Cadmium-free aqueous synthesis of ZnSe and ZnSe@ZnS core-shell quantum dots and their differential bioanalyte sensing potential

NASA Astrophysics Data System (ADS)

Mir, Irshad Ahmad; Rawat, Kamla; Bohidar, H. B.

2016-10-01

Herein we report a facile and cadmium-free approach to prepare water-soluble fluorescent ZnSe@ZnS core-shell quantum dots (QDs), using thioglycolic acid (TGA) ligand as a stabilizer and thiourea as a sulfur source. The optical properties and morphology of the obtained core-shell QDs were characterized by UV-vis and fluorescence spectroscopy, transmission electron microscopy (TEM), energy-dispersive x-ray analysis (EDX), x-ray diffraction (XRD), electrophoresis and dynamic light scattering (DLS) techniques. TEM analysis, and electrophoresis data showed that ZnSe core had an average size of 3.60 ± 0.12 nm and zeta potential of -38 mV; and for ZnSe@ZnS QDs, the mean size was 4.80 ± 0.20 nm and zeta potential was -45 mV. Compared to the core ZnSe QDs, the quantum yield of these core-shell structures was higher (13% versus 32%). These were interacted with five common bioanalytes such as, ascorbic acid, citric acid, oxalic acid, glucose and cholesterol which revealed fluorescence quenching due to concentration dependent binding of analytes to the core only, and core-shell QDs. The binding pattern followed the sequence: cholesterol < glucose < ascorbic acid < oxalic acid < citric acid for ZnSe, and cholesterol < glucose < oxalic acid < ascorbic acid < citric acid for core-shell QDs. Thus, enhanced binding was noticed for the analyte citric acid which may facilitate development of a fluorescence-based sensor based on the ZnSe core-only quantum dot platform. Further, the hydrophilic core-shell structure may find use in cell imaging applications.

Gold core@silver semishell Janus nanoparticles prepared by interfacial etching

NASA Astrophysics Data System (ADS)

Chen, Limei; Deming, Christopher P.; Peng, Yi; Hu, Peiguang; Stofan, Jake; Chen, Shaowei

2016-07-01

Gold core@silver semishell Janus nanoparticles were prepared by chemical etching of Au@Ag core-shell nanoparticles at the air/water interface. Au@Ag core-shell nanoparticles were synthesized by chemical deposition of a silver shell onto gold seed colloids followed by the self-assembly of 1-dodecanethiol onto the nanoparticle surface. The nanoparticles then formed a monolayer on the water surface of a Langmuir-Blodgett trough, and part of the silver shell was selectively etched away by the mixture of hydrogen peroxide and ammonia in the water subphase, where the etching was limited to the side of the nanoparticles that was in direct contact with water. The resulting Janus nanoparticles exhibited an asymmetrical distribution of silver on the surface of the gold cores, as manifested in transmission electron microscopy, UV-vis absorption, and X-ray photoelectron spectroscopy measurements. Interestingly, the Au@Ag semishell Janus nanoparticles exhibited enhanced electrocatalytic activity in oxygen reduction reactions, as compared to their Au@Ag and Ag@Au core-shell counterparts, likely due to a synergistic effect between the gold cores and silver semishells that optimized oxygen binding to the nanoparticle surface.Gold core@silver semishell Janus nanoparticles were prepared by chemical etching of Au@Ag core-shell nanoparticles at the air/water interface. Au@Ag core-shell nanoparticles were synthesized by chemical deposition of a silver shell onto gold seed colloids followed by the self-assembly of 1-dodecanethiol onto the nanoparticle surface. The nanoparticles then formed a monolayer on the water surface of a Langmuir-Blodgett trough, and part of the silver shell was selectively etched away by the mixture of hydrogen peroxide and ammonia in the water subphase, where the etching was limited to the side of the nanoparticles that was in direct contact with water. The resulting Janus nanoparticles exhibited an asymmetrical distribution of silver on the surface of the gold cores, as manifested in transmission electron microscopy, UV-vis absorption, and X-ray photoelectron spectroscopy measurements. Interestingly, the Au@Ag semishell Janus nanoparticles exhibited enhanced electrocatalytic activity in oxygen reduction reactions, as compared to their Au@Ag and Ag@Au core-shell counterparts, likely due to a synergistic effect between the gold cores and silver semishells that optimized oxygen binding to the nanoparticle surface. Electronic supplementary information (ESI) available: Additional TEM, UV-vis, XPS, and electrochemical data. See DOI: 10.1039/c6nr03368g

Valence-band and core-level photoemission study of single-crystal Bi2CaSr2Cu2O8 superconductors

NASA Astrophysics Data System (ADS)

Shen, Z.-X.; Lindberg, P. A. P.; Wells, B. O.; Mitzi, D. B.; Lindau, I.; Spicer, W. E.; Kapitulnik, A.

1988-12-01

High-quality single crystals of Bi2CaSr2Cu2O8 superconductors have been prepared and cleaved in ultrahigh vacuum. Low-energy electron diffraction measurements show that the surface structure is consistent with the bulk crystal structure. Ultraviolet photoemission and x-ray photoemission experiments were performed on these well-characterized sample surfaces. The valence-band and the core-level spectra obtained from the single-crystal surfaces are in agreement with spectra recorded from polycrystalline samples, justifying earlier results from polycrystalline samples. Cu satellites are observed both in the valence band and Cu 2p core level, signaling the strong correlation among the Cu 3d electrons. The O 1s core-level data exhibit a sharp, single peak at 529-eV binding energy without any clear satellite structures.

Electronic structure evolution of fullerene on CH 3NH 3PbI 3

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

Wang, Chenggong; Wang, Congcong; Liu, Xiaoliang

2015-03-19

The thickness dependence of fullerene on CH 3NH 3PbI 3 perovskitefilm surface has been investigated by using ultraviolet photoemission spectroscopy (UPS), X-ray photoemission spectroscopy(XPS), and inverse photoemission spectroscopy (IPES). The lowest unoccupied molecular orbital and highest occupied molecular orbital (HOMO) can be observed directly with IPES and UPS. It is observed that the HOMO level in fullerene shifts to lower binding energy. The XPS results show a strong initial shift of core levels to lower binding energy in the perovskite, which indicates that electrons transfer from the perovskitefilm to fullerene molecules. Further deposition of fullerene forms C 60 solid, accompaniedmore » by the reduction of the electron transfer. As a result, the strongest electron transfer happened at 1/4 monolayer of fullerene.« less

Electronic structure evolution of fullerene on CH{sub 3}NH{sub 3}PbI{sub 3}

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

Wang, Chenggong; Wang, Congcong; Kauppi, John

2015-03-16

The thickness dependence of fullerene on CH{sub 3}NH{sub 3}PbI{sub 3} perovskite film surface has been investigated by using ultraviolet photoemission spectroscopy (UPS), X-ray photoemission spectroscopy (XPS), and inverse photoemission spectroscopy (IPES). The lowest unoccupied molecular orbital and highest occupied molecular orbital (HOMO) can be observed directly with IPES and UPS. It is observed that the HOMO level in fullerene shifts to lower binding energy. The XPS results show a strong initial shift of core levels to lower binding energy in the perovskite, which indicates that electrons transfer from the perovskite film to fullerene molecules. Further deposition of fullerene forms C{submore » 60} solid, accompanied by the reduction of the electron transfer. The strongest electron transfer happened at 1/4 monolayer of fullerene.« less

Electronic Structure of Tl2Ba2CuO(6+Delta) Epitaxial Films Measured by X-Ray Photoemission

NASA Technical Reports Server (NTRS)

Vasquez, R. P.; Ren, Z. F.; Wang, J. H.

1996-01-01

The valence electronic structure and core levels of Tl2Ba2CuO(6 + delta) (Tl-2201) epitaxial films have been measured with X-ray photoelectron spectroscopy and are compared to those of Tl2Ba2CaCu2O(8 + delta) (Tl-2212). Changes in the Tl-2201 core-level binding energies with oxygen doping are consistent with a change in the chemical potential. Differences between the Tl-2201 and Tl-2212 measured densities of states are consistent with the calculated Cu 3d and Tl 6s partial densities of states.

CD/MCD/VTVH-MCD Studies of Escherichia coli Bacterioferritin Support a Binuclear Iron Cofactor Site.

PubMed

Kwak, Yeonju; Schwartz, Jennifer K; Huang, Victor W; Boice, Emily; Kurtz, Donald M; Solomon, Edward I

2015-12-01

Ferritins and bacterioferritins (Bfrs) utilize a binuclear non-heme iron binding site to catalyze oxidation of Fe(II), leading to formation of an iron mineral core within a protein shell. Unlike ferritins, in which the diiron site binds Fe(II) as a substrate, which then autoxidizes and migrates to the mineral core, the diiron site in Bfr has a 2-His/4-carboxylate ligand set that is commonly found in diiron cofactor enzymes. Bfrs could, therefore, utilize the diiron site as a cofactor rather than for substrate iron binding. In this study, we applied circular dichroism (CD), magnetic CD (MCD), and variable-temperature, variable-field MCD (VTVH-MCD) spectroscopies to define the geometric and electronic structures of the biferrous active site in Escherichia coli Bfr. For these studies, we used an engineered M52L variant, which is known to eliminate binding of a heme cofactor but to have very minor effects on either iron oxidation or mineral core formation. We also examined an H46A/D50A/M52L Bfr variant, which additionally disrupts a previously observed mononuclear non-heme iron binding site inside the protein shell. The spectral analyses define a binuclear and an additional mononuclear ferrous site. The biferrous site shows two different five-coordinate centers. After O2 oxidation and re-reduction, only the mononuclear ferrous signal is eliminated. The retention of the biferrous but not the mononuclear ferrous site upon O2 cycling supports a mechanism in which the binuclear site acts as a cofactor for the O2 reaction, while the mononuclear site binds the substrate Fe(II) that, after its oxidation to Fe(III), migrates to the mineral core.

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.

High resolution photoemission investigation: The oxidation of W

NASA Astrophysics Data System (ADS)

Morar, J. F.; Himpsel, F. J.; Hughes, G. J.; Jordan, J. L.; McFeely, F. R.; Hollinge, G.

High resolution photoemission measurements of surface oxide layers on tungsten has revealed a set of well resolved core level shifts characteristic of individual metal oxidation states. Measurement and analysis of this type of data can provide specific and quantitative chemical information about surface oxides. The formation of bonds between transition metals and strongly electronegative elements such as oxygen and fluorine results in charge transfer with the effect of shifting the metal core electron binding energies. The magnitude of such shifts depends primarily on two factors; the amount of charge transfer and the screening ability of the metals electrons. The size of core-level shifts tend to increase with additional charge transfer and be decreased by screening. In the case of tungsten the amount of screening should be a function of oxygen content since the oxygen ties up free electrons which are effective at screening. A continuous change in the tungsten core level shifts is observed with increasing oxygen content, i.e., as the screening changes from that characteristic of a metal screened to that characteristic of an insulator unscreened.

Electronic Voting Protocol Using Identity-Based Cryptography.

PubMed

Gallegos-Garcia, Gina; Tapia-Recillas, Horacio

2015-01-01

Electronic voting protocols proposed to date meet their properties based on Public Key Cryptography (PKC), which offers high flexibility through key agreement protocols and authentication mechanisms. However, when PKC is used, it is necessary to implement Certification Authority (CA) to provide certificates which bind public keys to entities and enable verification of such public key bindings. Consequently, the components of the protocol increase notably. An alternative is to use Identity-Based Encryption (IBE). With this kind of cryptography, it is possible to have all the benefits offered by PKC, without neither the need of certificates nor all the core components of a Public Key Infrastructure (PKI). Considering the aforementioned, in this paper we propose an electronic voting protocol, which meets the privacy and robustness properties by using bilinear maps.

Electronic Voting Protocol Using Identity-Based Cryptography

PubMed Central

Gallegos-Garcia, Gina; Tapia-Recillas, Horacio

2015-01-01

Electronic voting protocols proposed to date meet their properties based on Public Key Cryptography (PKC), which offers high flexibility through key agreement protocols and authentication mechanisms. However, when PKC is used, it is necessary to implement Certification Authority (CA) to provide certificates which bind public keys to entities and enable verification of such public key bindings. Consequently, the components of the protocol increase notably. An alternative is to use Identity-Based Encryption (IBE). With this kind of cryptography, it is possible to have all the benefits offered by PKC, without neither the need of certificates nor all the core components of a Public Key Infrastructure (PKI). Considering the aforementioned, in this paper we propose an electronic voting protocol, which meets the privacy and robustness properties by using bilinear maps. PMID:26090515

Temperature and hydrostatic pressure effects on single dopant states in hollow cylindrical core-shell quantum dot

NASA Astrophysics Data System (ADS)

El-Yadri, M.; Aghoutane, N.; El Aouami, A.; Feddi, E.; Dujardin, F.; Duque, C. A.

2018-05-01

This work reports on theoretical investigation of the temperature and hydrostatic pressure effects on the confined donor impurity in a AlGaAs-GaAs hollow cylindrical core-shell quantum dot. The charges are assumed to be completely confined to the interior of the shell with approximately rigid walls. Within the framework of the effective-mass approximation and by using a variational approach, we have computed the donor binding energies as a function of the shell size in order to study the behavior of the electron-impurity attraction for a very small thickness under the influence of both temperature and hydrostatic pressure. Our results show that the temperature and hydrostatic pressure have a significant influence on the impurity binding energy for large shell quantum dots. It will be shown that the binding energy is more pronounced with increasing pressure and decreasing temperature for any impurity position and quantum dot size. The photoionization cross section is also analyzed by considering only the in-plane incident radiation polarization. Its behavior is investigated as a function of photon energy for different values of pressure and temperature. The opposite effects caused by temperature and hydrostatic pressure reveal a big practical interest and offer an alternative way to tuning of correlated electron-impurity transitions in optoelectronic devices.

Theoretical studies of electronically excited states

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

Besley, Nicholas A.

2014-10-06

Time-dependent density functional theory is the most widely used quantum chemical method for studying molecules in electronically excited states. However, excited states can also be computed within Kohn-Sham density functional theory by exploiting methods that converge the self-consistent field equations to give excited state solutions. The usefulness of single reference self-consistent field based approaches for studying excited states is demonstrated by considering the calculation of several types of spectroscopy including the infrared spectroscopy of molecules in an electronically excited state, the rovibrational spectrum of the NO-Ar complex, core electron binding energies and the emission spectroscopy of BODIPY in water.

Constraints on the symmetry energy from neutron star observations

NASA Astrophysics Data System (ADS)

Newton, W. G.; Gearheart, M.; Wen, De-Hua; Li, Bao-An

2013-03-01

The modeling of many neutron star observables incorporates the microphysics of both the stellar crust and core, which is tied intimately to the properties of the nuclear matter equation of state (EoS). We explore the predictions of such models over the range of experimentally constrained nuclear matter parameters, focusing on the slope of the symmetry energy at nuclear saturation density L. We use a consistent model of the composition and EoS of neutron star crust and core matter to model the binding energy of pulsar B of the double pulsar system J0737-3039, the frequencies of torsional oscillations of the neutron star crust and the instability region for r-modes in the neutron star core damped by electron-electron viscosity at the crust-core interface. By confronting these models with observations, we illustrate the potential of astrophysical observables to offer constraints on poorly known nuclear matter parameters complementary to terrestrial experiments, and demonstrate that our models consistently predict L < 70 MeV.

Effect of K+ and Na+ on calcium-dependent electron-dense particles in the monoaminergic synaptic vesicles of rat pineal nerves fixed in Ca2+-containing solutions.

PubMed

Pellegrino de Iraldi, A; Corazza, J P

1983-01-01

The effect of K+ and Na+ on the Ca2+ binding site in the dense core of monoaminergic vesicles of pineal nerves was investigated in the rat. Rat pineal glands, bisected immediately after decapitation, were incubated at room temperature in solutions containing high K+ or high Na+ in the presence or absence of Ca2+. Fixation was performed in glutaraldehyde-osmium tetroxide in collidine buffer, with and without CaCl2. It was confirmed that, after fixation in Ca2+-containing solutions, an electron-dense particle, located in the vesicle core, which can be considered a calcium deposit, appears within the synaptic vesicles. It was observed that this Ca2+ deposit may be modified by incubation in a high K+ or high Na+ milieu before fixation in Ca2+ containing solutions. When the incubation was carried out with high K+ and high Ca2+ simultaneously, Ca2+ deposits were considerably increased. With K+ alone, no Ca2+ deposits were apparent, as when electrical stimulation is applied before fixation. This effect was not observed when the incubation was done in high Na+. Consecutive incubations in high K+ and high Na+, respectively, restored the capability of the vesicle cores to bind Ca2+. Prolonged incubation in high Na+ before fixation increased Ca2+ deposits within the vesicles. These findings are in line with data on the effect of these ions upon the storage and release of biogenic amines and suggest that these ions modify the capability of synaptic vesicles to bind Ca2+.

Distinct Rayleigh scattering from hot spot mutant p53 proteins reveals cancer cells.

PubMed

Jun, Ho Joon; Nguyen, Anh H; Kim, Yeul Hong; Park, Kyong Hwa; Kim, Doyoun; Kim, Kyeong Kyu; Sim, Sang Jun

2014-07-23

The scattering of light redirects and resonances when an electromagnetic wave interacts with electrons orbits in the hot spot core protein and oscillated electron of the gold nanoparticles (AuNP). This report demonstrates convincingly that resonant Rayleigh scattering generated from hot spot mutant p53 proteins is correspondence to cancer cells. Hot spot mutants have unique local electron density changes that affect specificity of DNA binding affinity compared with wild types. Rayleigh scattering changes introduced by hot-spot mutations were monitored by localized surface plasmon resonance (LSPR) shift changes. The LSPR λmax shift for hot-spot mutants ranged from 1.7 to 4.2 nm for mouse samples and from 0.64 nm to 2.66 nm for human samples, compared to 9.6 nm and 15 nm for wild type and mouse and human proteins, respectively with a detection sensitivity of p53 concentration at 17.9 nM. It is interesting that hot-spot mutants, which affect only interaction with DNA, launches affinitive changes as considerable as wild types. These changes propose that hot-spot mutants p53 proteins can be easily detected by local electron density alterations that disturbs the specificity of DNA binding of p53 core domain on the surface of the DNA probed-nanoplasmonic sensor. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Preparation and evaluation of magnetic core-shell mesoporous molecularly imprinted polymers for selective adsorption of tetrabromobisphenol S.

PubMed

Wang, Xuemei; Huang, Pengfei; Ma, Xiaomin; Wang, Huan; Lu, Xiaoquan; Du, Xinzhen

2017-05-01

Novel magnetic mesoporous molecularly imprinted polymers (MMIPs) with core-shell structure were prepared by simple surface molecular imprinting polymerization using tetrabromobisphenol-S (TBBPS) as the template. The MMIPs-TBBPS were characterized by fourier-transform infrared spectrometry (FTIR), scanning electron microscopy (SEM), transmission electron microscopy (TEM), N 2 adsorption-desorption transmission, and vibrating sample magnetometry. The resultant MMIPs-TBBPS were successfully applied magnetic solid-phase extraction (MSPE) coupled with HPLC determination of TBBPS in spiked real water samples with recoveries of 77.8-88.9%. The adsorption experiments showed that the binding capacity of MMIPs-TBBPS to TBBPS and six structural analogs were significantly higher than that of the magnetic nonimprinted polymers (MNIPs). Meanwhile, the MMIPs-TBBPS possessed rapid binding affinity, excellent magnetic response, specific selectivity and high adsorption capacity toward TBBPS with a maximum adsorption capacity of 1626.8µgg -1 . The analytical results indicate that the MMIPs-TBBPS are promising materials for selective separation and fast enrichment of TBBPS from complicated enviromental samples. Copyright © 2017 Elsevier B.V. All rights reserved.

Selective enrichment of metal-binding proteins based on magnetic core/shell microspheres functionalized with metal cations.

PubMed

Fang, Caiyun; Zhang, Lei; Zhang, Xiaoqin; Lu, Haojie

2015-06-21

Metal binding proteins play many important roles in a broad range of biological processes. Characterization of metal binding proteins is important for understanding their structure and biological functions, thus leading to a clear understanding of metal associated diseases. The present study is the first to investigate the effectiveness of magnetic microspheres functionalized with metal cations (Ca(2+), Cu(2+), Zn(2+) and Fe(3+)) as the absorbent matrix in IMAC technology to enrich metal containing/binding proteins. The putative metal binding proteins in rat liver were then globally characterized by using this strategy which is very easy to handle and can capture a number of metal binding proteins effectively. In total, 185 putative metal binding proteins were identified from rat liver including some known less abundant and membrane-bound metal binding proteins such as Plcg1, Acsl5, etc. The identified proteins are involved in many important processes including binding, catalytic activity, translation elongation factor activity, electron carrier activity, and so on.

When core competence is not enough: functional interplay of the DEAD-box helicase core with ancillary domains and auxiliary factors in RNA binding and unwinding.

PubMed

Rudolph, Markus G; Klostermeier, Dagmar

2015-08-01

DEAD-box helicases catalyze RNA duplex unwinding in an ATP-dependent reaction. Members of the DEAD-box helicase family consist of a common helicase core formed by two RecA-like domains. According to the current mechanistic model for DEAD-box mediated RNA unwinding, binding of RNA and ATP triggers a conformational change of the helicase core, and leads to formation of a compact, closed state. In the closed conformation, the two parts of the active site for ATP hydrolysis and of the RNA binding site, residing on the two RecA domains, become aligned. Closing of the helicase core is coupled to a deformation of the RNA backbone and destabilization of the RNA duplex, allowing for dissociation of one of the strands. The second strand remains bound to the helicase core until ATP hydrolysis and product release lead to re-opening of the core. The concomitant disruption of the RNA binding site causes dissociation of the second strand. The activity of the helicase core can be modulated by interaction partners, and by flanking N- and C-terminal domains. A number of C-terminal flanking regions have been implicated in RNA binding: RNA recognition motifs (RRM) typically mediate sequence-specific RNA binding, whereas positively charged, unstructured regions provide binding sites for structured RNA, without sequence-specificity. Interaction partners modulate RNA binding to the core, or bind to RNA regions emanating from the core. The functional interplay of the helicase core and ancillary domains or interaction partners in RNA binding and unwinding is not entirely understood. This review summarizes our current knowledge on RNA binding to the DEAD-box helicase core and the roles of ancillary domains and interaction partners in RNA binding and unwinding by DEAD-box proteins.

Effects of N-Substitutions on the Tetrahydroquinoline (THQ) Core of Mixed-Efficacy μ-Opioid Receptor (MOR)/δ-Opioid Receptor (DOR) Ligands.

PubMed

Harland, Aubrie A; Bender, Aaron M; Griggs, Nicholas W; Gao, Chao; Anand, Jessica P; Pogozheva, Irina D; Traynor, John R; Jutkiewicz, Emily M; Mosberg, Henry I

2016-05-26

N-Acetylation of the tetrahydroquinoline (THQ) core of a series of μ-opioid receptor (MOR) agonist/δ-opioid receptor (DOR) antagonist ligands increases DOR affinity, resulting in ligands with balanced MOR and DOR affinities. We report a series of N-substituted THQ analogues that incorporate various carbonyl-containing moieties to maintain DOR affinity and define the steric and electronic requirements of the binding pocket across the opioid receptors. 4h produced in vivo antinociception (ip) for 1 h at 10 mg/kg.

Effect on magnetic properties of germanium encapsulated C60 fullerene

NASA Astrophysics Data System (ADS)

Umran, Nibras Mossa; Kumar, Ranjan

2013-02-01

Structural and electronic properties of Gen(n = 1-4) doped C60 fullerene are investigated with ab initio density functional theory calculations by using an efficient computer code, known as SIESTA. The pseudopotentials are constructed using a Trouiller-Martins scheme, to describe the interaction of valence electrons with the atomic cores. In endohedral doped embedding of more germanium atoms complexes we have seen that complexes are stable and thereafter cage break down. We have also investigated that binding energy, electronic affinity increases and magnetic moment oscillating behavior as the number of semiconductor atoms in C60 fullerene goes on increasing.

Organization of chlorophyll biosynthesis and insertion of chlorophyll into the chlorophyll-binding proteins in chloroplasts.

PubMed

Wang, Peng; Grimm, Bernhard

2015-12-01

Oxygenic photosynthesis requires chlorophyll (Chl) for the absorption of light energy, and charge separation in the reaction center of photosystem I and II, to feed electrons into the photosynthetic electron transfer chain. Chl is bound to different Chl-binding proteins assembled in the core complexes of the two photosystems and their peripheral light-harvesting antenna complexes. The structure of the photosynthetic protein complexes has been elucidated, but mechanisms of their biogenesis are in most instances unknown. These processes involve not only the assembly of interacting proteins, but also the functional integration of pigments and other cofactors. As a precondition for the association of Chl with the Chl-binding proteins in both photosystems, the synthesis of the apoproteins is synchronized with Chl biosynthesis. This review aims to summarize the present knowledge on the posttranslational organization of Chl biosynthesis and current attempts to envision the proceedings of the successive synthesis and integration of Chl into Chl-binding proteins in the thylakoid membrane. Potential auxiliary factors, contributing to the control and organization of Chl biosynthesis and the association of Chl with the Chl-binding proteins during their integration into photosynthetic complexes, are discussed in this review.

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 .

Fabrication and characterization of ZnS/ZnO core shell nanostructures on silver wires

NASA Astrophysics Data System (ADS)

Kao, Chyuan Haur; Su, Wei Ming; Li, Cheng Yuan; Weng, Wei Chih; Weng, Chen Yuan; Cheng, Chin-Chi; Lin, Yung-Sen; Lin, Chia Feng; Chen, Hsiang

2018-06-01

In this research, ZnS nanoparticles were synthesized on ZnO/silver wires to form ZnS/ZnO core shell structures. Various outward appearance and colors could be observed by different ZnO growth and sulfurization conditions. To evaluate the properties of these nanostructures, optical properties and chemical bindings were analyzed by photoluminescence, Raman analysis, and X-ray photoelectron spectroscopy. Furthermore, material characterizations including transmission electron microscopy and X-ray diffraction confirmed that cubic ZnS (311)/ZnO nanostructures were grown on silver wires for the first time. ZnS/ZnO core shell structures on silver wires are promising for future optoelectronic and biomedical applications.

Developmental regulation of collagenase-3 mRNA in normal, differentiating osteoblasts through the activator protein-1 and the runt domain binding sites

NASA Technical Reports Server (NTRS)

Winchester, S. K.; Selvamurugan, N.; D'Alonzo, R. C.; Partridge, N. C.

2000-01-01

Collagenase-3 mRNA is initially detectable when osteoblasts cease proliferation, increasing during differentiation and mineralization. We showed that this developmental expression is due to an increase in collagenase-3 gene transcription. Mutation of either the activator protein-1 or the runt domain binding site decreased collagenase-3 promoter activity, demonstrating that these sites are responsible for collagenase-3 gene transcription. The activator protein-1 and runt domain binding sites bind members of the activator protein-1 and core-binding factor family of transcription factors, respectively. We identified core-binding factor a1 binding to the runt domain binding site and JunD in addition to a Fos-related antigen binding to the activator protein-1 site. Overexpression of both c-Fos and c-Jun in osteoblasts or core-binding factor a1 increased collagenase-3 promoter activity. Furthermore, overexpression of c-Fos, c-Jun, and core-binding factor a1 synergistically increased collagenase-3 promoter activity. Mutation of either the activator protein-1 or the runt domain binding site resulted in the inability of c-Fos and c-Jun or core-binding factor a1 to increase collagenase-3 promoter activity, suggesting that there is cooperative interaction between the sites and the proteins. Overexpression of Fra-2 and JunD repressed core-binding factor a1-induced collagenase-3 promoter activity. Our results suggest that members of the activator protein-1 and core-binding factor families, binding to the activator protein-1 and runt domain binding sites are responsible for the developmental regulation of collagenase-3 gene expression in osteoblasts.

Preparation and recognition of surface molecularly imprinted core-shell microbeads for protein in aqueous solutions

NASA Astrophysics Data System (ADS)

Lu, Yan; Yan, Chang-Ling; Gao, Shu-Yan

2009-04-01

In this paper, a surface molecular imprinting technique was reported for preparing core-shell microbeads of protein imprinting, and bovine hemoglobin or bovine serum albumin were used as model proteins for studying the imprinted core-shell microbeads. 3-Aminophenylboronic acid (APBA) was polymerized onto the surface of polystyrene microbead in the presence of the protein templates to create protein-imprinted core-shell microbeads. The various samples were characterized using scanning electron microscopy (SEM), transmission electron microscopy (TEM), Raman spectroscopy, X-ray photoelectron spectroscopy (XPS) and Brunauer-Emmett-Teller (BET) methods. The effect of pH on rebinding of the template hemoglobin, the specific binding and selective recognition were studied for the imprinted microbeads. The results show that the bovine hemoglobin-imprinted core-shell microbeads were successfully created. The shell was a sort of imprinted thin films with porous structure and larger surface areas. The imprinted microbeads have good selectivity for templates and high stability. Due to the recognition sites locating at or closing to the surface, these imprinted microbeads have good property of mass-transport. Unfortunately, the imprint technology was not successfully applied to imprinting bovine serum albumin (BSA).

Simple method for determining binding energies of fullerene and complex atomic negative ions

NASA Astrophysics Data System (ADS)

Felfli, Zineb; Msezane, Alfred

2017-04-01

A robust potential which embeds fully the vital core polarization interaction has been used in the Regge pole method to explore low-energy electron scattering from C60, Eu and Nb through the total cross sections (TCSs) calculations. From the characteristic dramatically sharp resonances in the TCSs manifesting negative ion formation in these systems, we extracted the binding energies for the C60, Euand Nbanions they are found to be in outstanding agreement with the measured electron affinities of C60, Eu and Nb. Common among these considered systems, including the standard atomic Au is the formation of their ground state negative ions at the second Ramsauer-Townsend (R-T) minima of their TCSs. Indeed, this is a signature of all the fullerenes and complex atoms considered thus far. Shape resonances, R-T minima and binding energies of the resultant anions are presented. This work was supported by U.S. DOE, Basic Energy Sciences, Office of Energy Research.

Electronic structure and mechanical properties of plasma nitrided ferrous alloys

NASA Astrophysics Data System (ADS)

Portolan, E.; Baumvol, I. J. R.; Figueroa, C. A.

2009-04-01

The electronic structures of the near-surface regions of two different nitrided steels (AISI 316 and 4140) were investigated using X-ray photoelectron spectroscopy. Photoelectron groups from all main chemical elements involved were addressed for steel samples with implanted-N concentrations in the range 16-32 at.%. As the implanted-N concentrations were increased, rather contrasting behaviors were observed for the two kinds of steel. The N1s photoelectrons had spectral shifts toward lower (nitrided AISI 316) or higher (nitrided AISI 4140) binding energies, whereas the Fe2p 3/2 photoelectron spectrum remains at a constant binding energy (nitrided AISI 316) or shifts toward higher binding energies (AISI 4140). These trends are discussed in terms of the metallic nitride formation and the overlapping of atomic orbitals. For nitrided AISI 316, a semi-classical approach of charge transfer between Cr and N is used to explain the experimental facts (formation of CrN), while for nitrided AISI 4140 we propose that the interaction between orbitals 4s from Fe and 2p from N promotes electrons to the conduction band increasing the electrical attraction of the N1s and Fe2p electrons in core shells (formation of FeN x). The increase in hardness of the steel upon N implantation is attributed to the localization of electrons in specific bonds, which diminishes the metallic bond character.

Ab initio molecular dynamics simulations reveal localization and time evolution dynamics of an excess electron in heterogeneous CO2-H2O systems.

PubMed

Liu, Ping; Zhao, Jing; Liu, Jinxiang; Zhang, Meng; Bu, Yuxiang

2014-01-28

In view of the important implications of excess electrons (EEs) interacting with CO2-H2O clusters in many fields, using ab initio molecular dynamics simulation technique, we reveal the structures and dynamics of an EE associated with its localization and subsequent time evolution in heterogeneous CO2-H2O mixed media. Our results indicate that although hydration can increase the electron-binding ability of a CO2 molecule, it only plays an assisting role. Instead, it is the bending vibrations that play the major role in localizing the EE. Due to enhanced attraction of CO2, an EE can stably reside in the empty, low-lying π(*) orbital of a CO2 molecule via a localization process arising from its initial binding state. The localization is completed within a few tens of femtoseconds. After EE trapping, the ∠OCO angle of the core CO2 (-) oscillates in the range of 127°∼142°, with an oscillation period of about 48 fs. The corresponding vertical detachment energy of the EE is about 4.0 eV, which indicates extreme stability of such a CO2-bound solvated EE in [CO2(H2O)n](-) systems. Interestingly, hydration occurs not only on the O atoms of the core CO2 (-) through formation of O⋯H-O H-bond(s), but also on the C atom, through formation of a C⋯H-O H-bond. In the latter binding mode, the EE cloud exhibits considerable penetration to the solvent water molecules, and its IR characteristic peak is relatively red-shifted compared with the former. Hydration on the C site can increase the EE distribution at the C atom and thus reduce the C⋯H distance in the C⋯H-O H-bonds, and vice versa. The number of water molecules associated with the CO2 (-) anion in the first hydration shell is about 4∼7. No dimer-core (C2O4 (-)) and core-switching were observed in the double CO2 aqueous media. This work provides molecular dynamics insights into the localization and time evolution dynamics of an EE in heterogeneous CO2-H2O media.

Ab initio density functional theory study on the atomic and electronic structure of GaP/Si(001) heterointerfaces

NASA Astrophysics Data System (ADS)

Romanyuk, O.; Supplie, O.; Susi, T.; May, M. M.; Hannappel, T.

2016-10-01

The atomic and electronic band structures of GaP/Si(001) heterointerfaces were investigated by ab initio density functional theory calculations. Relative total energies of abrupt interfaces and mixed interfaces with Si substitutional sites within a few GaP layers were derived. It was found that Si diffusion into GaP layers above the first interface layer is energetically unfavorable. An interface with Si/Ga substitution sites in the first layer above the Si substrate is energetically the most stable one in thermodynamic equilibrium. The electronic band structure of the epitaxial GaP/Si(001) heterostructure terminated by the (2 ×2 ) surface reconstruction consists of surface and interface electronic states in the common band gap of two semiconductors. The dispersion of the states is anisotropic and differs for the abrupt Si-Ga, Si-P, and mixed interfaces. Ga 2 p , P 2 p , and Si 2 p core-level binding-energy shifts were computed for the abrupt and the lowest-energy heterointerface structures. Negative and positive core-level shifts due to heterovalent bonds at the interface are predicted for the abrupt Si-Ga and Si-P interfaces, respectively. The distinct features in the heterointerface electronic structure and in the core-level shifts open new perspectives in the experimental characterization of buried polar-on-nonpolar semiconductor heterointerfaces.

Positron Annihilation Induced Auger Electron Spectroscopic Studies Of Reconstructed Semiconductor Surfaces

NASA Astrophysics Data System (ADS)

Fazleev, N. G.; Reed, J. A.; Starnes, S. G.; Weiss, A. H.

2011-06-01

The positron annihilation induced Auger spectrum from GaAs(100) displays six As and three Ga Auger peaks below 110 eV corresponding to M4,5VV, M2M4V, M2,3M4,5M4,5 Auger transitions for As and M2,3M4,5M4,5 Auger transitions for Ga. The integrated Auger peak intensities have been used to obtain experimental annihilation probabilities of surface trapped positrons with As 3p and 3d and Ga 3p core level electrons. PAES data is analyzed by performing calculations of positron surface and bulk states and annihilation characteristics of surface trapped positrons with relevant Ga and As core level electrons for both Ga- and As-rich (100) surfaces of GaAs, ideally terminated, non-reconstructed and with (2×8), (2×4), and (4×4) reconstructions. The orientation-dependent variations of the atomic and electron densities associated with reconstructions are found to affect localization of the positron wave function at the surface. Computed positron binding energy, work function, and annihilation characteristics demonstrate their sensitivity both to chemical composition and atomic structure of the topmost layers of the surface. Theoretical annihilation probabilities of surface trapped positrons with As 3d, 3p, and Ga 3p core level electrons are compared with the ones estimated from the measured Auger peak intensities.

Platinum Monolayer Shell on Non-Noble Metal Core Electrocatalysts for the Hydrogen Oxidation Reaction

NASA Astrophysics Data System (ADS)

Teeluck, Krishani Malini

According to the United States Environmental Protection Agency, as of 2015, transportation accounted for 32% of the carbon dioxide emissions in the United States (and all carbon dioxide emissions in the U.S. accounted for 82.2% of all greenhouse gases from human activity). A hydrogen fuel cell is a device that efficiently produces electrical energy directly from a chemical reaction, with zero carbon emissions, and therefore holds great promise in alleviating our dependence on harmful use of energy sources. Due to their clean emissions and high efficiencies, there has been focus on the hydrogen fuel cell for vehicle applications using proton exchange membrane and alkaline fuel cells. Although the proton exchange membrane fuel cell is currently being used in vehicles, their high cost limits their feasibility in the market. This has inspired the development of the alkaline fuel cell whose efficiency and simplicity suggest the possibility of manufacturing high power fuel cell vehicles at a low cost, since the electrocatalysts in the alkaline fuel cell can be made from non-noble metals. Although the hydrogen oxidation reaction is one of the fastest electrochemical reactions in acidic media, it is two orders of magnitude slower in alkaline media, which hinders the overall efficiency of the alkaline fuel cell. Pure platinum is currently the best catalyst for the hydrogen oxidation reaction, but platinum’s high cost and rarity yields economic issues, rendering the technology futile if it cannot be commercialized. Furthermore, platinum’s hydrogen binding energy is slightly stronger than the optimal hydrogen binding energy. As the hydrogen oxidation reaction happens only on the surface of the catalyst, there is no need for platinum content beyond the exterior. Since tungsten and nickel are cheap, as well as abundant, they are ideal elements to replace the core of the catalyst with, while leaving a platinum shell surrounding this core. The activity of the hydrogen oxidation reaction when using a platinum monolayer shell on a nickel tungsten core electrocatalyst is explored, and it was found that the novel catalyst created here exhibits kinetics that rival pure platinum, but at less than half the platinum content, suggesting that nickel and tungsten modify the electronic properties of platinum in a way that enhances its activity for the hydrogen oxidation reaction. Furthermore, the hydrogen binding energy of this novel electrocatalyst was found to be weaker than the optimal binding energy (rather than stronger, as seen in pure platinum), indicating the possibility of modifying the electronic properties of platinum for a more optimal hydrogen binding energy.

Formation, stability and dissociation dynamics of {{\\rm{N}}}_{2}{}^{{\\rm{n}}+} cations (n = 1 - 2) in 3.5 keV e - -N2 collisions studied using the energy resolved electron-ion coincidence technique

NASA Astrophysics Data System (ADS)

Kumar, S.; Prajapati, S.; Singh, B.; Singh, B. K.; Shanker, R.

2018-04-01

Coincidences between energy selected electrons and ions produced in the decay of a core hole ionized (excited) state in a free nitrogen molecule have been measured at three specified energies of emitted electrons to reveal the individual pathways produced in 3.5 keV electron-induced fragmentation processes. From these measurements, it has been possible to show, for the first time, that in addition to the normal Auger decay, the resonant Auger excitation channels also share their appreciable contributions in producing singly charged parent ions in an electron-induced collision system. The correlations between ion fragmentation products and electronic structures with a hole configuration in singly-, doubly- and possibly in triply charged molecular electronic states populated in the electronic decay of the initial core hole have been studied and discussed. KER values obtained from our experiments are found to be consistent with the previous results of photo absorption experiments for fragmentation channel {{{{N}}}2}2+ → N+ + N+ however, N2+ fragment ions are found to arise mainly from the fragmentation channel {{{{N}}}2}2+ → N2+ + N and to possess relatively low kinetic energies in the considered region of binding energies.

Evaluating Long-Term Impacts of Soil-Mixing Source-Zone Treatment using Cryogenic Core Collection

DTIC Science & Technology

2017-06-01

to (a) coring equipment freezing downhole, (b) freezing or binding of the core sample in barrel, and ( c ) running out of LN in the vicinity of sampling...encountered due to (a) coring equipment freezing downhole, (b) freezing or binding of the core sample in barrel, and ( c ) running out of LN in the...equipment freezing downhole, (b) freezing or binding of the core sample in barrel, and ( c ) running out of LN in the vicinity of sampling. Downhole

Studies of high coverage oxidation of the Cu(100) surface using low energy positrons

NASA Astrophysics Data System (ADS)

Fazleev, N. G.; Maddox, W. B.; Weiss, A. H.

2012-02-01

The study of oxidation of single crystal metal surfaces is important in understanding the corrosive and catalytic processes associated with thin film metal oxides. The structures formed on oxidized transition metal surfaces vary from simple adlayers of chemisorbed oxygen to more complex structures which result from the diffusion of oxygen into subsurface regions. In this work we present the results of theoretical studies of positron surface and bulk states and annihilation probabilities of surface-trapped positrons with relevant core electrons at the oxidized Cu(100) surface under conditions of high oxygen coverage. Calculations are performed for various high coverage missing row structures ranging between 0.50 and 1.50 ML oxygen coverage. The results of calculations of positron binding energy, positron work function, and annihilation characteristics of surface trapped positrons with relevant core electrons as function of oxygen coverage are compared with experimental data obtained from studies of oxidation of the Cu(100) surface using positron annihilation induced Auger electron spectroscopy (PAES).

A DFT and semiempirical model-based study of opioid receptor affinity and selectivity in a group of molecules with a morphine structural core.

PubMed

Bruna-Larenas, Tamara; Gómez-Jeria, Juan S

2012-01-01

We report the results of a search for model-based relationships between mu, delta, and kappa opioid receptor binding affinity and molecular structure for a group of molecules having in common a morphine structural core. The wave functions and local reactivity indices were obtained at the ZINDO/1 and B3LYP/6-31G(∗∗) levels of theory for comparison. New developments in the expression for the drug-receptor interaction energy expression allowed several local atomic reactivity indices to be included, such as local electronic chemical potential, local hardness, and local electrophilicity. These indices, together with a new proposal for the ordering of the independent variables, were incorporated in the statistical study. We found and discussed several statistically significant relationships for mu, delta, and kappa opioid receptor binding affinity at both levels of theory. Some of the new local reactivity indices incorporated in the theory appear in several equations for the first time in the history of model-based equations. Interaction pharmacophores were generated for mu, delta, and kappa receptors. We discuss possible differences regulating binding and selectivity in opioid receptor subtypes. This study, contrarily to the statistically backed ones, is able to provide a microscopic insight of the mechanisms involved in the binding process.

Substrate effect on the growth of Sn thin films

NASA Astrophysics Data System (ADS)

Chakraborty, Suvankar; Menon, Krishnakumar S. R.

2018-05-01

Growth of tin (Sn) on Ag(001), Ag(111) and W(110) substrate has been studied at elevated temperatures (473 K) using x-ray photoemission spectroscopy (XPS) and low energy electron diffraction (LEED). For Sn growth on silver substrates, it is noticed that both Sn 3d and Ag 3d core-level spectra shift in the higher binding energy direction due to the formation of surface alloy with the substrate. In both cases, surface alloy finally transforms into bulk alloy finally reaching bulk Sn value. For Sn growth on W(110) only Sn 3d core-level spectra shift in the higher binding energy direction due to surface core-level effect whereas no shift for tungsten core-level was noticed confirming no alloy formation. Sn is incorporated into the surface of substrate silver layer by removing every alternate or every third silver atoms to relieve the surface tensile stress as confirmed by LEED. On the other hand, tungsten being hard, Sn forms an overlayer structure by sitting in different energetically available positions rather than forming an alloy as energetically also it is not possible. Sn forms alloy with soft substrate silver and form overlayer films with tungsten. These studies are important in understanding the growth mechanism of Sn films on metal substrates.

DFT investigation of the interaction of gold nanoclusters with poly(amidoamine) PAMAM G0 dendrimer

NASA Astrophysics Data System (ADS)

Camarada, M. B.

2016-06-01

The interaction between PAMAM G0 and gold nanoclusters Aun (n = 2, 4, 6, and 8) was studied theoretically at DFT level. Different coordination sites were explored, including internal and superficial coordination. All stable complexes exhibited external interaction with the amine or carbonyl site, while the core site coordination was not favored. The more stable binding of Aun was registered with the terminal amine group, while the binding at the amide site was relatively weaker. The vertical first ionization potential, electron affinity, Fermi level, and the HOMO-LUMO gap of PAMAM and Aun-PAMAM G0 complexes were also analyzed.

Quantum confined stark effect on the binding energy of exciton in type II quantum heterostructure

NASA Astrophysics Data System (ADS)

Suseel, Rahul K.; Mathew, Vincent

2018-05-01

In this work, we have investigated the effect of external electric field on the strongly confined excitonic properties of CdTe/CdSe/CdTe/CdSe type-II quantum dot heterostructures. Within the effective mass approximation, we solved the Poisson-Schrodinger equations of the exciton in nanostructure using relaxation method in a self-consistent iterative manner. We changed both the external electric field and core radius of the quantum dot, to study the behavior of binding energy of exciton. Our studies show that the external electric field destroys the positional flipped state of exciton by modifying the confining potentials of electron and hole.

Diamagnetic susceptibility of a hydrogenic donor in a group IV-VI quantum dot-quantum well heterostructure

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

Saravanamoorthy, S. N.; Peter, A. John, E-mail: a.john.peter@gmail.com

2016-05-23

Electronic properties of a hydrogenic donor impurity in a CdSe/Pb{sub 0.8}Cd{sub 0.2}Se/CdSe quantum dot quantum well system are investigated for various radii of core with shell materials. Confined energies are obtained taking into account the geometrical size of the system and thereby the donor binding energies are found. The diamagnetic susceptibility is estimated for a confined shallow donor in the well system. The results show that the diamagnetic susceptibility strongly depends on core and shell radii and it is more sensitive to variations of the geometrical size of the well material.

A single amino-acid substitution in the Ets domain alters core DNA binding specificity of Ets1 to that of the related transcription factors Elf1 and E74.

PubMed

Bosselut, R; Levin, J; Adjadj, E; Ghysdael, J

1993-11-11

Ets proteins form a family of sequence specific DNA binding proteins which bind DNA through a 85 aminoacids conserved domain, the Ets domain, whose sequence is unrelated to any other characterized DNA binding domain. Unlike all other known Ets proteins, which bind specific DNA sequences centered over either GGAA or GGAT core motifs, E74 and Elf1 selectively bind to GGAA corecontaining sites. Elf1 and E74 differ from other Ets proteins in three residues located in an otherwise highly conserved region of the Ets domain, referred to as conserved region III (CRIII). We show that a restricted selectivity for GGAA core-containing sites could be conferred to Ets1 upon changing a single lysine residue within CRIII to the threonine found in Elf1 and E74 at this position. Conversely, the reciprocal mutation in Elf1 confers to this protein the ability to bind to GGAT core containing EBS. This, together with the fact that mutation of two invariant arginine residues in CRIII abolishes DNA binding, indicates that CRIII plays a key role in Ets domain recognition of the GGAA/T core motif and lead us to discuss a model of Ets proteins--core motif interaction.

Electronic structure and optical properties of the thiolate-protected Au28(SMe)20 cluster.

PubMed

Knoppe, Stefan; Malola, Sami; Lehtovaara, Lauri; Bürgi, Thomas; Häkkinen, Hannu

2013-10-10

The recently reported crystal structure of the Au28(TBBT)20 cluster (TBBT: p-tert-butylbenzenethiolate) is analyzed with (time-dependent) density functional theory (TD-DFT). Bader charge analysis reveals a novel trimeric Au3(SR)4 binding motif. The cluster can be formulated as Au14(Au2(SR)3)4(Au3(SR)4)2. The electronic structure of the Au14(6+) core and the ligand-protected cluster were analyzed, and their stability can be explained by formation of distorted eight-electron superatoms. Optical absorption and circular dichroism (CD) spectra were calculated and compared to the experiment. Assignment of handedness of the intrinsically chiral cluster is possible.

Surface states and annihilation characteristics of positrons trapped at the oxidized Cu(100) surface

NASA Astrophysics Data System (ADS)

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

2013-06-01

In this work we present the results of theoretical studies of positron surface and bulk states and annihilation probabilities of surface-trapped positrons with relevant core electrons at the oxidized Cu(100) surface under conditions of high oxygen coverage. Oxidation of the Cu(100) surface has been studied by performing an ab-initio investigation of the stability and electronic structure of the Cu(100) missing row reconstructed surface at various on-surface and subsurface oxygen coverages ranging from 0.5 to 1.5 monolayers using density functional theory (DFT). All studied structures have been found to be energetically more favorable as compared to structures formed by purely on-surface oxygen adsorption. The observed decrease in the positron work function when oxygen atoms occupy on-surface and subsurface sites has been attributed to a significant charge redistribution within the first two layers, buckling effects within each layer and an interlayer expansion. The computed positron binding energy, positron surface state wave function, and annihilation probabilities of the surface trapped positrons with relevant core electrons demonstrate their sensitivity to oxygen coverage, atomic structure of the topmost layers of surfaces, and charge transfer effects. Theoretical results are compared with experimental data obtained from studies of oxidation of the Cu(100) surface using positron annihilation induced Auger electron spectroscopy (PAES). The results presented provide an explanation for the changes observed in the probability of annihilation of surface trapped positrons with Cu 3p core-level electrons as a function of annealing temperature.

Ultrafast Dynamics of 1,3-Cyclohexadiene in Highly Excited States

DOE PAGES

Bühler, Christine C.; Minitti, Michael P.; Deb, Sanghamitra; ...

2011-01-01

The ultrafast dynamics of 1,3-cyclohexadiene has been investigated via structurally sensitive Rydberg electron binding energies and shown to differ upon excitation to the 1B state and the 3p Rydberg state. Excitation of the molecule with 4.63 eV photons into the ultrashort-lived 1B state yields the well-known ring opening to 1,3,5-hexatriene, while a 5.99 eV photon lifts the molecule directly into the 3p-Rydberg state. Excitation to 3p does not induce ring opening. In both experiments, time-dependent shifts of the Rydberg electron binding energy reflect the structural dynamics of the molecular core. Structural distortions associated with 3p-excitation cause a dynamical shift in the -more » and -binding energies by 10 and 26 meV/ps, respectively, whereas after excitation into 1B, more severe structural transformations along the ring-opening coordinate produce shifts at a rate of 40 to 60 meV/ps. The experiment validates photoionization-photoelectron spectroscopy via Rydberg states as a powerful technique to observe structural dynamics of polyatomic molecules.« less

Structural and electronic parameters of ferroelectric KWOF

NASA Astrophysics Data System (ADS)

Atuchin, V. V.; Gavrilova, T. A.; Kesler, V. G.; Molokeev, M. S.; Aleksandrov, K. S.

2010-11-01

The low-temperature ferroelectric G2 polymorph of K 3WO 3F 3 oxyfluoride is formed by chemical synthesis. The electronic parameters of G2-K 3WO 3F 3 have been measured by X-ray photoelectron spectroscopy under excitation with Al Kα radiation (1486.6 eV). Detailed spectra have been recorded for all element core levels and Auger lines. The chemical bonding effects in the WO 3F 3 and WO 6 octahedrons are considered by using the binding energy difference ΔBE(O-W)=BE(O 1s)-BE(W 4f).

d +i d chiral superconductivity in a triangular lattice from trigonal bipyramidal complexes

NASA Astrophysics Data System (ADS)

Lu, Chen; Zhang, Li-Da; Wu, Xianxin; Yang, Fan; Hu, Jiangping

2018-04-01

We model the newly predicted high-Tc superconducting candidates constructed by corner-shared trigonal bipyramidal complexes with an effective three-orbital tight-binding Hamiltonian and investigate the pairing symmetry of their superconducting states driven by electron-electron interactions. Our combined weak- and strong-coupling-based calculations consistently identify the chiral d +i d superconductivity as the leading pairing symmetry in a wide doping range with realistic interaction parameters. This pairing state has a nontrivial topological Chern number and can host gapless chiral edge modes, and the vortex cores under magnetic field can carry Majorana zero modes.

Gold core@silver semishell Janus nanoparticles prepared by interfacial etching.

PubMed

Chen, Limei; Deming, Christopher P; Peng, Yi; Hu, Peiguang; Stofan, Jake; Chen, Shaowei

2016-08-14

Gold core@silver semishell Janus nanoparticles were prepared by chemical etching of Au@Ag core-shell nanoparticles at the air/water interface. Au@Ag core-shell nanoparticles were synthesized by chemical deposition of a silver shell onto gold seed colloids followed by the self-assembly of 1-dodecanethiol onto the nanoparticle surface. The nanoparticles then formed a monolayer on the water surface of a Langmuir-Blodgett trough, and part of the silver shell was selectively etched away by the mixture of hydrogen peroxide and ammonia in the water subphase, where the etching was limited to the side of the nanoparticles that was in direct contact with water. The resulting Janus nanoparticles exhibited an asymmetrical distribution of silver on the surface of the gold cores, as manifested in transmission electron microscopy, UV-vis absorption, and X-ray photoelectron spectroscopy measurements. Interestingly, the Au@Ag semishell Janus nanoparticles exhibited enhanced electrocatalytic activity in oxygen reduction reactions, as compared to their Au@Ag and Ag@Au core-shell counterparts, likely due to a synergistic effect between the gold cores and silver semishells that optimized oxygen binding to the nanoparticle surface.

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

Löytynoja, T., E-mail: tuomas.loytynoja@oulu.fi; Division of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, SE-106 91 Stockholm; Li, X.

We study a newly devised quantum mechanics capacitance molecular mechanics (QMCMM) method for the calculation of core-electron binding energies in the case of molecules adsorbed on metal surfaces. This yet untested methodology is applied to systems with monolayer of methanol/methyl nitrite on an Ag(111) surface at 100 K temperature. It was found out that the studied C, N, and O 1s core-hole energies converge very slowly as a function of the radius of the metallic cluster, which was ascribed to build up of positive charge on the edge of the Ag slab. Further analysis revealed that an extrapolation process canmore » be used to obtain binding energies that deviated less than 0.5 eV against experiments, except in the case of methanol O 1s where the difference was as large as 1.8 eV. Additional QM-cluster calculations suggest that the latter error can be connected to the lack of charge transfer over the QM–CMM boundary. Thus, the results indicate that the QMCMM and QM-cluster methods can complement each other in a holistic picture of molecule-adsorbate core-ionization studies, where all types of intermolecular interactions are considered.« less

Electronic state and photoionization cross section of a single dopant in GaN/InGaN core/shell quantum dot under magnetic field and hydrostatic pressure

NASA Astrophysics Data System (ADS)

Aouami, A. El; Feddi, E.; Talbi, A.; Dujardin, F.; Duque, C. A.

2018-06-01

In this study, we have investigated the simultaneous influence of magnetic field combined to the hydrostatic pressure and the geometrical confinement on the behavior of a single dopant confined in GaN/InGaN core/shell quantum dots. Within the scheme of the effective-mass approximation, the eigenvalues equation has solved by using the variational method with one-parameter trial wavefunctions. Variation of the ground state binding energy of the single dopant is determined according to the magnetic field and hydrostatic pressure for several dimensions of the heterostructure. The results show that the binding energy is strongly dependent on the core/shell sizes, the magnetic field, and the hydrostatic pressure. The analysis of the photoionization cross section, corresponding to optical transitions associated to the first donor energy level and the conduction band, shows clearly that the reduction of the dot dimensions and/or the simultaneous influences of applied magnetic field, combined to the hydrostatic pressure strength, cause a shift in resonance peaks towards the higher energies with important variations in the magnitude of the resonant peaks.

Photoionization cross section and binding energy of single dopant in hollow cylindrical core/shell quantum dot

NASA Astrophysics Data System (ADS)

Feddi, E.; El-Yadri, M.; Dujardin, F.; Restrepo, R. L.; Duque, C. A.

2017-02-01

In this study, we have investigated the confined donor impurity in a hollow cylindrical-shell quantum dot. The charges are assumed to be completely confined to the interior of the shell with rigid walls. Within the framework of the effective-mass approximation and by using a simple variational approach, we have computed the donor binding energy as a function of the shell sizes in order to study the behavior of the electron-impurity attraction for a very small thickness. Our results show that the binding energy of a donor impurity placed at the center of cylindrical core/shell dots depends strongly on the shell size. The binding energy increases when the shell-wideness becomes smaller and shows the same behavior as in a simple cylindrical quantum dot. A special case has been studied, which corresponds to the ratio between the inner and outer radii near to one (a/b → 1) for which our model gives a non-significant behavior of the impurity binding energy. This fact implies the existence of a critical value (a/b) for which the binding energy of the donor impurity tends to the limit value of 4 effective Rydbergs as in a 2D quantum well. We also analyse the photoionization cross section considering only the in-plane incident radiation polarization. We determine its behavior as a function of photon energy, shell size, and donor position. The measurement of photoionization in such systems would be of great interest to understand the optical properties of carriers in quantum dots.

The Tom Core Complex

PubMed Central

Ahting, Uwe; Thun, Clemens; Hegerl, Reiner; Typke, Dieter; Nargang, Frank E.; Neupert, Walter; Nussberger, Stephan

1999-01-01

Translocation of nuclear-encoded preproteins across the outer membrane of mitochondria is mediated by the multicomponent transmembrane TOM complex. We have isolated the TOM core complex of Neurospora crassa by removing the receptors Tom70 and Tom20 from the isolated TOM holo complex by treatment with the detergent dodecyl maltoside. It consists of Tom40, Tom22, and the small Tom components, Tom6 and Tom7. This core complex was also purified directly from mitochondria after solubilization with dodecyl maltoside. The TOM core complex has the characteristics of the general insertion pore; it contains high-conductance channels and binds preprotein in a targeting sequence-dependent manner. It forms a double ring structure that, in contrast to the holo complex, lacks the third density seen in the latter particles. Three-dimensional reconstruction by electron tomography exhibits two open pores traversing the complex with a diameter of ∼2.1 nm and a height of ∼7 nm. Tom40 is the key structural element of the TOM core complex. PMID:10579717

Accurate quasiparticle calculation of x-ray photoelectron spectra of solids

NASA Astrophysics Data System (ADS)

Aoki, Tsubasa; Ohno, Kaoru

2018-05-01

It has been highly desired to provide an accurate and reliable method to calculate core electron binding energies (CEBEs) of crystals and to understand the final state screening effect on a core hole in high resolution x-ray photoelectron spectroscopy (XPS), because the ΔSCF method cannot be simply used for bulk systems. We propose to use the quasiparticle calculation based on many-body perturbation theory for this problem. In this study, CEBEs of band-gapped crystals, silicon, diamond, β-SiC, BN, and AlP, are investigated by means of the GW approximation (GWA) using the full ω integration and compared with the preexisting XPS data. The screening effect on a deep core hole is also investigated in detail by evaluating the relaxation energy (RE) from the core and valence contributions separately. Calculated results show that not only the valence electrons but also the core electrons have an important contribution to the RE, and the GWA have a tendency to underestimate CEBEs due to the excess RE. This underestimation can be improved by introducing the self-screening correction to the GWA. The resulting C1s, B1s, N1s, Si2p, and Al2p CEBEs are in excellent agreement with the experiments within 1 eV absolute error range. The present self-screening corrected GW approach has the capability to achieve the highly accurate prediction of CEBEs without any empirical parameter for band-gapped crystals, and provide a more reliable theoretical approach than the conventional ΔSCF-DFT method.

Accurate quasiparticle calculation of x-ray photoelectron spectra of solids.

PubMed

Aoki, Tsubasa; Ohno, Kaoru

2018-05-31

It has been highly desired to provide an accurate and reliable method to calculate core electron binding energies (CEBEs) of crystals and to understand the final state screening effect on a core hole in high resolution x-ray photoelectron spectroscopy (XPS), because the ΔSCF method cannot be simply used for bulk systems. We propose to use the quasiparticle calculation based on many-body perturbation theory for this problem. In this study, CEBEs of band-gapped crystals, silicon, diamond, β-SiC, BN, and AlP, are investigated by means of the GW approximation (GWA) using the full ω integration and compared with the preexisting XPS data. The screening effect on a deep core hole is also investigated in detail by evaluating the relaxation energy (RE) from the core and valence contributions separately. Calculated results show that not only the valence electrons but also the core electrons have an important contribution to the RE, and the GWA have a tendency to underestimate CEBEs due to the excess RE. This underestimation can be improved by introducing the self-screening correction to the GWA. The resulting C1s, B1s, N1s, Si2p, and Al2p CEBEs are in excellent agreement with the experiments within 1 eV absolute error range. The present self-screening corrected GW approach has the capability to achieve the highly accurate prediction of CEBEs without any empirical parameter for band-gapped crystals, and provide a more reliable theoretical approach than the conventional ΔSCF-DFT method.

Study of the phase composition of nanostructures produced by the local anodic oxidation of titanium films

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

Avilov, V. I.; Ageev, O. A.; Konoplev, B. G.

2016-05-15

The results of experimental studies of the phase composition of oxide nanostructures formed by the local anodic oxidation of a titanium thin film are reported. The data of the phase analysis of titanium-oxide nanostructures are obtained by X-ray photoelectron spectroscopy in the ion profiling mode of measurements. It is established that the surface of titanium-oxide nanostructures 4.5 ± 0.2 nm in height possesses a binding energy of core levels characteristic of TiO{sub 2} (458.4 eV). By analyzing the titanium-oxide nanostructures in depth by X-ray photoelectron spectroscopy, the formation of phases with binding energies of core levels characteristic of Ti{sub 2}O{submore » 3} (456.6 eV) and TiO (454.8 eV) is established. The results can be used in developing the technological processes of the formation of a future electronic-component base for nanoelectronics on the basis of titanium-oxide nanostructures and probe nanotechnologies.« less

Studies of the Ge(100) Surface Using a Low Energy Positron Beam: The Effects of Surface Reconstructions on Positron Trapping and Annihilation Characteristics

NASA Astrophysics Data System (ADS)

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

2008-03-01

Positron annihilation induced Auger electron spectroscopy (PAES) has been applied to study the Ge(100) surface. The PAES spectrum from the Ge(100) surface displays several strong Auger peaks corresponding to M4,5N1N2,3 , M2,3M4,5M4,5 , M2,3M4,5V, and M1M4,5M4,5 Auger transitions. The integrated peak intensities of Auger transitions are used to obtain experimental annihilation probabilities for the Ge 3d and 3p core level electrons. The experimental results are analyzed by performing calculations of positron surface states and annihilation characteristics of surface trapped positrons with relevant Ge core-level electrons for the reconstructed Ge(100)-p(2x1), Ge(100)-p(2x2), and Ge(100)-c(4x2) surfaces. Estimates of positron binding energy, work function, and annihilation characteristics reveal their sensitivity to surface reconstruction of the topmost layers of clean Ge(100). These results are compared to the ones obtained for the reconstructed Si(100)-(2x1) and Si(100)-p(2x2) surfaces. A comparison with PAES data reveals an agreement with theoretical core annihilation probabilities for the Auger transitions considered.

Predicted trends of core-shell preferences for 132 late transition-metal binary-alloy nanoparticles.

PubMed

Wang, Lin-Lin; Johnson, Duane D

2009-10-07

Transition-metal alloyed nanoparticles with core-shell features (shell enrichment by one of the metals) are becoming ubiquitous, from (electro-)catalysis to biomedical applications, due to their size control, performance, biocompatibility, and cost. We investigate 132 binary-alloyed nanoparticle systems (groups 8 to 11 in the Periodic Table) using density functional theory (DFT) and systematically explore their segregation energies to determine core-shell preferences. We find that core-shell preferences are generally described by two independent factors: (1) cohesive energy (related to vapor pressure) and (2) atomic size (quantified by the Wigner-Seitz radius), and the interplay between them. These independent factors are shown to provide general trends for the surface segregation preference for atoms in nanoparticles, as well as semi-infinite surfaces, and give a simple correlation (a "design map") for the alloying and catalytic behavior. Finally, we provide a universal description of core-shell preference via tight-binding theory (band-energy differences) that (i) quantitatively reproduces the DFT segregation energies and (ii) confirms the electronic origins and correlations for core-shell behavior.

Periodicity in Attachment Organelle Revealed by Electron Cryotomography Suggests Conformational Changes in Gliding Mechanism of Mycoplasma pneumoniae

PubMed Central

Kawamoto, Akihiro; Matsuo, Lisa; Kato, Takayuki; Yamamoto, Hiroki

2016-01-01

ABSTRACT Mycoplasma pneumoniae, a pathogenic bacterium, glides on host surfaces using a unique mechanism. It forms an attachment organelle at a cell pole as a protrusion comprised of knoblike surface structures and an internal core. Here, we analyzed the three-dimensional structure of the organelle in detail by electron cryotomography. On the surface, knoblike particles formed a two-dimensional array, albeit with limited regularity. Analyses using a nonbinding mutant and an antibody showed that the knoblike particles correspond to a naplike structure that has been observed by negative-staining electron microscopy and is likely to be formed as a complex of P1 adhesin, the key protein for binding and gliding. The paired thin and thick plates feature a rigid hexagonal lattice and striations with highly variable repeat distances, respectively. The combination of variable and invariant structures in the internal core and the P1 adhesin array on the surface suggest a model in which axial extension and compression of the thick plate along a rigid thin plate is coupled with attachment to and detachment from the substrate during gliding. PMID:27073090

Influence of strain on dislocation core in silicon

NASA Astrophysics Data System (ADS)

Pizzagalli, L.; Godet, J.; Brochard, S.

2018-05-01

First principles, density functional-based tight binding and semi-empirical interatomic potentials calculations are performed to analyse the influence of large strains on the structure and stability of a 60? dislocation in silicon. Such strains typically arise during the mechanical testing of nanostructures like nanopillars or nanoparticles. We focus on bi-axial strains in the plane normal to the dislocation line. Our calculations surprisingly reveal that the dislocation core structure largely depends on the applied strain, for strain levels of about 5%. In the particular case of bi-axial compression, the transformation of the dislocation to a locally disordered configuration occurs for similar strain magnitudes. The formation of an opening, however, requires larger strains, of about 7.5%. Furthermore, our results suggest that electronic structure methods should be favoured to model dislocation cores in case of large strains whenever possible.

Physical and Electronic Isolation of Carbon Nanotube Conductors

NASA Technical Reports Server (NTRS)

OKeeffe, James; Biegel, Bryan (Technical Monitor)

2001-01-01

Multi-walled nanotubes are proposed as a method to electrically and physically isolate nanoscale conductors from their surroundings. We use tight binding (TB) and density functional theory (DFT) to simulate the effects of an external electric field on multi-wall nanotubes. Two categories of multi-wall nanotube are investigated, those with metallic and semiconducting outer shells. In the metallic case, simulations show that the outer wall effectively screens the inner core from an applied electric field. This offers the ability to reduce crosstalk between nanotube conductors. A semiconducting outer shell is found not to perturb an electric field incident on the inner core, thereby providing physical isolation while allowing the tube to remain electrically coupled to its surroundings.

Synthesis and characterization of a poly(lactic-co-glycolic acid) core + poly(N-isopropylacrylamide) shell nanoparticle system

PubMed Central

Kosinski, Aaron M.; Brugnano, Jamie L.; Seal, Brandon L.; Knight, Frances C.; Panitch, Alyssa

2012-01-01

Poly(lactic-co-glycolic acid) (PLGA) is a popular material used to prepare nanoparticles for drug delivery. However, PLGA nanoparticles lack desirable attributes including active targeting abilities, resistance to aggregation during lyophilization, and the ability to respond to dynamic environmental stimuli. To overcome these issues, we fabricated a nanoparticle consisting of a PLGA core encapsulated within a shell of poly(N-isopropylacrylamide). Dynamic light scattering and transmission electron microscope imaging were used to characterize the nanoparticles, while an MTT assay and ELISA suggested biocompatibility in THP1 cells. Finally, a collagen type II binding assay showed successful modification of these nanoparticles with an active targeting moiety. PMID:23507885

Exciton and core-level electron confinement effects in transparent ZnO thin films

PubMed Central

Mosquera, Adolfo A.; Horwat, David; Rashkovskiy, Alexandr; Kovalev, Anatoly; Miska, Patrice; Wainstein, Dmitry; Albella, Jose M.; Endrino, Jose L.

2013-01-01

The excitonic light emission of ZnO films have been investigated by means of photoluminescence measurements in ultraviolet-visible region. Exciton confinement effects have been observed in thin ZnO coatings with thickness below 20 nm. This is enhanced by a rise of the intensity and a blue shift of the photoluminescence peak after extraction of the adsorbed species upon annealing in air. It is found experimentally that the free exciton energy (determined by the photoluminescence peak) is inversely proportional to the square of the thickness while core-level binding energy is inversely proportional to the thickness. These findings correlate very well with the theory of kinetic and potential confinements.

Design and Synthesis of Piperazine Sulfonamide Cores Leading to Highly Potent HIV-1 Protease Inhibitors.

PubMed

Bungard, Christopher J; Williams, Peter D; Schulz, Jurgen; Wiscount, Catherine M; Holloway, M Katharine; Loughran, H Marie; Manikowski, Jesse J; Su, Hua-Poo; Bennett, David J; Chang, Lehua; Chu, Xin-Jie; Crespo, Alejandro; Dwyer, Michael P; Keertikar, Kartik; Morriello, Gregori J; Stamford, Andrew W; Waddell, Sherman T; Zhong, Bin; Hu, Bin; Ji, Tao; Diamond, Tracy L; Bahnck-Teets, Carolyn; Carroll, Steven S; Fay, John F; Min, Xu; Morris, William; Ballard, Jeanine E; Miller, Michael D; McCauley, John A

2017-12-14

Using the HIV-1 protease binding mode of MK-8718 and PL-100 as inspiration, a novel aspartate binding bicyclic piperazine sulfonamide core was designed and synthesized. The resulting HIV-1 protease inhibitor containing this core showed an 60-fold increase in enzyme binding affinity and a 10-fold increase in antiviral activity relative to MK-8718 .

Positron probes of the Ge(1 0 0) surface: The effects of surface reconstructions and electron positron correlations on positron trapping and annihilation characteristics

NASA Astrophysics Data System (ADS)

Fazleev, N. G.; Jung, E.; Weiss, A. H.

2007-08-01

Positron annihilation induced Auger electron spectroscopy (PAES) has been applied to study the Ge(1 0 0) surface. The high-resolution PAES spectrum from the Ge(1 0 0) surface displays several strong Auger peaks corresponding to M4,5N1N2,3, M2,3M4,5M4,5, M2,3M4,5V and M1M4,5M4,5 Auger transitions. The integrated peak intensities of Auger transitions are used to obtain experimental annihilation probabilities for the Ge 3d and 3p core level electrons. These experimental results are analyzed by performing calculations of positron surface states and annihilation characteristics of surface trapped positrons with relevant Ge core-level electrons for the non-reconstructed and reconstructed Ge(1 0 0)-p(2 × 1), Ge(1 0 0)-p(2 × 2) and Ge(1 0 0)-c(4 × 2) surfaces. It is found that the positron surface state wave function extends into the Ge lattice in the regions where atoms are displaced from their ideal terminated positions due to reconstructions. Estimates of the positron binding energy and the positron annihilation characteristics reveal their sensitivity to the specific atomic structure of the topmost layers of Ge(1 0 0). A comparison with PAES data reveals an agreement with theoretical core annihilation probabilities for the Auger transitions considered.

Size effects in electronic and catalytic properties of unsupported palladium nanoparticles in electrooxidation of formic acid.

PubMed

Zhou, Wei Ping; Lewera, Adam; Larsen, Robert; Masel, Rich I; Bagus, Paul S; Wieckowski, Andrzej

2006-07-13

We report a combined X-ray photoelectron spectroscopy (XPS), cyclic voltammetry (CV), and chronoamperometry (CA) study of formic acid electrooxidation on unsupported palladium nanoparticle catalysts in the particle size range from 9 to 40 nm. The CV and CA measurements show that the most active catalyst is made of the smallest (9 and 11 nm) Pd nanoparticles. Besides the high reactivity, XPS data show that such nanoparticles display the highest core-level binding energy (BE) shift and the highest valence band (VB) center downshift with respect to the Fermi level. We believe therefore that we found a correlation between formic acid oxidation current and BE and VB center shifts, which, in turn, can directly be related to the electronic structure of palladium nanoparticles of different particle sizes. Clearly, such a trend using unsupported catalysts has never been reported. According to the density functional theory of heterogeneous catalysis, and mechanistic considerations, the observed shifts are caused by a weakening of the bond strength of the COOH intermediate adsorption on the catalyst surface. This, in turn, results in the increase in the formic acid oxidation rate to CO2 (and in the associated oxidation current). Overall, our measurements demonstrate the particle size effect on the electronic properties of palladium that yields different catalytic activity in the HCOOH oxidation reaction. Our work highlights the significance of the core-level binding energy and center of the d-band shifts in electrocatalysis and underlines the value of the theory that connects the center of the d-band shifts to catalytic reactivity.

Single-molecule fluorescence measurements reveal the reaction mechanisms of the core RISC, composed of human Argonaute 2 and a guide RNA.

PubMed

Jo, Myung Hyun; Song, Ji-Joon; Hohng, Sungchul

2015-12-01

In eukaryotes, small RNAs play important roles in both gene regulation and resistance to viral infection. Argonaute proteins have been identified as a key component of the effector complexes of various RNA-silencing pathways, but the mechanistic roles of Argonaute proteins in these pathways are not clearly understood. To address this question, we performed single-molecule fluorescence experiments using an RNA-induced silencing complex (core-RISC) composed of a small RNA and human Argonaute 2. We found that target binding of core-RISC starts at the seed region of the guide RNA. After target binding, four distinct reactions followed: target cleavage, transient binding, stable binding, and Argonaute unloading. Target cleavage required extensive sequence complementarity and accelerated core-RISC dissociation for recycling. In contrast, the stable binding of core-RISC to target RNAs required seed-match only, suggesting a potential explanation for the seed-match rule of microRNA (miRNA) target selection.

Kinetic modeling of electron transfer reactions in photosystem I complexes of various structures with substituted quinone acceptors.

PubMed

Milanovsky, Georgy E; Petrova, Anastasia A; Cherepanov, Dmitry A; Semenov, Alexey Yu

2017-09-01

The reduction kinetics of the photo-oxidized primary electron donor P 700 in photosystem I (PS I) complexes from cyanobacteria Synechocystis sp. PCC 6803 were analyzed within the kinetic model, which considers electron transfer (ET) reactions between P 700 , secondary quinone acceptor A 1 , iron-sulfur clusters and external electron donor and acceptors - methylviologen (MV), 2,3-dichloro-naphthoquinone (Cl 2 NQ) and oxygen. PS I complexes containing various quinones in the A 1 -binding site (phylloquinone PhQ, plastoquinone-9 PQ and Cl 2 NQ) as well as F X -core complexes, depleted of terminal iron-sulfur F A /F B clusters, were studied. The acceleration of charge recombination in F X -core complexes by PhQ/PQ substitution indicates that backward ET from the iron-sulfur clusters involves quinone in the A 1 -binding site. The kinetic parameters of ET reactions were obtained by global fitting of the P 700 + reduction with the kinetic model. The free energy gap ΔG 0 between F X and F A /F B clusters was estimated as -130 meV. The driving force of ET from A 1 to F X was determined as -50 and -220 meV for PhQ in the A and B cofactor branches, respectively. For PQ in A 1A -site, this reaction was found to be endergonic (ΔG 0  = +75 meV). The interaction of PS I with external acceptors was quantitatively described in terms of Michaelis-Menten kinetics. The second-order rate constants of ET from F A /F B , F X and Cl 2 NQ in the A 1 -site of PS I to external acceptors were estimated. The side production of superoxide radical in the A 1 -site by oxygen reduction via the Mehler reaction might comprise ≥0.3% of the total electron flow in PS I.

Thermally induced anchoring of a zinc-carboxyphenylporphyrin on rutile TiO2 (110)

NASA Astrophysics Data System (ADS)

Jöhr, Res; Hinaut, Antoine; Pawlak, Rémy; Zajac, Łukasz; Olszowski, Piotr; Such, Bartosz; Glatzel, Thilo; Zhang, Jun; Muntwiler, Matthias; Bergkamp, Jesse J.; Mateo, Luis-Manuel; Decurtins, Silvio; Liu, Shi-Xia; Meyer, Ernst

2017-05-01

Functionalization of surfaces has become of high interest for a wealth of applications such as sensors, hybrid photovoltaics, catalysis, and molecular electronics. Thereby molecule-surface interactions are of crucial importance for the understanding of interface properties. An especially relevant point is the anchoring of molecules to surfaces. In this work, we analyze this process for a zinc-porphyrin equipped with carboxylic acid anchoring groups on rutile TiO2 (110) using scanning probe microscopy. After evaporation, the porphyrins are not covalently bound to the surface. Upon annealing, the carboxylic acid anchors undergo deprotonation and bind to surface titanium atoms. The formation of covalent bonds is evident from the changed stability of the molecule on the surface as well as the adsorption configuration. Annealed porphyrins are rotated by 45° and adopt another adsorption site. The influence of binding on electronic coupling with the surface is investigated using photoelectron spectroscopy. The observed shifts of Zn 2p and N 1s levels to higher binding energies indicate charging of the porphyrin core, which is accompanied by a deformation of the macrocycle due to a strong interaction with the surface.

The Core Cysteines, (C909) of Islet Antigen-2 and (C945) of Islet Antigen-2β, Are Crucial to Autoantibody Binding in Type 1 Diabetes

PubMed Central

Elvers, Karen T.; Geoghegan, Ivey; Shoemark, Debbie K.; Lampasona, Vito; Bingley, Polly J.; Williams, Alistair J.K.

2013-01-01

Cysteines are thought integral to conformational epitopes of islet antigen-2 (IA-2) autoantibodies (IA-2A), possibly through disulfide bond formation. We therefore investigated which cysteines are critical to IA-2A binding in patients with newly diagnosed type 1 diabetes. All 10 cysteines in the intracellular domain of IA-2 were modified to serine by site-directed mutagenesis, and the effects of these changes on autoantibody binding in comparison with wild-type control were investigated by radiobinding assay. Mutation of the protein tyrosine phosphatase (PTP) core cysteine (C909) in IA-2 caused large reductions in autoantibody binding. In contrast, little or no reduction in binding was seen following substitution of the other cysteines. Modification of the core cysteine (C945) in IA-2β also greatly reduced autoantibody binding. Lysine substitution of glutamate-836 in IA-2 or glutamate-872 in IA-2β resulted in modest reductions in binding and identified a second epitope region. Binding to IA-2 PTP and IA-2β PTP was almost abolished by mutation of both the core cysteine and these glutamates. The core cysteine is key to the major PTP conformational epitope, but disulfide bonding contributes little to IA-2A epitope integrity. In most patients, at disease onset, >90% of antibodies binding to the PTP domain of IA-2 recognize just two epitope regions. PMID:22966073

Covalent immobilization of molecularly imprinted polymer nanoparticles using an epoxy silane.

PubMed

Kamra, Tripta; Chaudhary, Shilpi; Xu, Changgang; Johansson, Niclas; Montelius, Lars; Schnadt, Joachim; Ye, Lei

2015-05-01

Molecularly imprinted polymers (MIPs) can be used as antibody mimics to develop robust chemical sensors. One challenging problem in using MIPs for sensor development is the lack of reliable conjugation chemistry that allows MIPs to be fixed on transducer surface. In this work, we study the use of epoxy silane to immobilize MIP nanoparticles on model transducer surfaces without impairing the function of the immobilized nanoparticles. The MIP nanoparticles with a core-shell structure have selective molecular binding sites in the core and multiple amino groups in the shell. The model transducer surface is functionalized with a self-assembled monolayer of epoxy silane, which reacts with the core-shell MIP particles to enable straightforward immobilization. The whole process is characterized by studying the treated surfaces after each preparation step using atomic force microscopy, scanning electron microscopy, fluorescence microscopy, contact angle measurements and X-ray photoelectron spectroscopy. The microscopy results show that the MIP particles are immobilized uniformly on surface. The photoelectron spectroscopy results further confirm the action of each functionalization step. The molecular selectivity of the MIP-functionalized surface is verified by radioligand binding analysis. The particle immobilization approach described here has a general applicability for constructing selective chemical sensors in different formats. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Munc13 homology domain-1 in CAPS/UNC31 mediates SNARE binding required for priming vesicle exocytosis.

PubMed

Khodthong, Chuenchanok; Kabachinski, Greg; James, Declan J; Martin, Thomas F J

2011-08-03

Neuropeptide and peptide hormone secretion from neural and endocrine cells occurs by Ca(2+)-triggered dense-core vesicle exocytosis. The membrane fusion machinery consisting of vesicle and plasma membrane SNARE proteins needs to be assembled for Ca(2+)-triggered vesicle exocytosis. The related Munc13 and CAPS/UNC31 proteins that prime vesicle exocytosis are proposed to promote SNARE complex assembly. CAPS binds SNARE proteins and stimulates SNARE complex formation on liposomes, but the relevance of SNARE binding to CAPS function in cells had not been determined. Here we identify a core SNARE-binding domain in CAPS as corresponding to Munc13 homology domain-1 (MHD1). CAPS lacking a single helix in MHD1 was unable to bind SNARE proteins or to support the Ca(2+)-triggered exocytosis of either docked or newly arrived dense-core vesicles. The results show that MHD1 is a SNARE-binding domain and that SNARE protein binding is essential for CAPS function in dense-core vesicle exocytosis. Copyright © 2011 Elsevier Inc. All rights reserved.

Photoelectron spectroscopy study of the electronic structures at CoPc/Bi(111) interface

NASA Astrophysics Data System (ADS)

Sun, Haoliang; Liang, Zhaofeng; Shen, Kongchao; Hu, Jinbang; Ji, Gengwu; Li, Zheshen; Li, Haiyang; Zhu, Zhiyuan; Li, Jiong; Gao, Xingyu; Han, Huang; Jiang, Zheng; Song, Fei

2017-07-01

Self-assembly of functional molecules on solid substrate has been recognized as an appealing approach for the fabrication of diverse nanostructures for nanoelectronics. Herein, we investigate the growth of cobalt phthalocyanine (CoPc) on a Bi(111) surface with focus on the interface electronic structures utilizing photoelectron spectroscopy. While charge transfer from bismuth substrate to the molecule results in the emergence of an interface component in the Co 3p core level at lower binding energy, core-levels associated to the molecular ligand (C 1s and N 1s) are less influenced by the adsorption. In addition, density functional theory (DFT) calculations also support the empirical inference that the molecule-substrate interaction mainly involves the out-of-plane empty Co 3d orbital and bismuth states. Finally, valence band spectra demonstrate the molecule-substrate interaction is induced by interface charge transfer, agreeing well with core level measurements. Charge transfer is shown to be mainly from the underlying bismuth substrate to the empty states located at the central Co atom in the CoPc molecules. This report may provide a fundamental basis to the on-surface engineering of interfaces for molecular devices and spintronics.

Crystal Structure of the Marburg Virus Nucleoprotein Core Domain Chaperoned by a VP35 Peptide Reveals a Conserved Drug Target for Filovirus.

PubMed

Zhu, Tengfei; Song, Hao; Peng, Ruchao; Shi, Yi; Qi, Jianxun; Gao, George F

2017-09-15

Filovirus nucleoprotein (NP), viral protein 35 (VP35), and polymerase L are essential for viral replication and nucleocapsid formation. Here, we identify a 28-residue peptide (NP binding peptide [NPBP]) from Marburg virus (MARV) VP35 through sequence alignment with previously identified Ebola virus (EBOV) NPBP, which bound to the core region (residues 18 to 344) of the N-terminal portion of MARV NP with high affinity. The crystal structure of the MARV NP core/NPBP complex at a resolution of 2.6 Å revealed that NPBP binds to the C-terminal region of the NP core via electrostatic and nonpolar interactions. Further structural analysis revealed that the MARV and EBOV NP cores hold a conserved binding pocket for NPBP, and this pocket could serve as a promising target for the design of universal drugs against filovirus infection. In addition, cross-binding assays confirmed that the NP core of MARV or EBOV can bind the NPBP from the other virus, although with moderately reduced binding affinities that result from termini that are distinct between the MARV and EBOV NPBPs. IMPORTANCE Historically, Marburg virus (MARV) has caused severe disease with up to 90% lethality. Among the viral proteins produced by MARV, NP and VP35 are both multifunctional proteins that are essential for viral replication. In its relative, Ebola virus (EBOV), an N-terminal peptide from VP35 binds to the NP N-terminal region with high affinity. Whether this is a common mechanism among filoviruses is an unsolved question. Here, we present the crystal structure of a complex that consists of the core domain of MARV NP and the NPBP peptide from VP35. As we compared MARV NPBP with EBOV NPBP, several different features at the termini were identified. Although these differences reduce the affinity of the NP core for NPBPs across genera, a conserved pocket in the C-terminal region of the NP core makes cross-species binding possible. Our results expand our knowledge of filovirus NP-VP35 interactions and provide more details for therapeutic intervention. Copyright © 2017 American Society for Microbiology.

Studies of Positrons Trapped at Quantum-Dot Like Particles Embedded in Metal Surfaces

NASA Astrophysics Data System (ADS)

Fazleev, N. G.; Nadesalingam, M. P.; Weiss, A. H.

2009-03-01

Experimental studies of the positron annihilation induced Auger electron (PAES) spectra from the Fe-Cu alloy surfaces with quantum-dot like Cu nanoparticles embedded in Fe show that the PAES signal from Cu increase rapidly as the concentration of Cu is enhanced by vacuum annealing. These measurements indicate that almost 75% of positrons that annihilate with core electrons due so with Cu even though the surface concentration of Cu as measured by EAES is only 6%. This result suggests that positrons become localized at sites at the surface containing high concentration of Cu atoms before annihilation. These experimental results are investigated theoretically by performing calculations of the "image-potential" positron surface states and annihilation characteristics of the surface trapped positrons with relevant Fe and Cu core-level electrons for the clean Fe(100) and Cu(100) surfaces and for the Fe(100) surface with quantum-dot like Cu nanoparticles embedded in the top atomic layers of the host substrate. Estimates of the positron binding energy and positron annihilation characteristics reveal their strong sensitivity to the nanoparticle coverage. Computed core annihilation probabilities are compared with experimental ones estimated from the measured Auger peak intensities. The observed behavior of the Fe and Cu PAES signal intensities is explained by theoretical calculations as being due to trapping of positrons in the regions of Cu nanoparticles embedded in the top atomic layers of Fe.

Resonances in positron-potassium (e +-K) system with natural and unnatural parities

NASA Astrophysics Data System (ADS)

Umair, M.; Jonsell, S.

2016-01-01

We present an investigation of resonances with natural and unnatural parities in the positron-potassium system using the complex scaling method. A model potential is used to represent the interaction between the core and the valence electron. Explicitly correlated Gaussian wave functions are used to represent the correlation effects between the valence electron, the positron and the K+ core. Resonance energies and widths for two partial waves (S- and P-wave) below the {{K}}(4p,5 s,5p,4 d,4f) excitation thresholds and positronium n = 2 formation threshold are calculated for natural parity. Resonance states for P e below the {{K}}(4d) excitation threshold and positronium n = 2, 3 formation thresholds are calculated for unnatural parity which has not been previously reported. Below both positronium thresholds we have found a dipole series of resonances, with binding energies scaling in good agreement with exceptions from an analytical calculation. The present results are compared with those in the literature.

The protein inhibitor of nNOS (PIN/DLC1/LC8) binding does not inhibit the NADPH-dependent heme reduction in nNOS, a key step in NO synthesis

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

Parhad, Swapnil S.; Jaiswal, Deepa; TIFR Centre for Interdisciplinary Sciences, 21 Brundavan Colony, Narsingi, Hyderabad 500075

The neuronal nitric oxide synthase (nNOS) is an essential enzyme involved in the synthesis of nitric oxide (NO), a potent neurotransmitter. Although previous studies have indicated that the dynein light chain 1 (DLC1) binding to nNOS could inhibit the NO synthesis, the claim is challenged by contradicting reports. Thus, the mechanism of nNOS regulation remained unclear. nNOS has a heme-bearing, Cytochrome P450 core, and the functional enzyme is a dimer. The electron flow from NADPH to Flavin, and finally to the heme of the paired nNOS subunit within a dimer, is facilitated upon calmodulin (CaM) binding. Here, we show thatmore » DLC1 binding to nNOS-CaM complex does not affect the electron transport from the reductase to the oxygenase domain. Therefore, it cannot inhibit the rate of NADPH-dependent heme reduction in nNOS, which results in L-Arginine oxidation. Also, the NO release activity does not decrease with increasing DLC1 concentration in the reaction mix, which further confirmed that DLC1 does not inhibit nNOS activity. These findings suggest that the DLC1 binding may have other implications for the nNOS function in the cell. - Highlights: • The effect of interaction of nNOS with DLC1 has been debatable with contradicting reports in literature. • Purified DLC1 has no effect on electron transport between reductase and oxygenase domain of purified nNOS-CaM. • The NO release activity of nNOS was not altered by DLC1, supporting that DLC1 does not inhibit the enzyme. • These findings suggest that the DLC1 binding may have other implications for the nNOS function in the cell.« less

Virus-producing cells determine the host protein profiles of HIV-1 virion cores

PubMed Central

2012-01-01

Background Upon HIV entry into target cells, viral cores are released and rearranged into reverse transcription complexes (RTCs), which support reverse transcription and also protect and transport viral cDNA to the site of integration. RTCs are composed of viral and cellular proteins that originate from both target and producer cells, the latter entering the target cell within the viral core. However, the proteome of HIV-1 viral cores in the context of the type of producer cells has not yet been characterized. Results We examined the proteomic profiles of the cores purified from HIV-1 NL4-3 virions assembled in Sup-T1 cells (T lymphocytes), PMA and vitamin D3 activated THP1 (model of macrophages, mMΦ), and non-activated THP1 cells (model of monocytes, mMN) and assessed potential involvement of identified proteins in the early stages of infection using gene ontology information and data from genome-wide screens on proteins important for HIV-1 replication. We identified 202 cellular proteins incorporated in the viral cores (T cells: 125, mMΦ: 110, mMN: 90) with the overlap between these sets limited to 42 proteins. The groups of RNA binding (29), DNA binding (17), cytoskeleton (15), cytoskeleton regulation (21), chaperone (18), vesicular trafficking-associated (12) and ubiquitin-proteasome pathway-associated proteins (9) were most numerous. Cores of the virions from SupT1 cells contained twice as many RNA binding proteins as cores of THP1-derived virus, whereas cores of virions from mMΦ and mMN were enriched in components of cytoskeleton and vesicular transport machinery, most probably due to differences in virion assembly pathways between these cells. Spectra of chaperones, cytoskeletal proteins and ubiquitin-proteasome pathway components were similar between viral cores from different cell types, whereas DNA-binding and especially RNA-binding proteins were highly diverse. Western blot analysis showed that within the group of overlapping proteins, the level of incorporation of some RNA binding (RHA and HELIC2) and DNA binding proteins (MCM5 and Ku80) in the viral cores from T cells was higher than in the cores from both mMΦ and mMN and did not correlate with the abundance of these proteins in virus producing cells. Conclusions Profiles of host proteins packaged in the cores of HIV-1 virions depend on the type of virus producing cell. The pool of proteins present in the cores of all virions is likely to contain factors important for viral functions. Incorporation ratio of certain RNA- and DNA-binding proteins suggests their more efficient, non-random packaging into virions in T cells than in mMΦ and mMN. PMID:22889230

First-principle calculation of core level binding energies of Li{sub x}PO{sub y}N{sub z} solid electrolyte

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

Guille, Émilie; Vallverdu, Germain, E-mail: germain.vallverdu@univ-pau.fr; Baraille, Isabelle

2014-12-28

We present first-principle calculations of core-level binding energies for the study of insulating, bulk phase, compounds, based on the Slater-Janak transition state model. Those calculations were performed in order to find a reliable model of the amorphous Li{sub x}PO{sub y}N{sub z} solid electrolyte which is able to reproduce its electronic properties gathered from X-ray photoemission spectroscopy (XPS) experiments. As a starting point, Li{sub 2}PO{sub 2}N models were investigated. These models, proposed by Du et al. on the basis of thermodynamics and vibrational properties, were the first structural models of Li{sub x}PO{sub y}N{sub z}. Thanks to chemical and structural modifications appliedmore » to Li{sub 2}PO{sub 2}N structures, which allow to demonstrate the relevance of our computational approach, we raise an issue concerning the possibility of encountering a non-bridging kind of nitrogen atoms (=N{sup −}) in Li{sub x}PO{sub y}N{sub z} compounds.« less

The cyanobacterial cytochrome b6f subunit PetP adopts an SH3 fold in solution.

PubMed

Veit, Sebastian; Nagadoi, Aritaka; Rögner, Matthias; Rexroth, Sascha; Stoll, Raphael; Ikegami, Takahisa

2016-06-01

PetP is a peripheral subunit of the cytochrome b(6)f complex (b(6)f) present in both, cyanobacteria and red algae. It is bound to the cytoplasmic surface of this membrane protein complex where it greatly affects the efficiency of the linear photosynthetic electron flow although it is not directly involved in the electron transfer reactions. Despite the crystal structures of the b(6)f core complex, structural information for the transient regulatory b(6)f subunits is still missing. Here we present the first structure of PetP at atomic resolution as determined by solution NMR. The protein adopts an SH3 fold, which is a common protein motif in eukaryotes but comparatively rare in prokaryotes. The structure of PetP enabled the identification of the potential interaction site for b(6)f binding by conservation mapping. The interaction surface is mainly formed by two large loop regions and one short 310 helix which also exhibit an increased flexibility as indicated by heteronuclear steady-state {(1)H}-(15)N NOE and random coil index parameters. The properties of this potential b(6)f binding site greatly differ from the canonical peptide binding site which is highly conserved in eukaryotic SH3 domains. Interestingly, three other proteins of the photosynthetic electron transport chain share this SH3 fold with PetP: NdhS of the photosynthetic NADH dehydrogenase-like complex (NDH-1), PsaE of the photosystem 1 and subunit α of the ferredoxin-thioredoxin reductase have, similar to PetP, a great impact on the photosynthetic electron transport. Finally, a model is presented to illustrate how SH3 domains modulate the photosynthetic electron transport processes in cyanobacteria. Copyright © 2016 Elsevier B.V. All rights reserved.

Benchmark CCSD(T) and DFT study of binding energies in Be7 - 12: in search of reliable DFT functional for beryllium clusters

NASA Astrophysics Data System (ADS)

Labanc, Daniel; Šulka, Martin; Pitoňák, Michal; Černušák, Ivan; Urban, Miroslav; Neogrády, Pavel

2018-05-01

We present a computational study of the stability of small homonuclear beryllium clusters Be7 - 12 in singlet electronic states. Our predictions are based on highly correlated CCSD(T) coupled cluster calculations. Basis set convergence towards the complete basis set limit as well as the role of the 1s core electron correlation are carefully examined. Our CCSD(T) data for binding energies of Be7 - 12 clusters serve as a benchmark for performance assessment of several density functional theory (DFT) methods frequently used in beryllium cluster chemistry. We observe that, from Be10 clusters on, the deviation from CCSD(T) benchmarks is stable with respect to size, and fluctuating within 0.02 eV error bar for most examined functionals. This opens up the possibility of scaling the DFT binding energies for large Be clusters using CCSD(T) benchmark values for smaller clusters. We also tried to find analogies between the performance of DFT functionals for Be clusters and for the valence-isoelectronic Mg clusters investigated recently in Truhlar's group. We conclude that it is difficult to find DFT functionals that perform reasonably well for both beryllium and magnesium clusters. Out of 12 functionals examined, only the M06-2X functional gives reasonably accurate and balanced binding energies for both Be and Mg clusters.

Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification.

PubMed

Andreatta, Massimo; Karosiene, Edita; Rasmussen, Michael; Stryhn, Anette; Buus, Søren; Nielsen, Morten

2015-11-01

A key event in the generation of a cellular response against malicious organisms through the endocytic pathway is binding of peptidic antigens by major histocompatibility complex class II (MHC class II) molecules. The bound peptide is then presented on the cell surface where it can be recognized by T helper lymphocytes. NetMHCIIpan is a state-of-the-art method for the quantitative prediction of peptide binding to any human or mouse MHC class II molecule of known sequence. In this paper, we describe an updated version of the method with improved peptide binding register identification. Binding register prediction is concerned with determining the minimal core region of nine residues directly in contact with the MHC binding cleft, a crucial piece of information both for the identification and design of CD4(+) T cell antigens. When applied to a set of 51 crystal structures of peptide-MHC complexes with known binding registers, the new method NetMHCIIpan-3.1 significantly outperformed the earlier 3.0 version. We illustrate the impact of accurate binding core identification for the interpretation of T cell cross-reactivity using tetramer double staining with a CMV epitope and its variants mapped to the epitope binding core. NetMHCIIpan is publicly available at http://www.cbs.dtu.dk/services/NetMHCIIpan-3.1 .

Bidirectional Lipid Droplet Velocities Are Controlled by Differential Binding Strengths of HCV Core DII Protein

PubMed Central

Lyn, Rodney K.; Hope, Graham; Sherratt, Allison R.; McLauchlan, John; Pezacki, John Paul

2013-01-01

Host cell lipid droplets (LD) are essential in the hepatitis C virus (HCV) life cycle and are targeted by the viral capsid core protein. Core-coated LDs accumulate in the perinuclear region and facilitate viral particle assembly, but it is unclear how mobility of these LDs is directed by core. Herein we used two-photon fluorescence, differential interference contrast imaging, and coherent anti-Stokes Raman scattering microscopies, to reveal novel core-mediated changes to LD dynamics. Expression of core protein’s lipid binding domain II (DII-core) induced slower LD speeds, but did not affect directionality of movement on microtubules. Modulating the LD binding strength of DII-core further impacted LD mobility, revealing the temporal effects of LD-bound DII-core. These results for DII-core coated LDs support a model for core-mediated LD localization that involves core slowing down the rate of movement of LDs until localization at the perinuclear region is accomplished where LD movement ceases. The guided localization of LDs by HCV core protein not only is essential to the viral life cycle but also poses an interesting target for the development of antiviral strategies against HCV. PMID:24223760

Studying the Salt Dependence of the Binding of σ70 and σ32 to Core RNA Polymerase Using Luminescence Resonance Energy Transfer

PubMed Central

Glaser, Bryan T.; Bergendahl, Veit; Anthony, Larry C.; Olson, Brian; Burgess, Richard R.

2009-01-01

The study of protein-protein interactions is becoming increasingly important for understanding the regulation of many cellular processes. The ability to quantify the strength with which two binding partners interact is desirable but the accurate determination of equilibrium binding constants is a difficult process. The use of Luminescence Resonance Energy Transfer (LRET) provides a homogeneous binding assay that can be used for the detection of protein-protein interactions. Previously, we developed an LRET assay to screen for small molecule inhibitors of the interaction of σ70 with theβ' coiled-coil fragment (amino acids 100–309). Here we describe an LRET binding assay used to monitor the interaction of E. coli σ70 and σ32 with core RNA polymerase along with the controls to verify the system. This approach generates fluorescently labeled proteins through the random labeling of lysine residues which enables the use of the LRET assay for proteins for which the creation of single cysteine mutants is not feasible. With the LRET binding assay, we are able to show that the interaction of σ70 with core RNAP is much more sensitive to NaCl than to potassium glutamate (KGlu), whereas the σ32 interaction with core RNAP is insensitive to both salts even at concentrations >500 mM. We also find that the interaction of σ32 with core RNAP is stronger than σ70 with core RNAP, under all conditions tested. This work establishes a consistent set of conditions for the comparison of the binding affinities of the E.coli sigma factors with core RNA polymerase. The examination of the importance of salt conditions in the binding of these proteins could have implications in both in vitro assay conditions and in vivo function. PMID:19649256

Studies Of Oxidation And Thermal Reduction Of The Cu(100) Surface Using Positron Annihilation Induced Auger Electron Spectroscopy

NASA Astrophysics Data System (ADS)

Fazleev, N. G.; Nadesalingam, M. P.; Maddox, W.; Weiss, A. H.

2011-06-01

Positron annihilation induced Auger electron spectroscopy (PAES) measurements from the surface of an oxidized Cu(100) single crystal show a large increase in the intensity of the annihilation induced Cu M2,3VV Auger peak as the sample is subjected to a series of isochronal anneals in vacuum up to annealing temperature 300 °C. The PAES intensity then decreases monotonically as the annealing temperature is increased to ˜550 °C. Experimental positron annihilation probabilities with Cu 3p and O 1s core electrons are estimated from the measured intensities of the positron annihilation induced Cu M2,3VV and O KLL Auger transitions. PAES results are analyzed by performing calculations of positron surface states and annihilation probabilities of the surface-trapped positrons with relevant core electrons taking into account the charge redistribution at the surface and various surface structures associated with low and high oxygen coverages. The variations in atomic structure and chemical composition of the topmost layers of the oxidized Cu(100) surface are found to affect localization and spatial extent of the positron surface state wave function. The computed positron binding energy and annihilation characteristics reveal their sensitivity to charge transfer effects, atomic structure and chemical composition of the topmost layers of the oxidized Cu(100) surface. Theoretical positron annihilation probabilities with Cu 3p and O 1s core electrons computed for the oxidized Cu(100) surface are compared with experimental ones. The obtained results provide a demonstration of thermal reduction of the copper oxide surface after annealing at 300 °C followed by re-oxidation of the Cu(100) surface at higher annealing temperatures presumably due to diffusion of subsurface oxygen to the surface.

Studies Of Oxidation And Thermal Reduction Of The Cu(100) Surface Using Positron Annihilation Induced Auger Electron Spectroscopy

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

Fazleev, N. G.; Department of Physics, Kazan State University, Kazan 420008; Nadesalingam, M. P.

2011-06-01

Positron annihilation induced Auger electron spectroscopy (PAES) measurements from the surface of an oxidized Cu(100) single crystal show a large increase in the intensity of the annihilation induced Cu M2,3VV Auger peak as the sample is subjected to a series of isochronal anneals in vacuum up to annealing temperature 300 deg. C. The PAES intensity then decreases monotonically as the annealing temperature is increased to {approx}550 deg. C. Experimental positron annihilation probabilities with Cu 3p and O 1s core electrons are estimated from the measured intensities of the positron annihilation induced Cu M{sub 2,3}VV and O KLL Auger transitions. PAESmore » results are analyzed by performing calculations of positron surface states and annihilation probabilities of the surface-trapped positrons with relevant core electrons taking into account the charge redistribution at the surface and various surface structures associated with low and high oxygen coverages. The variations in atomic structure and chemical composition of the topmost layers of the oxidized Cu(100) surface are found to affect localization and spatial extent of the positron surface state wave function. The computed positron binding energy and annihilation characteristics reveal their sensitivity to charge transfer effects, atomic structure and chemical composition of the topmost layers of the oxidized Cu(100) surface. Theoretical positron annihilation probabilities with Cu 3p and O 1s core electrons computed for the oxidized Cu(100) surface are compared with experimental ones. The obtained results provide a demonstration of thermal reduction of the copper oxide surface after annealing at 300 deg. C followed by re-oxidation of the Cu(100) surface at higher annealing temperatures presumably due to diffusion of subsurface oxygen to the surface.« less

A Novel DNA Binding Mechanism for maf Basic Region-Leucine Zipper Factors Inferred from a MafA-DNA Complex Structure and Binding Specificities

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

Lu, Xun; Guanga, Gerald P; Wan, Cheng

2012-11-13

MafA is a proto-oncoprotein and is critical for insulin gene expression in pancreatic β-cells. Maf proteins belong to the AP1 superfamily of basic region-leucine zipper (bZIP) transcription factors. Residues in the basic helix and an ancillary N-terminal domain, the Extended Homology Region (EHR), endow maf proteins with unique DNA binding properties: binding a 13 bp consensus site consisting of a core AP1 site (TGACTCA) flanked by TGC sequences and binding DNA stably as monomers. To further characterize maf DNA binding, we determined the structure of a MafA–DNA complex. MafA forms base-specific hydrogen bonds with the flanking G –5C –4 andmore » central C 0/G 0 bases, but not with the core-TGA bases. However, in vitro binding studies utilizing a pulse–chase electrophoretic mobility shift assay protocol revealed that mutating either the core-TGA or flanking-TGC bases dramatically increases the binding off rate. Comparing the known maf structures, we propose that DNA binding specificity results from positioning the basic helix through unique phosphate contacts. The EHR does not contact DNA directly but stabilizes DNA binding by contacting the basic helix. Collectively, these results suggest a novel multistep DNA binding process involving a conformational change from contacting the core-TGA to contacting the flanking-TGC bases.« less

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

Dhaka, R. S.; Biswas, C.; Shukla, A. K.

We have studied xenon and argon bubbles formed in the subsurface region of Al(111) by x-ray photoelectron spectroscopy. As a consequence of the nanometer size of the bubbles, the photohole formed by Xe 3d or Ar 2p photoemission is screened by the Al conduction electrons, which substantially lowers the binding energy (BE) as compared to the gas phase. As the bubble size increases, the Al conduction electron screening decreases and the BE increases. On the basis of density functional theory, we show that the change in the bubble pressure with size is not responsible for the BE shift of innermore » shell core levels, such as Xe 3d or Ar 2p. On the other hand, an increase in BE with bubble size for outer shell core levels, such as Ar 3p, could be due to a decrease in both pressure and Al conduction electron screening. The core level line shape also changes with bubble size. For example, the spectra are broadened due to the distribution of the bubble radius around its mean value, and an asymmetry for small bubbles is observed that decreases for larger bubbles. An annealing of Xe and Ar bubbles after an implantation up to 640 K shows that the BE increases with annealing temperature. Since it is well known that bubble size increases with annealing temperature, this further supports our contention of BE shift with bubble size. A defect induced partial disorder of the Al(111) surface by Xe and Ar bombardment is observed by low energy electron diffraction, but this does not affect the Al 2p BE and line shape.« less

Electronic properties and bonding in Zr Hx thin films investigated by valence-band x-ray photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Magnuson, Martin; Schmidt, Susann; Hultman, Lars; Högberg, Hans

2017-11-01

The electronic structure and chemical bonding in reactively magnetron sputtered Zr Hx (x =0.15 , 0.30, 1.16) thin films with oxygen content as low as 0.2 at.% are investigated by 4d valence band, shallow 4p core-level, and 3d core-level x-ray photoelectron spectroscopy. With increasing hydrogen content, we observe significant reduction of the 4d valence states close to the Fermi level as a result of redistribution of intensity toward the H 1s-Zr 4d hybridization region at ˜6 eV below the Fermi level. For low hydrogen content (x =0.15 , 0.30), the films consist of a superposition of hexagonal closest-packed metal (α phase) and understoichiometric δ -Zr Hx (Ca F2 -type structure) phases, while for x =1.16 , the films form single-phase Zr Hx that largely resembles that of stoichiometric δ -Zr H2 phase. We show that the cubic δ -Zr Hx phase is metastable as thin film up to x =1.16 , while for higher H contents the structure is predicted to be tetragonally distorted. For the investigated Zr H1.16 film, we find chemical shifts of 0.68 and 0.51 eV toward higher binding energies for the Zr 4 p3 /2 and 3 d5 /2 peak positions, respectively. Compared to the Zr metal binding energies of 27.26 and 178.87 eV, this signifies a charge transfer from Zr to H atoms. The change in the electronic structure, spectral line shapes, and chemical shifts as a function of hydrogen content is discussed in relation to the charge transfer from Zr to H that affects the conductivity by charge redistribution in the valence band.

Ionic bonding of lanthanides, as influenced by d- and f-atomic orbitals, by core-shells and by relativity.

PubMed

Ji, Wen-Xin; Xu, Wei; Schwarz, W H Eugen; Wang, Shu-Guang

2015-03-15

Lanthanide trihalide molecules LnX3 (X = F, Cl, Br, I) were quantum chemically investigated, in particular detail for Ln = Lu (lutetium). We applied density functional theory (DFT) at the nonrelativistic and scalar and SO-coupled relativistic levels, and also the ab initio coupled cluster approach. The chemically active electron shells of the lanthanide atoms comprise the 5d and 6s (and 6p) valence atomic orbitals (AO) and also the filled inner 4f semivalence and outer 5p semicore shells. Four different frozen-core approximations for Lu were compared: the (1s(2) -4d(10) ) [Pd] medium core, the [Pd+5s(2) 5p(6) = Xe] and [Pd+4f(14) ] large cores, and the [Pd+4f(14) +5s(2) 5p(6) ] very large core. The errors of LuX bonding are more serious on freezing the 5p(6) shell than the 4f(14) shell, more serious upon core-freezing than on the effective-core-potential approximation. The LnX distances correlate linearly with the AO radii of the ionic outer shells, Ln(3+) -5p(6) and X(-) -np(6) , characteristic for dominantly ionic Ln(3+) -X(-) binding. The heavier halogen atoms also bind covalently with the Ln-5d shell. Scalar relativistic effects contract and destabilize the LuX bonds, spin orbit coupling hardly affects the geometries but the bond energies, owing to SO effects in the free atoms. The relativistic changes of bond energy BE, bond length Re , bond force k, and bond stretching frequency vs do not follow the simple rules of Badger and Gordy (Re ∼BE∼k∼vs ). The so-called degeneracy-driven covalence, meaning strong mixing of accidentally near-degenerate, nearly nonoverlapping AOs without BE contribution is critically discussed. © 2015 Wiley Periodicals, Inc.

Spin-labeled derivatives of cardiotonic steroids as tools for characterization of the extracellular entrance to the binding site on Na+ ,K+ -ATPase.

PubMed

Guo, Jin-Hua; Jiang, Ren-Wang; Andersen, Jacob Lauwring; Esmann, Mikael; Fedosova, Natalya U

2018-04-24

The information obtained from crystallized complexes of the Na + ,K + -ATPase with cardiotonic steroids (CTS) is not sufficient to explain differences in the inhibitory properties of CTS such as stereoselectivity of CTS binding or effect of glycosylation on the preference to enzyme isoforms. The uncertainty is related to the spatial organization of the hydrophilic cavity at the entrance of the CTS-binding site. Therefore, there is a need to supplement the crystallographic description with data obtained in aqueous solution, where molecules have significant degree of flexibility. This work addresses the applicability of the electron paramagnetic resonance (EPR) method for the purpose. We have designed and synthesized spin-labeled compounds based on the cinobufagin steroid core. The length of the spacer arms between the steroid core and the nitroxide group determines the position of the reporting group (N-O) confined to the binding site. High affinity to Na + ,K + -ATPase is inferred from their ability to inhibit enzymatic activity. The differences between the EPR spectra in the absence and presence of high ouabain concentrations identify the signature peaks originating from the fraction of the spin labels bound within the ouabain site. The degree of perturbations of the EPR spectra depends on the length of the spacer arm. Docking of the compounds into the CTS site suggests which elements of the protein structure might be responsible for interference with the spin label (e.g., steric clashes or immobilization). Thus, the method is suitable for gathering information on the cavity leading to the CTS-binding site in Na + ,K + -ATPase in all conformations with high affinity to CTS. © 2018 Federation of European Biochemical Societies.

On the validity of the basis set superposition error and complete basis set limit extrapolations for the binding energy of the formic acid dimer

NASA Astrophysics Data System (ADS)

Miliordos, Evangelos; Xantheas, Sotiris S.

2015-03-01

We report the variation of the binding energy of the Formic Acid Dimer with the size of the basis set at the Coupled Cluster with iterative Singles, Doubles and perturbatively connected Triple replacements [CCSD(T)] level of theory, estimate the Complete Basis Set (CBS) limit, and examine the validity of the Basis Set Superposition Error (BSSE)-correction for this quantity that was previously challenged by Kalescky, Kraka, and Cremer (KKC) [J. Chem. Phys. 140, 084315 (2014)]. Our results indicate that the BSSE correction, including terms that account for the substantial geometry change of the monomers due to the formation of two strong hydrogen bonds in the dimer, is indeed valid for obtaining accurate estimates for the binding energy of this system as it exhibits the expected decrease with increasing basis set size. We attribute the discrepancy between our current results and those of KKC to their use of a valence basis set in conjunction with the correlation of all electrons (i.e., including the 1s of C and O). We further show that the use of a core-valence set in conjunction with all electron correlation converges faster to the CBS limit as the BSSE correction is less than half than the valence electron/valence basis set case. The uncorrected and BSSE-corrected binding energies were found to produce the same (within 0.1 kcal/mol) CBS limits. We obtain CCSD(T)/CBS best estimates for De = - 16.1 ± 0.1 kcal/mol and for D0 = - 14.3 ± 0.1 kcal/mol, the later in excellent agreement with the experimental value of -14.22 ± 0.12 kcal/mol.

Suppression of grp78 core promoter element-mediated stress induction by the dbpA and dbpB (YB-1) cold shock domain proteins.

PubMed Central

Li, W W; Hsiung, Y; Wong, V; Galvin, K; Zhou, Y; Shi, Y; Lee, A S

1997-01-01

The highly conserved grp78 core promoter element plays an important role in the induction of grp78 under diverse stress signals. Previous studies have established a functional region in the 3' half of the core (stress-inducible change region [SICR]) which exhibits stress-inducible changes in stressed nuclei. The human transcription factor YY1 is shown to bind the SICR and transactivate the core element under stress conditions. Here we report that expression library screening with the core element has identified two new core binding proteins, YB-1 and dbpA. Both proteins belong to the Y-box family of proteins characterized by an evolutionarily conserved DNA binding motif, the cold shock domain (CSD). In contrast to YY1, which binds only double-stranded SICR, the Y-box/CSD proteins much prefer the lower strand of the SICR. The Y-box proteins can repress the inducibility of the grp78 core element mediated by treatment of cells with A23187, thapsigargin, and tunicamycin. In gel shift assays, YY1 binding to the core element is inhibited by either YB-1 or dbpA. A yeast interaction trap screen using LexA-YY1 as a bait and a HeLa cell cDNA-acid patch fusion library identified YB-1 as a YY1-interacting protein. In cotransfection experiments, the Y-box proteins antagonize the YY1-mediated enhancement of transcription directed by the grp78 core in stressed cells. Thus, the CSD proteins may be part of the stress signal transduction mechanism in the mammalian system. PMID:8972186

Importance of conduction electron correlation in a Kondo lattice, Ce₂CoSi₃.

PubMed

Patil, Swapnil; Pandey, Sudhir K; Medicherla, V R R; Singh, R S; Bindu, R; Sampathkumaran, E V; Maiti, Kalobaran

2010-06-30

Kondo systems are usually described by the interaction of the correlation induced local moments with the highly itinerant conduction electrons. Here, we study the role of electron correlations among conduction electrons in the electronic structure of a Kondo lattice compound, Ce₂CoSi₃, using high resolution photoemission spectroscopy and ab initio band structure calculations, where Co 3d electrons contribute in the conduction band. High energy resolution employed in the measurements helped to reveal the signatures of Ce 4f states derived Kondo resonance features at the Fermi level and the dominance of Co 3d contributions at higher binding energies in the conduction band. The lineshape of the experimental Co 3d band is found to be significantly different from that obtained from the band structure calculations within the local density approximations, LDA. Consideration of electron-electron Coulomb repulsion, U, among Co 3d electrons within the LDA + U method leads to a better representation of experimental results. The signature of an electron correlation induced satellite feature is also observed in the Co 2p core level spectrum. These results clearly demonstrate the importance of the electron correlation among conduction electrons in deriving the microscopic description of such Kondo systems.

Identification and Targeting of an Interaction between a Tyrosine Motif within Hepatitis C Virus Core Protein and AP2M1 Essential for Viral Assembly

PubMed Central

Ziv-Av, Amotz; Gerber, Doron; Jacob, Yves; Einav, Shirit

2012-01-01

Novel therapies are urgently needed against hepatitis C virus infection (HCV), a major global health problem. The current model of infectious virus production suggests that HCV virions are assembled on or near the surface of lipid droplets, acquire their envelope at the ER, and egress through the secretory pathway. The mechanisms of HCV assembly and particularly the role of viral-host protein-protein interactions in mediating this process are, however, poorly understood. We identified a conserved heretofore unrecognized YXXΦ motif (Φ is a bulky hydrophobic residue) within the core protein. This motif is homologous to sorting signals within host cargo proteins known to mediate binding of AP2M1, the μ subunit of clathrin adaptor protein complex 2 (AP-2), and intracellular trafficking. Using microfluidics affinity analysis, protein-fragment complementation assays, and co-immunoprecipitations in infected cells, we show that this motif mediates core binding to AP2M1. YXXΦ mutations, silencing AP2M1 expression or overexpressing a dominant negative AP2M1 mutant had no effect on HCV RNA replication, however, they dramatically inhibited intra- and extracellular infectivity, consistent with a defect in viral assembly. Quantitative confocal immunofluorescence analysis revealed that core's YXXΦ motif mediates recruitment of AP2M1 to lipid droplets and that the observed defect in HCV assembly following disruption of core-AP2M1 binding correlates with accumulation of core on lipid droplets, reduced core colocalization with E2 and reduced core localization to trans-Golgi network (TGN), the presumed site of viral particles maturation. Furthermore, AAK1 and GAK, serine/threonine kinases known to stimulate binding of AP2M1 to host cargo proteins, regulate core-AP2M1 binding and are essential for HCV assembly. Last, approved anti-cancer drugs that inhibit AAK1 or GAK not only disrupt core-AP2M1 binding, but also significantly inhibit HCV assembly and infectious virus production. These results validate viral-host interactions essential for HCV assembly and yield compounds for pharmaceutical development. PMID:22916011

Unexpected DNA affinity and sequence selectivity through core rigidity in guanidinium-based minor groove binders.

PubMed

Nagle, Padraic S; McKeever, Caitriona; Rodriguez, Fernando; Nguyen, Binh; Wilson, W David; Rozas, Isabel

2014-09-25

In this paper we report the design and biophysical evaluation of novel rigid-core symmetric and asymmetric dicationic DNA binders containing 9H-fluorene and 9,10-dihydroanthracene cores as well as the synthesis of one of these fluorene derivatives. First, the affinity toward particular DNA sequences of these compounds and flexible core derivatives was evaluated by means of surface plasmon resonance and thermal denaturation experiments finding that the position of the cations significantly influence the binding strength. Then their affinity and mode of binding were further studied by performing circular dichroism and UV studies and the results obtained were rationalized by means of DFT calculations. We found that the fluorene derivatives prepared have the ability to bind to the minor groove of certain DNA sequences and intercalate to others, whereas the dihydroanthracene compounds bind via intercalation to all the DNA sequences studied here.

In silico evolution of the Drosophila gap gene regulatory sequence under elevated mutational pressure.

PubMed

Chertkova, Aleksandra A; Schiffman, Joshua S; Nuzhdin, Sergey V; Kozlov, Konstantin N; Samsonova, Maria G; Gursky, Vitaly V

2017-02-07

Cis-regulatory sequences are often composed of many low-affinity transcription factor binding sites (TFBSs). Determining the evolutionary and functional importance of regulatory sequence composition is impeded without a detailed knowledge of the genotype-phenotype map. We simulate the evolution of regulatory sequences involved in Drosophila melanogaster embryo segmentation during early development. Natural selection evaluates gene expression dynamics produced by a computational model of the developmental network. We observe a dramatic decrease in the total number of transcription factor binding sites through the course of evolution. Despite a decrease in average sequence binding energies through time, the regulatory sequences tend towards organisations containing increased high affinity transcription factor binding sites. Additionally, the binding energies of separate sequence segments demonstrate ubiquitous mutual correlations through time. Fewer than 10% of initial TFBSs are maintained throughout the entire simulation, deemed 'core' sites. These sites have increased functional importance as assessed under wild-type conditions and their binding energy distributions are highly conserved. Furthermore, TFBSs within close proximity of core sites exhibit increased longevity, reflecting functional regulatory interactions with core sites. In response to elevated mutational pressure, evolution tends to sample regulatory sequence organisations with fewer, albeit on average, stronger functional transcription factor binding sites. These organisations are also shaped by the regulatory interactions among core binding sites with sites in their local vicinity.

Nuclear factor Y regulates ancient budgerigar hepadnavirus core promoter activity

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

Shen, Zhongliang; Liu, Yanfeng; Luo, Mengjun

Endogenous viral elements (EVE) in animal genomes are the fossil records of ancient viruses and provide invaluable information on the origin and evolution of extant viruses. Extant hepadnaviruses include avihepadnaviruses of birds and orthohepadnaviruses of mammals. The core promoter (Cp) of hepadnaviruses is vital for viral gene expression and replication. We previously identified in the budgerigar genome two EVEs that contain the full-length genome of an ancient budgerigar hepadnavirus (eBHBV1 and eBHBV2). Here, we found eBHBV1 Cp and eBHBV2 Cp were active in several human and chicken cell lines. A region from nt −85 to −11 in eBHBV1 Cp was critical formore » the promoter activity. Bioinformatic analysis revealed a putative binding site of nuclear factor Y (NF-Y), a ubiquitous transcription factor, at nt −64 to −50 in eBHBV1 Cp. The NF-Y core binding site (ATTGG, nt −58 to −54) was essential for eBHBV1 Cp activity. The same results were obtained with eBHBV2 Cp and duck hepatitis B virus Cp. The subunit A of NF-Y (NF-YA) was recruited via the NF-Y core binding site to eBHBV1 Cp and upregulated the promoter activity. Finally, the NF-Y core binding site is conserved in the Cps of all the extant avihepadnaviruses but not of orthohepadnaviruses. Interestingly, a putative and functionally important NF-Y core binding site is located at nt −21 to −17 in the Cp of human hepatitis B virus. In conclusion, our findings have pinpointed an evolutionary conserved and functionally critical NF-Y binding element in the Cps of avihepadnaviruses. - Highlights: • Endogenous budgerigar hepadnavirus (eBHBV) core promoters (Cps) are active in cells. • NF-Y binding site exists in the Cps of eBHBVs and all the extant avihepadnaviruses. • NF-Y binding and mediated upregulation is critical for eBHBV Cp activity.« less

Analysis of the NuRD subunits reveals a histone deacetylase core complex and a connection with DNA methylation

PubMed Central

Zhang, Yi; Ng, Huck-Hui; Erdjument-Bromage, Hediye; Tempst, Paul; Bird, Adrian; Reinberg, Danny

1999-01-01

ATP-dependent nucleosome remodeling and core histone acetylation and deacetylation represent mechanisms to alter nucleosome structure. NuRD is a multisubunit complex containing nucleosome remodeling and histone deacetylase activities. The histone deacetylases HDAC1 and HDAC2 and the histone binding proteins RbAp48 and RbAp46 form a core complex shared between NuRD and Sin3-histone deacetylase complexes. The histone deacetylase activity of the core complex is severely compromised. A novel polypeptide highly related to the metastasis-associated protein 1, MTA2, and the methyl-CpG-binding domain-containing protein, MBD3, were found to be subunits of the NuRD complex. MTA2 modulates the enzymatic activity of the histone deacetylase core complex. MBD3 mediates the association of MTA2 with the core histone deacetylase complex. MBD3 does not directly bind methylated DNA but is highly related to MBD2, a polypeptide that binds to methylated DNA and has been reported to possess demethylase activity. MBD2 interacts with the NuRD complex and directs the complex to methylated DNA. NuRD may provide a means of gene silencing by DNA methylation. PMID:10444591

Electronic structure of layered ferroelectric high-k titanate La2Ti2O7

NASA Astrophysics Data System (ADS)

Atuchin, V. V.; Gavrilova, T. A.; Grivel, J.-C.; Kesler, V. G.

2009-02-01

The electronic structure of binary titanate La2Ti2O7 has been studied by x-ray photoelectron spectroscopy. Spectral features of valence band and all constituent element core levels have been considered. The Auger parameters of titanium and oxygen in La2Ti2O7 are determined as αTi = 872.4 and αO = 1042.3 eV. Chemical bonding effects have been discussed with binding energy (BE) differences ΔTi = (BE O 1s - BE Ti 2p3/2) = 71.6 eV and ΔLa = (BE La 3d5/2 - BE O 1s) = 304.7 eV as key parameters in comparison with those in several titanium- and lanthanum-bearing oxides.

Electronic structure of layered titanate Nd 2Ti 2O 7

NASA Astrophysics Data System (ADS)

Atuchin, V. V.; Gavrilova, T. A.; Grivel, J.-C.; Kesler, V. G.

2008-10-01

The electronic structure of the binary titanate Nd 2Ti 2O 7 has been studied by X-ray photoelectron spectroscopy (XPS). Spectral features of the valence band and all constituent element core levels have been considered. The Auger parameters of titanium and oxygen in Nd 2Ti 2O 7 are determined as αTi = 873.5 and αO = 1042.2 eV. Chemical bonding effects have been discussed with the binding energies differences ΔTi = (BE O 1s - BE Ti 2p 3/2) = 71.5 eV and ΔNd = (BE Nd 3d 5/2 - BE O 1s) = 452.5 eV as key parameters in comparison with those in other titanium- and neodymium-bearing oxides.

Why three-body physics does not solve the proton-radius puzzle.

PubMed

Karr, Jean-Philippe; Hilico, Laurent

2012-09-07

The possible involvement of weakly bound three-body systems in the muonic hydrogen spectroscopy experiment, which could resolve the current discrepancy between determinations of the proton radius, is investigated. Using variational calculations with complex coordinate rotation, we show that in the pμe ion, which was recently proposed as a possible candidate, the pμ core fails to bind the outer electron tightly enough to explain the discrepancy. It is also shown that the ppμ molecular ion cannot play any role in the observed line.

Enhanced nitrogen diffusion induced by atomic attrition

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

Ochoa, E.A.; Figueroa, C.A.; Czerwiec, T.

2006-06-19

The nitrogen diffusion in steel is enhanced by previous atomic attrition with low energy xenon ions. The noble gas bombardment generates nanoscale texture surfaces and stress in the material. The atomic attrition increases nitrogen diffusion at lower temperatures than the ones normally used in standard processes. The stress causes binding energy shifts of the Xe 3d{sub 5/2} electron core level. The heavy ion bombardment control of the texture and stress of the material surfaces may be applied to several plasma processes where diffusing species are involved.

Facile transformation of FeO/Fe3O4 core-shell nanocubes to Fe3O4 via magnetic stimulation

NASA Astrophysics Data System (ADS)

Lak, Aidin; Niculaes, Dina; Anyfantis, George C.; Bertoni, Giovanni; Barthel, Markus J.; Marras, Sergio; Cassani, Marco; Nitti, Simone; Athanassiou, Athanassia; Giannini, Cinzia; Pellegrino, Teresa

2016-09-01

Here, we propose the use of magnetic hyperthermia as a means to trigger the oxidation of Fe1-xO/Fe3-δO4 core-shell nanocubes to Fe3-δO4 phase. As a first relevant consequence, the specific absorption rate (SAR) of the initial core-shell nanocubes doubles after exposure to 25 cycles of alternating magnetic field stimulation. The improved SAR value was attributed to a gradual transformation of the Fe1-xO core to Fe3-δO4, as evidenced by structural analysis including high resolution electron microscopy and Rietveld analysis of X-ray diffraction patterns. The magnetically oxidized nanocubes, having large and coherent Fe3-δO4 domains, reveal high saturation magnetization and behave superparamagnetically at room temperature. In comparison, the treatment of the same starting core-shell nanocubes by commonly used thermal annealing process renders a transformation to γ-Fe2O3. In contrast to other thermal annealing processes, the method here presented has the advantage of promoting the oxidation at a macroscopic temperature below 37 °C. Using this soft oxidation process, we demonstrate that biotin-functionalized core-shell nanocubes can undergo a mild self-oxidation transformation without losing their functional molecular binding activity.

Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids

PubMed Central

Sales, Mark; Plecs, Joseph J.; Holton, James M.; Alber, Tom

2007-01-01

The previous design of an unprecedented family of two-, three-, and four-helical, right-handed coiled coils utilized nonbiological amino acids to efficiently pack spaces in the oligomer cores. Here we show that a stable, right-handed parallel tetrameric coiled coil, called RH4B, can be designed entirely using biological amino acids. The X-ray crystal structure of RH4B was determined to 1.1 Å resolution using a designed metal binding site to coordinate a single Yb2+ ion per 33-amino acid polypeptide chain. The resulting experimental phases were particularly accurate, and the experimental electron density map provided an especially clear, unbiased view of the molecule. The RH4B structure closely matched the design, with equivalent core rotamers and an overall root-mean-square deviation for the N-terminal repeat of the tetramer of 0.24 Å. The clarity and resolution of the electron density map, however, revealed alternate rotamers and structural differences between the three sequence repeats in the molecule. These results suggest that the RH4B structure populates an unanticipated variety of structures. PMID:17766380

Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids.

PubMed

Sales, Mark; Plecs, Joseph J; Holton, James M; Alber, Tom

2007-10-01

The previous design of an unprecedented family of two-, three-, and four-helical, right-handed coiled coils utilized nonbiological amino acids to efficiently pack spaces in the oligomer cores. Here we show that a stable, right-handed parallel tetrameric coiled coil, called RH4B, can be designed entirely using biological amino acids. The X-ray crystal structure of RH4B was determined to 1.1 Angstrom resolution using a designed metal binding site to coordinate a single Yb(2+) ion per 33-amino acid polypeptide chain. The resulting experimental phases were particularly accurate, and the experimental electron density map provided an especially clear, unbiased view of the molecule. The RH4B structure closely matched the design, with equivalent core rotamers and an overall root-mean-square deviation for the N-terminal repeat of the tetramer of 0.24 Angstrom. The clarity and resolution of the electron density map, however, revealed alternate rotamers and structural differences between the three sequence repeats in the molecule. These results suggest that the RH4B structure populates an unanticipated variety of structures.

Protein Association and Dissociation Regulated by Ferric Ion

PubMed Central

Li, Chaorui; Fu, Xiaoping; Qi, Xin; Hu, Xiaosong; Chasteen, N. Dennis; Zhao, Guanghua

2009-01-01

Iron stored in phytoferritin plays an important role in the germination and early growth of seedlings. The protein is located in the amyloplast where it stores large amounts of iron as a hydrated ferric oxide mineral core within its shell-like structure. The present work was undertaken to study alternate mechanisms of core formation in pea seed ferritin (PSF). The data reveal a new mechanism for mineral core formation in PSF involving the binding and oxidation of iron at the extension peptide (EP) located on the outer surface of the protein shell. This binding induces aggregation of the protein into large assemblies of ∼400 monomers. The bound iron is gradually translocated to the mineral core during which time the protein dissociates back into its monomeric state. Either the oxidative addition of Fe2+ to the apoprotein to form Fe3+ or the direct addition of Fe3+ to apoPSF causes protein aggregation once the binding capacity of the 24 ferroxidase centers (48 Fe3+/shell) is exceeded. When the EP is enzymatically deleted from PSF, aggregation is not observed, and the rate of iron oxidation is significantly reduced, demonstrating that the EP is a critical structural component for iron binding, oxidation, and protein aggregation. These data point to a functional role for the extension peptide as an iron binding and ferroxidase center that contributes to mineralization of the iron core. As the iron core grows larger, the new pathway becomes less important, and Fe2+ oxidation and deposition occurs directly on the surface of the iron core. PMID:19398557

Determination of Histamine in Silages Using Nanomaghemite Core (γ-Fe2O3)-Titanium Dioxide Shell Nanoparticles Off-Line Coupled with Ion Exchange Chromatography

PubMed Central

Cernei, Natalia; Lackova, Zuzana; Guran, Roman; Hynek, David; Skladanka, Jiri; Horky, Pavel; Zitka, Ondrej; Adam, Vojtech

2016-01-01

The presence of biogenic amines is a hallmark of degraded food and its products. Herein, we focused on the utilization of magnetic nanoparticles off-line coupled with ion exchange chromatography with post-column ninhydrin derivatization and Vis detection for histamine (Him) separation and detection. Primarily, we described the synthesis of magnetic nanoparticles with nanomaghemite core (γ-Fe2O3) functionalized with titanium dioxide and, then, applied these particles to specific isolation of Him. To obtain further insight into interactions between paramagnetic particles’ (PMP) surface and Him, a scanning electron microscope was employed. It was shown that binding of histamine causes an increase of relative current response of deprotonated PMPs, which confirmed formation of Him-PMPs clusters. The recovery of the isolation showed that titanium dioxide-based particles were able to bind and preconcentrate Him with recovery exceeding 90%. Finally, we successfully carried out the analyses of real samples obtained from silage. We can conclude that our modified particles are suitable for Him isolation, and thus may serve as the first isolation step of Him from biological samples, as it is demonstrated on alfalfa seed variety Tereza silage. PMID:27626434

Neutrino Emission from Supernovae

NASA Astrophysics Data System (ADS)

Janka, Hans-Thomas

Supernovae are the most powerful cosmic sources of MeV neutrinos. These elementary particles play a crucial role when the evolution of a massive star is terminated by the collapse of its core to a neutron star or a black hole and the star explodes as supernova. The release of electron neutrinos, which are abundantly produced by electron captures, accelerates the catastrophic infall and causes a gradual neutronization of the stellar plasma by converting protons to neutrons as dominant constituents of neutron star matter. The emission of neutrinos and antineutrinos of all flavors carries away the gravitational binding energy of the compact remnant and drives its evolution from the hot initial to the cold final state. The absorption of electron neutrinos and antineutrinos in the surroundings of the newly formed neutron star can power the supernova explosion and determines the conditions in the innermost supernova ejecta, making them an interesting site for the nucleosynthesis of iron-group elements and trans-iron nuclei.

Analysis of the Structures and Properties of (GaSb)n (n = 4-9) Clusters through Density Functional Theory.

PubMed

Lu, Qi Liang; Luo, Qi Quan; Huang, Shou Guo; Li, Yi De; Wan, Jian Guo

2016-07-07

An optimization strategy combining global semiempirical quantum mechanical search with all-electron density functional theory was adopted to determine the lowest energy structure of (GaSb)n clusters up to n = 9. The growth pattern of the clusters differed from those of previously reported group III-V binary clusters. A cagelike configuration was found for cluster sizes n ≤ 7. The structure of (GaSb)6 deviated from that of other III-V clusters. Competition existed between core-shell and hollow cage structures of (GaSb)7. Novel noncagelike structures were energetically preferred over the cages for the (GaSb)8 and (GaSb)9 clusters. Electronic properties, such as vertical ionization potential, adiabatic electron affinities, HOMO-LUMO gaps, and average on-site charges on Ga or Sb atoms, as well as binding energies, were computed.

BI-2 destabilizes HIV-1 cores during infection and Prevents Binding of CPSF6 to the HIV-1 Capsid.

PubMed

Fricke, Thomas; Buffone, Cindy; Opp, Silvana; Valle-Casuso, Jose; Diaz-Griffero, Felipe

2014-12-11

The recently discovered small-molecule BI-2 potently blocks HIV-1 infection. BI-2 binds to the N-terminal domain of HIV-1 capsid. BI-2 utilizes the same capsid pocket used by the small molecule PF74. Although both drugs bind to the same pocket, it has been proposed that BI-2 uses a different mechanism to block HIV-1 infection when compared to PF74. This work demonstrates that BI-2 destabilizes the HIV-1 core during infection, and prevents the binding of the cellular factor CPSF6 to the HIV-1 core. Overall this short-form paper suggests that BI-2 is using a similar mechanism to the one used by PF74 to block HIV-1 infection.

The anti-sigma factor RsrA responds to oxidative stress by reburying its hydrophobic core

PubMed Central

Rajasekar, Karthik V.; Zdanowski, Konrad; Yan, Jun; Hopper, Jonathan T. S.; Francis, Marie-Louise R.; Seepersad, Colin; Sharp, Connor; Pecqueur, Ludovic; Werner, Jörn M.; Robinson, Carol V.; Mohammed, Shabaz; Potts, Jennifer R.; Kleanthous, Colin

2016-01-01

Redox-regulated effector systems that counteract oxidative stress are essential for all forms of life. Here we uncover a new paradigm for sensing oxidative stress centred on the hydrophobic core of a sensor protein. RsrA is an archetypal zinc-binding anti-sigma factor that responds to disulfide stress in the cytoplasm of Actinobacteria. We show that RsrA utilizes its hydrophobic core to bind the sigma factor σR preventing its association with RNA polymerase, and that zinc plays a central role in maintaining this high-affinity complex. Oxidation of RsrA is limited by the rate of zinc release, which weakens the RsrA–σR complex by accelerating its dissociation. The subsequent trigger disulfide, formed between specific combinations of RsrA's three zinc-binding cysteines, precipitates structural collapse to a compact state where all σR-binding residues are sequestered back into its hydrophobic core, releasing σR to activate transcription of anti-oxidant genes. PMID:27432510

Quantum confinement-induced tunable exciton states in graphene oxide.

PubMed

Lee, Dongwook; Seo, Jiwon; Zhu, Xi; Lee, Jiyoul; Shin, Hyeon-Jin; Cole, Jacqueline M; Shin, Taeho; Lee, Jaichan; Lee, Hangil; Su, Haibin

2013-01-01

Graphene oxide has recently been considered to be a potential replacement for cadmium-based quantum dots due to its expected high fluorescence. Although previously reported, the origin of the luminescence in graphene oxide is still controversial. Here, we report the presence of core/valence excitons in graphene-based materials, a basic ingredient for optical devices, induced by quantum confinement. Electron confinement in the unreacted graphitic regions of graphene oxide was probed by high resolution X-ray absorption near edge structure spectroscopy and first-principles calculations. Using experiments and simulations, we were able to tune the core/valence exciton energy by manipulating the size of graphitic regions through the degree of oxidation. The binding energy of an exciton in highly oxidized graphene oxide is similar to that in organic electroluminescent materials. These results open the possibility of graphene oxide-based optoelectronic device technology.

Estimation of Hammett sigma constants of substituted benzenes through accurate density-functional calculation of core-electron binding energy shifts

NASA Astrophysics Data System (ADS)

Takahata, Yuji; Chong, Delano P.

For substituted benzenes such as (p-F-C6H4-Z), Linderberg et al. 1 demonstrated the validity of an equation similar to: ΔCEBE ≈ κσ, where ΔCEBE is the difference in core-electron binding energies (CEBEs) of the fluorinated carbon in p-F-C6H4-Z and that in FC6H5, the parameter κ is a function of the type of reaction, and σ is the Hammett substituent (σ) constant. In this work, CEBEs of ring carbon atoms for a series of para disubstituted molecules p-F-C6H4-Z were first calculated using Density Functional Theory (DFT) with the scheme ΔEKS (PW86-PW91)/TZP+Crel//HF/6-31G*. An average absolute deviation of 0.13 eV from experiment was obtained for the CEBEs. Then we performed a linear regression analysis in the form of Y = A+B*X for a plot of Hammett σp constants against calculated shifts ΔCEBEs (in eV) for the fluorinated carbon. The results were: A = -0.08 and B = 1.01, with correlation coefficient R = 0.973, standard deviation = 0.12, and P < 0.0001. The intercept A of the fitted line, close to zero, shows that the Hammett σp constant is proportional to the calculated ΔCEBEs. On the other hand, the slope B of the straight line gives an estimate of the parameter κ. Similar statistical correlations were obtained for the carbon atoms ortho and meta to the substituent Z.

Interaction of ions, atoms, and small molecules with quantized vortex lines in superfluid (4)He.

PubMed

Mateo, David; Eloranta, Jussi; Williams, Gary A

2015-02-14

The interaction of a number of impurities (H2, Ag, Cu, Ag2, Cu2, Li, He3 (+), He(*) ((3)S), He2 (∗) ((3)Σu), and e(-)) with quantized rectilinear vortex lines in superfluid (4)He is calculated by using the Orsay-Trento density functional theory (DFT) method at 0 K. The Donnelly-Parks (DP) potential function binding ions to the vortex is combined with DFT data, yielding the impurity radius as well as the vortex line core parameter. The vortex core parameter at 0 K (0.74 Å) obtained either directly from the vortex line geometry or through the DP potential fitting is smaller than previously suggested but is compatible with the value obtained from re-analysis of the Rayfield-Reif experiment. All of the impurities have significantly higher binding energies to vortex lines below 1 K than the available thermal energy, where the thermally assisted escape process becomes exponentially negligible. Even at higher temperatures 1.5-2.0 K, the trapping times for larger metal clusters are sufficiently long that the previously observed metal nanowire assembly in superfluid helium can take place at vortex lines. The binding energy of the electron bubble is predicted to decrease as a function of both temperature and pressure, which allows adjusting the trap depth for either permanent trapping or to allow thermally assisted escape. Finally, a new scheme for determining the trapping of impurities on vortex lines by optical absorption spectroscopy is outlined and demonstrated for He(*).

Interaction of ions, atoms, and small molecules with quantized vortex lines in superfluid 4He

NASA Astrophysics Data System (ADS)

Mateo, David; Eloranta, Jussi; Williams, Gary A.

2015-02-01

The interaction of a number of impurities (H2, Ag, Cu, Ag2, Cu2, Li, He3 + , He* (3S), He2∗ (3Σu), and e-) with quantized rectilinear vortex lines in superfluid 4He is calculated by using the Orsay-Trento density functional theory (DFT) method at 0 K. The Donnelly-Parks (DP) potential function binding ions to the vortex is combined with DFT data, yielding the impurity radius as well as the vortex line core parameter. The vortex core parameter at 0 K (0.74 Å) obtained either directly from the vortex line geometry or through the DP potential fitting is smaller than previously suggested but is compatible with the value obtained from re-analysis of the Rayfield-Reif experiment. All of the impurities have significantly higher binding energies to vortex lines below 1 K than the available thermal energy, where the thermally assisted escape process becomes exponentially negligible. Even at higher temperatures 1.5-2.0 K, the trapping times for larger metal clusters are sufficiently long that the previously observed metal nanowire assembly in superfluid helium can take place at vortex lines. The binding energy of the electron bubble is predicted to decrease as a function of both temperature and pressure, which allows adjusting the trap depth for either permanent trapping or to allow thermally assisted escape. Finally, a new scheme for determining the trapping of impurities on vortex lines by optical absorption spectroscopy is outlined and demonstrated for He*.

A nanocomposite of Au-AgI core/shell dimer as a dual-modality contrast agent for x-ray computed tomography and photoacoustic imaging

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

Orza, Anamaria; Wu, Hui; Li, Yuancheng

Purpose: To develop a core/shell nanodimer of gold (core) and silver iodine (shell) as a dual-modal contrast-enhancing agent for biomarker targeted x-ray computed tomography (CT) and photoacoustic imaging (PAI) applications. Methods: The gold and silver iodine core/shell nanodimer (Au/AgICSD) was prepared by fusing together components of gold, silver, and iodine. The physicochemical properties of Au/AgICSD were then characterized using different optical and imaging techniques (e.g., HR- transmission electron microscope, scanning transmission electron microscope, x-ray photoelectron spectroscopy, energy-dispersive x-ray spectroscopy, Z-potential, and UV-vis). The CT and PAI contrast-enhancing effects were tested and then compared with a clinically used CT contrast agentmore » and Au nanoparticles. To confer biocompatibility and the capability for efficient biomarker targeting, the surface of the Au/AgICSD nanodimer was modified with the amphiphilic diblock polymer and then functionalized with transferrin for targeting transferrin receptor that is overexpressed in various cancer cells. Cytotoxicity of the prepared Au/AgICSD nanodimer was also tested with both normal and cancer cell lines. Results: The characterizations of prepared Au/AgI core/shell nanostructure confirmed the formation of Au/AgICSD nanodimers. Au/AgICSD nanodimer is stable in physiological conditions for in vivo applications. Au/AgICSD nanodimer exhibited higher contrast enhancement in both CT and PAI for dual-modality imaging. Moreover, transferrin functionalized Au/AgICSD nanodimer showed specific binding to the tumor cells that have a high level of expression of the transferrin receptor. Conclusions: The developed Au/AgICSD nanodimer can be used as a potential biomarker targeted dual-modal contrast agent for both or combined CT and PAI molecular imaging.« less

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

Kong, Leopold; Giang, Erick; Nieusma, Travis

Hepatitis C virus (HCV), a Hepacivirus, is a major cause of viral hepatitis, liver cirrhosis, and hepatocellular carcinoma. HCV envelope glycoproteins E1 and E2 mediate fusion and entry into host cells and are the primary targets of the humoral immune response. The crystal structure of the E2 core bound to broadly neutralizing antibody AR3C at 2.65 angstroms reveals a compact architecture composed of a central immunoglobulin-fold β sandwich flanked by two additional protein layers. The CD81 receptor binding site was identified by electron microscopy and site-directed mutagenesis and overlaps with the AR3C epitope. The x-ray and electron microscopy E2 structuresmore » differ markedly from predictions of an extended, three-domain, class II fusion protein fold and therefore provide valuable information for HCV drug and vaccine design.« less

Molecular mechanism of tau aggregation induced by anionic and cationic dyes.

PubMed

Lira-De León, Karla I; García-Gutiérrez, Ponciano; Serratos, Iris N; Palomera-Cárdenas, Marianela; Figueroa-Corona, María Del P; Campos-Peña, Victoria; Meraz-Ríos, Marco A

2013-01-01

Abnormal tau filaments are a hallmark of Alzheimer's disease. Anionic dyes such as Congo Red, Thiazine Red, and Thioflavin S are able to induce tau fibrillization in vitro. SH-SY5Y cells were incubated with each dye for seven days leading to intracellular aggregates of tau protein, with different morphological characteristics. Interestingly, these tau aggregates were not observed when the Methylene Blue dye was added to the cell culture. In order to investigate the molecular mechanisms underlying this phenomenon, we developed a computational model for the interaction of the tau paired helical filament (PHF) core with every dye by docking analysis. The polar/electrostatic and nonpolar contribution to the free binding energy in the tau PHF core-anionic dye interaction was determined. We found that the tau PHF core can generate a positive net charge within the binding site localized at residuesLys311 and Lys340 (numbering according to the longest isoform hTau40). These residues are important for the binding affinity of the negative charges present in the anionic dyes causing an electrostatic environment that stabilizes the complex. Tau PHF core protofibril-Congo Red interaction has a stronger binding affinity compared to Thiazine Red or Thioflavin S. By contrast, the cationic dye Methylene Blue does not bind to nor stabilize the tau PHF core protofibrils. These results characterize the driving forces responsible for the binding of tau to anionic dyes leading to their self-aggregation and suggest that Methylene Blue may act as a destabilizing agent of tau aggregates.

T-lymphoid, megakaryocyte, and granulocyte development are sensitive to decreases in CBFβ dosage.

PubMed Central

Talebian, Laleh; Li, Zhe; Guo, Yalin; Gaudet, Justin; Speck, Maren E.; Sugiyama, Daisuke; Kaur, Prabhjot; Pear, Warren S.; Maillard, Ivan; Speck, Nancy A.

2007-01-01

The family of core-binding factors includes the DNA-binding subunits Runx1-3 and their common non–DNA-binding partner CBFβ. We examined the collective role of core-binding factors in hematopoiesis with a hypomorphic Cbfb allelic series. Reducing CBFβ levels by 3- or 6-fold caused abnormalities in bone development, megakaryocytes, granulocytes, and T cells. T-cell development was very sensitive to an incremental reduction of CBFβ levels: mature thymocytes were decreased in number upon a 3-fold reduction in CBFβ levels, and were virtually absent when CBFβ levels were 6-fold lower. Partially penetrant consecutive differentiation blocks were found among early T-lineage progenitors within the CD4−CD8− double-negative 1 and downstream double-negative 2 thymocyte subsets. Our data define a critical CBFβ threshold for normal T-cell development, and situate an essential role for core-binding factors during the earliest stages of T-cell development. PMID:16940420

Molecular dynamics studies on the DNA-binding process of ERG.

PubMed

Beuerle, Matthias G; Dufton, Neil P; Randi, Anna M; Gould, Ian R

2016-11-15

The ETS family of transcription factors regulate gene targets by binding to a core GGAA DNA-sequence. The ETS factor ERG is required for homeostasis and lineage-specific functions in endothelial cells, some subset of haemopoietic cells and chondrocytes; its ectopic expression is linked to oncogenesis in multiple tissues. To date details of the DNA-binding process of ERG including DNA-sequence recognition outside the core GGAA-sequence are largely unknown. We combined available structural and experimental data to perform molecular dynamics simulations to study the DNA-binding process of ERG. In particular we were able to reproduce the ERG DNA-complex with a DNA-binding simulation starting in an unbound configuration with a final root-mean-square-deviation (RMSD) of 2.1 Å to the core ETS domain DNA-complex crystal structure. This allowed us to elucidate the relevance of amino acids involved in the formation of the ERG DNA-complex and to identify Arg385 as a novel key residue in the DNA-binding process. Moreover we were able to show that water-mediated hydrogen bonds are present between ERG and DNA in our simulations and that those interactions have the potential to achieve sequence recognition outside the GGAA core DNA-sequence. The methodology employed in this study shows the promising capabilities of modern molecular dynamics simulations in the field of protein DNA-interactions.

ETMB-RBF: discrimination of metal-binding sites in electron transporters based on RBF networks with PSSM profiles and significant amino acid pairs.

PubMed

Ou, Yu-Yen; Chen, Shu-An; Wu, Sheng-Cheng

2013-01-01

Cellular respiration is the process by which cells obtain energy from glucose and is a very important biological process in living cell. As cells do cellular respiration, they need a pathway to store and transport electrons, the electron transport chain. The function of the electron transport chain is to produce a trans-membrane proton electrochemical gradient as a result of oxidation-reduction reactions. In these oxidation-reduction reactions in electron transport chains, metal ions play very important role as electron donor and acceptor. For example, Fe ions are in complex I and complex II, and Cu ions are in complex IV. Therefore, to identify metal-binding sites in electron transporters is an important issue in helping biologists better understand the workings of the electron transport chain. We propose a method based on Position Specific Scoring Matrix (PSSM) profiles and significant amino acid pairs to identify metal-binding residues in electron transport proteins. We have selected a non-redundant set of 55 metal-binding electron transport proteins as our dataset. The proposed method can predict metal-binding sites in electron transport proteins with an average 10-fold cross-validation accuracy of 93.2% and 93.1% for metal-binding cysteine and histidine, respectively. Compared with the general metal-binding predictor from A. Passerini et al., the proposed method can improve over 9% of sensitivity, and 14% specificity on the independent dataset in identifying metal-binding cysteines. The proposed method can also improve almost 76% sensitivity with same specificity in metal-binding histidine, and MCC is also improved from 0.28 to 0.88. We have developed a novel approach based on PSSM profiles and significant amino acid pairs for identifying metal-binding sites from electron transport proteins. The proposed approach achieved a significant improvement with independent test set of metal-binding electron transport proteins.

ETMB-RBF: Discrimination of Metal-Binding Sites in Electron Transporters Based on RBF Networks with PSSM Profiles and Significant Amino Acid Pairs

PubMed Central

Ou, Yu-Yen; Chen, Shu-An; Wu, Sheng-Cheng

2013-01-01

Background Cellular respiration is the process by which cells obtain energy from glucose and is a very important biological process in living cell. As cells do cellular respiration, they need a pathway to store and transport electrons, the electron transport chain. The function of the electron transport chain is to produce a trans-membrane proton electrochemical gradient as a result of oxidation–reduction reactions. In these oxidation–reduction reactions in electron transport chains, metal ions play very important role as electron donor and acceptor. For example, Fe ions are in complex I and complex II, and Cu ions are in complex IV. Therefore, to identify metal-binding sites in electron transporters is an important issue in helping biologists better understand the workings of the electron transport chain. Methods We propose a method based on Position Specific Scoring Matrix (PSSM) profiles and significant amino acid pairs to identify metal-binding residues in electron transport proteins. Results We have selected a non-redundant set of 55 metal-binding electron transport proteins as our dataset. The proposed method can predict metal-binding sites in electron transport proteins with an average 10-fold cross-validation accuracy of 93.2% and 93.1% for metal-binding cysteine and histidine, respectively. Compared with the general metal-binding predictor from A. Passerini et al., the proposed method can improve over 9% of sensitivity, and 14% specificity on the independent dataset in identifying metal-binding cysteines. The proposed method can also improve almost 76% sensitivity with same specificity in metal-binding histidine, and MCC is also improved from 0.28 to 0.88. Conclusions We have developed a novel approach based on PSSM profiles and significant amino acid pairs for identifying metal-binding sites from electron transport proteins. The proposed approach achieved a significant improvement with independent test set of metal-binding electron transport proteins. PMID:23405059

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.

Multi-scale predictive modeling of nano-material and realistic electron devices

NASA Astrophysics Data System (ADS)

Palaria, Amritanshu

Among the challenges faced in further miniaturization of electronic devices, heavy influence of the detailed atomic configuration of the material(s) involved, which often differs significantly from that of the bulk material(s), is prominent. Device design has therefore become highly interrelated with material engineering at the atomic level. This thesis aims at outlining, with examples, a multi-scale simulation procedure that allows one to integrate material and device aspects of nano-electronic design to predict behavior of novel devices with novel material. This is followed in four parts: (1) An approach that combines a higher time scale reactive force field analysis with density functional theory to predict structure of new material is demonstrated for the first time for nanowires. Novel stable structures for very small diameter silicon nanowires are predicted. (2) Density functional theory is used to show that the new nanowire structures derived in 1 above have properties different from diamond core wires even though the surface bonds in some may be similar to the surface of bulk silicon. (3) Electronic structure of relatively large-scale germanium sections of realistically strained Si/strained Ge/ strained Si nanowire heterostructures is computed using empirical tight binding and it is shown that the average non-homogeneous strain in these structures drives their interesting non-conventional electronic characteristics such as hole effective masses which decrease as the wire cross-section is reduced. (4) It is shown that tight binding, though empirical in nature, is not necessarily limited to the material and atomic structure for which the parameters have been empirically derived, but that simple changes may adapt the derived parameters to new bond environments. Si (100) surface electronic structure is obtained from bulk Si parameters.

Incorporation of deoxyribonucleotides and ribonucleotides by a dNTP-binding cleft mutated reverse transcriptase in hepatitis B virus core particles

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

Kim, Hee-Young; Kim, Hye-Young; Jung, Jaesung

2008-01-05

Our recent observation that hepatitis B virus (HBV) DNA polymerase (P) might initiate minus-strand DNA synthesis without primer [Kim et al., (2004) Virology 322, 22-30], raised a possibility that HBV P protein may have the potential to function as an RNA polymerase. Thus, we mutated Phe 436, a bulky amino acid with aromatic side chain, at the putative dNTP-binding cleft in reverse transcriptase (RT) domain of P protein to smaller amino acids (Gly or Val), and examined RNA polymerase activity. HBV core particles containing RT dNTP-binding cleft mutant P protein were able to incorporate {sup 32}P-ribonucleotides, but not HBV coremore » particles containing wild type (wt), priming-deficient mutant, or RT-deficient mutant P proteins. Since all the experiments were conducted with core particles isolated from transfected cells, our results indicate that the HBV RT mutant core particles containing RT dNTP-binding cleft mutant P protein could incorporate both deoxyribonucleotides and ribonucleotides in replicating systems.« less

From clusters to bulk: A relativistic density functional investigation on a series of gold clusters Aun, n=6,…,147

NASA Astrophysics Data System (ADS)

Häberlen, Oliver D.; Chung, Sai-Cheong; Stener, Mauro; Rösch, Notker

1997-03-01

A series of gold clusters spanning the size range from Au6 through Au147 (with diameters from 0.7 to 1.7 nm) in icosahedral, octahedral, and cuboctahedral structure has been theoretically investigated by means of a scalar relativistic all-electron density functional method. One of the main objectives of this work was to analyze the convergence of cluster properties toward the corresponding bulk metal values and to compare the results obtained for the local density approximation (LDA) to those for a generalized gradient approximation (GGA) to the exchange-correlation functional. The average gold-gold distance in the clusters increases with their nuclearity and correlates essentially linearly with the average coordination number in the clusters. An extrapolation to the bulk coordination of 12 yields a gold-gold distance of 289 pm in LDA, very close to the experimental bulk value of 288 pm, while the extrapolated GGA gold-gold distance is 297 pm. The cluster cohesive energy varies linearly with the inverse of the calculated cluster radius, indicating that the surface-to-volume ratio is the primary determinant of the convergence of this quantity toward bulk. The extrapolated LDA binding energy per atom, 4.7 eV, overestimates the experimental bulk value of 3.8 eV, while the GGA value, 3.2 eV, underestimates the experiment by almost the same amount. The calculated ionization potentials and electron affinities of the clusters may be related to the metallic droplet model, although deviations due to the electronic shell structure are noticeable. The GGA extrapolation to bulk values yields 4.8 and 4.9 eV for the ionization potential and the electron affinity, respectively, remarkably close to the experimental polycrystalline work function of bulk gold, 5.1 eV. Gold 4f core level binding energies were calculated for sites with bulk coordination and for different surface sites. The core level shifts for the surface sites are all positive and distinguish among the corner, edge, and face-centered sites; sites in the first subsurface layer show still small positive shifts.

CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes

PubMed Central

Hestand, Matthew S; van Galen, Michiel; Villerius, Michel P; van Ommen, Gert-Jan B; den Dunnen, Johan T; 't Hoen, Peter AC

2008-01-01

Background The identification of transcription factor binding sites is difficult since they are only a small number of nucleotides in size, resulting in large numbers of false positives and false negatives in current approaches. Computational methods to reduce false positives are to look for over-representation of transcription factor binding sites in a set of similarly regulated promoters or to look for conservation in orthologous promoter alignments. Results We have developed a novel tool, "CORE_TF" (Conserved and Over-REpresented Transcription Factor binding sites) that identifies common transcription factor binding sites in promoters of co-regulated genes. To improve upon existing binding site predictions, the tool searches for position weight matrices from the TRANSFACR database that are over-represented in an experimental set compared to a random set of promoters and identifies cross-species conservation of the predicted transcription factor binding sites. The algorithm has been evaluated with expression and chromatin-immunoprecipitation on microarray data. We also implement and demonstrate the importance of matching the random set of promoters to the experimental promoters by GC content, which is a unique feature of our tool. Conclusion The program CORE_TF is accessible in a user friendly web interface at . It provides a table of over-represented transcription factor binding sites in the users input genes' promoters and a graphical view of evolutionary conserved transcription factor binding sites. In our test data sets it successfully predicts target transcription factors and their binding sites. PMID:19036135

Encapsulation of concentrated hemoglobin solution in phospholipid vesicles retards the reaction with NO, but not CO, by intracellular diffusion barrier.

PubMed

Sakai, Hiromi; Sato, Atsushi; Masuda, Kaoru; Takeoka, Shinji; Tsuchida, Eishun

2008-01-18

One physiological significance of the red blood cell (RBC) structure is that NO binding of Hb is retarded by encapsulation with the cell membrane. To clarify the mechanism, we analyzed Hb-vesicles (HbVs) with different intracellular Hb concentrations, [Hb](in), and different particle sizes using stopped-flow spectrophotometry. The apparent NO binding rate constant, k(on)('(NO)), of HbV at [Hb](in) = 1 g/dl was 2.6 x 10(7) m(-1) s(-1), which was almost equal to k(on)((NO)) of molecular Hb, indicating that the lipid membrane presents no obstacle for NO binding. With increasing [Hb](in) to 35 g/dl, k(on)('(NO)) decreased to 0.9 x 10(7) m(-1) s(-1), which was further decreased to 0.5 x 10(7) m(-1) s(-1) with enlarging particle diameter from 265 to 452 nm. For CO binding, which is intrinsically much slower than NO binding, k(on)('(CO)) did not change greatly with [Hb](in) and the particle diameter. Results obtained using diffusion simulations coupled with elementary binding reactions concur with these tendencies and clarify that NO is trapped rapidly by Hb from the interior surface region to the core of HbV at a high [Hb](in), retarding NO diffusion toward the core of HbV. In contrast, slow CO binding allows time for further CO-diffusion to the core. Simulations extrapolated to larger particles (8 mum) showing retardation even for CO binding. The obtained k(on)('(NO)) and k(on)('(NO)) yield values similar to those reported for RBCs. In summary, the intracellular, not extracellular, diffusion barrier is predominant due to the rapid NO binding that induces a rapid sink of NO from the interior surface to the core, retarding further NO diffusion and binding.

Exploring the core level shift origin of sulfur and thiolates on Pd(111) surfaces.

PubMed

Salvarezza, Roberto Carlos; Carro, Pilar

2015-10-07

Thiol molecules on planar metal surfaces are widely used for building sensing and electronic devices and also as capping agents to protect and to control the size and shape of nanoparticles. In the case of Pd the thiol molecules exhibit a complex behavior because C-S bond scission is possible, resulting in a significant amount of co-adsorbed S. Therefore identification of these species on Pd is a key point for many applications, a task that is usually achieved by XPS. Here we show, from DFT calculations, that the core level shift (CLS) of the S 2p binding energy (BE) of thiol and sulfur on different thiol-Pd(111) surface models strongly depends on the adsorbed or subsurface state of sulfur atoms. Our results reflect the complexity of S 2p BE behavior and contribute to understanding and reanalyzing the experimental data of thiolated Pd surfaces.

Quantum confinement-induced tunable exciton states in graphene oxide

PubMed Central

Lee, Dongwook; Seo, Jiwon; Zhu, Xi; Lee, Jiyoul; Shin, Hyeon-Jin; Cole, Jacqueline M.; Shin, Taeho; Lee, Jaichan; Lee, Hangil; Su, Haibin

2013-01-01

Graphene oxide has recently been considered to be a potential replacement for cadmium-based quantum dots due to its expected high fluorescence. Although previously reported, the origin of the luminescence in graphene oxide is still controversial. Here, we report the presence of core/valence excitons in graphene-based materials, a basic ingredient for optical devices, induced by quantum confinement. Electron confinement in the unreacted graphitic regions of graphene oxide was probed by high resolution X-ray absorption near edge structure spectroscopy and first-principles calculations. Using experiments and simulations, we were able to tune the core/valence exciton energy by manipulating the size of graphitic regions through the degree of oxidation. The binding energy of an exciton in highly oxidized graphene oxide is similar to that in organic electroluminescent materials. These results open the possibility of graphene oxide-based optoelectronic device technology. PMID:23872608

Plasmonic Nanodiamonds – Targeted Core-shell Type Nanoparticles for Cancer Cell Thermoablation

PubMed Central

Rehor, Ivan; Lee, Karin L.; Chen, Kevin; Hajek, Miroslav; Havlik, Jan; Lokajova, Jana; Masat, Milan; Slegerova, Jitka; Shukla, Sourabh; Heidari, Hamed; Bals, Sara

2015-01-01

Targeted biocompatible nanostructures with controlled plasmonic and morphological parameters are promising materials for cancer treatment based on selective thermal ablation of cells. Here, core-shell plasmonic nanodiamonds consisting of a silica-encapsulated diamond nanocrystal coated in a gold shell is designed and synthesized. The architecture of particles is analyzed and confirmed in detail using 3-dimensional transmission electron microscope tomography. The particles are biocompatibilized using a PEG polymer terminated with bioorthogonally reactive alkyne groups. Azide-modified transferrin is attached to these particles, and their high colloidal stability and successful targeting to cancer cells overexpressing the transferrin receptor is demonstrated. The particles are nontoxic to the cells and they are readily internalized upon binding to the transferrin receptor. The high plasmonic cross section of the particles in the near-infrared region is utilized to quantitatively ablate the cancer cells with a short, one-minute irradiation by a pulse 750-nm laser. PMID:25336437

Amine-functionalized magnetic mesoporous silica nanoparticles for DNA separation

NASA Astrophysics Data System (ADS)

Sheng, Wei; Wei, Wei; Li, Junjian; Qi, Xiaoliang; Zuo, Gancheng; Chen, Qi; Pan, Xihao; Dong, Wei

2016-11-01

We report a modified approach for the functionalized magnetic mesoporous silica nanoparticles (MMSN) using polymer microspheres incorporated with magnetic nanoparticles in the presence of cetyltrimethylammonium bromide (CTAB) and the core-shell magnetic silica nanoparticles (MSN). These particles were functionalized with amino groups via the addition of aminosilane directly to the particle sol. We then evaluate their DNA separation abilities and find the capacity of DNA binding significantly increased (210.22 μg/mg) compared with normal magnetic silica spheres (138.44 μg/mg) by using an ultraviolet and visible spectrophotometer (UV). The morphologies, magnetic properties, particle size, pore size, core-shell structure and Zeta potential are characterized by Fourier transform infrared spectroscopy (FT-IR), vibrating sample magnetometer (VSM), Transmission electron microscopy (TEM), Powder X-ray diffraction (XRD), and dynamic light scattering (DLS). This work demonstrates that our MMSN own an excellent potential application in bioseparation and drug delivery.

p53 targets chromatin structure alteration to repress alpha-fetoprotein gene expression.

PubMed

Ogden, S K; Lee, K C; Wernke-Dollries, K; Stratton, S A; Aronow, B; Barton, M C

2001-11-09

Many of the functions ascribed to p53 tumor suppressor protein are mediated through transcription regulation. We have shown that p53 represses hepatic-specific alpha-fetoprotein (AFP) gene expression by direct interaction with a composite HNF-3/p53 DNA binding element. Using solid-phase, chromatin-assembled AFP DNA templates and analysis of chromatin structure and transcription in vitro, we find that p53 binds DNA and alters chromatin structure at the AFP core promoter to regulate transcription. Chromatin assembled in the presence of hepatoma extracts is activated for AFP transcription with an open, accessible core promoter structure. Distal (-850) binding of p53 during chromatin assembly, but not post-assembly, reverses transcription activation concomitant with promoter inaccessibility to restriction enzyme digestion. Inhibition of histone deacetylase activity by trichostatin-A (TSA) addition, prior to and during chromatin assembly, activated chromatin transcription in parallel with increased core promoter accessibility. Chromatin immunoprecipitation analyses showed increased H3 and H4 acetylated histones at the core promoter in the presence of TSA, while histone acetylation remained unchanged at the site of distal p53 binding. Our data reveal that p53 targets chromatin structure alteration at the core promoter, independently of effects on histone acetylation, to establish repressed AFP gene expression.

Binding energy of e^+Li using the Peach model potential.

NASA Astrophysics Data System (ADS)

Shertzer, Janine; Ward, Sandra

2006-05-01

The l-independent, parametric model potential developed by Peach^1 for describing the electron interaction with the alkali ion core yields energy levels that are in excellent agreement with experiment. Because of its relative simplicity, this model potential is an attractive choice for studying e^+- Li collisions;^2,3 the e^+-ion core interaction is obtained by changing the sign of the static term in the interaction. In order to test the usefulness of the potential for describing the physics of an effective three-body system, we calculated the binding energy of e^+Li. This is a stringent test, because the system is very weakly bound. Our results are in excellent agreement with previous calculations,^4 including those using the exact four-body Hamiltonian.^5 This work was funded by NSF under collaborative Grant PHYS-0440714 (JS) and PHYS-0440565 (SJW). ^1G. Peach, H.E. Saraph and M.J. Seaton, J. Phys. B 21, 3669 (1988). ^2M.S.T. Watts and J.W. Humberston, J. Phys. B 25, L491 (1992). ^3S. J. Ward and J. Shertzer, Phys. Rev. A 68, 032720 (2003). ^4J. Mitroy, M.W.J. Bromley, and G.G. Ryzhikh, J. Phys. B 35, R81 (2002). ^5Massimo Mella, Gabriele Morosi, and Dario Bressanini, J. Chem. Phys. 111, 108 (1999).

Human Retroviruses: Methods and Protocols

PubMed Central

Zhao, Gongpu; Zhang, Peijun

2015-01-01

Summary After virus fusion with a target cell, the viral core is released into the host cell cytoplasm and undergoes a controlled disassembly process, termed uncoating, before or as reverse transcription takes place. The cellular protein TRIM5α is a host cell restriction factor that blocks HIV-1 infection in rhesus macaque cells by targeting the viral capsid and inducing premature uncoating. The molecular mechanism of the interaction between capsid and TRIM5α remains unclear. Here, we describe an approach that utilizes cryo-electron microscopy (cryoEM) to examine the structural changes exerted on HIV-1 capsid (CA) assembly by TRIM5α binding. The TRIM5α interaction sites on CA assembly were further dissected by combining cryoEM with pair-wise cysteine mutations that crosslink CA either within a CA hexamer or between CA hexamers. Based on the structural information from cryoEM and crosslinking results from in vitro CA assemblies and purified intact HIV-1 cores, we demonstrate that direct binding of TRIM5α CC-SPRY domains to the viral capsid results in disruption and fragmentation of the surface lattice of HIV-1 capsid, specifically at inter-hexamer interfaces. The method described here can be easily adopted to study other important interactions in multi-protein complexes. PMID:24158810

The electronic structure of Bi 2.0Sr 1.8La 0.3Ca 0.8Cu 2.1O 8+δ superconductors studied using ultraviolet and X-ray photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Lindberg, P. A. P.; Shen, Z.-X.; Dessau, D. S.; Wells, B. O.; Borg, A.; Ellis, W.; Mitzi, D. B.; Lindau, I.; Spicer, W. E.; Kapitulnik, A.

1989-07-01

Photoemission measurements on single crystals of La-doped 2212 (Bi 2.0Sr 1.8La 0.3Ca 0.8Cu 2.1O 8+δ) superconductors were carried out utilizing both synchrotron and Al K α (1486.6 eV) radiation. A quantitative analysis of the photoemission data in comparison with similar data for the undoped 2212 material indicates that the La atoms preferentially occupy the Sr sites in the SrO layer next to the BiO plane. Evidence of alternation of the electronic environment of the Bi atoms is found in the Bi 5d core level spectra which show a shoulder at ≈ 1.2 eV higher binding energy, presumably due to the partial substitution of trivalent La ions (La 3+) for divalent Sr ions (Sr 2+). As for the undoped 2212 material, the photoemission spectra reveal a clear Fermi level cut-off at room temperature, single component O ls core level emission, and a Cu 2p satellite to main line intensity ratio of 0.4.

Elucidating the role of surface passivating ligand structural parameters in hole wave function delocalization in semiconductor cluster molecules.

PubMed

Teunis, Meghan B; Nagaraju, Mulpuri; Dutta, Poulami; Pu, Jingzhi; Muhoberac, Barry B; Sardar, Rajesh; Agarwal, Mangilal

2017-09-28

This article describes the mechanisms underlying electronic interactions between surface passivating ligands and (CdSe) 34 semiconductor cluster molecules (SCMs) that facilitate band-gap engineering through the delocalization of hole wave functions without altering their inorganic core. We show here both experimentally and through density functional theory calculations that the expansion of the hole wave function beyond the SCM boundary into the ligand monolayer depends not only on the pre-binding energetic alignment of interfacial orbitals between the SCM and surface passivating ligands but is also strongly influenced by definable ligand structural parameters such as the extent of their π-conjugation [π-delocalization energy; pyrene (Py), anthracene (Anth), naphthalene (Naph), and phenyl (Ph)], binding mode [dithiocarbamate (DTC, -NH-CS 2 - ), carboxylate (-COO - ), and amine (-NH 2 )], and binding head group [-SH, -SeH, and -TeH]. We observe an unprecedentedly large ∼650 meV red-shift in the lowest energy optical absorption band of (CdSe) 34 SCMs upon passivating their surface with Py-DTC ligands and the trend is found to be Ph- < Naph- < Anth- < Py-DTC. This shift is reversible upon removal of Py-DTC by triethylphosphine gold(i) chloride treatment at room temperature. Furthermore, we performed temperature-dependent (80-300 K) photoluminescence lifetime measurements, which show longer lifetime at lower temperature, suggesting a strong influence of hole wave function delocalization rather than carrier trapping and/or phonon-mediated relaxation. Taken together, knowledge of how ligands electronically interact with the SCM surface is crucial to semiconductor nanomaterial research in general because it allows the tuning of electronic properties of nanomaterials for better charge separation and enhanced charge transfer, which in turn will increase optoelectronic device and photocatalytic efficiencies.

Metal-Free Photoinduced Electron Transfer-Atom Transfer Radical Polymerization Integrated with Bioinspired Polydopamine Chemistry as a Green Strategy for Surface Engineering of Magnetic Nanoparticles.

PubMed

Yang, Yang; Liu, Xuegang; Ye, Gang; Zhu, Shan; Wang, Zhe; Huo, Xiaomei; Matyjaszewski, Krzysztof; Lu, Yuexiang; Chen, Jing

2017-04-19

Developing green and efficient technologies for surface modification of magnetic nanoparticles (MNPs) is of crucial importance for their biomedical and environmental applications. This study reports, for the first time, a novel strategy by integrating metal-free photoinduced electron transfer-atom transfer radical polymerization (PET-ATRP) with the bioinspired polydopamine (PDA) chemistry for controlled architecture of functional polymer brushes from MNPs. Conformal PDA encapsulation layers were initially generated on the surfaces of MNPs, which served as the protective shells while providing an ideal platform for tethering 2-bromo-2-phenylacetic acid (BPA), a highly efficient initiator. Metal-free PET-ATRP technique was then employed for controlled architecture of poly(glycidyl methacrylate) (PGMA) brushes from the core-shell MNPs by using diverse organic dyes as photoredox catalysts. Impacts of light sources (including UV and visible lights), photoredox catalysts, and polymerization time on the composition and morphology of the PGMA brushes were investigated. Moreover, the versatility of the PGMA-functionalized core-shell MNPs was demonstrated by covalent attachment of ethylenediamine (EDA), a model functional molecule, which afforded the MNPs with improved hydrophilicity, dispersibility, and superior binding ability to uranyl ions. The green methodology by integrating metal-free PET-ATRP with facile PDA chemistry would provide better opportunities for surface modification of MNPs and miscellaneous nanomaterials for biomedical and electronic applications.

Tuning the Activity of Carbon for Electrocatalytic Hydrogen Evolution via an Iridium-Cobalt Alloy Core Encapsulated in Nitrogen-Doped Carbon Cages.

PubMed

Jiang, Peng; Chen, Jitang; Wang, Changlai; Yang, Kang; Gong, Shipeng; Liu, Shuai; Lin, Zhiyu; Li, Mengsi; Xia, Guoliang; Yang, Yang; Su, Jianwei; Chen, Qianwang

2018-03-01

Graphene, a 2D material consisting of a single layer of sp 2 -hybridized carbon, exhibits inert activity as an electrocatalyst, while the incorporation of heteroatoms (such as N) into the framework can tune its electronic properties. Because of the different electronegativity between N and C atoms, electrons will transfer from C to N in N-doped graphene nanosheets, changing inert C atoms adjacent to the N-dopants into active sites. Notwithstanding the achieved progress, its intrinsic activity in acidic media is still far from Pt/C. Here, a facile annealing strategy is adopted for Ir-doped metal-organic frameworks to synthesize IrCo nanoalloys encapsulated in N-doped graphene layers. The highly active electrocatalyst, with remarkably reduced Ir loading (1.56 wt%), achieves an ultralow Tafel slope of 23 mV dec -1 and an overpotential of only 24 mV at a current density of 10 mA cm -2 in 0.5 m sulfuric acid solution. Such superior performance is even superior to the noble-metal catalyst Pt. Surface structural and computational studies reveal that the superior behavior originates from the decreased ΔG H* for HER induced by the electrons transferred from the alloy core to the graphene layers, which is beneficial for enhancing CH binding. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Binding of two-electron metastable states in semiconductor quantum dots under a magnetic field

NASA Astrophysics Data System (ADS)

Garagiola, Mariano; Pont, Federico M.; Osenda, Omar

2018-04-01

Applying a strong enough magnetic field results in the binding of few-electron resonant states. The mechanism was proposed many years ago but its verification in laboratory conditions is far more recent. In this work we study the binding of two-electron resonant states. The electrons are confined in a cylindrical quantum dot which is embedded in a semiconductor wire. The geometry considered is similar to the one used in actual experimental setups. The low-energy two-electron spectrum is calculated numerically from an effective-mass approximation Hamiltonian modelling the system. Methods for binding threshold calculations in systems with one and two electrons are thoroughly studied; in particular, we use quantum information quantities to assess when the strong lateral confinement approximation can be used to obtain reliable low-energy spectra. For simplicity, only cases without bound states in the absence of an external field are considered. Under these conditions, the binding threshold for the one-electron case is given by the lowest Landau energy level. Moreover, the energy of the one-electron bounded resonance can be used to obtain the two-electron binding threshold. It is shown that for realistic values of the two-electron model parameters it is feasible to bind resonances with field strengths of a few tens of tesla.

The vaccinia virus I3L gene product is localized to a complex endoplasmic reticulum-associated structure that contains the viral parental DNA.

PubMed

Welsch, Sonja; Doglio, Laura; Schleich, Sibylle; Krijnse Locker, Jacomine

2003-05-01

The vaccinia virus (VV) I3L gene product is a single-stranded DNA-binding protein made early in infection that localizes to the cytoplasmic sites of viral DNA replication (S. C. Rochester and P. Traktman, J. Virol. 72:2917-2926, 1998). Surprisingly, when replication was blocked, the protein localized to distinct cytoplasmic spots (A. Domi and G. Beaud, J. Gen. Virol. 81:1231-1235, 2000). Here these I3L-positive spots were characterized in more detail. By using an anti-I3L peptide antibody we confirmed that the protein localized to the cytoplasmic sites of viral DNA replication by both immunofluorescence and electron microscopy (EM). Before replication had started or when replication was inhibited with hydroxyurea or cytosine arabinoside, I3L localized to distinct cytoplasmic punctate structures of homogeneous size. We show that these structures are not incoming cores or cytoplasmic sites of VV early mRNA accumulation. Instead, morphological and quantitative data indicate that they are specialized sites where the parental DNA accumulates after its release from incoming viral cores. By EM, these sites appeared as complex, electron-dense structures that were intimately associated with the cellular endoplasmic reticulum (ER). By double labeling of cryosections we show that they contain DNA and a viral early protein, the gene product of E8R. Since E8R is a membrane protein that is able to bind to DNA, the localization of this protein to the I3L puncta suggests that they are composed of membranes. The results are discussed in relation to our previous data showing that the process of viral DNA replication also occurs in close association with the ER.

Novel interactions of complex carbohydrates with peanut (PNA), Ricinus communis (RCA-I), Sambucus nigra (SNA-I) and wheat germ (WGA) agglutinins as revealed by the binding specificities of these lectins towards mucin core-2 O-linked and N-linked glycans and related structures.

PubMed

Chandrasekaran, E V; Xue, Jun; Xia, Jie; Khaja, Siraj D; Piskorz, Conrad F; Locke, Robert D; Neelamegham, Sriram; Matta, Khushi L

2016-10-01

Plant lectins through their multivalent quaternary structures bind intrinsically flexible oligosaccharides. They recognize fine structural differences in carbohydrates and interact with different sequences in mucin core 2 or complex-type N-glycan chain and also in healthy and malignant tissues. They are used in characterizing cellular and extracellular glycoconjugates modified in pathological processes. We study here, the complex carbohydrate-lectin interactions by determining the effects of substituents in mucin core 2 tetrasaccharide Galβ1-4GlcNAcβ1-6(Galβ1-3)GalNAcα-O-R and fetuin glycopeptides on their binding to agarose-immobilized lectins PNA, RCA-I, SNA-I and WGA. Briefly, in mucin core 2 tetrasaccharide (i) structures modified by α2-3/6-Sialyl LacNAc, LewisX and α1-3-Galactosyl LacNAc resulted in regular binding to PNA whereas compounds with 6-sulfo LacNAc displayed no-binding; (ii) strucures bearing α2-6-sialyl 6-sulfo LacNAc, or 6-sialyl LacdiNAc carbohydrates displayed strong binding to SNA-I; (iii) structures with α2-3/6-sialyl, α1-3Gal LacNAc or LewisX were non-binder to RCA-I and compounds with 6-sulfo LacNAc only displayed weak binding; (iv) structures containing LewisX, 6-Sulfo LewisX, α2-3/6-sialyl LacNAc, α2-3/6-sialyl 6-sulfo LacNAc and GalNAc Lewis-a were non-binding to WGA, those with α1-2Fucosyl, α1-3-Galactosyl LacNAc, α2-3-sialyl T-hapten plus 3'/6'sulfo LacNAc displayed weak binding, and compounds with α2-3-sialyl T-hapten, α2.6-Sialyl LacdiNAc, α2-3-sialyl D-Fucβ1-3 GalNAc and Fucα-1-2 D-Fucβ-1-3GalNAc displaying regular binding and GalNAc LewisX and LacdiNAc plus D-Fuc β-1-3 GalNAcα resulting in tight binding. RCA-I binds Fetuin triantennary asialoglycopeptide 100 % after α-2-3 and 25 % after α-2-6 sialylation, 30 % after α-1-2 and 100 % after α-1-3 fucosylation, and 50 % after α-1-3 galactosylation. WGA binds 3-but not 6-Fucosyl chitobiose core. Thus, information on the influence of complex carbohydrate chain constituents on lectin binding is apparently essential for the potential application of lectins in glycoconjugate research.

Structural characterization of core-bradavidin in complex with biotin

PubMed Central

Agrawal, Nitin; Määttä, Juha A. E.; Kulomaa, Markku S.; Hytönen, Vesa P.; Johnson, Mark S.; Airenne, Tomi T.

2017-01-01

Bradavidin is a tetrameric biotin-binding protein similar to chicken avidin and bacterial streptavidin, and was originally cloned from the nitrogen-fixing bacteria Bradyrhizobium diazoefficiens. We have previously reported the crystal structure of the full-length, wild-type (wt) bradavidin with 138 amino acids, where the C-terminal residues Gly129-Lys138 (“Brad-tag”) act as an intrinsic ligand (i.e. Gly129-Lys138 bind into the biotin-binding site of an adjacent subunit within the same tetramer) and has potential as an affinity tag for biotechnological purposes. Here, the X-ray structure of core-bradavidin lacking the C-terminal residues Gly114-Lys138, and hence missing the Brad-tag, was crystallized in complex with biotin at 1.60 Å resolution [PDB:4BBO]. We also report a homology model of rhodavidin, an avidin-like protein from Rhodopseudomonas palustris, and of an avidin-like protein from Bradyrhizobium sp. Ai1a-2, both of which have the Brad-tag sequence at their C-terminus. Moreover, core-bradavidin V1, an engineered variant of the original core-bradavidin, was also expressed at high levels in E. coli, as well as a double mutant (Cys39Ala and Cys69Ala) of core-bradavidin (CC mutant). Our data help us to further engineer the core-bradavidin–Brad-tag pair for biotechnological assays and chemical biology applications, and provide deeper insight into the biotin-binding mode of bradavidin. PMID:28426764

High resolution spectroscopy of the 12Lambda B hypernucleus produced by the (e,e'K+) reaction.

PubMed

Miyoshi, T; Sarsour, M; Yuan, L; Zhu, X; Ahmidouch, A; Ambrozewicz, P; Androic, D; Angelescu, T; Asaturyan, R; Avery, S; Baker, O K; Bertovic, I; Breuer, H; Carlini, R; Cha, J; Chrien, R; Christy, M; Cole, L; Danagoulian, S; Dehnhard, D; Elaasar, M; Empl, A; Ent, R; Fenker, H; Fujii, Y; Furic, M; Gan, L; Garrow, K; Gasparian, A; Gueye, P; Harvey, M; Hashimoto, O; Hinton, W; Hu, B; Hungerford, E; Jackson, C; Johnston, K; Juengst, H; Keppel, C; Lan, K; Liang, Y; Likhachev, V P; Liu, J H; Mack, D; Margaryan, A; Markowitz, P; Martoff, J; Mkrtchyan, H; Nakamura, S N; Petkovic, T; Reinhold, J; Roche, J; Sato, Y; Sawafta, R; Simicevic, N; Smith, G; Stepanyan, S; Tadevosyan, V; Takahashi, T; Tanida, K; Tang, L; Ukai, M; Uzzle, A; Vulcan, W; Wells, S; Wood, S; Xu, G; Yamaguchi, H; Yan, C

2003-06-13

High-energy, cw electron beams at new accelerator facilities allow electromagnetic production and precision study of hypernuclear structure, and we report here on the first experiment demonstrating the potential of the (e,e'K+) reaction for hypernuclear spectroscopy. This experiment is also the first to take advantage of the enhanced virtual photon flux available when electrons are scattered at approximately zero degrees. The observed energy resolution was found to be approximately 900 keV for the (12)(Lambda)B spectrum, and is substantially better than any previous hypernuclear experiment using magnetic spectrometers. The positions of the major excitations are found to be in agreement with a theoretical prediction and with a previous binding energy measurement, but additional structure is also observed in the core excited region, underlining the future promise of this technique.

34. DESPATCH CORE OVENS, GREY IRON FOUNDRY CORE ROOM, BAKES ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

34. DESPATCH CORE OVENS, GREY IRON FOUNDRY CORE ROOM, BAKES CORES THAT ARE NOT MADE ON HEATED OR COLD BOX CORE MACHINES, TO SET BINDING AGENTS MIXED WITH THE SAND CREATING CORES HARD ENOUGH TO WITHSTAND THE FLOW OF MOLTEN IRON INSIDE A MOLD. - Stockham Pipe & Fittings Company, Grey Iron Foundry, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

The baculovirus core gene ac83 is required for nucleocapsid assembly and per os infectivity of Autographa californica nucleopolyhedrovirus.

PubMed

Zhu, Shimao; Wang, Wei; Wang, Yan; Yuan, Meijin; Yang, Kai

2013-10-01

Autographa californica multiple nucleopolyhedrovirus (AcMNPV) ac83 is a baculovirus core gene whose function in the AcMNPV life cycle is unknown. In the present study, an ac83-knockout AcMNPV (vAc83KO) was constructed to investigate the function of ac83 through homologous recombination in Escherichia coli. No budded virions were produced in vAc83KO-transfected Sf9 cells, although viral DNA replication was unaffected. Electron microscopy revealed that nucleocapsid assembly was aborted due to the ac83 deletion. Domain-mapping studies revealed that the expression of Ac83 amino acid residues 451 to 600 partially rescued the ability of AcMNPV to produce infectious budded virions. Bioassays indicated that deletion of the chitin-binding domain of Ac83 resulted in the failure of oral infection of Trichoplusia ni larvae by AcMNPV, but AcMNPV remained infectious following intrahemocoelic injection, suggesting that the domain is involved in the binding of occlusion-derived virions to the peritrophic membrane and/or to other chitin-containing insect tissues. It has been demonstrated that Ac83 is the only component with a chitin-binding domain in the per os infectivity factor complex on the occlusion-derived virion envelope. Interestingly, a functional inner nuclear membrane sorting motif, which may facilitate the localization of Ac83 to the envelopes of occlusion-derived virions, was identified by immunofluorescence analysis. Taken together, these results demonstrate that Ac83 plays an important role in nucleocapsid assembly and the establishment of oral infection.

Cisplatin Radiosensitization of DNA Irradiated with 2-20 eV Electrons: Role of Transient Anions.

PubMed

Bao, Qianhong; Chen, Yunfeng; Zheng, Yi; Sanche, Léon

2014-06-20

Platinum chemotherapeutic agents, such as cisplatin ( cis -diamminedichloroplatinum(II)), can act as radiosensitizers when bound covalently to nuclear DNA in cancer cells. This radiosensitization is largely due to an increase in DNA damage induced by low-energy secondary electrons, produced in large quantities by high-energy radiation. We report the yields of single- and double-strand breaks (SSB and DSB) and interduplex cross-links (CL) induced by electrons of 1.6-19.6 eV (i.e., the yield functions) incident on 5 monolayer (ML) films of cisplatin-DNA complexes. These yield functions are compared with those previously recorded with 5 ML films of unmodified plasmid DNA. Binding of five cisplatin molecules to plasmid DNA (3197 base pairs) enhances SSB, DSB, and CL by factors varying, from 1.2 to 2.8, 1.4 to 3.5, and 1.2 to 2.7, respectively, depending on electron energy. All yield functions exhibit structures around 5 and 10 eV that can be attributed to enhancement of bond scission, via the initial formation of core-excited resonances associated with π → π * transitions of the bases. This increase in damage is interpreted as arising from a modification of the parameters of the corresponding transient anions already present in nonmodified DNA, particularly those influencing molecular dissociation. Two additional resonances, specific to cisplatin-modified DNA, are formed at 13.6 and 17.6 eV in the yield function of SSB. Furthermore, cisplatin binding causes the induction of DSB by electrons of 1.6-3.6 eV, i.e., in an energy region where a DSB cannot be produced by a single electron in pure DNA. Breaking two bonds with a subexcitation-energy electron is tentatively explained by a charge delocalization mechanism, where a single electron occupies simultaneously two σ * bonds linking the Pt atom to guanine bases on opposite strands.

Cisplatin Radiosensitization of DNA Irradiated with 2–20 eV Electrons: Role of Transient Anions

PubMed Central

Bao, Qianhong; Chen, Yunfeng; Zheng, Yi; Sanche, Léon

2015-01-01

Platinum chemotherapeutic agents, such as cisplatin (cis-diamminedichloroplatinum(II)), can act as radiosensitizers when bound covalently to nuclear DNA in cancer cells. This radiosensitization is largely due to an increase in DNA damage induced by low-energy secondary electrons, produced in large quantities by high-energy radiation. We report the yields of single- and double-strand breaks (SSB and DSB) and interduplex cross-links (CL) induced by electrons of 1.6–19.6 eV (i.e., the yield functions) incident on 5 monolayer (ML) films of cisplatin–DNA complexes. These yield functions are compared with those previously recorded with 5 ML films of unmodified plasmid DNA. Binding of five cisplatin molecules to plasmid DNA (3197 base pairs) enhances SSB, DSB, and CL by factors varying, from 1.2 to 2.8, 1.4 to 3.5, and 1.2 to 2.7, respectively, depending on electron energy. All yield functions exhibit structures around 5 and 10 eV that can be attributed to enhancement of bond scission, via the initial formation of core-excited resonances associated with π → π* transitions of the bases. This increase in damage is interpreted as arising from a modification of the parameters of the corresponding transient anions already present in nonmodified DNA, particularly those influencing molecular dissociation. Two additional resonances, specific to cisplatin-modified DNA, are formed at 13.6 and 17.6 eV in the yield function of SSB. Furthermore, cisplatin binding causes the induction of DSB by electrons of 1.6–3.6 eV, i.e., in an energy region where a DSB cannot be produced by a single electron in pure DNA. Breaking two bonds with a subexcitation-energy electron is tentatively explained by a charge delocalization mechanism, where a single electron occupies simultaneously two σ* bonds linking the Pt atom to guanine bases on opposite strands. PMID:26793285

Recognition of chromatin by the plant alkaloid, ellipticine as a dual binder

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

Banerjee, Amrita; Sanyal, Sulagna; Majumder, Parijat

Recognition of core histone components of chromatin along with chromosomal DNA by a class of small molecule modulators is worth examining to evaluate their intracellular mode of action. A plant alkaloid ellipticine (ELP) which is a putative anticancer agent has so far been reported to function via DNA intercalation, association with topoisomerase II and binding to telomere region. However, its effect upon the potential intracellular target, chromatin is hitherto unreported. Here we have characterized the biomolecular recognition between ELP and different hierarchical levels of chromatin. The significant result is that in addition to DNA, it binds to core histone(s) andmore » can be categorized as a ‘dual binder’. As a sequel to binding with histone(s) and core octamer, it alters post-translational histone acetylation marks. We have further demonstrated that it has the potential to modulate gene expression thereby regulating several key biological processes such as nuclear organization, transcription, translation and histone modifications. - Highlights: • Ellipticine acts a dual binder binding to both DNA and core histone(s). • It induces structural perturbations in chromatin, chromatosome and histone octamer. • It alters histones acetylation and affects global gene expression.« less

Theoretical studies of the electronic spectrum of tellurium monosulfide.

PubMed

Chattopadhyaya, Surya; Nath, Abhijit; Das, Kalyan Kumar

2013-08-01

Ab initio based multireference singles and doubles configuration interaction (MRDCI) study including spin-orbit coupling is carried out to explore the electronic structure and spectroscopic properties of tellurium monosulfide (TeS) molecule by employing relativistic effective core potentials (RECP) and suitable Gaussian basis sets of the constituent atoms. Potential energy curves correlating with the lowest and second dissociation limit are constructed and spectroscopic constants (T(e), r(e), and ω(e)) of several low-lying bound Λ-S electronic states up to 3.68 eV of energy are computed. The binding energies and electric dipole moments (μ(e)) of the ground and the low-lying excited Λ-S states are also computed. The effects of the spin-orbit coupling on the electronic spectrum of the species are studied in details and compared with the available data. The transition probabilities of some dipole-allowed and spin-forbidden transitions are computed and radiative lifetimes of some excited states at lowest vibrational level are estimated from the transition probability data. Copyright © 2013 Elsevier B.V. All rights reserved.

Identification of the DNA-Binding Domains of Human Replication Protein A That Recognize G-Quadruplex DNA

PubMed Central

Prakash, Aishwarya; Natarajan, Amarnath; Marky, Luis A.; Ouellette, Michel M.; Borgstahl, Gloria E. O.

2011-01-01

Replication protein A (RPA), a key player in DNA metabolism, has 6 single-stranded DNA-(ssDNA-) binding domains (DBDs) A-F. SELEX experiments with the DBDs-C, -D, and -E retrieve a 20-nt G-quadruplex forming sequence. Binding studies show that RPA-DE binds preferentially to the G-quadruplex DNA, a unique preference not observed with other RPA constructs. Circular dichroism experiments show that RPA-CDE-core can unfold the G-quadruplex while RPA-DE stabilizes it. Binding studies show that RPA-C binds pyrimidine- and purine-rich sequences similarly. This difference between RPA-C and RPA-DE binding was also indicated by the inability of RPA-CDE-core to unfold an oligonucleotide containing a TC-region 5′ to the G-quadruplex. Molecular modeling studies of RPA-DE and telomere-binding proteins Pot1 and Stn1 reveal structural similarities between the proteins and illuminate potential DNA-binding sites for RPA-DE and Stn1. These data indicate that DBDs of RPA have different ssDNA recognition properties. PMID:21772997

Histidine-rich stabilized polyplexes for cMet-directed tumor-targeted gene transfer

NASA Astrophysics Data System (ADS)

Kos, Petra; Lächelt, Ulrich; Herrmann, Annika; Mickler, Frauke Martina; Döblinger, Markus; He, Dongsheng; Krhač Levačić, Ana; Morys, Stephan; Bräuchle, Christoph; Wagner, Ernst

2015-03-01

Overexpression of the hepatocyte growth factor receptor/c-Met proto oncogene on the surface of a variety of tumor cells gives an opportunity to specifically target cancerous tissues. Herein, we report the first use of c-Met as receptor for non-viral tumor-targeted gene delivery. Sequence-defined oligomers comprising the c-Met binding peptide ligand cMBP2 for targeting, a monodisperse polyethylene glycol (PEG) for polyplex surface shielding, and various cationic (oligoethanamino) amide cores containing terminal cysteines for redox-sensitive polyplex stabilization, were assembled by solid-phase supported syntheses. The resulting oligomers exhibited a greatly enhanced cellular uptake and gene transfer over non-targeted control sequences, confirming the efficacy and target-specificity of the formed polyplexes. Implementation of endosomal escape-promoting histidines in the cationic core was required for gene expression without additional endosomolytic agent. The histidine-enriched polyplexes demonstrated stability in serum as well as receptor-specific gene transfer in vivo upon intratumoral injection. The co-formulation with an analogous PEG-free cationic oligomer led to a further compaction of pDNA polyplexes with an obvious change of shape as demonstrated by transmission electron microscopy. Such compaction was critically required for efficient intravenous gene delivery which resulted in greatly enhanced, cMBP2 ligand-dependent gene expression in the distant tumor.Overexpression of the hepatocyte growth factor receptor/c-Met proto oncogene on the surface of a variety of tumor cells gives an opportunity to specifically target cancerous tissues. Herein, we report the first use of c-Met as receptor for non-viral tumor-targeted gene delivery. Sequence-defined oligomers comprising the c-Met binding peptide ligand cMBP2 for targeting, a monodisperse polyethylene glycol (PEG) for polyplex surface shielding, and various cationic (oligoethanamino) amide cores containing terminal cysteines for redox-sensitive polyplex stabilization, were assembled by solid-phase supported syntheses. The resulting oligomers exhibited a greatly enhanced cellular uptake and gene transfer over non-targeted control sequences, confirming the efficacy and target-specificity of the formed polyplexes. Implementation of endosomal escape-promoting histidines in the cationic core was required for gene expression without additional endosomolytic agent. The histidine-enriched polyplexes demonstrated stability in serum as well as receptor-specific gene transfer in vivo upon intratumoral injection. The co-formulation with an analogous PEG-free cationic oligomer led to a further compaction of pDNA polyplexes with an obvious change of shape as demonstrated by transmission electron microscopy. Such compaction was critically required for efficient intravenous gene delivery which resulted in greatly enhanced, cMBP2 ligand-dependent gene expression in the distant tumor. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr06556e

Structural and functional organization of the ESCRT-I trafficking complex

PubMed Central

Kostelansky, Michael S.; Sun, Ji; Lee, Sangho; Kim, Jaewon; Ghirlando, Rodolfo; Hierro, Aitor; Emr, Scott D.; Hurley, James H.

2006-01-01

Summary The Endosomal Sorting Complex Required for Transport (ESCRT) complexes are central to receptor downregulation, lysosome biogenesis, and budding of HIV. The yeast ESCRT-I complex contains the Vps23, Vps28, and Vps37 proteins and its assembly is directed by the C-terminal steadiness box of Vps23, the N-terminal half of Vps28, and the C-terminal half of Vps37. The crystal structures of a Vps23:Vps28 core subcomplex and the Vps23:Vps28:Vps37 core were solved at 2.1 and 2.8 Å resolution. Each subunit contains a structurally similar pair of helices that form the core. The N-terminal domain of Vps28 has a hydrophobic binding site on its surface that is conformationally dynamic. The C-terminal domain of Vps28 binds the ESCRT-II complex. The structure shows how ESCRT-I is assembled by a compact core from which the Vps23 UEVdomain, the Vps28 C-domain, and other domains project to bind their partners. PMID:16615894

Structural basis for diversity in the SAM clan of riboswitches.

PubMed

Trausch, Jeremiah J; Xu, Zhenjiang; Edwards, Andrea L; Reyes, Francis E; Ross, Phillip E; Knight, Rob; Batey, Robert T

2014-05-06

In bacteria, sulfur metabolism is regulated in part by seven known families of riboswitches that bind S-adenosyl-l-methionine (SAM). Direct binding of SAM to these mRNA regulatory elements governs a downstream secondary structural switch that communicates with the transcriptional and/or translational expression machinery. The most widely distributed SAM-binding riboswitches belong to the SAM clan, comprising three families that share a common SAM-binding core but differ radically in their peripheral architecture. Although the structure of the SAM-I member of this clan has been extensively studied, how the alternative peripheral architecture of the other families supports the common SAM-binding core remains unknown. We have therefore solved the X-ray structure of a member of the SAM-I/IV family containing the alternative "PK-2" subdomain shared with the SAM-IV family. This structure reveals that this subdomain forms extensive interactions with the helix housing the SAM-binding pocket, including a highly unusual mode of helix packing in which two helices pack in a perpendicular fashion. Biochemical and genetic analysis of this RNA reveals that SAM binding induces many of these interactions, including stabilization of a pseudoknot that is part of the regulatory switch. Despite strong structural similarity between the cores of SAM-I and SAM-I/IV members, a phylogenetic analysis of sequences does not indicate that they derive from a common ancestor.

Binding properties of SUMO-interacting motifs (SIMs) in yeast.

PubMed

Jardin, Christophe; Horn, Anselm H C; Sticht, Heinrich

2015-03-01

Small ubiquitin-like modifier (SUMO) conjugation and interaction play an essential role in many cellular processes. A large number of yeast proteins is known to interact non-covalently with SUMO via short SUMO-interacting motifs (SIMs), but the structural details of this interaction are yet poorly characterized. In the present work, sequence analysis of a large dataset of 148 yeast SIMs revealed the existence of a hydrophobic core binding motif and a preference for acidic residues either within or adjacent to the core motif. Thus the sequence properties of yeast SIMs are highly similar to those described for human. Molecular dynamics simulations were performed to investigate the binding preferences for four representative SIM peptides differing in the number and distribution of acidic residues. Furthermore, the relative stability of two previously observed alternative binding orientations (parallel, antiparallel) was assessed. For all SIMs investigated, the antiparallel binding mode remained stable in the simulations and the SIMs were tightly bound via their hydrophobic core residues supplemented by polar interactions of the acidic residues. In contrary, the stability of the parallel binding mode is more dependent on the sequence features of the SIM motif like the number and position of acidic residues or the presence of additional adjacent interaction motifs. This information should be helpful to enhance the prediction of SIMs and their binding properties in different organisms to facilitate the reconstruction of the SUMO interactome.

Assemblies of Boron Dipyrromethene/Porphyrin, Phthalocyanine, and C60 Moieties as Artificial Models of Photosynthesis: Synthesis, Supramolecular Interactions, and Photophysical Studies.

PubMed

Chen, Xiao-Fei; El-Khouly, Mohamed E; Ohkubo, Kei; Fukuzumi, Shunichi; Ng, Dennis K P

2018-03-12

A series of light-harvesting conjugates based on a zinc(II) phthalocyanine core with either two or four boron dipyrromethene (BODIPY) or porphyrin units have been synthesized and characterized. The conjugation of BODIPY/porphyrin units can extend the absorptions of the phthalocyanine core to cover most of the visible region. Upon addition of an imidazole-substituted C 60 (C 60 Im), it can axially bind to the zinc(II) center of the phthalocyanine core through metal-ligand interactions. The resulting complexes form photosynthetic antenna-reaction center mimics in which the BODIPY/porphyrin units serve as the antennas to capture the light and transfer the energy to the phthalocyanine core by efficient excitation energy transfer. The excited phthalocyanine is then quenched by the axially bound C 60 Im moiety by electron transfer, which has been supported by computational studies. The photoinduced processes of the assemblies have been studied in detail by various steady-state and time-resolved spectroscopic methods. By femtosecond transient absorption spectroscopic studies, the lifetimes of the charge-separated state of the bis(BODIPY) and bis(porphyrin) systems have been determined to be 3.2 and 4.0 ns, respectively. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Solvation and Evolution Dynamics of an Excess Electron in Supercritical CO2

NASA Astrophysics Data System (ADS)

Wang, Zhiping; Liu, Jinxiang; Zhang, Meng; Cukier, Robert I.; Bu, Yuxiang

2012-05-01

We present an ab initio molecular dynamics simulation of the dynamics of an excess electron solvated in supercritical CO2. The excess electron can exist in three types of states: CO2-core localized, dual-core localized, and diffuse states. All these states undergo continuous state conversions via a combination of long lasting breathing oscillations and core switching, as also characterized by highly cooperative oscillations of the excess electron volume and vertical detachment energy. All of these oscillations exhibit a strong correlation with the electron-impacted bending vibration of the core CO2, and the core-switching is controlled by thermal fluctuations.

Fractal dimension study of polaron effects in cylindrical GaAs/Al x Ga1- x As core-shell nanowires

NASA Astrophysics Data System (ADS)

Sun, Hui; Li, Hua; Tian, Qiang

2018-04-01

Polaron effects in cylindrical GaAs/Al x Ga1- x As core-shell nanowires are studied by applying the fractal dimension method. In this paper, the polaron properties of GaAs/Al x Ga1- x As core-shell nanowires with different core radii and aluminum concentrations are discussed. The polaron binding energy, polaron mass shift, and fractal dimension parameter are numerically determined as functions of shell width. The calculation results reveal that the binding energy and mass shift of the polaron first increase and then decrease as the shell width increases. A maximum value appears at a certain shell width for different aluminum concentrations and a given core radius. By using the fractal dimension method, polaron problems in cylindrical GaAs/Al x Ga1- x As core-shell nanowires are solved in a simple manner that avoids complex and lengthy calculations.

Nitric oxide activation by distal redox modulation in tetranuclear iron nitrosyl complexes.

PubMed

de Ruiter, Graham; Thompson, Niklas B; Lionetti, Davide; Agapie, Theodor

2015-11-11

A series of tetranuclear iron complexes displaying a site-differentiated metal center was synthesized. Three of the metal centers are coordinated to our previously reported ligand, based on a 1,3,5-triarylbenzene motif with nitrogen and oxygen donors. The fourth (apical) iron center is coordinatively unsaturated and appended to the trinuclear core through three bridging pyrazolates and an interstitial μ4-oxide moiety. Electrochemical studies of complex [LFe3(PhPz)3OFe][OTf]2 revealed three reversible redox events assigned to the Fe(II)4/Fe(II)3Fe(III) (-1.733 V), Fe(II)3Fe(III)/Fe(II)2Fe(III)2 (-0.727 V), and Fe(II)2Fe(III)2/Fe(II)Fe(III)3 (0.018 V) redox couples. Combined Mössbauer and crystallographic studies indicate that the change in oxidation state is exclusively localized at the triiron core, without changing the oxidation state of the apical metal center. This phenomenon is assigned to differences in the coordination environment of the two metal sites and provides a strategy for storing electron and hole equivalents without affecting the oxidation state of the coordinatively unsaturated metal. The presence of a ligand-binding site allowed the effect of redox modulation on nitric oxide activation by an Fe(II) metal center to be studied. Treatment of the clusters with nitric oxide resulted in binding of NO to the apical iron center, generating a {FeNO}(7) moiety. As with the NO-free precursors, the three reversible redox events are localized at the iron centers distal from the NO ligand. Altering the redox state of the triiron core resulted in significant change in the NO stretching frequency, by as much as 100 cm(-1). The increased activation of NO is attributed to structural changes within the clusters, in particular, those related to the interaction of the metal centers with the interstitial atom. The differences in NO activation were further shown to lead to differential reactivity, with NO disproportionation and N2O formation performed by the more electron-rich cluster.

Hot spot analysis for driving the development of hits into leads in fragment based drug discovery

PubMed Central

Hall, David R.; Ngan, Chi Ho; Zerbe, Brandon S.; Kozakov, Dima; Vajda, Sandor

2011-01-01

Fragment based drug design (FBDD) starts with finding fragment-sized compounds that are highly ligand efficient and can serve as a core moiety for developing high affinity leads. Although the core-bound structure of a protein facilitates the construction of leads, effective design is far from straightforward. We show that protein mapping, a computational method developed to find binding hot spots and implemented as the FTMap server, provides information that complements the fragment screening results and can drive the evolution of core fragments into larger leads with a minimal loss or, in some cases, even a gain in ligand efficiency. The method places small molecular probes, the size of organic solvents, on a dense grid around the protein, and identifies the hot spots as consensus clusters formed by clusters of several probes. The hot spots are ranked based on the number of probe clusters, which predicts the binding propensity of the subsites and hence their importance for drug design. Accordingly, with a single exception the main hot spot identified by FTMap binds the core compound found by fragment screening. The most useful information is provided by the neighboring secondary hot spots, indicating the regions where the core can be extended to increase its affinity. To quantify this information, we calculate the density of probes from mapping, which describes the binding propensity at each point, and show that the change in the correlation between a ligand position and the probe density upon extending or repositioning the core moiety predicts the expected change in ligand efficiency. PMID:22145575

Impact of cadmium, cobalt and nickel on sequence-specific DNA binding of p63 and p73 in vitro and in cells

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

Adámik, Matej; Bažantová, Pavla; Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 701 03 Ostrava

Highlights: • DNA binding of p53 family core domains is inhibited by cadmium, cobalt and nickel. • Binding to DNA protects p53 family core domains from metal induced inhibition. • Cadmium, cobalt and nickel induced inhibition was reverted by EDTA in vitro. - Abstract: Site-specific DNA recognition and binding activity belong to common attributes of all three members of tumor suppressor p53 family proteins: p53, p63 and p73. It was previously shown that heavy metals can affect p53 conformation, sequence-specific binding and suppress p53 response to DNA damage. Here we report for the first time that cadmium, nickel and cobalt,more » which have already been shown to disturb various DNA repair mechanisms, can also influence p63 and p73 sequence-specific DNA binding activity and transactivation of p53 family target genes. Based on results of electrophoretic mobility shift assay and luciferase reporter assay, we conclude that cadmium inhibits sequence-specific binding of all three core domains to p53 consensus sequences and abolishes transactivation of several promoters (e.g. BAX and MDM2) by 50 μM concentrations. In the presence of specific DNA, all p53 family core domains were partially protected against loss of DNA binding activity due to cadmium treatment. Effective cadmium concentration to abolish DNA–protein interactions was about two times higher for p63 and p73 proteins than for p53. Furthermore, we detected partial reversibility of cadmium inhibition for all p53 family members by EDTA. DTT was able to reverse cadmium inhibition only for p53 and p73. Nickel and cobalt abolished DNA–p53 interaction at sub-millimolar concentrations while inhibition of p63 and p73 DNA binding was observed at millimolar concentrations. In summary, cadmium strongly inhibits p53, p63 and p73 DNA binding in vitro and in cells in comparison to nickel and cobalt. The role of cadmium inhibition of p53 tumor suppressor family in carcinogenesis is discussed.« less

Sequences Flanking the Gephyrin-Binding Site of GlyRβ Tune Receptor Stabilization at Synapses

PubMed Central

Grünewald, Nora; Salvatico, Charlotte; Kress, Vanessa

2018-01-01

Abstract The efficacy of synaptic transmission is determined by the number of neurotransmitter receptors at synapses. Their recruitment depends upon the availability of postsynaptic scaffolding molecules that interact with specific binding sequences of the receptor. At inhibitory synapses, gephyrin is the major scaffold protein that mediates the accumulation of heteromeric glycine receptors (GlyRs) via the cytoplasmic loop in the β-subunit (β-loop). This binding involves high- and low-affinity interactions, but the molecular mechanism of this bimodal binding and its implication in GlyR stabilization at synapses remain unknown. We have approached this question using a combination of quantitative biochemical tools and high-density single molecule tracking in cultured rat spinal cord neurons. The high-affinity binding site could be identified and was shown to rely on the formation of a 310-helix C-terminal to the β-loop core gephyrin-binding motif. This site plays a structural role in shaping the core motif and represents the major contributor to the synaptic confinement of GlyRs by gephyrin. The N-terminal flanking sequence promotes lower affinity interactions by occupying newly identified binding sites on gephyrin. Despite its low affinity, this binding site plays a modulatory role in tuning the mobility of the receptor. Together, the GlyR β-loop sequences flanking the core-binding site differentially regulate the affinity of the receptor for gephyrin and its trapping at synapses. Our experimental approach thus bridges the gap between thermodynamic aspects of receptor-scaffold interactions and functional receptor stabilization at synapses in living cells. PMID:29464196

Observation of hole accumulation in Ge/Si core/shell nanowires using off-axis electron holography.

PubMed

Li, Luying; Smith, David J; Dailey, Eric; Madras, Prashanth; Drucker, Jeff; McCartney, Martha R

2011-02-09

Hole accumulation in Ge/Si core/shell nanowires (NWs) has been observed and quantified using off-axis electron holography and other electron microscopy techniques. The epitaxial [110]-oriented Ge/Si core/shell NWs were grown on Si (111) substrates by chemical vapor deposition through the vapor-liquid-solid growth mechanism. High-angle annular-dark-field scanning transmission electron microscopy images and off-axis electron holograms were obtained from specific NWs. The excess phase shifts measured by electron holography across the NWs indicated the presence of holes inside the Ge cores. Calculations based on a simplified coaxial cylindrical model gave hole densities of (0.4 ± 0.2) /nm(3) in the core regions.

A SERS-active sensor based on heterogeneous gold nanostar core-silver nanoparticle satellite assemblies for ultrasensitive detection of aflatoxinB1

NASA Astrophysics Data System (ADS)

Li, Aike; Tang, Lijuan; Song, Dan; Song, Shanshan; Ma, Wei; Xu, Liguang; Kuang, Hua; Wu, Xiaoling; Liu, Liqiang; Chen, Xin; Xu, Chuanlai

2016-01-01

A surface-enhanced Raman scattering (SERS) sensor based on gold nanostar (Au NS) core-silver nanoparticle (Ag NP) satellites was fabricated for the first time to detect aflatoxinB1 (AFB1). We constructed the SERS sensor using AFB1 aptamer (DNA1)-modified Ag satellites and a complementary sequence (DNA2)-modified Au NS core. The Raman label (ATP) was modified on the surface of Ag satellites. The SERS signal was enhanced when the satellite NP was attached to the Au core NS. The AFB1 aptamer on the surface of Ag satellites would bind to the targets when AFB1 was present in the system, Ag satellites were then removed and the SERS signal decreased. This SERS sensor showed superior specificity for AFB1 and the linear detection range was from 1 to 1000 pg mL-1 with the limit of detection (LOD) of 0.48 pg mL-1. The excellent recovery experiment using peanut milk demonstrated that the sensor could be applied in food and environmental detection.A surface-enhanced Raman scattering (SERS) sensor based on gold nanostar (Au NS) core-silver nanoparticle (Ag NP) satellites was fabricated for the first time to detect aflatoxinB1 (AFB1). We constructed the SERS sensor using AFB1 aptamer (DNA1)-modified Ag satellites and a complementary sequence (DNA2)-modified Au NS core. The Raman label (ATP) was modified on the surface of Ag satellites. The SERS signal was enhanced when the satellite NP was attached to the Au core NS. The AFB1 aptamer on the surface of Ag satellites would bind to the targets when AFB1 was present in the system, Ag satellites were then removed and the SERS signal decreased. This SERS sensor showed superior specificity for AFB1 and the linear detection range was from 1 to 1000 pg mL-1 with the limit of detection (LOD) of 0.48 pg mL-1. The excellent recovery experiment using peanut milk demonstrated that the sensor could be applied in food and environmental detection. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr08372a

Acanthamoeba castellanii contains a ribosomal RNA enhancer binding protein which stimulates TIF-IB binding and transcription under stringent conditions.

PubMed

Yang, Q; Radebaugh, C A; Kubaska, W; Geiss, G K; Paule, M R

1995-11-11

The intergenic spacer (IGS) of Acanthamoeba castellanii rRNA genes contains repeated elements which are weak enhancers for transcription by RNA polymerase I. A protein, EBF, was identified and partially purified which binds to the enhancers and to several other sequences within the IGS, but not to other DNA fragments, including the rRNA core promoter. No consensus binding sequence could be discerned in these fragments and bound factor is in rapid equilibrium with unbound. EBF has functional characteristics similar to vertebrate upstream binding factors (UBF). Not only does it bind to the enhancer and other IGS elements, but it also stimulates binding of TIF-IB, the fundamental transcription initiation factor, to the core promoter and stimulates transcription from the promoter. Attempts to identify polypeptides with epitopes similar to rat or Xenopus laevis UBF suggest that structurally the protein from A.castellanii is not closely related to vertebrate UBF.

Acanthamoeba castellanii contains a ribosomal RNA enhancer binding protein which stimulates TIF-IB binding and transcription under stringent conditions.

PubMed Central

Yang, Q; Radebaugh, C A; Kubaska, W; Geiss, G K; Paule, M R

1995-01-01

The intergenic spacer (IGS) of Acanthamoeba castellanii rRNA genes contains repeated elements which are weak enhancers for transcription by RNA polymerase I. A protein, EBF, was identified and partially purified which binds to the enhancers and to several other sequences within the IGS, but not to other DNA fragments, including the rRNA core promoter. No consensus binding sequence could be discerned in these fragments and bound factor is in rapid equilibrium with unbound. EBF has functional characteristics similar to vertebrate upstream binding factors (UBF). Not only does it bind to the enhancer and other IGS elements, but it also stimulates binding of TIF-IB, the fundamental transcription initiation factor, to the core promoter and stimulates transcription from the promoter. Attempts to identify polypeptides with epitopes similar to rat or Xenopus laevis UBF suggest that structurally the protein from A.castellanii is not closely related to vertebrate UBF. Images PMID:7501455

Vaccinia Virus Mutations in the L4R Gene Encoding a Virion Structural Protein Produce Abnormal Mature Particles Lacking a Nucleocapsid

PubMed Central

Moussatche, Nissin; Condit, Richard C.

2014-01-01

ABSTRACT Electron micrographs from the 1960s revealed the presence of an S-shaped tubular structure in the center of the vaccinia virion core. Recently, we showed that packaging of virus transcription enzymes is necessary for the formation of the tubular structure, suggesting that the structure is equivalent to a nucleocapsid. Based on this study and on what is known about nucleocapsids of other viruses, we hypothesized that in addition to transcription enzymes, the tubular structure also contains the viral DNA and a structural protein as a scaffold. The vaccinia virion structural protein L4 stands out as the best candidate for the role of a nucleocapsid structural protein because it is abundant, it is localized in the center of the virion core, and it binds DNA. In order to gain more insight into the structure and relevance of the nucleocapsid, we analyzed thermosensitive and inducible mutants in the L4R gene. Using a cryo-fixation method for electron microscopy (high-pressure freezing followed by freeze-substitution) to preserve labile structures like the nucleocapsid, we were able to demonstrate that in the absence of functional L4, mature particles with defective internal structures are produced under nonpermissive conditions. These particles do not contain a nucleocapsid. In addition, the core wall of these virions is abnormal. This suggests that the nucleocapsid interacts with the core wall and that the nucleocapsid structure might be more complex than originally assumed. IMPORTANCE The vaccinia virus nucleocapsid has been neglected since the 1960s due to a lack of electron microscopy techniques to preserve this labile structure. With the advent of cryo-fixation techniques, like high-pressure freezing/freeze-substitution, we are now able to consistently preserve and visualize the nucleocapsid. Because vaccinia virus early transcription is coupled to the viral core structure, detailing the structure of the nucleocapsid is indispensable for determining the mechanisms of vaccinia virus core-directed transcription. The present study represents our second attempt to understand the structure and biological significance of the nucleocapsid. We demonstrate the importance of the protein L4 for the formation of the nucleocapsid and reveal in addition that the nucleocapsid and the core wall may be associated, suggesting a higher level of complexity of the nucleocapsid than predicted. In addition, we prove the utility of high-pressure freezing in preserving the vaccinia virus nucleocapsid. PMID:25253347

Transcription Factors Encoded on Core and Accessory Chromosomes of Fusarium oxysporum Induce Expression of Effector Genes

PubMed Central

van der Does, H. Charlotte; Schmidt, Sarah M.; Langereis, Léon; Hughes, Timothy R.

2016-01-01

Proteins secreted by pathogens during host colonization largely determine the outcome of pathogen-host interactions and are commonly called ‘effectors’. In fungal plant pathogens, coordinated transcriptional up-regulation of effector genes is a key feature of pathogenesis and effectors are often encoded in genomic regions with distinct repeat content, histone code and rate of evolution. In the tomato pathogen Fusarium oxysporum f. sp. lycopersici (Fol), effector genes reside on one of four accessory chromosomes, known as the ‘pathogenicity’ chromosome, which can be exchanged between strains through horizontal transfer. The three other accessory chromosomes in the Fol reference strain may also be important for virulence towards tomato. Expression of effector genes in Fol is highly up-regulated upon infection and requires Sge1, a transcription factor encoded on the core genome. Interestingly, the pathogenicity chromosome itself contains 13 predicted transcription factor genes and for all except one, there is a homolog on the core genome. We determined DNA binding specificity for nine transcription factors using oligonucleotide arrays. The binding sites for homologous transcription factors were highly similar, suggesting that extensive neofunctionalization of DNA binding specificity has not occurred. Several DNA binding sites are enriched on accessory chromosomes, and expression of FTF1, its core homolog FTF2 and SGE1 from a constitutive promoter can induce expression of effector genes. The DNA binding sites of only these three transcription factors are enriched among genes up-regulated during infection. We further show that Ftf1, Ftf2 and Sge1 can activate transcription from their binding sites in yeast. RNAseq analysis revealed that in strains with constitutive expression of FTF1, FTF2 or SGE1, expression of a similar set of plant-responsive genes on the pathogenicity chromosome is induced, including most effector genes. We conclude that the Fol pathogenicity chromosome may be partially transcriptionally autonomous, but there are also extensive transcriptional connections between core and accessory chromosomes. PMID:27855160

Magnetic, core-shell structured and surface molecularly imprinted polymers for the rapid and selective recognition of salicylic acid from aqueous solutions

NASA Astrophysics Data System (ADS)

Zhang, Zulei; Niu, Dechao; Li, Yongsheng; Shi, Jianlin

2018-03-01

In this work, a novel kind of magnetic, core-shell structured and surface molecularly imprinted polymers (MMIPs) for the recognition of salicylic acid (SA) was facilely synthesized through a surface imprinting and sol-gel polymerization approach. The as-synthesized MMIPs exhibit uniform core-shell structure and favorable magnetic properties with a saturation magnetization of 22.8 emu g-1. The binding experiments demonstrated that MMIPs possessed high binding and specific recognition capacity, as well as fast binding kinetics and phase separation rate. The maximum binding capacity of MMIPs is around 36.8 mg g-1, nearly 6 times that of the magnetic non-imprinted polymers (MNIPs). Moreover, the selectivity experiments show that all the relative selectivity coefficients towards SA over its structure analogs are higher than 18, further indicating the markedly enhanced binding selectivity of MMIPs. Furthermore, the MMIPs were successfully applied for the determination of SA in environmental water samples with the recovery rates ranging from 94.0 to 108.0 %. This strategy may provide a versatile approach for the fabrication of well-defined molecularly imprinted polymers on nanomaterials for the analysis of complicated matrixes.

Intranuclear binding in space and time of exon junction complex and NXF1 to premRNPs/mRNPs in vivo

PubMed Central

Björk, Petra; Persson, Jan-Olov

2015-01-01

Eukaryotic gene expression requires the ordered association of numerous factors with precursor messenger RNAs (premRNAs)/messenger RNAs (mRNAs) to achieve efficiency and regulation. Here, we use the Balbiani ring (BR) genes to demonstrate the temporal and spatial association of the exon junction complex (EJC) core with gene-specific endogenous premRNAs and mRNAs. The EJC core components bind cotranscriptionally to BR premRNAs during or very rapidly after splicing. The EJC core does not recruit the nonsense-mediated decay mediaters UPF2 and UPF3 until the BR messenger RNA protein complexes (mRNPs) enter the interchromatin. Even though several known adapters for the export factor NXF1 become part of BR mRNPs already at the gene, NXF1 binds to BR mRNPs only in the interchromatin. In steady state, a subset of the BR mRNPs in the interchromatin binds NXF1, UPF2, and UPF3. This binding appears to occur stochastically, and the efficiency approximately equals synthesis and export of the BR mRNPs. Our data provide unique in vivo information on how export competent eukaryotic mRNPs are formed. PMID:26459599

Intrinsic Conformational Preferences and Interactions in α-Synuclein Fibrils: Insights from Molecular Dynamics Simulations.

PubMed

Ilie, Ioana M; Nayar, Divya; den Otter, Wouter K; van der Vegt, Nico F A; Briels, Wim J

2018-06-12

Amyloid formation by the intrinsically disordered α-synuclein protein is the hallmark of Parkinson's disease. We present atomistic Molecular Dynamics simulations of the core of α-synuclein using enhanced sampling techniques to describe the conformational and binding free energy landscapes of fragments implicated in fibril stabilization. The theoretical framework is derived to combine the free energy profiles of the fragments into the reaction free energy of a protein binding to a fibril. Our study shows that individual fragments in solution have a propensity toward attaining non-β conformations, indicating that in a fibril β-strands are stabilized by interactions with other strands. We show that most dimers of hydrogen-bonded fragments are unstable in solution, while hydrogen bonding stabilizes the collective binding of five fragments to the end of a fibril. Hydrophobic effects make further contributions to the stability of fibrils. This study is the first of its kind where structural and binding preferences of the five major fragments of the hydrophobic core of α-synuclein have been investigated. This approach improves sampling of intrinsically disordered proteins, provides information on the binding mechanism between the core sequences of α-synuclein, and enables the parametrization of coarse grained models.

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

Kononchik, Joseph P.; Vancini, Ricardo; Brown, Dennis T., E-mail: dennis_brown@ncsu.edu

Sindbis Virus (SV), the prototype alphavirus in the family togaviridae, infects both mammalian and insect cells. The ability of SV to infect cells possessing significantly different biochemical environments suggests that there may be a common mode of entry into each cell type. Previous studies show that up to 4 h post infection cells are permeable to small ions and alpha sarcin suggesting that the plasma membrane is compromised as infection takes place. Thin-section electron microscopy has also shown SV to bind to the plasma membrane and lose its electron dense core through a pore like structure developed upon interaction ofmore » the virus with the cell surface. Using freeze-fracture replicas, thin-sections and antibody labeling the data presented herein show virus associated with intramembrane particles on mosquito cells. These data suggest that the intramembrane particles associated with SV may be part of the pore structure consisting of virus proteins and cell receptor.« less

Electronic structure of layered ferroelectric high-k titanate Pr2Ti2O7

NASA Astrophysics Data System (ADS)

Atuchin, V. V.; Gavrilova, T. A.; Grivel, J.-C.; Kesler, V. G.; Troitskaia, I. B.

2012-11-01

The spectroscopic parameters and electronic structure of binary titanate Pr2Ti2O7 have been studied by IR-, Raman and X-ray photoelectron spectroscopy (XPS) for the powder sample prepared by solid state synthesis. The spectral features of valence band and all constituent element core levels have been considered. The Auger parameters of titanium and oxygen in Pr2Ti2O7 have been determined as αTi=872.8 and αO=1042.3 eV. Variations of cation-anion bond ionicity have been discussed using binding energy differences ΔTi=(BE O 1s-BE Ti 2p3/2)=71.6 eV and ΔPr=BE(Pr 3d5/2)-BE(O 1s)=403.8 eV as key parameters in comparison with those of other titanium- and praseodymium-bearing oxides.

Electronic Structures of Purple Bronze KMo6O17 Studied by X-Ray Photoemission Spectra

NASA Astrophysics Data System (ADS)

Qin, Xiaokui; Wei, Junyin; Shi, Jing; Tian, Mingliang; Chen, Hong; Tian, Decheng

X-ray photoemission spectroscopy study has been performed for the purple bronze KMo6O17. The structures of conduction band and valence band are analogous to the results of ultraviolet photoemission spectra and are also consistent with the model of Travaglini et al., but the gap between conduction and valence band is insignificant. The shape of asymmetric and broadening line of O-1s is due to unresolved contributions from the many inequivalent oxygen sites in this crystal structure. Mo 3d core-level spectrum reveals that there are two kinds of valence states of Molybdenum (Mo+5 and Mo+6). The calculated average valence state is about +5.6, which is consistent with the expectation value from the composition of this material. The tail of Mo-3d spectrum toward higher binding energy is the consequence of the excitation of electron-hole pairs with singularity index of 0.21.

Size-dependent electronic structure controls activity for ethanol electro-oxidation at Ptn/indium tin oxide (n = 1 to 14).

PubMed

von Weber, Alexander; Baxter, Eric T; Proch, Sebastian; Kane, Matthew D; Rosenfelder, Michael; White, Henry S; Anderson, Scott L

2015-07-21

Understanding the factors that control electrochemical catalysis is essential to improving performance. We report a study of electrocatalytic ethanol oxidation - a process important for direct ethanol fuel cells - over size-selected Pt centers ranging from single atoms to Pt14. Model electrodes were prepared by soft-landing of mass-selected Ptn(+) on indium tin oxide (ITO) supports in ultrahigh vacuum, and transferred to an in situ electrochemical cell without exposure to air. Each electrode had identical Pt coverage, and differed only in the size of Pt clusters deposited. The small Ptn have activities that vary strongly, and non-monotonically with deposited size. Activity per gram Pt ranges up to ten times higher than that of 5 to 10 nm Pt particles dispersed on ITO. Activity is anti-correlated with the Pt 4d core orbital binding energy, indicating that electron rich clusters are essential for high activity.

JunB is required for endothelial cell morphogenesis by regulating core-binding factor β

PubMed Central

Licht, Alexander H.; Pein, Oliver T.; Florin, Lore; Hartenstein, Bettina; Reuter, Hendrik; Arnold, Bernd; Lichter, Peter; Angel, Peter; Schorpp-Kistner, Marina

2006-01-01

The molecular mechanism triggering the organization of endothelial cells (ECs) in multicellular tubules is mechanistically still poorly understood. We demonstrate that cell-autonomous endothelial functions of the AP-1 subunit JunB are required for proper endothelial morphogenesis both in vivo in mouse embryos with endothelial-specific ablation of JunB and in in vitro angiogenesis models. By cDNA microarray analysis, we identified core-binding factor β (CBFβ), which together with the Runx proteins forms the heterodimeric core-binding transcription complex CBF, as a novel JunB target gene. In line with our findings, expression of the CBF target MMP-13 was impaired in JunB-deficient ECs. Reintroduction of CBFβ into JunB-deficient ECs rescued the tube formation defect and MMP-13 expression, indicating an important role for CBFβ in EC morphogenesis. PMID:17158955

Ultrafast Structural Dynamics in Combustion Relevant Model Systems

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

Weber, Peter M.

2014-03-31

The research project explored the time resolved structural dynamics of important model reaction system using an array of novel methods that were developed specifically for this purpose. They include time resolved electron diffraction, time resolved relativistic electron diffraction, and time resolved Rydberg fingerprint spectroscopy. Toward the end of the funding period, we also developed time-resolved x-ray diffraction, which uses ultrafast x-ray pulses at LCLS. Those experiments are just now blossoming, as the funding period expired. In the following, the time resolved Rydberg Fingerprint Spectroscopy is discussed in some detail, as it has been a very productive method. The binding energymore » of an electron in a Rydberg state, that is, the energy difference between the Rydberg level and the ground state of the molecular ion, has been found to be a uniquely powerful tool to characterize the molecular structure. To rationalize the structure sensitivity we invoke a picture from electron diffraction: when it passes the molecular ion core, the Rydberg electron experiences a phase shift compared to an electron in a hydrogen atom. This phase shift requires an adjustment of the binding energy of the electron, which is measurable. As in electron diffraction, the phase shift depends on the molecular, geometrical structure, so that a measurement of the electron binding energy can be interpreted as a measurement of the molecule’s structure. Building on this insight, we have developed a structurally sensitive spectroscopy: the molecule is first elevated to the Rydberg state, and the binding energy is then measured using photoelectron spectroscopy. The molecule’s structure is read out as the binding energy spectrum. Since the photoionization can be done with ultrafast laser pulses, the technique is inherently capable of a time resolution in the femtosecond regime. For the purpose of identifying the structures of molecules during chemical reactions, and for the analysis of molecular species in the hot environments of combustion processes, there are several features that make the Rydberg ionization spectroscopy uniquely useful. First, the Rydberg electron’s orbit is quite large and covers the entire molecule for most molecular structures of combustion interest. Secondly, the ionization does not change vibrational quantum numbers, so that even complicated and large molecules can be observed with fairly well resolved spectra. In fact, the spectroscopy is blind to vibrational excitation of the molecule. This has the interesting consequence for the study of chemical dynamics, where the molecules are invariably very energetic, that the molecular structures are observed unobstructed by the vibrational congestion that dominates other spectroscopies. This implies also that, as a tool to probe the time-dependent structural dynamics of chemically interesting molecules, Rydberg spectroscopy may well be better suited than electron or x-ray diffraction. With recent progress in calculating Rydberg binding energy spectra, we are approaching the point where the method can be evolved into a structure determination method. To implement the Rydberg ionization spectroscopy we use a molecular beam based, time-resolved pump-probe multi-photon ionization/photoelectron scheme in which a first laser pulse excites the molecule to a Rydberg state, and a probe pulse ionizes the molecule. A time-of-flight detector measures the kinetic energy spectrum of the photoelectrons. The photoelectron spectrum directly provides the binding energy of the electron, and thereby reveals the molecule’s time-dependent structural fingerprint. Only the duration of the laser pulses limits the time resolution. With a new laser system, we have now reached time resolutions better than 100 fs, although very deep UV wavelengths (down to 190 nm) have slightly longer instrument functions. The structural dynamics of molecules in Rydberg-excited states is obtained by delaying the probe ionization photon from the pump photon; the structural dynamics of molecules in their ground state or excited valence states is measured by inducing the dynamics using a near UV laser pulse, and employing a multi-photon ionization scheme via the Rydberg states as a probe process. Thus, the technique is capable of measuring the reaction dynamics in any electronic state of neutral molecules.« less

Plant Proanthocyanidins Bind to and Neutralize Bacterial Lipopolysaccharides

DTIC Science & Technology

2008-01-01

2008 NRL REVIEW 101 Plant Proanthocyanidins Bind to and Neutralize Bacterial Lipopolysaccharides J.B. Delehanty,1 B.J. Johnson,1 T.E. Hickey,1 T...polymers derived from higher plants and they have recently been associated with several potential positive health benefits such as antibacterial...and 2) a core oligosaccharide region which gives rise to 3) the O-antigen, a branched polysaccharide that extends from the core oligosaccharide .2

Multifunctional cellulase and hemicellulase

DOEpatents

Fox, Brian G.; Takasuka, Taichi; Bianchetti, Christopher M.

2015-09-29

A multifunctional polypeptide capable of hydrolyzing cellulosic materials, xylan, and mannan is disclosed. The polypeptide includes the catalytic core (cc) of Clostridium thermocellum Cthe_0797 (CelE), the cellulose-specific carbohydrate-binding module CBM3 of the cellulosome anchoring protein cohesion region (CipA) of Clostridium thermocellum (CBM3a), and a linker region interposed between the catalytic core and the cellulose-specific carbohydrate binding module. Methods of using the multifunctional polypeptide are also disclosed.

Molecular modelling study of changes induced by netropsin binding to nucleosome core particles.

PubMed Central

Pérez, J J; Portugal, J

1990-01-01

It is well known that certain sequence-dependent modulators in structure appear to determine the rotational positioning of DNA on the nucleosome core particle. That preference is rather weak and could be modified by some ligands as netropsin, a minor-groove binding antibiotic. We have undertaken a molecular modelling approach to calculate the relative energy of interaction between a DNA molecule and the protein core particle. The histones particle is considered as a distribution of positive charges on the protein surface that interacts with the DNA molecule. The molecular electrostatic potentials for the DNA, simulated as a discontinuous cylinder, were calculated using the values for all the base pairs. Computing these parameters, we calculated the relative energy of interaction and the more stable rotational setting of DNA. The binding of four molecules of netropsin to this model showed that a new minimum of energy is obtained when the DNA turns toward the protein surface by about 180 degrees, so a new energetically favoured structure appears where netropsin binding sites are located facing toward the histones surface. The effect of netropsin could be explained in terms of an induced change in the phasing of DNA on the core particle. The induced rotation is considered to optimize non-bonded contacts between the netropsin molecules and the DNA backbone. PMID:2165249

Distinct effects of Cr bulk doping and surface deposition on the chemical environment and electronic structure of the topological insulator Bi2Se3

NASA Astrophysics Data System (ADS)

Yilmaz, Turgut; Hines, William; Sun, Fu-Chang; Pletikosić, Ivo; Budnick, Joseph; Valla, Tonica; Sinkovic, Boris

2017-06-01

In this report, it is shown that Cr doped into the bulk and Cr deposited on the surface of Bi2Se3 films produced by molecular beam epitaxy (MBE) have strikingly different effects on both the electronic structure and chemical environment. Angle resolved photoemission spectroscopy (ARPES) shows that Cr doped into the bulk opens a surface state energy gap which can be seen at room temperature; much higher than the measured ferromagnetic transition temperature of ≈10 K. On the other hand, similar ARPES measurements show that the surface states remain gapless down to 15 K for films with Cr surface deposition. In addition, core-level photoemission spectroscopy of the Bi 5d, Se 3d, and Cr 3p core levels show distinct differences in the chemical environment for the two methods of Cr introduction. Surface deposition of Cr results in the formation of shoulders on the lower binding energy side for the Bi 5d peaks and two distinct Cr 3p peaks indicative of two Cr sites. These striking differences suggests an interesting possibility that better control of doping at only near surface region may offer a path to quantum anomalous Hall states at higher temperatures than reported in the literature.

Core-Shell ZIF-8@ZIF-67-Derived CoP Nanoparticle-Embedded N-Doped Carbon Nanotube Hollow Polyhedron for Efficient Overall Water Splitting.

PubMed

Pan, Yuan; Sun, Kaian; Liu, Shoujie; Cao, Xing; Wu, Konglin; Cheong, Weng-Chon; Chen, Zheng; Wang, Yu; Li, Yang; Liu, Yunqi; Wang, Dingsheng; Peng, Qing; Chen, Chen; Li, Yadong

2018-02-21

The construction of highly active and stable non-noble-metal electrocatalysts for hydrogen and oxygen evolution reactions is a major challenge for overall water splitting. Herein, we report a novel hybrid nanostructure with CoP nanoparticles (NPs) embedded in a N-doped carbon nanotube hollow polyhedron (NCNHP) through a pyrolysis-oxidation-phosphidation strategy derived from core-shell ZIF-8@ZIF-67. Benefiting from the synergistic effects between highly active CoP NPs and NCNHP, the CoP/NCNHP hybrid exhibited outstanding bifunctional electrocatalytic performances. When the CoP/NCNHP was employed as both the anode and cathode for overall water splitting, a potential as low as 1.64 V was needed to achieve the current density of 10 mA·cm -2 , and it still exhibited superior activity after continuously working for 36 h with nearly negligible decay in potential. Density functional theory calculations indicated that the electron transfer from NCNHP to CoP could increase the electronic states of the Co d-orbital around the Fermi level, which could increase the binding strength with H and therefore improve the electrocatalytic performance. The strong stability is attributed to high oxidation resistance of the CoP surface protected by the NCNHP.

Effect of Molecular Guest Binding on the d-d Transitions of Ni2+ of CPO-27-Ni: A Combined UV-Vis, Resonant-Valence-to-Core X-ray Emission Spectroscopy, and Theoretical Study.

PubMed

Gallo, Erik; Gorelov, Evgeny; Guda, Alexander A; Bugaev, Aram L; Bonino, Francesca; Borfecchia, Elisa; Ricchiardi, Gabriele; Gianolio, Diego; Chavan, Sachin; Lamberti, Carlo

2017-12-04

We used Ni K-edge resonant-valence-to-core X-ray emission spectroscopy (RVtC-XES, also referred to as direct RIXS), an element-selective bulk-sensitive synchrotron-based technique, to investigate the electronic structure of the CPO-27-Ni metal-organic framework (MOF) upon molecular adsorption of significant molecular probes: H 2 O, CO, H 2 S, and NO. We compare RVtC-XES with UV-vis spectroscopy, and we show that the element selectivity of RVtC-XES is of strategic significance to observe the full set of d-d excitations in Ni 2+ , which are partially overshadowed by the low-energy π-π* transitions of the Ni ligands in standard diffuse-reflectance UV-vis experiments. Our combined RVtC-XES/UV-vis approach provides access to the whole set of d-d excitations, allowing us a complete discussion of the changes undergone by the electronic configuration of the Ni 2+ sites hosted within the MOF upon molecular adsorption. The experimental data have been interpreted by multiplet ligand-field theory calculations based on Wannier orbitals. This study represents a step further in understanding the ability of the CPO-27-Ni MOFs in molecular sorption and separation applications.

Shell effect on the electron and hole reorganization energy of core-shell II-VI nanoclusters

NASA Astrophysics Data System (ADS)

Cui, Xianhui; Wang, Xinqin; Yang, Fang; Cui, Yingqi; Yang, Mingli

2017-09-01

Density functional theory calculations were performed to study the effect of shell encapsulation on the geometrical and electronic properties of pure and hybrid core-shell CdSe nanoclusters. The CdSe cores are distorted by the shells, and the shells exhibit distinct surface activity from the cores, which leads to remarkable changes in their electron transition behaviors. Although the electron and hole reorganization energies, which are related to the formation and recombination of electron-hole pairs, vary in a complicated way, their itemized contributions, potentials of electron extraction, ionization and affinity, and hole extraction (HEP), are dependent on the cluster size, shell composition and/or solvent. Our calculations suggest that the behaviors of charge carriers, free electrons and holes, in the semiconductor core-shell nanoclusters can be modulated by selecting appropriate cluster size and controlling the chemical composition of the shells.

Spectroscopic Studies of the Super Relaxed State of Skeletal Muscle

PubMed Central

Naber, Nariman; Pate, Edward; Canton, Marcella; Reggiani, Carlo; Cooke, Roger

2016-01-01

In the super-relaxed state of myosin, ATPase activity is strongly inhibited by binding of the myosin heads to the core of the thick filament in a structure known as the interacting-heads motif. In the disordered relaxed state myosin heads are not bound to the core of the thick filament and have an ATPase rate that is 10 fold greater. In the interacting-heads motif the two regulatory light chains appear to bind to each other. We have made single cysteine mutants of the regulatory light chain, placed both paramagnetic and fluorescent probes on them, and exchanged them into skinned skeletal muscle fibers. Many of the labeled light chains tended to disrupt the stability of the super-relaxed state, and showed spectral changes in the transition from the disordered relaxed state to the super-relaxed state. These data support the putative interface between the two regulatory light chains identified by cryo electron microscopy and show that both the divalent cation bound to the regulatory light chain and the N-terminus of the regulatory light chain play a role in the stability of the super-relaxed state. One probe showed a shift to shorter wavelengths in the super-relaxed state such that a ratio of intensities at 440nm to that at 520nm provided a measure of the population of the super-relaxed state amenable for high throughput screens for finding potential pharmaceuticals. The results provide a proof of concept that small molecules that bind to this region can destabilize the super-relaxed state and provide a method to search for small molecules that do so leading to a potentially effective treatment for Type 2 diabetes and obesity. PMID:27479128

E-novo: an automated workflow for efficient structure-based lead optimization.

PubMed

Pearce, Bradley C; Langley, David R; Kang, Jia; Huang, Hongwei; Kulkarni, Amit

2009-07-01

An automated E-Novo protocol designed as a structure-based lead optimization tool was prepared through Pipeline Pilot with existing CHARMm components in Discovery Studio. A scaffold core having 3D binding coordinates of interest is generated from a ligand-bound protein structural model. Ligands of interest are generated from the scaffold using an R-group fragmentation/enumeration tool within E-Novo, with their cores aligned. The ligand side chains are conformationally sampled and are subjected to core-constrained protein docking, using a modified CHARMm-based CDOCKER method to generate top poses along with CDOCKER energies. In the final stage of E-Novo, a physics-based binding energy scoring function ranks the top ligand CDOCKER poses using a more accurate Molecular Mechanics-Generalized Born with Surface Area method. Correlation of the calculated ligand binding energies with experimental binding affinities were used to validate protocol performance. Inhibitors of Src tyrosine kinase, CDK2 kinase, beta-secretase, factor Xa, HIV protease, and thrombin were used to test the protocol using published ligand crystal structure data within reasonably defined binding sites. In-house Respiratory Syncytial Virus inhibitor data were used as a more challenging test set using a hand-built binding model. Least squares fits for all data sets suggested reasonable validation of the protocol within the context of observed ligand binding poses. The E-Novo protocol provides a convenient all-in-one structure-based design process for rapid assessment and scoring of lead optimization libraries.

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.

DNA-polymer micelles as nanoparticles with recognition ability.

PubMed

Talom, Renée Mayap; Fuks, Gad; Kaps, Leonard; Oberdisse, Julian; Cerclier, Christel; Gaillard, Cédric; Mingotaud, Christophe; Gauffre, Fabienne

2011-11-25

The Watson-Crick binding of DNA single strands is a powerful tool for the assembly of nanostructures. Our objective is to develop polymer nanoparticles equipped with DNA strands for surface-patterning applications, taking advantage of the DNA technology, in particular, recognition and reversibility. A hybrid DNA copolymer is synthesized through the conjugation of a ssDNA (22-mer) with a poly(ethylene oxide)-poly(caprolactone) diblock copolymer (PEO-b-PCl). It is shown that, in water, the PEO-b-PCl-ssDNA(22) polymer forms micelles with a PCl hydrophobic core and a hydrophilic corona made of PEO and DNA. The micelles are thoroughly characterized using electron microscopy (TEM and cryoTEM) and small-angle neutron scattering. The binding of these DNA micelles to a surface through DNA recognition is monitored using a quartz crystal microbalance and imaged by atomic force microscopy. The micelles can be released from the surface by a competitive displacement event. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electronic and Structural Parameters of Phosphorus-Oxygen Bonds in Inorganic Phosphate Crystals

NASA Astrophysics Data System (ADS)

Atuchin, V. V.; Kesler, V. G.; Pervukhina, N. V.

Wide set of experimental results on binding energy of photoelectrons emitted from P 2p, P 2s, and O 1s core levels has been observed for inorganic phosphate crystals and the parameters were compared using energy differences Δ(O 1s - P 2p) and Δ (O 1s - P 2s) as most robust characteristics. Linear dependence of the binding energy difference on mean chemical bond length L(P-O) between phosphorus and oxygen atoms has been found. The functions are of the forms: Δ (O 1s - P 2p) (eV) = 375.54 + 0.146 · L(P-O) (pm) and Δ (O 1s - P 2s) (eV) = 320.77 + 0.129 · L(P-O) (pm). The dependencies are general for inorganic phosphates and may be used in quantitative component analysis of X-ray photoemission spectra of complex oxide compounds including functional groups with different coordination of P and O atoms.

DNA sequence determinants controlling affinity, stability and shape of DNA complexes bound by the nucleoid protein Fis

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

Hancock, Stephen P.; Stella, Stefano; Cascio, Duilio

The abundant Fis nucleoid protein selectively binds poorly related DNA sequences with high affinities to regulate diverse DNA reactions. Fis binds DNA primarily through DNA backbone contacts and selects target sites by reading conformational properties of DNA sequences, most prominently intrinsic minor groove widths. High-affinity binding requires Fis-stabilized DNA conformational changes that vary depending on DNA sequence. In order to better understand the molecular basis for high affinity site recognition, we analyzed the effects of DNA sequence within and flanking the core Fis binding site on binding affinity and DNA structure. X-ray crystal structures of Fis-DNA complexes containing variable sequencesmore » in the noncontacted center of the binding site or variations within the major groove interfaces show that the DNA can adapt to the Fis dimer surface asymmetrically. We show that the presence and position of pyrimidine-purine base steps within the major groove interfaces affect both local DNA bending and minor groove compression to modulate affinities and lifetimes of Fis-DNA complexes. Sequences flanking the core binding site also modulate complex affinities, lifetimes, and the degree of local and global Fis-induced DNA bending. In particular, a G immediately upstream of the 15 bp core sequence inhibits binding and bending, and A-tracts within the flanking base pairs increase both complex lifetimes and global DNA curvatures. Taken together, our observations support a revised DNA motif specifying high-affinity Fis binding and highlight the range of conformations that Fis-bound DNA can adopt. Lastly, the affinities and DNA conformations of individual Fis-DNA complexes are likely to be tailored to their context-specific biological functions.« less

DNA sequence determinants controlling affinity, stability and shape of DNA complexes bound by the nucleoid protein Fis

DOE PAGES

Hancock, Stephen P.; Stella, Stefano; Cascio, Duilio; ...

2016-03-09

The abundant Fis nucleoid protein selectively binds poorly related DNA sequences with high affinities to regulate diverse DNA reactions. Fis binds DNA primarily through DNA backbone contacts and selects target sites by reading conformational properties of DNA sequences, most prominently intrinsic minor groove widths. High-affinity binding requires Fis-stabilized DNA conformational changes that vary depending on DNA sequence. In order to better understand the molecular basis for high affinity site recognition, we analyzed the effects of DNA sequence within and flanking the core Fis binding site on binding affinity and DNA structure. X-ray crystal structures of Fis-DNA complexes containing variable sequencesmore » in the noncontacted center of the binding site or variations within the major groove interfaces show that the DNA can adapt to the Fis dimer surface asymmetrically. We show that the presence and position of pyrimidine-purine base steps within the major groove interfaces affect both local DNA bending and minor groove compression to modulate affinities and lifetimes of Fis-DNA complexes. Sequences flanking the core binding site also modulate complex affinities, lifetimes, and the degree of local and global Fis-induced DNA bending. In particular, a G immediately upstream of the 15 bp core sequence inhibits binding and bending, and A-tracts within the flanking base pairs increase both complex lifetimes and global DNA curvatures. Taken together, our observations support a revised DNA motif specifying high-affinity Fis binding and highlight the range of conformations that Fis-bound DNA can adopt. Lastly, the affinities and DNA conformations of individual Fis-DNA complexes are likely to be tailored to their context-specific biological functions.« less

A near ambient pressure XPS study of subnanometer silver clusters on Al 2O 3 and TiO 2 ultrathin film supports

DOE PAGES

Mao, Bao -Hua; Chang, Rui; Shi, Lei; ...

2014-10-29

Here, we have investigated model systems of silver clusters with different sizes (3 and 15 atoms) deposited on alumina and titania supports using ambient pressure X-ray photoelectron spectroscopy. The electronic structures of silver clusters and support materials are studied upon exposure to various atmospheres (ultrahigh vacuum, O 2 and CO) at different temperatures. Compared to bulk silver, the binding energies of silver clusters are about 0.55 eV higher on TiO 2 and 0.95 eV higher on Al 2O 3 due to the final state effect and the interaction with supports. No clear size effect of the silver XPS peak ismore » observed on different silver clusters among these samples. Silver clusters on titania show better stability against sintering. Al 2p and Ti 2p core level peak positions of the alumina and titania support surfaces change upon exposure to oxygen while the Ag 3d core level position remains unchanged. We discuss the origin of these core level shifts and their implications for catalytic properties of Ag clusters.« less

Prediction of FAD binding sites in electron transport proteins according to efficient radial basis function networks and significant amino acid pairs.

PubMed

Le, Nguyen-Quoc-Khanh; Ou, Yu-Yen

2016-07-30

Cellular respiration is a catabolic pathway for producing adenosine triphosphate (ATP) and is the most efficient process through which cells harvest energy from consumed food. When cells undergo cellular respiration, they require a pathway to keep and transfer electrons (i.e., the electron transport chain). Due to oxidation-reduction reactions, the electron transport chain produces a transmembrane proton electrochemical gradient. In case protons flow back through this membrane, this mechanical energy is converted into chemical energy by ATP synthase. The convert process is involved in producing ATP which provides energy in a lot of cellular processes. In the electron transport chain process, flavin adenine dinucleotide (FAD) is one of the most vital molecules for carrying and transferring electrons. Therefore, predicting FAD binding sites in the electron transport chain is vital for helping biologists understand the electron transport chain process and energy production in cells. We used an independent data set to evaluate the performance of the proposed method, which had an accuracy of 69.84 %. We compared the performance of the proposed method in analyzing two newly discovered electron transport protein sequences with that of the general FAD binding predictor presented by Mishra and Raghava and determined that the accuracy of the proposed method improved by 9-45 % and its Matthew's correlation coefficient was 0.14-0.5. Furthermore, the proposed method enabled reducing the number of false positives significantly and can provide useful information for biologists. We developed a method that is based on PSSM profiles and SAAPs for identifying FAD binding sites in newly discovered electron transport protein sequences. This approach achieved a significant improvement after we added SAAPs to PSSM features to analyze FAD binding proteins in the electron transport chain. The proposed method can serve as an effective tool for predicting FAD binding sites in electron transport proteins and can help biologists understand the functions of the electron transport chain, particularly those of FAD binding sites. We also developed a web server which identifies FAD binding sites in electron transporters available for academics.

Plasmonic nanodiamonds: targeted core-shell type nanoparticles for cancer cell thermoablation.

PubMed

Rehor, Ivan; Lee, Karin L; Chen, Kevin; Hajek, Miroslav; Havlik, Jan; Lokajova, Jana; Masat, Milan; Slegerova, Jitka; Shukla, Sourabh; Heidari, Hamed; Bals, Sara; Steinmetz, Nicole F; Cigler, Petr

2015-02-18

Targeted biocompatible nanostructures with controlled plasmonic and morphological parameters are promising materials for cancer treatment based on selective thermal ablation of cells. Here, core-shell plasmonic nanodiamonds consisting of a silica-encapsulated diamond nanocrystal coated in a gold shell are designed and synthesized. The architecture of particles is analyzed and confirmed in detail using electron tomography. The particles are biocompatibilized using a PEG polymer terminated with bioorthogonally reactive alkyne groups. Azide-modified transferrin is attached to these particles, and their high colloidal stability and successful targeting to cancer cells overexpressing the transferrin receptor are demonstrated. The particles are nontoxic to the cells and they are readily internalized upon binding to the transferrin receptor. The high plasmonic cross section of the particles in the near-infrared region is utilized to quantitatively ablate the cancer cells with a short, one-minute irradiation by a pulse 750-nm laser. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Target binding influences permeability in aptamer-polyelectrolyte microcapsules.

PubMed

Sultan, Yasir; DeRosa, Maria C

2011-05-09

Aptamer-polyelectrolyte microcapsules are prepared for potential use as triggered delivery vehicles and microreactors. The hollow microcapsules are prepared from the sulforhodamine B aptamer and the polyelectrolytes poly(allylamine hydrochloride) and poly(sodium 4-styrene-sulfonate), using layer-by-layer (LbL) film deposition templated on a sacrificial CaCO(3) spherical core. Scanning electron microscopy and confocal microscopy confirm the formation of spherical CaCO(3) cores and LbL-aptamer microcapsules. Colocalization studies with fluorescently-tagged aptamer and sulforhodamine B verify the ability of the aptamer to recognize its cognate target in the presence of the K(+) ions that are required for its characteristic G-quadruplex formation. Fluorescence recovery after photobleaching studies confirms a significant difference in the permeability of the aptamer-polyelectrolyte microcapsules for the sulforhodamine B dye target compared to control microcapsules prepared with a random oligonucleotide. These results suggest that aptamer-based 'smart' responsive films and microcapsules could be applied to problems of catalysis and controlled release. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantum Effects in Cation Interactions with First and Second Coordination Shell Ligands in Metalloproteins

PubMed Central

2015-01-01

Despite decades of investigations, the principal mechanisms responsible for the high affinity and specificity of proteins for key physiological cations K+, Na+, and Ca2+ remain a hotly debated topic. At the core of the debate is an apparent need (or lack thereof) for an accurate description of the electrostatic response of the charge distribution in a protein to the binding of an ion. These effects range from partial electronic polarization of the directly ligating atoms to long-range effects related to partial charge transfer and electronic delocalization effects. While accurate modeling of cation recognition by metalloproteins warrants the use of quantum-mechanics (QM) calculations, the most popular approximations used in major biomolecular simulation packages rely on the implicit modeling of electronic polarization effects. That is, high-level QM computations for ion binding to proteins are desirable, but they are often unfeasible, because of the large size of the reactive-site models and the need to sample conformational space exhaustively at finite temperature. Several solutions to this challenge have been proposed in the field, ranging from the recently developed Drude polarizable force-field for simulations of metalloproteins to approximate tight-binding density functional theory (DFTB). To delineate the usefulness of different approximations, we examined the accuracy of three recent and commonly used theoretical models and numerical algorithms, namely, CHARMM C36, the latest developed Drude polarizable force fields, and DFTB3 with the latest 3OB parameters. We performed MD simulations for 30 cation-selective proteins with high-resolution X-ray structures to create ensembles of structures for analysis with different levels of theory, e.g., additive and polarizable force fields, DFTB3, and DFT. The results from DFT computations were used to benchmark CHARMM C36, Drude, and DFTB3 performance. The explicit modeling of quantum effects unveils the key electrostatic properties of the protein sites and the importance of specific ion-protein interactions. One of the most interesting findings is that secondary coordination shells of proteins are noticeably perturbed in a cation-dependent manner, showing significant delocalization and long-range effects of charge transfer and polarization upon binding Ca2+. PMID:26574284

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.

A study of planar anchor groups for graphene-based single-molecule electronics.

PubMed

Bailey, Steven; Visontai, David; Lambert, Colin J; Bryce, Martin R; Frampton, Harry; Chappell, David

2014-02-07

To identify families of stable planar anchor groups for use in single molecule electronics, we report detailed results for the binding energies of two families of anthracene and pyrene derivatives adsorbed onto graphene. We find that all the selected derivatives functionalized with either electron donating or electron accepting substituents bind more strongly to graphene than the parent non-functionalized anthracene or pyrene. The binding energy is sensitive to the detailed atomic alignment of substituent groups over the graphene substrate leading to larger than expected binding energies for -OH and -CN derivatives. Furthermore, the ordering of the binding energies within the anthracene and pyrene series does not simply follow the electron affinities of the substituents. Energy barriers to rotation or displacement on the graphene surface are much lower than binding energies for adsorption and therefore at room temperature, although the molecules are bound to the graphene, they are almost free to move along the graphene surface. Binding energies can be increased by incorporating electrically inert side chains and are sensitive to the conformation of such chains.

A study of planar anchor groups for graphene-based single-molecule electronics

NASA Astrophysics Data System (ADS)

Bailey, Steven; Visontai, David; Lambert, Colin J.; Bryce, Martin R.; Frampton, Harry; Chappell, David

2014-02-01

To identify families of stable planar anchor groups for use in single molecule electronics, we report detailed results for the binding energies of two families of anthracene and pyrene derivatives adsorbed onto graphene. We find that all the selected derivatives functionalized with either electron donating or electron accepting substituents bind more strongly to graphene than the parent non-functionalized anthracene or pyrene. The binding energy is sensitive to the detailed atomic alignment of substituent groups over the graphene substrate leading to larger than expected binding energies for -OH and -CN derivatives. Furthermore, the ordering of the binding energies within the anthracene and pyrene series does not simply follow the electron affinities of the substituents. Energy barriers to rotation or displacement on the graphene surface are much lower than binding energies for adsorption and therefore at room temperature, although the molecules are bound to the graphene, they are almost free to move along the graphene surface. Binding energies can be increased by incorporating electrically inert side chains and are sensitive to the conformation of such chains.

Probing a 2-aminobenzimidazole library for binding to RNA internal loops via two-dimensional combinatorial screening.

PubMed

Velagapudi, Sai Pradeep; Pushechnikov, Alexei; Labuda, Lucas P; French, Jonathan M; Disney, Matthew D

2012-11-16

There are many potential RNA drug targets in bacterial, viral, and human transcriptomes. However, there are few small molecules that modulate RNA function. This is due, in part, to a lack of fundamental understanding about RNA-ligand interactions including the types of small molecules that bind to RNA structural elements and the RNA structural elements that bind to small molecules. In an effort to better understand RNA-ligand interactions, we diversified the 2-aminobenzimidazole core (2AB) and probed the resulting library for binding to a library of RNA internal loops. We chose the 2AB core for these studies because it is a privileged scaffold for binding RNA based on previous reports. These studies identified that N-methyl pyrrolidine, imidazole, and propylamine diversity elements at the R1 position increase binding to internal loops; variability at the R2 position is well tolerated. The preferred RNA loop space was also determined for five ligands using a statistical approach and identified trends that lead to selective recognition.

Decorin is a Zn(2+) Metalloprotein

NASA Technical Reports Server (NTRS)

Yang, Vivian W.-C.; LaBrenz, Steven R.; Rosenberg, Lawrence C.; McQuillan, David; Hoeoek, Magnus

1998-01-01

Decorin is ubiquitously distributed in the extracellular matrix of mammals and a member of the proteoglycan family characterized by a core protein dominated by Leucine Rich Repeat motifs. We here demonstrate that decorin extracted from bovine tissues under denaturing conditions or produced in recombinant "native" form by cultured mammalian cells, has a high affinity for Zn(2+). Binding of Zn(2+) to decorin is demonstrated by Zn(2+) chelating chromatography and equilibrium dialyses. The Zn(2+) binding sites are localized to the N-terminal domain of the core protein that contains 4 Cys residues in the spacing reminiscent of a Zn finger. A recombinant 41 amino acid long peptide representing the N-terminal domain of decorin has full Zn(2+) binding activity and binds two Zn(2+) ions with an average K(D) of 3 x 10(exp -7) M. Biglycan, a proteoglycan that is structurally closely related to decorin contains a similar high affinity Zn(2+) binding segment, whereas the structurally more distantly related proteoglycans, epiphycan and osteoglycin, did not bind Zn(2+) with high affinity.

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

Wu, Kailang; Li, Weikai; Peng, Guiqing

NL63 coronavirus (NL63-CoV), a prevalent human respiratory virus, is the only group I coronavirus known to use angiotensin-converting enzyme 2 (ACE2) as its receptor. Incidentally, ACE2 is also used by group II SARS coronavirus (SARS-CoV). We investigated how different groups of coronaviruses recognize the same receptor, whereas homologous group I coronaviruses recognize different receptors. We determined the crystal structure of NL63-CoV spike protein receptor-binding domain (RBD) complexed with human ACE2. NL63-CoV RBD has a novel {beta}-sandwich core structure consisting of 2 layers of {beta}-sheets, presenting 3 discontinuous receptor-binding motifs (RBMs) to bind ACE2. NL63-CoV and SARS-CoV have no structural homologymore » in RBD cores or RBMs; yet the 2 viruses recognize common ACE2 regions, largely because of a 'virus-binding hotspot' on ACE2. Among group I coronaviruses, RBD cores are conserved but RBMs are variable, explaining how these viruses recognize different receptors. These results provide a structural basis for understanding viral evolution and virus-receptor interactions.« less

P20A inhibits HIV-1 fusion through its electrostatic interaction with the distal region of the gp41 fusion core.

PubMed

Fu, Shushu; Tong, Pei; Tan, Yue; Zhu, Yun; Chen, Ying-Hua

2015-09-01

We previously identified an HIV-1 fusion inhibitor P20A targeting HIV-1 gp41 6-HB fusion core. Using alanine scanning mutagenesis, we investigated the effect of 6-HB surface residue mutations on the binding affinity between P20A and 6-HB. Substitution of positively or negatively charged residues in the distal region of 6-HB with alanines resulted in significant decrease or increase of its binding affinity to P20A, respectively. The 6-HB with E630K, D632K, or E634K mutation exhibited enhanced binding affinity with P20A, suggesting that P20A blocks HIV-1 fusion through electrostatic interaction with the positively charged residues in the distal region of the gp41 fusion core. Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Host-Guest Complexes with Protein-Ligand-Like Affinities: Computational Analysis and Design

PubMed Central

Moghaddam, Sarvin; Inoue, Yoshihisa

2009-01-01

It has recently been discovered that guests combining a nonpolar core with cationic substituents bind cucurbit[7]uril (CB[7]) in water with ultra-high affinities. The present study uses the Mining Minima algorithm to study the physics of these extraordinary associations and to computationally test a new series of CB[7] ligands designed to bind with similarly high affinity. The calculations reproduce key experimental observations regarding the affinities of ferrocene-based guests with CB[7] and β-cyclodextrin and provide a coherent view of the roles of electrostatics and configurational entropy as determinants of affinity in these systems. The newly designed series of compounds is based on a bicyclo[2.2.2]octane core, which is similar in size and polarity to the ferrocene core of the existing series. Mining Minima predicts that these new compounds will, like the ferrocenes, bind CB[7] with extremely high affinities. PMID:19133781

Solid charged-core model of ball lightning

NASA Astrophysics Data System (ADS)

Muldrew, D. B.

2010-01-01

In this study, ball lightning (BL) is assumed to have a solid, positively-charged core. According to this underlying assumption, the core is surrounded by a thin electron layer with a charge nearly equal in magnitude to that of the core. A vacuum exists between the core and the electron layer containing an intense electromagnetic (EM) field which is reflected and guided by the electron layer. The microwave EM field applies a ponderomotive force (radiation pressure) to the electrons preventing them from falling into the core. The energetic electrons ionize the air next to the electron layer forming a neutral plasma layer. The electric-field distributions and their associated frequencies in the ball are determined by applying boundary conditions to a differential equation given by Stratton (1941). It is then shown that the electron and plasma layers are sufficiently thick and dense to completely trap and guide the EM field. This model of BL is exceptional in that it can explain all or nearly all of the peculiar characteristics of BL. The ES energy associated with the core charge can be extremely large which can explain the observations that occasionally BL contains enormous energy. The mass of the core prevents the BL from rising like a helium-filled balloon - a problem with most plasma and burning-gas models. The positively charged core keeps the negatively charged electron layer from diffusing away, i.e. it holds the ball together; other models do not have a mechanism to do this. The high electrical charges on the core and in the electron layer explains why some people have been electrocuted by BL. Experiments indicate that BL radiates microwaves upon exploding and this is consistent with the model. The fact that this novel model of BL can explain these and other observations is strong evidence that the model should be taken seriously.

Thiophene-Core Estrogen Receptor Ligands Having Superagonist Activity

PubMed Central

Min, Jian; Wang, Pengcheng; Srinivasan, Sathish; Nwachukwu, Jerome C.; Guo, Pu; Huang, Minjian; Carlson, Kathryn E.; Katzenellenbogen, John A.; Nettles, Kendall W.; Zhou, Hai-Bing

2013-01-01

To probe the importance of the heterocyclic core of estrogen receptor (ER) ligands, we prepared a series of thiophene-core ligands by Suzuki cross-coupling of aryl boronic acids with bromo-thiophenes, and we assessed their receptor binding and cell biological activities. The disposition of the phenol substituents on the thiophene core, at alternate or adjacent sites, and the nature of substituents on these phenols all contribute to binding affinity and subtype selectivity. Most of the bis(hydroxyphenyl)-thiophenes were ERβ selective, whereas the tris(hydroxyphenyl)-thiophenes were ERα selective; analogous furan-core compounds generally have lower affinity and less selectivity. Some diarylthiophenes show distinct superagonist activity in reporter gene assays, giving maximal activities 2–3 times that of estradiol, and modeling suggests that these ligands have a different interaction with a hydrogen-bonding residue in helix-11. Ligand-core modification may be a new strategy for developing ER ligands whose selectivity is based on having transcriptional activity greater than that of estradiol. PMID:23586645

HCV Core Residues Critical for Infectivity Are Also Involved in Core-NS5A Complex Formation

PubMed Central

Gawlik, Katarzyna; Baugh, James; Chatterji, Udayan; Lim, Precious J.; Bobardt, Michael D.; Gallay, Philippe A.

2014-01-01

Hepatitis C virus (HCV) infection is a major cause of liver disease. The molecular machinery of HCV assembly and particle release remains obscure. A better understanding of the assembly events might reveal new potential antiviral strategies. It was suggested that the nonstructural protein 5A (NS5A), an attractive recent drug target, participates in the production of infectious particles as a result of its interaction with the HCV core protein. However, prior to the present study, the NS5A-binding site in the viral core remained unknown. We found that the D1 domain of core contains the NS5A-binding site with the strongest interacting capacity in the basic P38-K74 cluster. We also demonstrated that the N-terminal basic residues of core at positions 50, 51, 59 and 62 were required for NS5A binding. Analysis of all substitution combinations of R50A, K51A, R59A, and R62A, in the context of the HCVcc system, showed that single, double, triple, and quadruple mutants were fully competent for viral RNA replication, but deficient in secretion of viral particles. Furthermore, we found that the extracellular and intracellular infectivity of all the mutants was abolished, suggesting a defect in the formation of infectious particles. Importantly, we showed that the interaction between the single and quadruple core mutants and NS5A was impaired in cells expressing full-length HCV genome. Interestingly, mutations of the four basic residues of core did not alter the association of core or NS5A with lipid droplets. This study showed for the first time that basic residues in the D1 domain of core that are critical for the formation of infectious extracellular and intracellular particles also play a role in core-NS5A interactions. PMID:24533158

Structure of the C-terminal effector-binding domain of AhrC bound to its corepressor l-arginine

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

Garnett, James A.; Baumberg, Simon; Stockley, Peter G.

2007-11-01

The crystal structure of the C-terminal domain hexameric core of AhrC, with bound corepressor (l-arginine), has been solved at 1.95 Å resolution. Binding of l-arginine results in a rotation between the two trimers of the hexamer, leading to the activation of the DNA-binding state. The arginine repressor/activator protein (AhrC) from Bacillus subtilis belongs to a large family of multifunctional transcription factors that are involved in the regulation of bacterial arginine metabolism. AhrC interacts with operator sites in the promoters of arginine biosynthetic and catabolic operons, acting as a transcriptional repressor at biosynthetic sites and an activator of transcription at catabolicmore » sites. AhrC is a hexamer of identical subunits, each having two domains. The C-terminal domains form the core of the protein and are involved in oligomerization and l-arginine binding. The N-terminal domains lie on the outside of the compact core and play a role in binding to 18 bp DNA operators called ARG boxes. The C-terminal domain of AhrC has been expressed, purified and characterized, and also crystallized as a hexamer with the bound corepressor l-arginine. Here, the crystal structure refined to 1.95 Å is presented.« less

Isolation and functional characterization of TIF-IB, a factor that confers promoter specificity to mouse RNA polymerase I.

PubMed

Schnapp, A; Clos, J; Hädelt, W; Schreck, R; Cvekl, A; Grummt, I

1990-03-25

The murine ribosomal gene promoter contains two cis-acting control elements which operate in concert to promote efficient and accurate transcription initiation by RNA polymerase I. The start site proximal core element which is indispensable for promoter recognition by RNA polymerase I (pol I) encompasses sequences from position -39 to -1. An upstream control element (UCE) which is located between nucleotides -142 and -112 stimulates the efficiency of transcription initiation both in vivo and in vitro. Here we report the isolation and functional characterization of a specific rDNA binding protein, the transcription initiation factor TIF-IB, which specifically interacts with the core region of the mouse ribosomal RNA gene promoter. Highly purified TIF-IB complements transcriptional activity in the presence of two other essential initiation factors TIF-IA and TIF-IC. We demonstrate that the binding efficiency of purified TIF-IB to the core promoter is strongly enhanced by the presence in cis of the UCE. This positive effect of upstream sequences on TIF-IB binding is observed throughout the purification procedure suggesting that the synergistic action of the two distant promoter elements is not mediated by a protein different from TIF-IB. Increasing the distance between both control elements still facilitates stable factor binding but eliminates transcriptional activation. The results demonstrate that TIF-IB binding to the rDNA promoter is an essential early step in the assembly of a functional transcription initiation complex. The subsequent interaction of TIF-IB with other auxiliary transcription initiation factors, however, requires the correct spacing between the UCE and the core promoter element.

A Study of the Vacancy-Impurity Interaction in Dilute Nickel Alloys by Core Electron Annihilation

NASA Astrophysics Data System (ADS)

Arbuzov, V. L.; Danilov, S. E.; Druzhkov, A. P.

1997-08-01

It is shown that the angular correlation of annihilation radiation can be used to identify vacancy-impurity complexes in dilute alloys. Annihilation of trapped positrons with core electrons bears information about the chemical environment of a vacancy defect. The method is especially effective for d-matrices doped with sp-impurities since annihilation parameters of positrons with d- and sp-shell electrons differ considerably. The potentialities of the method of core-electron annihilation of positrons are demonstrated taking electron-irradiated dilute Ni-P and Ni-Si alloys as an example. It is shown that the interaction between the vacancies, which migrate at the III stage of annealing, and P atoms in Ni-P causes a considerable change in the annihilation parameters of positrons with core electrons compared to pure Ni. In Ni-Si alloys the annihilation parameters of trapped positrons with core electrons do not differ from those in Ni. This fact is an evidence that Si atoms do not interact with vacancies in Ni.

Molecular Characterization of Lipopolysaccharide Binding to Human α-1-Acid Glycoprotein

PubMed Central

Huang, Johnny X.; Azad, Mohammad A. K.; Yuriev, Elizabeth; Baker, Mark A.; Nation, Roger L.; Li, Jian; Cooper, Matthew A.; Velkov, Tony

2012-01-01

The ability of AGP to bind circulating lipopolysaccharide (LPS) in plasma is believed to help reduce the proinflammatory effect of bacterial lipid A molecules. Here, for the first time we have characterized human AGP binding characteristics of the LPS from a number of pathogenic Gram-negative bacteria: Escherichia coli, Salmonella typhimurium, Klebsiella pneumonia, Pseudomonas aeruginosa, and Serratia marcescens. The binding affinity and structure activity relationships (SAR) of the AGP-LPS interactions were characterized by surface plasma resonance (SPR). In order to dissect the contribution of the lipid A, core oligosaccharide and O-antigen polysaccharide components of LPS, the AGP binding affinity of LPS from smooth strains, were compared to lipid A, Kdo2-lipid A, Ra, Rd, and Re rough LPS mutants. The SAR analysis enabled by the binding data suggested that, in addition to the important role played by the lipid A and core components of LPS, it is predominately the unique species- and strain-specific carbohydrate structure of the O-antigen polysaccharide that largely determines the binding affinity for AGP. Together, these data are consistent with the role of AGP in the binding and transport of LPS in plasma during acute-phase inflammatory responses to invading Gram-negative bacteria. PMID:23316371

Crystal structure of the Escherichia coli regulator of sigma70, Rsd, in complex with sigma70 domain 4.

PubMed

Patikoglou, Georgia A; Westblade, Lars F; Campbell, Elizabeth A; Lamour, Valérie; Lane, William J; Darst, Seth A

2007-09-21

The Escherichia coli Rsd protein binds tightly and specifically to the RNA polymerase (RNAP) sigma(70) factor. Rsd plays a role in alternative sigma factor-dependent transcription by biasing the competition between sigma(70) and alternative sigma factors for the available core RNAP. Here, we determined the 2.6 A-resolution X-ray crystal structure of Rsd bound to sigma(70) domain 4 (sigma(70)(4)), the primary determinant for Rsd binding within sigma(70). The structure reveals that Rsd binding interferes with the two primary functions of sigma(70)(4), core RNAP binding and promoter -35 element binding. Interestingly, the most highly conserved Rsd residues form a network of interactions through the middle of the Rsd structure that connect the sigma(70)(4)-binding surface with three cavities exposed on distant surfaces of Rsd, suggesting functional coupling between sigma(70)(4) binding and other binding surfaces of Rsd, either for other proteins or for as yet unknown small molecule effectors. These results provide a structural basis for understanding the role of Rsd, as well as its ortholog, AlgQ, a positive regulator of Pseudomonas aeruginosa virulence, in transcription regulation.

Crystal structure of the Escherichia coli regulator of σ70, Rsd, in complex with σ70 domain 4

PubMed Central

Patikoglou, Georgia A.; Westblade, Lars F.; Campbell, Elizabeth A.; Lamour, Valérie; Lane, William J.; Darst, Seth A.

2007-01-01

Summary The Escherichia coli Rsd protein binds tightly and specifically to the RNA polymerase (RNAP) σ70 factor. Rsd plays a role in alternative σ factor-dependent transcription by biasing the competition between σ70 and alternative σ factors for the available core RNAP. Here, we determined the 2.6 Å-resolution X-ray crystal structure of Rsd bound to σ70 domain 4 (σ704), the primary determinant for Rsd binding within σ70. The structure reveals that Rsd binding interferes with the two primary functions of σ704, core RNAP binding and promoter –35 element binding. Interestingly, the most highly conserved Rsd residues form a network of interactions through the middle of the Rsd structure that connect the σ704-binding surface with three cavities exposed on distant surfaces of Rsd, suggesting functional coupling between σ704 binding and other binding surfaces of Rsd, either for other proteins or for as yet unknown small molecule effectors. These results provide a structural basis for understanding the role of Rsd, as well as its ortholog, AlgQ, a positive regulator of Pseudomonas aeruginosa virulence, in transcription regulation. PMID:17681541

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

Patikoglou,G.; Westblade, L.; Campbell, E.

The Escherichia coli Rsd protein binds tightly and specifically to the RNA polymerase (RNAP) {sigma}{sup 70} factor. Rsd plays a role in alternative {sigma} factor-dependent transcription by biasing the competition between {sigma}{sup 70} and alternative {sigma} factors for the available core RNAP. Here, we determined the 2.6 {angstrom}-resolution X-ray crystal structure of Rsd bound to {sigma}{sup 70} domain 4 ({sigma}{sup 70}{sub 4}), the primary determinant for Rsd binding within {sigma}{sup 70}. The structure reveals that Rsd binding interferes with the two primary functions of {sigma}{sup 70}{sub 4}, core RNAP binding and promoter -35 element binding. Interestingly, the most highly conservedmore » Rsd residues form a network of interactions through the middle of the Rsd structure that connect the {sigma}{sup 70}{sub 4}-binding surface with three cavities exposed on distant surfaces of Rsd, suggesting functional coupling between {sigma}{sup 70}{sub 4} binding and other binding surfaces of Rsd, either for other proteins or for as yet unknown small molecule effectors. These results provide a structural basis for understanding the role of Rsd, as well as its ortholog, AlgQ, a positive regulator of Pseudomonas aeruginosa virulence, in transcription regulation.« less

Stable MOB1 interaction with Hippo/MST is not essential for development and tissue growth control.

PubMed

Kulaberoglu, Yavuz; Lin, Kui; Holder, Maxine; Gai, Zhongchao; Gomez, Marta; Assefa Shifa, Belul; Mavis, Merdiye; Hoa, Lily; Sharif, Ahmad A D; Lujan, Celia; Smith, Ewan St John; Bjedov, Ivana; Tapon, Nicolas; Wu, Geng; Hergovich, Alexander

2017-09-25

The Hippo tumor suppressor pathway is essential for development and tissue growth control, encompassing a core cassette consisting of the Hippo (MST1/2), Warts (LATS1/2), and Tricornered (NDR1/2) kinases together with MOB1 as an important signaling adaptor. However, it remains unclear which regulatory interactions between MOB1 and the different Hippo core kinases coordinate development, tissue growth, and tumor suppression. Here, we report the crystal structure of the MOB1/NDR2 complex and define key MOB1 residues mediating MOB1's differential binding to Hippo core kinases, thereby establishing MOB1 variants with selective loss-of-interaction. By studying these variants in human cancer cells and Drosophila, we uncovered that MOB1/Warts binding is essential for tumor suppression, tissue growth control, and development, while stable MOB1/Hippo binding is dispensable and MOB1/Trc binding alone is insufficient. Collectively, we decrypt molecularly, cell biologically, and genetically the importance of the diverse interactions of Hippo core kinases with the pivotal MOB1 signal transducer.The Hippo tumor suppressor pathway is essential for development and tissue growth control. Here the authors employ a multi-disciplinary approach to characterize the interactions of the three Hippo kinases with the signaling adaptor MOB1 and show how they differently affect development, tissue growth and tumor suppression.

Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses.

PubMed

Narusaka, Yoshihiro; Nakashima, Kazuo; Shinwari, Zabta K; Sakuma, Yoh; Furihata, Takashi; Abe, Hiroshi; Narusaka, Mari; Shinozaki, Kazuo; Yamaguchi-Shinozaki, Kazuko

2003-04-01

Many abiotic stress-inducible genes contain two cis-acting elements, namely a dehydration-responsive element (DRE; TACCGACAT) and an ABA-responsive element (ABRE; ACGTGG/TC), in their promoter regions. We precisely analyzed the 120 bp promoter region (-174 to -55) of the Arabidopsis rd29A gene whose expression is induced by dehydration, high-salinity, low-temperature, and abscisic acid (ABA) treatments and whose 120 bp promoter region contains the DRE, DRE/CRT-core motif (A/GCCGAC), and ABRE sequences. Deletion and base substitution analyses of this region showed that the DRE-core motif functions as DRE and that the DRE/DRE-core motif could be a coupling element of ABRE. Gel mobility shift assays revealed that DRE-binding proteins (DREB1s/CBFs and DREB2s) bind to both DRE and the DRE-core motif and that ABRE-binding proteins (AREBs/ABFs) bind to ABRE in the 120 bp promoter region. In addition, transactivation experiments using Arabidopsis leaf protoplasts showed that DREBs and AREBs cumulatively transactivate the expression of a GUS reporter gene fused to the 120 bp promoter region of rd29A. These results indicate that DRE and ABRE are interdependent in the ABA-responsive expression of the rd29A gene in response to ABA in Arabidopsis.

Apparatus and method for compensating for electron beam emittance in synchronizing light sources

DOEpatents

Neil, George R.

1996-01-01

A focused optical beam is used to change the path length of the core electrons in electron light sources thereby boosting their efficiency of conversion of electron beam energy to light. Both coherent light in the free electron laser and incoherent light in the synchrotron is boosted by this technique. By changing the path length of the core electrons by the proper amount, the core electrons are caused to stay in phase with the electrons in the outer distribution of the electron beam. This increases the fraction of the electron beam energy that is converted to light thereby improving the efficiency of conversion of energy to light and therefore boosting the power output of the free electron laser and synchrotron.

Apparatus and method for compensating for electron beam emittance in synchronizing light sources

DOEpatents

Neil, G.R.

1996-07-30

A focused optical beam is used to change the path length of the core electrons in electron light sources thereby boosting their efficiency of conversion of electron beam energy to light. Both coherent light in the free electron laser and incoherent light in the synchrotron is boosted by this technique. By changing the path length of the core electrons by the proper amount, the core electrons are caused to stay in phase with the electrons in the outer distribution of the electron beam. This increases the fraction of the electron beam energy that is converted to light thereby improving the efficiency of conversion of energy to light and therefore boosting the power output of the free electron laser and synchrotron. 4 figs.

Identification and characterization of a novel high affinity metal-binding site in the hammerhead ribozyme.

PubMed Central

Hansen, M R; Simorre, J P; Hanson, P; Mokler, V; Bellon, L; Beigelman, L; Pardi, A

1999-01-01

A novel metal-binding site has been identified in the hammerhead ribozyme by 31P NMR. The metal-binding site is associated with the A13 phosphate in the catalytic core of the hammerhead ribozyme and is distinct from any previously identified metal-binding sites. 31P NMR spectroscopy was used to measure the metal-binding affinity for this site and leads to an apparent dissociation constant of 250-570 microM at 25 degrees C for binding of a single Mg2+ ion. The NMR data also show evidence of a structural change at this site upon metal binding and these results are compared with previous data on metal-induced structural changes in the core of the hammerhead ribozyme. These NMR data were combined with the X-ray structure of the hammerhead ribozyme (Pley HW, Flaherty KM, McKay DB. 1994. Nature 372:68-74) to model RNA ligands involved in binding the metal at this A13 site. In this model, the A13 metal-binding site is structurally similar to the previously identified A(g) metal-binding site and illustrates the symmetrical nature of the tandem G x A base pairs in domain 2 of the hammerhead ribozyme. These results demonstrate that 31P NMR represents an important method for both identification and characterization of metal-binding sites in nucleic acids. PMID:10445883

Structure-Function Analysis of the Drosophila melanogaster Caudal Transcription Factor Provides Insights into Core Promoter-preferential Activation.

PubMed

Shir-Shapira, Hila; Sharabany, Julia; Filderman, Matan; Ideses, Diana; Ovadia-Shochat, Avital; Mannervik, Mattias; Juven-Gershon, Tamar

2015-07-10

Regulation of RNA polymerase II transcription is critical for the proper development, differentiation, and growth of an organism. The RNA polymerase II core promoter is the ultimate target of a multitude of transcription factors that control transcription initiation. Core promoters encompass the RNA start site and consist of functional elements such as the TATA box, initiator, and downstream core promoter element (DPE), which confer specific properties to the core promoter. We have previously discovered that Drosophila Caudal, which is a master regulator of genes involved in development and differentiation, is a DPE-specific transcriptional activator. Here, we show that the mouse Caudal-related homeobox (Cdx) proteins (mCdx1, mCdx2, and mCdx4) are also preferential core promoter transcriptional activators. To elucidate the mechanism that enables Caudal to preferentially activate DPE transcription, we performed structure-function analysis. Using a systematic series of deletion mutants (all containing the intact DNA-binding homeodomain) we discovered that the C-terminal region of Caudal contributes to the preferential activation of the fushi tarazu (ftz) Caudal target gene. Furthermore, the region containing both the homeodomain and the C terminus of Caudal was sufficient to confer core promoter-preferential activation to the heterologous GAL4 DNA-binding domain. Importantly, we discovered that Drosophila CREB-binding protein (dCBP) is a co-activator for Caudal-regulated activation of ftz. Strikingly, dCBP conferred the ability to preferentially activate the DPE-dependent ftz reporter to mini-Caudal proteins that were unable to preferentially activate ftz transcription themselves. Taken together, it is the unique combination of dCBP and Caudal that enables the co-activation of ftz in a core promoter-preferential manner. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Chemical bonding in aqueous hexacyano cobaltate from photon- and electron-detection perspectives

PubMed Central

Lalithambika, Sreeju Sreekantan Nair; Atak, Kaan; Seidel, Robert; Neubauer, Antje; Brandenburg, Tim; Xiao, Jie; Winter, Bernd; Aziz, Emad F.

2017-01-01

The electronic structure of the [Co(CN)6]3− complex dissolved in water is studied using X-ray spectroscopy techniques. By combining electron and photon detection methods from the solutions ionized or excited by soft X-rays we experimentally identify chemical bonding between the metal center and the CN ligand. Non-resonant photoelectron spectroscopy provides solute electron binding energies, and nitrogen 1 s and cobalt 2p resonant core-level photoelectron spectroscopy identifies overlap between metal and ligand orbitals. By probing resonances we are able to qualitatively determine the ligand versus metal character of the respective occupied and non-occupied orbitals, purely by experiment. For the same excitations we also detect the emitted X-rays, yielding the complementary resonant inelastic X-ray scattering spectra. For a quantitative interpretation of the spectra, we perform theoretical electronic-structure calculations. The latter provide both orbital energies and orbital character which are found to be in good agreement with experimental energies and with experimentally inferred orbital mixing. We also report calculated X-ray absorption spectra, which in conjunction with our orbital-structure analysis, enables us to quantify various bonding interactions with a particular focus on the water-solvent – ligand interaction and the strength of π-backbonding between metal and ligand. PMID:28098216

A BPTTF-based self-assembled electron-donating triangle capable of C60 binding.

PubMed

Goeb, Sébastien; Bivaud, Sébastien; Dron, Paul Ionut; Balandier, Jean-Yves; Chas, Marcos; Sallé, Marc

2012-03-25

A kinetically stable self-assembled redox-active triangle is isolated. The resulting electron-donating cavity, which incorporates three BPTTF units, exhibits a remarkable binding ability for electron-deficient C(60), supported by a favorable combination of structural and electronic features.

Yeast one-hybrid system used to identify the binding proteins for rat glutathione S-transferase P enhancer I.

PubMed

Liao, Ming-Xiang; Liu, Dong-Yuan; Zuo, Jin; Fang, Fu-De

2002-03-01

To detect the trans-factors specifically binding to the strong enhancer element (GPEI) in the upstream of rat glutathione S-transferase P (GST-P) gene. Yeast one-hybrid system was used to screen rat lung MATCHMAKER cDNA library to identify potential trans-factors that can interact with core sequence of GPEI(cGPEI). Electrophoresis mobility shift assay (EMSA) was used to analyze the binding of transfactors to cGPEI. cDNA fragments coding for the C-terminal part of the transcription factor c-Jun and rat adenine nucleotide translocator (ANT) were isolated. The binding of c-Jun and ANT to GPEI core sequence were confirmed. Rat c-jun transcriptional factor and ANT may interact with cGPEI. They could play an important role in the induced expression of GST-P gene.

ELECTRON-CAPTURE AND β-DECAY RATES FOR sd-SHELL NUCLEI IN STELLAR ENVIRONMENTS RELEVANT TO HIGH-DENSITY O–NE–MG CORES

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

Suzuki, Toshio; Toki, Hiroshi; Nomoto, Ken’ichi, E-mail: suzuki@phys.chs.nihon-u.ac.jp

Electron-capture and β-decay rates for nuclear pairs in the sd-shell are evaluated at high densities and high temperatures relevant to the final evolution of electron-degenerate O–Ne–Mg cores of stars with initial masses of 8–10 M{sub ⊙}. Electron capture induces a rapid contraction of the electron-degenerate O–Ne–Mg core. The outcome of rapid contraction depends on the evolutionary changes in the central density and temperature, which are determined by the competing processes of contraction, cooling, and heating. The fate of the stars is determined by these competitions, whether they end up with electron-capture supernovae or Fe core-collapse supernovae. Since the competing processes aremore » induced by electron capture and β-decay, the accurate weak rates are crucially important. The rates are obtained for pairs with A = 20, 23, 24, 25, and 27 by shell-model calculations in the sd-shell with the USDB Hamiltonian. Effects of Coulomb corrections on the rates are evaluated. The rates for pairs with A = 23 and 25 are important for nuclear Urca processes that determine the cooling rate of the O–Ne–Mg core, while those for pairs with A = 20 and 24 are important for the core contraction and heat generation rates in the core. We provide these nuclear rates at stellar environments in tables with fine enough meshes at various densities and temperatures for studies of astrophysical processes sensitive to the rates. In particular, the accurate rate tables are crucially important for the final fates of not only O–Ne–Mg cores but also a wider range of stars, such as C–O cores of lower-mass stars.« less

Distinct peptide binding specificities of Src homology 3 (SH3) protein domains can be determined by modulation of local energetics across the binding interface.

PubMed

Gorelik, Maryna; Davidson, Alan R

2012-03-16

The yeast Nbp2p SH3 and Bem1p SH3b domains bind certain target peptides with similar high affinities, yet display vastly different affinities for other targets. To investigate this unusual behavior, we have solved the structure of the Nbp2p SH3-Ste20 peptide complex and compared it with the previously determined structure of the Bem1p SH3b bound to the same peptide. Although the Ste20 peptide interacts with both domains in a structurally similar manner, extensive in vitro studies with domain and peptide mutants revealed large variations in interaction strength across the binding interface of the two complexes. Whereas the Nbp2p SH3 made stronger contacts with the peptide core RXXPXXP motif, the Bem1p SH3b domain made stronger contacts with residues flanking the core motif. Remarkably, this modulation of local binding energetics can explain the distinct and highly nuanced binding specificities of these two domains.

Probing a 2-Aminobenzimidazole Library for Binding to RNA Internal Loops via Two-Dimensional Combinatorial Screening

PubMed Central

Velegapudi, Sai Pradeep; Pushechnikov, Alexei; Labuda, Lucas P.; French, Jonathan M.; Disney, Matthew D.

2012-01-01

There are many potential RNA drug targets in bacterial, viral, and the human transcriptomes. However, there are few small molecules that modulate RNA function. This is due, in part, to a lack of fundamental understanding about RNA-ligand interactions including the types of small molecules that bind to RNA structural elements and the RNA structural elements that bind to small molecules. In an effort to better understand RNA-ligand interactions, we diversified the 2-aminobenzimidazole core (2AB) and probed the resulting library for binding to a library of RNA internal loops. We chose the 2AB core for these studies because it is a privileged scaffold for binding RNA based on previous reports. These studies identified that N-methyl pyrrolidine, imidazole, and propylamine diversity elements at the R1 position increase binding to internal loops; variability at the R2 position is well tolerated. The preferred RNA loop space was also determined for five ligands using a statistical approach and identified trends that lead to selective recognition. PMID:22958065

Crystal structure of mouse coronavirus receptor-binding domain complexed with its murine receptor

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

Peng, Guiqing; Sun, Dawei; Rajashankar, Kanagalaghatta R.

2011-09-28

Coronaviruses have evolved diverse mechanisms to recognize different receptors for their cross-species transmission and host-range expansion. Mouse hepatitis coronavirus (MHV) uses the N-terminal domain (NTD) of its spike protein as its receptor-binding domain. Here we present the crystal structure of MHV NTD complexed with its receptor murine carcinoembryonic antigen-related cell adhesion molecule 1a (mCEACAM1a). Unexpectedly, MHV NTD contains a core structure that has the same {beta}-sandwich fold as human galectins (S-lectins) and additional structural motifs that bind to the N-terminal Ig-like domain of mCEACAM1a. Despite its galectin fold, MHV NTD does not bind sugars, but instead binds mCEACAM1a through exclusivemore » protein-protein interactions. Critical contacts at the interface have been confirmed by mutagenesis, providing a structural basis for viral and host specificities of coronavirus/CEACAM1 interactions. Sugar-binding assays reveal that galectin-like NTDs of some coronaviruses such as human coronavirus OC43 and bovine coronavirus bind sugars. Structural analysis and mutagenesis localize the sugar-binding site in coronavirus NTDs to be above the {beta}-sandwich core. We propose that coronavirus NTDs originated from a host galectin and retained sugar-binding functions in some contemporary coronaviruses, but evolved new structural features in MHV for mCEACAM1a binding.« less

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

Bosanac, Ivan; Yamazaki, Haruka; Matsu-ura, Toru

Binding of inositol 1,4,5-trisphosphate (IP{sub 3}) to the amino-terminal region of IP{sub 3} receptor promotes Ca{sup 2+} release from the endoplasmic reticulum. Within the amino terminus, the first 220 residues directly preceding the IP{sub 3} binding core domain play a key role in IP{sub 3} binding suppression and regulatory protein interaction. Here we present a crystal structure of the suppressor domain of the mouse type 1 IP{sub 3} receptor at 1.8 {angstrom}. Displaying a shape akin to a hammer, the suppressor region contains a Head subdomain forming the {beta}-trefoil fold and an Arm subdomain possessing a helix-turn-helix structure. The conservedmore » region on the Head subdomain appeared to interact with the IP{sub 3} binding core domain and is in close proximity to the previously proposed binding sites of Homer, RACK1, calmodulin, and CaBP1. The present study sheds light onto the mechanism underlying the receptor's sensitivity to the ligand and its communication with cellular signaling proteins.« less

Direct Heating of a Laser-Imploded Core by Ultraintense Laser-Driven Ions

NASA Astrophysics Data System (ADS)

Kitagawa, Y.; Mori, Y.; Komeda, O.; Ishii, K.; Hanayama, R.; Fujita, K.; Okihara, S.; Sekine, T.; Satoh, N.; Kurita, T.; Takagi, M.; Watari, T.; Kawashima, T.; Kan, H.; Nishimura, Y.; Sunahara, A.; Sentoku, Y.; Nakamura, N.; Kondo, T.; Fujine, M.; Azuma, H.; Motohiro, T.; Hioki, T.; Kakeno, M.; Miura, E.; Arikawa, Y.; Nagai, T.; Abe, Y.; Ozaki, S.; Noda, A.

2015-05-01

A novel direct core heating fusion process is introduced, in which a preimploded core is predominantly heated by energetic ions driven by LFEX, an extremely energetic ultrashort pulse laser. Consequently, we have observed the D (d ,n )He 3 -reacted neutrons (DD beam-fusion neutrons) with the yield of 5 ×108 n /4 π sr . Examination of the beam-fusion neutrons verified that the ions directly collide with the core plasma. While the hot electrons heat the whole core volume, the energetic ions deposit their energies locally in the core, forming hot spots for fuel ignition. As evidenced in the spectrum, the process simultaneously excited thermal neutrons with the yield of 6 ×107 n /4 π sr , raising the local core temperature from 0.8 to 1.8 keV. A one-dimensional hydrocode STAR 1D explains the shell implosion dynamics including the beam fusion and thermal fusion initiated by fast deuterons and carbon ions. A two-dimensional collisional particle-in-cell code predicts the core heating due to resistive processes driven by hot electrons, and also the generation of fast ions, which could be an additional heating source when they reach the core. Since the core density is limited to 2 g /cm3 in the current experiment, neither hot electrons nor fast ions can efficiently deposit their energy and the neutron yield remains low. In future work, we will achieve the higher core density (>10 g /cm3 ); then hot electrons could contribute more to the core heating via drag heating. Together with hot electrons, the ion contribution to fast ignition is indispensable for realizing high-gain fusion. By virtue of its core heating and ignition, the proposed scheme can potentially achieve high gain fusion.

Direct heating of a laser-imploded core by ultraintense laser-driven ions.

PubMed

Kitagawa, Y; Mori, Y; Komeda, O; Ishii, K; Hanayama, R; Fujita, K; Okihara, S; Sekine, T; Satoh, N; Kurita, T; Takagi, M; Watari, T; Kawashima, T; Kan, H; Nishimura, Y; Sunahara, A; Sentoku, Y; Nakamura, N; Kondo, T; Fujine, M; Azuma, H; Motohiro, T; Hioki, T; Kakeno, M; Miura, E; Arikawa, Y; Nagai, T; Abe, Y; Ozaki, S; Noda, A

2015-05-15

A novel direct core heating fusion process is introduced, in which a preimploded core is predominantly heated by energetic ions driven by LFEX, an extremely energetic ultrashort pulse laser. Consequently, we have observed the D(d,n)^{3}He-reacted neutrons (DD beam-fusion neutrons) with the yield of 5×10^{8} n/4π sr. Examination of the beam-fusion neutrons verified that the ions directly collide with the core plasma. While the hot electrons heat the whole core volume, the energetic ions deposit their energies locally in the core, forming hot spots for fuel ignition. As evidenced in the spectrum, the process simultaneously excited thermal neutrons with the yield of 6×10^{7} n/4π sr, raising the local core temperature from 0.8 to 1.8 keV. A one-dimensional hydrocode STAR 1D explains the shell implosion dynamics including the beam fusion and thermal fusion initiated by fast deuterons and carbon ions. A two-dimensional collisional particle-in-cell code predicts the core heating due to resistive processes driven by hot electrons, and also the generation of fast ions, which could be an additional heating source when they reach the core. Since the core density is limited to 2 g/cm^{3} in the current experiment, neither hot electrons nor fast ions can efficiently deposit their energy and the neutron yield remains low. In future work, we will achieve the higher core density (>10 g/cm^{3}); then hot electrons could contribute more to the core heating via drag heating. Together with hot electrons, the ion contribution to fast ignition is indispensable for realizing high-gain fusion. By virtue of its core heating and ignition, the proposed scheme can potentially achieve high gain fusion.

Ta-Pt Alloys as Gate Materials for Metal-Oxide-Semiconductor Field Effect Transistor Application

NASA Astrophysics Data System (ADS)

Huang, Chih-Feng; Tsui, Bing-Yue

2009-03-01

In this work we explore the thermal stability of sputter-deposited Ta-rich Ta-Pt alloys. The effects of group III and V impurities on their work function are also investigated. The Ta content ranges from 65 to 82 at. %. The main phase is σ Ta-Pt. The binding energies of core-level electrons of Ta and Pt are changed due to the intermixing of Ta and Pt, which is evidence that the work function of alloys is changed in metallic alloy systems. Binding energies are thermally stable up to 800 °C. Moreover, the incorporation of Pt in Ta film induces poor crystallization and a compound phase of Ta-Pt alloys. Transmission electron microscopy analysis confirmed the absence of a clear grain boundary in Ta-Pt alloys. The Ta and Pt depth profile shows uniformity in depth after 800 °C annealing for 30 min. The diffusion and distribution of impurities in the alloys were studied by secondary ion mass spectroscopy. Arsenic cannot diffuse in the alloys following annealing at 800 °C for 30 s. In contrast, boron can easily diffuse at 800 °C. The incorporation of impurities with a dosage of 5 ×1015 cm-2 in 60 nm Ta-Pt alloy by implantation did not significantly change the flat-band voltage following annealing at 800 °C.

Deformability in the cleavage site of primary microRNA is not sensed by the double-stranded RNA binding domains in the microprocessor component DGCR8.

PubMed

Quarles, Kaycee A; Chadalavada, Durga; Showalter, Scott A

2015-06-01

The prevalence of double-stranded RNA (dsRNA) in eukaryotic cells has only recently been appreciated. Of interest here, RNA silencing begins with dsRNA substrates that are bound by the dsRNA-binding domains (dsRBDs) of their processing proteins. Specifically, processing of microRNA (miRNA) in the nucleus minimally requires the enzyme Drosha and its dsRBD-containing cofactor protein, DGCR8. The smallest recombinant construct of DGCR8 that is sufficient for in vitro dsRNA binding, referred to as DGCR8-Core, consists of its two dsRBDs and a C-terminal tail. As dsRBDs rarely recognize the nucleotide sequence of dsRNA, it is reasonable to hypothesize that DGCR8 function is dependent on the recognition of specific structural features in the miRNA precursor. Previously, we demonstrated that noncanonical structural elements that promote RNA flexibility within the stem of miRNA precursors are necessary for efficient in vitro cleavage by reconstituted Microprocessor complexes. Here, we combine gel shift assays with in vitro processing assays to demonstrate that neither the N-terminal dsRBD of DGCR8 in isolation nor the DGCR8-Core construct is sensitive to the presence of noncanonical structural elements within the stem of miRNA precursors, or to single-stranded segments flanking the stem. Extending DGCR8-Core to include an N-terminal heme-binding region does not change our conclusions. Thus, our data suggest that although the DGCR8-Core region is necessary for dsRNA binding and recruitment to the Microprocessor, it is not sufficient to establish the previously observed connection between RNA flexibility and processing efficiency. © 2015 Wiley Periodicals, Inc.

Nup153 and Nup98 bind the HIV-1 core and contribute to the early steps of HIV-1 replication

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

Di Nunzio, Francesca, E-mail: francesca.di-nunzio@pasteur.fr; Fricke, Thomas; Miccio, Annarita

The early steps of HIV-1 replication involve the entry of HIV-1 into the nucleus, which is characterized by viral interactions with nuclear pore components. HIV-1 developed an evolutionary strategy to usurp the nuclear pore machinery and chromatin in order to integrate and efficiently express viral genes. In the current work, we studied the role of nucleoporins 153 and 98 (Nup153 and Nup98) in infection of human Jurkat lymphocytes by HIV-1. We showed that Nup153-depleted cells exhibited a defect in nuclear import, while depletion of Nup 98 caused a slight defect in HIV integration. To explore the biochemical viral determinants formore » the requirement of Nup153 and Nup98 during HIV-1 infection, we tested the ability of these nucleoporins to interact with HIV-1 cores. Our findings showed that both nucleoporins bind HIV-1 cores suggesting that this interaction is important for HIV-1 nuclear import and/or integration. Distribution analysis of integration sites in Nup153-depleted cells revealed a reduced tendency of HIV-1 to integrate in intragenic sites, which in part could account for the large infectivity defect observed in Nup153-depleted cells. Our work strongly supports a role for Nup153 in HIV-1 nuclear import and integration. - Highlights: ► We studied the role of Nup98 and Nup153 in HIV-1 infection. ► Nup98 binds the HIV-1 core and is involved in HIV-1 integration. ► Nup153 binds the HIV-1 core and is involved in HIV-1 nuclear import. ► Depletion of Nup153 decreased the integration of HIV-1 in transcriptionally active sites.« less

Crystallization and preliminary X-ray crystallographic analysis of the GluR0 ligand-binding core from Nostoc punctiforme

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

Lee, Jun Hyuck; Park, Soo Jeong; Rho, Seong-Hwan

2005-11-01

The GluR0 ligand-binding core from N. punctiforme was expressed, purified and crystallized in the presence of l-glutamate. A diffraction data set was collected to a resolution of 2.1 Å. GluR0 from Nostoc punctiforme (NpGluR0) is a bacterial homologue of the ionotropic glutamate receptor. The ligand-binding core of NpGluR0 was crystallized at 294 K using the hanging-drop vapour-diffusion method. The l-glutamate-complexed crystal belongs to space group C222{sub 1}, with unit-cell parameters a = 78.0, b = 145.1, c = 132.1 Å. The crystals contain three subunits in the asymmetric unit, with a V{sub M} value of 2.49 Å{sup 3} Da{sup −1}.more » The diffraction limit of the l-glutamate complex data set was 2.1 Å using synchrotron X-ray radiation at beamline BL-4A of the Pohang Accelerator Laboratory (Pohang, Korea)« less

The H3-H4 N-Terminal Tail Domains Are the Primary Mediators of Transcription Factor IIIA Access to 5S DNA within a Nucleosome

PubMed Central

Vitolo, Joseph M.; Thiriet, Christophe; Hayes, Jeffrey J.

2000-01-01

Reconstitution of a DNA fragment containing a Xenopus borealis somatic type 5S rRNA gene into a nucleosome greatly restricts the binding of transcription factor IIIA (TFIIIA) to its cognate DNA sequence within the internal promoter of the gene. Removal of all core histone tail domains by limited trypsin proteolysis or acetylation of the core histone tails significantly relieves this inhibition and allows TFIIIA to exhibit high-affinity binding to nucleosomal DNA. Since only a single tail or a subset of tails may be primarily responsible for this effect, we determined whether removal of the individual tail domains of the H2A-H2B dimer or the H3-H4 tetramer affects TFIIIA binding to its cognate DNA site within the 5S nucleosome in vitro. The results show that the tail domains of H3 and H4, but not those of H2A and/or H2B, directly modulate the ability of TFIIIA to bind nucleosomal DNA. In vitro transcription assays carried out with nucleosomal templates lacking individual tail domains show that transcription efficiency parallels the binding of TFIIIA. In addition, we show that the stoichiometry of core histones within the 5S DNA-core histone-TFIIIA triple complex is not changed upon TFIIIA association. Thus, TFIIIA binding occurs by displacement of H2A-H2B–DNA contacts but without complete loss of the dimer from the nucleoprotein complex. These data, coupled with previous reports (M. Vettese-Dadey, P. A. Grant, T. R. Hebbes, C. Crane-Robinson, C. D. Allis, and J. L. Workman, EMBO J. 15:2508–2518, 1996; L. Howe, T. A. Ranalli, C. D. Allis, and J. Ausio, J. Biol. Chem. 273:20693–20696, 1998), suggest that the H3/H4 tails are the primary arbiters of transcription factor access to intranucleosomal DNA. PMID:10688663

TAF(II)250: a transcription toolbox.

PubMed

Wassarman, D A; Sauer, F

2001-08-01

Activation of RNA-polymerase-II-dependent transcription involves conversion of signals provided by gene-specific activator proteins into the synthesis of messenger RNA. This conversion requires dynamic structural changes in chromatin and assembly of general transcription factors (GTFs) and RNA polymerase II at core promoter sequence elements surrounding the transcription start site of genes. One hallmark of transcriptional activation is the interaction of DNA-bound activators with coactivators such as the TATA-box binding protein (TBP)-associated factors (TAF(II)s) within the GTF TFIID. TAF(II)250 possesses a variety of activities that are likely to contribute to the initial steps of RNA polymerase II transcription. TAF(II)250 is a scaffold for assembly of other TAF(II)s and TBP into TFIID, TAF(II)250 binds activators to recruit TFIID to particular promoters, TAF(II)250 regulates binding of TBP to DNA, TAF(II)250 binds core promoter initiator elements, TAF(II)250 binds acetylated lysine residues in core histones, and TAF(II)250 possesses protein kinase, ubiquitin-activating/conjugating and acetylase activities that modify histones and GTFs. We speculate that these activities achieve two goals--(1) they aid in positioning and stabilizing TFIID at particular promoters, and (2) they alter chromatin structure at the promoter to allow assembly of GTFs--and we propose a model for how TAF(II)250 converts activation signals into active transcription.

Serotonin storage pools in basophil leukemia and mast cells: characterization of two types of serotonin binding protein and radioautographic analysis of the intracellular distribution of (/sup 3/H)serotonin

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

Tamir, H.; Theoharides, T.C.; Gershon, M.D.

1982-06-01

The binding of serotonin to protein(s) derived from rat basophil leukemia (RBL) cells and mast cells was studied. Two types of serotonin binding protein in RBL cells was found. These proteins differed from one another in molecular weight and eluted in separate peaks from sephadex G-200 columns. Peak I protein (KD = 1.9 x 10/sup -6/ M) was a glycoprotein that bound to concanavalin A (Con A); Peak II protein (KD/sub 1/ = 4.5 x 10/sup -/8 M; KD/sub 2/ = 3.9 x 10/sup -6/ M) did not bind to Con A. Moreover, binding of (/sup 3/H)serotonin to protein ofmore » Peak I was sensitive to inhibition by reserpine, while binding of (/sup 3/H)serotonin to protein of Peak II resisted inhibition by that drug. Other differences between the two types of binding protein were found, the most significant of which was the far more vigorous conditions of homogenization required to extract Peak I than Peak II protein. Electron microscope radioautographic analysis of the intracellular distribution of (/sup 3/H) serotonin taken up in vitro by RBL cells or in vivo by murine mast cells indicated that essentially all of the labeled amine was located in cytoplasmic granules.No evidence for a pool in the cytosol was found and all granules were capable of becoming labeled. The presence of two types of intracellular serotonin binding proteins in these cells may indicate that there are two intracellular storage compartments for the amine. Both may be intragranular, but Peak I protein may be associated with the granular membrane while Peak II protein may be more free within the granular core. Different storage proteins may help to explain the differential release of amines from mast cell granules.« less

Electronic Interactions of Size-Selected Oxide Clusters on Metallic and Thin Film Oxide Supports

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

Xue, Meng; Nakayama, Miki; Liu, Ping

The interfacial electronic structure of various size-selected metal oxide nanoclusters (M 3O x; M = Mo, Nb, Ti) on Cu(111) and a thin film of Cu 2O supports were investigated in this paper by a combination of experimental methods and density functional theory (DFT). These systems explore electron transfer at the metal–metal oxide interface which can modify surface structure, metal oxidation states, and catalytic activity. Electron transfer was probed by measurements of surface dipoles derived from coverage dependent work function measurements using two-photon photoemission (2PPE) and metal core level binding energy spectra from X-ray photoelectron spectroscopy (XPS). The measured surfacemore » dipoles are negative for all clusters on Cu(111) and Cu 2O/Cu(111), but those on the Cu 2O surface are much larger in magnitude. In addition, sub-stoichiometric or “reduced” clusters exhibit smaller surface dipoles on both the Cu(111) and Cu 2O surfaces. Negative surface dipoles for clusters on Cu(111) suggest Cu → cluster electron transfer, which is generally supported by DFT-calculated Bader charge distributions. For Cu 2O/Cu(111), calculations of the surface electrostatic potentials show that the charge distributions associated with cluster adsorption structures or distortions at the cluster–Cu 2O–Cu(111) interface are largely responsible for the observed negative surface dipoles. Changes observed in the XPS spectra for the Mo 3d, Nb 3d, and Ti 2p core levels of the clusters on Cu(111) and Cu 2O/Cu(111) are interpreted with help from the calculated Bader charges and cluster adsorption structures, the latter providing information about the presence of inequivalent cation sites. Finally, the results presented in this work illustrate how the combined use of different experimental probes along with theoretical calculations can result in a more realistic picture of cluster–support interactions and bonding.« less

Electronic Interactions of Size-Selected Oxide Clusters on Metallic and Thin Film Oxide Supports

DOE PAGES

Xue, Meng; Nakayama, Miki; Liu, Ping; ...

2017-09-13

The interfacial electronic structure of various size-selected metal oxide nanoclusters (M 3O x; M = Mo, Nb, Ti) on Cu(111) and a thin film of Cu 2O supports were investigated in this paper by a combination of experimental methods and density functional theory (DFT). These systems explore electron transfer at the metal–metal oxide interface which can modify surface structure, metal oxidation states, and catalytic activity. Electron transfer was probed by measurements of surface dipoles derived from coverage dependent work function measurements using two-photon photoemission (2PPE) and metal core level binding energy spectra from X-ray photoelectron spectroscopy (XPS). The measured surfacemore » dipoles are negative for all clusters on Cu(111) and Cu 2O/Cu(111), but those on the Cu 2O surface are much larger in magnitude. In addition, sub-stoichiometric or “reduced” clusters exhibit smaller surface dipoles on both the Cu(111) and Cu 2O surfaces. Negative surface dipoles for clusters on Cu(111) suggest Cu → cluster electron transfer, which is generally supported by DFT-calculated Bader charge distributions. For Cu 2O/Cu(111), calculations of the surface electrostatic potentials show that the charge distributions associated with cluster adsorption structures or distortions at the cluster–Cu 2O–Cu(111) interface are largely responsible for the observed negative surface dipoles. Changes observed in the XPS spectra for the Mo 3d, Nb 3d, and Ti 2p core levels of the clusters on Cu(111) and Cu 2O/Cu(111) are interpreted with help from the calculated Bader charges and cluster adsorption structures, the latter providing information about the presence of inequivalent cation sites. Finally, the results presented in this work illustrate how the combined use of different experimental probes along with theoretical calculations can result in a more realistic picture of cluster–support interactions and bonding.« less

Surface Chemistry in Cobalt Phosphide-Stabilized Lithium-Sulfur Batteries.

PubMed

Zhong, Yiren; Yin, Lichang; He, Peng; Liu, Wen; Wu, Zishan; Wang, Hailiang

2018-01-31

Chemistry at the cathode/electrolyte interface plays an important role for lithium-sulfur batteries in which stable cycling of the sulfur cathode requires confinement of the lithium polysulfide intermediates and their fast electrochemical conversion on the electrode surface. While many materials have been found to be effective for confining polysulfides, the underlying chemical interactions remain poorly understood. We report a new and general lithium polysulfide-binding mechanism enabled by surface oxidation layers of transition-metal phosphide and chalcogenide materials. We for the first time find that CoP nanoparticles strongly adsorb polysulfides because their natural oxidation (forming Co-O-P-like species) activates the surface Co sites for binding polysulfides via strong Co-S bonding. With a surface oxidation layer capable of confining polysulfides and an inner core suitable for conducting electrons, the CoP nanoparticles are thus a desirable candidate for stabilizing and improving the performance of sulfur cathodes in lithium-sulfur batteries. We demonstrate that sulfur electrodes that hold a high mass loading of 7 mg cm -2 and a high areal capacity of 5.6 mAh cm -2 can be stably cycled for 200 cycles. We further reveal that this new surface oxidation-induced polysulfide-binding scheme applies to a series of transition-metal phosphide and chalcogenide materials and can explain their stabilizing effects for lithium-sulfur batteries.

Crystal structures and atomic model of NADPH oxidase.

PubMed

Magnani, Francesca; Nenci, Simone; Millana Fananas, Elisa; Ceccon, Marta; Romero, Elvira; Fraaije, Marco W; Mattevi, Andrea

2017-06-27

NADPH oxidases (NOXs) are the only enzymes exclusively dedicated to reactive oxygen species (ROS) generation. Dysregulation of these polytopic membrane proteins impacts the redox signaling cascades that control cell proliferation and death. We describe the atomic crystal structures of the catalytic flavin adenine dinucleotide (FAD)- and heme-binding domains of Cylindrospermum stagnale NOX5. The two domains form the core subunit that is common to all seven members of the NOX family. The domain structures were then docked in silico to provide a generic model for the NOX family. A linear arrangement of cofactors (NADPH, FAD, and two membrane-embedded heme moieties) injects electrons from the intracellular side across the membrane to a specific oxygen-binding cavity on the extracytoplasmic side. The overall spatial organization of critical interactions is revealed between the intracellular loops on the transmembrane domain and the NADPH-oxidizing dehydrogenase domain. In particular, the C terminus functions as a toggle switch, which affects access of the NADPH substrate to the enzyme. The essence of this mechanistic model is that the regulatory cues conformationally gate NADPH-binding, implicitly providing a handle for activating/deactivating the very first step in the redox chain. Such insight provides a framework to the discovery of much needed drugs that selectively target the distinct members of the NOX family and interfere with ROS signaling.

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

Chaudhury, Paushali; Neiner, Tomasz; D'Imprima, Edoardo

The motor of the membrane-anchored archaeal motility structure, the archaellum, contains FlaX, FlaI and FlaH. FlaX forms a 30 nm ring structure that acts as a scaffold protein and was shown to interact with the bifunctional ATPase FlaI and FlaH. However, the structure and function of FlaH has been enigmatic. Here we present structural and functional analyses of isolated FlaH and archaellum motor subcomplexes. The FlaH crystal structure reveals a RecA/Rad51 family fold with an ATP bound on a conserved and exposed surface, which presumably forms an oligomerization interface. FlaH does not hydrolyze ATP in vitro, but ATP binding tomore » FlaH is essential for its interaction with FlaI and for archaellum assembly. FlaH interacts with the C-terminus of FlaX, which was earlier shown to be essential for FlaX ring formation and to mediate interaction with FlaI. Electron microscopy reveals that FlaH assembles as a second ring inside the FlaX ring in vitro. Collectively these data reveal central structural mechanisms for FlaH interactions in mediating archaellar assembly: FlaH binding within the FlaX ring and nucleotide-regulated FlaH binding to FlaI form the archaellar basal body core.« less

Distinct effects of Cr bulk doping and surface deposition on the chemical environment and electronic structure of the topological insulator Bi 2 Se 3

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

Yilmaz, Turgut; Hines, William; Sun, Fu-Chang

In this report, it is shown that Cr doped into the bulk and Cr deposited on the surface of Bi2Se3 films produced by molecular beam epitaxy (MBE) have strikingly different effects on both the electronic structure and chemical environment. Angle resolved photoemission spectroscopy (ARPES) shows that Cr doped into the bulk opens a surface state energy gap which can be seen at room temperature; much higher than the measured ferromagnetic transition temperature of ≈ 10 K. On the other hand, similar ARPES measurements show that the surface states remain gapless down to 15 K for films with Cr surface deposition.more » In addition, core-level photoemission spectroscopy of the Bi 5d, Se 3d, and Cr 3p core levels show distinct differences in the chemical environment for the two methods of Cr introduction. Surface deposition of Cr results in the formation of shoulders on the lower binding energy side for the Bi 5d peaks and two distinct Cr 3p peaks indicative of two Cr sites. These striking differences suggests an interesting possibility that better control of doping at only near surface region may offer a path to quantum anomalous Hall states at higher temperatures than reported in the literature.« less

Distinct effects of Cr bulk doping and surface deposition on the chemical environment and electronic structure of the topological insulator Bi 2 Se 3

DOE PAGES

Yilmaz, Turgut; Hines, William; Sun, Fu-Chang; ...

2017-02-21

In this report, it is shown that Cr doped into the bulk and Cr deposited on the surface of Bi2Se3 films produced by molecular beam epitaxy (MBE) have strikingly different effects on both the electronic structure and chemical environment. Angle resolved photoemission spectroscopy (ARPES) shows that Cr doped into the bulk opens a surface state energy gap which can be seen at room temperature; much higher than the measured ferromagnetic transition temperature of ≈ 10 K. On the other hand, similar ARPES measurements show that the surface states remain gapless down to 15 K for films with Cr surface deposition.more » In addition, core-level photoemission spectroscopy of the Bi 5d, Se 3d, and Cr 3p core levels show distinct differences in the chemical environment for the two methods of Cr introduction. Surface deposition of Cr results in the formation of shoulders on the lower binding energy side for the Bi 5d peaks and two distinct Cr 3p peaks indicative of two Cr sites. These striking differences suggests an interesting possibility that better control of doping at only near surface region may offer a path to quantum anomalous Hall states at higher temperatures than reported in the literature.« less

Structure and assembly of the mouse ASC inflammasome by combined NMR spectroscopy and cryo-electron microscopy

PubMed Central

Sborgi, Lorenzo; Ravotti, Francesco; Dandey, Venkata P.; Dick, Mathias S.; Mazur, Adam; Reckel, Sina; Chami, Mohamed; Scherer, Sebastian; Huber, Matthias; Böckmann, Anja; Egelman, Edward H.; Stahlberg, Henning; Broz, Petr; Meier, Beat H.; Hiller, Sebastian

2015-01-01

Inflammasomes are multiprotein complexes that control the innate immune response by activating caspase-1, thus promoting the secretion of cytokines in response to invading pathogens and endogenous triggers. Assembly of inflammasomes is induced by activation of a receptor protein. Many inflammasome receptors require the adapter protein ASC [apoptosis-associated speck-like protein containing a caspase-recruitment domain (CARD)], which consists of two domains, the N-terminal pyrin domain (PYD) and the C-terminal CARD. Upon activation, ASC forms large oligomeric filaments, which facilitate procaspase-1 recruitment. Here, we characterize the structure and filament formation of mouse ASC in vitro at atomic resolution. Information from cryo-electron microscopy and solid-state NMR spectroscopy is combined in a single structure calculation to obtain the atomic-resolution structure of the ASC filament. Perturbations of NMR resonances upon filament formation monitor the specific binding interfaces of ASC-PYD association. Importantly, NMR experiments show the rigidity of the PYD forming the core of the filament as well as the high mobility of the CARD relative to this core. The findings are validated by structure-based mutagenesis experiments in cultured macrophages. The 3D structure of the mouse ASC-PYD filament is highly similar to the recently determined human ASC-PYD filament, suggesting evolutionary conservation of ASC-dependent inflammasome mechanisms. PMID:26464513

DNA Packaging Mutant: Repression of the Vaccinia Virus A32 Gene Results in Noninfectious, DNA-Deficient, Spherical, Enveloped Particles

PubMed Central

Cassetti, Maria Cristina; Merchlinsky, Michael; Wolffe, Elizabeth J.; Weisberg, Andrea S.; Moss, Bernard

1998-01-01

The vaccinia virus A32 open reading frame was predicted to encode a protein with a nucleoside triphosphate-binding motif and a mass of 34 kDa. To investigate the role of this protein, we constructed a mutant in which the original A32 gene was replaced by an inducible copy. The recombinant virus, vA32i, has a conditional lethal phenotype: infectious virus formation was dependent on isopropyl-β-d-thiogalactopyranoside (IPTG). Under nonpermissive conditions, the mutant synthesized early- and late-stage viral proteins, as well as viral DNA that was processed into unit-length genomes. Electron microscopy of cells infected in the absence of IPTG revealed normal-appearing crescents and immature virus particles but very few with nucleoids. Instead of brick-shaped mature particles with defined core structures, there were numerous electron-dense, spherical particles. Some of these spherical particles were wrapped with cisternal membranes, analogous to intracellular and extracellular enveloped virions. Mutant viral particles, purified by sucrose density gradient centrifugation, had low infectivity and transcriptional activity, and the majority were spherical and lacked DNA. Nevertheless, the particle preparation contained representative membrane proteins, cleaved and uncleaved core proteins, the viral RNA polymerase, the early transcription factor and several enzymes, suggesting that incorporation of these components is not strictly coupled to DNA packaging. PMID:9621036

Metal centre effects on HNO binding in porphyrins and the electronic origin: metal's electronic configuration, position in the periodic table, and oxidation state.

PubMed

Yang, Liu; Fang, Weihai; Zhang, Yong

2012-04-21

HNO binds to many different metals in organometallic and bioinorganic chemistry. To help understand experimentally observed metal centre effects, a quantum chemical investigation was performed, revealing clear general binding trends with respect to metal centre characteristics and the electronic origin for the first time. This journal is © The Royal Society of Chemistry 2012

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

Kwon, Deug-Nam; Park, Mi-Ryung; Park, Jong-Yi

Highlights: {yields} The sequences of -604 to -84 bp of the pUPII promoter contained the region of a putative negative cis-regulatory element. {yields} The core promoter was located in the 5F-1. {yields} Transcription factor HNF4 can directly bind in the pUPII core promoter region, which plays a critical role in controlling promoter activity. {yields} These features of the pUPII promoter are fundamental to development of a target-specific vector. -- Abstract: Uroplakin II (UPII) is a one of the integral membrane proteins synthesized as a major differentiation product of mammalian urothelium. UPII gene expression is bladder specific and differentiation dependent, butmore » little is known about its transcription response elements and molecular mechanism. To identify the cis-regulatory elements in the pig UPII (pUPII) gene promoter region, we constructed pUPII 5' upstream region deletion mutants and demonstrated that each of the deletion mutants participates in controlling the expression of the pUPII gene in human bladder carcinoma RT4 cells. We also identified a new core promoter region and putative negative cis-regulatory element within a minimal promoter region. In addition, we showed that hepatocyte nuclear factor 4 (HNF4) can directly bind in the pUPII core promoter (5F-1) region, which plays a critical role in controlling promoter activity. Transient cotransfection experiments showed that HNF4 positively regulates pUPII gene promoter activity. Thus, the binding element and its binding protein, HNF4 transcription factor, may be involved in the mechanism that specifically regulates pUPII gene transcription.« less

A dimer of the lymphoid protein RAG1 recognizes the recombination signal sequence and the complex stably incorporates the high mobility group protein HMG2.

PubMed

Rodgers, K K; Villey, I J; Ptaszek, L; Corbett, E; Schatz, D G; Coleman, J E

1999-07-15

RAG1 and RAG2 are the two lymphoid-specific proteins required for the cleavage of DNA sequences known as the recombination signal sequences (RSSs) flanking V, D or J regions of the antigen-binding genes. Previous studies have shown that RAG1 alone is capable of binding to the RSS, whereas RAG2 only binds as a RAG1/RAG2 complex. We have expressed recombinant core RAG1 (amino acids 384-1008) in Escherichia coli and demonstrated catalytic activity when combined with RAG2. This protein was then used to determine its oligomeric forms and the dissociation constant of binding to the RSS. Electrophoretic mobility shift assays show that up to three oligomeric complexes of core RAG1 form with a single RSS. Core RAG1 was found to exist as a dimer both when free in solution and as the minimal species bound to the RSS. Competition assays show that RAG1 recognizes both the conserved nonamer and heptamer sequences of the RSS. Zinc analysis shows the core to contain two zinc ions. The purified RAG1 protein overexpressed in E.coli exhibited the expected cleavage activity when combined with RAG2 purified from transfected 293T cells. The high mobility group protein HMG2 is stably incorporated into the recombinant RAG1/RSS complex and can increase the affinity of RAG1 for the RSS in the absence of RAG2.

Dynamic constitutional frameworks for DNA biomimetic recognition.

PubMed

Catana, Romina; Barboiu, Mihail; Moleavin, Ioana; Clima, Lilia; Rotaru, Alexandru; Ursu, Elena-Laura; Pinteala, Mariana

2015-02-07

Linear and cross-linked dynamic constitutional frameworks generated from reversibly interacting linear PEG/core constituents and cationic sites shed light on the dominant coiling versus linear DNA binding behaviours, closer to the histone DNA binding wrapping mechanism.

Early stages of clathrin aggregation at a membrane in coarse-grained simulations

NASA Astrophysics Data System (ADS)

Giani, M.; den Otter, W. K.; Briels, W. J.

2017-04-01

The self-assembly process of clathrin coated pits during endocytosis has been simulated by combining and extending coarse grained models of the clathrin triskelion, the adaptor protein AP2, and a flexible network membrane. The AP2's core, upon binding to membrane and cargo, releases a motif that can bind clathrin. In conditions where the core-membrane-cargo binding is weak, the binding of this motif to clathrin can result in a stable complex. We characterize the conditions and mechanisms resulting in the formation of clathrin lattices that curve the membrane, i.e., clathrin coated pits. The mechanical properties of the AP2 β linker appear crucial to the orientation of the curved clathrin lattice relative to the membrane, with wild-type short linkers giving rise to the inward curving buds enabling endocytosis while long linkers produce upside-down cages and outward curving bulges.

Specificity determinants for the abscisic acid response element.

PubMed

Sarkar, Aditya Kumar; Lahiri, Ansuman

2013-01-01

Abscisic acid (ABA) response elements (ABREs) are a group of cis-acting DNA elements that have been identified from promoter analysis of many ABA-regulated genes in plants. We are interested in understanding the mechanism of binding specificity between ABREs and a class of bZIP transcription factors known as ABRE binding factors (ABFs). In this work, we have modeled the homodimeric structure of the bZIP domain of ABRE binding factor 1 from Arabidopsis thaliana (AtABF1) and studied its interaction with ACGT core motif-containing ABRE sequences. We have also examined the variation in the stability of the protein-DNA complex upon mutating ABRE sequences using the protein design algorithm FoldX. The high throughput free energy calculations successfully predicted the ability of ABF1 to bind to alternative core motifs like GCGT or AAGT and also rationalized the role of the flanking sequences in determining the specificity of the protein-DNA interaction.

Electronic, Optical, and Thermal Properties of Reduced-Dimensional Semiconductors

NASA Astrophysics Data System (ADS)

Huang, Shouting

Reduced-dimensional materials have attracted tremendous attention because of their new physics and exotic properties, which are of great interests for fundamental science. More importantly, the manipulation and engineering of matter on an atomic scale yield promising applications for many fields including nanoelectronics, nanobiotechnology, environments, and renewable energy. Because of the unusual quantum confinement and enhanced surface effect of reduced-dimensional materials, traditional empirical models suffer from necessary but unreliable parameters extracted from previously-studied bulk materials. In this sense, quantitative, parameter-free approaches are highly useful for understanding properties of reduced-dimensional materials and, furthermore, predicting their novel applications. The first-principles density functional theory (DFT) is proven to be a reliable and convenient tool. In particular, recent progress in many-body perturbation theory (MBPT) makes it possible to calculate excited-state properties, e.g., quasiparticle (QP) band gap and optical excitations, by the first-principles approach based on DFT. Therefore, during my PhD study, I employed first-principles calculations based on DFT and MBPT to systematically study fundamental properties of typical reduced-dimensional semiconductors, i.e., the electronic structure, phonons, and optical excitations of core-shell nanowires (NWs) and graphene-like two-dimensional (2D) structures of current interests. First, I present first-principles studies on how to engineer band alignments of nano-sized radial heterojunctions, Si/Ge core-shell NWs. Our calculation reveals that band offsets in these one-dimensional (1D) nanostructures can be tailored by applying axial strain or varying core-shell sizes. In particular, the valence band offset can be efficiently tuned across a wide range and even be diminished via applied strain. Two mechanisms contribute to this tuning of band offsets. Furthermore, varying the size of Si/Ge core-shell NWs and corresponding quantum confinement is shown to be efficient for modifying both valence and conduction band offsets simultaneously. Our proposed approaches to control band offsets in nano-sized heterojunctions may be of practical interest for nanoelectronic and photovoltaic applications. Additionally, I also studied the lattice vibrational modes of Si/Ge core-shell N-Ws. Our calculations show that the internal strain induced by the lattice mismatch between core and shell plays an important role in significantly shifting the frequency of characteristic optical modes of core-shell NWs. In particular, our simulation demonstrates that these frequency shifts can be detected by Raman-scattering experiments, giving rise to a convenient and nondestructive way to obtain structural information of core-shell materials. Meanwhile, another type of collective modes, the radial breathing modes (RBM), is identified in Si-core/Ge-shell NWs and their frequency dependence is explained by an elastic media model. Our studied vibrational modes and their frequency evolution are useful for thermoelectric applications based on core-shell nanostructures. Then I studied optical properties and exciton spectra of 2D semiconducting carbon structures. The energy spectra and wavefunctions of excitons in the 2D graphene derivatives, i.e., graphyne and graphane, are found to be strongly modified by quantum confinement, making them qualitatively different from the usual Rydberg series. However, their parity and optical selection rules are preserved. Thus a one-parameter hydrogenic model is applied to quantitatively explain the ab initio exciton spectra, and allows one to extrapolate the electron-hole binding energy from optical spectroscopies of 2D semiconductors without costly simulations. Meanwhile, our calculated optical absorption spectrum and enhanced spin singlet-triplet splitting project graphyne, an allotrope of graphene, as a good candidate for intriguing energy and biomedical applications. Lastly, we report first-principles results on electronic structures of 2D graphene-like system, i.e., silicene. For planar and simply buckled silicene structures, we confirm their zero-gap nature and show a significant renormalization of their Fermi velocity by including many-electron effects. However, the other two recently proposed silicene structures exhibit a finite band gap, indicating that they are gapped semiconductors instead of expected Dirac-fermion semimetals. This finite band gap of the latter two structures is preserved even with the Ag substrate included. The gap opening is explained by the symmetry breaking of the buckled structures. Moreover, our GW calculation reveals enhanced many-electron effects in these 2D structures. Finally the band gap of the latter two structures can be tuned in a wide range by applying strain.

Critical Nuclear Charge for Two-electron Atoms

NASA Astrophysics Data System (ADS)

Estienne, C. S.; Drake, G. W. F.

2014-05-01

There has been a recent revival of interest in the critical nuclear charge Zc that is just sufficient to bind a nucleus of charge Z and two electrons in the 1s21 S ground state. It is conjectured that the inverse of critical charge is related to the radius of convergence 1 /Z* for a 1 / Z expansion of the energy of the form E (Z) =Z2 (E0 +E1 / Z +E2 /Z2 + ⋯) . We have performed high precision variational calculations in Hylleraas coordinates, using the double basis set method, for values of Z very close to Zc, with basis sets containing up to 2809 terms (Ω = 24). Our preliminary result is Zc = 0 . 911 028 224 077 260 (15) , corresponding to 1 /Zc = 1 . 097 660 833 738 555 (18) . Well-defined eigenvalues continue to appear for Z

Electronic structure of Fe- vs. Ru-based dye molecules

NASA Astrophysics Data System (ADS)

Johnson, Phillip S.; Cook, Peter L.; Zegkinoglou, Ioannis; García-Lastra, J. M.; Rubio, Angel; Ruther, Rose E.; Hamers, Robert J.; Himpsel, F. J.

2013-01-01

In order to explore whether Ru can be replaced by inexpensive Fe in dye molecules for solar cells, the differences in the electronic structure of Fe- and Ru-based dyes are investigated by X-ray absorption spectroscopy and first-principles calculations. Molecules with the metal in a sixfold, octahedral N cage, such as tris(bipyridines) and tris(phenanthrolines), exhibit a systematic downward shift of the N 1s-to-π* transition when Ru is replaced by Fe. This shift is explained by an extra transfer of negative charge from the metal to the N ligands in the case of Fe, which reduces the binding energy of the N 1s core level. The C 1s-to-π* transitions show the opposite trend, with an increase in the transition energy when replacing Ru by Fe. Molecules with the metal in a fourfold, planar N cage (porphyrins) exhibit a more complex behavior due to a subtle competition between the crystal field, axial ligands, and the 2+ vs. 3+ oxidation states.

Structural Changes in a Marine Podovirus Associated with Release of its Genome into Prochlorococcus

PubMed Central

Liu, Xiangan; Zhang, Qinfen; Murata, Kazuyoshi; Baker, Matthew L.; Sullivan, Matthew B.; Fu, Caroline; Dougherty, Matthew; Schmid, Michael F.; Osburne, Marcia S.; Chisholm, Sallie W.; Chiu, Wah

2010-01-01

Podovirus P-SSP7 infects Prochlorococcus marinus, the most abundant oceanic photosynthetic microorganism. Single particle cryo-electron microscopy (cryo-EM) yields icosahedral and asymmetrical structures of infectious P-SSP7 with 4.6 Å and 9 Å resolution, respectively. The asymmetric reconstruction reveals how symmetry mismatches are accommodated among 5 of the gene products at the portal vertex. Reconstructions of infectious and empty particles show a conformational change of the “valve” density in the nozzle, an orientation difference in the tail fibers, a disordering of the C-terminus of the portal protein, and disappearance of the core proteins. In addition, cryo-electron tomography (cryo-ET) of P-SSP7 infecting Prochlorococcus demonstrated the same tail fiber conformation as in empty particles. Our observations suggest a mechanism whereby, upon binding to the host cell, the tail fibers induce a cascade of structural alterations of the portal vertex complex that triggers DNA release. PMID:20543830

Surface electronic properties of polycrystalline bulk and thin film In2O3(ZnO)k compounds

NASA Astrophysics Data System (ADS)

Hopper, E. Mitchell; Zhu, Qimin; Gassmann, Jürgen; Klein, Andreas; Mason, Thomas O.

2013-01-01

The surface electronic potentials of In2O3(ZnO)k compounds were measured by X-ray and ultraviolet photoelectron spectroscopy. Both thin film (k = 2) and bulk specimens (k = 3, 5, 7, 9) were studied. All bulk specimens exhibited In enrichment at the surface. All samples showed an increase of In core level binding energies compared to pure and Sn-doped In2O3. The work functions and Fermi levels spanned a range similar to those of the basis oxides In2O3 and ZnO, and the ionization potential was similar to that of both In2O3 and ZnO processed under similar conditions (7.7 eV). This ionization potential was independent of both composition and post-deposition oxidation and reduction treatments. Kelvin probe measurements of cleaned and UV-ozone treated specimens under ambient conditions were in agreement with the photoelectron spectroscopy measurements.

a Photoemission Study of the Electronic Structure Induced by Potassium Adsorption on TiO2(110)

NASA Astrophysics Data System (ADS)

Heise, Rainer; Courths, Ralf

Electronic structure effects induced by potassium adsorption up to one monolayer (ML) on a nearly stoichiometric TiO2(110) surface has been studied by means of angle-resolved photoemission spectroscopy (ARUPS and ARXPS) from valence states and core levels. In agreement with the observations on K/TiO2(100) [P.J. Hardman et al., Surf. Sci. 269/270, 677 (1992)], potassium adsorption at room temperature leads—due to K-to-substrate charge transfer—to the reduction of surface Ti ions (to nominally Ti3+ ions), evidenced by lowered Ti 2p core-level binding energy (ΔBE=-1.6 eV) and occupation of Ti 3d-like band-gap states centered at 0.9 eV BE. The gap-state intensity exhibits a pronounced maximum at 0.37 ML coverage, where the work function has a weak minimum. This behavior is in agreement with a ionic-to-neutral transition of the K-substrate bonding with increasing K coverage, as suggested recently [Souda et al., Surf. Sci. 285, 265 (1993)]. Annealing of a surface precovered with 0.27 ML potassium up to 1000 K results in metallization of the surface, evidenced by (i) the occupation of a second gap-state centered at 0.4 BE and with a considerable state-density at the Fermi energy, and (ii) Ti 2p core-levels lowered by 3.2 eV in BE (nominally “Ti2+” ions). This dramatic reduction of the surface is healed out with complete desorption of potassium. A discussion in terms of desorption of KOx species and oxygen diffusion from the bulk to the surface is given.

[Spectroscopic Study of Salbutamol Molecularly Imprinted Polymers].

PubMed

Ren, Hui-peng; Guan, Yu-yu; Dai, Rong-hua; Liu, Guo-yan; Chai, Chun-yan

2016-02-01

In order to solve the problem of on-site rapid detection of salbutamol residues in feed and animal products, and develop a new method of fast detection of salbutamol on the basis of the molecular imprinting technology, this article uses the salbutamol (SAL) working as template molecule, methacrylic acid (MAA) working as functional monomer. On this basis, a new type of core-shell type salbutamol molecularly imprinted polymers were prepared with colloidal gold particles as triggering core. Superficial characteristics of the MIPs and the related compounds were investigated by ultraviolet (UV) spectra and infrared (IR) spectra, Raman spectra, Scanning electron microscopy (SEM) respectively. The results indicated that a stable hydrogen bonding complex has been formed between the carboxyl groups of SAL and MA with a matching ratio of 1:1. The complex can be easily eluted by the reagent containing hydrogen bonding. The chemical binding constant K reaches -0.245 x 10⁶ L² · mol⁻². The possible binding sites of the hydrogen bonding was formed between the hydrogen atoms of -COOH in MA and the oxygen atoms of C==O in SAL. IR and Raman spectrum showed that, compared with MA, a significant red shift of -OH absorption peak was manifested in MIPs, which proved that SAL as template molecule occurred a specific bond between MA. Red shift of stretching vibration absorption peak of C==O was also detected in the un-eluted MIPs and obvious energy loss happened, which demonstrated a possible binding sites is SAL intramolecular of C==O atom of oxygen. If the hydrogen atoms of -COOH in MA wanted to generate hydrogen bond. However, the shapes of absorption peak of other functional groups including C==C, C==O, and -OH were very similar both in MIPs and NIPs. Specific cavities were formed after the template molecules in MIPs were removed. It was proved by the adsorption experiment that the specific sites in these cavities highly match with the chemical and space structure of SAL. Besides, colloidal gold type core-shell molecularly imprinted polymers have looser surface, more cavities in the surface compared with ordinary molecularly imprinted polymers, which increased the effective area of adsorption to target molecules. So it have better performance in adsorption. Based on the principle that these cavities can specificly recognize and combine with target molecule in the test sample, and the excellent ability of colloidal gold core-shell molecularly imprinted polymers, the development of novel methods for fast determination of SAL based on the molecular imprinting technology can be expected in the near future.

Predicting the relative binding affinity of mineralocorticoid receptor antagonists by density functional methods

NASA Astrophysics Data System (ADS)

Roos, Katarina; Hogner, Anders; Ogg, Derek; Packer, Martin J.; Hansson, Eva; Granberg, Kenneth L.; Evertsson, Emma; Nordqvist, Anneli

2015-12-01

In drug discovery, prediction of binding affinity ahead of synthesis to aid compound prioritization is still hampered by the low throughput of the more accurate methods and the lack of general pertinence of one method that fits all systems. Here we show the applicability of a method based on density functional theory using core fragments and a protein model with only the first shell residues surrounding the core, to predict relative binding affinity of a matched series of mineralocorticoid receptor (MR) antagonists. Antagonists of MR are used for treatment of chronic heart failure and hypertension. Marketed MR antagonists, spironolactone and eplerenone, are also believed to be highly efficacious in treatment of chronic kidney disease in diabetes patients, but is contra-indicated due to the increased risk for hyperkalemia. These findings and a significant unmet medical need among patients with chronic kidney disease continues to stimulate efforts in the discovery of new MR antagonist with maintained efficacy but low or no risk for hyperkalemia. Applied on a matched series of MR antagonists the quantum mechanical based method gave an R2 = 0.76 for the experimental lipophilic ligand efficiency versus relative predicted binding affinity calculated with the M06-2X functional in gas phase and an R2 = 0.64 for experimental binding affinity versus relative predicted binding affinity calculated with the M06-2X functional including an implicit solvation model. The quantum mechanical approach using core fragments was compared to free energy perturbation calculations using the full sized compound structures.

Conformational control and DNA-binding mechanism of the metazoan origin recognition complex.

PubMed

Bleichert, Franziska; Leitner, Alexander; Aebersold, Ruedi; Botchan, Michael R; Berger, James M

2018-06-26

In eukaryotes, the heterohexameric origin recognition complex (ORC) coordinates replication onset by facilitating the recruitment and loading of the minichromosome maintenance 2-7 (Mcm2-7) replicative helicase onto DNA to license origins. Drosophila ORC can adopt an autoinhibited configuration that is predicted to prevent Mcm2-7 loading; how the complex is activated and whether other ORC homologs can assume this state are not known. Using chemical cross-linking and mass spectrometry, biochemical assays, and electron microscopy (EM), we show that the autoinhibited state of Drosophila ORC is populated in solution, and that human ORC can also adopt this form. ATP binding to ORC supports a transition from the autoinhibited state to an active configuration, enabling the nucleotide-dependent association of ORC with both DNA and Cdc6. An unstructured N-terminal region adjacent to the conserved ATPase domain of Orc1 is shown to be required for high-affinity ORC-DNA interactions, but not for activation. ORC optimally binds DNA duplexes longer than the predicted footprint of the ORC ATPases associated with a variety of cellular activities (AAA + ) and winged-helix (WH) folds; cryo-EM analysis of Drosophila ORC bound to DNA and Cdc6 indicates that ORC contacts DNA outside of its central core region, bending the DNA away from its central DNA-binding channel. Our findings indicate that ORC autoinhibition may be common to metazoans and that ORC-Cdc6 remodels origin DNA before Mcm2-7 recruitment and loading.

Brightness analysis of an electron beam with a complex profile

NASA Astrophysics Data System (ADS)

Maesaka, Hirokazu; Hara, Toru; Togawa, Kazuaki; Inagaki, Takahiro; Tanaka, Hitoshi

2018-05-01

We propose a novel analysis method to obtain the core bright part of an electron beam with a complex phase-space profile. This method is beneficial to evaluate the performance of simulation data of a linear accelerator (linac), such as an x-ray free electron laser (XFEL) machine, since the phase-space distribution of a linac electron beam is not simple, compared to a Gaussian beam in a synchrotron. In this analysis, the brightness of undulator radiation is calculated and the core of an electron beam is determined by maximizing the brightness. We successfully extracted core electrons from a complex beam profile of XFEL simulation data, which was not expressed by a set of slice parameters. FEL simulations showed that the FEL intensity was well remained even after extracting the core part. Consequently, the FEL performance can be estimated by this analysis without time-consuming FEL simulations.

X-ray excited Auger transitions of Pu compounds

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

Nelson, Art J., E-mail: nelson63@llnl.gov; Grant, William K.; Stanford, Jeff A.

2015-05-15

X-ray excited Pu core–valence–valence and core–core–valence Auger line-shapes were used in combination with the Pu 4f photoelectron peaks to characterize differences in the oxidation state and local electronic structure for Pu compounds. The evolution of the Pu 4f core-level chemical shift as a function of sputtering depth profiling and hydrogen exposure at ambient temperature was quantified. The combination of the core–valence–valence Auger peak energies with the associated chemical shift of the Pu 4f photoelectron line defines the Auger parameter and results in a reliable method for definitively determining oxidation states independent of binding energy calibration. Results show that PuO{sub 2},more » Pu{sub 2}O{sub 3}, PuH{sub 2.7}, and Pu have definitive Auger line-shapes. These data were used to produce a chemical state (Wagner) plot for select plutonium oxides. This Wagner plot allowed us to distinguish between the trivalent hydride and the trivalent oxide, which cannot be differentiated by the Pu 4f binding energy alone.« less

SOCS1 and SOCS3 Are Targeted by Hepatitis C Virus Core/gC1qR Ligation To Inhibit T-Cell Function

PubMed Central

Yao, Zhi Qiang; Waggoner, Stephen N.; Cruise, Michael W.; Hall, Caroline; Xie, Xuefang; Oldach, David W.; Hahn, Young S.

2005-01-01

T cells play an important role in the control of hepatitis C virus (HCV) infection. We have previously demonstrated that the HCV core inhibits T-cell responses through interaction with gC1qR. We show here that core proteins from chronic and resolved HCV patients differ in sequence, gC1qR-binding ability, and T-cell inhibition. Specifically, chronic core isolates bind to gC1qR more efficiently and inhibit T-cell proliferation as well as gamma interferon (IFN-γ) production more profoundly than resolved core isolates. This inhibition is mediated by the disruption of STAT phosphorylation through the induction of SOCS molecules. Silencing either SOCS1 or SOCS3 by small interfering RNA dramatically augments the production of IFN-γ in T cells, thereby abrogating the inhibitory effect of core. Additionally, the ability of core proteins from patients with chronic infections to induce SOCS proteins and suppress STAT activation greatly exceeds that of core proteins from patients with resolved infections. These results suggest that the HCV core/gC1qR-induced T-cell dysfunction involves the induction of SOCS, a powerful inhibitor of cytokine signaling, which represents a novel mechanism by which a virus usurps the host machinery for persistence. PMID:16306613

Toward an Experimental Quantum Chemistry: Exploring a New Energy Partitioning.

PubMed

Rahm, Martin; Hoffmann, Roald

2015-08-19

Following the work of L. C. Allen, this work begins by relating the central chemical concept of electronegativity with the average binding energy of electrons in a system. The average electron binding energy, χ̅, is in principle accessible from experiment, through photoelectron and X-ray spectroscopy. It can also be estimated theoretically. χ̅ has a rigorous and understandable connection to the total energy. That connection defines a new kind of energy decomposition scheme. The changing total energy in a reaction has three primary contributions to it: the average electron binding energy, the nuclear-nuclear repulsion, and multielectron interactions. This partitioning allows one to gain insight into the predominant factors behind a particular energetic preference. We can conclude whether an energy change in a transformation is favored or resisted by collective changes to the binding energy of electrons, the movement of nuclei, or multielectron interactions. For example, in the classical formation of H2 from atoms, orbital interactions dominate nearly canceling nuclear-nuclear repulsion and two-electron interactions. While in electron attachment to an H atom, the multielectron interactions drive the reaction. Looking at the balance of average electron binding energy, multielectron, and nuclear-nuclear contributions one can judge when more traditional electronegativity arguments can be justifiably invoked in the rationalization of a particular chemical event.

Very Facile Polarity Umpolung and Noncovalent Functionalization of Inorganic Nanoparticles: A Tool Kit for Supramolecular Materials Chemistry.

PubMed

Zeininger, Lukas; Petzi, Stefanie; Schönamsgruber, Jörg; Portilla, Luis; Halik, Marcus; Hirsch, Andreas

2015-09-28

The facile assembly of shell-by-shell (SbS)-coated nanoparticles [TiO2-PAC16]@shell 1-7 (PAC16 = hexadecylphosphonic acid), which are soluble in water and can be isolated as stable solids, is reported. In these functional architectures, an umpolung of dispersibility (organic apolar versus water) was accomplished by the noncovalent binding of ligands 1-7 to titania nanoparticles [TiO2-PAC16] containing a first covalent coating with PAC16. Ligands 1-7 are amphiphilic and form the outer second shell of [TiO2-PAC16]@shell 1-7. The tailor-designed dendritic building blocks 3-5 contain negative and positive charges in the same molecule, and ligands 6 and 7 contain a perylenetetracarboxylic acid dimide (PDI) core (6/7) as a photoactive reporter component. In the redox and photoactive system [TiO2-PAC16]@shell 7, electronic communication between the inorganic core to the PDI ligands was observed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Antibacterial action mode of quaternized carboxymethyl chitosan/poly(amidoamine) dendrimer core-shell nanoparticles against Escherichia coli correlated with molecular chain conformation.

PubMed

Wen, Yan; Yao, Fanglian; Sun, Fang; Tan, Zhilei; Tian, Liang; Xie, Lei; Song, Qingchao

2015-03-01

The action mode of quaternized carboxymethyl chitosan/poly(amidoamine) dendrimer core-shell nanoparticles (CM-HTCC/PAMAM) against Escherichia coli (E. coli) was investigated via a combination of approaches including measurements of cell membrane integrity, outer membrane (OM) and inner membrane (IM) permeability, and scanning electron microscopy (SEM). CM-HTCC/PAMAM dendrimer nanoparticles likely acted in a sequent event-driven mechanism, beginning with the binding of positively charged groups from nanoparticle surface with negative cell surface, thereby causing the disorganization of cell membrane, and subsequent leakage of intracellular components which might ultimately lead to cell death. Moreover, the chain conformation of polymers was taken into account for a better understanding of the antibacterial action mode by means of viscosity and GPC measurements. High utilization ratio of positive charge and large specific surface area generated from a compacted conformation of CM-HTCC/PAMAM, significantly different from the extended conformation of HTCC, were proposed to be involved in the antibacterial action. Copyright © 2014 Elsevier B.V. All rights reserved.

Apolipoprotein E3 Mediated Targeted Brain Delivery of Reconstituted High Density Lipoprotein Bearing 3, 10, And 17 Nm Hydrophobic Core Gold Nanoparticles

NASA Astrophysics Data System (ADS)

Chuang, Skylar T.

We have developed a high density lipoprotein (HDL)-based platform for transport and delivery of hydrophobic gold nanoparticles (AuNP). The ability of apolipoprotein E3 (apoE3) to act as a ligand for the low-density lipoprotein receptor (LDLr) was exploited to gain entry of HDL with AuNP into glioblastoma cells. AuNP of 3, 10 and 17 nm diameter, the latter two synthesized by phase transfer process, were solubilized by integration into reconstituted HDL (rHDL). Absorption spectroscopy indicated the presence of stable particles with signature surface plasmon bands, while electron microscopy revealed AuNP embedded in rHDL core. The rHDL-AuNP complexes displayed robust binding to the LDLr, were internalized by the glioblastoma cells, and appeared as aggregated AuNP in the endosomal-lysosomal compartments. The rHDL-AuNP generated little cytotoxicity and were able to cross the blood brain barrier. The findings bear significance since they offer an effective means of delivering AuNP across tumor cell membrane.

Preparation and characterisation of core-shell CNTs@MIPs nanocomposites and selective removal of estrone from water samples.

PubMed

Gao, Ruixia; Su, Xiaoqian; He, Xiwen; Chen, Langxing; Zhang, Yukui

2011-01-15

This paper reports the preparation of carbon nanotubes (CNTs) functionalized with molecularly imprinted polymers (MIPs) for advanced removal of estrone. CNTs@Est-MIPs nanocomposites with a well-defined core-shell structure were obtained using a semi-covalent imprinting strategy, which employed a thermally reversible covalent bond at the surface of silica-coated CNTs for a large-scale production. The morphology and structure of the products were characterised by transmission electron microscopy and Fourier transform infrared spectroscopy. The adsorption properties were demonstrated by equilibrium rebinding experiments and Scatchard analysis. The results demonstrate that the imprinted nanocomposites possess favourable selectivity, high capacity and fast kinetics for template molecule uptake, yielding an adsorption capacity of 113.5 μmol/g. The synthetic process is quite simple, and the different batches of synthesized CNTs@Est-MIPs nanocomposites showed good reproducibility in template binding. The feasibility of removing estrogenic compounds from environmental water using the CNTs@Est-MIPs nanocomposites was demonstrated using water samples spiked with estrone. Copyright © 2010 Elsevier B.V. All rights reserved.

Structures of cycloserine and 2-oxazolidinone probed by X-ray photoelectron spectroscopy: theory and experiment.

PubMed

Ahmed, Marawan; Wang, Feng; Acres, Robert G; Prince, Kevin C

2014-05-22

The electronic structures and properties of 2-oxazolidinone and the related compound cycloserine (CS) have been investigated using theoretical calculations and core and valence photoelectron spectroscopy. Isomerization of the central oxazolidine heterocycle and the addition of an amino group yield cycloserine. Theory correctly predicts the C, N, and O 1s core spectra, and additionally, we report theoretical natural bond orbital (NBO) charges. The valence ionization energies are also in agreement with theory and previous measurements. Although the lowest binding energy part of the spectra of the two compounds shows superficial similarities, further analysis of the charge densities of the frontier orbitals indicates substantial reorganization of the wave functions as a result of isomerization. The highest occupied molecular orbital (HOMO) of CS shows leading carbonyl π character with contributions from other heavy (non-H) atoms in the molecule, while the HOMO of 2-oxazolidinone (OX2) has leading nitrogen, carbon, and oxygen pπ characters. The present study further theoretically predicts bond resonance effects of the compounds, evidence for which is provided by our experimental measurements and published crystallographic data.

Electronic structure of rare-earth chromium antimonides RECrSb{sub 3} (RE=La-Nd, Sm, Gd-Dy, Yb) by X-ray photoelectron spectroscopy

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

Crerar, Shane J.; Mar, Arthur, E-mail: arthur.mar@ualberta.ca; Grosvenor, Andrew P.

The electronic structure of the ternary rare-earth chromium antimonides RECrSb{sub 3} (RE=La-Nd, Sm, Gd-Dy, Yb) has been examined by high-resolution X-ray photoelectron spectroscopy (XPS) for the first time. The RE 3d or 4d core-line spectra are substantially complicated by the presence of satellite peaks but their general resemblance to those of RE{sub 2}O{sub 3} tends to support the presence of trivalent RE atoms in RECrSb{sub 3}. However, the Yb 4d spectrum of YbCrSb{sub 3} also shows peaks that are characteristic of divalent ytterbium. The Cr 2p core-line spectra exhibit asymmetric lineshapes and little change in binding energy (BE) relative tomore » Cr metal, providing strong evidence for electronic delocalization. The Sb 3d core-line spectra reveal slightly negative BE shifts relative to elemental antimony, supporting the presence of anionic Sb species in RECrSb{sub 3}. The experimental valence band spectrum of LaCrSb{sub 3} matches well with the calculated density of states, and it can be fitted to component peaks belonging to individual atoms to yield an average formulation that agrees well with expectations ('La{sup 3+}Cr{sup 3+}(Sb{sup 2-}){sub 3}'). On progressing from LaCrSb{sub 3} to NdCrSb{sub 3}, the 4f-band in the valence band spectra grows in intensity and shifts to higher BE. The valence band spectrum for YbCrSb{sub 3} also supports the presence of divalent ytterbium. - Graphical Abstract: In their valence band spectra, the 4f-band intensifies and shifts to higher BE on progressing from LaCrSb{sub 3} to NdCrSb{sub 3}. Highlights: Black-Right-Pointing-Pointer High-resolution core-line and valence band XPS spectra were measured for RECrSb{sub 3}. Black-Right-Pointing-Pointer Divalent Yb is present in YbCrSb{sub 3}, in contrast to trivalent RE in other members. Black-Right-Pointing-Pointer Asymmetric Cr 2p spectral lineshape confirms delocalization of Cr valence electrons. Black-Right-Pointing-Pointer Small negative Sb 3d BE shifts support assignment of anionic Sb atoms. Black-Right-Pointing-Pointer Fitted valence band spectra show shifts in the 4f band as RE is changed.« less

Theory and X-ray Absorption Spectroscopy for Aluminum Coordination Complexes – Al K-Edge Studies of Charge and Bonding in (BDI)Al, (BDI)AlR2, and (BDI)AlX2 Complexes.

PubMed

Altman, Alison B; Pemmaraju, C D; Camp, Clément; Arnold, John; Minasian, Stefan G; Prendergast, David; Shuh, David K; Tyliszczak, Tolek

2015-08-19

Polarized aluminum K-edge X-ray absorption near edge structure (XANES) spectroscopy and first-principles calculations were used to probe electronic structure in a series of (BDI)Al, (BDI)AlX2, and (BDI)AlR2 coordination compounds (X = F, Cl, I; R = H, Me; BDI = 2,6-diisopropylphenyl-β-diketiminate). Spectral interpretations were guided by examination of the calculated transition energies and polarization-dependent oscillator strengths, which agreed well with the XANES spectroscopy measurements. Pre-edge features were assigned to transitions associated with the Al 3p orbitals involved in metal-ligand bonding. Qualitative trends in Al 1s core energy and valence orbital occupation were established through a systematic comparison of excited states derived from Al 3p orbitals with similar symmetries in a molecular orbital framework. These trends suggested that the higher transition energies observed for (BDI)AlX2 systems with more electronegative X(1-) ligands could be ascribed to a decrease in electron density around the aluminum atom, which causes an increase in the attractive potential of the Al nucleus and concomitant increase in the binding energy of the Al 1s core orbitals. For (BDI)Al and (BDI)AlH2 the experimental Al K-edge XANES spectra and spectra calculated using the eXcited electron and Core-Hole (XCH) approach had nearly identical energies for transitions to final state orbitals of similar composition and symmetry. These results implied that the charge distributions about the aluminum atoms in (BDI)Al and (BDI)AlH2 are similar relative to the (BDI)AlX2 and (BDI)AlMe2 compounds, despite having different formal oxidation states of +1 and +3, respectively. However, (BDI)Al was unique in that it exhibited a low-energy feature that was attributed to transitions into a low-lying p-orbital of b1 symmetry that is localized on Al and orthogonal to the (BDI)Al plane. The presence of this low-energy unoccupied molecular orbital on electron-rich (BDI)Al distinguishes its valence electronic structure from that of the formally trivalent compounds (BDI)AlX2 and (BDI)AlR2. The work shows that Al K-edge XANES spectroscopy can be used to provide valuable insight into electronic structure and reactivity relationships for main-group coordination compounds.

Relativistic semiempirical-core-potential calculations in Ca+,Sr+ , and Ba+ ions on Lagrange meshes

NASA Astrophysics Data System (ADS)

Filippin, Livio; Schiffmann, Sacha; Dohet-Eraly, Jérémy; Baye, Daniel; Godefroid, Michel

2018-01-01

Relativistic atomic structure calculations are carried out in alkaline-earth-metal ions using a semiempirical-core-potential approach. The systems are partitioned into frozen-core electrons and an active valence electron. The core orbitals are defined by a Dirac-Hartree-Fock calculation using the grasp2k package. The valence electron is described by a Dirac-like Hamiltonian involving a core-polarization potential to simulate the core-valence electron correlation. The associated equation is solved with the Lagrange-mesh method, which is an approximate variational approach having the form of a mesh calculation because of the use of a Gauss quadrature to calculate matrix elements. Properties involving the low-lying metastable D 3 /2 ,5 /2 2 states of Ca+, Sr+, and Ba+ are studied, such as polarizabilities, one- and two-photon decay rates, and lifetimes. Good agreement is found with other theory and observation, which is promising for further applications in alkalilike systems.

Electronic wave function and binding effects in M-shell ionization of gold by protons

NASA Astrophysics Data System (ADS)

Pajek, M.; Banaś, D.; Jabłoński, Ł.; Mukoyama, T.

2018-02-01

The measured M-X-ray production cross sections for protons, which are used in the particle induced X-ray emission (PIXE) technique, are systematically underestimated for low impact energies by the ECPSSR and ECUSAR theories. These theories, which are based on the plane wave Born approximation (PWBA) and use the screened hydrogenic wave functions, include corrections for the projectile Coulomb deflection and electron relativistic and binding effects. In the present paper, in order to interpret the observed disagreement at low impact energies, the systematic calculations of the M-shell ionization cross sections for gold were performed using the semiclassical (SCA) and the binary encounter (BEA) approximations in order to identify a role of the electronic wave function and electron binding effects. In these calculations the different wave functions, from nonrelativistic hydrogenic to selfconsistent Dirac-Hartree-Fock, were considered and the binding effect was treated within extreme separated- (SA) and united-atoms (UA) limits. The results are discussed in details and the observed discrepancies are attributed to inadequate description of the electron binding effect at the lowest impact energies for which the molecular approach is required.

Endogenous Hot Spots of De Novo Telomere Addition in the Yeast Genome Contain Proximal Enhancers That Bind Cdc13

PubMed Central

Obodo, Udochukwu C.; Epum, Esther A.; Platts, Margaret H.; Seloff, Jacob; Dahlson, Nicole A.; Velkovsky, Stoycho M.; Paul, Shira R.

2016-01-01

DNA double-strand breaks (DSBs) pose a threat to genome stability and are repaired through multiple mechanisms. Rarely, telomerase, the enzyme that maintains telomeres, acts upon a DSB in a mutagenic process termed telomere healing. The probability of telomere addition is increased at specific genomic sequences termed sites of repair-associated telomere addition (SiRTAs). By monitoring repair of an induced DSB, we show that SiRTAs on chromosomes V and IX share a bipartite structure in which a core sequence (Core) is directly targeted by telomerase, while a proximal sequence (Stim) enhances the probability of de novo telomere formation. The Stim and Core sequences are sufficient to confer a high frequency of telomere addition to an ectopic site. Cdc13, a single-stranded DNA binding protein that recruits telomerase to endogenous telomeres, is known to stimulate de novo telomere addition when artificially recruited to an induced DSB. Here we show that the ability of the Stim sequence to enhance de novo telomere addition correlates with its ability to bind Cdc13, indicating that natural sites at which telomere addition occurs at high frequency require binding by Cdc13 to a sequence 20 to 100 bp internal from the site at which telomerase acts to initiate de novo telomere addition. PMID:27044869

Positron annihilation induced Auger electron emission

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

Weiss, A.; Jibaly, M.; Lei, Chun

1988-01-01

We report on measurements of Auger electron emission from Cu and Fe due to core hole excitations produced by the removal of core electrons by matter-antimatter annihilation. Estimates are developed of the probability of positrons annihilating with a 3p electron in these materials. Several important advantages of Positron annihilation induced Auger Electron Spectroscopy (PAES) for surface analysis are suggested. 10 refs., 2 figs.

Discovery of a small-molecule HIV-1 integrase inhibitor-binding site | Center for Cancer Research

Cancer.gov

The lowest energy-binding conformation of an inhibitor bound to the dimeric interface of HIV-1 integrase core domain. The yellow region represents a unique allosteric binding site identified by affinity labeling and mass spectrometry and validated through mutagenesis. This site can provide a potential platform for the rational design of inhibitors selective for disruption of

HMG-D is an architecture-specific protein that preferentially binds to DNA containing the dinucleotide TG.

PubMed Central

Churchill, M E; Jones, D N; Glaser, T; Hefner, H; Searles, M A; Travers, A A

1995-01-01

The high mobility group (HMG) protein HMG-D from Drosophila melanogaster is a highly abundant chromosomal protein that is closely related to the vertebrate HMG domain proteins HMG1 and HMG2. In general, chromosomal HMG domain proteins lack sequence specificity. However, using both NMR spectroscopy and standard biochemical techniques we show that binding of HMG-D to a single DNA site is sequence selective. The preferred duplex DNA binding site comprises at least 5 bp and contains the deformable dinucleotide TG embedded in A/T-rich sequences. The TG motif constitutes a common core element in the binding sites of the well-characterized sequence-specific HMG domain proteins. We show that a conserved aromatic residue in helix 1 of the HMG domain may be involved in recognition of this core sequence. In common with other HMG domain proteins HMG-D binds preferentially to DNA sites that are stably bent and underwound, therefore HMG-D can be considered an architecture-specific protein. Finally, we show that HMG-D bends DNA and may confer a superhelical DNA conformation at a natural DNA binding site in the Drosophila fushi tarazu scaffold-associated region. Images PMID:7720717

Self-Assembled Multivalent (SAMul) Polyanion Binding-Impact of Hydrophobic Modifications in the Micellar Core on DNA and Heparin Binding at the Peripheral Cationic Ligands.

PubMed

Albanyan, Buthaina; Laurini, Erik; Posocco, Paola; Pricl, Sabrina; Smith, David K

2017-05-05

This paper reports a small family of cationic surfactants designed to bind polyanions such as DNA and heparin. Each molecule has the same hydrophilic cationic ligand and a hydrophobic aliphatic group with eighteen carbon atoms with one, two, or three alkene groups within the hydrophobic chain (C18-1, C18-2 and C18-3). Dynamic light scattering indicates that more alkenes lead to geometric distortion, giving rise to larger self-assembled multivalent (SAMul) nanostructures. Mallard Blue and Ethidium Bromide dye displacement assays demonstrate that heparin and DNA have markedly different binding preferences, with heparin binding most effectively to C18-1, and DNA to C18-3, even though the molecular structural differences of these SAMul systems are buried in the hydrophobic core. Multiscale modelling suggests that adaptive heparin maximises enthalpically favourable interactions with C18-1, while shape-persistent DNA forms a similar number of interactions with each ligand display, but with slightly less entropic cost for binding to C18-3-fundamental thermodynamic differences in SAMul binding of heparin or DNA. This study therefore provides unique insight into electrostatic molecular recognition between highly charged nanoscale surfaces in biologically relevant systems. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

ACFIS: a web server for fragment-based drug discovery

PubMed Central

Hao, Ge-Fei; Jiang, Wen; Ye, Yuan-Nong; Wu, Feng-Xu; Zhu, Xiao-Lei; Guo, Feng-Biao; Yang, Guang-Fu

2016-01-01

In order to foster innovation and improve the effectiveness of drug discovery, there is a considerable interest in exploring unknown ‘chemical space’ to identify new bioactive compounds with novel and diverse scaffolds. Hence, fragment-based drug discovery (FBDD) was developed rapidly due to its advanced expansive search for ‘chemical space’, which can lead to a higher hit rate and ligand efficiency (LE). However, computational screening of fragments is always hampered by the promiscuous binding model. In this study, we developed a new web server Auto Core Fragment in silico Screening (ACFIS). It includes three computational modules, PARA_GEN, CORE_GEN and CAND_GEN. ACFIS can generate core fragment structure from the active molecule using fragment deconstruction analysis and perform in silico screening by growing fragments to the junction of core fragment structure. An integrated energy calculation rapidly identifies which fragments fit the binding site of a protein. We constructed a simple interface to enable users to view top-ranking molecules in 2D and the binding mode in 3D for further experimental exploration. This makes the ACFIS a highly valuable tool for drug discovery. The ACFIS web server is free and open to all users at http://chemyang.ccnu.edu.cn/ccb/server/ACFIS/. PMID:27150808

ACFIS: a web server for fragment-based drug discovery.

PubMed

Hao, Ge-Fei; Jiang, Wen; Ye, Yuan-Nong; Wu, Feng-Xu; Zhu, Xiao-Lei; Guo, Feng-Biao; Yang, Guang-Fu

2016-07-08

In order to foster innovation and improve the effectiveness of drug discovery, there is a considerable interest in exploring unknown 'chemical space' to identify new bioactive compounds with novel and diverse scaffolds. Hence, fragment-based drug discovery (FBDD) was developed rapidly due to its advanced expansive search for 'chemical space', which can lead to a higher hit rate and ligand efficiency (LE). However, computational screening of fragments is always hampered by the promiscuous binding model. In this study, we developed a new web server Auto Core Fragment in silico Screening (ACFIS). It includes three computational modules, PARA_GEN, CORE_GEN and CAND_GEN. ACFIS can generate core fragment structure from the active molecule using fragment deconstruction analysis and perform in silico screening by growing fragments to the junction of core fragment structure. An integrated energy calculation rapidly identifies which fragments fit the binding site of a protein. We constructed a simple interface to enable users to view top-ranking molecules in 2D and the binding mode in 3D for further experimental exploration. This makes the ACFIS a highly valuable tool for drug discovery. The ACFIS web server is free and open to all users at http://chemyang.ccnu.edu.cn/ccb/server/ACFIS/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Hollow Electron Beam Collimation for HL-LHC - Effects on the Beam Core

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

Fitterer, M.; Stancari, G.; Valishev, A.

2017-06-13

Collimation with hollow electron beams is currently one of the most promising concepts for active halo control in the High Luminosity Large Hadron Collider (HL-LHC). To ensure the successful operation of the hollow beam collimator the unwanted effects on the beam core, which might arise from the operation with a pulsed electron beam, must be minimized. This paper gives a summary of the effect of hollow electron lenses on the beam core in terms of sources, provides estimates for HL-LHC and discusses the possible mitigation methods.

Expression of a functional intrabody against hepatitis C virus core protein in Escherichia coli and silkworm pupae.

PubMed

Kato, Tatsuya; Hasegawa, Moeko; Yamamoto, Takeshi; Miyazaki, Takatsugu; Suzuki, Ryosuke; Wakita, Takaji; Suzuki, Tetsuro; Park, Enoch Y

2018-10-01

It has been shown that the single-domain intrabody 2H9-L against the hepatitis C virus (HCV) capsid (core) protein inhibits the viral propagation and NF-κB promoter activity induced by the HCV core. In this study, 2H9-L fused with the FLAG tag sequence was expressed in both Escherichia coli and silkworm pupae and then purified. In addition, the full-length and its C terminal deletions of the HCV core protein, i.e., 1-123 amino acid residues (C123), 1-152 amino acid residues (C152), 1-177 amino acid residues (C177) and 1-191 amino acid residues (C191), were expressed as fusion proteins with a 6 × His tag at their N-terminus in E. coli and then purified. Approximately 175 and 132 μg of the intrabody were purified from 100 ml of E. coli culture and 10 silkworm pupae, respectively, by affinity chromatography. The C123, C152, C177 and C191 HCV core protein variants were purified to approximately 152, 127, 103 and 155 μg, respectively, from 100 ml of E. coli culture. An ELISA in which the intrabodies were immobilized revealed that the intrabodies purified from both hosts were bound to all HCV core protein variants. However, their binding to the C191 appeared to be weak compared to their bindings to the other HCV core protein variants. When C152 was immobilized in the ELISA, the binding of each intrabody to the core protein was also observed. These purified intrabodies can be used in biochemical analyses of the inhibitory mechanism of HCV propagation and as protein interference reagents, thus providing a potential pathway to developing a new type of antiviral drug. Copyright © 2018 Elsevier Inc. All rights reserved.

Temperature dependent electron delocalization in CdSe/CdS type-I core-shell systems: An insight from scanning tunneling spectroscopy

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

Kundu, Biswajit; Chakrabarti, Sudipto; Pal, Amlan J., E-mail: sspajp@iacs.res.in

2016-03-14

Core-shell nanocrystals having a type-I band-alignment confine charge carriers to the core. In this work, we choose CdSe/CdS core-shell nano-heterostructures that evidence confinement of holes only. Such a selective confinement occurs in the core-shell nanocrystals due to a low energy-offset of conduction band (CB) edges resulting in delocalization of electrons and thus a decrease in the conduction band-edge. Since the delocalization occurs through a thermal assistance, we study temperature dependence of selective delocalization process through scanning tunneling spectroscopy. From the density of states (DOS), we observe that the electrons are confined to the core at low temperatures. Above a certainmore » temperature, they become delocalized up to the shell leading to a decrease in the CB of the core-shell system due to widening of quantum confinement effect. With holes remaining confined to the core due to a large offset in the valence band (VB), we record the topography of the core-shell nanocrystals by probing their CB and VB edges separately. The topographies recorded at different temperatures representing wave-functions of electrons and holes corresponded to the results obtained from the DOS spectra. The results evidence temperature-dependent wave-function delocalization of one-type of carriers up to the shell layer in core-shell nano-heterostructures.« less

Time-dependent Schrödinger equation for molecular core-hole dynamics

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

Picón, A.

2017-02-01

X-ray spectroscopy is an important tool for the investigation of matter. X rays primarily interact with inner-shell electrons, creating core (inner-shell) holes that will decay on the time scale of attoseconds to a few femtoseconds through electron relaxations involving the emission of a photon or an electron. Furthermore, the advent of femtosecond x-ray pulses expands x-ray spectroscopy to the time domain and will eventually allow the control of core-hole population on time scales comparable to core-vacancy lifetimes. For both cases, a theoretical approach that accounts for the x-ray interaction while the electron relaxations occur is required. We describe a time-dependentmore » framework, based on solving the time-dependent Schrödinger equation, that is suitable for describing the induced electron and nuclear dynamics.« less

Electronic and Spatial Structures of Water-Soluble Dinitrosyl Iron Complexes with Thiol-Containing Ligands Underlying Their Ability to Act as Nitric Oxide and Nitrosonium Ion Donors

PubMed Central

Vanin, Anatoly F.; Burbaev, Dosymzhan Sh.

2011-01-01

The ability of mononuclear dinitrosyl iron commplexes (M-DNICs) with thiolate ligands to act as NO donors and to trigger S-nitrosation of thiols can be explain only in the paradigm of the model of the [Fe+(NO+)2] core ({Fe(NO)2}7 according to the Enemark-Feltham classification). Similarly, the {(RS−)2Fe+(NO+)2}+ structure describing the distribution of unpaired electron density in M-DNIC corresponds to the low-spin (S = 1/2) state with a d7 electron configuration of the iron atom and predominant localization of the unpaired electron on MO(dz2) and the square planar structure of M-DNIC. On the other side, the formation of molecular orbitals of M-DNIC including orbitals of the iron atom, thiolate and nitrosyl ligands results in a transfer of electron density from sulfur atoms to the iron atom and nitrosyl ligands. Under these conditions, the positive charge on the nitrosyl ligands diminishes appreciably, the interaction of the ligands with hydroxyl ions or with thiols slows down and the hydrolysis of nitrosyl ligands and the S-nitrosating effect of the latter are not manifested. Most probably, the S-nitrosating effect of nitrosyl ligands is a result of weak binding of thiolate ligands to the iron atom under conditions favoring destabilization of M-DNIC. PMID:22505886

Electronic and spatial structures of water-soluble dinitrosyl iron complexes with thiol-containing ligands underlying their ability to act as nitric oxide and nitrosonium ion donors.

PubMed

Vanin, Anatoly F; Burbaev, Dosymzhan Sh

2011-01-01

The ability of mononuclear dinitrosyl iron commplexes (M-DNICs) with thiolate ligands to act as NO donors and to trigger S-nitrosation of thiols can be explain only in the paradigm of the model of the [Fe(+)(NO(+))(2)] core ({Fe(NO)(2)}(7) according to the Enemark-Feltham classification). Similarly, the {(RS(-))(2)Fe(+)(NO(+))(2)}(+) structure describing the distribution of unpaired electron density in M-DNIC corresponds to the low-spin (S = 1/2) state with a d(7) electron configuration of the iron atom and predominant localization of the unpaired electron on MO(d(z2)) and the square planar structure of M-DNIC. On the other side, the formation of molecular orbitals of M-DNIC including orbitals of the iron atom, thiolate and nitrosyl ligands results in a transfer of electron density from sulfur atoms to the iron atom and nitrosyl ligands. Under these conditions, the positive charge on the nitrosyl ligands diminishes appreciably, the interaction of the ligands with hydroxyl ions or with thiols slows down and the hydrolysis of nitrosyl ligands and the S-nitrosating effect of the latter are not manifested. Most probably, the S-nitrosating effect of nitrosyl ligands is a result of weak binding of thiolate ligands to the iron atom under conditions favoring destabilization of M-DNIC.

The Effects of Surface Reconstruction and Electron-Positron Correlation on the Annihilation Characteristics of Positrons Trapped at Semiconductor Surfaces

NASA Astrophysics Data System (ADS)

Fazleev, N. G.; Jung, E.; Weiss, A. H.

2009-03-01

Experimental positron annihilation induced Auger electron spectroscopy (PAES) data from Ge(100) and Ge(111) surfaces display several strong Auger peaks corresponding to M4,5N1N2,3, M2,3M4,5M4,5, M2,3M4,5V, and M1M4,5M4,5 Auger transitions. The integrated peak intensities of Auger transitions have been used to obtain experimental annihilation probabilities for the Ge 3d and 3p core electrons. The experimental data were analyzed by performing theoretical studies of the effects of surface reconstructions and electron-positron correlations on image potential induced surface states and annihilation characteristics of positrons trapped at the reconstructed Ge(100) and Ge(111) surfaces. Calculations of positron surface states and annihilation characteristics have been performed for Ge(100) surface with (2×1), (2×2), and (4×2) reconstructions, and for Ge(111) surface with c(2×8) reconstruction. Estimates of the positron binding energy and annihilation characteristics reveal their sensitivity to the specific atomic structure of the topmost layers of the semiconductor and to the approximations used to describe electron-positron correlations. The results of these theoretical studies are compared with the ones obtained for the reconstructed Si(100)-(2×1) and Si(111)-(7×7) surfaces.

Effects of excitation frequency on high-order terahertz sideband generation in semiconductors

NASA Astrophysics Data System (ADS)

Xie, Xiao-Tao; Zhu, Bang-Fen; Liu, Ren-Bao

2013-10-01

We theoretically investigate the effects of the excitation frequency on the plateau of high-order terahertz sideband generation (HSG) in semiconductors driven by intense terahertz (THz) fields. We find that the plateau of the sideband spectrum strongly depends on the detuning between the near-infrared laser field and the band gap. We use the quantum trajectory theory (three-step model) to understand the HSG. In the three-step model, an electron-hole pair is first excited by a weak laser, then driven by the strong THz field, and finally recombined to emit a photon with energy gain. When the laser is tuned below the band gap (negative detuning), the electron-hole generation is a virtual process that requires quantum tunneling to occur. When the energy gained by the electron-hole pair from the THz field is less than 3.17 times the ponderomotive energy (Up), the electron and the hole can be driven to the same position and recombined without quantum tunneling, so that the HSG will have large probability amplitude. This leads to a plateau feature of the HSG spectrum with a high-frequency cutoff at about 3.17Up above the band gap. Such a plateau feature is similar to the case of high-order harmonics generation in atoms where electrons have to overcome the binding energy to escape the atomic core. A particularly interesting excitation condition in HSG is that the laser can be tuned above the band gap (positive detuning), corresponding to the unphysical ‘negative’ binding energy in atoms for high-order harmonic generation. Now the electron-hole pair is generated by real excitation, but the recombination process can be real or virtual depending on the energy gained from the THz field, which determines the plateau feature in HSG. Both the numerical calculation and the quantum trajectory analysis reveal that for positive detuning, the HSG plateau cutoff depends on the frequency of the excitation laser. In particular, when the laser is tuned more than 3.17Up above the band gap, the HSG spectrum presents no plateau feature but instead sharp peaks near the band edge and near the excitation frequency.

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

Lyn, Rodney K.; Department of Chemistry, University of Ottawa, Ottawa; Kennedy, David C.

Research highlights: {yields} Hepatitis C virus uses lipid droplets (LD) onto which HCV core proteins bind. {yields} HCV core proteins on LDs facilitate viral particle assembly. {yields} We used a novel combination of CARS, two-photon fluorescence, and DIC microscopies. {yields} Particle tracking experiments show that core slowly affects LD localization. {yields} Particle tracking measured the change in speed and directionality of LD movement. -- Abstract: The hepatitis C virus (HCV) is a global health problem, with limited treatment options and no vaccine available. HCV uses components of the host cell to proliferate, including lipid droplets (LD) onto which HCV coremore » proteins bind and facilitate viral particle assembly. We have measured the dynamics of HCV core protein-mediated changes in LDs and rates of LD movement on microtubules using a combination of coherent anti-Stokes Raman scattering (CARS), two-photon fluorescence (TPF), and differential interference contrast (DIC) microscopies. Results show that the HCV core protein induces rapid increases in LD size. Particle tracking experiments show that HCV core protein slowly affects LD localization by controlling the directionality of LD movement on microtubules. These dynamic processes ultimately aid HCV in propagating and the molecules and interactions involved represent novel targets for potential therapeutic intervention.« less

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.

Complexes of DNA bases and Watson-Crick base pairs interaction with neutral silver Agn (n = 8, 10, 12) clusters: a DFT and TDDFT study.

PubMed

Srivastava, Ruby

2018-03-01

We study the binding of the neutral Ag n (n = 8, 10, 12) to the DNA base-adenine (A), guanine (G) and Watson-Crick -adenine-thymine, guanine-cytosine pairs. Geometries of complexes were optimized at the DFT level using the hybrid B3LYP functional. LANL2DZ effective core potential was used for silver and 6-31 + G ** was used for all other atoms. NBO charges were analyzed using the Natural population analysis. The absorption properties of Ag n -A,G/WC complexes were also studied using time-dependent density functional theory. The absorption spectra for these complexes show wavelength in the visible region. It was revealed that silver clusters interact more strongly with WC pairs than with isolated DNA complexes. Furthermore, it was found that the electronic charge transferred from silver to isolated DNA clusters are less than the electronic charge transferred from silver to the Ag n -WC complexes. The vertical ionization potential, vertical electron affinity, hardness, and electrophilicity index of Ag n -DNA/WC complexes have also been discussed.

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.

Density-functional theory study of the geometries, stabilities, and electronic properties of Au n Rb (n = 1-10) clusters: comparison with pure gold clusters

NASA Astrophysics Data System (ADS)

Hu, Yan-Fei; Jiang, Gang; Meng, Da-Qiao

2012-01-01

The density functional method with the relativistic effective core potential has been employed to investigate systematically the geometric structures, relative stabilities, growth-pattern behavior, and electronic properties of small bimetallic Au n Rb (n = 1-10) and pure gold Au n (n ≤ 11) clusters. For the geometric structures of the Au n Rb (n = 1-10) clusters, the dominant growth pattern is for a Rb-substituted Au n +1 cluster or one Au atom capped on a Au n -1Rb cluster, and the turnover point from a two-dimensional to a three-dimensional structure occurs at n = 4. Moreover, the stability of the ground-state structures of these clusters has been examined via an analysis of the average atomic binding energies, fragmentation energies, and the second-order difference of energies as a function of cluster size. The results exhibit a pronounced even-odd alternation phenomenon. The same pronounced even-odd alternations are found for the HOMO-LUMO gap, VIPs, VEAs, and the chemical hardness. In addition, about one electron charge transfers from the Au n host to the Rb atom in each corresponding Au n Rb cluster.

Atomistic Description of Thiostannate-Capped CdSe Nanocrystals: Retention of Four-Coordinate SnS4 Motif and Preservation of Cd-Rich Stoichiometry

PubMed Central

2016-01-01

Colloidal semiconductor nanocrystals (NCs) are widely studied as building blocks for novel solid-state materials. Inorganic surface functionalization, used to displace native organic capping ligands from NC surfaces, has been a major enabler of electronic solid-state devices based on colloidal NCs. At the same time, very little is known about the atomistic details of the organic-to-inorganic ligand exchange and binding motifs at the NC surface, severely limiting further progress in designing all-inorganic NCs and NC solids. Taking thiostannates (K4SnS4, K4Sn2S6, K6Sn2S7) as typical examples of chalcogenidometallate ligands and oleate-capped CdSe NCs as a model NC system, in this study we address these questions through the combined application of solution 1H NMR spectroscopy, solution and solid-state 119Sn NMR spectroscopy, far-infrared and X-ray absorption spectroscopies, elemental analysis, and by DFT modeling. We show that through the X-type oleate-to-thiostannate ligand exchange, CdSe NCs retain their Cd-rich stoichiometry, with a stoichiometric CdSe core and surface Cd adatoms serving as binding sites for terminal S atoms of the thiostannates ligands, leading to all-inorganic (CdSe)core[Cdm(Sn2S7)yK(6y-2m)]shell (taking Sn2S76– ligand as an example). Thiostannates SnS44– and Sn2S76– retain (distorted) tetrahedral SnS4 geometry upon binding to NC surface. At the same time, experiments and simulations point to lower stability of Sn2S64– (and SnS32–) in most solvents and its lower adaptability to the NC surface caused by rigid Sn2S2 rings. PMID:25597625

The Hexamer Structure of the Rift Valley Fever Virus Nucleoprotein Suggests a Mechanism for its Assembly into Ribonucleoprotein Complexes

PubMed Central

Ferron, François; Li, Zongli; Danek, Eric I.; Luo, Dahai; Wong, Yeehwa; Coutard, Bruno; Lantez, Violaine; Charrel, Rémi; Canard, Bruno; Walz, Thomas; Lescar, Julien

2011-01-01

Rift Valley fever virus (RVFV), a Phlebovirus with a genome consisting of three single-stranded RNA segments, is spread by infected mosquitoes and causes large viral outbreaks in Africa. RVFV encodes a nucleoprotein (N) that encapsidates the viral RNA. The N protein is the major component of the ribonucleoprotein complex and is also required for genomic RNA replication and transcription by the viral polymerase. Here we present the 1.6 Å crystal structure of the RVFV N protein in hexameric form. The ring-shaped hexamers form a functional RNA binding site, as assessed by mutagenesis experiments. Electron microscopy (EM) demonstrates that N in complex with RNA also forms rings in solution, and a single-particle EM reconstruction of a hexameric N-RNA complex is consistent with the crystallographic N hexamers. The ring-like organization of the hexamers in the crystal is stabilized by circular interactions of the N terminus of RVFV N, which forms an extended arm that binds to a hydrophobic pocket in the core domain of an adjacent subunit. The conformation of the N-terminal arm differs from that seen in a previous crystal structure of RVFV, in which it was bound to the hydrophobic pocket in its own core domain. The switch from an intra- to an inter-molecular interaction mode of the N-terminal arm may be a general principle that underlies multimerization and RNA encapsidation by N proteins from Bunyaviridae. Furthermore, slight structural adjustments of the N-terminal arm would allow RVFV N to form smaller or larger ring-shaped oligomers and potentially even a multimer with a super-helical subunit arrangement. Thus, the interaction mode between subunits seen in the crystal structure would allow the formation of filamentous ribonucleocapsids in vivo. Both the RNA binding cleft and the multimerization site of the N protein are promising targets for the development of antiviral drugs. PMID:21589902

Focused library with a core structure extracted from natural products and modified: application to phosphatase inhibitors and several biochemical findings.

PubMed

Hirai, Go; Sodeoka, Mikiko

2015-05-19

Synthesis of a focused library is an important strategy to create novel modulators of specific classes of proteins. Compounds in a focused library are composed of a common core structure and different diversity structures. In this Account, we describe our design and synthesis of libraries focused on selective inhibitors of protein phosphatases (PPases). We considered that core structures having structural and electronic features similar to those of PPase substrates, phosphate esters, would be a reasonable choice. Therefore, we extracted core structures from natural products already identified as PPase inhibitors. Since many PPases share similar active-site structures, such phosphate-mimicking core structures should interact with many enzymes in the same family, and therefore the choice of diversity structures is pivotal both to increase the binding affinity and to achieve specificity for individual enzymes. Here we present case studies of application of focused libraries to obtain PPase inhibitors, covering the overall process from selection of core structures to identification and evaluation of candidates in the focused libraries. To synthesize a library focused on protein serine-threonine phosphatases (PPs), we chose norcantharidin as a core structure, because norcantharidin dicarboxylate shows a broad inhibition profile toward several PPs. From the resulting focused library, we identified a highly selective PP2B inhibitor, NCA-01. On the other hand, to find inhibitors of dual-specificity protein phosphatases (DSPs), we chose 3-acyltetronic acid extracted from natural product RK-682 as a core structure, because its structure resembles the transition state in the dephosphorylation reaction of DSPs. However, a highly selective inhibitor was not found in the resulting focused library. Furthermore, an inherent drawback of compounds having the highly acidic 3-acyltetronic acid as a core structure is very weak potency in cellulo, probably due to poor cell membrane permeability. Therefore, we next modified the core structure from acidic to neutral by transformation to the enamine derivative and constructed a second-generation focused library (RE derivatives). The resulting compounds showed dramatically improved cell membrane permeability and inhibitory selectivity and included VHR (vaccinia VH1-related)-selective RE12 and CDC25A/B (cell division cycle 25A/B)-selective RE44. These inhibitors act on target enzymes in cellulo and do not generate reactive oxygen species, which is a potential problem with quinoid-type inhibitors of CDC25s. The cellular activity of RE12 was further improved by replacement of the side chain to afford RE176, which showed more potent antiproliferative activity than RE12 against HeLa cells. The dramatic change of inhibitory selectivity obtained by core structure modification from 3-acyltetronic acid to its enamine derivative was associated with a change in the mode of action. Namely, RE derivatives were found to be noncompetitive inhibitors with respect to a small-molecular substrate of CDC25A/B, whereas RK-682 was a competitive inhibitor of VHR. We identified the binding site of RE derivatives on the CDC25A as a pocket adjacent to the active site; this appears to be a promising target site for development of further novel inhibitors of CDC25s.

Electron temperatures within magnetic clouds between 2 and 4 AU: Voyager 2 observations

NASA Astrophysics Data System (ADS)

Sittler, E. C.; Burlaga, L. F.

1998-08-01

We have performed an analysis of Voyager 2 plasma electron observations within magnetic clouds between 2 and 4 AU identified by Burlaga and Behannon [1982]. The analysis has been confined to three of the magnetic clouds identified by Burlaga and Behannon that had high-quality data. The general properties of the plasma electrons within a magnetic cloud are that (1) the moment electron temperature anticorrelates with the electron density within the cloud, (2) the ratio Te/Tp tends to be >1, and (3) on average, Te/Tp~7.0. All three results are consistent with previous electron observations within magnetic clouds. Detailed analyses of the core and halo populations within the magnetic clouds show no evidence of either an anticorrelation between the core temperature TC and the electron density Ne or an anticorrelation between the halo temperature TH and the electron density. Within the magnetic clouds the halo component can contribute more than 50% of the electron pressure. The anticorrelation of Te relative to Ne can be traced to the density of the halo component relative to the density of the core component. The core electrons dominate the electron density. When the density goes up, the halo electrons contribute less to the electron pressure, so we get a lower Te. When the electron density goes down, the halo electrons contribute more to the electron pressure, and Te goes up. We find a relation between the electron pressure and density of the form Pe=αNeγ with γ~0.5.

FAAP20: a novel ubiquitin-binding FA nuclear core-complex protein required for functional integrity of the FA-BRCA DNA repair pathway

PubMed Central

Ali, Abdullah Mahmood; Pradhan, Arun; Singh, Thiyam Ramsingh; Du, Changhu; Li, Jie; Wahengbam, Kebola; Grassman, Elke; Auerbach, Arleen D.; Pang, Qishen

2012-01-01

Fanconi anemia (FA) nuclear core complex is a multiprotein complex required for the functional integrity of the FA-BRCA pathway regulating DNA repair. This pathway is inactivated in FA, a devastating genetic disease, which leads to hematologic defects and cancer in patients. Here we report the isolation and characterization of a novel 20-kDa FANCA-associated protein (FAAP20). We show that FAAP20 is an integral component of the FA nuclear core complex. We identify a region on FANCA that physically interacts with FAAP20, and show that FANCA regulates stability of this protein. FAAP20 contains a conserved ubiquitin-binding zinc-finger domain (UBZ), and binds K-63–linked ubiquitin chains in vitro. The FAAP20-UBZ domain is not required for interaction with FANCA, but is required for DNA-damage–induced chromatin loading of FANCA and the functional integrity of the FA pathway. These findings reveal critical roles for FAAP20 in the FA-BRCA pathway of DNA damage repair and genome maintenance. PMID:22343915

Hexameric supramolecular scaffold orients carbohydrates to sense bacteria.

PubMed

Grünstein, Dan; Maglinao, Maha; Kikkeri, Raghavendra; Collot, Mayeul; Barylyuk, Konstantin; Lepenies, Bernd; Kamena, Faustin; Zenobi, Renato; Seeberger, Peter H

2011-09-07

Carbohydrates are integral to biological signaling networks and cell-cell interactions, yet the detection of discrete carbohydrate-lectin interactions remains difficult since binding is generally weak. A strategy to overcome this problem is to create multivalent sensors, where the avidity rather than the affinity of the interaction is important. Here we describe the development of a series of multivalent sensors that self-assemble via hydrophobic supramolecular interactions. The multivalent sensors are comprised of a fluorescent ruthenium(II) core surrounded by a heptamannosylated β-cyclodextrin scaffold. Two additional series of complexes were synthesized as proof-of-principle for supramolecular self-assembly, the fluorescent core alone and the core plus β-cyclodextrin. Spectroscopic analyses confirmed that the three mannosylated sensors displayed 14, 28, and 42 sugar units, respectively. Each complex adopted original and unique spatial arrangements. The sensors were used to investigate the influence of carbohydrate spatial arrangement and clustering on the mechanistic and qualitative properties of lectin binding. Simple visualization of binding between a fluorescent, multivalent mannose complex and the Escherichia coli strain ORN178 that possesses mannose-specific receptor sites illustrates the potential for these complexes as biosensors.

Electron microscopy investigations of nanoparticles for cancer diagnostic applications

NASA Astrophysics Data System (ADS)

Koh, Ai Leen

This dissertation concerns electron microscopy characterization of magnetic (MNP) and surface enhanced Raman scattering (SERS) nanoparticles for in-vitro cancer diagnostic applications. Electron microscopy is an essential characterization tool owing to its (sub) nanometer spatial resolution. Structural information about the nanoparticles can be obtained using transmission electron microscopy (TEM), which can in turn be correlated to their physical characteristics. The scanning electron microscope (SEM) has excellent depth of field and can be effectively utilized to obtain high resolution information about nanoparticles binding onto cell surfaces. Part One of this thesis focuses on MNPs for bio-sensing and detection applications. As a preliminary study, chemically-synthesized, commercially-available iron oxide nanoparticles were compared against their laboratory-synthesized counterparts to assess their suitability for this application. The motivation for this initial study came about due to the lack of published data on commercially available iron oxide nanoparticles. TEM studies show that the latter are "beads" composed of multiple iron oxide cores encapsulated by a polymer shell, with large standard deviations in core diameter. Laboratory-synthesized iron oxide nanoparticles, on the other hand, are single core particles with small variations in diameter and therefore are expected to be better candidates for the required application. A key limitation in iron oxide nanoparticles is their relatively weak magnetic signals. The development of high moment Synthetic Anti-Ferromagnetic (SAF) nanoparticles aims to overcome this issue. SAFs are a novel class of MNPs fabricated using nanoimprint lithography, direct deposition of multilayer structure and final suspension into liquid medium (water). TEM analyses of cross-section specimens reveal that the SAFs possess characteristics similar to those of sputtered magnetic multilayer thin films. Their layered structure is preserved after a chemical etch. Magnetic measurements show a slight decrease in magnetic moment after ion milling. From TEM characterization, the introduction of oxygen into the copper release layer, prior the film deposition process, can effectively control the topography of the oxidized-copper grains and, consequently, lead to the production of SAF nanoparticles with flatter layers. Size distribution studies performed on SAFs fabricated using self-assembled stamps show that it is possible to produce monodisperse nanoparticles with diameters from 70 nm up. Part Two of the dissertation describes structural characterization experiments performed on Composite Organic-Inorganic Nanoparticles (COINs), which are a novel type of SERS nanoclusters formed by aggregating silver nanoparticles with Raman molecules, and then encapsulating them with an organic coating that stabilizes the aggregates and promotes subsequent functionalization with antibodies. Part Three of this dissertation focuses on the development and application of electron microscopy-based techniques to characterize the nanomaterial-biology interactions, to assess how, or indeed whether, nanoparticles are attaching to the cancer cells. The technique of negative staining was applied to simultaneously visualize inorganic nanoparticles and their biofunctionalized entities under the TEM and to verify the successful functionalization of nanoparticles with antibodies. The interpretation of the negatively-stained COINs was consistent with the EFTEM data. Next, the localization and characterization of CD54-functionalized COINs on the apicolateral portions of U937 leukemia cell lines was determined using TEM, SEM and Scanning Auger Microscopy. The analyses show that CD54 antigens are localized at a specific region on U937 leukemia cell surfaces. SEM imaging and SER spectroscopy correlation studies of different antibody-conjugated COINs attached onto different cancer cell lines show a direct correlation between the number of COINs binding to cells and the corresponding SER intensity. Finally, TEM was used to locate intra-cellularly labeled COINs and to trace the phospho-stat6 signaling pathway in U937 leukemia cells, demonstrating that COINs can be used to detect intracellular phosphorylation signaling events. These experiments demonstrate the importance of electron microscopy for analyzing the material-biology interface and for validating the attachment of nanoparticles on and in cells. Thus, electron microscope provides complementary imaging and spectroscopic information to current magnetic and SERS bio-detection technologies. (Abstract shortened by UMI.)

Posttranslational events leading to the assembly of photosystem II protein complex: a study using photosynthesis mutants from Chlamydomonas reinhardtii

PubMed Central

1989-01-01

We studied the assembly of photosystem II (PSII) in several mutants from Chlamydomonas reinhardtii which were unable to synthesize either one PSII core subunit (P6 [43 kD], D1, or D2) or one oxygen-evolving enhancer (OEE1 or OEE2) subunit. Synthesis of the PSII subunits was analyzed on electrophoretograms of cells pulse labeled with [14C]acetate. Their accumulation in thylakoid membranes was studied on immunoblots, their chlorophyll-binding ability on nondenaturating gels, their assembly by detergent fractionation, their stability by pulse- chase experiments and determination of in vitro protease sensitivity, and their localization by immunocytochemistry. In Chlamydomonas, the PSII core subunits P5 (47 kD), D1, and D2 are synthesized in a concerted manner while P6 synthesis is independent. P5 and P6 accumulate independently of each other in the stacked membranes. They bind chlorophyll soon after, or concomitantly with, their synthesis and independently of the presence of the other PSII subunits. Resistance to degradation increases step by step: beginning with assembly of P5, D1, and D2, then with binding of P6, and, finally, with binding of the OEE subunits on two independent high affinity sites (one for OEE1 and another for OEE2 to which OEE3 binds). In the absence of PSII cores, the OEE subunits accumulate independently in the thylakoid lumen and bind loosely to the membranes; OEE1 was found on stacked membranes, but OEE2 was found on either stacked or unstacked membranes depending on whether or not P6 was synthesized. PMID:2670960

Posttranslational events leading to the assembly of photosystem II protein complex: a study using photosynthesis mutants from Chlamydomonas reinhardtii.

PubMed

de Vitry, C; Olive, J; Drapier, D; Recouvreur, M; Wollman, F A

1989-09-01

We studied the assembly of photosystem II (PSII) in several mutants from Chlamydomonas reinhardtii which were unable to synthesize either one PSII core subunit (P6 [43 kD], D1, or D2) or one oxygen-evolving enhancer (OEE1 or OEE2) subunit. Synthesis of the PSII subunits was analyzed on electrophoretograms of cells pulse labeled with [14C]acetate. Their accumulation in thylakoid membranes was studied on immunoblots, their chlorophyll-binding ability on nondenaturating gels, their assembly by detergent fractionation, their stability by pulse-chase experiments and determination of in vitro protease sensitivity, and their localization by immunocytochemistry. In Chlamydomonas, the PSII core subunits P5 (47 kD), D1, and D2 are synthesized in a concerted manner while P6 synthesis is independent. P5 and P6 accumulate independently of each other in the stacked membranes. They bind chlorophyll soon after, or concomitantly with, their synthesis and independently of the presence of the other PSII subunits. Resistance to degradation increases step by step: beginning with assembly of P5, D1, and D2, then with binding of P6, and, finally, with binding of the OEE subunits on two independent high affinity sites (one for OEE1 and another for OEE2 to which OEE3 binds). In the absence of PSII cores, the OEE subunits accumulate independently in the thylakoid lumen and bind loosely to the membranes; OEE1 was found on stacked membranes, but OEE2 was found on either stacked or unstacked membranes depending on whether or not P6 was synthesized.

Structural investigation of C4b-binding protein by molecular modeling: localization of putative binding sites.

PubMed

Villoutreix, B O; Härdig, Y; Wallqvist, A; Covell, D G; García de Frutos, P; Dahlbäck, B

1998-06-01

C4b-binding protein (C4BP) contributes to the regulation of the classical pathway of the complement system and plays an important role in blood coagulation. The main human C4BP isoform is composed of one beta-chain and seven alpha-chains essentially built from three and eight complement control protein (CCP) modules, respectively, followed by a nonrepeat carboxy-terminal region involved in polymerization of the chains. C4BP is known to interact with heparin, C4b, complement factor I, serum amyloid P component, streptococcal Arp and Sir proteins, and factor VIII/VIIIa via its alpha-chains and with protein S through its beta-chain. The principal aim of the present study was to localize regions of C4BP involved in the interaction with C4b, Arp, and heparin. For this purpose, a computer model of the 8 CCP modules of C4BP alpha-chain was constructed, taking into account data from previous electron microscopy (EM) studies. This structure was investigated in the context of known and/or new experimental data. Analysis of the alpha-chain model, together with monoclonal antibody studies and heparin binding experiments, suggests that a patch of positively charged residues, at the interface between the first and second CCP modules, plays an important role in the interaction between C4BP and C4b/Arp/Sir/heparin. Putative binding sites, secondary-structure prediction for the central core, and an overall reevaluation of the size of the C4BP molecule are also presented. An understanding of these intermolecular interactions should contribute to the rational design of potential therapeutic agents aiming at interfering specifically some of these protein-protein interactions.

Structure and Mutagenesis of the Parainfluenza Virus 5 Hemagglutinin-Neuraminidase Stalk Domain Reveals a Four-Helix Bundle and the Role of the Stalk in Fusion Promotion

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

Bose, Sayantan; Welch, Brett D.; Kors, Christopher A.

2014-10-02

Paramyxovirus entry into cells requires the fusion protein (F) and a receptor binding protein (hemagglutinin-neuraminidase [HN], H, or G). The multifunctional HN protein of some paramyxoviruses, besides functioning as the receptor (sialic acid) binding protein (hemagglutinin activity) and the receptor-destroying protein (neuraminidase activity), enhances F activity, presumably by lowering the activation energy required for F to mediate fusion of viral and cellular membranes. Before or upon receptor binding by the HN globular head, F is believed to interact with the HN stalk. Unfortunately, until recently none of the receptor binding protein crystal structures have shown electron density for the stalkmore » domain. Parainfluenza virus 5 (PIV5) HN exists as a noncovalent dimer-of-dimers on the surface of cells, linked by a single disulfide bond in the stalk. Here we present the crystal structure of the PIV5-HN stalk domain at a resolution of 2.65 {angstrom}, revealing a four-helix bundle (4HB) with an upper (N-terminal) straight region and a lower (C-terminal) supercoiled part. The hydrophobic core residues are a mix of an 11-mer repeat and a 3- to 4-heptad repeat. To functionally characterize the role of the HN stalk in F interactions and fusion, we designed mutants along the PIV5-HN stalk that are N-glycosylated to physically disrupt F-HN interactions. By extensive study of receptor binding, neuraminidase activity, oligomerization, and fusion-promoting functions of the mutant proteins, we found a correlation between the position of the N-glycosylation mutants on the stalk structure and their neuraminidase activities as well as their abilities to promote fusion.« less

Annexin-A6 presents two modes of association with phospholipid membranes. A combined QCM-D, AFM and cryo-TEM study.

PubMed

Buzhynskyy, Nikolay; Golczak, Marcin; Lai-Kee-Him, Joséphine; Lambert, Olivier; Tessier, Béatrice; Gounou, Céline; Bérat, Rémi; Simon, Anne; Granier, Thierry; Chevalier, Jean-Marc; Mazères, Serge; Bandorowicz-Pikula, Joanna; Pikula, Slawomir; Brisson, Alain R

2009-10-01

Annexins are soluble proteins that bind to biological membranes in a Ca(2+)-dependent manner. Annexin-A6 (AnxA6) is unique in the annexin family as it consists of the repeat of two annexin core modules, while all other annexins consist of a single module. AnxA6 has been proposed to participate in various membrane-related processes, including endocytosis and exocytosis, yet the molecular mechanism of association of AnxA6 with biological membranes, especially its ability to aggregate membranes, is still unclear. To address this question, we studied the association of AnxA6 with model phospholipid membranes by combining the techniques of quartz crystal microbalance with dissipation monitoring (QCM-D), (cryo-) transmission electron microscopy (TEM) and atomic force microscopy (AFM). The properties of membrane binding and membrane aggregation of AnxA6 were compared to two reference systems, annexin A5 (AnxA5), which is the annexin prototype, and a chimerical AnxA5-dimer molecule, which is able to aggregate two membranes in a symmetrical manner. We show that AnxA6 presents two modes of association with lipid membranes depending on Ca(2+)-concentration. At low Ca(2+)-concentration ( approximately 60-150microM), AnxA6 binds to membranes via its two coplanar annexin modules and is not able to associate two separate membranes. At high Ca(2+)-concentration ( approximately 2mM), AnxA6 molecules are able to bind two adjacent phospholipid membranes and present a conformation similar to the AnxA6 3D crystallographic structure. Possible biological implications of these novel membrane-binding properties of AnxA6 are discussed.

Structure and Mutagenesis of the Parainfluenza Virus 5 Hemagglutinin-Neuraminidase Stalk Domain Reveals a Four-Helix Bundle and the Role of the Stalk in Fusion Promotion▿

PubMed Central

Bose, Sayantan; Welch, Brett D.; Kors, Christopher A.; Yuan, Ping; Jardetzky, Theodore S.; Lamb, Robert A.

2011-01-01

Paramyxovirus entry into cells requires the fusion protein (F) and a receptor binding protein (hemagglutinin-neuraminidase [HN], H, or G). The multifunctional HN protein of some paramyxoviruses, besides functioning as the receptor (sialic acid) binding protein (hemagglutinin activity) and the receptor-destroying protein (neuraminidase activity), enhances F activity, presumably by lowering the activation energy required for F to mediate fusion of viral and cellular membranes. Before or upon receptor binding by the HN globular head, F is believed to interact with the HN stalk. Unfortunately, until recently none of the receptor binding protein crystal structures have shown electron density for the stalk domain. Parainfluenza virus 5 (PIV5) HN exists as a noncovalent dimer-of-dimers on the surface of cells, linked by a single disulfide bond in the stalk. Here we present the crystal structure of the PIV5-HN stalk domain at a resolution of 2.65 Å, revealing a four-helix bundle (4HB) with an upper (N-terminal) straight region and a lower (C-terminal) supercoiled part. The hydrophobic core residues are a mix of an 11-mer repeat and a 3- to 4-heptad repeat. To functionally characterize the role of the HN stalk in F interactions and fusion, we designed mutants along the PIV5-HN stalk that are N-glycosylated to physically disrupt F-HN interactions. By extensive study of receptor binding, neuraminidase activity, oligomerization, and fusion-promoting functions of the mutant proteins, we found a correlation between the position of the N-glycosylation mutants on the stalk structure and their neuraminidase activities as well as their abilities to promote fusion. PMID:21994464

To Bind or Not To Bind: Pros & Cons of Maintaining Paper Periodicals in the Library's Collection.

ERIC Educational Resources Information Center

Anderson, Iris W.

1999-01-01

Explores controversial questions related to libraries' decision-making on paper journals and electronic journals. Notes that the critical mass of scholarly publishing is still in print. Discusses benefits and drawbacks of electronic journals and paper journals. Presents comments on the pros and cons to binding paper periodicals gathered from an…

Atomic structure of a peptide coated gold nanocluster identified using theoretical and experimental studies

NASA Astrophysics Data System (ADS)

Wang, Hui; Li, Xu; Gao, Liang; Zhai, Jiao; Liu, Ru; Gao, Xueyun; Wang, Dongqi; Zhao, Lina

2016-06-01

Peptide coated gold nanoclusters (AuNCs) have a precise molecular formula and atomic structure, which are critical for their unique applications in targeting specific proteins either for protein analysis or drug design. To date, a study of the crystal structure of peptide coated AuNCs is absent primarily due to the difficulty of obtaining their crystalline phases in an experiment. Here we study a typical peptide coated AuNC (Au24Peptide8, Peptide = H2N-CCYKKKKQAGDV-COOH, Anal. Chem., 2015, 87, 2546) to figure out its atomic structure and electronic structure using a theoretical method for the first time. In this work, we identify the explicit configuration of the essential structure of Au24Peptide8, Au24(Cys-Cys)8, using density functional theory (DFT) computations and optical spectroscopic experiments, where Cys denotes cysteine without H bonded to S. As the first multidentate ligand binding AuNC, Au24(Cys-Cys)8 is characterized as a distorted Au13 core with Oh symmetry covered by two Au(Cys-Cys) and three Au3(Cys-Cys)2 staple motifs in its atomic structure. The most stable configuration of Au24(Cys-Cys)8 is confirmed by comparing its UV-vis absorption spectrum from time-dependent density-functional theory (TDDFT) calculations with optical absorption measurements, and these results are consistent with each other. Furthermore, we carry out frontier molecular orbital (FMO) calculations to elucidate that the electronic structure of Au24(Cys-Cys)8 is different from that of Au24(SR)20 as they have a different Au/S ratio, where SR represents alkylthiolate. Importantly, the different ligand coatings, Cys-Cys and SR, in Au24(Cys-Cys)8 and Au24(SR)20 cause the different Au/S ratios in the coated Au24. The reason is that the Au/S ratio is crucial in determining the size of the Au core of the ligand protected AuNC, and the size of the Au core corresponds to a specific electronic structure. By the adjustment of ligand coatings from alkylthiolate to peptide, the Au/S ratio could be controlled to generate different AuNCs with versatile electronic structures, optical properties and reaction stabilities. Therefore, we propose a universal approach to obtain a specific Au/S ratio of ligand coated AuNCs by adjusting the ligand composition, thus controlling the chemicophysical properties of AuNCs with ultimately the same number of Au atoms.Peptide coated gold nanoclusters (AuNCs) have a precise molecular formula and atomic structure, which are critical for their unique applications in targeting specific proteins either for protein analysis or drug design. To date, a study of the crystal structure of peptide coated AuNCs is absent primarily due to the difficulty of obtaining their crystalline phases in an experiment. Here we study a typical peptide coated AuNC (Au24Peptide8, Peptide = H2N-CCYKKKKQAGDV-COOH, Anal. Chem., 2015, 87, 2546) to figure out its atomic structure and electronic structure using a theoretical method for the first time. In this work, we identify the explicit configuration of the essential structure of Au24Peptide8, Au24(Cys-Cys)8, using density functional theory (DFT) computations and optical spectroscopic experiments, where Cys denotes cysteine without H bonded to S. As the first multidentate ligand binding AuNC, Au24(Cys-Cys)8 is characterized as a distorted Au13 core with Oh symmetry covered by two Au(Cys-Cys) and three Au3(Cys-Cys)2 staple motifs in its atomic structure. The most stable configuration of Au24(Cys-Cys)8 is confirmed by comparing its UV-vis absorption spectrum from time-dependent density-functional theory (TDDFT) calculations with optical absorption measurements, and these results are consistent with each other. Furthermore, we carry out frontier molecular orbital (FMO) calculations to elucidate that the electronic structure of Au24(Cys-Cys)8 is different from that of Au24(SR)20 as they have a different Au/S ratio, where SR represents alkylthiolate. Importantly, the different ligand coatings, Cys-Cys and SR, in Au24(Cys-Cys)8 and Au24(SR)20 cause the different Au/S ratios in the coated Au24. The reason is that the Au/S ratio is crucial in determining the size of the Au core of the ligand protected AuNC, and the size of the Au core corresponds to a specific electronic structure. By the adjustment of ligand coatings from alkylthiolate to peptide, the Au/S ratio could be controlled to generate different AuNCs with versatile electronic structures, optical properties and reaction stabilities. Therefore, we propose a universal approach to obtain a specific Au/S ratio of ligand coated AuNCs by adjusting the ligand composition, thus controlling the chemicophysical properties of AuNCs with ultimately the same number of Au atoms. Electronic supplementary information (ESI) available: The MALDI-TOF-MS identification of Au24Peptide8, the structural divisions of Au24(Cys-Cys)8 obtained based on the ``divide and protect'' approach, the structure of level-1 and -3 staple motifs, the relative energies of all stable configurations of Au24(Cys-Cys)8, orbital components of Iso1 of Au24(Cys-Cys)8, electronic structure comparison between Au24(Cys-Cys)8 and Au24(SR)20, and the coordination of Iso1. See DOI: 10.1039/c5nr08727a

Revisiting the origin of satellites in core-level photoemission of transparent conducting oxides: The case of n -doped SnO2

NASA Astrophysics Data System (ADS)

Borgatti, Francesco; Berger, J. A.; Céolin, Denis; Zhou, Jianqiang Sky; Kas, Joshua J.; Guzzo, Matteo; McConville, C. F.; Offi, Francesco; Panaccione, Giancarlo; Regoutz, Anna; Payne, David J.; Rueff, Jean-Pascal; Bierwagen, Oliver; White, Mark E.; Speck, James S.; Gatti, Matteo; Egdell, Russell G.

2018-04-01

The longstanding problem of interpretation of satellite structures in core-level photoemission spectra of metallic systems with a low density of conduction electrons is addressed using the specific example of Sb-doped SnO2. Comparison of ab initio many-body calculations with experimental hard x-ray photoemission spectra of the Sn 4 d states shows that strong satellites are produced by coupling of the Sn core hole to the plasma oscillations of the free electrons introduced by doping. Within the same theoretical framework, spectral changes of the valence band spectra are also related to dynamical screening effects. These results demonstrate that, for the interpretation of electron correlation features in the core-level photoelectron spectra of such narrow-band materials, going beyond the homogeneous electron gas electron-plasmon coupling model is essential.

Metal Ion Interactions with Immunoglobulin G (IgG). 1. Preliminary Studies with Electron Paramagnetic Resonance (EPR) Spectroscopy and Ultrafiltration

DTIC Science & Technology

1978-12-12

EPR and ultrafiltration studies are recommceided to conduct luture metal ion- IgG binding research. Using Scatchard plots, bind.ng levels can be...of the binding sites can be best pursued by EPR and ultrafiltration using the fragments of IgG . This report noted some difference in the binding...immunoelectrophoresis, ultrafiltration, UV spectroscopy, atomic absorption spectroscopy, and electron paramagnetic resonance (EPR). IgG used ,- ,is non

An Evolutionary/Biochemical Connection Between Promoter- and Primer-Dependent Polymerases Revealed by Selective Evolution of Ligands by Exponential Enrichment (SELEX).

PubMed

Fenstermacher, Katherine J; Achuthan, Vasudevan; Schneider, Thomas D; DeStefano, Jeffrey J

2018-01-16

DNA polymerases (DNAPs) recognize 3' recessed termini on duplex DNA and carry out nucleotide catalysis. Unlike promoter-specific RNA polymerases (RNAPs), no sequence specificity is required for binding or initiation of catalysis. Despite this, previous results indicate that viral reverse transcriptases bind much more tightly to DNA primers that mimic the polypurine tract. In the current report, primer sequences that bind with high affinity to Taq and Klenow polymerases were identified using a modified Selective Evolution of Ligands by Exponential Enrichment (SELEX) approach. Two Taq -specific primers that bound ∼10 (Taq1) and over 100 (Taq2) times more stably than controls to Taq were identified. Taq1 contained 8 nucleotides (5' -CACTAAAG-3') that matched the phage T3 RNAP "core" promoter. Both primers dramatically outcompeted primers with similar binding thermodynamics in PCR reactions. Similarly, exonuclease minus Klenow polymerase also selected a high affinity primer that contained a related core promoter sequence from phage T7 RNAP (5' -ACTATAG-3'). For both Taq and Klenow, even small modifications to the sequence resulted in large losses in binding affinity suggesting that binding was highly sequence-specific. The results are discussed in the context of possible effects on multi-primer (multiplex) PCR assays, molecular information theory, and the evolution of RNAPs and DNAPs. Importance This work further demonstrates that primer-dependent DNA polymerases can have strong sequence biases leading to dramatically tighter binding to specific sequences. These may be related to biological function, or be a consequences of the structural architecture of the enzyme. New sequence specificity for Taq and Klenow polymerases were uncovered and among them were sequences that contained the core promoter elements from T3 and T7 phage RNA polymerase promoters. This suggests the intriguing possibility that phage RNA polymerases exploited intrinsic binding affinities of ancestral DNA polymerases to develop their promotors. Conversely, DNA polymerases could have evolved from related RNA polymerases and retained the intrinsic binding preference despite there being no clear function for such a preference in DNA biology. Copyright © 2018 American Society for Microbiology.

A novel core 1 O-linked glycan-specific binding lectin from the fruiting body of Hericium erinaceus.

PubMed

Kim, Seonghun

2018-02-01

Mucin-type O-glycans are involved in biological functions on the cell surface as well as the glycoproteins and can also be used as specific carbohydrate biomarkers of many diseases. In this study, I purified a novel core 1 O-linked glycan specific lectin, Hericium erinaceus lecin (HeL), from the fruiting body of the mushroom Hericium erinaceus, which is known as the natural source for a sialic acid-binding lectin. Upon optimization of the purification conditions, a sequence of ion exchange, affinity, ion exchange, and size-exclusion chromatography resulted in the highest yield and best quality of lectin without protease activity. The resulting purified HeL is an apparent hexameric protein with a subunit molecular weight of 15kDa, and a pI of 4.3. In hemagglutination inhibition assay, the purified lectin was only inhibited by glycoproteins containing mucin-type O-glycans and reacted weakly with Galβ(1,3)GalNAc. Glycan array analyses showed that HeL specifically interacts with core 1 O-linked glycans as well as extended O-glycan structures containing sialylation or fucosylation. The glycan binding specificity of HeL is comparable to that of peanut agglutinin for detection of a broader range of extended core 1 O-glycan structures. Taken together, these results provide an efficient and optimized procedure for the purification of HeL from the fruiting body of the mushroom Hericium erinaceus. Moreover, HeL represents a powerful tool for analyzing core 1 and extended core 1 O- glycan structures in diagnosis assays. Copyright © 2017 Elsevier B.V. All rights reserved.

Effects of rare earth doping on multi-core iron oxide nanoparticles properties

NASA Astrophysics Data System (ADS)

Petran, Anca; Radu, Teodora; Borodi, Gheorghe; Nan, Alexandrina; Suciu, Maria; Turcu, Rodica

2018-01-01

New multi-core iron oxide magnetic nanoparticles doped with rare earth metals (Gd, Eu) were obtained by a one step synthesis procedure using a solvothermal method for potential biomedical applications. The obtained clusters were characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM), energy-dispersive X-ray microanalysis (EDX), X-ray photoelectron spectroscopy (XPS) and magnetization measurements. They possess high colloidal stability, a saturation magnetization of up to 52 emu/g, and nearly spherical shape. The presence of rare earth ions in the obtained samples was confirmed by EDX and XPS. XRD analysis proved the homogeneous distribution of the trivalent rare earth ions in the inverse-spinel structure of magnetite and the increase of crystal strain upon doping the samples. XPS study reveals the valence state and the cation distribution on the octahedral and tetrahedral sites of the analysed samples. The observed shift of the XPS valence band spectra maximum in the direction of higher binding energies after rare earth doping, as well as theoretical valence band calculations prove the presence of Gd and Eu ions in octahedral sites. The blood protein adsorption ability of the obtained samples surface, the most important factor of the interaction between biomaterials and body fluids, was assessed by interaction with bovine serum albumin (BSA). The rare earth doped clusters surface show higher afinity for binding BSA. In vitro cytotoxicity test results for the studied samples showed no cytotoxicity in low and medium doses, establishing a potential perspective for rare earth doped MNC to facilitate multiple therapies in a single formulation for cancer theranostics.

Measurement of Conformational Changes Accompanying Desensitization in an Ionotropic Glutamate Receptor

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

Armstrong,N.; Jasti, J.; Beich-Frandsen, M.

2006-01-01

The canonical conformational states occupied by most ligand-gated ion channels, and many cell-surface receptors, are the resting, activated, and desensitized states. While the resting and activated states of multiple receptors are well characterized, elaboration of the structural properties of the desensitized state, a state that is by definition inactive, has proven difficult. Here we use electrical, chemical, and crystallographic experiments on the AMPA-sensitive GluR2 receptor, defining the conformational rearrangements of the agonist binding cores that occur upon desensitization of this ligand-gated ion channel. These studies demonstrate that desensitization involves the rupture of an extensive interface between domain 1 of 2-foldmore » related glutamate-binding core subunits, compensating for the ca. 21{sup o} of domain closure induced by glutamate binding. The rupture of the domain 1 interface allows the ion channel to close and thereby provides a simple explanation to the long-standing question of how agonist binding is decoupled from ion channel gating upon receptor desensitization.« less

Incorporating electron-transfer functionality into synthetic metalloproteins from the bottom-up.

PubMed

Hong, Jing; Kharenko, Olesya A; Ogawa, Michael Y

2006-12-11

The alpha-helical coiled-coil motif serves as a robust scaffold for incorporating electron-transfer (ET) functionality into synthetic metalloproteins. These structures consist of a supercoiling of two or more aplha helices that are formed by the self-assembly of individual polypeptide chains whose sequences contain a repeating pattern of hydrophobic and hydrophilic residues. Early work from our group attached abiotic Ru-based redox sites to the most surface-exposed positions of two stranded coiled-coils and used electron-pulse radiolysis to study both intra- and intermolecular ET reactions in these systems. Later work used smaller metallopeptides to investigate the effects of conformational gating within electrostatic peptide-protein complexes. We have recently designed the C16C19-GGY peptide, which contains Cys residues located at both the "a" and "d" positions of its third heptad repeat in order to construct a nativelike metal-binding domain within its hydrophobic core. It was shown that the binding of both Cd(II) and Cu(I) ions induces the peptide to undergo a conformational change from a disordered random coil to a metal-bridged coiled-coil. However, whereas the Cd(II)-protein exists as a two-stranded coiled-coil, the Cu(I) derivative exists as a four-stranded coiled-coil. Upon the incorporation of other metal ions, metal-bridged peptide dimers, tetramers, and hexamers are formed. The Cu(I)-protein is of particular interest because it exhibits a long-lived (microsecond) room-temperature luminescence at 600 nm. The luminophore in this protein is thought to be a multinuclear CuI4Cys4(N/O)4 cage complex, which can be quenched by exogenous electron acceptors in solution, as shown by emission-lifetime and transient-absorption experiments. It is anticipated that further investigation into these systems will contribute to the expanding effort of bioinorganic chemists to prepare new kinds of functionally active synthetic metalloproteins.

Ab initio study of structural, electronic, optical, and vibrational properties of Zn x S y ( x + y = 2 to 5) nanoclusters

NASA Astrophysics Data System (ADS)

Yadav, P. S.; Pandey, D. K.; Agrawal, S.; Agrawal, B. K.

2010-03-01

An ab initio study of the stability, structural, electronic. and optical properties has been performed for 46 zinc sulfide nanoclusters Zn x S y ( x + y = n = 2 to 5). Five out of them are seen to be unstable as their vibrational frequencies are found to be imaginary. A B3LYP-DFT/6-311G(3df) method is employed to optimize the geometries and a TDDFT method is used for the study of the optical properties. The binding energies (BE), HOMO-LUMO gaps and the bond lengths have been obtained for all the clusters. For the ZnS2, ZnS3, and ZnS4 nanoclusters, our stable structures are seen to be different from those obtained earlier by using the effective core potentials. We have also considered the zero point energy (ZPE) corrections ignored by the earlier workers. For a fixed value of n, we designate the most stable structure the one, which has maximum final binding energy per atom. The adiabatic and vertical ionization potentials (IP) and electron affinities (EA), charges on the atoms, dipole moments, optical properties, vibrational frequencies, infrared intensities, relative infrared intensities, and Raman scattering activities have been investigated for the most stable structures. The nanoclusters containing large number of S atoms for each n is found to be most stable. The HOMO-LUMO gap decreases from n = 2-3 and then increases above n = 3. The IP and EA both fluctuate with the cluster size n. The optical absorption is quite weak in visible region but strong in the ultraviolet region in most of the nanoclusters except a few. The optical absorption spectrum or electron energy loss spectrum (EELS) is unique for every nanocluster and may be used to characterize a specific nanocluster. The growth of most stable nanoclusters may be possible in the experiments.

The pressure distribution inside the proton

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

Burkert, V. D.; Elouadrhiri, L.; Girod, F. X.

The proton, one of the components of atomic nuclei, is composed of fundamental particles called quarks and gluons. Gluons are the carriers of the force that binds quarks together, and free quarks are never found in isolation—that is, they are confined within the composite particles in which they reside. The origin of quark confinement is one of the most important questions in modern particle and nuclear physics because confinement is at the core of what makes the proton a stable particle and thus provides stability to the Universe. The internal quark structure of the proton is revealed by deeply virtualmore » Compton scattering1,2, a process in which electrons are scattered off quarks inside the protons, which subsequently emit high-energy photons, which are detected in coincidence with the scattered electrons and recoil protons. Here we report a measurement of the pressure distribution experienced by the quarks in the proton. We find a strong repulsive pressure near the centre of the proton (up to 0.6 femtometres) and a binding pressure at greater distances. The average peak pressure near the centre is about 1035 pascals, which exceeds the pressure estimated for the most densely packed known objects in the Universe, neutron stars3. This work opens up a new area of research on the fundamental gravitational properties of protons, neutrons and nuclei, which can provide access to their physical radii, the internal shear forces acting on the quarks and their pressure distributions.« less

Cryo-electron microscopy and single molecule fluorescent microscopy detect CD4 receptor induced HIV size expansion prior to cell entry

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

Pham, Son; CSIRO Australian Animal Health Laboratory, Victoria 3220; Tabarin, Thibault

Viruses are often thought to have static structure, and they only remodel after the viruses have entered target cells. Here, we detected a size expansion of virus particles prior to viral entry using cryo-electron microscopy (cryo-EM) and single molecule fluorescence imaging. HIV expanded both under cell-free conditions with soluble receptor CD4 (sCD4) targeting the CD4 binding site on the HIV-1 envelope protein (Env) and when HIV binds to receptor on cellular membrane. We have shown that the HIV Env is needed to facilitate receptor induced virus size expansions, showing that the ‘lynchpin’ for size expansion is highly specific. We demonstratemore » that the size expansion required maturation of HIV and an internal capsid core with wild type stability, suggesting that different HIV compartments are linked and are involved in remodelling. Our work reveals a previously unknown event in HIV entry, and we propose that this pre-entry priming process enables HIV particles to facilitate the subsequent steps in infection. - Highlights: • Cell free viruses are able to receive external trigger that leads to apparent size expansion. • Virus envelope and CD4 receptor engagement is the lynchpin of virus size expansion. • Internal capsid organisation can influence receptor mediated virus size expansion. • Pre-existing virus-associated lipid membrane in cell free virus can accommodate the receptor mediated virus size expansion.« less

The pressure distribution inside the proton.

PubMed

Burkert, V D; Elouadrhiri, L; Girod, F X

2018-05-01

The proton, one of the components of atomic nuclei, is composed of fundamental particles called quarks and gluons. Gluons are the carriers of the force that binds quarks together, and free quarks are never found in isolation-that is, they are confined within the composite particles in which they reside. The origin of quark confinement is one of the most important questions in modern particle and nuclear physics because confinement is at the core of what makes the proton a stable particle and thus provides stability to the Universe. The internal quark structure of the proton is revealed by deeply virtual Compton scattering 1,2 , a process in which electrons are scattered off quarks inside the protons, which  subsequently emit high-energy photons, which are detected in coincidence with the scattered electrons and recoil protons. Here we report a measurement of the pressure distribution experienced by the quarks in the proton. We find a strong repulsive pressure near the centre of the proton (up to 0.6 femtometres) and a binding pressure at greater distances. The average peak pressure near the centre is about 10 35 pascals, which exceeds the pressure estimated for the most densely packed known objects in the Universe, neutron stars 3 . This work opens up a new area of research on the fundamental gravitational properties of protons, neutrons and nuclei, which can provide access to their physical radii, the internal shear forces acting on the quarks and their pressure distributions.

Neutral-atom electron binding energies from relaxed-orbital relativistic Hartree-Fock-Slater calculations for Z between 2 and 106

NASA Technical Reports Server (NTRS)

Huang, K.-N.; Aoyagi, M.; Mark, H.; Chen, M. H.; Crasemann, B.

1976-01-01

Electron binding energies in neutral atoms have been calculated relativistically, with the requirement of complete relaxation. Hartree-Fock-Slater wave functions served as zeroth-order eigenfunctions to compute the expectation of the total Hamiltonian. A first-order correction to the local approximation was thus included. Quantum-electrodynamic corrections were made. For all elements with atomic numbers ranging from 2 to 106, the following quantities are listed: total energies, electron kinetic energies, electron-nucleus potential energies, electron-electron potential energies consisting of electrostatic and Breit interaction (magnetic and retardation) terms, and vacuum polarization energies. Binding energies including relaxation are listed for all electrons in all atoms over the indicated range of atomic numbers. A self-energy correction is included for the 1s, 2s, and 2p(1/2) levels. Results for selected atoms are compared with energies calculated by other methods and with experimental values.

Genuine binding energy of the hydrated electron

PubMed Central

Luckhaus, David; Yamamoto, Yo-ichi; Suzuki, Toshinori; Signorell, Ruth

2017-01-01

The unknown influence of inelastic and elastic scattering of slow electrons in water has made it difficult to clarify the role of the solvated electron in radiation chemistry and biology. We combine accurate scattering simulations with experimental photoemission spectroscopy of the hydrated electron in a liquid water microjet, with the aim of resolving ambiguities regarding the influence of electron scattering on binding energy spectra, photoelectron angular distributions, and probing depths. The scattering parameters used in the simulations are retrieved from independent photoemission experiments of water droplets. For the ground-state hydrated electron, we report genuine values devoid of scattering contributions for the vertical binding energy and the anisotropy parameter of 3.7 ± 0.1 eV and 0.6 ± 0.2, respectively. Our probing depths suggest that even vacuum ultraviolet probing is not particularly surface-selective. Our work demonstrates the importance of quantitative scattering simulations for a detailed analysis of key properties of the hydrated electron. PMID:28508051

Nanosized cancer cell-targeted polymeric immunomicelles loaded with superparamagnetic iron oxide nanoparticles

NASA Astrophysics Data System (ADS)

Sawant, Rishikesh M.; Sawant, Rupa R.; Gultepe, Evin; Nagesha, Dattatri; Papahadjopoulos-Sternberg, Brigitte; Sridhar, Srinivas; Torchilin, Vladimir P.

2009-10-01

Stable 30-50 nm polymeric polyethylene glycol-phosphatidylethanolamine (PEG-PE)-based micelles entrapping superparamagnetic iron oxide nanoparticles (SPION) have been prepared. At similar concentrations of SPION, the SPION-micelles had significantly better magnetic resonance imaging (MRI) T2 relaxation signal compared to `plain' SPION. Freeze-fracture electron microscopy confirmed SPION entrapment in the lipid core of the PEG-PE micelles. To enhance the targeting capability of these micelles, their surface was modified with the cancer cell-specific anti-nucleosome monoclonal antibody 2C5 (mAb 2C5). Such mAb 2C5-SPION immunomicelles demonstrated specific binding with cancer cells in vitro and were able to bring more SPION to the cancer cells thus demonstrating the potential to be used as targeted MRI contrast agents for tumor imaging.

Structural correlates of affinity in fetal versus adult endplate nicotinic receptors

NASA Astrophysics Data System (ADS)

Nayak, Tapan Kumar; Chakraborty, Srirupa; Zheng, Wenjun; Auerbach, Anthony

2016-04-01

Adult-type nicotinic acetylcholine receptors (AChRs) mediate signalling at mature neuromuscular junctions and fetal-type AChRs are necessary for proper synapse development. Each AChR has two neurotransmitter binding sites located at the interface of a principal and a complementary subunit. Although all agonist binding sites have the same core of five aromatic amino acids, the fetal site has ~30-fold higher affinity for the neurotransmitter ACh. Here we use molecular dynamics simulations of adult versus fetal homology models to identify complementary-subunit residues near the core that influence affinity, and use single-channel electrophysiology to corroborate the results. Four residues in combination determine adult versus fetal affinity. Simulations suggest that at lower-affinity sites, one of these unsettles the core directly and the others (in loop E) increase backbone flexibility to unlock a key, complementary tryptophan from the core. Swapping only four amino acids is necessary and sufficient to exchange function between adult and fetal AChRs.

Self-Assembly of a Strong Polyhedral Oligomeric Silsesquioxane Core-Based Aspartate Derivative Dendrimer Supramolecular Gelator in Different Polarity Solvents.

PubMed

He, Huiwen; Chen, Si; Tong, Xiaoqian; An, Zhihang; Ma, Meng; Wang, Xiaosong; Wang, Xu

2017-11-21

Aromatic groups are introduced into the end peripherals of polyhedral oligomeric silsesquioxane (POSS) core-based organic/inorganic hybrid supramolecules to get a novel dendrimer gelator POSS-Z-Asp(OBzl) (POSS-ASP), which have eight aspartate derivative arms to make full use of strong π-π stacking forces to get strong supramolecular gels in addition to multiple hydrogen bindings and van der Waals interactions. POSS-ASP can self-assemble into three-dimensional nanoscale gel networks to provide hybrid physical gels especially with strong mechanical properties and fast-recovery behaviors. Two totally different morphologies of the connected spherical particle structures and banded ultralong fibers are observed owing to the polarity of solvents confirmed by the scanning electron microscopy, polarized optical microscopy, and transmission electron microscopy techniques, expecting the existing various self-assembly models and illustrating the peripherals of the dendrimer and the polarity of solvents having huge influences in the supramolecular self-assembly mechanism. What is more, the thermal stability, rheological properties, and network architecture information have also been investigated via tube-inversion, rotational rheometer, and powder X-ray diffraction methods, the results of which confirm the two different gel formation mechanisms that make POSS-ASP to exhibit two totally different thermal and mechanical properties. Such a study reports a new gelation system in organic or organic/aqueous mixed solvents, which can be helpful for investigating the relationship of dendritic supramolecular gelation and different polarity solvents during the supramolecular self-assembly process of gelators.

The nucleotide-dependent interaction of FlaH and FlaI is essential for assembly and function of the archaellum motor

DOE PAGES

Chaudhury, Paushali; Neiner, Tomasz; D'Imprima, Edoardo; ...

2015-10-28

The motor of the membrane-anchored archaeal motility structure, the archaellum, contains FlaX, FlaI and FlaH. FlaX forms a 30 nm ring structure that acts as a scaffold protein and was shown to interact with the bifunctional ATPase FlaI and FlaH. However, the structure and function of FlaH has been enigmatic. Here we present structural and functional analyses of isolated FlaH and archaellum motor subcomplexes. The FlaH crystal structure reveals a RecA/Rad51 family fold with an ATP bound on a conserved and exposed surface, which presumably forms an oligomerization interface. FlaH does not hydrolyze ATP in vitro, but ATP binding tomore » FlaH is essential for its interaction with FlaI and for archaellum assembly. FlaH interacts with the C-terminus of FlaX, which was earlier shown to be essential for FlaX ring formation and to mediate interaction with FlaI. Electron microscopy reveals that FlaH assembles as a second ring inside the FlaX ring in vitro. Collectively these data reveal central structural mechanisms for FlaH interactions in mediating archaellar assembly: FlaH binding within the FlaX ring and nucleotide-regulated FlaH binding to FlaI form the archaellar basal body core.« less

Diamond fiber field emitters

DOEpatents

Blanchet-Fincher, Graciela B.; Coates, Don M.; Devlin, David J.; Eaton, David F.; Silzars, Aris K.; Valone, Steven M.

1996-01-01

A field emission electron emitter comprising an electrode formed of at least one diamond, diamond-like carbon or glassy carbon composite fiber, said composite fiber having a non-diamond core and a diamond, diamond-like carbon or glassy carbon coating on said non-diamond core, and electronic devices employing such a field emission electron emitter.

Cyclic perylene diimide: Selective ligand for tetraplex DNA binding over double stranded DNA.

PubMed

Vasimalla, Suresh; Sato, Shinobu; Takenaka, Fuminori; Kurose, Yui; Takenaka, Shigeori

2017-12-15

Synthesized cyclic perylene diimide, cPDI, showed the binding constant of 6.3 × 10 6  M -1 with binding number of n = 2 with TA-core as a tetraplex DNA in 50 mM Tris-HCl buffer (pH = 7.4) containing 100 mM KCl using Schatchard analysis and showed a higher preference for tetraplex DNA than for double stranded DNA with over 10 3 times. CD spectra showed that TA-core induced its antiparallel conformation upon addition of cPDI in the absence or presence of K + or Na + ions. The cPDI inhibits the telomerase activity with IC 50 of 0.3 µM using TRAP assay which is potential anti-cancer drug with low side effect. Copyright © 2017 Elsevier Ltd. All rights reserved.

Predominance of multielectron processes contributing to the intrinsic spectra of low-energy Auger transitions in copper and gold

NASA Astrophysics Data System (ADS)

Mukherjee, S. F.; Shastry, K.; Weiss, A. H.

2011-10-01

Positron-annihilation-induced Auger electron spectroscopy (PAES) was used to obtain Cu and Au Auger spectra that are free of primary-beam-induced backgrounds by impinging the positrons at an energy below the secondary-electron-emission threshold. The removal of the core electron via annihilation in the PAES process resulted in the elimination of postcollision effects. The spectra indicate that there is an intense low-energy tail (LET) associated with the Auger peak that extends all the way to 0 eV. The LET is interpreted as indicative of processes in which filling of the core hole by a valence electron results in the ejection of two or more valence electrons which share the energy of the conventional core-valence-valence Auger electron.

Binding modes and functional surface of anti-mammalian scorpion α-toxins to sodium channels.

PubMed

Chen, Rong; Chung, Shin-Ho

2012-10-02

Scorpion α-toxins bind to the voltage-sensing domains of voltage-gated sodium (Na(V)) channels and interfere with the inactivation mechanisms. The functional surface of α-toxins has been shown to contain an NC-domain consisting of the five-residue turn (positions 8-12) and the C-terminus (positions 56-64) and a core-domain centered on the residue 18. The NC- and core-domains are interconnected by the linker-domain (positions 8-18). Here with atomistic molecular dynamics simulations, we examine the binding modes between two α-toxins, the anti-mammalian AahII and the anti-insect LqhαIT, and the voltage-sensing domain of rat Na(V)1.2, a subtype of Na(V) channels expressed in nerve cells. Both toxins are docked to the extracellular side of the voltage-sensing domain of Na(V)1.2 using molecular dynamics simulations, with the linker-domain assumed to wedge into the binding pocket. Several salt bridges and hydrophobic clusters are observed to form between the NC- and core-domains of the toxins and Na(V)1.2 and stabilize the toxin-channel complexes. The binding modes predicted are consistent with available mutagenesis data and can readily explain the relative affinities of AahII and LqhαIT for Na(V)1.2. The dissociation constants for the two toxin-channel complexes are derived, which compare favorably with experiment. Our models demonstrate that the functional surface of anti-mammalian scorpion α-toxins is centered on the linker-domain, similar to that of β-toxins.

Actin-binding and cell proliferation activities of angiomotin family members are regulated by Hippo pathway-mediated phosphorylation.

PubMed

Chan, Siew Wee; Lim, Chun Jye; Guo, Fusheng; Tan, Ivan; Leung, Thomas; Hong, Wanjin

2013-12-27

Whether the Hippo pathway has downstream targets other than YAP and TAZ is unknown. In this report, we have identified angiomotin (Amot) family members as novel substrates of Hippo core kinases. The N-terminal regions of Amot proteins contain a conserved HXRXXS consensus site for LATS1/2-mediated phosphorylation. Phospho-specific antibodies showed that Hippo core kinases could mediate phosphorylation of endogenous as well as exogenous Amot family members. Knockdown of LATS1 and LATS2 endogenously reduced the phosphorylation of Amots detected by the phospho-specific antibodies. Mutation of the serine to alanine within this HXRXXS site in Amot and AmotL2 established that this site was essential for Hippo core kinase-mediated phosphorylation. Wild-type and non-phosphorylated Amot (Amot-S175A) were targeted to actin filaments, whereas phospho-mimic Amot (Amot-S175D) failed to be localized with actin. Overexpression of LATS2 caused dissociation of Amot from actin but not Amot-S175A. Mapping of the actin-binding site of Amot showed that serine 175 of Amot was important for the actin-binding activity. Amot-S175A promoted, whereas Amot and Amot-S175D inhibited, cell proliferation. These results collectively suggest that the Hippo pathway negatively regulates the actin-binding activity of Amot family members through direct phosphorylation.

Structural evidence for the role of polar core residue Arg175 in arrestin activation

PubMed Central

Granzin, Joachim; Stadler, Andreas; Cousin, Anneliese; Schlesinger, Ramona; Batra-Safferling, Renu

2015-01-01

Binding mechanism of arrestin requires photoactivation and phosphorylation of the receptor protein rhodopsin, where the receptor bound phosphate groups cause displacement of the long C-tail ‘activating’ arrestin. Mutation of arginine 175 to glutamic acid (R175E), a central residue in the polar core and previously predicted as the ‘phosphosensor’ leads to a pre-active arrestin that is able to terminate phototransduction by binding to non-phosphorylated, light-activated rhodopsin. Here, we report the first crystal structure of a R175E mutant arrestin at 2.7 Å resolution that reveals significant differences compared to the basal state reported in full-length arrestin structures. These differences comprise disruption of hydrogen bond network in the polar core, and three-element interaction including disordering of several residues in the receptor-binding finger loop and the C-terminus (residues 361–404). Additionally, R175E structure shows a 7.5° rotation of the amino and carboxy-terminal domains relative to each other. Consistent to the biochemical data, our structure suggests an important role of R29 in the initial activation step of C-tail release. Comparison of the crystal structures of basal arrestin and R175E mutant provide insights into the mechanism of arrestin activation, where binding of the receptor likely induces structural changes mimicked as in R175E. PMID:26510463

Structural evidence for the role of polar core residue Arg175 in arrestin activation.

PubMed

Granzin, Joachim; Stadler, Andreas; Cousin, Anneliese; Schlesinger, Ramona; Batra-Safferling, Renu

2015-10-29

Binding mechanism of arrestin requires photoactivation and phosphorylation of the receptor protein rhodopsin, where the receptor bound phosphate groups cause displacement of the long C-tail 'activating' arrestin. Mutation of arginine 175 to glutamic acid (R175E), a central residue in the polar core and previously predicted as the 'phosphosensor' leads to a pre-active arrestin that is able to terminate phototransduction by binding to non-phosphorylated, light-activated rhodopsin. Here, we report the first crystal structure of a R175E mutant arrestin at 2.7 Å resolution that reveals significant differences compared to the basal state reported in full-length arrestin structures. These differences comprise disruption of hydrogen bond network in the polar core, and three-element interaction including disordering of several residues in the receptor-binding finger loop and the C-terminus (residues 361-404). Additionally, R175E structure shows a 7.5° rotation of the amino and carboxy-terminal domains relative to each other. Consistent to the biochemical data, our structure suggests an important role of R29 in the initial activation step of C-tail release. Comparison of the crystal structures of basal arrestin and R175E mutant provide insights into the mechanism of arrestin activation, where binding of the receptor likely induces structural changes mimicked as in R175E.

Correlation between core ion energization, suprathermal electron bursts, and broadband ELF plasma waves

NASA Astrophysics Data System (ADS)

Knudsen, David J.; Clemmons, James H.; Wahlund, Jan-Erik

1998-03-01

Observations of the lowest energy or core ions provide a particularly sensitive measure of the early stages of auroral ion energization. Freja satellite observations of 0-20 eV core ions in the topside auroral ionosphere and cusp/cleft show signs of heating within both regions of VLF hiss and broadband ELF plasma waves. However, heating to several eV or more is associated predominantly with the ELF waves. A correlation analysis of wave and core ion data formed from orbital segments shows that, on average, correlations are highest for wave frequencies below several hundred Hz, and less at VLF hiss frequencies. A similar analysis shows a higher correlation between electron precipitation and ion heating for electron energies below several hundred eV (i.e., the energies associated with suprathermal electron bursts) and a lower correlation above the 1 keV energies associated with auroral inverted-V's. Signs of core ion heating begin to appear when wave power at the O+ gyrofrequency exceeds about 10-3(mVm-1)2/Hz, and when the integrated field-aligned electron flux exceeds a few times 107cm-2s-1sr-1. This electron energy flux threshold is at least an order of magnitude lower than previously inferred from earlier studies comparing suprathermal electron fluxes and energetic ions. Almost all observed heating events occur during enhanced or active geomagnetic conditions; i.e., Kp>=4. While the most intense core ion heating is correlated with broadband ELF waves, we also present one example of weak ion heating of a few eV in a region of VLF auroral hiss.

The Role of Core Grammar in Pidgin Development.

ERIC Educational Resources Information Center

Macedo, Donaldo P.

1986-01-01

Examines the process of pidgin development within the context of the Government and Binding Theory proposed by Chomsky in 1981. Hypothesizes that the contact of various languages may produce a new experience which subsequently fixes the parameters of Universal Grammar, providing a pidgin core gammar. (SED)

Fast Heating of Imploded Core with Counterbeam Configuration.

PubMed

Mori, Y; Nishimura, Y; Hanayama, R; Nakayama, S; Ishii, K; Kitagawa, Y; Sekine, T; Sato, N; Kurita, T; Kawashima, T; Kan, H; Komeda, O; Nishi, T; Azuma, H; Hioki, T; Motohiro, T; Sunahara, A; Sentoku, Y; Miura, E

2016-07-29

A tailored-pulse-imploded core with a diameter of 70  μm is flashed by counterirradiating 110 fs, 7 TW laser pulses. Photon emission (>40  eV) from the core exceeds the emission from the imploded core by 6 times, even though the heating pulse energies are only one seventh of the implosion energy. The coupling efficiency from the heating laser to the core using counterirradiation is 14% from the enhancement of photon emission. Neutrons are also produced by counterpropagating fast deuterons accelerated by the photon pressure of the heating pulses. A collisional two-dimensional particle-in-cell simulation reveals that the collisionless two counterpropagating fast-electron currents induce mega-Gauss magnetic filaments in the center of the core due to the Weibel instability. The counterpropagating fast-electron currents are absolutely unstable and independent of the core density and resistivity. Fast electrons with energy below a few MeV are trapped by these filaments in the core region, inducing an additional coupling. This might lead to the observed bright photon emissions.

Extended Impact of Pin1 Catalytic Loop Phosphorylation Revealed by S71E Phosphomimetic.

PubMed

Mahoney, Brendan J; Zhang, Meiling; Zintsmaster, John S; Peng, Jeffrey W

2018-03-02

Pin1 is a two-domain human protein that catalyzes the cis-trans isomerization of phospho-Ser/Thr-Pro (pS/T-P) motifs in numerous cell-cycle regulatory proteins. These pS/T-P motifs bind to Pin1's peptidyl-prolyl isomerase (PPIase) domain in a catalytic pocket, between an extended catalytic loop and the PPIase domain core. Previous studies showed that post-translational phosphorylation of S71 in the catalytic loop decreases substrate binding affinity and isomerase activity. To define the origins for these effects, we investigated a phosphomimetic Pin1 mutant, S71E-Pin1, using solution NMR. We find that S71E perturbs not only its host loop but also the nearby PPIase core. The perturbations identify a local network of hydrogen bonds and salt bridges that is more extended than previously thought, and includes interactions between the catalytic loop and the α2/α3 turn in the PPIase core. Explicit-solvent molecular dynamics simulations and phylogenetic analysis suggest that these interactions act as conserved "latches" between the loop and PPIase core that enhance binding of phosphorylated substrates, as they are absent in PPIases lacking pS/T-P specificity. Our results suggest that S71 is a hub residue within an electrostatic network primed for phosphorylation, and may illustrate a common mechanism of phosphorylation-mediated allostery. Copyright © 2018 Elsevier Ltd. All rights reserved.

Unexpected electronic perturbation effects of simple PEG environments on the optical properties of small cadmium chalcogenide clusters

NASA Astrophysics Data System (ADS)

Fukunaga, Naoto; Konishi, Katsuaki

2015-12-01

Poly(ethylene glycol) (PEG) has been widely used for the surface protection of inorganic nanoobjects because of its virtually `inert' nature, but little attention has been paid to its inherent electronic impacts on inorganic cores. Herein, we definitively show, through studies on optical properties of a series of PEG-modified Cd10Se4(SR)10 clusters, that the surrounding PEG environments can electronically affect the properties of the inorganic core. For the clusters with PEG units directly attached to an inorganic core (R = (CH2CH2O)nOCH3, 1-PEGn, n = 3, ~7, ~17, ~46), the absorption bands, associated with the low-energy transitions, continuously blue-shifted with the increasing PEG chain length. The chain length dependencies were also observed in the photoluminescence properties, particularly in the excitation spectral profiles. By combining the spectral features of several PEG17-modified clusters (2-Cm-PEG17 and 3) whose PEG and core units are separated by various alkyl chain-based spacers, it was demonstrated that sufficiently long PEG units, including PEG17 and PEG46, cause electronic perturbations in the cluster properties when they are arranged near the inorganic core. These unique effects of the long-PEG environments could be correlated with their large dipole moments, suggesting that the polarity of the proximal chemical environment is critical when affecting the electronic properties of the inorganic cluster core.Poly(ethylene glycol) (PEG) has been widely used for the surface protection of inorganic nanoobjects because of its virtually `inert' nature, but little attention has been paid to its inherent electronic impacts on inorganic cores. Herein, we definitively show, through studies on optical properties of a series of PEG-modified Cd10Se4(SR)10 clusters, that the surrounding PEG environments can electronically affect the properties of the inorganic core. For the clusters with PEG units directly attached to an inorganic core (R = (CH2CH2O)nOCH3, 1-PEGn, n = 3, ~7, ~17, ~46), the absorption bands, associated with the low-energy transitions, continuously blue-shifted with the increasing PEG chain length. The chain length dependencies were also observed in the photoluminescence properties, particularly in the excitation spectral profiles. By combining the spectral features of several PEG17-modified clusters (2-Cm-PEG17 and 3) whose PEG and core units are separated by various alkyl chain-based spacers, it was demonstrated that sufficiently long PEG units, including PEG17 and PEG46, cause electronic perturbations in the cluster properties when they are arranged near the inorganic core. These unique effects of the long-PEG environments could be correlated with their large dipole moments, suggesting that the polarity of the proximal chemical environment is critical when affecting the electronic properties of the inorganic cluster core. Electronic supplementary information (ESI) available: Details of synthetic procedures and characterisation data of the PEGylated thiols and clusters and additional absorption, photoluminescence emission and excitation spectral data. See DOI: 10.1039/c5nr06307h

Prediction of core level binding energies in density functional theory: Rigorous definition of initial and final state contributions and implications on the physical meaning of Kohn-Sham energies.

PubMed

Pueyo Bellafont, Noèlia; Bagus, Paul S; Illas, Francesc

2015-06-07

A systematic study of the N(1s) core level binding energies (BE's) in a broad series of molecules is presented employing Hartree-Fock (HF) and the B3LYP, PBE0, and LC-BPBE density functional theory (DFT) based methods with a near HF basis set. The results show that all these methods give reasonably accurate BE's with B3LYP being slightly better than HF but with both PBE0 and LCBPBE being poorer than HF. A rigorous and general decomposition of core level binding energy values into initial and final state contributions to the BE's is proposed that can be used within either HF or DFT methods. The results show that Koopmans' theorem does not hold for the Kohn-Sham eigenvalues. Consequently, Kohn-Sham orbital energies of core orbitals do not provide estimates of the initial state contribution to core level BE's; hence, they cannot be used to decompose initial and final state contributions to BE's. However, when the initial state contribution to DFT BE's is properly defined, the decompositions of initial and final state contributions given by DFT, with several different functionals, are very similar to those obtained with HF. Furthermore, it is shown that the differences of Kohn-Sham orbital energies taken with respect to a common reference do follow the trend of the properly calculated initial state contributions. These conclusions are especially important for condensed phase systems where our results validate the use of band structure calculations to determine initial state contributions to BE shifts.

Crystal Structure of Thioesterase SgcE10 Supporting Common Polyene Intermediates in 9- and 10-Membered Enediyne Core Biosynthesis

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

Annaval, Thibault; Rudolf, Jeffrey D.; Chang, Chin-Yuan

Enediynes are potent natural product anticancer antibiotics, and are classified as 9- or 10-membered according to the size of their enediyne core carbon skeleton. Both 9- and 10-membered enediyne cores are biosynthesized by the enediyne polyketide synthase (PKSE), thioesterase (TE), and PKSE-associated enzymes. Though the divergence between 9- and 10-membered enediyne core biosynthesis remains unclear, it has been observed that nascent polyketide intermediates, tethered to the acyl carrier protein (ACP) domain of PKSE, could be released by TE in the absence of the PKSE-associated enzymes. Here, we determined the crystal structure of SgcE10, the TE that participates in the biosynthesismore » of the 9-membered enediyne C-1027. Structural comparison of SgcE10 with CalE7 and DynE7, two TEs that participate in the biosynthesis of the 10-membered enediynes calicheamicin and dynemicin, respectively, revealed that they share a common α/β hot-dog fold. The amino acids involved in both substrate binding and catalysis are conserved among SgcE10, CalE7, and DynE7. The volume and the shape of the substrate-binding channel and active site in SgcE10, CalE7, and DynE7 confirm that TEs from both 9- and 10-membered enediyne biosynthetic machineries bind the linear form of similar ACP-tethered polyene intermediates. Taken together, our findings further support the proposal that the divergence between 9- and 10-membered enediyne core biosynthesis occurs beyond PKSE and TE catalysis.« less

Crystal Structure of Thioesterase SgcE10 Supporting Common Polyene Intermediates in 9- and 10-Membered Enediyne Core Biosynthesis

DOE PAGES

Annaval, Thibault; Rudolf, Jeffrey D.; Chang, Chin-Yuan; ...

2017-08-30

Enediynes are potent natural product anticancer antibiotics, and are classified as 9- or 10-membered according to the size of their enediyne core carbon skeleton. Both 9- and 10-membered enediyne cores are biosynthesized by the enediyne polyketide synthase (PKSE), thioesterase (TE), and PKSE-associated enzymes. Though the divergence between 9- and 10-membered enediyne core biosynthesis remains unclear, it has been observed that nascent polyketide intermediates, tethered to the acyl carrier protein (ACP) domain of PKSE, could be released by TE in the absence of the PKSE-associated enzymes. Here, we determined the crystal structure of SgcE10, the TE that participates in the biosynthesismore » of the 9-membered enediyne C-1027. Structural comparison of SgcE10 with CalE7 and DynE7, two TEs that participate in the biosynthesis of the 10-membered enediynes calicheamicin and dynemicin, respectively, revealed that they share a common α/β hot-dog fold. The amino acids involved in both substrate binding and catalysis are conserved among SgcE10, CalE7, and DynE7. The volume and the shape of the substrate-binding channel and active site in SgcE10, CalE7, and DynE7 confirm that TEs from both 9- and 10-membered enediyne biosynthetic machineries bind the linear form of similar ACP-tethered polyene intermediates. Taken together, our findings further support the proposal that the divergence between 9- and 10-membered enediyne core biosynthesis occurs beyond PKSE and TE catalysis.« less

Electron mobility limited by optical phonons in wurtzite InGaN/GaN core-shell nanowires

NASA Astrophysics Data System (ADS)

Liu, W. H.; Qu, Y.; Ban, S. L.

2017-09-01

Based on the force-balance and energy-balance equations, the optical phonon-limited electron mobility in InxGa1-xN/GaN core-shell nanowires (CSNWs) is discussed. It is found that the electrons tend to distribute in the core of the CSNWs due to the strong quantum confinement. Thus, the scattering from first kind of the quasi-confined optical (CO) phonons is more important than that from the interface (IF) and propagating (PR) optical phonons. Ternary mixed crystal and size effects on the electron mobility are also investigated. The results show that the PR phonons exist while the IF phonons disappear when the indium composition x < 0.047, and vice versa. Accordingly, the total electron mobility μ first increases and then decreases with indium composition x, and reaches a peak value of approximately 3700 cm2/(V.s) when x = 0.047. The results also show that the mobility μ increases as increasing the core radius of CSNWs due to the weakened interaction between the electrons and CO phonons. The total electron mobility limited by the optical phonons exhibits an obvious enhancement as decreasing temperature or increasing line electron density. Our theoretical results are expected to be helpful to develop electronic devices based on CSNWs.

The punctilious RNA polymerase II core promoter

PubMed Central

Vo ngoc, Long; Wang, Yuan-Liang; Kassavetis, George A.; Kadonaga, James T.

2017-01-01

The signals that direct the initiation of transcription ultimately converge at the core promoter, which is the gateway to transcription. Here we provide an overview of the RNA polymerase II core promoter in bilateria (bilaterally symmetric animals). The core promoter is diverse in terms of its composition and function yet is also punctilious, as it acts with strict rules and precision. We additionally describe an expanded view of the core promoter that comprises the classical DNA sequence motifs, sequence-specific DNA-binding transcription factors, chromatin signals, and DNA structure. This model may eventually lead to a more unified conceptual understanding of the core promoter. PMID:28808065

The "Core Concepts Plus" Paradigm for Creating an Electronic Textbook for Introductory Business and Economic Statistics

ERIC Educational Resources Information Center

Haley, M. Ryan

2013-01-01

This paper describes a flexible paradigm for creating an electronic "Core Concepts Plus" textbook (CCP-text) for a course in Introductory Business and Economic Statistics (IBES). In general terms, "core concepts" constitute the intersection of IBES course material taught by all IBES professors at the author's university. The…

Investigation of the electronic structure of Be2+He and Be+He, and static dipole polarisabilities of the helium atom

NASA Astrophysics Data System (ADS)

Dhiflaoui, J.; Bejaoui, M.; Farjallah, M.; Berriche, H.

2018-05-01

The potential energy and spectroscopic constants of the ground and many excited states of the Be+He van der Waals system have been investigated using a one-electron pseudo-potential approach, which is used to replace the effect of the Be2+ core and the electron-He interactions by effective potentials. Furthermore, the core-core interactions are incorporated. This permits the reduction of the number of active electrons of the Be+He van der Waals system to only one electron. Therefore, the potential energy of the ground state as well as the excited states is performed at the SCF level and considering the spin-orbit interaction. The core-core interaction for Be2+He ground state is included using accurate CCSD (T) calculations. Then, the spectroscopic properties of the Be+He electronic states are extracted and compared with the previous theoretical and experimental studies. This comparison has shown a very good agreement for the ground and the first excited states. Moreover, the transition dipole moment has been determined for a large and dense grid of internuclear distances including the spin orbit effect. In addition, a vibrational spacing analysis for the Be2+He and Be+He ground states is performed to extract the He atomic polarisability.

Structure of electron transfer flavoprotein-ubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool

PubMed Central

Zhang, Jian; Frerman, Frank E.; Kim, Jung-Ja P.

2006-01-01

Electron transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO) is a 4Fe4S flavoprotein located in the inner mitochondrial membrane. It catalyzes ubiquinone (UQ) reduction by ETF, linking oxidation of fatty acids and some amino acids to the mitochondrial respiratory chain. Deficiencies in ETF or ETF-QO result in multiple acyl-CoA dehydrogenase deficiency, a human metabolic disease. Crystal structures of ETF-QO with and without bound UQ were determined, and they are essentially identical. The molecule forms a single structural domain. Three functional regions bind FAD, the 4Fe4S cluster, and UQ and are closely packed and share structural elements, resulting in no discrete structural domains. The UQ-binding pocket consists mainly of hydrophobic residues, and UQ binding differs from that of other UQ-binding proteins. ETF-QO is a monotopic integral membrane protein. The putative membrane-binding surface contains an α-helix and a β-hairpin, forming a hydrophobic plateau. The UQ—flavin distance (8.5 Å) is shorter than the UQ—cluster distance (18.8 Å), and the very similar redox potentials of FAD and the cluster strongly suggest that the flavin, not the cluster, transfers electrons to UQ. Two possible electron transfer paths can be envisioned. First, electrons from the ETF flavin semiquinone may enter the ETF-QO flavin one by one, followed by rapid equilibration with the cluster. Alternatively, electrons may enter via the cluster, followed by equilibration between centers. In both cases, when ETF-QO is reduced to a two-electron reduced state (one electron at each redox center), the enzyme is primed to reduce UQ to ubiquinol via FAD. PMID:17050691

Structure of electron transfer flavoprotein-ubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool.

PubMed

Zhang, Jian; Frerman, Frank E; Kim, Jung-Ja P

2006-10-31

Electron transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO) is a 4Fe4S flavoprotein located in the inner mitochondrial membrane. It catalyzes ubiquinone (UQ) reduction by ETF, linking oxidation of fatty acids and some amino acids to the mitochondrial respiratory chain. Deficiencies in ETF or ETF-QO result in multiple acyl-CoA dehydrogenase deficiency, a human metabolic disease. Crystal structures of ETF-QO with and without bound UQ were determined, and they are essentially identical. The molecule forms a single structural domain. Three functional regions bind FAD, the 4Fe4S cluster, and UQ and are closely packed and share structural elements, resulting in no discrete structural domains. The UQ-binding pocket consists mainly of hydrophobic residues, and UQ binding differs from that of other UQ-binding proteins. ETF-QO is a monotopic integral membrane protein. The putative membrane-binding surface contains an alpha-helix and a beta-hairpin, forming a hydrophobic plateau. The UQ-flavin distance (8.5 A) is shorter than the UQ-cluster distance (18.8 A), and the very similar redox potentials of FAD and the cluster strongly suggest that the flavin, not the cluster, transfers electrons to UQ. Two possible electron transfer paths can be envisioned. First, electrons from the ETF flavin semiquinone may enter the ETF-QO flavin one by one, followed by rapid equilibration with the cluster. Alternatively, electrons may enter via the cluster, followed by equilibration between centers. In both cases, when ETF-QO is reduced to a two-electron reduced state (one electron at each redox center), the enzyme is primed to reduce UQ to ubiquinol via FAD.

On the atomic-number similarity of the binding energies of electrons in filled shells of elements of the periodic table

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

Karpov, V. Ya.; Shpatakovskaya, G. V., E-mail: shpagalya@yandex.ru

An expression for the binding energies of electrons in the ground state of an atom is derived on the basis of the Bohr–Sommerfeld quantization rule within the Thomas–Fermi model. The validity of this relation for all elements from neon to uranium is tested within a more perfect quantum-mechanical model with and without the inclusion of relativistic effects, as well as with experimental binding energies. As a result, the ordering of electronic levels in filled atomic shells is established, manifested in an approximate atomic-number similarity. It is proposed to use this scaling property to analytically estimate the binding energies of electronsmore » in an arbitrary atom.« less

Core-shell nanophosphor architecture: toward efficient energy transport in inorganic/organic hybrid solar cells.

PubMed

Li, Qinghua; Yuan, Yongbiao; Chen, Zihan; Jin, Xiao; Wei, Tai-huei; Li, Yue; Qin, Yuancheng; Sun, Weifu

2014-08-13

In this work, a core-shell nanostructure of samarium phosphates encapsulated into a Eu(3+)-doped silica shell has been successfully fabricated, which has been confirmed by X-ray diffraction, transmission electron microscopy (TEM), and high-resolution TEM. Moreover, we report the energy transfer process from the Sm(3+) to emitters Eu(3+) that widens the light absorption range of the hybrid solar cells (HSCs) and the strong enhancement of the electron-transport of TiO2/poly(3-hexylthiophene) (P3HT) bulk heterojunction (BHJ) HSCs by introducing the unique core-shell nanoarchitecture. Furthermore, by applying femtosecond transient absorption spectroscopy, we successfully obtain the electron transport lifetimes of BHJ systems with or without incorporating the core-shell nanophosphors (NPs). Concrete evidence has been provided that the doping of core-shell NPs improves the efficiency of electron transfers from donor to acceptor, but the hole transport almost remains unchanged. In particular, the hot electron transfer lifetime was shortened from 30.2 to 16.7 ps, i.e., more than 44% faster than pure TiO2 acceptor. Consequently, a notable power conversion efficiency of 3.30% for SmPO4@Eu(3+):SiO2 blended TiO2/P3HT HSCs is achieved at 5 wt % as compared to 1.98% of pure TiO2/P3HT HSCs. This work indicates that the core-shell NPs can efficiently broaden the absorption region, facilitate electron-transport of BHJ, and enhance photovoltaic performance of inorganic/organic HSCs.

Binding energies of benzene on coinage metal surfaces: Equal stability on different metals

NASA Astrophysics Data System (ADS)

Maaß, Friedrich; Jiang, Yingda; Liu, Wei; Tkatchenko, Alexandre; Tegeder, Petra

2018-06-01

Interfaces between organic molecules and inorganic solids adapt a prominent role in fundamental science, catalysis, molecular sensors, and molecular electronics. The molecular adsorption geometry, which is dictated by the strength of lateral and vertical interactions, determines the electronic structure of the molecule/substrate system. In this study, we investigate the binding properties of benzene on the noble metal surfaces Au(111), Ag(111), and Cu(111), respectively, using temperature-programmed desorption and first-principles calculations that account for non-locality of both electronic exchange and correlation effects. In the monolayer regime, we observed for all three systems a decrease of the binding energy with increasing coverage due to repulsive adsorbate/adsorbate interactions. Although the electronic properties of the noble metal surfaces are rather different, the binding strength of benzene on these surfaces is equal within the experimental error (accuracy of 0.05 eV), in excellent agreement with our calculations. This points toward the existence of a universal trend for the binding energy of aromatic molecules resulting from a subtle balance between Pauli repulsion and many-body van der Waals attraction.

The Structural Basis for Recognition of the PreQ0 Metabolite by an Unusually Small Riboswitch Aptamer Domain*S⃞♦

PubMed Central

Spitale, Robert C.; Torelli, Andrew T.; Krucinska, Jolanta; Bandarian, Vahe; Wedekind, Joseph E.

2009-01-01

Riboswitches are RNA elements that control gene expression through metabolite binding. The preQ1 riboswitch exhibits the smallest known ligand-binding domain and is of interest for its economical organization and high affinity interactions with guanine-derived metabolites required to confer tRNA wobbling. Here we present the crystal structure of a preQ1 aptamer domain in complex with its precursor metabolite preQ0. The structure is highly compact with a core that features a stem capped by a well organized decaloop. The metabolite is recognized within a deep pocket via Watson-Crick pairing with C15. Additional hydrogen bonds are made to invariant bases U6 and A29. The ligand-bound state confers continuous helical stacking throughout the core fold, thus providing a platform to promote Watson-Crick base pairing between C9 of the decaloop and the first base of the ribosome-binding site, G33. The structure offers insight into the mode of ribosome-binding site sequestration by a minimal RNA fold stabilized by metabolite binding and has implications for understanding the molecular basis by which bacterial genes are regulated. PMID:19261617

CryoEM and Molecular Dynamics of the Circadian KaiB-KaiC Complex Indicates That KaiB Monomers Interact with KaiC and Block ATP Binding Clefts

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

Villarreal, Seth A.; Pattanayek, Rekha; Williams, Dewight R.

The circadian control of cellular processes in cyanobacteria is regulated by a posttranslational oscillator formed by three Kai proteins. During the oscillator cycle, KaiA serves to promote autophosphorylation of KaiC while KaiB counteracts this effect. Here, we present a crystallographic structure of the wild-type Synechococcus elongatus KaiB and a cryo-electron microscopy (cryoEM) structure of a KaiBC complex. The crystal structure shows the expected dimer core structure and significant conformational variations of the KaiB C-terminal region, which is functionally important in maintaining rhythmicity. The KaiBC sample was formed with a C-terminally truncated form of KaiC, KaiC-Δ489, which is persistently phosphorylated. Themore » KaiB–KaiC-Δ489 structure reveals that the KaiC hexamer can bind six monomers of KaiB, which form a continuous ring of density in the KaiBC complex. We performed cryoEM-guided molecular dynamics flexible fitting simulations with crystal structures of KaiB and KaiC to probe the KaiBC protein–protein interface. This analysis indicated a favorable binding mode for the KaiB monomer on the CII end of KaiC, involving two adjacent KaiC subunits and spanning an ATP binding cleft. A KaiC mutation, R468C, which has been shown to affect the affinity of KaiB for KaiC and lengthen the period in a bioluminescence rhythm assay, is found within the middle of the predicted KaiBC interface. The proposed KaiB binding mode blocks access to the ATP binding cleft in the CII ring of KaiC, which provides insight into how KaiB might influence the phosphorylation status of KaiC.« less

Synthesis and characterization of the core-shell magnetic molecularly imprinted polymers (Fe₃O₄@MIPs) adsorbents for effective extraction and determination of sulfonamides in the poultry feed.

PubMed

Kong, Xuan; Gao, Ruixia; He, Xiwen; Chen, Langxing; Zhang, Yukui

2012-07-06

In this study, we present a general method to prepare the core-shell magnetic molecularly imprinted polymers (MIPs) nanoparticles (NPs) for sulfamethazine (SMZ). The resulting Fe₃O₄@MIPs NPs possess a highly improved imprinting effect, fast adsorption kinetics and high adsorption capacity, and can be applied to extract sulfonamide in the poultry feed. In this protocol, the magnetite NPs were synthesized by co-precipitating Fe²⁺ and Fe³⁺ in an ammonia solution first. Silica was then coated on the Fe₃O₄ NPs using a sol-gel method to obtain silica shell magnetic NPs. Subsequently, the vinyl groups were grated onto silica-modified Fe₃O₄ surface by 3-methacryloyloxypropyltrimethoxysilane. Finally, the MIPs films were formed on the surface of Fe₃O₄@SiO₂ by the copolymerization of vinyl end groups with functional monomer, methacrylic acid, cross-linking agent, ethylene glycol dimethacrylate, the initiator azo-bis-isobutyronitrile and template molecule, sulfamethazine. The morphology, magnetic, adsorption and recognition properties of Fe₃O₄@MIPs NPs were characterized using transmission electron microscope (TEM), scanning electron microscope (SEM), Fourier transform infrared (FT-IR) spectrometer, vibrating sample magnetometer (VSM) and re-binding experiments. The results showed that the binding sites of Fe₃O₄@MIPs were good accessibility, fast adsorption rate and the maximum adsorption capacity of Fe₃O₄@MIPs to SMZ was 344.8 μg g⁻¹. The selectivity of the obtained Fe₃O₄@MIPs NPs were elucidated by the different rebinding capability of SMZ and structural related sulfonamides in the mixed solution. The results indicated that the Fe₃O₄@MIPs had high imprinting factor 9.5 and significant selectivity. A method was developed for enrichment and determination of SMZ in the poultry feed samples with recoveries of duck and chicken feed ranging from 63.3 to 76.5% and 68.7 to 74.7%, respectively and the relative standard deviations (RSD) (<6.7%). Copyright © 2012 Elsevier B.V. All rights reserved.

Introduction to Time of Flight Positron Annihilation Induced Auger Spectroscopy (TOF-PAES)

NASA Astrophysics Data System (ADS)

Joglekar, Prasad; Kalaskar, Sushant; Shastry, Karthik; Satyal, Suman; Weiss, Alex

2009-10-01

Time of flight- positron annihilation induced auger electron spectroscopy (TOF-PAES) is extremely surface selective with close to 95% of the PAES signal stemming from the top-most atomic layer. In PAES, a beam of low energy (1eV -- 25eV) positrons is made incident on a surface where they become trapped in an image potential well. A fraction (up to several percent) of the positrons in the surface state annihilate with the core electrons of atoms at the surface resulting in core-holes. Electrons in higher levels can fill these core-hole via an Auger transition in which the energy associated with this filling the core hole is transferred to another electron which can leave the atom and the surface. The energy of the outgoing (Auger) electrons is characteristic of the energy levels of the atom and can be used to identify the specific element taking part in the transition. In this talk I will present a brief review of how the TOF PAES technique can be used to obtain Auger spectra that is completely free of secondary electron background.

Acid-base-controlled stereoselective metalation of overhanging carboxylic acid porphyrins: consequences for the formation of heterobimetallic complexes.

PubMed

Le Gac, Stéphane; Najjari, Btissam; Dorcet, Vincent; Roisnel, Thierry; Fusaro, Luca; Luhmer, Michel; Furet, Eric; Halet, Jean-François; Boitrel, Bernard

2013-08-12

Overhanging carboxylic acid porphyrins have revealed promising ditopic ligands offering a new entry in the field of supramolecular coordination chemistry of porphyrinoids. Notably, the adjunction of a so-called hanging-atop (HAT) Pb(II) cation to regular Pb(II) porphyrin complexes allowed a stereoselective incorporation of the N-core bound cation, and an allosterically controlled Newton's cradle-like motion of the two Pb(II) ions also emerged from such bimetallic complexes. In this contribution, we have extended this work to other ligands and metal ions, aiming at understanding the parameters that control the HAT Pb(II) coordination. The nature of the N-core bound metal ion (Zn(II), Cd(II)), the influence of the deprotonation state of the overhanging COOH group and the presence of a neutral ligand on the opposite side (exogenous or intramolecular), have been examined through (1)H NMR spectroscopic experiments with the help of radiocrystallographic structures and DFT calculations. Single and bis-strap ligands have been considered. They all incorporate a COOH group hung over the N-core on one side. For the bis-strap ligands, either an ester or an amide group has been introduced on the other side. In the presence of a base, the mononuclear Zn(II) or Cd(II) complexes incorporate the carbonyl of the overhanging carboxylate as apical ligand, decreasing its availability for the binding of a HAT Pb(II). An allosteric effector (e.g., 4-dimethylaminopyridine (DMAP), in the case of a single-strap ligand) or an intramolecular ligand (e.g., an amide group), strong enough to compete with the carbonyl of the hung COO(-), is required to switch the N-core bound cation to the opposite side with concomitant release of the COO(-), thereby allowing HAT Pb(II) complexation. In the absence of a base, Zn(II) or Cd(II) binds preferentially the carbonyl of the intramolecular ester or amide groups in apical position rather than that of the COOH. This better preorganization, with the overhanging COOH fully available, is responsible for a stronger binding of the HAT Pb(II). Thus, either allosteric or acid-base control is achieved through stereoselective metalation of Zn(II) or Cd(II). In the latter case, according to the deprotonation state of the COOH group, the best electron-donating ligand is located on one or the other side of the porphyrin (COO(-)>CONHR>COOR>COOH): the lower affinity of COOH for Zn(II) and Cd(II), the higher for a HAT Pb(II). These insights provide new opportunities for the elaboration of innovative bimetallic molecular switches. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Alloy and heterostructure architectures as promising tools for controlling electronic properties of semiconductor quantum dots

NASA Astrophysics Data System (ADS)

Vaxenburg, Roman; Lifshitz, Efrat

2012-02-01

Tunability of energy levels and wavefunctions of carriers in colloidal quantum dots (CQDs) has a marked effect on numerous physical aspects, such as Coulomb interactions and charge separation, which in turn has a direct impact on the functioning of CQD-based opto-electronic devices. The electronic properties of CQDs are conventionally controlled by variation of their size. Here we demonstrate a theoretical approach to engineer the electronic properties of IV-VI CQDs by introducing an alloy composition in core and core/shell heterostructures, having the general chemical formula PbSexS1-x/PbSeyS1-y (0 ≤ x ≤ 1, 0 ≤ y ≤ 1), while maintaining a constant size. The theoretical model considered an effective mass anisotropy and smooth potential step at the core/shell interface. The model revealed the influence induced by variation of chemical composition and core-to-shell division on the band-gap energy, remote states’ density, internal charge separation, electron-hole Coulomb interaction, and optical transition oscillator strength.

Physical property control in core/shell inorganic nanostructures for fluorescence and magnetic targeting applications

NASA Astrophysics Data System (ADS)

Roberts, Stephen K.

Nanomaterials show immense promise for the future in numerous areas of application. Properties that are unique from the bulk material and are tunable allow for innovation in material design. This thesis will focus on controlling the physical properties of core/shell nanostructures to enhance the utility of the materials. The first focus is on the impact of different solvent mixtures during the shell growth phase of SILAR based core/shell quantum dot synthesis is studied. Gaining insight into the mechanism for SILAR growth of core/shell nanoparticles allows improved synthetic yields and precursor binding, providing enhanced control to synthesis of core/shell nanoparticles. The second focus of this thesis is exploring the use of magnetic nanoparticles for magnetic drug targeting for cardiovascular conditions. Magnetic targeting for drug delivery enables increased local drug concentration, while minimizing non-specific interactions. In order to be effective for magnetic targeting, it must be shown that low magnetic strength is sufficient to capture flowing nanoparticles. By demonstrating the binding of a therapeutic agent to the surface at medicinal levels, the viability for use as a nanoparticle drug delivery system is improved.

Structural and Histone Binding Ability Characterizations of Human PWWP Domains

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

Wu, Hong; Zeng, Hong; Lam, Robert

2013-09-25

The PWWP domain was first identified as a structural motif of 100-130 amino acids in the WHSC1 protein and predicted to be a protein-protein interaction domain. It belongs to the Tudor domain 'Royal Family', which consists of Tudor, chromodomain, MBT and PWWP domains. While Tudor, chromodomain and MBT domains have long been known to bind methylated histones, PWWP was shown to exhibit histone binding ability only until recently. The PWWP domain has been shown to be a DNA binding domain, but sequence analysis and previous structural studies show that the PWWP domain exhibits significant similarity to other 'Royal Family' members,more » implying that the PWWP domain has the potential to bind histones. In order to further explore the function of the PWWP domain, we used the protein family approach to determine the crystal structures of the PWWP domains from seven different human proteins. Our fluorescence polarization binding studies show that PWWP domains have weak histone binding ability, which is also confirmed by our NMR titration experiments. Furthermore, we determined the crystal structures of the BRPF1 PWWP domain in complex with H3K36me3, and HDGF2 PWWP domain in complex with H3K79me3 and H4K20me3. PWWP proteins constitute a new family of methyl lysine histone binders. The PWWP domain consists of three motifs: a canonical {beta}-barrel core, an insertion motif between the second and third {beta}-strands and a C-terminal {alpha}-helix bundle. Both the canonical {beta}-barrel core and the insertion motif are directly involved in histone binding. The PWWP domain has been previously shown to be a DNA binding domain. Therefore, the PWWP domain exhibits dual functions: binding both DNA and methyllysine histones.« less

Predominance of multielectron processes contributing to the intrinsic spectra of low-energy Auger transitions in copper and gold

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

Mukherjee, S. F.; Shastry, K.; Weiss, A. H.

2011-10-15

Positron-annihilation-induced Auger electron spectroscopy (PAES) was used to obtain Cu and Au Auger spectra that are free of primary-beam-induced backgrounds by impinging the positrons at an energy below the secondary-electron-emission threshold. The removal of the core electron via annihilation in the PAES process resulted in the elimination of postcollision effects. The spectra indicate that there is an intense low-energy tail (LET) associated with the Auger peak that extends all the way to 0 eV. The LET is interpreted as indicative of processes in which filling of the core hole by a valence electron results in the ejection of two ormore » more valence electrons which share the energy of the conventional core-valence-valence Auger electron.« less

De novo modeling of the F420-reducing [NiFe]-hydrogenase from a methanogenic archaeon by cryo-electron microscopy

PubMed Central

Mills, Deryck J; Vitt, Stella; Strauss, Mike; Shima, Seigo; Vonck, Janet

2013-01-01

Methanogenic archaea use a [NiFe]-hydrogenase, Frh, for oxidation/reduction of F420, an important hydride carrier in the methanogenesis pathway from H2 and CO2. Frh accounts for about 1% of the cytoplasmic protein and forms a huge complex consisting of FrhABG heterotrimers with each a [NiFe] center, four Fe-S clusters and an FAD. Here, we report the structure determined by near-atomic resolution cryo-EM of Frh with and without bound substrate F420. The polypeptide chains of FrhB, for which there was no homolog, was traced de novo from the EM map. The 1.2-MDa complex contains 12 copies of the heterotrimer, which unexpectedly form a spherical protein shell with a hollow core. The cryo-EM map reveals strong electron density of the chains of metal clusters running parallel to the protein shell, and the F420-binding site is located at the end of the chain near the outside of the spherical structure. DOI: http://dx.doi.org/10.7554/eLife.00218.001 PMID:23483797

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

Michael, Alicia K.; Fribourgh, Jennifer L.; Chelliah, Yogarany

The basic helix-loop-helix PAS domain (bHLH-PAS) transcription factor CLOCK:BMAL1 (brain and muscle Arnt-like protein 1) sits at the core of the mammalian circadian transcription/translation feedback loop. Precise control of CLOCK:BMAL1 activity by coactivators and repressors establishes the ~24-h periodicity of gene expression. Formation of a repressive complex, defined by the core clock proteins cryptochrome 1 (CRY1):CLOCK:BMAL1, plays an important role controlling the switch from repression to activation each day. Here in this paper, we show that CRY1 binds directly to the PAS domain core of CLOCK: BMAL1, driven primarily by interaction with the CLOCK PAS-B domain. Integrative modeling and solutionmore » X-ray scattering studies unambiguously position a key loop of the CLOCK PAS-B domain in the secondary pocket of CRY1, analogous to the antenna chromophore-binding pocket of photolyase. CRY1 docks onto the transcription factor alongside the PAS domains, extending above the DNA-binding bHLH domain. Single point mutations at the interface on either CRY1 or CLOCK disrupt formation of the ternary complex, highlighting the importance of this interface for direct regulation of CLOCK:BMAL1 activity by CRY1.« less

Exploring the effect of band alignment and surface states on photoinduced electron transfer from CuInS2/CdS core/shell quantum dots to TiO2 electrodes.

PubMed

Sun, Mingye; Zhu, Dehua; Ji, Wenyu; Jing, Pengtao; Wang, Xiuying; Xiang, Weidong; Zhao, Jialong

2013-12-11

Photoinduced electron transfer (ET) processes from CuInS2/CdS core/shell quantum dots (QDs) with different core sizes and shell thicknesses to TiO2 electrodes were investigated by time-resolved photoluminescence (PL) spectroscopy. The ET rates and efficiencies from CuInS2/CdS QDs to TiO2 were superior to those of CuInS2/ZnS QDs. An enhanced ET efficiency was surprisingly observed for 2.0 nm CuInS2 core QDs after growth of the CdS shell. On the basis of the experimental and theoretical analysis, the improved performances of CuInS2/CdS QDs were attributed to the passivation of nonradiative traps by overcoating shell and enhanced delocalization of electron wave function from core to CdS shell due to lower conduction band offset. These results indicated that the electron distribution regulated by the band alignment between core and shell of QDs and the passivation of surface defect states could improve ET performance between donor and acceptor.

Analysis of DNA binding by human factor xeroderma pigmentosum complementation group A (XPA) provides insight into its interactions with nucleotide excision repair substrates.

PubMed

Sugitani, Norie; Voehler, Markus W; Roh, Michelle S; Topolska-Woś, Agnieszka M; Chazin, Walter J

2017-10-13

Xeroderma pigmentosum (XP) complementation group A (XPA) is an essential scaffolding protein in the multiprotein nucleotide excision repair (NER) machinery. The interaction of XPA with DNA is a core function of this protein; a number of mutations in the DNA-binding domain (DBD) are associated with XP disease. Although structures of the central globular domain of human XPA and data on binding of DNA substrates have been reported, the structural basis for XPA's DNA-binding activity remains unknown. X-ray crystal structures of the central globular domain of yeast XPA (Rad14) with lesion-containing DNA duplexes have provided valuable insights, but the DNA substrates used for this study do not correspond to the substrates of XPA as it functions within the NER machinery. To better understand the DNA-binding activity of human XPA in NER, we used NMR to investigate the interaction of its DBD with a range of DNA substrates. We found that XPA binds different single-stranded/double-stranded junction DNA substrates with a common surface. Comparisons of our NMR-based mapping of binding residues with the previously reported Rad14-DNA crystal structures revealed similarities and differences in substrate binding between XPA and Rad14. This includes direct evidence for DNA contacts to the residues extending C-terminally from the globular core, which are lacking in the Rad14 construct. Moreover, mutation of the XPA residue corresponding to Phe-262 in Rad14, previously reported as being critical for DNA binding, had only a moderate effect on the DNA-binding activity of XPA. The DNA-binding properties of several disease-associated mutations in the DBD were investigated. These results suggest that for XPA mutants exhibiting altered DNA-binding properties, a correlation exists between the extent of reduction in DNA-binding affinity and the severity of symptoms in XP patients. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Positron-annihilation-induced ion desorption from TiO2(110)

NASA Astrophysics Data System (ADS)

Tachibana, T.; Hirayama, T.; Nagashima, Y.

2014-05-01

We have investigated the positron-stimulated desorption of ions from a TiO2(110) surface. Desorbed O+ ions were detected in coincidence with the emission of annihilation γ rays. The energy dependence of the ion yields shows that the O+ ions were detected at energies much lower than the previously reported threshold for electron impact desorption corresponding to the excitation energy of Ti(3p) core electrons. These results provide evidence that core-hole creation by positron annihilation with electrons in the core levels leads to ion desorption.

Flavins in Marine Sediments: A Potentially Ubiquitous Intermediary In Microbial Electron Transfer

NASA Astrophysics Data System (ADS)

Monteverde, D.; Sylvan, J. B.; Suffridge, C.; Berelson, W.; Sanudo-Wilhelmy, S. A.; Baronas, J. J.

2016-12-01

The flavins (riboflavin, flavin mononucleotide [FMN], flavin adenine dinucleotide [FA­­D]) are a class of organic compounds synthesized by organisms to assist in redox reactions. They represent the largest class of required coenzymes, rivaled only by iron in the number of unique enzymes they bind. In addition to internal use, cultured metal-reducing organisms such as Shewanella and Geobacter have been known to release flavins into the extracellular pool to aid in external electron transfer. So called "electron shuttles" can allow organisms to overcome unfavorable geochemical zonation by transferring electrons onto a relatively distant insoluble acceptor. Despite the extensive culture work, flavins have not been systematically measured in the environment. Here we present the first set of flavin profiles from the water column and pore waters of a marine environment. Samples were taken from San Pedro Basin, a 900 meter deep, silled basin, with high seasonal inputs of organic carbon, low bottom water oxygen concentrations, and laminated sediments - making it ideal to explore variations in sediment geochemical zonations. Dissolved flavin concentrations in the water column and pore waters collected from two cores were preconcentrated via solid phase extraction and measured via LC/MS. Flavin profiles are compared to a suite of geochemical parameters as well as sediment microbial 16s rRNA data. Preliminary results show that FMN is typically an order of magnitude higher concentration than riboflavin (800-300pM versus 100-50pM). Porewater concentrations were elevated over water column values for all analytes (ranging from 100-2000pM) and displayed an increasing trend with depth in both cores. This increasing trend correlated with a decrease in dissolved Fe (ranging from 160 µM in surface sediments to 65 µM at 40 cm) and shifts in microbial diversity from sediments shallower than 5 cm depth dominated by Delta- and Gammaproteobacteria to subsurface sediments dominated by Chloroflexi and Archaea at 20-40 cm. These first environmental profiles of flavins in the marine environmental support previous observations of the importance of electron transfer intermediaries in culture and point to an important role for flavins in modern marine microbial communities.

First principles study of structural, electronic and magnetic properties of SnGe n (0, ±1) ( n = 1–17) clusters

NASA Astrophysics Data System (ADS)

Djaadi, Soumaia; Eddine Aiadi, Kamal; Mahtout, Sofiane

2018-04-01

The structures, relative stability and magnetic properties of pure Ge n +1, neutral cationic and anionic SnGe n (n = 1–17) clusters have been investigated by using the first principles density functional theory implemented in SIESTA packages. We find that with the increasing of cluster size, the Ge n +1 and SnGe n (0, ±1) clusters tend to adopt compact structures. It has been also found that the Sn atom occupied a peripheral position for SnGe n clusters when n < 12 and occupied a core position for n > 12. The structural and electronic properties such as optimized geometries, fragmentation energy, binding energy per atom, HOMO–LUMO gaps and second-order differences in energy of the pure Ge n +1 and SnGe n clusters in their ground state are calculated and analyzed. All isomers of neutral SnGe n clusters are generally nonmagnetic except for n = 1 and 4, where the total spin magnetic moments is 2μ b. The total (DOS) and partial density of states of these clusters have been calculated to understand the origin of peculiar magnetic properties. The cluster size dependence of vertical ionization potentials, vertical electronic affinities, chemical hardness, adiabatic electron affinities and adiabatic ionization potentials have been calculated and discussed.

The Effects of Surface Reconstruction and Electron-Positron Correlation on the Annihilation Characteristics of Positrons Trapped at Semiconductor Surfaces

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

Fazleev, N. G.; Department of Physics, Kazan State University, Kazan 420008; Jung, E.

2009-03-10

Experimental positron annihilation induced Auger electron spectroscopy (PAES) data from Ge(100) and Ge(111) surfaces display several strong Auger peaks corresponding to M{sub 4,5}N{sub 1}N{sub 2,3}, M{sub 2,3}M{sub 4,5}M{sub 4,5}, M{sub 2,3}M{sub 4,5}V, and M{sub 1}M{sub 4,5}M{sub 4,5} Auger transitions. The integrated peak intensities of Auger transitions have been used to obtain experimental annihilation probabilities for the Ge 3d and 3p core electrons. The experimental data were analyzed by performing theoretical studies of the effects of surface reconstructions and electron-positron correlations on image potential induced surface states and annihilation characteristics of positrons trapped at the reconstructed Ge(100) and Ge(111) surfaces. Calculationsmore » of positron surface states and annihilation characteristics have been performed for Ge(100) surface with (2x1), (2x2), and (4x2) reconstructions, and for Ge(111) surface with c(2x8) reconstruction. Estimates of the positron binding energy and annihilation characteristics reveal their sensitivity to the specific atomic structure of the topmost layers of the semiconductor and to the approximations used to describe electron-positron correlations. The results of these theoretical studies are compared with the ones obtained for the reconstructed Si(100)-(2x1) and Si(111)-(7x7) surfaces.« less

Gene disruption of dematin causes precipitous loss of erythrocyte membrane stability and severe hemolytic anemia.

PubMed

Lu, Yunzhe; Hanada, Toshihiko; Fujiwara, Yuko; Nwankwo, Jennifer O; Wieschhaus, Adam J; Hartwig, John; Huang, Sha; Han, Jongyoon; Chishti, Athar H

2016-07-07

Dematin is a relatively low abundance actin binding and bundling protein associated with the spectrin-actin junctions of mature erythrocytes. Primary structure of dematin includes a loosely folded core domain and a compact headpiece domain that was originally identified in villin. Dematin's actin binding properties are regulated by phosphorylation of its headpiece domain by cyclic adenosine monophosphate-dependent protein kinase. Here, we used a novel gene disruption strategy to generate the whole body dematin gene knockout mouse model (FLKO). FLKO mice, while born at a normal Mendelian ratio, developed severe anemia and exhibited profound aberrations of erythrocyte morphology and membrane stability. Having no apparent effect on primitive erythropoiesis, FLKO mice show significant enhancement of erythroblast enucleation during definitive erythropoiesis. Using membrane protein analysis, domain mapping, electron microscopy, and dynamic deformability measurements, we investigated the mechanism of membrane instability in FLKO erythrocytes. Although many membrane and cytoskeletal proteins remained at their normal levels, the major peripheral membrane proteins spectrin, adducin, and actin were greatly reduced in FLKO erythrocytes. Our results demonstrate that dematin plays a critical role in maintaining the fundamental properties of the membrane cytoskeleton complex. © 2016 by The American Society of Hematology.

Gene disruption of dematin causes precipitous loss of erythrocyte membrane stability and severe hemolytic anemia

PubMed Central

Lu, Yunzhe; Hanada, Toshihiko; Fujiwara, Yuko; Nwankwo, Jennifer O.; Wieschhaus, Adam J.; Hartwig, John; Huang, Sha; Han, Jongyoon

2016-01-01

Dematin is a relatively low abundance actin binding and bundling protein associated with the spectrin–actin junctions of mature erythrocytes. Primary structure of dematin includes a loosely folded core domain and a compact headpiece domain that was originally identified in villin. Dematin’s actin binding properties are regulated by phosphorylation of its headpiece domain by cyclic adenosine monophosphate–dependent protein kinase. Here, we used a novel gene disruption strategy to generate the whole body dematin gene knockout mouse model (FLKO). FLKO mice, while born at a normal Mendelian ratio, developed severe anemia and exhibited profound aberrations of erythrocyte morphology and membrane stability. Having no apparent effect on primitive erythropoiesis, FLKO mice show significant enhancement of erythroblast enucleation during definitive erythropoiesis. Using membrane protein analysis, domain mapping, electron microscopy, and dynamic deformability measurements, we investigated the mechanism of membrane instability in FLKO erythrocytes. Although many membrane and cytoskeletal proteins remained at their normal levels, the major peripheral membrane proteins spectrin, adducin, and actin were greatly reduced in FLKO erythrocytes. Our results demonstrate that dematin plays a critical role in maintaining the fundamental properties of the membrane cytoskeleton complex. PMID:27073223

Pseudopotentials for quantum Monte Carlo studies of transition metal oxides

DOE PAGES

Krogel, Jaron T.; Santana Palacio, Juan A.; Reboredo, Fernando A.

2016-02-22

Quantum Monte Carlo (QMC) calculations of transition metal oxides are partially limited by the availability of high-quality pseudopotentials that are both accurate in QMC and compatible with major plane-wave electronic structure codes. We have generated a set of neon-core pseudopotentials with small cutoff radii for the early transition metal elements Sc to Zn within the local density approximation of density functional theory. The pseudopotentials have been directly tested for accuracy within QMC by calculating the first through fourth ionization potentials of the isolated transition metal (M) atoms and the binding curve of each M-O dimer. We find the ionization potentialsmore » to be accurate to 0.16(1) eV, on average, relative to experiment. The equilibrium bond lengths of the dimers are within 0.5(1)% of experimental values, on average, and the binding energies are also typically accurate to 0.18(3) eV. The level of accuracy we find for atoms and dimers is comparable to what has recently been observed for bulk metals and oxides using the same pseudopotentials. Our QMC pseudopotential results compare well with the findings of previous QMC studies and benchmark quantum chemical calculations.« less

Core binding factors are necessary for natural killer cell development and cooperate with Notch signaling during T-cell specification

PubMed Central

Guo, Yalin; Maillard, Ivan; Chakraborti, Sankhamala; Rothenberg, Ellen V.

2008-01-01

CBFβ is the non-DNA binding subunit of the core binding factors (CBFs). Mice with reduced CBFβ levels display profound, early defects in T-cell but not B-cell development. Here we show that CBFβ is also required at very early stages of natural killer (NK)–cell development. We also demonstrate that T-cell development aborts during specification, as the expression of Gata3 and Tcf7, which encode key regulators of T lineage specification, is substantially reduced, as are functional thymic progenitors. Constitutively active Notch or IL-7 signaling cannot restore T-cell expansion or differentiation of CBFβ insufficient cells, nor can overexpression of Runx1 or CBFβ overcome a lack of Notch signaling. Therefore, the ability of the prethymic cell to respond appropriately to Notch is dependent on CBFβ, and both signals converge to activate the T-cell developmental program. PMID:18390836

Alkyl Chain Ordering of Asymmetric Phosphatidyicholines Adsorbed at a Liquid-Liquid Interface

DTIC Science & Technology

1998-05-30

the blood bind to the PL surface and begin to hydrolyze the triglyceride core and only a small fraction of the phospholipids, such that the core...which surface-adsorbed proteins are able to hydrolyze the triglyceride core has been shown to depend on the acyl chain composition of monolayer PCs...in the commercial use of natural phosphatidylcholines (or lecithins ) as emulsifiers, including their use in delivery of water-insoluble drugs (Davis

High-order harmonic generation enhanced by XUV light

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

Buth, Christian; Kohler, Markus C.; Ullrich, Joachim

2012-03-19

The combination of high-order harmonic generation (HHG) with resonant XUV excitation of a core electron into the transient valence vacancy that is created in the course of the HHG process is investigated theoretically. In this setup, the first electron performs a HHG three-step process, whereas the second electron Rabi flops between the core and the valence vacancy. The modified HHG spectrum due to recombination with the valence and the core is determined and analyzed for krypton on the 3d {yields} 4p resonance in the ion. We assume an 800 nm laser with an intensity of about 10{sup 14} Wcm{sup 2}more » and XUV radiation from the Free Electron Laser in Hamburg (FLASH) with an intensity in the range 10{sup 13}-10{sup 16} Wcm{sup 2}. Our prediction opens perspectives for nonlinear XUV physics, attosecond x rays, and HHG-based spectroscopy involving core orbitals.« less

Enhanced bioactivity of internally functionalized cationic dendrimers with PEG cores

PubMed Central

Albertazzi, Lorenzo; Mickler, Frauke M.; Pavan, Giovanni M.; Salomone, Fabrizio; Bardi, Giuseppe; Panniello, Mariangela; Amir, Elizabeth; Kang, Taegon; Killops, Kato L.; Bräuchle, Christoph; Amir, Roey J.; Hawker, Craig J.

2012-01-01

Hybrid dendritic-linear block copolymers based on a 4-arm polyethylene glycol (PEG) core were synthesized using an accelerated AB2/CD2 dendritic growth approach through orthogonal amine/epoxy and thiol-yne chemistries. The biological activity of these 4-arm and the corresponding 2-arm hybrid dendrimers revealed an enhanced, dendritic effect with an exponential increase in cell internalization concomitant with increasing amine end-groups and low cytotoxicity. Furthermore, the ability of these hybrid dendrimers to induce endosomal escape combined with their facile and efficient synthesis makes them attractive platforms for gene transfection. The 4-arm-based dendrimer showed significantly improved DNA binding and gene transfection capabilities in comparison with the 2-arm derivative. These results combined with the MD simulation indicate a significant effect of both the topology of the PEG core and the multivalency of these hybrid macromolecules, on their DNA binding and delivery capablities. PMID:23140570

An enhanceosome containing the Jun B/Fra-2 heterodimer and the HMG-I(Y) architectural protein controls HPV 18 transcription.

PubMed

Bouallaga, I; Massicard, S; Yaniv, M; Thierry, F

2000-11-01

Recent studies have reported new mechanisms that mediate the transcriptional synergy of strong tissue-specific enhancers, involving the cooperative assembly of higher-order nucleoprotein complexes called enhanceosomes. Here we show that the HPV18 enhancer, which controls the epithelial-specific transcription of the E6 and E7 transforming genes, exhibits characteristic features of these structures. We used deletion experiments to show that a core enhancer element cooperates, in a specific helical phasing, with distant essential factors binding to the ends of the enhancer. This core sequence, binding a Jun B/Fra-2 heterodimer, cooperatively recruits the architectural protein HMG-I(Y) in a nucleoprotein complex, where they interact with each other. Therefore, in HeLa cells, HPV18 transcription seems to depend upon the assembly of an enhanceosome containing multiple cellular factors recruited by a core sequence interacting with AP1 and HMG-I(Y).

Functionalization of paramagnetic nanoparticles for protein immobilization and purification.

PubMed

Carneiro, Lara A B C; Ward, Richard J

2018-01-01

A paramagnetic nanocomposite coated with chitosan and N-(5-Amino-1-carboxy-pentyl) iminodiacetic acid (NTA) that is suitable for protein immobilization applications has been prepared and characterized. The nanoparticle core was synthesized by controlled aggregation of Fe 3 O 4 under alkaline conditions, and Transmission Electron Microscopy revealed a size distribution of 10-50 nm. The nanoparticle core was coated with chitosan and derivatized with glutaraldehyde and NTA, as confirmed by Fourier Transform Infrared Spectroscopy. The final nanoparticles were used as a metal affinity matrix to separate a recombinant polyhistidine-tagged β-galactosidase from Bacillus subtilis directly from E. coli cell lysates with high purity (>95%). After loading with Ni 2+ , nanoparticles demonstrated a binding capacity of 250 μg of a polyhistidine-tagged β-galactosidase per milligram of support. The immobilized enzyme retained 80% activity after 9 cycles of washing, and the immobilized recombinant protein could be eluted with high purity with imidazole. The applications for these nanomagnetic composites extend beyond protein purification, and can also be used for immobilizing enzymes, where the β-galactosidase immobilized on the nanomagnetic support was used in multiple cycles of catalytic reactions with no significant loss of catalytic activity. Copyright © 2017. Published by Elsevier Inc.

Shape transformation of bimetallic Au–Pd core–shell nanocubes to multilayered Au–Pd–Au core–shell hexagonal platelets

DOE PAGES

Bhattarai, Nabraj; Prozorov, Tanya

2015-11-05

Transformation of metallic or bimetallic (BM) nanoparticles (NPs) from one shape to another desired shape is of importance to nanoscience and nanotechnology, where new morphologies of NPs lead to enhancement of their exploitable properties. In this report, we present the shape transformation of Au octahedral NPs to Au–Pd core–shell nanocubes, followed by their transformation to nanostars and finally to multilayered Au–Pd–Au core–shell hexagonal platelets in the presence of T30 DNA. The weaker binding affinity of T30 DNA directs the growth to favor the formation of lower energy {111} facets, changing the morphology from nanocubes to nanostar. The nanostars, exhibiting unusualmore » intermediate morphologies, are comprised two sets of shell layers and have Au core, Pd intermediate shell, and Au outer shell. Similarly, the hexagonal platelets, which also have Au core and inner Pd shell, are encased in an external gold shell. As a result, the formation of multilayered Au–Pd–Au core–shell hexagonal platelets from Au–Pd core–shell nanocubes via the multilayered nanostars is monitored using scanning/transmission electron microscopy analysis.« less

Shape transformation of bimetallic Au–Pd core–shell nanocubes to multilayered Au–Pd–Au core–shell hexagonal platelets

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

Bhattarai, Nabraj; Prozorov, Tanya

Transformation of metallic or bimetallic (BM) nanoparticles (NPs) from one shape to another desired shape is of importance to nanoscience and nanotechnology, where new morphologies of NPs lead to enhancement of their exploitable properties. In this report, we present the shape transformation of Au octahedral NPs to Au–Pd core–shell nanocubes, followed by their transformation to nanostars and finally to multilayered Au–Pd–Au core–shell hexagonal platelets in the presence of T30 DNA. The weaker binding affinity of T30 DNA directs the growth to favor the formation of lower energy {111} facets, changing the morphology from nanocubes to nanostar. The nanostars, exhibiting unusualmore » intermediate morphologies, are comprised two sets of shell layers and have Au core, Pd intermediate shell, and Au outer shell. Similarly, the hexagonal platelets, which also have Au core and inner Pd shell, are encased in an external gold shell. As a result, the formation of multilayered Au–Pd–Au core–shell hexagonal platelets from Au–Pd core–shell nanocubes via the multilayered nanostars is monitored using scanning/transmission electron microscopy analysis.« less

Communication: Two-step explosion processes of highly charged fullerene cations C{sub 60}{sup q+} (q = 20–60)

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

Yamazaki, Kaoru; Nakamura, Takashi; Kanno, Manabu

2014-09-28

To establish the fundamental understanding of the fragmentation dynamics of highly positive charged nano- and bio-materials, we carried out on-the-fly classical trajectory calculations on the fragmentation dynamics of C{sub 60}{sup q+} (q = 20–60). We used the UB3LYP/3-21G level of density functional theory and the self-consistent charge density-functional based tight-binding theory. For q ≥ 20, we found that a two-step explosion mechanism governs the fragmentation dynamics: C{sub 60}{sup q+} first ejects singly and multiply charged fast atomic cations C{sup z+} (z ≥ 1) via Coulomb explosions on a timescale of 10 fs to stabilize the remaining core cluster. Thermal evaporationsmore » of slow atomic and molecular fragments from the core cluster subsequently occur on a timescale of 100 fs to 1 ps. Increasing the charge q makes the fragments smaller. This two-step mechanism governs the fragmentation dynamics in the most likely case that the initial kinetic energy accumulated upon ionization to C{sub 60}{sup q+} by ion impact or X-ray free electron laser is larger than 100 eV.« less

Measurement of the spectra of low energy electrons resulting from Auger transitions induced by the annihilation of low energy positrons implanted at The Ag (100) surface

NASA Astrophysics Data System (ADS)

Shastry, Karthik; Joglekar, Prasad; Weiss, A. H.; Fazleev, N. G.

2013-04-01

A few percent of positrons bound to a solid surface annihilate with core electrons resulting in highly excited atoms containing core holes. These core holes may be filled in an auto-ionizing process in which a less tightly bound electron drops into the hole and the energy difference transferred to an outgoing "Auger electron." Because the core holes are created by annihilation and not impact it is possible to use very low energy positron beams to obtain annihilation induced Auger signals. The Auger signals so obtained have little or none of the large impact induced secondary electron background that interferes with measurements of the low energy Auger spectra obtained using the much higher incident energies necessary when using electron or photon beams. Here we present the results of measurements of the energy spectrum of low energy electrons emitted as a result of Positron Annihilation Induce Auger Electron Emission [1] from a clean Ag (100) surface. The measurements were performed using the University of Texas Arlington Time of Flight Positron Annihilation induced Auger Electron Spectrometer (T-O-F-PAES) System [2]. A strong double peak was observed at ˜35eV corresponding to the N2VV and N3VV Auger transitions in agreement with previous PAES studies [3].

Architecture of the Saccharomyces cerevisiae SAGA transcription coactivator complex

PubMed Central

Han, Yan; Luo, Jie; Ranish, Jeffrey; Hahn, Steven

2014-01-01

The conserved transcription coactivator SAGA is comprised of several modules that are involved in activator binding, TBP binding, histone acetylation (HAT) and deubiquitination (DUB). Crosslinking and mass spectrometry, together with genetic and biochemical analyses, were used to determine the molecular architecture of the SAGA-TBP complex. We find that the SAGA Taf and Taf-like subunits form a TFIID-like core complex at the center of SAGA that makes extensive interactions with all other SAGA modules. SAGA-TBP binding involves a network of interactions between subunits Spt3, Spt8, Spt20, and Spt7. The HAT and DUB modules are in close proximity, and the DUB module modestly stimulates HAT function. The large activator-binding subunit Tra1 primarily connects to the TFIID-like core via its FAT domain. These combined results were used to derive a model for the arrangement of the SAGA subunits and its interactions with TBP. Our results provide new insight into SAGA function in gene regulation, its structural similarity with TFIID, and functional interactions between the SAGA modules. PMID:25216679

Sanguinarine interacts with chromatin, modulates epigenetic modifications, and transcription in the context of chromatin.

PubMed

Selvi B, Ruthrotha; Pradhan, Suman Kalyan; Shandilya, Jayasha; Das, Chandrima; Sailaja, Badi Sri; Shankar G, Naga; Gadad, Shrikanth S; Reddy, Ashok; Dasgupta, Dipak; Kundu, Tapas K

2009-02-27

DNA-binding anticancer agents cause alteration in chromatin structure and dynamics. We report the dynamic interaction of the DNA intercalator and potential anticancer plant alkaloid, sanguinarine (SGR), with chromatin. Association of SGR with different levels of chromatin structure was enthalpy driven with micromolar dissociation constant. Apart from DNA, it binds with comparable affinity with core histones and induces chromatin aggregation. The dual binding property of SGR leads to inhibition of core histone modifications. Although it potently inhibits H3K9 methylation by G9a in vitro, H3K4 and H3R17 methylation are more profoundly inhibited in cells. SGR inhibits histone acetylation both in vitro and in vivo. It does not affect the in vitro transcription from DNA template but significantly represses acetylation-dependent chromatin transcription. SGR-mediated repression of epigenetic marks and the alteration of chromatin geography (nucleography) also result in the modulation of global gene expression. These data, conclusively, show an anticancer DNA binding intercalator as a modulator of chromatin modifications and transcription in the chromatin context.

Nitrogen reduction and functionalization by a multimetallic uranium nitride complex

NASA Astrophysics Data System (ADS)

Falcone, Marta; Chatelain, Lucile; Scopelliti, Rosario; Živković, Ivica; Mazzanti, Marinella

2017-07-01

Molecular nitrogen (N2) is cheap and widely available, but its unreactive nature is a challenge when attempting to functionalize it under mild conditions with other widely available substrates (such as carbon monoxide, CO) to produce value-added compounds. Biological N2 fixation can do this, but the industrial Haber-Bosch process for ammonia production operates under harsh conditions (450 degrees Celsius and 300 bar), even though both processes are thought to involve multimetallic catalytic sites. And although molecular complexes capable of binding and even reducing N2 under mild conditions are known, with co-operativity between metal centres considered crucial for the N2 reduction step, the multimetallic species involved are usually not well defined, and further transformation of N2-binding complexes to achieve N-H or N-C bond formation is rare. Haber noted, before an iron-based catalyst was adopted for the industrial Haber-Bosch process, that uranium and uranium nitride materials are very effective heterogeneous catalysts for ammonia production from N2. However, few examples of uranium complexes binding N2 are known, and soluble uranium complexes capable of transforming N2 into ammonia or organonitrogen compounds have not yet been identified. Here we report the four-electron reduction of N2 under ambient conditions by a fully characterized complex with two UIII ions and three K+ centres held together by a nitride group and a flexible metalloligand framework. The addition of H2 and/or protons, or CO to the resulting complex results in the complete cleavage of N2 with concomitant N2 functionalization through N-H or N-C bond-forming reactions. These observations establish that a molecular uranium complex can promote the stoichiometric transformation of N2 into NH3 or cyanate, and that a flexible, electron-rich, multimetallic, nitride-bridged core unit is a promising starting point for the design of molecular complexes capable of cleaving and functionalizing N2 under mild conditions.

Increasing the affinity of selective bZIP-binding peptides through surface residue redesign.

PubMed

Kaplan, Jenifer B; Reinke, Aaron W; Keating, Amy E

2014-07-01

The coiled-coil dimer is a prevalent protein interaction motif that is important for many cellular processes. The basic leucine-zipper (bZIP) transcription factors are one family of proteins for which coiled-coil mediated dimerization is essential for function, and misregulation of bZIPs can lead to disease states including cancer. This makes coiled coils attractive protein-protein interaction targets to disrupt using engineered molecules. Previous work designing peptides to compete with native coiled-coil interactions focused primarily on designing the core residues of the interface to achieve affinity and specificity. However, folding studies on the model bZIP GCN4 show that coiled-coil surface residues also contribute to binding affinity. Here we extend a prior study in which peptides were designed to bind tightly and specifically to representative members of each of 20 human bZIP families. These "anti-bZIP" peptides were designed with an emphasis on target-binding specificity, with contributions to design-target specificity and affinity engineered considering only the coiled-coil core residues. High-throughput testing using peptide arrays indicated many successes. We have now measured the binding affinities and specificities of anti-bZIPs that bind to FOS, XBP1, ATF6, and CREBZF in solution and tested whether redesigning the surface residues can increase design-target affinity. Incorporating residues that favor helix formation into the designs increased binding affinities in all cases, providing low-nanomolar binders of each target. However, changes in surface electrostatic interactions sometimes changed the binding specificity of the designed peptides. © 2014 The Protein Society.

(±)-Japonones A and B, two pairs of new enantiomers with anti-KSHV activities from Hypericum japonicum

NASA Astrophysics Data System (ADS)

Hu, Linzhen; Zhu, Hucheng; Li, Lei; Huang, Jinfeng; Sun, Weiguang; Liu, Junjun; Li, Hua; Luo, Zengwei; Wang, Jianping; Xue, Yongbo; Zhang, Yu; Zhang, Yonghui

2016-06-01

Two pairs of new enantiomers with unusual 5,5-spiroketal cores, termed (±)-japonones A and B [(±)-1 and (±)-2], were obtained from Hypericum japonicum Thunb. The absolute configurations of (±)-1 and (±)-2 were characterized by extensive analyses of spectroscopic data and calculated electronic circular dichroism (ECD) spectra, the application of modified Mosher’s methods, and the assistance of quantum chemical predictions (QCP) of 13C NMR chemical shifts. Among these metabolites, (+)-1 exhibited some inhibitory activity on Kaposi’s sarcoma associated herpesvirus (KSHV). Virtual screening of (±)-1 and (±)-2 were conducted using the Surflex-Dock module in the Sybyl software, and (+)-1 exhibited ability to bind with ERK to form key interactions with residues Lys52, Pro56, Ile101, Asp165, Gly167 and Val99.

Spiral wound extraction cartridge

DOEpatents

Wisted, Eric E.; Lundquist, Susan H.

1999-01-01

A cartridge device for removing an analyte from a fluid comprises a hollow core, a sheet composite comprising a particulate-loaded porous membrane and optionally at least one reinforcing spacer sheet, the particulate being capable of binding the analyte, the sheet composite being formed into a spiral configuration about the core, wherein the sheet composite is wound around itself and wherein the windings of sheet composite are of sufficient tightness so that adjacent layers are essentially free of spaces therebetween, two end caps which are disposed over the core and the lateral ends of the spirally wound sheet composite, and means for securing the end caps to the core, the end caps also being secured to the lateral ends of the spirally wound sheet composite. A method for removing an analyte from a fluid comprises the steps of providing a spirally wound element of the invention and passing the fluid containing the analyte through the element essentially normal to a surface of the sheet composite so as to bind the analyte to the particulate of the particulate-loaded porous membrane, the method optionally including the step of eluting the bound analyte from the sheet composite.

Detection of Hepatitis C core antibody by dual-affinity yeast chimera and smartphone-based electrochemical sensing.

PubMed

Aronoff-Spencer, Eliah; Venkatesh, A G; Sun, Alex; Brickner, Howard; Looney, David; Hall, Drew A

2016-12-15

Yeast cell lines were genetically engineered to display Hepatitis C virus (HCV) core antigen linked to gold binding peptide (GBP) as a dual-affinity biobrick chimera. These multifunctional yeast cells adhere to the gold sensor surface while simultaneously acting as a "renewable" capture reagent for anti-HCV core antibody. This streamlined functionalization and detection strategy removes the need for traditional purification and immobilization techniques. With this biobrick construct, both optical and electrochemical immunoassays were developed. The optical immunoassays demonstrated detection of anti-HCV core antibody down to 12.3pM concentrations while the electrochemical assay demonstrated higher binding constants and dynamic range. The electrochemical format and a custom, low-cost smartphone-based potentiostat ($20 USD) yielded comparable results to assays performed on a state-of-the-art electrochemical workstation. We propose this combination of synthetic biology and scalable, point-of-care sensing has potential to provide low-cost, cutting edge diagnostic capability for many pathogens in a variety of settings. Copyright © 2016 Elsevier B.V. All rights reserved.

The Effect of Lipopolysaccharide Core Oligosaccharide Size on the Electrostatic Binding of Antimicrobial Proteins to Models of the Gram Negative Bacterial Outer Membrane

PubMed Central

2016-01-01

Understanding the electrostatic interactions between bacterial membranes and exogenous proteins is crucial to designing effective antimicrobial agents against Gram-negative bacteria. Here we study, using neutron reflecometry under multiple isotopic contrast conditions, the role of the uncharged sugar groups in the outer core region of lipopolysaccharide (LPS) in protecting the phosphate-rich inner core region from electrostatic interactions with antimicrobial proteins. Models of the asymmetric Gram negative outer membrane on silicon were prepared with phopshatidylcholine (PC) in the inner leaflet (closest to the silicon), whereas rough LPS was used to form the outer leaflet (facing the bulk solution). We show how salt concentration can be used to reversibly alter the binding affinity of a protein antibiotic colicin N (ColN) to the anionic LPS confirming that the interaction is electrostatic in nature. By examining the interaction of ColN with two rough LPS types with different-sized core oligosaccharide regions we demonstrate the role of uncharged sugars in blocking short-range electrostatic interactions between the cationic antibiotics and the vulnerable anionic phosphate groups. PMID:27003358

Functional contributions of N- and O-glycans to L-selectin ligands in murine and human lymphoid organs.

PubMed

Arata-Kawai, Hanayo; Singer, Mark S; Bistrup, Annette; Zante, Annemieke van; Wang, Yang-Qing; Ito, Yuki; Bao, Xingfeng; Hemmerich, Stefan; Fukuda, Minoru; Rosen, Steven D

2011-01-01

L-selectin initiates lymphocyte interactions with high endothelial venules (HEVs) of lymphoid organs through binding to ligands with specific glycosylation modifications. 6-Sulfo sLe(x), a sulfated carbohydrate determinant for L-selectin, is carried on core 2 and extended core 1 O-glycans of HEV-expressed glycoproteins. The MECA-79 monoclonal antibody recognizes sulfated extended core 1 O-glycans and partially blocks lymphocyte-HEV interactions in lymphoid organs. Recent evidence has identified the contribution of 6-sulfo sLe(x) carried on N-glycans to lymphocyte homing in mice. Here, we characterize CL40, a novel IgG monoclonal antibody. CL40 equaled or surpassed MECA-79 as a histochemical staining reagent for HEVs and HEV-like vessels in mouse and human. Using synthetic carbohydrates, we found that CL40 bound to 6-sulfo sLe(x) structures, on both core 2 and extended core 1 structures, with an absolute dependency on 6-O-sulfation. Using transfected CHO cells and gene-targeted mice, we observed that CL40 bound its epitope on both N-glycans and O-glycans. Consistent with its broader glycan-binding, CL40 was superior to MECA-79 in blocking lymphocyte-HEV interactions in both wild-type mice and mice deficient in forming O-glycans. This superiority was more marked in human, as CL40 completely blocked lymphocyte binding to tonsillar HEVs, whereas MECA-79 inhibited only 60%. These findings extend the evidence for the importance of N-glycans in lymphocyte homing in mouse and indicate that this dependency also applies to human lymphoid organs. Copyright © 2011 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

Interaction of sigma factor sigmaN with Escherichia coli RNA polymerase core enzyme.

PubMed

Scott, D J; Ferguson, A L; Gallegos, M T; Pitt, M; Buck, M; Hoggett, J G

2000-12-01

The equilibrium binding and kinetics of assembly of the DNA-dependent RNA polymerase (RNAP) sigma(N)-holoenzyme has been investigated using biosynthetically labelled 7-azatryptophyl- (7AW)sigma(N). The spectroscopic properties of such 7AW proteins allows their absorbance and fluorescence to be monitored selectively, even in the presence of high concentrations of other tryptophan-containing proteins. The 7AWsigma(N) retained its biological activity in stimulating transcription from sigma(N)-specific promoters, and in in vitro gel electrophoresis assays of binding to core RNAP from Escherichia coli. Furthermore, five Trp-->Ala single mutants of sigma(N) were shown to support growth under conditions of nitrogen limitation, and showed comparable efficiency in activating the sigma(N)-dependent nifH promoter in vivo, indicating that none of the tryptophan residues were essential for activity. The equilibrium binding of 7AWsigma(N) to core RNAP was examined by analytical ultracentrifugation. In sedimentation equilibrium experiments, absorbance data at 315 nm (which reports selectively on the distribution of free and bound 7AWsigma(N)) established that a 1:1 complex was formed, with a dissociation constant lower than 2 microM. The kinetics of the interaction between 7AWsigma(N) and core RNAP was investigated using stopped-flow spectrofluorimetry. A biphasic decrease in fluorescence intensity was observed when samples were excited at 280 nm, whereas only the slower of the two phases was observed at 315 nm. The kinetic data were analysed in terms of a mechanism in which a fast bimolecular association of sigma(N) with core RNAP is followed by a relatively slow isomerization step. The consequences of these findings on the competition between sigma(N) and the major sigma factor, sigma(70), in Escherichia coli are discussed.

Interaction of sigma factor sigmaN with Escherichia coli RNA polymerase core enzyme.

PubMed Central

Scott, D J; Ferguson, A L; Gallegos, M T; Pitt, M; Buck, M; Hoggett, J G

2000-01-01

The equilibrium binding and kinetics of assembly of the DNA-dependent RNA polymerase (RNAP) sigma(N)-holoenzyme has been investigated using biosynthetically labelled 7-azatryptophyl- (7AW)sigma(N). The spectroscopic properties of such 7AW proteins allows their absorbance and fluorescence to be monitored selectively, even in the presence of high concentrations of other tryptophan-containing proteins. The 7AWsigma(N) retained its biological activity in stimulating transcription from sigma(N)-specific promoters, and in in vitro gel electrophoresis assays of binding to core RNAP from Escherichia coli. Furthermore, five Trp-->Ala single mutants of sigma(N) were shown to support growth under conditions of nitrogen limitation, and showed comparable efficiency in activating the sigma(N)-dependent nifH promoter in vivo, indicating that none of the tryptophan residues were essential for activity. The equilibrium binding of 7AWsigma(N) to core RNAP was examined by analytical ultracentrifugation. In sedimentation equilibrium experiments, absorbance data at 315 nm (which reports selectively on the distribution of free and bound 7AWsigma(N)) established that a 1:1 complex was formed, with a dissociation constant lower than 2 microM. The kinetics of the interaction between 7AWsigma(N) and core RNAP was investigated using stopped-flow spectrofluorimetry. A biphasic decrease in fluorescence intensity was observed when samples were excited at 280 nm, whereas only the slower of the two phases was observed at 315 nm. The kinetic data were analysed in terms of a mechanism in which a fast bimolecular association of sigma(N) with core RNAP is followed by a relatively slow isomerization step. The consequences of these findings on the competition between sigma(N) and the major sigma factor, sigma(70), in Escherichia coli are discussed. PMID:11085949

Bond-order potential for magnetic body-centered-cubic iron and its transferability

NASA Astrophysics Data System (ADS)

Lin, Yi-Shen; Mrovec, M.; Vitek, V.

2016-06-01

We derived and thoroughly tested a bond-order potential (BOP) for body-centered-cubic (bcc) magnetic iron that can be employed in atomistic calculations of a broad variety of crystal defects that control structural, mechanical, and thermodynamic properties of this technologically important metal. The constructed BOP reflects correctly the mixed nearly free electron and covalent bonding arising from the partially filled d band as well as the ferromagnetism that is actually responsible for the stability of the bcc structure of iron at low temperatures. The covalent part of the cohesive energy is determined within the tight-binding bond model with the Green's function of the Schrödinger equation determined using the method of continued fractions terminated at a sufficient level of the moments of the density of states. This makes the BOP an O (N ) method usable for very large numbers of particles. Only d d bonds are included explicitly, but the effect of s electrons on the covalent energy is included via their screening of the corresponding d d bonds. The magnetic part of the cohesive energy is included using the Stoner model of itinerant magnetism. The repulsive part of the cohesive energy is represented, as in any tight-binding scheme, by an empirical formula. Its functional form is physically justified by studies of the repulsion in face-centered-cubic (fcc) solid argon under very high pressure where the repulsion originates from overlapping s and p closed-shell electrons just as it does from closed-shell s electrons in transition metals squeezed into the ion core under the influence of the large covalent d bonding. Testing of the transferability of the developed BOP to environments significantly different from those of the ideal bcc lattice was carried out by studying crystal structures and magnetic states alternative to the ferromagnetic bcc lattice, vacancies, divacancies, self-interstitial atoms (SIAs), paths continuously transforming the bcc structure to different less symmetric structures and phonons. The results of these calculations are compared with either experiments or calculations based on the density functional theory (DFT), and they all show very good agreement. Importantly, the lowest energy configuration of SIAs agrees with DFT calculations that show that it is an exception within bcc transition metals controlled by magnetism. Moreover, the migration energy of interstitials is significantly lower than that of vacancies, which is essential for correct analysis of the effects of irradiation. Finally, the core structure and glide of ½ <111 > screw dislocations that control the plastic flow in single crystals of bcc metals was explored. The results fully agree with available DFT based studies and with experimental observations of the slip geometry of bcc iron at low temperatures.

Structural and compositional evolution of Al{sub 3}(Zr,Y) precipitates in Al-Zr-Y alloy

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

Gao, Haiyan, E-mail: gaohaiyan@sjtu.edu.cn

Structural and compositional evolution of Al{sub 3}(Zr,Y) precipitates in aged Al-Zr-Y alloy was investigated through atom probe tomography (APT) and transmission electron microscope (TEM) analysis and first principles calculations. The results show that short-bar-shaped D0{sub 19}-Al{sub 3}Y with some Zr atoms dissolved in precipitated at the very beginning of decomposition and worked as heterogeneous nuclei for L1{sub 2}-Al{sub 3}Zr with spherical morphology after being aged at 400 °C for 2 h. Quasi-static coarsening happened as the aging treatment lasted from 2 h to 200 h. However, distribution of Zr and Y atoms in Al{sub 3}(Zr,Y) is nearly uniform and Al{submore » 3}(Zr,Y) do not have the typical “Al{sub 3}RE core-Al{sub 3}Zr shell” structure which observed in other RE containing Al-Zr-RE alloys with L1{sub 2}-Al{sub 3}RE as nuclei. First principles calculations revealed that binding energy between Y and Zr is strong during the growth of Al{sub 3}(Zr,Y), which led to the co-precipitation of Y and Zr atoms and attribute to the evolution of Al{sub 3}(Zr,Y). - Highlights: •Al{sub 3}Y precipitated firstly and then became nuclei for Al{sub 3}Zr during aging of Al-Zr-Y. •Al{sub 3}(Zr,Y) precipitates do not have the typical “Al{sub 3}Y core-Al{sub 3}Zr shell” structure. •Strong binding between Y and Zr led to the co-precipitation of Y and Zr atoms.« less

Band line-up determination at p- and n-type Al/4H-SiC Schottky interfaces using photoemission spectroscopy

NASA Astrophysics Data System (ADS)

Kohlscheen, J.; Emirov, Y. N.; Beerbom, M. M.; Wolan, J. T.; Saddow, S. E.; Chung, G.; MacMillan, M. F.; Schlaf, R.

2003-09-01

The band lineup of p- and n-type 4H-SiC/Al interfaces was determined using x-ray photoemission spectroscopy (XPS). Al was deposited in situ on ex situ cleaned SiC substrates in several steps starting at 1.2 Å up to 238 Å nominal film thickness. Before growth and after each growth step, the sample surface was characterized in situ by XPS. The analysis of the spectral shifts indicated that during the initial deposition stages the Al films react with the ambient surface contamination layer present on the samples after insertion into vacuum. At higher coverage metallic Al clusters are formed. The band lineups were determined from the analysis of the core level peak shifts and the positions of the valence bands maxima (VBM) depending on the Al overlayer thickness. Shifts of the Si 2p and C 1s XPS core levels occurred to higher (lower) binding energy for the p-(n-)type substrates, which was attributed to the occurrence of band bending due to Fermi-level equilibration at the interface. The hole injection barrier at the p-type interface was determined to be 1.83±0.1 eV, while the n-type interface revealed an electron injection barrier of 0.98±0.1 eV. Due to the weak features in the SiC valence bands measured by XPS, the VBM positions were determined using the Si 2p peak positions. This procedure required the determination of the Si 2p-to-VBM binding energy difference (99.34 eV), which was obtained from additional measurements.

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.

Electronic Structure of TlBa2CaCu2O(7-Delta)

NASA Technical Reports Server (NTRS)

Vasquez, R. P.; Novikov, D. L.; Freeman, A. J.; Siegal, M. P.

1997-01-01

The core levels of TlBa2CaCu2O(7-delta) (Tl-1212) epitaxial films have been measured with X-ray photoelectron spectroscopy (XPS). The valence electronic structure has been determined using the full-potential linear muffin-tin-orbital band-structure method and measured with XPS. The calculations show that a van Hove singularity (VHS) lies above the Fermi level (E(sub F)) for the stoichiometric compound (delta = 0.5), while for 50% oxygen vacancies in the Tl-O layer (delta = 0.5) E(sub F) is in close proximity to the VHS. Samples annealed in nitrogen (to reduce the hole overdoping by the removal of oxygen) exhibit higher core-level binding energies and a higher T(sub c), consistent with a shift of E(sub F) closer to the VHS. Comparisons are made to the core levels and valence bands of Tl2Ba2CaCu2O(8 + delta)(Tl-2212) and HgBa2CaCu2O)6 + delta) (Hg- 1212). The similarity of the Cu 2p(sub 3/2) spectra for Tl-1212 and Tl-2212 indicates that the number of Tl-O layers has little effect on the Cu-O bonding. However, the Tl-1212 and Hg-1212 Cu 2p(sub 3/2) signals exhibit differences which suggest that the replacement of T(sup 3+) with Hg(sup 2+) results in a decrease in the O 2p right arrow Cu 3d charge-transfer energy and differences in the probabilities of planar vs apical oxygen charge transfer and/or Zhang-Rice singlet-state formation. Differences between the Tl-1212 and the Tl-2212 and Hg-1212 measured valence bands are consistent with the calculated Cu 3d and (Tl,Hg) 6s/5d partial densities of states.

Designing Superoxide-Generating Quantum Dots for Selective Light-Activated Nanotherapy

NASA Astrophysics Data System (ADS)

Goodman, Samuel M.; Levy, Max; Li, Fei-Fei; Ding, Yuchen; Courtney, Colleen M.; Chowdhury, Partha P.; Erbse, Annette; Chatterjee, Anushree; Nagpal, Prashant

2018-03-01

The rapid emergence of superbugs or multi-drug resistant (MDR) organisms has prompted a search for novel antibiotics, beyond traditional small-molecule therapies. Nanotherapeutics are being investigated as alternatives, and recently superoxide-generating quantum dots (QDs) have been shown as important candidates for selective light-activated therapy and potentiating existing antibiotics against MDR superbugs. Their therapeutic action is selective, can be tailored by simply changing their quantum-confined conduction-valence bands and their alignment with different redox half-reactions, and hence their ability to generate specific radical species in biological media. Here, we show the design of superoxide-generating QDs using optimal QD material and size well matched to superoxide redox potential, charged ligands to modulate their uptake in cells and selective redox interventions, and core/shell structures to improve their stability for therapeutic action. We show that cadmium telluride (CdTe) QDs with conduction band position at -0.5V with respect to Normal Hydrogen Electron (NHE) and visible 2.4 eV bandgap generate a large flux of selective superoxide radicals, thereby demonstrating the most effective light-activated therapy. Although the positively charged QDs demonstrate large cellular uptake, they bind indiscriminately to cell surfaces and cause non-selective cell death, while negatively charged and zwitterionic QD ligands reduce the uptake and allow selective therapeutic action via interaction with redox species. The stability of designed QDs in biologically-relevant media increases with the formation of core-shell QD structures, but an appropriate design of core-shell structures is needed to minimize any reduction in charge injection efficiency to adsorbed oxygen molecules (to form superoxide) and maintain similar quantitative generation of tailored redox species, as measured using electron paramagnetic resonance (EPR) spectroscopy and electrochemical impedance spectroscopy. Using these findings, we demonstrate the rational design of QDs as selective therapeutic kills more than 99% of priority class I pathogens, thus providing an effective therapy against MDR superbugs.

Designing Superoxide-Generating Quantum Dots for Selective Light-Activated Nanotherapy.

PubMed

Goodman, Samuel M; Levy, Max; Li, Fei-Fei; Ding, Yuchen; Courtney, Colleen M; Chowdhury, Partha P; Erbse, Annette; Chatterjee, Anushree; Nagpal, Prashant

2018-01-01

The rapid emergence of superbugs, or multi-drug resistant (MDR) organisms, has prompted a search for novel antibiotics, beyond traditional small-molecule therapies. Nanotherapeutics are being investigated as alternatives, and recently superoxide-generating quantum dots (QDs) have been shown as important candidates for selective light-activated therapy, while also potentiating existing antibiotics against MDR superbugs. Their therapeutic action is selective, can be tailored by simply changing their quantum-confined conduction-valence band (CB-VB) positions and alignment with different redox half-reactions-and hence their ability to generate specific radical species in biological media. Here, we show the design of superoxide-generating QDs using optimal QD material and size well-matched to superoxide redox potential, charged ligands to modulate their uptake in cells and selective redox interventions, and core/shell structures to improve their stability for therapeutic action. We show that cadmium telluride (CdTe) QDs with conduction band (CB) position at -0.5 V with respect to Normal Hydrogen Electron (NHE) and visible 2.4 eV bandgap generate a large flux of selective superoxide radicals, thereby demonstrating the effective light-activated therapy. Although the positively charged QDs demonstrate large cellular uptake, they bind indiscriminately to cell surfaces and cause non-selective cell death, while negatively charged and zwitterionic QD ligands reduce the uptake and allow selective therapeutic action via interaction with redox species. The stability of designed QDs in biologically-relevant media increases with the formation of core-shell QD structures, but an appropriate design of core-shell structures is needed to minimize any reduction in charge injection efficiency to adsorbed oxygen molecules (to form superoxide) and maintain similar quantitative generation of tailored redox species, as measured using electron paramagnetic resonance (EPR) spectroscopy and electrochemical impedance spectroscopy (EIS). Using these findings, we demonstrate the rational design of QDs as selective therapeutic to kill more than 99% of a priority class I pathogen, thus providing an effective therapy against MDR superbugs.

Biotin-decorated silica coated PbS nanocrystals emitting in the second biological near infrared window for bioimaging

NASA Astrophysics Data System (ADS)

Corricelli, M.; Depalo, N.; di Carlo, E.; Fanizza, E.; Laquintana, V.; Denora, N.; Agostiano, A.; Striccoli, M.; Curri, M. L.

2014-06-01

Nanoparticles (NPs) emitting in the second biological near infrared (NIR) window of the electromagnetic spectrum have been successfully synthesized by growing a silica shell on the hydrophobic surface of OLEA/TOP PbS nanocrystals (NCs), by means of a reverse microemulsion approach, and subsequently decorated with biotin molecules. The fabrication of very uniform and monodisperse NPs, formed of SiO2 shell coated single core PbS NCs, has been demonstrated by means of a set of complementary optical and structural techniques (Vis-NIR absorption and photoluminescence spectroscopy, transmission electron microscopy) that have highlighted how experimental parameters, such as PbS NC and silica precursor concentration, are crucial to direct the morphology and optical properties of silica coated PbS NPs. Subsequently, the silica surface of the core-shell NPs has been grafted with amino groups, in order to achieve covalent binding of biotin to NIR emitting silica coated NPs. Finally the successful reaction with a green-fluorescent labelled streptavidin has verified the molecular recognition response of the biotin molecules decorating the PbS@SiO2 NP surface. Dynamic light scattering (DLS) and ζ-potential techniques have been used to monitor the hydrodynamic diameter and colloidal stability of both PbS@SiO2 and biotin decorated NPs, showing their high colloidal stability in physiological media, as needed for biomedical applications. Remarkably the obtained biotinylated PbS@SiO2 NPs have been found to retain emission properties in the `second optical window' of the NIR region of the electromagnetic spectrum, thus representing attractive receptor-targeted NIR fluorescent probes for in vivo tumour imaging.Nanoparticles (NPs) emitting in the second biological near infrared (NIR) window of the electromagnetic spectrum have been successfully synthesized by growing a silica shell on the hydrophobic surface of OLEA/TOP PbS nanocrystals (NCs), by means of a reverse microemulsion approach, and subsequently decorated with biotin molecules. The fabrication of very uniform and monodisperse NPs, formed of SiO2 shell coated single core PbS NCs, has been demonstrated by means of a set of complementary optical and structural techniques (Vis-NIR absorption and photoluminescence spectroscopy, transmission electron microscopy) that have highlighted how experimental parameters, such as PbS NC and silica precursor concentration, are crucial to direct the morphology and optical properties of silica coated PbS NPs. Subsequently, the silica surface of the core-shell NPs has been grafted with amino groups, in order to achieve covalent binding of biotin to NIR emitting silica coated NPs. Finally the successful reaction with a green-fluorescent labelled streptavidin has verified the molecular recognition response of the biotin molecules decorating the PbS@SiO2 NP surface. Dynamic light scattering (DLS) and ζ-potential techniques have been used to monitor the hydrodynamic diameter and colloidal stability of both PbS@SiO2 and biotin decorated NPs, showing their high colloidal stability in physiological media, as needed for biomedical applications. Remarkably the obtained biotinylated PbS@SiO2 NPs have been found to retain emission properties in the `second optical window' of the NIR region of the electromagnetic spectrum, thus representing attractive receptor-targeted NIR fluorescent probes for in vivo tumour imaging. Electronic supplementary information (ESI) available: Size statistical analysis of silanized PbS NPs, TLC plate showing the ninhydrin test results and a table summarizing the DH and ζ-potential values for the investigated samples. See DOI: 10.1039/c4nr01025f

Two Aromatic Rings Coupled a Sulfur-Containing Group to Favor Protein Electron Transfer by Instantaneous Formations of π∴S:π↔π:S∴π or π∴π:S↔π:π∴S Five-Electron Bindings

PubMed Central

Sun, Weichao; Ren, Haisheng; Tao, Ye; Xiao, Dong; Qin, Xin; Deng, Li; Shao, Mengyao; Gao, Jiali; Chen, Xiaohua

2015-01-01

The cooperative interactions among two aromatic rings with a S-containing group are described, which may participate in electron hole transport in proteins. Ab initio calculations reveal the possibility for the formations of the π∴S:π↔π:S∴π and π∴π:S↔π:π∴S five-electron bindings in the corresponding microsurrounding structures in proteins, both facilitating electron hole transport as efficient relay stations. The relay functionality of these two special structures comes from their low local ionization energies and proper binding energies, which varies with the different aromatic amino acids, S-containing residues, and the arrangements of the same aromatic rings according to the local microsurroundings in proteins. PMID:26120374

Interaction of Hepatitis C Virus Core Protein with Janus Kinase Is Required for Efficient Production of Infectious Viruses

PubMed Central

Lee, Choongho

2013-01-01

Chronic hepatitis C virus (HCV) infection is responsible for the development of liver cirrhosis and hepatocellular carcinoma. HCV core protein plays not only a structural role in the virion morphogenesis by encapsidating a virus RNA genome but also a non-structural role in HCV-induced pathogenesis by blocking innate immunity. Especially, it has been shown to regulate JAK-STAT signaling pathway through its direct interaction with Janus kinase (JAK) via its proline-rich JAK-binding motif (79PGYPWP84). However, little is known about the physiological significance of this HCV core-JAK association in the context of the virus life cycle. In order to gain an insight, a mutant HCV genome (J6/JFH1-79A82A) was constructed to express the mutant core with a defective JAK-binding motif (79AGYAWP84) using an HCV genotype 2a infectious clone (J6/JFH1). When this mutant HCV genome was introduced into hepatocarcinoma cells, it was found to be severely impaired in its ability to produce infectious viruses in spite of its robust RNA genome replication. Taken together, all these results suggest an essential requirement of HCV core-JAK protein interaction for efficient production of infectious viruses and the potential of using core-JAK blockers as a new anti-HCV therapy. PMID:24009866

Conformational Entropy from NMR Relaxation in Proteins: The SRLS Perspective.

PubMed

Tchaicheeyan, Oren; Meirovitch, Eva

2017-02-02

Conformational entropy changes associated with bond-vector motions in proteins contribute to the free energy of ligand-binding. To derive such contributions, we apply the slowly relaxing local structure (SRLS) approach to NMR relaxation from 15 N-H bonds or C-CDH 2 moieties of several proteins in free and ligand-bound form. The spatial restraints on probe motion, which determine the extent of local order, are expressed in SRLS by a well-defined potential, u(θ). The latter yields the orientational probability density, P eq  = exp(-u(θ)), and hence the related conformational entropy, Ŝ = -∫P eq (θ) ln[P eq (θ)] sin θ dθ (Ŝ is "entropy" in units of k B T, and θ represents the bond-vector orientation in the protein). SRLS is applied to 4-oxalocrotonate tautomerase (4-OT), the acyl-coenzyme A binding protein (ACBP), the C-terminal SH2 domain of phospholipase C γ 1 (PLC γ 1C SH2), the construct dihydrofolate reductase-E:folate (DHFR-E:folate), and their complexes with appropriate ligands, to determine ΔŜ. Eglin C and its V18A and V34A mutants are also studied. Finally, SRLS is applied to the structurally homologous proteins TNfn3 and FNfn10 to characterize within its scope the unusual "dynamics" of the TNfn3 core. Upon ligand-binding, the backbones of 4-OT, ACBP, and PLC γ 1C SH2 show limited, increased, and decreased order, respectively; the cores of DHFR-E:folate and PLC γ 1C SH2 become more ordered. The V18A (V34A) mutation increases (decreases) the order within the eglin C core. The core of TNfn3 is less ordered structurally and more mobile kinetically. Secondary structure versus loops, surface-binding versus core insertion, and ligand size emerged as being important in rationalizing ΔŜ. The consistent and general tool developed herein is expected to provide further insights in future work.

Positron annihilation induced Auger electron spectroscopy

NASA Technical Reports Server (NTRS)

Weiss, Alex; Koymen, A. R.; Mehl, David; Jensen, K. O.; Lei, Chun; Lee, K. H.

1990-01-01

Recently, Weiss et al. have demonstrated that it is possible to excite Auger transitions by annihilating core electrons using a low energy (less than 30eV) beam of positrons. This mechanism makes possible a new electron spectroscopy, Positron annihilation induced Auger Electron Spectroscopy (PAES). The probability of exciting an Auger transition is proportional to the overlap of the positron wavefunction with atomic core levels. Since the Auger electron energy provides a signature of the atomic species making the transition, PAES makes it possible to determine the overlap of the positron wavefunction with a particular element. PAES may therefore provide a means of detecting positron-atom complexes. Measurements of PAES intensities from clean and adsorbate covered Cu surfaces are presented which indicate that approx. 5 percent of positrons injected into CU at 25eV produce core annihilations that result in Auger transitions.

Enhanced Electron Mobility in Nonplanar Tensile Strained Si Epitaxially Grown on SixGe1-x Nanowires.

PubMed

Wen, Feng; Tutuc, Emanuel

2018-01-10

We report the growth and characterization of epitaxial, coherently strained Si x Ge 1-x -Si core-shell nanowire heterostructure through vapor-liquid-solid growth mechanism for the Si x Ge 1-x core, followed by an in situ ultrahigh-vacuum chemical vapor deposition for the Si shell. Raman spectra acquired from individual nanowire reveal the Si-Si, Si-Ge, and Ge-Ge modes of the Si x Ge 1-x core and the Si-Si mode of the shell. Because of the compressive (tensile) strain induced by lattice mismatch, the core (shell) Raman modes are blue (red) shifted compared to those of unstrained bare Si x Ge 1-x (Si) nanowires, in good agreement with values calculated using continuum elasticity model coupled with lattice dynamic theory. A large tensile strain of up to 2.3% is achieved in the Si shell, which is expected to provide quantum confinement for electrons due to a positive core-to-shell conduction band offset. We demonstrate n-type metal-oxide-semiconductor field-effect transistors using Si x Ge 1-x -Si core-shell nanowires as channel and observe a 40% enhancement of the average electron mobility compared to control devices using Si nanowires due to an increased electron mobility in the tensile-strained Si shell.

Electronically cloaked nanoparticles

NASA Astrophysics Data System (ADS)

Shen, Wenqing

The concept of electronic cloaking is to design objects invisible to conduction electrons. The approach of electronic cloaking has been recently suggested to design invisible nanoparticle dopants with electronic scattering cross section smaller than 1% of the physical cross section (pi a2), and therefore to enhance the carrier mobility of bulk materials. The proposed nanoparticles have core-shell structures. The dopants are incorporated inside the core, while the shell layer serves both as a spacer to separate the charge carriers from their parent atoms and as a cloaking shell to minimize the scattering cross section of the electrons from the ionized nanoparticles. Thermoelectric materials are usually highly doped to have enough carrier density. Using invisible dopants could achieve larger thermoelectric power factors by enhancing the electronic mobility. Core-shell nanoparticles show an advantage over one-layer nanoparticles, which are proposed in three-dimensional modulation doping. However designing such nanoparticles is not easy as there are too many parameters to be considered. This thesis first shows an approach to design hollow nanoparticles by applying constrains on variables. In the second part, a simple mapping approach is introduced where one can identify possible core-shell particles by comparing the dimensionless parameters of chosen materials with provided maps. In both parts of this work, several designs with realistic materials were made and proven to achieve electronic cloaking. Improvement in the thermoelectric power factor compared to the traditional impurity doping method was demonstrated in several cases.

Hydrogenic impurity bound polaron in an anisotropic quantum dot

NASA Astrophysics Data System (ADS)

Chen, Shi-Hua

2018-01-01

The effect of the electron-phonon interaction on an electron bound to a hydrogenic impurity in a three-dimensional (3D) anisotropic quantum dot (QD) is studied theoretically. We use the Landau-Pekar variational approach to calculate the binding energy of ground state (GS) and first-excited state (ES) with considering electron-phonon interaction. The expressions of the GS and ES energies under investigation depict a rich variety of dependent relationship with the variational parameters in three different limiting cases. Numerical calculations were performed for ZnSe QDs with different confinement lengths in the xy-plane and the z-direction, respectively. It is illustrated that binding energies of impurity polarons corresponding to each level are larger in small QDs. Furthermore, the contribution to binding energy from phonon is about 15% of the total binding energy.

Binding and Energetics of Electron Transfer between an Artificial Four-Helix Mn-Protein and Reaction Centers from Rhodobacter sphaeroides.

PubMed

Espiritu, Eduardo; Olson, Tien L; Williams, JoAnn C; Allen, James P

2017-12-12

The ability of an artificial four-helix bundle Mn-protein, P1, to bind and transfer an electron to photosynthetic reaction centers from the purple bacterium Rhodobacter sphaeroides was characterized using optical spectroscopy. Upon illumination of reaction centers, an electron is transferred from P, the bacteriochlorophyll dimer, to Q A , the primary electron acceptor. The P1 Mn-protein can bind to the reaction center and reduce the oxidized bacteriochlorophyll dimer, P + , with a dissociation constant of 1.2 μM at pH 9.4, comparable to the binding constant of c-type cytochromes. Amino acid substitutions of surface residues on the Mn-protein resulted in increases in the dissociation constant to 8.3 μM. The extent of reduction of P + by the P1 Mn-protein was dependent on the P/P + midpoint potential and the pH. Analysis of the free energy difference yielded a midpoint potential of approximately 635 mV at pH 9.4 for the Mn cofactor of the P1 Mn-protein, a value similar to those found for other Mn cofactors in proteins. The linear dependence of -56 mV/pH is consistent with one proton being released upon Mn oxidation, allowing the complex to maintain overall charge neutrality. These outcomes demonstrate the feasibility of designing four-helix bundles and other artificial metalloproteins to bind and transfer electrons to bacterial reaction centers and establish the usefulness of this system as a platform for designing sites to bind novel metal cofactors capable of performing complex oxidation-reduction reactions.

Conformation of glycomimetics in the free and protein-bound state: structural and binding features of the C-glycosyl analogue of the core trisaccharide alpha-D-Man-(1 --> 3)-[alpha-D-Man-(1 --> 6)]-D-Man.

PubMed

Mikkelsen, Lise Munch; Hernáiz, María José; Martín-Pastor, M; Skrydstrup, Troels; Jiménez-Barbero, Jesús

2002-12-18

The conformational properties of the C-glycosyl analogue of the core trisaccharide alpha-D-Man-(1 --> 3)-[alpha-D-Man-(1 --> 6)]-D-Man in solution have been carefully analyzed by a combination of NMR spectroscopy and time-averaged restrained molecular dynamics. It has been found that both the alpha-1,3- and the alpha-1,6-glycosidic linkages show a major conformational averaging. Unusual Phi ca. 60 degrees orientations for both Phi torsion angles are found. Moreover, a major conformational distinction between the natural compound and the glycomimetic affects to the behavior of the omega(16) torsion angle around the alpha-1 --> 6-linkage. Despite this increased flexibility, the C-glycosyl analogue is recognized by three mannose binding lectins, as shown by NMR (line broadening, TR-NOE, and STD) and surface plasmon resonance (SPR) methods. Moreover, a process of conformational selection takes place, so that these lectins probably bind the glycomimetic similarly to the way they recognize the natural analogue. Depending upon the architecture and extension of the binding site of the lectin, loss or gain of binding affinity with respect to the natural analogue is found.

Smart multifunctional core-shell nanospheres with drug and gene co-loaded for enhancing the therapeutic effect in a rat intracranial tumor model

NASA Astrophysics Data System (ADS)

Wang, Hanjie; Su, Wenya; Wang, Sheng; Wang, Xiaomin; Liao, Zhenyu; Kang, Chunsheng; Han, Lei; Chang, Jin; Wang, Guangxiu; Pu, Peiyu

2012-09-01

Glioblastoma with high mortality has been one of the most serious cancers threatening human health. Because of the present treatment limitations, there is an urgent need to construct a multifunctional vesicle for enhancing the treatment of in situ malignant glioblastoma. In our study, drug and gene co-loaded magnetic PLGA/multifunctional polymeric liposome (magnetic PLGA/MPLs) core-shell nanospheres were constructed. They were mainly self-assembled from two parts: hydrophobic PLGA cores that can load drugs and magnetic nanocrystals; and polymeric lipid shells anchored with functional molecules such as PEG chains, TAT peptides and RGD peptides that can help the vectors to condense the gene, prolong the circulation time, cross the blood brain barrier and target delivery to the cancer tissue. The results showed that the magnetic PLGA/MPLs nanosphere has a nanosized core-shell structure, can achieve sustained drug release and has good DNA binding abilities. Importantly, compared with the control group and other groups with single functionality, it can co-deliver the drug and gene into the same cell in vitro and show the strongest inhibiting effect on the growth of the in situ malignant glioblastoma in vivo. All of these results indicated that the different functional components of magnetic PLGA/MPLs, can form an organic whole and none of them can be dispensed with. The magnetic PLGA/MPLs nanosphere may be another option for treatment of glioblastoma.Glioblastoma with high mortality has been one of the most serious cancers threatening human health. Because of the present treatment limitations, there is an urgent need to construct a multifunctional vesicle for enhancing the treatment of in situ malignant glioblastoma. In our study, drug and gene co-loaded magnetic PLGA/multifunctional polymeric liposome (magnetic PLGA/MPLs) core-shell nanospheres were constructed. They were mainly self-assembled from two parts: hydrophobic PLGA cores that can load drugs and magnetic nanocrystals; and polymeric lipid shells anchored with functional molecules such as PEG chains, TAT peptides and RGD peptides that can help the vectors to condense the gene, prolong the circulation time, cross the blood brain barrier and target delivery to the cancer tissue. The results showed that the magnetic PLGA/MPLs nanosphere has a nanosized core-shell structure, can achieve sustained drug release and has good DNA binding abilities. Importantly, compared with the control group and other groups with single functionality, it can co-deliver the drug and gene into the same cell in vitro and show the strongest inhibiting effect on the growth of the in situ malignant glioblastoma in vivo. All of these results indicated that the different functional components of magnetic PLGA/MPLs, can form an organic whole and none of them can be dispensed with. The magnetic PLGA/MPLs nanosphere may be another option for treatment of glioblastoma. Electronic supplementary information (ESI) available. See DOI: 10.1039/c2nr31263h

Ex(2)Box: interdependent modes of binding in a two-nanometer-long synthetic receptor.

PubMed

Juríček, Michal; Barnes, Jonathan C; Dale, Edward J; Liu, Wei-Guang; Strutt, Nathan L; Bruns, Carson J; Vermeulen, Nicolaas A; Ghooray, Kala C; Sarjeant, Amy A; Stern, Charlotte L; Botros, Youssry Y; Goddard, William A; Stoddart, J Fraser

2013-08-28

Incorporation of two biphenylene-bridged 4,4'-bipyridinium extended viologen units into a para-phenylene-based cyclophane results in a synthetic receptor that is ~2 nm long and adopts a box-like geometry. This cyclophane, Ex(2)Box(4+), possesses the ability to form binary and ternary complexes with a myriad of guest molecules ranging from long π-electron-rich polycyclic aromatic hydrocarbons, such as tetracene, tetraphene, and chrysene, to π-electron-poor 2,6-dinitrotoluene, 1,2,4-trichlorobenzene, and both the 9,10- and 1,4-anthraquinone molecules. Moreover, Ex(2)Box(4+) is capable of forming one-to-one complexes with polyether macrocycles that consist of two π-electron-rich dioxynaphthalene units, namely, 1,5-dinaphtho[38]crown-10. This type of broad molecular recognition is possible because the electronic constitution of Ex(2)Box(4+) is such that the pyridinium rings located at the "ends" of the cyclophane are electron-poor and prefer to enter into donor-acceptor interactions with π-electron-rich guests, while the "middle" of the cyclophane, consisting of the biphenylene spacer, is more electron-rich and can interact with π-electron-poor guests. In some cases, these different modes of binding can act in concert to generate one-to-one complexes which possess high stability constants in organic media. The binding affinity of Ex(2)Box(4+) was investigated in the solid state by way of single-crystal X-ray diffraction and in solution by using UV-vis and NMR spectroscopy for 12 inclusion complexes consisting of the tetracationic cyclophane and the corresponding guests of different sizes, shapes, and electronic compositions. Additionally, density functional theory was carried out to elucidate the relative energetic differences between the different modes of binding of Ex(2)Box(4+) with anthracene, 9,10-anthraquinone, and 1,4-anthraquinone in order to understand the degree with which each mode of binding contributes to the overall encapsulation of each guest.

Structural comparison of four different antibodies interacting with human papillomavirus 16 and mechanisms of neutralization

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

Guan, Jian; Bywaters, Stephanie M.; Brendle, Sarah A.

2015-09-15

Cryo-electron microscopy (cryo-EM) was used to solve the structures of human papillomavirus type 16 (HPV16) complexed with fragments of antibody (Fab) from three different neutralizing monoclonals (mAbs): H16.1A, H16.14J, and H263.A2. The structure-function analysis revealed predominantly monovalent binding of each Fab with capsid interactions that involved multiple loops from symmetry related copies of the major capsid protein. The residues identified in each Fab-virus interface map to a conformational groove on the surface of the capsomer. In addition to the known involvement of the FG and HI loops, the DE loop was also found to constitute the core of each epitope.more » Surprisingly, the epitope mapping also identified minor contributions by EF and BC loops. Complementary immunological assays included mAb and Fab neutralization. The specific binding characteristics of mAbs correlated with different neutralizing behaviors in pre- and post-attachment neutralization assays. - Highlights: • We present HPV16-Fab complexes from neutralizing mAbs: H16.1A, H16.14J, and H263.A2. • The structure-function analysis revealed predominantly monovalent binding of each mAb. • Capsid–Fab interactions involved multiple loops from symmetry related L1 proteins. • Besides the known FG and HI loops, epitope mapping also identified DE, EF, and BC loops. • Neutralizing assays complement the structures to show multiple neutralization mechanisms.« less

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.

Single d-metal atoms on F(s) and F(s+) defects of MgO(001): a theoretical study across the periodic table.

PubMed

Neyman, Konstantin M; Inntam, Chan; Matveev, Alexei V; Nasluzov, Vladimir A; Rösch, Notker

2005-08-24

Single d-metal atoms on oxygen defects F(s) and F(s+) of the MgO(001) surface were studied theoretically. We employed an accurate density functional method combined with cluster models, embedded in an elastic polarizable environment, and we applied two gradient-corrected exchange-correlation functionals. In this way, we quantified how 17 metal atoms from groups 6-11 of the periodic table (Cu, Ag, Au; Ni, Pd, Pt; Co, Rh, Ir; Fe, Ru, Os; Mn, Re; and Cr, Mo, W) interact with terrace sites of MgO. We found bonding with F(s) and F(s+) defects to be in general stronger than that with O2- sites, except for Mn-, Re-, and Fe/F(s) complexes. In M/F(s) systems, electron density is accumulated on the metal center in a notable fashion. The binding energy on both kinds of O defects increases from 3d- to 4d- to 5d-atoms of a given group, at variance with the binding energy trend established earlier for the M/O2- complexes, 4d < 3d < 5d. Regarding the evolution of the binding energy along a period, group 7 atoms are slightly destabilized compared to their group 6 congeners in both the F(s) and F(s+) complexes; for later transition elements, the binding energy increases gradually up to group 10 and finally decreases again in group 11, most strongly on the F(s) site. This trend is governed by the negative charge on the adsorbed atoms. We discuss implications for an experimental detection of metal atoms on oxide supports based on computed core-level energies.

Ultra-High-Contrast Laser Acceleration of Relativistic Electrons in Solid Targets

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

Higginson, Drew Pitney

2013-01-01

The cone-guided fast ignition approach to Inertial Con nement Fusion requires laser-accelerated relativistic electrons to deposit kilojoules of energy within an imploded fuel core to initiate fusion burn. One obstacle to coupling electron energy into the core is the ablation of material, known as preplasma, by laser energy proceeding nanoseconds prior to the main pulse. This causes the laser-absorption surface to be pushed back hundreds of microns from the initial target surface; thus increasing the distance that electrons must travel to reach the imploded core. Previous experiments have shown an order of magnitude decrease in coupling into surrogate targets whenmore » intentionally increasing the amount of preplasma. Additionally, for electrons to deposit energy within the core, they should have kinetic energies on the order of a few MeV, as less energetic electrons will be stopped prior to the core and more energetic electrons will pass through the core without depositing much energy. Thus a quantitative understanding of the electron energy spectrum and how it responds to varied laser parameters is paramount for fast ignition. For the rst time, this dissertation quantitatively investigates the acceleration of electrons using an ultra-high-contrast laser. Ultra-high-contrast lasers reduce the laser energy that reaches the target prior to the main pulse; drastically reducing the amount of preplasma. Experiments were performed in a cone-wire geometry relevant to fast ignition. These experiments irradiated the inner-tip of a Au cone with the laser and observed electrons that passed through a Cu wire attached to the outer-tip of the cone. The total emission of K x-rays is used as a diagnostic to infer the electron energy coupled into the wire. Imaging the x-ray emission allowed an e ective path-length of electrons within the wire to be determined, which constrained the electron energy spectrum. Experiments were carried out on the ultra-high-contrast Trident laser at Los Alamos National Laboratory and at the low-contrast Titan laser at Lawrence Livermore National Laboratory. The targets were irradiated using these 1.054 μm wavelength lasers at intensities from 1019 to 1020 W/cm2. The coupling of energy into the Cu wire was found to be 2.7x higher when the preplasma was reduced using high-contrast. Additionally, higher laser intensity elongated the e ective path-length of electrons within the wire, indicating that their kinetic energy was higher.« less

Probing electronic binding potentials with attosecond photoelectron wavepackets

NASA Astrophysics Data System (ADS)

Kiesewetter, D.; Jones, R. R.; Camper, A.; Schoun, S. B.; Agostini, P.; Dimauro, L. F.

2018-01-01

The central goal of attosecond science is to visualize, understand and ultimately control electron dynamics in matter over the fastest relevant timescales. To date, numerous schemes have demonstrated exquisite temporal resolution, on the order of ten attoseconds, in measurements of the response of photo-excited electrons to time-delayed probes. However, attributing this response to specific dynamical mechanisms is difficult, requiring guidance from advanced calculations. Here we show that energy transfer between an oscillating field and low-energy attosecond photoelectron wavepackets directly provides coarse-grained information on the effective binding potential from which the electrons are liberated. We employ a dense extreme ultraviolet (XUV) harmonic comb to photoionize He, Ne and Ar atoms and record the electron spectra as a function of the phase of a mid-infrared dressing field. The amplitude and phase of the resulting interference modulations in the electron spectra reveal the average momentum and change in momentum of the electron wavepackets during the first quarter-period of the dressing field after their creation, reflecting the corresponding coarse characteristics of the binding potential.

Renormalization of myoglobin–ligand binding energetics by quantum many-body effects

PubMed Central

Weber, Cédric; Cole, Daniel J.; O’Regan, David D.; Payne, Mike C.

2014-01-01

We carry out a first-principles atomistic study of the electronic mechanisms of ligand binding and discrimination in the myoglobin protein. Electronic correlation effects are taken into account using one of the most advanced methods currently available, namely a linear-scaling density functional theory (DFT) approach wherein the treatment of localized iron 3d electrons is further refined using dynamical mean-field theory. This combination of methods explicitly accounts for dynamical and multireference quantum physics, such as valence and spin fluctuations, of the 3d electrons, while treating a significant proportion of the protein (more than 1,000 atoms) with DFT. The computed electronic structure of the myoglobin complexes and the nature of the Fe–O2 bonding are validated against experimental spectroscopic observables. We elucidate and solve a long-standing problem related to the quantum-mechanical description of the respiration process, namely that DFT calculations predict a strong imbalance between O2 and CO binding, favoring the latter to an unphysically large extent. We show that the explicit inclusion of the many-body effects induced by the Hund’s coupling mechanism results in the correct prediction of similar binding energies for oxy- and carbonmonoxymyoglobin. PMID:24717844

Green synthesis of CuInS2/ZnS core-shell quantum dots by facile solvothermal route with enhanced optical properties

NASA Astrophysics Data System (ADS)

Jindal, Shikha; Giripunje, Sushama M.; Kondawar, Subhash B.; Koinkar, Pankaj

2018-03-01

We report an eco-friendly green synthesis of highly luminescent CuInS2/ZnS core-shell quantum dots (QDs) with average particle size ∼ 3.9 nm via solvothermal process. The present study embodies the intensification of CuInS2/ZnS QDs properties by the shell growth on the CuInS2 QDs. The as-prepared CuInS2 core and CuInS2/ZnS core-shell QDs have been characterized using a range of optical and structural techniques. By adopting a low temperature growth of CuInS2 core and high temperature growth of CuInS2/ZnS core-shell growth, the tuning of absorption and photoluminescence emission spectra were observed. Optical absorption and photoluminescence spectroscopy probe the effect of ZnS passivation on the electronic structure of the CuInS2 dots. In addition, QDs have been scrutinized using ultra violet photoelectron spectroscopy (UPS) to explore their electronic band structure. The band level positions of CuInS2 and CuInS2/ZnS QDs suffices the demand of non-toxic acceptor material for electronic devices. The variation in electronic energy levels of CuInS2 core with the coating of wide band gap ZnS shell influence the removal of trap assisted recombination on the surface of the core. QDs exhibited tunable emission from red to orange region. These studies reveal the feasibility of QDs in photovoltaic and light emitting diodes.

Changes in divertor conditions in response to changing core density with RMPs

DOE PAGES

Briesemeister, Alexis R.; Ahn, Joon -Wook; Canik, John M.; ...

2017-06-07

The effects of changes in core density on divertor electron temperature, density and heat flux when resonant magnetic perturbations (RMPs) are applied are presented, notably a reduction in RMP induced secondary radial peaks in the electron temperature profile at the target plate is observed when the core density is increased, which is consistent with modeling. RMPs is used here to indicated non-axisymmetric magnetic field perturbations, created using in-vessel control coils, which have components which has at least one but typically many resonances with the rotational transform of the plasma. RMPs are found to alter inter-ELM heat flux to the divertormore » by modifying the core plasma density. It is shown that applying RMPs reduces the core density and increases the inter-ELM heat flux to both the inner and outer targets. Using gas puffing to return the core density to the pre-RMP levels more than eliminates the increase in inter-ELM heat flux, but a broadening of the heat flux to the outer target remains. These measurements were made at a single toroidal location, but the peak in the heat flux profile was found near the outer strike point where simulations indicate little toroidal variation should exist and tangentially viewing diagnostics showed no evidence of strong asymmetries. In experiments where divertor Thomson scattering measurements were available it is shown that, local secondary peaks in the divertor electron temperature profile near the target plate are reduced as the core density is increased, while peaks in the divertor electron density profile near the target are increased. Furthermore, these trends observed in the divertor electron temperature and density are qualitatively reproduced by scanning the upstream density in EMC3-Eirene modeling. Measurements are presented showing that higher densities are needed to induce detachment of the outer strike point in a case where an increase in electron temperature, likely due to a change in MHD activity, is seen after RMPs are applied.« less

Changes in divertor conditions in response to changing core density with RMPs

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

Briesemeister, Alexis R.; Ahn, Joon -Wook; Canik, John M.

The effects of changes in core density on divertor electron temperature, density and heat flux when resonant magnetic perturbations (RMPs) are applied are presented, notably a reduction in RMP induced secondary radial peaks in the electron temperature profile at the target plate is observed when the core density is increased, which is consistent with modeling. RMPs is used here to indicated non-axisymmetric magnetic field perturbations, created using in-vessel control coils, which have components which has at least one but typically many resonances with the rotational transform of the plasma. RMPs are found to alter inter-ELM heat flux to the divertormore » by modifying the core plasma density. It is shown that applying RMPs reduces the core density and increases the inter-ELM heat flux to both the inner and outer targets. Using gas puffing to return the core density to the pre-RMP levels more than eliminates the increase in inter-ELM heat flux, but a broadening of the heat flux to the outer target remains. These measurements were made at a single toroidal location, but the peak in the heat flux profile was found near the outer strike point where simulations indicate little toroidal variation should exist and tangentially viewing diagnostics showed no evidence of strong asymmetries. In experiments where divertor Thomson scattering measurements were available it is shown that, local secondary peaks in the divertor electron temperature profile near the target plate are reduced as the core density is increased, while peaks in the divertor electron density profile near the target are increased. Furthermore, these trends observed in the divertor electron temperature and density are qualitatively reproduced by scanning the upstream density in EMC3-Eirene modeling. Measurements are presented showing that higher densities are needed to induce detachment of the outer strike point in a case where an increase in electron temperature, likely due to a change in MHD activity, is seen after RMPs are applied.« less

Electronic and Optical Properties of Core/Shell Pb16X16/Cd52X52 (X =S, Se, Te) Quantum Dots

NASA Astrophysics Data System (ADS)

Tamukong, Patrick; Mayo, Michael; Kilina, Svetlana

2015-03-01

The electronic and optoelectronic properties of semiconductor quantum dots (QDs) are mediated by surface defects due to the presence of dangling bonds producing trap states within the HOMO-LUMO energy gap, and contributing to fluorescence quenching. Surface capping ligands are generally used to alleviate this problem and increase the quantum yields of QDs. An alternative way is to synthesize core-shell QD structures; i.e., a QD core with a shell of another semiconductor material. We have investigated the effects of Cd52X52 shells on the photoexcited dynamics of Pb16X16 (X =S, Se, Te) QDs. The thin (~ 0.50 nm) shells were found to result largely in type I core/shell structures and a blue shift of the absorption spectra. Our studies revealed fairly strong core-shell hybridization in the electronic states close to the conduction band (CB) edge for Pb16S16andPb16Se16 cores, whereas for the Pb16Te16 core, such CB states were largely shell-like in nature. Nonadiabatic DFT-based dynamics, coupled with the surface hopping method, was used to study the effects of the core and shell compositions on energy relaxation rates in these systems.

The effects of the chemical composition and strain on the electronic properties of GaSb/InAs core-shell nanowires

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

Ning, Feng; Wang, Dan; Tang, Li-Ming, E-mail: lmtang@hnu.edu.cn

2014-09-07

The effects of the chemical composition and strain on the electronic properties of [111] zinc-blende (ZB) and [0001] wurtzite (WZ) GaSb/InAs core-shell nanowires (NWs) with different core diameters and shell thicknesses are studied using first-principles methods. The band structures of the [111] ZB GaSb/InAs core-shell NWs underwent a noticeable type-I/II band alignment transition, associated with a direct-to-indirect band gap transition under a compressive uniaxial strain. The band structures of the [0001] WZ GaSb/InAs core-shell NWs preserved the direct band gap under either compressive or tensile uniaxial strains. In addition, the band gaps and the effective masses of the carriers couldmore » be tuned by their composition. For the core-shell NWs with a fixed GaSb-core size, the band gaps decreased linearly with an increasing InAs-shell thickness, caused by the significant downshift of the conduction bands. For the [111] ZB GaSb/InAs core-shell NWs, the calculated effective masses indicated that the transport properties could be changed from hole-dominated conduction to electron-dominated conduction by changing the InAs-shell thickness.« less

A distal point mutation in the streptavidin-biotin complex preserves structure but diminishes binding affinity: experimental evidence of electronic polarization effects?

PubMed

Baugh, Loren; Le Trong, Isolde; Cerutti, David S; Gülich, Susanne; Stayton, Patrick S; Stenkamp, Ronald E; Lybrand, Terry P

2010-06-08

We have identified a distal point mutation in streptavidin that causes a 1000-fold reduction in biotin binding affinity without disrupting the equilibrium complex structure. The F130L mutation creates a small cavity occupied by a water molecule; however, all neighboring side chain positions are preserved, and protein-biotin hydrogen bonds are unperturbed. Molecular dynamics simulations reveal a reduced mobility of biotin binding residues but no observable destabilization of protein-ligand interactions. Our combined structural and computational studies suggest that the additional water molecule may affect binding affinity through an electronic polarization effect that impacts the highly cooperative hydrogen bonding network in the biotin binding pocket.

Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1

DOE PAGES

Michael, Alicia K.; Fribourgh, Jennifer L.; Chelliah, Yogarany; ...

2017-01-31

The basic helix-loop-helix PAS domain (bHLH-PAS) transcription factor CLOCK:BMAL1 (brain and muscle Arnt-like protein 1) sits at the core of the mammalian circadian transcription/translation feedback loop. Precise control of CLOCK:BMAL1 activity by coactivators and repressors establishes the ~24-h periodicity of gene expression. Formation of a repressive complex, defined by the core clock proteins cryptochrome 1 (CRY1):CLOCK:BMAL1, plays an important role controlling the switch from repression to activation each day. Here in this paper, we show that CRY1 binds directly to the PAS domain core of CLOCK: BMAL1, driven primarily by interaction with the CLOCK PAS-B domain. Integrative modeling and solutionmore » X-ray scattering studies unambiguously position a key loop of the CLOCK PAS-B domain in the secondary pocket of CRY1, analogous to the antenna chromophore-binding pocket of photolyase. CRY1 docks onto the transcription factor alongside the PAS domains, extending above the DNA-binding bHLH domain. Single point mutations at the interface on either CRY1 or CLOCK disrupt formation of the ternary complex, highlighting the importance of this interface for direct regulation of CLOCK:BMAL1 activity by CRY1.« less

CORE-COLLAPSE SUPERNOVA EQUATIONS OF STATE BASED ON NEUTRON STAR OBSERVATIONS

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

Steiner, A. W.; Hempel, M.; Fischer, T.

2013-09-01

Many of the currently available equations of state for core-collapse supernova simulations give large neutron star radii and do not provide large enough neutron star masses, both of which are inconsistent with some recent neutron star observations. In addition, one of the critical uncertainties in the nucleon-nucleon interaction, the nuclear symmetry energy, is not fully explored by the currently available equations of state. In this article, we construct two new equations of state which match recent neutron star observations and provide more flexibility in studying the dependence on nuclear matter properties. The equations of state are also provided in tabularmore » form, covering a wide range in density, temperature, and asymmetry, suitable for astrophysical simulations. These new equations of state are implemented into our spherically symmetric core-collapse supernova model, which is based on general relativistic radiation hydrodynamics with three-flavor Boltzmann neutrino transport. The results are compared with commonly used equations of state in supernova simulations of 11.2 and 40 M{sub Sun} progenitors. We consider only equations of state which are fitted to nuclear binding energies and other experimental and observational constraints. We find that central densities at bounce are weakly correlated with L and that there is a moderate influence of the symmetry energy on the evolution of the electron fraction. The new models also obey the previously observed correlation between the time to black hole formation and the maximum mass of an s = 4 neutron star.« less

Core-valence stockholder AIM analysis and its connection to nonadiabatic effects in small molecules.

PubMed

Amaral, Paulo H R; Mohallem, José R

2017-05-21

A previous theory of separation of motions of core and valence fractions of electrons in a molecule [J. R. Mohallem et al., Chem. Phys. Lett. 501, 575 (2011)] is invoked as basis for the useful concept of Atoms-in-Molecules (AIM) in the stockholder scheme. The output is a new tool for the analysis of the chemical bond that identifies core and valence electron density fractions (core-valence stockholder AIM (CVSAIM)). One-electron effective potentials for each atom are developed, which allow the identification of the parts of the AIM which move along with the nuclei (cores). This procedure results in a general method for obtaining effective masses that yields accurate non-adiabatic corrections to vibrational energies, necessary to attain cm -1 accuracy in molecular spectroscopy. The clear-cut determination of the core masses is exemplified for either homonuclear (H 2 + , H 2 ) or heteronuclear (HeH + , LiH) molecules. The connection of CVSAIM with independent physically meaningful quantities can resume the question of whether they are observable or not.

Core-valence stockholder AIM analysis and its connection to nonadiabatic effects in small molecules

PubMed Central

Amaral, Paulo H. R.; Mohallem, José R.

2017-01-01

A previous theory of separation of motions of core and valence fractions of electrons in a molecule [J. R. Mohallem et al., Chem. Phys. Lett. 501, 575 (2011)] is invoked as basis for the useful concept of Atoms-in-Molecules (AIM) in the stockholder scheme. The output is a new tool for the analysis of the chemical bond that identifies core and valence electron density fractions (core-valence stockholder AIM (CVSAIM)). One-electron effective potentials for each atom are developed, which allow the identification of the parts of the AIM which move along with the nuclei (cores). This procedure results in a general method for obtaining effective masses that yields accurate non-adiabatic corrections to vibrational energies, necessary to attain cm−1 accuracy in molecular spectroscopy. The clear-cut determination of the core masses is exemplified for either homonuclear (H2+, H2) or heteronuclear (HeH+, LiH) molecules. The connection of CVSAIM with independent physically meaningful quantities can resume the question of whether they are observable or not. PMID:28527456

The Rydberg electronic transitions of the hydrogen molecule

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

Babb, J.F.; Chang, E.S.

1992-01-01

Transition energies and relative line strengths, without Boltzmann weighting, for the electric dipole transitions between Rydberg states n{prime}L{prime} and nL of the hydrogen molecule (one electron in a near-hydrogenic state of high n and L, with n the principal quantum number and L the orbital angular momentum quantum number of the electron) are calculated. Since the H{sup +}{sub 2} core is loosely coupled to the Rydberg electron, numerous lines occur, depending on the vector sum of L and the core rotational angular momentum. For the core vibrational quantum numbers v = 0 to 5 the strongest lines among the P,more » Q, and R branches for the lowest 12 core rotational levels are given for the particular transition arrays 6h-5g, 8i-6h, 7i-6h, 8k-7i, and 9l-8k, for which transitions occur in the wave number range 350 to 1,400 cm {sup {minus}1}.« less

A two-pronged structural analysis of retroviral maturation indicates that core formation proceeds by a disassembly-reassembly pathway rather than a displacive transition.

PubMed

Keller, Paul W; Huang, Rick K; England, Matthew R; Waki, Kayoko; Cheng, Naiqian; Heymann, J Bernard; Craven, Rebecca C; Freed, Eric O; Steven, Alasdair C

2013-12-01

Retrovirus maturation involves sequential cleavages of the Gag polyprotein, initially arrayed in a spherical shell, leading to formation of capsids with polyhedral or conical morphology. Evidence suggests that capsids assemble de novo inside maturing virions from dissociated capsid (CA) protein, but the possibility persists of a displacive pathway in which the CA shell remains assembled but is remodeled. Inhibition of the final cleavage between CA and spacer peptide SP1/SP blocks the production of mature capsids. We investigated whether retention of SP might render CA assembly incompetent by testing the ability of Rous sarcoma virus (RSV) CA-SP to assemble in vitro into icosahedral capsids. Capsids were indeed assembled and were indistinguishable from those formed by CA alone, indicating that SP was disordered. We also used cryo-electron tomography to characterize HIV-1 particles produced in the presence of maturation inhibitor PF-46396 or with the cleavage-blocking CA5 mutation. Inhibitor-treated virions have a shell that resembles the CA layer of the immature Gag shell but is less complete. Some CA protein is generated but usually not enough for a mature core to assemble. We propose that inhibitors like PF-46396 bind to the Gag lattice where they deny the protease access to the CA-SP1 cleavage site and prevent the release of CA. CA5 particles, which exhibit no cleavage at the CA-SP1 site, have spheroidal shells with relatively thin walls. It appears that this lattice progresses displacively toward a mature-like state but produces neither conical cores nor infectious virions. These observations support the disassembly-reassembly pathway for core formation.

Towards well-defined gold nanomaterials via diafiltration and aptamer mediated synthesis

NASA Astrophysics Data System (ADS)

Sweeney, Scott Francis

Gold nanoparticles have garnered recent attention due to their intriguing size- and shape-dependent properties. Routine access to well-defined gold nanoparticle samples in terms of core diameter, shape, peripheral functionality and purity is required in order to carry out fundamental studies of their properties and to utilize these properties in future applications. For this reason, the development of methods for preparing well-defined gold nanoparticle samples remains an area of active research in materials science. In this dissertation, two methods, diafiltration and aptamer mediated synthesis, are explored as possible routes towards well-defined gold nanoparticle samples. It is shown that diafiltration has considerable potential for the efficient and convenient purification and size separation of water-soluble nanoparticles. The suitability of diafiltration for (i) the purification of water-soluble gold nanoparticles, (ii) the separation of a bimodal distribution of nanoparticles into fractions, (iii) the fractionation of a polydisperse sample and (iv) the isolation of [rimers from monomers and aggregates is studied. NMR, thermogravimetric analysis (TGA), and X-ray photoelectron spectroscopy (XPS) measurements demonstrate that diafiltration produces highly pure nanoparticles. UV-visible spectroscopic and transmission electron microscopic analyses show that diafiltration offers the ability to separate nanoparticles of disparate core size, including linked nanoparticles. These results demonstrate the applicability of diafiltration for the rapid and green preparation of high-purity gold nanoparticle samples and the size separation of heterogeneous nanoparticle samples. In the second half of the dissertation, the identification of materials specific aptamers and their use to synthesize shaped gold nanoparticles is explored. The use of in vitro selection for identifying materials specific peptide and oligonucleotide aptamers is reviewed, outlining the specific requirements of in vitro selection for materials and the ways in which the field can be advanced. A promising new technique, in vitro selection on surfaces (ISOS), is developed and the discovery using ISOS of RNA aptamers that bind to evaporated gold is discussed. Analysis of the isolated gold binding RNA aptamers indicates that they are highly structured with single-stranded polyadenosine binding motifs. These aptamers, and similarly isolated peptide aptamers, are briefly explored for their ability to synthesize gold nanoparticles. This dissertation contains both previously published and unpublished co-authored material.

Core Histones and HIRIP3, a Novel Histone-Binding Protein, Directly Interact with WD Repeat Protein HIRA

PubMed Central

Lorain, Stéphanie; Quivy, Jean-Pierre; Monier-Gavelle, Frédérique; Scamps, Christine; Lécluse, Yann; Almouzni, Geneviève; Lipinski, Marc

1998-01-01

The human HIRA gene has been named after Hir1p and Hir2p, two corepressors which together appear to act on chromatin structure to control gene transcription in Saccharomyces cerevisiae. HIRA homologs are expressed in a regulated fashion during mouse and chicken embryogenesis, and the human gene is a major candidate for the DiGeorge syndrome and related developmental disorders caused by a reduction to single dose of a fragment of chromosome 22q. Western blot analysis and double-immunofluorescence experiments using a specific antiserum revealed a primary nuclear localization of HIRA. Similar to Hir1p, HIRA contains seven amino-terminal WD repeats and probably functions as part of a multiprotein complex. HIRA and core histone H2B were found to physically interact in a yeast double-hybrid protein interaction trap, in GST pull-down assays, and in coimmunoprecipitation experiments performed from cellular extracts. In vitro, HIRA also interacted with core histone H4. H2B- and H4-binding domains were overlapping but distinguishable in the carboxy-terminal region of HIRA, and the region for HIRA interaction was mapped to the amino-terminal tail of H2B and the second α helix of H4. HIRIP3 (HIRA-interacting protein 3) is a novel gene product that was identified from its HIRA-binding properties in the yeast protein interaction trap. In vitro, HIRIP3 directly interacted with HIRA but also with core histones H2B and H3, suggesting that a HIRA-HIRIP3-containing complex could function in some aspects of chromatin and histone metabolism. Insufficient production of HIRA, which we report elsewhere interacts with homeodomain-containing DNA-binding factors during mammalian embryogenesis, could perturb the stoichiometric assembly of multimolecular complexes required for normal embryonic development. PMID:9710638

Magnetic field generation in core-sheath jets via the kinetic Kelvin-Helmholtz instability

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

Nishikawa, K.-I.; Hardee, P. E.; Duţan, I.

2014-09-20

We have investigated magnetic field generation in velocity shears via the kinetic Kelvin-Helmholtz instability (kKHI) using a relativistic plasma jet core and stationary plasma sheath. Our three-dimensional particle-in-cell simulations consider plasma jet cores with Lorentz factors of 1.5, 5, and 15 for both electron-proton and electron-positron plasmas. For electron-proton plasmas, we find generation of strong large-scale DC currents and magnetic fields that extend over the entire shear surface and reach thicknesses of a few tens of electron skin depths. For electron-positron plasmas, we find generation of alternating currents and magnetic fields. Jet and sheath plasmas are accelerated across the shearmore » surface in the strong magnetic fields generated by the kKHI. The mixing of jet and sheath plasmas generates a transverse structure similar to that produced by the Weibel instability.« less

In Silico Characterization of the Binding Affinity of Dendrimers to Penicillin-Binding Proteins (PBPs): Can PBPs be Potential Targets for Antibacterial Dendrimers?

PubMed

Ahmed, Shaimaa; Vepuri, Suresh B; Ramesh, Muthusamy; Kalhapure, Rahul; Suleman, Nadia; Govender, Thirumala

2016-04-01

We have shown that novel silver salts of poly (propyl ether) imine (PETIM) dendron and dendrimers developed in our group exhibit preferential antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) and Staphylococcus aureus. This led us to examine whether molecular modeling methods could be used to identify the key structural design principles for a bioactive lead molecule, explore the mechanism of binding with biological targets, and explain their preferential antibacterial activity. The current article reports the conformational landscape as well as mechanism of binding of generation 1 PETIM dendron and dendrimers to penicillin-binding proteins (PBPs) in order to understand the antibacterial activity profiles of their silver salts. Molecular dynamics at different simulation protocols and conformational analysis were performed to elaborate on the conformational features of the studied dendrimers, as well as to create the initial structure for further binding studies. The results showed that for all compounds, there were no significant conformational changes due to variation in simulation conditions. Molecular docking calculations were performed to investigate the binding theme between the studied dendrimers and PBPs. Interestingly, in significant accordance with the experimental data, dendron and dendrimer with aliphatic cores were found to show higher activity against S. aureus than the dendrimer with an aromatic core. The latter showed higher activity against MRSA. The findings from this computational and molecular modeling report together with the experimental results serve as a road map toward designing more potent antibacterial dendrimers against resistant bacterial strains.

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.

Disentangling formation of multiple-core holes in aminophenol molecules exposed to bright X-FEL radiation

NASA Astrophysics Data System (ADS)

Zhaunerchyk, V.; Kamińska, M.; Mucke, M.; Squibb, R. J.; Eland, J. H. D.; Piancastelli, M. N.; Frasinski, L. J.; Grilj, J.; Koch, M.; McFarland, B. K.; Sistrunk, E.; Gühr, M.; Coffee, R. N.; Bostedt, C.; Bozek, J. D.; Salén, P.; Meulen, P. v. d.; Linusson, P.; Thomas, R. D.; Larsson, M.; Foucar, L.; Ullrich, J.; Motomura, K.; Mondal, S.; Ueda, K.; Richter, R.; Prince, K. C.; Takahashi, O.; Osipov, T.; Fang, L.; Murphy, B. F.; Berrah, N.; Feifel, R.

2015-12-01

Competing multi-photon ionization processes, some leading to the formation of double core hole states, have been examined in 4-aminophenol. The experiments used the linac coherent light source (LCLS) x-ray free electron laser, in combination with a time-of-flight magnetic bottle electron spectrometer and the correlation analysis method of covariance mapping. The results imply that 4-aminophenol molecules exposed to the focused x-ray pulses of the LCLS sequentially absorb more than two x-ray photons, resulting in the formation of multiple core holes as well as in the sequential removal of photoelectrons and Auger electrons (so-called PAPA sequences).

Ultrafast core-loss spectroscopy in four-dimensional electron microscopy

PubMed Central

van der Veen, Renske M.; Penfold, Thomas J.; Zewail, Ahmed H.

2015-01-01

We demonstrate ultrafast core-electron energy-loss spectroscopy in four-dimensional electron microscopy as an element-specific probe of nanoscale dynamics. We apply it to the study of photoexcited graphite with femtosecond and nanosecond resolutions. The transient core-loss spectra, in combination with ab initio molecular dynamics simulations, reveal the elongation of the carbon-carbon bonds, even though the overall behavior is a contraction of the crystal lattice. A prompt energy-gap shrinkage is observed on the picosecond time scale, which is caused by local bond length elongation and the direct renormalization of band energies due to temperature-dependent electron–phonon interactions. PMID:26798793

Disentangling formation of multiple-core holes in aminophenol molecules exposed to bright X-FEL radiation

DOE PAGES

Zhaunerchyk, V.; Kaminska, M.; Mucke, M.; ...

2015-10-28

Competing multi-photon ionization processes, some leading to the formation of double core hole states, have been examined in 4-aminophenol. The experiments used the linac coherent light source (LCLS) x-ray free electron laser, in combination with a time-of-flight magnetic bottle electron spectrometer and the correlation analysis method of covariance mapping. Furthermore, the results imply that 4-aminophenol molecules exposed to the focused x-ray pulses of the LCLS sequentially absorb more than two x-ray photons, resulting in the formation of multiple core holes as well as in the sequential removal of photoelectrons and Auger electrons (so-called PAPA sequences).

The Green Bank Ammonia Survey: Dense Cores under Pressure in Orion A

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

Kirk, Helen; Di Francesco, James; Friesen, Rachel K.

We use data on gas temperature and velocity dispersion from the Green Bank Ammonia Survey and core masses and sizes from the James Clerk Maxwell Telescope Gould Belt Survey to estimate the virial states of dense cores within the Orion A molecular cloud. Surprisingly, we find that almost none of the dense cores are sufficiently massive to be bound when considering only the balance between self-gravity and the thermal and non-thermal motions present in the dense gas. Including the additional pressure binding imposed by the weight of the ambient molecular cloud material and additional smaller pressure terms, however, suggests thatmore » most of the dense cores are pressure-confined.« less

The Green Bank Ammonia Survey: Dense Cores under Pressure in Orion A

NASA Astrophysics Data System (ADS)

Kirk, Helen; Friesen, Rachel K.; Pineda, Jaime E.; Rosolowsky, Erik; Offner, Stella S. R.; Matzner, Christopher D.; Myers, Philip C.; Di Francesco, James; Caselli, Paola; Alves, Felipe O.; Chacón-Tanarro, Ana; Chen, How-Huan; Chun-Yuan Chen, Michael; Keown, Jared; Punanova, Anna; Seo, Young Min; Shirley, Yancy; Ginsburg, Adam; Hall, Christine; Singh, Ayushi; Arce, Héctor G.; Goodman, Alyssa A.; Martin, Peter; Redaelli, Elena

2017-09-01

We use data on gas temperature and velocity dispersion from the Green Bank Ammonia Survey and core masses and sizes from the James Clerk Maxwell Telescope Gould Belt Survey to estimate the virial states of dense cores within the Orion A molecular cloud. Surprisingly, we find that almost none of the dense cores are sufficiently massive to be bound when considering only the balance between self-gravity and the thermal and non-thermal motions present in the dense gas. Including the additional pressure binding imposed by the weight of the ambient molecular cloud material and additional smaller pressure terms, however, suggests that most of the dense cores are pressure-confined.

Supramolecular Ex plorations: Ex hibiting the Ex tent of Ex tended Cationic Cyclophanes

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

Dale, Edward J.; Vermeulen, Nicolaas A.; Juricek, Michal

Acting as hosts, cationic cyclophanes, consisting of π-electron-poor bipyridinium units, are capable of entering into strong donor–acceptor interactions to form host–guest complexes with various guests when the size and electronic constitution are appropriately matched. A synthetic protocol has been developed that utilizes catalytic quantities of tetrabutylammonium iodide to make a wide variety of cationic pyridinium-based cyclophanes in a quick and easy manner. Members of this class of cationic cyclophanes with boxlike geometries, dubbed ExnBoxm4+ for short, have been prepared by altering a number of variables: (i) n, the number of “horizontal” p-phenylene spacers between adjoining pyridinium units, to modulate themore » “length” of the cavity; (ii) m, the number of “vertical” p-phenylene spacers, to modulate the “width” of the cavity; and (iii) the aromatic linkers, namely, 1,4-di- and 1,3,5-trisubstituted units for the construction of macrocycles (ExBoxes) and macrobicycles (ExCages), respectively. This Account serves as an exploration of the properties that emerge from these structural modifications of the pyridinium-based hosts, coupled with a call for further investigation into the wealth of properties inherent in this class of compounds. By variation of only the aforementioned components, the role of these cationic receptors covers ground that spans (i) synthetic methodology, (ii) extraction and sequestration, (iii) catalysis, (iv) molecular electronics, (v) physical organic chemistry, and (vi) supramolecular chemistry. Ex1Box4+ (or simply ExBox4+) has been shown to be a multipurpose receptor capable of binding a wide range of polycyclic aromatic hydrocarbons (PAHs), while also being a suitable component in switchable mechanically interlocked molecules. Additionally, the electronic properties of some host–guest complexes allow the development of artificial photosystems. Ex2Box4+ boasts the ability to bind both π-electron-rich and -poor aromatic guests in different binding sites located within the same cavity. ExBox24+ forms complexes with C60 in which discrete arrays of aligned fullerenes result in single cocrystals, leading to improved material conductivities. When the substitution pattern of the ExnBox4+ series is changed to 1,3,5-trisubstituted benzenoid cores, the hexacationic cagelike compound, termed ExCage6+, exhibits different kinetics of complexation with guests of varying sizes—a veritable playground for physical organic chemists. The organization of functionality with respect to structure becomes valuable as the number of analogues continues to grow. With each of these minor structural modifications, a wealth of properties emerge, begging the question as to what discoveries await and what properties will be realized with the continued exploration of this area of supramolecular chemistry based on a unique class of receptor molecules.« less

Supramolecular Ex plorations: Ex hibiting the Ex tent of Ex tended Cationic Cyclophanes

DOE PAGES

Dale, Edward J.; Vermeulen, Nicolaas A.; Juricek, Michal; ...

2016-01-19

Acting as hosts, cationic cyclophanes, consisting of π-electron-poor bipyridinium units, are capable of entering into strong donor–acceptor interactions to form host–guest complexes with various guests when the size and electronic constitution are appropriately matched. A synthetic protocol has been developed that utilizes catalytic quantities of tetrabutylammonium iodide to make a wide variety of cationic pyridinium-based cyclophanes in a quick and easy manner. Members of this class of cationic cyclophanes with boxlike geometries, dubbed ExnBoxm4+ for short, have been prepared by altering a number of variables: (i) n, the number of “horizontal” p-phenylene spacers between adjoining pyridinium units, to modulate themore » “length” of the cavity; (ii) m, the number of “vertical” p-phenylene spacers, to modulate the “width” of the cavity; and (iii) the aromatic linkers, namely, 1,4-di- and 1,3,5-trisubstituted units for the construction of macrocycles (ExBoxes) and macrobicycles (ExCages), respectively. This Account serves as an exploration of the properties that emerge from these structural modifications of the pyridinium-based hosts, coupled with a call for further investigation into the wealth of properties inherent in this class of compounds. By variation of only the aforementioned components, the role of these cationic receptors covers ground that spans (i) synthetic methodology, (ii) extraction and sequestration, (iii) catalysis, (iv) molecular electronics, (v) physical organic chemistry, and (vi) supramolecular chemistry. Ex1Box4+ (or simply ExBox4+) has been shown to be a multipurpose receptor capable of binding a wide range of polycyclic aromatic hydrocarbons (PAHs), while also being a suitable component in switchable mechanically interlocked molecules. Additionally, the electronic properties of some host–guest complexes allow the development of artificial photosystems. Ex2Box4+ boasts the ability to bind both π-electron-rich and -poor aromatic guests in different binding sites located within the same cavity. ExBox24+ forms complexes with C60 in which discrete arrays of aligned fullerenes result in single cocrystals, leading to improved material conductivities. When the substitution pattern of the ExnBox4+ series is changed to 1,3,5-trisubstituted benzenoid cores, the hexacationic cagelike compound, termed ExCage6+, exhibits different kinetics of complexation with guests of varying sizes—a veritable playground for physical organic chemists. The organization of functionality with respect to structure becomes valuable as the number of analogues continues to grow. With each of these minor structural modifications, a wealth of properties emerge, begging the question as to what discoveries await and what properties will be realized with the continued exploration of this area of supramolecular chemistry based on a unique class of receptor molecules.« less

Microwave emulations and tight-binding calculations of transport in polyacetylene

NASA Astrophysics Data System (ADS)

Stegmann, Thomas; Franco-Villafañe, John A.; Ortiz, Yenni P.; Kuhl, Ulrich; Mortessagne, Fabrice; Seligman, Thomas H.

2017-01-01

A novel approach to investigate the electron transport of cis- and trans-polyacetylene chains in the single-electron approximation is presented by using microwave emulation measurements and tight-binding calculations. In the emulation we take into account the different electronic couplings due to the double bonds leading to coupled dimer chains. The relative coupling constants are adjusted by DFT calculations. For sufficiently long chains a transport band gap is observed if the double bonds are present, whereas for identical couplings no band gap opens. The band gap can be observed also in relatively short chains, if additional edge atoms are absent, which cause strong resonance peaks within the band gap. The experimental results are in agreement with our tight-binding calculations using the nonequilibrium Green's function method. The tight-binding calculations show that it is crucial to include third nearest neighbor couplings to obtain the gap in the cis-polyacetylene.

Electron core ionization in compressed alkali metal cesium

NASA Astrophysics Data System (ADS)

Degtyareva, V. F.

2018-01-01

Elements of groups I and II in the periodic table have valence electrons of s-type and are usually considered as simple metals. Crystal structures of these elements at ambient pressure are close-packed and high-symmetry of bcc and fcc-types, defined by electrostatic (Madelung) energy. Diverse structures were found under high pressure with decrease of the coordination number, packing fraction and symmetry. Formation of complex structures can be understood within the model of Fermi sphere-Brillouin zone interactions and supported by Hume-Rothery arguments. With the volume decrease there is a gain of band structure energy accompanied by a formation of many-faced Brillouin zone polyhedra. Under compression to less than a half of the initial volume the interatomic distances become close to or smaller than the ionic radius which should lead to the electron core ionization. At strong compression it is necessary to assume that for alkali metals the valence electron band overlaps with the upper core electrons, which increases the valence electron count under compression.

Low temperature nano-spin filtering using a diluted magnetic semiconductor core-shell quantum dot

NASA Astrophysics Data System (ADS)

Chattopadhyay, Saikat; Sen, Pratima; Andrews, Joshep Thomas; Sen, Pranay Kumar

2014-07-01

The spin polarized electron transport properties and spin polarized tunneling current have been investigated analytically in a diluted magnetic semiconductor core-shell quantum dot in the presence of applied electric and magnetic fields. Assuming the electron wave function to satisfy WKB approximation, the electron energy eigenvalues have been calculated. The spin polarized tunneling current and the spin dependent tunneling coefficient are obtained by taking into account the exchange interaction and Zeeman splitting. Numerical estimates made for a specific diluted magnetic semiconductor, viz., Zn1-xMnxSe/ZnS core-shell quantum dot establishes the possibility of a nano-spin filter for a particular biasing voltage and applied magnetic field. Influence of applied voltage on spin polarized electron transport has been investigated in a CSQD.

Core excitation effects on oscillator strengths for transitions in four electron atomic systems

NASA Astrophysics Data System (ADS)

Chang, T. N.; Luo, Yuxiang

2007-06-01

By including explicitly the electronic configurations with two and three simultaneously excited electronic orbital, we have extended the BSCI (B-spline based configuration interaction) method [1] to estimate directly the effect of inner shell core excitation to oscillator strengths for transitions in four-electron atomic systems. We will present explicitly the change in oscillator strengths due to core excitations, especially for transitions involving doubly excited states and those with very small oscillator strengths. The length and velocity results are typically in agreement better than 1% or less. [1] Tu-nan Chang, in Many-body Theory of Atomic Structure and Photoionization, edited by T. N. Chang (World Scientific, Singapore, 1993), p. 213-47; and T. N. Chang and T. K. Fang, Elsevier Radiation Physics and Chemistry 70, 173-190 (2004).

Theory of long-range interactions for Rydberg states attached to hyperfine-split cores

NASA Astrophysics Data System (ADS)

Robicheaux, F.; Booth, D. W.; Saffman, M.

2018-02-01

The theory is developed for one- and two-atom interactions when the atom has a Rydberg electron attached to a hyperfine-split core state. This situation is relevant for some of the rare-earth and alkaline-earth atoms that have been proposed for experiments on Rydberg-Rydberg interactions. For the rare-earth atoms, the core electrons can have a very substantial total angular momentum J and a nonzero nuclear spin I . In the alkaline-earth atoms there is a single (s ) core electron whose spin can couple to a nonzero nuclear spin for odd isotopes. The resulting hyperfine splitting of the core state can lead to substantial mixing between the Rydberg series attached to different thresholds. Compared to the unperturbed Rydberg series of the alkali-metal atoms, the series perturbations and near degeneracies from the different parity states could lead to qualitatively different behavior for single-atom Rydberg properties (polarizability, Zeeman mixing and splitting, etc.) as well as Rydberg-Rydberg interactions (C5 and C6 matrices).

The radial gradients and collisional properties of solar wind electrons

NASA Technical Reports Server (NTRS)

Gilvie, K. W.; Scudder, J. D.

1977-01-01

The plasma instrument on Mariner 10 carried out measurements of electron density and temperature in the interplanetary medium between heliocentric distances of 0.85 and 0.45 AU. Due to the stable coronal configuration and low solar activity during the period of observation, the radial variations of these quantities could be obtained. The power-law exponent of the core temperature was measured to be -0.3 + or - 0.04, and the halo temperature was found to be almost independent of heliocentric distance. The exponent of the power law for the density variation was 2.5 + or - 0.2 and the extrapolated value at 1 AU was consistent with measured values during the same period. Calculations of the core electron self-collision time, and the core-halo equipartition time were made as a function of radial distance. These measurements indicate a macroscale picture of a Coulomb-collisional core and a collisionless isothermal halo. Extrapolating back to the sun, core and halo temperatures become equal at a radial distance of approx. 2-15 radii.

Catching the electron in action in real space inside a Ge-Si core-shell nanowire transistor.

PubMed

Jaishi, Meghnath; Pati, Ranjit

2017-09-21

Catching the electron in action in real space inside a semiconductor Ge-Si core-shell nanowire field effect transistor (FET), which has been demonstrated (J. Xiang, W. Lu, Y. Hu, Y. Wu, H. Yan and C. M. Lieber, Nature, 2006, 441, 489) to outperform the state-of-the-art metal oxide semiconductor FET, is central to gaining unfathomable access into the origin of its functionality. Here, using a quantum transport approach that does not make any assumptions on electronic structure, charge, and potential profile of the device, we unravel the most probable tunneling pathway for electrons in a Ge-Si core-shell nanowire FET with orbital level spatial resolution, which demonstrates gate bias induced decoupling of electron transport between the core and the shell region. Our calculation yields excellent transistor characteristics as noticed in the experiment. Upon increasing the gate bias beyond a threshold value, we observe a rapid drop in drain current resulting in a gate bias driven negative differential resistance behavior and switching in the sign of trans-conductance. We attribute this anomalous behavior in drain current to the gate bias induced modification of the carrier transport pathway from the Ge core to the Si shell region of the nanowire channel. A new experiment involving a four probe junction is proposed to confirm our prediction on gate bias induced decoupling.

Soft Landing of Bare Nanoparticles with Controlled Size, Composition, and Morphology

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

Johnson, Grant E.; Colby, Robert J.; Laskin, Julia

2015-01-01

A kinetically-limited physical synthesis method based on magnetron sputtering and gas aggregation has been coupled with size-selection and ion soft landing to prepare bare metal nanoparticles on surfaces with controlled coverage, size, composition, and morphology. Employing atomic force microscopy (AFM) and scanning electron microscopy (SEM), it is demonstrated that the size and coverage of bare nanoparticles soft landed onto flat glassy carbon and silicon as well as stepped graphite surfaces may be controlled through size-selection with a quadrupole mass filter and the length of deposition, respectively. The bare nanoparticles are observed with AFM to bind randomly to the flat glassymore » carbon surface when soft landed at relatively low coverage (1012 ions). In contrast, on stepped graphite surfaces at intermediate coverage (1013 ions) the soft landed nanoparticles are shown to bind preferentially along step edges forming extended linear chains of particles. At the highest coverage (5 x 1013 ions) examined in this study the nanoparticles are demonstrated with both AFM and SEM to form a continuous film on flat glassy carbon and silicon surfaces. On a graphite surface with defects, however, it is shown with SEM that the presence of localized surface imperfections results in agglomeration of nanoparticles onto these features and the formation of neighboring depletion zones that are devoid of particles. Employing high resolution scanning transmission electron microscopy in the high angular annular dark field imaging mode (STEM-HAADF) and electron energy loss spectroscopy (EELS) it is demonstrated that the magnetron sputtering/gas aggregation synthesis technique produces single metal particles with controlled morphology as well as bimetallic alloy nanoparticles with clearly defined core-shell structure. Therefore, this kinetically-limited physical synthesis technique, when combined with ion soft landing, is a versatile complementary method for preparing a wide range of bare supported nanoparticles with selected properties that are free of the solvent, organic capping agents, and residual reactants present with nanoparticles synthesized in solution.« less

Evidence-based use of electronic clinical tracking systems in advanced practice registered nurse education: an integrative review.

PubMed

Branstetter, M Laurie; Smith, Lynette S; Brooks, Andrea F

2014-07-01

Over the past decade, the federal government has mandated healthcare providers to incorporate electronic health records into practice by 2015. This technological update in healthcare documentation has generated a need for advanced practice RN programs to incorporate information technology into education. The National Organization of Nurse Practitioner Faculties created core competencies to guide program standards for advanced practice RN education. One core competency is Technology and Information Literacy. Educational programs are moving toward the utilization of electronic clinical tracking systems to capture students' clinical encounter data. The purpose of this integrative review was to evaluate current research on advanced practice RN students' documentation of clinical encounters utilizing electronic clinical tracking systems to meet advanced practice RN curriculum outcome goals in information technology as defined by the National Organization of Nurse Practitioner Faculties. The state of the science depicts student' and faculty attitudes, preferences, opinions, and data collections of students' clinical encounters. Although electronic clinical tracking systems were utilized to track students' clinical encounters, these systems have not been evaluated for meeting information technology core competency standards. Educational programs are utilizing electronic clinical tracking systems with limited evidence-based literature evaluating the ability of these systems to meet the core competencies in advanced practice RN programs.

Decorin binds myostatin and modulates its activity to muscle cells

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

Miura, Takayuki; Kishioka, Yasuhiro; Wakamatsu, Jun-ichi

2006-02-10

Myostatin, a member of TGF-{beta} superfamily of growth factors, acts as a negative regulator of skeletal muscle mass. The mechanism whereby myostatin controls the proliferation and differentiation of myogenic cells is mostly clarified. However, the regulation of myostatin activity to myogenic cells after its secretion in the extracellular matrix (ECM) is still unknown. Decorin, a small leucine-rich proteoglycan, binds TGF-{beta} and regulates its activity in the ECM. Thus, we hypothesized that decorin could also bind to myostatin and participate in modulation of its activity to myogenic cells. In order to test the hypothesis, we investigated the interaction between myostatin andmore » decorin by surface plasmon assay. Decorin interacted with mature myostatin in the presence of concentrations of Zn{sup 2+} greater than 10 {mu}M, but not in the absence of Zn{sup 2+}. Kinetic analysis with a 1:1 binding model resulted in dissociation constants (K {sub D}) of 2.02 x 10{sup -8} M and 9.36 x 10{sup -9} M for decorin and the core protein of decorin, respectively. Removal of the glycosaminoglycan chain by chondroitinase ABC digestion did not affect binding, suggesting that decorin could bind to myostatin with its core protein. Furthermore, we demonstrated that immobilized decorin could rescue the inhibitory effect of myostatin on myoblast proliferation in vitro. These results suggest that decorin could trap myostatin and modulate its activity to myogenic cells in the ECM.« less

Core drug-drug interaction alerts for inclusion in pediatric electronic health records with computerized prescriber order entry.

PubMed

Harper, Marvin B; Longhurst, Christopher A; McGuire, Troy L; Tarrago, Rod; Desai, Bimal R; Patterson, Al

2014-03-01

The study aims to develop a core set of pediatric drug-drug interaction (DDI) pairs for which electronic alerts should be presented to prescribers during the ordering process. A clinical decision support working group composed of Children's Hospital Association (CHA) members was developed. CHA Pharmacists and Chief Medical Information Officers participated. Consensus was reached on a core set of 19 DDI pairs that should be presented to pediatric prescribers during the order process. We have provided a core list of 19 high value drug pairs for electronic drug-drug interaction alerts to be recommended for inclusion as high value alerts in prescriber order entry software used with a pediatric patient population. We believe this list represents the most important pediatric drug interactions for practical implementation within computerized prescriber order entry systems.

Oxidations of N-(3-indoleethyl) cyclic aliphatic amines by horseradish peroxidase: the indole ring binds to the enzyme and mediates electron-transfer amine oxidation.

PubMed

Ling, Ke-Qing; Li, Wen-Shan; Sayre, Lawrence M

2008-01-23

Although oxidations of aromatic amines by horseradish peroxidase (HRP) are well-known, typical aliphatic amines are not substrates of HRP. In this study, the reactions of N-benzyl and N-methyl cyclic amines with HRP were found to be slow, but reactions of N-(3-indoleethyl) cyclic amines were 2-3 orders of magnitude faster. Analyses of pH-rate profiles revealed a dominant contribution to reaction by the amine-free base forms, the only species found to bind to the enzyme. A metabolic study on a family of congeneric N-(3-indoleethyl) cyclic amines indicated competition between amine and indole oxidation pathways. Amine oxidation dominated for the seven- and eight-membered azacycles, where ring size supports the change in hybridization from sp3 to sp2 that occurs upon one-electron amine nitrogen oxidation, whereas only indole oxidation was observed for the six-membered ring congener. Optical difference spectroscopic binding data and computational docking simulations suggest that all the arylalkylamine substrates bind to the enzyme through their aromatic termini with similar binding modes and binding affinities. Kinetic saturation was observed for a particularly soluble substrate, consistent with an obligatory role of an enzyme-substrate complexation preceding electron transfer. The significant rate enhancements seen for the indoleethylamine substrates suggest the ability of the bound indole ring to mediate what amounts to medium long-range electron-transfer oxidation of the tertiary amine center by the HRP oxidants. This is the first systematic investigation to document aliphatic amine oxidation by HRP at rates consistent with normal metabolic turnover, and the demonstration that this is facilitated by an auxiliary electron-rich aromatic ring.

Fluctuation Dynamics Analysis of gp120 Envelope Protein Reveals a Topologically Based Communication Network

PubMed Central

Shrivastava, Indira; LaLonde, Judith M.

2012-01-01

HIV infection is initiated by binding of the viral glycoprotein gp120, to the cellular receptor CD4. Upon CD4 binding, gp120 undergoes conformational change, permitting binding to the chemokine receptor. Crystal structures of gp120 ternary complex reveal the CD4 bound conformation of gp120. We report here the application of Gaussian Network Model (GNM) to the crystal structures of gp120 bound to CD4 or CD4 mimic and 17b, to study the collective motions of the gp120 core and determine the communication propensities of the residue network. The GNM fluctuation profiles identify residues in the inner domain and outer domain that may facilitate conformational change or stability, respectively. Communication propensities delineate a residue network that is topologically suited for signal propagation from the Phe43 cavity throughout the gp120 outer domain. . These results provide a new context for interpreting gp120 core envelope structure-function relationships. PMID:20718047

Temperature dependent dispersion and electron-phonon coupling surface states on Be(1010)

NASA Astrophysics Data System (ADS)

Tang, Shu-Jung; Ismail; Sprunger, Philip; Plummer, Ward

2002-03-01

Temperature dependent dispersion and electron-phonon coupling surface states on Be(10-10) S.-J Tang*, Ismail* , P.T . Sprunger#, E. W. Plummer* * Department of Physics and Astronomy, University of Tennessee, Knoxville, TN37996 , # Center for Advanced Microstructures and Devices (CAMD), Louisiana State University The surface states dispersing in a large band gap from -A to -Γ in Be(10-10) were studied with high-resolution, angle-resolved photoemission. Spectra reveal that the two zone-boundary surface states, S1 and S2, behave significantly different with respect to band dispersion, the temperature dependence of binding energies, and the electron-phonon coupling. The band dispersion of S1 is purely free-electron like with the maximum binding energy of 0.37+-0.05 eV at -A and effective mass m*/m =0835. However, the maximum binding energy 2.74+-0.05 eV of the S2 is located 0.2Åaway from -A and disperses into the bulk band edge at a binding energy of 1.75+-0.05 eV. Temperature dependent data reveal that the binding energies of S1 and S2 at -A shift in opposite directions at the rate of (-0.61+-0.3)+- 10E-4 eV/K and (1.71+-0.8)+-10E-4 eV/K, respectively. Moreover, from the temperature-dependent spectral widths of the surface states S1 and S2 at , the electron-phonon coupling parameters,λ, have been determined. Unusually different, the coupling strength λ for S1 and S2 are 0.67+-0.03 and 0.51+-0.04, respectively. The differences between the electron-phonon coupling, temperature dependent binding energies, and dispersions between these two zone-centered surface states will be discussed in light unique bonding at the surface and localization.

Esrrb Unlocks Silenced Enhancers for Reprogramming to Naive Pluripotency.

PubMed

Adachi, Kenjiro; Kopp, Wolfgang; Wu, Guangming; Heising, Sandra; Greber, Boris; Stehling, Martin; Araúzo-Bravo, Marcos J; Boerno, Stefan T; Timmermann, Bernd; Vingron, Martin; Schöler, Hans R

2018-06-11

Transcription factor (TF)-mediated reprogramming to pluripotency is a slow and inefficient process, because most pluripotency TFs fail to access relevant target sites in a refractory chromatin environment. It is still unclear how TFs actually orchestrate the opening of repressive chromatin during the long latency period of reprogramming. Here, we show that the orphan nuclear receptor Esrrb plays a pioneering role in recruiting the core pluripotency factors Oct4, Sox2, and Nanog to inactive enhancers in closed chromatin during the reprogramming of epiblast stem cells. Esrrb binds to silenced enhancers containing stable nucleosomes and hypermethylated DNA, which are inaccessible to the core factors. Esrrb binding is accompanied by local loss of DNA methylation, LIF-dependent engagement of p300, and nucleosome displacement, leading to the recruitment of core factors within approximately 2 days. These results suggest that TFs can drive rapid remodeling of the local chromatin structure, highlighting the remarkable plasticity of stable epigenetic information. Copyright © 2018 Elsevier Inc. All rights reserved.

TRF2 and the evolution of the bilateria

PubMed Central

Duttke, Sascha H.C.; Doolittle, Russell F.; Wang, Yuan-Liang

2014-01-01

The development of a complex body plan requires a diversity of regulatory networks. Here we consider the concept of TATA-box-binding protein (TBP) family proteins as “system factors” that each supports a distinct set of transcriptional programs. For instance, TBP activates TATA-box-dependent core promoters, whereas TBP-related factor 2 (TRF2) activates TATA-less core promoters that are dependent on a TCT or downstream core promoter element (DPE) motif. These findings led us to investigate the evolution of TRF2. TBP occurs in Archaea and eukaryotes, but TRF2 evolved prior to the emergence of the bilateria and subsequent to the evolutionary split between bilaterians and nonbilaterian animals. Unlike TBP, TRF2 does not bind to the TATA box and could thus function as a new system factor that is largely independent of TBP. We postulate that this TRF2-based system served as the foundation for new transcriptional programs, such as those involved in triploblasty and body plan development, that facilitated the evolution of bilateria. PMID:25274724

Preparation and application of hollow molecularly imprinted polymers with a super-high selectivity to the template protein.

PubMed

Chen, Yang; He, Xi-Wen; Mao, Jie; Li, Wen-You; Zhang, Yu-Kui

2013-10-01

Protein-imprinted polymers with hollow cores that have a super-high imprinting factor were prepared by etching the core of the surface-imprinted polymers that used silica particles as the support. Lysozyme as template was modified onto the surface of silica particles by a covalent method, and after polymerization and the removal of template molecules, channels through the polymer layer were formed, which allowed a single-protein molecule to come into the hollow core and attach to the binding sites inside the polymer layer. The adsorption experiments demonstrated that the hollow imprinted polymers had an extremely high binding capacity and selectivity, and thus a super-high imprinting factor was obtained. The as-prepared imprinted polymers were used to separate the template lysozyme from egg white successfully, indicating its high selectivity and potential application in the field of separation of protein from real samples. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Carbohydrate–Aromatic Interactions in Proteins

PubMed Central

2015-01-01

Protein–carbohydrate interactions play pivotal roles in health and disease. However, defining and manipulating these interactions has been hindered by an incomplete understanding of the underlying fundamental forces. To elucidate common and discriminating features in carbohydrate recognition, we have analyzed quantitatively X-ray crystal structures of proteins with noncovalently bound carbohydrates. Within the carbohydrate-binding pockets, aliphatic hydrophobic residues are disfavored, whereas aromatic side chains are enriched. The greatest preference is for tryptophan with an increased prevalence of 9-fold. Variations in the spatial orientation of amino acids around different monosaccharides indicate specific carbohydrate C–H bonds interact preferentially with aromatic residues. These preferences are consistent with the electronic properties of both the carbohydrate C–H bonds and the aromatic residues. Those carbohydrates that present patches of electropositive saccharide C–H bonds engage more often in CH−π interactions involving electron-rich aromatic partners. These electronic effects are also manifested when carbohydrate–aromatic interactions are monitored in solution: NMR analysis indicates that indole favorably binds to electron-poor C–H bonds of model carbohydrates, and a clear linear free energy relationships with substituted indoles supports the importance of complementary electronic effects in driving protein–carbohydrate interactions. Together, our data indicate that electrostatic and electronic complementarity between carbohydrates and aromatic residues play key roles in driving protein–carbohydrate complexation. Moreover, these weak noncovalent interactions influence which saccharide residues bind to proteins, and how they are positioned within carbohydrate-binding sites. PMID:26561965

Carbohydrate-Aromatic Interactions in Proteins.

PubMed

Hudson, Kieran L; Bartlett, Gail J; Diehl, Roger C; Agirre, Jon; Gallagher, Timothy; Kiessling, Laura L; Woolfson, Derek N

2015-12-09

Protein-carbohydrate interactions play pivotal roles in health and disease. However, defining and manipulating these interactions has been hindered by an incomplete understanding of the underlying fundamental forces. To elucidate common and discriminating features in carbohydrate recognition, we have analyzed quantitatively X-ray crystal structures of proteins with noncovalently bound carbohydrates. Within the carbohydrate-binding pockets, aliphatic hydrophobic residues are disfavored, whereas aromatic side chains are enriched. The greatest preference is for tryptophan with an increased prevalence of 9-fold. Variations in the spatial orientation of amino acids around different monosaccharides indicate specific carbohydrate C-H bonds interact preferentially with aromatic residues. These preferences are consistent with the electronic properties of both the carbohydrate C-H bonds and the aromatic residues. Those carbohydrates that present patches of electropositive saccharide C-H bonds engage more often in CH-π interactions involving electron-rich aromatic partners. These electronic effects are also manifested when carbohydrate-aromatic interactions are monitored in solution: NMR analysis indicates that indole favorably binds to electron-poor C-H bonds of model carbohydrates, and a clear linear free energy relationships with substituted indoles supports the importance of complementary electronic effects in driving protein-carbohydrate interactions. Together, our data indicate that electrostatic and electronic complementarity between carbohydrates and aromatic residues play key roles in driving protein-carbohydrate complexation. Moreover, these weak noncovalent interactions influence which saccharide residues bind to proteins, and how they are positioned within carbohydrate-binding sites.

Electrostatic Interactions in Aminoglycoside-RNA Complexes

PubMed Central

Kulik, Marta; Goral, Anna M.; Jasiński, Maciej; Dominiak, Paulina M.; Trylska, Joanna

2015-01-01

Electrostatic interactions often play key roles in the recognition of small molecules by nucleic acids. An example is aminoglycoside antibiotics, which by binding to ribosomal RNA (rRNA) affect bacterial protein synthesis. These antibiotics remain one of the few valid treatments against hospital-acquired infections by Gram-negative bacteria. It is necessary to understand the amplitude of electrostatic interactions between aminoglycosides and their rRNA targets to introduce aminoglycoside modifications that would enhance their binding or to design new scaffolds. Here, we calculated the electrostatic energy of interactions and its per-ring contributions between aminoglycosides and their primary rRNA binding site. We applied either the methodology based on the exact potential multipole moment (EPMM) or classical molecular mechanics force field single-point partial charges with Coulomb formula. For EPMM, we first reconstructed the aspherical electron density of 12 aminoglycoside-RNA complexes from the atomic parameters deposited in the University at Buffalo Databank. The University at Buffalo Databank concept assumes transferability of electron density between atoms in chemically equivalent vicinities and allows reconstruction of the electron densities from experimental structural data. From the electron density, we then calculated the electrostatic energy of interaction using EPMM. Finally, we compared the two approaches. The calculated electrostatic interaction energies between various aminoglycosides and their binding sites correlate with experimentally obtained binding free energies. Based on the calculated energetic contributions of water molecules mediating the interactions between the antibiotic and rRNA, we suggest possible modifications that could enhance aminoglycoside binding affinity. PMID:25650932

Fanconi anemia (FA) binding protein FAAP20 stabilizes FA complementation group A (FANCA) and participates in interstrand cross-link repair.

PubMed

Leung, Justin Wai Chung; Wang, Yucai; Fong, Ka Wing; Huen, Michael Shing Yan; Li, Lei; Chen, Junjie

2012-03-20

The Fanconi anemia (FA) pathway participates in interstrand cross-link (ICL) repair and the maintenance of genomic stability. The FA core complex consists of eight FA proteins and two Fanconi anemia-associated proteins (FAAP24 and FAAP100). The FA core complex has ubiquitin ligase activity responsible for monoubiquitination of the FANCI-FANCD2 (ID) complex, which in turn initiates a cascade of biochemical events that allow processing and removal of cross-linked DNA and thereby promotes cell survival following DNA damage. Here, we report the identification of a unique component of the FA core complex, namely, FAAP20, which contains a RAD18-like ubiquitin-binding zinc-finger domain. Our data suggest that FAAP20 promotes the functional integrity of the FA core complex via its direct interaction with the FA gene product, FANCA. Indeed, somatic knockout cells devoid of FAAP20 displayed the hallmarks of FA cells, including hypersensitivity to DNA cross-linking agents, chromosome aberrations, and reduced FANCD2 monoubiquitination. Taking these data together, our study indicates that FAAP20 is an important player involved in the FA pathway.

Fanconi anemia (FA) binding protein FAAP20 stabilizes FA complementation group A (FANCA) and participates in interstrand cross-link repair

PubMed Central

Leung, Justin Wai Chung; Wang, Yucai; Fong, Ka Wing; Huen, Michael Shing Yan; Li, Lei; Chen, Junjie

2012-01-01

The Fanconi anemia (FA) pathway participates in interstrand cross-link (ICL) repair and the maintenance of genomic stability. The FA core complex consists of eight FA proteins and two Fanconi anemia-associated proteins (FAAP24 and FAAP100). The FA core complex has ubiquitin ligase activity responsible for monoubiquitination of the FANCI-FANCD2 (ID) complex, which in turn initiates a cascade of biochemical events that allow processing and removal of cross-linked DNA and thereby promotes cell survival following DNA damage. Here, we report the identification of a unique component of the FA core complex, namely, FAAP20, which contains a RAD18-like ubiquitin-binding zinc-finger domain. Our data suggest that FAAP20 promotes the functional integrity of the FA core complex via its direct interaction with the FA gene product, FANCA. Indeed, somatic knockout cells devoid of FAAP20 displayed the hallmarks of FA cells, including hypersensitivity to DNA cross-linking agents, chromosome aberrations, and reduced FANCD2 monoubiquitination. Taking these data together, our study indicates that FAAP20 is an important player involved in the FA pathway. PMID:22396592

Albumin-Encapsulated Liposomes: A Novel Drug Delivery Carrier With Hydrophobic Drugs Encapsulated in the Inner Aqueous Core.

PubMed

Okamoto, Yuko; Taguchi, Kazuaki; Yamasaki, Keishi; Sakuragi, Mina; Kuroda, Shun'ichi; Otagiri, Masaki

2018-01-01

Liposomes are clinically used in drug delivery, but loading hydrophobic substances is limited to the hydrophobic space of a lipid membrane, despite the fact that it is favorable to encapsulate substances into the inner aqueous core of liposome, from a drug stability of view. We report herein on the preparation of a liposome with bovine serum albumin encapsulated (BSA-liposome). Using this system, it is possible to encapsulate hydrophobic drugs in the inner aqueous core of the liposome based on the hypothesis that the water solubility of hydrophobic drugs is increased when bound to albumin. The physicochemical properties of the prepared BSA-liposomes could be easily regulated and the loading of hydrophobic drugs in the inner aqueous core of the liposome was dramatically improved by virtue of the drug-binding properties of albumin. An in vivo safety and pharmacokinetic study showed that BSA-liposomes possess favorable properties as a drug carrier, including biocompatibility and a stealth effect. This new type of hydrophobic drug carrier, an albumin-liposome, has the potential for use in delivering numerous hydrophobic drugs that typically bind to albumin. Copyright © 2018 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Spiral wound extraction cartridge

DOEpatents

Wisted, E.E.; Lundquist, S.H.

1999-04-27

A cartridge device for removing an analyte from a fluid comprises a hollow core, a sheet composite comprising a particulate-loaded porous membrane and optionally at least one reinforcing spacer sheet, the particulate being capable of binding the analyte, the sheet composite being formed into a spiral configuration about the core, wherein the sheet composite is wound around itself and wherein the windings of sheet composite are of sufficient tightness so that adjacent layers are essentially free of spaces therebetween, two end caps which are disposed over the core and the lateral ends of the spirally wound sheet composite, and means for securing the end caps to the core, the end caps also being secured to the lateral ends of the spirally wound sheet composite. A method for removing an analyte from a fluid comprises the steps of providing a spirally wound element of the invention and passing the fluid containing the analyte through the element essentially normal to a surface of the sheet composite so as to bind the analyte to the particulate of the particulate-loaded porous membrane, the method optionally including the step of eluting the bound analyte from the sheet composite. 4 figs.

Microcavity surface plasmon resonance bio-sensors

NASA Astrophysics Data System (ADS)

Mosavian, Nazanin

This work discusses a miniature surface plasmon biosensor which uses a dielectric sub- micron diameter core with gold spherical shell. The shell has a subwavelength nanoaperture believed to excite stationary plasmon resonances at the biosensor's surface. The sub-micron cavity enhances the measurement sensitivity of molecules binding to the sensor surface. We used visible-range optical spectroscopy to study the wavelength shift as bio-molecules absorbed-desorbed at the shell surface. We also used Scanning Electron Microscopy (SEM) and Focused Ion Beam (FIB) ablation to study the characteristics of microcavity surface plasmon resonance sensor (MSPRS) and the inner structure formed with metal deposition and its spectrum. We found that resonances at 580 nm and 670 nm responded to bound test agents and that Surface Plasmon Resonance (SPR) sensor intensity could be used to differentiate between D-glucose and L-glucose. The responsiveness of the system depended upon the mechanical integrity of the metallic surface coating.

Observing Graphene Grow: Catalyst–Graphene Interactions during Scalable Graphene Growth on Polycrystalline Copper

PubMed Central

2013-01-01

Complementary in situ X-ray photoelectron spectroscopy (XPS), X-ray diffractometry, and environmental scanning electron microscopy are used to fingerprint the entire graphene chemical vapor deposition process on technologically important polycrystalline Cu catalysts to address the current lack of understanding of the underlying fundamental growth mechanisms and catalyst interactions. Graphene forms directly on metallic Cu during the high-temperature hydrocarbon exposure, whereby an upshift in the binding energies of the corresponding C1s XPS core level signatures is indicative of coupling between the Cu catalyst and the growing graphene. Minor carbon uptake into Cu can under certain conditions manifest itself as carbon precipitation upon cooling. Postgrowth, ambient air exposure even at room temperature decouples the graphene from Cu by (reversible) oxygen intercalation. The importance of these dynamic interactions is discussed for graphene growth, processing, and device integration. PMID:24041311

Mono and bimetallic nanoparticles of gold, silver and palladium-catalyzed NADH oxidation-coupled reduction of Eosin-Y

NASA Astrophysics Data System (ADS)

Santhanalakshmi, J.; Venkatesan, P.

2011-02-01

Mono metallic (Au, Ag, Pd) and bimetallic (Au-Ag, Ag-Pd, Au-Pd) with 1:1 mol stoichiometry, nanoparticles are synthesized using one-pot, temperature controlled chemical method using cetyltrimethylammonium bromide (CTAB) as the capping agent. The particle sizes (Au = 5.6, Ag = 5.0, Pd = 6.0, Au-Ag = 9.2, Ag-Pd = 9.6, Au-Pd = 9.4 nm) are characterized by UV-Vis, HRTEM, and XRD measurements, respectively. CTAB bindings onto mono and bimetallic nanoparticles are analyzed by FTIR spectra. The catalytic activities of mono and bimetallic nanoparticles are tested on the reaction between NADH oxidation and Eosin-Y reduction. The effects of base, pH, ionic strength, nature of mono and bimetallic catalysts are studied and the reaction conditions are optimized. Bimetallic nanoparticles exhibited better catalysis than the mono metallic nanoparticles, which may be due to the electronic effects of the core to shell metal atoms.

Theoretical study of transition-metal ions bound to benzene

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Partridge, Harry; Langhoff, Stephen R.

1992-01-01

Theoretical binding energies are reported for all first-row and selected second-row transition metal ions (M+) bound to benzene. The calculations employ basis sets of at least double-zeta plus polarization quality and account for electron correlation using the modified coupled-pair functional method. While the bending is predominantly electrostatic, the binding energies are significantly increased by electron correlation, because the donation from the metal d orbitals to the benzene pi* orbitals is not well described at the self-consistent-field level. The uncertainties in the computed binding energies are estimated to be about 5 kcal/mol. Although the calculated and experimental binding energies generally agree to within their combined uncertainties, it is likely that the true binding energies lie in the lower portion of the experimental range. This is supported by the very good agreement between the theoretical and recent experimental binding energies for AgC6H6(+).

Non-intercalative, deoxyribose binding of boric acid to calf thymus DNA.

PubMed

Ozdemir, Ayse; Gursaclı, Refiye Tekiner; Tekinay, Turgay

2014-05-01

The present study characterizes the effects of the boric acid binding on calf thymus DNA (ct-DNA) by spectroscopic and calorimetric methods. UV-Vis absorbance spectroscopy, circular dichroism (CD) spectroscopy, transmission electron microscopy (TEM), isothermal titration calorimetry (ITC), and Fourier transform infrared (FT-IR) spectroscopy were employed to characterize binding properties. Changes in the secondary structure of ct-DNA were determined by CD spectroscopy. Sizes and morphologies of boric acid-DNA complexes were determined by transmission electron microscopy (TEM). The kinetics of boric acid binding to calf thymus DNA (ct-DNA) was investigated by isothermal titration calorimetry (ITC). ITC results revealed that boric acid exhibits a moderate affinity to ct-DNA with a binding constant (K a) of 9.54 × 10(4) M(-1). FT-IR results revealed that boric acid binds to the deoxyribose sugar of DNA without disrupting the B-conformation at tested concentrations.

Fabrication of core-shell micro/nanoparticles for programmable dual drug release by emulsion electrospraying

NASA Astrophysics Data System (ADS)

Wang, Yazhou; Zhang, Yiqiong; Wang, Bochu; Cao, Yang; Yu, Qingsong; Yin, Tieying

2013-06-01

The study aimed at constructing a novel drug delivery system for programmable multiple drug release controlled with core-shell structure. The core-shell structure consisted of chitosan nanoparticles as core and polyvinylpyrrolidone micro/nanocoating as shell to form core-shell micro/nanoparticles, which was fabricated by ionic gelation and emulsion electrospray methods. As model drug agents, Naproxen and rhodamine B were encapsulated in the core and shell regions, respectively. The core-shell micro/nanoparticles thus fabricated were characterized and confirmed by scanning electron microscope, transmission electron microscope, and fluorescence optical microscope. The core-shell micro/nanoparticles showed good release controllability through drug release experiment in vitro. It was noted that a programmable release pattern for dual drug agents was also achieved by adjusting their loading regions in the core-shell structures. The results indicate that emulsion electrospraying technology is a promising approach in fabrication of core-shell micro/nanoparticles for programmable dual drug release. Such a novel multi-drug delivery system has a potential application for the clinical treatment of cancer, tuberculosis, and tissue engineering.

Interactions of Escherichia coli σ70 within the transcription elongation complex

PubMed Central

Daube, Shirley S.; von Hippel, Peter H.

1999-01-01

A functional transcription elongation complex can be formed without passing through a promoter by adding a complementary RNA primer and core Escherichia coli RNA polymerase in trans to an RNA-primed synthetic bubble-duplex DNA framework. This framework consists of a double-stranded DNA sequence with an internal noncomplementary DNA “bubble” containing a hybridized RNA primer. On addition of core polymerase and the requisite NTPs, the RNA primer is extended in a process that manifests most of the properties of in vitro transcription elongation. This synthetic elongation complex can also be assembled by using holo rather than core RNA polymerase, and in this study we examine the interactions and fate of the σ70 specificity subunit of the holopolymerase in the assembly process. We show that the addition of holopolymerase to the bubble-duplex construct triggers the dissociation of the sigma factor from some complexes, whereas in others the RNA oligomer is released into solution instead. These results are consistent with an allosteric competition between σ70 and the nascent RNA strand within the elongation complex and suggest that both cannot be bound to the core polymerase simultaneously. However, the dissociation of σ70 from the complex can also be stimulated by binding of the holopolymerase to the DNA bubble duplex in the absence of a hybridized RNA primer, suggesting that the binding of the core polymerase to the bubble-duplex construct also triggers a conformational change that additionally weakens the sigma–core interaction. PMID:10411885

Photoswitchable Janus glycodendrimer micelles as multivalent inhibitors of LecA and LecB from Pseudomonas aeruginosa.

PubMed

Hu, Yingxue; Beshr, Ghamdan; Garvey, Christopher J; Tabor, Rico F; Titz, Alexander; Wilkinson, Brendan L

2017-11-01

The first example of the self-assembly and lectin binding properties of photoswitchable glycodendrimer micelles is reported. Light-addressable micelles were assembled from a library of 12 amphiphilic Janus glycodendrimers composed of variable carbohydrate head groups and hydrophobic tail groups linked to an azobenzene core. Spontaneous association in water gave cylindrical micelles with uniform size distribution as determined by dynamic light scattering (DLS) and small angle neutron scattering (SANS). Trans-cis photoisomerization of the azobenzene dendrimer core was used to probe the self-assembly behaviour and lectin binding properties of cylindrical micelles, revealing moderate-to-potent inhibition of lectins LecA and LecB from Pseudomonas aeruginosa. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Core-level binding energy shifts in Pt Ru nanoparticles: A puzzle resolved

NASA Astrophysics Data System (ADS)

Lewera, Adam; Zhou, Wei Ping; Hunger, Ralf; Jaegermann, Wolfram; Wieckowski, Andrzej; Yockel, Scott; Bagus, Paul S.

2007-10-01

Synchrotron measurements of Pt and Ru core-level binding energies, BE's, in Pt-Ru nanoparticles, as a function of Pt content, quantify earlier indications that the Pt 4f BE shift is much larger than the Ru 3d BE shift. A complementary theoretical analysis relates the BE shifts to changes in the metal-metal distances as the composition of the nanoparticle changes. We establish that the large Pt and small Ru BE shifts arise from the different response of these metals to changes in the bond distances, an unexpected result. Our results give evidence that the magnitudes of the BE shifts depend on whether the d band is open, as for Ru, or essentially filled, as for Pt.

Electronic structures of U X3 (X =Al , Ga, and In) studied by photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Fujimori, Shin-ichi; Kobata, Masaaki; Takeda, Yukiharu; Okane, Tetsuo; Saitoh, Yuji; Fujimori, Atsushi; Yamagami, Hiroshi; Haga, Yoshinori; Yamamoto, Etsuji; Ōnuki, Yoshichika

2017-09-01

The electronic structures of U X3 (X =Al , Ga , and In ) were studied by photoelectron spectroscopy to understand the relationship between their electronic structures and magnetic properties. The band structures and Fermi surfaces of UAl3 and UGa3 were revealed experimentally by angle-resolved photoelectron spectroscopy (ARPES), and they were compared with the result of band-structure calculations. The topologies of the Fermi surfaces and the band structures of UAl3 and UGa3 were explained reasonably well by the calculation, although bands near the Fermi level (EF) were renormalized owing to the finite electron correlation effect. The topologies of the Fermi surfaces of UAl3 and UGa3 are very similar to each other, except for some minor differences. Such minor differences in their Fermi surface or electron correlation effect might take an essential role in their different magnetic properties. No significant changes were observed between the ARPES spectra of UGa3 in the paramagnetic and antiferromagnetic phases, suggesting that UGa3 is an itinerant weak antiferromagnet. The effect of chemical pressure on the electronic structures of U X3 compounds was also studied by utilizing the smaller lattice constants of UAl3 and UGa3 than that of UIn3. The valence band spectrum of UIn3 is accompanied by a satellitelike structure on the high-binding-energy side. The core-level spectrum of UIn3 is also qualitatively different from those of UAl3 and UGa3. These findings suggest that the U 5 f states in UIn3 are more localized than those in UAl3 and UGa3.

Stability of a Bifunctional Cu-Based Core@Zeolite Shell Catalyst for Dimethyl Ether Synthesis Under Redox Conditions Studied by Environmental Transmission Electron Microscopy and In Situ X-Ray Ptychography.

PubMed

Baier, Sina; Damsgaard, Christian D; Klumpp, Michael; Reinhardt, Juliane; Sheppard, Thomas; Balogh, Zoltan; Kasama, Takeshi; Benzi, Federico; Wagner, Jakob B; Schwieger, Wilhelm; Schroer, Christian G; Grunwaldt, Jan-Dierk

2017-06-01

When using bifunctional core@shell catalysts, the stability of both the shell and core-shell interface is crucial for catalytic applications. In the present study, we elucidate the stability of a CuO/ZnO/Al2O3@ZSM-5 core@shell material, used for one-stage synthesis of dimethyl ether from synthesis gas. The catalyst stability was studied in a hierarchical manner by complementary environmental transmission electron microscopy (ETEM), scanning electron microscopy (SEM) and in situ hard X-ray ptychography with a specially designed in situ cell. Both reductive activation and reoxidation were applied. The core-shell interface was found to be stable during reducing and oxidizing treatment at 250°C as observed by ETEM and in situ X-ray ptychography, although strong changes occurred in the core on a 10 nm scale due to the reduction of copper oxide to metallic copper particles. At 350°C, in situ X-ray ptychography indicated the occurrence of structural changes also on the µm scale, i.e. the core material and parts of the shell undergo restructuring. Nevertheless, the crucial core-shell interface required for full bifunctionality appeared to remain stable. This study demonstrates the potential of these correlative in situ microscopy techniques for hierarchically designed catalysts.

PMMA/PS coaxial electrospinning: core-shell fiber morphology as a function of material parameters

NASA Astrophysics Data System (ADS)

Rahmani, Shahrzad; Arefazar, Ahmad; Latifi, Masoud

2017-03-01

Core-shell fibers of polymethyl methacrylate (PMMA) and polystyrene (PS) have been successfully electrospun by coaxial electrospinning. To evaluate the influence of the solvent on the final fiber morphology, four types of organic solvents were used in the shell solution while the core solvent was preserved. Morphological observations with scanning electron microscopy, transmission electron microscopy and optical microscopy revealed that both core and shell solvent properties were involved in the final fiber morphology. To explain this involvement, alongside a discussion of the Bagley solubility graph of PS and PMMA, a novel criterion based on solvent physical properties was introduced. A theoretical model based on the momentum conservation principle was developed and applied for describing the dependence of the core and shell diameters to their solvent combinations. Different concentrations of core and shell were also investigated in the coaxial electrospinning of PMMA/PS. The core-shell fiber morphologies with different core and shell concentrations were compared with their single electrospun fibers.

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.

Electron-ion relaxation in a dense plasma. [supernovae core physics

NASA Technical Reports Server (NTRS)

Littleton, J. E.; Buchler, J.-R.

1974-01-01

The microscopic physics of the thermonuclear runaway in highly degenerate carbon-oxygen cores is investigated to determine if and how a detonation wave is generated. An expression for the electron-ion relaxation time is derived under the assumption of large degeneracy and extreme relativity of the electrons in a two-temperature plasma. Since the nuclear burning time proves to be several orders of magnitude shorter than the relaxation time, it is concluded that in studying the structure of the detonation wave the electrons and ions must be treated as separate fluids.

The Role of Glycine Residues 140 and 141 of Subunit B in the Functional Ubiquinone Binding Site of the Na+-pumping NADH:quinone Oxidoreductase from Vibrio cholerae*

PubMed Central

Juárez, Oscar; Neehaul, Yashvin; Turk, Erin; Chahboun, Najat; DeMicco, Jessica M.; Hellwig, Petra; Barquera, Blanca

2012-01-01

The Na+-pumping NADH:quinone oxidoreductase (Na+-NQR) is the main entrance for electrons into the respiratory chain of many marine and pathogenic bacteria. The enzyme accepts electrons from NADH and donates them to ubiquinone, and the free energy released by this redox reaction is used to create an electrochemical gradient of sodium across the cell membrane. Here we report the role of glycine 140 and glycine 141 of the NqrB subunit in the functional binding of ubiquinone. Mutations at these residues altered the affinity of the enzyme for ubiquinol. Moreover, mutations in residue NqrB-G140 almost completely abolished the electron transfer to ubiquinone. Thus, NqrB-G140 and -G141 are critical for the binding and reaction of Na+-NQR with its electron acceptor, ubiquinone. PMID:22645140

Core-binding factor beta interacts with Runx2 and is required for skeletal development.

PubMed

Yoshida, Carolina A; Furuichi, Tatsuya; Fujita, Takashi; Fukuyama, Ryo; Kanatani, Naoko; Kobayashi, Shinji; Satake, Masanobu; Takada, Kenji; Komori, Toshihisa

2002-12-01

Core-binding factor beta (CBFbeta, also called polyomavirus enhancer binding protein 2beta (PEBP2B)) is associated with an inversion of chromosome 16 and is associated with acute myeloid leukemia in humans. CBFbeta forms a heterodimer with RUNX1 (runt-related transcription factor 1), which has a DNA binding domain homologous to the pair-rule protein runt in Drosophila melanogaster. Both RUNX1 and CBFbeta are essential for hematopoiesis. Haploinsufficiency of another runt-related protein, RUNX2 (also called CBFA1), causes cleidocranial dysplasia in humans and is essential in skeletal development by regulating osteoblast differentiation and chondrocyte maturation. Mice deficient in Cbfb (Cbfb(-/-)) die at midgestation, so the function of Cbfbeta in skeletal development has yet to be ascertained. To investigate this issue, we rescued hematopoiesis of Cbfb(-/-) mice by introducing Cbfb using the Gata1 promoter. The rescued Cbfb(-/-) mice recapitulated fetal liver hematopoiesis in erythroid and megakaryocytic lineages and survived until birth, but showed severely delayed bone formation. Although mesenchymal cells differentiated into immature osteoblasts, intramembranous bones were poorly formed. The maturation of chondrocytes into hypertrophic cells was markedly delayed, and no endochondral bones were formed. Electrophoretic mobility shift assays and reporter assays showed that Cbfbeta was necessary for the efficient DNA binding of Runx2 and for Runx2-dependent transcriptional activation. These findings indicate that Cbfbeta is required for the function of Runx2 in skeletal development.