Surface acoustic wave oxygen sensor

NASA Technical Reports Server (NTRS)

Collman, James P.; Oglesby, Donald M.; Upchurch, Billy T.; Leighty, Bradley D.; Zhang, Xumu; Herrmann, Paul C.

1994-01-01

A surface acoustic wave (SAW) device that responds to oxygen pressure was developed by coating a 158 MHz quartz surface acoustic wave (SAW) device with an oxygen binding agent. Two types of coatings were used. One type was prepared by dissolving an oxygen binding agent in a toluene solution of a copolymer containing the axial ligand. A second type was prepared with an oxygen binding porphyrin solution containing excess axial ligand without a polymer matrix. In the polymer based coatings, the copolymer served to provide the axial ligand to the oxygen binding agent and as a coating matrix on the surface of the SAW device. The oxygen sensing SAW device has been shown to bind oxygen following a Langmuir isotherm and may be used to measure the equilibrium constant of the oxygen binding compound in the coating matrix.

Redox-inactive metal ions modulate the reactivity and oxygen release of mononuclear non-haem iron(III)–peroxo complexes

DOE PAGES

Bang, Suhee; Lee, Yong -Min; Hong, Seungwoo; ...

2014-09-14

Redox-inactive metal ions that function as Lewis acids play pivotal roles in modulating the reactivity of oxygen-containing metal complexes and metalloenzymes, such as the oxygen-evolving complex in photosystem II and its small-molecule mimics. Here we report the synthesis and characterization of non-haem iron(III)–peroxo complexes that bind redox-inactive metal ions, (TMC)FeIII–(μ,η 2:η 2-O 2)–M n+ (M n+ = Sr 2+, Ca 2+, Zn 2+, Lu 3+, Y 3+ and Sc 3+; TMC, 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane). We demonstrate that the Ca 2+ and Sr 2+ complexes showed similar electrochemical properties and reactivities in one-electron oxidation or reduction reactions. However, the properties and reactivities ofmore » complexes formed with stronger Lewis acidities were found to be markedly different. In conclusion, complexes that contain Ca 2+ or Sr 2+ ions were oxidized by an electron acceptor to release O 2, whereas the release of O 2 did not occur for complexes that bind stronger Lewis acids. Furthermore, we discuss these results in the light of the functional role of the Ca 2+ ion in the oxidation of water to dioxygen by the oxygen-evolving complex.« less

Redox-inactive metal ions modulate the reactivity and oxygen release of mononuclear non-haem iron(III)–peroxo complexes

PubMed Central

Bang, Suhee; Lee, Yong-Min; Hong, Seungwoo; Cho, Kyung-Bin; Nishida, Yusuke; Seo, Mi Sook; Sarangi, Ritimukta; Fukuzumi, Shunichi; Nam, Wonwoo

2014-01-01

Redox-inactive metal ions that function as Lewis acids play pivotal roles in modulating the reactivity of oxygen-containing metal complexes and metalloenzymes, such as the oxygen-evolving complex in photosystem II and its small-molecule mimics. Here we report the synthesis and characterization of non-haem iron(III)–peroxo complexes that bind redox-inactive metal ions, (TMC)FeIII–(μ,η2:η2-O2)–Mn+ (Mn+ = Sr2+, Ca2+, Zn2+, Lu3+, Y3+ and Sc3+; TMC, 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane). We demonstrate that the Ca2+ and Sr2+ complexes showed similar electrochemical properties and reactivities in one-electron oxidation or reduction reactions. However, the properties and reactivities of complexes formed with stronger Lewis acidities were found to be markedly different. Complexes that contain Ca2+ or Sr2+ ions were oxidized by an electron acceptor to release O2, whereas the release of O2 did not occur for complexes that bind stronger Lewis acids. We discuss these results in the light of the functional role of the Ca2+ ion in the oxidation of water to dioxygen by the oxygen-evolving complex. PMID:25242490

[THE INFLUENCE OF NITROGLYCERIN ON SPECTRAL AND OXYGEN-BINDING CHARACTERISTICS OF HUMAN INTRACELLULAR HEMOGLOBIN.

PubMed

Kalaeva, E A; Artyukhov, V G; Putintseva, O V; Polyubez'eva, A I

2016-01-01

The spectral and oxygen-binding characteristics of human intracellular hemoglobin in the presence of nitroglycerin at concentrations of 5 ng/mL and 5 μg/mL have been studied. Short incubation (20 min) of erythrocytes with the drug led increasing hemoglobin affinity to oxygen and weakening of cooperative interactions in hemoprotein molecules. As a result, the amount of O(2) supplied to tissues in the process of gas exchange decreased by 23.96% (5 ng/mL) and 26.68% (5 μg/ml), p < 0.05. Incubation of cells for 24 h resulted in oxidation of the heme iron atom, accumulation of methemoglobin, and partial hemolysis. Nitroglycerin reduces the intensity of oxidative processes. However, no dependence of the degree of changes in the physical and chemical properties of hemoglobin on the concentration of nitroglycerin was found.

From intermolecular interactions to structures and properties of a novel cocrystal explosive: a first-principles study.

PubMed

Zhang, Lei; Wu, Ji-Zhou; Jiang, Sheng-Li; Yu, Yi; Chen, Jun

2016-09-29

By employing a first-principles method, we conducted a thorough study on a novel cocrystal explosive 1 : 1 NTO : TZTN and gained insight into the interaction-structure-property interrelationship. Mulliken bond orders, Hirshfeld surfaces, intermolecular binding energies, packing coefficients, and oxygen balance were calculated to analyze the intermolecular interactions and structures of the cocrystal explosive. The cocrystallization of NTO and TZTN molecules enhances the intermolecular binding force, which drives the synthesis of the cocrystal. However, the cocrystallization decreases the molecular packing density along the closest packed directions, which reduces the density by 10.5% and deteriorates the oxygen balance. All of these lead to a reduction in the detonation performance compared to NTO explosives. We have also proposed a new method to evaluate the impact sensitivity according to the lattice dynamics calculation. The cocrystal explosive has a lower impact sensitivity than TZTN but higher than NTO, which agrees well with experiments.

On optima: the case of myoglobin-facilitated oxygen diffusion.

PubMed

Wittenberg, Jonathan B

2007-08-15

The process of myoglobin/leghemoglobin-facilitated oxygen diffusion is adapted to function in different environments in diverse organisms. We enquire how the functional parameters of the process are optimized in particular organisms. The ligand-binding properties of the proteins, myoglobin and plant symbiotic hemoglobins, we discover, suggest that they have been adapted under genetic selection pressure for optimal performance. Since carrier-mediated oxygen transport has probably evolved independantly many times, adaptation of diverse proteins for a common functionality exemplifies the process of convergent evolution. The progenitor proteins may be built on the myoglobin scaffold or may be very different.

Aspects of Protein, Chemistry, Part II: Oxygen-Binding Proteins

ERIC Educational Resources Information Center

Nixon, J. E.

1977-01-01

Compares differences in function and behavior of two oxygen-binding proteins, myoglobin found in muscle and hemoglobin found in blood. Describes the mechanism of oxygen-binding and allosteric effect in hemoglobin; also describes the effect of pH on the affinity of hemoglobin for oxygen. (CS)

Effect of oxygen deficiency on electronic properties and local structure of amorphous tantalum oxide thin films

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

Denny, Yus Rama; Firmansyah, Teguh; Oh, Suhk Kun

2016-10-15

Highlights: • The effect of oxygen flow rate on electronic properties and local structure of tantalum oxide thin films was studied. • The oxygen deficiency induced the nonstoichiometric state a-TaOx. • A small peak at 1.97 eV above the valence band side appeared on nonstoichiometric Ta{sub 2}O{sub 5} thin films. • The oxygen flow rate can change the local electronic structure of tantalum oxide thin films. - Abstract: The dependence of electronic properties and local structure of tantalum oxide thin film on oxygen deficiency have been investigated by means of X-ray photoelectron spectroscopy (XPS), Reflection Electron Energy Loss Spectroscopy (REELS),more » and X-ray absorption spectroscopy (XAS). The XPS results showed that the oxygen flow rate change results in the appearance of features in the Ta 4f at the binding energies of 23.2 eV, 24.4 eV, 25.8, and 27.3 eV whose peaks are attributed to Ta{sup 1+}, Ta{sup 2+}, Ta{sup 3+}/Ta{sup 4+}, and Ta{sup 5+}, respectively. The presence of nonstoichiometric state from tantalum oxide (TaOx) thin films could be generated by the oxygen vacancies. In addition, XAS spectra manifested both the increase of coordination number of the first Ta-O shell and a considerable reduction of the Ta-O bond distance with the decrease of oxygen deficiency.« less

[Peroxynitrite effect on the haemoglobin oxygen affinity in vitro in presence of different partial pressure of carbon dioxide].

PubMed

Stepuro, T L; Zinchuk, V V

2011-08-01

Peroxynitrite (ONOO-) besides its toxic possesses regulatory action that includes the modulation of oxygen binding properties of blood. The aim of this work was to estimate ONOO- effect on the haemoglobin oxygen affinity (HOA) in vitro in presence of different partial pressure of carbon dioxide (CO2). The ONOO- presence in venous blood in conditions of hypercapnia induced oxyhaemoglobin dissociation curve shift leftward while in hypocapnic conditions the result of a different character was obtained. The revealed effect of ONOO- is realized, possibly, through various modifications ofhaemoglobin whose formation is dependent on the CO2 pressure. The ONOO- influences the HOA in different manner that can be important in regulation of blood oxygenation in lungs and maintenance of oxygen consumption in tissues.

Genetic Diversity of Coastal Bottlenose Dolphins Revealed by Structurally and Functionally Diverse Hemoglobins

PubMed Central

Remington, Nicole; Stevens, Robert D.; Wells, Randall S.; Hohn, Aleta; Dhungana, Suraj; Taboy, Celine H.; Crumbliss, Alvin L.; Henkens, Robert; Bonaventura, Celia

2007-01-01

Studies of structure-function relationships in the respiratory proteins of marine mammals revealed unexpected variations in the number and types of hemoglobins (Hbs) present in coastal bottlenose dolphins, Tursiops truncatus. We obtained blood samples from free-ranging coastal bottlenose dolphins as a component of capture-release studies. We found that the oxygen-binding functions of bottlenose dolphin blood are poised between effector-saturated and unsaturated levels, enabling exercise-dependent shifts in oxygen transfer functions. Isolated bottlenose dolphin Hbs showed elevated pH sensitivities (Bohr effects) and appreciably lower oxygen affinities than adult human Hb in the absence of allosteric effectors. These properties may be an adaptive modification that enhance oxygen delivery during diving episodes when oxygen tensions and effector levels are low. The Hbs of individual dolphins showed similar oxygen affinities, responses to effectors, and expression of heme-heme interaction in oxygen binding, but differed in their redox potentials and rates of autoxidation. The heterogeneity suggested by these functional variations in Hbs of individual dolphins was born out by variations in the molecular weights and numbers of their α and β globin chains. Although coastal bottlenose dolphins were expected to have a single type of Hb, the mass differences observed revealed considerable genetic diversity. There were multiple Hb forms in some individuals and differences in Hb patterns among individuals within the same community. PMID:17604574

Genetic diversity of coastal bottlenose dolphins revealed by structurally and functionally diverse hemoglobins.

PubMed

Remington, Nicole; Stevens, Robert D; Wells, Randall S; Holn, Aleta; Dhungana, Suraj; Taboy, Celine H; Crumbliss, Alvin L; Henkens, Robert; Bonaventura, Celia

2007-08-15

Studies of structure-function relationships in the respiratory proteins of marine mammals revealed unexpected variations in the number and types of hemoglobins (Hbs) present in coastal bottlenose dolphins, Tursiops truncatus. We obtained blood samples from free-ranging coastal bottlenose dolphins as a component of capture-release studies. We found that the oxygen-binding functions of bottlenose dolphin blood are poised between effector-saturated and unsaturated levels, enabling exercise-dependent shifts in oxygen transfer functions. Isolated bottlenose dolphin Hbs showed elevated pH sensitivities (Bohr effects) and appreciably lower oxygen affinities than adult human Hb in the absence of allosteric effectors. These properties may be an adaptive modification that enhances oxygen delivery during diving episodes when oxygen tensions and effector levels are low. The Hbs of individual dolphins showed similar oxygen affinities, responses to effectors, and expression of heme-heme interaction in oxygen binding, but differed in their redox potentials and rates of autoxidation. The heterogeneity suggested by these functional variations in Hbs of individual dolphins was born out by variations in the molecular weights and numbers of their alpha and beta globin chains. Although coastal bottlenose dolphins were expected to have a single type of Hb, the mass differences observed revealed considerable genetic diversity. There were multiple Hb forms in some individuals and differences in Hb patterns among individuals within the same community.

Photophysical and photochemical properties of Bauhinia megalandra (Caesalpinaceae) extracts as new PDT photosensitizer

NASA Astrophysics Data System (ADS)

Vargas Tovar, Franklin R.; Rivas, C.; Estrada, O.; Marcano O., Aristides A.; Echevarria, Lorenzo; Diaz, Yrene; Alexander, I.; Rodriguez, L.; Padron, L.; Rivera, I. R.

2004-10-01

Recently new photosensitizers, chlorophyll "a and b" derivatives, for photodynamic therapy (PDT) have been presented. It already passed complete pre-clinical investigations. This prompted us to carry out an extensive study of photophysical properties of chlorine derivatives, important both for optimization of their clinic applications and for study of mechanisms of chlorine PDT&. The fresh leaves of Bauhinia megalandra (Caesalpinaceae) were extracted with methanol by percolation, and re-extract with a mixture of methanol-water (1:1), the insoluble fraction was then separated by column chromatography [RP18/hexane-ethylacetate (9:1)] to obtain four fractions named 1 to 4. These compounds were identified by NMR data. We found that 3 and 4 efficiently generates singlet oxygen when irradiated with visible light. Detection of the singlet oxygen was fulfilled by its reaction with histidine and detected by bleaching p-nitrosodimethylaniline under 440 nm irradiation. The quantum yields of singlet oxygen determined by us were 0.088 (1), 0.151 (2), 0.219 (3) and 0.301 (4). We measured absorption and fluorescence spectra of compounds 1 to 4 (Mg-chlorophyll-a, Pheophytin, Mg-chlorophyll-b and chlorophyll-b respectively) in different media and in aqueous solutions of human serum albumin. The association constant of the compounds 1, 2, 3 and 4 in the presence of HSA were estimated. The binding and quenching studies suggest that only 1 and 3 may serve as a useful fluorescence probe for structure/function studies of different chlorophyll binding proteins. No photoinduced binding was observed after irradiation by all the studied compounds in presence of human serum albumin.

Ion adsorption at the rutile-water interface: linking molecular and macroscopic properties.

PubMed

Zhang, Z; Fenter, P; Cheng, L; Sturchio, N C; Bedzyk, M J; Predota, M; Bandura, A; Kubicki, J D; Lvov, S N; Cummings, P T; Chialvo, A A; Ridley, M K; Bénézeth, P; Anovitz, L; Palmer, D A; Machesky, M L; Wesolowski, D J

2004-06-08

A comprehensive picture of the interface between aqueous solutions and the (110) surface of rutile (alpha-TiO2) is being developed by combining molecular-scale and macroscopic approaches, including experimental measurements, quantum calculations, molecular simulations, and Gouy-Chapman-Stern models. In situ X-ray reflectivity and X-ray standing-wave measurements are used to define the atomic arrangement of adsorbed ions, the coordination of interfacial water molecules, and substrate surface termination and structure. Ab initio calculations and molecular dynamics simulations, validated through direct comparison with the X-ray results, are used to predict ion distributions not measured experimentally. Potentiometric titration and ion adsorption results for rutile powders having predominant (110) surface expression provide macroscopic constraints of electrical double layer (EDL) properties (e.g., proton release) which are evaluated by comparison with a three-layer EDL model including surface oxygen proton affinities calculated using ab initio bond lengths and partial charges. These results allow a direct correlation of the three-dimensional, crystallographically controlled arrangements of various species (H2O, Na+, Rb+, Ca2+, Sr2+, Zn2+, Y3+, Nd3+) with macroscopic observables (H+ release, metal uptake, zeta potential) and thermodynamic/electrostatic constraints. All cations are found to be adsorbed as "inner sphere" species bonded directly to surface oxygen atoms, while the specific binding geometries and reaction stoichiometries are dependent on ionic radius. Ternary surface complexes of sorbed cations with electrolyte anions are not observed. Finally, surface oxygen proton affinities computed using the MUSIC model are improved by incorporation of ab initio bond lengths and hydrogen bonding information derived from MD simulations. This multitechnique and multiscale approach demonstrates the compatibility of bond-valence models of surface oxygen proton affinities and Stern-based models of the EDL structure, with the actual molecular interfacial distributions observed experimentally, revealing new insight into EDL properties including specific binding sites and hydration states of sorbed ions, interfacial solvent properties (structure, diffusivity, dielectric constant), surface protonation and hydrolysis, and the effect of solution ionic strength.

Role of oxygen on the optical properties of borate glass doped with ZnO

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

Abdel-Baki, Manal; El-Diasty, Fouad, E-mail: fdiasty@yahoo.com

2011-10-15

Lithium tungsten borate glass (0.56-x)B{sub 2}O{sub 3}-0.4Li{sub 2}O-xZnO-0.04WO{sub 3} (0{<=}x{<=}0.1 mol%) is prepared by the melt quenching technique for photonic applications. Small relative values of ZnO are used to improve the glass optical dispersion and to probe as well the role of oxygen electronic polarizability on its optical characteristics. The spectroscopic properties of the glass are determined in a wide spectrum range (200-2500 nm) using a Fresnel-based spectrophotometric technique. Based on the Lorentz-Lorenz theory, as ZnO content increases on the expense of B{sub 2}O{sub 3} the glass molar polarizability increased due to an enhanced unshared oxide ion 2p electron density,more » which increases ionicity of the chemical bonds of glass. The role of oxide ion polarizability is explained in accordance with advanced measures and theories such as optical basicity, O 1s binding energy, the outer most cation binding energy in Yamashita-Kurosawa's interionic interaction parameter and Sun's average single bond strength. FT-IR measurements confirm an increase in bridging oxygen bonds, as a result of replacement of ZnO by B{sub 2}O{sub 3}, which increase the UV glass transmission window and transmittance. - Graphical abstract: O1s, Yamashita-Kurosawa's parameter and average single bond strength of charge overlapping between electronic shells are used to explain enhanced oxide ion 2p electron density, which increases refractive index of glasses. Highlights: > New borate glass for photonic application is prepared. > The dispersion property of the glass is effectively controlled using small amounts of ZnO. > ZnO is used to probe the glass structure and investigate the role of oxygen on the obtained optical properties of the glasses. > Modern theories are used to explain enhanced unshared oxide ion 2p electron density, which increases ionicity of chemical bonds of the glass.« less

Oxygen binding by alpha(Fe2+)2beta(Ni2+)2 hemoglobin crystals.

PubMed Central

Bruno, S.; Bettati, S.; Manfredini, M.; Mozzarelli, A.; Bolognesi, M.; Deriu, D.; Rosano, C.; Tsuneshige, A.; Yonetani, T.; Henry, E. R.

2000-01-01

Oxygen binding by hemoglobin fixed in the T state either by crystallization or by encapsulation in silica gels is apparently noncooperative. However, cooperativity might be masked by different oxygen affinities of alpha and beta subunits. Metal hybrid hemoglobins, where the noniron metal does not bind oxygen, provide the opportunity to determine the oxygen affinities of alpha and beta hemes separately. Previous studies have characterized the oxygen binding by alpha(Ni2+)2beta(Fe2+)2 crystals. Here, we have determined the three-dimensional (3D) structure and oxygen binding of alpha(Fe2+)2beta(Ni2+)2 crystals grown from polyethylene glycol solutions. Polarized absorption spectra were recorded at different oxygen pressures with light polarized parallel either to the b or c crystal axis by single crystal microspectrophotometry. The oxygen pressures at 50% saturation (p50s) are 95 +/- 3 and 87 +/- 4 Torr along the b and c crystal axes, respectively, and the corresponding Hill coefficients are 0.96 +/- 0.06 and 0.90 +/- 0.03. Analysis of the binding curves, taking into account the different projections of the alpha hemes along the optical directions, indicates that the oxygen affinity of alpha1 hemes is 1.3-fold lower than alpha2 hemes. Inspection of the 3D structure suggests that this inequivalence may arise from packing interactions of the Hb tetramer within the monoclinic crystal lattice. A similar inequivalence was found for the beta subunits of alpha(Ni2+)2beta(Fe2+)2 crystals. The average oxygen affinity of the alpha subunits (p50 = 91 Torr) is about 1.2-fold higher than the beta subunits (p50 = 110 Torr). In the absence of cooperativity, this heterogeneity yields an oxygen binding curve of Hb A with a Hill coefficient of 0.999. Since the binding curves of Hb A crystals exhibit a Hill coefficient very close to unity, these findings indicate that oxygen binding by T-state hemoglobin is noncooperative, in keeping with the Monod, Wyman, and Changeux model. PMID:10794410

Redox process is crucial for inhibitory properties of aurintricarboxylic acid against activity of YopH: virulence factor of Yersinia pestis

PubMed Central

Kuban-Jankowska, Alicja; Gorska, Magdalena; Tuszynski, Jack A; Ossowski, Tadeusz; Wozniak, Michal

2015-01-01

YopH is a bacterial protein tyrosine phosphatase, which is essential for the viability and pathogenic virulence of the plague-causing Yersinia sp. bacteria. Inactivation of YopH activity would lead to the loss of bacterial pathogenicity. We have studied the inhibitory properties of aurintricarboxylic acid (ATA) against YopH phosphatase and found that at nanomolar concentrations ATA reversibly decreases the activity of YopH. Computational docking studies indicated that in all binding poses ATA binds in the YopH active site. Molecular dynamics simulations showed that in the predicted binding pose, ATA binds to the essential Cys403 and Arg409 residues in the active site and has a stronger binding affinity than the natural substrate (pTyr). The cyclic voltammetry experiments suggest that ATA reacts remarkably strongly with molecular oxygen. Additionally, the electrochemical reduction of ATA in the presence of a negative potential from −2.0 to 2.5 V generates a current signal, which is observed for hydrogen peroxide. Here we showed that ATA indicates a unique mechanism of YopH inactivation due to a redox process. We proposed that the potent inhibitory properties of ATA are a result of its strong binding in the YopH active site and in situ generation of hydrogen peroxide near catalytic cysteine residue. PMID:26286963

Twisted cyanines: a non-planar fluorogenic dye with superior photostability and its use in a protein-based fluoromodule.

PubMed

Shank, Nathaniel I; Pham, Ha H; Waggoner, Alan S; Armitage, Bruce A

2013-01-09

The cyanine dye thiazole orange (TO) is a well-known fluorogenic stain for DNA and RNA, but this property precludes its use as an intracellular fluorescent probe for non-nucleic acid biomolecules. Further, as is the case with many cyanines, the dye suffers from low photostability. Here, we report the synthesis of a bridge-substituted version of TO named α-CN-TO, where the central methine hydrogen of TO is replaced by an electron withdrawing cyano group, which was expected to decrease the susceptibility of the dye toward singlet oxygen-mediated degradation. An X-ray crystal structure shows that α-CN-TO is twisted drastically out of plane, in contrast to TO, which crystallizes in the planar conformation. α-CN-TO retains the fluorogenic behavior of the parent dye TO in viscous glycerol/water solvent, but direct irradiation and indirect bleaching studies showed that α-CN-TO is essentially inert to visible light and singlet oxygen. In addition, the twisted conformation of α-CN-TO mitigates nonspecific binding and fluorescence activation by DNA and a previously selected TO-binding protein and exhibits low background fluorescence in HeLa cell culture. α-CN-TO was then used to select a new protein that binds and activates fluorescence from the dye. The new α-CN-TO/protein fluoromodule exhibits superior photostability to an analogous TO/protein fluoromodule. These properties indicate that α-CN-TO will be a useful fluorogenic dye in combination with specific RNA and protein binding partners for both in vitro and cell-based applications. More broadly, structural features that promote nonplanar conformations can provide an effective method for reducing nonspecific binding of cationic dyes to nucleic acids and other biomolecules.

Twisted Cyanines: A Non-Planar Fluorogenic Dye with Superior Photostability and its Use in a Protein-Based Fluoromodule

PubMed Central

Shank, Nathaniel I.; Pham, Ha; Waggoner, Alan S.; Armitage, Bruce A.

2013-01-01

The cyanine dye thiazole orange (TO) is a well-known fluorogenic stain for DNA and RNA, but this property precludes its use as an intracellular fluorescent probe for non-nucleic acid biomolecules. Further, as is the case with many cyanines, the dye suffers from low photostability. Here we report the synthesis of a bridge-substituted version of TO named α-CN-TO, where the central methine hydrogen of TO is replaced by an electron withdrawing cyano group, which was expected to decrease the susceptibility of the dye toward singlet oxygen-mediated degradation. An X-ray crystal structure shows that α-CN-TO is twisted drastically out of plane, in contrast to TO, which crystallizes in the planar conformation. α-CN-TO retains the fluorogenic behavior of the parent dye TO in viscous glycerol/water solvent, but direct irradiation and indirect bleaching studies showed that α-CN-TO is essentially inert to visible light and singlet oxygen. In addition, the twisted conformation of α-CN-TO mitigates non-specific binding and fluorescence activation by DNA and a previously selected TO-binding protein and exhibits low background fluorescence in HeLa cell culture. α-CN-TO was then used to select a new protein that binds and activates fluorescence from the dye. The new α-CN-TO/protein fluoromodule exhibits superior photostability to an analogous TO/protein fluoromodule. These properties indicate that α-CN-TO will be a useful fluorogenic dye in combination with specific RNA and protein binding partners for both in vitro and cell-based applications. More broadly, structural features that promote nonplanar conformations can provide an effective method for reducing nonspecific binding of cationic dyes to nucleic acids and other biomolecules. PMID:23252842

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

Parkes, Marie V.; Sava Gallis, Dorina F.; Greathouse, Jeffery A.

Computational screening of metal-organic framework (MOF) materials for selective oxygen adsorption from air could lead to new sorbents for the oxyfuel combustion process feedstock streams. A comprehensive study on the effect of MOF metal chemistry on gas binding energies in two common but structurally disparate metal-organic frameworks has been undertaken. Dispersion-corrected density functional theory methods were used to calculate the oxygen and nitrogen binding energies with each of fourteen metals, respectively, substituted into two MOF series, M 2(dobdc) and M 3(btc) 2. The accuracy of DFT methods was validated by comparing trends in binding energy with experimental gas sorption measurements.more » A periodic trend in oxygen binding energies was found, with greater oxygen binding energies for early transition-metal-substituted MOFs compared to late transition metal MOFs; this was independent of MOF structural type. The larger binding energies were associated with oxygen binding in a side-on configuration to the metal, with concomitant lengthening of the O-O bond. In contrast, nitrogen binding energies were similar across the transition metal series, regardless of both MOF structural type and metal identity. Altogether, these findings suggest that early transition metal MOFs are best suited to separating oxygen from nitrogen, and that the MOF structural type is less important than the metal identity.« less

Nickel-quinolones interaction. Part 4. Structure and biological evaluation of nickel(II)-enrofloxacin complexes compared to zinc(II) analogues.

PubMed

Skyrianou, Kalliopi C; Psycharis, Vassilis; Raptopoulou, Catherine P; Kessissoglou, Dimitris P; Psomas, George

2011-01-01

The nickel(II) complexes with the second-generation quinolone antibacterial agent enrofloxacin in the presence or absence of the nitrogen-donor heterocyclic ligands 1,10-phenanthroline, 2,2'-bipyridine or pyridine have been synthesized and characterized. Enrofloxacin acts as bidentate ligand coordinated to Ni(II) ion through the ketone oxygen and a carboxylato oxygen. The crystal structure of (1,10-phenanthroline)bis(enrofloxacinato)nickel(II) has been determined by X-ray crystallography. UV study of the interaction of the complexes with calf-thymus DNA (CT DNA) has shown that they bind to CT DNA and bis(pyridine)bis(enrofloxacinato)nickel(II) exhibits the highest binding constant to CT DNA. The cyclic voltammograms of the complexes have shown that in the presence of CT DNA the complexes can bind to CT DNA by the intercalative binding mode which has also been verified by DNA solution viscosity measurements. Competitive study with ethidium bromide (EB) has shown that the complexes can displace the DNA-bound EB indicating that they bind to DNA in strong competition with EB. The complexes exhibit good binding propensity to human or bovine serum albumin protein having relatively high binding constant values. The biological properties of the complexes have been evaluated in comparison to the corresponding Zn(II) enrofloxacinato complexes as well as Ni(II) complexes with the first-generation quinolone oxolinic acid. Copyright © 2010 Elsevier Inc. All rights reserved.

Low affinity PEGylated hemoglobin from Trematomus bernacchii, a model for hemoglobin-based blood substitutes

PubMed Central

2011-01-01

Background Conjugation of human and animal hemoglobins with polyethylene glycol has been widely explored as a means to develop blood substitutes, a novel pharmaceutical class to be used in surgery or emergency medicine. However, PEGylation of human hemoglobin led to products with significantly different oxygen binding properties with respect to the unmodified tetramer and high NO dioxygenase reactivity, known causes of toxicity. These recent findings call for the biotechnological development of stable, low-affinity PEGylated hemoglobins with low NO dioxygenase reactivity. Results To investigate the effects of PEGylation on protein structure and function, we compared the PEGylation products of human hemoglobin and Trematomus bernacchii hemoglobin, a natural variant endowed with a remarkably low oxygen affinity and high tetramer stability. We show that extension arm facilitated PEGylation chemistry based on the reaction of T. bernacchii hemoglobin with 2-iminothiolane and maleimido-functionalyzed polyethylene glycol (MW 5000 Da) leads to a tetraPEGylated product, more homogeneous than the corresponding derivative of human hemoglobin. PEGylated T. bernacchii hemoglobin largely retains the low affinity of the unmodified tetramer, with a p50 50 times higher than PEGylated human hemoglobin. Moreover, it is still sensitive to protons and the allosteric effector ATP, indicating the retention of allosteric regulation. It is also 10-fold less reactive towards nitrogen monoxide than PEGylated human hemoglobin. Conclusions These results indicate that PEGylated hemoglobins, provided that a suitable starting hemoglobin variant is chosen, can cover a wide range of oxygen-binding properties, potentially meeting the functional requirements of blood substitutes in terms of oxygen affinity, tetramer stability and NO dioxygenase reactivity. PMID:22185675

Structure and Ligand Binding Properties of the Epoxidase Component of Styrene Monooxygenase

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

Ukaegbu, Uchechi E.; Kantz, Auric; Beaton, Michelle

2010-07-23

Styrene monooxygenase (SMO) is a two-component flavoprotein monooxygenase that transforms styrene to styrene oxide in the first step of the styrene catabolic and detoxification pathway of Pseudomonas putida S12. The crystal structure of the N-terminally histidine-tagged epoxidase component of this system, NSMOA, determined to 2.3 {angstrom} resolution, indicates the enzyme exists as a homodimer in which each monomer forms two distinct domains. The overall architecture is most similar to that of p-hydroxybenzoate hydroxylase (PHBH), although there are some significant differences in secondary structure. Structural comparisons suggest that a large cavity open to the surface forms the FAD binding site. Atmore » the base of this pocket is another cavity that likely represents the styrene binding site. Flavin binding and redox equilibria are tightly coupled such that reduced FAD binds apo NSMOA {approx}8000 times more tightly than the oxidized coenzyme. Equilibrium fluorescence and isothermal titration calorimetry data using benzene as a substrate analogue indicate that the oxidized flavin and substrate analogue binding equilibria of NSMOA are linked such that the binding affinity of each is increased by 60-fold when the enzyme is saturated with the other. A much weaker {approx}2-fold positive cooperative interaction is observed for the linked binding equilibria of benzene and reduced FAD. The low affinity of the substrate analogue for the reduced FAD complex of NSMOA is consistent with a preferred reaction order in which flavin reduction and reaction with oxygen precede the binding of styrene, identifying the apoenzyme structure as the key catalytic resting state of NSMOA poised to bind reduced FAD and initiate the oxygen reaction.« less

A molecular model for cocaine binding by the immunotherapeutic human/mouse chimeric monoclonal antibody 2E2.

PubMed

Lape, Michael; Paula, Stefan; Ball, William J

2010-06-01

Immunotherapy by cocaine-binding monoclonal antibodies (mAbs) has emerged as a promising strategy for the treatment of cocaine addiction. The human (gamma1 heavy chain)/murine (lambda light chain) chimeric mAb 2E2 has excellent affinity and specificity for cocaine and recent animal studies have demonstrated 2E2's ability in vivo to reduce cocaine levels in the brain as well as alter cocaine self-administration behavior in rats. In this study, we used mAb 2E2 amino acid sequence information to create a homology model for the 3-D structure of its Fv fragment. Subsequent computational docking studies revealed the intermolecular interactions potentially responsible for mAb 2E2's cocaine binding properties. The driving force of cocaine binding was identified as a combination of hydrophobic interactions and a single hydrogen bond between a light chain tyrosine residue and a carbonyl oxygen atom of cocaine. The model also allowed for an in silico evaluation of single/double residue mutations in the heavy and light chain variable regions that might further enhance mAb 2E2's cocaine binding properties. Copyright (c) 2010 Elsevier Masson SAS. All rights reserved.

A Molecular Model for Cocaine Binding by the Immunotherapeutic Human/Mouse Chimeric Monoclonal Antibody 2E2

PubMed Central

Lape, Michael; Paula, Stefan; Ball, William J.

2010-01-01

Immunotherapy by cocaine-binding monoclonal antibodies (mAbs) has emerged as a promising strategy for the treatment of cocaine addiction. The human (γ1 heavy chain)/murine (λ light chain) chimeric mAb 2E2 has excellent affinity and specificity for cocaine and recent animal studies have demonstrated 2E2’s ability in vivo to reduce cocaine levels in the brain as well as alter cocaine self-administration behavior in rats. In this study, we used mAb 2E2 amino acid sequence information to create a homology model for the 3-D structure of its Fv fragment. Subsequent computational docking studies revealed the intermolecular interactions potentially responsible for mAb 2E2’s cocaine binding properties. The driving force of cocaine binding was identified as a combination of hydrophobic interactions and a single hydrogen bond between a light chain tyrosine residue and a carbonyl oxygen atom of cocaine. The model also allowed for an in silico evaluation of single/double residue mutations in the heavy and light chain variable regions that might further enhance mAb 2E2’s cocaine binding properties. PMID:20185210

Analysis of zinc binding sites in protein crystal structures.

PubMed

Alberts, I L; Nadassy, K; Wodak, S J

1998-08-01

The geometrical properties of zinc binding sites in a dataset of high quality protein crystal structures deposited in the Protein Data Bank have been examined to identify important differences between zinc sites that are directly involved in catalysis and those that play a structural role. Coordination angles in the zinc primary coordination sphere are compared with ideal values for each coordination geometry, and zinc coordination distances are compared with those in small zinc complexes from the Cambridge Structural Database as a guide of expected trends. We find that distances and angles in the primary coordination sphere are in general close to the expected (or ideal) values. Deviations occur primarily for oxygen coordinating atoms and are found to be mainly due to H-bonding of the oxygen coordinating ligand to protein residues, bidentate binding arrangements, and multi-zinc sites. We find that H-bonding of oxygen containing residues (or water) to zinc bound histidines is almost universal in our dataset and defines the elec-His-Zn motif. Analysis of the stereochemistry shows that carboxyl elec-His-Zn motifs are geometrically rigid, while water elec-His-Zn motifs show the most geometrical variation. As catalytic motifs have a higher proportion of carboxyl elec atoms than structural motifs, they provide a more rigid framework for zinc binding. This is understood biologically, as a small distortion in the zinc position in an enzyme can have serious consequences on the enzymatic reaction. We also analyze the sequence pattern of the zinc ligands and residues that provide elecs, and identify conserved hydrophobic residues in the endopeptidases that also appear to contribute to stabilizing the catalytic zinc site. A zinc binding template in protein crystal structures is derived from these observations.

Effect of metal in M 3(btc) 2 and M 2(dobdc) MOFs for O 2/N 2 separations: A combined density functional theory and experimental study

DOE PAGES

Parkes, Marie V.; Sava Gallis, Dorina F.; Greathouse, Jeffery A.; ...

2015-03-02

Computational screening of metal-organic framework (MOF) materials for selective oxygen adsorption from air could lead to new sorbents for the oxyfuel combustion process feedstock streams. A comprehensive study on the effect of MOF metal chemistry on gas binding energies in two common but structurally disparate metal-organic frameworks has been undertaken. Dispersion-corrected density functional theory methods were used to calculate the oxygen and nitrogen binding energies with each of fourteen metals, respectively, substituted into two MOF series, M 2(dobdc) and M 3(btc) 2. The accuracy of DFT methods was validated by comparing trends in binding energy with experimental gas sorption measurements.more » A periodic trend in oxygen binding energies was found, with greater oxygen binding energies for early transition-metal-substituted MOFs compared to late transition metal MOFs; this was independent of MOF structural type. The larger binding energies were associated with oxygen binding in a side-on configuration to the metal, with concomitant lengthening of the O-O bond. In contrast, nitrogen binding energies were similar across the transition metal series, regardless of both MOF structural type and metal identity. Altogether, these findings suggest that early transition metal MOFs are best suited to separating oxygen from nitrogen, and that the MOF structural type is less important than the metal identity.« less

Unusually weak oxygen binding, physical properties, partial sequence, autoxidation rate and a potential phosphorylation site of beluga whale (Delphinapterus leucas) myoglobin.

PubMed

Stewart, J M; Blakely, J A; Karpowicz, P A; Kalanxhi, E; Thatcher, B J; Martin, B M

2004-03-01

We purified myoglobin from beluga whale (Delphinapterus leucas) muscle (longissimus dorsi) with size exclusion and cation exchange chromatographies. The molecular mass was determined by mass spectrometry (17,081 Da) and the isoelectric pH (9.4) by capillary isoelectric focusing. The near-complete amino acid sequence was determined and a phylogeny indicated that beluga was in the same clad as Dall's and harbor porpoises. There were consensus motifs for a phosphorylation site on the protein surface with the most likely site at serine-117. This motif was common to all cetacean myoglobins examined. Two oxygen-binding studies at 37 degrees C indicated dissociation constants (20.5 and 23.6 microM) 5.7-6.6 times larger than horse myoglobin (3.6 microM). The autoxidation rate of beluga myoglobin at 37 degrees C, pH 7.2 was 0.218+/-0.028 h(-1), 1/3 larger than reported for myoglobin of terrestrial mammals. There was no clear sequence change to explain the difference in oxygen binding or autoxidation although substitutions (N66 and T67) in an invariant rich sequence (HGNTV) distal to the heme may play a role. Structural models based on the protein sequence and constructed on topologies of known templates (horse and sperm whale crystal structures) were not adequate to assess perturbation of the heme pocket.

Cobalt porphyrin-mediated oxygen transport in a polymer membrane. Effect of the cobalt porphyrin structure on the oxygen-binding reaction, oxygen-diffusion constants, and oxygen-transport efficiency

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

Nishide, Hiroyuki; Suzuki, Takayuki; Kawakami, Hiroyoshi

1994-05-12

New derivatives of (meso-[alpha],[alpha],[alpha],[alpha]-tetrakis(o-pivalamidophenyl)porphinato)cobalt (CoPs) were characterized by oxygen-binding equilibrium and rate constants of the cobalt centered in the porphyrins. They depended on the structure of the porphyrin; for example, the rate constants of oxygen binding and dissociation (k[sub on] and k[sub off]) for [alpha][sup 3][beta]-CoP[sub 4]P were 3 and 20 times as large as those for [alpha][sup 4]-CoB[sub 4]P, respectively. Oxygen transport through the polymer membranes containing CoPs as the fixed oxygen carriers was facilitated and was affected by the oxygen-binding character or the structure of CoPs. The logarithmically linear correlation of the oxygen-dissociation rate constant of CoPs (k[submore » off] = (3-66) x 10[sup 3] S[sup [minus]1]) with the diffusion constant of oxygen via CoPs fixed in the membranes (D[sub cc] = (3-140) x 10[sup [minus]9] cm[sup 2] s[sup [minus]1]) was given for those six CoP derivatives. 26 refs., 5 figs., 2 tabs.« less

Free energy changes and components implicit in the MWC allosteric model for the cooperative oxygen binding of hemoglobin.#

PubMed Central

Bucci, Enrico

2013-01-01

Hill’s plots of oxygen binding isotherms reveal the presence of a transition between two different oxygen affinities at the beginning and end of the isotherm. They correspond to the two conformations anticipated by the MWC model, namely the T and R conformations at the beginning and end of oxygen binding, when the lower affinity of the T form develops into the higher affinity of the R form. The difference between the binding Gibbs free energies changes of the two affinities (ΔGL) is the free energy of binding cooperativity. Notably ΔGL is positive in favor of the T form, that moves to a higher energy level upon oxygen release. Osmotic stress reveals a higher volume/surface ratio of deoxyHb, with a positive ΔGW also in favor of the T form . Increasing protein concentration shifts the isotherms to the right indicating the formation of intermediate polymeric forms. Enthalpy of the intermediates show a strong absorption of heat at the third oxygenation step due to polymers formation with quinary, and above, structures. The disassembly of intermediate polymers releases energy with a negative ΔG that compensates and allow the positivity of ΔGL. High energy polymers are the barrier preventing the relaxation of the T and R conformations into one another. The MWC allosteric model is the best justification of oxygen binding cooperativity . PMID:23710673

The Nernst equation applied to oxidation-reduction reactions in myoglobin and hemoglobin. Evaluation of the parameters.

PubMed

Saroff, Harry A

Analyses of the binding of oxygen to monomers such as myoglobin employ the Mass Action equation. The Mass Action equation, as such, is not directly applicable for the analysis of the binding of oxygen to oligomers such as hemoglobin. When the binding of oxygen to hemoglobin is analyzed, models incorporating extensions of mass action are employed. Oxidation-reduction reactions of the heme group in myoglobin and hemoglobin involve the binding and dissociation of electrons. This reaction is described with the Nernst equation. The Nernst equation is applicable only to a monomeric species even if the number of electrons involved is greater than unity. To analyze the oxidation-reduction reaction in a molecule such as hemoglobin a model is required which incorporates extensions of the Nernst equation. This communication develops models employing the Nernst equation for oxidation-reduction reactions analogous to those employed for hemoglobin in the analysis of the oxygenation (binding of oxygen) reaction.

Should modulation of p50 be a therapeutic target in the critically ill?

PubMed

Srinivasan, Amudan J; Morkane, Clare; Martin, Daniel S; Welsby, Ian J

2017-05-01

A defining feature of human hemoglobin is its oxygen binding affinity, quantified by the partial pressure of oxygen at which hemoglobin is 50% saturated (p50), and the variability of this parameter over a range of physiological and environmental states. Modulation of this property of hemoglobin can directly affect the degree of peripheral oxygen offloading and tissue oxygenation. Areas covered: This review summarizes the role of hemoglobin oxygen affinity in normal and abnormal physiology and discusses the current state of the literature regarding artificial modulation of p50. Hypoxic tumors, sickle cell disease, heart failure, and transfusion medicine are discussed in the context of recent advances in hemoglobin oxygen affinity manipulation. Expert commentary: Of particular clinical interest is the possibility of maintaining adequate end-organ oxygen availability in patients with anemia or compromised cardiac function via an increase in systemic p50. This increase in systemic p50 can be achieved with small molecule drugs or a packed red blood cell unit processing variant called rejuvenation, and human trials are needed to better understand the potential clinical benefits to modulating p50.

Rhodium clustering process on defective (8,0) SWCNT: Analysis of chemical and physical properties using density functional theory

NASA Astrophysics Data System (ADS)

Ambrusi, Ruben E.; Luna, C. Romina; Sandoval, Mario G.; Bechthold, Pablo; Pronsato, M. Estela; Juan, Alfredo

2017-12-01

The Spin-polarized density functional theory is used to study the effect of a single vacancy in a (8,0) single-walled carbon nanotube (SWCNT) on the Rh clustering process. The vacancy is considered oxygenated and non-oxygenated and, in each case, different Rhn cluster sizes (n = 1-4) are taken into account. For the analysis of these systems some physical and chemical properties are calculated, such as binding energy (Eb), work function (WF), magnetic moment, charge transfer, bond length, band gap (Eg), and density of state (DOS). From this analysis it can be concluded that: a single Rh atom and Rh2 dimer are adsorbed on vacancy without oxygen, whereas Rh3 and Rh4 clusters prefer to be adsorbed on oxygenated vacancy. In all cases, Rh adsorption induces a magnetic moment. When the Rh atom and Rh2 dimer are bonded to the defective SWCNT, it has been found that they show a semiconductor behavior that could be interesting to use in the spintronic area. In the case of Rh3 and Rh4 clusters our results show a metallic behavior suggesting that these systems are good candidates for nanotube contact.

Magnetism and Metal-Insulator Transition in Oxygen Deficient SrTiO 3

DOE PAGES

Lopez-Bezanilla, Alejandro; Ganesh, Panchapakesan; Littlewood, Peter B.

2015-09-08

First-principles calculations to study the electronic and magnetic properties of bulk, oxygen-deficient SrTiO 3 (STO) under different doping conditions and densities have been conducted. The appearance of magnetism in oxygen-deficient STO is not determined solely by the presence of a single oxygen vacancy but by the density of free carriers and the relative proximity of the vacant sites. We find that while an isolated vacancy behaves as a nonmagnetic double donor, manipulation of the doping conditions allows the stability of a single-donor state, with emergent local moments coupled ferromagnetically by carriers in the conduction band. Strong local lattice distortions enhancemore » the binding of this state. As a result, the energy of the in-gap local moment can be further tuned by orthorhombic strain. Consequently we find that the free-carrier density and strain are fundamental components to obtaining trapped spin-polarized electrons in oxygen-deficient STO, which may have important implications in the design of optical devices.« less

Oxygen Vacancies in ZnO Nanosheets Enhance CO2 Electrochemical Reduction to CO.

PubMed

Geng, Zhigang; Kong, Xiangdong; Chen, Weiwei; Su, Hongyang; Liu, Yan; Cai, Fan; Wang, Guoxiong; Zeng, Jie

2018-05-22

As electron transfer to CO 2 is generally considered to be the critical step during the activation of CO 2 , it is important to develop approaches to engineer the electronic properties of catalysts to improve their performance in CO 2 electrochemical reduction. Herein, we developed an efficient strategy to facilitate CO 2 activation by introducing oxygen vacancies into electrocatalysts with electronic-rich surface. ZnO nanosheets rich in oxygen vacancies exhibited a current density of -16.1 mA cm -2 with a Faradaic efficiency of 83 % for CO production. Based on density functional theory (DFT) calculations, the introduction of oxygen vacancies increased the charge density of ZnO around the valence band maximum, resulting in the enhanced activation of CO 2 . Mechanistic studies further revealed that the enhancement of CO production by introducing oxygen vacancies into ZnO nanosheets originated from the increased binding strength of CO 2 and the eased CO 2 activation. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tuning the Redox Properties of a Nonheme Iron(III)-Peroxo Complex Binding Redox-Inactive Zinc Ions by Water Molecules.

PubMed

Lee, Yong-Min; Bang, Suhee; Yoon, Heejung; Bae, Seong Hee; Hong, Seungwoo; Cho, Kyung-Bin; Sarangi, Ritimukta; Fukuzumi, Shunichi; Nam, Wonwoo

2015-07-20

Redox-inactive metal ions play important roles in tuning chemical properties of metal-oxygen intermediates. Herein we report the effect of water molecules on the redox properties of a nonheme iron(III)-peroxo complex binding redox-inactive metal ions. The coordination of two water molecules to a Zn(2+) ion in (TMC)Fe(III) -(O2 )-Zn(CF3 SO3 )2 (1-Zn(2+) ) decreases the Lewis acidity of the Zn(2+) ion, resulting in the decrease of the one-electron oxidation and reduction potentials of 1-Zn(2+) . This further changes the reactivities of 1-Zn(2+) in oxidation and reduction reactions; no reaction occurred upon addition of an oxidant (e.g., cerium(IV) ammonium nitrate (CAN)) to 1-Zn(2+) , whereas 1-Zn(2+) coordinating two water molecules, (TMC)Fe(III) -(O2 )-Zn(CF3 SO3 )2 -(OH2 )2 [1-Zn(2+) -(OH2 )2 ], releases the O2 unit in the oxidation reaction. In the reduction reactions, 1-Zn(2+) was converted to its corresponding iron(IV)-oxo species upon addition of a reductant (e.g., a ferrocene derivative), whereas such a reaction occurred at a much slower rate in the case of 1-Zn(2+) -(OH2 )2 . The present results provide the first biomimetic example showing that water molecules at the active sites of metalloenzymes may participate in tuning the redox properties of metal-oxygen intermediates. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tuning the Redox Properties of a Nonheme Iron(III)-Peroxo Complex Binding Redox-Inactive Zinc Ions by Water Molecules

DOE PAGES

Lee, Yong-Min; Bang, Suhee; Yoon, Heejung; ...

2015-06-19

Here we report redox-inactive metal ions play important roles in tuning chemical properties of metal–oxygen intermediates. We describe the effect of water molecules on the redox properties of a nonheme iron(III)–peroxo complex binding redox-inactive metal ions. The coordination of two water molecules to a Zn 2+ ion in (TMC)Fe III-(O 2)-Zn(CF 3SO 3) 2 (1-Zn 2+) decreases the Lewis acidity of the Zn 2+ ion, resulting in the decrease of the one-electron oxidation and reduction potentials of 1-Zn 2+. This further changes the reactivities of 1-Zn 2+ in oxidation and reduction reactions; no reaction occurred upon addition of an oxidantmore » (e.g., cerium(IV) ammonium nitrate (CAN)) to 1-Zn 2+, whereas 1-Zn 2+ coordinating two water molecules, (TMC)Fe III-(O 2)-Zn(CF 3SO 3) 2-(OH 2) 2 [1-Zn 2+-(OH 2) 2], releases the O 2 unit in the oxidation reaction. In the reduction reactions, 1-Zn 2+ was converted to its corresponding iron(IV)–oxo species upon addition of a reductant (e.g., a ferrocene derivative), whereas such a reaction occurred at a much slower rate in the case of 1-Zn 2+-(OH 2) 2. Finally, the present results provide the first biomimetic example showing that water molecules at the active sites of metalloenzymes may participate in tuning the redox properties of metal–oxygen intermediates.« less

Cloned Hemoglobin Genes Enhance Growth Of Cells

NASA Technical Reports Server (NTRS)

Khosla, Chaitan; Bailey, James E.

1991-01-01

Experiments show that portable deoxyribonucleic acid (DNA) sequences incorporated into host cells make them produce hemoglobins - oxygen-binding proteins essential to function of red blood cells. Method useful in several biotechnological applications. One, enhancement of growth of cells at higher densities. Another, production of hemoglobin to enhance supplies of oxygen in cells, for use in chemical reactions requiring oxygen, as additive to serum to increase transport of oxygen, and for binding and separating oxygen from mixtures of gases.

Three-state combinatorial switch models as applied to the binding of oxygen by human hemoglobin.

PubMed

Straume, M; Johnson, M L

1988-02-23

We have generated a series of all 6561 unique, discrete three-state combinatorial switch models to describe the partitioning of the cooperative oxygen-binding free change among the 10 variously ligated forms of human hemoglobin tetramers. These models were inspired by the experimental observation of Smith and Ackers that the cooperative free energy of the intersubunit contact regions of the 10 possible ligated forms of human hemoglobin tetramers can be represented by a particular distribution of three distinct energy levels [Smith, F. R., & Ackers, G. K. (1985) Proc. Natl. Acad. Sci. U.S.A. 82, 5347-5351]. A statistical thermodynamic formulation accounting for both dimer-tetramer equilibria and ligand binding properties of hemoglobin solutions as a function of oxygen and protein concentrations was utilized to exhaustively test these thermodynamic models. In this series of models each of the 10 ligated forms of the hemoglobin tetramer can exist in one, and only one, of three possible energy levels; i.e., each ligated form was assumed to be associated with a discrete energy state. This series of models includes all possible ways that the 10 ligation states of hemoglobin can be distributed into three distinct cooperative energy levels. The mathematical models, as presented here, do not permit equilibria between energy states to exist for any of the 10 unique ligated forms of hemoglobin tetramers. These models were analyzed by nonlinear least-squares estimation of the free energy parameters characteristic of this statistical thermodynamic development.(ABSTRACT TRUNCATED AT 250 WORDS)

The PpaA/AerR regulators of photosynthesis gene expression from anoxygenic phototrophic proteobacteria contain heme-binding SCHIC domains.

PubMed

Moskvin, Oleg V; Gilles-Gonzalez, Marie-Alda; Gomelsky, Mark

2010-10-01

The SCHIC domain of the B12-binding domain family present in the Rhodobacter sphaeroides AppA protein binds heme and senses oxygen. Here we show that the predicted SCHIC domain PpaA/AerR regulators also bind heme and respond to oxygen in vitro, despite their low sequence identity with AppA.

Purification, crystallization and preliminary X-ray analysis of haemoglobin from ostrich (Struthio camelus).

PubMed

Sundaresan, S S; Ramesh, P; Sivakumar, K; Ponnuswamy, M N

2009-07-01

Haemoglobin is a tetrameric protein that carries oxygen from the lungs to tissues and carbon dioxide from tissues back to the lungs. The oxygen-binding properties of haemoglobin are regulated through the binding of allosteric effectors. The respiratory system of avian species is unique and complex in nature when compared with that of mammals. In avian species, inositol pentaphosphate (inositol-P(5)) is present in the erythrocytes of the adult and is thought to be the major factor responsible for the relatively high oxygen affinity of the whole blood. The ostrich (Struthio camelus) is a large flightless bird which contains inositol tetrakisphosphate (inositol-P(4)) in its erythrocytes and its whole blood oxygen affinity is higher. Efforts have been made to explore the structure-function relationship of ostrich haemoglobin. Ostrich haemoglobin was purified using ion-exchange chromatography. Haemoglobin crystals were grown by the hanging-drop vapour-diffusion method using PEG 3350 as the precipitant in 50 mM phosphate buffer pH 7.2. Data were collected using a MAR345 image-plate detector system. The crystals of ostrich haemoglobin diffracted to 2.2 A resolution. They belonged to the orthorhombic space group P2(1)2(1)2(1) with one whole biological molecule in the asymmetric unit; the unit-cell parameters were a = 80.93, b = 81.68, c = 102.05 A.

An Unprecedented NADPH Domain Conformation in Lysine Monooxygenase NbtG Provides Insights into Uncoupling of Oxygen Consumption from Substrate Hydroxylation

DOE PAGES

Binda, Claudia; Robinson, Reeder M.; Martin del Campo, Julia S.; ...

2015-03-23

N-hydroxylating monooxygenases (NMOs) are involved in the biosynthesis of iron-chelating hydroxamate-containing siderophores that play a role in microbial virulence. These flavoenzymes catalyze the NADPH- and oxygen-dependent hydroxylation of amines, such as those found on the side chains of lysine and ornithine. In this work we report the biochemical and structural characterization of Nocardia farcinica Lys monooxygenase (NbtG), which has similar biochemical properties to mycobacterial homologs. NbtG is also active on D-Lys although it binds L-Lys with a higher affinity. Differently from the ornithine monooxygenases PvdA, SidA and KtzI, NbtG can use both NADH and NADPH and is highly uncoupled, producingmore » more superoxide and hydrogen peroxide than hydroxylated Lys. The crystal structure of NbtG solved at 2.4 Å resolution revealed an unexpected protein conformation with a 30° rotation of the NAD(P)H domain with respect to the FAD domain that precludes binding of the nicotinamide cofactor. This “occluded” structure may explain the biochemical properties of NbtG, specifically with regard to the substantial uncoupling and limited stabilization of the C4a-hydroperoxyflavin intermediate. We discuss the biological implications of these findings.« less

Three-dimensional quantitative structure-activity relationship modeling of cocaine binding by a novel human monoclonal antibody.

PubMed

Paula, Stefan; Tabet, Michael R; Farr, Carol D; Norman, Andrew B; Ball, W James

2004-01-01

Human monoclonal antibodies (mAbs) designed for immunotherapy have a high potential for avoiding the complications that may result from human immune system responses to the introduction of nonhuman mAbs into patients. This study presents a characterization of cocaine/antibody interactions that determine the binding properties of the novel human sequence mAb 2E2 using three-dimensional quantitative structure-activity relationship (3D-QSAR) methodology. We have experimentally determined the binding affinities of mAb 2E2 for cocaine and 38 cocaine analogues. The K(d) of mAb 2E2 for cocaine was 4 nM, indicating a high affinity. Also, mAb 2E2 displayed good cocaine specificity, as reflected in its 10-, 1500-, and 25000-fold lower binding affinities for the three physiologically relevant cocaine metabolites benzoylecgonine, ecgonine methyl ester, and ecgonine, respectively. 3D-QSAR models of cocaine binding were developed by comparative molecular similarity index analysis (CoMSIA). A model of high statistical quality was generated showing that cocaine binds to mAb 2E2 in a sterically restricted binding site that leaves the methyl group attached to the ring nitrogen of cocaine solvent-exposed. The methyl ester group of cocaine appears to engage in attractive van der Waals interactions with mAb 2E2, whereas the phenyl group contributes to the binding primarily via hydrophobic interactions. The model further indicated that an increase in partial positive charge near the nitrogen proton and methyl ester carbonyl group enhances binding affinity and that the ester oxygen likely forms an intermolecular hydrogen bond with mAb 2E2. Overall, the cocaine binding properties of mAb 2E2 support its clinical potential for development as a treatment of cocaine overdose and addiction.

Water-Soluble Chlorophyll Protein (WSCP) Stably Binds Two or Four Chlorophylls.

PubMed

Palm, Daniel M; Agostini, Alessandro; Tenzer, Stefan; Gloeckle, Barbara M; Werwie, Mara; Carbonera, Donatella; Paulsen, Harald

2017-03-28

Water-soluble chlorophyll proteins (WSCPs) of class IIa from Brassicaceae form tetrameric complexes containing one chlorophyll (Chl) per apoprotein but no carotenoids. The complexes are remarkably stable toward dissociation and protein denaturation even at 100 °C and extreme pH values, and the Chls are partially protected against photooxidation. There are several hypotheses that explain the biological role of WSCPs, one of them proposing that they function as a scavenger of Chls set free upon plant senescence or pathogen attack. The biochemical properties of WSCP described in this paper are consistent with the protein acting as an efficient and flexible Chl scavenger. At limiting Chl concentrations, the recombinant WSCP apoprotein binds substoichiometric amounts of Chl (two Chls per tetramer) to form complexes that are as stable toward thermal dissociation, denaturation, and photodamage as the fully pigmented ones. If more Chl is added, these two-Chl complexes can bind another two Chls to reach the fully pigmented state. The protection of WSCP Chls against photodamage has been attributed to the apoprotein serving as a diffusion barrier for oxygen, preventing its access to triplet excited Chls and, thus, the formation of singlet oxygen. By contrast, the sequential binding of Chls by WSCP suggests a partially open or at least flexible structure, raising the question of how WSCP photoprotects its Chls without the help of carotenoids.

A Specific Peptide with Calcium-Binding Capacity from Defatted Schizochytrium sp. Protein Hydrolysates and the Molecular Properties.

PubMed

Cai, Xixi; Yang, Qian; Lin, Jiaping; Fu, Nanyan; Wang, Shaoyun

2017-03-29

Marine microorganisms have been proposed as a new kind of protein source. Efforts are needed in order to transform the protein-rich biological wastes left after lipid extraction into value-added bio-products. Thus, the utilization of protein recovered from defatted Schizochytrium sp. by-products presents an opportunity. A specific peptide Tyr-Leu (YL) with calcium-binding capacity was purified from defatted Schizochytrium sp. protein hydrolysates through gel filtration chromatography and RP-HPLC. The calcium-binding activity of YL reached 126.34 ± 3.40 μg/mg. The calcium-binding mechanism was investigated through ultraviolet, fluorescence and infrared spectroscopy. The results showed that calcium ions could form dative bonds with carboxyl oxygen atoms and amino nitrogen atoms as well as the nitrogen and oxygen atoms of amide bonds. YL-Ca exhibited excellent thermal stability and solubility, which was beneficial for its absorption and transport in the basic intestinal tract of the human body. Moreover, the cellular uptake of calcium in Caco-2 cells showed that YL-Ca could enhance calcium uptake efficiency and protect calcium ions against precipitation caused by dietary inhibitors such as tannic acid, oxalate, phytate and metal ions. The findings indicate that the by-product of Schizochytrium sp. is a promising source for making peptide-calcium bio-products as algae-based functional supplements for human beings.

Electrostatic interaction of positive charges on the surface of Psb31 with photosystem II in the diatom Chaetoceros gracilis.

PubMed

Nagao, Ryo; Suzuki, Takehiro; Okumura, Akinori; Kihira, Tomohiro; Toda, Ayaka; Dohmae, Naoshi; Nakazato, Katsuyoshi; Tomo, Tatsuya

2017-09-01

Psb31, a novel extrinsic protein found in diatom photosystem II (PSII), directly binds to PSII core subunits, independent of the other extrinsic proteins, and functions to maintain optimum oxygen evolution. However, how Psb31 electrostatically interacts with PSII intrinsic proteins remains to be clarified. In this study, we examined electrostatic interaction of Psb31 with PSII complexes isolated from the diatom Chaetoceros gracilis. Positive or negative charges of isolated Psb31 proteins were modified with N-succinimidyl propionate (NSP) or glycine methyl ester (GME), respectively, resulting in formation of uncharged groups. NSP-modified Psb31 did not bind to PSII with a concomitant increase in NSP concentration, whereas GME-modified Psb31 clearly bound to PSII with retention of oxygen-evolving activity, indicating that positive charges of Lys residues and the N-terminus on the surface of Psb31 are involved in electrostatic interactions with PSII intrinsic proteins. Mass spectrometry analysis of NSP-modified Psb31 and sequence comparisons of Psb31 from C. gracilis with other chromophyte algae led to identification of three Lys residues as possible binding sites to PSII. Based on these findings, together with our previous cross-linking study in diatom PSII and a red algal PSII structure, we discuss binding properties of Psb31 with PSII core proteins. Copyright © 2017 Elsevier B.V. All rights reserved.

First-second shell interactions in metal binding sites in proteins: a PDB survey and DFT/CDM calculations.

PubMed

Dudev, Todor; Lin, Yen-lin; Dudev, Minko; Lim, Carmay

2003-03-12

The role of the second shell in the process of metal binding and selectivity in metalloproteins has been elucidated by combining Protein Data Bank (PDB) surveys of Mg, Mn, Ca, and Zn binding sites with density functional theory/continuum dielectric methods (DFT/CDM). Peptide backbone groups were found to be the most common second-shell ligand in Mg, Mn, Ca, and Zn binding sites, followed (in decreasing order) by Asp/Glu, Lys/Arg, Asn/Gln, and Ser/Thr side chains. Aromatic oxygen- or nitrogen-containing side chains (Tyr, His, and Trp) and sulfur-containing side chains (Cys and Met) are seldom found in the second coordination layer. The backbone and Asn/Gln side chain are ubiquitous in the metal second coordination layer as their carbonyl oxygen and amide hydrogen can act as a hydrogen-bond acceptor and donor, respectively, and can therefore partner practically every first-shell ligand. The second most common outer-shell ligand, Asp/Glu, predominantly hydrogen bonds to a metal-bound water or Zn-bound histidine and polarizes the H-O or H-N bond. In certain cases, a second-shell Asp/Glu could affect the protonation state of the metal ligand. It could also energetically stabilize a positively charged metal complex more than a neutral ligand such as the backbone and Asn/Gln side chain. As for the first shell, the second shell is predicted to contribute to the metal selectivity of the binding site by discriminating between metal cations of different ionic radii and coordination geometries. The first-shell-second-shell interaction energies decay rapidly with increasing solvent exposure of the metal binding site. They are less favorable but are of the same order of magnitude as compared to the respective metal-first-shell interaction energies. Altogether, the results indicate that the structure and properties of the second shell are dictated by those of the first layer. The outer shell is apparently designed to stabilize/protect the inner-shell and complement/enhance its properties.

Electron paramagnetic resonance spectral study of [Mn(acs){sub 2}(2–pic){sub 2}(H{sub 2}O){sub 2}] single crystals

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

Kocakoç, Mehpeyker, E-mail: mkocakoc@cu.edu.tr; Tapramaz, Recep, E-mail: recept@omu.edu.tr

Acesulfame potassium salt is a synthetic and non-caloric sweetener. It is also important chemically for its capability of being ligand in coordination compounds, because it can bind over Nitrogen and Oxygen atoms of carbonyl and sulfonyl groups and ring oxygen. Some acesulfame containing transition metal ion complexes with mixed ligands exhibit solvato and thermo chromic properties and these properties make them physically important. In this work single crystals of Mn{sup +2} ion complex with mixed ligand, [Mn(acs){sub 2}(2-pic){sub 2}(H{sub 2}O){sub 2}], was studied with electron paramagnetic resonance (EPR) spectroscopy. EPR parameters were determined. Zero field splitting parameters indicated that themore » complex was highly symmetric. Variable temperature studies showed no detectable chance in spectra.« less

Passive transport and binding of lead by human red blood cells.

PubMed

Simons, T J

1986-09-01

The uptake of Pb into human red blood cells has been studied using Pb buffers. Passive Pb movements can be studied conveniently when the cells are depleted of adenosine 5'-triphosphate (ATP), to eliminate active transport, and of inorganic phosphate, to prevent precipitation of lead phosphate. Pb can cross the membrane passively in either direction. Influx and efflux show similar properties. Passive Pb transport is strongly stimulated by HCO3-, and is reduced by replacing Cl- with ClO4-. It is inhibited by low concentrations of 4-acetamido-4'-isothiocyanostilbene-2,2'-disulphonic acid (SITS) and 4,4'-diisothiocyanostilbene-2.2'-disulphonic acid (DIDS), characteristic inhibitors of anion transport. Pb uptake is unaffected by varying the external concentrations of Na+, K+ and Ca2+. When Pb enters the cell, it binds mainly to haemoglobin. The ratio of bound Pb:free Pb2+ in the cytosol is estimated to be 6000:1. Pb binding to haemoglobin is unaffected by oxygenation. Binding to albumin is quantitatively similar to binding to haemoglobin. The implications of these results for the transport and binding of Pb in the blood are discussed.

The complex of hypericin with β-lactoglobulin has antimicrobial activity with potential applications in dairy industry.

PubMed

Rodríguez-Amigo, Beatriz; Delcanale, Pietro; Rotger, Gabriel; Juárez-Jiménez, Jordi; Abbruzzetti, Stefania; Summer, Andrea; Agut, Montserrat; Luque, F Javier; Nonell, Santi; Viappiani, Cristiano

2015-01-01

Using a combination of molecular modeling and spectroscopic experiments, the naturally occurring, pharmacologically active hypericin compound is shown to form a stable complex with the dimeric form of β-lactoglobulin (β-LG). Binding is predicted to occur at the narrowest cleft found at the interface between monomers in the dimeric β-LG. The complex is able to preserve the fluorescence and singlet oxygen photosensitizing properties of the dye. The equilibrium constant for hypericin binding has been determined as Ka=1.40±0.07µM(-1), equivalent to a dissociation constant, Kd=0.71±0.03µM. The complex is active against Staphylococcus aureus bacteria. Overall, the results are encouraging for pursuing the potential application of the complex between hypericin and β-LG as a nanodevice with bactericidal properties for disinfection. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Subsurface Oxygen in Oxide-Derived Copper Electrocatalysts for Carbon Dioxide Reduction

DOE PAGES

Eilert, Andre; Cavalca, Filippo; Roberts, F. Sloan; ...

2016-12-16

Copper electrocatalysts derived from an oxide have shown extraordinary electrochemical properties for the carbon dioxide reduction reaction (CO 2RR). Using in situ ambient pressure X-ray photoelectron spectroscopy and quasi in situ electron energy-loss spectroscopy in a transmission electron microscope, we show that there is a substantial amount of residual oxygen in nanostructured, oxide-derived copper electrocatalysts but no residual copper oxide. On the basis of these findings in combination with density functional theory simulations, we propose that residual subsurface oxygen changes the electronic structure of the catalyst and creates sites with higher carbon monoxide binding energy. If such sites are stablemore » under the strongly reducing conditions found in CO 2RR, these findings would explain the high efficiencies of oxide-derived copper in reducing carbon dioxide to multicarbon compounds such as ethylene.« less

Novel single-cell functional analysis of red blood cells using laser tweezers Raman spectroscopy: application for sickle cell disease.

PubMed

Liu, Rui; Mao, Ziliang; Matthews, Dennis L; Li, Chin-Shang; Chan, James W; Satake, Noriko

2013-07-01

Laser tweezers Raman spectroscopy was used to characterize the oxygenation response of single normal adult, sickle, and cord blood red blood cells (RBCs) to an applied mechanical force. Individual cells were subjected to different forces by varying the laser power of a single-beam optical trap, and the intensities of several oxygenation-specific Raman spectral peaks were monitored to determine the oxygenation state of the cells. For all three cell types, an increase in laser power (or mechanical force) induced a greater deoxygenation of the cell. However, sickle RBCs deoxygenated more readily than normal RBCs when subjected to the same optical forces. Conversely, cord blood RBCs were able to maintain their oxygenation better than normal RBCs. These results suggest that differences in the chemical or mechanical properties of fetal, normal, and sickle cells affect the degree to which applied mechanical forces can deoxygenate the cell. Populations of normal, sickle, and cord RBCs were identified and discriminated based on this mechanochemical phenomenon. This study demonstrates the potential application of laser tweezers Raman spectroscopy as a single-cell, label-free analytical tool to characterize the functional (e.g., mechanical deformability, oxygen binding) properties of normal and diseased RBCs. Copyright © 2013 ISEH - Society for Hematology and Stem Cells. Published by Elsevier Inc. All rights reserved.

Theoretical studies of Pt-Ti nanoparticles for potential use as PEMFC electrocatalysts.

PubMed

Jennings, Paul C; Pollet, Bruno G; Johnston, Roy L

2012-03-07

A theoretical investigation is presented of alloying platinum with titanium to form binary Pt-Ti nanoalloys as an alternative to the expensive pure platinum catalysts commonly used for Proton Exchange Membrane Fuel Cell cathode electrocatalysts. Density Functional Theory calculations are performed to investigate compositional effects on structural properties as well as Oxygen Reduction Reaction kinetics and poisoning effects. High symmetry A(32)-B(6) clusters are studied to investigate structural properties. From these structures binding energies of hydroxyl and carbon monoxide are studied on a range of sites on the surface of the clusters. Promising results are obtained suggesting that the bimetallic Pt-Ti nanoalloys may exhibit enhanced properties compared to pure platinum catalysts.

Direct Measurement of Equilibrium Constants for High-Affinity Hemoglobins

PubMed Central

Kundu, Suman; Premer, Scott A.; Hoy, Julie A.; Trent, James T.; Hargrove, Mark S.

2003-01-01

The biological functions of heme proteins are linked to their rate and affinity constants for ligand binding. Kinetic experiments are commonly used to measure equilibrium constants for traditional hemoglobins comprised of pentacoordinate ligand binding sites and simple bimolecular reaction schemes. However, kinetic methods do not always yield reliable equilibrium constants with more complex hemoglobins for which reaction mechanisms are not clearly understood. Furthermore, even where reaction mechanisms are clearly understood, it is very difficult to directly measure equilibrium constants for oxygen and carbon monoxide binding to high-affinity (KD ≪ 1 μM) hemoglobins. This work presents a method for direct measurement of equilibrium constants for high-affinity hemoglobins that utilizes a competition for ligands between the "target" protein and an array of "scavenger" hemoglobins with known affinities. This method is described for oxygen and carbon monoxide binding to two hexacoordinate hemoglobins: rice nonsymbiotic hemoglobin and Synechocystis hemoglobin. Our results demonstrate that although these proteins have different mechanisms for ligand binding, their affinities for oxygen and carbon monoxide are similar. Their large affinity constants for oxygen, 285 and ∼100 μM−1 respectively, indicate that they are not capable of facilitating oxygen transport. PMID:12770899

Identical linkage and cooperativity of oxygen and carbon monoxide binding to Octopus dofleini hemocyanin

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

Connelly, P.R.; Gill, S.J.; Miller, K.I.

1989-02-21

Employment of high-precision thin-layer methods has enabled detailed functional characterization of oxygen and carbon monoxide binding for (1) the fully assembled form with 70 binding sites and (2) the isolated chains with 7 binding sites of octopus dofleini hemocyanin. The striking difference in the cooperativities of the two ligands for the assembled decamer is revealed through an examination of the binding capacities and the partition coefficient, determined as functions of the activities of both ligands. A global analysis of the data sets supported by a two-state allosteric model assuming an allosteric unit of 7. Higher level allosteric interactions were notmore » indicated. This contrasts to results obtained for arthropod hemocyanins. Oxygen and carbon monoxide experiments performed on the isolated subunit chain confirmed the presence of functional heterogeneity reported previously. The analysis shows two types of binding sites in the ratio of 4:3.« less

Structural Basis of the Lactate-dependent Allosteric Regulation of Oxygen Binding in Arthropod Hemocyanin

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

Hirota, S.; Tanaka, N; Micetic, I

2010-01-01

Hemocyanin (Hc) is an oxygen carrier protein in which oxygen binding is regulated by allosteric effectors such as H{sup +} and L-lactate. Isothermal titration calorimetric measurements showed that L-lactate binds to dodecameric and heterohexameric Hc and to the CaeSS3 homohexamer but not to the CaeSS2 monomer. The binding of lactate caused no change in the optical absorption and x-ray absorption spectra of either oxy- or deoxy-Hc, suggesting that no structural rearrangement of the active site occurred. At pH 6.5, the oxygen binding rate constant k{sub obs} obtained by flash photolysis showed a significant increase upon addition of L-lactate, whereas L-lactatemore » addition had little effect at pH 8.3. Lactate binding caused a concentration-dependent shift in the interhexameric distances at pH 6.5 based on small angle x-ray scattering measurements. These results show that L-lactate affects oxygen affinity at pH 6.5 by modulating the global structure of Hc without affecting its binuclear copper center (the active site). In contrast to this, the active site structure of deoxy-Hc is affected by changes in pH (Hirota, S., Kawahara, T., Beltramini, M., Di Muro, P., Magliozzo, R. S., Peisach, J., Powers, L. S., Tanaka, N., Nagao, S., and Bubacco, L. (2008) J. Biol. Chem. 283, 31941-31948). Upon addiction of lactate, the kinetic behavior of oxygen rebinding for Hc was heterogeneous under low oxygen concentrations at pH 6.5 due to changes in the T and R state populations, and the equilibrium was found to shift from the T toward the R state with addition of lactate.« less

Novel FeII and CoII Complexes of Natural Product Tryptanthrin: Synthesis and Binding with G-Quadruplex DNA

PubMed Central

Zhong, Yi-ning; Zhang, Yan; Gu, Yun-qiong; Wu, Shi-yun; Shen, Wen-ying

2016-01-01

Tryptanthrin is one of the most important members of indoloquinoline alkaloids. We obtained this alkaloid from Isatis. Two novel FeII and CoII complexes of tryptanthrin were first synthesized. Single-crystal X-ray diffraction analyses show that these complexes display distorted four-coordinated tetrahedron geometry via two heterocyclic nitrogen and oxygen atoms from tryptanthrin ligand. Binding with G-quadruplex DNA properties revealed that both complexes were found to exhibit significant interaction with G-quadruplex DNA. This study may potentially serve as the basis of future rational design of metal-based drugs from natural products that target the G-quadruplex DNA. PMID:27698647

Aryloxyalkanoic Acids as Non-Covalent Modifiers of the Allosteric Properties of Hemoglobin

PubMed Central

Omar, Abdelsattar M.; Mahran, Mona A.; Ghatge, Mohini S.; Bamane, Faida H. A.; Ahmed, Mostafa H.; El-Araby, Moustafa E.; Abdulmalik, Osheiza; Safo, Martin K.

2017-01-01

Hemoglobin (Hb) modifiers that stereospecifically inhibit sickle hemoglobin polymer formation and/or allosterically increase Hb affinity for oxygen have been shown to prevent the primary pathophysiology of sickle cell disease (SCD), specifically, Hb polymerization and red blood cell sickling. Several such compounds are currently being clinically studied for the treatment of SCD. Based on the previously reported non-covalent Hb binding characteristics of substituted aryloxyalkanoic acids that exhibited antisickling properties, we designed, synthesized and evaluated 18 new compounds (KAUS II series) for enhanced antisickling activities. Surprisingly, select test compounds showed no antisickling effects or promoted erythrocyte sickling. Additionally, the compounds showed no significant effect on Hb oxygen affinity (or in some cases, even decreased the affinity for oxygen). The X-ray structure of deoxygenated Hb in complex with a prototype compound, KAUS-23, revealed that the effector bound in the central water cavity of the protein, providing atomic level explanations for the observed functional and biological activities. Although the structural modification did not lead to the anticipated biological effects, the findings provide important direction for designing candidate antisickling agents, as well as a framework for novel Hb allosteric effectors that conversely, decrease the protein affinity for oxygen for potential therapeutic use for hypoxic- and/or ischemic-related diseases. PMID:27529207

New insight into multifunctional role of peroxiredoxin family protein: Determination of DNA protection properties of bacterioferritin comigratory protein under hyperthermal and oxidative stresses

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

Lee, Sangmin, E-mail: taeinlee2011@kangwon.ac.kr; Chung, Jeong Min; Yun, Hyung Joong

Bacterioferritin comigratory protein (BCP) is a monomeric conformer acting as a putative thiol-dependent bacterial peroxidase, however molecular basis of DNA-protection via DNA-binding has not been clearly understood. In this study, we characterized the DNA binding properties of BCP using various lengths and differently shaped architectures of DNA. An electrophoretic mobility shift assay and electron microscopy analysis showed that recombinant TkBCP bound to DNA of a circular shape (double-stranded DNA and single-stranded DNA) and a linear shape (16–1000 bp) as well as various architectures of DNA. In addition, DNA protection experiments indicated that TkBCP can protect DNA against hyperthermal and oxidative stressmore » by removing highly reactive oxygen species (ROS) or by protecting DNA from thermal degradation. Based on these results, we suggest that TkBCP is a multi-functional DNA-binding protein which has DNA chaperon and antioxidant functions. - Highlights: • Bacterioferritin comigratory protein (BCP) protects DNA from oxidative stress by reducing ROS. • TkBCP does not only scavenge ROS, but also protect DNA from hyperthermal stress. • BCP potentially adopts the multi-functional role in DNA binding activities and anti-oxidant functions.« less

Allosteric modulation of ATP-gated P2X receptor channels

PubMed Central

Coddou, Claudio; Stojilkovic, Stanko S.; Huidobro-Toro, J. Pablo

2013-01-01

Seven mammalian purinergic receptor subunits, denoted P2X1 to P2X7, and several spliced forms of these subunits have been cloned. When heterologously expressed, these cDNAs encode ATP-gated non-selective cation channels organized as trimers. All activated receptors produce cell depolarization and promote Ca2+ influx through their pores and indirectly by activating voltage-gated calcium channels. However, the biophysical and pharmacological properties of these receptors differ considerably, and the majority of these subunits are also capable of forming heterotrimers with other members of the P2X receptor family, which confers further different properties. These channels have three ATP binding domains, presumably located between neighboring subunits, and occupancy of at least two binding sites is needed for their activation. In addition to the orthosteric binding sites for ATP, these receptors have additional allosteric sites that modulate the agonist action at receptors, including sites for trace metals, protons, neurosteroids, reactive oxygen species and phosphoinositides. The allosteric regulation of P2X receptors is frequently receptor-specific and could be a useful tool to identify P2X members in native tissues and their roles in signaling. The focus of this review is on common and receptor-specific allosteric modulation of P2X receptors and the molecular base accounting for allosteric binding sites. PMID:21639805

Periodic DFT study of acidic trace atmospheric gas molecule adsorption on Ca- and Fe-doped MgO(001) surface basic sites.

PubMed

Baltrusaitis, Jonas; Hatch, Courtney; Orlando, Roberto

2012-08-02

The electronic properties of undoped and Ca- or Fe-doped MgO(001) surfaces, as well as their propensity toward atmospheric acidic gas (CO2, SO2, and NO2) uptake was investigated with an emphasis on gas adsorption on the basic MgO oxygen surface sites, O(surf), using periodic density functional theory (DFT) calculations. Adsorption energy calculations show that MgO doping will provide stronger interactions of the adsorbate with the O(surf) sites than the undoped MgO for a given adsorbate molecule. Charge transfer from the iron atom in Fe-doped MgO(001) to NO2 was shown to increase the binding interaction between adsorbate by an order of magnitude, when compared to that of undoped and Ca-doped MgO(001) surfaces. Secondary binding interactions of adsorbate oxygen atoms were observed with surface magnesium sites at distances close to those of the Mg-O bond within the crystal. These interactions may serve as a preliminary step for adsorption and facilitate further adsorbate transformations into other binding configurations. Impacts on global atmospheric chemistry are discussed as these adsorption phenomena can affect atmospheric gas budgets via altered partitioning and retention on mineral aerosol surfaces.

Periodic DFT study of acidic trace atmospheric gas molecule adsorption on Ca and Fe doped MgO (001) surface basic sites

PubMed Central

Hatch, Courtney; Orlando, Roberto

2012-01-01

The electronic properties of undoped and Ca or Fe doped MgO (001) surfaces, as well as their propensity towards atmospheric acidic gas (CO2, SO2 and NO2) uptake was investigated with an emphasis on gas adsorption on the basic MgO oxygen surface sites, Osurf, using periodic Density Functional Theory (DFT) calculations. Adsorption energy calculations show that MgO doping will provide stronger interactions of the adsorbate with the Osurf sites than the undoped MgO for a given adsorbate molecule. Charge transfer from the iron atom in Fe doped MgO (001) to NO2 was shown to increase the binding interaction between adsorbate by an order of magnitude, when compared to that of undoped and Ca doped MgO (001) surfaces. Secondary binding interactions of adsorbate oxygen atoms were observed with surface magnesium sites at distances close to those of the Mg-O bond within the crystal. These interactions may serve as a preliminary step for adsorption and facilitate further adsorbate transformations into other binding configurations. Impacts on global atmospheric chemistry are discussed as these adsorption phenomena can affect atmospheric gas budgets via altered partitioning and retention on mineral aerosol surfaces. PMID:22775293

Human Cells Cultured under Physiological Oxygen Utilize Two Cap-binding Proteins to recruit Distinct mRNAs for Translation*

PubMed Central

Timpano, Sara; Uniacke, James

2016-01-01

Translation initiation is a focal point of translational control and requires the binding of eIF4E to the 5′ cap of mRNA. Under conditions of extreme oxygen depletion (hypoxia), human cells repress eIF4E and switch to an alternative cap-dependent translation mediated by a homolog of eIF4E, eIF4E2. This homolog forms a complex with the oxygen-regulated hypoxia-inducible factor 2α and can escape translation repression. This complex mediates cap-dependent translation under cell culture conditions of 1% oxygen (to mimic tumor microenvironments), whereas eIF4E mediates cap-dependent translation at 21% oxygen (ambient air). However, emerging evidence suggests that culturing cells in ambient air, or “normoxia,” is far from physiological or “normal.” In fact, oxygen in human tissues ranges from 1–11% or “physioxia.” Here we show that two distinct modes of cap-dependent translation initiation are active during physioxia and act on separate pools of mRNAs. The oxygen-dependent activities of eIF4E and eIF4E2 are elucidated by observing their polysome association and the status of mammalian target of rapamycin complex 1 (eIF4E-dependent) or hypoxia-inducible factor 2α expression (eIF4E2-dependent). We have identified oxygen conditions where eIF4E is the dominant cap-binding protein (21% normoxia or standard cell culture conditions), where eIF4E2 is the dominant cap-binding protein (1% hypoxia or ischemic diseases and cancerous tumors), and where both cap-binding proteins act simultaneously to initiate the translation of distinct mRNAs (1–11% physioxia or during development and stem cell differentiation). These data suggest that the physioxic proteome is generated by initiating translation of mRNAs via two distinct but complementary cap-binding proteins. PMID:27002144

Copper attachment to prion protein at a non-octarepeat site

NASA Astrophysics Data System (ADS)

Hodak, Miroslav; Bernholc, Jerry

2011-03-01

Prion protein (PrP) plays a causative role in a group of neurodegenerative diseases, which include ``mad cow disease'' or its human form variant Creutzfeld-Jacob disease. Normal function of PrP remains unknown, but it is now well established that PrP can efficiently bind copper ions and this ability has been linked to its function. The primary binding sites are located in the so-called octarepeat region located between residues 60-91. While these are by now well characterized, the sites located outside these region remain mostly undetermined. In this work, we investigate the properties of Cu binding site located at His 111 using recently developed hybrid Kohn-Sham/orbital-free density functional simulations. Experimental data indicate that copper is coordinated by either four nitrogens or three nitrogens and one oxygen. We investigate both possibilities, comparing their energetics and attachment geometries. Similarities and differences with other binding sites and implications for PrP function will also be discussed.

NADPH as a potential intrinsic probe for tumour margin estimation

NASA Astrophysics Data System (ADS)

Stewart, Hazel; Hupp, Ted R.; Birch, David J. S.

2018-03-01

The fluorescent properties of the reduced coenzyme NADH and its phosphorylated derivative (NADPH) have been explored in order to assess their potential as an intrinsic probe for cancer surgery. NADPH production is increased in cancer cells to quench reactive oxygen species and meet higher demands for biosynthesis, and has attractive fluorescent properties such as emission towards the visible part of the spectrum and a relatively long fluorescence lifetime upon binding to enzymes ( 1 - 6.5 ns) that helps discriminate against other endogenous species. Different environmental effects on NAD(P)H fluorescence are reported here, including an increase in lifetime upon oxygen removal, an ability to retain its fluorescent properties in a complex medium (a silica phantom) and its fluorescence lifetime also being distinguishable in a cell environment. In addition, the development of a miniaturized liquid light guide filter-based timecorrelated single photon counting fluorescence lifetime system is reported as a step towards time-resolved visual imaging in cancer surgery. This system has been demonstrated as being capable of accurately measuring NAD(P)H fluorescence lifetimes in both simple solvent and cellular environments.

Role of conserved cysteine residues in Herbaspirillum seropedicae NifA activity.

PubMed

Oliveira, Marco A S; Baura, Valter A; Aquino, Bruno; Huergo, Luciano F; Kadowaki, Marco A S; Chubatsu, Leda S; Souza, Emanuel M; Dixon, Ray; Pedrosa, Fábio O; Wassem, Roseli; Monteiro, Rose A

2009-01-01

Herbaspirillum seropedicae is an endophytic diazotrophic bacterium that associates with economically important crops. NifA protein, the transcriptional activator of nif genes in H. seropedicae, binds to nif promoters and, together with RNA polymerase-sigma(54) holoenzyme, catalyzes the formation of open complexes to allow transcription initiation. The activity of H. seropedicae NifA is controlled by ammonium and oxygen levels, but the mechanisms of such control are unknown. Oxygen sensitivity is attributed to a conserved motif of cysteine residues in NifA that spans the central AAA+ domain and the interdomain linker that connects the AAA+ domain to the C-terminal DNA binding domain. Here we mutagenized this conserved motif of cysteines and assayed the activity of mutant proteins in vivo. We also purified the mutant variants of NifA and tested their capacity to bind to the nifB promoter region. Chimeric proteins between H. seropedicae NifA, an oxygen-sensitive protein, and Azotobacter vinelandii NifA, an oxygen-tolerant protein, were constructed and showed that the oxygen response is conferred by the central AAA+ and C-terminal DNA binding domains of H. seropedicae NifA. We conclude that the conserved cysteine motif is essential for NifA activity, although single cysteine-to-serine mutants are still competent at binding DNA.

XPS of oxygen atoms on Ag(111) and Ag(110) surfaces: accurate study with SAC/SAC-CI combined with dipped adcluster model.

PubMed

Ishikawa, Atsushi; Nakatsuji, Hiroshi

2013-08-05

O1s core-electron binding energies (CEBE) of the atomic oxygens on different Ag surfaces were investigated by the symmetry adapted cluster-configuration interaction (SAC-CI) method combined with the dipped adcluster model, in which the electron exchange between bulk metal and adsorbate is taken into account properly. Electrophilic and nucleophilic oxygens (O(elec) and O(nuc)) that might be important for olefin epoxidation in a low-oxygen coverage condition were focused here. We consider the O1s CEBE as a key property to distinguish the surface oxygen states, and series of calculation was carried out by the Hartree-Fock, Density functional theory, and SAC/SAC-CI methods. The experimental information and our SAC/SAC-CI results indicate that O(elec) is the atomic oxygen adsorbed on the fcc site of Ag(111) and that O(nuc) is the one on the reconstructed added-row site of Ag(110) and that one- and two-electron transfers occur, respectively, to the O(elec) and O(nuc) adclusters from the silver surface. Copyright © 2013 Wiley Periodicals, Inc.

Properties of the glycoprotein laccase immobilized by two methods.

PubMed

Froehner, S C; Eriksson, K

1975-01-01

Laccase (p-diphenol:oxygen oxidoreductase; EC 1.10.3.2) from Neurospora crassa has been immobilized by two different procedures: (1) Covalent attachment to Sepharose 4B activated with cyanogen bromide, and (2) Adsorption to Concanavalin A-Sepharose via the carbohydrate moiety. Except for small changes in the Michaelis-Menten constants, no differences were noted in the enzymological properties of the immobilized enzymes when compared to free enzyme. The carbohydrate moiety of laccase involved in the interaction with Concanavalin A does not appear to be closely associated with the active center since binding to the lectin has no effect on the enzymological parameters investigated.

Hemoglobin Rahere, a human hemoglobin variant with amino acid substitution at the 2,3-diphosphoglycerate binding site. Functional consequences of the alteration and effects of bezafibrate on the oxygen bindings.

PubMed

Sugihara, J; Imamura, T; Nagafuchi, S; Bonaventura, J; Bonaventura, C; Cashon, R

1985-09-01

We encountered an abnormal hemoglobin (Rahere), with a threonine residue replacing the beta 82 (EF6) lysine residue at the binding site of 2,3-diphosphoglycerate, which was responsible for overt erythrocytosis in two individuals of a Japanese family. Hemoglobin Rahere shows a lower oxygen affinity on the binding of 2,3-diphosphoglycerate or chloride ions than hemoglobin A. Although a decrease in the positive charge density at the binding sites of 2,3-diphosphoglycerate in hemoglobin Rahere apparently shifts the allosteric equilibrium toward the low affinity state, it greatly diminishes the cofactor effects by anions. The oxygen affinity of the patient's erythrocytes is substantially lowered by the presence of bezafibrate, which combines with sites different from those of 2,3-diphosphoglycerate in either hemoglobin Rahere or hemoglobin A.

Hemoglobin Rahere, a human hemoglobin variant with amino acid substitution at the 2,3-diphosphoglycerate binding site. Functional consequences of the alteration and effects of bezafibrate on the oxygen bindings.

PubMed Central

Sugihara, J; Imamura, T; Nagafuchi, S; Bonaventura, J; Bonaventura, C; Cashon, R

1985-01-01

We encountered an abnormal hemoglobin (Rahere), with a threonine residue replacing the beta 82 (EF6) lysine residue at the binding site of 2,3-diphosphoglycerate, which was responsible for overt erythrocytosis in two individuals of a Japanese family. Hemoglobin Rahere shows a lower oxygen affinity on the binding of 2,3-diphosphoglycerate or chloride ions than hemoglobin A. Although a decrease in the positive charge density at the binding sites of 2,3-diphosphoglycerate in hemoglobin Rahere apparently shifts the allosteric equilibrium toward the low affinity state, it greatly diminishes the cofactor effects by anions. The oxygen affinity of the patient's erythrocytes is substantially lowered by the presence of bezafibrate, which combines with sites different from those of 2,3-diphosphoglycerate in either hemoglobin Rahere or hemoglobin A. PMID:3930571

Dynamics, magnetic properties, and electron binding energies of H2O2 in water.

PubMed

C Cabral, Benedito J

2017-06-21

Results for the magnetic properties and electron binding energies of H 2 O 2 in liquid water are presented. The adopted methodology relies on the combination of Born-Oppenheimer molecular dynamics and electronic structure calculations. The Keal-Tozer functional was applied for predicting magnetic shieldings and H 2 O 2 intramolecular spin-spin coupling constants. Electron binding energies were calculated with electron propagator theory. In water, H 2 O 2 is a better proton donor than proton acceptor, and the present results indicate that this feature is important for understanding magnetic properties in solution. In comparison with the gas-phase, H 2 O 2 atoms are deshielded in water. For oxygen atoms, the deshielding is mainly determined by structural/conformational changes. Hydrogen-bond interactions explain the deshielding of protons in water. The predicted chemical shift for the H 2 O 2 protons in water (δ∼11.8 ppm) is in good agreement with experimental information (δ=11.2 ppm). The two lowest electron binding energies of H 2 O 2 in water (10.7±0.5 and 11.2±0.5 eV) are in reasonable agreement with experiment. In keeping with data from photoelectron spectroscopy, an ∼1.6 eV red-shift of the two first ionisation energies relative to the gas-phase is observed in water. The strong dependence of magnetic properties on changes of the electronic density in the nuclei environment is illustrated by a correlation between the σ( 17 O) magnetic shielding constant and the energy gap between the [2a] lowest valence and [1a] core orbitals of H 2 O 2 .

Binding of tetramethylammonium to polyether side-chained aromatic hosts. Evaluation of the binding contribution from ether oxygen donors.

PubMed

Bartoli, Sandra; De Nicola, Gina; Roelens, Stefano

2003-10-17

A set of macrocyclic and open-chain aromatic ligands endowed with polyether side chains has been prepared to assess the contribution of ether oxygen donors to the binding of tetramethylammonium (TMA), a cation believed incapable of interacting with oxygen donors. The open-chain hosts consisted of an aromatic binding site and side chains possessing a variable number of ether oxygen donors; the macrocyclic ligands were based on the structure of a previously investigated host, the dimeric cyclophane 1,4-xylylene-1,4-phenylene diacetate (DXPDA), implemented with polyether-type side chains in the backbone. Association to tetramethylammonium picrate (TMAP) was measured in CDCl(3) at T = 296 K by (1)H NMR titrations. Results confirm that the main contribution to the binding of TMA comes from the cation-pi interaction established with the aromatic binding sites, but they unequivocally show that polyether chains participate with cooperative contributions, although of markedly smaller entity. Water is also bound, but the two guests interact with aromatic rings and oxygen donors in an essentially noncompetitive way. An improved procedure for the preparation of cyclophanic tetraester derivatives has been developed that conveniently recycles the oligomeric ester byproducts formed in the one-pot cyclization reaction. An alternative entry to benzylic diketones has also been provided that makes use of a low-order cyanocuprate reagent to prepare in fair yields a class of compounds otherwise uneasily accessible.

Passive transport and binding of lead by human red blood cells.

PubMed Central

Simons, T J

1986-01-01

The uptake of Pb into human red blood cells has been studied using Pb buffers. Passive Pb movements can be studied conveniently when the cells are depleted of adenosine 5'-triphosphate (ATP), to eliminate active transport, and of inorganic phosphate, to prevent precipitation of lead phosphate. Pb can cross the membrane passively in either direction. Influx and efflux show similar properties. Passive Pb transport is strongly stimulated by HCO3-, and is reduced by replacing Cl- with ClO4-. It is inhibited by low concentrations of 4-acetamido-4'-isothiocyanostilbene-2,2'-disulphonic acid (SITS) and 4,4'-diisothiocyanostilbene-2.2'-disulphonic acid (DIDS), characteristic inhibitors of anion transport. Pb uptake is unaffected by varying the external concentrations of Na+, K+ and Ca2+. When Pb enters the cell, it binds mainly to haemoglobin. The ratio of bound Pb:free Pb2+ in the cytosol is estimated to be 6000:1. Pb binding to haemoglobin is unaffected by oxygenation. Binding to albumin is quantitatively similar to binding to haemoglobin. The implications of these results for the transport and binding of Pb in the blood are discussed. PMID:3795106

Short-range correlations in carbon-12, oxygen-16, and neon-20: Intrinsic properties

NASA Technical Reports Server (NTRS)

Braley, R. C.; Ford, W. F.; Becker, R. L.; Patterson, M. R.

1972-01-01

The Brueckner-Hartree-Fock (BHF) method has been applied to nuclei whose intrinsic structure is nonspherical. Reaction matrix elements were calculated as functions of starting energy for the Hamada-Johnston interaction using the Pauli operator appropriate to O-16 and a shifted oscillator spectrum for virtual excited states. Binding energies, single particle energies, radii, and shape deformations of the intrinsic state, in ordinary as well as renormalized BHF, are discussed and compared with previous HF studies and with experiment when possible. Results are presented for C-12, 0-16 and Ne-20. It is found that the binding energies and radii are too small, but that separation energies are well reproduced when the renormalized theory is used.

More accurate depiction of adsorption energy on transition metals using work function as one additional descriptor.

PubMed

Shen, Xiaochen; Pan, Yanbo; Liu, Bin; Yang, Jinlong; Zeng, Jie; Peng, Zhenmeng

2017-05-24

The reaction mechanism and properties of a catalytic process are primarily determined by the interactions between reacting species and catalysts. However, the interactions are often challenging to be experimentally measured, especially for unstable intermediates. Therefore, it is of significant importance to establish an exact relationship between chemical-catalyst interactions and catalyst parameters, which will allow calculation of these interactions and thus advance their mechanistic understanding. Herein we report the description of adsorption energy on transition metals by considering both ionic bonding and covalent bonding contributions and introduce the work function as one additional responsible parameter. We find that the adsorption energy can be more accurately described using a two-dimensional (2D) polynomial model, which shows a significant improvement compared with the current adsorption energy-d-band center linear correlation. We also demonstrate the utilization of this new 2D polynomial model to calculate oxygen binding energy of different transition metals to help understand their catalytic properties in oxygen reduction reactions.

Structural changes at the metal ion binding site during the phosphoglucomutase reaction.

PubMed

Ray, W J; Post, C B; Liu, Y; Rhyu, G I

1993-01-12

An electron density map of the reactive, Cd2+ form of crystalline phosphoglucomutase from X-ray diffraction studies shows that the enzymic phosphate donates a nonbridging oxygen to the ligand sphere of the bound metal ion, which appears to be tetracoordinate. 31P and 113Cd NMR spectroscopy are used to assess changes in the properties of bound Cd2+ produced by substrate/product and by substrate/product analog inhibitors. The approximately 50 ppm downfield shift of the 113Cd resonance on formation of the complex of dephosphoenzyme and glucose 1,6-bisphosphate is associated with the initial sugar-phosphate binding step and likely involves a change in the geometry of the coordinating ligands. This interpretation is supported by spectral studies involving various complexes of the active Co2+ and Ni(2+)-enzyme. In addition, there is a loss of the 31P-113Cd J coupling that characterizes the monophosphate complexes of the Cd2+ enzyme either during or immediately after the PO3- transfer step that produces the bisphosphate complex, indicating a further change at the metal binding site. The implications of these observations with respect to the PO3- transfer process in the phosphoglucomutase reaction are considered. The apparent plasticity of the ligand sphere of the active site metal ion in this system may allow a single metal ion to act as a chaperone for a nonbridging oxygen during PO3- transfer or to allow a change in metal ion coordination during catalysis. A general NMR line shape/chemical-exchange analysis for evaluating binding in protein-ligand systems when exchange is intermediate to fast on the NMR time scale is described. Its application to the present system involves multiple exchange sites that depend on a single binding rate, thereby adding further constraints to the analysis.

Dynamic Factors Affecting Gaseous Ligand Binding in an Artificial Oxygen Transport Protein‡

PubMed Central

Zhang, Lei; Andersen, Eskil M.E.; Khajo, Abdelahad; Magliozzo, Richard S.; Koder, Ronald L.

2013-01-01

We report the functional analysis of an artificial hexacoordinate oxygen transport protein, HP7, which operates via a mechanism similar to that of human neuroglobin and cytoglobin: the destabilization of one of two heme-ligating histidine residues. In the case of HP7 this is the result of the coupling of histidine side chain ligation with the burial of three charged glutamate residues on the same helix. Here we compare gaseous ligand binding, including rates, affinities and oxyferrous state lifetimes, of both heme binding sites in HP7. We find that despite the identical sequence of helices in both binding sites, there are differences in oxygen affinity and oxyferrous state lifetime which may be the result of differences in the freedom of motion imposed by the candelabra fold on the two sites of the protein. We further examine the effect of mutational removal of the buried glutamates on function. Heme iron in the ferrous state of this mutant is rapidly oxidized when when exposed to oxygen. Compared to HP7, distal histidine affinity is increased by a 22-fold decrease in the histidine ligand off-rate. EPR comparison of these ferric hemoproteins demonstrates that the mutation increases disorder at the heme binding site. NMR-detected deuterium exchange demonstrates that the mutation greatly increases water penetration into the protein core. The inability of the mutant protein to bind oxygen may be due to increased water penetration, the large decrease in binding rate caused by the increase in distal histidine affinity, or a combination of the two factors. Together these data underline the importance of the control of protein dynamics in the design of functional artificial proteins. PMID:23249163

Dynamic factors affecting gaseous ligand binding in an artificial oxygen transport protein.

PubMed

Zhang, Lei; Andersen, Eskil M E; Khajo, Abdelahad; Magliozzo, Richard S; Koder, Ronald L

2013-01-22

We report the functional analysis of an artificial hexacoordinate oxygen transport protein, HP7, which operates via a mechanism similar to that of human neuroglobin and cytoglobin: the destabilization of one of two heme-ligating histidine residues. In the case of HP7, this is the result of the coupling of histidine side chain ligation with the burial of three charged glutamate residues on the same helix. Here we compare gaseous ligand binding, including rates, affinities, and oxyferrous state lifetimes, of both heme binding sites in HP7. We find that despite the identical sequence of helices in both binding sites, there are differences in oxygen affinity and oxyferrous state lifetime that may be the result of differences in the freedom of motion imposed by the candelabra fold on the two sites of the protein. We further examine the effect of mutational removal of the buried glutamates on function. Heme iron in the ferrous state of this mutant is rapidly oxidized when exposed to oxygen. Compared to that of HP7, the distal histidine affinity is increased by a 22-fold decrease in the histidine ligand off rate. Electron paramagnetic resonance comparison of these ferric hemoproteins demonstrates that the mutation increases the level of disorder at the heme binding site. Nuclear magnetic resonance-detected deuterium exchange demonstrates that the mutation greatly increases the degree of penetration of water into the protein core. The inability of the mutant protein to bind oxygen may be due to an increased level of water penetration, the large decrease in binding rate caused by the increase in distal histidine affinity, or a combination of the two factors. Together, these data underline the importance of the control of protein dynamics in the design of functional artificial proteins.

An oxygen pressure sensor using surface acoustic wave devices

NASA Technical Reports Server (NTRS)

Leighty, Bradley D.; Upchurch, Billy T.; Oglesby, Donald M.

1993-01-01

Surface acoustic wave (SAW) piezoelectric devices are finding widespread applications in many arenas, particularly in the area of chemical sensing. We have developed an oxygen pressure sensor based on coating a SAW device with an oxygen binding agent which can be tailored to provide variable sensitivity. The coating is prepared by dissolving an oxygen binding agent in a toluene solution of a copolymer which is then sprayed onto the surface of the SAW device. Experimental data shows the feasibility of tailoring sensors to measure the partial pressure of oxygen from 2.6 to 67 KPa (20 to 500 torr). Potential applications of this technology are discussed.

Engineering cofactor and ligand binding in an artificial neuroglobin

NASA Astrophysics Data System (ADS)

Zhang, Lei

HP-7 is one artificial mutated oxygen transport protein, which operates via a mechanism akin to human neuroglobin and cytoglobin. This protein destabilizes one of two heme-ligating histidine residues by coupling histidine side chain ligation with the burial of three charged glutamate residues on the same helix. Replacement of these glutamate residues with alanine, which has a neutral hydrophobicity, slows gaseous ligand binding 22-fold, increases the affinity of the distal histidine ligand by a factor of thirteen, and decreases the binding affinity of carbon monoxide, a nonreactive oxygen analogue, three-fold. Paradoxically, it also decreases heme binding affinity by a factor of three in the reduced state and six in the oxidized state. Application of a two-state binding model, in which an initial pentacoordinate binding event is followed by a protein conformational change to hexacoordinate, provides insight into the mechanism of this seemingly counterintuitive result: the initial pentacoordinate encounter complex is significantly destabilized by the loss of the glutamate side chains, and the increased affinity for the distal histidine only partially compensates. These results point to the importance of considering each oxidation and conformational state in the design of functional artificial proteins. We have also examined the effects these mutations have on function. The K d of the nonnreactive oxygen analogue carbon monoxide (CO) is only decreased three-fold, despite the large increase in distal histidine affinity engendered by the 22-fold decrease in the histidine ligand off-rate. This is a result of the four-fold increase in affinity for CO binding to the pentacoordinate state. Oxygen binds to HP7 with a Kd of 117 µM, while the mutant rapidly oxidizes when exposed to oxygen. EPR analysis of both ferric hemoproteins demonstrates that the mutation increases disorder at the heme binding site. NMR-detected deuterium exchange demonstrates that the mutation causes a large increase in water penetration into the protein core. The inability of the mutant protein may thus either be due to increased water penetration, the large decrease in binding rate caused by the increase in distal histidine affinity, or a combination of the two factors.

On the elusive nature of oxygen binding at coordinatively unsaturated 3d transition metal centers in metal–organic frameworks

DOE PAGES

Rosnes, Mali H.; Sheptyakov, Denis; Franz, Alexandra; ...

2017-09-18

Low and ambient temperature binding of oxygen, O 2, in MOF-74, CPO-27-M (M = Mn, Co, Ni, Cu, Zn) framework materials remains in the physisorption regime, with energetics very similar to that of nitrogen, N 2, sorption.

On the elusive nature of oxygen binding at coordinatively unsaturated 3d transition metal centers in metal–organic frameworks

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

Rosnes, Mali H.; Sheptyakov, Denis; Franz, Alexandra

Low and ambient temperature binding of oxygen, O 2, in MOF-74, CPO-27-M (M = Mn, Co, Ni, Cu, Zn) framework materials remains in the physisorption regime, with energetics very similar to that of nitrogen, N 2, sorption.

Systematic shell-model study on spectroscopic properties from light to heavy nuclei

NASA Astrophysics Data System (ADS)

Yuan, Cenxi

2018-05-01

A systematic shell-model study is performed to study the spectroscopic properties from light to heavy nuclei, such as binding energies, energy levels, electromagnetic properties, and β decays. The importance of cross-shell excitation is shown in the spectroscopic properties of neutron-rich boron, carbon, nitrogen, and oxygen isotopes. A special case is presented for low-lying structure of 14C. The weakly bound effect of proton 1s1/2 orbit is necessary for the description of the mirror energy difference in the nuclei around A=20. Some possible isomers are predicted in the nuclei in the southeast region of 132Sn based on a newly suggested Hamiltonian. A preliminary study on the nuclei around 208Pb are given to show the ability of the shell model in the heavy nuclei.

Exploration of the effect of sequence variations located inside the binding pocket of HIV-1 and HIV-2 proteases.

PubMed

Triki, Dhoha; Billot, Telli; Visseaux, Benoit; Descamps, Diane; Flatters, Delphine; Camproux, Anne-Claude; Regad, Leslie

2018-04-10

HIV-2 protease (PR2) is naturally resistant to most FDA (Food and Drug Administration)-approved HIV-1 protease inhibitors (PIs), a major antiretroviral class. In this study, we compared the PR1 and PR2 binding pockets extracted from structures complexed with 12 ligands. The comparison of PR1 and PR2 pocket properties showed that bound PR2 pockets were more hydrophobic with more oxygen atoms and fewer nitrogen atoms than PR1 pockets. The structural comparison of PR1 and PR2 pockets highlighted structural changes induced by their sequence variations and that were consistent with these property changes. Specifically, substitutions at residues 31, 46, and 82 induced structural changes in their main-chain atoms that could affect PI binding in PR2. In addition, the modelling of PR1 mutant structures containing V32I and L76M substitutions revealed a cooperative mechanism leading to structural deformation of flap-residue 45 that could modify PR2 flexibility. Our results suggest that substitutions in the PR1 and PR2 pockets can modify PI binding and flap flexibility, which could underlie PR2 resistance against PIs. These results provide new insights concerning the structural changes induced by PR1 and PR2 pocket variation changes, improving the understanding of the atomic mechanism of PR2 resistance to PIs.

Relative Propensities of Cytochrome c Oxidase and Cobalt Corrins for Reaction with Cyanide and Oxygen: Implications for Amelioration of Cyanide Toxicity.

PubMed

Yuan, Quan; Pearce, Linda L; Peterson, Jim

2017-12-18

In aqueous media at neutral pH, the binding of two cyanide molecules per cobinamide can be described by two formation constants, K f1 = 1.1 (±0.6) × 10 5 M -1 and K f2 = 8.5 (±0.1) × 10 4 M -1 , or an overall cyanide binding constant of ∼1 × 10 10 M -2 . In comparison, the cyanide binding constants for cobalamin and a fully oxidized form of cytochrome c oxidase, each binding a single cyanide anion, were found to be 7.9 (±0.5) × 10 4 M -1 and 1.6 (±0.2) × 10 7 M -1 , respectively. An examination of the cyanide-binding properties of cobinamide at neutral pH by stopped-flow spectrophotometry revealed two kinetic phases, rapid and slow, with apparent second-order rate constants of 3.2 (±0.5) × 10 3 M -1 s -1 and 45 (±1) M -1 s -1 , respectively. Under the same conditions, cobalamin exhibited a single slow cyanide-binding kinetic phase with a second-order rate constant of 35 (±1) M -1 s -1 . All three of these processes are significantly slower than the rate at which cyanide is bound by complex IV during enzyme turnover (>10 6 M -1 s -1 ). Overall, it can be understood from these findings why cobinamide is a measurably better cyanide scavenger than cobalamin, but it is unclear how either cobalt corrin can be antidotal toward cyanide intoxication as neither compound, by itself, appears able to out-compete cytochrome c oxidase for available cyanide. Furthermore, it has also been possible to unequivocally show in head-to-head comparison assays that the enzyme does indeed have greater affinity for cyanide than both cobalamin and cobinamide. A plausible resolution of the paradox that both cobalamin and cobinamide clearly are antidotal toward cyanide intoxication, involving the endogenous auxiliary agent nitric oxide, is suggested. Additionally, the catalytic consumption of oxygen by the cobalt corrins is demonstrated and, in the case of cobinamide, the involvement of cytochrome c when present. Particularly in the case of cobinamide, these oxygen-dependent reactions could potentially lead to erroneous assessment of the ability of the cyanide scavenger to restore the activity of cyanide-inhibited cytochrome c oxidase.

Artificial oxygen transport protein

DOEpatents

Dutton, P. Leslie

2014-09-30

This invention provides heme-containing peptides capable of binding molecular oxygen at room temperature. These compounds may be useful in the absorption of molecular oxygen from molecular oxygen-containing atmospheres. Also included in the invention are methods for treating an oxygen transport deficiency in a mammal.

Homogenous Electrocatalytic Oxygen Reduction Rates Correlate with Reaction Overpotential in Acidic Organic Solutions

PubMed Central

2016-01-01

Improved electrocatalysts for the oxygen reduction reaction (ORR) are critical for the advancement of fuel cell technologies. Herein, we report a series of 11 soluble iron porphyrin ORR electrocatalysts that possess turnover frequencies (TOFs) from 3 s–1 to an unprecedented value of 2.2 × 106 s–1. These TOFs correlate with the ORR overpotential, which can be modulated by changing the E1/2 of the catalyst using different ancillary ligands, by changing the solvent and solution acidity, and by changing the catalyst’s protonation state. The overpotential is well-defined for these homogeneous electrocatalysts by the E1/2 of the catalyst and the proton activity of the solution. This is the first such correlation for homogeneous ORR electrocatalysis, and it demonstrates that the remarkably fast TOFs are a consequence of high overpotential. The correlation with overpotential is surprising since the turnover limiting steps involve oxygen binding and protonation, as opposed to turnover limiting electron transfer commonly found in Tafel analysis of heterogeneous ORR materials. Computational studies show that the free energies for oxygen binding to the catalyst and for protonation of the superoxide complex are in general linearly related to the catalyst E1/2, and that this is the origin of the overpotential correlations. This analysis thus provides detailed understanding of the ORR barriers. The best catalysts involve partial decoupling of the influence of the second coordination sphere from the properties of the metal center, which is suggested as new molecular design strategy to avoid the limitations of the traditional scaling relationships for these catalysts. PMID:27924314

Study of positron annihilation with core electrons at the clean and oxygen covered Ag(001) surface

NASA Astrophysics Data System (ADS)

Joglekar, P.; Shastry, K.; Olenga, A.; Fazleev, N. G.; Weiss, A. H.

2013-03-01

In this paper we present measurements of the energy spectrum of electrons emitted as a result of Positron Annihilation Induce Auger Electron Emission from a clean and oxygen covered Ag (100) surface using a series of incident beam energies ranging from 20 eV down to 2 eV. A peak was observed at ~ 40 eV corresponding to the N23VV Auger transition in agreement with previous PAES studies. Experimental results were investigated theoretically by calculations of positron states and annihilation probabilities of surface-trapped positrons with relevant core electrons at the clean and oxygen covered Ag(100) surface. An ab-initio investigation of stability and associated electronic properties of different adsorption phases of oxygen on Ag(100) has been performed on the basis of density functional theory and using DMOl3 code. The computed positron binding energy, positron surface state wave function, and positron annihilation probabilities of surface trapped positrons with relevant core electrons demonstrate their sensitivity to oxygen coverage, elemental content, atomic structure of the topmost layers of surfaces, and charge transfer effects. Theoretical results are compared with experimental data. This work was supported in part by the National Science Foundation Grant # DMR-0907679.

Casein kinase 1 regulates sterol regulatory element-binding protein (SREBP) to control sterol homeostasis.

PubMed

Brookheart, Rita T; Lee, Chih-Yung S; Espenshade, Peter J

2014-01-31

Sterol homeostasis is tightly controlled by the sterol regulatory element-binding protein (SREBP) transcription factor that is highly conserved from fungi to mammals. In fission yeast, SREBP functions in an oxygen-sensing pathway to promote adaptation to decreased oxygen supply that limits oxygen-dependent sterol synthesis. Low oxygen stimulates proteolytic cleavage of the SREBP homolog Sre1, generating the active transcription factor Sre1N that drives expression of sterol biosynthetic enzymes. In addition, low oxygen increases the stability and DNA binding activity of Sre1N. To identify additional signals controlling Sre1 activity, we conducted a genetic overexpression screen. Here, we describe our isolation and characterization of the casein kinase 1 family member Hhp2 as a novel regulator of Sre1N. Deletion of Hhp2 increases Sre1N protein stability and ergosterol levels in the presence of oxygen. Hhp2-dependent Sre1N degradation by the proteasome requires Hhp2 kinase activity, and Hhp2 binds and phosphorylates Sre1N at specific residues. Our results describe a role for casein kinase 1 as a direct regulator of sterol homeostasis. Given the role of mammalian Hhp2 homologs, casein kinase 1δ and 1ε, in regulation of the circadian clock, these findings may provide a mechanism for coordinating circadian rhythm and lipid metabolism.

Excitonic states and defect physics of two-dimensional group-IV monochalcogenides.

NASA Astrophysics Data System (ADS)

Gomes, Lidia; Carvalho, Alexandra; Trevisanutto, Paolo; Rodin, Aleksandr; Neto, Antonio

Layered group-IV monochalcogenides have become an important group of materials within the ever-growing family of two-dimensional crystals. Among the binary IV-VI compounds, SnS, SnSe, GeS, and GeSe form a subgroup with orthorhombic structure which has shown exciting particularities and has been considered of high potential for numerous application. We give a brief overview of some important properties of the 2D form of this group and focus on recent results addressing the excitonic properties and the impact of the introduction of point defects on their structures. Vacancies and oxygen defects are modeled using first principles calculations. Energetic and structural analysis of five different models for chemisorbed oxygen atoms, reveals a better resistance of these materials to oxidation if compared to their isostructural partner, phosphorene. We also discuss a parallel work where quasi-particle band structure and excitonic properties of GeS and GeSe monolayers are investigated through ab initio GW and Bethe-Salpeter equation calculations. Within the main results, we show that the optical spectra of both materials are dominated by excitonic effects, however, GeS presents a remarkably larger binding energy of 1 eV. NRF-CRP award Novel 2D materials with tailored properties: beyond graphene (R-144-000-295-281) 1.

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

Eilert, Andre; Cavalca, Filippo; Roberts, F. Sloan

Copper electrocatalysts derived from an oxide have shown extraordinary electrochemical properties for the carbon dioxide reduction reaction (CO 2RR). Using in situ ambient pressure X-ray photoelectron spectroscopy and quasi in situ electron energy-loss spectroscopy in a transmission electron microscope, we show that there is a substantial amount of residual oxygen in nanostructured, oxide-derived copper electrocatalysts but no residual copper oxide. On the basis of these findings in combination with density functional theory simulations, we propose that residual subsurface oxygen changes the electronic structure of the catalyst and creates sites with higher carbon monoxide binding energy. If such sites are stablemore » under the strongly reducing conditions found in CO 2RR, these findings would explain the high efficiencies of oxide-derived copper in reducing carbon dioxide to multicarbon compounds such as ethylene.« less

Predicting the Oxygen-Binding Properties of Platinum Nanoparticle Ensembles by Combining High-Precision Electron Microscopy and Density Functional Theory.

PubMed

Aarons, Jolyon; Jones, Lewys; Varambhia, Aakash; MacArthur, Katherine E; Ozkaya, Dogan; Sarwar, Misbah; Skylaris, Chris-Kriton; Nellist, Peter D

2017-07-12

Many studies of heterogeneous catalysis, both experimental and computational, make use of idealized structures such as extended surfaces or regular polyhedral nanoparticles. This simplification neglects the morphological diversity in real commercial oxygen reduction reaction (ORR) catalysts used in fuel-cell cathodes. Here we introduce an approach that combines 3D nanoparticle structures obtained from high-throughput high-precision electron microscopy with density functional theory. Discrepancies between experimental observations and cuboctahedral/truncated-octahedral particles are revealed and discussed using a range of widely used descriptors, such as electron-density, d-band centers, and generalized coordination numbers. We use this new approach to determine the optimum particle size for which both detrimental surface roughness and particle shape effects are minimized.

The crystal structure of a cyanobacterial water-soluble carotenoid binding protein.

PubMed

Kerfeld, Cheryl A; Sawaya, Michael R; Brahmandam, Vishnu; Cascio, Duilio; Ho, Kwok Ki; Trevithick-Sutton, Colleen C; Krogmann, David W; Yeates, Todd O

2003-01-01

Carotenoids undergo a wide range of photochemical reactions in animal, plant, and microbial systems. In photosynthetic organisms, in addition to light harvesting, they perform an essential role in protecting against light-induced damage by quenching singlet oxygen, superoxide anion radicals, or triplet-state chlorophyll. We have determined the crystal structure of a water-soluble orange carotenoid protein (OCP) isolated from the cyanobacterium Arthrospira maxima at a resolution of 2.1 A. OCP forms a homodimer with one carotenoid molecule per monomer. The carotenoid binding site is lined by a striking number of methionine residues. The structure reveals several possible ways in which the protein environment influences the spectral properties of the pigment and provides insight into how the OCP carries out its putative functions in photoprotection.

Incorporation of Tyrosine and Glutamine Residues into the Soluble Guanylate Cyclase Heme Distal Pocket Alters NO and O2 Binding*

PubMed Central

Derbyshire, Emily R.; Deng, Sarah; Marletta, Michael A.

2010-01-01

Nitric oxide (NO) is the physiologically relevant activator of the mammalian hemoprotein soluble guanylate cyclase (sGC). The heme cofactor of α1β1 sGC has a high affinity for NO but has never been observed to form a complex with oxygen. Introduction of a key tyrosine residue in the sGC heme binding domain β1(1–385) is sufficient to produce an oxygen-binding protein, but this mutation in the full-length enzyme did not alter oxygen affinity. To evaluate ligand binding specificity in full-length sGC we mutated several conserved distal heme pocket residues (β1 Val-5, Phe-74, Ile-145, and Ile-149) to introduce a hydrogen bond donor in proximity to the heme ligand. We found that the NO coordination state, NO dissociation, and enzyme activation were significantly affected by the presence of a tyrosine in the distal heme pocket; however, the stability of the reduced porphyrin and the proteins affinity for oxygen were unaltered. Recently, an atypical sGC from Drosophila, Gyc-88E, was shown to form a stable complex with oxygen. Sequence analysis of this protein identified two residues in the predicted heme pocket (tyrosine and glutamine) that may function to stabilize oxygen binding in the atypical cyclase. The introduction of these residues into the rat β1 distal heme pocket (Ile-145 → Tyr and Ile-149 → Gln) resulted in an sGC construct that oxidized via an intermediate with an absorbance maximum at 417 nm. This absorbance maximum is consistent with globin FeII-O2 complexes and is likely the first observation of a FeII-O2 complex in the full-length α1β1 protein. Additionally, these data suggest that atypical sGCs stabilize O2 binding by a hydrogen bonding network involving tyrosine and glutamine. PMID:20231286

Molecular dynamic simulations on TKX-50/RDX cocrystal.

PubMed

Xiong, Shuling; Chen, Shusen; Jin, Shaohua

2017-06-01

Dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50) is a newly synthesized energetic material with excellent comprehensive properties. Cyclotrimethylenetrinitramine (RDX) is currently one of the most widely used energetic materials in the world. TKX-50 and RDX supercell models and TKX-50/RDX cocrystal model were constructed based on their crystal cell parameters and the formation mechanism of cocrystal, respectively, then they were simulated by molecular dynamics (MD) simulations. The maximum trigger bond (NNO 2 ) length(L max ), binding energy (E bind ), radial distribution function (RDF), cohesive energy density(CED) and mechanical properties were simulated at different temperatures based on the simulated equilibrium structures of the models. The simulated results indicate that hydrogen bond and van der Waals force interactions exist in the cocrystal system and the hydrogen bonds are mainly derived from the hydrogen atom of TKX-50 with the oxygen or nitrogen atom of RDX. Moreover, TKX-50/RDX cocrystal structure significantly reduces the sensitivity and improves the thermodynamic stability of RDX, and it also shows better mechanical properties than pure TKX-50 and RDX, indicating that it will vastly expand the application scope of the single compound explosives. Copyright © 2017 Elsevier Inc. All rights reserved.

Lanthanide ions induce hydrolysis of hemoglobin-bound 2,3-diphosphoglycerate (2,3-DPG), conformational changes of globin and bidirectional changes of 2,3-DPG-hemoglobin's oxygen affinity.

PubMed

Cheng, Y; Lin, H; Xue, D; Li, R; Wang, K

2001-02-14

The changes in structure and function of 2,3-diphosphoglycerate-hemoglobin (2,3-DPG-Hb) induced by Ln(3+) binding were studied by spectroscopic methods. The binding of lanthanide cations to 2,3-DPG is prior to that to Hb. Ln(3+) binding causes the hydrolysis of either one from the two phosphomonoester bonds in 2,3-DPG non-specifically. The results using the ultrafiltration method indicate that Ln(3+) binding sites for Hb can be classified into three categories: i.e. positive cooperative sites (N(I)), non-cooperative strong sites (N(S)) and non-cooperative weak sites (N(W)) with binding constants in decreasing order: K(I)>K(S)>K(W). The total number of binding sites amounts to about 65 per Hb tetramer. Information on reaction kinetics was obtained from the change of intrinsic fluorescence in Hb monitored by stopped-flow fluorometry. Fluctuation of fluorescence dependent on Ln(3+) concentration and temperature was observed and can be attributed to the successive conformational changes induced by Ln(3+) binding. The results also reveal the bidirectional changes of the oxygen affinity of Hb in the dependence on Ln(3+) concentration. At the range of [Ln(3+)]/[Hb]<2, the marked increase of oxygen affinity (P(50) decrease) with the Ln(3+) concentration can be attributed to the hydrolysis of 2,3-DPG, while the slight rebound of oxygen affinity in higher Ln(3+) concentration can be interpreted by the transition to the T-state of the Hb tetramer induced by Ln(3+) binding. This was indicated by the changes in secondary structure characterized by the decrease of alpha-helix content.

In vitro phototoxic potential and photochemical properties of imidazopyridine derivative: a novel 5-HT4 partial agonist.

PubMed

Onoue, Satomi; Igarashi, Naoko; Yamauchi, Yukinori; Kojima, Takashi; Murase, Noriaki; Zhou, Yu; Yamada, Shizuo; Tsuda, Yoshiko

2008-10-01

Drug-induced phototoxic skin responses have been recognized as undesirable side effects, and as we previously proposed the determination of reactive oxygen species (ROS) from photo-irradiated compounds can be effective for the prediction of phototoxic potential. In this investigation, we evaluated the photosensitizing properties of imidazopyridine derivative, a novel 5-HT(4) partial agonist, using ROS assay and several analytical/biochemical techniques. Exposure of the compound to simulated sunlight resulted in the significant production of singlet oxygen, which is indicative of its phototoxic potential. In practice, an imidazopyridine derivative under UVA/B light exposure also showed significant photodegradation and even photobiochemical events; peroxidation of fatty acid and genetic damage after DNA-binding, which are considered as causative agents for phototoxic dermatitis. Interestingly, both photodegradation and lipoperoxidation were dramatically attenuated by the addition of radical scavengers, especially singlet oxygen quenchers, suggesting the possible involvement of ROS generation in the phototoxic pathways. In the 3T3 neutral red uptake phototoxicity test, imidazopyridine derivative also showed the phototoxic effect on 3T3 mouse fibroblast cells. These results suggest the phototoxic risk of newly synthesized imidazopyridine derivative and also verify the usefulness of ROS assay for phototoxicity prediction. (c) 2008 Wiley-Liss, Inc. and the American Pharmacists Association

[KEEPING THE ELECTRON-DONOR PROPERTIES OF DRINKING WATER].

PubMed

Gibert, K K; Stekhin, A A; Iakovleva, G V; Sul'ina, Iu S

2015-01-01

In a study there was performed the experimental evaluation of long-term structural--physical changes of the phase of associated water in drinking water treated in hypomagnetic conditions according to the the technology providing the retention of of ortho/para isomers of water in the presence of a catalyst--triplet oxygen. According to the results of measurements ofparameters of nano-associates formed in the water there was found a series ofconsistencies, allowing to determine the mechanisms of the impact of hypomagnetic treatment on the catalytic properties ofwater and long-term stability of its activated state, that provides the long-term maintenance of high biological activity of drinking water. In particular, under hypomagnetic conditions of the treatment there is formed denser packing of amorphous ice--VI in the composition of associates peroxide, serving as a kind of "reservoir" of atmospheric gases. In such a "reservoir" there realized higher pressure, compared with normal geophysical conditions, that stimulates the gas-phase reactions with the formation of dimers and trimers of oxygen existing in the 2-electron--active configurations with binding energies of 0.3 eVand ~0.2 eV providing phase modulation, resulting in condensation of environment additional electrons on paramagnetic oxygen, which provides the long-term maintenance of the electron--donor ability of water and electrically non-equilibrium state.

Detection of Singlet Oxygen Formation inside Photoactive Biohybrid Composite Material.

PubMed

Hajdu, Kata; Ur Rehman, Ateeq; Vass, Imre; Nagy, László

2017-12-26

Photosynthetic reaction center proteins (RCs) are the most efficient light energy converter systems in nature. The first steps of the primary charge separation in photosynthesis take place in these proteins. Due to their unique properties, combining RCs with nano-structures promising applications can be predicted in optoelectronic systems. In the present work RCs purified from Rhodobacter sphaeroides purple bacteria were immobilized on multiwalled carbon nanotubes (CNTs). Carboxyl-and amine-functionalised CNTs were used, so different binding procedures, physical sorption and chemical sorption as well, could be applied as immobilization techniques. Light-induced singlet oxygen production was measured in the prepared photoactive biocomposites in water-based suspension by histidine mediated chemical trapping. Carbon nanotubes were applied under different conditions in order to understand their role in the equilibration of singlet oxygen concentration in the suspension. CNTs acted as effective quenchers of ¹O₂ either by physical (resonance) energy transfer or by chemical (oxidation) reaction and their efficiency showed dependence on the diffusion distance of ¹O₂.

Hemoglobin isoform differentiation and allosteric regulation of oxygen binding in the turtle, Trachemys scripta

PubMed Central

Damsgaard, Christian; Storz, Jay F.; Hoffmann, Federico G.

2013-01-01

When freshwater turtles acclimatize to winter hibernation, there is a gradual transition from aerobic to anaerobic metabolism, which may require adjustments of blood O2 transport before turtles become anoxic. Here, we report the effects of protons, anionic cofactors, and temperature on the O2-binding properties of isolated hemoglobin (Hb) isoforms, HbA and HbD, in the turtle Trachemys scripta. We determined the primary structures of the constituent subunits of the two Hb isoforms, and we related the measured functional properties to differences in O2 affinity between untreated hemolysates from turtles that were acclimated to normoxia and anoxia. Our data show that HbD has a consistently higher O2 affinity compared with HbA, whereas Bohr and temperature effects, as well as thiol reactivity, are similar. Although sequence data show amino acid substitutions at two known β-chain ATP-binding site positions, we find high ATP affinities for both Hb isoforms, suggesting an alternative and stronger binding site for ATP. The high ATP affinities indicate that, although ATP levels decrease in red blood cells of turtles acclimating to anoxia, the O2 affinity would remain largely unchanged, as confirmed by O2-binding measurements of untreated hemolysates from normoxic and anoxic turtles. Thus, the increase in blood-O2 affinity that accompanies winter acclimation is mainly attributable to a decrease in temperature rather than in concentrations of organic phosphates. This is the first extensive study on freshwater turtle Hb isoforms, providing molecular evidence for adaptive changes in O2 transport associated with acclimation to severe hypoxia. PMID:23986362

Structural evidence of the species-dependent albumin binding of the modified cyclic phosphatidic acid with cytotoxic properties

PubMed Central

Sekula, Bartosz; Ciesielska, Anna; Rytczak, Przemyslaw; Koziołkiewicz, Maria; Bujacz, Anna

2016-01-01

Cyclic phosphatidic acids (cPAs) are naturally occurring, very active signalling molecules, which are involved in several pathological states, such as cancer, diabetes or obesity. As molecules of highly lipidic character found in the circulatory system, cPAs are bound and transported by the main extracellular lipid binding protein–serum albumin. Here, we present the detailed interactions between human serum albumin (HSA) and equine serum albumin (ESA) with a derivative of cPA, 1-O-myristoyl-sn-glycerol-2,3-cyclic phosphorodithioate (Myr-2S-cPA). Initial selection of the ligand used for the structural study was made by the analysis of the therapeutically promising properties of the sulfur containing analogues of cPA in respect to the unmodified lysophospholipids (LPLs). Substitution of one or two non-bridging oxygen atoms in the phosphate group with one or two sulfur atoms increases the cytotoxic effect of cPAs up to 60% on the human prostate cancer (PC) cells. Myr-2S-cPA reduces cancer cell viability in a dose-dependent manner, with IC50 value of 29.0 μM after 24 h incubation, which is almost 30% lower than IC50 of single substituted phosphorothioate cPA. Although, the structural homology between HSA and ESA is big, their crystal complexes with Myr-2S-cPA demonstrate significantly different mode of binding of this LPL analogue. HSA binds three molecules of Myr-2S-cPA, whereas ESA only one. Moreover, none of the identified Myr-2S-cPA binding sites overlap in both albumins. PMID:27129297

Diphosphoglycerate and Inosine Hexaphosphate Control of Oxygen Binding by Hemoglobin: A Theoretical Interpretation of Experimental Data*

PubMed Central

Ling, Gilbert N.

1970-01-01

A theoretical equation is presented for the control of cooperative adsorption on proteins and other linear macromolecules by hormones, drugs, ATP, and other „cardinal adsorbents.” With reasonable accuracy, this equation describes quantitatively the control of oxygen binding to hemoglobin by 2,3-diphosphoglycerate and by inosine hexaphosphate. PMID:5272319

Crown oxygen-doping graphene with embedded main-group metal atoms

NASA Astrophysics Data System (ADS)

Wu, Liyuan; Wang, Qian; Yang, Chuanghua; Quhe, Ruge; Guan, Pengfei; Lu, Pengfei

2018-02-01

Different main-group metal atoms embedded in crown oxygen-doping graphene (metal@OG) systems are studied by the density functional theory. The binding energies and electronic structures are calculated by using first-principles calculations. The binding energy of metal@OG system mainly depends on the electronegativity of the metal atom. The lower the value of the electronegativity, the larger the binding energy, indicating the more stable the system. The electronic structure of metal@OG arouses the emergence of bandgap and shift of Dirac point. It is shown that interaction between metal atom and crown oxygen-doping graphene leads to the graphene's stable n-doping, and the metal@OG systems are stable semiconducting materials, which can be used in technological applications.

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

Garbuio, Viviana; Pulci, Olivia; Cascella, Michele

The proton disorder in ice has a key role in several properties such as the growth mode, thermodynamical properties, and ferroelectricity. While structural phase transitions from proton disordered to proton ordered ices have been extensively studied, much less is known about their electronic and optical properties. Here, we present ab initio many body perturbation theory-based calculations of the electronic and optical properties of cubic ice at different levels of proton disorder. We compare our results with those from liquid water, that acts as an example of a fully (proton- and oxygen-)disordered system. We find that by increasing the proton disorder,more » a shrinking of the electronic gap occurs in ice, and it is smallest in the liquid water. Simultaneously, the excitonic binding energy decreases, so that the final optical gaps result to be almost independent on the degree of proton disorder. We explain these findings as an interplay between the local dipolar disorder and the electronic correlation.« less

Systematic spatial and stoichiometric screening towards understanding the surface of ultrasmall oxygenated silicon nanocrystal

NASA Astrophysics Data System (ADS)

Niaz, Shanawer; Zdetsis, Aristides D.; Koukaras, Emmanuel N.; Gülseren, Oǧuz; Sadiq, Imran

2016-11-01

In most of the realistic ab initio and model calculations which have appeared on the emission of light from silicon nanocrystals, the role of surface oxygen has been usually ignored, underestimated or completely ruled out. We investigate theoretically, by density functional theory (DFT/B3LYP) possible modes of oxygen bonding in hydrogen terminated silicon quantum dots using as a representative case of the Si29 nanocrystal. We have considered Bridge-bonded oxygen (BBO), Doubly-bonded oxygen (DBO), hydroxyl (OH) and Mix of these oxidizing agents. Due to stoichiometry, all comparisons performed are unbiased with respect to composition whereas spatial distribution of oxygen species pointed out drastic change in electronic and cohesive characteristics of nanocrytals. From an overall perspective of this study, it is shown that bridge bonded oxygenated Si nanocrystals accompanied by Mix have higher binding energies and large electronic gap compared to nanocrystals with doubly bonded oxygen atoms. In addition, it is observed that the presence of OH along with BBO, DBO and mixed configurations further lowers electronic gaps and binding energies but trends in same fashion. It is also demonstrated that within same composition, oxidizing constituent, along with their spatial distribution substantially alters binding energy, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) gap (up to 1.48 eV) and localization of frontier orbitals.

Cation Effects on the Electron-Acceptor Side of Photosystem II.

PubMed

Khan, Sahr; Sun, Jennifer S; Brudvig, Gary W

2015-06-18

The normal pathway of electron transfer on the electron-acceptor side of photosystem II (PSII) involves electron transfer from quinone A, QA, to quinone B, QB. It is possible to redirect electrons from QA(-) to water-soluble Co(III) complexes, which opens a new avenue for harvesting electrons from water oxidation by immobilization of PSII on electrode surfaces. Herein, the kinetics of electron transfer from QA(-) to [Co(III)(terpy)2](3+) (terpy = 2,2';6',2″-terpyridine) are investigated with a spectrophotometric assay revealing that the reaction follows Michaelis-Menten saturation kinetics, is inhibited by cations, and is not affected by variation of the QA reduction potential. A negatively charged site on the stromal surface of the PSII protein complex, composed of glutamic acid residues near QA, is hypothesized to bind cations, especially divalent cations. The cations are proposed to tune the redox properties of QA through electrostatic interactions. These observations may thus explain the molecular basis of the effect of divalent cations like Ca(2+), Sr(2+), Mg(2+), and Zn(2+) on the redox properties of the quinones in PSII, which has previously been attributed to long-range conformational changes propagated from divalent cations binding to the Ca(II)-binding site in the oxygen-evolving complex on the lumenal side of the PSII complex.

N-Terminal Cu-Binding Motifs (Xxx-Zzz-His, Xxx-His) and Their Derivatives: Chemistry, Biology and Medicinal Applications.

PubMed

Gonzalez, Paulina; Bossak, Karolina; Stefaniak, Ewelina; Hureau, Christelle; Raibaut, Laurent; Bal, Wojciech; Faller, Peter

2018-06-07

Peptides and proteins with N-terminal amino acid sequences NH 2 -Xxx-His (XH) and NH 2 -Xxx-Zzz-His (XZH) form well-established high-affinity Cu II -complexes. Key examples are Asp-Ala-His (in serum albumin) and Gly-His-Lys, the wound healing factor. This opens a straightforward way to add a high-affinity Cu II -binding site to almost any peptide or protein, by chemical or recombinant approaches. Thus, these motifs, NH 2 -Xxx-Zzz-His in particular, have been used to equip peptides and proteins with a multitude of functions based on the redox activity of Cu, including nuclease, protease, glycosidase, or oxygen activation properties, useful in anticancer or antimicrobial drugs. More recent research suggests novel biological functions, mainly based on the redox inertness of Cu II in XZH, like PET imaging (with 64 Cu), chelation therapies (for instance in Alzheimer's disease and other types of neurodegeneration), antioxidant units, Cu transporters and activation of biological functions by strong Cu II binding. This Review gives an overview of the chemical properties of Cu-XH and -XZH motifs and discusses the pros and cons of the vastly different biological applications, and how they could be improved depending on the application. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cyanide-insensitive quinol oxidase (CIO) from Gluconobacter oxydans is a unique terminal oxidase subfamily of cytochrome bd.

PubMed

Miura, Hiroshi; Mogi, Tatsushi; Ano, Yoshitaka; Migita, Catharina T; Matsutani, Minenosuke; Yakushi, Toshiharu; Kita, Kiyoshi; Matsushita, Kazunobu

2013-06-01

Cyanide-insensitive terminal quinol oxidase (CIO) is a subfamily of cytochrome bd present in bacterial respiratory chain. We purified CIO from the Gluconobacter oxydans membranes and characterized its properties. The air-oxidized CIO showed some or weak peaks of reduced haemes b and of oxygenated and ferric haeme d, differing from cytochrome bd. CO- and NO-binding difference spectra suggested that haeme d serves as the ligand-binding site of CIO. Notably, the purified CIO showed an extraordinary high ubiquinol-1 oxidase activity with the pH optimum of pH 5-6. The apparent Vmax value of CIO was 17-fold higher than that of G. oxydans cytochrome bo3. In addition, compared with Escherichia coli cytochrome bd, the quinol oxidase activity of CIO was much more resistant to cyanide, but sensitive to azide. The Km value for O2 of CIO was 7- to 10-fold larger than that of G. oxydans cytochrome bo3 or E. coli cytochrome bd. Our results suggest that CIO has unique features attributable to the structure and properties of the O2-binding site, and thus forms a new sub-group distinct from cytochrome bd. Furthermore, CIO of acetic acid bacteria may play some specific role for rapid oxidation of substrates under acidic growth conditions.

Analyte chemisorption and sensing on n- and p-channel copper phthalocyanine thin-film transistors.

PubMed

Yang, Richard D; Park, Jeongwon; Colesniuc, Corneliu N; Schuller, Ivan K; Royer, James E; Trogler, William C; Kummel, Andrew C

2009-04-28

Chemical sensing properties of phthalocyanine thin-film transistors have been investigated using nearly identical n- and p-channel devices. P-type copper phthalocyanine (CuPc) has been modified with fluorine groups to convert the charge carriers from holes to electrons. The sensor responses to the tight binding analyte dimethyl methylphosphonate (DMMP) and weak binding analyte methanol (MeOH) were compared in air and N(2). The results suggest that the sensor response involves counterdoping of pre-adsorbed oxygen (O(2)). A linear dependence of chemical response to DMMP concentration was observed in both n- and p- type devices. For DMMP, there is a factor of 2.5 difference in the chemical sensitivity between n- and p-channel CuPc thin-film transistors, even though it has similar binding strength to n- and p-type CuPc molecules as indicated by the desorption times. The effect is attributed to the difference in the analyte perturbation of electron and hole trap energies in n- and p-type materials.

Aza-Bambusurils En Route to Anion Transporters.

PubMed

Singh, Mandeep; Solel, Ephrath; Keinan, Ehud; Reany, Ofer

2016-06-20

Previous calculations of anion binding with various bambusuril analogs predicted that the replacement of oxygen by nitrogen atoms to produce semiaza-bambus[6]urils would award these new cavitands with multiple anion binding properties. This study validates the hypothesis by efficient synthesis, crystallography, thermogravimetric analysis and calorimetry. These unique host molecules are easily accessible from the corresponding semithio-bambusurils in a one-pot reaction, which converts a single anion receptor into a potential anion channel. Solid-state structures exhibit simultaneous accommodation of three anions, linearly positioned within the cavity along the main symmetry axis. The ability to hold anions at a short distance of about 4 Å is reminiscent of natural chloride channels in E. coli, which exhibit similar distances between their adjacent anion binding sites. The calculated transition-state energy for double-anion movement through the channel suggests that although these host-guest complexes are thermodynamically stable they enjoy high kinetic flexibility to render them efficient anion channels. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Reversible binding of hemoglobin to band 3 constitutes the molecular switch that mediates O2 regulation of erythrocyte properties

PubMed Central

McKenna, Mary M.; Krump, Nathan A.; Zheng, Suilan; Mendelsohn, Laurel; Thein, Swee Lay; Garrett, Lisa J.; Bodine, David M.

2016-01-01

Functional studies have shown that the oxygenation state of the erythrocyte regulates many important pathways, including glucose metabolism, membrane mechanical stability, and cellular adenosine triphosphate (ATP) release. Deoxyhemoglobin (deoxyHb), but not oxyhemoglobin, binds avidly and reversibly to band 3, the major erythrocyte membrane protein. Because band 3 associates with multiple metabolic, solute transport, signal transduction, and structural proteins, the hypothesis naturally arises that the O2-dependent regulation of erythrocyte properties might be mediated by the reversible association of deoxyHb with band 3. To explore whether the band 3–deoxyHb interaction constitutes a “molecular switch” for regulating erythrocyte biology, we have generated transgenic mice with mutations in the deoxyHb-binding domain of band 3. One strain of mouse contains a “humanized” band 3 in which the N-terminal 45 residues of mouse band 3 are replaced by the homologous sequence from human band 3, including the normal human band 3 deoxyHb-binding site. The second mouse contains the same substitution as the first, except the deoxyHb site on band 3 (residues 12-23) has been deleted. Comparison of these animals with wild-type mice demonstrates that the following erythrocyte properties are controlled by the O2-dependent association of hemoglobin with band 3: (1) assembly of a glycolytic enzyme complex on the erythrocyte membrane which is associated with a shift in glucose metabolism between the pentose phosphate pathway and glycolysis, (2) interaction of ankyrin with band 3 and the concomitant regulation of erythrocyte membrane stability, and (3) release of ATP from the red cell which has been linked to vasodilation. PMID:27688804

Peer reviewed: Characterizing aquatic dissolved organic matter

USGS Publications Warehouse

Leenheer, Jerry A.; Croué, Jean-Philippe

2003-01-01

Whether it causes aesthetic concerns such as color, taste, and odor; leads to the binding and transport of organic and inorganic contaminants; produces undesirable disinfection byproducts; provides sources and sinks for carbon; or mediates photochemical processes, the nature and properties of dissolved organic matter (DOM) in water are topics of significant environmental interest. DOM is also a major reactant in and product of biogeochemical processes in which the material serves as a carbon and energy source for biota and controls levels of dissolved oxygen, nitrogen, phosphorus, sulfur, numerous trace metals, and acidity.

RNA-binding properties and RNA chaperone activity of human peroxiredoxin 1

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

Kim, Ji-Hee; Lee, Jeong-Mi; Lee, Hae Na

2012-09-07

Highlights: Black-Right-Pointing-Pointer hPrx1 has RNA-binding properties. Black-Right-Pointing-Pointer hPrx1 exhibits helix-destabilizing activity. Black-Right-Pointing-Pointer Cold stress increases hPrx1 level in the nuclear fraction. Black-Right-Pointing-Pointer hPrx1 enhances the viability of cells exposed to cold stress. -- Abstract: Human peroxiredoxin 1 (hPrx1), a member of the peroxiredoxin family, detoxifies peroxide substrates and has been implicated in numerous biological processes, including cell growth, proliferation, differentiation, apoptosis, and redox signaling. To date, Prx1 has not been implicated in RNA metabolism. Here, we investigated the ability of hPrx1 to bind RNA and act as an RNA chaperone. In vitro, hPrx1 bound to RNA and DNA, and unwoundmore » nucleic acid duplexes. hPrx1 also acted as a transcription anti-terminator in an assay using an Escherichia coli strain containing a stem-loop structure upstream of the chloramphenicol resistance gene. The overall cellular level of hPrx1 expression was not increased at low temperatures, but the nuclear level of hPrx1 was increased. In addition, hPrx1 overexpression enhanced the survival of cells exposed to cold stress, whereas hPrx1 knockdown significantly reduced cell survival under the same conditions. These findings suggest that hPrx1 may perform biological functions as a RNA-binding protein, which are distinctive from known functions of hPrx1 as a reactive oxygen species scavenger.« less

Characterization of the Sr(2+)- and Cd(2+)-Substituted Oxygen-Evolving Complex of Photosystem II by Quantum Mechanics/Molecular Mechanics Calculations.

PubMed

Pitari, Fabio; Bovi, Daniele; Narzi, Daniele; Guidoni, Leonardo

2015-09-29

The Mn4CaO5 cluster in the oxygen-evolving complex is the catalytic core of the Photosystem II (PSII) enzyme, responsible for the water splitting reaction in oxygenic photosynthesis. The role of the redox-inactive ion in the cluster has not yet been fully clarified, although several experimental data are available on Ca2+-depleted and Ca2+-substituted PSII complexes, indicating Sr2+-substituted PSII as the only modification that preserves oxygen evolution. In this work, we investigated the structural and electronic properties of the PSII catalytic core with Ca2+ replaced with Sr2+ and Cd2+ in the S2 state of the Kok−Joliot cycle by means of density functional theory and ab initio molecular dynamics based on a quantum mechanics/ molecular mechanics approach. Our calculations do not reveal significant differences between the substituted and wild-type systems in terms of geometries, thermodynamics, and kinetics of two previously identified intermediate states along the S2 to S3 transition, namely, the open cubane S2 A and closed cubane S2 B conformers. Conversely, our calculations show different pKa values for the water molecule bound to the three investigated heterocations. Specifically, for Cd-substituted PSII, the pKa value is 5.3 units smaller than the respective value in wild type Ca-PSII. On the basis of our results, we conclude that, assuming all the cations sharing the same binding site, the induced difference in the acidity of the binding pocket might influence the hydrogen bonding network and the redox levels to prevent the further evolution of the cycle toward the S3 state.

The hemoglobin system of the serpent eel Ophisurus serpens: structural and functional characterization.

PubMed

Manconi, Barbara; Pellegrini, Mariagiuseppina; Messana, Irene; Sanna, Maria Teresa; Castagnola, Massimo; Iavarone, Federica; Coluccia, Elisabetta; Giardina, Bruno; Olianas, Alessandra

2013-10-01

The hemoglobin system of the serpent eel Ophisurus serpens was structurally and functionally characterized with the aim of comparing it to the hemoglobin system of other fish species, as oxygen loading under the severe habitat conditions experienced by O. serpens could have necessitated specific adaptation mechanisms during evolution. The hemoglobin system of O. serpens includes one cathodic and four anodic components. The molecular mass of the α and β chains of the cathodic component as well as the 2 α and 4 β of the anodic components were determined. Analysis of the intact α and β chains from cathodic hemoglobin and their proteolytic digestion products by high-resolution MS and MS/MS experiments resulted in 92 and 95 % sequence coverage of the α and β globins, respectively. The oxygen binding properties of both hemoglobin components were analyzed with respect to their interactions with their physiological effectors. Stripped cathodic hemoglobin displayed the highest oxygen affinity among Anguilliformes with no significant effect of pH on O2-affinity. In the presence of both chloride and organic phosphates, O2-affinity was strongly reduced, and cooperativity was enhanced; moreover, cathodic hemoglobin contains two indistinguishable GTP-binding sites. Stripped anodic hemoglobins exhibited both low O2-affinity and low cooperativity and a larger Bohr effect than cathodic hemoglobin. The cathodic hemoglobin of O. serpens and the corresponding component of Conger conger share the greatest structural and functional similarity among hemoglobin systems of Anguilliformes studied to date, consistent with their phylogenetic relationship.

Adenylosuccinate synthetase: recent developments.

PubMed

Honzatko, R B; Stayton, M M; Fromm, H J

1999-01-01

By exerting strategic control on purine nucleotide biosynthesis, and by engaging GTP-dependent transphosphorylation of IMP to activate loss of an oxygen atom during catalysis, adenylosuccinate synthetase remains as enzyme that justifiably fascinates students of enzyme catalysis. This review describes how the balanced application of X-ray crystallography and enzyme kinetics has advanced the comprehension of the catalytic and regulatory properties of adenylosuccinate synthetase. Detailed analysis has demonstrated the formation of 6-phosphoryl-IMP, an intermediate originally postulated over 40 years ago on the basis of oxygen-18 exchange experiments showing that position-6 oxygen of IMP becomes incorporated into phosphate. Inferences about the participation of amino acid side-chains that stabilize 6-P-IMP during catalysis have also been confirmed by site-directed mutagenesis and examination of such mutations on various kinetic parameters. Moreover, the action of certain regulatory ligands have also been viewed at atomic level resolution. For example, magnesium ion and GDP can induce conformational changes linked to the stabilization of one of two known conformations of the so-called 40s loop. Another significant finding is that two magnesium ions play fundamental roles: one binding with high affinity to the substrate GTP, and a second binding with lower affinity to the co-substrate aspartate. These structural and kinetic studies have also formed the basis for clarifying the action of various inhibitors and potentially important pharmacologic agents with this key regulatory enzyme. Finally, this review explores the current status of investigations on gene structure and gene expression in a number of organisms.

DNA-binding and oxidative properties of cationic phthalocyanines and their dimeric complexes with anionic phthalocyanines covalently linked to oligonucleotides.

PubMed

Kuznetsova, A A; Lukyanets, E A; Solovyeva, L I; Knorre, D G; Fedorova, O S

2008-12-01

Design of chemically modified oligonucleotides for regulation of gene expression has attracted considerable attention over the past decades. One actively pursued approach involves antisense or antigene oligonucleotide constructs carrying reactive groups, many of these based on transition metal complexes. The complexes of Fe(II) and Co(II) with phthalocyanines are extremely good catalysts of oxidation of organic compounds with molecular oxygen and hydrogen peroxide. The binding of positively charged Fe(II) and Co(II) phthalocyanines with single- and double-stranded DNA was investigated. It was shown that these phthalocyanines interact with nucleic acids through an outside binding mode. The site-directed modification of single-stranded DNA by O2 and H2O2 in the presence of dimeric complexes of negatively and positively charged Fe(II) and Co(II) phthalocyanines was investigated. These complexes were formed directly on single-stranded DNA through interaction between negatively charged phthalocyanine in conjugate and positively charged phthalocyanine in solution. The resulting oppositely charged phthalocyanine complexes showed significant increase of catalytic activity compared with monomeric forms of phthalocyanines Fe(II) and Co(II). These complexes catalyzed the DNA oxidation with high efficacy and led to direct DNA strand cleavage. It was determined that oxidation of DNA by molecular oxygen catalyzed by complex of Fe(II)-phthalocyanines proceeds with higher rate than in the case of Co(II)-phthalocyanines but the latter led to a greater extent of target DNA modification.

Pretreatment with apoaequorin protects hippocampal CA1 neurons from oxygen-glucose deprivation.

PubMed

Detert, Julia A; Adams, Erin L; Lescher, Jacob D; Lyons, Jeri-Anne; Moyer, James R

2013-01-01

Ischemic stroke affects ∼795,000 people each year in the U.S., which results in an estimated annual cost of $73.7 billion. Calcium is pivotal in a variety of neuronal signaling cascades, however, during ischemia, excess calcium influx can trigger excitotoxic cell death. Calcium binding proteins help neurons regulate/buffer intracellular calcium levels during ischemia. Aequorin is a calcium binding protein isolated from the jellyfish Aequorea victoria, and has been used for years as a calcium indicator, but little is known about its neuroprotective properties. The present study used an in vitro rat brain slice preparation to test the hypothesis that an intra-hippocampal infusion of apoaequorin (the calcium binding component of aequorin) protects neurons from ischemic cell death. Bilaterally cannulated rats received an apoaequorin infusion in one hemisphere and vehicle control in the other. Hippocampal slices were then prepared and subjected to 5 minutes of oxygen-glucose deprivation (OGD), and cell death was assayed by trypan blue exclusion. Apoaequorin dose-dependently protected neurons from OGD--doses of 1% and 4% (but not 0.4%) significantly decreased the number of trypan blue-labeled neurons. This effect was also time dependent, lasting up to 48 hours. This time dependent effect was paralleled by changes in cytokine and chemokine expression, indicating that apoaequorin may protect neurons via a neuroimmunomodulatory mechanism. These data support the hypothesis that pretreatment with apoaequorin protects neurons against ischemic cell death, and may be an effective neurotherapeutic.

DNA Damage: Quantum Mechanics/Molecular Mechanics Study on the Oxygen Binding and Substrate Hydroxylation Step in AlkB Repair Enzymes

PubMed Central

Quesne, Matthew G; Latifi, Reza; Gonzalez-Ovalle, Luis E; Kumar, Devesh; de Visser, Sam P

2014-01-01

AlkB repair enzymes are important nonheme iron enzymes that catalyse the demethylation of alkylated DNA bases in humans, which is a vital reaction in the body that heals externally damaged DNA bases. Its mechanism is currently controversial and in order to resolve the catalytic mechanism of these enzymes, a quantum mechanics/molecular mechanics (QM/MM) study was performed on the demethylation of the N1-methyladenine fragment by AlkB repair enzymes. Firstly, the initial modelling identified the oxygen binding site of the enzyme. Secondly, the oxygen activation mechanism was investigated and a novel pathway was found, whereby the catalytically active iron(IV)–oxo intermediate in the catalytic cycle undergoes an initial isomerisation assisted by an Arg residue in the substrate binding pocket, which then brings the oxo group in close contact with the methyl group of the alkylated DNA base. This enables a subsequent rate-determining hydrogen-atom abstraction on competitive σ-and π-pathways on a quintet spin-state surface. These findings give evidence of different locations of the oxygen and substrate binding channels in the enzyme and the origin of the separation of the oxygen-bound intermediates in the catalytic cycle from substrate. Our studies are compared with small model complexes and the effect of protein and environment on the kinetics and mechanism is explained. PMID:24339041

Ionophoric polyphenols selectively bind Cu(2+), display potent antioxidant and anti-amyloidogenic properties, and are non-toxic toward Tetrahymena thermophila.

PubMed

Martínez, Alberto; Alcendor, Ralph; Rahman, Tanzeen; Podgorny, Magdalena; Sanogo, Ismaila; McCurdy, Rebecca

2016-08-15

Alzheimer's disease (AD) is the most common form of dementia affecting more than 28million people in the world. Only symptomatic treatments are currently available. Anticipated tri-fold increase of AD incidence in the next 50years has established the need to explore new possible treatments. Accumulation of extracellular amyloid-β (Aβ) plaques, intracellular tangles in the brain, and formation of reactive oxygen species (ROS) are the major hallmarks of the disease. The active role of some metal ions, especially Cu(2+), in promoting both Aβ aggregation and reactive oxygen species formation has rendered ionophoric drugs as a promising treatment strategy. In this work, a series of 5 disease-modifying and multi-target ionophoric polyphenols (1-5), inspired on the structure of natural resveratrol, have been synthesized and characterized. All compounds bind Cu(2+) selectively over other biologically relevant metal ions. They form 2:1 (compound/Cu(2+)) complexes with association constants logKa 12-14 depending on the molecular design. Our results indicate that compounds 1-5 possess excellent antioxidant properties: they inhibit the Cu(2+)-catalyzed reactive oxygen species production between 47% and 100%, and they scavenge DPPH (1,1-diphenyl-2-picryl-hydrazyl) and AAPH (2,2'-azobis(2-amindino-propane)dihydrochloride) free radicals in general better than clioquinol, resveratrol and ascorbic acid. In addition, compounds 1-5 interact with Aβ peptides and inhibit both the Cu(2+)-catalyzed aggregation and the self-assembly of Aβ(1-40) up to a ∼92% extent. Interestingly, 1-5 are also able to disaggregate up to ∼91% of pre-formed Aβ(1-40) aggregates. Furthermore, cytotoxic studies show remarkably low toxicity of 1-5 toward Tetrahymena thermophila with LD50 values higher than 150μM, comparable to non-toxic natural resveratrol. Published by Elsevier Ltd.

Recent advances in α-synuclein functions, advanced glycation, and toxicity: implications for Parkinson's disease.

PubMed

Guerrero, Erika; Vasudevaraju, P; Hegde, Muralidhar L; Britton, G B; Rao, K S

2013-04-01

The toxicity of α-synuclein in the neuropathology of Parkinson's disease which includes its hallmark aggregation has been studied scrupulously in the last decade. Although little is known regarding the normal functions of α-synuclein, its association with membrane phospholipids suggests its potential role in signaling pathways. Following extensive evidences for its nuclear localization, we and others recently demonstrated DNA binding activity of α-synuclein that modulates its conformation as well as aggregation properties. Furthermore, we also underscored the similarities among various amyloidogenic proteins involved in neurodegenerative diseases including amyloid beta peptides and tau. Our more recent studies show that α-synuclein is glycated and glycosylated both in vitro and in neurons, significantly affecting its folding, oligomeric, and DNA binding properties. Glycated α-synuclein causes increased genome damage both via its direct interaction with DNA and by increased generation of reactive oxygen species as glycation byproduct. In this review, we discuss the mechanisms of glycation and other posttranslational modifications of α-synuclein, including phosphorylation and nitration, and their role in neuronal death in Parkinson's disease.

Trojan Horse for Light-Triggered Bifurcated Production of Singlet Oxygen and Fenton-Reactive Iron within Cancer Cells.

PubMed

Cioloboc, Daniela; Kennedy, Christopher; Boice, Emily N; Clark, Emily R; Kurtz, Donald M

2018-01-08

Traditional photodynamic therapy for cancer relies on dye-photosensitized generation of singlet oxygen. However, therapeutically effective singlet oxygen generation requires well-oxygenated tissues, whereas many tumor environments tend to be hypoxic. We describe a platform for targeted enhancement of photodynamic therapy that produces singlet oxygen in oxygenated environments and hydroxyl radical, which is typically regarded as the most toxic reactive oxygen species, in hypoxic environments. The 24-subunit iron storage protein bacterioferritin (Bfr) has the unique property of binding 12 heme groups in its protein shell. We inserted the isostructural photosensitizer, zinc(II) protoporphyrin IX (ZnP), in place of the hemes and extended the surface-exposed N-terminal ends of the Bfr subunits with a peptide targeting a receptor that is hyperexpressed on the cell surface of many tumors and tumor vasculature. We then loaded the inner cavity with ∼2500 irons as a ferric oxyhydroxide polymer and finally conjugated 2 kDa polyethylene glycol to the outer surface. We showed that the inserted ZnP photosensitizes generation of both singlet oxygen and the hydroxyl radical, the latter via the reaction of photoreleased ferrous iron with hydrogen peroxide. This targeted iron-loaded ZnP-Bfr construct was endocytosed by C32 melanoma cells and localized to lysosomes. Irradiating the treated cells with light at wavelengths overlapping the ZnP Soret absorption band induced photosensitized intracellular Fe 2+ release and substantial lowering of cell viability. This targeted, light-triggered production of intracellular singlet oxygen and Fenton-reactive iron could potentially be developed into a phototherapeutic adjunct for many types of cancers.

Laboratory Investigations of Mesospheric Ice Surfaces: Absence of Dangling Bonds in the Presence of Atomic Oxygen

NASA Astrophysics Data System (ADS)

Boulter, J. E.; Morgan, C. G.; Marschall, J.

2006-05-01

Remote observations of PMCs have become more sophisticated and have increased in geographic and temporal coverage, while numerical models have advanced in detail and predictive power. Together, these advances enable new questions of PMC morphology, optical properties, and microphysical processes in their formation and dissipation. Laboratory investigations also advance this understanding, simulating physical and chemical processes unique to this atmospheric region under comparable conditions. In this work, ice deposition experiments in the presence of microwave discharge-dissociated molecular oxygen suggest heterogeneous interactions between dangling OH bonds on the ice surface and atomic oxygen. Ice films deposited on a gold substrate at temperatures of 115, 130, and 140 K from oxygen/water gas mixtures representative of the summertime polar mesosphere exhibit infrared absorption features characteristic of dangling bonds, whereas films grown in the presence of atomic oxygen do not. Dangling bond spectral features are shown to diminish rapidly when the microwave discharge is activated during ice deposition. Similar decreases were not seen when the gas stream was heated or when the ice film was slowly annealed from 130 to 160 K. One interpretation of these results is that atomic oxygen binds to dangling bond sites during ice growth, a phenomenon that may also occur during the formation of ice particles observed just below the cold summertime mesopause.

Diffusion of oxygen interstitials in UO2+x using kinetic Monte Carlo simulations: Role of O/M ratio and sensitivity analysis

NASA Astrophysics Data System (ADS)

Behera, Rakesh K.; Watanabe, Taku; Andersson, David A.; Uberuaga, Blas P.; Deo, Chaitanya S.

2016-04-01

Oxygen interstitials in UO2+x significantly affect the thermophysical properties and microstructural evolution of the oxide nuclear fuel. In hyperstoichiometric Urania (UO2+x), these oxygen interstitials form different types of defect clusters, which have different migration behavior. In this study we have used kinetic Monte Carlo (kMC) to evaluate diffusivities of oxygen interstitials accounting for mono- and di-interstitial clusters. Our results indicate that the predicted diffusivities increase significantly at higher non-stoichiometry (x > 0.01) for di-interstitial clusters compared to a mono-interstitial only model. The diffusivities calculated at higher temperatures compare better with experimental values than at lower temperatures (< 973 K). We have discussed the resulting activation energies achieved for diffusion with all the mono- and di-interstitial models. We have carefully performed sensitivity analysis to estimate the effect of input di-interstitial binding energies on the predicted diffusivities and activation energies. While this article only discusses mono- and di-interstitials in evaluating oxygen diffusion response in UO2+x, future improvements to the model will primarily focus on including energetic definitions of larger stable interstitial clusters reported in the literature. The addition of larger clusters to the kMC model is expected to improve the comparison of oxygen transport in UO2+x with experiment.

Seasonal changes in blood oxygen transport and acid-base status in the tegu lizard, Tupinambis merianae.

PubMed

Andrade, Denis V; Brito, Simone P; Toledo, Luís Felipe; Abe, Augusto S

2004-05-20

Oxygen-binding properties, blood gases, and acid-base parameters were studied in tegu lizards, Tupinambis merianae, at different seasons and temperatures. Independent of temperature and pH, blood oxygen affinity was higher in dormant lizards than in those active during the summer. Haematocrit (Hct) and hemoglobin content ([Hb]) were greater in active lizards resulting in a higher oxygen-carrying capacity. Nucleoside triphosphate content ([NTP]) was reduced during dormancy, but the ratio between [NTP] and [Hb] remained unchanged. Dormancy was accompanied by an increase in plasma bicarbonate ([HCO-(3)]pl) and an elevation of arterial CO2 partial pressure (PaCO2) and CO2 content in the plasma (CplCO2). These changes in acid-base parameters persist over a broad range of body temperatures. In vivo, arterial O2 partial pressure (PaO2) and O2 content (CaO2) were not affected by season and tended to increase with temperature. Arterial pH (pHa) of dormant animals is reduced compared to active lizards at body temperatures below 15 degrees C, while no significant difference was noticed at higher temperatures. Copyright 2003 Elsevier B.V.

Effect of dye localization and self-interactions on the photosensitized generation of singlet oxygen by rose bengal bound to bovine serum albumin.

PubMed

Turbay, María Beatriz Espeche; Rey, Valentina; Argañaraz, Natalia M; Morán Vieyra, Faustino E; Aspée, Alexis; Lissi, Eduardo A; Borsarelli, Claudio D

2014-12-01

The spectroscopic and photophysical properties of rose bengal (RB) encased in bovine serum albumin (BSA) have been examined to evaluate the photosensitized generation of singlet molecular oxygen ((1)O2). The results show that RB photophysical and photosensitizing properties are highly modulated by the average number of dye molecules per protein (n). At n ≪ 1, the dye molecule is tightly located into the hydrophobic nanocavity site I of the BSA molecule with a binding constant Kb = 0.15 ± 0.01 μM(-1). The interaction with surrounding amino acids induces heterogeneous decay of both singlet and triplet excited states of RB and partially reduce its triplet quantum yield as compared with that in buffer solution. However, despite of the diffusive barrier imposed by the protein nanocavity to (3)O2, the quenching of (3)RB(∗):BSA generates (1)O2 with quantum yield ΦΔ = 0.35 ± 0.05. In turns, the intraprotein generated (1)O2 is able to diffuse through the bulk solution, where is dynamically quenched by BSA itself with an overall quenching rate constant of 7.3 × 10(8) M(-1) s(-1). However, at n>1, nonspecific binding of up to ≈ 6RB molecules per BSA is produced, allowing efficient static quenching of excited states of RB preventing photosensitization of (1)O2. These results provide useful information for development of dye-protein adducts suitable for using as potential intracellular photosensitizers. Copyright © 2014 Elsevier B.V. All rights reserved.

Structural evidence of the species-dependent albumin binding of the modified cyclic phosphatidic acid with cytotoxic properties.

PubMed

Sekula, Bartosz; Ciesielska, Anna; Rytczak, Przemyslaw; Koziołkiewicz, Maria; Bujacz, Anna

2016-07-01

Cyclic phosphatidic acids (cPAs) are naturally occurring, very active signalling molecules, which are involved in several pathological states, such as cancer, diabetes or obesity. As molecules of highly lipidic character found in the circulatory system, cPAs are bound and transported by the main extracellular lipid binding protein-serum albumin. Here, we present the detailed interactions between human serum albumin (HSA) and equine serum albumin (ESA) with a derivative of cPA, 1-O-myristoyl-sn-glycerol-2,3-cyclic phosphorodithioate (Myr-2S-cPA). Initial selection of the ligand used for the structural study was made by the analysis of the therapeutically promising properties of the sulfur containing analogues of cPA in respect to the unmodified lysophospholipids (LPLs). Substitution of one or two non-bridging oxygen atoms in the phosphate group with one or two sulfur atoms increases the cytotoxic effect of cPAs up to 60% on the human prostate cancer (PC) cells. Myr-2S-cPA reduces cancer cell viability in a dose-dependent manner, with IC50 value of 29.0 μM after 24 h incubation, which is almost 30% lower than IC50 of single substituted phosphorothioate cPA. Although, the structural homology between HSA and ESA is big, their crystal complexes with Myr-2S-cPA demonstrate significantly different mode of binding of this LPL analogue. HSA binds three molecules of Myr-2S-cPA, whereas ESA only one. Moreover, none of the identified Myr-2S-cPA binding sites overlap in both albumins. © 2016 The Author(s).

Photophysical, photochemical and BSA binding/BQ quenching properties of quaternizable coumarin containing water soluble zinc phthalocyanine complexes

NASA Astrophysics Data System (ADS)

Esenpınar, Aliye Aslı; Durmuş, Mahmut; Bulut, Mustafa

2011-08-01

The non-peripherally ( np-QZnPc) and peripherally ( p-QZnPc) tetrakis-[7-oxo-(3-[(2-diethylaminomethyliodide)ethyl)]-4-methylcoumarin]-phthalocyaninatozinc complexes have been prepared by quaternization of non-peripherally and peripherally tetrakis[7-oxo-(3-[(2-diethylamino)ethyl)]-methylcoumarin] phthalocyaninato zinc complexes with methyliodide in dimethylsulfoxide (DMSO). The new quaternized zinc phthalocyanine complex ( np-QZnPc) has been characterized by elementel analysis, MALDI-TOF, IR and UV-vis spectral data. The photophysical and photochemical properties of the peripherally and non-peripherally quaternized tetrakis-3-[(2-diethylamino)ethyl]-7-oxo-4-methylcoumarin substituted zinc phthalocyanines are reported. The effects of the position of the substituents and the aggregation of the phthalocyanine molecules on the photophysical and photochemical properties are also investigated. General trends are described for photodegradation, singlet oxygen and fluorescence quantum yields, and fluorescence lifetimes for complexes np-ZnPc/ p-ZnPc in DMSO and for complexes np-QZnPc/p-QZnPc in DMSO, phosphate buffered solution (PBS) and PBS+Triton-X 100 solutions. The fluorescence of the tetra-substituted quaternized zinc phthalocyanine complexes ( np-QZnPc/ p-QZnPc) are effectively quenched addition of 1,4-benzoquinone (BQ) and this study also presented the ionic zinc phthalocyanine complexes strongly bind to bovine serum albumin (BSA).

Optimization of ionic conductivity in doped ceria

PubMed Central

Andersson, David A.; Simak, Sergei I.; Skorodumova, Natalia V.; Abrikosov, Igor A.; Johansson, Börje

2006-01-01

Oxides with the cubic fluorite structure, e.g., ceria (CeO2), are known to be good solid electrolytes when they are doped with cations of lower valence than the host cations. The high ionic conductivity of doped ceria makes it an attractive electrolyte for solid oxide fuel cells, whose prospects as an environmentally friendly power source are very promising. In these electrolytes, the current is carried by oxygen ions that are transported by oxygen vacancies, present to compensate for the lower charge of the dopant cations. Ionic conductivity in ceria is closely related to oxygen-vacancy formation and migration properties. A clear physical picture of the connection between the choice of a dopant and the improvement of ionic conductivity in ceria is still lacking. Here we present a quantum-mechanical first-principles study of the influence of different trivalent impurities on these properties. Our results reveal a remarkable correspondence between vacancy properties at the atomic level and the macroscopic ionic conductivity. The key parameters comprise migration barriers for bulk diffusion and vacancy–dopant interactions, represented by association (binding) energies of vacancy–dopant clusters. The interactions can be divided into repulsive elastic and attractive electronic parts. In the optimal electrolyte, these parts should balance. This finding offers a simple and clear way to narrow the search for superior dopants and combinations of dopants. The ideal dopant should have an effective atomic number between 61 (Pm) and 62 (Sm), and we elaborate that combinations of Nd/Sm and Pr/Gd show enhanced ionic conductivity, as compared with that for each element separately. PMID:16478802

Optimization of ionic conductivity in doped ceria.

PubMed

Andersson, David A; Simak, Sergei I; Skorodumova, Natalia V; Abrikosov, Igor A; Johansson, Börje

2006-03-07

Oxides with the cubic fluorite structure, e.g., ceria (CeO2), are known to be good solid electrolytes when they are doped with cations of lower valence than the host cations. The high ionic conductivity of doped ceria makes it an attractive electrolyte for solid oxide fuel cells, whose prospects as an environmentally friendly power source are very promising. In these electrolytes, the current is carried by oxygen ions that are transported by oxygen vacancies, present to compensate for the lower charge of the dopant cations. Ionic conductivity in ceria is closely related to oxygen-vacancy formation and migration properties. A clear physical picture of the connection between the choice of a dopant and the improvement of ionic conductivity in ceria is still lacking. Here we present a quantum-mechanical first-principles study of the influence of different trivalent impurities on these properties. Our results reveal a remarkable correspondence between vacancy properties at the atomic level and the macroscopic ionic conductivity. The key parameters comprise migration barriers for bulk diffusion and vacancy-dopant interactions, represented by association (binding) energies of vacancy-dopant clusters. The interactions can be divided into repulsive elastic and attractive electronic parts. In the optimal electrolyte, these parts should balance. This finding offers a simple and clear way to narrow the search for superior dopants and combinations of dopants. The ideal dopant should have an effective atomic number between 61 (Pm) and 62 (Sm), and we elaborate that combinations of Nd/Sm and Pr/Gd show enhanced ionic conductivity, as compared with that for each element separately.

Controlling n-type doping in MoO 3

DOE PAGES

Peelaers, H.; Chabinyc, M. L.; Van de Walle, C. G.

2017-02-27

Here, we study the electronic properties of native defects and intentional dopant impurities in MoO 3, a widely used transparent conductor. Using first-principles hybrid functional calculations, we show that electron polarons can be self-trapped, but they can also bind to defects; thus, they play an important role in understanding the properties of doped MoO 3. Our calculations show that oxygen vacancies can cause unintentional n-type doping in MoO 3. Mo vacancies are unlikely to form. Tc and Re impurities on the Mo site and halogens (F, Cl, and Br) on the O site all act as shallow donors but trapmore » electron polarons. Fe, Ru, and Os impurities are amphoteric and will compensate n-type MoO 3. Mn dopants are also amphoteric, and they show interesting magnetic properties. These results support the design of doping approaches that optimally exploit functionality.« less

Effects of 8-mer acidic peptide concentration on the morphology and photoluminescence of synthesized ZnO nanomaterials

NASA Astrophysics Data System (ADS)

Moon, Chung Hee; Tousi, Marzieh; Cheeney, Joseph; Ngo-Duc, Tam-Triet; Zuo, Zheng; Liu, Jianlin; Haberer, Elaine D.

2015-11-01

An 8-mer ZnO-binding peptide, VPGAAEHT, was identified using a M13 pVIII phage display library and employed as an additive during aqueous-based ZnO synthesis at 65 °C. Unlike most other well-studied ZnO-binding sequences which are strongly basic (pI > pH 7), the 8-mer peptide was overall acidic (pI < pH 7) in character, including only a single basic residue. The selected peptide strongly influenced ZnO nanostructure formation. Morphology and optical emission properties were found to be dependent on the concentration of peptide additive. Using lower peptide concentrations (<0.1 mM), single crystal hexagonal rods and platelets were produced, and using higher peptide concentrations (≥0.1 mM), polycrystalline layered platelets, yarn-like structures, and microspheres were assembled. Photoluminescence analysis revealed a characteristic ZnO band-edge peak, as well as sub-bandgap emission peaks. Defect-related green emission, typically associated with surface-related oxygen and zinc vacancies, was significantly reduced by the peptide additive, while blue emission, attributable to oxygen and zinc interstitials, emerged with increased peptide concentrations. Peptide-directed synthesis of ZnO materials may be useful for gas sensing and photocatalytic applications in which properly engineered morphology and defect levels have demonstrated enhanced performance.

Cardiovascular and haematological responses of Atlantic cod (Gadus morhua) to acute temperature increase.

PubMed

Gollock, M J; Currie, S; Petersen, L H; Gamperl, A K

2006-08-01

For fish to survive large acute temperature increases (i.e. >10.0 degrees C) that may bring them close to their critical thermal maximum (CTM), oxygen uptake at the gills and distribution by the cardiovascular system must increase to match tissue oxygen demand. To examine the effects of an acute temperature increase ( approximately 1.7 degrees C h(-1) to CTM) on the cardiorespiratory physiology of Atlantic cod, we (1) carried out respirometry on 10.0 degrees C acclimated fish, while simultaneously measuring in vivo cardiac parameters using Transonic probes, and (2) constructed in vitro oxygen binding curves on whole blood from 7.0 degrees C acclimated cod at a range of temperatures. Both cardiac output (Q) and heart rate (fh) increased until near the fish's CTM (22.2+/-0.2 degrees C), and then declined rapidly. Q(10) values for Q and fh were 2.48 and 2.12, respectively, and increases in both parameters were tightly correlated with O(2) consumption. The haemoglobin (Hb)-oxygen binding curve at 24.0 degrees C showed pronounced downward and rightward shifts compared to 20.0 degrees C and 7.0 degrees C, indicating that both binding capacity and affinity decreased. Further, Hb levels were lower at 24.0 degrees C than at 20.0 degrees C and 7.0 degrees C. This was likely to be due to cell swelling, as electrophoresis of Hb samples did not suggest protein denaturation, and at 24.0 degrees C Hb samples showed peak absorbance at the expected wavelength (540 nm). Our results show that cardiac function is unlikely to limit metabolic rate in Atlantic cod from Newfoundland until close to their CTM, and we suggest that decreased blood oxygen binding capacity may contribute to the plateau in oxygen consumption.

Deposition of TiOxNy Thin Films with Various Nitrogen Flow Rate:. Growth Behavior and Structural Properties

NASA Astrophysics Data System (ADS)

Cho, S.-J.; Jung, C.-K.; Bae, I.-S.; Song, Y.-H.; Boo, J.-H.

2011-06-01

We have deposited TiOxNy thin films on Si(100) substrates at 500 °C using RF PECVD system. Titanium iso-propoxide was used as precursor with different nitrogen flow rate to control oxygen and nitrogen contents in the films. Changes of chemical states of constituent elements in the deposited films were examined by XPS analysis. The data showed that with increasing nitrogen flow rate, the total amounts of nitrogen and titanium were increased while that of oxygen was decreased, resulting in a binding energy shift toward high energy side. The characteristics of film growth orientation and structure as well as morphology change behavior were also analyzed by XRD, TED, FT-IR, TEM, and SEM. Deposition at higher nitrogen flow rate results in finer clusters with a nanograin size and more effective photocatalytic TiOxNy thin films with hydrophilic surface.

Understanding PGM-free Catalysts by Linking Density Functional Theory Calculations and Structural Analysis: Perspectives and Challenges

DOE PAGES

Gonzales, Ivana; Artyushkova, Kateryna; Atanassov, Plamen

2018-03-13

Here, we discuss perspectives and challenges in applying density functional theory for the calculation of spectroscopic properties of platinum group metal (PGM)-free electrocatalysts for oxygen reduction. More specifically, we discuss recent advances in the density functional theory calculations of core-level shifts in binding energies of N 1s electrons as measured by X-ray photoelectron spectroscopy. The link between the density functional theory calculations, the electrocatalytic performance of the catalysts, and structural analysis using modern spectroscopic techniques is expected to significantly increase our understanding of PGM-free catalysts at the molecular level.

Understanding PGM-free Catalysts by Linking Density Functional Theory Calculations and Structural Analysis: Perspectives and Challenges

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

Gonzales, Ivana; Artyushkova, Kateryna; Atanassov, Plamen

Here, we discuss perspectives and challenges in applying density functional theory for the calculation of spectroscopic properties of platinum group metal (PGM)-free electrocatalysts for oxygen reduction. More specifically, we discuss recent advances in the density functional theory calculations of core-level shifts in binding energies of N 1s electrons as measured by X-ray photoelectron spectroscopy. The link between the density functional theory calculations, the electrocatalytic performance of the catalysts, and structural analysis using modern spectroscopic techniques is expected to significantly increase our understanding of PGM-free catalysts at the molecular level.

Phosphate forms an unusual tripodal complex with the Fe–Mn center of sweet potato purple acid phosphatase

PubMed Central

Schenk, Gerhard; Gahan, Lawrence R.; Carrington, Lyle E.; Mitić, Nataša; Valizadeh, Mohsen; Hamilton, Susan E.; de Jersey, John; Guddat, Luke W.

2005-01-01

Purple acid phosphatases (PAPs) are a family of binuclear metalloenzymes that catalyze the hydrolysis of phosphoric acid esters and anhydrides. A PAP in sweet potato has a unique, strongly antiferromagnetically coupled Fe(III)–Mn(II) center and is distinguished from other PAPs by its increased catalytic efficiency for a range of activated and unactivated phosphate esters, its strict requirement for Mn(II), and the presence of a μ-oxo bridge at pH 4.90. This enzyme displays maximum catalytic efficiency (kcat/Km) at pH 4.5, whereas its catalytic rate constant (kcat) is maximal at near-neutral pH, and, in contrast to other PAPs, its catalytic parameters are not dependent on the pKa of the leaving group. The crystal structure of the phosphate-bound Fe(III)–Mn(II) PAP has been determined to 2.5-Å resolution (final Rfree value of 0.256). Structural comparisons of the active site of sweet potato, red kidney bean, and mammalian PAPs show several amino acid substitutions in the sweet potato enzyme that can account for its increased catalytic efficiency. The phosphate molecule binds in an unusual tripodal mode to the two metal ions, with two of the phosphate oxygen atoms binding to Fe(III) and Mn(II), a third oxygen atom bridging the two metal ions, and the fourth oxygen pointing toward the substrate binding pocket. This binding mode is unique among the known structures in this family but is reminiscent of phosphate binding to urease and of sulfate binding to λ protein phosphatase. The structure and kinetics support the hypothesis that the bridging oxygen atom initiates hydrolysis. PMID:15625111

Specific Interactions of Antitumor Metallocenes with Deoxydinucleoside Monophosphates

NASA Astrophysics Data System (ADS)

Eberle, Rahel P.; Hari, Yvonne; Schürch, Stefan

2017-09-01

Bent metallocenes Cp2MCl2 (M = Ti, V, Nb, Mo) are known to exhibit cytotoxic activity against a variety of cancer types. Though the mechanism of action is not fully understood yet, the accumulation of the metal ions in the nucleus points towards DNA as one of the primary targets. A set of eight deoxydinucleoside monophosphates was used to study the adduct yields with metallocenes and cisplatin. The binding affinities are reflected by the relative intensities of the adducts and were found to follow the order of Pt > V > Ti > Mo (no adducts were detected with Nb). High-resolution tandem mass spectrometry was applied to locate the binding patterns in the deoxydinucleoside monophosphates. Whereas cisplatin binds to the soft nitrogen atoms in the purine nucleobases, the metallocenes additionally interact with the hard phosphate oxygen, which is in good agreement with the hard and soft (Lewis) acids and bases (HSAB) concept. However, the binding specificities were found to be unique for each metallocene. The hard Lewis acids titanium and vanadium predominantly bind to the deprotonated phosphate oxygen, whereas molybdenum, an intermediate Lewis acid, preferentially interacts with the nucleobases. Nucleobases comprise alternative binding sites for titanium and vanadium, presumably oxygen atoms for the first and nitrogen atoms for the latter. In summary, the intrinsic binding behavior of the different metallodrugs is reflected by the gas-phase dissociation of the adducts. Consequently, MS/MS can provide insights into therapeutically relevant interactions between metallodrugs and their cellular targets. [Figure not available: see fulltext.

Structure and spectroscopic investigations of a bi-dentate N‧-[(4-ethylphenyl)methylidene]-4-hydroxybenzohydrazide and its Co(II), Ni(II), Cu(II) and Cd(II) complexes: Insights relevant to biological properties

NASA Astrophysics Data System (ADS)

Gopal Reddy, N. B.; Krishna, P. Murali; Shantha Kumar, S. S.; Patil, Yogesh P.; Nethaji, Munirathinam

2017-06-01

The present paper describes the synthesis of novel ligand, N‧-[(4-ethylphenyl)methylidene]-4-hydroxy benzohydrazide (HL) and its Co(II), Ni(II), Cu(II) and Cd(II) complexes. The ligand (HL) crystallizes in orthorhombic lattice in P212121 space group with a = 7.9941 (7) Å, b = 11.6154 (10) Å, c = 15.2278 (13) Å, α = β = γ = 90°. Spectroscopic data gives the strong evidence that ligand is coordinated through azomethine nitrogen and enolic oxygen with metal ion. The DNA binding studies revealed that the complexes bind to CT-DNA via intercalation/electrostatic interaction. All the targeted compounds showed more pronounced DNA cleavage activity in the presence of H2O2 and also inhibit the growth of in vitro antibacterial activity against Gram-positive and Gram-negative bacteria.

NOx Binding and Dissociation: Enhanced Ferroelectric Surface Chemistry by Catalytic Monolayers

NASA Astrophysics Data System (ADS)

Kakekhani, Arvin; Ismail-Beigi, Sohrab

2013-03-01

NOx molecules are regulated air pollutants produced during automotive combustion. As part of an effort to design viable catalysts for NOx decomposition operating at higher temperatures that would allow for improved fuel efficiency, we examine NOx chemistry on ferroelectric perovskite surfaces. Changing the direction of ferroelectric polarization can modify surface electronic properties and may lead to switchable surface chemistry. Here, we describe our recent work on potentially enhanced surface chemistry using catalytic RuO2 monolayers on perovskite ferroelectric substrates. In addition to thermodynamic stabilization of the RuO2 layer, we present results on the polarization-dependent binding of NO, O2, N2, and atomic O and N. We present results showing that one key problem with current catalysts, involving the difficulty of releasing dissociation products (especially oxygen), can be ameliorated by this method. Primary support from Toyota Motor Engineering and Manufacturing, North America, Inc.

Carbon-Coated Core-Shell Fe-Cu Nanoparticles as Highly Active and Durable Electrocatalysts for a Zn-Air Battery.

PubMed

Nam, Gyutae; Park, Joohyuk; Choi, Min; Oh, Pilgun; Park, Suhyeon; Kim, Min Gyu; Park, Noejung; Cho, Jaephil; Lee, Jang-Soo

2015-06-23

Understanding the interaction between a catalyst and oxygen has been a key step in designing better electrocatalysts for the oxygen reduction reaction (ORR) as well as applying them in metal-air batteries and fuel cells. Alloying has been studied to finely tune the catalysts' electronic structures to afford proper binding affinities for oxygen. Herein, we synthesized a noble-metal-free and nanosized transition metal CuFe alloy encapsulated with a graphitic carbon shell as a highly efficient and durable electrocatalyst for the ORR in alkaline solution. Theoretical models and experimental results demonstrated that the CuFe alloy has a more moderate binding strength for oxygen molecules as well as the final product, OH(-), thus facilitating the oxygen reduction process. Furthermore, the nitrogen-doped graphitic carbon-coated layer, formed catalytically under the influence of iron, affords enhanced charge transfer during the oxygen reduction process and superior durability. These benefits were successfully confirmed by realizing the catalyst application in a mechanically rechargeable Zn-air battery.

Reverse engineering the cooperative machinery of human hemoglobin.

PubMed

Ren, Zhong

2013-01-01

Hemoglobin transports molecular oxygen from the lungs to all human tissues for cellular respiration. Its α2β2 tetrameric assembly undergoes cooperative binding and releasing of oxygen for superior efficiency and responsiveness. Over past decades, hundreds of hemoglobin structures were determined under a wide range of conditions for investigation of molecular mechanism of cooperativity. Based on a joint analysis of hemoglobin structures in the Protein Data Bank (Ren, companion article), here I present a reverse engineering approach to elucidate how two subunits within each dimer reciprocate identical motions that achieves intradimer cooperativity, how ligand-induced structural signals from two subunits are integrated to drive quaternary rotation, and how the structural environment at the oxygen binding sites alter their binding affinity. This mechanical model reveals the intricate design that achieves the cooperative mechanism and has previously been masked by inconsistent structural fluctuations. A number of competing theories on hemoglobin cooperativity and broader protein allostery are reconciled and unified.

Deep analysis of N-cadherin/ADH-1 interaction: a computational survey.

PubMed

Eslami, Mahboobeh; Nezafat, Navid; Khajeh, Sahar; Mostafavi-Pour, Zohreh; Bagheri Novir, Samaneh; Negahdaripour, Manica; Ghasemi, Younes; Razban, Vahid

2018-01-19

Due to the considerable role of N-cadherin in cancer metastasis, tumor growth, and progression, inhibition of this protein has been highly regarded in recent years. Although ADH-1 has been known as an appropriate inhibitor of N-cadherin in clinical trials, its chemical nature and binding mode with N-cadherin have not been precisely specified yet. Accordingly, in this study, quantum mechanics calculations were used to investigate the chemical nature of ADH-1. These calculations clarify the molecular properties of ADH-1 and determine its reactive sites. Based on the results, the oxygen atoms are suitable for electrophilic reactivity, while the hydrogen atoms that are connected to nitrogen atoms are the favorite sites for nucleophilic reactivity. The higher electronegativity of the oxygen atoms makes them the most reactive portions in this molecule. Molecular docking and molecular dynamics (MD) simulation have also been applied to specify the binding mode of ADH-1 with N-cadherin and determine the important residues of N-cadherin involving in the interaction with ADH-1. Moreover, the verified model by MD simulation has been studied to extract the free energy value and find driving forces. These calculations and molecular electrostatic potential map of ADH-1 indicated that hydrophobic and electrostatic interactions are almost equally involved in the implantation of ADH-1 in the N-cadherin binding site. The presented results not only enable a closer examination of N-cadherin in complex with ADH-1 molecule, but also are very beneficial in designing new inhibitors for N-cadherin and can help to save time and cost in this field.

Expression, subcellular localization and regulation of sigma receptor in retinal Müller cells

PubMed Central

Jiang, Guoliang; Mysona, Barbara; Dun, Ying; Gnana-Prakasam, Jaya P.; Pabla, Navjotsin; Li, Weiguo; Dong, Zheng; Ganapathy, Vadivel; Smith, Sylvia B.

2013-01-01

Purpose Sigma receptors (σR) are non-opioid, non-phencyclidine binding sites with robust neuroprotective properties. σR1 is expressed in brain oligodendrocytes, but its expression and binding capacity have not been analyzed in retinal glial cells. This study examined the expression, subcellular localization, binding activity and regulation of σR1 in retinal Müller cells. Methods Primary mouse Müller cells (1°MC) were analyzed by RT-PCR, immunoblotting and immunocytochemistry for the expression of σR1 and data were compared to the rat Müller cell line, rMC-1 and rat ganglion cell line, RGC-5. Confocal microscopy was used to determine the subcellular σR1 location in 1°MC. Membranes prepared from these cells were used for binding assays using [3H]-pentazocine (PTZ). The kinetics of binding, the ability of various σR1 ligands to compete with σR1 binding and the effects of nitric oxide (NO) and reactive oxygen species (ROS) donors on binding were examined. Results σR1 is expressed in 1°MC and is localized to the nuclear and endoplasmic reticulum membranes. Binding assays showed that in 1°MCs, rMC-1 and RGC-5 cells, the binding of PTZ was saturable. [3H]-PTZ bound with high affinity in RGC-5 and rMC-1 cells and the binding was similarly robust in 1°MC. Competition studies showed marked inhibition of [3H]-PTZ binding in the presence of σR1-specific ligands. Incubation of cells with NO and ROS donors markedly increased σR1 binding activity. Conclusions Müller cells express σR1 and demonstrate robust σR1 binding activity, which is inhibited by σR1 ligands and is stimulated during oxidative stress. The potential of Müller cells to bind σR1 ligands may prove beneficial in retinal degenerative diseases such as diabetic retinopathy. PMID:17122151

Expression, subcellular localization, and regulation of sigma receptor in retinal muller cells.

PubMed

Jiang, Guoliang; Mysona, Barbara; Dun, Ying; Gnana-Prakasam, Jaya P; Pabla, Navjotsin; Li, Weiguo; Dong, Zheng; Ganapathy, Vadivel; Smith, Sylvia B

2006-12-01

Sigma receptors (sigmaRs) are nonopioid, nonphencyclidine binding sites with robust neuroprotective properties. Type 1 sigmaR1 (sigmaR1) is expressed in brain oligodendrocytes, but its expression and binding capacity have not been analyzed in retinal glial cells. This study examined the expression, subcellular localization, binding activity, and regulation of sigmaR1 in retinal Müller cells. Primary mouse Müller cells (MCs) were analyzed by RT-PCR, immunoblotting, and immunocytochemistry for the expression of sigmaR1, and data were compared with those of the rat Müller cell line (rMC-1) and the rat ganglion cell line (RGC-5). Confocal microscopy was used to determine the subcellular sigmaR1 location in primary mouse MCs. Membranes prepared from these cells were used for binding assays with [3H]-pentazocine (PTZ). The kinetics of binding, the ability of various sigmaR1 ligands to compete with sigmaR1 binding, and the effects of donated nitric oxide (NO) and reactive oxygen species (ROS) on binding were examined. sigmaR1 is expressed in primary mouse MCs and is localized to the nuclear and endoplasmic reticulum membranes. Binding assays showed that in primary mouse MCs, rMC-1, and RGC-5, the binding of PTZ was saturable. [3H]-PTZ bound with high affinity in RGC-5 and rMC-1 cells, and the binding was similarly robust in primary mouse MCs. Competition studies showed marked inhibition of [3H]-PTZ binding in the presence of sigmaR1-specific ligands. Incubation of cells with NO and ROS donors markedly increased sigmaR1 binding activity. MCs express sigmaR1 and demonstrate robust sigmaR1 binding activity, which is inhibited by sigmaR1 ligands and is stimulated during oxidative stress. The potential of Müller cells to bind sigmaR1 ligands may prove beneficial in retinal degenerative diseases such as diabetic retinopathy.

Oxygenation-linked subunit interactions in human hemoglobin: analysis of linkage functions for constituent energy terms.

PubMed

Johnson, M L; Halvorson, H R; Ackers, G K

1976-11-30

Resolution of the linkage functions between oxygenation and subunit association-dissociation equilibria in human hemoglobin into the constituent microscopic terms has been explored by numerical simulation and least-squares analysis. The correlation properties between parameters has been studied using several choices of parameter sets in order to optimize resolution. It is found that, with currently available levels of experimental precision and ranges of variables, neither linkage function can provide sufficient resolution of all the desired energy terms. The most difficult quantities to resolve always include the dimer-tetramer association constant for unliganded hemoglobin and the oxygen binding constants to alphabeta dimers. A feasible experimental strategy for overcoming these difficulties lies in independent determination of the dimer-tetramer association constants for unliganded and fully oxygenated hemoglobin. These constants, in combination with the median lignad concentration, provide an estimate of the energy for total oxygenation of tetramers which is essentially independent of the other constituent energies. It is shown that if these separately determinable parameters are fixed, the remaining terms may be estimated to good accuracy using data which represents either linkage function. In general it is desirable to combine information from both types of experimental quantities. A previous paper (Mills, F.C., Johnson, M.L., and Ackers, G.K. (1976), Biochemestry, 15, the preceding paper in this issue) describes the experimental implementation of this strategy.

USE OF OXYGEN-18 ISOTOPE LABELING FOR MEASUREMENT OF OXIDATIVE STRESS

EPA Science Inventory

Oxygen-18 (18-O) labeling provides a sensitive means for quantifying oxygen
binding that occurs during in vivo oxidations. Oxidants (ozone, nitrogen
oxides, hydrogen peroxide, etc.) are first synthesized using 18-O, then cells
or tissues are exposed to the labeled ...

Electronic structure and surface properties of MgB2(0001) upon oxygen adsorption

NASA Astrophysics Data System (ADS)

Kim, Chang-Eun; Ray, Keith G.; Bahr, David F.; Lordi, Vincenzo

2018-05-01

We use density-functional theory to investigate the bulk and surface properties of MgB2. The unique bonding structure of MgB2 is investigated by Bader's atoms-in-molecules, charge density difference, and occupancy projected band structure analyses. Oxygen adsorption on the charge-depleted surfaces of MgB2 is studied by a surface potential energy mapping method, reporting a complete map including low-symmetry binding sites. The B-terminated MgB2(0001) demonstrates reconstruction of the graphenelike B layer, and the reconstructed geometry exposes a threefold site of the subsurface Mg, making it accessible from the surface. Detailed reconstruction mechanisms are studied by simulated annealing method based on ab initio molecular dynamics and nudged elastic band calculations. The surface clustering of B atoms significantly modifies the B 2 p states to occupy low energy valence states. The present paper emphasizes that a thorough understanding of the surface phase may explain an apparent inconsistency in the experimental surface characterization of MgB2. Furthermore, these results suggest that the surface passivation can be an important technical challenge when it comes to development of a superconducting device using MgB2.

The influence of tumor oxygenation on hypoxia imaging in murine squamous cell carcinoma using [64Cu]Cu-ATSM or [18F]Fluoromisonidazole positron emission tomography.

PubMed

Matsumoto, Ken-Ichiro; Szajek, Lawrence; Krishna, Murali C; Cook, John A; Seidel, Jurgen; Grimes, Kelly; Carson, Joann; Sowers, Anastasia L; English, Sean; Green, Michael V; Bacharach, Stephen L; Eckelman, William C; Mitchell, James B

2007-04-01

[64Cu]Cu(II)-ATSM (64Cu-ATSM) and [18F]-Fluoromisonidazole (18F-FMiso) tumor binding as assessed by positron emisson topography (PET) was used to determine the responsiveness of each probe to modulation in tumor oxygenation levels in the SCCVII tumor model. Animals bearing the SCCVII tumor were injected with 64Cu-ATSM or 18F-FMiso followed by dynamic small animal PET imaging. Animals were imaged with both agents using different inspired oxygen mixtures (air, 10% oxygen, carbogen) which modulated tumor hypoxia as independently assessed by the hypoxia marker pimonidazole. The extent of hypoxia in the SCCVII tumor as monitored by the pimonidazole hypoxia marker was found to be in the following order: 10% oxygen>air>carbogen. Tumor uptake of 64Cu-ATSM could not be changed if the tumor was oxygenated using carbogen inhalation 90 min post-injection suggesting irreversible cellular uptake of the 64Cu-ATSM complex. A small but significant paradoxical increase in 64Cu-ATSM tumor uptake was observed for animals breathing air or carbogen compared to 10% oxygen. There was a positive trend toward 18F-FMiso tumor uptake as a function of changing hypoxia levels in agreement with the pimonidazole data. 64Cu-ATSM tumor uptake was unable to predictably detect changes in varying amounts of hypoxia when oxygenation levels in SCCVII tumors were modulated. 18F-FMiso tumor uptake was more responsive to changing levels of hypoxia. While the mechanism of nitroimidazole binding to hypoxic cells has been extensively studied, the avid binding of Cu-ATSM to tumors may involve other mechanisms independent of hypoxia that warrant further study.

DNA binding by a new metallointercalator that contains a proflavine group bearing a hanging chelating unit.

PubMed

Bazzicalupi, Carla; Bencini, Andrea; Bianchi, Antonio; Biver, Tarita; Boggioni, Alessia; Bonacchi, Sara; Danesi, Andrea; Giorgi, Claudia; Gratteri, Paola; Ingraín, Antonio Marchal; Secco, Fernando; Sissi, Claudia; Valtancoli, Barbara; Venturini, Marcella

2008-01-01

The new bifunctional molecule 3,6-diamine-9-[6,6-bis(2-aminoethyl)-1,6-diaminohexyl]acridine (D), which is characterised by both an aromatic moiety and a separate metal-complexing polyamine centre, has been synthesised. The characteristics of D and its ZnII complex ([ZnD]) (protonation and metal-complexing constants, optical properties and self-aggregation phenomena) have been analysed by means of NMR spectroscopy, potentiometric, spectrophotometric and spectrofluorimetric techniques. The equilibria and kinetics of the binding process of D and [ZnD] to calf thymus DNA have been investigated at I=0.11 M (NaCl) and 298.1 K by using spectroscopic methods and the stopped-flow technique. Static measurements show biphasic behaviour for both D-DNA and [ZnD]-DNA systems; this reveals the occurrence of two different binding processes depending on the polymer-to-dye molar ratio (P/D). The binding mode that occurs at low P/D values is interpreted in terms of external binding with a notable contribution from the polyamine residue. The binding mode at high P/D values corresponds to intercalation of the proflavine residue. Stopped-flow, circular dichroism and supercoiled-DNA unwinding experiments corroborate the proposed mechanism. Molecular-modelling studies support the intercalative process and evidence the influence of NH+...O interactions between the protonated acridine nitrogen atom and the oxygen atoms of the polyanion; these interactions play a key role in determining the conformation of DNA adducts.

Oxygen- and Lithium-Doped Hybrid Boron-Nitride/Carbon Networks for Hydrogen Storage.

PubMed

Shayeganfar, Farzaneh; Shahsavari, Rouzbeh

2016-12-20

Hydrogen storage capacities have been studied on newly designed three-dimensional pillared boron nitride (PBN) and pillared graphene boron nitride (PGBN). We propose these novel materials based on the covalent connection of BNNTs and graphene sheets, which enhance the surface and free volume for storage within the nanomaterial and increase the gravimetric and volumetric hydrogen uptake capacities. Density functional theory and molecular dynamics simulations show that these lithium- and oxygen-doped pillared structures have improved gravimetric and volumetric hydrogen capacities at room temperature, with values on the order of 9.1-11.6 wt % and 40-60 g/L. Our findings demonstrate that the gravimetric uptake of oxygen- and lithium-doped PBN and PGBN has significantly enhanced the hydrogen sorption and desorption. Calculations for O-doped PGBN yield gravimetric hydrogen uptake capacities greater than 11.6 wt % at room temperature. This increased value is attributed to the pillared morphology, which improves the mechanical properties and increases porosity, as well as the high binding energy between oxygen and GBN. Our results suggest that hybrid carbon/BNNT nanostructures are an excellent candidate for hydrogen storage, owing to the combination of the electron mobility of graphene and the polarized nature of BN at heterojunctions, which enhances the uptake capacity, providing ample opportunities to further tune this hybrid material for efficient hydrogen storage.

Enhanced nitrite reductase activity associated with the haptoglobin complexed hemoglobin dimer: Functional and antioxidative implications

PubMed Central

Roche, Camille J.; Dantsker, David; Alayash, Abdu I.; Friedman, Joel M.

2012-01-01

The presence of acellular hemoglobin (Hb) within the circulation is generally viewed as a pathological state that can result in toxic consequences. Haptoglobin (Hp), a globular protein found in the plasma, binds with high avidity the αβ dimers derived from the dissociation of Hb tetramer and thus helps clear free Hb. More recently there have been compelling indications that the redox properties of the Hp bound dimer (Hb–Hp) may play a more active role in controlling toxicity by limiting the potential tissue damage caused by propagation of the free-radicals generated within the heme containing globin chains. The present study further examines the potential protective effect of Hp through its impact on the production of nitric oxide (NO) from nitrite through nitrite reductase activity of the Hp bound αβ Hb dimer. The presented results show that the Hb dimer in the Hb–Hp complex has oxygen binding, CO recombination and spectroscopic properties consistent with an Hb species having properties similar to but not exactly the same as the R quaternary state of the Hb tetramer. Consistent with these observations is the finding that the initial nitrite reductase rate for Hb–Hp is approximately ten times that of HbA under the same conditions. These results in conjunction with the earlier redox properties of the Hb–Hp are discussed in terms of limiting the pathophysiological consequences of acellular Hb in the circulation. PMID:22521791

Spectroscopic and Theoretical Study of CuI Binding to His111 in the Human Prion Protein Fragment 106–115

PubMed Central

2016-01-01

The ability of the cellular prion protein (PrPC) to bind copper in vivo points to a physiological role for PrPC in copper transport. Six copper binding sites have been identified in the nonstructured N-terminal region of human PrPC. Among these sites, the His111 site is unique in that it contains a MKHM motif that would confer interesting CuI and CuII binding properties. We have evaluated CuI coordination to the PrP(106–115) fragment of the human PrP protein, using NMR and X-ray absorption spectroscopies and electronic structure calculations. We find that Met109 and Met112 play an important role in anchoring this metal ion. CuI coordination to His111 is pH-dependent: at pH >8, 2N1O1S species are formed with one Met ligand; in the range of pH 5–8, both methionine (Met) residues bind to CuI, forming a 1N1O2S species, where N is from His111 and O is from a backbone carbonyl or a water molecule; at pH <5, only the two Met residues remain coordinated. Thus, even upon drastic changes in the chemical environment, such as those occurring during endocytosis of PrPC (decreased pH and a reducing potential), the two Met residues in the MKHM motif enable PrPC to maintain the bound CuI ions, consistent with a copper transport function for this protein. We also find that the physiologically relevant CuI-1N1O2S species activates dioxygen via an inner-sphere mechanism, likely involving the formation of a copper(II) superoxide complex. In this process, the Met residues are partially oxidized to sulfoxide; this ability to scavenge superoxide may play a role in the proposed antioxidant properties of PrPC. This study provides further insight into the CuI coordination properties of His111 in human PrPC and the molecular mechanism of oxygen activation by this site. PMID:26930130

Enhanced binding of hydrophobic organic contaminants by microwave-assisted humification of soil organic matter.

PubMed

Hur, Jin; Park, Sung-Won; Kim, Min Chan; Kim, Han S

2013-11-01

Enhanced binding of hydrophobic organic contaminants (HOCs) with soil organic matter (SOM) by microwave (MW) irradiation was investigated in this study. We used fluorescence excitation emission matrix, humification index (HIX), and organic carbon partitioning coefficient (Koc) to examine characteristic changes in SOM and its sorptive capacity for HOCs. When MW was irradiated to soils, protein-like fluorescence decreased but fulvic- and humic-like fluorescence increased. The addition of activated carbon in the presence of oxygen facilitated the humification-like alteration of SOM more significantly, evidenced by increases in fulvic- and humic-like fluorescence signals. The extent of SOM-phenanthrene binding also increased with MW treatment, supported by a notable increase in Koc value from 1.8×10(4) to 7.3×10(5)Lkg(-1). Various descriptors indicating the physical and chemical properties of SOM along with the relative percentage of humic-like fluorescence and HIX values demonstrated strong linear relationships with Koc values. These linear relationships indicated that the increased binding affinity of SOM for phenanthrene was attributed to enhanced SOM humification, which was stimulated by MW irradiation. Thus, our results demonstrate that MW irradiation could be effectively used for remediation or for assessing the environmental risks of HOC-contaminated soils and groundwater. Copyright © 2013 Elsevier Ltd. All rights reserved.

Electron transfer function versus oxygen delivery: a comparative study for several hexacoordinated globins across the animal kingdom.

PubMed

Kiger, Laurent; Tilleman, Lesley; Geuens, Eva; Hoogewijs, David; Lechauve, Christophe; Moens, Luc; Dewilde, Sylvia; Marden, Michael C

2011-01-01

Caenorhabditis elegans globin GLB-26 (expressed from gene T22C1.2) has been studied in comparison with human neuroglobin (Ngb) and cytoglobin (Cygb) for its electron transfer properties. GLB-26 exhibits no reversible binding for O(2) and a relatively low CO affinity compared to myoglobin-like globins. These differences arise from its mechanism of gaseous ligand binding since the heme iron of GLB-26 is strongly hexacoordinated in the absence of external ligands; the replacement of this internal ligand, probably the E7 distal histidine, is required before binding of CO or O(2) as for Ngb and Cygb. Interestingly the ferrous bis-histidyl GLB-26 and Ngb, another strongly hexacoordinated globin, can transfer an electron to cytochrome c (Cyt-c) at a high bimolecular rate, comparable to those of inter-protein electron transfer in mitochondria. In addition, GLB-26 displays an unexpectedly rapid oxidation of the ferrous His-Fe-His complex without O(2) actually binding to the iron atom, since the heme is oxidized by O(2) faster than the time for distal histidine dissociation. These efficient mechanisms for electron transfer could indicate a family of hexacoordinated globin which are functionally different from that of pentacoordinated globins.

The Impact of Atmosphere on the Local Luminescence Properties of Metal Halide Perovskite Grains.

PubMed

Brenes, Roberto; Eames, Christopher; Bulović, Vladimir; Islam, M Saiful; Stranks, Samuel D

2018-04-01

Metal halide perovskites are exceptional candidates for inexpensive yet high-performing optoelectronic devices. Nevertheless, polycrystalline perovskite films are still limited by nonradiative losses due to charge carrier trap states that can be affected by illumination. Here, in situ microphotoluminescence measurements are used to elucidate the impact of light-soaking individual methylammonium lead iodide grains in high-quality polycrystalline films while immersing them with different atmospheric environments. It is shown that emission from each grain depends sensitively on both the environment and the nature of the specific grain, i.e., whether it shows good (bright grain) or poor (dark grain) luminescence properties. It is found that the dark grains show substantial rises in emission, while the bright grain emission is steady when illuminated in the presence of oxygen and/or water molecules. The results are explained using density functional theory calculations, which reveal strong adsorption energies of the molecules to the perovskite surfaces. It is also found that oxygen molecules bind particularly strongly to surface iodide vacancies which, in the presence of photoexcited electrons, lead to efficient passivation of the carrier trap states that arise from these vacancies. The work reveals a unique insight into the nature of nonradiative decay and the impact of atmospheric passivation on the microscale properties of perovskite films. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Lee, Yong-Min; Bang, Suhee; Yoon, Heejung

Here we report redox-inactive metal ions play important roles in tuning chemical properties of metal–oxygen intermediates. We describe the effect of water molecules on the redox properties of a nonheme iron(III)–peroxo complex binding redox-inactive metal ions. The coordination of two water molecules to a Zn 2+ ion in (TMC)Fe III-(O 2)-Zn(CF 3SO 3) 2 (1-Zn 2+) decreases the Lewis acidity of the Zn 2+ ion, resulting in the decrease of the one-electron oxidation and reduction potentials of 1-Zn 2+. This further changes the reactivities of 1-Zn 2+ in oxidation and reduction reactions; no reaction occurred upon addition of an oxidantmore » (e.g., cerium(IV) ammonium nitrate (CAN)) to 1-Zn 2+, whereas 1-Zn 2+ coordinating two water molecules, (TMC)Fe III-(O 2)-Zn(CF 3SO 3) 2-(OH 2) 2 [1-Zn 2+-(OH 2) 2], releases the O 2 unit in the oxidation reaction. In the reduction reactions, 1-Zn 2+ was converted to its corresponding iron(IV)–oxo species upon addition of a reductant (e.g., a ferrocene derivative), whereas such a reaction occurred at a much slower rate in the case of 1-Zn 2+-(OH 2) 2. Finally, the present results provide the first biomimetic example showing that water molecules at the active sites of metalloenzymes may participate in tuning the redox properties of metal–oxygen intermediates.« less

The Greenland shark Somniosus microcephalus-Hemoglobins and ligand-binding properties.

PubMed

Russo, Roberta; Giordano, Daniela; Paredi, Gianluca; Marchesani, Francesco; Milazzo, Lisa; Altomonte, Giovanna; Del Canale, Pietro; Abbruzzetti, Stefania; Ascenzi, Paolo; di Prisco, Guido; Viappiani, Cristiano; Fago, Angela; Bruno, Stefano; Smulevich, Giulietta; Verde, Cinzia

2017-01-01

A large amount of data is currently available on the adaptive mechanisms of polar bony fish hemoglobins, but structural information on those of cartilaginous species is scarce. This study presents the first characterisation of the hemoglobin system of one of the longest-living vertebrate species (392 ± 120 years), the Arctic shark Somniosus microcephalus. Three major hemoglobins are found in its red blood cells and are made of two copies of the same α globin combined with two copies of three very similar β subunits. The three hemoglobins show very similar oxygenation and carbonylation properties, which are unaffected by urea, a very important compound in marine elasmobranch physiology. They display identical electronic absorption and resonance Raman spectra, indicating that their heme-pocket structures are identical or highly similar. The quaternary transition equilibrium between the relaxed (R) and the tense (T) states is more dependent on physiological allosteric effectors than in human hemoglobin, as also demonstrated in polar teleost hemoglobins. Similar to other cartilaginous fishes, we found no evidence for functional differentiation among the three isoforms. The very similar ligand-binding properties suggest that regulatory control of O2 transport may be at the cellular level and that it may involve changes in the cellular concentrations of allosteric effectors and/or variations of other systemic factors. The hemoglobins of this polar shark have evolved adaptive decreases in O2 affinity in comparison to temperate sharks.

The Greenland shark Somniosus microcephalus—Hemoglobins and ligand-binding properties

PubMed Central

Paredi, Gianluca; Marchesani, Francesco; Milazzo, Lisa; Altomonte, Giovanna; Del Canale, Pietro; Abbruzzetti, Stefania; Ascenzi, Paolo; di Prisco, Guido; Viappiani, Cristiano; Fago, Angela; Bruno, Stefano; Smulevich, Giulietta

2017-01-01

A large amount of data is currently available on the adaptive mechanisms of polar bony fish hemoglobins, but structural information on those of cartilaginous species is scarce. This study presents the first characterisation of the hemoglobin system of one of the longest-living vertebrate species (392 ± 120 years), the Arctic shark Somniosus microcephalus. Three major hemoglobins are found in its red blood cells and are made of two copies of the same α globin combined with two copies of three very similar β subunits. The three hemoglobins show very similar oxygenation and carbonylation properties, which are unaffected by urea, a very important compound in marine elasmobranch physiology. They display identical electronic absorption and resonance Raman spectra, indicating that their heme-pocket structures are identical or highly similar. The quaternary transition equilibrium between the relaxed (R) and the tense (T) states is more dependent on physiological allosteric effectors than in human hemoglobin, as also demonstrated in polar teleost hemoglobins. Similar to other cartilaginous fishes, we found no evidence for functional differentiation among the three isoforms. The very similar ligand-binding properties suggest that regulatory control of O2 transport may be at the cellular level and that it may involve changes in the cellular concentrations of allosteric effectors and/or variations of other systemic factors. The hemoglobins of this polar shark have evolved adaptive decreases in O2 affinity in comparison to temperate sharks. PMID:29023598

Novel graphene-oxide-coated SPR interfaces for biosensing applications

NASA Astrophysics Data System (ADS)

Volkov, V. S.; Stebunov, Yu. V.; Yakubovsky, D. I.; Fedyanin, D. Yu.; Arsenin, A. V.

2017-09-01

Carbon allotropes-based nanomaterials possess unique physical and chemical properties including high surface area, the possibility of pi-stacking interaction with a wide range of biological objects, rich availability of oxygen-containing functional groups in graphene-oxide (GO), and excellent optical properties, which make them an ideal candidate for use as a universal immobilization platform in SPR biosensing. Here, we propose a new surface plasmon resonance (SPR) biosensing interface for sensitive and selective detection of small molecules. This interface is based on the GO linking layers deposited on the gold/copper surface of SPR sensor chips. To estimate the binding capacity of GO layers, modification of carboxyl groups to N-Hydroxysuccinimide esters was performed in the flow cell of SPR instrument. For comparison, the same procedure was applied to commercial sensor chips based on linking layers of carboxymethylated dextran.

Oxygen content tailored magnetic and electronic properties in cobaltite double perovskite thin films

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

Harrell, Zach John; Enriquez, Erik M.; Chen, Aiping

Oxygen content in transition metal oxides is one of the most important parameters to control for the desired physical properties. Recently, we have systematically studied the oxygen content and property relationship of the double perovskite PrBaCo 2O 5.5+δ (PBCO) thin films deposited on the LaAlO 3 substrates. The oxygen content in the films was varied by in-situ annealing in a nitrogen, oxygen, or ozone environment. Associated with the oxygen content, the out-of-plane lattice parameter progressively decreases with increasing oxygen content in the films. The saturated magnetization shows a drastic increase and resistivity is significantly reduced in the ozone annealed samples,more » indicating the strong coupling between physical properties and oxygen content. Furthermore, these results demonstrate that the magnetic properties of PBCO films are highly dependent on the oxygen contents, or the film with higher oxygen uptake has the largest magnetization.« less

Oxygen content tailored magnetic and electronic properties in cobaltite double perovskite thin films

DOE PAGES

Harrell, Zach John; Enriquez, Erik M.; Chen, Aiping; ...

2017-02-27

Oxygen content in transition metal oxides is one of the most important parameters to control for the desired physical properties. Recently, we have systematically studied the oxygen content and property relationship of the double perovskite PrBaCo 2O 5.5+δ (PBCO) thin films deposited on the LaAlO 3 substrates. The oxygen content in the films was varied by in-situ annealing in a nitrogen, oxygen, or ozone environment. Associated with the oxygen content, the out-of-plane lattice parameter progressively decreases with increasing oxygen content in the films. The saturated magnetization shows a drastic increase and resistivity is significantly reduced in the ozone annealed samples,more » indicating the strong coupling between physical properties and oxygen content. Furthermore, these results demonstrate that the magnetic properties of PBCO films are highly dependent on the oxygen contents, or the film with higher oxygen uptake has the largest magnetization.« less

Functional characterization of mutant strains of the cyanobacterium Synechocystis sp. PCC 6803 lacking short domains within the large, lumen-exposed loop of the chlorophyll protein CP47 in photosystem II.

PubMed

Gleiter, H M; Haag, E; Shen, J R; Eaton-Rye, J J; Inoue, Y; Vermaas, W F; Renger, G

1994-10-11

Several autotrophic mutant strains of Synechocystis sp. PCC 6803 carrying short deletions or a single-site mutation within the large, lumen-exposed loop (loop E) of the chlorophyll a-binding photosystem II core protein, CP47, are analyzed for their functional properties by measuring the flash-induced pattern of thermoluminescence, oxygen yield, and fluorescence quantum yield. A physiological and biochemical characterization of these mutant strains has been given in two previous reports [Eaton-Rye, J.J., & Vermaas, W.F.J. (1991) Plant Mol. Biol. 17, 1165-1177; Haag, E., Eaton-Rye, J.J., Renger, G., & Vermaas, S. F.J. (1993) Biochemistry 32, 4444-4454]. The results of the present study show that deletion of charged and conserved amino acids in a region roughly located between residues 370 and 390 decreases the binding affinity of the extrinsic PS II-O protein to photosystem II. Marked differences with PSII-O deletion mutants are observed with respect to Ca2+ requirement and the flash-induced pattern of oxygen evolution. Under conditions where a sufficient light activation is provided, the psbB mutants assayed in this study reveal normal S-state parameters and lifetimes. The results bear two basic implications: (i) the manganese involved in water oxidation can still be bound in a functionally normal or only slightly distorted manner, and (ii) the binding of the extrinsic PS II-O protein to photosystem II is impaired in mutants carrying a deletion in the domain between residues 370 and 390, but the presence of the PS II-O protein is still of functional relevance for the PS II complex, e.g., for maintenance of a high-affinity binding site for Ca2+ and/or involvement during the process of photoactivation.

Active and stable Ir@Pt core–shell catalysts for electrochemical oxygen reduction

DOE PAGES

Strickler, Alaina L.; Jackson, Ariel; Jaramillo, Thomas F.

2016-12-28

Electrochemical oxygen reduction is an important reaction for many sustainable energy technologies, such as fuel cells and metal–air batteries. Kinetic limitations of this reaction, expensive electrocatalysts, and catalyst instability, however, limit the commercial viability of such devices. Herein, we report an active Ir@Pt core–shell catalyst that combines platinum overlayers with nanostructure effects to tune the oxygen binding to the Pt surface, thereby achieving enhanced activity and stability for the oxygen reduction reaction. Ir@Pt nanoparticles with several shell thicknesses were synthesized in a scalable, inexpensive, one-pot polyol method. Electrochemical analysis demonstrates the activity and stability of the Ir@Pt catalyst, with specificmore » and mass activities increasing to 2.6 and 1.8 times that of commercial Pt/C (TKK), respectively, after 10 000 stability cycles. Furthermore, activity enhancement of the Ir@Pt catalyst is attributed to weakening of the oxygen binding to the Pt surface induced by the Ir core.« less

Experimental and DFT studies of gold nanoparticles supported on MgO(111) nano-sheets and their catalytic activity.

PubMed

Li, Zhi; Ciobanu, Cristian V; Hu, Juncheng; Palomares-Báez, Juan-Pedro; Rodríguez-López, José-Luis; Richards, Ryan

2011-02-21

A wet chemical preparation of MgO with the (111) facet as the primary surface has recently been reported and with alternating layers of oxygen anions and magnesium cations, this material shows unique chemical and physical properties. The potential to utilize the MgO(111) surface for the immobilization of metal particles is intriguing because the surface itself offers a very different environment for the metal particle with an all oxygen interface, as opposed to the typical (100) facet that possesses alternating oxygen anion and magnesium cation sites on the surface. Gold nanoparticles have demonstrated a broad range of interesting catalytic properties, but are often susceptible to aggregation at high temperatures and are very sensitive to substrate effects. Here, we investigate gold-supported on MgO(111) nanosheets as a catalyst system for the aerobic oxidation of benzyl alcohol. Gold nanoparticles deposited on MgO(111) show an increased level of activity in the solvent-free benzyl alcohol aerobic oxidation as compared to gold nanoparticles deposited on a typical MgO aerogel. TEM studies reveal that the gold nanoparticles have a hemispherical shape while sitting on the main surface of MgO(111) nanosheets, with a large Au-MgO interface. Given that the gold nanoparticles deposited on the two types of MgO have similar size, and that the two types of unmodified MgO show almost the same activities in the blank reaction, we infer that the high activity of Au/MgO(111) is due to the properties of the (111) support and/or those of the gold-support interface. To understand the binding of Au on low-index MgO surfaces and the charge distribution at the surface of the support, we have performed density functional theory (DFT) calculations on all low-index MgO substrates (with and without gold), using a model Au(10) cluster. Due to similar lattice constants of Au(111) and MgO(111) planes, the Au cluster retains its structural integrity and binds strongly on MgO(111) with either oxygen or magnesium termination. Furthermore, we have found that for the (001) and (110) substrates the charges of the ions in the top surface layer have similar values as in bulk MgO, but that on (111) surfaces these charges are significantly different. This difference in surface charge determines the direction of the electronic transfer upon adsorption of gold, such transfer occurring so as to restore the bulk MgO charge values. Using the results from theoretical calculations, we provide an explanation of our observations of increased catalytic activity in the case of the Au/MgO(111) system.

Inhibition of human Na(v)1.5 sodium channels by strychnine and its analogs.

PubMed

Yuan, Chunhua; Sun, Lirong; Zhang, Meng; Li, Shuji; Wang, Xuemin; Gao, Tianming; Zhu, Xinhong

2011-08-15

Strychnine and brucine from the seeds of the plant Strychnos nux vomica have been shown to have interesting pharmacological effects on several neurotransmitter receptors. In this study, we have characterized the pharmacological properties of strychnine and its analogs on human Na(v)1.5 channels to assess their potential therapeutic advantage in certain arrhythmias. Among the eight alkaloids, only strychnine and icajine exhibited inhibition potency on the Na(v)1.5 channel with the half-maximum inhibition (IC(50)) values of 83.1μM and 104.6μM, respectively. Structure-function analysis indicated that the increased bulky methoxy groups on the phenyl ring or the negatively charged oxygen atom may account for this lack of inhibition on the Na(v)1.5 channel. Strychnine and icajine may bind to the channel by cation-π interactions. The substitution with a large side chain on the phenyl ring or the increased molecular volume may alter the optimized position for the compound close to the binding sites of the channel. Strychnine and icajine bind to the Na(v)1.5 channel with a new mechanism that is different from TTX and local anesthetics. They bind to the outer vestibule of the channel pore with fast association and dissociation rates at resting state. Strychnine and icajine had little effect on steady-state fast inactivation but markedly shifted the slow inactivation of Na(v)1.5 currents toward more hyperpolarized potentials. The property of icajine influencing slow-inactivated state of Na(v)1.5 channel would be potential therapeutic advantages in certain arrhythmias. Copyright © 2011 Elsevier Inc. All rights reserved.

Synthesis and biophysical properties of 5'-thio-2',4'-BNA/LNA oligonucleotide.

PubMed

Islam, Md Ariful; Fujisaka, Aki; Mori, Shohei; Ito, Kosuke Ramon; Yamaguchi, Takao; Obika, Satoshi

2018-07-23

Phosphorothioate modification of oligonucleotides is one of the most promising chemical modifications in nucleic acid therapeutics. Structurally similar 5'-thio or phosphorothiolate-modified nucleotides, in which the 5'-bridging oxygen atom is replaced with a sulfur atom, are attracting attention and gaining importance in oligonucleotide-based research. In our present study, we synthesized 5'-thio-2',4'-BNA/LNA monomers bearing thymine or 5-methylcytosine nucleobase. The 5'-thio-2',4'-BNA/LNA monomers were successfully incorporated into target oligonucleotides, and their nuclease stability and binding affinity with complementary strands were evaluated. Copyright © 2018 Elsevier Ltd. All rights reserved.

Quantum mechanics/molecular mechanics study on the oxygen binding and substrate hydroxylation step in AlkB repair enzymes.

PubMed

Quesne, Matthew G; Latifi, Reza; Gonzalez-Ovalle, Luis E; Kumar, Devesh; de Visser, Sam P

2014-01-07

AlkB repair enzymes are important nonheme iron enzymes that catalyse the demethylation of alkylated DNA bases in humans, which is a vital reaction in the body that heals externally damaged DNA bases. Its mechanism is currently controversial and in order to resolve the catalytic mechanism of these enzymes, a quantum mechanics/molecular mechanics (QM/MM) study was performed on the demethylation of the N(1) -methyladenine fragment by AlkB repair enzymes. Firstly, the initial modelling identified the oxygen binding site of the enzyme. Secondly, the oxygen activation mechanism was investigated and a novel pathway was found, whereby the catalytically active iron(IV)-oxo intermediate in the catalytic cycle undergoes an initial isomerisation assisted by an Arg residue in the substrate binding pocket, which then brings the oxo group in close contact with the methyl group of the alkylated DNA base. This enables a subsequent rate-determining hydrogen-atom abstraction on competitive σ- and π-pathways on a quintet spin-state surface. These findings give evidence of different locations of the oxygen and substrate binding channels in the enzyme and the origin of the separation of the oxygen-bound intermediates in the catalytic cycle from substrate. Our studies are compared with small model complexes and the effect of protein and environment on the kinetics and mechanism is explained. © 2013 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

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

Electron Paramagnetic Resonance Studies of Spin-Labeled Hemoglobins and Their Implications to the Nature of Cooperative Oxygen Binding to Hemoglobin*

PubMed Central

Ho, Chien; Baldassare, Joseph J.; Charache, Samuel

1970-01-01

The spin label technique has been used to study human hemoglobins A, F, Zürich, and Chesapeake as a function of carbon monoxide saturation. The experimental results suggest that the changes in the electron paramagnetic resonance spectra of hemoglobin labeled with N-(1-oxyl-2,2,6,6-tetramethyl-4-piperidinyl)iodoacetamide depend on the state of ligation of more than one heme group. For those hemoglobins with full or large cooperative ligand binding (such as A, F, and Zürich), there is a lack of isosbestic points in the spectra as a function of CO saturation. However, for those hemoglobins with little or no cooperative ligand binding (such as Chesapeake and methemoglobins), there is a sharp set of isosbestic points. These findings confirm and extend the early work of McConnell and co-workers. The absence of a set of isosbestic points in those hemoglobins with full cooperative ligand binding is consistent with the sequential model of Koshland, Némethy, and Filmer for cooperative oxygen binding to hemoglobin. The present results, with hemoglobin variants having known amino acid substitutions, also focus on the importance of the interactions among the amino acid residues located at α1-β2 or α2-β1 subunit contacts for the functioning of hemoglobin as an oxygen carrier. In addition, the resonance spectra of the spin label are very sensitive to small structural variations around the heme groups in the β- or γ-chains where the labels are attached. The results of the spin label experiment are discussed in relation to recent findings on the mechanism of oxygenation of hemoglobin from the nuclear magnetic resonance studies of this laboratory and the x-ray crystallographic analysis of Perutz and co-workers. PMID:4316679

Cationic composition and acid-base state of the extracellular fluid, and specific buffer value of hemoglobin from the branchiopod crustacean Triops cancriformis.

PubMed

Pirow, Ralph; Buchen, Ina; Richter, Marc; Allmer, Carsten; Nunes, Frank; Günsel, Andreas; Heikens, Wiebke; Lamkemeyer, Tobias; von Reumont, Björn M; Hetz, Stefan K

2009-04-01

Recent insights into the allosteric control of oxygen binding in the extracellular hemoglobin (Hb) of the tadpole shrimp Triops cancriformis raised the question about the physico-chemical properties of the protein's native environment. This study determined the cationic composition and acid-base state of the animal's extracellular fluid. The physiological concentrations of potential cationic effectors (calcium, magnesium) were more than one order of magnitude below the level effective to increase Hb oxygen affinity. The extracellular fluid in the pericardial space had a typical bicarbonate concentration of 7.6 mM but a remarkably high CO(2) partial pressure of 1.36 kPa at pH 7.52 and 20 degrees C. The discrepancy between this high CO(2) partial pressure and the comparably low values for water-breathing decapods could not solely be explained by the hemolymph-sampling procedure but may additionally arise from differences in cardiovascular complexity and efficiency. T. cancriformis hemolymph had a non-bicarbonate buffer value of 2.1 meq L(-1) pH(-1). Hb covered 40-60% of the non-bicarbonate buffering power. The specific buffer value of Hb of 1.1 meq (mmol heme)(-1) pH(-1) suggested a minimum requirement of two titratable histidines per heme-binding domain, which is supported by available information from N-terminal sequencing and expressed sequence tags.

Deciphering the GPER/GPR30-agonist and antagonists interactions using molecular modeling studies, molecular dynamics, and docking simulations.

PubMed

Méndez-Luna, D; Martínez-Archundia, M; Maroun, Rachid C; Ceballos-Reyes, G; Fragoso-Vázquez, M J; González-Juárez, D E; Correa-Basurto, J

2015-01-01

The G-protein coupled estrogen receptor 1 GPER/GPR30 is a transmembrane seven-helix (7TM) receptor involved in the growth and proliferation of breast cancer. Due to the absence of a crystal structure of GPER/GPR30, in this work, molecular modeling studies have been carried out to build a three-dimensional structure, which was subsequently refined by molecular dynamics (MD) simulations (up to 120 ns). Furthermore, we explored GPER/GPR30's molecular recognition properties by using reported agonist ligands (G1, estradiol (E2), tamoxifen, and fulvestrant) and the antagonist ligands (G15 and G36) in subsequent docking studies. Our results identified the E2 binding site on GPER/GPR30, as well as other receptor cavities for accepting large volume ligands, through GPER/GPR30 π-π, hydrophobic, and hydrogen bond interactions. Snapshots of the MD trajectory at 14 and 70 ns showed almost identical binding motifs for G1 and G15. It was also observed that C107 interacts with the acetyl oxygen of G1 (at 14 ns) and that at 70 ns the residue E275 interacts with the acetyl group and with the oxygen from the other agonist whereas the isopropyl group of G36 is oriented toward Met141, suggesting that both C107 and E275 could be involved in the protein activation. This contribution suggest that GPER1 has great structural changes which explain its great capacity to accept diverse ligands, and also, the same ligand could be recognized in different binding pose according to GPER structural conformations.

Effects of bottom water dissolved oxygen variability on copper and lead fractionation in the sediments across the oxygen minimum zone, western continental margin of India.

PubMed

Chakraborty, Parthasarathi; Chakraborty, Sucharita; Jayachandran, Saranya; Madan, Ritu; Sarkar, Arindam; Linsy, P; Nath, B Nagender

2016-10-01

This study describes the effect of varying bottom-water oxygen concentration on geochemical fractionation (operational speciation) of Cu and Pb in the underneath sediments across the oxygen minimum zone (Arabian Sea) in the west coast of India. Both, Cu and Pb were redistributed among the different binding phases of the sediments with changing dissolved oxygen level (from oxic to hypoxic and close to suboxic) in the bottom water. The average lability of Cu-sediment complexes gradually decreased (i.e., stability increased) with the decreasing dissolved oxygen concentrations of the bottom water. Decreasing bottom-water oxygen concentration increased Cu association with sedimentary organic matter. However, Pb association with Fe/Mn-oxyhydroxide phases in the sediments gradually decreased with the decreasing dissolved oxygen concentration of the overlying bottom water (due to dissolution of Fe/Mn oxyhydroxide phase). The lability of Pb-sediment complexes increased with the decreasing bottom-water oxygen concentration. This study suggests that bottom-water oxygen concentration is one of the key factors governing stability and lability of Cu and Pb complexes in the underneath sediment. Sedimentary organic matter and Fe/Mn oxyhydroxide binding phases were the major hosting phases for Cu and Pb respectively in the study area. Increasing lability of Pb-complexes in bottom sediments may lead to positive benthic fluxes of Pb at low oxygen environment. Copyright © 2016 Elsevier B.V. All rights reserved.

Deep vs shallow nature of oxygen vacancies and consequent n -type carrier concentrations in transparent conducting oxides

NASA Astrophysics Data System (ADS)

Buckeridge, J.; Catlow, C. R. A.; Farrow, M. R.; Logsdail, A. J.; Scanlon, D. O.; Keal, T. W.; Sherwood, P.; Woodley, S. M.; Sokol, A. A.; Walsh, A.

2018-05-01

The source of n -type conductivity in undoped transparent conducting oxides has been a topic of debate for several decades. The point defect of most interest in this respect is the oxygen vacancy, but there are many conflicting reports on the shallow versus deep nature of its related electronic states. Here, using a hybrid quantum mechanical/molecular mechanical embedded cluster approach, we have computed formation and ionization energies of oxygen vacancies in three representative transparent conducting oxides: In2O3 ,SnO2, and ZnO. We find that, in all three systems, oxygen vacancies form well-localized, compact donors. We demonstrate, however, that such compactness does not preclude the possibility of these states being shallow in nature, by considering the energetic balance between the vacancy binding electrons that are in localized orbitals or in effective-mass-like diffuse orbitals. Our results show that, thermodynamically, oxygen vacancies in bulk In2O3 introduce states above the conduction band minimum that contribute significantly to the observed conductivity properties of undoped samples. For ZnO and SnO2, the states are deep, and our calculated ionization energies agree well with thermochemical and optical experiments. Our computed equilibrium defect and carrier concentrations, however, demonstrate that these deep states may nevertheless lead to significant intrinsic n -type conductivity under reducing conditions at elevated temperatures. Our study indicates the importance of oxygen vacancies in relation to intrinsic carrier concentrations not only in In2O3 , but also in SnO2 and ZnO.

Positron states and annihilation characteristics of surface-trapped positrons at the oxidized Cu(110) surface

NASA Astrophysics Data System (ADS)

Fazleev, N. G.; Olenga, Antoine; Weiss, A. H.

2013-03-01

The process by which oxide layers are formed on metal surfaces is still not well understood. In this work we present the results of theoretical studies of positron states and annihilation characteristics of surface-trapped positrons at the oxidized Cu(110) surface. An ab-initio investigation of stability and associated electronic properties of different adsorption phases of oxygen on Cu(110) has been performed on the basis of density functional theory and using DMOl3 code. The changes in the positron work function and the surface dipole moment when oxygen atoms occupy on-surface and sub-surface sites have been attributed to charge redistribution within the first two layers, buckling effects within each layer and interlayer expansion. The computed positron binding energy, positron surface state wave function, and annihilation probabilities of surface trapped positrons with relevant core electrons demonstrate their sensitivity to oxygen coverage, elemental content, atomic structure of the topmost layers of surfaces, and charge transfer effects. Theoretical results are compared with experimental data obtained from studies of oxidized transition metal surfaces using positron annihilation induced Auger electron spectroscopy. This work was supported in part by the National Science Foundation Grant DMR-0907679.

Fe3O4@NiSx/rGO composites with amounts of heterointerfaces and enhanced electrocatalytic properties for oxygen evolution

NASA Astrophysics Data System (ADS)

Zhu, Guoxing; Xie, Xulan; Liu, Yuanjun; Li, Xiaoyun; Xu, Keqiang; Shen, Xiaoping; Yao, Yinjie; Shah, Sayyar Ali

2018-06-01

The sluggish oxygen evolution kinetics involved in water splitting and various metal-air batteries makes the effective and inexpensive electrocatalysts be highly desirable for oxygen evolution reaction (OER). Herein, an effective and facile two-step route is developed to construct Fe3O4@NiSx composite loaded on reduced graphene oxide (rGO). The morphology and microstructure of the composites were characterized by different characterization techniques. The obtained composites show amounts of heterointerfaces. The shift of binding energy in X-ray photoelectron spectrum demonstrates the existence of interfacial charge transfer effect between Fe3O4 and NiSx. The optimized Fe3O4@NiSx/rGO sample exhibits excellent electrocatalytic performance toward OER in alkaline media, showing 10 mA·cm-2 at η = 330 mV, lower Tafel slope (35.5 mV·dec-1), and good durability, demonstrating a great perspective. The excellent OER performance can be ascribed to the synergetic effect between Fe and Ni species. It is believed that the heterointerfaces between Fe3O4 and NiSx perform as active centers for OER.

Positron trapping at defects in copper oxide superconductors

NASA Astrophysics Data System (ADS)

McMullen, T.; Jena, P.; Khanna, S. N.; Li, Yi; Jensen, Kjeld O.

1991-05-01

Positron states and lifetimes at defects in the copper oxide superconductors La2-xSrxCuO4, YBa2Cu3O7-x, and Bi2Sr2CaCu2O8+x are calculated with use of the superposed-atom model. In the Bi2Sr2CaCu2O8+x compound, we find that the smaller metal-ion vacancies appear to only bind positrons weakly, while missing oxygens do not trap positrons. In contrast, metal-ion vacancies in La2-xSrxCuO4 and YBa2Cu3O7-x bind positrons by ~1 eV, and oxygen-related defects appear to be the weak-binding sites in these materials. The sites that bind positrons only weakly, by energies ~kBT, are of particular interest in view of the complex temperature dependences of the annihilation characteristics that are observed in these materials.

Relaxation Process of Photoexcited meso-Naphthylporphyrins while Interacting with DNA and Singlet Oxygen Generation.

PubMed

Hirakawa, Kazutaka; Taguchi, Makoto; Okazaki, Shigetoshi

2015-10-15

Electron donor-connecting cationic porphyrins meso-(1-naphthyl)-tris(N-methyl-p-pyridinio)porphyrin (1-NapTMPyP) and meso-(2-naphthyl)-tris(N-methyl-p-pyridinio)porphyrin (2-NapTMPyP) were designed and synthesized. DFT calculations speculate that the photoexcited states of 1- and 2-NapTMPyPs can be deactivated via intramolecular electron transfer from the naphthyl moiety to the porphyrin moiety. However, the quenching effect through the intramolecular electron transfer is insufficient, possibly due to the orthogonal position of the electron donor and the porphyrin ring and the relatively small driving force: Gibbs energies are 0.11 and 0.07 eV for 1- and 2-NapTMPyPs, respectively. It was speculated that more than 0.3 eV of the driving force is required to realize effective electron transfer in similar electron-donor connecting porphyrin systems. These porphyrins aggregated around the DNA strand, accelerating the deactivation of their excited singlet state and decreasing their photosensitized singlet oxygen-generating activities. In the presence of a sufficiently large concentration of DNA, these porphyrins can bind to a DNA strand stably, leading to an increased fluorescence quantum yield and lifetime. Singlet oxygen generation was also suppressed by the aggregation of porphyrins around DNA. Although the quantum yield of singlet oxygen generation was recovered in the presence of sufficient DNA, the singlet oxygen generated by DNA-binding porphyrins was significantly smaller than that without DNA. These results suggest that DNA-binding drugs limit the generation of photosensitized singlet oxygen by quenching the DNA strand.

Pixel-based absorption correction for dual-tracer fluorescence imaging of receptor binding potential

PubMed Central

Kanick, Stephen C.; Tichauer, Kenneth M.; Gunn, Jason; Samkoe, Kimberley S.; Pogue, Brian W.

2014-01-01

Ratiometric approaches to quantifying molecular concentrations have been used for decades in microscopy, but have rarely been exploited in vivo until recently. One dual-tracer approach can utilize an untargeted reference tracer to account for non-specific uptake of a receptor-targeted tracer, and ultimately estimate receptor binding potential quantitatively. However, interpretation of the relative dynamic distribution kinetics is confounded by differences in local tissue absorption at the wavelengths used for each tracer. This study simulated the influence of absorption on fluorescence emission intensity and depth sensitivity at typical near-infrared fluorophore wavelength bands near 700 and 800 nm in mouse skin in order to correct for these tissue optical differences in signal detection. Changes in blood volume [1-3%] and hemoglobin oxygen saturation [0-100%] were demonstrated to introduce substantial distortions to receptor binding estimates (error > 30%), whereas sampled depth was relatively insensitive to wavelength (error < 6%). In response, a pixel-by-pixel normalization of tracer inputs immediately post-injection was found to account for spatial heterogeneities in local absorption properties. Application of the pixel-based normalization method to an in vivo imaging study demonstrated significant improvement, as compared with a reference tissue normalization approach. PMID:25360349

Novel water soluble morpholine substituted Zn(II) phthalocyanine: Synthesis, characterization, DNA/BSA binding, DNA photocleavage and topoisomerase I inhibition.

PubMed

Barut, Burak; Demirbaş, Ümit; Özel, Arzu; Kantekin, Halit

2017-12-01

In this study, novel peripherally tetra 3-morpholinophenol substituted zinc(II) phthalocyanine (4) and its water soluble form quaternized zinc(II) phthalocyanine (ZnQ) were synthesized for the first time. These novel compounds were characterized by a combination of different spectroscopic techniques such as FT-IR, 1 H NMR, 13 C NMR, UV-vis and mass. The DNA binding of ZnQ was investigated using UV-vis absorption titration, competitive ethidium bromide, thermal denaturation and viscosity experiments that the ZnQ bound to CT-DNA via intercalation mode. ZnQ indicated photocleavage activity on supercoiled pBR322 plasmid DNA via formation of singlet oxygen under irradiation at 700nm. Besides, the topoisomerase I inhibitory effect experiments showed that ZnQ inhibited topoisomerase I enzyme in a concentration-dependent manner. The bovine serum albumin (BSA) binding experiments indicated that ZnQ bound to proteins through a static quenching mechanism. All of these results claim that ZnQ has potential agent for photodynamic therapy owing to its nucleic acid interactions and photobiological or photochemical properties. Copyright © 2017 Elsevier B.V. All rights reserved.

Structural and optoelectronic properties of ZnGaO thin film by pulsed laser deposition

NASA Astrophysics Data System (ADS)

Han, Xiaowei; Wang, Li; Li, Shufeng; Gao, Dongwen; Pan, Yong

2018-01-01

ZnO has attracted much attention because of its high-energy gap and exciton binding energy at room temperature. Compared to ZnO thin films, ZnGaO thin films are more resistive to oxidation and have smaller deformation of lattice. In this study, the high purity ZnSe and Ga2O3 powders were weighted at a molar ratio of 18:1. Se was oxidized to Se2O3 and separated from the mixture powders by using conventional solid state reaction method in air, and the ZnGaO ceramic target was prepared. We fabricated the ZnGaO films on silica glass by pulsed laser deposition (PLD) method under different oxygen pressure at room temperature. The as-grown films were tested by X-ray diffraction and atomic force microscope (AFM) to diagnose the crystal structure and surface morphology. Moreover, we obtained the optical transmittance of ZnGaO film and found that the electrical conductivity capacity varied with the increase of oxygen pressure.

Aspergillus fumigatus Copper Export Machinery and Reactive Oxygen Intermediate Defense Counter Host Copper-Mediated Oxidative Antimicrobial Offense.

PubMed

Wiemann, Philipp; Perevitsky, Adi; Lim, Fang Yun; Shadkchan, Yana; Knox, Benjamin P; Landero Figueora, Julio A; Choera, Tsokyi; Niu, Mengyao; Steinberger, Andrew J; Wüthrich, Marcel; Idol, Rachel A; Klein, Bruce S; Dinauer, Mary C; Huttenlocher, Anna; Osherov, Nir; Keller, Nancy P

2017-05-02

The Fenton-chemistry-generating properties of copper ions are considered a potent phagolysosome defense against pathogenic microbes, yet our understanding of underlying host/microbe dynamics remains unclear. We address this issue in invasive aspergillosis and demonstrate that host and fungal responses inextricably connect copper and reactive oxygen intermediate (ROI) mechanisms. Loss of the copper-binding transcription factor AceA yields an Aspergillus fumigatus strain displaying increased sensitivity to copper and ROI in vitro, increased intracellular copper concentrations, decreased survival in challenge with murine alveolar macrophages (AMΦs), and reduced virulence in a non-neutropenic murine model. ΔaceA survival is remediated by dampening of host ROI (chemically or genetically) or enhancement of copper-exporting activity (CrpA) in A. fumigatus. Our study exposes a complex host/microbe multifactorial interplay that highlights the importance of host immune status and reveals key targetable A. fumigatus counter-defenses. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

New cobalt(II) and nickel(II) complexes of benzyl carbazate Schiff bases: Syntheses, crystal structures, in vitro DNA and HSA binding studies.

PubMed

Nithya, Palanivelu; Helena, Sannasi; Simpson, Jim; Ilanchelian, Malaichamy; Muthusankar, Aathi; Govindarajan, Subbiah

2016-12-01

In the present study, new Schiff base complexes with the composition [M(NCS) 2 (L1) 2 ]·nH 2 O, where M=Co (n=0) (1) and Ni (n=2) (2); [M(NCS) 2 (L2) 2 ], M=Co (3) and Ni (4) as well as [M(NCS) 2 (L3) 2 ], M=Co (5) and Ni (6); (L1=benzyl 2-(propan-2-ylidene)hydrazinecarboxylate, L2=benzyl 2-(butan-2-ylidene)hydrazinecarboxylate and L3=benzyl 2-(pentan-3-ylidene)hydrazinecarboxylate) have been synthesized by a template method. The complexes were characterised by analytical methods, spectroscopic studies, thermal and X-ray diffraction techniques. The structures of all the complexes explore that the metal(II) cation has a trans-planar coordination environment, the monomeric units containing a six-coordinated metal center in octahedral geometry with N-bound isothiocyanate anions coordinated as terminal ligands. Furthermore, the binding of the two Schiff base ligands to the metal centers involves the azomethine nitrogen and the carbonyl oxygen in mutually trans configuration. The binding interactions of all the complexes with Calf thymus-deoxyribonucleic acid (CT-DNA) and human serum albumin (HSA) have been investigated using absorption and emission spectral techniques. The CT-DNA binding properties of these complexes reveal that they bind to CT-DNA through a partial intercalation mode and the binding constant values were calculated using the absorption and emission spectral data. The binding constant values (~10×10 6 moldm -3 ) indicate strong binding of metal complexes with CT-DNA. HSA binding interaction studies showed that the cobalt and nickel complexes can quench the intrinsic fluorescence of HSA through static quenching process. Also, molecular docking studies were supported out to apprehend the binding interactions of these complexes with DNA and HSA which offer new understandings into the experimental model observations. Copyright © 2016 Elsevier B.V. All rights reserved.

Solid-State Gas Adsorption Studies with Discrete Palladium(II) [Pd2 (L)4 ]4+ Cages.

PubMed

Preston, Dan; White, Keith F; Lewis, James E M; Vasdev, Roan A S; Abrahams, Brendan F; Crowley, James D

2017-08-04

The need for effective CO 2 capture systems remains high, and due to their tunability, metallosupramolecular architectures are an attractive option for gas sorption. While the use of extended metal organic frameworks for gas adsorption has been extensively explored, the exploitation of discrete metallocage architectures to bind gases remains in its infancy. Herein the solid state gas adsorption properties of a series of [Pd 2 (L) 4 ] 4+ lantern shaped coordination cages (L = variants of 2,6-bis(pyridin-3-ylethynyl)pyridine), which had solvent accessible internal cavities suitable for gas binding, have been investigated. The cages showed little interaction with dinitrogen gas but were able to take up CO 2 . The best performing cage reversibly sorbed 1.4 mol CO 2 per mol cage at 298 K, and 2.3 mol CO 2 per mol cage at 258 K (1 bar). The enthalpy of binding was calculated to be 25-35 kJ mol -1 , across the number of equivalents bound, while DFT calculations on the CO 2 binding in the cage gave ΔE for the cage-CO 2 interaction of 23-28 kJ mol -1 , across the same range. DFT modelling suggested that the binding mode is a hydrogen bond between the carbonyl oxygen of CO 2 and the internally directed hydrogen atoms of the cage. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Method for producing an atomic oxygen beam

NASA Technical Reports Server (NTRS)

Outlaw, Ronald A. (Inventor)

1989-01-01

A method for producing an atomic oxygen beam is provided by the present invention. First, a material 10' is provided which dissociates molecular oxygen and dissolves atomic oxygen into its bulk. Next, molecular oxygen is exposed to entrance surface 11' of material 10'. Next, material 10' is heated by heater 17' to facilitate the permeation of atomic oxygen through material 10' to the UHV side 12'. UHV side 12' is interfaced with an ultra-high vacuum (UHV) environment provided by UHV pump 15'. The atomic oxygen on the UHV side 12' is excited to a non-binding state by exciter 14' thus producing the release of atomic oxygen to form an atomic oxygen beam 35'.

Monomeric Yeast Frataxin is an Iron-Binding Protein

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

Cook,J.; Bencze, K.; Jankovic, A.

Friedreich's ataxia, an autosomal cardio- and neurodegenerative disorder that affects 1 in 50 000 humans, is caused by decreased levels of the protein frataxin. Although frataxin is nuclear-encoded, it is targeted to the mitochondrial matrix and necessary for proper regulation of cellular iron homeostasis. Frataxin is required for the cellular production of both heme and iron-sulfur (Fe-S) clusters. Monomeric frataxin binds with high affinity to ferrochelatase, the enzyme involved in iron insertion into porphyrin during heme production. Monomeric frataxin also binds to Isu, the scaffold protein required for assembly of Fe-S cluster intermediates. These processes (heme and Fe-S cluster assembly)more » share requirements for iron, suggesting that monomeric frataxin might function as the common iron donor. To provide a molecular basis to better understand frataxin's function, we have characterized the binding properties and metal-site structure of ferrous iron bound to monomeric yeast frataxin. Yeast frataxin is stable as an iron-loaded monomer, and the protein can bind two ferrous iron atoms with micromolar binding affinity. Frataxin amino acids affected by the presence of iron are localized within conserved acidic patches located on the surfaces of both helix-1 and strand-1. Under anaerobic conditions, bound metal is stable in the high-spin ferrous state. The metal-ligand coordination geometry of both metal-binding sites is consistent with a six-coordinate iron-(oxygen/nitrogen) based ligand geometry, surely constructed in part from carboxylate and possibly imidazole side chains coming from residues within these conserved acidic patches on the protein. On the basis of our results, we have developed a model for how we believe yeast frataxin interacts with iron.« less

Monomeric Yeast Frataxin is an Iron Binding Protein†

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

Cook, J.; Bencze, K; Jankovic, A

Friedreich's ataxia, an autosomal cardio- and neurodegenerative disorder that affects 1 in 50000 humans, is caused by decreased levels of the protein frataxin. Although frataxin is nuclear-encoded, it is targeted to the mitochondrial matrix and necessary for proper regulation of cellular iron homeostasis. Frataxin is required for the cellular production of both heme and iron-sulfur (Fe-S) clusters. Monomeric frataxin binds with high affinity to ferrochelatase, the enzyme involved in iron insertion into porphyrin during heme production. Monomeric frataxin also binds to Isu, the scaffold protein required for assembly of Fe-S cluster intermediates. These processes (heme and Fe-S cluster assembly) sharemore » requirements for iron, suggesting that monomeric frataxin might function as the common iron donor. To provide a molecular basis to better understand frataxin's function, we have characterized the binding properties and metal-site structure of ferrous iron bound to monomeric yeast frataxin. Yeast frataxin is stable as an iron-loaded monomer, and the protein can bind two ferrous iron atoms with micromolar binding affinity. Frataxin amino acids affected by the presence of iron are localized within conserved acidic patches located on the surfaces of both helix-1 and strand-1. Under anaerobic conditions, bound metal is stable in the high-spin ferrous state. The metal-ligand coordination geometry of both metal-binding sites is consistent with a six-coordinate iron-(oxygen/nitrogen) based ligand geometry, surely constructed in part from carboxylate and possibly imidazole side chains coming from residues within these conserved acidic patches on the protein. On the basis of our results, we have developed a model for how we believe yeast frataxin interacts with iron.« less

Hemoglobin in Frankia, a Nitrogen-Fixing Actinomycete†

PubMed Central

Tjepkema, John D.; Cashon, Robert E.; Beckwith, Jason; Schwintzer, Christa R.

2002-01-01

Frankia strain CcI3 grown in culture produced a hemoglobin which had optical absorption bands typical of a hemoglobin and a molecular mass of 14.1 kDa. Its equilibrium oxygen binding constant was 274 nM, the oxygen dissociation rate constant was 56 s−1, and the oxygen association rate constant was 206 μM−1 s−1. PMID:11976149

The Oxygen Dissociation Curve of Hemoglobin: Bridging the Gap between Biochemistry and Physiology

NASA Astrophysics Data System (ADS)

Gómez-Cambronero, Julian

2001-06-01

Cooperativity is a very difficult concept for biochemistry students in the health sciences. An analogy between breaking salt bonds and tearing apart a block of four stamps has been proposed for hemoglobin (Hb). However, since tearing is equated to binding of molecules, two intrinsically contradictory terms, students still have difficulty. I apply the pictorial analogy to the releasing of oxygen instead of the binding, thus bridging biochemistry (cooperativity) with physiology (oxygen dissociation). I embark on an imaginary journey from the lungs (saturation at 100 mmHg) to the oxygen-starved tissues. The stamps represent fully loaded Hb. By making two cuts the first "oxygen" is released. For the second, only one cut is needed. With one final cut, the last two stamps are separated. This means that less energy is needed to unload oxygen: just small drops in partial pressure do the trick in the right place (tissues) but not in the wrong one (lungs). In doing this, I use the three main models of learning: association, discovery and mentoring. Additionally, by guiding students to discover the truth by themselves, I can use hemoglobin as a wonderful excuse to apply the "Socratic method" in the classroom.

Exploring the effect of oxygen-containing functional groups on the water-holding capacity of lignite.

PubMed

Liu, Jie; Jiang, Xiangang; Cao, Yu; Zhang, Chen; Zhao, Guangyao; Zhao, Maoshuang; Feng, Li

2018-05-07

Graphene oxide with different degrees of oxidation was prepared and selected as a model compound of lignite to study quantitatively, using both experiment and theoretical calculation methods, the effect on water-holding capacity of oxygen-containing functional groups. The experimental results showed that graphite can be oxidized, and forms epoxy groups most easily, followed by hydroxyl and carboxyl groups. The prepared graphene oxide forms a membrane-state as a single layer structure, with an irregular surface. The water-holding capacity of lignite increased with the content of oxygen-containing functional groups. The influence on the configuration of water molecule clusters and binding energy of water molecules of different oxygen-containing functional groups was calculated by density functional theory. The calculation results indicated that the configuration of water molecule clusters was totally changed by oxygen-containing functional groups. The order of binding energy produced by oxygen-containing functional groups and water molecules was as follows: carboxyl > edge phenol hydroxyl >epoxy group. Finally, it can be concluded that the potential to form more hydrogen bonds is the key factor influencing the interaction energy between model compounds and water molecules.

Hemoglobin crystals immersed in liquid oxygen reveal diffusion channels.

PubMed

Terrell, James Ross; Gumpper, Ryan H; Luo, Ming

2018-01-08

Human hemoglobin (HbA) transports molecular oxygen (O 2 ) from the lung to tissues where the partial pressure of O 2 is lower. O 2 binds to HbA at the heme cofactor and is stabilized by a distal histidine (HisE7). HisE7 has been observed to occupy opened and closed conformations, and is postulated to act as a gate controlling the binding/release of O 2 . However, it has been suggested that HbA also contains intraprotein oxygen channels for entrances/exits far from the heme. In this study, we developed a novel method of crystal immersion in liquid oxygen prior to X-ray data collection. In the crystals immersed in liquid oxygen, the heme center was oxidized to generate aquomethemoglobin. Increases of structural flexibility were also observed in regions that are synonymous with previously postulated oxygen channels. These regions also correspond to medically relevant mutations which affect O 2 affinity. The way HbA utilizes these O 2 channels could have a profound impact on understanding the relationship of HbA O 2 transport within these disease conditions. Finally, the liquid oxygen immersion technique can be utilized as a new tool to crystallographically examine proteins and protein complexes which utilize O 2 for enzyme catalysis or transport. Copyright © 2017 Elsevier Inc. All rights reserved.

Element specificity of ortho-positronium annihilation for alkali-metal loaded SiO2 glasses.

PubMed

Sato, K; Hatta, T

2015-03-07

Momentum distributions associated with ortho-positronium (o-Ps) pick-off annihilation photon are often influenced by light elements, as, e.g., carbon, oxygen, and fluorine. This phenomenon, so-called element specificity of o-Ps pick-off annihilation, has been utilized for studying the elemental environment around the open spaces. To gain an insight into the element specificity of o-Ps pick-off annihilation, the chemical shift of oxygen 1s binding energy and the momentum distributions associated with o-Ps pick-off annihilation were systematically investigated for alkali-metal loaded SiO2 glasses by means of X-ray photoelectron spectroscopy and positron-age-momentum correlation spectroscopy, respectively. Alkali metals introduced into the open spaces surrounded by oxygen atoms cause charge transfer from alkali metals to oxygen atoms, leading to the lower chemical shift for the oxygen 1s binding energy. The momentum distribution of o-Ps localized into the open spaces is found to be closely correlated with the oxygen 1s chemical shift. This correlation with the deepest 1s energy level evidences that the element specificity of o-Ps originates from pick-off annihilation with orbital electrons, i.e., dominantly with oxygen 2p valence electrons and s electrons with lower probability.

Tailoring oxide properties: An impact on adsorption characteristics of molecules and metals

NASA Astrophysics Data System (ADS)

Honkala, Karoliina

2014-12-01

Both density functional theory calculations and numerous experimental studies demonstrate a variety of unique features in metal supported oxide films and transition metal doped simple oxides, which are markedly different from their unmodified counterparts. This review highlights, from the computational perspective, recent literature on the properties of the above mentioned surfaces and how they adsorb and activate different species, support metal aggregates, and even catalyse reactions. The adsorption of Au atoms and clusters on metal-supported MgO films are reviewed together with the cluster's theoretically predicted ability to activate and dissociate O2 at the Au-MgO(100)/Ag(100) interface, as well as the impact of an interface vacancy to the binding of an Au atom. In contrast to a bulk MgO surface, an Au atom binds strongly on a metal-supported ultra-thin MgO film and becomes negatively charged. Similarly, Au clusters bind strongly on a supported MgO(100) film and are negatively charged favouring 2D planar structures. The adsorption of other metal atoms is briefly considered and compared to that of Au. Existing computational literature of adsorption and reactivity of simple molecules including O2, CO, NO2, and H2O on mainly metal-supported MgO(100) films is discussed. Chemical reactions such as CO oxidation and O2 dissociation are discussed on the bare thin MgO film and on selected Au clusters supported on MgO(100)/metal surfaces. The Au atoms at the perimeter of the cluster are responsible for catalytic activity and calculations predict that they facilitate dissociative adsorption of oxygen even at ambient conditions. The interaction of H2O with a flat and stepped Ag-supported MgO film is summarized and compared to bulk MgO. The computational results highlight spontaneous dissociation on MgO steps. Furthermore, the impact of water coverage on adsorption and dissociation is addressed. The modifications, such as oxygen vacancies and dopants, at the oxide-metal interface and their effect on the adsorption characteristics of water and Au are summarized. Finally, more limited computational literature on transition metal (TM) doped CaO(100) and MgO(100) surfaces is presented. Again, Au is used as a probe species. Similar to metal-supported MgO films, Au binds more strongly than on undoped CaO(100) and becomes negatively charged. The discussion focuses on rationalization of Au adsorption with the help of Born-Haber cycle, which reveals that the so-called redox energy including the electron transfer from the dopant to the Au atom together with the simultaneous structural relaxation of lattice atoms is responsible for enhanced binding. In addition, adsorption energy dependence on the position and type of the dopant is summarized.

Broad Phylogenetic Occurrence of the Oxygen-Binding Hemerythrins in Bilaterians

PubMed Central

Schrago, Carlos G.; Halanych, Kenneth M.

2017-01-01

Abstract Animal tissues need to be properly oxygenated for carrying out catabolic respiration and, as such, natural selection has presumably favored special molecules that can reversibly bind and transport oxygen. Hemoglobins, hemocyanins, and hemerythrins (Hrs) fulfill this role, with Hrs being the least studied. Knowledge of oxygen-binding proteins is crucial for understanding animal physiology. Hr genes are present in the three domains of life, Archaea, Bacteria, and Eukaryota; however, within Animalia, Hrs has been reported only in marine species in six phyla (Annelida, Brachiopoda, Priapulida, Bryozoa, Cnidaria, and Arthropoda). Given this observed Hr distribution, whether all metazoan Hrs share a common origin is circumspect. We investigated Hr diversity and evolution in metazoans, by employing in silico approaches to survey for Hrs from of 120 metazoan transcriptomes and genomes. We found 58 candidate Hr genes actively transcribed in 36 species distributed in 11 animal phyla, with new records in Echinodermata, Hemichordata, Mollusca, Nemertea, Phoronida, and Platyhelminthes. Moreover, we found that “Hrs” reported from Cnidaria and Arthropoda were not consistent with that of other metazoan Hrs. Contrary to previous suggestions that Hr genes were absent in deuterostomes, we find Hr genes present in deuterostomes and were likely present in early bilaterians, but not in nonbilaterian animal lineages. As expected, the Hr gene tree did not mirror metazoan phylogeny, suggesting that Hrs evolutionary history was complex and besides the oxygen carrying capacity, the drivers of Hr evolution may also consist of secondary functional specializations of the proteins, like immunological functions. PMID:29016798

Polyphenolic chemistry of tea and coffee: a century of progress.

PubMed

Wang, Yu; Ho, Chi-Tang

2009-09-23

Tea and coffee, the most popular beverages in the world, have been consumed for thousands of years for their alluring flavors and health benefits. Polyphenols, particularly flavonoids and phenolic acids, are of great abundance in tea and coffee and contribute a lot to their flavor and health properties. This paper reviews the polyphenol chemistry of tea and coffee, specifically their stability, and scavenging ability of reactive oxygen species (ROS) and reactive carbonyl species (RCS). During the manufacturing and brewing process, green tea and black tea polyphenols undergo epimerization and oxidation, respectively. Meanwhile, the lactonization and the polymerization of chlorogenic acid are the major causes for the degradation of polyphenols in coffee. Tea catechins, besides having antioxidant properties, have the novel characteristic of trapping reactive carbonyl species. The A ring of the catechins is the binding site for RCS trapping, whereas the B ring is the preferred site for antioxidation.

Electronic-property dependent interactions between tetracycline and graphene nanomaterials in aqueous solution.

PubMed

He, Lin; Liu, Fei-Fei; Zhao, Mengyao; Qi, Zhen; Sun, Xuefei; Afzal, Muhammad Zaheer; Sun, Xiaomin; Li, Yanhui; Hao, Jingcheng; Wang, Shuguang

2018-04-01

Understanding the interactions between graphene nanomaterials (GNMs) and antibiotics in aqueous solution is critical to both the engineering applications of GNMs and the assessment of their potential impact on the fate and transport of antibiotics in the aquatic environment. In this study, adsorption of one common antibiotic, tetracycline, by graphene oxide (GO) and reduced graphene oxide (RGO) was examined with multi-walled carbon nanotubes (MWCNTs) and graphite as comparison. The results showed that the tetracycline adsorption capacity by the four selected carbonaceous materials on the unit mass basis followed an order of GO>RGO>MWCNTs>graphite. Upon normalization by surface area, graphite, RGO and MWCNTs had almost the same high tetracycline adsorption affinity while GO exhibited the lowest. We proposed π-electron-property dependent interaction mechanisms to explain the observed different adsorption behaviors. Density functional theory (DFT) calculations suggested that the oxygen-containing functional groups on GO surface reduced its π-electron-donating ability, and thus decreased the π-based interactions between tetracycline and GO surface. Comparison of adsorption efficiency at different pH indicated that electrostatic interaction also played an important role in tetracycline-GO interactions. Site energy analysis confirmed a highly heterogeneous distribution of the binding sites and strong tetracycline binding affinity of GO surface. Copyright © 2017. Published by Elsevier B.V.

Singlet oxygen-dependent translational control in the tigrina-d.12 mutant of barley.

PubMed

Khandal, Dhriti; Samol, Iga; Buhr, Frank; Pollmann, Stephan; Schmidt, Holger; Clemens, Stephan; Reinbothe, Steffen; Reinbothe, Christiane

2009-08-04

The tigrina (tig)-d.12 mutant of barley is impaired in the negative control limiting excess protochlorophyllide (Pchlide) accumulation in the dark. Upon illumination, Pchlide operates as photosensitizer and triggers singlet oxygen production and cell death. Here, we show that both Pchlide and singlet oxygen operate as signals that control gene expression and metabolite accumulation in tig-d.12 plants. In vivo labeling, Northern blotting, polysome profiling, and protein gel blot analyses revealed a selective suppression of synthesis of the small and large subunits of ribulose-1,5-bisphosphate carboxylase/oxygenase (RBCSs and RBCLs), the major light-harvesting chlorophyll a/b-binding protein of photosystem II (LHCB2), as well as other chlorophyll-binding proteins, in response to singlet oxygen. In part, these effects were caused by an arrest in translation initiation of photosynthetic transcripts at 80S cytoplasmic ribosomes. The observed changes in translation correlated with a decline in the phosphorylation level of ribosomal protein S6. At later stages, ribosome dissociation occurred. Together, our results identify translation as a major target of singlet oxygen-dependent growth control and cell death in higher plants.

Camphor revisited: studies of 2,5-diketocamphane 1,2-monooxygenase from Pseudomonas putida ATCC 17453.

PubMed Central

Taylor, D G; Trudgill, P W

1986-01-01

The oxygenating component of 2,5-diketocamphane 1,2-monooxygenase from Pseudomonas putida ATCC 17453 was purified to homogeneity by a combination of ammonium sulfate fractionation and chromatography on DEAE-cellulose and polyanion SI-17 columns. It had an Mr of 78,000, bound one molecule of nonautooxidizable flavin mononucleotide (FMN), consisted of two subunits of equal molecular weight, and existed in two electrophoretically distinguishable active forms. The oxygenating complex was constructed from equimolecular amounts of an NADH oxidase, which could be purified separately (Mr, 36,000), and the oxygenating component. Most of the NADH oxidase dissociated from the oxygenating component during purification, although traces remained, to give the final preparation of the oxygenating component significant oxygenase activity. FMN did not dissociate significantly from the oxygenating component during purification, but it was not covalently bound and could be removed under a variety of conditions. Binding between the two proteins that made up the active complex was fairly weak and freely reversible. It probably occurred through the FMN which was strongly bound to the oxygenating component and for which the NADH had a weak binding site. Iron was not present at a significant level in the oxygenating component, and in common with other characterized Baeyer Villiger monooxygenases, 2,5-diketocamphane 1,2-monooxygenase was found to be a simple flavoprotein. Images PMID:3944058

Camphor revisited: studies of 2,5-diketocamphane 1,2-monooxygenase from Pseudomonas putida ATCC 17453.

PubMed

Taylor, D G; Trudgill, P W

1986-02-01

The oxygenating component of 2,5-diketocamphane 1,2-monooxygenase from Pseudomonas putida ATCC 17453 was purified to homogeneity by a combination of ammonium sulfate fractionation and chromatography on DEAE-cellulose and polyanion SI-17 columns. It had an Mr of 78,000, bound one molecule of nonautooxidizable flavin mononucleotide (FMN), consisted of two subunits of equal molecular weight, and existed in two electrophoretically distinguishable active forms. The oxygenating complex was constructed from equimolecular amounts of an NADH oxidase, which could be purified separately (Mr, 36,000), and the oxygenating component. Most of the NADH oxidase dissociated from the oxygenating component during purification, although traces remained, to give the final preparation of the oxygenating component significant oxygenase activity. FMN did not dissociate significantly from the oxygenating component during purification, but it was not covalently bound and could be removed under a variety of conditions. Binding between the two proteins that made up the active complex was fairly weak and freely reversible. It probably occurred through the FMN which was strongly bound to the oxygenating component and for which the NADH had a weak binding site. Iron was not present at a significant level in the oxygenating component, and in common with other characterized Baeyer Villiger monooxygenases, 2,5-diketocamphane 1,2-monooxygenase was found to be a simple flavoprotein.

Molecular evolution and expression of oxygen transport genes in livebearing fishes (Poeciliidae) from hydrogen sulfide rich springs.

PubMed

Barts, Nicholas; Greenway, Ryan; Passow, Courtney N; Arias-Rodriguez, Lenin; Kelley, Joanna L; Tobler, Michael

2018-04-01

Hydrogen sulfide (H 2 S) is a natural toxicant in some aquatic environments that has diverse molecular targets. It binds to oxygen transport proteins, rendering them non-functional by reducing oxygen-binding affinity. Hence, organisms permanently inhabiting H 2 S-rich environments are predicted to exhibit adaptive modifications to compensate for the reduced capacity to transport oxygen. We investigated 10 lineages of fish of the family Poeciliidae that have colonized freshwater springs rich in H 2 S-along with related lineages from non-sulfidic environments-to test hypotheses about the expression and evolution of oxygen transport genes in a phylogenetic context. We predicted shifts in the expression of and signatures of positive selection on oxygen transport genes upon colonization of H 2 S-rich habitats. Our analyses indicated significant shifts in gene expression for multiple hemoglobin genes in lineages that have colonized H 2 S-rich environments, and three hemoglobin genes exhibited relaxed selection in sulfidic compared to non-sulfidic lineages. However, neither changes in gene expression nor signatures of selection were consistent among all lineages in H 2 S-rich environments. Oxygen transport genes may consequently be predictable targets of selection during adaptation to sulfidic environments, but changes in gene expression and molecular evolution of oxygen transport genes in H 2 S-rich environments are not necessarily repeatable across replicated lineages.

Gene expression profile differences in left and right liver lobes from mid-gestation fetal baboons: a cautionary tale

PubMed Central

Cox, Laura A; Schlabritz-Loutsevitch, Natalia; Hubbard, Gene B; Nijland, Mark J; McDonald, Thomas J; Nathanielsz, Peter W

2006-01-01

Interpretation of gene array data presents many potential pitfalls in adult tissues. Gene array techniques applied to fetal tissues present additional confounding pitfalls. The left lobe of the fetal liver is supplied with blood containing more oxygen than the right lobe. Since synthetic activity and cell function are oxygen dependent, we hypothesized major differences in mRNA expression between the fetal right and left liver lobes. Our aim was to demonstrate the need to evaluate RNA samples from both lobes. We performed whole genome expression profiling on left and right liver lobe RNA from six 90-day gestation baboon fetuses (term 180 days). Comparing right with left, we found 875 differentially expressed genes – 312 genes were up-regulated and 563 down-regulated. Pathways for damaged DNA binding, endonuclease activity, interleukin binding and receptor activity were up-regulated in right lobe; ontological pathways related to cell signalling, cell organization, cell biogenesis, development, intracellular transport, phospholipid metabolism, protein biosynthesis, protein localization, protein metabolism, translational regulation and vesicle mediated transport were down-regulated in right lobe. Molecular pathway analysis showed down-regulation of pathways related to heat shock protein binding, ion channel and transporter activities, oxygen binding and transporter activities, translation initiation and translation regulator activities. Genes involved in amino acid biosynthesis, lipid biosynthesis and oxygen transport were also differentially expressed. This is the first demonstration of RNA differences between the two lobes of the fetal liver. The data support the argument that a complete interpretation of gene expression in the developing liver requires data from both lobes. PMID:16484296

[Hemoglobin oxygen transport capacity in surgical endotoxicosis ].

PubMed

Poryadin, G V; Vlasov, A P; Trofimov, V A; Vlasova, T I; Kamkina, O V; Grigoryev, A G; Vlasov, P A

2016-01-01

In surgical endointoxication hemoglobin oxygen transport capacity of red blood cells (hemoglobin affinity ligands: the ability to bind and release ligands) is reduced and is associated with the severity of endogenous intoxication. Violation of oxygen transport function of hemoglobin at endogenous intoxication is associated with conformational changes of a biomolecule, and its possible influence on reactive oxygen species, which confirmed in experiments in vitro: under the influence of oxygen-iron ascorbate ability of hemoglobin deteriorates. Largely similar structural and functional changes in hemoglobin occur in patients with surgical endotoxicosis.

(1)H, (13)C, (15)N backbone and side-chain resonance assignment of Nostoc sp. C139A variant of the heme-nitric oxide/oxygen binding (H-NOX) domain.

PubMed

Alexandropoulos, Ioannis I; Argyriou, Aikaterini I; Marousis, Kostas D; Topouzis, Stavros; Papapetropoulos, Andreas; Spyroulias, Georgios A

2016-10-01

The H-NOX (Heme-nitric oxide/oxygen binding) domain is conserved across eukaryotes and bacteria. In human soluble guanylyl cyclase (sGC) the H-NOX domain functions as a sensor for the gaseous signaling agent nitric oxide (NO). sGC contains the heme-binding H-NOX domain at its N-terminus, which regulates the catalytic site contained within the C-terminal end of the enzyme catalyzing the conversion of GTP (guanosine 5'-triphosphate) to GMP (guanylyl monophosphate). Here, we present the backbone and side-chain assignments of the (1)H, (13)C and (15)N resonances of the 183-residue H-NOX domain from Nostoc sp. through solution NMR.

Influence of Mechanical Stretching on Adsorption Properties of Nitrogen-Doped Graphene

NASA Astrophysics Data System (ADS)

Dolinskii, I. Yu.; Katin, K. P.; Grishakov, K. S.; Prudkovskii, V. S.; Kargin, N. I.; Maslov, M. M.

2018-04-01

This paper presents the results of quantum chemical modeling of chemisorption of atomic hydrogen and epoxy, carboxyl, and hydroxyl functional groups on nitrogen-doped graphene. It is shown that the substitutional nitrogen atom does not bind to adsorbing groups directly, but significantly increases the adsorption activity of neighboring carbon atoms. Mechanical stretching of doped graphene reduces the adsorption energy of all the aforementioned radicals. This reduction is significantly greater for the epoxy group than for the other functional groups. The results obtained confirm that, upon a sufficient stretching of a nitrogen-doped graphene sheet, the dissociation of molecular hydrogen and oxygen with subsequent precipitation of the resulting radicals onto graphene can be energetically favorable.

Electronic-topological study of the structure-activity relationships in a series of steroids with mineralocorticoid binding affinity.

PubMed

Kandemirli, Fatma; Tokay, Nesrin; Shvets, Nataly M; Dimoglo, Anatoly S

2003-01-01

Conformational analysis and quantum chemical calculations were carried out using molecular mechanics (MMP2) and semi-empirical quantum chemistry (CNDO/2) methods for 51 steroid homologues belonging to a series of 17-spirolactones. Matrices called Electronic-Topological Matrices of Conjunction (ETMCs) were formed using data obtained from quantum chemical calculations. A structural fragment of activity was identified in the series of steroids. As seen from the fragment's properties, active compounds are characterized by the presence of two atoms of oxygen, O1 and O3, which are situated at a distance of 13.5 A and possess high negative charges (-0.29 to -0.31 e).

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

Cho, Byungsu; Samsung Display Co. Ltd., Tangjeong, Chungcheongnam-Do 336-741; Choi, Yonghyuk

We demonstrate an enhanced electrical stability through a Ti oxide (TiO{sub x}) layer on the amorphous InGaZnO (a-IGZO) back-channel; this layer acts as a surface polarity modifier. Ultrathin Ti deposited on the a-IGZO existed as a TiO{sub x} thin film, resulting in oxygen cross-binding with a-IGZO surface. The electrical properties of a-IGZO thin film transistors (TFTs) with TiO{sub x} depend on the surface polarity change and electronic band structure evolution. This result indicates that TiO{sub x} on the back-channel serves as not only a passivation layer protecting the channel from ambient molecules or process variables but also a control layermore » of TFT device parameters.« less

Successful Treatment of Severe Carbon Monoxide Poisoning and Refractory Shock Using Extracorporeal Membrane Oxygenation.

PubMed

Teerapuncharoen, Krittika; Sharma, Nirmal S; Barker, Andrew B; Wille, Keith M; Diaz-Guzman, Enrique

2015-09-01

Carbon monoxide (CO) is the most common cause of poisoning and poisoning-related death in the United States. It is a tasteless and odorless poisonous gas produced from incomplete combustion of hydrocarbons, such as those produced by cars and heating systems. CO rapidly binds to hemoglobin to form carboxyhemoglobin, leading to tissue hypoxia, multiple-organ failure, and cardiovascular collapse. CO also binds to myocardial myoglobin, preventing oxidative phosphorylation in cardiac mitochondria and resulting in cardiac ischemia or stunning and cardiogenic pulmonary edema. Treatment of CO poisoning is mainly supportive, and supplemental oxygen remains the cornerstone of therapy, whereas hyperbaric oxygen therapy is considered for patients with evidence of neurological and myocardial injury. Extracorporeal membrane oxygenation (ECMO) has been utilized effectively in patients with respiratory failure and hemodynamic instability, but its use has rarely been reported in patients with CO poisoning. We report the successful use of venoarterial ECMO in a patient with severe CO poisoning and multiple-organ failure. Copyright © 2015 by Daedalus Enterprises.

Oxygen Vacancy-Tuned Physical Properties in Perovskite Thin Films with Multiple B-site Valance States

DOE PAGES

Enriquez, Erik; Chen, Aiping; Harrell, Zach; ...

2017-04-18

Controlling oxygen content in perovskite oxides with ABO 3 structure is one of most critical steps for tuning their functionality. Notably, there have been tremendous efforts to understand the effect of changes in oxygen content on the properties of perovskite thin films that are not composed of cations with multiple valance states. Here, we study the effect of oxygen vacancies on structural and electrical properties in epitaxial thin films of SrFeO 3-δ (SFO), where SFO is a compound with multiple valance states at the B site. Various annealing treatments are used to produce different oxygen contents in the films, whichmore » has resulted in significant structural changes in the fully strained SFO films. The out-of-plane lattice parameter and tetragonality increase with decreasing oxygen concentration, indicating the crystal structure is closely related to the oxygen content. Importantly, variation of the oxygen content in the films significantly affects the dielectric properties, leakage conduction mechanisms, and the resistive hysteresis of the materials. These results establish the relationship between oxygen content and structural and functional properties for a range of multivalent transition metal oxides.« less

Oxygen Vacancy-Tuned Physical Properties in Perovskite Thin Films with Multiple B-site Valance States

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

Enriquez, Erik; Chen, Aiping; Harrell, Zach

Controlling oxygen content in perovskite oxides with ABO 3 structure is one of most critical steps for tuning their functionality. Notably, there have been tremendous efforts to understand the effect of changes in oxygen content on the properties of perovskite thin films that are not composed of cations with multiple valance states. Here, we study the effect of oxygen vacancies on structural and electrical properties in epitaxial thin films of SrFeO 3-δ (SFO), where SFO is a compound with multiple valance states at the B site. Various annealing treatments are used to produce different oxygen contents in the films, whichmore » has resulted in significant structural changes in the fully strained SFO films. The out-of-plane lattice parameter and tetragonality increase with decreasing oxygen concentration, indicating the crystal structure is closely related to the oxygen content. Importantly, variation of the oxygen content in the films significantly affects the dielectric properties, leakage conduction mechanisms, and the resistive hysteresis of the materials. These results establish the relationship between oxygen content and structural and functional properties for a range of multivalent transition metal oxides.« less

Photophysicochemical, calf thymus DNA binding and in vitro photocytotoxicity properties of tetra-morpholinoethoxy-substituted phthalocyanines and their water-soluble quaternized derivatives.

PubMed

Koçan, Halit; Kaya, Kerem; Özçeşmeci, İbrahim; Sesalan, B Şebnem; Göksel, Meltem; Durmuş, Mahmut; Burat, Ayfer Kalkan

2017-12-01

In this study, morpholinoethoxy-substituted metal-free (3), zinc(II) (4) and indium(III) (5) phthalocyanines were synthesized. These phthalocyanines were converted to their water-soluble quaternized derivatives (3Q-5Q) using excess methyl iodide as a quaternization agent. All these phthalocyanines (Pcs) were characterized by elemental analysis and different spectroscopic methods such as FT-IR, 1 H NMR, UV-Vis and mass spectrometry. The photophysical and photochemical properties such as fluorescence and generation of singlet oxygen were investigated for determination of these phthalocyanines as photosensitizers in photodynamic therapy (PDT) applications. The binding properties of quaternized phthalocyanines (3Q-5Q) to calf thymus DNA (CT-DNA) were investigated by UV-Vis and fluorescence spectrophotometric methods. The quenching effect of all quaternized phthalocyanines on the fluorescence intensity of SYBR Green-DNA complex was determined. The mixtures of 3Q, 4Q or 5Q and DNA solutions were used to determine the change in T m of double helix DNA with thermal denaturation profile. In addition, thermodynamic parameters considering their aggregation in buffer solution, which shows the spontaneity of the reactions between DNA and quaternized Pcs were investigated. On the other hand, in vitro phototoxicity and cytotoxicity behavior of the quaternized water-soluble phthalocyanine photosensitizers (3Q-5Q) were tested against the cervical cancer cell line named HeLa for evaluation of their suitability for treatment of cancer by PDT method. Peripherally tetra-substituted neutral and quaternized metal-free and metallophthalocyanines (MPcs) (Zn, In) bearing morpholinoethoxy groups were prepared. The binding of quaternized compounds (3Q-5Q) to CT-DNA were examined using UV-Vis, fluorescence spectra, thermal denaturation profiles and K SV values. Besides, thermodynamic studies indicated that binding of 3Q-5Q to DNA was spontaneous. On the other hand, in vitro phototoxicity and cytotoxicity behavior of the quaternized water-soluble phthalocyanine photosensitizers (3Q-5Q) were tested against the cervical cancer cell line named HeLa for evaluation of their suitability for treatment of cancer by PDT method.

pH-Specific structural speciation of the ternary V(V)-peroxido-betaine system: a chemical reactivity-structure correlation.

PubMed

Gabriel, C; Kioseoglou, E; Venetis, J; Psycharis, V; Raptopoulou, C P; Terzis, A; Voyiatzis, G; Bertmer, M; Mateescu, C; Salifoglou, A

2012-06-04

Vanadium involvement in cellular processes requires deep understanding of the nature and properties of its soluble and bioavailable forms arising in aqueous speciations of binary and ternary systems. In an effort to understand the ternary vanadium-H(2)O(2)-ligand interactions relevant to that metal ion's biological role, synthetic efforts were launched involving the physiological ligands betaine (Me(3)N(+)CH(2)CO(2)(-)) and H(2)O(2). In a pH-specific fashion, V(2)O(5), betaine, and H(2)O(2) reacted and afforded three new, unusual, and unique compounds, consistent with the molecular formulation K(2)[V(2)O(2)(O(2))(4){(CH(3))(3)NCH(2)CO(2))}]·H(2)O (1), (NH(4))(2)[V(2)O(2)(O(2))(4){(CH(3))(3)NCH(2)CO(2))}]·0.75H(2)O (2), and {Na(2)[V(2)O(2)(O(2))(4){(CH(3))(3)NCH(2)CO(2))}(2)]}(n)·4nH(2)O (3). All complexes 1-3 were characterized by elemental analysis; UV/visible, FT-IR, Raman, and NMR spectroscopy in solution and the solid state; cyclic voltammetry; TGA-DTG; and X-ray crystallography. The structures of 1 and 2 reveal the presence of unusual ternary dinuclear vanadium-tetraperoxido-betaine complexes containing [(V(V)═O)(O(2))(2)] units interacting through long V-O bonds. The two V(V) ions are bridged through the oxygen terminal of one of the peroxide groups bound to the vanadium centers. The betaine ligand binds only one of the two V(V) ions. In the case of the third complex 3, the two vanadium centers are not immediate neighbors, with Na(+) ions (a) acting as efficient oxygen anchors and through Na-O bonds holding the two vanadium ions in place and (b) providing for oxygen-containing ligand binding leading to a polymeric lattice. In 1 and 3, interesting 2D (honeycomb) and 1D (zigzag chains) topologies of potassium nine-coordinate polyhedra (1) and sodium octahedra (3), respectively, form. The collective physicochemical properties of the three ternary species 1-3 project the chemical role of the low molecular mass biosubstrate betaine in binding V(V)-diperoxido units, thereby stabilizing a dinuclear V(V)-tetraperoxido dianion. Structural comparisons of the anions in 1-3 with other known dinuclear V(V)-tetraperoxido binary anionic species provide insight into the chemical reactivity of V(V)-diperoxido systems and their potential link to cellular events such as insulin mimesis and anitumorigenicity modulated by the presence of betaine.

Adsorption Energies of Carbon, Nitrogen, and Oxygen Atoms on the Low-temperature Amorphous Water Ice: A Systematic Estimation from Quantum Chemistry Calculations

NASA Astrophysics Data System (ADS)

Shimonishi, Takashi; Nakatani, Naoki; Furuya, Kenji; Hama, Tetsuya

2018-03-01

We propose a new simple computational model to estimate the adsorption energies of atoms and molecules to low-temperature amorphous water ice, and we present the adsorption energies of carbon (3 P), nitrogen (4 S), and oxygen (3 P) atoms based on quantum chemistry calculations. The adsorption energies were estimated to be 14,100 ± 420 K for carbon, 400 ± 30 K for nitrogen, and 1440 ± 160 K for oxygen. The adsorption energy of oxygen is consistent with experimentally reported values. We found that the binding of a nitrogen atom is purely physisorption, while that of a carbon atom is chemisorption, in which a chemical bond to an O atom of a water molecule is formed. That of an oxygen atom has a dual character, with both physisorption and chemisorption. The chemisorption of atomic carbon also implies the possibility of further chemical reactions to produce molecules bearing a C–O bond, though this may hinder the formation of methane on water ice via sequential hydrogenation of carbon atoms. These properties would have a large impact on the chemical evolution of carbon species in interstellar environments. We also investigated the effects of newly calculated adsorption energies on the chemical compositions of cold dense molecular clouds with the aid of gas-ice astrochemical simulations. We found that abundances of major nitrogen-bearing molecules, such as N2 and NH3, are significantly altered by applying the calculated adsorption energy, because nitrogen atoms can thermally diffuse on surfaces, even at 10 K.

Spectroscopic analysis of the impact of oxidative stress on the structure of human serum albumin (HSA) in terms of its binding properties

NASA Astrophysics Data System (ADS)

Maciążek-Jurczyk, M.; Sułkowska, A.

2015-02-01

Oxygen metabolism has an important role in the pathogenesis of rheumatoid arthritis (RA). Reactive oxygen species (ROS) are produced in the course of cellular oxidative phosphorylation and by activated phagocytic cells during oxidative bursts, exceed the physiological buffering capacity and result in oxidative stress. ROS result in oxidation of serum albumin, which causes a number of structural changes in the spatial structure, may influence the binding and cause significant drug interactions, particularly in polytherapy. During the oxidation modification of amino acid residues, particularly cysteine and methionine may occur. The aim of the study was to investigate the influence of oxidative stress on human serum albumin (HSA) structure and evaluate of possible alterations in the binding of the drug to oxidized human serum albumin (oHSA). HSA was oxidized by a chloramine-T (CT). CT reacts rapidly with sulfhydryl groups and at pH 7.4 the reaction was monitored by spectroscopic techniques. Modification of free thiol group in the Cys residue in HSA was quantitatively determined by the use of Ellman's reagent. Changes of albumin conformation were examined by comparison of modified (oHSA) and nonmodified human serum albumin (HSA) absorption spectra, emission spectra, red-edge shift (REES) and synchronous spectroscopy. Studies of absorption spectra indicated that changes in the value of absorbance associated with spectral changes in the region of 200-250 nm involve structural alterations in peptide backbone conformation. Synchronous fluorescence spectroscopy technique confirmed changes of position of tryptophanyl and tyrosyl residues fluorescent band caused by CT. Moreover analysis of REES effect allowed to observe structural changes caused by CT in the region of the hydrophobic pocket containing the tryptophanyl residue. Effect of oxidative stress on binding of anti-rheumatic drugs, sulfasalazine (SSZ) and sulindac (SLD) in the high and low affinity binding sites was investigated by spectrofluorescence, ITC and 1H NMR spectroscopy, respectively. SSZ and SLD change the affinity of each other to the binding site in non- and modified human serum albumin. The presence of SLD causes the increase of association constant (Ka) of SSZ-oHSA system and the strength of binding and the stability of the complexes has been observed while in the presence of SSZ a displacement of SLD from the SLD-HSA has been recorded. The analysis of 1H NMR spectral parameters i.e. changes of chemical shifts of the drug indicate that the presence of SSZ and SLD have a mutual influence on changes in the affinity of human serum albumin binding site and this competition takes place not only due to the additional drug but also to the oxidation of HSA.

In vitro covalent binding of new brain tracer, para-125I-amphetamine, to rat liver and lung microsomes

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

Joulin, Y.; Delaforge, M.; Hoellinger, H.

1990-01-01

p-125I-amphetamine (I-Amp) is retained significantly in liver and lung during brain tomoscintigraphy. To attempt to explain this clinical observation, we have investigated the interaction of I-Amp with rat liver and lung microsomal proteins. Studies using spectral shift technique indicate that low concentration of I-Amp gives a type I complex and high concentration appears very stable type II complex with cytochrome P-450 Fe III. In the presence of NADPH, I-Amp gives rise to a 455 nm absorbing complex with similar properties to the Fe-RNO complexes. This complex formation was greatly enhanced with phenobarbital treated liver microsomes. The in vitro binding studymore » shows that I-Amp and/or its metabolites was covalently bound to macromolecules in the presence of the molecular oxygen and NADPH-generating system. Incubation in the presence of glutathione, cystein and radical scavengers decreases binding. Mixed function oxydase (MFO) inhibitors diminish the amount of covalent binding and alter the extent of metabolite formation. The total covalent binding level increased with liver microsomes from PB pretreated rats as it was observed with the 455nm complex formation. The radioactivity distribution on microsomal proteins was examinated with SDS polyacrylamide gel electrophoresis and autoradiography. This experiment proves that the radiolabelled compounds are bound on the cytochrome P-450. The radioactivity bound increased when the PB induced rat liver microsomes were used. All these results indicate that I-Amp was activated by an oxydative process dependent on the MFO system which suggests a N-oxydation of I-Amp and the formation of reactive entities which covalently bind to proteins.« less

Red blood cells serve as intravascular carriers of myeloperoxidase.

PubMed

Adam, Matti; Gajdova, Silvie; Kolarova, Hana; Kubala, Lukas; Lau, Denise; Geisler, Anne; Ravekes, Thorben; Rudolph, Volker; Tsao, Philip S; Blankenberg, Stefan; Baldus, Stephan; Klinke, Anna

2014-09-01

Myeloperoxidase (MPO) is a heme enzyme abundantly expressed in polymorphonuclear neutrophils. MPO is enzymatically capable of catalyzing the generation of reactive oxygen species (ROS) and the consumption of nitric oxide (NO). Thus MPO has both potent microbicidal and, upon binding to the vessel wall, pro-inflammatory properties. Interestingly, MPO - a highly cationic protein - has been shown to bind to both endothelial cells and leukocyte membranes. Given the anionic surface charge of red blood cells, we investigated binding of MPO to erythrocytes. Red blood cells (RBCs) derived from patients with elevated MPO plasma levels showed significantly higher amounts of MPO by flow cytometry and ELISA than healthy controls. Heparin-induced MPO-release from patient-derived RBCs was significantly increased compared to controls. Ex vivo experiments revealed dose and time dependency for MPO-RBC binding, and immunofluorescence staining as well as confocal microscopy localized MPO-RBC interaction to the erythrocyte plasma membrane. NO-consumption by RBC-membrane fragments (erythrocyte "ghosts") increased with incrementally greater concentrations of MPO during incubation, indicating preserved catalytic MPO activity. In vivo infusion of MPO-loaded RBCs into C57BL/6J mice increased local MPO tissue concentrations in liver, spleen, lung, and heart tissue as well as within the cardiac vasculature. Further, NO-dependent relaxation of aortic rings was altered by RBC bound-MPO and systemic vascular resistance significantly increased after infusion of MPO-loaded RBCs into mice. In summary, we find that MPO binds to RBC membranes in vitro and in vivo, is transported by RBCs to remote sites in mice, and affects endothelial function as well as systemic vascular resistance. RBCs may avidly bind circulating MPO, and act as carriers of this leukocyte-derived enzyme. Copyright © 2014 Elsevier Ltd. All rights reserved.

Unifying the 2e(-) and 4e(-) Reduction of Oxygen on Metal Surfaces.

PubMed

Viswanathan, Venkatasubramanian; Hansen, Heine Anton; Rossmeisl, Jan; Nørskov, Jens K

2012-10-18

Understanding trends in selectivity is of paramount importance for multi-electron electrochemical reactions. The goal of this work is to address the issue of 2e(-) versus 4e(-) reduction of oxygen on metal surfaces. Using a detailed thermodynamic analysis based on density functional theory calculations, we show that to a first approximation an activity descriptor, ΔGOH*, the free energy of adsorbed OH*, can be used to describe trends for the 2e(-) and 4e(-) reduction of oxygen. While the weak binding of OOH* on Au(111) makes it an unsuitable catalyst for the 4e(-) reduction, this weak binding is optimal for the 2e(-) reduction to H2O2. We find quite a remarkable agreement between the predictions of the model and experimental results spanning nearly 30 years.

Ultrasound-assisted interaction between chlorin-e6 and human serum albumin: pH dependence, singlet oxygen production, and formulation effect

NASA Astrophysics Data System (ADS)

Mocanu, Mihaela N.; Yan, Fei

2018-02-01

The interaction between chlorin e6 (Ce6) and human serum albumin (HSA) in the presence and absence of ultrasound have been investigated by ultraviolet-visible absorption spectroscopy and fluorescence spectroscopy. Ce6 is found to bind strongly to HSA at or near physiological pH conditions, but the strength of the binding is significantly weakened at lower pHs. The intrinsic fluorescence of HSA is incrementally quenched with increasing concentration of Ce6, and the quenching is enhanced after exposure to high-frequency ultrasound. Our experimental results suggest that Ce6-induced sonodynamic oxidation of HSA is mainly mediated by singlet oxygen. The formulation of Ce6 by high molecular weight polyvinylpyrrolidone (PVP) increased its stability in aqueous solutions and its quantum yield of singlet oxygen under ultrasound irradiation.

Broad Phylogenetic Occurrence of the Oxygen-Binding Hemerythrins in Bilaterians.

PubMed

Costa-Paiva, Elisa M; Schrago, Carlos G; Halanych, Kenneth M

2017-10-01

Animal tissues need to be properly oxygenated for carrying out catabolic respiration and, as such, natural selection has presumably favored special molecules that can reversibly bind and transport oxygen. Hemoglobins, hemocyanins, and hemerythrins (Hrs) fulfill this role, with Hrs being the least studied. Knowledge of oxygen-binding proteins is crucial for understanding animal physiology. Hr genes are present in the three domains of life, Archaea, Bacteria, and Eukaryota; however, within Animalia, Hrs has been reported only in marine species in six phyla (Annelida, Brachiopoda, Priapulida, Bryozoa, Cnidaria, and Arthropoda). Given this observed Hr distribution, whether all metazoan Hrs share a common origin is circumspect. We investigated Hr diversity and evolution in metazoans, by employing in silico approaches to survey for Hrs from of 120 metazoan transcriptomes and genomes. We found 58 candidate Hr genes actively transcribed in 36 species distributed in 11 animal phyla, with new records in Echinodermata, Hemichordata, Mollusca, Nemertea, Phoronida, and Platyhelminthes. Moreover, we found that "Hrs" reported from Cnidaria and Arthropoda were not consistent with that of other metazoan Hrs. Contrary to previous suggestions that Hr genes were absent in deuterostomes, we find Hr genes present in deuterostomes and were likely present in early bilaterians, but not in nonbilaterian animal lineages. As expected, the Hr gene tree did not mirror metazoan phylogeny, suggesting that Hrs evolutionary history was complex and besides the oxygen carrying capacity, the drivers of Hr evolution may also consist of secondary functional specializations of the proteins, like immunological functions. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Effects of Fiber Type and Size on the Heterogeneity of Oxygen Distribution in Exercising Skeletal Muscle

PubMed Central

Liu, Gang; Mac Gabhann, Feilim; Popel, Aleksander S.

2012-01-01

The process of oxygen delivery from capillary to muscle fiber is essential for a tissue with variable oxygen demand, such as skeletal muscle. Oxygen distribution in exercising skeletal muscle is regulated by convective oxygen transport in the blood vessels, oxygen diffusion and consumption in the tissue. Spatial heterogeneities in oxygen supply, such as microvascular architecture and hemodynamic variables, had been observed experimentally and their marked effects on oxygen exchange had been confirmed using mathematical models. In this study, we investigate the effects of heterogeneities in oxygen demand on tissue oxygenation distribution using a multiscale oxygen transport model. Muscles are composed of different ratios of the various fiber types. Each fiber type has characteristic values of several parameters, including fiber size, oxygen consumption, myoglobin concentration, and oxygen diffusivity. Using experimentally measured parameters for different fiber types and applying them to the rat extensor digitorum longus muscle, we evaluated the effects of heterogeneous fiber size and fiber type properties on the oxygen distribution profile. Our simulation results suggest a marked increase in spatial heterogeneity of oxygen due to fiber size distribution in a mixed muscle. Our simulations also suggest that the combined effects of fiber type properties, except size, do not contribute significantly to the tissue oxygen spatial heterogeneity. However, the incorporation of the difference in oxygen consumption rates of different fiber types alone causes higher oxygen heterogeneity compared to control cases with uniform fiber properties. In contrast, incorporating variation in other fiber type-specific properties, such as myoglobin concentration, causes little change in spatial tissue oxygenation profiles. PMID:23028531

The mechanism and high-free-energy transition state of lac repressor–lac operator interaction

PubMed Central

Sengupta, Rituparna; Capp, Michael W.; Shkel, Irina A.

2017-01-01

Abstract Significant, otherwise-unavailable information about mechanisms and transition states (TS) of protein folding and binding is obtained from solute effects on rate constants. Here we characterize TS for lac repressor(R)–lac operator(O) binding by analyzing effects of RO-stabilizing and RO-destabilizing solutes on association (ka) and dissociation (kd) rate constants. RO-destabilizing solutes (urea, KCl) reduce ka comparably (urea) or more than (KCl) they increase kd, demonstrating that they destabilize TS relative to reactants and RO, and that TS exhibits most of the Coulombic interactions between R and O. Strikingly, three solutes which stabilize RO by favoring burial/dehydration of amide oxygens and anionic phosphate oxygens all reduce kd without affecting ka significantly. The lack of stabilization of TS by these solutes indicates that O phosphates remain hydrated in TS and that TS preferentially buries aromatic carbons and amide nitrogens while leaving amide oxygens exposed. In our proposed mechanism, DNA-binding-domains (DBD) of R insert in major grooves of O pre-TS, forming most Coulombic interactions of RO and burying aromatic carbons. Nucleation of hinge helices creates TS, burying sidechain amide nitrogens. Post-TS, hinge helices assemble and the DBD-hinge helix-O-DNA module docks on core repressor, partially dehydrating phosphate oxygens and tightening all interfaces to form RO. PMID:29036376

Deep levels due to hydrogen in ZnO single crystals

NASA Astrophysics Data System (ADS)

Parmar, Narendra; Weber, Marc; Lynn, Kelvin

2009-05-01

Hydrogen impurities and oxygen vacancies are involved in the ˜0.7 eV shift of the optical absorption edge of ZnO. Deuterium causes a smaller shift. Titanium metal is used to bind hydrogen as it diffuses out of ZnO. Positron annihilation spectroscopy coupled with other techniques point to the presence of oxygen vacancies. Removing hydrogen followed by annealing in oxygen reduces the carrier concentration.

Surface acoustic wave oxygen pressure sensor

NASA Technical Reports Server (NTRS)

Oglesby, Donald M. (Inventor); Upchurch, Billy T. (Inventor); Leighty, Bradley D. (Inventor)

1994-01-01

A transducer for the measurement of absolute gas-state oxygen pressure from pressures of less than 100 Pa to atmospheric pressure (1.01 x 10(exp 5) Pa) is based on a standard surface acoustic wave (SAW) device. The piezoelectric material of the SAW device is coated with a compound which will selectively and reversibly bind oxygen. When oxygen is bound by the coating, the mass of the coating increases by an amount equal to the mass of the bound oxygen. Such an increase in the mass of the coating causes a corresponding decrease in the resonant frequency of the SAW device.

Novel optical oxy/deoxy hemoglobin monitoring as a modality for non-invasive real-time monitoring of cognitive activity and beyond

NASA Astrophysics Data System (ADS)

Davies-Shaw, Dana; Huser, Thomas R.

2008-02-01

We report on the successful development of a custom in vitro system that provides a physiologically relevant means of demonstrating optical methodologies for the calibration and validation of oxygen delivery and hemoglobin oxygen binding dynamics in the brain. While measured optical signals have generally been equated to heme absorbance values that are, in turn, presumed to correspond to oxygen delivery, there has been little specific study of the sigmoidal oxygen binding dynamics of hemoglobin, a tetrameric protein, within physiologically relevant parameters. Our development of this novel analytical device addresses this issue, and is a significant step towards the minimally invasive and real-time monitoring of spatially resolved cognitive processes. As such, it is of particular interest for the detection of autistic brain activity in infants and young children. Moreover, our device and approach bring with them the ability to quantify and spatially resolve oxygen delivery down to volumes relevant to individual cell oxygen uptake, without any oxygen consumption, and with a temporal resolution that is physically unachievable by any oxygen tracking modality such as fMRI etc. Such a capability opens up myriad possibilities for further investigation, such as real-time tumor biopsy and resection; the tracking and quantification of cellular proliferation, as well as metabolic measures of tissue viability, to name but a few. Our system has also been engineered to be synergistic with virtually all imaging techniques, optical and otherwise.

Kinetic mechanism of L-α-glycerophosphate oxidase from Mycoplasma pneumoniae.

PubMed

Maenpuen, Somchart; Watthaisong, Pratchaya; Supon, Pacharee; Sucharitakul, Jeerus; Parsonage, Derek; Karplus, P Andrew; Claiborne, Al; Chaiyen, Pimchai

2015-08-01

L-α-glycerophosphate oxidase is an FAD-dependent enzyme that catalyzes the oxidation of L-α-glycerophosphate (Glp) by molecular oxygen to generate dihydroxyacetone phosphate (DHAP) and hydrogen peroxide (H2O2). The catalytic properties of recombinant His6-GlpO from Mycoplasma pneumoniae (His6-MpGlpO) were investigated through transient and steady-state kinetics and ligand binding studies. The results indicate that the reaction mechanism of His6-MpGlpO follows a ping-pong model. Double-mixing mode stopped-flow experiments show that, after flavin-mediated substrate oxidation, DHAP leaves rapidly prior to the oxygen reaction. The values determined for the individual rate constants and kcat (4.2 s(-1) at 4 °C), in addition to the finding that H2 O2 binds to the oxidized enzyme, suggest that H2O2 release is the rate-limiting step for the overall reaction. The results indicate that His6 -MpGlpO contains mixed populations of fast- and slow-reacting species. It is predominantly the fast-reacting species that participates in turnover. In contrast to other GlpO enzymes previously described, His6-MpGlpO is able to catalyze the reverse reaction of reduced enzyme and DHAP. This result may be explained by the standard reduction potential value of His6-MpGlpO (-167 ± 1 mV), which is lower than those of GlpO from other species. We found that D,L-glyceraldehyde 3-phosphate (GAP) may be used as a substrate in the His6-MpGlpO reaction, although it exhibited an approximately 100-fold lower kcat value in comparison with the reaction of Glp. These results also imply involvement of GlpO in glycolysis, as well as in lipid and glycerol metabolism. The kinetic models and distinctive properties of His6-MpGlpO reported here should be useful for future drug development against Mycoplasma pneumoniae infection. © 2015 FEBS.

Density functional theory studies of oxygen and carbonate binding to a dicopper patellamide complex.

PubMed

Latifi, Reza; Bagherzadeh, Mojtaba; Milne, Bruce F; Jaspars, Marcel; de Visser, Sam P

2008-12-01

In this work we present results of density functional theory (DFT) calculations on dicopper patellamides and their affinity for molecular oxygen and carbonate. Patellamides are cyclic octapeptides that are produced by a cyanobacterium, and may show promise as therapeutics. Thus, carbonate binding to a dicopper patellamide center gives a stable cyclic octapeptide with a twist of almost 90 degrees . The system exists in close-lying open-shell singlet and triplet spin states with two unpaired electrons in orthogonal sigma* orbitals on each metal center. Subsequently, we replaced carbonate with dioxygen and found a stable Cu2(mu-O)2 diamond shaped patellamide core. In this structure the original dioxygen bond is significantly weakened to essentially a single bond, which should enable the system to transfer these oxygen atoms to substrates. We predicted the IR and Raman spectra of the Cu2(mu-O)2 diamond shaped patellamide structure using density functional theory and found a considerable isotope effect on the O-O stretch vibration for 16O2 versus 18O2 bound structures. Our studies reveal that carbonate forms an extremely stable complex with dicopper patellamide, but that additional molecular oxygen to this system does not give a potential oxidant. Therefore, it is more likely that carbonate prepares the system for dioxygen binding by folding it into the correct configuration followed in the proposed catalytic cycle by a protonation event preceding dioxygen binding to enable the system to reorganize to form a stable Cu2(mu-O)2-patellamide cluster. Alternatively, carbonate may act as an inhibitor that blocks the catalytic activity of the system. It is anticipated that the Cu2(mu-O)2-patellamide structure is a potential active oxidant of the dicopper patellamide complex.

The QSAR and docking calculations of fullerene derivatives as HIV-1 protease inhibitors

NASA Astrophysics Data System (ADS)

Saleh, Noha A.

2015-02-01

The inhibition of HIV-1 protease is considered as one of the most important targets for drug design and the deactivation of HIV-1. In the present work, the fullerene surface (C60) is modified by adding oxygen atoms as well as hydroxymethylcarbonyl (HMC) groups to form 6 investigated fullerene derivative compounds. These compounds have one, two, three, four or five O atoms + HMC groups at different positions on phenyl ring. The effect of the repeating of these groups on the ability of suggested compounds to inhibit the HIV protease is studied by calculating both Quantitative Structure Activity Relationship (QSAR) properties and docking simulation. Based on the QSAR descriptors, the solubility and the hydrophilicity of studied fullerene derivatives increased with increasing the number of oxygen atoms + HMC groups in the compound. While docking calculations indicate that, the compound with two oxygen atoms + HMC groups could interact and binds with HIV-1 protease active site. This is could be attributed to the active site residues of HIV-1 protease are hydrophobic except the two aspartic acids. So that, the increase in the hydrophilicity and polarity of the compound is preventing and/or decreasing the hydrophobic interaction between the compound and HIV-1 protease active site.

NOx Direct Decomposition: Potentially Enhanced Thermodynamics and Kinetics on Chemically Modified Ferroelectric Surfaces

NASA Astrophysics Data System (ADS)

Kakekhani, Arvin; Ismail-Beigi, Sohrab

2014-03-01

NOx are regulated pollutants produced during automotive combustion. As part of an effort to design catalysts for NOx decomposition that operate in oxygen rich environment and permit greater fuel efficiency, we study chemistry of NOx on (001) ferroelectric surfaces. Changing the polarization at such surfaces modifies electronic properties and leads to switchable surface chemistry. Using first principles theory, our previous work has shown that addition of catalytic RuO2 monolayer on ferroelectric PbTiO3 surface makes direct decomposition of NO thermodynamically favorable for one polarization. Furthermore, the usual problem of blockage of catalytic sites by strong oxygen binding is overcome by flipping polarization that helps desorb the oxygen. We describe a thermodynamic cycle for direct NO decomposition followed by desorption of N2 and O2. We provide energy barriers and transition states for key steps of the cycle as well as describing their dependence on polarization direction. We end by pointing out how a switchable order parameter of substrate,in this case ferroelectric polarization, allows us to break away from some standard compromises for catalyst design(e.g. the Sabatier principle). This enlarges the set of potentially catalytic metals. Primary support from Toyota Motor Engineering and Manufacturing, North America, Inc.

Chances and limitations of nanosized titanium dioxide practical application in view of its physicochemical properties

NASA Astrophysics Data System (ADS)

Bogdan, Janusz; Jackowska-Tracz, Agnieszka; Zarzyńska, Joanna; Pławińska-Czarnak, Joanna

2015-02-01

Nanotechnology is a field of science that is nowadays developing in a dynamic way. It seems to offer almost endless opportunities of contribution to many areas of economy and human activity, in general. Thanks to nanotechnology, the so-called nanomaterials can be designed. They present structurally altered materials, with their physical, chemical and biological properties entirely differing from properties of the same materials manufactured in microtechnology. Nanotechnology creates a unique opportunity to modify the matter at the level of atoms and particles. Therefore, it has become possible to obtain items displaying new, useful properties, i.e. self-disinfecting and self-cleaning surfaces. Those surfaces are usually covered by a thin layer of a photocatalyst. The role of the photocatalyst is most of the time performed by the nanosized titanium dioxide (nano-TiO2). Excitation of nano-TiO2 by ultraviolet radiation initiates advanced oxidation processes and reactions leading to the creation of oxygen vacancies that bind water particles. As a result, photocatalytic surfaces are given new properties. Those properties can then be applied in a variety of disciplines, such as medicine, food hygiene, environmental protection or building industry. Practically, the applications include inactivation of microorganisms, degradation of toxins, removing pollutants from buildings and manufacturing of fog-free windows or mirrors.

DNA incision evaluation, binding investigation and biocidal screening of Cu(II), Ni(II) and Co(II) complexes with isoxazole Schiff bases.

PubMed

Ganji, Nirmala; Chityala, Vijay Kumar; Marri, Pradeep Kumar; Aveli, Rambabu; Narendrula, Vamsikrishna; Daravath, Sreenu; Shivaraj

2017-10-01

Two new series of binary metal complexes [M(L 1 ) 2 ] and [M(L 2 ) 2 ] where, M=Cu(II), Ni(II) & Co(II) and L 1 =4-((3,4-dimethylisoxazol-5-ylimino)methyl)benzene-1,3-diol; L 2 =2-((3,4-dimethylisoxazol-5-ylimino)methyl)-5-methoxyphenol were synthesized and characterized by elemental analysis, 1 H NMR, 13 C NMR, FT-IR, ESI mass, UV-Visible, magnetic moment, ESR, SEM and powder XRD studies. Based on these results, a square planar geometry is assigned for all the metal complexes where the Schiff base acts as uninegatively charged bidentate chelating agent via the hydroxyl oxygen and azomethine nitrogen atoms. DNA binding studies of all the complexes with calf thymus DNA have been comprehensively investigated using electronic absorption spectroscopy, fluorescence quenching and viscosity studies. The oxidative and photo cleavage affinity of metal complexes towards supercoiled pBR322 DNA has been ascertained by agarose gel electrophoresis assay. From the results, it is observed that all the metal complexes bind effectively to CT-DNA via an intercalative mode of binding and also cleave pBR322 DNA in a promising manner. Further the Cu(II) complexes have shown better binding and cleavage properties towards DNA. The antimicrobial activities of the Schiff bases and their metal complexes were studied on bacterial and fungal strains and the results denoted that the complexes are more potent than their Schiff base ligands. Copyright © 2017 Elsevier B.V. All rights reserved.

Electronic properties of high-temperature superconductors

NASA Astrophysics Data System (ADS)

Richert, Brent Armand

1989-08-01

A semiempirical tight-binding model was developed for the electronic energy bands, the local and total densities of states, and the atomic valences in the high temperature superconductors La(1.85)Sr(0.15)CuO4, YBaCu307, Bi2Sr2CuO6, Bi2CaSr2Cu2O8, Tl2Ba2CuO6, Tl2CaBa2Cu2O8, Tl2Ca2Ba2Cu3O10, TlCa3Ba2Cu4O11, BaPb(0.75)Bi(0.25)O3, and Ba(0.6)K(0.4)BiO3. Calculations of the changes in electronic properties associated with atomic substitutions in YBa2Cu3O7, Bi2CaSr2Cu2O8, and Tl2CaBa2Cu2O8 give results in agreement with expected chemical trends and consistent with observed changes in the superconducting properties. For example, substitution of Lead for Bismuth in BiMCaSr2Cu2O8 increases the concentration of hole carriers within the CuO2 planes. Similarly, doping with Mercury or Pb in TlMCaBa2Cu2O8 also affects the carrier concentration, with Hg creating holes and Pb destroying them. Oxygen vacancies in both La(1.85)Sr(0.15)CuO(4-y) and YBa2Cu3O(7-y) act as electron donors. This is consistent with the observations that oxygen vacancies degrade the superconductivity and metallic conductivity in these materials. Lanthanum vacancies in La2-xCuO4 donate holes, giving the same electronic effect as doping with divalent metal atoms or excess oxygen initially stoichiometric La2CuO4. A specific excitonic mechanism for high temperature superconductivity is proposed which requires insulating metal oxide layers adjacent to the superconducting planes.

The Synthetic Analogs of Oxygen-Binding Heme Proteins.

ERIC Educational Resources Information Center

Suslick, Kenneth S.; Reinert, Thomas J.

1985-01-01

Discusses model studies aimed at elucidating various ways in which molecular oxygen interacts with metalloproteins. The focus is on the chemistry of iron(II) porphyrins and their adducts with nitrogenous bases, carbon monoxide, and dioxygen, which are most relevant to the functional proteries of the heme proteins, hemoglobin, and myoglobin. (JN)

Early Implementation of Large Scale Carbon Dioxide Removal Projects through the Cement Industry

NASA Astrophysics Data System (ADS)

Zeman, F. S.

2014-12-01

The development of large-scale carbon dioxide reduction projects requires high purity CO2and a reactive cation source. A project seeking to provide both of these requirements will likely face cost barriers with current carbon prices. The cement industry is a suitable early implementation site for such projects by virtue of the properties of its exhaust gases and those of waste concrete. Cement plants are the second largest source of industrial CO2 emissions, globally. It is also the second largest commodity after water, has no ready substitute and is literally the foundation of society. Finally, half of the CO2 emissions originate from process reactions rather than fossil fuel combustion resulting in higher flue gas CO2concentrations. These properties, with the co-benefits of oxygen combustion, create a favorable environment for spatially suitable projects. Oxygen combustion involves substituting produced oxygen for air in a combustion reaction. The absence of gaseous N2 necessitates the recirculation of exhaust gases to maintain kiln temperatures, which increase the CO2 concentrations from 28% to 80% or more. Gas exit temperatures are also elevated (>300oC) and can reach higher temperatures if the multi stage pre-heater towers, that recover heat, are re-designed in light of FGR. A ready source of cations can be found in waste concrete, a by-product of construction and demolition activities. These wastes can be processed to remove cations and then reacted with atmospheric CO2 to produce carbonate minerals. While not carbon negative, they represent a demonstration opportunity for binding atmospheric CO2while producing a saleable product (precipitated calcium carbonate). This paper will present experimental results on PCC production from waste concrete along with modeling results for oxygen combustion at cement facilities. The results will be presented with a view to mineral sequestration process design and implementation.

Singlet oxygen-dependent translational control in the tigrina-d.12 mutant of barley

PubMed Central

Khandal, Dhriti; Samol, Iga; Buhr, Frank; Pollmann, Stephan; Schmidt, Holger; Clemens, Stephan; Reinbothe, Steffen; Reinbothe, Christiane

2009-01-01

The tigrina (tig)-d.12 mutant of barley is impaired in the negative control limiting excess protochlorophyllide (Pchlide) accumulation in the dark. Upon illumination, Pchlide operates as photosensitizer and triggers singlet oxygen production and cell death. Here, we show that both Pchlide and singlet oxygen operate as signals that control gene expression and metabolite accumulation in tig-d.12 plants. In vivo labeling, Northern blotting, polysome profiling, and protein gel blot analyses revealed a selective suppression of synthesis of the small and large subunits of ribulose-1,5-bisphosphate carboxylase/oxygenase (RBCSs and RBCLs), the major light-harvesting chlorophyll a/b-binding protein of photosystem II (LHCB2), as well as other chlorophyll-binding proteins, in response to singlet oxygen. In part, these effects were caused by an arrest in translation initiation of photosynthetic transcripts at 80S cytoplasmic ribosomes. The observed changes in translation correlated with a decline in the phosphorylation level of ribosomal protein S6. At later stages, ribosome dissociation occurred. Together, our results identify translation as a major target of singlet oxygen-dependent growth control and cell death in higher plants. PMID:19620736

Dioxygen Binding in the Active Site of Histone Demethylase JMJD2A and the Role of the Protein Environment.

PubMed

Cortopassi, Wilian A; Simion, Robert; Honsby, Charles E; França, Tanos C C; Paton, Robert S

2015-12-21

JMJD2A catalyses the demethylation of di- and trimethylated lysine residues in histone tails and is a target for the development of new anticancer medicines. Mechanistic details of demethylation are yet to be elucidated and are important for the understanding of epigenetic processes. We have evaluated the initial step of histone demethylation by JMJD2A and demonstrate the dramatic effect of the protein environment upon oxygen binding using quantum mechanics/molecular mechanics (QM/MM) calculations. The changes in electronic structure have been studied for possible spin states and different conformations of O2 , using a combination of quantum and classical simulations. O2 binding to this histone demethylase is computed to occur preferentially as an end-on superoxo radical bound to a high-spin ferric centre, yielding an overall quintet ground state. The favourability of binding is strongly influenced by the surrounding protein: we have quantified this effect using an energy decomposition scheme into electrostatic and dispersion contributions. His182 and the methylated lysine assist while Glu184 and the oxoglutarate cofactor are deleterious for O2 binding. Charge separation in the superoxo-intermediate benefits from the electrostatic stabilization provided by the surrounding residues, stabilizing the binding process significantly. This work demonstrates the importance of the extended protein environment in oxygen binding, and the role of energy decomposition in understanding the physical origin of binding/recognition. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Discovery of 4-Methyl-N-(4-((4-methylpiperazin-1-yl)methyl)-3-(trifluoromethyl)phenyl)-3-((1-nicotinoylpiperidin-4-yl)oxy)benzamide (CHMFL-ABL/KIT-155) as a Novel Highly Potent Type II ABL/KIT Dual Kinase Inhibitor with a Distinct Hinge Binding.

PubMed

Wang, Qiang; Liu, Feiyang; Wang, Beilei; Zou, Fengming; Qi, Ziping; Chen, Cheng; Yu, Kailin; Hu, Chen; Qi, Shuang; Wang, Wenchao; Hu, Zhenquan; Liu, Juan; Wang, Wei; Wang, Li; Liang, Qianmao; Zhang, Shanchun; Ren, Tao; Liu, Qingsong; Liu, Jing

2017-01-12

The discovery of a novel potent type II ABL/c-KIT dual kinase inhibitor compound 34 (CHMFL-ABL/KIT-155), which utilized a hydrogen bond formed by NH on the kinase backbone and carbonyl oxygen of 34 as a unique hinge binding, is described. 34 potently inhibited purified ABL (IC 50 : 46 nM) and c-KIT kinase (IC 50 : 75 nM) in the biochemical assays and displayed high selectivity (S Score (1) = 0.03) at the concentration of 1 μM among 468 kinases/mutants in KINOMEscan assay. It exhibited strong antiproliferative activities against BCR-ABL/c-KIT driven CML/GISTs cancer cell lines through blockage of the BCR-ABL/c-KIT mediated signaling pathways, arresting cell cycle progression and induction of apoptosis. 34 possessed a good oral PK property and effectively suppressed the tumor progression in the K562 (CML) and GIST-T1 (GISTs) cells mediated xenograft mouse model. The distinct hinge-binding mode of 34 provided a novel pharmacophore for expanding the chemical structure diversity for the type II kinase inhibitors discovery.

Molluskan Hemocyanins Activate the Classical Pathway of the Human Complement System through Natural Antibodies

PubMed Central

Pizarro-Bauerle, Javier; Maldonado, Ismael; Sosoniuk-Roche, Eduardo; Vallejos, Gerardo; López, Mercedes N.; Salazar-Onfray, Flavio; Aguilar-Guzmán, Lorena; Valck, Carolina; Ferreira, Arturo; Becker, María Inés

2017-01-01

Molluskan hemocyanins are enormous oxygen-carrier glycoproteins that show remarkable immunostimulatory properties when inoculated in mammals, such as the generation of high levels of antibodies, a strong cellular reaction, and generation of non-specific antitumor immune responses in some types of cancer, particularly for superficial bladder cancer. These proteins have the ability to bias the immune response toward a Th1 phenotype. However, despite all their current uses with beneficial clinical outcomes, a clear mechanism explaining these properties is not available. Taking into account reports of natural antibodies against the hemocyanin of the gastropod Megathura crenulata [keyhole limpet hemocyanin (KLH)] in humans as well as other vertebrate species, we report here for the first time, the presence, in sera from unimmunized healthy donors, of antibodies recognizing, in addition to KLH, two other hemocyanins from gastropods with documented immunomodulatory capacities: Fisurella latimarginata hemocyanin (FLH) and Concholepas concholepas hemocyanin (CCH). Through an ELISA screening, we found IgM and IgG antibodies reactive with these hemocyanins. When the capacity of these antibodies to bind deglycosylated hemocyanins was studied, no decreased interaction was detected. Moreover, in the case of FLH, deglycosylation increased antibody binding. We evaluated through an in vitro complement deposition assay whether these antibodies activated the classical pathway of the human complement system. The results showed that all three hemocyanins and their deglycosylated counterparts elicited this activation, mediated by C1 binding to immunoglobulins. Thus, this work contributes to the understanding on how the complement system could participate in the immunostimulatory properties of hemocyanins, through natural, complement-activating antibodies reacting with these proteins. Although a role for carbohydrates cannot be completely ruled out, in our experimental setting, glycosylation status had a limited effect. Finally, our data open possibilities for further studies leading to the design of improved hemocyanin-based research tools for diagnosis and immunotherapy. PMID:28286504

Molluskan Hemocyanins Activate the Classical Pathway of the Human Complement System through Natural Antibodies.

PubMed

Pizarro-Bauerle, Javier; Maldonado, Ismael; Sosoniuk-Roche, Eduardo; Vallejos, Gerardo; López, Mercedes N; Salazar-Onfray, Flavio; Aguilar-Guzmán, Lorena; Valck, Carolina; Ferreira, Arturo; Becker, María Inés

2017-01-01

Molluskan hemocyanins are enormous oxygen-carrier glycoproteins that show remarkable immunostimulatory properties when inoculated in mammals, such as the generation of high levels of antibodies, a strong cellular reaction, and generation of non-specific antitumor immune responses in some types of cancer, particularly for superficial bladder cancer. These proteins have the ability to bias the immune response toward a T h 1 phenotype. However, despite all their current uses with beneficial clinical outcomes, a clear mechanism explaining these properties is not available. Taking into account reports of natural antibodies against the hemocyanin of the gastropod Megathura crenulata [keyhole limpet hemocyanin (KLH)] in humans as well as other vertebrate species, we report here for the first time, the presence, in sera from unimmunized healthy donors, of antibodies recognizing, in addition to KLH, two other hemocyanins from gastropods with documented immunomodulatory capacities: Fisurella latimarginata hemocyanin (FLH) and Concholepas concholepas hemocyanin (CCH). Through an ELISA screening, we found IgM and IgG antibodies reactive with these hemocyanins. When the capacity of these antibodies to bind deglycosylated hemocyanins was studied, no decreased interaction was detected. Moreover, in the case of FLH, deglycosylation increased antibody binding. We evaluated through an in vitro complement deposition assay whether these antibodies activated the classical pathway of the human complement system. The results showed that all three hemocyanins and their deglycosylated counterparts elicited this activation, mediated by C1 binding to immunoglobulins. Thus, this work contributes to the understanding on how the complement system could participate in the immunostimulatory properties of hemocyanins, through natural, complement-activating antibodies reacting with these proteins. Although a role for carbohydrates cannot be completely ruled out, in our experimental setting, glycosylation status had a limited effect. Finally, our data open possibilities for further studies leading to the design of improved hemocyanin-based research tools for diagnosis and immunotherapy.

Oxygen plasma surface modification augments poly(L-lactide-co-glycolide) cytocompatibility toward osteoblasts and minimizes immune activation of macrophages.

PubMed

Scislowska-Czarnecka, Anna; Szmigiel, Dariusz; Genet, Michel; Dupont-Gillain, Christine; Pamula, Elzbieta; Kolaczkowska, Elzbieta

2015-12-01

Here, we report on modification of one of the model biomedical polymers, poly L-lactide-co-glycolide (PLGA; 85:15), by reactive ion etching (RIE) oxygen plasma treatment. PLGA's major disadvantage is high hydrophobicity which restrains binding of cell-adhesive proteins and host cells. In the current approach, we aimed to answer two questions: (1) will only short (10 s) and moderate (20-200 mTorr, 45-90 W) RIE oxygen plasma treatment, leading to decrease of water contact angle by only up to 10°, sufficiently improve PLGA adherence to cells, and (2) how will this affect osteoblasts and activation of the immune system? All obtained modified PLGAs had improved hydrophilicity but unaltered roughness (as revealed by water contact angle measurements, X-ray photoelectron spectroscopy, and atomic force microscopy) resulting in significantly improved adhesion of osteoblasts (MG-63) and their low activation. Importantly, macrophages (RAW 264.7), one of the key cells initiating inflammation and bone resorption, responded significantly less vigorously to the modified polymers, expressing/releasing lower amounts of nitric oxide, matrix metalloproteinases (MMP-9), and pro-inflammatory cytokines (TNF-α, IL-6, IL-12p70, IFN-γ, IL-10). We conclude that already slight RIE oxygen plasma modification of PLGA is sufficient to improve its surface properties, and enhance cytocompatibility. Most importantly, this type of modification prevents excessive immune response. © 2015 Wiley Periodicals, Inc.

Computational and Experimental Study of Neuroglobin and Mutants

NASA Astrophysics Data System (ADS)

Nelson, Lauren; Cho, Samuel; Kim-Shaprio, Daniel

Neuroglobin (Ngb) is a hexacoordinated heme protein that is closely related to hemoglobin and myoglobin and normally found in the brain and nervous systems. It is involved in cellular oxygen homeostasis and reversibly binds to oxygen with a higher binding affinity than hemoglobin. To protect the brain tissue from hypoxic or ischemic conditions, Ngb increases oxygen availability. We have previously shown that a mutant form of Ngb reduces nitrite to nitric oxide 50x faster than myoglobin and 500x faster than hemoglobin. It also tightly binds to carbon monoxide (CO) with an association rate that is 500x faster than hemoglobin. To analyze the structure of neuroglobin and the characteristics causing these phenomena, we performed 3 sets of 1 microsecond molecular dynamic (MD) simulations of wild-type oxidized and reduced human Ngb and their C46A, C55A, H64L, and H64Q mutants. We also directly compare our MD simulations with time-resolved absorption spectroscopy. These studies will help identify treatments for diseases involving low nitric oxide availability and carbon monoxide poisoning. This research was supported by an NIH NSRA predoctoral fellowship in the Structural and Computational Biophysics Program training Grant (T32GM095440-05).

Tunable optical and excitonic properties of phosphorene via oxidation

NASA Astrophysics Data System (ADS)

Sadki, S.; Drissi, L. B.

2018-06-01

The optical properties and excitonic wave function of phosphorene oxides (PO) are studied using the first principle many-body Green function and the Bethe–Salpeter equation formalism. In this work, the optical properties are determined using ab initio calculations of the dielectric function. At the long wavelength limit q of EM wave (i.e. ), the dielectric function, the absorption spectrum, the lectivity, the electron energy loss spectra (EELS) and the wave function are calculated. The results show an excitonic binding energy of 818 meV with a bright exciton located in the armchair direction in pristine phosphorene. For PO, the arrangement of the oxygen atoms significantly influences the optical properties. In particular, the absorption spectrum is extended along the solar spectrum, with a high absorption coefficient observed in the dangling structures. The maximum lectivity values are observed for the high energies of the light spectrum. Moreover, the first EELS peak is located in the visible region in all the structures except for one configuration that exhibits the same behavior as pure phosphorene. Finally, the exciton effect reveals that all PO conformers have a dark exciton state, which is suitable for long-lived applications.

Predicting and analyzing DNA-binding domains using a systematic approach to identifying a set of informative physicochemical and biochemical properties

PubMed Central

2011-01-01

Background Existing methods of predicting DNA-binding proteins used valuable features of physicochemical properties to design support vector machine (SVM) based classifiers. Generally, selection of physicochemical properties and determination of their corresponding feature vectors rely mainly on known properties of binding mechanism and experience of designers. However, there exists a troublesome problem for designers that some different physicochemical properties have similar vectors of representing 20 amino acids and some closely related physicochemical properties have dissimilar vectors. Results This study proposes a systematic approach (named Auto-IDPCPs) to automatically identify a set of physicochemical and biochemical properties in the AAindex database to design SVM-based classifiers for predicting and analyzing DNA-binding domains/proteins. Auto-IDPCPs consists of 1) clustering 531 amino acid indices in AAindex into 20 clusters using a fuzzy c-means algorithm, 2) utilizing an efficient genetic algorithm based optimization method IBCGA to select an informative feature set of size m to represent sequences, and 3) analyzing the selected features to identify related physicochemical properties which may affect the binding mechanism of DNA-binding domains/proteins. The proposed Auto-IDPCPs identified m=22 features of properties belonging to five clusters for predicting DNA-binding domains with a five-fold cross-validation accuracy of 87.12%, which is promising compared with the accuracy of 86.62% of the existing method PSSM-400. For predicting DNA-binding sequences, the accuracy of 75.50% was obtained using m=28 features, where PSSM-400 has an accuracy of 74.22%. Auto-IDPCPs and PSSM-400 have accuracies of 80.73% and 82.81%, respectively, applied to an independent test data set of DNA-binding domains. Some typical physicochemical properties discovered are hydrophobicity, secondary structure, charge, solvent accessibility, polarity, flexibility, normalized Van Der Waals volume, pK (pK-C, pK-N, pK-COOH and pK-a(RCOOH)), etc. Conclusions The proposed approach Auto-IDPCPs would help designers to investigate informative physicochemical and biochemical properties by considering both prediction accuracy and analysis of binding mechanism simultaneously. The approach Auto-IDPCPs can be also applicable to predict and analyze other protein functions from sequences. PMID:21342579

Fluorescence properties and conformational stability of the beta-hemocyanin of Helix pomatia.

PubMed

Idakieva, Krassimira; Siddiqui, Nurul I; Parvanova, Katja; Nikolov, Peter; Gielens, Constant

2006-04-01

The beta-hemocyanin (beta-HpH) is one of the three dioxygen-binding proteins found freely dissolved in the hemolymph of the gastropodan mollusc Helix pomatia. The didecameric molecule (molecular mass 9 MDa) is built up of only one type of subunits. The fluorescence properties of the oxygenated and apo-form (copper-deprived) of the didecamer and its subunits were characterized. Upon excitation of the hemocyanins at 295 or 280 nm, tryptophyl residues buried in the hydrophobic interior of the protein determine the fluorescence emission. This is confirmed by quenching experiments with acrylamide, cesium chloride and potassium iodide. The copper-dioxygen system at the binuclear active site quenches the tryptophan emission of the oxy-beta-HpH. The removal of this system increases the fluorescence quantum yield and causes structural rearrangement of the microenvironment of the emitting tryptophyl residues in the apo-form. Time-resolved fluorescence measurements show that the oxygenated and copper-deprived forms of the beta-HpH and its subunits exist in different conformations. The thermal stability of the oxy- and apo-beta-HpH is characterized by a transition temperature (Tm) of 84 degrees C and 63 degrees C, respectively, obtained by differential scanning calorimetry. Increase of the temperature influences the active site at lower temperatures than the environments of tryptophans and tyrosines causing a loss of oxygen bound to the copper atoms. This process is, at least partially, reversible as after cooling of the protein samples, around 60% reinstatement of the copper-peroxide band has been observed. The results confirm the role of the copper-dioxygen complex for the stabilization of the hemocyanin structure in solution. The other important stabilizing factor is oligomerization of the hemocyanin molecule.

Preparation and characterization of ceramic sensors for use at elevated temperatures

NASA Astrophysics Data System (ADS)

You, Tao

Ceramic ITO strain sensors were prepared by reactive sputtering in various nitrogen/oxygen/argon partial pressures. The thickness of the active ITO strain elements played a significant role in the high temperature stability and piezoresistive properties, specifically, these results indicated that both gauge factor and drift rate were affected by the thickness of ITO films comprising the active strain elements. The influence of nitrogen in the reactive sputtered ITO films on the microstructure and the high temperature piezoresistive properties was also investigated. Scanning electron microscopy (SEM) revealed a partially sintered microstructure consisting of a contiguous network of sub-micron ITO particles with well-defined necks and isolated nanoporosity. Sintering and densification of the ITO particles containing these nitrogen rich grain boundaries was retarded and a contiguous network of nano-sized ITO particles was established. Aluminum doped indium tin oxide thin film exhibited an enhanced high temperature stability compared with undoped ITO thin film. The effect of aluminum doped ITO was investigated under various preparation and testing environments. Electron spectroscopy for chemical analysis (ESCA) studies indicated that interfacial reactions between ITO and aluminum increased the stability of ITO at elevated temperatures. These binding energies of indium-indium are significantly higher than those associated with stoichiometric indium oxide. A robust ceramic temperature sensor was fabricated by two different ITO elements, each with substantially different charge carrier concentrations. Thermal cycling of ITO thin films in a varied of partial oxygen pressures conditions showed that temperature coefficient of resistance (TCR) was nearly independent of oxygen partial pressure. A thermoelectric power of 6.0muV/°C and a linear voltage-temperature response were measured for an ITO thin film ceramic thermocouple over the temperature range 25--1250°C.

Probing the diphosphoglycerate binding pocket of HbA and HbPresbyterian (beta 108Asn --> Lys).

PubMed

Gottfried, D S; Manjula, B N; Malavalli, A; Acharya, A S; Friedman, J M

1999-08-31

HbPresbyterian (beta 108Asn --> Lys, HbP) contains an additional positive charge (per alpha beta dimer) in the middle of the central cavity and exhibits a lower oxygen affinity than wild-type HbA in the presence of chloride. However, very little is known about the molecular origins of its altered functional properties. In this study, we have focused on the beta beta cleft of the Hb tetramer. Recently, we developed an approach for quantifying the ligand binding affinity to the beta-end of the Hb central cavity using fluorescent analogues of the natural allosteric effector 2, 3-diphosphoglycerate (DPG) [Gottfried, D. S., et al. (1997) J. Biol. Chem. 272, 1571-1578]. Time-correlated single-photon counting fluorescence lifetime studies were used to assess the binding of pyrenetetrasulfonate to both HbA and HbP in the deoxy and CO ligation states under acidic and neutral pH conditions. Both the native and mutant proteins bind the probe at a weak binding site and a strong binding site; in all cases, the binding to HbP was stronger than to HbA. The most striking finding was that for HbA the binding affinity varies as follows: deoxy (pH 6.35) > deoxy (pH 7.20) > CO (pH 6.35); however, the binding to HbP is independent of ligation or pH. The mutant oxy protein also hydrolyzes p-nitrophenyl acetate, through a reversible acyl-imidazole pathway linked to the His residues of the beta beta cleft, at a considerably higher rate than does HbA. This implies a perturbation of the microenvironment of these residues at the DPG binding pocket. Structural consequences due to the presence of the new positive charge in the middle of the central cavity have been transmitted to the beta beta cleft of the protein, even in its liganded conformation. This is consistent with a newly described quaternary state (B) for liganded HbPresbyterian and an associated change in the allosteric control mechanism.

A natural xanthone increases catalase activity but decreases NF-kappa B and lipid peroxidation in U-937 and HepG2 cell lines.

PubMed

Sahoo, Binay K; Zaidi, Adeel H; Gupta, Pankaj; Mokhamatam, Raveendra B; Raviprakash, Nune; Mahali, Sidhartha K; Manna, Sunil K

2015-10-05

Mangiferin, a C-glycosyl xanthone, has shown anti-inflammatory, antioxidant, and anti-tumorigenic activities. In the present study, we investigated the molecular mechanism for the antioxidant property of mangiferin. Considering the role of nuclear transcription factor kappa B (NF-κB) in inflammation and tumorigenesis, we hypothesized that modulating its activity will be a viable therapeutic target in regulating the redox-sensitive ailments. Our results show that mangiferin blocks several inducers, such as tumor necrosis factor (TNF), lypopolysaccharide (LPS), phorbol-12-myristate-13-acetate (PMA) or hydrogen peroxide (H2O2) mediated NF-κB activation via inhibition of reactive oxygen species generation. In silico docking studies predicted strong binding energy of mangiferin to the active site of catalase (-9.13 kcal/mol), but not with other oxidases such as myeloperoxidase, glutathione peroxidase, or inducible nitric oxide synthase. Mangiferin increased activity of catalase by 44%, but had no effect on myeloperoxidase activity in vitro. Fluorescence spectroscopy further revealed the binding of mangiferin to catalase at the single site with binding constant and binding affinity of 3.1×10(-7) M(-1) and 1.046 respectively. Mangiferin also inhibits TNF-induced lipid peroxidation and thereby protects apoptosis. Hence, mangiferin with its ability to inhibit NF-κB and increase the catalase activity may prove to be a potent therapeutic. Copyright © 2015 Elsevier B.V. All rights reserved.

A review of theoretical study of graphene chemical vapor deposition synthesis on metals: nucleation, growth, and the role of hydrogen and oxygen

NASA Astrophysics Data System (ADS)

Rezwan Habib, Mohammad; Liang, Tao; Yu, Xuegong; Pi, Xiaodong; Liu, Yingchun; Xu, Mingsheng

2018-03-01

Graphene has attracted intense research interest due to its extraordinary properties and great application potential. Various methods have been proposed for the synthesis of graphene, among which chemical vapor deposition has drawn a great deal of attention for synthesizing large-area and high-quality graphene. Theoretical understanding of the synthesis mechanism is crucial for optimizing the experimental design for desired graphene production. In this review, we discuss the three fundamental steps of graphene synthesis in details, i.e. (1) decomposition of carbon feedstocks and formation of various active carbon species, (2) nucleation, and (3) attachment and extension. We provide a complete scenario of graphene synthesis on metal surfaces at atomistic level by means of density functional theory, molecular dynamics (MD), Monte Carlo (MC) and their combination and interface with other simulation methods such as quantum mechanical molecular dynamics, density functional tight binding molecular dynamics, and combination of MD and MC. We also address the latest investigation of the influences of the hydrogen and oxygen on the synthesis and the quality of the synthesized graphene.

Interspecific correlation between red blood cell mitochondrial ROS production, cardiolipin content and longevity in birds.

PubMed

Delhaye, Jessica; Salamin, Nicolas; Roulin, Alexandre; Criscuolo, François; Bize, Pierre; Christe, Philippe

2016-12-01

Mitochondrial respiration releases reactive oxygen species (ROS) as by-products that can damage the soma and may in turn accelerate ageing. Hence, according to "the oxidative stress theory of ageing", longer-lived organisms may have evolved mechanisms that improve mitochondrial function, reduce ROS production and/or increase cell resistance to oxidative damage. Cardiolipin, an important mitochondrial inner-membrane phospholipid, has these properties by binding and stabilizing mitochondrial inner-membrane proteins. Here, we investigated whether ROS production, cardiolipin content and cell membrane resistance to oxidative attack in freshly collected red blood cells (RBCs) are associated with longevity (range 5-35 years) in 21 bird species belonging to seven Orders. After controlling for phylogeny, body size and oxygen consumption, variation in maximum longevity was significantly explained by mitochondrial ROS production and cardiolipin content, but not by membrane resistance to oxidative attack. RBCs of longer-lived species produced less ROS and contained more cardiolipin than RBCs of shorter-lived species did. These results support the oxidative stress theory of ageing and shed light on mitochondrial cardiolipin as an important factor linking ROS production to longevity.

A highly Selective Fluorescent Sensor for Monitoring Cu2+ Ion: Synthesis, Characterization and Photophysical Properties.

PubMed

Aderinto, Stephen Opeyemi; Xu, Yuling; Peng, Hongping; Wang, Fei; Wu, Huilu; Fan, Xuyang

2017-01-01

A new fluorescent sensor, 4-allylamine-N-(N-salicylidene)-1,8-naphthalimide (1), anchoring a naphthalimide moiety as fluorophore and a Schiff base group as receptor, was synthesized and characterized. The photophysical properties of sensor 1 were conducted in organic solvents of different polarities. Our study revealed that, depending on the solvent polarity, the fluorescence quantum yields varied from 0.59 to 0.89. The fluorescent activity of the sensor was monitored and the sensor was consequently applied for the detection of Cu 2+ with high selectivity over various metal ions by fluorescence quenching in Tris-HCl (pH = 7.2) buffer/DMF (1:1, v/v) solution. From the binding stoichiometry, it was indicated that a 1:1 complex was formed between Cu 2+ and the sensor 1. The fluorescence intensity was linear with Cu 2+ in the concentration range 0.5-5 μM. Moreso, the detection limit was calculated to be 0.32 μM, which is sufficiently low for good sensitivity of Cu 2+ ion. The binding mode was due to the intramolecular charge transfer (ICT) and the coordination of Cu 2+ with C = N and hydroxyl oxygen groups of the sensor 1. The sensor proved effective for Cu 2+ monitoring in real water samples with recovery rates of 95-112.6 % obtained.

Atomic scale simulations of pyrochlore oxides with a tight-binding variable-charge model: implications for radiation tolerance.

PubMed

Sattonnay, G; Tétot, R

2014-02-05

Atomistic simulations with new interatomic potentials derived from a tight-binding variable-charge model were performed in order to investigate the lattice properties and the defect formation energies in Gd2Ti2O7 and Gd2Zr2O7 pyrochlores. The main objective was to determine the role played by the defect stability on the radiation tolerance of these compounds. Calculations show that the titanate has a more covalent character than the zirconate. Moreover, the properties of oxygen Frenkel pairs, cation antisite defects and cation Frenkel pairs were studied. In Gd2Ti2O7 the cation antisite defect and the Ti-Frenkel pair are not stable: they evolve towards more stable defect configurations during the atomic relaxation process. This phenomenon is driven by a decrease of the Ti coordination number down to five which leads to a local atomic reorganization and strong structural distortions around the defects. These kinds of atomic rearrangements are not observed around defects in Gd2Zr2O7. Therefore, the defect stability in A2B2O7 depends on the ability of B atoms to accommodate high coordination number (higher than six seems impossible for Ti). The accumulation of structural distortions around Ti-defects due to this phenomenon could drive the Gd2Ti2O7 amorphization induced by irradiation.

Understanding Ion Binding Affinity and Selectivity in β-Parvalbumin Using Molecular Dynamics and Mean Spherical Approximation Theory.

PubMed

Kucharski, Amir N; Scott, Caitlin E; Davis, Jonathan P; Kekenes-Huskey, Peter M

2016-08-25

Parvalbumin (PV) is a globular calcium (Ca(2+))-selective protein expressed in a variety of biological tissues. Our computational studies of the rat β-parvalbumin (β-PV) isoform seek to elucidate the molecular thermodynamics of Ca(2+) versus magnesium (Mg(2+)) binding at the protein's two EF-hand motifs. Specifically, we have utilized molecular dynamics (MD) simulations and a mean-field electrolyte model (mean spherical approximation (MSA) theory) to delineate how the EF-hand scaffold controls the "local" thermodynamics of Ca(2+) binding selectivity over Mg(2+). Our MD simulations provide the probability density of metal-chelating oxygens within the EF-hand scaffolds for both Ca(2+) and Mg(2+), as well the conformational strain induced by Mg(2+) relative to Ca(2+) binding. MSA theory utilizes the binding domain oxygen and charge distributions to predict the chemical potential of ion binding, as well as their corresponding concentrations within the binding domain. We find that the electrostatic and steric contributions toward ion binding were similar for Mg(2+) and Ca(2+), yet the latter was 5.5 kcal/mol lower in enthalpy when internal strain within the EF hand was considered. We therefore speculate that beyond differences in dehydration energies for the Ca(2+) versus Mg(2+), strain induced in the β-PV EF hand by cation binding significantly contributes to the nearly 10,000-fold difference in binding affinity reported in the literature. We further complemented our analyses of local factors governing cation binding selectivity with whole-protein (global) contributions, such as interhelical residue-residue contacts and solvent exposure of hydrophobic surface. These contributions were found to be comparable for both Ca(2+)- and Mg(2+)-bound β-PV, which may implicate local factors, EF-hand strain, and dehydration, in providing the primary means of selectivity. We anticipate these methods could be used to estimate metal binding thermodynamics across a broad range of PV sequence homologues and EF-hand-containing, Ca(2+) binding proteins.

Haemoglobin Rahere (beta Lys-Thr): A new high affinity haemoglobin associated with decreased 2, 3-diphosphoglycerate binding and relative polycythaemia.

PubMed Central

Lorkin, P A; Stephens, A D; Beard, M E; Wrigley, P F; Adams, L; Lehmann, H

1975-01-01

A new haemoglobin with increased oxygen affinity, beta82 (EF6) lysine leads to threonine (Hb Rahere), was found during the investigation of a patient who was found to have a raised haemoglobin concentration after a routine blood count. The substitution affects one of the 2, 3-diphosphoglycerate binding sites, resulting in an increased affinity for oxygen, but both the haem-haem interaction and the alkaline Bohr effect are normal in the haemolysate. This variant had the same mobility as haemoglobin A on electrophoresis at alkaline pH but was detected by measuring the whole blood oxygen affinity; it could be separated from haemoglobin A, however, by electrophoresis in agar at acid pH. The raised haemoglobin concentration was mainly due to a reduction in plasma volume (a relative polycythaemia) and was associated with a persistently raised white blood count. This case emphasises the need to measure the oxygen affinity of haemoglobin in all patients with absolute or relative polycythaemia when some obvious cause is not evident. PMID:124

First Principle Calculation : Investigation on interaction of Pt/Graphene as Catalyst

NASA Astrophysics Data System (ADS)

Anugrah Putri Namari, Nuning; Suprijadi

2017-07-01

The increasing in energy needs and the lack of non-renewable energy sources becomes a challenge for the human being to be able to use renewable energy sources. One of the devices to process renewable energy is Polymer Electrolyte Membrane Fuel Cell (PEMFC) . PEMFC use hydrogen and Oxygen as an energy sources . The most important reaction in fuel cell is Oxidation and reduction process. Therefore, a catalyst is needed to help the OR process. Study of catalyst shows that the most effective fuel cell for now is Platinum. Many fuel cell have use platinum as the catalyst. However, Platinum is a rare and expensive element. Therefore, to reduce the cost of fuel cell fabrication, we need to increase the activity of platinum. In this research, we use graphene as a support material. Then, we will study about the interaction of platinum on graphene and analyze its morphological change and electronic properties.The research conduct using Density Functional Theory (DFT). The calculation result shows that Pt/graphene can break H2 into H+ and the binding between Pt cluster is stronger than binding with the substrate.

Phosphorothioate backbone modifications of nucleotide-based drugs are potent platelet activators

PubMed Central

Flierl, Ulrike; Nero, Tracy L.; Lim, Bock; Arthur, Jane F.; Yao, Yu; Jung, Stephanie M.; Gitz, Eelo; Pollitt, Alice Y.; Zaldivia, Maria T.K.; Jandrot-Perrus, Martine; Schäfer, Andreas; Nieswandt, Bernhard; Andrews, Robert K.; Parker, Michael W.; Gardiner, Elizabeth E.

2015-01-01

Nucleotide-based drug candidates such as antisense oligonucleotides, aptamers, immunoreceptor-activating nucleotides, or (anti)microRNAs hold great therapeutic promise for many human diseases. Phosphorothioate (PS) backbone modification of nucleotide-based drugs is common practice to protect these promising drug candidates from rapid degradation by plasma and intracellular nucleases. Effects of the changes in physicochemical properties associated with PS modification on platelets have not been elucidated so far. Here we report the unexpected binding of PS-modified oligonucleotides to platelets eliciting strong platelet activation, signaling, reactive oxygen species generation, adhesion, spreading, aggregation, and thrombus formation in vitro and in vivo. Mechanistically, the platelet-specific receptor glycoprotein VI (GPVI) mediates these platelet-activating effects. Notably, platelets from GPVI function–deficient patients do not exhibit binding of PS-modified oligonucleotides, and platelet activation is fully abolished. Our data demonstrate a novel, unexpected, PS backbone–dependent, platelet-activating effect of nucleotide-based drug candidates mediated by GPVI. This unforeseen effect should be considered in the ongoing development programs for the broad range of upcoming and promising DNA/RNA therapeutics. PMID:25646267

High blood oxygen affinity in the air-breathing swamp eel Monopterus albus.

PubMed

Damsgaard, Christian; Findorf, Inge; Helbo, Signe; Kocagoz, Yigit; Buchanan, Rasmus; Huong, Do Thi Thanh; Weber, Roy E; Fago, Angela; Bayley, Mark; Wang, Tobias

2014-12-01

The Asian swamp eel (Monopterus albus, Zuiew 1793) is a facultative air-breathing fish with reduced gills. Previous studies have shown that gas exchange seems to occur across the epithelium of the buccopharyngeal cavity, the esophagus and the integument, resulting in substantial diffusion limitations that must be compensated by adaptations in others steps of the O₂ transport system to secure adequate O₂ delivery to the respiring tissues. We therefore investigated O₂ binding properties of whole blood, stripped hemoglobin (Hb), two major isoHb components and the myoglobin (Mb) from M. albus. Whole blood was sampled using indwelling catheters for blood gas analysis and determination of O₂ equilibrium curves. Hb was purified to assess the effects of endogenous allosteric effectors, and Mb was isolated from heart and skeletal muscle to determine its O₂ binding properties. The blood of M. albus has a high O₂ carrying capacity [hematocrit (Hct) of 42.4±4.5%] and binds O₂ with an unusually high affinity (P₅₀=2.8±0.4mmHg at 27°C and pH7.7), correlating with insensitivity of the Hb to the anionic allosteric effectors that normally decrease Hb-O₂ affinity. In addition, Mb is present at high concentrations in both heart and muscle (5.16±0.99 and 1.08±0.19mg ∙ g wet tissue⁻¹, respectively). We suggest that the high Hct and high blood O₂ affinity serve to overcome the low diffusion capacity in the relatively inefficient respiratory surfaces, while high Hct and Mb concentration aid in increasing the O₂ flux from the blood to the muscles. Copyright © 2014 Elsevier Inc. All rights reserved.

Omega-oxidation impairs oxidizability of polyenoic fatty acids by 15-lipoxygenases: consequences for substrate orientation at the active site.

PubMed Central

Ivanov, I; Schwarz, K; Holzhütter, H G; Myagkova, G; Kühn, H

1998-01-01

During oxygenation by 15-lipoxygenases, polyenoic fatty acids are bound at the active site in such a way that the omega-terminus of the fatty acids penetrates into the substrate binding pocket. In contrast, for arachidonic acid 5-lipoxygenation, an inverse head to tail orientation has been suggested. However, an inverse orientation may be hindered by the large energy barrier associated with burying the charged carboxylate group in the hydrophobic environment of the substrate binding cleft. We studied the oxygenation kinetics of omega-modified fatty acids by 15-lipoxygenases and found that omega-hydroxylation strongly impaired substrate affinity (higher Km), but only moderately altered Vmax. In contrast, omega-carboxylation completely prevented the lipoxygenase reaction; however, methylation of the additional carboxylate group restored the activity. Arg403 of the human 15-lipoxygenase has been implicated in fatty acid binding by forming a salt bridge with the carboxylate group, and thus mutation of this amino acid to an uncharged residue was supposed to favour an inverse substrate orientation. The prepared Arg403-->Leu mutant of the rabbit 15-lipoxygenase was found to be a less effective catalyst of linoleic acid oxygenation. However, the oxygenation rate of omega-hydroxyarachidonic acid was similar when the wild-type and mutant enzyme were compared, and the patterns of oxygenation products were identical for both enzyme species. These data suggest that introduction of a polar, or even charged residue, at the omega-terminus of substrate fatty acids in connection with mutation of Arg403 may not alter substrate alignment at the active site of 15-lipoxygenases. PMID:9820810

Low abdominal NIRS values and elevated plasma intestinal fatty acid-binding protein in a premature piglet model of necrotizing enterocolitis

USDA-ARS?s Scientific Manuscript database

To identify early markers of necrotizing enterocolitis (NEC), we hypothesized that continuous abdominal near-infrared spectroscopy (A-NIRS) measurement of splanchnic tissue oxygen saturation and intermittent plasma intestinal fatty-acid binding protein (pI-FABP) measured every 6 hours can detect NEC...

Mechanism of the enhancement of the Bohr effect in mammalian hemoglobins by diphosphoglycerate.

PubMed

Riggs, A

1971-09-01

The number of protons released from several mammalian hemoglobins as a consequence of oxygenation is greater in the presence of low concentrations of 2,3-diphosphoglycerate than in its absence. A mechanism for this enhancement of proton release is proposed. The basis of this mechanism is that 2,3-diphosphoglycerate binds primarily between the protonated alpha-NH(2) terminal groups of the two beta chains in deoxyhemoglobin. This binding will shift the ionization equilibria in favor of the protonation of the deoxyhemoglobin. Partial release of 2,3-diphosphoglycerate upon oxygenation of the hemoglobin is then accompanied by a release of protons. The apparent enthalpy of diphosphoglycerate binding appears to be close to zero. The previously reported temperature dependence appears to be due entirely to the associated protonation reaction. If only a single diphosphoglycerate binding site is assumed, the intrinsic association constant is estimated to be 3.9 x 10(5) M(-1) for deoxyhemoglobin and 1.05 x 10(4) M(-1) for oxyhemoglobin at 20 degrees C in 0.1 M NaCl.

Mechanism of the Enhancement of the Bohr Effect in Mammalian Hemoglobins by Diphosphoglycerate

PubMed Central

Riggs, Austen

1971-01-01

The number of protons released from several mammalian hemoglobins as a consequence of oxygenation is greater in the presence of low concentrations of 2,3-diphosphoglycerate than in its absence. A mechanism for this enhancement of proton release is proposed. The basis of this mechanism is that 2,3-diphosphoglycerate binds primarily between the protonated α-NH2 terminal groups of the two β chains in deoxyhemoglobin. This binding will shift the ionization equilibria in favor of the protonation of the deoxyhemoglobin. Partial release of 2,3-diphosphoglycerate upon oxygenation of the hemoglobin is then accompanied by a release of protons. The apparent enthalpy of diphosphoglycerate binding appears to be close to zero. The previously reported temperature dependence appears to be due entirely to the associated protonation reaction. If only a single diphosphoglycerate binding site is assumed, the intrinsic association constant is estimated to be 3.9 × 105 M-1 for deoxyhemoglobin and 1.05 × 104 M-1 for oxyhemoglobin at 20°C in 0.1 M NaCl. PMID:5289365

Roles of Neuroglobin Binding to Mitochondrial Complex III Subunit Cytochrome c1 in Oxygen-Glucose Deprivation-Induced Neurotoxicity in Primary Neurons.

PubMed

Yu, Zhanyang; Zhang, Yu; Liu, Ning; Yuan, Jing; Lin, Li; Zhuge, Qichuan; Xiao, Jian; Wang, Xiaoying

2016-07-01

Neuroglobin (Ngb) is a tissue globin specifically expressed in brain neurons. Recent studies by our laboratory and others have demonstrated that Ngb is protective against stroke and related neurological disorders, but the mechanisms remain poorly understood. We previously identified cytochrome c1 (Cyc1) as an Ngb-interacting molecule by yeast two-hybrid screening. Cyc1 is a subunit of mitochondria complex III, which is a component of mitochondrial respiratory chain and a major source of reactive oxygen species (ROS) production under both physiological and pathological conditions. In this study, we for the first time defined Ngb-Cyc1 binding, and investigated its roles in oxygen-glucose deprivation (OGD)/reoxygenation-induced neurotoxicity and ROS production in primary neurons. Immunocytochemistry and co-immunoprecipitation validated Ngb-Cyc1 binding, which was significantly increased by OGD and Ngb overexpression. We found 4 h OGD with/without 4 h reoxygenation significantly increased complex III activity, but this activity elevation was significantly attenuated in three groups of neurons: Ngb overexpression, specific complex III inhibitor stigmatellin, or stigmatellin plus Ngb overexpression, whereas there was no significant differences between these three groups, suggesting Ngb-Cyc1 binding may function in suppressing OGD-mediated complex III activity elevation. Importantly, these three groups of neurons also showed significant decreases in OGD-induced superoxide anion generation and neurotoxicity. These results suggest that Ngb can bind to mitochondrial complex III subunit Cyc1, leading to suppression of OGD-mediated complex III activity and subsequent ROS production elevation, and eventually reduction of OGD-induced neurotoxicity. This molecular signaling cascade may be at least part of the mechanisms of Ngb neuroprotection against OGD-induced neurotoxicity.

Determination of the Bridging Ligand in the Active Site of Tyrosinase.

PubMed

Zou, Congming; Huang, Wei; Zhao, Gaokun; Wan, Xiao; Hu, Xiaodong; Jin, Yan; Li, Junying; Liu, Junjun

2017-10-28

Tyrosinase is a type-3 copper enzyme that is widely distributed in plants, fungi, insects, and mammals. Developing high potent inhibitors against tyrosinase is of great interest in diverse fields including tobacco curing, food processing, bio-insecticides development, cosmetic development, and human healthcare-related research. In the crystal structure of Agaricus bisporus mushroom tyrosinase, there is an oxygen atom bridging the two copper ions in the active site. It is unclear whether the identity of this bridging oxygen is a water molecule or a hydroxide anion. In the present study, we theoretically determine the identity of this critical bridging oxygen by performing first-principles hybrid quantum mechanics/molecular mechanics/Poisson-Boltzmann-surface area (QM/MM-PBSA) calculations along with a thermodynamic cycle that aim to improve the accuracy. Our results show that the binding with water molecule is energy favored and the QM/MM-optimized structure is very close to the crystal structure, whereas the binding with hydroxide anions causes the increase of energy and significant structural changes of the active site, indicating that the identity of the bridging oxygen must be a water molecule rather than a hydroxide anion. The different binding behavior between water and hydroxide anions may explain why molecules with a carboxyl group or too many negative charges have lower inhibitory activity. In light of this, the design of high potent active inhibitors against tyrosinase should satisfy both the affinity to the copper ions and the charge neutrality of the entire molecule.

Proanthocyanidin-containing polyphenol extracts from fruits prevent the inhibitory effect of hydrogen sulfide on human colonocyte oxygen consumption.

PubMed

Andriamihaja, Mireille; Lan, Annaïg; Beaumont, Martin; Grauso, Marta; Gotteland, Martin; Pastene, Edgar; Cires, Maria Jose; Carrasco-Pozo, Catalina; Tomé, Daniel; Blachier, François

2018-06-01

Hydrogen sulfide (H 2 S), a metabolic end product synthesized by the microbiota from L-cysteine, has been shown to act at low micromolar concentration as a mineral oxidative substrate in colonocytes while acting as an inhibitor of oxygen consumption at higher luminal concentrations (65 µM and above). From the previous works showing that polyphenols can bind volatile sulfur compounds, we hypothesized that different dietary proanthocyanidin-containing polyphenol (PACs) plant extracts might modulate the inhibitory effect of H 2 S on colonocyte respiration. Using the model of human HT-29 Glc-/+ cell colonocytes, we show here that pre-incubation of 65 µM of the H 2 S donor NaHS with the different polyphenol extracts markedly reduced the inhibitory effect of NaHS on colonocyte oxygen consumption. Our studies on HT-29 Glc-/+ cell respiration performed in the absence or the presence of PACs reveal rapid binding of H 2 S with the sulfide-oxidizing unit and slower binding of H 2 S to the cytochrome c oxidase (complex IV of the respiratory chain). Despite acute inhibition of colonocyte respiration, no measurable effect of NaHS on paracellular permeability was recorded after 24 h treatment using the Caco-2 colonocyte monolayer model. The results are discussed in the context of the binding of excessive bacterial metabolites by unabsorbed dietary compounds and of the capacity of colonocytes to adapt to changing luminal environment.

On the nature of the {SO2-4}/{Ag(111) } and {SO2-4}/{Au(111) } surface bonding

NASA Astrophysics Data System (ADS)

Patrito, E. M.; Olivera, P. Paredes; Sellers, Harrell

1997-05-01

The nature of sulfate-Ag(111) and sulfate-Au(111) surface bonding has been investigated at the SCF + MP2 level of theory. Convergence of binding energy with cluster size is investigated and, unlike neutral adsorbates, large clusters are required in order to obtain reliable binding energies. In the most stable adsorption mode, sulfate binds to the surface via three oxygen atoms (C 3v symmetry) with a binding energy of 159.3 kcal/mol on Ag(111) and 143.9 kcal/mol on Au(111). The geometry of adsorbed sulfate was optimized at the SCF level. While the bond length between sulfur and the oxygens coordinated to the surface increases, the sulfur-uncoordinated oxygen bond length decreases. This weakening and strengthening of the bonds, respectively, is consistent with bond order conservation in adsorbates on metal surfaces. Although a charge transfer of 0.4 electrons towards the metal is observed, the adsorbate remains very much sulfate-like. The molecular orbital analysis indicates that there is also some charge back-donation towards unoccupied orbitals of sulfate. This results in an increased electron density around sulfur as revealed in the electron density difference maps. Analysis of the Laplacian of the charge density of free sulfate provides a suitable framework to understand the nature of the different charge transfer processes and allows us to establish some similarities with the CO- and SO 2-metal bondings.

H2O incorporation in the phosphorene/a-SiO2 interface: a first-principles study

NASA Astrophysics Data System (ADS)

Scopel, Wanderlã L.; Souza, Everson S.; Miwa, R. H.

2017-02-01

Based on first-principles calculations, we investigate (i) the energetic stability and electronic properties of single-layer phosphorene (SLP) adsorbed on an amorphous SiO2 surface (SLP/a-SiO2), and (ii) the further incorporation of water molecules at the phosphorene/a-SiO2 interface. In (i), we find that the phosphorene sheet binds to a-SiO2 through van der Waals interactions, even in the presence of oxygen vacancies on the surface. The SLP/a-SiO2 system presents a type-I band alignment, with the valence (conduction) band maximum (minimum) of the phosphorene lying within the energy gap of the a-SiO2 substrate. The structure and the surface-potential corrugations promote the formation of electron-rich and electron-poor regions on the phosphorene sheet and at the SLP/a-SiO2 interface. Such charge density puddles are strengthened by the presence of oxygen vacancies in a-SiO2. In (ii), because of the amorphous structure of the surface, we consider a number of plausible geometries for H2O embedded in the SLP/a-SiO2 interface. There is an energetic preference for the formation of hydroxyl (OH) groups on the a-SiO2 surface. Meanwhile, in the presence of oxygenated water or interstitial oxygen in the phosphorene sheet, we observe the formation of metastable OH bonded to the phosphorene, and the formation of energetically stable P-O-Si chemical bonds at the SLP/a-SiO2 interface. Further x-ray absorption spectra simulations are performed, which aim to provide additional structural/electronic information on the oxygen atoms forming hydroxyl groups or P-O-Si chemical bonds at the interface region.

H2O incorporation in the phosphorene/a-SiO2 interface: a first-principles study.

PubMed

Scopel, Wanderlã L; Souza, Everson S; Miwa, R H

2017-02-22

Based on first-principles calculations, we investigate (i) the energetic stability and electronic properties of single-layer phosphorene (SLP) adsorbed on an amorphous SiO 2 surface (SLP/a-SiO 2 ), and (ii) the further incorporation of water molecules at the phosphorene/a-SiO 2 interface. In (i), we find that the phosphorene sheet binds to a-SiO 2 through van der Waals interactions, even in the presence of oxygen vacancies on the surface. The SLP/a-SiO 2 system presents a type-I band alignment, with the valence (conduction) band maximum (minimum) of the phosphorene lying within the energy gap of the a-SiO 2 substrate. The structure and the surface-potential corrugations promote the formation of electron-rich and electron-poor regions on the phosphorene sheet and at the SLP/a-SiO 2 interface. Such charge density puddles are strengthened by the presence of oxygen vacancies in a-SiO 2 . In (ii), because of the amorphous structure of the surface, we consider a number of plausible geometries for H 2 O embedded in the SLP/a-SiO 2 interface. There is an energetic preference for the formation of hydroxyl (OH) groups on the a-SiO 2 surface. Meanwhile, in the presence of oxygenated water or interstitial oxygen in the phosphorene sheet, we observe the formation of metastable OH bonded to the phosphorene, and the formation of energetically stable P-O-Si chemical bonds at the SLP/a-SiO 2 interface. Further x-ray absorption spectra simulations are performed, which aim to provide additional structural/electronic information on the oxygen atoms forming hydroxyl groups or P-O-Si chemical bonds at the interface region.

Densification and Electrical Properties of Zinc Oxide Varistors Microwave-Sintered Under Different Oxygen Partial Pressures

NASA Astrophysics Data System (ADS)

Lin, Cong; Wang, Bo; Xu, Zheng; Peng, Hu

2012-11-01

ZnO varistors were prepared by microwave sintering under different oxygen partial pressures. The temperature profile and the densification behavior in different atmospheres were investigated. It was found that the density of ZnO varistors during sintering was the key factor affecting the absorption of microwave energy. The electrical properties, including the nonlinear properties and capacitance-voltage ( C- V) characteristics, were also carefully studied. The results showed that the oxygen partial pressure has significant effects on the electrical properties of ZnO varistors by changing the concentration of defects through a series of reactions involving oxygen during sintering.

Rp-phosphorothioate modifications in RNase P RNA that interfere with tRNA binding.

PubMed Central

Hardt, W D; Warnecke, J M; Erdmann, V A; Hartmann, R K

1995-01-01

We have used Rp-phosphorothioate modifications and a binding interference assay to analyse the role of phosphate oxygens in tRNA recognition by Escherichia coli ribonuclease P (RNase P) RNA. Total (100%) Rp-phosphorothioate modification at A, C or G positions of RNase P RNA strongly impaired tRNA binding and pre-tRNA processing, while effects were less pronounced at U positions. Partially modified E. coli RNase P RNAs were separated into tRNA binding and non-binding fractions by gel retardation. Rp-phosphorothioate modifications that interfered with tRNA binding were found 5' of nucleotides A67, G68, U69, C70, C71, G72, A130, A132, A248, A249, G300, A317, A330, A352, C353 and C354. Manganese rescue at positions U69, C70, A130 and A132 identified, for the first time, sites of direct metal ion coordination in RNase P RNA. Most sites of interference are at strongly conserved nucleotides and nine reside within a long-range base-pairing interaction present in all known RNase P RNAs. In contrast to RNase P RNA, 100% Rp-phosphorothioate substitutions in tRNA showed only moderate effects on binding to RNase P RNAs from E. coli, Bacillus subtilis and Chromatium vinosum, suggesting that pro-Rp phosphate oxygens of mature tRNA contribute relatively little to the formation of the tRNA-RNase P RNA complex. Images PMID:7540978

Investigation of the photophysical and photochemical properties of peripherally tetra-substituted water-soluble zwitterionic and cationic zinc(ii) phthalocyanines.

PubMed

Çolak, Senem; Durmuş, Mahmut; Yıldız, Salih Zeki

2016-06-21

In this study, 4-{4-[N-((3-dimethylamino)propyl)amide]phenoxy}phthalonitrile () and its zinc(ii) phthalocyanine derivative () were synthesized for the first time. 4-(N-((3-Dimethylamino)propyl)amide)phenoxy substituted zinc(ii) phthalocyanine () was converted to its water-soluble sulfobetaine (), betaine () and N-oxide () containing zwitterionic and quaternized cationic () derivatives. All newly synthesized compounds () were characterized by the combination of UV-vis, FT-IR, (1)H NMR, mass spectroscopy techniques and elemental analysis. The photophysical (fluorescence quantum yields and lifetimes) and photochemical (singlet oxygen quantum yields) properties were investigated in DMSO for all the synthesized zinc(ii) phthalocyanines () and in both DMSO and aqueous solutions for zwitterionic and cationic phthalocyanines () for the specification of their capability as photosensitizers in photodynamic therapy (PDT). The binding behavior of water soluble phthalocyanines () to the bovine serum albumin protein was also examined for the determination of their transportation ability in the blood stream.

Laccase/HBT and laccase-CBM/HBT treatment of softwood kraft pulp: impact on pulp bleachability and physical properties.

PubMed

Ravalason, Holy; Bertaud, Frédérique; Herpoël-Gimbert, Isabelle; Meyer, Valérie; Ruel, Katia; Joseleau, Jean-Paul; Grisel, Sacha; Olivé, Caroline; Sigoillot, Jean-Claude; Petit-Conil, Michel

2012-10-01

Pycnoporus cinnabarinus laccase and a chimeric laccase-CBM were applied in softwood kraft pulp biobleaching in the presence of 1-hydroxybenzotriazole (HBT). The presence of CBM could enhance the laccase biobleaching potential as a decrease in the enzymatic charge and chlorine dioxide consumption, as well as an increase in pulp brightness were observed. Laccase/HBT treatment could be improved by increasing oxygen pressure from 1 to 3bar and pulp consistency from 5% to 10%. Conversely, under the same conditions, no improvement of laccase-CBM/HBT treatment was observed, indicating a different behavior of both systems. However, laccase-CBM/HBT treatment led to a better preservation of pulp properties. This effect was probably due to fiber surface modifications involving the action of the CBM. Transmission electron microscopy examination of pulp fibers indicated a retention of laccase-CBM inside the pulp fibers due to CBM binding and an increased external microfibrillation of the fibers due to enzymatic treatments. Copyright © 2012 Elsevier Ltd. All rights reserved.

Dopant-Modulating Mechanism of Lithium Adsorption and Diffusion at the Graphene /Li2S Interface

NASA Astrophysics Data System (ADS)

Guo, Lichao; Li, Jiajun; Wang, Huayu; Zhao, Naiqin; Shi, Chunsheng; Ma, Liying; He, Chunnian; He, Fang; Liu, Enzuo

2018-02-01

Graphene modification is one of the most effective routes to enhance the electrochemical properties of the transition-metal sulfide anode for Li-ion batteries and the Li2S cathode for Li-S batteries. Boron, nitrogen, oxygen, phosphorus, and sulfur doping greatly affect the electrochemical properties of Li2S /graphene . Here, we investigate the interfacial binding energy, lithium adsorption energy, interface diffusion barrier, and electronic structure by first-principles calculations to unveil the diverse effects of different dopants during interfacial lithiation reactions. The interfacial lithium storage follows the pseudocapacitylike mechanism with intercalation character. Two different mechanisms are revealed to enhance the interfacial lithium adsorption and diffusion, which are the electron-deficiency host doping and the vacancylike structure evolutions with bond breaking. The synergistic effect between different dopants with diverse doping effects is also proposed. The results give a theoretical basis for the materials design with doped graphene as advanced materials modification for energy storage.

Introduction of a new regulatory mechanism into human hemoglobin.

PubMed

Fronticelli, Clara; Bobofchak, Kevin M; Karavitis, Michael; Sanna, Maria Teresa; Brinigar, William S

2002-07-10

Previous studies on bovine hemoglobin (HbBv) have suggested amino acid substitutions, which might introduce into human hemoglobin (HbA) functional characteristics of HbBv, namely a low intrinsic oxygen affinity regulated by Cl(-). Accordingly, we have constructed and characterized a multiple mutant, PB5, [beta(V1M + H2 Delta + T4I + P5A + A76K)] replacing four amino acid residues of HbA with those present at structurally analogous positions in HbBv, plus an additional substitution, beta T4I, which does not occur in either HbBv or HbA. This 'pseudobovine' hemoglobin has oxygen binding properties very similar to those of HbBv: the P(50) of HbA, PB5 and HbBv in the absence of Cl(-) are 1.6, 4.6 and 4.8 torr, respectively, and in 100 mM Cl(-) are 3.7, 10.5 and 12 torr, respectively. Moreover, PB5 has 3-fold slower autoxidation rate compared to HbA and HbBv. These are desirable characteristics for a human hemoglobin to be considered for use as a clinical artificial oxygen carrier. Although the functional properties of PB5 and HbBv are similar, van't Hoff plots indicate that the two hemoglobins interact differently with water, suggesting that factors regulating the R to T equilibrium are not the same in the two proteins. A further indication that PB5 is not a functional mimic of HbBv derives from PB5(control), a human hemoglobin with the same substitutions as PB5, except the beta T4I replacement. PB5(control) has a high oxygen affinity (P(50)=2.3 torr) in the absence of Cl(-), but retains the Cl(-) effect of PB5. The Cl(-) regulation of oxygen affinity in PB5 involves lysine residues at beta 8 and beta 76. PB4, which has the same substitutions as PB5 except beta A76K, and PB6, which has all the substitutions of PB5 plus beta K8Q, both have a low intrinsic oxygen affinity, like HbBv and PB5, but exhibit a decreased sensitivity to Cl(-). Since HbBv has lysine residues at both beta 8 and beta 76, these results imply that Cl(-) regulation in HbBv likewise involves these two residues. The mechanism responsible for the low intrinsic oxygen affinity of HbBv remains unclear. It is suggested that residues peculiar to HbBv at the alpha(1)beta(1) interface may play a role.

Involvement of DPP-IV catalytic residues in enzyme–saxagliptin complex formation

PubMed Central

Metzler, William J.; Yanchunas, Joseph; Weigelt, Carolyn; Kish, Kevin; Klei, Herbert E.; Xie, Dianlin; Zhang, Yaqun; Corbett, Martin; Tamura, James K.; He, Bin; Hamann, Lawrence G.; Kirby, Mark S.; Marcinkeviciene, Jovita

2008-01-01

The inhibition of DPP-IV by saxagliptin has been proposed to occur through formation of a covalent but reversible complex. To evaluate further the mechanism of inhibition, we determined the X-ray crystal structure of the DPP-IV:saxagliptin complex. This structure reveals covalent attachment between S630 and the inhibitor nitrile carbon (C–O distance <1.3 Å). To investigate whether this serine addition is assisted by the catalytic His-Asp dyad, we generated two mutants of DPP-IV, S630A and H740Q, and assayed them for ability to bind inhibitor. DPP-IVH740Q bound saxagliptin with an ∼1000-fold reduction in affinity relative to DPP-IVWT, while DPP-IVS630A showed no evidence for binding inhibitor. An analog of saxagliptin lacking the nitrile group showed unchanged binding properties to the both mutant proteins, highlighting the essential role S630 and H740 play in covalent bond formation between S630 and saxagliptin. Further supporting mechanism-based inhibition by saxagliptin, NMR spectra of enzyme–saxagliptin complexes revealed the presence of three downfield resonances with low fractionation factors characteristic of short and strong hydrogen bonds (SSHB). Comparison of the NMR spectra of various wild-type and mutant DPP-IV:ligand complexes enabled assignment of a resonance at ∼14 ppm to H740. Two additional DPP-IV mutants, Y547F and Y547Q, generated to probe potential stabilization of the enzyme–inhibitor complex by this residue, did not show any differences in inhibitor binding either by ITC or NMR. Together with the previously published enzymatic data, the structural and binding data presented here strongly support a histidine-assisted covalent bond formation between S630 hydroxyl oxygen and the nitrile group of saxagliptin. PMID:18227430

Involvement of DPP-IV Catalytic Residues in Enzyme-Saxagliptin Complex Formation

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

Metzler,W.; Yanchunas, J.; Weigelt, C.

The inhibition of DPP-IV by saxagliptin has been proposed to occur through formation of a covalent but reversible complex. To evaluate further the mechanism of inhibition, we determined the X-ray crystal structure of the DPP-IV:saxagliptin complex. This structure reveals covalent attachment between S630 and the inhibitor nitrile carbon (C-O distance <1.3 Angstroms). To investigate whether this serine addition is assisted by the catalytic His-Asp dyad, we generated two mutants of DPP-IV, S630A and H740Q, and assayed them for ability to bind inhibitor. DPP-IVH740Q bound saxagliptin with an {approx}1000-fold reduction in affinity relative to DPP-IVWT, while DPP-IVS630A showed no evidence formore » binding inhibitor. An analog of saxagliptin lacking the nitrile group showed unchanged binding properties to the both mutant proteins, highlighting the essential role S630 and H740 play in covalent bond formation between S630 and saxagliptin. Further supporting mechanism-based inhibition by saxagliptin, NMR spectra of enzyme-saxagliptin complexes revealed the presence of three downfield resonances with low fractionation factors characteristic of short and strong hydrogen bonds (SSHB). Comparison of the NMR spectra of various wild-type and mutant DPP-IV:ligand complexes enabled assignment of a resonance at {approx}14 ppm to H740. Two additional DPP-IV mutants, Y547F and Y547Q, generated to probe potential stabilization of the enzyme-inhibitor complex by this residue, did not show any differences in inhibitor binding either by ITC or NMR. Together with the previously published enzymatic data, the structural and binding data presented here strongly support a histidine-assisted covalent bond formation between S630 hydroxyl oxygen and the nitrile group of saxagliptin.« less

A Comparative Study of the Application of Fluorescence Excitation-Emission Matrices Combined with Parallel Factor Analysis and Nonnegative Matrix Factorization in the Analysis of Zn Complexation by Humic Acids

PubMed Central

Boguta, Patrycja; Pieczywek, Piotr M.; Sokołowska, Zofia

2016-01-01

The main aim of this study was the application of excitation-emission fluorescence matrices (EEMs) combined with two decomposition methods: parallel factor analysis (PARAFAC) and nonnegative matrix factorization (NMF) to study the interaction mechanisms between humic acids (HAs) and Zn(II) over a wide concentration range (0–50 mg·dm−3). The influence of HA properties on Zn(II) complexation was also investigated. Stability constants, quenching degree and complexation capacity were estimated for binding sites found in raw EEM, EEM-PARAFAC and EEM-NMF data using mathematical models. A combination of EEM fluorescence analysis with one of the proposed decomposition methods enabled separation of overlapping binding sites and yielded more accurate calculations of the binding parameters. PARAFAC and NMF processing allowed finding binding sites invisible in a few raw EEM datasets as well as finding totally new maxima attributed to structures of the lowest humification. Decomposed data showed an increase in Zn complexation with an increase in humification, aromaticity and molecular weight of HAs. EEM-PARAFAC analysis also revealed that the most stable compounds were formed by structures containing the highest amounts of nitrogen. The content of oxygen-functional groups did not influence the binding parameters, mainly due to fact of higher competition of metal cation with protons. EEM spectra coupled with NMF and especially PARAFAC processing gave more adequate assessments of interactions as compared to raw EEM data and should be especially recommended for modeling of complexation processes where the fluorescence intensities (FI) changes are weak or where the processes are interfered with by the presence of other fluorophores. PMID:27782078

Oxidative phosphorylation. The relation between the specific binding of trimethlytin and triethyltin to mitochondria and their effects on various mitochondrial functions

PubMed Central

Aldridge, W. N.; Street, B. W.

1971-01-01

1. A binding site (site 1) is present in mitochondria with affinity for trimethyltin and triethyltin adequate for a site to which they could be attached when the processes of energy conservation are inhibited. 2. The quantitative relationships between the binding of trimethyltin and triethyltin to site 1 and their effects on various mitochondrial functions have been examined. 3. ATP synthesis linked to the oxidation of pyruvate, succinate and intramitochondrial substrate, ATP synthesis and oxygen uptake (succinate or pyruvate as substrate) stimulated by uncoupling agents are all inhibited by trimethyltin and triethyltin; when inhibition is less than 50% the ratio (percentage inhibition)/(percentage of binding site 1 complexed) is approx. 10:1. 4. ATP synthesis linked to the oxidation of reduced cytochrome c (ascorbate+NNN′N′-tetramethyl-p-phenylenediamine), ATP hydrolysis and oxygen uptake in the presence of low concentrations of trimethyltin and triethyltin approach zero activity as the proportion of binding site 1 complexed approaches 100%. 5. Possible interpretations of these findings are discussed with reference to published arrangements for coupling of electron transport to ATP synthesis and also to our present knowledge of the chemical and biological specificity of trialkyltin compounds. PMID:5126473

Rapid comparison of protein binding site surfaces with Property Encoded Shape Distributions (PESD)

PubMed Central

Das, Sourav; Kokardekar, Arshad

2009-01-01

Patterns in shape and property distributions on the surface of binding sites are often conserved across functional proteins without significant conservation of the underlying amino-acid residues. To explore similarities of these sites from the viewpoint of a ligand, a sequence and fold-independent method was created to rapidly and accurately compare binding sites of proteins represented by property-mapped triangulated Gauss-Connolly surfaces. Within this paradigm, signatures for each binding site surface are produced by calculating their property-encoded shape distributions (PESD), a measure of the probability that a particular property will be at a specific distance to another on the molecular surface. Similarity between the signatures can then be treated as a measure of similarity between binding sites. As postulated, the PESD method rapidly detected high levels of similarity in binding site surface characteristics even in cases where there was very low similarity at the sequence level. In a screening experiment involving each member of the PDBBind 2005 dataset as a query against the rest of the set, PESD was able to retrieve a binding site with identical E.C. (Enzyme Commission) numbers as the top match in 79.5% of cases. The ability of the method in detecting similarity in binding sites with low sequence conservations were compared with state-of-the-art binding site comparison methods. PMID:19919089

Molecular mechanisms of the impact of smoke-oxidants.

PubMed

Milnerowicz, Halina; Ściskalska, Milena; Dul, Magdalena

2015-01-01

Tobacco smoke is a source of many xenobiotics and free radicals. Reactive oxygen species can affect the body both directly and indirectly, through the activation of both signalling pathways and transcription factors (NF-κB and AP-1). One of the most important signalling cascades which can affect the oxidants in smoke are mitogen-activated protein kinases (MAPK). The mechanism of MAPK pathways activation by reactive oxygen species depends on the stimulation of specific tyrosine kinases and protein tyrosine phosphatases inactivation. An activated MAP protein can initiate AP-1 signalling and interact with many other transcription factors. The components of tobacco smoke with oxidation-reduction properties can have an effect on NF-κB signalling. Binding of NF-κB and AP-1 with DNA is a complicated process, in which coactivators exhibiting internal histone acetyltransferase activity are involved. The balance between histone deacetylases and acetylases is important for the regulation of inflammatory response in the lungs. Tobacco smoke causes increased acetylase activity and decreased deacetylase activity in epithelial lung cells. The result is an increase in the activation of NF-κB and AP-1. Oxygen free radicals from tobacco smoke can change the redox status of cells, which can in turn induce the activation of transcription factors, chromatin remodelling and intensified genes transcription for inflammatory mediators. Copyright © 2015 Elsevier GmbH. All rights reserved.

Tailoring properties of reduced graphene oxide by oxygen plasma treatment

NASA Astrophysics Data System (ADS)

Kondratowicz, Izabela; Nadolska, Małgorzata; Şahin, Samet; Łapiński, Marcin; Prześniak-Welenc, Marta; Sawczak, Mirosław; Yu, Eileen H.; Sadowski, Wojciech; Żelechowska, Kamila

2018-05-01

We report an easily controllable, eco-friendly method for tailoring the properties of reduced graphene oxide (rGO) by means of oxygen plasma. The effect of oxygen plasma treatment time (1, 5 and 10 min) on the surface properties of rGO was evaluated. Physicochemical characterization using microscopic, spectroscopic and thermal techniques was performed. The results revealed that different oxygen-containing groups (e.g. carboxyl, hydroxyl) were introduced on the rGO surface enhancing its wettability. Furthermore, upon longer treatment time, other functionalities were created (e.g. quinones, lactones). Moreover, external surface of rGO was partially etched resulting in an increase of the material surface area and porosity. Finally, the oxygen plasma-treated rGO electrodes with bilirubin oxidase were tested for oxygen reduction reaction. The study showed that rGO treated for 10 min exhibited twofold higher current density than untreated rGO. The oxygen plasma treatment may improve the enzyme adsorption on rGO electrodes by introduction of oxygen moieties and increasing the porosity.

Effect of blood viscosity on oxygen transport in residual stenosed artery following angioplasty.

PubMed

Kwon, Ohwon; Krishnamoorthy, Mahesh; Cho, Young I; Sankovic, John M; Banerjee, Rupak K

2008-02-01

The effect of blood viscosity on oxygen transport in a stenosed coronary artery during the postangioplasty scenario is studied. In addition to incorporating varying blood viscosity using different hematocrit (Hct) concentrations, oxygen consumption by the avascular wall and its supply from vasa vasorum, nonlinear oxygen binding capacity of the hemoglobin, and basal to hyperemic flow rate changes are included in the calculation of oxygen transport in both the lumen and the avascular wall. The results of this study show that oxygen transport in the postangioplasty residual stenosed artery is affected by non-Newtonian shear-thinning property of the blood viscosity having variable Hct concentration. As Hct increases from 25% to 65%, the diminished recirculation zone for the increased Hct causes the commencement of pO(2) decrease to shift radially outward by approximately 20% from the center of the artery for the basal flow, but by approximately 10% for the hyperemic flow at the end of the diverging section. Oxygen concentration increases from a minimum value at the core of the recirculation zone to over 90 mm Hg before the lumen-wall interface at the diverging section for the hyperemic flow, which is attributed to increased shear rate and thinner lumen boundary layer for the hyperemic flow, and below 90 mm Hg for the basal flow. As Hct increases from 25% to 65%, the average of pO(2,min) beyond the diverging section drops by approximately 25% for the basal flow, whereas it increases by approximately 15% for the hyperemic flow. Thus, current results with the moderate stenosed artery indicate that reducing Hct might be favorable in terms of increasing O(2) flux and pO(2,min), in the medial region of the wall for the basal flow, while higher Hct is advantageous for the hyperemic flow beyond the diverging section. The results of this study not only provide significant details of oxygen transport under varying pathophysiologic blood conditions such as unusually high blood viscosity and flow rate, but might also be extended to offer implications for drug therapy related to blood-thinning medication and for blood transfusion and hemorrhage.

dsRNA binding properties of RDE-4 and TRBP reflect their distinct roles in RNAi.

PubMed

Parker, Greg S; Maity, Tuhin Subhra; Bass, Brenda L

2008-12-26

Double-stranded RNA (dsRNA)-binding proteins facilitate Dicer functions in RNA interference. Caenorhabditis elegans RDE-4 facilitates cleavage of long dsRNA to small interfering RNA (siRNA), while human trans-activation response RNA-binding protein (TRBP) functions downstream to pass siRNA to the RNA-induced silencing complex. We show that these distinct in vivo roles are reflected in in vitro binding properties. RDE-4 preferentially binds long dsRNA, while TRBP binds siRNA with an affinity that is independent of dsRNA length. These properties are mechanistically based on the fact that RDE-4 binds cooperatively, via contributions from multiple domains, while TRBP binds noncooperatively. Our studies offer a paradigm for how dsRNA-binding proteins, which are not sequence specific, discern dsRNA length. Additionally, analyses of the ability of RDE-4 deletion constructs and RDE-4/TRBP chimeras to reconstitute Dicer activity suggest RDE-4 promotes activity using its dsRNA-binding motif 2 to bind dsRNA, its linker region to interact with Dicer, and its C-terminus for Dicer activation.

Structural insight into the substrate- and dioxygen-binding manner in the catalytic cycle of rieske nonheme iron oxygenase system, carbazole 1,9a-dioxygenase.

PubMed

Ashikawa, Yuji; Fujimoto, Zui; Usami, Yusuke; Inoue, Kengo; Noguchi, Haruko; Yamane, Hisakazu; Nojiri, Hideaki

2012-06-24

Dihydroxylation of tandemly linked aromatic carbons in a cis-configuration, catalyzed by multicomponent oxygenase systems known as Rieske nonheme iron oxygenase systems (ROs), often constitute the initial step of aerobic degradation pathways for various aromatic compounds. Because such RO reactions inherently govern whether downstream degradation processes occur, novel oxygenation mechanisms involving oxygenase components of ROs (RO-Os) is of great interest. Despite substantial progress in structural and physicochemical analyses, no consensus exists on the chemical steps in the catalytic cycles of ROs. Thus, determining whether conformational changes at the active site of RO-O occur by substrate and/or oxygen binding is important. Carbazole 1,9a-dioxygenase (CARDO), a RO member consists of catalytic terminal oxygenase (CARDO-O), ferredoxin (CARDO-F), and ferredoxin reductase. We have succeeded in determining the crystal structures of oxidized CARDO-O, oxidized CARDO-F, and both oxidized and reduced forms of the CARDO-O: CARDO-F binary complex. In the present study, we determined the crystal structures of the reduced carbazole (CAR)-bound, dioxygen-bound, and both CAR- and dioxygen-bound CARDO-O: CARDO-F binary complex structures at 1.95, 1.85, and 2.00 Å resolution. These structures revealed the conformational changes that occur in the catalytic cycle. Structural comparison between complex structures in each step of the catalytic mechanism provides several implications, such as the order of substrate and dioxygen bindings, the iron-dioxygen species likely being Fe(III)-(hydro)peroxo, and the creation of room for dioxygen binding and the promotion of dioxygen binding in desirable fashion by preceding substrate binding. The RO catalytic mechanism is proposed as follows: When the Rieske cluster is reduced, substrate binding induces several conformational changes (e.g., movements of the nonheme iron and the ligand residue) that create room for oxygen binding. Dioxygen bound in a side-on fashion onto nonheme iron is activated by reduction to the peroxo state [Fe(III)-(hydro)peroxo]. This state may react directly with the bound substrate, or O-O bond cleavage may occur to generate Fe(V)-oxo-hydroxo species prior to the reaction. After producing a cis-dihydrodiol, the product is released by reducing the nonheme iron. This proposed scheme describes the catalytic cycle of ROs and provides important information for a better understanding of the mechanism.

Enzymatic function of loop movement in enolase: preparation and some properties of H159N, H159A, H159F, and N207A enolases.

PubMed

Brewer, John M; Glover, Claiborne V C; Holland, Michael J; Lebioda, Lukasz

2003-05-01

The hypothesis that His159 in yeast enolase moves on a polypeptide loop to protonate the phosphoryl of 2-phosphoglycerate to initiate its conversion to phosphoenolpyruvate was tested by preparing H159N, H159A, and H159F enolases. These have 0.07%-0.25% of the native activity under standard assay conditions and the pH dependence of maximum velocities of H159A and H159N mutants is markedly altered. Activation by Mg2+ is biphasic, with the smaller Mg2+ activation constant closer to that of the "catalytic" Mg2+ binding site of native enolase and the larger in the mM range in which native enolase is inhibited. A third Mg2+ may bind to the phosphoryl, functionally replacing proton donation by His159. N207A enolase lacks an intersubunit interaction that stabilizes the closed loop(s) conformation when 2-phosphoglycerate binds. It has 21% of the native activity, also exhibits biphasic Mg2+ activation, and its reaction with the aldehyde analogue of the substrate is more strongly inhibited than is its normal enzymatic reaction. Polypeptide loop(s) closure may keep a proton from His159 interacting with the substrate phosphoryl oxygen long enough to stabilize a carbanion intermediate.

Kinetic bottlenecks to chemical exchange rates for deep-sea animals - Part 1: Oxygen

NASA Astrophysics Data System (ADS)

Hofmann, A. F.; Peltzer, E. T.; Brewer, P. G.

2012-10-01

Ocean warming will reduce dissolved oxygen concentrations which can pose challenges to marine life. Oxygen limits are traditionally reported simply as a static concentration thresholds with no temperature, pressure or flow rate dependency. Here we treat the oceanic oxygen supply potential for heterotrophic consumption as a dynamic molecular exchange problem analogous to familiar gas exchange processes at the sea surface. A combination of the purely physico-chemical oceanic properties temperature, hydrostatic pressure, and oxygen concentration defines the ability of the ocean to supply oxygen to any given animal. This general oceanic oxygen supply potential is modulated by animal specific properties such as the diffusive boundary layer thickness to define and limit maximal oxygen supply rates. Here we combine all these properties into formal, mechanistic equations defining novel oceanic properties that subsume various relevant classical oceanographic parameters to better visualize, map, comprehend, and predict the impact of ocean deoxygenation on aerobic life. By explicitly including temperature and hydrostatic pressure into our quantities, various ocean regions ranging from the cold deep-sea to warm, coastal seas can be compared. We define purely physico-chemical quantities to describe the oceanic oxygen supply potential, but also quantities that contain organism-specific properties which in a most generalized way describe general concepts and dependencies. We apply these novel quantities to example oceanic profiles around the world and find that temperature and pressure dependencies of diffusion and partial pressure create zones of greatest physical constriction on oxygen supply typically at around 1000 m depth, which coincides with oxygen concentration minimum zones. In these zones, which comprise the bulk of the world ocean, ocean warming and deoxygenation have a clear negative effect for aerobic life. In some shallow and warm waters the enhanced diffusion and higher partial pressure due to higher temperatures might slightly overcompensate for oxygen concentration decreases due to decreases in solubility.

Quantum mechanical calculations suggest that lytic polysaccharide monooxygenases use a copper-oxyl, oxygen-rebound mechanism

PubMed Central

Kim, Seonah; Ståhlberg, Jerry; Sandgren, Mats; Paton, Robert S.; Beckham, Gregg T.

2014-01-01

Lytic polysaccharide monooxygenases (LPMOs) exhibit a mononuclear copper-containing active site and use dioxygen and a reducing agent to oxidatively cleave glycosidic linkages in polysaccharides. LPMOs represent a unique paradigm in carbohydrate turnover and exhibit synergy with hydrolytic enzymes in biomass depolymerization. To date, several features of copper binding to LPMOs have been elucidated, but the identity of the reactive oxygen species and the key steps in the oxidative mechanism have not been elucidated. Here, density functional theory calculations are used with an enzyme active site model to identify the reactive oxygen species and compare two hypothesized reaction pathways in LPMOs for hydrogen abstraction and polysaccharide hydroxylation; namely, a mechanism that employs a η1-superoxo intermediate, which abstracts a substrate hydrogen and a hydroperoxo species is responsible for substrate hydroxylation, and a mechanism wherein a copper-oxyl radical abstracts a hydrogen and subsequently hydroxylates the substrate via an oxygen-rebound mechanism. The results predict that oxygen binds end-on (η1) to copper, and that a copper-oxyl–mediated, oxygen-rebound mechanism is energetically preferred. The N-terminal histidine methylation is also examined, which is thought to modify the structure and reactivity of the enzyme. Density functional theory calculations suggest that this posttranslational modification has only a minor effect on the LPMO active site structure or reactivity for the examined steps. Overall, this study suggests the steps in the LPMO mechanism for oxidative cleavage of glycosidic bonds. PMID:24344312

Molecular Basis of the Bohr Effect in Arthropod Hemocyanin

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

Hirota, S.; Kawahara, T; Beltramini, M

2008-01-01

Flash photolysis and K-edge x-ray absorption spectroscopy (XAS) were used to investigate the functional and structural effects of pH on the oxygen affinity of three homologous arthropod hemocyanins (Hcs). Flash photolysis measurements showed that the well-characterized pH dependence of oxygen affinity (Bohr effect) is attributable to changes in the oxygen binding rate constant, kon, rather than changes in koff. In parallel, coordination geometry of copper in Hc was evaluated as a function of pH by XAS. It was found that the geometry of copper in the oxygenated protein is unchanged at all pH values investigated, while significant changes were observedmore » for the deoxygenated protein as a function of pH. The interpretation of these changes was based on previously described correlations between spectral lineshape and coordination geometry obtained for model compounds of known structure A pH-dependent change in the geometry of cuprous copper in the active site of deoxyHc, from pseudotetrahedral toward trigonal was assigned from the observed intensity dependence of the 1s ? 4pz transition in x-ray absorption near edge structure (XANES) spectra. The structural alteration correlated well with increase in oxygen affinity at alkaline pH determined in flash photolysis experiments. These results suggest that the oxygen binding rate in deoxyHc depends on the coordination geometry of Cu(I) and suggest a structural origin for the Bohr effect in arthropod Hcs.« less

Absorption process for producing oxygen and nitrogen and solution therefor

DOEpatents

Roman, Ian C.

1984-01-01

Process for the separation and purification of oxygen and nitrogen is disclosed which utilizes solutions of oxygen carriers to selectively absorb oxygen from a gaseous stream, leaving nitrogen as a byproduct. In the process, an oxygen carrier capable of reversibly binding molecular oxygen is dissolved in a solvent solution, which absorbs oxygen from an oxygen-containing gaseous feed stream such as atmospheric air and desorbs oxygen to a gaseous product stream. The feed stream is maintained at a sufficiently high oxygen pressure to keep the oxygen carrier in its oxygenated form during absorption, while the product stream is maintained at a sufficiently low oxygen pressure to keep the carrier in its deoxygenated form during desorption. In an alternate mode of operation, the carrier solution is maintained at a sufficiently low temperature and high oxygen pressure to keep the oxygen carrier in its oxygenated form during absorption, and at a sufficiently high temperature to keep the carrier in its deoxygenated form during desorption. Under such conditions, exceptionally high oxygen concentrations on the order of 95% to 99% are obtained, as well as a long carrier lifetime in excess of 3 months, making the process commercially feasible.

Absorption process for producing oxygen and nitrogen and solution therefor

DOEpatents

Roman, Ian C. [Wilmington, DE; Baker, Richard W. [Palo Alto, CA

1990-09-25

Process for the separation and purification of oxygen and nitrogen is disclosed which utilizes solutions of oxygen carriers to selectively absorb oxygen from a gaseous stream, leaving nitrogen as a byproduct. In the process, an oxygen carrier capable of reversibly binding molecular oxygen is dissolved in a solvent solution, which absorbs oxygen from an oxygen-containing gaseous feed stream such as atmospheric air and desorbs oxygen to a gaseous product stream. The feed stream is maintained at a sufficiently high oxygen pressure to keep the oxygen carrier in its oxygenated form during absorption, while the product stream is maintained at a sufficiently low oxygen pressure to keep the carrier in its deoxygenated form during desorption. In an alternate mode of operation, the carrier solution is maintained at a sufficiently low temperature and high oxygen pressure to keep the oxygen carrier in its oxygenated form during absorption, and at a sufficiently high temperature to keep the carrier in its deoxygenated form during desorption. Under such conditions, exceptionally high oxygen concentrations on the order of 95% to 99% are obtained, as well as a long carrier lifetime in excess of 3 months, making the process commercially feasible.

Absorption process for producing oxygen and nitrogen and solution therefor

DOEpatents

Roman, I.C.; Baker, R.W.

1990-09-25

Process for the separation and purification of oxygen and nitrogen is disclosed which utilizes solutions of oxygen carriers to selectively absorb oxygen from a gaseous stream, leaving nitrogen as a byproduct. In the process, an oxygen carrier capable of reversibly binding molecular oxygen is dissolved in a solvent solution, which absorbs oxygen from an oxygen-containing gaseous feed stream such as atmospheric air and desorbs oxygen to a gaseous product stream. The feed stream is maintained at a sufficiently high oxygen pressure to keep the oxygen carrier in its oxygenated form during absorption, while the product stream is maintained at a sufficiently low oxygen pressure to keep the carrier in its deoxygenated form during desorption. In an alternate mode of operation, the carrier solution is maintained at a sufficiently low temperature and high oxygen pressure to keep the oxygen carrier in its oxygenated form during absorption, and at a sufficiently high temperature to keep the carrier in its deoxygenated form during desorption. Under such conditions, exceptionally high oxygen concentrations on the order of 95% to 99% are obtained, as well as a long carrier lifetime in excess of 3 months, making the process commercially feasible. 1 figure

Thermodynamic and NMR analyses of NADPH binding to lipocalin-type prostaglandin D synthase

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

Qin, Shubin; Shimamoto, Shigeru; Maruno, Takahiro

2015-12-04

Lipocalin-type prostaglandin D synthase (L-PGDS) is one of the most abundant proteins in human cerebrospinal fluid (CSF) with dual functions as a prostaglandin D{sub 2} (PGD{sub 2}) synthase and a transporter of lipophilic ligands. Recent studies revealed that L-PGDS plays important roles in protecting against various neuronal diseases induced by reactive oxygen species (ROS). However, the molecular mechanisms of such protective actions of L-PGDS remain unknown. In this study, we conducted thermodynamic and nuclear magnetic resonance (NMR) analyses, and demonstrated that L-PGDS binds to nicotinamide coenzymes, including NADPH, NADP{sup +}, and NADH. Although a hydrophilic ligand is not common formore » L-PGDS, these ligands, especially NADPH showed specific interaction with L-PGDS at the upper pocket of its ligand-binding cavity with an unusually bifurcated shape. The binding affinity of L-PGDS for NADPH was comparable to that previously reported for NADPH oxidases and NADPH in vitro. These results suggested that L-PGDS potentially attenuates the activities of NADPH oxidases through interaction with NADPH. Given that NADPH is the substrate for NADPH oxidases that play key roles in neuronal cell death by generating excessive ROS, these results imply a novel linkage between L-PGDS and ROS. - Highlights: • Interactions of L-PGDS with nicotinamide coenzymes were studied by ITC and NMR. • The binding affinity of L-PGDS was strongest to NADPH among nicotinamide coenzymes. • NADPH binds to the upper part of L-PGDS ligand-binding cavity. • L-PGDS binds to both lipophilic and hydrophilic ligands. • This study implies a novel linkage between L-PGDS and reactive oxygen species.« less

Donor assists acceptor binding and catalysis of human α1,6-fucosyltransferase.

PubMed

Kötzler, Miriam P; Blank, Simon; Bantleon, Frank I; Wienke, Martin; Spillner, Edzard; Meyer, Bernd

2013-08-16

α1,6-Core-fucosyltransferase (FUT8) is a vital enzyme in mammalian physiological and pathophysiological processes such as tumorigenesis and progress of, among others, non-small cell lung cancer and colon carcinoma. It was also shown that therapeutic antibodies have a dramatically higher efficacy if the α1,6-fucosyl residue is absent. However, specific and potent inhibitors for FUT8 and related enzymes are lacking. Hence, it is crucial to elucidate the structural basis of acceptor binding and the catalytic mechanism. We present here the first structural model of FUT8 in complex with its acceptor and donor molecules. An unusually large acceptor, i.e., a hexasaccharide from the core of N-glycans, is required as minimal structure. Acceptor substrate binding of FUT8 is being dissected experimentally by STD NMR and SPR and theoretically by molecular dynamics simulations. The acceptor binding site forms an unusually large and shallow binding site. Binding of the acceptor to the enzyme is much faster and stronger if the donor is present. This is due to strong hydrogen bonding between O6 of the proximal N-acetylglucosamine and an oxygen atom of the β-phosphate of GDP-fucose. Therefore, we propose an ordered Bi Bi mechanism for FUT8 where the donor molecule binds first. No specific amino acid is present that could act as base during catalysis. Our results indicate a donor-assisted mechanism, where an oxygen of the β-phosphate deprotonates the acceptor. Knowledge of the mechanism of FUT8 is now being used for rational design of targeted inhibitors to address metastasis and prognosis of carcinomas.

Molecular controls of the oxygenation and redox reactions of hemoglobin.

PubMed

Bonaventura, Celia; Henkens, Robert; Alayash, Abdu I; Banerjee, Sambuddha; Crumbliss, Alvin L

2013-06-10

The broad classes of O(2)-binding proteins known as hemoglobins (Hbs) carry out oxygenation and redox functions that allow organisms with significantly different physiological demands to exist in a wide range of environments. This is aided by allosteric controls that modulate the protein's redox reactions as well as its O(2)-binding functions. The controls of Hb's redox reactions can differ appreciably from the molecular controls for Hb oxygenation and come into play in elegant mechanisms for dealing with nitrosative stress, in the malarial resistance conferred by sickle cell Hb, and in the as-yet unsuccessful designs for safe and effective blood substitutes. An important basic principle in consideration of Hb's redox reactions is the distinction between kinetic and thermodynamic reaction control. Clarification of these modes of control is critical to gaining an increased understanding of Hb-mediated oxidative processes and oxidative toxicity in vivo. This review addresses emerging concepts and some unresolved questions regarding the interplay between the oxygenation and oxidation reactions of structurally diverse Hbs, both within red blood cells and under acellular conditions. Developing methods that control Hb-mediated oxidative toxicity will be critical to the future development of Hb-based blood substitutes.

Numerical modeling of fluid and oxygen exchanges through microcirculation for the assessment of microcirculation alterations caused by type 2 diabetes.

PubMed

Tang, Yuanliang; He, Ying

2018-05-01

Type 2 diabetes mellitus (DM2) is frequently accompanied by microcirculation complications, including structural and functional alterations, which may have serious effects on substance exchanges between blood and interstitial tissue and the health of organs. In this paper, we aim to study the influence of microcirculation alterations in DM2 patients on fluid and oxygen exchanges through a model analysis. A fluid flow and oxygen transport model were developed by considering the interplay between blood in capillary network and interstitial tissue. The two regions were separately represented by 1D network model and 3D volume model, and the immersed boundary method (IBM) was adopted to solve fluid and mass transfer between these two regions. By using the model, the steady flow field and the distributions of oxygen in capillary network and surrounding tissue were firstly simulated. In the interstitial volume, fluid pressure and oxygen tension decreased with the increase of distance from the network; in the network, oxygen tension in blood plasma dropped from 100 mm Hg at the entrance to about 40 mm Hg at the exit. We further tested several structural and functional disorders related to diabetic pathological conditions. Simulated results show that the impaired connectivity of the network could result in poor robustness in maintaining blood flow and perfused surface; under high fluid permeability conditions of capillary walls, the pressure gradient was much larger around the capillary bed, and this alteration led to a saturation level of the interstitial pressure when lymphatic flow drainage can't work effectively; the variations in network connectivity and permeability of capillary wall also had unfavorable influence on oxygen distributions in interstitial tissue. In addition, when the oxygen releasing capacity of hemoglobin was confined by glycosylated hemoglobin (HbA1) in the case of diabetes, the plasma could not be complemented with adequate oxygen and thus the hypoxic tissue range will be extended. This study illustrates that when microcirculation disturbances, including the structure of capillary network, the wall osmosis property and the capacity of blood binding oxygen occur in DM2, some negative impacts are raised on microvascular hemodynamics and metabolism circumstance of interstitial tissue. Copyright © 2018 Elsevier Inc. All rights reserved.

Non-site-specific allosteric effect of oxygen on human hemoglobin under high oxygen partial pressure

PubMed Central

Takayanagi, Masayoshi; Kurisaki, Ikuo; Nagaoka, Masataka

2014-01-01

Protein allostery is essential for vital activities. Allosteric regulation of human hemoglobin (HbA) with two quaternary states T and R has been a paradigm of allosteric structural regulation of proteins. It is widely accepted that oxygen molecules (O2) act as a “site-specific” homotropic effector, or the successive O2 binding to the heme brings about the quaternary regulation. However, here we show that the site-specific allosteric effect is not necessarily only a unique mechanism of O2 allostery. Our simulation results revealed that the solution environment of high O2 partial pressure enhances the quaternary change from T to R without binding to the heme, suggesting an additional “non-site-specific” allosteric effect of O2. The latter effect should play a complementary role in the quaternary change by affecting the intersubunit contacts. This analysis must become a milestone in comprehensive understanding of the allosteric regulation of HbA from the molecular point of view. PMID:24710521

Non-site-specific allosteric effect of oxygen on human hemoglobin under high oxygen partial pressure.

PubMed

Takayanagi, Masayoshi; Kurisaki, Ikuo; Nagaoka, Masataka

2014-04-08

Protein allostery is essential for vital activities. Allosteric regulation of human hemoglobin (HbA) with two quaternary states T and R has been a paradigm of allosteric structural regulation of proteins. It is widely accepted that oxygen molecules (O2) act as a "site-specific" homotropic effector, or the successive O2 binding to the heme brings about the quaternary regulation. However, here we show that the site-specific allosteric effect is not necessarily only a unique mechanism of O2 allostery. Our simulation results revealed that the solution environment of high O2 partial pressure enhances the quaternary change from T to R without binding to the heme, suggesting an additional "non-site-specific" allosteric effect of O2. The latter effect should play a complementary role in the quaternary change by affecting the intersubunit contacts. This analysis must become a milestone in comprehensive understanding of the allosteric regulation of HbA from the molecular point of view.

Selective Sensitization of Zinc Finger Protein Oxidation by Reactive Oxygen Species through Arsenic Binding*

PubMed Central

Zhou, Xixi; Cooper, Karen L.; Sun, Xi; Liu, Ke J.; Hudson, Laurie G.

2015-01-01

Cysteine oxidation induced by reactive oxygen species (ROS) on redox-sensitive targets such as zinc finger proteins plays a critical role in redox signaling and subsequent biological outcomes. We found that arsenic exposure led to oxidation of certain zinc finger proteins based on arsenic interaction with zinc finger motifs. Analysis of zinc finger proteins isolated from arsenic-exposed cells and zinc finger peptides by mass spectrometry demonstrated preferential oxidation of C3H1 and C4 zinc finger configurations. C2H2 zinc finger proteins that do not bind arsenic were not oxidized by arsenic-generated ROS in the cellular environment. The findings suggest that selectivity in arsenic binding to zinc fingers with three or more cysteines defines the target proteins for oxidation by ROS. This represents a novel mechanism of selective protein oxidation and demonstrates how an environmental factor may sensitize certain target proteins for oxidation, thus altering the oxidation profile and redox regulation. PMID:26063799

Molecular origin of the selectivity differences between palladium and gold-palladium in benzyl alcohol oxidation: Different oxygen adsorption properties

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

Savara, Aditya Ashi; Chan-Thaw, Carine E.; Sutton, Jonathan E.

The same mechanism and microkinetic model used for benzyl alcohol oxidation over Pd/C was shown to apply to benzyl alcohol oxidation over AuPd/C. Almost all of the selectivity differences could be explained by a decrease in oxygen adsorption on AuPd. After isolating oxygen adsorption as being the origin of the selectivity differences, density functional theory was used to investigate the oxygen adsorption properties of a pure Pd surface, a pure Au surface, and an alloyed AuPd surface. Finally, the calculations showed that Au–Pd alloying decreased the oxygen adsorption properties relative to pure Pd, which explained the selectivity differences, consistent withmore » the microkinetic modeling.« less

Relationship of oxygen dose to angiogenesis induction in irradiated tissue

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

Marx, R.E.; Ehler, W.J.; Tayapongsak, P.

1990-11-01

This study was accomplished in an irradiated rabbit model to assess the angiogenic properties of normobaric oxygen and hyperbaric oxygen as compared with air-breathing controls. Results indicated that normobaric oxygen had no angiogenic properties above normal revascularization of irradiated tissue than did air-breathing controls (p = 0.89). Hyperbaric oxygen demonstrated an eight- to ninefold increased vascular density over both normobaric oxygen and air-breathing controls (p = 0.001). Irradiated tissue develops a hypovascular-hypocellular-hypoxic tissue that does not revascularize spontaneously. Results failed to demonstrate an angiogenic effect of normobaric oxygen. It is suggested that oxygen in this sense is a drug requiringmore » hyperbaric pressures to generate therapeutic effects on chronically hypovascular irradiated tissue.« less

The transition in hemoglobin proton-binding characteristics within the basal actinopterygian fishes.

PubMed

Regan, Matthew Daniel; Brauner, Colin J

2010-04-01

Carbon dioxide (CO(2)) transport in the blood of fishes is aided by the proton-binding properties of hemoglobin (Hb) through either a high-intrinsic buffer value and small oxylabile proton binding (Haldane effect), or a low buffer value and large Haldane effect. Primitive species, such as elasmobranchs and sarcopterygians have been shown to rely on the former, while derived species, such as teleosts rely on the latter. Both strategies are effective in the transport of CO(2) in the blood. However, there is a paucity of information on the nature of the transition between these two strategies that appears to occur within the intermediate group of fishes, the basal actinopterygians. The objective of the present study was to simultaneously assess the intrinsic Hb buffer values and Haldane effects of species within the basal actinopterygian lineage to characterize the transition in Hb-proton-binding strategy seen among the fishes. Expressed in order of most basal to most derived, the species investigated included American paddlefish (Polyodon spathula), white sturgeon (Acipenser transmontanus), spotted gar (Lepisosteus oculatus), alligator gar (Atractosteus spatula), bowfin (Amia calva), and mooneye (Hiodon tergisus). Hemolysates from these species were prepared and Hb titrations (under oxygenated and deoxygenated conditions) were performed in both the presence and absence of saturating levels of organic phosphates (GTP). The findings suggest that the nature of the Hb-proton-binding transition may have been punctuated rather than gradual, with the Hb buffer value decreasing and the Haldane effect increasing significantly in bowfin from fairly steady ancestral levels in the four more basal species. This change is coupled with the initial appearance of the choroid rete, as well as an increase in the magnitude and onset pH of the Root effect in bowfin, suggesting that the change in Hb-proton-binding strategy may be associated with the evolution of enhanced O(2) delivery to the eye and an in vivo operational Root effect.

[Role of erythrocyte cytoplasmic structures in changes in the affinity of haemoglobin for oxygen].

PubMed

Bryzgalova, N Iu; Brazhe, N A; Iusipovich, A U; Maksimov, G V; Rubin, A B

2009-01-01

Changes in the refractive index of the cytoplasm and the affinity of haemoporphyrin of erythrocyte haemoglobin to oxygen (pH, 2,3-diphosphoglycerate) have been investigated using laser interference microscopy and Raman spectroscopy. It has been established that a decrease in pH and an increase in the content of 2,3-diphosphoglycerate are accompanied by changes in both the form of the cell and the refractive index of the cytoplasm and the affinity of haemoporphyrin of hemoglobin to oxygen. It has been shown that as pH is reduced, the capacity of haemoporphyrin for binding oxygen decreases and as the concentration of 2,3-diphosphoglycerate is increased, the ability of haemoporphyrin for oxygen reabsorption increases.

The effect of 2,3-diphosphoglycerate on the oxygen dissociation curve of human haemoglobin.

PubMed Central

Goodford, P J; Norrington, F E; Paterson, R A; Wootton, R

1977-01-01

1. Oxygen dissociation curves for concentrated human haemoglobin solutions (1.6 mmol dm-3 in haem) have been measured by mixing known quantities of oxy- and deoxyhaemoglobin solutions and measuring the resulting partial pressure of oxygen with an oxygen electrode. 2. Observations in the presence of 2,3-diphosphoglycerate support previous conclusions derived from experiments at low haemoglobin concentrations, the validity of which has been questioned. 3. The two affinity state model of Monod, Wyman & Changeux (1965) does not fully describe the actions of 2,3-diphosphoglycerate and a model in which this allosteric effector not only binds preferentially to the T state but also lowers the oxygen affinity of this state gives an improved fit to the data. PMID:604451

Antioxidant properties of geroprotective peptides of the pineal gland.

PubMed

Kozina, L S; Arutjunyan, A V; Khavinson, V Kh

2007-01-01

It was shown that peptide preparations from the pineal gland (epithalamin and epitalon) possess antioxidant properties exceeding in some cases the effects of the well-known scavenger of reactive oxygen species (ROS), the melatonin, which is also produced by the pineal gland. The methods used in our experiments in old rats included determination of total antioxidant and antiradical activities, as well as those of antioxidant enzymes (superoxide dismutase=SOD, glutathione peroxidase, glutathione-S-transferase, etc.) in blood serum, liver and brain. It has been revealed that epithalamin (polipeptide preparation from bovine brain) and its active fragment, epitalon (Ala-Glu-Asp-Gly) along with their ability to stimulate melatonin production, have an antioxidant mechanism that is quite different from the action of melatonin. Epithalamin can be more beneficial than melatonin because the former not only produces direct antioxidant effects, but also is able to stimulate the expression of SOD, ceruloplasmin and other antioxidant enzymes. The possibility of oxidation chains by their interaction with different ROS by means of binding of transition metals (Fe(2+)) cannot also be excluded. Thus, the results of our experiments testify that the pineal gland peptides enhance the antioxidant defense system, which can contribute to their geroprotective properties.

Plasma membrane order and fluidity are diversely triggered by elicitors of plant defence

PubMed Central

Sandor, Roman; Der, Christophe; Grosjean, Kevin; Anca, Iulia; Noirot, Elodie; Leborgne-Castel, Nathalie; Lochman, Jan; Simon-Plas, Françoise; Gerbeau-Pissot, Patricia

2016-01-01

Although plants are exposed to a great number of pathogens, they usually defend themselves by triggering mechanisms able to limit disease development. Alongside signalling events common to most such incompatible interactions, modifications of plasma membrane (PM) physical properties could be new players in the cell transduction cascade. Different pairs of elicitors (cryptogein, oligogalacturonides, and flagellin) and plant cells (tobacco and Arabidopsis) were used to address the issue of possible modifications of plant PM biophysical properties induced by elicitors and their links to other events of the defence signalling cascade. We observed an increase of PM order whatever the elicitor/plant cell pair used, provided that a signalling cascade was induced. Such membrane modification is dependent on the NADPH oxidase-mediated reactive oxygen species production. Moreover, cryptogein, which is the sole elicitor able to trap sterols, is also the only one able to trigger an increase in PM fluidity. The use of cryptogein variants with altered sterol-binding properties confirms the strong correlation between sterol removal from the PM and PM fluidity enhancement. These results propose PM dynamics as a player in early signalling processes triggered by elicitors of plant defence. PMID:27604805

Structural and elastic properties and stability characteristics of oxygenated carbon nanotubes under physical adsorption of polymers

NASA Astrophysics Data System (ADS)

Ansari, R.; Ajori, S.; Rouhi, S.

2015-03-01

The importance of covalent and non-covalent functionalization approaches for modification the properties of carbon nanotubes is being more widely recognized. To this end, elastic properties and buckling behavior of oxygenated CNT with atomic oxygen and hydroxyl under physical adsorption of PE (Polyethylene) and PEO (Poly (ethylene oxide)) are determined through employing the molecular dynamics (MD) simulations. The results demonstrate that non-covalent bonding of polymer on the surface of oxygenated CNT causes reductions in the variations of critical buckling load and critical strain compared to oxygenated CNTs. Critical buckling load and critical strain of oxygenated CNT/polymer are higher than those of oxygenated CNT. Also, it is demonstrated that critical buckling load and critical strain values in the case of oxygenated CNT/polymer are independent of polymer type unlike the value of Young's modulus. It is shown that variations of Young's modulus decrease as PE adsorbed on the surface of oxygenated CNT. Moreover, the presence of oxygen atom on PEO chain leads to bigger variations of Young's modulus with weight percentage of chemisorbed component, i.e. atomic oxygen and hydroxyl. It is also demonstrated that Young's modulus reduces more considerably in the presence of PEO chain compared to PE one.

Probing the General Time Scale Question of Boronic Acid Binding with Sugars in Aqueous Solution at Physiological pH

PubMed Central

Ni, Nanting; Laughlin, Sarah; Wang, Yingji; Feng, You; Zheng, Yujun

2012-01-01

The boronic acid group is widely used in chemosensor design due to its ability to reversibly bind diol-containing compounds. The thermodynamic properties of the boronic acid-diol binding process have been investigated extensively. However, there are few studies of the kinetic properties of such binding processes. In this report, stopped-flow method was used for the first time to study the kinetic properties of the binding between three model arylboronic acids, 4-, 5-, and 8-isoquinolinylboronic acids, and various sugars. With all the boronic acid-diol pair sexamined, reactions were complete within seconds. The kon values with various sugars follow the order of D-fructose >D-tagatose>D-mannose >D-glucose. This trend tracks the thermodynamic binding affinities for these sugars and demonstrates that the “on” rate is the key factor determining the binding constant. PMID:22464680

Synthesis of iron oxide nanoparticles in Listeria innocua Dps (DNA-binding protein from starved cells): a study with the wild-type protein and a catalytic centre mutant.

PubMed

Ceci, Pierpaolo; Chiancone, Emilia; Kasyutich, Oksana; Bellapadrona, Giuliano; Castelli, Lisa; Fittipaldi, Maria; Gatteschi, Dante; Innocenti, Claudia; Sangregorio, Claudio

2010-01-11

A comparative analysis of the magnetic properties of iron oxide nanoparticles grown in the cavity of the DNA-binding protein from starved cells of the bacterium Listeria innocua, LiDps, and of its triple-mutant lacking the catalytic ferroxidase centre, LiDps-tm, is presented. TEM images and static and dynamic magnetic and electron magnetic resonance (EMR) measurements reveal that, under the applied preparation conditions, namely alkaline pH, high temperature (65 degrees C), exclusion of oxygen, and the presence of hydrogen peroxide, maghemite and/or magnetite nanoparticles with an average diameter of about 3 nm are mineralised inside the cavities of both LiDps and LiDps-tm. The magnetic nanoparticles (MNPs) thus formed show similar magnetic properties, with superparamagnetic behaviour above 4.5 K and a large magnetic anisotropy. Interestingly, in the EMR spectra an absorption at half-field is observed, which can be considered as a manifestation of the quantum behaviour of the MNPs. These results indicate that Dps proteins can be advantageously used for the production of nanomagnets at the interface between molecular clusters and traditional MNPs and that the presence of the ferroxidase centre, though increasing the efficiency of nanoparticle formation, does not affect the nature and fine structure of the MNPs. Importantly, the self-organisation of MNP-containing Dps on HRTEM grids suggests that Dps-enclosed MNPs can be deposited on surfaces in an ordered fashion.

[Effects of glycerol on the spectral properties of sodium caseinate].

PubMed

Li, Yan; Chang, Fen-fen; Gao, Huan-yuan; Cao, Qing; Jin, Li-e

2015-01-01

Although the immigration of water molecule, and diffusion and traversing of oxygen can be prevented by the edible film prepared through sodium caseinate, which plays a good protection role for the food, the strong hydrophilicity makes its watertightness and mechanical properties become inferior. Because the toughness and water resistance of SC films can be enhanced by glycerol (G) as an additive, it is necessary to elucidate the interaction between G and SC through the spectral characteristics such as fluorescence spectra, infrared spectra and UV spectra. The results show that the fluorescence intensity of SC decreases due to the addition of G. The binding constant obtained by the double logarithmic regression curve analysis is 1. 127 x 10(3) L . mol-1 and the number of binding sites reaches 1. 161. It indicates that the weak chemical bond is primary between G and SC molecules; From IR the absorption peaks of SC are almost the same before and after adding G. However, there is a certain difference among their absorption intensities. It reveals that the secondary structure of SC is affected, β folding length decreases, α helix, random coil structure, β angle structure increases, and the intermolecular hydrogen bond is strengthened; From UV the peptide bond structure of SC is not changed after the addition of G, but the polymer with larger molecular weight, which is formed by non-covalent bond, makes the peak intensity decrease. The research gives the mode of G and SC from the molecular level.

Heme biomolecule as redox mediator and oxygen shuttle for efficient charging of lithium-oxygen batteries

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

Ryu, Won-Hee; Gittleson, Forrest S.; Thomsen, Julianne M.

One of the greatest challenges with lithium-oxygen batteries involves identifying catalysts that facilitate the growth and evolution of cathode species on an oxygen electrode. Heterogeneous solid catalysts cannot adequately address the problematic overpotentials when the surfaces become passivated. But, there exists a class of biomolecules which have been designed by nature to guide complex solution-based oxygen chemistries. We show that the heme molecule, a common porphyrin cofactor in blood, can function as a soluble redox catalyst and oxygen shuttle for efficient oxygen evolution in non-aqueous Li-O 2 batteries. The heme’s oxygen binding capability facilitates battery recharge by accepting and releasingmore » dissociated oxygen species while benefiting charge transfer with the cathode. We reveal the chemical change of heme redox molecules where synergy exists with the electrolyte species. Our study brings focus to the rational design of solution-based catalysts and suggests a sustainable cross-link between biomolecules and advanced energy storage.« less

Optical Oxygen Micro- and Nanosensors for Plant Applications

PubMed Central

Ast, Cindy; Schmälzlin, Elmar; Löhmannsröben, Hans-Gerd; van Dongen, Joost T.

2012-01-01

Pioneered by Clark's microelectrode more than half a century ago, there has been substantial interest in developing new, miniaturized optical methods to detect molecular oxygen inside cells. While extensively used for animal tissue measurements, applications of intracellular optical oxygen biosensors are still scarce in plant science. A critical aspect is the strong autofluorescence of the green plant tissue that interferes with optical signals of commonly used oxygen probes. A recently developed dual-frequency phase modulation technique can overcome this limitation, offering new perspectives for plant research. This review gives an overview on the latest optical sensing techniques and methods based on phosphorescence quenching in diverse tissues and discusses the potential pitfalls for applications in plants. The most promising oxygen sensitive probes are reviewed plus different oxygen sensing structures ranging from micro-optodes to soluble nanoparticles. Moreover, the applicability of using heterologously expressed oxygen binding proteins and fluorescent proteins to determine changes in the cellular oxygen concentration are discussed as potential non-invasive cellular oxygen reporters. PMID:22969334

Heme biomolecule as redox mediator and oxygen shuttle for efficient charging of lithium-oxygen batteries

PubMed Central

Ryu, Won-Hee; Gittleson, Forrest S.; Thomsen, Julianne M.; Li, Jinyang; Schwab, Mark J.; Brudvig, Gary W.; Taylor, André D.

2016-01-01

One of the greatest challenges with lithium-oxygen batteries involves identifying catalysts that facilitate the growth and evolution of cathode species on an oxygen electrode. Heterogeneous solid catalysts cannot adequately address the problematic overpotentials when the surfaces become passivated. However, there exists a class of biomolecules which have been designed by nature to guide complex solution-based oxygen chemistries. Here, we show that the heme molecule, a common porphyrin cofactor in blood, can function as a soluble redox catalyst and oxygen shuttle for efficient oxygen evolution in non-aqueous Li-O2 batteries. The heme's oxygen binding capability facilitates battery recharge by accepting and releasing dissociated oxygen species while benefiting charge transfer with the cathode. We reveal the chemical change of heme redox molecules where synergy exists with the electrolyte species. This study brings focus to the rational design of solution-based catalysts and suggests a sustainable cross-link between biomolecules and advanced energy storage. PMID:27759005

Heme biomolecule as redox mediator and oxygen shuttle for efficient charging of lithium-oxygen batteries

DOE PAGES

Ryu, Won-Hee; Gittleson, Forrest S.; Thomsen, Julianne M.; ...

2016-10-19

One of the greatest challenges with lithium-oxygen batteries involves identifying catalysts that facilitate the growth and evolution of cathode species on an oxygen electrode. Heterogeneous solid catalysts cannot adequately address the problematic overpotentials when the surfaces become passivated. But, there exists a class of biomolecules which have been designed by nature to guide complex solution-based oxygen chemistries. We show that the heme molecule, a common porphyrin cofactor in blood, can function as a soluble redox catalyst and oxygen shuttle for efficient oxygen evolution in non-aqueous Li-O 2 batteries. The heme’s oxygen binding capability facilitates battery recharge by accepting and releasingmore » dissociated oxygen species while benefiting charge transfer with the cathode. We reveal the chemical change of heme redox molecules where synergy exists with the electrolyte species. Our study brings focus to the rational design of solution-based catalysts and suggests a sustainable cross-link between biomolecules and advanced energy storage.« less

Structure Evolution of Graphene Oxide during Thermally Driven Phase Transformation: Is the Oxygen Content Really Preserved?

PubMed Central

Sun, Pengzhan; Wang, Yanlei; Liu, He; Wang, Kunlin; Wu, Dehai; Xu, Zhiping; Zhu, Hongwei

2014-01-01

A mild annealing procedure was recently proposed for the scalable enhancement of graphene oxide (GO) properties with the oxygen content preserved, which was demonstrated to be attributed to the thermally driven phase separation. In this work, the structure evolution of GO with mild annealing is closely investigated. It reveals that in addition to phase separation, the transformation of oxygen functionalities also occurs, which leads to the slight reduction of GO membranes and furthers the enhancement of GO properties. These results are further supported by the density functional theory based calculations. The results also show that the amount of chemically bonded oxygen atoms on graphene decreases gradually and we propose that the strongly physisorbed oxygen species constrained in the holes and vacancies on GO lattice might be responsible for the preserved oxygen content during the mild annealing procedure. The present experimental results and calculations indicate that both the diffusion and transformation of oxygen functional groups might play important roles in the scalable enhancement of GO properties. PMID:25372142

Influence of oxygen impurity on electronic properties of carbon and boron nitride nanotubes: A comparative study

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

Singh, Ram Sevak, E-mail: singh915@gmail.com

2015-11-15

Influence of oxygen impurity on electronic properties of carbon and boron nitride nanotubes (CNTs and BNNTs) is systematically studied using first principle calculations based on density functional theory. Energy band structures and density of states of optimized zigzag (5, 0), armchair (3, 3), and chiral (4, 2) structures of CNT and BNNT are calculated. Oxygen doping in zigzag CNT exhibits a reduction in metallicity with opening of band gap in near-infrared region while metallicity is enhanced in armchair and chiral CNTs. Unlike oxygen-doped CNTs, energy bands are drastically modulated in oxygen-doped zigzag and armchair BNNTs, showing the nanotubes to havemore » metallic behaviour. Furthermore, oxygen impurity in chiral BNNT induces narrowing of band gap, indicating a gradual modification of electronic band structure. This study underscores the understanding of different electronic properties induced in CNTs and BNNTs under oxygen doping, and has potential in fabrication of various nanoelectronic devices.« less

Inflight resistance measurement on high-T(sub c) superconducting thin films exposed to orbital atomic oxygen on CONCAP-2 (STS-46)

NASA Technical Reports Server (NTRS)

Gregory, J. C.; Raiker, G. N.; Bijvoet, J. A.; Nerren, P. D.; Sutherland, W. T.; Mogro-Camperso, A.; Turner, L. G.; Kwok, Hoi; Raistrick, I. D.; Cross, J. B.

1995-01-01

In 1992, UAH (University of Alabama in Huntsville) conducted a unique experiment on STS-46 in which YBa2Cu3O7 (commonly known as '1-2-3' superconductor) high-T(c) superconducting thin film samples prepared at three different laboratories were exposed to 5 eV atomic oxygen in low Earth orbit on the ambient and 320 C hot plate during the first flight of the CONCAP-2 (Complex Autonomous Payload) experiment carrier. The resistance of the thin films was measured in flight during the atomic oxygen exposure and heating cycle. Superconducting properties were measured in the laboratory before and after the flight by the individual experimenters. Films with good superconducting properties, and which were exposed to the oxygen flux, survived the flight including those heated to 320 C (600 K) with properties essentially unchanged, while other samples which were heated but not exposed to oxygen were degraded. The properties of other flight controls held at ambient temperature appear unchanged and indistinguishable from those of ground controls, whether exposed to oxygen or not.

dsRNA binding properties of RDE-4 and TRBP reflect their distinct roles in RNAi

PubMed Central

Parker, Greg S.; Maity, Tuhin Subhra; Bass, Brenda L.

2008-01-01

SUMMARY dsRNA binding proteins (dsRBPs) facilitate Dicer functions in RNAi. C. elegans RDE-4 facilitates cleavage of long dsRNA to siRNA, while human TRBP functions downstream to pass siRNA to RISC. We show that these distinct in vivo roles are reflected in in vitro binding properties. RDE-4 preferentially binds long dsRNA, while TRBP binds siRNA with an affinity that is independent of dsRNA length. These properties are mechanistically based in the fact that RDE-4 binds cooperatively, via contributions from multiple domains, while TRBP binds non-cooperatively. Our studies offer a paradigm for how dsRBPs, which are not sequence-specific, discern dsRNA length. Additionally, analyses of the ability of RDE-4 deletion constructs and RDE-4/TRBP chimeras to reconstitute Dicer activity suggest RDE-4 promotes activity using its dsRBM2 to bind dsRNA, its linker region to interact with Dicer, and its C-terminus for Dicer activation. PMID:18948111

Docking modes of BB-3497 into the PDF active site--a comparison of the pure MM and QM/MM based docking strategies.

PubMed

Kumari, Tripti; Issar, Upasana; Kakkar, Rita

2014-01-01

Peptide deformylase (PDF) has emerged as an important antibacterial drug target. Considerable effort is being directed toward developing peptidic and non-peptidic inhibitors for this metalloprotein. In this work, the known peptidic inhibitor BB-3497 and its various ionization and tautomeric states are evaluated for their inhibition efficiency against PDF using a molecular mechanics (MM) approach as well as a mixed quantum mechanics/molecular mechanics (QM/MM) approach, with an aim to understand the interactions in the binding site. The evaluated Gibbs energies of binding with the mixed QM/MM approach are shown to have the best predictive power. The experimental pose is found to have the most negative Gibbs energy of binding, and also the smallest strain energy. A quantum mechanical evaluation of the active site reveals the requirement of strong chelation by the ligand with the metal ion. The investigated ligand chelates the metal ion through the two oxygens of its reverse hydroxamate moiety, particularly the N-O(-) oxygen, forming strong covalent bonds with the metal ion, which is penta-coordinated. In the uninhibited state, the metal ion is tetrahedrally coordinated, and hence chelation with the inhibitor is associated with an increase of the metal ion coordination. Thus, the strong binding of the ligand at the binding site is accounted for.

Oxygen sensation and social feeding mediated by a C. elegans guanylate cyclase homologue.

PubMed

Gray, Jesse M; Karow, David S; Lu, Hang; Chang, Andy J; Chang, Jennifer S; Ellis, Ronald E; Marletta, Michael A; Bargmann, Cornelia I

2004-07-15

Specialized oxygen-sensing cells in the nervous system generate rapid behavioural responses to oxygen. We show here that the nematode Caenorhabditis elegans exhibits a strong behavioural preference for 5-12% oxygen, avoiding higher and lower oxygen levels. 3',5'-cyclic guanosine monophosphate (cGMP) is a common second messenger in sensory transduction and is implicated in oxygen sensation. Avoidance of high oxygen levels by C. elegans requires the sensory cGMP-gated channel tax-2/tax-4 and a specific soluble guanylate cyclase homologue, gcy-35. The GCY-35 haem domain binds molecular oxygen, unlike the haem domains of classical nitric-oxide-regulated guanylate cyclases. GCY-35 and TAX-4 mediate oxygen sensation in four sensory neurons that control a naturally polymorphic social feeding behaviour in C. elegans. Social feeding and related behaviours occur only when oxygen exceeds C. elegans' preferred level, and require gcy-35 activity. Our results suggest that GCY-35 is regulated by molecular oxygen, and that social feeding can be a behavioural strategy for responding to hyperoxic environments.

Reactivity of 12-tungstophosphoric acid and its inhibitor potency toward Na+/K+-ATPase: A combined 31P NMR study, ab initio calculations and crystallographic analysis.

PubMed

Bošnjaković-Pavlović, Nada; Bajuk-Bogdanović, Danica; Zakrzewska, Joanna; Yan, Zeyin; Holclajtner-Antunović, Ivanka; Gillet, Jean-Michel; Spasojević-de Biré, Anne

2017-11-01

Influence of 12-tungstophosphoric acid (WPA) on conversion of adenosine triphosphate (ATP) to adenosine diphosphate (ADP) in the presence of Na + /K + -ATPase was monitored by 31 P NMR spectroscopy. It was shown that WPA exhibits inhibitory effect on Na + /K + -ATPase activity. In order to study WPA reactivity and intermolecular interactions between WPA oxygen atoms and different proton donor types (D=O, N, C), we have considered data for WPA based compounds from the Cambridge Structural Database (CSD), the Crystallographic Open Database (COD) and the Inorganic Crystal Structure Database (ICSD). Binding properties of Keggin's anion in biological systems are illustrated using Protein Data Bank (PDB). This work constitutes the first determination of theoretical Bader charges on polyoxotungstate compound via the Atom In Molecule theory. An analysis of electrostatic potential maps at the molecular surface and charge of WPA, resulting from DFT calculations, suggests that the preferred protonation site corresponds to WPA bridging oxygen. These results enlightened WPA chemical reactivity and its potential biological applications such as the inhibition of the ATPase activity. Copyright © 2017 Elsevier Inc. All rights reserved.

Computational insights of water droplet transport on graphene sheet with chemical density

NASA Astrophysics Data System (ADS)

Zhang, Liuyang; Wang, Xianqiao

2014-05-01

Surface gradient has been emerging as an intriguing technique for nanoscale particle manipulation and transportation. Owing to its outstanding and stable chemical properties, graphene with covalently bonded chemical groups represents extraordinary potential for the investigation of nanoscale transport in the area of physics and biology. Here, we employ molecular dynamics simulations to investigate the fundamental mechanism of utilizing a chemical density on a graphene sheet to control water droplet motions on it. Simulation results have demonstrated that the binding energy difference among distinct segment of graphene in terms of interaction between the covalently bonded oxygen atoms on graphene and the water molecules provides a fundamental driving force to transport the water droplet across the graphene sheet. Also, the velocity of the water droplet has showed a strong dependence on the relative concentration of oxygen atoms between successive segments. Furthermore, a multi-direction channel provides insights to guide the transportation of objects towards a targeted position, separating the mixtures with a system of specific chemical functionalization. Our findings shed illuminating lights on the surface gradient method and therefore provide a feasible way to control nanoscale motion on the surface and mimic the channelless microfluidics.

Photoactive platinum(II) complexes of nonsteroidal anti-inflammatory drug naproxen: Interaction with biological targets, antioxidant activity and cytotoxicity.

PubMed

Srivastava, Payal; Singh, Khushbu; Verma, Madhu; Sivakumar, Sri; Patra, Ashis K

2018-01-20

The effect on the therapeutic efficacy of Pt(II) complexes on combining non-steroidal anti-inflammatory drugs (NSAIDs) is an attractive strategy to circumvent chronic inflammation mediated by cancer and metastasis. Two square-planar platinum(II) complexes: [Pt(dach)(nap)Cl] (1) and [Pt(dach)(nap) 2 ] (2), where dach = (1R,2R)-dichloro(cyclohexane-1,2-diamine) and NSAID drug naproxen (nap), have been designed for studying their biological activity. The naproxen bound to the Pt(II) centre get released upon photoirradiation with low-power UV-A light as confirmed by the significant enhancement in emission intensities of the complexes. The compounds were evaluated for their photophysical properties, photostability, reactivity with 5'-guanosine monophophosphate (5'-GMP), interactions with CT-DNA and BSA, antioxidant activity and reactive oxygen species mediated photo-induced DNA damage properties. ESI-MS studies demonstrated the formation of bis-adduct with 5'-GMP and the formation of Pt II -DNA crosslinks by gel electrophoretic mobility shift assay and ITC studies. The interaction of the complexes 1 and 2 with the CT-DNA exhibits potential binding affinity (K b  ∼ 10 4  M -1 , K app ∼ 10 5  M -1 ), implying intercalation to CT-DNA through planar naphthyl ring of the complexes. Both the complexes also exhibit strong binding affinity towards BSA (K BSA ∼ 10 5  M -1 ). The complexes exhibit efficient DNA damage activity on irradiation at 365 nm via formation of singlet oxygen ( 1 O 2 ) and hydroxyl radical ( • OH) under physiological conditions. Both the complexes were cytotoxic in dark and exhibit significant enhancement of cytotoxicity upon photo-exposure against HeLa and HepG2 cancer cells giving IC 50 values ranging from 8 to 12 μM for 1 and 2. The cellular internalization data showed cytosolic and nuclear localization of the complexes in the HeLa cells. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

High temperature thermoelectric properties of strontium titanate thin films with oxygen vacancy and niobium doping.

PubMed

Kumar, S R Sarath; Barasheed, Abeer Z; Alshareef, H N

2013-08-14

We report the evolution of high temperature thermoelectric properties of SrTiO3 thin films doped with Nb and oxygen vacancies. Structure-property relations in this important thermoelectric oxide are elucidated and the variation of transport properties with dopant concentrations is discussed. Oxygen vacancies are incorporated during growth or annealing in Ar/H2 above 800 K. An increase in lattice constant due to the inclusion of Nb and oxygen vacancies is found to result in an increase in carrier density and electrical conductivity with simultaneous decrease in carrier effective mass and Seebeck coefficient. The lattice thermal conductivity at 300 K is found to be 2.22 W m(-1) K(-1), and the estimated figure of merit is 0.29 at 1000 K.

Hemoglobin

DTIC Science & Technology

1993-03-08

affinity, which is less at low levels of hemoglobin saturation, increases markedly as fractional saturation increases. Thus, high affinity for 02 at... diphosphoglycerate (2,3-DPG), and carbon dioxide (Co 2). Since they are linked to 02 binding, they are called oxygen-linked effectors. The oxygen...hemoglobin molecule because of the negative charge of the ions. 2,3- Diphosphoglycerate is a molecule formed during the breakdown of sugar in normal human

Measurement of antiphotooxidative properties of isoquinoline alkaloids using transient thermal lens spectroscopy

NASA Astrophysics Data System (ADS)

Hung, J.; Castillo, J.; Laboren, I.; Rodríguez, M.; Hassegawa, M.

2005-11-01

The antiphotooxidative properties of boldine and chloride berberine were studied by time-resolved thermal lensing technique. These compounds belong to isoquinoline alkaloids possessing interesting biological activity (e.g. antibacterial, antimalarial, antitumor). Antiphotooxidative properties of the alkaloids were studied by mechanism of energy transference between powerful oxidizing agents such as singlet oxygen. Singlet oxygen was produced by energy transfer from chlorophyll-sensitized photooxidation of oil by exposure of high light intensities like laser. The lifetimes of singlet oxygen in dimethylsulfoxide, methanol and water were determined to confirm the assignment of the singlet molecular oxygen O II (1Δ g) in the experiments. In order to understand the effect of the alkaloids on active oxygen species, we carried out in detail an analysis of the thermal lensing signal. It was shown that the alkaloids can act as quenchers of singlet oxygen. To demonstrate the ability of the alkaloids to act efficient singlet oxygen acceptors, we have measured the fluorescence spectra of the studied alkaloids in the presence and in the absence of singlet oxygen. The antiphotooxidative activity of boldine and chloride berberine can be explained by the ability to quench singlet oxygen.

31P-NMR measurements of ATP, ADP, 2,3-diphosphoglycerate and Mg2+ in human erythrocytes.

PubMed

Petersen, A; Kristensen, S R; Jacobsen, J P; Hørder, M

1990-08-17

Absolute 31P-NMR measurements of ATP, ADP and 2,3-diphosphoglycerate (2,3-DPG) in oxygenated and partly deoxygenated human erythrocytes, compared to measurements by standard assays after acid extraction, show that ATP is only 65% NMR visible, ADP measured by NMR is unexpectedly 400% higher than the enzymatic measurement and 2,3-DPG is fully NMR visible, regardless of the degree of oxygenation. These results show that binding to hemoglobin is unlikely to cause the decreased visibility of ATP in human erythrocytes as deoxyhemoglobin binds the phosphorylated metabolites more tightly than oxyhemoglobin. The high ADP visibility is unexplained. The levels of free Mg2+ [( Mg2+]free) in human erythrocytes are 225 mumol/l at an oxygen saturation of 98.6% and instead of the expected increase, the level decreased to 196 mumol/l at an oxygen saturation of 38.1% based on the separation between the alpha- and beta-ATP peaks. [Mg2+]free in the erythrocytes decreased to 104 mumol/l at a high 2,3-DPG concentration of 25.4 mmol/l red blood cells (RBC) and a normal ATP concentration of 2.05 mmol/l RBC. By increasing the ATP concentration to 3.57 mmol/l RBC, and with a high 2,3-DPG concentration of 24.7 mmol/l RBC, the 31P-NMR measured [Mg2+]free decreased to 61 mumol/l. These results indicate, that the 31P-NMR determined [Mg2+]free in human erythrocytes, based solely on the separation of the alpha- and beta-ATP peaks, does not give a true measure of intracellular free Mg2+ changes with different oxygen saturation levels. Furthermore the measurement is influenced by the concentration of the Mg2+ binding metabolites ATP and 2,3-DPG. Failure to take these factors into account when interpreting 31P-NMR data from human erythrocytes may explain some discrepancies in the literature regarding [Mg2+]free.

Potassium-induced effect on structure and chemical activity of Cu xO/Cu(111) (x≤2) surface: A combined scanning tunneling microscopy and density functional theory study

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

Liu, Ping; An, Wei; Stacchiola, Dario

2015-10-16

Potassium (K) plays an essential role in promoting catalytic reaction in many established industrial catalytic processes. Here, we report a combined study using scanning tunneling microscopy (STM) and density functional theory (DFT) in understanding the effect of depositing K on the atomic and electronic structures as well as chemical activities of Cu xO/Cu(111) (x≤2). The DFT calculations observe a pseudomorphic growth of K on Cu xO/Cu(111) up to 0.19 monolayer (ML) of coverage, where K binds the surface via strong ionic interaction with chemisorbed oxygen and the relatively weak electrostatic interactions with copper ions, lower and upper oxygen on themore » Cu xO rings. The simulated STM pattern based on the DFT results agrees well with the experimental observations. The deposited K displays great impact on the surface electronic structure of Cu xO/Cu(111), which induces significant reduction in work function and leads to a strong electron polarization on the surface. The promotion of K on the surface binding properties is selective. It varies depending on the nature of adsorbates. According to our results, K has little effect on surface acidity, while it enhances the surface basicity significantly. As a consequence, the presence of K does not help for CO adsorption on Cu xO/Cu(111), but being able to accelerate the activation of CO 2. Thus, such promotion strongly depends on the combinations from both geometric and electronic effects. Our results highlight the origin of promoting effect of alkalis in the design of catalysts for the complex reactions.« less

Native Alanine Substitution in the Glycine Hinge Modulates Conformational Flexibility of Heme Nitric Oxide/Oxygen (H-NOX) Sensing Proteins.

PubMed

Hespen, Charles W; Bruegger, Joel J; Guo, Yirui; Marletta, Michael A

2018-06-15

Heme nitric oxide/oxygen sensing (H-NOX) domains are direct NO sensors that regulate a variety of biological functions in both bacteria and eukaryotes. Previous work on H-NOX proteins has shown that upon NO binding, a conformational change occurs along two glycine residues on adjacent helices (termed the glycine hinge). Despite the apparent importance of the glycine hinge, it is not fully conserved in all H-NOX domains. Several H-NOX sensors from the family Flavobacteriaceae contain a native alanine substitution in one of the hinge residues. In this work, the effect of the increased steric bulk within the Ala-Gly hinge on H-NOX function was investigated. The hinge in Kordia algicida OT-1 ( Ka H-NOX) is composed of A71 and G145. Ligand-binding properties and signaling function for this H-NOX were characterized. The variant A71G was designed to convert the hinge region of Ka H-NOX to the typical Gly-Gly motif. In activity assays with its cognate histidine kinase (HnoK), the wild type displayed increased signal specificity compared to A71G. Increasing titrations of unliganded A71G gradually inhibits HnoK autophosphorylation, while increasing titrations of unliganded wild type H-NOX does not inhibit HnoK. Crystal structures of both wild type and A71G Ka H-NOX were solved to 1.9 and 1.6 Å, respectively. Regions of H-NOX domains previously identified as involved in protein-protein interactions with HnoK display significantly higher b-factors in A71G compared to wild-type H-NOX. Both biochemical and structural data indicate that the hinge region controls overall conformational flexibility of the H-NOX, affecting NO complex formation and regulation of its HnoK.

Lectin conjugates as biospecific contrast agents for MRI. Coupling of Lycopersicon esculentum agglutinin to linear water-soluble DTPA-loaded oligomers.

PubMed

Pashkunova-Martic, Irena; Kremser, Christian; Galanski, Markus; Schluga, Petra; Arion, Vladimir; Debbage, Paul; Jaschke, Werner; Keppler, Bernhard

2011-06-01

Magnetic resonance imaging (MRI) requires synthesis of contrast media bearing targeting groups and numerous gadolinium chelating groups generating high relaxivity. This paper explores the results of linking the gadolinium chelates to the targeting group, a protein molecule, via various types of linkers. Polycondensates of diethylenetriaminepentaacetic acid (DTPA) with either diols or diamines were synthesised and coupled to the targeting group, a lectin (Lycopersicon esculentum agglutinin, tomato lectin) which binds with high affinity to specific oligosaccharide configurations in the endothelial glycocalyx. The polycondensates bear up to four carboxylic groups per constitutive unit. Gd-chelate bonds are created through dative interactions with the unshared pair of electrons on each oxygen and nitrogen atom on DTPA. This is mandatory for complexation of Gd(III) and avoidance of the severe toxicity of free gadolinium ions. The polymer-DTPA compounds were characterised by (1)H NMR and mass spectrometry. The final lectin-DTPA-polycondensate conjugates were purified by fast protein liquid chromatography (FPLC). The capacity for specific binding was assessed, and the MRI properties were examined in order to evaluate the use of these oligomers as components of selective perfusional contrast agents.

Numerical Optimization of Density Functional Tight Binding Models: Application to Molecules Containing Carbon, Hydrogen, Nitrogen, and Oxygen

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

Krishnapriyan, A.; Yang, P.; Niklasson, A. M. N.

New parametrizations for semiempirical density functional tight binding (DFTB) theory have been developed by the numerical optimization of adjustable parameters to minimize errors in the atomization energy and interatomic forces with respect to ab initio calculated data. Initial guesses for the radial dependences of the Slater- Koster bond integrals and overlap integrals were obtained from minimum basis density functional theory calculations. The radial dependences of the pair potentials and the bond and overlap integrals were represented by simple analytic functions. The adjustable parameters in these functions were optimized by simulated annealing and steepest descent algorithms to minimize the value ofmore » an objective function that quantifies the error between the DFTB model and ab initio calculated data. The accuracy and transferability of the resulting DFTB models for the C, H, N, and O system were assessed by comparing the predicted atomization energies and equilibrium molecular geometries of small molecules that were not included in the training data from DFTB to ab initio data. The DFTB models provide accurate predictions of the properties of hydrocarbons and more complex molecules containing C, H, N, and O.« less

The Nature of the Interactions in Triethanolammonium-Based Ionic Liquids. A Quantum Chemical Study.

PubMed

Fedorova, Irina V; Safonova, Lyubov P

2018-05-10

Structural features and interionic interactions play a crucial role in determining the overall stability of ionic liquids and their physicochemical properties. Therefore, we performed high-level quantum-chemical study of different cation-anion pairs representing the building units of protic ionic liquids based on triethanolammonium cation and anions of sulfuric, nitric, phosphoric, and phosphorus acids to provide essential insight into these phenomena at the molecular level. It was shown that every structure is stabilized through multiple H bonds between the protons in the N-H and O-H groups of the cation and different oxygen atoms of the anion acid. Using atoms in molecules topological parameters and natural bond orbital analysis, we determined the nature and strength of these interactions. Our calculations suggest that the N-H group of the cation has more proton donor-like character than the O-H group that makes the N-H···O hydrogen bonds stronger. A close relation between the binding energies of these ion pairs and experimental melting points was established: the smaller the absolute value of the binding energy between ions, the lower is the melting point.

Numerical Optimization of Density Functional Tight Binding Models: Application to Molecules Containing Carbon, Hydrogen, Nitrogen, and Oxygen

DOE PAGES

Krishnapriyan, A.; Yang, P.; Niklasson, A. M. N.; ...

2017-10-17

New parametrizations for semiempirical density functional tight binding (DFTB) theory have been developed by the numerical optimization of adjustable parameters to minimize errors in the atomization energy and interatomic forces with respect to ab initio calculated data. Initial guesses for the radial dependences of the Slater- Koster bond integrals and overlap integrals were obtained from minimum basis density functional theory calculations. The radial dependences of the pair potentials and the bond and overlap integrals were represented by simple analytic functions. The adjustable parameters in these functions were optimized by simulated annealing and steepest descent algorithms to minimize the value ofmore » an objective function that quantifies the error between the DFTB model and ab initio calculated data. The accuracy and transferability of the resulting DFTB models for the C, H, N, and O system were assessed by comparing the predicted atomization energies and equilibrium molecular geometries of small molecules that were not included in the training data from DFTB to ab initio data. The DFTB models provide accurate predictions of the properties of hydrocarbons and more complex molecules containing C, H, N, and O.« less

Steap4 Plays a Critical Role in Osteoclastogenesis in Vitro by Regulating Cellular Iron/Reactive Oxygen Species (ROS) Levels and cAMP Response Element-binding Protein (CREB) Activation*

PubMed Central

Zhou, Jian; Ye, Shiqiao; Fujiwara, Toshifumi; Manolagas, Stavros C.; Zhao, Haibo

2013-01-01

Iron is essential for osteoclast differentiation, and iron overload in a variety of hematologic diseases is associated with excessive bone resorption. Iron uptake by osteoclast precursors via the transferrin cycle increases mitochondrial biogenesis, reactive oxygen species production, and activation of cAMP response element-binding protein, a critical transcription factor downstream of receptor activator of NF-κB-ligand-induced calcium signaling. These changes are required for the differentiation of osteoclast precursors to mature bone-resorbing osteoclasts. However, the molecular mechanisms regulating cellular iron metabolism in osteoclasts remain largely unknown. In this report, we provide evidence that Steap4, a member of the six-transmembrane epithelial antigen of prostate (Steap) family proteins, is an endosomal ferrireductase with a critical role in cellular iron utilization in osteoclasts. Specifically, we show that Steap4 is the only Steap family protein that is up-regulated during osteoclast differentiation. Knocking down Steap4 expression in vitro by lentivirus-mediated short hairpin RNAs inhibits osteoclast formation and decreases cellular ferrous iron, reactive oxygen species, and the activation of cAMP response element-binding protein. These results demonstrate that Steap4 is a critical enzyme for cellular iron uptake and utilization in osteoclasts and, thus, indispensable for osteoclast development and function. PMID:23990467

Mechanism-based inactivation of dopamine beta-hydroxylase by p-cresol and related alkylphenols

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

Goodhart, P.J.; DeWolf, W.E. Jr.; Kruse, L.I.

1987-05-05

The mechanism-based inhibition of dopamine beta-hydroxylase by p-cresol (4-methylphenol) and other simple structural analogues of dopamine, which lack a basic side-chain nitrogen, is reported. p-Cresol binds DBH by a mechanism that is kinetically indistinguishable from normal dopamine substrate binding. Under conditions (pH 6.6) of random oxygen and phenethylamine substrate addition p-cresol adds randomly, whereas at pH 4.5 or in the presence of fumarate activator addition of p-cresol precedes oxygen binding as is observed with phenethylamine substrate. p-Cresol is shown to be a rapid (kinact = 2.0 min-1, pH 5.0) mechanism-based inactivator of DBH. This inactivation exhibits pseudo-first-order kinetics, is irreversible,more » is prevented by tyramine substrate or competitive inhibitor, and is dependent upon oxygen and ascorbic acid cosubstrates. Inhibition occurs with partial covalent incorporation of p-cresol into DBH. A plot of -log kinact vs. pH shows maximal inactivation occurs at pH 5.0 with dependence upon enzymatic groups with apparent pK values of 4.51 +/- 0.06 and 5.12 +/- 0.06. p-Cresol and related alkylphenols, unlike other mechanism-based inhibitors of DBH, lack a latent electrophile. These inhibitors are postulated to covalently modify DBH by a direct insertion of an aberrant substrate-derived benzylic radical into an active site residue.« less

Effect of oxygen vacancy distribution on the thermoelectric properties of La-doped SrTiO3 epitaxial thin films

NASA Astrophysics Data System (ADS)

Sarath Kumar, S. R.; Abutaha, A. I.; Hedhili, M. N.; Alshareef, H. N.

2012-12-01

A detailed study of the role of oxygen vacancies in determining the effective mass and high temperature (300-1000 K) thermoelectric properties of La-doped epitaxial SrTiO3 thin films is presented. It is observed that at intermediate temperatures, a transition from degenerate to non-degenerate behavior is observed in the Seebeck coefficient, but not electrical conductivity, which is attributed to heterogeneous oxygen non-stoichiometry. Heikes formula is found to be invalid for the films with oxygen vacancies. By fitting the spectroscopic ellipsometry (SE) data, obtained in the range 300-2100 nm, using a Drude-Lorentz dispersion relation with two Lorentz oscillators, the electrical and optical properties of the films are extracted. Using the excellent agreement between the transport properties extracted from SE modeling and direct electrical measurements, we demonstrate that an increase in concentration of oxygen vacancies results in a simultaneous increase of both carrier concentration and electron effective mass, resulting in a higher power factor.

Novel regulation of Skp1 by the Dictyostelium AgtA α-galactosyltransferase involves the Skp1-binding activity of its WD40 repeat domain.

PubMed

Schafer, Christopher M; Sheikh, M Osman; Zhang, Dongmei; West, Christopher M

2014-03-28

The role of Skp1 as an adaptor protein that links Cullin-1 to F-box proteins in E3 Skp1/Cullin-1/F-box protein (SCF) ubiquitin ligases is well characterized. In the social amoeba Dictyostelium and probably many other unicellular eukaryotes, Skp1 is modified by a pentasaccharide attached to a hydroxyproline near its C terminus. This modification is important for oxygen-sensing during Dictyostelium development and is mediated by a HIF-α type prolyl 4-hydroxylase and five sequentially acting cytoplasmic glycosyltransferase activities. Gene disruption studies show that AgtA, the enzyme responsible for addition of the final two galactose residues, in α-linkages to the Skp1 core trisaccharide, is unexpectedly critical for oxygen-dependent terminal development. AgtA possesses a WD40 repeat domain C-terminal to its single catalytic domain and, by use of domain deletions, binding studies, and enzyme assays, we find that the WD40 repeats confer a salt-sensitive second-site binding interaction with Skp1 that mediates novel catalytic activation in addition to simple substrate recognition. In addition, AgtA binds similarly well to precursor isoforms of Skp1 by a salt-sensitive mechanism that competes with binding to an F-box protein and recognition by early modification enzymes, and the effect of binding is diminished when AgtA modifies Skp1. Genetic studies show that loss of AgtA is more severe when an earlier glycosylation step is blocked, and overexpressed AgtA is deleterious if catalytically inactivated. Together, the findings suggest that AgtA mediates non-enzymatic control of unmodified and substrate precursor forms of Skp1 by a binding mechanism that is normally relieved by switch-like activation of its glycosylation function.

Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones

PubMed Central

Glass, Jennifer B.; Kretz, Cecilia B.; Ganesh, Sangita; Ranjan, Piyush; Seston, Sherry L.; Buck, Kristen N.; Landing, William M.; Morton, Peter L.; Moffett, James W.; Giovannoni, Stephen J.; Vergin, Kevin L.; Stewart, Frank J.

2015-01-01

Iron (Fe) and copper (Cu) are essential cofactors for microbial metalloenzymes, but little is known about the metalloenyzme inventory of anaerobic marine microbial communities despite their importance to the nitrogen cycle. We compared dissolved O2, NO3−, NO2−, Fe and Cu concentrations with nucleic acid sequences encoding Fe and Cu-binding proteins in 21 metagenomes and 9 metatranscriptomes from Eastern Tropical North and South Pacific oxygen minimum zones and 7 metagenomes from the Bermuda Atlantic Time-series Station. Dissolved Fe concentrations increased sharply at upper oxic-anoxic transition zones, with the highest Fe:Cu molar ratio (1.8) occurring at the anoxic core of the Eastern Tropical North Pacific oxygen minimum zone and matching the predicted maximum ratio based on data from diverse ocean sites. The relative abundance of genes encoding Fe-binding proteins was negatively correlated with O2, driven by significant increases in genes encoding Fe-proteins involved in dissimilatory nitrogen metabolisms under anoxia. Transcripts encoding cytochrome c oxidase, the Fe- and Cu-containing terminal reductase in aerobic respiration, were positively correlated with O2 content. A comparison of the taxonomy of genes encoding Fe- and Cu-binding vs. bulk proteins in OMZs revealed that Planctomycetes represented a higher percentage of Fe genes while Thaumarchaeota represented a higher percentage of Cu genes, particularly at oxyclines. These results are broadly consistent with higher relative abundance of genes encoding Fe-proteins in the genome of a marine planctomycete vs. higher relative abundance of genes encoding Cu-proteins in the genome of a marine thaumarchaeote. These findings highlight the importance of metalloenzymes for microbial processes in oxygen minimum zones and suggest preferential Cu use in oxic habitats with Cu > Fe vs. preferential Fe use in anoxic niches with Fe > Cu. PMID:26441925

Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones.

PubMed

Glass, Jennifer B; Kretz, Cecilia B; Ganesh, Sangita; Ranjan, Piyush; Seston, Sherry L; Buck, Kristen N; Landing, William M; Morton, Peter L; Moffett, James W; Giovannoni, Stephen J; Vergin, Kevin L; Stewart, Frank J

2015-01-01

Iron (Fe) and copper (Cu) are essential cofactors for microbial metalloenzymes, but little is known about the metalloenyzme inventory of anaerobic marine microbial communities despite their importance to the nitrogen cycle. We compared dissolved O2, NO[Formula: see text], NO[Formula: see text], Fe and Cu concentrations with nucleic acid sequences encoding Fe and Cu-binding proteins in 21 metagenomes and 9 metatranscriptomes from Eastern Tropical North and South Pacific oxygen minimum zones and 7 metagenomes from the Bermuda Atlantic Time-series Station. Dissolved Fe concentrations increased sharply at upper oxic-anoxic transition zones, with the highest Fe:Cu molar ratio (1.8) occurring at the anoxic core of the Eastern Tropical North Pacific oxygen minimum zone and matching the predicted maximum ratio based on data from diverse ocean sites. The relative abundance of genes encoding Fe-binding proteins was negatively correlated with O2, driven by significant increases in genes encoding Fe-proteins involved in dissimilatory nitrogen metabolisms under anoxia. Transcripts encoding cytochrome c oxidase, the Fe- and Cu-containing terminal reductase in aerobic respiration, were positively correlated with O2 content. A comparison of the taxonomy of genes encoding Fe- and Cu-binding vs. bulk proteins in OMZs revealed that Planctomycetes represented a higher percentage of Fe genes while Thaumarchaeota represented a higher percentage of Cu genes, particularly at oxyclines. These results are broadly consistent with higher relative abundance of genes encoding Fe-proteins in the genome of a marine planctomycete vs. higher relative abundance of genes encoding Cu-proteins in the genome of a marine thaumarchaeote. These findings highlight the importance of metalloenzymes for microbial processes in oxygen minimum zones and suggest preferential Cu use in oxic habitats with Cu > Fe vs. preferential Fe use in anoxic niches with Fe > Cu.

Borrelia oxidative stress response regulator, BosR: A distinctive Zn-dependent transcriptional activator

PubMed Central

Boylan, Julie A.; Posey, James E.; Gherardini, Frank C.

2003-01-01

The ability of a pathogen to cause infection depends on successful colonization of the host, which, in turn, requires adaptation to various challenges presented by that host. For example, host immune cells use a variety of mechanisms to control infection by bacterial pathogens, including the production of bactericidal reactive oxygen species. Prokaryotic and eukaryotic cells have developed ways of protecting themselves against this oxidative damage; for instance, Borrelia burgdorferi alters the expression of oxidative-stress-related proteins, such as a Dps/Dpr homolog NapA (BB0690), in response to increasing levels of oxygen and reactive oxygen species. These stress-related genes appear to be regulated by a putative metal-dependent DNA-binding protein (BB0647) that has 50.7% similarity to the peroxide-specific stress response repressor of Bacillus subtilis, PerR. We overexpressed and purified this protein from Escherichia coli and designated it Borrelia oxidative stress regulator, BosR. BosR bound to a 50-nt region 180 bp upstream of the napA transcriptional start site and required DTT and Zn2+ for optimal binding. Unlike the Bacillus subtilis PerR repressor, BosR did not require Fe2+ and Mn2+ for binding, and oxidizing agents, such as t-butyl peroxide, enhanced, not eliminated, BosR binding to the napA promoter region. Surprisingly, transcriptional fusion analysis indicated that BosR exerted a positive regulatory effect on napA that is inducible with t-butyl peroxide. On the basis of these data, we propose that, despite the similarity to PerR, BosR functions primarily as a transcriptional activator, not a repressor of oxidative stress response, in B. burgdorferi. PMID:12975527

Molecular Docking, Molecular Dynamics, and Structure–Activity Relationship Explorations of 14-Oxygenated N-Methylmorphinan-6-ones as Potent μ-Opioid Receptor Agonists

PubMed Central

2017-01-01

Among opioids, morphinans are of major importance as the most effective analgesic drugs acting primarily via μ-opioid receptor (μ-OR) activation. Our long-standing efforts in the field of opioid analgesics from the class of morphinans led to N-methylmorphinan-6-ones differently substituted at positions 5 and 14 as μ-OR agonists inducing potent analgesia and fewer undesirable effects. Herein we present the first thorough molecular modeling study and structure–activity relationship (SAR) explorations aided by docking and molecular dynamics (MD) simulations of 14-oxygenated N-methylmorphinan-6-ones to gain insights into their mode of binding to the μ-OR and interaction mechanisms. The structure of activated μ-OR provides an essential model for how ligand/μ-OR binding is encoded within small chemical differences in otherwise structurally similar morphinans. We reveal important molecular interactions that these μ-agonists share and distinguish them. The molecular docking outcomes indicate the crucial role of the relative orientation of the ligand in the μ-OR binding site, influencing the propensity of critical non-covalent interactions that are required to facilitate ligand/μ-OR interactions and receptor activation. The MD simulations point out minor differences in the tendency to form hydrogen bonds by the 4,5α-epoxy group, along with the tendency to affect the 3–7 lock switch. The emerged SARs reveal the subtle interplay between the substituents at positions 5 and 14 in the morphinan scaffold by enabling the identification of key structural elements that determine the distinct pharmacological profiles. This study provides a significant structural basis for understanding ligand binding and μ-OR activation by the 14-oxygenated N-methylmorphinan-6-ones, which should be useful for guiding drug design. PMID:28125215

Molecular Docking, Molecular Dynamics, and Structure-Activity Relationship Explorations of 14-Oxygenated N-Methylmorphinan-6-ones as Potent μ-Opioid Receptor Agonists.

PubMed

Noha, Stefan M; Schmidhammer, Helmut; Spetea, Mariana

2017-06-21

Among opioids, morphinans are of major importance as the most effective analgesic drugs acting primarily via μ-opioid receptor (μ-OR) activation. Our long-standing efforts in the field of opioid analgesics from the class of morphinans led to N-methylmorphinan-6-ones differently substituted at positions 5 and 14 as μ-OR agonists inducing potent analgesia and fewer undesirable effects. Herein we present the first thorough molecular modeling study and structure-activity relationship (SAR) explorations aided by docking and molecular dynamics (MD) simulations of 14-oxygenated N-methylmorphinan-6-ones to gain insights into their mode of binding to the μ-OR and interaction mechanisms. The structure of activated μ-OR provides an essential model for how ligand/μ-OR binding is encoded within small chemical differences in otherwise structurally similar morphinans. We reveal important molecular interactions that these μ-agonists share and distinguish them. The molecular docking outcomes indicate the crucial role of the relative orientation of the ligand in the μ-OR binding site, influencing the propensity of critical non-covalent interactions that are required to facilitate ligand/μ-OR interactions and receptor activation. The MD simulations point out minor differences in the tendency to form hydrogen bonds by the 4,5α-epoxy group, along with the tendency to affect the 3-7 lock switch. The emerged SARs reveal the subtle interplay between the substituents at positions 5 and 14 in the morphinan scaffold by enabling the identification of key structural elements that determine the distinct pharmacological profiles. This study provides a significant structural basis for understanding ligand binding and μ-OR activation by the 14-oxygenated N-methylmorphinan-6-ones, which should be useful for guiding drug design.

Effect of altitude on oxygen binding by hemoglobin and on organic phosphate levels

PubMed Central

Lenfant, Claude; Torrance, John; English, Eugenia; Finch, Clement A.; Reynafarje, Cesar; Ramos, Jose; Faura, Jose

1968-01-01

The relationship between oxygen dissociation and 2,3-diphosphoglycerate (2,3-DPG) in the red cell has been studied in subjects moving from low to high altitude and vice versa. Within 24 hr following the change in altitude there was a change in hemoglobin affinity for oxygen; this modification therefore represents an important rapid adaptive mechanism to anoxia. A parallel change occurred in the organic phosphate content of the red cell. While this study does not provide direct evidence of a cause-effect relationship, the data strongly suggest that with anoxia, the observed rise in organic phosphate content of the red cell is responsible for increased availability of oxygen to tissues. Images PMID:5725278

Adsorption and diffusion of atomic oxygen and sulfur at pristine and doped Ni surfaces with implications for stress corrosion cracking

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

Alexandrov, Vitaly; Sushko, Maria L.; Schreiber, Daniel K.

A density-functional-theory modeling study of atomic oxygen/sulfur adsorption and diffusion at pristine and doped Ni(111) and (110) surfaces is presented. We find that oxygen and sulfur feature comparable adsorption energies over the same surface sites, however, the surface diffusion of sulfur is characterized by an activation barrier about one half that of oxygen. Calculations with different alloying elements at Ni surfaces show that Cr strongly enhances surface binding of both species in comparison to Al. These results in combination with previous modeling studies help explain the observed differences in selective grain boundary oxidation mechanisms of Ni-Cr and Ni-Al alloys.

Activity of N-coordinated multi-metal-atom active site structures for Pt-free oxygen reduction reaction catalysis: Role of *OH ligands

DOE PAGES

Holby, Edward F.; Taylor, Christopher D.

2015-03-19

We report calculated oxygen reduction reaction energy pathways on multi-metal-atom structures that have previously been shown to be thermodynamically favorable. We predict that such sites have the ability to spontaneously cleave the O₂ bond and then will proceed to over-bind reaction intermediates. In particular, the *OH bound state has lower energy than the final 2 H₂O state at positive potentials. Contrary to traditional surface catalysts, this *OH binding does not poison the multi-metal-atom site but acts as a modifying ligand that will spontaneously form in aqueous environments leading to new active sites that have higher catalytic activities. These *OH boundmore » structures have the highest calculated activity to date.« less

Effects of oxygen plasma treatment on domestic aramid fiber III reinforced bismaleimide composite interfacial properties

NASA Astrophysics Data System (ADS)

Shi, Chen; Wang, Jing; Chen, Ping; Feng, Jiayue; Cui, Jinyuan; Yang, Faze

2017-12-01

Domestic Aramid Fiber III (DAF III) was modified by oxygen plasma treatment. The fiber surface characteristics was observed by Scanning Electron Microscopy. The results showed that oxygen plasma treatment changed surface morphologies. The effects of oxygen plasma treatment on DAF III reinforced bismaleimides (BMI) composite bending and interfacial properties were investigated, respectively. The ILSS value increased from 49.3 MPa to 56.0 MPa (by 13.5%) after oxygen plasma treatment. The bending strength changed a little. Furthermore, the composite rupture mode changed from interfacial rupture to fiber or resin bulk rupture.

Oxygen defect induced photoluminescence of HfO2 thin films

NASA Astrophysics Data System (ADS)

Ni, Jie; Zhou, Qin; Li, Zhengcao; Zhang, Zhengjun

2008-07-01

Amorphous HfO2 films prepared by e-beam deposition exhibited room-temperature photoluminescence (PL) in the visible range, i.e., at ˜620 and 700nm, due to oxygen vacancies involved during deposition. This PL can be enhanced by two orders in intensity by crystallizing the amorphous films in flowing argon, where a large amount of oxygen vacancies were introduced, and can be diminished by removal of the oxygen vacancies by annealing HfO2 films in oxygen. This study could help understand the defect-property relationship and provides ways to tune the PL property of HfO2 films.

Oxygen vacancy effect on dielectric and hysteretic properties of zigzag ferroelectric iron dioxide nanoribbon

NASA Astrophysics Data System (ADS)

Zriouel, S.; Taychour, B.; Yahyaoui, F. El; Drissi, L. B.

2017-07-01

Zigzag FeO2 nanoribbon defected by the removal of oxygen atoms is simulated using Monte Carlo simulations. All possible arrangements of positions and number of oxygen vacancy are investigated. Temperature dependence of polarization, dielectric susceptibility, internal energy, specific heat and dielectric hysteresis loops are all studied. Results show the presence of second order phase transition and Q - type behavior. Dielectric properties dependence on ribbon's edge, positions and number of oxygen vacancy are discussed in detail. Moreover, single and square hysteresis loops are observed whatever the number of oxygen vacancy in the system.

Reversible Oxygenation of 2,4-Diaminobutanoic Acid-Co(II) Complexes

PubMed Central

Li, Hui; Yue, Fan; Wen, Hongmei

2016-01-01

This paper introduces the structural characterization and studies on reversible oxygenation behavior of a new oxygen carrier Co(II)-2,4-diaminobutanoic acid (DABA) complex in aqueous solution. The composition of the oxygenated complex was determined by gas volumetric method, molar ratio method, and mass spectrometry, and the formula of the oxygenated complex was determined to be [Co(DABA)2O2]. In aqueous solution, the complex can continuously uptake and release dioxygen and exhibit excellent reversibility of oxygenation and deoxygenation ability. This complex can maintain 50% of its original oxygenation capacity after 30 cycles in 24 h and retain 5% of the original oxygenation capacity after more than 260 cycles after 72 h. When a ligand analogue was linked to histidine (His), the new complex exhibited as excellent reversible oxygenation property as His-Co(II) complex. Insight into the relationship between structural detail and oxygenation properties will provide valuable suggestion for a new family of oxygen carriers. PMID:27648004

Exploring high-affinity binding properties of octamer peptides by principal component analysis of tetramer peptides.

PubMed

Kume, Akiko; Kawai, Shun; Kato, Ryuji; Iwata, Shinmei; Shimizu, Kazunori; Honda, Hiroyuki

2017-02-01

To investigate the binding properties of a peptide sequence, we conducted principal component analysis (PCA) of the physicochemical features of a tetramer peptide library comprised of 512 peptides, and the variables were reduced to two principal components. We selected IL-2 and IgG as model proteins and the binding affinity to these proteins was assayed using the 512 peptides mentioned above. PCA of binding affinity data showed that 16 and 18 variables were suitable for localizing IL-2 and IgG high-affinity binding peptides, respectively, into a restricted region of the PCA plot. We then investigated whether the binding affinity of octamer peptide libraries could be predicted using the identified region in the tetramer PCA. The results show that octamer high-affinity binding peptides were also concentrated in the tetramer high-affinity binding region of both IL-2 and IgG. The average fluorescence intensity of high-affinity binding peptides was 3.3- and 2.1-fold higher than that of low-affinity binding peptides for IL-2 and IgG, respectively. We conclude that PCA may be used to identify octamer peptides with high- or low-affinity binding properties from data from a tetramer peptide library. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Oxygen "getter" effects on microstructure and carrier transport in low temperature combustion-processed a-InXZnO (X = Ga, Sc, Y, La) transistors.

PubMed

Hennek, Jonathan W; Smith, Jeremy; Yan, Aiming; Kim, Myung-Gil; Zhao, Wei; Dravid, Vinayak P; Facchetti, Antonio; Marks, Tobin J

2013-07-24

In oxide semiconductors, such as those based on indium zinc oxide (IXZO), a strong oxygen binding metal ion ("oxygen getter"), X, functions to control O vacancies and enhance lattice formation, hence tune carrier concentration and transport properties. Here we systematically study, in the IXZO series, the role of X = Ga(3+) versus the progression X = Sc(3+) → Y(3+) → La(3+), having similar chemical characteristics but increasing ionic radii. IXZO films are prepared from solution over broad composition ranges for the first time via low-temperature combustion synthesis. The films are characterized via thermal analysis of the precursor solutions, grazing incidence angle X-ray diffraction (GIAXRD), atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and scanning transmission electron microscopy (STEM) with high angle annular dark field (HAADF) imaging. Excellent thin-film transistor (TFT) performance is achieved for all X, with optimal compositions after 300 °C processing exhibiting electron mobilities of 5.4, 2.6, 2.4, and 1.8 cm(2) V(-1) s(-1) for Ga(3+), Sc(3+), Y(3+), and La(3+), respectively, and with I(on)/I(off) = 10(7)-10(8). Analysis of the IXZO TFT positive bias stress response shows X = Ga(3+) to be superior with mobilities (μ) retaining >95% of the prestress values and threshold voltage shifts (ΔV(T)) of <1.6 V, versus <85% μ retention and ΔV(T) ≈ 20 V for the other trivalent ions. Detailed microstructural analysis indicates that Ga(3+) most effectively promotes oxide lattice formation. We conclude that the metal oxide lattice formation enthalpy (ΔH(L)) and metal ionic radius are the best predictors of IXZO oxygen getter efficacy.

Evolution of Structural and Electrical Properties of Oxygen-Deficient VO2 under Low Temperature Heating Process.

PubMed

Zhang, Jiasong; Zhao, Zhengjing; Li, Jingbo; Jin, Haibo; Rehman, Fida; Chen, Pengwan; Jiang, Yijie; Chen, Chunxu; Cao, Maosheng; Zhao, Yongjie

2017-08-16

Structural stability and functional performances of vanadium dioxide (VO 2 ) are strongly influenced by oxygen vacancies. However, the mechanism of metal-insulator transition (MIT) influenced by defects is still under debate. Here, we study the evolution of structure and electrical property of oxygen-deficient VO 2 by a low temperature annealing process (LTP) based on a truss-structured VO 2 nanonet. The oxygenation process of the oxygen-deficient VO 2 is greatly prolonged, which enables us to probe the gradual change of properties of the oxygen-deficient VO 2 . A continuous lattice reduction is observed during LTP. No recrystallization and structural collapse of the VO 2 nanonet can be found after LTP. The valence-band X-ray photoelectron spectroscopy (XPS) measurements indicate that the oxygen deficiency strongly affects the energy level of the valence band edge. Correspondingly, the resistance changes of the VO 2 films from 1 to 4.5 orders of magnitude are achieved by LTP. The effect of oxygen vacancy on the electric field driven MIT is investigated. The threshold value of voltage triggering the MIT decreases with increasing the oxygen vacancy concentration. This work demonstrates a novel and effective way to control the content of oxygen vacancies in VO 2 and the obvious impact of oxygen vacancy on MIT, facilitating further research on the role of oxygen vacancy in structure and MIT of VO 2 , which is important for the deep understanding of MIT and exploiting innovative functional application of VO 2 .

Systems for the Storage of Molecular Oxygen - A Study.

DTIC Science & Technology

1980-11-25

form adducts with certain chemical compounds . This process, which will be called chemical absorption, generally uses a transition metal coordination... compound as the absorber. The study of oxygen binding to metal complexes has become of great interest over the past three decades (21), and some...for iron, most notably cobalt (33-35) manganese (36,37) and ruthenium (38), usually to serve as model compounds for biologically important heme

Molecular Controls of the Oxygenation and Redox Reactions of Hemoglobin

PubMed Central

Henkens, Robert; Alayash, Abdu I.; Banerjee, Sambuddha; Crumbliss, Alvin L.

2013-01-01

Abstract Significance: The broad classes of O2-binding proteins known as hemoglobins (Hbs) carry out oxygenation and redox functions that allow organisms with significantly different physiological demands to exist in a wide range of environments. This is aided by allosteric controls that modulate the protein's redox reactions as well as its O2-binding functions. Recent Advances: The controls of Hb's redox reactions can differ appreciably from the molecular controls for Hb oxygenation and come into play in elegant mechanisms for dealing with nitrosative stress, in the malarial resistance conferred by sickle cell Hb, and in the as-yet unsuccessful designs for safe and effective blood substitutes. Critical Issues: An important basic principle in consideration of Hb's redox reactions is the distinction between kinetic and thermodynamic reaction control. Clarification of these modes of control is critical to gaining an increased understanding of Hb-mediated oxidative processes and oxidative toxicity in vivo. Future Directions: This review addresses emerging concepts and some unresolved questions regarding the interplay between the oxygenation and oxidation reactions of structurally diverse Hbs, both within red blood cells and under acellular conditions. Developing methods that control Hb-mediated oxidative toxicity will be critical to the future development of Hb-based blood substitutes. Antioxid. Redox Signal. 18, 2298–2313. PMID:23198874

The Properties of Oxygen Investigated with Easily Accessible Instrumentation: The "One-Photon-Two-Molecule" Mechanism Revisited

ERIC Educational Resources Information Center

Adelhelm, Manfred; Aristov, Natasha; Habekost, Achim

2010-01-01

The physical properties of oxygen, in particular, the blue color of the liquid phase, the red glow of its chemiluminescence, and its paramagnetism as shown by the entrapment or deflection of liquid oxygen by a magnetic field, can be investigated in a regular school setting with hand-held spectrophotometers and digital cameras. In college-level…

The globins of cyanobacteria and algae.

PubMed

Johnson, Eric A; Lecomte, Juliette T J

2013-01-01

Approximately, 20 years ago, a haemoglobin gene was identified within the genome of the cyanobacterium Nostoc commune. Haemoglobins have now been confirmed in multiple species of photosynthetic microbes beyond N. commune, and the diversity of these proteins has recently come under increased scrutiny. This chapter summarizes the state of knowledge concerning the phylogeny, physiology and chemistry of globins in cyanobacteria and green algae. Sequence information is by far the best developed and the most rapidly expanding aspect of the field. Structural and ligand-binding properties have been described for just a few proteins. Physiological data are available for even fewer. Although activities such as nitric oxide dioxygenation and oxygen scavenging are strong candidates for cellular function, dedicated studies will be required to complete the story on this intriguing and ancient group of proteins. © 2013 Elsevier Ltd. All rights reserved.

Dexrazoxane for the prevention of cardiac toxicity and treatment of extravasation injury from the anthracycline antibiotics.

PubMed

Doroshow, James H

2012-08-01

The cumulative cardiac toxicity of the anthracycline antibiotics and their propensity to produce severe tissue injury following extravasation from a peripheral vein during intravenous administration remain significant problems in clinical oncologic practice. Understanding of the free radical metabolism of these drugs and their interactions with iron proteins led to the development of dexrazoxane, an analogue of EDTA with intrinsic antineoplastic activity as well as strong iron binding properties, as both a prospective cardioprotective therapy for patients receiving anthracyclines and as an effective treatment for anthracycline extravasations. In this review, the molecular mechanisms by which the anthracyclines generate reactive oxygen species and interact with intracellular iron are examined to understand the cardioprotective mechanism of action of dexrazoxane and its ability to protect the subcutaneous tissues from anthracycline-induced tissue necrosis.

Proinflammatory Activity of a Cecropin-Like Antibacterial Peptide from Helicobacter pylori

PubMed Central

Bylund, Johan; Christophe, Thierry; Boulay, Francois; Nyström, Thomas; Karlsson, Anna; Dahlgren, Claes

2001-01-01

Helicobacter pylori, the bacterial pathogen associated with gastritis and peptic ulcers, is highly successful in establishing infection in the human gastric mucosa, a process typically associated with massive infiltration of inflammatory cells. Colonization of the mucosa is suggested to be facilitated by H. pylori-produced cecropin-like peptides with antibacterial properties, giving the microbe a competitive advantage over other bacteria. We show that a cecropin-like antibacterial peptide from H. pylori, Hp(2-20), not only has a potent bactericidal effect but also induces proinflammatory activities in human neutrophils, e.g., upregulation of integrins (Mac-1), induction of chemotaxis, and activation of the oxygen radical producing NADPH-oxidase. Furthermore, we show that these effects are mediated through binding of Hp(2-20) to the promiscuous, G-protein-linked lipoxin A4 receptor–formyl peptide-like receptor 1. PMID:11353614

Spectral and in vitro antimicrobial properties of 2-oxo-4-phenyl-6-styryl-1,2,3,4-tetrahydro-pyrimidine-5-carboxylic acid transition metal complexes

NASA Astrophysics Data System (ADS)

Dhankar, Raksha P.; Rahatgaonkar, Anjali M.; Chorghade, Mukund S.; Tiwari, Ashutosh

2-oxo-4-phenyl-6-styryl-1,2,3,4-tetrahydro-pyrimidine-5-carboxylic acid (ADP) was complexed with acetates of Mn(II), Ni(II), Cu(II) and Zn(II). The structures of the ligand and its metal complexes were characterized by microanalysis, IR, NMR, UV-vis spectroscopy, magnetic susceptibility and TGA-DTA analyses. Octahedral and square planar geometries were suggested for the complexes in which the central metal ion coordinated with sbnd O donors of ligand and acetate ions. Each ligand binds the metal using carboxylate oxygens. The ligand and complexes were evaluated for their antimicrobial activities against different species of pathogenic bacteria and fungi. The present novel pyrimidine containing complexes could constitute a new group of antibacterial and antifungal agents.

Swertiajaponin as an anti-browning and antioxidant flavonoid.

PubMed

Moon, Kyoung Mi; Lee, Bonggi; Cho, Won-Kyung; Lee, Bong-Seon; Kim, Choon Young; Ma, Jin Yeul

2018-06-30

Enzymatic browning is a major issue that needs to be solved in the food industry. Although swertiajaponin is a flavonoid rich in the whole herb of Swertia japonica that has been clinically used, its biological functions and applicat​ion in the foods have not been fully elucidated. Here, we showed that swertiajaponin efficiently blocked enzymatic browning in potatoes possibly by direct binding to and inactivating polyphenol oxidase. Furthermore, swertiajaponin showed potent antioxidant activity proven by markedly suppressed reactive oxygen species. Swertiajaponin significantly increased antioxidant properties of potato extract when it is added since it additively elevated total flavonoid content. Considering numerous beneficial effects of antioxidants, swertiajaponin may be used as a functional food additive to suppress enzymatic browning and elevate the antioxidant capacity of foods including beverages and soups by fortification of flavonoids. Copyright © 2018 Elsevier Ltd. All rights reserved.

Surface charge effects in protein adsorption on nanodiamonds

NASA Astrophysics Data System (ADS)

Aramesh, M.; Shimoni, O.; Ostrikov, K.; Prawer, S.; Cervenka, J.

2015-03-01

Understanding the interaction of proteins with charged diamond nanoparticles is of fundamental importance for diverse biomedical applications. Here we present a thorough study of protein binding, adsorption kinetics and structure on strongly positively (hydrogen-terminated) and negatively (oxygen-terminated) charged nanodiamond particles using a quartz crystal microbalance by dissipation and infrared spectroscopy. By using two model proteins (bovine serum albumin and lysozyme) of different properties (charge, molecular weight and rigidity), the main driving mechanism responsible for the protein binding to the charged nanoparticles was identified. Electrostatic interactions were found to dominate the protein adsorption dynamics, attachment and conformation. We developed a simple electrostatic model that can qualitatively explain the observed adsorption behaviour based on charge-induced pH modifications near the charged nanoparticle surfaces. Under neutral conditions, the local pH around the positively and negatively charged nanodiamonds becomes very high (11-12) and low (1-3) respectively, which has a profound impact on the protein charge, hydration and affinity to the nanodiamonds. Small proteins (lysozyme) were found to form multilayers with significant conformational changes to screen the surface charge, while larger proteins (albumin) formed monolayers with minor conformational changes. The findings of this study provide a step forward toward understanding and eventually predicting nanoparticle interactions with biofluids.Understanding the interaction of proteins with charged diamond nanoparticles is of fundamental importance for diverse biomedical applications. Here we present a thorough study of protein binding, adsorption kinetics and structure on strongly positively (hydrogen-terminated) and negatively (oxygen-terminated) charged nanodiamond particles using a quartz crystal microbalance by dissipation and infrared spectroscopy. By using two model proteins (bovine serum albumin and lysozyme) of different properties (charge, molecular weight and rigidity), the main driving mechanism responsible for the protein binding to the charged nanoparticles was identified. Electrostatic interactions were found to dominate the protein adsorption dynamics, attachment and conformation. We developed a simple electrostatic model that can qualitatively explain the observed adsorption behaviour based on charge-induced pH modifications near the charged nanoparticle surfaces. Under neutral conditions, the local pH around the positively and negatively charged nanodiamonds becomes very high (11-12) and low (1-3) respectively, which has a profound impact on the protein charge, hydration and affinity to the nanodiamonds. Small proteins (lysozyme) were found to form multilayers with significant conformational changes to screen the surface charge, while larger proteins (albumin) formed monolayers with minor conformational changes. The findings of this study provide a step forward toward understanding and eventually predicting nanoparticle interactions with biofluids. Electronic supplementary information (ESI) available: The FTIR spectrum of nanodiamonds, QCM-D profiles of 50 nm nanodiamond adsorption on silica surfaces, QCM-D profiles of protein desorption after rinsing with water (rinsing experiment) and the full FTIR spectrum of proteins before and after adsorption on ND particles. See DOI: 10.1039/c5nr00250h

Evidence of room temperature ferromagnetism in argon/oxygen annealed TiO2 thin films deposited by electron beam evaporation technique

NASA Astrophysics Data System (ADS)

Mohanty, P.; Kabiraj, D.; Mandal, R. K.; Kulriya, P. K.; Sinha, A. S. K.; Rath, Chandana

2014-04-01

TiO2 thin films deposited by electron beam evaporation technique annealed in either O2 or Ar atmosphere showed ferromagnetism at room temperature. The pristine amorphous film demonstrates anatase phase after annealing under Ar/O2 atmosphere. While the pristine film shows a super-paramagnetic behavior, both O2 and Ar annealed films display hysteresis at 300 K. X-ray photo emission spectroscopy (XPS), Raman spectroscopy, Rutherford's backscattering spectroscopy (RBS), cross-sectional transmission electron microscopy (TEM) and energy dispersive X-ray spectroscopy (EDS) were used to refute the possible role of impurities/contaminants in magnetic properties of the films. The saturation magnetization of the O2 annealed film is found to be higher than the Ar annealed one. It is revealed from shifting of O 1s and Ti 2p core level spectra as well as from the enhancement of high binding energy component of O 1s spectra that the higher magnetic moment is associated with higher oxygen vacancies. In addition, O2 annealed film demonstrates better crystallinity, uniform deposition and smoother surface than that of the Ar annealed one from glancing angle X-ray diffraction (GAXRD) and atomic force microscopy (AFM). We conclude that although ferromagnetism is due to oxygen vacancies, the higher magnetization in O2 annealed film could be due to crystallinity, which has been observed earlier in Co doped TiO2 film deposited by pulsed laser deposition (Mohanty et al., 2012 [10]).

Effect of Ion Binding in Palmitoyl-Oleoyl Phosphatidylserine Monolayers

NASA Astrophysics Data System (ADS)

Eckler, Matthew; Matysiak, Silvina

2013-03-01

Molecular dynamics simulations of palmitoyl-oleoyl phosphatidylserine (POPS) monolayers at the air-water interface were performed with different ionic strengths with the aim of determining the specific organization and dynamics of counterion binding events. Na + ions penetrated the monolayers into both the ester carbonyl and carboxylate regions of the phospholipids. The binding events increase with the addition of salt. Differences in lipid order parameter, headgroup orientation, and prevalence of inter- and intramolecular hydrogen bonding events between the amine group of the lipid and oxygen groups are observed depending on whether the Na + is binding near the carboxylate or ester region of the lipid. The observed changes are explained in terms of the salting-out effect.

Critical Role of Water and Oxygen Defects in C-O Scission during CO2 Reduction on Zn2GeO4(010).

PubMed

Yang, Jing; Li, Yanlu; Zhao, Xian; Fan, Weiliu

2018-03-27

Exploration of catalyst structure and environmental sensitivity for C-O bond scission is essential for improving the conversion efficiency because of the inertness of CO 2 . We performed density functional theory calculations to understand the influence of the properties of adsorbed water and the reciprocal action with oxygen vacancy on the CO 2 dissociation mechanism on Zn 2 GeO 4 (010). When a perfect surface was hydrated, the introduction of H 2 O was predicted to promote the scission step by two modes based on its appearance, with the greatest enhancement from dissociative adsorbed H 2 O. The dissociative H 2 O lowers the barrier and reaction energy of CO 2 dissociation through hydrogen bonding to preactivate the C-O bond and assisted scission via a COOH intermediate. The perfect surface with bidentate-binding H 2 O was energetically more favorable for CO 2 dissociation than the surface with monodentate-binding H 2 O. Direct dissociation was energetically favored by the former, whereas monodentate H 2 O facilitated the H-assisted pathway. The defective surface exhibited a higher reactivity for CO 2 decomposition than the perfect surface because the generation of oxygen vacancies could disperse the product location. When the defective surface was hydrated, the reciprocal action for vacancy and surface H 2 O on CO 2 dissociation was related to the vacancy type. The presence of H 2 O substantially decreased the reaction energy for the direct dissociation of CO 2 on O 2c1 - and O 3c2 -defect surfaces, which converts the endoergic reaction to an exoergic reaction. However, the increased decomposition barrier made the step kinetically unfavorable and reduced the reaction rate. When H 2 O was present on the O 2c2 -defect surface, both the barrier and reaction energy for direct dissociation were invariable. This result indicated that the introduction of H 2 O had little effect on the kinetics and thermodynamics. Moreover, the H-assisted pathway was suppressed on all hydrated defect surfaces. These results provide a theoretical perspective for the design of highly efficient catalysts.

Autoxidation and Oxygen Binding Properties of Recombinant Hemoglobins with Substitutions at the αVal-62 or βVal-67 Position of the Distal Heme Pocket*

PubMed Central

Tam, Ming F.; Rice, Natalie W.; Maillett, David H.; Simplaceanu, Virgil; Ho, Nancy T.; Tam, Tsuey Chyi S.; Shen, Tong-Jian; Ho, Chien

2013-01-01

The E11 valine in the distal heme pocket of either the α- or β-subunit of human adult hemoglobin (Hb A) was replaced by leucine, isoleucine, or phenylalanine. Recombinant proteins were expressed in Escherichia coli and purified for structural and functional studies. 1H NMR spectra were obtained for the CO and deoxy forms of Hb A and the mutants. The mutations did not disturb the α1β2 interface in either form, whereas the H-bond between αHis-103 and βGln-131 in the α1β1 interfaces of the deoxy α-subunit mutants was weakened. Localized structural changes in the mutated heme pocket were detected for the CO form of recombinant Hb (rHb) (αV62F), rHb (βV67I), and rHb (βV67F) compared with Hb A. In the deoxy form the proximal histidyl residue in the β-subunit of rHb (βV67F) has been altered. Furthermore, the interactions between the porphyrin ring and heme pocket residues have been perturbed in rHb (αV62I), rHb (αV62F), and rHb (βV67F). Functionally, the oxygen binding affinity (P50), cooperativity (n50), and the alkaline Bohr Effect of the three α-subunit mutants and rHb (βV67L) are similar to those of Hb A. rHb (βV67I) and rHb (βV67F) exhibit low and high oxygen affinity, respectively. rHb (βV67F) has P50 values lower that those reported for rHb (αL29F), a B10 mutant studied previously in our laboratory (Wiltrout, M. E., Giovannelli, J. L., Simplaceanu, V., Lukin, J. A., Ho, N. T., and Ho, C. (2005) Biochemistry 44, 7207–7217). These E11 mutations do not slow down the autoxidation and azide-induced oxidation rates of the recombinant proteins. Results from this study provide new insights into the roles of E11 mutants in the structure-function relationship in hemoglobin. PMID:23867463

Time-resolved studies define the nature of toxic IAPP intermediates, providing insight for anti-amyloidosis therapeutics

PubMed Central

Abedini, Andisheh; Plesner, Annette; Cao, Ping; Ridgway, Zachary; Zhang, Jinghua; Tu, Ling-Hsien; Middleton, Chris T; Chao, Brian; Sartori, Daniel J; Meng, Fanling; Wang, Hui; Wong, Amy G; Zanni, Martin T; Verchere, C Bruce; Raleigh, Daniel P; Schmidt, Ann Marie

2016-01-01

Islet amyloidosis by IAPP contributes to pancreatic β-cell death in diabetes, but the nature of toxic IAPP species remains elusive. Using concurrent time-resolved biophysical and biological measurements, we define the toxic species produced during IAPP amyloid formation and link their properties to induction of rat INS-1 β-cell and murine islet toxicity. These globally flexible, low order oligomers upregulate pro-inflammatory markers and induce reactive oxygen species. They do not bind 1-anilnonaphthalene-8-sulphonic acid and lack extensive β-sheet structure. Aromatic interactions modulate, but are not required for toxicity. Not all IAPP oligomers are toxic; toxicity depends on their partially structured conformational states. Some anti-amyloid agents paradoxically prolong cytotoxicity by prolonging the lifetime of the toxic species. The data highlight the distinguishing properties of toxic IAPP oligomers and the common features that they share with toxic species reported for other amyloidogenic polypeptides, providing information for rational drug design to treat IAPP induced β-cell death. DOI: http://dx.doi.org/10.7554/eLife.12977.001 PMID:27213520

First-Principles Study of Carbon and Vacancy Structures in Niobium

DOE PAGES

Ford, Denise C.; Zapol, Peter; Cooley, Lance D.

2015-04-03

The interstitial chemical impurities hydrogen, oxygen, nitrogen, and carbon are important for niobium metal production, and particularly for the optimization of niobium SRF technology. These atoms are present in refined sheets and can be absorbed into niobium during processing treatments, resulting in changes to the residual resistance and the performance of SRF cavities. A first-principles approach is taken to study the properties of carbon in niobium, and the results are compared and contrasted with the properties of the other interstitial impurities. The results indicate that C will likely form precipitates or atmospheres around defects rather than strongly bound complexes withmore » other impurities. Based on the analysis of carbon and hydrogen near niobium lattice vacancies and small vacancy chains and clusters, the formation of extended carbon chains and hydrocarbons is not likely to occur. Association of carbon with hydrogen atoms can, however, occur through the strain fields created by interstitial binding of the impurity atoms. In conclusion, calculated electronic densities of states indicate that interstitial C may have a similar effect as interstitial O on the superconducting transition temperature of Nb.« less

Ice surfaces in the mesosphere: Absence of dangling bonds in the presence of atomic oxygen

NASA Astrophysics Data System (ADS)

Boulter, James E.; Morgan, Christopher G.; Marschall, Jochen

2005-07-01

Ice deposition experiments in the presence of microwave discharge-dissociated molecular oxygen suggest heterogeneous interactions between dangling OH bonds on the ice surface and atomic oxygen. Ice films deposited on a gold substrate at temperatures of 115, 130, and 140 K from oxygen/water gas mixtures representative of the summertime polar mesosphere exhibit infrared absorption features characteristic of dangling bonds, whereas films grown in the presence of atomic oxygen do not. Dangling bond spectral features are shown to diminish rapidly when the microwave discharge is activated during ice deposition. Similar decreases were not seen when the gas stream was heated or when the ice film was slowly annealed from 130 to 160 K. One interpretation of these results is that atomic oxygen binds to dangling bond sites during ice growth, a phenomenon that may also occur during the formation of ice particles observed just below the cold summertime mesopause.

Improvement of oxygen storage properties of hexagonal YMnO3+δ by microstructural modifications

NASA Astrophysics Data System (ADS)

Klimkowicz, Alicja; Świerczek, Konrad; Kobayashi, Shuntaro; Takasaki, Akito; Allahyani, Wadiah; Dabrowski, Bogdan

2018-02-01

Hexagonal YMnO3+δ is shown to be an effective temperature-swing oxygen storage material working at low temperatures (150-300 °C) in pure oxygen if adequately processed or obtained having sub-micrometer primary particles with limited number of big agglomerates. A substantial increase of a practical oxygen storage capacity is observed for a sample synthesized by a solid-state method, which was subjected to a high impact mechanical milling. However, even better properties can be achieved for the sol-gel technique-produced YMnO3+δ. The reversible incorporation and release of the oxygen is associated with a structural transformation between stoichiometric YMnO3 (Hex0) phase and a mixture of oxygen-loaded Hex1 with δ ≈ 0.28 and Hex2 with δ ≈ 0.41 phases, as documented by in situ structural X-ray diffraction studies, supported by thermogravimetric experiments. Contrary to HoMnO3+δ, it was not possible to obtain single phase Hex1 material in oxygen, as well as to oxidize YMnO3 in air. Results confirm crucial role of the ionic size of rare earth element Ln on the oxygen storage-related properties and stability of the oxygen-loaded LnMnO3+δ phases.

Variations in oxygen and ellagitannins, and organoleptic properties of red wine aged in French oak barrels classified by a near infrared system.

PubMed

Michel, Julien; Albertin, Warren; Jourdes, Michael; Le Floch, Alexandra; Giordanengo, Thomas; Mourey, Nicolas; Teissedre, Pierre-Louis

2016-08-01

During wine aging in barrels, antioxidant molecules from wood, such as ellagitannins, are solubilized and react with wine molecules and oxygen. However, their concentrations are highly variable. Oxygen is an important factor, as it plays a role in wine parameters and organoleptic perceptions. Five barrel modalities were used; three polyphenol indices (IP), classified using the NIRS procedure, and three grain qualities. Barrels were equipped with windows to measure the oxygen using luminescence technology. The ellagitannin concentrations in the wine and its organoleptic properties were monitored. Oxygen concentrations decreased quickly during the first 8days of aging and this phenomenon was significantly more marked in barrels with a higher IP and medium grain. The ellagitannin concentrations were believed to be correlated with wood classification and oxygen consumption. Furthermore, the organoleptic properties were significantly impacted, as the wine with the lowest ellagitannin level was described as less astringent, bitter, woody, and smoky/toasty. Copyright © 2016 Elsevier Ltd. All rights reserved.

Tensile properties of V-Cr-Ti alloys after exposure in helium and low-partial-pressure oxygen environments

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

Natesan, K.; Soppet, W.K.

1997-04-01

A test program is in progress to evaluate the effect of oxygen at low pO{sub 2} on the tensile properties of V-(4-5)wt% Cr-(4-5)wt% Ti alloys. Some of the tensile specimens were precharged with oxygen at low pO{sub 2} at 500{degrees}C and reannealed in vacuum at 500{degrees}C in environments with various pO{sub 2} levels and subsequently tensile tested at room temperature. The preliminary results indicate that both approaches are appropriate for evaluating the effect of oxygen uptake on the tensile properties of the alloys. The data showed that in the relatively short-time tests conducted thus far, the maximum engineering stress slightlymore » increased after oxygen exposure but the uniform and total elongation values exhibited significant decrease after exposure in oxygen-containing environments. The data for a specimen exposed to a helium environment were similar to those obtained in low pO{sub 2} environments.« less

Effect of the oxygen content in solution on the static and cyclic deformation of titanium foams.

PubMed

Lefebvre, L P; Baril, E; Bureau, M N

2009-11-01

It is well known that interstitials affect the mechanical properties of titanium and titanium alloys. Their effects on the fatigue properties of titanium foams have not, however, been documented in the literature. This paper presents the effect of the oxygen content on the static and dynamic compression properties of titanium foams. Increasing the oxygen content from 0.24 to 0.51 wt% O in solution significantly increases the yield strength and reduces the ductility of the foams. However, the fatigue limit is not significantly affected by the oxygen content and falls within the 92 MPa +/- 12 MPa range for all specimens investigated in this study. During cyclic loading, deformation is initially coming from cumulative creep followed by the formation of microcracks. The coalescence of these microcracks is responsible for the rupture of the specimens. Fracture surfaces of the specimens having lower oxygen content show a more ductile aspect than the specimens having higher oxygen content.

The effects of oxygen pressure on disordering and magneto-transport properties of Ba{sub 2}FeMoO{sub 6} thin films grown via pulsed laser deposition

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

Kim, Kyeong-Won; Mhin, Sungwook; Jones, Jacob L.

2015-07-21

Epitaxial Ba{sub 2}FeMoO{sub 6} thin films were grown via pulsed laser deposition under low oxygen pressure and their structural, chemical, and magnetic properties were examined, focusing on the effects of oxygen pressure. The chemical disorder, off-stoichiometry in B site cations (Fe and Mo) increased with increasing oxygen pressure and thus magnetic properties were degraded. Interestingly, in contrast, negative magneto-resistance, which is the characteristics of this double perovskite material, was enhanced with increasing oxygen pressure. It is believed that phase segregation of highly disordered thin films is responsible for the increased magneto-resistance of thin films grown at high oxygen pressure. Themore » anomalous Hall effect, which behaves hole-like, was also observed due to spin-polarized itinerant electrons under low magnetic field below 1 T and the ordinary electron-like Hall effect was dominant at higher magnetic fields.« less

Characterization of the DNA binding properties of polyomavirus capsid protein

NASA Technical Reports Server (NTRS)

Chang, D.; Cai, X.; Consigli, R. A.; Spooner, B. S. (Principal Investigator)

1993-01-01

The DNA binding properties of the polyomavirus structural proteins VP1, VP2, and VP3 were studied by Southwestern analysis. The major viral structural protein VP1 and host-contributed histone proteins of polyomavirus virions were shown to exhibit DNA binding activity, but the minor capsid proteins VP2 and VP3 failed to bind DNA. The N-terminal first five amino acids (Ala-1 to Lys-5) were identified as the VP1 DNA binding domain by genetic and biochemical approaches. Wild-type VP1 expressed in Escherichia coli (RK1448) exhibited DNA binding activity, but the N-terminal truncated VP1 mutants (lacking Ala-1 to Lys-5 and Ala-1 to Cys-11) failed to bind DNA. The synthetic peptide (Ala-1 to Cys-11) was also shown to have an affinity for DNA binding. Site-directed mutagenesis of the VP1 gene showed that the point mutations at Pro-2, Lys-3, and Arg-4 on the VP1 molecule did not affect DNA binding properties but that the point mutation at Lys-5 drastically reduced DNA binding affinity. The N-terminal (Ala-1 to Lys-5) region of VP1 was found to be essential and specific for DNA binding, while the DNA appears to be non-sequence specific. The DNA binding domain and the nuclear localization signal are located in the same N-terminal region.

Studies of the Interaction of Influenza Virus RNA Polymerase PAN with Endonuclease Inhibitors.

PubMed

Dong, Li-Hua; Cao, Xiao-Rong

2018-06-01

Influenza virus is a major causative agent of respiratory viral infections, and RNA polymerase catalyzes its replication and transcription activities in infected cell nuclei. Since it is highly conserved in all virus strains, RNA polymerase becomes a key target of anti-influenza virus agents. Although experimental studies have revealed the good inhibitory activity of endonuclease inhibitors to RNA polymerase, the mechanism is still unclear. In this study, the docking and molecular dynamics simulations have been performed to explore the interaction of three kinds of endonuclease inhibitors with the subunit (PA N ) of RNA polymerase. Our calculations indicate that all these endonuclease inhibitors can bind to the binding pocket of PA N , in which the electronegative oxygen atoms of the inhibitors form a chelated structure with the two Mn 2+ cations of the active center. The most important interaction between these inhibitors and PA N is electrostatic interaction. The electron density of the chelate oxygen atoms determines the magnitude of the electrostatic energy, and the chelated structure and orientation of inhibitors depend largely on the distance between the chelate oxygen atoms.

Method of making an electrode

DOEpatents

Isenberg, Arnold O.

1986-01-01

Disclosed is a method of coating an electrode on a solid oxygen conductive oxide layer. A coating of particles of an electronic conductor is formed on one surface of the oxide layer and a source of oxygen is applied to the opposite surface of the oxide layer. A metal halide vapor is applied over the electronic conductor and the oxide layer is heated to a temperature sufficient to induce oxygen to diffuse through the oxide layer and react with the metal halide vapor. This results in the growing of a metal oxide coating on the particles of electronic conductor, thereby binding them to the oxide layer.

Interrogating the relationship between rat in vivo tissue distribution and drug property data for >200 structurally unrelated molecules

PubMed Central

Harrell, Andrew W; Sychterz, Caroline; Ho, May Y; Weber, Andrew; Valko, Klara; Negash, Kitaw

2015-01-01

The ability to explain distribution patterns from drug physicochemical properties and binding characteristics has been explored for more than 200 compounds by interrogating data from quantitative whole body autoradiography studies (QWBA). These in vivo outcomes have been compared to in silico and in vitro drug property data to determine the most influential properties governing drug distribution. Consistent with current knowledge, in vivo distribution was most influenced by ionization state and lipophilicity which in turn affected phospholipid and plasma protein binding. Basic and neutral molecules were generally better distributed than acidic counterparts demonstrating weaker plasma protein and stronger phospholipid binding. The influence of phospholipid binding was particularly evident in tissues with high phospholipid content like spleen and lung. Conversely, poorer distribution of acidic drugs was associated with stronger plasma protein and weaker phospholipid binding. The distribution of a proportion of acidic drugs was enhanced, however, in tissues known to express anionic uptake transporters such as the liver and kidney. Greatest distribution was observed into melanin containing tissues of the eye, most likely due to melanin binding. Basic molecules were consistently better distributed into parts of the eye and skin containing melanin than those without. The data, therefore, suggest that drug binding to macromolecules strongly influences the distribution of total drug for a large proportion of molecules in most tissues. Reducing lipophilicity, a strategy often used in discovery to optimize pharmacokinetic properties such as absorption and clearance, also decreased the influence of nonspecific binding on drug distribution. PMID:26516585

Structure of a Premicellar Complex of Alkyl Sulfates with the Interfacial Binding Surfaces of 4 Subunits of Phospholipase A2✰

PubMed Central

Pan, Ying H.; Bahnson, Brian J.

2010-01-01

The properties of three discrete premicellar complexes (E1#, E2#, E3#) of pig pancreatic group-IB secreted phospholipase A2 (sPLA2) with monodisperse alkyl sulfates has been characterized [Berg, O. G., et al., Biochemistry 43, 7999–8013, 2004]. Here we have solved the 2.7 Å crystal structure of group-IB sPLA2 complexed with 12 molecules of octyl sulfate (C8S) in a form consistent with a tetrameric oligomeric that exists during the E1# phase of premicellar complexes. The alkyl tails of the C8S molecules are centered in the middle of the tetrameric cluster of sPLA2 subunits. Three of the four sPLA2 subunits also contain a C8S molecule in the active site pocket. The sulfate oxygen of a C8S ligand is complexed to the active site calcium in 3 of the 4 protein active sites. The interactions of the alkyl sulfate head group with Arg-6 and Lys-10, as well as the backbone amide of Met-20, are analogous to those observed in the previously solved sPLA2 crystal structures with bound phosphate and sulfate anions. The cluster of three anions found in the present structure is postulated to be the site for nucleating the binding of anionic amphiphiles to the interfacial surface of the protein, and therefore this binding interaction has implications for interfacial activation of the enzyme. PMID:20302975

Hydration of cations: a key to understanding of specific cation effects on aggregation behaviors of PEO-PPO-PEO triblock copolymers.

PubMed

Lutter, Jacob C; Wu, Tsung-yu; Zhang, Yanjie

2013-09-05

This work reports results from the interactions of a series of monovalent and divalent cations with a triblock copolymer, poly(ethylene oxide)-b-poly(propylene oxide)-b-poly(ethylene oxide) (PEO-PPO-PEO). Phase transition temperatures of the polymer in the presence of chloride salts with six monovalent and eight divalent cations were measured using an automated melting point apparatus. The polymer undergoes a two-step phase transition, consisting of micellization of the polymer followed by aggregation of the micelles, in the presence of all the salts studied herein. The results suggest that hydration of cations plays a key role in determining the interactions between the cations and the polymer. The modulation of the phase transition temperature of the polymer by cations can be explained as a balance between three interactions: direct binding of cations to the oxygen in the polymer chains, cations sharing one water molecule with the polymer in their hydration layer, and cations interacting with the polymer via two water molecules. Monovalent cations Na(+), K(+), Rb(+), and Cs(+) do not bind to the polymer, while Li(+) and NH4(+) and all the divalent cations investigated including Mg(2+), Ca(2+), Sr(2+), Ba(2+), Co(2+), Ni(2+), Cu(2+), and Cd(2+) bind to the polymer. The effects of the cations correlate well with their hydration thermodynamic properties. Mechanisms for cation-polymer interactions are discussed.

Synthesis, spectral characterization and DNA binding of Schiff-base metal complexes derived from 2-amino-3-hydroxyprobanoic acid and acetylacetone

NASA Astrophysics Data System (ADS)

Hosny, Nasser Mohammed; Hussien, Mostafa A.; Radwan, Fatima M.; Nawar, Nagwa

2014-11-01

Four new metal complexes derived from the reaction of Cu(II), Co(II), Ni(II) and Zn(II) acetates with the Schiff-base ligand (H3L) resulted from the condensation of the amino acid 2-amino-3-hydroxyprobanoic acid (serine) and acetylacetone have been synthesized and characterized by, elemental analyses, ES-MS, IR, UV-Vis., 1H NMR, 13C NMR, ESR, thermal analyses (TGA and DTG) and magnetic measurements. The results showed that the Schiff-base ligand acts as bi-negative tridentate through the azomethine nitrogen, the deprotonated carboxylate oxygen and the enolic carbonyl oxygen. The optical band gaps measurements indicated the semi-conducting nature of these complexes. Molecular docking was used to predict the binding between the Schiff base ligand with the receptor of prostate cancer mutant H874Y. The interactions between the Cu(II) complex and calf thymus DNA (CT-DNA) have been studied by UV spectra. The results confirm that the Cu(II) complex binds to CT-DNA in an intercalative mode.

Zinc Bioavailability from Phytate-Rich Foods and Zinc Supplements. Modeling the Effects of Food Components with Oxygen, Nitrogen, and Sulfur Donor Ligands.

PubMed

Tang, Ning; Skibsted, Leif H

2017-10-04

Aqueous solubility of zinc phytate (K sp = (2.6 ± 0.2) × 10 -47 mol 7 /L 7 ), essential for zinc bioavailability from plant foods, was found to decrease with increasing temperature corresponding to ΔH dis of -301 ± 22 kJ/mol and ΔS dis of -1901 ± 72 J/(mol K). Binding of zinc to phytate was found to be exothermic for the stronger binding site and endothermic for the weaker binding site. The solubility of the slightly soluble zinc citrate and insoluble zinc phytate was found to be considerably enhanced by the food components with oxygen donor, nitrogen donor, and sulfur donor ligands. The driving force for the enhanced solubility is mainly due to the complex formation between zinc and the investigated food components rather than ligand exchange and ternary complex formation as revealed by quantum mechanical calculations and isothermal titration calorimetry. Histidine and citrate are promising ligands for improving zinc absorption from phytate-rich foods.

Development of biodegradable materials; balancing degradability and performance

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

Mayer, J.M.; Allen, A.L.; Dell, P.A.

1993-12-31

The development of biodegradable materials suitable for packaging must take into consideration various performance criteria such as mechanical and barrier properties, as well as rate of biodegradability in given environments. Individual or blended biopolymer films were obtained commercially or blown into film in the laboratory and tested for tensile strength, ultimate elongation and oxygen barrier. These films were then subjected to accelerated marine biodegradation tests as well as simulated marine respirometry. Starch/ethylene vinyl alcohol films exhibited good mechanical and excellent oxygen barrier properties, but were very slow to biodegrade in the simulated and excellent oxygen barrier properties, but were verymore » slow to biodegrade in the simulated marine environment. Polyhydroxyalkanoates had good mechanical properties, average oxygen barrier and good biodegradability. Data indicate that performance and biodegradability of packaging can be tailored to needs by combining individual biopolymers in different proportions in blends and laminates.« less

Properties of tungsten coating deposited onto copper by high-speed atmospheric plasma spraying

NASA Astrophysics Data System (ADS)

Jianjun, Huang; Fan, Wang; Ying, Liu; Shishou, Jiang; Xisheng, Wang; Bing, Qi; Liang, Gao

2011-07-01

Tungsten (W) coatings were fabricated on copper (Cu) by high-speed atmospheric plasma spray (HAPS) technique. The properties of the porosity, oxygen content, bonding strength and microhardness were measured. The results obtained indicated that the HAPS-W coating showed good properties particularly in terms of porosity and oxygen content. The porosity of the HAPS-W coating was 2.3% and the distribution of pore size diameter was mainly concentrated in the range of 0.01-1 μm. The oxygen content of the coating measured by means of Nitrogen/Oxygen Determinator was about 0.10 wt.%. These initial results suggest that the HAPS-W coating has achieved the reported properties of the vacuum plasma spray (VPS) W coating. Compared with VPS, HAPS-W technique could provide a convenient and low cost way to obtain adequate W coatings for fusion applications.

RNA-binding properties and mapping of the RNA-binding domain from the movement protein of Prunus necrotic ringspot virus.

PubMed

Herranz, M Carmen; Pallás, Vicente

2004-03-01

The movement protein (MP) of Prunus necrotic ringspot virus (PNRSV) is involved in intercellular virus transport. In this study, putative RNA-binding properties of the PNRSV MP were studied. The PNRSV MP was produced in Escherichia coli using an expression vector. Electrophoretic mobility shift assays (EMSAs) using DIG-labelled riboprobes demonstrated that PNRSV MP bound ssRNA cooperatively without sequence specificity. Two different ribonucleoprotein complexes were found to be formed depending on the molar MP : PNRSV RNA ratio. The different responses of the complexes to urea treatment strongly suggested that they have different structural properties. Deletion mutagenesis followed by Northwestern analysis allowed location of a nucleic acid binding domain to aa 56-88. This 33 aa RNA-binding motif is the smallest region delineated among members of the family Bromoviridae for which RNA-binding properties have been demonstrated. This domain is highly conserved within all phylogenetic subgroups previously described for PNRSV isolates. Interestingly, the RNA-binding domain described here and the one described for Alfamovirus are located at the N terminus of their corresponding MPs, whereas similar domains previously characterized in members of the genera Bromovirus and Cucumovirus are present at the C terminus, strongly reflecting their corresponding phylogenetic relationships. The evolutionary implications of this observation are discussed.

Effect of time varying phosphorus implantation on optoelectronics properties of RF sputtered ZnO thin-films

NASA Astrophysics Data System (ADS)

Murkute, Punam; Ghadi, Hemant; Saha, Shantanu; Chavan, Vinayak; Chakrabarti, Subhananda

2018-03-01

ZnO has potential application in the field of short wavelength devices like LED's, laser diodes, UV detectors etc, because of its wide band gap (3.34 eV) and high exciton binding energy (60 meV). ZnO possess N-type conductivity due to presence of defects arising from oxygen and zinc interstitial vacancies. In order to achieve P-type or intrinsic carrier concentration an implantation study is preferred. In this report, we have varied phosphorous implantation time and studied its effect on optical as well structural properties of RF sputtered ZnO thin-films. Implantation was carried out using Plasma Immersion ion implantation technique for 10 and 20 s. These films were further annealed at 900°C for 10 s in oxygen ambient to activate phosphorous dopants. Low temperature photoluminescence (PL) spectra measured two distinct peaks at 3.32 and 3.199 eV for 20 s implanted sample annealed at 900°C. Temperature dependent PL measurement shows slightly blue shift in peak position from 18 K to 300 K. 3.199 eV peak can be attributed to donoracceptor pair (DAP) emission and 3.32 eV peak corresponds to conduction-band-to-acceptor (eA0) transition. High resolution x-ray diffraction revels dominant (002) peak from all samples. Increasing implantation time resulted in low peak intensity suggesting a formation of implantation related defects. Compression in C-axis with implantation time indicates incorporation of phosphorus in the formed film. Improvement in surface quality was observed from 20 s implanted sample which annealed at 900°C.

Performance and properties of atomic oxygen protective coatings for polymeric materials

NASA Technical Reports Server (NTRS)

Banks, Bruce A.; Lamoreaux, Cynthia

1992-01-01

Such large LEO spacecraft as the Space Station Freedom will encounter high atomic oxygen fluences which entail the use of protective coatings for their polymeric structural materials. Such coatings have demonstrated polymer mass losses due to oxidation that are much smaller than those of unprotected materials. Attention is here given to protective and/or electrically conductive coatings of SiO(x), Ge, and indium-tin oxide which have been exposed to atomic oxygen in order to ascertain mass loss, electrical conductivity, and optical property dependence on atomic oxygen exposure.

Determination of optical properties, drug concentration, and tissue oxygenation in human pleural tissue before and after Photofrin-mediated photodynamic therapy

NASA Astrophysics Data System (ADS)

Ong, Yi Hong; Padawer-Curry, Jonah; Finlay, Jarod C.; Kim, Michele M.; Dimofte, Andreea; Cengel, Keith; Zhu, Timothy C.

2018-02-01

PDT efficacy depends on the concentration of photosensitizer, oxygen, and light delivery in patient tissues. In this study, we measure the in-vivo distribution of important dosimetric parameters, namely the tissue optical properties (absorption μa (λ) and scattering μs ' (λ) coefficients), photofrin concentration (cphotofrin), blood oxygen saturation (%StO2), and total hemoglobin concentration (THC), before and after PDT. We characterize the inter- and intra-patient heterogeneity of these quantities and explore how these properties change as a result of PDT treatment. The result suggests the need for real-time dosimetry during PDT to optimize the treatment condition depending on the optical and physiological properties.

The effect of the morphology of supported subnanometer Pt clusters on the first and key step of CO 2 photoreduction [Morphology effect of supported subnanometer Pt clusters on first and key step of CO 2 photoreduction

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

Yang, Chi -Ta; Wood, Brandon C.; Bhethanabotla, Venkat R.

2015-09-04

In this study, using density functional theory calculations, we investigate the influence of size-dependent cluster morphology on the synergistic catalytic properties of anatase TiO 2(101) surfaces decorated with subnanometer Pt clusters. Focusing on the formation of the key precursor in the CO 2 photoreduction reaction (bent CO 2 –), we find that flatter (2D-like) Pt clusters that “wet” the TiO 2 surface offer significantly less benefit than 3D-like Pt clusters. We attribute the differences to three factors. First, the 3D clusters provide a greater number of accessible Pt–TiO 2 interfacial sites with geometries that can aid CO 2 bond bendingmore » and charge transfer processes. Second, binding competition among each Pt–CO 2 bonding interaction mitigates maximum orbital overlaps, leading to insufficient CO 2 binding. Third and also most interestingly, the 3D clusters tend to possess higher structural fluxionality than the flatter clusters, which is shown to correlate positively with CO2 binding strength. The preferred morphology adopted by the clusters depends on several factors, including the cluster size and the presence of oxygen vacancies on the TiO 2 surface; this suggests a strategy for optimizing the synergistic effect between Pt clusters and TiO 2 surfaces for CO 2 photocatalysis. Clusters of ~6–8 atoms should provide the largest benefit, since they retain the desired 3D morphology, yet are small enough to exhibit high structural fluxionality. Electronic structure analysis provides additional insight into the electronic motivations for the enhanced binding of CO 2 on TiO 2-supported 3D Pt clusters, as well as suppressed binding on flattened, 2D-like clusters.« less

Modulation of hemoglobin dynamics by an allosteric effector

DOE PAGES

Lal, Jyotsana; Maccarini, Marco; Fouquet, Peter; ...

2016-12-15

Hemoglobin (Hb) is an extensively studied paradigm of proteins that alter their function in response to allosteric effectors. Models of its action have been used as prototypes for structure-function relationships in many proteins, and models for the molecular basis of its function have been deeply studied and extensively argued. Recent reports suggest that dynamics may play an important role in its function. Relatively little is known about the slow, correlated motions of hemoglobin subunits in various structural states because experimental and computational strategies for their characterization are challenging. Allosteric effectors such as inositol hexaphosphate (IHP) bind to both deoxy-Hb andmore » HbCO, albeit at different sites, leading to a lowered oxygen affinity. The manner in which these effectors impact oxygen binding is unclear and may involve changes in structure, dynamics or both. Here we use neutron spin echo (NSE) measurements accompanied by wideangle x-ray scattering (WAXS) to show that binding of IHP to HbCO results in an increase in the rate of coordinated motions of Hb subunits relative to one another with little if any change in large scale structure. This increase of large-scale dynamics seems to be coupled with a decrease in the average magnitude of higher frequency modes of individual residues. Furthermore, these observations indicate that enhanced dynamic motions contribute to the functional changes induced by IHP and suggest that they may be responsible for the lowered oxygen affinity triggered by these effectors.« less

Static and dynamic optical properties of La 1-xSr xFeO 3-δ: The effects of A-site and oxygen stoichiometry

DOE PAGES

Sergey Y. Smolin; Sfeir, Matthew Y.; Scafetta, Mark D.; ...

2015-12-09

Perovskite oxides are a promising material class for photovoltaic and photocatalytic applications due to their visible band gaps, nanosecond recombination lifetimes, and great chemical diversity. However, there is limited understanding of the link between composition and static and dynamic optical properties, despite the critical role these properties play in the design of light-harvesting devices. To clarify these relationships, we systemically studied the optoelectronic properties in La 1-xSr xFeO 3-δ epitaxial films, uncovering the effects of A-site cation substitution and oxygen stoichiometry. Variable-angle spectroscopic ellipsometry was used to measure static optical properties, revealing a linear increase in absorption coefficient at 1.25more » eV and a red-shifting of the optical absorption edge with increasing Sr fraction. The absorption spectra can be similarly tuned through the introduction of oxygen vacancies, indicating the critical role that nominal Fe valence plays in optical absorption. Dynamic optoelectronic properties were studied with ultrafast transient reflectance spectroscopy, revealing similar nanosecond photoexcited carrier lifetimes for oxygen deficient and stoichiometric films with the same nominal Fe valence. Furthermore, these results demonstrate that while the static optical absorption is strongly dependent on nominal Fe valence tuned through cation or anion stoichiometry, oxygen vacancies do not appear to play a significantly detrimental role in the recombination kinetics.« less

Plasma treatment of p-GaN/n-ZnO nanorod light-emitting diodes

NASA Astrophysics Data System (ADS)

Leung, Yu Hang; Ng, Alan M. C.; Djurišic, Aleksandra B.; Chan, Wai Kin; Fong, Patrick W. K.; Lui, Hsien Fai; Surya, Charles

2014-03-01

Zinc oxide (ZnO) is a material of great interest for short-wavelength optoelectronic applications due to its wide band gap (3.37 eV) and high exciton binding energy (60 meV). Due to the difficulty in stable p-type doping of ZnO, other p-type materials such as gallium nitride (GaN) have been used to form heterojunctions with ZnO. p-GaN/n-ZnO heterojunction devices, in particular light-emitting diodes (LED) have been extensively studied. There was a huge variety of electronic properties and emission colors on the reported devices. It is due to the different energy alignment at the interface caused by different properties of the GaN layer and ZnO counterpart in the junction. Attempts have been made on modifying the heterojunction by various methods, such as introducing a dielectric interlayer and post-growth surface treatment, and changing the growth methods of ZnO. In this study, heterojunction LED devices with p-GaN and ZnO nanorods array are demonstrated. The ZnO nanorods were grown by a solution method. The ZnO nanorods were exposed to different kinds of plasma treatments (such as nitrogen and oxygen) after the growth. It was found that the treatment could cause significant change on the optical properties of the ZnO nanorods, as well as the electronic properties and light emissions of the resultant LED devices.

Study of Al-Si Alloy Oxygen Saturation on Its Microstructure and Mechanical Properties.

PubMed

Finkelstein, Arkady; Schaefer, Arseny; Chikova, Оlga; Borodianskiy, Konstantin

2017-07-11

One of the main goals of modern materials research is obtaining different microstructures and studying their influence on the mechanical properties of metals; aluminum alloys are particularly of interest due to their advanced performance. Traditionally, their required properties are obtained by alloying process, modification, or physical influence during solidification. The present work describes a saturation of the overheated AlSi₇Fe₁ casting alloy by oxides using oxygen blowing approach in overheated alloy. Changes in metals' microstructural and mechanical properties are also described in the work. An Al 10 SiFe intermetallic complex compound was obtained as a preferable component to Al₂O₃ precipitation on it, and its morphology was investigated by scanning electron microscopy. The mechanical properties of the alloy after the oxygen blowing treatment are discussed in this work.

Implementation of steady state approximation for modelling of reaction kinetic of UV catalysed hydrogen peroxide oxidation of starch

NASA Astrophysics Data System (ADS)

Kumoro, Andri Cahyo; Retnowati, Diah Susetyo; Ratnawati, Budiyati, Catarina Sri

2015-12-01

With regard to its low viscosity, high stability, clarity, film forming and binding properties, oxidised starch has been widely used in various applications specifically in the food, paper, textile, laundry finishing and binding materials industries. A number of methods have been used to produce oxidised starch through reactions with various oxidizing agents, such as hydrogen peroxide, air oxygen, ozone, bromine, chromic acid, permanganate, nitrogen dioxide and hypochlorite. Unfortunately, most of previous works reported in the literatures were focused on the study of reaction mechanism and physicochemical properties characterization of the oxidised starches produced without investigation of the reaction kinetics of the oxidation process. This work aimed to develop a simple kinetic model for UV catalysed hydrogen peroxide oxidation of starch through implementation of steady state approximation for the radical reaction rates. The model was then verified using experimental data available in the literature. The model verification revealed that the proposed model shows its good agreement with the experimental data as indicated by an average absolute relative error of only 2.45%. The model also confirmed that carboxyl groups are oxidised further by hydroxyl radical. The carbonyl production rate was found to follow first order reaction with respect to carbonyl concentration. Similarly, carboxyl production rate also followed first order reaction with respect to carbonyl concentration. The apparent reaction rate constant for carbonyl formation and oxidation were 6.24 × 104 s-1 and 1.01 × 104 M-1.s-1, respectively. While apparent reaction rate constant for carboxyl oxidation was 4.86 × 104 M-1.s-1.

Charge doping and large lattice expansion in oxygen-deficient heteroepitaxial WO3

NASA Astrophysics Data System (ADS)

Mattoni, Giordano; Filippetti, Alessio; Manca, Nicola; Zubko, Pavlo; Caviglia, Andrea D.

2018-05-01

Tungsten trioxide (WO3) is a versatile material with widespread applications ranging from electrochromics and optoelectronics to water splitting and catalysis of chemical reactions. For technological applications, thin films of WO3 are particularly appealing, taking advantage from a high surface-to-volume ratio and tunable physical properties. However, the growth of stoichiometric crystalline thin films is challenging because the deposition conditions are very sensitive to the formation of oxygen vacancies. In this paper, we show how background oxygen pressure during pulsed laser deposition can be used to tune the structural and electronic properties of WO3 thin films. By performing x-ray diffraction and low-temperature electrical transport measurements, we find changes in the WO3 lattice volume of up to 10% concomitantly with a resistivity drop of more than five orders of magnitude at room temperature as a function of increased oxygen deficiency. We use advanced ab initio calculations to describe in detail the properties of the oxygen vacancy defect states and their evolution in terms of excess charge concentration. Our results depict an intriguing scenario where structural, electronic, optical, and transport properties of WO3 single-crystal thin films can all be purposely tuned by controlling the oxygen vacancy formation during growth.

Functional assignment to JEV proteins using SVM.

PubMed

Sahoo, Ganesh Chandra; Dikhit, Manas Ranjan; Das, Pradeep

2008-01-01

Identification of different protein functions facilitates a mechanistic understanding of Japanese encephalitis virus (JEV) infection and opens novel means for drug development. Support vector machines (SVM), useful for predicting the functional class of distantly related proteins, is employed to ascribe a possible functional class to Japanese encephalitis virus protein. Our study from SVMProt and available JE virus sequences suggests that structural and nonstructural proteins of JEV genome possibly belong to diverse protein functions, are expected to occur in the life cycle of JE virus. Protein functions common to both structural and non-structural proteins are iron-binding, metal-binding, lipid-binding, copper-binding, transmembrane, outer membrane, channels/Pores - Pore-forming toxins (proteins and peptides) group of proteins. Non-structural proteins perform functions like actin binding, zinc-binding, calcium-binding, hydrolases, Carbon-Oxygen Lyases, P-type ATPase, proteins belonging to major facilitator family (MFS), secreting main terminal branch (MTB) family, phosphotransfer-driven group translocators and ATP-binding cassette (ABC) family group of proteins. Whereas structural proteins besides belonging to same structural group of proteins (capsid, structural, envelope), they also perform functions like nuclear receptor, antibiotic resistance, RNA-binding, DNA-binding, magnesium-binding, isomerase (intra-molecular), oxidoreductase and participate in type II (general) secretory pathway (IISP).

Functional assignment to JEV proteins using SVM

PubMed Central

Sahoo, Ganesh Chandra; Dikhit, Manas Ranjan; Das, Pradeep

2008-01-01

Identification of different protein functions facilitates a mechanistic understanding of Japanese encephalitis virus (JEV) infection and opens novel means for drug development. Support vector machines (SVM), useful for predicting the functional class of distantly related proteins, is employed to ascribe a possible functional class to Japanese encephalitis virus protein. Our study from SVMProt and available JE virus sequences suggests that structural and nonstructural proteins of JEV genome possibly belong to diverse protein functions, are expected to occur in the life cycle of JE virus. Protein functions common to both structural and non-structural proteins are iron-binding, metal-binding, lipid-binding, copper-binding, transmembrane, outer membrane, channels/Pores - Pore-forming toxins (proteins and peptides) group of proteins. Non-structural proteins perform functions like actin binding, zinc-binding, calcium-binding, hydrolases, Carbon-Oxygen Lyases, P-type ATPase, proteins belonging to major facilitator family (MFS), secreting main terminal branch (MTB) family, phosphotransfer-driven group translocators and ATP-binding cassette (ABC) family group of proteins. Whereas structural proteins besides belonging to same structural group of proteins (capsid, structural, envelope), they also perform functions like nuclear receptor, antibiotic resistance, RNA-binding, DNA-binding, magnesium-binding, isomerase (intra-molecular), oxidoreductase and participate in type II (general) secretory pathway (IISP). PMID:19052658

The tyrosine B10 hydroxyl is crucial for oxygen avidity of Ascaris hemoglobin.

PubMed

Kloek, A P; Yang, J; Mathews, F S; Frieden, C; Goldberg, D E

1994-01-28

The parasitic nematode Ascaris suum has a gene encoding a two-domain hemoglobin with remarkable oxygen avidity. The strong interaction with oxygen is a consequence of a particularly slow oxygen off-rate. The single polypeptide chain consists of two domains, each of which can be expressed separately in Escherichia coli as a globin-like protein exhibiting oxygen binding characteristics comparable with the native molecule. Site-directed mutagenesis was performed on the gene segment encoding domain one. The E7 position, involved in forming a hydrogen bond with the liganded oxygen in vertebrate globins, is a glutamine in both Ascaris domains. Conversion of this residue to leucine or alanine produced a hemoglobin variant with an oxygen off-rate 5- or 60-fold faster than that of unaltered domain one. Replacement of the tyrosine B10 with either phenylalanine or leucine (as found in vertebrate globins) yielded hemoglobin mutants with oxygen off-rates 280- or 570-fold faster, approaching rates found with vertebrate myoglobins. The data suggest that the distal glutamine hydrogen bonds with the liganded oxygen and that the tyrosine B10 hydroxyl contributes an additional hydrogen bond that appears substantially responsible for the extreme oxygen avidity of Ascaris hemoglobin.

Visible-light activate Ag/WO3 films based on wood with enhanced negative oxygen ions production properties

NASA Astrophysics Data System (ADS)

Gao, Likun; Gan, Wentao; Cao, Guoliang; Zhan, Xianxu; Qiang, Tiangang; Li, Jian

2017-12-01

The Ag/WO3-wood was fabricated through a hydrothermal method and a silver mirror reaction. The system of visible-light activate Ag/WO3-wood was used to produce negative oxygen ions, and the effect of Ag nanoparticles on negative oxygen ions production was investigated. From the results of negative oxygen ions production tests, it can be observed that the sample doped with Ag nanoparticles, the concentration of negative oxygen ions is up to 1660 ions/cm3 after 60 min visible light irradiation. Moreover, for the Ag/WO3-wood, even after 60 min without irradiation, the concentration of negative oxygen ions could keep more than 1000 ions/cm3, which is up to the standard of the fresh air. Moreover, due to the porous structure of wood, the wood acted as substrate could promote the nucleation of nanoparticles, prevent the agglomeration of the particles, and thus lead the improvement of photocatalytic properties. And such wood-based functional materials with the property of negative oxygen ions production could be one of the most promising materials in the application of indoor decoration materials, which would meet people's pursuit of healthy, environment-friendly life.

Effect of oxygen vacancies on the electronic and optical properties of tungsten oxide from first principles calculations

NASA Astrophysics Data System (ADS)

Mehmood, Faisal; Pachter, Ruth; Murphy, Neil R.; Johnson, Walter E.; Ramana, Chintalapalle V.

2016-12-01

In this work, we investigated theoretically the role of oxygen vacancies on the electronic and optical properties of cubic, γ-monoclinic, and tetragonal phases of tungsten oxide (WO3) thin films. Following the examination of structural properties and stability of the bulk tungsten oxide polymorphs, we analyzed band structures and optical properties, applying density functional theory (DFT) and GW (Green's (G) function approximation with screened Coulomb interaction (W)) methods. Careful benchmarking of calculated band gaps demonstrated the importance of using a range-separated functional, where results for the pristine room temperature γ-monoclinic structure indicated agreement with experiment. Further, modulation of the band gap for WO3 structures with oxygen vacancies was quantified. Dielectric functions for cubic WO3, calculated at both the single-particle, essentially time-dependent DFT, as well as many-body GW-Bethe-Salpeter equation levels, indicated agreement with experimental data for pristine WO3. Interestingly, we found that introducing oxygen vacancies caused appearance of lower energy absorptions. A smaller refractive index was indicated in the defective WO3 structures. These predictions could lead to further experiments aimed at tuning the optical properties of WO3 by introducing oxygen vacancies, particularly for the lower energy spectral region.

An Origin of Cooperative Oxygen Binding of Human Adult Hemoglobin: Different Roles of the α and β Subunits in the α2β2 Tetramer

PubMed Central

Sakurai, Hiroshi; Imai, Kiyohiro; Mizusawa, Naoki; Ogura, Takashi

2015-01-01

Human hemoglobin (Hb), which is an α2β2 tetramer and binds four O2 molecules, changes its O2-affinity from low to high as an increase of bound O2, that is characterized by ‘cooperativity’. This property is indispensable for its function of O2 transfer from a lung to tissues and is accounted for in terms of T/R quaternary structure change, assuming the presence of a strain on the Fe-histidine (His) bond in the T state caused by the formation of hydrogen bonds at the subunit interfaces. However, the difference between the α and β subunits has been neglected. To investigate the different roles of the Fe-His(F8) bonds in the α and β subunits, we investigated cavity mutant Hbs in which the Fe-His(F8) in either α or β subunits was replaced by Fe-imidazole and F8-glycine. Thus, in cavity mutant Hbs, the movement of Fe upon O2-binding is detached from the movement of the F-helix, which is supposed to play a role of communication. Recombinant Hb (rHb)(αH87G), in which only the Fe-His in the α subunits is replaced by Fe-imidazole, showed a biphasic O2-binding with no cooperativity, indicating the coexistence of two independent hemes with different O2-affinities. In contrast, rHb(βH92G), in which only the Fe-His in the β subunits is replaced by Fe-imidazole, gave a simple high-affinity O2-binding curve with no cooperativity. Resonance Raman, 1H NMR, and near-UV circular dichroism measurements revealed that the quaternary structure change did not occur upon O2-binding to rHb(αH87G), but it did partially occur with O2-binding to rHb(βH92G). The quaternary structure of rHb(αH87G) appears to be frozen in T while its tertiary structure is changeable. Thus, the absence of the Fe-His bond in the α subunit inhibits the T to R quaternary structure change upon O2-binding, but its absence in the β subunit simply enhances the O2-affinity of α subunit. PMID:26244770

Increased viscosity of hemoglobin-based oxygen carriers retards NO-binding when perfused through narrow gas-permeable tubes.

PubMed

Sakai, Hiromi; Okuda, Naoto; Takeoka, Shinji; Tsuchida, Eishun

2011-03-01

Increased fluid viscosity of a solution of hemoglobin-based oxygen carriers (HBOCs) reduces vasoconstrictive effects because increased shear stress on the vascular wall enhances the production of vasorelaxation factors such as NO. Nevertheless, on a microcirculatory level, it remains unclear how viscosity affects the reaction of HBOCs and NO. In this study, different HBOCs were perfused through narrow gas-permeable tubes (25 μm inner diameter at 1 mm/s centerline velocity; hemoglobin concentration [Hb]=5 g/dL). The reaction was examined microscopically based on the Hb visible-light absorption spectrum. When immersed in a NO atmosphere, the NO-binding of deoxygenated Hb solution (viscosity, 1.1 cP at 1000 s(-1)) in the tube occurred about twice as rapidly as that of red blood cells (RBCs): 1.6 cP. Binding was reduced by PEGylation (PEG-Hb, 7.7 cP), by addition of a high molecular weight hydroxyethyl starch (HES) (2.8 cP), and by encapsulation to form Hb-vesicles (HbVs, 1.5 cP; particle size 279 nm). However, the reduction was not as great as that shown for RBCs. A mixture of HbVs and HES (6.2 cP) showed almost identical NO-binding to that of RBCs. Higher viscosity and particle size might reduce lateral diffusion when particles are flowing. The HbVs with HES showed the slowest NO-binding. Furthermore, Hb encapsulation and PEGylation, but not HES-addition, tended to retard CO-binding. Increased viscosity reportedly enhances production of endothelium NO. In addition, our results show that the increased viscosity also inhibits the reaction with NO. Each effect might mitigate vasoconstriction. Copyright © 2010 Elsevier Inc. All rights reserved.

Impact of oxygen dissolved at bottling and transmitted through closures on the composition and sensory properties of a Sauvignon Blanc wine during bottle storage.

PubMed

Lopes, Paulo; Silva, Maria A; Pons, Alexandre; Tominaga, Takatoshi; Lavigne, Valérie; Saucier, Cédric; Darriet, Philippe; Teissedre, Pierre-Louis; Dubourdieu, Denis

2009-11-11

This work outlines the results from an investigation to determine the effect of the oxygen dissolved at bottling and the specific oxygen barrier properties of commercially available closures on the composition, color and sensory properties of a Bordeaux Sauvignon Blanc wine during two years of storage. The importance of oxygen for wine development after bottling was also assessed using an airtight bottle ampule. Wines were assessed for the antioxidants (SO(2) and ascorbic acid), varietal thiols (4-mercapto-4-methylpentan-2-one, 3-mercaptohexan-1-ol), hydrogen sulfide and sotolon content, and color throughout 24 months of storage. In addition, the aroma and palate properties of wines were also assessed. The combination of oxygen dissolved at bottling and the oxygen transferred through closures has a significant effect on Sauvignon Blanc development after bottling. Wines highly exposed to oxygen at bottling and those sealed with a synthetic, Nomacorc classic closure, highly permeable to oxygen, were relatively oxidized in aroma, brown in color, and low in antioxidants and volatile compounds compared to wines sealed with other closures. Conversely, wines sealed under more airtight conditions, bottle ampule and screw cap Saran-tin, have the slowest rate of browning, and displayed the greatest contents of antioxidants and varietal thiols, but also high levels of H(2)S, which were responsible for the reduced dominating character found in these wines, while wines sealed with cork stoppers and screw cap Saranex presented negligible reduced and oxidized characters.

Plasma membrane order and fluidity are diversely triggered by elicitors of plant defence.

PubMed

Sandor, Roman; Der, Christophe; Grosjean, Kevin; Anca, Iulia; Noirot, Elodie; Leborgne-Castel, Nathalie; Lochman, Jan; Simon-Plas, Françoise; Gerbeau-Pissot, Patricia

2016-09-01

Although plants are exposed to a great number of pathogens, they usually defend themselves by triggering mechanisms able to limit disease development. Alongside signalling events common to most such incompatible interactions, modifications of plasma membrane (PM) physical properties could be new players in the cell transduction cascade. Different pairs of elicitors (cryptogein, oligogalacturonides, and flagellin) and plant cells (tobacco and Arabidopsis) were used to address the issue of possible modifications of plant PM biophysical properties induced by elicitors and their links to other events of the defence signalling cascade. We observed an increase of PM order whatever the elicitor/plant cell pair used, provided that a signalling cascade was induced. Such membrane modification is dependent on the NADPH oxidase-mediated reactive oxygen species production. Moreover, cryptogein, which is the sole elicitor able to trap sterols, is also the only one able to trigger an increase in PM fluidity. The use of cryptogein variants with altered sterol-binding properties confirms the strong correlation between sterol removal from the PM and PM fluidity enhancement. These results propose PM dynamics as a player in early signalling processes triggered by elicitors of plant defence. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Hyperoxia, unlike phorbol ester, induces glutathione peroxidase through a protein kinase C-independent mechanism.

PubMed Central

Jornot, L; Junod, A F

1997-01-01

Human selenium-dependent glutathione peroxidase (GP) is implicated as a mechanism of resistance against oxygen free radicals. The 5' flanking sequence upstream from the coding region of GP contained an oxygen-responsive element termed ORE1 that is responsive to hypoxia, as well as several copies of the activator protein-1 (AP-1)- and AP-1-like-binding sites. In this study, we sought to define the molecular events that lead to GP gene transcription in response to hyperoxia in human umbilical-vein endothelial cells, and asked whether such induction is mimicked and sustained by activation of protein kinase C (PKC) by phorbol esters. Treatment of cells with 100 nM phorbol 12,13-dibutyrate (PdBu) induced a delayed (24-48 h) but significant (2-fold) increase in steady-state GP mRNA levels. Steady-state GP mRNA levels also rose after exposure to 95% O2, again after considerable delay (48-72 h). For both PdBu and oxygen, induction was transcriptionally regulated, as demonstrated by nuclear run-on experiments. The simulations by PdBu and oxygen were additive. In contrast with PdBu, hyperoxia did not stimulate translocation of PKC from the cytosol to the particulate fraction, although the specific activity of both cytosolic and particulate-associated PKC was increased 2-fold in cells exposed to 95% O2 for 5 days. In addition, gel mobility-shift assays using double-stranded tumour-promoting-agent-responsive element (TRE) and nuclear extracts derived from phorbol- and oxygen-treated cells revealed that PdBu, but not hyperoxia, increased AP-1 DNA-binding activity. On the other hand, the up-regulation of GP expression by oxygen could not be accounted for by the ORE1 core sequence, since no specific protein-DNA binding activity could be detected using nuclear extracts from hyperoxic cells and ORE1. Taken together, these results suggest that there may be different molecular mechanisms controlling GP expression. After exposure to PdBu, GP undergoes transcriptional activation via a process that can be readily explained by a classic AP-1 interaction with the TRE sites in the GP promoter. During hyperoxia, GP also undergoes transcriptional activity, but via a process that appears to involve neither TRE nor ORE1. PMID:9337858

Acid-base and copper-binding properties of three organic matter fractions isolated from a forest floor soil solution

NASA Astrophysics Data System (ADS)

van Schaik, Joris W. J.; Kleja, Dan B.; Gustafsson, Jon Petter

2010-02-01

Vast amounts of knowledge about the proton- and metal-binding properties of dissolved organic matter (DOM) in natural waters have been obtained in studies on isolated humic and fulvic (hydrophobic) acids. Although macromolecular hydrophilic acids normally make up about one-third of DOM, their proton- and metal-binding properties are poorly known. Here, we investigated the acid-base and Cu-binding properties of the hydrophobic (fulvic) acid fraction and two hydrophilic fractions isolated from a soil solution. Proton titrations revealed a higher total charge for the hydrophilic acid fractions than for the hydrophobic acid fraction. The most hydrophilic fraction appeared to be dominated by weak acid sites, as evidenced by increased slope of the curve of surface charge versus pH at pH values above 6. The titration curves were poorly predicted by both Stockholm Humic Model (SHM) and NICA-Donnan model calculations using generic parameter values, but could be modelled accurately after optimisation of the proton-binding parameters (pH ⩽ 9). Cu-binding isotherms for the three fractions were determined at pH values of 4, 6 and 9. With the optimised proton-binding parameters, the SHM model predictions for Cu binding improved, whereas the NICA-Donnan predictions deteriorated. After optimisation of Cu-binding parameters, both models described the experimental data satisfactorily. Iron(III) and aluminium competed strongly with Cu for binding sites at both pH 4 and pH 6. The SHM model predicted this competition reasonably well, but the NICA-Donnan model underestimated the effects significantly at pH 6. Overall, the Cu-binding behaviour of the two hydrophilic acid fractions was very similar to that of the hydrophobic acid fraction, despite the differences observed in proton-binding characteristics. These results show that for modelling purposes, it is essential to include the hydrophilic acid fraction in the pool of 'active' humic substances.

Innovative oxide materials for electrochemical energy conversion and oxygen separation

NASA Astrophysics Data System (ADS)

Belousov, V. V.

2017-10-01

Ion-conducting solid metal oxides are widely used in high-temperature electrochemical devices for energy conversion and oxygen separation. However, liquid metal oxides possessing unique electrochemical properties still remain of limited use. The review demonstrates the potential for practical applications of molten oxides. The transport properties of molten oxide materials are discussed. The emphasis is placed on the chemical diffusion of oxygen in the molten oxide membrane materials for electrochemical energy conversion and oxygen separation. The thermodynamics of these materials is considered. The dynamic polymer chain model developed to describe the oxygen ion transport in molten oxides is discussed. Prospects for further research into molten oxide materials are outlined. The bibliography includes 145 references.

The effect of oxygen-plasma treatment on Kevlar fibers and the properties of Kevlar fibers/bismaleimide composites

NASA Astrophysics Data System (ADS)

Su, Min; Gu, Aijuan; Liang, Guozheng; Yuan, Li

2011-02-01

The effect of oxygen-plasma treatment for Kevlar fibers on the interfacial adhesion and typical macro-properties of Kevlar fiber/bismaleimide composites was intensively studied. It is found that oxygen-plasma treatment significantly affects the interfacial adhesion by changing the chemistry and morphology of the surfaces of the fibers, and thus leading to improved interlaminar shear strength, water resistance and dielectric properties of the composites. However, the improvement is closely related to the treatment power and time. The best condition for treating Kevlar fiber is 70 W for 5 min. Oxygen-plasma treatment provides an effective technique for overcoming the poor interfacial adhesion of Kevlar fiber based composites, and thus showing great potential in fabricating high performance copper clad laminates.

Space charge characteristics of fluorinated polyethylene: Different effects of fluorine and oxygen

NASA Astrophysics Data System (ADS)

Zhao, Ni; Nie, Yongjie; Li, Shengtao

2018-04-01

Direct fluorination are proved having obvious effect on space charge characteristics of polyethylene. It is believed that fluorine has a positive effect on suppressing space charge injection while oxygen impurity has a negative effect. However, the mechanism for the opposite effect of fluorine and oxygen is still not clear. In this paper, the different effects of fluorine and oxygen on space charge characteristics of fluorinated low density polyethylene (LDPE) are investigated on the basis of dielectric property, chemical constitutes and trap performance of surface fluorinated layers. The results show that direct fluorination has obvious effect on chemical constitutes and dielectric properties of surface fluorinated layer. Introduced fluorine is the main factor for suppressing charge injection from the electrodes, because it seriously changes the chemical constitutes and further the trap properties of the surface fluorinated layer. While introduction of oxygen results in heterocharges and makes space charge distribution complex, due to the ionization of generated small groups like C=O containing groups. Moreover, direct fluorination will result in cleavage of some LDPE molecules whatever there is oxygen impurity or not.

Electronic and energetics properties of oxygen defects in La2-xSrxCuO4 in relation to doping and strain

NASA Astrophysics Data System (ADS)

Park, Sohee; Park, Changwon; Yoon, Mina

The level of oxygen defects in La2-xSrxCuO4 (LSCO), a high temperature superconductor, is known to drastically change LSCO's structural and electronic properties. However, the atomistic understanding of the role of oxygen defects is far from being complete. Using first-principles calculations, we investigated the electronic and energetic properties of oxygen vacancies in LSCO in relation to external parameters such as degree of Sr doping amount and external strain. We find that the relative stabilities between the equatorial vacancy induced in the CuO2 layer and the apical vacancy in the LaO layer can be altered by strain. In addition, Sr doping plays a crucial role in their relative stabilities. Therefore, the complex interplay between those key parameters essentially determines the overall oxygen density. Our finding can be instrumental in the experimental development of LSCO with desired oxygen density. Work supported by the LDRD Program of ORNL managed by UT-Battle, LLC, for the U.S. DOE.

Growth control of oxygen stoichiometry in homoepitaxial SrTiO3 films by pulsed laser epitaxy in high vacuum

PubMed Central

Lee, Ho Nyung; Ambrose Seo, Sung S.; Choi, Woo Seok; Rouleau, Christopher M.

2016-01-01

In many transition metal oxides, oxygen stoichiometry is one of the most critical parameters that plays a key role in determining the structural, physical, optical, and electrochemical properties of the material. However, controlling the growth to obtain high quality single crystal films having the right oxygen stoichiometry, especially in a high vacuum environment, has been viewed as a challenge. In this work, we show that, through proper control of the plume kinetic energy, stoichiometric crystalline films can be synthesized without generating oxygen defects even in high vacuum. We use a model homoepitaxial system of SrTiO3 (STO) thin films on single crystal STO substrates. Physical property measurements indicate that oxygen vacancy generation in high vacuum is strongly influenced by the energetics of the laser plume, and it can be controlled by proper laser beam delivery. Therefore, our finding not only provides essential insight into oxygen stoichiometry control in high vacuum for understanding the fundamental properties of STO-based thin films and heterostructures, but expands the utility of pulsed laser epitaxy of other materials as well. PMID:26823119

The Effect of Oxygen on Organic Haze Properties

NASA Astrophysics Data System (ADS)

Ugelow, Melissa S.; De Haan, David O.; Hörst, Sarah M.; Tolbert, Margaret A.

2018-05-01

Atmospheric organic hazes are present on many planetary bodies, possibly including the ancient Earth and exoplanets, and can greatly influence surface and atmospheric properties. Here we examine the physical and optical properties of organic hazes produced with molecular nitrogen, methane, carbon dioxide, and increasing amounts of molecular oxygen, and compare them to hazes produced without added oxygen. As molecular oxygen is included in increasing amounts from 0 to 200 ppmv, the mass loading of haze produced decreases nonlinearly. With 200 ppmv molecular oxygen, the mass loading of particles produced is on the order of the amount of organic aerosol in modern Earth’s atmosphere, suggesting that while not a thick organic haze, haze particles produced with 200 ppmv molecular oxygen could still influence planetary climates. Additionally, the hazes produced with increasing amounts of oxygen become increasingly oxidized and the densities increase. For hazes produced with 0, 2 and 20 ppmv oxygen, the densities were found to be 0.94, 1.03 and 1.12 g cm‑3, respectively. Moreover, the hazes produced with 0, 2, and 20 ppmv oxygen are found to have real refractive indices of n = 1.58 ± 0.04, 1.53 ± 0.03 and 1.67 ± 0.03, respectively, and imaginary refractive indices of k={0.001}-0.001+0.002, 0.002 ± 0.002 and {0.002}-0.002+0.003, respectively. These k values demonstrate that the particles formed with oxygen have no absorption within our experimental error, and could result in a light scattering layer in an oxygen-containing atmosphere.

Surface properties of thermionic electrodes

NASA Technical Reports Server (NTRS)

Stickney, R. E.

1972-01-01

A quasi-equilibrium model which provides semiquantitative predictions of the oxygen reaction with refractory metals was developed at high temperature and low pressure. Extensive experimental data was obtained on adsorption and work function properties for a wide variety of adsorbates (Cs, K, Na, I, Br, Cl, and O) on several refractory metals (W, Ta, Mo, and Re). Conclusions and recommendations for research on alkali metal adsorption, oxygen adsorption, and adsorption of cesium - oxygen mixtures are included.

Electrocatalysis of fuel cell reactions: Investigation of alternate electrolytes

NASA Technical Reports Server (NTRS)

Chin, D. T.; Hsueh, K. L.; Chang, H. H.

1983-01-01

Oxygen reduction and transport properties of the electrolyte in the phosphoric acid fuel cell are studied. A theoretical expression for the rotating ring-disk electrode technique; the intermediate reaction rate constants for oxygen reduction on platinum in phosphoric acid electrolyte; oxygen reduction mechanism in trifluoromethanesulfonic acid (TFMSA), considered as an alternate electrolyte for the acid fuel cells; and transport properties of the phosphoric acid electrolyte at high concentrations and temperatures are covered.

Destruction of a distal hypoxia response element abolishes trans-activation of the PAG1 gene mediated by HIF-independent chromatin looping

PubMed Central

Schörg, Alexandra; Santambrogio, Sara; Platt, James L.; Schödel, Johannes; Lindenmeyer, Maja T.; Cohen, Clemens D.; Schrödter, Katrin; Mole, David R.; Wenger, Roland H.; Hoogewijs, David

2015-01-01

A crucial step in the cellular adaptation to oxygen deficiency is the binding of hypoxia-inducible factors (HIFs) to hypoxia response elements (HREs) of oxygen-regulated genes. Genome-wide HIF-1α/2α/β DNA-binding studies revealed that the majority of HREs reside distant to the promoter regions, but the function of these distal HREs has only been marginally studied in the genomic context. We used chromatin immunoprecipitation (ChIP), gene editing (TALEN) and chromosome conformation capture (3C) to localize and functionally characterize a 82 kb upstream HRE that solely drives oxygen-regulated expression of the newly identified HIF target gene PAG1. PAG1, a transmembrane adaptor protein involved in Src signalling, was hypoxically induced in various cell lines and mouse tissues. ChIP and reporter gene assays demonstrated that the −82 kb HRE regulates PAG1, but not an equally distant gene further upstream, by direct interaction with HIF. Ablation of the consensus HRE motif abolished the hypoxic induction of PAG1 but not general oxygen signalling. 3C assays revealed that the −82 kb HRE physically associates with the PAG1 promoter region, independent of HIF-DNA interaction. These results demonstrate a constitutive interaction between the −82 kb HRE and the PAG1 promoter, suggesting a physiologically important rapid response to hypoxia. PMID:26007655

Molecular identification of an ABC transporter complex for manganese: analysis of a cyanobacterial mutant strain impaired in the photosynthetic oxygen evolution process.

PubMed Central

Bartsevich, V V; Pakrasi, H B

1995-01-01

During photosynthesis, the photosystem II (PSII) pigment-protein complex catalyzes oxygen evolution, a reaction in which a four-manganese ensemble plays a crucial role. Using a newly developed selection scheme, we have isolated BP13, a random photosynthesis-deficient mutant strain of the cyanobacterium, Synechocystis 6803. This mutant grew slowly under photoautotrophic conditions, and had a low oxygen evolution activity. Biochemical analysis revealed that the lesion in this mutant strain had specifically affected the Mn ensemble in PSII. Interestingly, incubation of BP13 cells with micromolar levels of added Mn induced rapid recovery of oxygen evolution activity. The mutant could be complemented with a fragment of wild-type chromosomal DNA containing three closely linked genes, mntA, mntB and mntC. These gene products showed significant sequence similarities with polypeptide components of bacterial permeases that are members of the 'ABC (ATP binding cassette) superfamily' of transporter proteins. We determined that in the BP13 strain, a single nucleotide change had resulted in the replacement of an alanine by an aspartic acid residue in MntA, a soluble protein containing ATP binding motifs. These results suggest that the mntCAB gene cluster encodes polypeptide components of a Mn transporter, the first such protein complex identified in any organism. PMID:7743991

Analysis of calcium-induced conformational changes in calcium-binding allergens and quantitative determination of their IgE binding properties.

PubMed

Parody, Nuria; Fuertes, Miguel Angel; Alonso, Carlos; Pico de Coaña, Yago

2013-01-01

The polcalcin family is one of the most epidemiologically relevant families of calcium-binding allergens. Polcalcins are potent plant allergens that contain one or several EF-hand motifs and their allergenicity is primarily associated with the Ca(2+)-bound form of the protein. Conformation, stability, as well as IgE recognition of calcium-binding allergens greatly depend on the presence of protein-bound calcium ions. We describe a protocol that uses three techniques (SDS-PAGE, circular dichroism spectroscopy, and ELISA) to describe the effects that calcium has on the structural changes in an allergen and its IgE binding properties.

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

Water-gas-shift over metal-free nanocrystalline ceria: An experimental and theoretical study

DOE PAGES

Guild, Curtis J.; Vovchok, Dimitriy; Kriz, David A.; ...

2017-01-23

A tandem experimental and theoretical investigation of a mesoporous ceria catalyst reveals the properties of the metal oxide are conducive for activity typically ascribed to metals, suggesting reduced Ce 3+ and oxygen vacancies are responsible for the inherent bi-functionality of CO oxidation and dissociation of water required for facilitating the production of H 2. The degree of reduction of the ceria, specifically the (1 0 0) face, is found to significantly influence the binding of reagents, suggesting reduced surfaces harbor the necessary reactive sites. The metal-free catalysis of the reaction is significant for catalyst design considerations, and the suite ofmore » in situ analyses provides a comprehensive study of the dynamic nature of the high surface area catalyst system. Finally, this study postulates feasible improvements in catalytic activity may redirect the purpose of the water-gas shift reaction from CO purification to primary hydrogen production.« less

Water-gas-shift over metal-free nanocrystalline ceria: An experimental and theoretical study

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

Guild, Curtis J.; Vovchok, Dimitriy; Kriz, David A.

A tandem experimental and theoretical investigation of a mesoporous ceria catalyst reveals the properties of the metal oxide are conducive for activity typically ascribed to metals, suggesting reduced Ce 3+ and oxygen vacancies are responsible for the inherent bi-functionality of CO oxidation and dissociation of water required for facilitating the production of H 2. The degree of reduction of the ceria, specifically the (1 0 0) face, is found to significantly influence the binding of reagents, suggesting reduced surfaces harbor the necessary reactive sites. The metal-free catalysis of the reaction is significant for catalyst design considerations, and the suite ofmore » in situ analyses provides a comprehensive study of the dynamic nature of the high surface area catalyst system. Finally, this study postulates feasible improvements in catalytic activity may redirect the purpose of the water-gas shift reaction from CO purification to primary hydrogen production.« less

Synthesis, crystal structures, spectral, thermal and antimicrobial properties of new Zn(II) 5-iodo- and 5-bromosalicylates

NASA Astrophysics Data System (ADS)

Košická, Petra; Győryová, Katarína; Smolko, Lukáš; Gyepes, Róbert; Hudecová, Daniela

2018-03-01

Two new analogous zinc(II) complexes containing 5-iodo- and 5-bromosalicylate ligands, respectively, were prepared in single-crystal form and characterized by IR spectroscopy, thermal analysis and elemental analysis. The solid-state structures of prepared complexes were determined by single crystal X-ray crystallography. Both complexes are isostructural and their crystal structures composed of neutral molecules [Zn(5-Xsal)2(H2O)2] (where X = Br, I, sal = salicylato). Central Zn(II) atom is in both complexes coordinated by six oxygen atoms, four of which are from two chelate bonded 5-halosalicylates and remaining two from coordinated water molecules. The found chelate binding mode is in line with the Δ values calculated from IR spectral data. Antimicrobial activity of prepared complexes was studied against selected bacteria, yeast and filamentous fungi. Obtained results indicate that 5-iodosalicylate complex is more antimicrobially active than its 5-bromo substituted analogue.

Structural and functional characterization of a calcium-activated cation channel from Tsukamurella paurometabola

NASA Astrophysics Data System (ADS)

Dhakshnamoorthy, Balasundaresan; Rohaim, Ahmed; Rui, Huan; Blachowicz, Lydia; Roux, Benoît

2016-09-01

The selectivity filter is an essential functional element of K+ channels that is highly conserved both in terms of its primary sequence and its three-dimensional structure. Here, we investigate the properties of an ion channel from the Gram-positive bacterium Tsukamurella paurometabola with a selectivity filter formed by an uncommon proline-rich sequence. Electrophysiological recordings show that it is a non-selective cation channel and that its activity depends on Ca2+ concentration. In the crystal structure, the selectivity filter adopts a novel conformation with Ca2+ ions bound within the filter near the pore helix where they are coordinated by backbone oxygen atoms, a recurrent motif found in multiple proteins. The binding of Ca2+ ion in the selectivity filter controls the widening of the pore as shown in crystal structures and in molecular dynamics simulations. The structural, functional and computational data provide a characterization of this calcium-gated cationic channel.

Wear and interfacial transport of material

NASA Technical Reports Server (NTRS)

Buckley, D. H.

1975-01-01

Bonding across the interface for two solids in contact and the subsequent transfer of material from one surface to another is a direct result of the interfacial bonds being stronger than the cohesive bonds in either of the two solids. Surface tools such as LEED, Auger emission spectroscopy, field ion microscopy, and the atom probe are used to examine adhesive contacts and to determine the direction, nature, quantity of material transfer and properties of the solids which effect transfer and wear. The electronic nature, cohesive binding energies, surface structure, lattice disregistry and distribution of species in surface layers are all found to effect adhesion and transfer or transport for clean surfaces in solid state contact. The influence of adsorbed and reacted surface films from fractions of a monolayer to multilayer reactive films are considered. It is shown that even fractions of a monolayer of surface active species such as oxygen and sulfur can markedly inhibit adhesion and transport.

Self-catalytic crystal growth, formation mechanism, and optical properties of indium tin oxide nanostructures

NASA Astrophysics Data System (ADS)

Liang, Yuan-Chang; Zhong, Hua

2013-08-01

In-Sn-O nanostructures with rectangular cross-sectional rod-like, sword-like, and bowling pin-like morphologies were successfully synthesized through self-catalytic growth. Mixed metallic In and Sn powders were used as source materials, and no catalyst layer was pre-coated on the substrates. The distance between the substrate and the source materials affected the size of the Sn-rich alloy particles during crystal growth in a quartz tube. This caused In-Sn-O nanostructures with various morphologies to form. An X-ray photoelectron spectroscope and a transmittance electron microscope with an energy-dispersive X-ray spectrometer were used to investigate the elemental binding states and compositions of the as-synthesized nanostructures. The Sn doping and oxygen vacancies in the In2O3 crystals corresponded to the blue-green and yellow-orange emission bands of the nanostructures, respectively.

A gadolinium(III) complex of a carboxylic-phosphorus acid derivative of diethylenetriamine covalently bound to inulin, a potential macromolecular MRI contrast agent.

PubMed

Lebdusková, Petra; Kotek, Jan; Hermann, Petr; Vander Elst, Luce; Muller, Robert N; Lukes, Ivan; Peters, Joop A

2004-01-01

A novel conjugate of a polysaccharide and a Gd(III) chelate with potential as contrast agent for magnetic resonance imaging (MRI) was synthesized. The structure of the chelate was derived from H5DTPA by replacing the central pendant arm by a phosphinic acid functional group, which was covalently bound to the polysaccharide inulin. On the average, each monosaccharide unit of the inulin was attached to approximately one (0.9) chelate moiety. The average molecular weight is 23110 and the average number of Gd3+ ions per molecule is 24. The ligand binds the Gd3+ ion in an octadentate fashion via three nitrogen atoms, four carboxylate oxygen atoms, and one P-O oxygen atom, and its first coordination sphere is completed by a water molecule. This compound shows promising properties for application as a contrast agent for MRI thanks to a favorable residence lifetime of this water molecule (170 ns at 298 K), a relatively long rotational correlation time (866 ps at 298 K), and the presence of two water molecules in the second coordination sphere of the Gd3+ ion. Furthermore, its stability toward transmetalation with Zn(II) is as high as that of the clinically used [Gd(DTPA)(H2O)]2-.

Coordination properties of the oxime analogue of glycine to Cu(II).

PubMed

Georgieva, I; Trendafilova, N; Rodríguez-Santiago, L; Sodupe, M

2005-06-30

The coordination of Cu2+ by glyoxilic acid oxime (gao)--the oxime analogue of glycine amino acid--and its deprotonated (gao- and gao2-) species has been studied with different density functional methods. Single-point calculations have also been carried out at the single- and double- (triple) excitation coupled-cluster (CCSD(T)) level of theory. The isomers studied involve coordination of Cu2+ to electron-rich sites (O,N) of neutral, anionic, and dianionic gao species in different conformations. In contrast to Cu2+-glycine, for which the ground-state structure is bidentate with the CO2(-) terminus of zwitterionic glycine, for Cu2+-gao the most stable isomer shows monodentate binding of Cu2+ with the carbonylic oxygen of the neutral form. The most stable complexes of Cu2+ interacting with deprotonated gao species (gao- and gao2-) also take place through the carboxylic oxygens but in a bidentate manner. The results with different functionals show that, for these open shell (Cu2+-L) systems, the relative stability of complexes with different coordination environments (and so, different spin distribution) can be quite sensitive to the amount of "Hartree-Fock" exchange included in the functional. Among all the functionals tested in this work, the BHandHLYP is the one that better compares to CCSD(T) results.

Theoretical insights into effects of molar ratios on stabilities, mechanical properties and detonation performance of CL-20/RDX cocrystal explosives by molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Hang, Gui-yun; Yu, Wen-li; Wang, Tao; Wang, Jin-tao; Li, Zhen

2017-08-01

The CL-20/RDX cocrystal models with different molar ratios were established by substitution method and molecular dynamics (MD) simulation method was applied to investigate the influences of molar ratios on mechanical properties, stabilities and detonation performance of cocrystal explosives. The crystal parameters, structures, binding energies, mechanical properties and some detonation parameters of different cocrystal explosives were got and compared. The results illustrate that the molar ratio has a direct influence on properties of cocrystal explosive and each of the cocrystal model holds different mechanical properties, binding energies and detonation parameters. The mechanical properties of CL-20/RDX cocrystal explosive can be effectively improved and the cocrystal model with molar ratio in 1:1 has the best mechanical properties. Besides, it has the highest binding energy, so the stability and compatibility is the best. The detonation parameters show that the cocrystal explosive has better detonation performance than RDX. In a word, the cocrystal explosive with molar ratio in 1:1 has the best mechanical properties, highest binding energy and excellent energy density and detonation performance, it is quite promising and can satisfy the requirements of high energy density compounds (HEDC). This paper could offer some theoretical instructions and novel insights for the CL-20 cocrystal explosive designing.

[Sauna effect on blood oxygen transport function and proxidant/antioxidant balance in youths].

PubMed

Zinchuk, V V; Zhad'ko, D D

2012-01-01

There was investigated sauna effect on blood oxygen transport function and proxidant/antioxidant balance in 18 to 22 years old males. Subjects being tested underwent thermal exposure once per week over a period of 5 months (20 procedures). There were two exposure over the course of sauna bathing (temperature 85-90 degrees C, humidity 10-15%): the first exposure lasted for 5 minutes and the second one for 10 minutes. Dry air sauna in youth's leads to respiratory alkalosis, increases pO2, decreases haemoglobin binding capacity to venous blood oxygen thus facilitating oxygen transport into body tissues. Single sauna visit results in oxidative stress (augmentation of free radical processes and deterioration of antioxidant defence mechanisms), while its manifestations being diminished after multiple thermal exposures. Increase in nitrogen monoxide formation being observed might matter for the modification of the oxygen dependent processes of the human body.

Symposium on Oxygen Binding Heme Proteins Structure, Dynamics, Function and Genetics Held in Pacific Grove, California on 9-13 October 1988

DTIC Science & Technology

1989-08-15

hemoglobin, hemoglobin that has been internally crosslinked, polymerized crosslinked-hemoglobin, and I hemoglobin that is conjugated to carriers such as...dextran and polyethyleneglycol are also under intense study. To date, only unmodified hemoglobin and crosslinked- polymerized hemoglobin have been...complement and may bind bacterial endotoxins in vivo . I During the past 3 years, the US Army has supported the industrial scaleup of one such product

Crystal structure of a lipoxygenase from Cyanothece sp. may reveal novel features for substrate acquisition[S

PubMed Central

Newie, Julia; Andreou, Alexandra; Neumann, Piotr; Einsle, Oliver; Feussner, Ivo; Ficner, Ralf

2016-01-01

In eukaryotes, oxidized PUFAs, so-called oxylipins, are vital signaling molecules. The first step in their biosynthesis may be catalyzed by a lipoxygenase (LOX), which forms hydroperoxides by introducing dioxygen into PUFAs. Here we characterized CspLOX1, a phylogenetically distant LOX family member from Cyanothece sp. PCC 8801 and determined its crystal structure. In addition to the classical two domains found in plant, animal, and coral LOXs, we identified an N-terminal helical extension, reminiscent of the long α-helical insertion in Pseudomonas aeruginosa LOX. In liposome flotation studies, this helical extension, rather than the β-barrel domain, was crucial for a membrane binding function. Additionally, CspLOX1 could oxygenate 1,2-diarachidonyl-sn-glycero-3-phosphocholine, suggesting that the enzyme may act directly on membranes and that fatty acids bind to the active site in a tail-first orientation. This binding mode is further supported by the fact that CspLOX1 catalyzed oxygenation at the n-10 position of both linoleic and arachidonic acid, resulting in 9R- and 11R-hydroperoxides, respectively. Together these results reveal unifying structural features of LOXs and their function. While the core of the active site is important for lipoxygenation and thus highly conserved, peripheral domains functioning in membrane and substrate binding are more variable. PMID:26667668

Controlling the bond scission sequence of oxygenates for energy applications

NASA Astrophysics Data System (ADS)

Stottlemyer, Alan L.

The so called "Holy Grail" of heterogeneous catalysis is a fundamental understanding of catalyzed chemical transformations which span multidimensional scales of both length and time, enabling rational catalyst design. Such an undertaking is realizable only with an atomic level understanding of bond formation and destruction with respect to intrinsic properties of the metal catalyst. In this study, we investigate the bond scission sequence of small oxygenates (methanol, ethanol, ethylene glycol) on bimetallic transition metal catalysts and transition metal carbide catalysts. Oxygenates are of interest both as hydrogen carriers for reforming to H2 and CO and as fuels in direct alcohol fuel cells (DAFC). To address the so-called "materials gap" and "pressure gap" this work adopted three parallel research approaches: (1) ultra high vacuum (UHV) studies including temperature programmed desorption (TPD) and high-resolution electron energy loss spectroscopy (HREELS) on polycrystalline surfaces; (2) DFT studies including thermodynamic and kinetic calculations; (3) electrochemical studies including cyclic voltammetry (CV) and chronoamperometry (CA). Recent studies have suggested that tungsten monocarbide (WC) may behave similarly to Pt for the electrooxidation of oxygenates. TPD was used to quantify the activity and selectivity of oxygenate decomposition for WC and Pt-modifiedWC (Pt/WC) as compared to Pt. While decomposition activity was generally higher on WC than on Pt, scission of the C-O bond resulted in alkane/alkene formation on WC, an undesired product for DAFC. When Pt was added to WC by physical vapor deposition C-O bond scission was limited, suggesting that Pt synergistically modifies WC to improve the selectivity toward C-H bond scission to produce H2 and CO. Additionally, TPD confirmed WC and Pt/WC to be more CO tolerant than Pt. HREELS results verified that surface intermediates were different on Pt/WC as compared to Pt or WC and evidence of aldehyde intermediates was observed on the Pt and Pt/WC surfaces. For CH3OH decomposition, DFT calculations suggested that the bond scission sequence could be controlled using monolayer coverage of Pt on WC. The Ni/Pt bimetallic system was studied as an example for using oxygenates as a hydrogen source. There are two well characterized surface structures for the Ni/Pt system: the surface configuration, in which the Ni atoms reside primarily on the surface of the Pt bulk, and the subsurface configuration, in which the second atomic layer is enriched in Ni atoms and the surface is enriched in Pt atoms. These configurations are denoted NiPtPt and PtNiPt, respectively. DFT results revealed that trends established for the Ni/Pt(111) system extend to the Ni/Pt(100) analogue. TPD studies revealed that the NiPtPt surface was more active for oxygenate reforming than the Pt or PtNiPt surfaces. HREELS confirmed the presence of strongly bound reaction intermediates, including aldehyde-like species, and suggested that the first decomposition step was likely O-H bond scission. Thus, the binding energies of the deprotonated reaction intermediates are important parameters in controlling the decomposition pathways of oxygenates. These studies have demonstrated that the bond scission sequence of oxygenate decomposition can be controlled using bimetallic and transition metal carbide catalysts. While this study has focused on oxygenate decomposition for energy applications, the principles and methodology applied herein are universally applicable to the development of novel and marketable value-added products. The value in such a methodology is in the combination of both calculations to predict catalytic and chemical properties, and experiments to fine-tune theoretical predictions.

Influence of Food with High Moisture Content on Oxygen Barrier Property of Polyvinyl Alcohol (PVA)/Vermiculite Nanocomposite Coated Multilayer Packaging Film.

PubMed

Kim, Jung Min; Lee, Min Hyeock; Ko, Jung A; Kang, Dong Ho; Bae, Hojae; Park, Hyun Jin

2018-02-01

This study investigates the potential complications in applying nanoclay-based waterborne coating to packaging films for food with high moisture content. Multilayer packaging films were prepared by dry laminating commercially available polyvinyl alcohol (PVA)/vermiculite nanocomposite coating films and linear low-density polyethylene film, and the changes in oxygen barrier properties were investigated according to different relative humidity using 3 types of food simulants. When the relative humidity was above 60%, the oxygen permeability increased sharply, but this was reversible. Deionized water and 3% acetic acid did not cause any large structural change in the PVA/vermiculite nanocomposite but caused a reversible deterioration of the oxygen barrier properties. In contrast, 50% ethanol, a simulant for the semifatty food, induced irreversible structural changes with deterioration of the oxygen barrier property. These changes are due to the characteristics of PVA rather than vermiculite. We believe this manuscript would be of interest to the wide group of researchers, organizations, and companies in the field of developing nanoclay-based gas barrier packaging for foods with high moisture content. Hence, we wish to diffuse our knowledge to the scientific community. © 2018 Institute of Food Technologists®.

Determination of binding-dioxygen in dioxygen complexes by headspace gas chromatography.

PubMed

Wang, Wei; Feng, Shun; Li, Ya-ni; Wu, Meiying; Wang, Jide

2008-06-06

Dioxygen complexes play important roles in organisms' bodies, so the determination of binding-dioxygen has practical significance. A simple and robust method based on headspace gas chromatography was proposed to determine the binding-dioxygen in dioxygen complexes. By measuring the content change of nitrogen gas in a vial, the amount of oxygen released from dixoygen complexes can be determined. The method was validated using potassium chlorate as model sample, and the results exhibited good recoveries (90-99%) with the relative standard deviation less than 8%. It was also used to analyze dioxygen complex of cobalt bis(salicylaldehyde) ethylenediimine and polyamine cobalt complexes prepared by solid-phase reaction.

Magnetic properties of solid oxygen under pressure (Review Article)

NASA Astrophysics Data System (ADS)

Freiman, Yu. A.

2015-11-01

Solid oxygen is a unique crystal combining properties of a simple molecular solid and a magnet. Unlike ordinary magnets, the exchange interaction in solid oxygen acts on a background of weak Van der Waals forces, providing a significant part of the total lattice energy. Therefore, the magnetic and lattice properties of solid oxygen are very closely related. This manifests itself in a very rich phase diagram and numerous anomalies of thermal, magnetic and optical properties. Low-temperature low-pressure α-O2 is a two-sublattice collinear Neel antiferromagnet. At a pressure of ˜6 GPa, α-O2 is transformed into δ-O2, in which three different magnetic structures are realized upon increasing temperature. At ˜8 GPa δ-O2 is transformed into ɛ-O2. In this transition, O2 molecules combine into four-molecule clusters (O2)4. This transformation is accompanied by a magnetic collapse. This review describes the evolution of the magnetic structure with increasing pressure, and analyzes the causes behind this behavior.

Dispersion of SiC nanoparticles in cellulose for study of tensile, thermal and oxygen barrier properties.

PubMed

Kisku, Sudhir K; Dash, Satyabrata; Swain, Sarat K

2014-01-01

Cellulose/silicon carbide (cellulose/SiC) nanobiocomposites were prepared by solution technique. The interaction of SiC nanoparticles with cellulose were confirmed by Fourier transformed infrared (FTIR) spectroscopy. The structure of cellulose/SiC nanobiocomposites was investigated by X-ray diffraction (XRD), and transmission electron microscopy (TEM). The tensile properties of the nanobiocomposites were improved as compared with virgin cellulose. Thermal stabilities of cellulose/SiC nanobiocomposites were studied by thermogravimetric analysis (TGA). The cellulose/SiC nanobiocomposites were thermally more stable than the raw cellulose. It may be due to the delamination of SiC with cellulose matrix. The oxygen barrier properties of cellulose composites were measured using gas permeameter. A substantial reduction in oxygen permeability was obtained with increase in silicon carbide concentrations. The thermally resistant and oxygen barrier properties of the prepared nanobiocomposites may enable the materials for the packaging applications. Copyright © 2013 Elsevier Ltd. All rights reserved.

Tuning of electronic properties and dynamical stability of graphene oxide with different functional groups

NASA Astrophysics Data System (ADS)

Dabhi, Shweta D.; Jha, Prafulla K.

2017-09-01

The structural, electronic and vibrational properties of graphene oxide (GO) with varying proportion of epoxy and hydroxyl functional groups have been studied using density functional theory. The functional groups and oxygen density have an obvious influence on the electronic and vibrational properties. The dependence of band gap on associated functional groups and oxygen density shows a possibility of tuning the band gap of graphene by varying the functional groups as well as oxidation level. The absorption of high oxygen content in graphene leads to the gap opening and resulting in a transition from semimetal to semiconductor. Phonon dispersion curves show no imaginary frequency or no softening of any phonon mode throughout the Brillouin zone which confirms the dynamical stability of all considered GO models. Different groups and different oxygen density result into the varying characteristics of phonon modes. The computed results show good agreement with the experimental observations. Our results present interesting possibilities for engineering the electronic properties of graphene and GO and impact the fabrication of new electronics.

Optoelectronic properties of valence-state-controlled amorphous niobium oxide

NASA Astrophysics Data System (ADS)

Onozato, Takaki; Katase, Takayoshi; Yamamoto, Akira; Katayama, Shota; Matsushima, Koichi; Itagaki, Naho; Yoshida, Hisao; Ohta, Hiromichi

2016-06-01

In order to understand the optoelectronic properties of amorphous niobium oxide (a-NbO x ), we have investigated the valence states, local structures, electrical resistivity, and optical absorption of a-NbO x thin films with various oxygen contents. It was found that the valence states of Nb ion in a-NbO x films can be controlled from 5+  to 4+  by reducing oxygen pressure during film deposition at room temperature, together with changing the oxide-ion arrangement around Nb ion from Nb2O5-like to NbO2-like local structure. As a result, a four orders of magnitude reduction in the electrical resistivity of a-NbO x films was observed with decreasing oxygen content, due to the carrier generation caused by the appearance and increase of an oxygen-vacancy-related subgap state working as an electron donor. The tunable optoelectronic properties of a-NbO x films by valence-state-control with oxygen-vacancy formation will be useful for potential flexible optoelectronic device applications.

Influence of oxygen partial pressure on the microstructural and magnetic properties of Er-doped ZnO thin films

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

Chen, Wei-Bin; Li, Fei; Chen, Hong-Ming

2015-06-15

Er-doped ZnO thin films have been prepared by using inductively coupled plasma enhanced physical vapor deposition at different O{sub 2}:Ar gas flow ratio (R = 0:30, 1:30, 1:15, 1:10 and 1:6). The influence of oxygen partial pressure on the structural, optical and magnetic properties was studied. It is found that an appropriate oxygen partial pressure (R=1:10) can produce the best crystalline quality with a maximum grain size. The internal strain, estimated by fitting the X-ray diffraction peaks, varied with oxygen partial pressure during growth. PL measurements show that plenty of defects, especially zinc vacancy, exist in Er-doped ZnO films. Allmore » the samples show room-temperature ferromagnetism. Importantly, the saturation magnetization exhibits similar dependency on oxygen partial pressure with the internal strain, which indicates that internal strain has an important effect on the magnetic properties of Er-doped ZnO thin films.« less

Binding properties and colour of Bologna sausage made with varying fat levels, protein levels and cooking temperatures.

PubMed

Carballo, J; Mota, N; Barreto, G; Colmenero, F J

1995-01-01

A little-studied procedure for adjusting the properties of low-fat products is to use the influence that both composition and certain processing factors exert on these properties. The object of the present work was to assess the effects of protein level (P, ranging from 10% to 16%), fat level (F, ranging from 10.1% to 22%) and cooking temperature (HT, ranging from 77 °C to 105 °C) on the binding properties and colour of meat emulsions. Protein content was the variable that most influenced total expressible fluid (TEF) and purge loss. Heating rate had scarcely any effect on the binding properties of Bologna sausages. Analysis of variance indicated that the regression models for parameters L, a and b were not significant.

Hydrogen-Deuterium Exchange Mass Spectrometry Reveals Calcium Binding Properties and Allosteric Regulation of Downstream Regulatory Element Antagonist Modulator (DREAM).

PubMed

Zhang, Jun; Li, Jing; Craig, Theodore A; Kumar, Rajiv; Gross, Michael L

2017-07-18

Downstream regulatory element antagonist modulator (DREAM) is an EF-hand Ca 2+ -binding protein that also binds to a specific DNA sequence, downstream regulatory elements (DRE), and thereby regulates transcription in a calcium-dependent fashion. DREAM binds to DRE in the absence of Ca 2+ but detaches from DRE under Ca 2+ stimulation, allowing gene expression. The Ca 2+ binding properties of DREAM and the consequences of the binding on protein structure are key to understanding the function of DREAM. Here we describe the application of hydrogen-deuterium exchange mass spectrometry (HDX-MS) and site-directed mutagenesis to investigate the Ca 2+ binding properties and the subsequent conformational changes of full-length DREAM. We demonstrate that all EF-hands undergo large conformation changes upon calcium binding even though the EF-1 hand is not capable of binding to Ca 2+ . Moreover, EF-2 is a lower-affinity site compared to EF-3 and -4 hands. Comparison of HDX profiles between wild-type DREAM and two EF-1 mutated constructs illustrates that the conformational changes in the EF-1 hand are induced by long-range structural interactions. HDX analyses also reveal a conformational change in an N-terminal leucine-charged residue-rich domain (LCD) remote from Ca 2+ -binding EF-hands. This LCD domain is responsible for the direct interaction between DREAM and cAMP response element-binding protein (CREB) and regulates the recruitment of the co-activator, CREB-binding protein. These long-range interactions strongly suggest how conformational changes transmit the Ca 2+ signal to CREB-mediated gene transcription.

Enhanced O-2 Selectivity versus N-2 by Partial Metal Substitution in Cu-BTC

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

Sava Gallis, Dorina F.; Parkes, Marie V.; Greathouse, Jeffery A.

2015-03-24

Here, we describe the homogeneous substitution of Mn, Fe, and Co at various levels into a prototypical metal organic framework (MOP), namely Cu-BTC (HKUST-1), and the effect of that substitution on preferential gas sorption. Using a combination of density functional theory (DFT) calculations, postsynthetic metal substitutions, materials characterization, and gas sorption testing, we demonstrate that the identity of the metal ion has a quantifiable effect on their oxygen and nitrogen sorption properties at cryogenic temperatures. An excellent correlation is found between O-2/N-2 selectivities determined experimentally at 77 K and the difference in O-2 and N-2 binding energies calculated from DFTmore » modeling data: Mn > Fe Co >> Cu. Room temperature gas sorption studies were also performed and correlated with metal substitution. The Fe-exchanged sample shows a significantly higher nitrogen isosteric heat of adsorption at temperatures close to ambient conditions (273-298 K) as compared to all other metals studied, indicative of favorable interactions between N-2 and coordinatively unsaturated Fe metal centers. Interestingly, differences in gas adsorption results at cryogenic and room temperatures are evident; they are explained by comparing experimental results with DFT binding energies (0 K) and room temperature Grand Canonical Monte Carlo simulations.« less

Surface charge effects in protein adsorption on nanodiamonds.

PubMed

Aramesh, M; Shimoni, O; Ostrikov, K; Prawer, S; Cervenka, J

2015-03-19

Understanding the interaction of proteins with charged diamond nanoparticles is of fundamental importance for diverse biomedical applications. Here we present a thorough study of protein binding, adsorption kinetics and structure on strongly positively (hydrogen-terminated) and negatively (oxygen-terminated) charged nanodiamond particles using a quartz crystal microbalance by dissipation and infrared spectroscopy. By using two model proteins (bovine serum albumin and lysozyme) of different properties (charge, molecular weight and rigidity), the main driving mechanism responsible for the protein binding to the charged nanoparticles was identified. Electrostatic interactions were found to dominate the protein adsorption dynamics, attachment and conformation. We developed a simple electrostatic model that can qualitatively explain the observed adsorption behaviour based on charge-induced pH modifications near the charged nanoparticle surfaces. Under neutral conditions, the local pH around the positively and negatively charged nanodiamonds becomes very high (11-12) and low (1-3) respectively, which has a profound impact on the protein charge, hydration and affinity to the nanodiamonds. Small proteins (lysozyme) were found to form multilayers with significant conformational changes to screen the surface charge, while larger proteins (albumin) formed monolayers with minor conformational changes. The findings of this study provide a step forward toward understanding and eventually predicting nanoparticle interactions with biofluids.

Enhanced O 2 selectivity versus N 2 by partial metal substitution in Cu-BTC

DOE PAGES

Sava Gallis, Dorina F.; Parkes, Marie V.; Greathouse, Jeffery A.; ...

2015-03-05

Here we describe the homogeneous substitution of Mn, Fe and Co at various levels into a prototypical metal-organic framework (MOF), namely Cu-BTC (HKUST-1), and the effect of that substitution on preferential gas sorption. Using a combination of density functional theory (DFT) calculations, postsynthetic metal substitutions, materials characterization, and gas sorption testing, we demonstrate that the identity of the metal ion has a quantifiable effect on their oxygen and nitrogen sorption properties at cryogenic temperatures. An excellent correlation is found between O 2/N 2 selectivities determined experimentally at 77 K and the difference in O 2 and N 2 binding energiesmore » calculated from DFT modeling data: Mn > Fe > Co > Cu. Room temperature gas sorption studies were also performed and correlated with metal substitution. The Fe-exchanged sample shows a significantly higher nitrogen isosteric heat of adsorption at temperatures close to ambient conditions (273 K - 298 K) as compared to all other metals studied, indicative of favorable interactions between N 2 and coordinatively unsaturated Fe metal centers. Furthermore, differences in gas adsorption results at cryogenic and room temperatures are evident; they are explained by comparing experimental results with DFT binding energies (0 K) and room temperature Grand Canonical Monte Carlo simulations.« less

Orientation-Dependent Oxygen Evolution on RuO 2 without Lattice Exchange

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

Stoerzinger, Kelsey A.; Diaz-Morales, Oscar; Kolb, Manuel

RuO2 catalysts exhibit record activities towards the oxygen evolution reaction (OER), which is crucial to enable efficient and sustainable energy storage. Here we examine the RuO2 OER kinetics on rutile (110), (100), (101), and (111) orientations, finding (100) the most active. We assess the potential involvement of lattice oxygen in the OER mechanism with online 3 electrochemical mass spectrometry, which showed no evidence of oxygen exchange on these oriented facets in acidic or basic electrolytes. Similar results were obtained for polyoriented RuO2 films and particles, in contrast to previous work, suggesting lattice oxygen is not exchanged in catalyzing OER onmore » crystalline RuO2 surfaces. This hypothesis is supported by the correlation of activity with the number of active Ru-sites calculated by DFT, where more active facets bind oxygen more weakly. This new understanding of the active sites provides a design strategy to enhance the OER activity of RuO2 nanoparticles by facet engineering.« less

Complexes of horseradish peroxidase with formate, acetate, and carbon monoxide.

PubMed

Carlsson, Gunilla H; Nicholls, Peter; Svistunenko, Dimitri; Berglund, Gunnar I; Hajdu, Janos

2005-01-18

Carbon monoxide, formate, and acetate interact with horseradish peroxidase (HRP) by binding to subsites within the active site. These ligands also bind to catalases, but their interactions are different in the two types of enzymes. Formate (notionally the "hydrated" form of carbon monoxide) is oxidized to carbon dioxide by compound I in catalase, while no such reaction is reported to occur in HRP, and the CO complex of ferrocatalase can only be obtained indirectly. Here we describe high-resolution crystal structures for HRP in its complexes with carbon monoxide and with formate, and compare these with the previously determined HRP-acetate structure [Berglund, G. I., et al. (2002) Nature 417, 463-468]. A multicrystal X-ray data collection strategy preserved the correct oxidation state of the iron during the experiments. Absorption spectra of the crystals and electron paramagnetic resonance data for the acetate and formate complexes in solution correlate electronic states with the structural results. Formate in ferric HRP and CO in ferrous HRP bind directly to the heme iron with iron-ligand distances of 2.3 and 1.8 A, respectively. CO does not bind to the ferric iron in the crystal. Acetate bound to ferric HRP stacks parallel with the heme plane with its carboxylate group 3.6 A from the heme iron, and without an intervening solvent molecule between the iron and acetate. The positions of the oxygen atoms in the bound ligands outline a potential access route for hydrogen peroxide to the iron. We propose that interactions in this channel ensure deprotonation of the proximal oxygen before binding to the heme iron.

Formation of a dinitrosyl iron complex by NorA, a nitric oxide-binding di-iron protein from Ralstonia eutropha H16.

PubMed

Strube, Katja; de Vries, Simon; Cramm, Rainer

2007-07-13

In Ralstonia eutropha H16, two genes, norA and norB, form a dicistronic operon that is controlled by the NO-responsive transcriptional regulator NorR. NorB has been identified as a membrane-bound NO reductase, but the physiological function of NorA is unknown. We found that, in a NorA deletion mutant, the promoter activity of the norAB operon was increased 3-fold, indicating that NorA attenuates activation of NorR. NorA shows limited sequence similarity to the oxygen carrier hemerythrin, which contains a di-iron center. Indeed, optical and EPR spectroscopy of purified NorA revealed the presence of a di-iron center, which binds oxygen in a similar way as hemerythrin. Diferrous NorA binds two molecules of NO maximally. Unexpectedly, binding of NO to the diferrous NorA required an external reductant. Two different NorA-NO species could be resolved. A minor species (up to 20%) showed an S = (1/2) EPR signal with g( perpendicular) = 2.041, and g( parallel) = 2.018, typical of a paramagnetic dinitrosyl iron complex. The major species was EPR-silent, showing characteristic signals at 420 nm and 750 nm in the optical spectrum. This species is proposed to represent a novel dinitrosyl iron complex of the form Fe(2+)-[NO](2)(2-), i.e. NO is bound as NO(-). The NO binding capacity of NorA in conjunction with its high cytoplasmic concentration (20 mum) suggests that NorA regulates transcription by lowering the free cytoplasmic concentration of NO.

Physical origins of weak H 2 binding on carbon nanostructures: Insight from ab initio studies of chemically functionalized graphene nanoribbons

DOE PAGES

Ulman, Kanchan; Bhaumik, Debarati; Wood, Brandon C.; ...

2014-05-05

Here, we have performed ab initio density functional theory calculations, incorporating London dispersion corrections, to study the absorption of molecular hydrogen on zigzag graphene nanoribbons whose edges have been functionalized by OH, NH 2, COOH, NO 2, or H 2PO 3. We find that hydrogen molecules always preferentially bind at or near the functionalized edge, and display induced dipole moments. Binding is generally enhanced by the presence of polar functional groups. Furthermore, the largest gains are observed for groups with oxygen lone pairs that can facilitate local charge reorganization, with the biggest single enhancement in adsorption energy found for “strongmore » functionalization” by H 2PO 3 (115 meV/H 2 versus 52 meV/H 2 on bare graphene). We show that for binding on the “outer edge” near the functional group, the presence of the group can introduce appreciable contributions from Debye interactions and higher-order multipole electrostatic terms, in addition to the dominant London dispersion interactions. For those functional groups that contain the OH moiety, the adsorption energy is linearly proportional to the number of lone pairs on oxygen atoms. Mixed functionalization with two different functional groups on a graphene edge can also have a synergistic effect, particularly when electron-donating and electron-withdrawing groups are combined. For binding on the “inner edge” somewhat farther from the functional group, most of the binding again arises from London interactions; however, there is also significant charge redistribution in the π manifold, which directly reflects the electron donating or withdrawing capacity of the functional group. These results offer insight into the specific origins of weak binding of gas molecules on graphene, and suggest that edge functionalization could perhaps be used in combination with other strategies to increase the uptake of hydrogen in graphene. They also have relevance for the storage of hydrogen in porous carbon materials, such as activated carbons.« less

Novel Regulation of Skp1 by the Dictyostelium AgtA α-Galactosyltransferase Involves the Skp1-binding Activity of Its WD40 Repeat Domain*

PubMed Central

Schafer, Christopher M.; Sheikh, M. Osman; Zhang, Dongmei; West, Christopher M.

2014-01-01

The role of Skp1 as an adaptor protein that links Cullin-1 to F-box proteins in E3 Skp1/Cullin-1/F-box protein (SCF) ubiquitin ligases is well characterized. In the social amoeba Dictyostelium and probably many other unicellular eukaryotes, Skp1 is modified by a pentasaccharide attached to a hydroxyproline near its C terminus. This modification is important for oxygen-sensing during Dictyostelium development and is mediated by a HIF-α type prolyl 4-hydroxylase and five sequentially acting cytoplasmic glycosyltransferase activities. Gene disruption studies show that AgtA, the enzyme responsible for addition of the final two galactose residues, in α-linkages to the Skp1 core trisaccharide, is unexpectedly critical for oxygen-dependent terminal development. AgtA possesses a WD40 repeat domain C-terminal to its single catalytic domain and, by use of domain deletions, binding studies, and enzyme assays, we find that the WD40 repeats confer a salt-sensitive second-site binding interaction with Skp1 that mediates novel catalytic activation in addition to simple substrate recognition. In addition, AgtA binds similarly well to precursor isoforms of Skp1 by a salt-sensitive mechanism that competes with binding to an F-box protein and recognition by early modification enzymes, and the effect of binding is diminished when AgtA modifies Skp1. Genetic studies show that loss of AgtA is more severe when an earlier glycosylation step is blocked, and overexpressed AgtA is deleterious if catalytically inactivated. Together, the findings suggest that AgtA mediates non-enzymatic control of unmodified and substrate precursor forms of Skp1 by a binding mechanism that is normally relieved by switch-like activation of its glycosylation function. PMID:24550398

The hemoglobin system of the primitive fish, Amia calva: isolation and functional characterization of the individual hemoglobin components.

PubMed

Weber, R E; Sullivan, B; Bonaventura, J; Bonaventura, C

1976-05-20

Blood from the primitive holostean fish, the bowfin, Amia calva, contains 2 mo of ATP per mol of hemoglobin. The hemolysates contain at least five tetrameric hemoglobin components which differ in their oxygen affinities and their response to cofactors such as ATP. The binding of oxygen by each chromatographically isolated component, including a cathodal component, is influenced by pH and organic phosphates; there is no significant differentiation of function or structure as seen in trout and certain other fish hemolysates. Kinetic analyses of ligand binding indicate that the Bohr and Root effects of Amia calva hemoglobins are best explained by changes in both the "on" and "off" constants. At low pH, the increase in the "off" constant is smaller than for most other Root hemoglobins. The hemoglobin system of Amina calva is functionally undifferentiated and may be representative of the ancestral condition in teleosts.

Interactions of chloride and formate at the donor and the acceptor side of photosystem II.

PubMed

Jajoo, Anjana; Bharti, Sudhakar; Kawamori, Asako

2005-02-01

Chloride is required for the maximum activity of the oxygen evolving complex (OEC) while formate inhibits the function of OEC. On the basis of the measurements of oxygen evolution rates and the S(2) state multiline EPR signal, an interaction between the action of chloride and formate at the donor side of PS II has been suggested. Moreover, the Fe(2)+Q-A EPR signals were measured to investigate a common binding site of both these anions at the PS II acceptor side. Other monovalent anions like bromide, nitrate etc. could influence the effects of formate to a small extent at the donor side of PS II, but not significantly at the acceptor side of PS II. The results presented in this paper clearly suggest a competitive binding of formate and chloride at the PS II acceptor side.

Mixing of acrylic bone cement: effect of oxygen on setting properties.

PubMed

He, Shulin; Scott, Christopher; Higham, Paul

2003-12-01

The present study investigates the effect of different mixing methods on the setting properties of bone cement. It was found that vacuum mixing decreased the setting time of the bone cement by nearly 2 min (10%), compared to mixing in air. Two additional experiments, in which the bone cement powders were purged with argon or oxygen, and mixed with the methyl methacrylate monomer, revealed that oxygen concentrations in the bone cement had a great effect on the setting time. The setting time increases significantly as the oxygen concentration increases, which suggests that the decrease in the setting time by vacuum mixing may be attributed to the lower oxygen levels present in the mixer. No significant effect was observed on dough time or maximum exothermic temperature by varying oxygen concentrations in the bone cement mixer.

Pyrene maleimide as a probe of microenvironmental and dynamics properties of protein binding sites

NASA Astrophysics Data System (ADS)

Benci, S.; Vaccari, S.; Schianchi, G.; Locatelli, Donata; Vaghi, P.; Bottiroli, Giovanni F.

1995-01-01

N-(1-Pyrene)maleimide is highly fluorescent upon covalent binding with sulfhydryl and amino groups of the proteins. Multiexponential fluorescence decays were observed for the dye bound to different proteins even when a single binding site is involved. The lack of information about the fluorescence decay of free dye does not allow to define the variations of fluorescence parameter following the conjugation and their correlation with the binding properties of the fluorophore. In this work, a study of the fluorescence of the probe, free in solution, bound to different antibodies and to the antigen-antibody complex both in solution and in cell, has been performed. The experimental results showed that chemico-physical properties of the medium influence the fluorescence decay of the probe in both the free and bound forms, although to a different extent. The variations of fluorescence decay and anisotropy of the bound probe are related to the electronic characteristics of microenvironment and show an increased stabilization of the probe binding site with the increasing complexity of the substrate. The sensitivity of the fluorescence properties of the probe to the binding site environment opens interesting perspectives concerning the application of Py- maleimide fluorochromization to assess the degree of specificity of immunocytochemical labelling.

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

Detwiler, Michael D.; Majumdar, Paulami; Gu, Xiang-Kui

Changes in surface chemistry and morphology of Re–Pt surfaces synthesized by ultra-high vacuum chemical vapor deposition (UHV-CVD) of Re on Pt(111) were studied by a combination of experiment and density functional theory (DFT) modeling. A Re oxide formed following exposure of the as-deposited Re to 1 × 10- 6 mbar oxygen at 600–673 K. Subsequent annealing at 973 K resulted in oxygen desorption and a decrease in Re coverage, as calculated by XPS and as observed by STM. This observation was explained by DFT calculations which showed that a clean Pt surface slab with subsurface Re is thermodynamically more favorablemore » than Pt(111) with Re on the surface. DFT calculations also predicted weaker O and CO binding on this surface compared to both monometallic Pt and Re, and HREELS and temperature desorption measurements suggested that O binds weakly to the Pt skin surface, with oxygen on the Pt skin desorbing from this surface following annealing at 373 K. Trends in adsorption energies were consistent with DFT calculated d-band centers of surface atoms for model Pt–Re structures. Comparison of HREELS data and STM images with DFT calculated vibrational frequencies have been used to understand the structure of rhenium oxide on Pt(111).« less

Zolpidem reduces the blood oxygen level-dependent signal during visual system stimulation

PubMed Central

Licata, Stephanie C.; Lowen, Steven B.; Trksak, George H.; MacLean, Robert R.; Lukas, Scott E.

2011-01-01

Zolpidem is a short-acting imidazopyridine hypnotic that binds at the benzodiazepine binding site on specific GABAA receptors to enhance fast inhibitory neurotransmission. The behavioral and receptor pharmacology of zolpidem has been studied extensively, but little is known about its neuronal substrates in vivo. In the present within-subject, double-blind, and placebo-controlled study, blood oxygen level-dependent functional magnetic resonance imaging (BOLD fMRI) at 3 Tesla was used to assess the effects of zolpidem within the brain. Healthy participants (n=12) were scanned 60 minutes after acute oral administration of zolpidem (0, 5, 10, or 20 mg), and changes in BOLD signal were measured in the visual cortex during presentation of a flashing checkerboard. Heart rate and oxygen saturation were monitored continuously throughout the session. Zolpidem (10 and 20 mg) reduced the robust visual system activation produced by presentation of this stimulus, but had no effects on physiological activity during the fMRI scan. Zolpidem’s modulation of the BOLD signal within the visual cortex is consistent with the abundant distribution of GABAA receptors localized in this region, as well as previous studies showing a relationship between increased GABA-mediated neuronal inhibition and a reduction in BOLD activation. PMID:21640782

Molecular packing and magnetic properties of lithium naphthalocyanine crystals: hollow channels enabling permeability and paramagnetic sensitivity to molecular oxygen

PubMed Central

Pandian, Ramasamy P.; Dolgos, Michelle; Marginean, Camelia; Woodward, Patrick M.; Hammel, P. Chris; Manoharan, Periakaruppan T.; Kuppusamy, Periannan

2009-01-01

The synthesis, structural framework, magnetic and oxygen-sensing properties of a lithium naphthalocyanine (LiNc) radical probe are presented. LiNc was synthesized in the form of a microcrystalline powder using a chemical method and characterized by electron paramagnetic resonance (EPR) spectroscopy, magnetic susceptibility, powder X-ray diffraction analysis, and mass spectrometry. X-Ray powder diffraction studies revealed a structural framework that possesses long, hollow channels running parallel to the packing direction. The channels measured approximately 5.0 × 5.4 Å2 in the two-dimensional plane perpendicular to the length of the channel, enabling diffusion of oxygen molecules (2.9 × 3.9 Å2) through the channel. The powdered LiNc exhibited a single, sharp EPR line under anoxic conditions, with a peak-to-peak linewidth of 630 mG at room temperature. The linewidth was sensitive to surrounding molecular oxygen, showing a linear increase in pO2 with an oxygen sensitivity of 31.2 mG per mmHg. The LiNc microcrystals can be further prepared as nano-sized crystals without the loss of its high oxygen-sensing properties. The thermal variation of the magnetic properties of LiNc, such as the EPR linewidth, EPR intensity and magnetic susceptibility revealed the existence of two different temperature regimes of magnetic coupling and hence differing columnar packing, both being one-dimensional antiferromagnetic chains but with differing magnitudes of exchange coupling constants. At a temperature of ∼50 K, LiNc crystals undergo a reversible phase transition. The high degree of oxygen-sensitivity of micro- and nano-sized crystals of LiNc, combined with excellent stability, should enable precise and accurate measurements of oxygen concentration in biological systems using EPR spectroscopy. PMID:19809598

Characterization of a unique [FeS] cluster in the electron transfer chain of the oxygen tolerant [NiFe] hydrogenase from Aquifex aeolicus.

PubMed

Pandelia, Maria-Eirini; Nitschke, Wolfgang; Infossi, Pascale; Giudici-Orticoni, Marie-Thérèse; Bill, Eckhard; Lubitz, Wolfgang

2011-04-12

Iron-sulfur clusters are versatile electron transfer cofactors, ubiquitous in metalloenzymes such as hydrogenases. In the oxygen-tolerant Hydrogenase I from Aquifex aeolicus such electron "wires" form a relay to a diheme cytb, an integral part of a respiration pathway for the reduction of O(2) to water. Amino acid sequence comparison with oxygen-sensitive hydrogenases showed conserved binding motifs for three iron-sulfur clusters, the nature and properties of which were unknown so far. Electron paramagnetic resonance spectra exhibited complex signals that disclose interesting features and spin-coupling patterns; by redox titrations three iron-sulfur clusters were identified in their usual redox states, a [3Fe4S] and two [4Fe4S], but also a unique high-potential (HP) state was found. On the basis of (57)Fe Mössbauer spectroscopy we attribute this HP form to a superoxidized state of the [4Fe4S] center proximal to the [NiFe] site. The unique environment of this cluster, characterized by a surplus cysteine coordination, is able to tune the redox potentials and make it compliant with the [4Fe4S](3+) state. It is actually the first example of a biological [4Fe4S] center that physiologically switches between 3+, 2+, and 1+ oxidation states within a very small potential range. We suggest that the (1 + /2+) redox couple serves the classical electron transfer reaction, whereas the superoxidation step is associated with a redox switch against oxidative stress.

Characterization of a unique [FeS] cluster in the electron transfer chain of the oxygen tolerant [NiFe] hydrogenase from Aquifex aeolicus

PubMed Central

Pandelia, Maria-Eirini; Nitschke, Wolfgang; Infossi, Pascale; Giudici-Orticoni, Marie-Thérèse; Bill, Eckhard; Lubitz, Wolfgang

2011-01-01

Iron-sulfur clusters are versatile electron transfer cofactors, ubiquitous in metalloenzymes such as hydrogenases. In the oxygen-tolerant Hydrogenase I from Aquifex aeolicus such electron “wires” form a relay to a diheme cytb, an integral part of a respiration pathway for the reduction of O2 to water. Amino acid sequence comparison with oxygen-sensitive hydrogenases showed conserved binding motifs for three iron-sulfur clusters, the nature and properties of which were unknown so far. Electron paramagnetic resonance spectra exhibited complex signals that disclose interesting features and spin-coupling patterns; by redox titrations three iron-sulfur clusters were identified in their usual redox states, a [3Fe4S] and two [4Fe4S], but also a unique high-potential (HP) state was found. On the basis of 57Fe Mössbauer spectroscopy we attribute this HP form to a superoxidized state of the [4Fe4S] center proximal to the [NiFe] site. The unique environment of this cluster, characterized by a surplus cysteine coordination, is able to tune the redox potentials and make it compliant with the [4Fe4S]3+ state. It is actually the first example of a biological [4Fe4S] center that physiologically switches between 3+, 2+, and 1+ oxidation states within a very small potential range. We suggest that the (1 + /2+) redox couple serves the classical electron transfer reaction, whereas the superoxidation step is associated with a redox switch against oxidative stress. PMID:21444783

Effect of oxygen concentration on the magnetic properties of La2CoMnO6 thin films

NASA Astrophysics Data System (ADS)

Guo, H. Z.; Gupta, A.; Zhang, Jiandi; Varela, M.; Pennycook, S. J.

2007-11-01

The dependence of the magnetic properties on oxygen concentration in epitaxial La2CoMnO6 thin films deposited on (100)-oriented SrTiO3 substrates has been investigated by varying the oxygen background pressure during growth using pulsed laser deposition. Two distinct ferromagnetic (FM) phases are revealed, and the relative fraction varies with the oxygen concentration. The existence of oxygen vacancies induces the local vibronic Mn3+-O -Co3+ superexchange interactions in direct competition with the static FM Mn4+-O-Co2+ interactions. This results in the appearance of a new low temperature FM phase and suppression of the high-temperature FM phase, creating two distinct magnetic phase transitions.

The In Vivo DNA Binding Properties of Wild-Type and Mutant p53 Proteins in Mammary Cell Lines During the Course of Cell Cycle.

DTIC Science & Technology

1996-08-01

J-4030 TITLE: The In Vivo DNA Binding Properties of Wild-Type and Mutant p53 Proteins in Mammary Cell Lines During the Course of Cell Cycle PRINCIPAL...The In Vivo DNA Binding Properties of 5. FUNDING NUMBERS Wild-Type and Mutant p53 Proteins in Mammary Cell Lines DAMD17-94-J-4030 During the Course of...ABSTRACT (Maximum 200 Using a pair of murine cell lines, one lacking p53 and a derivative cell line containing temperature sensitive p53 val 135

Crystal structure of the Alpha subunit PAS domain from soluble guanylyl cyclase

PubMed Central

Purohit, Rahul; Weichsel, Andrzej; Montfort, William R

2013-01-01

Soluble guanylate cyclase (sGC) is a heterodimeric heme protein of ∼150 kDa and the primary nitric oxide receptor. Binding of NO stimulates cyclase activity, leading to regulation of cardiovascular physiology and providing attractive opportunities for drug discovery. How sGC is stimulated and where candidate drugs bind remains unknown. The α and β sGC chains are each composed of Heme-Nitric Oxide Oxygen (H-NOX), Per-ARNT-Sim (PAS), coiled-coil and cyclase domains. Here, we present the crystal structure of the α1 PAS domain to 1.8 Å resolution. The structure reveals the binding surfaces of importance to heterodimer function, particularly with respect to regulating NO binding to heme in the β1 H-NOX domain. It also reveals a small internal cavity that may serve to bind ligands or participate in signal transduction. PMID:23934793

Thermophysical properties and oxygen transport in (Th x,Pu 1-x)O 2

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

Galvin, C. O. T.; Cooper, M. W. D.; Rushton, M. J. D.

Using Molecular Dynamics, this paper investigates the thermophysical properties and oxygen transport of (Th x,Pu 1–x)O 2 (0 ≤ x ≤ 1) between 300–3500 K. Specifically, the superionic transition is investigated and viewed via the thermal dependence of lattice parameter, linear thermal expansion coefficient, enthalpy and specific heat at constant pressure. Oxygen diffusivity and activation enthalpy are also investigated. Below the superionic temperature an increase of oxygen diffusivity for certain compositions of (Th x,Pu 1–x)O 2 compared to the pure end members is predicted. Oxygen defect formation enthalpies are also examined, as they underpin the superionic transition temperature and themore » increase in oxygen diffusivity. The increase in oxygen diffusivity for (Th x,Pu 1–x)O 2 is explained in terms of lower oxygen defect formation enthalpies for (Th x,Pu 1–x)O 2 than PuO 2 and ThO 2, while links are drawn between the superionic transition temperature and oxygen Frenkel disorder.« less

Thermophysical properties and oxygen transport in (Th x,Pu 1-x)O 2

DOE PAGES

Galvin, C. O. T.; Cooper, M. W. D.; Rushton, M. J. D.; ...

2016-10-31

Using Molecular Dynamics, this paper investigates the thermophysical properties and oxygen transport of (Th x,Pu 1–x)O 2 (0 ≤ x ≤ 1) between 300–3500 K. Specifically, the superionic transition is investigated and viewed via the thermal dependence of lattice parameter, linear thermal expansion coefficient, enthalpy and specific heat at constant pressure. Oxygen diffusivity and activation enthalpy are also investigated. Below the superionic temperature an increase of oxygen diffusivity for certain compositions of (Th x,Pu 1–x)O 2 compared to the pure end members is predicted. Oxygen defect formation enthalpies are also examined, as they underpin the superionic transition temperature and themore » increase in oxygen diffusivity. The increase in oxygen diffusivity for (Th x,Pu 1–x)O 2 is explained in terms of lower oxygen defect formation enthalpies for (Th x,Pu 1–x)O 2 than PuO 2 and ThO 2, while links are drawn between the superionic transition temperature and oxygen Frenkel disorder.« less

The specificity of binding of growth hormone and prolactin to purified plasma membranes from pregnant-rabbit liver.

PubMed Central

Webb, C F; Cadman, H F; Wallis, M

1986-01-01

The binding of 125I-labelled human growth hormone (hGH) to a purified plasma membrane preparation from the liver of pregnant rabbit, and to receptors solubilized from this fraction with Triton X-100, was dependent on time, temperature, the cations used and the receptor concentration. Solubilization did not affect the binding properties of the receptors at low concentrations of Triton X-100. Some somatogenic hormones, such as bovine GH, and some lactogenic hormones, such as ovine prolactin, displaced 125I-labelled hGH from purified plasma membranes and solubilized receptor preparations, but GHs and prolactins from various other species were rather ineffective. The results indicate that although there are binding sites for hGH in these pregnant rabbit liver membranes, few of these are specifically somatogenic or lactogenic. The binding properties of the purified plasma membranes are similar to those of a microsomal preparation studied previously, suggesting that the complex nature of the binding of hGH is not due to the heterogeneity of cellular membranes used to study binding, but is a property of the receptors associated with plasma membranes. PMID:3790086

The mechanism of the molecular interaction between cerium (III) and ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco).

PubMed

Liu, Chao; Hong, Fa-shui; Tao, Ye; Liu, Tao; Xie, Ya-ning; Xu, Jian-hua; Li, Zhong-rui

2011-11-01

The mechanism of the molecular interaction between Ce3+, a member of rare earth elements, and Rubisco in vitro is investigated. The carboxylase activity of Rubisco greatly increased under low concentrations of Ce3+ and decreased under high concentrations of Ce3+. The ultraviolet absorption spectra show that the various concentrations of Ce3+ treatment do not shift the characteristic peaks of Rubisco while the characteristic peak intensity of Rubisco increases with increasing Ce3+ concentration. The Rubisco-Ce3+ interactions also do not cause any noticeable change in the λmax of Rubisco fluorescence spectra. However, the fluorescence intensity of Rubisco is found quenched by the addition of Ce3+, which strongly suggests that Ce3+ could directly bind to the Rubisco protein. and the binding sites is estimated to 1.52 per protein. The binding between Ce3+ and Rubisco is also proved by extended X-ray absorption fine-structure essay; Ce3+ coordinated with eight oxygen atoms of Rubisco in first shells and six oxygen atoms in second shells. The results implied that Ce3+ might improve the microenvironment of Rubisco and, in turn, affected the carboxylase capacity of Rubisco greatly.

Metal binding of flavonoids and their distinct inhibition mechanisms toward the oxidation activity of Cu2+-β-amyloid: not just serving as suicide antioxidants!

PubMed

Tay, William Maung; da Silva, Giordano F Z; Ming, Li-June

2013-01-18

The accumulation of plagues of β-amyloid (Aβ) peptides in the brain is a hallmark of Alzheimer's disease (AD). The redox-active Cu and Fe complexes of Aβ can cause damage to the neurons potentially via reactive oxygen species (ROS). The significant metal-mediated oxidative activity of CuAβ suggests that its presence can be chemically devastating regardless whether it is a cause or a result of AD. Flavonoids exhibit various benefits to human health, attributable to their metal-binding and antioxidation activities to certain extents. Despite broad interests and extensive studies of their metal-binding properties and anti/pro-oxidation activities, these properties and the mechanisms of the activities toward metal-centered oxidation reactions have not been fully revealed and concluded. We report herein distinctive antioxidation mechanisms between two flavonoid families toward the oxidation reactions by CuAβ(1-20), wherein the flavonols quercetin (Qr) and myricetin (Mr) competitively inhibit the oxidation of catechol by CuAβ(1-20) with K(i) of 11.2 and 32.6 μM, respectively, whereas the flavanols catechin (Ct) and epicatechin (Et) are substrates with k(cat) = 1.01 × 10(-2) and 1.55 × 10(-3) s(-1) and K(m) = 0.94 and 0.55 mM, respectively. Qr has a nearly 10-fold higher antioxidative efficacy than Ct against the oxidation activity of CuAβ, while Ct is effectively oxidized, which further decreases its antioxidant capacity. Similar inhibition patterns are observed toward oxidation of the catecholamine neurotransmitter dopamine by CuAβ(1-20). Metal ions and CuAβ bind Qr with a 1:1 ratio under our experimental conditions through the α-ketoenolate moiety as determined by the use of Co(2+) and Yb(3+) as paramagnetic NMR probes. Unlike flavanols, which are merely suicide antioxidative substrates, flavonols bind to the metal center and prevent metal-mediated redox reactions. We suggest flavonols may serve as leads for drug discovery and/or as agents toward preventing metal-mediated oxidative stress due to AD and other disorders. Moreover, CuAβ shows 8.6- and 4.2-fold higher kinetic regioselectivity in terms of k(cat) and k(cat)/K(m), respectively, toward the peroxidation of Ct than that of the enantiomer Et, suggesting potential development of metallo-catalysts in regioselective catalysis by the use of metallopeptides as templates.

B 36N 36 fullerene-like nanocages: A novel material for drug delivery

NASA Astrophysics Data System (ADS)

Ganji, M. D.; Yazdani, H.; Mirnejad, A.

2010-07-01

We study interaction between B 36N 36 fullerene-like nanocage and glycine amino acid from the first- principles. Binding energy is calculated and glycine binding to the pure C 60 fullerene is compared. We also analyze the electronic structure and charge Mulliken population for the energetically most favorable complexes. Our results indicate that glycine can form stable bindings with B 36N 36 nanocage via their carbonyl oxygen (O) active site while, the C 60 fullerene might be unable to form stable bindings to glycine amino acid via their active sites, which is consistence with recent experimental and theoretical investigations. Thus, we arrive at the prediction that the B 36N 36 nanocage can be implemented as a novel material for drug delivery applications.

The Molecular Structure of Epoxide Hydrolase B From And Its Complex With Urea-Based Inhibitor

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

Biswal, B.K.; Morisseau, C.; Garen, G.

2009-05-11

Mycobacterium tuberculosis (Mtb), the intracellular pathogen that infects macrophages primarily, is the causative agent of the infectious disease tuberculosis in humans. The Mtb genome encodes at least six epoxide hydrolases (EHs A to F). EHs convert epoxides to trans-dihydrodiols and have roles in drug metabolism as well as in the processing of signaling molecules. Herein, we report the crystal structures of unbound Mtb EHB and Mtb EHB bound to a potent, low-nanomolar (IC(50) approximately 19 nM) urea-based inhibitor at 2.1 and 2.4 A resolution, respectively. The enzyme is a homodimer; each monomer adopts the classical alpha/beta hydrolase fold that composesmore » the catalytic domain; there is a cap domain that regulates access to the active site. The catalytic triad, comprising Asp104, His333 and Asp302, protrudes from the catalytic domain into the substrate binding cavity between the two domains. The urea portion of the inhibitor is bound in the catalytic cavity, mimicking, in part, the substrate binding; the two urea nitrogen atoms donate hydrogen bonds to the nucleophilic carboxylate of Asp104, and the carbonyl oxygen of the urea moiety receives hydrogen bonds from the phenolic oxygen atoms of Tyr164 and Tyr272. The phenolic oxygen groups of these two residues provide electrophilic assistance during the epoxide hydrolytic cleavage. Upon inhibitor binding, the binding-site residues undergo subtle structural rearrangement. In particular, the side chain of Ile137 exhibits a rotation of around 120 degrees about its C(alpha)-C(beta) bond in order to accommodate the inhibitor. These findings have not only shed light on the enzyme mechanism but also have opened a path for the development of potent inhibitors with good pharmacokinetic profiles against all Mtb EHs of the alpha/beta type.« less

Immunohistochemical detection of a hypoxia marker in spontaneous canine tumours.

PubMed Central

Cline, J. M.; Thrall, D. E.; Page, R. L.; Franko, A. J.; Raleigh, J. A.

1990-01-01

An immunoperoxidase technique has been used to detect the in vivo binding of a 2-nitroimidazole hypoxia marker in histochemical sections of a variety of excised canine tumours. The binding occurred 10-12 cell diameters away from tumour blood vessels, consistent with the expected location of hypoxic cells in tissues in which oxygen concentration gradients are established by diffusion. Hypoxic fractions ranging from 4 to 13% have been estimated on the basis of morphometric analysis of multiple tumour sections. The binding of the marker was restricted to the cytoplasm of the cells. The marker appeared in regions adjacent to necrosis but also in regions free of necrosis. As in earlier autoradiography studies, binding was occasionally observed in cells adjacent to tumour blood vessels. Generally, binding to normal tissues was not observed. However, binding to smooth muscle cells surrounding arterioles in some sections of normal tissue and tumour tissue was observed. Images Figure 1 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 PMID:1701659

Fulvic acid-sulfide ion competition for mercury ion binding in the Florida everglades

USGS Publications Warehouse

Reddy, M.M.; Aiken, G.R.

2001-01-01

Negatively charged functional groups of fulvic acid compete with inorganic sulfide ion for mercury ion binding. This competition is evaluated here by using a discrete site-electrostatic model to calculate mercury solution speciation in the presence of fulvic acid. Model calculated species distributions are used to estimate a mercury-fulvic acid apparent binding constant to quantify fulvic acid and sulfide ion competition for dissolved inorganic mercury (Hg(II)) ion binding. Speciation calculations done with PHREEQC, modified to use the estimated mercury-fulvic acid apparent binding constant, suggest that mercury-fulvic acid and mercury-sulfide complex concentrations are equivalent for very low sulfide ion concentrations (about 10-11 M) in Everglades' surface water. Where measurable total sulfide concentration (about 10-7 M or greater) is present in Everglades' surface water, mercury-sulfide complexes should dominate dissolved inorganic mercury solution speciation. In the absence of sulfide ion (for example, in oxygenated Everglades' surface water), fulvic acid binding should dominate Everglades' dissolved inorganic mercury speciation.

41 CFR 50-204.67 - Oxygen.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 41 Public Contracts and Property Management 1 2013-07-01 2013-07-01 false Oxygen. 50-204.67..., Vapors, Fumes, Dusts, and Mists § 50-204.67 Oxygen. The in-plant transfer, handling, storage, and utilization of oxygen as a liquid or a compressed gas shall be in accordance with Compressed Gas Association...

41 CFR 50-204.67 - Oxygen.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 41 Public Contracts and Property Management 1 2014-07-01 2014-07-01 false Oxygen. 50-204.67..., Vapors, Fumes, Dusts, and Mists § 50-204.67 Oxygen. The in-plant transfer, handling, storage, and utilization of oxygen as a liquid or a compressed gas shall be in accordance with Compressed Gas Association...

Genome analysis and signature discovery for diving and sensory properties of the endangered Chinese alligator

PubMed Central

Wan, Qiu-Hong; Pan, Sheng-Kai; Hu, Li; Zhu, Ying; Xu, Peng-Wei; Xia, Jin-Quan; Chen, Hui; He, Gen-Yun; He, Jing; Ni, Xiao-Wei; Hou, Hao-Long; Liao, Sheng-Guang; Yang, Hai-Qiong; Chen, Ying; Gao, Shu-Kun; Ge, Yun-Fa; Cao, Chang-Chang; Li, Peng-Fei; Fang, Li-Ming; Liao, Li; Zhang, Shu; Wang, Meng-Zhen; Dong, Wei; Fang, Sheng-Guo

2013-01-01

Crocodilians are diving reptiles that can hold their breath under water for long periods of time and are crepuscular animals with excellent sensory abilities. They comprise a sister lineage of birds and have no sex chromosome. Here we report the genome sequence of the endangered Chinese alligator (Alligator sinensis) and describe its unique features. The next-generation sequencing generated 314 Gb of raw sequence, yielding a genome size of 2.3 Gb. A total of 22 200 genes were predicted in Alligator sinensis using a de novo, homology- and RNA-based combined model. The genetic basis of long-diving behavior includes duplication of the bicarbonate-binding hemoglobin gene, co-functioning of routine phosphate-binding and special bicarbonate-binding oxygen transport, and positively selected energy metabolism, ammonium bicarbonate excretion and cardiac muscle contraction. Further, we elucidated the robust Alligator sinensis sensory system, including a significantly expanded olfactory receptor repertoire, rapidly evolving nerve-related cellular components and visual perception, and positive selection of the night vision-related opsin and sound detection-associated otopetrin. We also discovered a well-developed immune system with a considerable number of lineage-specific antigen-presentation genes for adaptive immunity as well as expansion of the tripartite motif-containing C-type lectin and butyrophilin genes for innate immunity and expression of antibacterial peptides. Multifluorescence in situ hybridization showed that alligator chromosome 3, which encodes DMRT1, exhibits significant synteny with chicken chromosome Z. Finally, population history analysis indicated population admixture 0.60-1.05 million years ago, when the Qinghai-Tibetan Plateau was uplifted. PMID:23917531

Structure of a premicellar complex of alkyl sulfates with the interfacial binding surfaces of four subunits of phospholipase A2.

PubMed

Pan, Ying H; Bahnson, Brian J

2010-07-01

The properties of three discrete premicellar complexes (E1#, E2#, E3#) of pig pancreatic group-IB secreted phospholipase A2 (sPLA2) with monodisperse alkyl sulfates have been characterized [Berg, O. G. et al., Biochemistry 43, 7999-8013, 2004]. Here we have solved the 2.7 A crystal structure of group-IB sPLA2 complexed with 12 molecules of octyl sulfate (C8S) in a form consistent with a tetrameric oligomeric that exists during the E1# phase of premicellar complexes. The alkyl tails of the C8S molecules are centered in the middle of the tetrameric cluster of sPLA2 subunits. Three of the four sPLA2 subunits also contain a C8S molecule in the active site pocket. The sulfate oxygen of a C8S ligand is complexed to the active site calcium in three of the four protein active sites. The interactions of the alkyl sulfate head group with Arg-6 and Lys-10, as well as the backbone amide of Met-20, are analogous to those observed in the previously solved sPLA2 crystal structures with bound phosphate and sulfate anions. The cluster of three anions found in the present structure is postulated to be the site for nucleating the binding of anionic amphiphiles to the interfacial surface of the protein, and therefore this binding interaction has implications for interfacial activation of the enzyme. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Plant Flavone Apigenin Binds to Nucleic Acid Bases and Reduces Oxidative DNA Damage in Prostate Epithelial Cells

PubMed Central

Bhaskaran, Natarajan; Gupta, Sanjay

2014-01-01

Oxidative stress has been linked to prostate carcinogenesis as human prostate tissue is vulnerable to oxidative DNA damage. Apigenin, a dietary plant flavone, possesses anti-proliferative and anticancer effects; however, its antioxidant properties have not been fully elucidated. We investigated sub-cellular distribution of apigenin, it’s binding to DNA and protective effects against H2O2-induced DNA damage using transformed human prostate epithelial RWPE-1 cells and prostate cancer LNCaP, PC-3 and DU145 cells. Exposure of cells to apigenin exhibited higher accumulation in RWPE-1 and LNCaP cells, compared to PC-3 and DU145 cells. The kinetics of apigenin uptake in LNCaP cells was estimated with a Km value of 5 µmole/L and Vmax of 190 pmoles/million cells/h. Sub-cellular fractionation demonstrated that nuclear matrix retains the highest concentration of apigenin (45.3%), followed by cytosol (23.9%), nuclear membranes (17.9%) and microsomes (12.9%), respectively. Spectroscopic analysis of apigenin with calf-thymus DNA exhibited intercalation as the dominant binding mode to DNA duplex. Apigenin exposure resulted in significant genoprotective effects in H2O2-stressed RWPE-1 cells by reduction in reactive oxygen species levels. In addition, apigenin exposure suppressed the formation of 8-hydroxy-2′ deoxyguanosine and protected exposed cells from apoptosis. Our studies demonstrate that apigenin is readily taken up by normal prostatic epithelial cells and prostate cancer cells, and is incorporated into their nuclei, where its intercalation with nucleic acid bases may account for its antioxidant and chemopreventive activities. PMID:24614817

Plant flavone apigenin binds to nucleic acid bases and reduces oxidative DNA damage in prostate epithelial cells.

PubMed

Sharma, Haripaul; Kanwal, Rajnee; Bhaskaran, Natarajan; Gupta, Sanjay

2014-01-01

Oxidative stress has been linked to prostate carcinogenesis as human prostate tissue is vulnerable to oxidative DNA damage. Apigenin, a dietary plant flavone, possesses anti-proliferative and anticancer effects; however, its antioxidant properties have not been fully elucidated. We investigated sub-cellular distribution of apigenin, it's binding to DNA and protective effects against H2O2-induced DNA damage using transformed human prostate epithelial RWPE-1 cells and prostate cancer LNCaP, PC-3 and DU145 cells. Exposure of cells to apigenin exhibited higher accumulation in RWPE-1 and LNCaP cells, compared to PC-3 and DU145 cells. The kinetics of apigenin uptake in LNCaP cells was estimated with a Km value of 5 µmole/L and Vmax of 190 pmoles/million cells/h. Sub-cellular fractionation demonstrated that nuclear matrix retains the highest concentration of apigenin (45.3%), followed by cytosol (23.9%), nuclear membranes (17.9%) and microsomes (12.9%), respectively. Spectroscopic analysis of apigenin with calf-thymus DNA exhibited intercalation as the dominant binding mode to DNA duplex. Apigenin exposure resulted in significant genoprotective effects in H2O2-stressed RWPE-1 cells by reduction in reactive oxygen species levels. In addition, apigenin exposure suppressed the formation of 8-hydroxy-2' deoxyguanosine and protected exposed cells from apoptosis. Our studies demonstrate that apigenin is readily taken up by normal prostatic epithelial cells and prostate cancer cells, and is incorporated into their nuclei, where its intercalation with nucleic acid bases may account for its antioxidant and chemopreventive activities.

Genome analysis and signature discovery for diving and sensory properties of the endangered Chinese alligator.

PubMed

Wan, Qiu-Hong; Pan, Sheng-Kai; Hu, Li; Zhu, Ying; Xu, Peng-Wei; Xia, Jin-Quan; Chen, Hui; He, Gen-Yun; He, Jing; Ni, Xiao-Wei; Hou, Hao-Long; Liao, Sheng-Guang; Yang, Hai-Qiong; Chen, Ying; Gao, Shu-Kun; Ge, Yun-Fa; Cao, Chang-Chang; Li, Peng-Fei; Fang, Li-Ming; Liao, Li; Zhang, Shu; Wang, Meng-Zhen; Dong, Wei; Fang, Sheng-Guo

2013-09-01

Crocodilians are diving reptiles that can hold their breath under water for long periods of time and are crepuscular animals with excellent sensory abilities. They comprise a sister lineage of birds and have no sex chromosome. Here we report the genome sequence of the endangered Chinese alligator (Alligator sinensis) and describe its unique features. The next-generation sequencing generated 314 Gb of raw sequence, yielding a genome size of 2.3 Gb. A total of 22 200 genes were predicted in Alligator sinensis using a de novo, homology- and RNA-based combined model. The genetic basis of long-diving behavior includes duplication of the bicarbonate-binding hemoglobin gene, co-functioning of routine phosphate-binding and special bicarbonate-binding oxygen transport, and positively selected energy metabolism, ammonium bicarbonate excretion and cardiac muscle contraction. Further, we elucidated the robust Alligator sinensis sensory system, including a significantly expanded olfactory receptor repertoire, rapidly evolving nerve-related cellular components and visual perception, and positive selection of the night vision-related opsin and sound detection-associated otopetrin. We also discovered a well-developed immune system with a considerable number of lineage-specific antigen-presentation genes for adaptive immunity as well as expansion of the tripartite motif-containing C-type lectin and butyrophilin genes for innate immunity and expression of antibacterial peptides. Multifluorescence in situ hybridization showed that alligator chromosome 3, which encodes DMRT1, exhibits significant synteny with chicken chromosome Z. Finally, population history analysis indicated population admixture 0.60-1.05 million years ago, when the Qinghai-Tibetan Plateau was uplifted.

Coating magnesium hydroxide on surface of carbon microspheres and interface binding with poly (ethylene terephthalate) matrix

NASA Astrophysics Data System (ADS)

Xue, Baoxia; Niu, Mei; Yang, Yongzhen; Bai, Jie; Song, Yinghao; Peng, Yun; Liu, Xuguang

2017-08-01

In this account, magnesium hydroxide (MH) employed as a capsule wall was firstly coated on the surface of carbon microspheres (CMSs) to obtain MH@CMSs using liquid phase deposition, then was modified by 3-Aminopropyltriethoxysilane (APTS) to form FMH@CMSs. To investigate the interface binding forces, a series of PET composites was prepared by melt compounding with MH@CMSs or FMH@CMSs. Field-emission scanning electron microscopy (FESEM), Transmission electron microscopy (TEM), Fourier-transform Infrared spectrometry (FTIR) and X-ray photoelectron spectroscopy (XPS) were used to characterize the morphology, chemical structure, and effect of functionalization of CMSs. The coating degree and thermal stability were investigated by thermogravimetry analysis. The results showed that CMSs were coated by an inorganic shell layer of MH as a capsule wall. On the other hand, MH@CMSs were coated with an organic layer of APTS. When compared to MH@CMSs, the interface binding forces between FMH@CMSs and PET matrix were significantly improved, and the tensile strength of FMH@CMSs/PET was higher than that of MH@CMSs/PET. At 1 wt% mass fraction of FMH@CMSs, the limiting oxygen index (LOI) value of PET composites increased from 21% to 27.6% following a V-0 rating. The tensile strength of FMH@CMSs/PET increased by 66.2% to reach 47.20 MPa, a value nearly similar to that of PET. Overall, the formed two layers provided the FMH@CMSs/PET with good mechanical and flame-retardant properties, which would broaden their scope of application.

A computational model of oxygen transport in the cerebrocapillary levels for normal and pathologic brain function.

PubMed

Safaeian, Navid; David, Tim

2013-10-01

The oxygen exchange and correlation between the cerebral blood flow (CBF) and cerebral metabolic rate of oxygen consumption (CMRO2) in the cortical capillary levels for normal and pathologic brain functions remain the subject of debate. A 3D realistic mesoscale model of the cortical capillary network (non-tree like) is constructed using a random Voronoi tessellation in which each edge represents a capillary segment. The hemodynamics and oxygen transport are numerically simulated in the model, which involves rheological laws in the capillaries, oxygen diffusion, and non-linear binding of oxygen to hemoglobin, respectively. The findings show that the cerebral hypoxia due to a significant decreased perfusion (as can occur in stroke) can be avoided by a moderate reduction in oxygen demand. Oxygen extraction fraction (OEF) can be an important indicator for the brain oxygen metabolism under normal perfusion and misery-perfusion syndrome (leading to ischemia). The results demonstrated that a disproportionately large increase in blood supply is required for a small increase in the oxygen demand, which, in turn, is strongly dependent on the resting OEF. The predicted flow-metabolism coupling in the model supports the experimental studies of spatiotemporal stimulations in humans by positron emission tomography and functional magnetic resonance imaging.

A computational model of oxygen transport in the cerebrocapillary levels for normal and pathologic brain function

PubMed Central

Safaeian, Navid; David, Tim

2013-01-01

The oxygen exchange and correlation between the cerebral blood flow (CBF) and cerebral metabolic rate of oxygen consumption (CMRO2) in the cortical capillary levels for normal and pathologic brain functions remain the subject of debate. A 3D realistic mesoscale model of the cortical capillary network (non-tree like) is constructed using a random Voronoi tessellation in which each edge represents a capillary segment. The hemodynamics and oxygen transport are numerically simulated in the model, which involves rheological laws in the capillaries, oxygen diffusion, and non-linear binding of oxygen to hemoglobin, respectively. The findings show that the cerebral hypoxia due to a significant decreased perfusion (as can occur in stroke) can be avoided by a moderate reduction in oxygen demand. Oxygen extraction fraction (OEF) can be an important indicator for the brain oxygen metabolism under normal perfusion and misery-perfusion syndrome (leading to ischemia). The results demonstrated that a disproportionately large increase in blood supply is required for a small increase in the oxygen demand, which, in turn, is strongly dependent on the resting OEF. The predicted flow-metabolism coupling in the model supports the experimental studies of spatiotemporal stimulations in humans by positron emission tomography and functional magnetic resonance imaging. PMID:23921901

Crystal structures of RIalpha subunit of cyclic adenosine 5'-monophosphate (cAMP)-dependent protein kinase complexed with (Rp)-adenosine 3',5'-cyclic monophosphothioate and (Sp)-adenosine 3',5'-cyclic monophosphothioate, the phosphothioate analogues of cAMP.

PubMed

Wu, Jian; Jones, John M; Nguyen-Huu, Xuong; Ten Eyck, Lynn F; Taylor, Susan S

2004-06-01

Cyclic adenosine 5'-monophosphate (cAMP) is an ancient signaling molecule, and in vertebrates, a primary target for cAMP is cAMP-dependent protein kinase (PKA). (R(p))-adenosine 3',5'-cyclic monophosphothioate ((R(p))-cAMPS) and its analogues are the only known competitive inhibitors and antagonists for cAMP activation of PKA, while (S(p))-adenosine 3',5'-cyclic monophosphothioate ((S(p))-cAMPS) functions as an agonist. The crystal structures of a Delta(1-91) deletion mutant of the RIalpha regulatory subunit of PKA bound to (R(p))-cAMPS and (S(p))-cAMPS were determined at 2.4 and 2.3 A resolution, respectively. While the structures are similar to each other and to the crystal structure of RIalpha bound to cAMP, differences in the dynamical properties of the protein when (R(p))-cAMPS is bound are apparent. The structures highlight the critical importance of the exocyclic oxygen's interaction with the invariant arginine in the phosphate binding cassette (PBC) and the importance of this interaction for the dynamical properties of the interactions that radiate out from the PBC. The conformations of the phosphate binding cassettes containing two invariant arginine residues (Arg209 on domain A, and Arg333 on domain B) are somewhat different due to the sulfur interacting with this arginine. Furthermore, the B-site ligand together with the entire domain B show significant differences in their overall dynamic properties in the crystal structure of Delta(1-91) RIalpha complexed with (R(p))-cAMPS phosphothioate analogue ((R(p))-RIalpha) compared to the cAMP- and (S(p))-cAMPS-bound type I and II regulatory subunits, based on the temperature factors. In all structures, two structural solvent molecules exist within the A-site ligand binding pocket; both mediate water-bridged interactions between the ligand and the protein. No structured waters are in the B-site pocket. Owing to the higher resolution data, the N-terminal segment (109-117) of the RIalpha subunit can also be traced. This strand forms an intermolecular antiparallel beta-sheet with the same strand in an adjacent molecule and implies that the RIalpha subunit can form a weak homodimer even in the absence of its dimerization domain.

Adaptation of avian influenza A (H6N1) virus from avian to human receptor-binding preference

PubMed Central

Wang, Fei; Qi, Jianxun; Bi, Yuhai; Zhang, Wei; Wang, Min; Zhang, Baorong; Wang, Ming; Liu, Jinhua; Yan, Jinghua; Shi, Yi; Gao, George F

2015-01-01

The receptor-binding specificity of influenza A viruses is a major determinant for the host tropism of the virus, which enables interspecies transmission. In 2013, the first human case of infection with avian influenza A (H6N1) virus was reported in Taiwan. To gather evidence concerning the epidemic potential of H6 subtype viruses, we performed comprehensive analysis of receptor-binding properties of Taiwan-isolated H6 HAs from 1972 to 2013. We propose that the receptor-binding properties of Taiwan-isolated H6 HAs have undergone three major stages: initially avian receptor-binding preference, secondarily obtaining human receptor-binding capacity, and recently human receptor-binding preference, which has been confirmed by receptor-binding assessment of three representative virus isolates. Mutagenesis work revealed that E190V and G228S substitutions are important to acquire the human receptor-binding capacity, and the P186L substitution could reduce the binding to avian receptor. Further structural analysis revealed how the P186L substitution in the receptor-binding site of HA determines the receptor-binding preference change. We conclude that the human-infecting H6N1 evolved into a human receptor preference. PMID:25940072

The effect of different oxygen exchange layers on TaO x based RRAM devices

NASA Astrophysics Data System (ADS)

Alamgir, Zahiruddin; Holt, Joshua; Beckmann, Karsten; Cady, Nathaniel C.

2018-01-01

In this work, we investigated the effect of the oxygen exchange layer (OEL) on the resistive switching properties of TaO x based memory cells. It was found that the forming voltage, SET-RESET voltage, R off, R on and retention properties are strongly correlated with the oxygen scavenging ability of the OEL, and the resulting oxygen vacancy formation ability of this layer. Higher forming voltage was observed for OELs having lower electronegativity/lower Gibbs free energy for oxide formation, and devices fabricated with these OELs exhibited an increased memory window, when using similar SET-RESET voltage range.

Structural and electrical properties of sputter deposited ZnO thin films

NASA Astrophysics Data System (ADS)

Muhammed Shameem P., V.; Mekala, Laxman; Kumar, M. Senthil

2018-05-01

The growth of zinc oxide thin films having different oxygen content was achieved at ambient temperature by reactive dc magnetron sputtering technique and their structural and electrical properties are studied. The structural studies show that the films are polycrystalline with a preferential orientation of the grains along the c-axis [002], which increases with increase in oxygen partial pressure. The grain size and the surface roughness of the zinc oxide films are found to decrease with increasing oxygen partial pressure. It is observed that the resistivity of the zinc oxide films can be tuned from semiconducting to insulating regime by varying the oxygen content.

Growth control of oxygen stoichiometry in homoepitaxial SrTiO 3 films by pulsed laser epitaxy in high vacuum

DOE PAGES

Lee, Ho Nyung; Ambrose Seo, Sung S.; Choi, Woo Seok; ...

2016-01-29

In many transition metal oxides, oxygen stoichiometry is one of the most critical parameters that plays a key role in determining the structural, physical, optical, and electrochemical properties of the material. However, controlling the growth to obtain high quality single crystal films having the right oxygen stoichiometry, especially in a high vacuum environment, has been viewed as a challenge. In this work, we show that, through proper control of the plume kinetic energy, stoichiometric crystalline films can be synthesized without generating oxygen defects even in high vacuum. We use a model homoepitaxial system of SrTiO 3 (STO) thin films onmore » single crystal STO substrates. Physical property measurements indicate that oxygen vacancy generation in high vacuum is strongly influenced by the energetics of the laser plume, and it can be controlled by proper laser beam delivery. Thus, our finding not only provides essential insight into oxygen stoichiometry control in high vacuum for understanding the fundamental properties of STO-based thin films and heterostructures, but it expands the utility of pulsed laser epitaxy of other materials as well.₃« less

Oxygen mobility in CeO{sub 2} and Ce{sub x}Zr({sub 1-x})O{sub 2} compounds: Study by CO transient oxidation and {sup 18}O/{sup 16}O isotopic exchange

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

Madier, Y.; Descorme, C.; Govic, A.M. Le

Cerium-zirconium mixed oxides (Ce{sub x}Zr{sub 1{minus}x}O{sub 2}), precalcined at 900 C in dry air, were supplied by Rhodia Terres Rares as monophasic solid solutions. Introduction of some zirconium atoms in the ceria lattice by isomorphous substitution clearly influences the final properties of these materials as long as the cubic structure of ceria is maintained. Modifications in oxygen storage capacity (OSC measurements), redox properties (CO TPR), and oxygen exchange processes (TPIE) were studied. Ce{sub 0.63}Zr{sub 0.37}O{sub 2} was shown to have the most promising properties with the largest OSC at 400 C and the highest reactivity in O{sub 2} exchange. Allmore » mixed oxides are able to exchange very large amounts of oxygen compared to ceria, implying the participation of bulk oxygen. Furthermore, on Ce{sub x}Zr{sub (1{minus}x)}O{sub 2} samples, oxygen is predominantly exchanged via a multiple heteroexchange mechanism involving surface dioxygen species as superoxides or peroxides.« less

Exhaustive Exercise-induced Oxidative Stress Alteration of Erythrocyte Oxygen Release Capacity.

PubMed

Xiong, Yanlian; Xiong, Yanlei; Wang, Yueming; Zhao, Yajin; Li, Yaojin; Ren, Yang; Wang, Ruofeng; Zhao, Mingzi; Hao, Yitong; Liu, Haibei; Wang, Xiang

2018-05-24

The aim of the present study is to explore the effect of exhaustive running exercise (ERE) in the oxygen release capacity of rat erythrocytes. Rats were divided into sedentary control (C), moderate running exercise (MRE) and exhaustive running exercise groups. The thermodynamics and kinetics properties of the erythrocyte oxygen release process of different groups were tested. We also determined the degree of band-3 oxidative and phosphorylation, anion transport activity and carbonic anhydrase isoform II(CAII) activity. Biochemical studies suggested that exhaustive running significantly increased oxidative injury parameters in TBARS and methaemoglobin levels. Furthermore, exhaustive running significantly decreased anion transport activity and carbonic anhydrase isoform II(CAII) activity. Thermodynamic analysis indicated that erythrocytes oxygen release ability also significantly increased due to elevated 2,3-DPG level after exhaustive running. Kinetic analysis indicated that exhaustive running resulted in significantly decreased T50 value. We presented evidence that exhaustive running remarkably impacted thermodynamics and kinetics properties of RBCs oxygen release. In addition, changes in 2,3-DPG levels and band-3 oxidation and phosphorylation could be the driving force for exhaustive running induced alterations in erythrocytes oxygen release thermodynamics and kinetics properties.

Combined effects of Ag nanoparticles and oxygen plasma treatment on PLGA morphological, chemical, and antibacterial properties.

PubMed

Fortunati, Elena; Mattioli, Samantha; Visai, Livia; Imbriani, Marcello; Fierro, Josè Luis G; Kenny, Josè Maria; Armentano, Ilaria

2013-03-11

The purpose of this study is to investigate the combined effects of oxygen plasma treatments and silver nanoparticles (Ag) on PLGA in order to modulate the surface antimicrobial properties through tunable bacteria adhesion mechanisms. PLGA nanocomposite films, produced by solvent casting with 1 wt % and 7 wt % of Ag nanoparticles were investigated. The PLGA and PLGA/Ag nanocomposite surfaces were treated with oxygen plasma. Surface properties of PLGA were investigated by field emission scanning electron microscopy (FESEM), atomic force microscopy (AFM), static contact angle (CA), and high resolution X-ray photoelectron spectroscopy (XPS). Antibacterial tests were performed using an Escherichia coli RB (a Gram negative) and Staphylococcus aureus 8325-4 (a Gram positive). The PLGA surface becomes hydrophilic after the oxygen treatment and its roughness increases with the treatment time. The surface treatment and the Ag nanoparticle introduction have a dominant influence on the bacteria adhesion and growth. Oxygen-treated PLGA/Ag systems promote higher reduction of the bacteria viability in comparison to the untreated samples and neat PLGA. The combination of Ag nanoparticles with the oxygen plasma treatment opens new perspectives for the studied biodegradable systems in biomedical applications.