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At least 487 records · Page 27Linked to original sources
PubMed2005

Topological analysis of the electron density in model azolium systems for thiamin structure-function: sulfur is the electron sink and positively polarized carbanions act as nucleophiles.

The mechanism of thiamin diphosphate-dependent enzyme reactions requires two carbanion intermediates 1a and 1b. Neither has been isolated nor detected, but resonance stabilization is assumed to occur with the thiazolium quaternary nitrogen being the electron sink. We have questioned the electronic nature of these carbanion intermediates and, in a broader sense, the role of sulfur in the thiazolium moiety. To address these issues the theory of atoms in molecules (AIM) was used to acquire quantitative electron distributions in thiazolium 2, oxazolium 3, and imidazolium 4 as cations and zwitterions. Among the heteroatoms, only sulfur acts as an electron sink. This is corroborated by a similar behavior in phosphorothioates. Further, the formal carbanion at C2 and Calpha of the intermediates are positively charged and their nucleophilic character is explained with AIM theory by comparison with the sigmaC(-) of model 5a and piC(-) of model 6a. C2 of 2a excels in lone-pair coverage in the sigma-plane, surpassing the sigmaC(-) in acyclic 5a and other cyclic ylidenes, and hence, is a more effective nucleophile. The piC(-) of 6a reveals a depletion area centered in the sigma-plane but shows lone-pair concentration above and below the plane. Unlike 6a, the AIM properties, bond length, and bond order of 2b indicate no lone-pair on Calpha but essentially a double bond across C2-Calpha. Thus, the nucleophilic behavior at Calpha of 1b is based on the enamine chemistry induced by an electrophile.

Anions↗
PubMed2005

Electron spin-echo envelope modulation and pulse electron nuclear double resonance studies of Cu2+...beta-carotene interactions in Cu-MCM-41 molecular sieves.

Perdeuterated all-trans beta-carotene imbedded in activated Cu-MCM-41 was examined by electron paramagnetic resonance (EPR) and electron spin-echo envelope modulation (ESEEM) spectroscopies. The EPR study showed that complexation and electron transfer between Cu2+ and deuterated beta-carotene occurs. The interaction was confirmed by detecting the spin-echo modulation of deuterium in the ESEEM spectra of Cu2+. Ratio analysis of ESEEM was used to determine the number of deuterons which interact with Cu2+ and the distance between deuteron(s) and Cu2+. The bonding site of beta- carotene determined by ESEEM and pulse electron nuclear double resonance is the C15=C15' double bond.

Copper↗
PubMed2005

First-principles simulations of inelastic electron tunneling spectroscopy of molecular electronic devices.

Inelastic electron tunneling spectroscopy (IETS) is a powerful experimental tool for studying the molecular and metal contact geometries in molecular electronic devices. A first-principles computational method based on the hybrid density functional theory is developed to simulate the IETS of realistic molecular electronic devices. The calculated spectra of a real device with an octanedithiolate embedded between two gold contacts are in excellent agreement with recent experimental results. Strong temperature dependence of the experimental IETS spectra is also reproduced. It is shown that the IETS is extremely sensitive to the intramolecular conformation and the molecule-metal contact geometry changes. With the help of theoretical calculations, it has finally become possible to fully understand and assign the complicated experimental IETS and, more importantly, provide the structural information of the molecular electronic devices.

Computer Simulation↗
PubMed1987

Reactions of electron-transfer flavoprotein and electron-transfer flavoprotein: ubiquinone oxidoreductase.

Electron-transfer flavoprotein:ubiquinone oxidoreductase (ETF-Q oxidoreductase) catalyses the re-oxidation of reduced electron-transfer flavoprotein (ETF) with ubiquinone-1 (Q-1) as the electron acceptor. A kinetic assay for the enzyme was devised in which glutaryl-CoA in the presence of glutaryl-CoA dehydrogenase was used to reduce ETFox. and the reduction of Q-1 was monitored at 275 nm. The partial reactions involved in the overall assay system were examined. Glutaryl-CoA dehydrogenase catalyses the rapid reduction of ETFox. to the anionic semiquinone (ETF.-), but reduces ETF.- to the fully reduced form (ETFhq) at a rate that is about 6-fold lower. ETF.-, but not ETFhq, is directly re-oxidized by Q-1 at a rate that, depending on the steady-state concentration of ETF.-, may contribute significantly to the overall reaction. ETF-Q oxidoreductase catalyses rapid disproportionation of ETF.- with an equilibrium constant of about 1.0 at pH 7.8. In the presence of Q-1 it also catalyses the re-oxidation of ETFhq at a rate that is faster than that of the overall reaction. Rapid-scan experiments indicated the formation of ETF.-, but its fractional concentration in the early stages of the re-oxidation of ETFhq is low. The data indicate that the re-oxidation of ETFhq proceeds at a rate that is adequate to account for the overall rate of electron transfer from glutaryl-CoA to Q-1. An unusual property of ETF-Q oxidoreductase seems to be that it not only catalyses the re-oxidation of the reduced forms of ETF but also facilitates the complete reduction of ETFox. to ETFhq by disproportionation of the radical.

Catalysis↗
PubMed2003

Measurement of the electric field distribution and potentials on the object surface in an emission electron microscope without restriction of the electron beams.

An emission electron microscope without restriction of the electron beams was used to visualize and measure the distribution of electric fields and potentials on the surface under study. Investigations of this kind can be performed in an emission electron microscope without any aperture diaphragm. The potentialities of this method have been demonstrated using measurements with a silicon p-n junction to which a voltage has been applied in the reverse direction. The quantitative analysis becomes more complicated if the specimen is characterized by a heterogeneous intensity distribution of the electron emission from different areas of its surface. In the latter case two images obtained at different accelerating voltages (i.e. different voltages of the microscope extractor) provide the information necessary for an analysis of electric field and potential distributions.

Beta Particles↗
PubMed1985

[Experimental studies of the scatter behavior of fast electrons in the use of electron applicators in radiotherapy].

When using high energy electrons in radiotherapy, there is frequently undesirable electron scatter, which is derived from the applicators used to delimit the field. In order to improve our understanding of the factors which influence scatter, this was studied using fast electrons and a variety of materials to reduce this scatter. The geometry and angulation of the scattering plate and the electron energies were varied during these experiments.

Electrons↗
PubMed2005

Absolute electronic excitation cross sections for low-energy electron (5-12 eV) scattering from condensed thymine.

The absolute cross sections for electronic excitations of thymine by electron impact between 5 and 12 eV are determined by means of electron-energy loss (EEL) spectroscopy for the molecule deposited at submonolayer coverage on an inert Ar substrate. The lowest EEL features at 3.7 and 4.0 eV are attributed to the excitation of the triplet 1 3A'(pi --> pi*) and 1 3A''(n --> pi*) valence states of the molecule. The higher EEL features located at 4.9, 6.3, 7.3, and 9 eV with a weak shoulder around 6 eV are ascribed mostly to triplet valence (pi --> pi*) excitation manifold of the molecule. The energy dependence of the cross section for both the lowest triplet valence excitations shows essentially a peak at about 5 eV reaching a value of 2.9 x 10(-17) cm2. The cross sections for the higher EEL features are generally characterized by a common broad maximum around 8 eV. The latter reaches a value of 1.36 x 10(-16) cm2 for the combined 6 and 6.3 eV excitation region. The maxima in the present cross sections are found to correspond to the resonances that have been reported at about the same energies in the O- yield from electron impact on thymine in the gas phase.

Models, Chemical↗
PubMed1993

Electron self-exchange in azurin: calculation of the superexchange electron tunneling rate.

Electronic coupling between the copper atoms in an azurin dimer has been calculated in this conformationally well-defined system by using many-electronic wave functions. When one of the two water molecules forming intermolecular hydrogen bonds between the copper-ligating His-117 of the two azurins is removed, the calculated coupling element is reduced from 2.5 x 10(-6) to 1.1 x 10(-7) eV (1 eV = 1.602 x 10(-19) J). Also, the effects of the relative orientations of the two water molecules have been analyzed. The results show that water molecules may play an important role as switches for biological electron transfer. The rate of electron self-exchange between two azurins has been calculated, and the result is in very good agreement with the rate found experimentally.

Azurin↗
PubMed2000

Chlororespiration and poising of cyclic electron transport. Plastoquinone as electron transporter between thylakoid NADH dehydrogenase and peroxidase.

Polypeptides encoded by plastid ndh genes form a complex (Ndh) which could reduce plastoquinone with NADH. Through a terminal oxidase, reduced plastoquinone would be oxidized in chlororespiration. However, isolated Ndh complex has low activity with plastoquinone and no terminal oxidase has been found in chloroplasts, thus the function of Ndh complex is unknown. Alternatively, thylakoid hydroquinone peroxidase could oxidize reduced plastoquinone with H(2)O(2). By immunoaffinity chromatography, we have purified the plastid Ndh complex of barley (Hordeum vulgare L.) to investigate the electron donor and acceptor specificity. A detergent-containing system was reconstructed with thylakoid Ndh complex and peroxidase which oxidized NADH with H(2)O(2) in a plastoquinone-dependent process. This system and the increases of thylakoid Ndh complex and peroxidase activities under photooxidative stress suggest that the chlororespiratory process consists of the sequence of reactions catalyzed by Ndh complex, peroxidase (acting on reduced plastoquinone), superoxide dismutase, and the non-enzymic one-electron transfer from reduced iron-sulfur protein (FeSP) to O(2). When FeSP is a component of cytochrome b(6).f complex or of the same Ndh complex, O(2) may be reduced with NADH, without requirement of light. Chlororespiration consumes reactive species of oxygen and, eventually, may decrease their production by lowering O(2) concentration in chloroplasts. The common plastoquinone pool with photosynthetic electron transport suggests that chlororespiratory reactions may poise reduced and oxidized forms of the intermediates of cyclic electron transport under highly fluctuating light intensities.

Ascorbate Peroxidases↗
PubMed2001

Protein dynamics enhance electronic coupling in electron transfer complexes.

Electron-transferring flavoproteins (ETFs) from human and Paracoccus denitrificans have been analyzed by small angle x-ray scattering, showing that neither molecule exists in a rigid conformation in solution. Both ETFs sample a range of conformations corresponding to a large rotation of domain II with respect to domains I and III. A model of the human ETF.medium chain acyl-CoA dehydrogenase complex, consistent with x-ray scattering data, indicates that optimal electron transfer requires domain II of ETF to rotate by approximately 30 to 50 degrees toward domain I relative to its position in the x-ray structure. Domain motion establishes a new "robust engineering principle" for electron transfer complexes, tolerating multiple configurations of the complex while retaining efficient electron transfer.

Electron Transport↗
PubMed2004

Extensive domain motion and electron transfer in the human electron transferring flavoprotein.medium chain Acyl-CoA dehydrogenase complex.

The crystal structure of the human electron transferring flavoprotein (ETF).medium chain acyl-CoA dehydrogenase (MCAD) complex reveals a dual mode of protein-protein interaction, imparting both specificity and promiscuity in the interaction of ETF with a range of structurally distinct primary dehydrogenases. ETF partitions the functions of partner binding and electron transfer between (i) the recognition loop, which acts as a static anchor at the ETF.MCAD interface, and (ii) the highly mobile redox active FAD domain. Together, these enable the FAD domain of ETF to sample a range of conformations, some compatible with fast interprotein electron transfer. Disorders in amino acid or fatty acid catabolism can be attributed to mutations at the protein-protein interface. Crucially, complex formation triggers mobility of the FAD domain, an induced disorder that contrasts with general models of protein-protein interaction by induced fit mechanisms. The subsequent interfacial motion in the MCAD.ETF complex is the basis for the interaction of ETF with structurally diverse protein partners. Solution studies using ETF and MCAD with mutations at the protein-protein interface support this dynamic model and indicate ionic interactions between MCAD Glu(212) and ETF Arg alpha(249) are likely to transiently stabilize productive conformations of the FAD domain leading to enhanced electron transfer rates between both partners.

Acyl-CoA Dehydrogenase↗
PubMed2003

Giant electron dense chains, clusters and granules in megakaryocytes and platelets with normal dense bodies: an inherited thrombocytopenic disorder III. Platelet analytical electron microscopy.

A woman and her son were referred because of prolonged thrombocytopenia. Ultrastructural studies revealed the presence of giant organelles in their cells never observed previously in human platelets. Our initial reports described the evolution of two types of giant organelles in patient megakaryocytes and platelets. The last report also demonstrated that the large organelles in platelet whole mount preparations were inherently electron opaque like serotonin-rich dense bodies in normal and patient platelets. In the present study analytical electron microscopy of whole mount preparations from the patients and controls revealed that the inherently electron opaque dense and hexagonal precursor fragments, chains, clusters and giant organelles contained high concentrations of calcium and phosphorous, the major elements in normal dense bodies. The ratio of calcium to phosphorous in patient giant organelles was nearly the same as in normal platelet dense bodies. However, as shown in the previous study, levels of serotonin and adenine nucleotides were normal in patient platelets, and giant organelles and their contents were not secreted following activation of platelets with thrombin. Thus, despite the similarity in mineral content responsible for electron density, the giant organelles in patient platelets do no appear to be aberrant serotonin storage organelles.

Adenine Nucleotides↗
PubMed1968

Microincineration, electron microscopy, and electron diffraction of calcium phosphate-loaded mitochondria.

Isolated rat liver mitochondria were incubated in vitro under conditions supporting the massive accumulation of calcium and phosphate. Samples were embedded, thin sectioned, and examined in the electron microscope. The intramitochondrial distribution of insoluble or structure-bound mineral substances was studied by electron microscopy coupled with recently developed techniques of high resolution microincineration. As shown previously, the ion-loaded mitochondria acquire large, internal granules which have inherent electron opacity indicative of high mineral content. Study of ash patterns in preselected areas of sections directly confirmed the high mineral content of the granules, and the appearance of the residues was consistent with the copresence in the granules of some organic material. Other mitochondrial structures were almost devoid of mineral. Thin sections of unincubated control mitochondria also were incinerated. They were found to contain appreciable amounts of intrinsic mineral, seemingly associated with membranes. The normal, dense matrix granules commonly seen in unaltered mitochondria could be seen in intact sections of these control preparations, but after burning no definite correspondence of any ash to the granules could be demonstrated. The normal granules perhaps do not contain mineral. Heating experiments on ash patterns of all the preparations demonstrated the thermal stability and crystallizability of the ash. The crystallized ash of the in vitro-produced dense granules was tentatively shown by electron diffraction to be beta-tricalcium phosphate (whitlockite). This, together with evidence from the literature, suggests that the original, noncrystalline mineral may be a colloidal, subcrystalline precursor of calcium-deficient hydroxyapatite. Experiments were performed on synthetic calcium phosphates for comparison. Other possible applications of the microincineration techniques are briefly discussed.

Animals↗
PubMed2003

Theoretical cross sections for electron collisions in water: structure of electron tracks.

To understand what happens when biological matter is irradiated needs a detailed knowledge of the microscopic distribution of interactions and especially of the energy deposited in irradiated matter. Monte Carlo event-by-event simulations are particularly suitable for this task. However, the development of these track-structure codes necessitates accurate interaction cross sections for all the electronic processes: ionization, excitation and elastic scattering. In these conditions, we have recently developed a Monte Carlo code for electrons in water, this latter being commonly used to simulate the biological medium. All the electronic processes are studied in detail via theoretical differential and total cross-section calculations. The purpose of this work is to make an inter-comparison of our cross sections with those used in the electron track-structure codes developed in the literature, and to compare macroscopic quantities such as stopping powers and mean energy transfer distributions to available experimental data and/or to theoretical predictions in liquid water.

Algorithms↗
PubMed2002

Computer-assisted simulation of high-voltage electron microscopy using serial images recorded by conventional transmission electron microscopy.

Here we describe a computer-assisted method which, based on conventional transmission electron microscopy, renders simulated high-voltage electron micrographs. We perform arithmetic minimum filtering on stacks of aligned serial transmission electron microscopic images. In this way, the structural information of the separate images is fused into one compound image that highlights organization patterns otherwise easily overlooked or impossible to comprehend. Our method, like high-voltage electron microscopy, offers the possibility to build stereo-pairs for high-resolution three-dimensional analysis of tissue layers 1-2 microm thick. The use of background elimination and the development of a depth enhancement routine improved the three-dimensional effect and facilitated the analysis of the interior of objects. As an example, we use the method to display the distribution of axonal organelles at nodes of Ranvier and the shape and contents of a highly branched hippocampal dendritic spine.

Animals↗
PubMed1993

Characterization of the electron acceptors of old yellow enzyme: mechanistic approach to the mode of one electron transfer from the enzyme to menadione or dyestuffs.

Molecular oxygen or cytochrome c has been described as the electron acceptor of the reaction of old yellow enzyme with NADPH. In this study, menadione was found to be a sensitive electron acceptor of the reaction under aerobic as well as anaerobic conditions. The Km value of menadione for old yellow enzyme is as low as 2-3 x 10(-7) M in the presence or absence of superoxide dismutase. The rate enhancement of the cytochrome c reduction of old yellow enzyme with NADPH was about eight times in the presence of menadione. The rate increment was slightly higher under aerobic than anaerobic conditions. The rate enhancement by menadione enabled sensitive determination of the enzyme activity in the assay system, which contained NADPH, cytochrome c, menadione, and old yellow enzyme. In the reaction course, the semiquinone species of menadione was trapped by the reaction with t-butyl-alpha-phenylnitrone. The radical adduct was detected on EPR. The dyestuff, 2,6-dichlorophenolindophenol, was found to be reduced ineffectively even in the presence of menadione; moreover, it was inhibitory in the NADPH consumption reaction. Methylene blue or Lauth's violet, known to be capable of semiquinone formation, also behaved, like menadione, as a mediator of electron transport to cytochrome c. On the basis of the experimental results, the occurrence of the one electron transfer of the old yellow enzyme reaction was emphasized.

2,6-Dichloroindophenol↗
PubMed2005

CO2 response of cyclic electron flow around PSI (CEF-PSI) in tobacco leaves--relative electron fluxes through PSI and PSII determine the magnitude of non-photochemical quenching (NPQ) of Chl fluorescence.

We hypothesized that cyclic electron flow around photosystem I (CEF-PSI) participates in the induction of non-photochemical quenching (NPQ) of chlorophyll (Chl) fluorescence when the rate of photosynthetic linear electron flow (LEF) is electron-acceptor limited. To test this hypothesis, the relationships among photosynthesis rate, electron fluxes through both PSI and PSII [Je(PSI) and Je(PSII)] and Chl fluorescence parameters were analyzed simultaneously in intact leaves of tobacco plants at several light intensities and partial pressures of ambient CO2 (Ca). At low light intensities, decreasing Ca lowered the photosynthesis rate, but Je(PSI) and Je(PSII) remained constant. Je(PSI) was larger than Je(PSII), indicating the existence of CEF-PSI. Increasing the light intensity enhanced photosynthesis and both Je(PSI) and Je (PSII). Je(PSI)/Je(PSII) also increased at high light and at high light and low Ca combined, showing a strong, positive relationship with NPQ of Chl fluorescence. These results indicated that CEF-PSI contributed to the dissipation of photon energy in excess of that consumed by photosynthesis by driving NPQ of Chl fluorescence. The main physiological function of CEF-PSI in photosynthesis of higher plants is discussed.

Carbon Dioxide↗
PubMed1992

3D structure determination from electron-microscope images: electron crystallography of staurolite.

Resolution of better than 2 A has been obtained in many crystals by high-resolution electron microscopy. Although this resolution is sufficient to resolve interatomic spacings, structures are traditionally interpreted by comparing experimental images with contrast calculations. A drawback of this method is that images are 2D projections in which information is invariably obscured by overlap of atoms. 3D electron crystallography, developed by biophysicists to study proteins, has been used to investigate the crystal structure of staurolite. Amplitudes and phases of structure factors are obtained experimentally from high-resolution images (JEOL ARM 1000 at the National Center for Electron Microscopy at LBL), taken in different directions from thin regions where dynamic scattering is minimal. From images in five orientations (containing 59 independent reflections to a resolution of 1.38 A), a 3D electron potential map is constructed which resolves clearly all cations (Al, Si, Fe, including those with partial occupancy) and all O atoms. This method has great potential in crystal structure determinations of small domains in heterogeneous crystals which are inaccessible to X-ray analysis. It is estimated that 3D structure determinations should be possible on regions only about ten unit cells wide and should resolve not only atom positions but also site occupancies. The method is also applicable to space-group determination.

Chemical Phenomena↗