Oligomerization and protein-protein interactions of the sensory histidine kinase DcuS in Escherichia coli

DcuS is a membrane-integral sensory histidine kinase involved in the DcuSR two-component regulatory system in Escherichia coli by regulating the gene expression of C4-dicarboxylate metabolism in response to external stimuli. How DcuS mediates the signal transduction across the membrane remains little understood. This study focused on the oligomerization and protein-protein interactions of DcuS by using quantitative Fluorescence Resonance Energy Transfer (FRET) spectroscopy. A quantitative FRET analysis for fluorescence spectroscopy has been developed in this study, consisting of three steps: (1) flexible background subtraction to yield background-free spectra, (2) a FRET quantification method to determine FRET efficiency (E) and donor fraction (fD = [donor] / ([donor]+[acceptor])) from the spectra, and (3) a model to determine the degree of oligomerization (interaction stoichiometry) in the protein complexes based on E vs. fD. The accuracy and applicability of this analysis was validated by theoretical simulations and experimental systems. These three steps were integrated into a computer procedure as an automatic quantitative FRET analysis which is easy, fast, and allows high-throughout to quantify FRET accurately and robustly, even in living cells. This method was subsequently applied to investigate oligomerization and protein-protein interactions, in particular in living cells. Cyan (CFP) and yellow fluorescent protein (YFP), two spectral variants of green fluorescent protein, were used as a donor-acceptor pair for in vivo measurements. Based on CFP- and YFP-fusions of non-interacting membrane proteins in the cell membrane, a minor FRET signal (E = 0.06 ± 0.01) can be regarded as an estimate of direct interaction between CFP and YFP moieties of fusion proteins co-localized in the cell membrane (false-positive). To confirm if the FRET occurrence is specific to the interaction of the investigated proteins, their FRET efficiency should be clearly above E = 0.06. The oligomeric state of DcuS was examined both in vivo (CFP/YFP) and in vitro (two different donor-acceptor pairs of organic dyes) by three independent experimental systems. The consistent occurrence of FRET in vitro and in vivo provides the evidence for the homo-dimerization of DcuS as full-length protein for the first time. Moreover, novel interactions (hetero-complexes) between DcuS and its functionally related proteins, citrate-specific sensor kinase CitA and aerobic dicarboxylate transporter DctA respectively, have been identified for the first time by intermolecular FRET in vivo. This analysis can be widely applied as a robust method to determine the interaction stoichiometry of protein complexes for other proteins of interest labeled with adequate fluorophores in vitro or in vivo.

Energy transfer to a proton-transfer fluorescence probe: Tryptophan to a flavonol in human serum albumin

A protein fluorescence probe system, coupling excited-state intermolecular Förster energy transfer and intramolecular proton transfer (PT), is presented. As an energy donor for this system, we used tryptophan, which transfers its excitation energy to 3-hydroxyflavone (3-HF) as a flavonol prototype, an acceptor exhibiting excited-state intramolecular PT. We demonstrate such a coupling in human serum albumin–3-HF complexes, excited via the single intrinsic tryptophan (Trp-214). Besides the PT tautomer fluorescence (λmax = 526 nm), these protein–probe complexes exhibit a 3-HF anion emission (λmax = 500 nm). Analysis of spectroscopic data leads to the conclusion that two binding sites are involved in the human serum albumin–3-HF interaction. The 3-HF molecule bound in the higher affinity binding site, located in the IIIA subdomain, has the association constant (k1) of 7.2 × 105 M−1 and predominantly exists as an anion. The lower affinity site (k2 = 2.5 × 105 M−1), situated in the IIA subdomain, is occupied by the neutral form of 3-HF (normal tautomer). Since Trp-214 is situated in the immediate vicinity of the 3-HF normal tautomer bound in the IIA subdomain, the intermolecular energy transfer for this donor/acceptor pair has a 100% efficiency and is followed by the PT tautomer fluorescence. Intermolecular energy transfer from the Trp-214 to the 3-HF anion bound in the IIIA subdomain is less efficient and has the rate of 1.61 × 108 s−1, thus giving for the donor/acceptor distance a value of 25.5 Å.

A comparative Raman study of the interaction of electron donor and acceptor molecules with graphene prepared by different methods

Interaction of tetrathiafulvalene (TTF) and tetracyanoethylene (TCNE) with few-layer graphene samples prepared by the exfoliation of graphite oxide (EG), conversion of nanodiamond (DG) and arc-evaporation of graphite in hydrogen (HG) has been investigated by Raman spectroscopy to understand the role of the graphene surface. The position and full-width at half maximum of the Raman G-band are affected on interaction with TTF and TCNE and the effect is highest with EG and least with HG. The effect of TTF and TCNE on the 2D-band is also maximum with EG. The magnitude of interaction between the donor/acceptor molecules varies in the same order as the surface areas of the graphenes. (C) 2009 Published by Elsevier B. V.

Estimation of electronic coupling in π -stacked donor-bridge-acceptor systems: correction of the two-state model

Comparison of donor-acceptor electronic couplings calculated within two-state and three-state models suggests that the two-state treatment can provide unreliable estimates of Vda because of neglecting the multistate effects. We show that in most cases accurate values of the electronic coupling in a π stack, where donor and acceptor are separated by a bridging unit, can be obtained as Ṽ da = (E2 - E1) μ12 Rda + (2 E3 - E1 - E2) 2 μ13 μ23 Rda2, where E1, E2, and E3 are adiabatic energies of the ground, charge-transfer, and bridge states, respectively, μij is the transition dipole moments between the states i and j, and Rda is the distance between the planes of donor and acceptor. In this expression based on the generalized Mulliken-Hush approach, the first term corresponds to the coupling derived within a two-state model, whereas the second term is the superexchange correction accounting for the bridge effect. The formula is extended to bridges consisting of several subunits. The influence of the donor-acceptor energy mismatch on the excess charge distribution, adiabatic dipole and transition moments, and electronic couplings is examined. A diagnostic is developed to determine whether the two-state approach can be applied. Based on numerical results, we showed that the superexchange correction considerably improves estimates of the donor-acceptor coupling derived within a two-state approach. In most cases when the two-state scheme fails, the formula gives reliable results which are in good agreement (within 5%) with the data of the three-state generalized Mulliken-Hush model

Extended donor and acceptor molecules for organic electronics

Die Untersuchung von halbleitenden Materialien auf der Basis von organischen Molekülen stellt ein Gebiet der angewandten Forschung an der Schwelle zur industriellen Nutzung dar. Geringes Gewicht und hohe mechanische Flexibilität ermöglichen völlig neue Produkte, die mit anorganischen Halbleitern nicht zu realisieren sind. Die Herstellung von Bauteilen wie Transistoren, Solarzellen oder Leuchtdioden aus organischen Materialien ist ein komplexes Gebiet, das einer Vielzahl von unterschiedlichen Optimierungen bedarf, um eine konkurrenzfähige Leistung zu erreichen. Die synthetische organische Chemie bietet vielfältige Möglichkeiten, mit maßgeschneiderten Lösungen zum Optimierungsprozess beizutragen. Zum einen können neue aktive Materialien hergestellt werden mit besserer Leistung und leichterer Verarbeitbarkeit. Zum anderen sind Substanzen zugänglich, die z.B. bei der Ladungsträgerinjektion hilfreich sein können.rnIn dieser Arbeit wurde an beiden dieser Fronten gearbeitet. Dabei lag die Entwicklungsstrategie darin, ausgedehnte π-konjugierte Moleküle herzustellen, die entweder besonders elektronenarme Akzeptoren oder elektronenreiche Donoren darstellen. Die genaue Kontrolle der elektronischen Niveaus stellt einen wichtigen Bestandteil dar, um niedrige elektrische Kontaktbarrieren zu Metallen zu erreichen und ausreichend stabile Materialien zu erreichen.rnDer erste Fokus der Arbeiten lag in der Funktionalisierung von Coronen. Dieser PAH stellt einen guten Kompromiss bezüglich seiner Größe dar: Er ist groß genug, um Diffusion in andere Schichten von Bauteilen zu vermeiden, aber nicht zu groß, um Verarbeitung durch Vakuumsublimation zu ermöglichen. Bislang sind praktisch keine Coronen-Derivate in der Literatur beschrieben, weshalb eine neue Synthese entwickelt werden musste, die die Einführung starker Donor- und Akzeptorfunktionalitäten erlaubt. Die photochemische Cyclodehydrierung von substituierten [2.2.2]paracyclophan-trienen stellte sich als hervorragende Möglichkeit heraus, dies zu bewerkstelligen. Es wurde eine Reihe von methoxy-substitutierten Coronenen mit unterschiedlicher Symmetrie hergestellt. Mittels optischer Spektroskopie konnte gezeigt werden, dass Methoxygruppen wenig Einfluss auf die elektronischen Eigenschaften von Coronen haben. Unter Spaltung der Methylether und anschließender Oxidation allerdings sind Coronenketone zugänglich, welche bis zu drei α-Diketongruppen besitzen. Diese Moleküle sind enorm starke Akzeptoren, was durch Cyclovoltammetrie und Vergleich zu anderen Akzeptoren eindrucksvoll gezeigt werden konnte. Die Sublimation dieses Akzeptors auf die Oberfläche von Metallen zeigt einen dramatischen Einfluss auf die Austrittsarbeit dieses Metalls, was zur Herstellung eines ohmschen Kontakts zu organischen Halbleitern von außerordentlichem Nutzen ist. rnDen zweiten Teil der Arbeit bilden Benzodithiophen enthaltende Polymere, die für den Einsatz als aktive Komponente in elektronischen Bauteilen entwickelt wurden. Nach systematischer Strukturoptimierung wurde ein Polymer enthalten, welches in einem Feldeffekt-Transistor auf Standard-Silizium-Substraten Ladungsträger-Mobilitäten über 0,1 cm2/Vs erreicht mit großer Reproduzierbarkeit und ausgezeichneter Transistor-Charakteristik. Es konnte gezeigt werden, dass die durch die Monomergeometrie erzeugte Kurvung des Polymers zu einem optimalen Kompromiss aus Löslichkeit und effektiver Packung darstellt. Auf für industrielle Anwendungen besonders interessanten polymer-basierten Substraten wurde eine noch erheblich bessere Leistung gezeigt. Auf einem PET-Substrat wurden Feldeffekt-Mobilitäten von 0,5 cm2/Vs gemessen mit überzeugenden Reproduzierbarkeit und Stabilität.rnDamit konnte in der Arbeit ein bedeutender Beitrag zur Weiterentwicklung von Materialien für den Einsatz in elektronischen Bauteilen geleistet werden. Die Substanzen versprechen noch erhebliches Potenzial nach intensiver Optimierung und wurden deshalb zum Patent angemeldet.rn

Single-pair fluorescence resonance energy transfer on freely diffusing molecules: Observation of Förster distance dependence and subpopulations

Photon bursts from single diffusing donor-acceptor labeled macromolecules were used to measure intramolecular distances and identify subpopulations of freely diffusing macromolecules in a heterogeneous ensemble. By using DNA as a rigid spacer, a series of constructs with varying intramolecular donor-acceptor spacings were used to measure the mean and distribution width of fluorescence resonance energy transfer (FRET) efficiencies as a function of distance. The mean single-pair FRET efficiencies qualitatively follow the distance dependence predicted by Förster theory. Possible contributions to the widths of the FRET efficiency distributions are discussed, and potential applications in the study of biopolymer conformational dynamics are suggested. The ability to measure intramolecular (and intermolecular) distances for single molecules implies the ability to distinguish and monitor subpopulations of molecules in a mixture with different distances or conformational states. This is demonstrated by monitoring substrate and product subpopulations before and after a restriction endonuclease cleavage reaction. Distance measurements at single-molecule resolution also should facilitate the study of complex reactions such as biopolymer folding. To this end, the denaturation of a DNA hairpin was examined by using single-pair FRET.

Water-based nanoparticulate solar cells using a diketopyrrolopyrrole donor polymer

Organic photovoltaic devices with either bulk heterojunction (BHJ) or nanoparticulate (NP) active layers have been prepared from a 1:2 blend of (poly{3,6-dithiophene-2-yl-2,5-di(2-octyldodecyl)-pyrrolo[3,4-c]pyrrole-1, 4-dione-alt-naphthalene}) (PDPP-TNT) and the fullerene acceptor, ([6,6]-phenyl C71-butyric acid methyl ester) (PC70BM). Atomic force microscopy (AFM) and scanning electron microscopy (SEM) have been used to investigate the morphology of the active layers of the two approaches. Mild thermal treatment of the NP film is required to promote initial joining of the NPs in order for the devices to function, however the NP structure is retained. Consequently, whereas gross phase segregation of the active layer occurs in the BHJ device spin cast from chloroform, the nanoparticulate approach retains control of the material domain sizes on the length scale of exciton diffusion in the materials. As a result, NP devices are found to generate more than twice the current density of BHJ devices and have a substantially greater overall efficiency. The use of aqueous nanoparticulate dispersions offers a promising approach to control the donor acceptor morphology on the nanoscale with the benefit of environmentally- friendly, solution-based fabrication. © 2014 the Owner Societies.

Fluorescent resonant excitation energy transfer in linear polyenes

We have studied the dynamics of excitation transfer between two conjugated polyene molecules whose intermolecular separation is comparable to the molecular dimensions. We have employed a correlated electron model that includes both the charge-charge, charge-bond, and bond-bond intermolecular electron repulsion integrals. We have shown that the excitation transfer rate varies as inverse square of donor-acceptor separation R-2 rather than as R-6, suggested by the Foumlrster type of dipolar approximation. Our time-evolution study alsom shows that the orientational dependence on excitation transfer at a fixed short donor-acceptor separation cannot be explained by Foumlrster type of dipolar approximation beyond a certain orientational angle of rotation of an acceptor polyene with respect to the donor polyene. The actual excitation transfer rate beyond a certain orientational angle is faster than the Foumlrster type of dipolar approximation rate. We have also studied the excitation transfer process in a pair of push-pull polyenes for different push-pull strengths. We have seen that, depending on the push-pull strength, excitation transfer could occur to other dipole coupled states. Our study also allows for the excitation energy transfer to optically dark states which are excluded by Foumlrster theory since the one-photon transition intensity to these states (from the ground state) is zero.

Non-Marcus energy gap dependence of electron transfer rate in contact ion pairs. Novel interplay between relaxation and reaction in solution

Electron transfer reactions between donor-acceptor pairs in solution and in organized media exhibit diverse behaviour. Recent experiments have indicated an interesting breakdown of the Marcus parabolic energy gap dependence in the normal regime for back electron transfer from contact ion pairs. A novel explanation of this breakdown has recently been proposed (M. Tachiya and S. Murata, J. Am. Chem. Sec., 116(1994) 2434) which attributes the breakdown to the interplay between the relaxation in the reactant well and the reaction. A particularly interesting aspect of the model is that it envisages the electron transfer in the normal regime to take place from a completely non-equilibrium condition. In this article a time dependent solution of the model is presented for the first time, after generalizing it to include a realistic initial population distribution. The decay of the contact ion pair population is completely non-exponential. This can be used to check the validity of the Tachiya-Murata model. The dynamics of electron transfer from the solvent separated ion pair, which seem to obey the Marcus relation, is exponential.

Effect of orientational motion of mobile chromophores on the dynamics of Forster energy transfer in polymers

Brownian dynamics (BD) simulations have been carried out to explore the effects of the orientational motion of the donor-acceptor (D-A) chromophore pair on the Forster energy transfer between the D-A pair embedded in a polymer chain in solution. It is found that the usually employed orientational averaging (that is, replacing the orientational factor, kappa, by kappa (2) = 2/3) may lead to an error in the estimation of the rate of the reaction by about 20%. In the limit of slow orientational relaxation, the preaveraging of the orientational factor leads to an overestimation of the rate, while in the opposite limit of very fast orientational relaxation, the usual scheme underestimates the rate. The latter results from an interesting interplay between reaction and diffusion. On the other hand, when one of the chromophores is fixed, the preaveraged rate is found to be fairly reliable if the rotational relaxation of the chromophore is sufficiently fast. The present study also reveals a power law dependence of the FRET rate on the chain length (rate proportional to N- alpha, with alpha approximate to 2.6).

Electrophile-Induced C-C Bond Activation of Vinylcyclopropanes for the Synthesis of Z-Alkylidenetetrahydrofurans

We present a detailed study on the behavior of vinylcyclopropanes as masked donor acceptor system toward the stereoselective synthesis of Z-alkylidenetetrahydrofurans. Results of bromenium catalyzed indirect activation of C-C bond of vinylcyclopropanes and concomitant cyclization to alkylidenetetrahydrofuran and other heterocycles have been discussed. The stereoselective formation of the Z-isomer is strongly controlled by the extent of destabilization of one of the gauche conformers of the vinylcyclopropane. The ring-opening/cyclization step was found to be stereospecific as in the case of DA cyclopropanes. The activation of the C-C bond leads to a tight-carbocation intermediate, which is evident from the complete retention of the stereochemistry. The retention of configuration has been established by a necessary control experiment that rules out the possibility of a double inversion pathway. The present results serve as direct stereochemical evidence in support of a tight ion-pair intermediate versus the controversial S(N)2 pathway. A 2D potential energy scan has been carried out at B3LYP/6-31G(d) level theory to obtain the relative energies of the conformers. The Z-selectivity observed has been explained on the basis of the relative population of the conformers and modeling the intermediate and transition state involved in the reaction at M06-2x/6-31+G(d) level. Energy profile for the cyclization step was modeled considering various possible pathways through which cyclization can happen. The methodology has been successfully demonstrated on vinylcyclobutanes as well.

Synthesis, morphology, optical and photocatalytic performance of nanostructured beta-Ga2O3

Fine powders of beta-Ga2O3 nanostructures were prepared via low temperature reflux condensation method by varying the pH value without using any surfactant. The pH value of reaction mixture had great influence on the morphology of final products. High crystalline single phase beta-Ga2O3 nanostructures were obtained by thermal treatment at 900 degrees C which was confirmed by X-ray diffraction and Raman spectroscopy. The morphological analysis revealed rod like nanostructures at lower and higher pH values of 6 and 10, while spindle like structures were obtained at pH = 8. The phase purity and presence of vibrational bands were identified using Fourier transform infrared spectroscopy. The optical absorbance spectrum showed intense absorption features in the UV spectral region. A broad blue emission peak centered at 441 nm due to donor-acceptor gallium-oxygen vacancy pair recombination appeared. The photocatalytic activity toward Rhodamine B under visible light irradiation was higher for nanorods at pH 10.

Ring opening of activated cyclopropanes with NIS/NaN3: synthesis of C-1 linked pseudodisaccharides

NIS/NaN3 mediated ring opening of various donor-acceptor cyclopropanes has been investigated. The study shows the necessity of the donor oxygen lone pair in such ring opening reactions. This methodology has been utilized in the synthesis of C-1 linked pseudodisaccharides through the use of click chemistry. (C) 2013 Elsevier Ltd. All rights reserved.

Photophysical, electrochemical and solid state properties of diketopyrrolopyrrole based molecular materials: importance of the donor group

Diketopyrrolopyrrole (DPP) based molecular semiconductors have emerged as promising materials for high performance active layers in organic solar cells. It is imperative to comprehend the origin of such a property by investigating the fundamental structure property correlation. In this report we have investigated the role of the donor group in DPP based donor-acceptor- donor (D-A-D) structure to govern the solid state, photophysical and electrochemical properties. We have prepared three derivatives of DPP with varying strengths of the donor groups, such as phenyl (PDPP-Hex), thiophene (TDPP-Hex) and selenophene (SeDPP-Hex). The influence of the donor units on the solid state packing was studied by single crystal X-ray diffraction. The photophysical, electrochemical and density functional theory ( DFT) results were combined to elucidate the structural and electronic properties of three DPP derivatives. We found that these DPP derivatives crystallized in the monoclinic space group P21/c and show herringbone packing in the crystal lattice. The derivatives exhibit weak p-p stacking interactions as two neighboring molecules slip away from each other with varied torsional angles at the donor units. The high torsional angle of 32 degrees ( PDPP-Hex) between the phenyl and lactam ring results in weak intramolecular interactions between the donor and acceptor, while TDPP-Hex and SeDPP-Hex show lower torsional angles of 9 degrees and 12 degrees with a strong overlap between the donor and acceptor units. The photophysical properties reveal that PDPP-Hex exhibits a high Stokes shift of 0.32 eV and SeDPP- Hex shows a high molar absorption co-efficient of 33 600 L mol -1 1 cm -1 1 with a low band gap of similar to 2.2 eV. The electrochemical studies of SeDPP- Hex indicate the pronounced effect of selenium in stabilizing the LUMO energy levels and this further emphasizes the importance of chalcogens in developing new n-type organic semiconductors for optoelectronic devices.

Energy bands and acceptor binding energies of GaN

The energy bands of zinc-blende and wurtzite GaN are calculated with the empirical pseudopotential method, and the pseudopotential parameters for Ga and N atoms are-given. The calculated energy bands are in agreement with those obtained by the ab initio method. The effective-mass theory for the semiconductors of wurtzite structure is established, and the effective-mass parameters of GaN for both structures are given The binding energies of acceptor states are calculated by solving strictly the effective-mass equations. The binding energies of donor and acceptor are 24 and 142 meV for the zinc-blende structure, 20 and 131, and 97 meV for the wurtzite structure, respectively, which are consistent with recent experimental results. It is proposed that there are two kinds of acceptor in wurtzite GaN. One kind is the general acceptor such as C, which substitutes N, which satisfies the effective-mass theory. The other kind of acceptor includes Mg, Zn, Cd, etc., the binding energy of these accepters is deviated from that given by the effective mass theory. In this report, wurtzite GaN is grown by the molecular-beam epitaxy method, and the photoluminescence spectra were measured. Three main peaks are assigned to the donor-acceptor transitions from two kinds of accepters. Some of the transitions were identified as coming from the cubic phase of GaN, which appears randomly within the predominantly hexagonal material. [S0163-1829(99)15915-0].