Surface defect free growth of a spin dimer TlCuCl{sub 3} compound crystals and investigations on its optical and magnetic properties

Energy Technology Data Exchange (ETDEWEB)

Ryu, Gihun, E-mail: G.Ryu@fkf.mpg.de [Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart (Germany); Son, Kwanghyo [Max Planck Institute for Intelligent Systems, Heisenbergstraße 3, 70569 Stuttgart (Germany)

2016-05-15

A defect-free high quality single crystal of spin dimer TlCuCl{sub 3} compound is firstly synthesized at the optimal growth temperature using the vertical Bridgman method. In this study, we clearly found that the cupric chloride is easily decomposed into the Cl{sup −} deficient composition at ≥470 °C. The Cl{sup −}- related gas phase at the high temperature region also always gives rise to a pinhole-like surface defect at the surface of crystal. Therefore, we clearly verified an exotic anisotropic magnetic behavior (anisotropic ratio of M{sub b}/M{sub (201)} at 2 K, 7 T=10) using the defect-free TlCuCl{sub 3} crystals in this three-dimensional spin dimer TlCuCl{sub 3} compound, relatively stronger magnetic ordering in the H//b than that of H//(201) direction at above the transition magnetic field. - Graphical abstract: A single crystal of spin dimer TlCuCl{sub 3} compound with a defect free is successfully synthesized on the basis of TG/DTA result. We newly found that this cupric chloride compound is easily decomposed into the Cl{sup −} deficient composition at ≥470 °C and Cl{sup −} related gas phases also give rise to the defects like a pinhole on the surface of TlCuCl{sub 3} crystal. Using the crystals with a surface defect free, we also clearly verified the crystal structure of spin dimer TlCuCl{sub 3} compound.

Calix[4]arene supported clusters: a dimer of [Mn(III)Mn(II)] dimers

DEFF Research Database (Denmark)

Taylor, Stephanie M; McIntosh, Ruaraidh D; Beavers, Christine M

2011-01-01

Phosphinate ligands allow for the transformation of a calix[4]arene supported [Mn(III)(2)Mn(II)(2)] tetramer cluster motif into an unusual [Mn(III)Mn(II)](2) dimer of dimers; the clusters self-assemble in the crystal to form bi-layer arrays reminiscent of the typical packing of calixarene solvates....

Inverse colloidal crystal membranes for hydrophobic interaction membrane chromatography.

Science.gov (United States)

Vu, Anh T; Wang, Xinying; Wickramasinghe, S Ranil; Yu, Bing; Yuan, Hua; Cong, Hailin; Luo, Yongli; Tang, Jianguo

2015-08-01

Hydrophobic interaction membrane chromatography has gained interest due to its excellent performance in the purification of humanized monoclonal antibodies. The membrane material used in hydrophobic interaction membrane chromatography has typically been commercially available polyvinylidene fluoride. In this contribution, newly developed inverse colloidal crystal membranes that have uniform pores, high porosity and, therefore, high surface area for protein binding are used as hydrophobic interaction membrane chromatography membranes for humanized monoclonal antibody immunoglobulin G purification. The capacity of the inverse colloidal crystal membranes developed here is up to ten times greater than commercially available polyvinylidene fluoride membranes with a similar pore size. This work highlights the importance of developing uniform pore size high porosity membranes in order to maximize the capacity of hydrophobic interaction membrane chromatography. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Crystal structure of N′-hydroxypyrimidine-2-carboximidamide

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Nithianantham Jeeva Jasmine

2014-10-01

Full Text Available The title compound, C5H6N4O, is approximately planar, with an angle of 11.04 (15° between the planes of the pyrimidine ring and the non-H atoms of the carboximidamide unit. The molecule adopts an E configuration about the C=N double bond. In the crystal, adjacent molecules are linked by pairs of N—H...O hydrogen bonds, forming inversion dimers with an R22(10 ring motif. The dimers are further linked via N—H...N and O—H...N hydrogen bonds into a sheet structure parallel to the ac plane. The crystal structure also features N—H...O and weak C—H...O hydrogen bonds and offset π–π stacking interactions between adjacent pyrimidine rings [centroid–centroid distance = 3.622 (1 Å].

Rapid fabrication of 2D and 3D photonic crystals and their inversed structures

International Nuclear Information System (INIS)

Huang, C-K; Chan, C-H; Chen, C-Y; Tsai, Y-L; Chen, C-C; Han, J-L; Hsieh, K-H

2007-01-01

In this paper a new technique is proposed for the fabrication of two-dimensional (2D) and three-dimensional (3D) photonic crystals using monodisperse polystyrene microspheres as the templates. In addition, the approaches toward the creation of their corresponding inversed structures are described. The inversed structures were prepared by subjecting an introduced silica source to a sol-gel process; programmed heating was then performed to remove the template without spoiling the inversed structures. Utilizing these approaches, 2D and 3D photonic crystals and their highly ordered inversed hexagonal multilayer or monolayer structures were obtained on the substrate

Stretched inverse opal colloid crystal substrates-induced orientation of fibroblast

International Nuclear Information System (INIS)

Wang, Y C; Tang, Z M; Feng, Z Q; Xie, Z Y; Gu, Z Z

2010-01-01

Recently, there has been increasing interest in studying the interaction between mammalian cells and nanometer-sized structures. However, the effect of nanostructures on cell behavior, such as cell morphology and alignment, is still largely unknown. Inverse opal colloid crystal substrates, which can be stretched to produce nano-scale pore structures of different degrees of orientation, serve as a convenient model system to study the effect of nanotopography on cell morphology and cell alignment. In this work, we fabricated inverse opal colloidal crystal films that were either unstretched or stretched to three, four or six times their original length, producing pore structures of increasing degree of orientation. Human dermal fibroblast-fetal (HDF-f) cells were seeded and cultured on these four types of substrates. The results from fluorescence microscopy and scanning electron microscopy indicated that cells showed the highest degree of alignment when cultured on inverse opal colloid crystal films that were stretched the most (six times original length). The results also demonstrated that the orientation of nanostructures could affect both the morphology and growth direction of fibroblasts. The ability to control the direction of cell growth through the engineering of nanostructures could have important applications in tissue engineering, especially for tissues with anisotropic structures, such as cardiac muscle, blood vessel, tendon and ligament.

Stretched inverse opal colloid crystal substrates-induced orientation of fibroblast

Energy Technology Data Exchange (ETDEWEB)

Wang, Y C; Tang, Z M; Feng, Z Q; Xie, Z Y; Gu, Z Z, E-mail: gu@seu.edu.c [State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096 (China)

2010-06-01

Recently, there has been increasing interest in studying the interaction between mammalian cells and nanometer-sized structures. However, the effect of nanostructures on cell behavior, such as cell morphology and alignment, is still largely unknown. Inverse opal colloid crystal substrates, which can be stretched to produce nano-scale pore structures of different degrees of orientation, serve as a convenient model system to study the effect of nanotopography on cell morphology and cell alignment. In this work, we fabricated inverse opal colloidal crystal films that were either unstretched or stretched to three, four or six times their original length, producing pore structures of increasing degree of orientation. Human dermal fibroblast-fetal (HDF-f) cells were seeded and cultured on these four types of substrates. The results from fluorescence microscopy and scanning electron microscopy indicated that cells showed the highest degree of alignment when cultured on inverse opal colloid crystal films that were stretched the most (six times original length). The results also demonstrated that the orientation of nanostructures could affect both the morphology and growth direction of fibroblasts. The ability to control the direction of cell growth through the engineering of nanostructures could have important applications in tissue engineering, especially for tissues with anisotropic structures, such as cardiac muscle, blood vessel, tendon and ligament.

Selective amine catalysed steroidal dimerization

Indian Academy of Sciences (India)

of cholesterol is the formation of a green colour in concentrated sulphuric acid, and this was shown to be due to a polyenyl steroidal dimer carbocation.7–9 Many dimeric and oligomeric steroids exhibit interesting micellular, detergent and liquid crystal behaviour.10,11. Most of the steroidal dimmers are also well-known.

Crystal structure of 1,3-dicyclohexyl-1-[3-(pyren-1-ylpropanoyl]urea

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Edgar González-Juárez

2015-10-01

Full Text Available In the title compound, C33H38N2O2, each of the cyclohexyl rings adopts a chair conformation. The two planes involving carbonyl groups, C—(C=O—N and N—(C=O—N, are oriented at a dihedral angle of 62.28 (10°. In the crystal, two neighboring molecules are linked by a pair of N—H...O interactions, generating an inversion dimer. The dimers are interconnected by C—H...O hydrogen bonds into a supramolecular chain along the a-axis direction.

Preparation and Optical Properties of Spherical Inverse Opals by Liquid Phase Deposition Using Spherical Colloidal Crystals

International Nuclear Information System (INIS)

Aoi, Y; Tominaga, T

2013-01-01

Titanium dioxide (TiO 2 ) inverse opals in spherical shape were prepared by liquid phase deposition (LPD) using spherical colloidal crystals as templates. Spherical colloidal crystals were produced by ink-jet drying technique. Aqueous emulsion droplets that contain polystyrene latex particles were ejected into air and dried. Closely packed colloidal crystals with spherical shape were obtained. The obtained spherical colloidal crystals were used as templates for the LPD. The templates were dispersed in the deposition solution of the LPD, i.e. a mixed solution of ammonium hexafluorotitanate and boric acid and reacted for 4 h at 30 °C. After the LPD process, the interstitial spaces of the spherical colloidal crystals were completely filled with titanium oxide. Subsequent heat treatment resulted in removal of templates and spherical titanium dioxide inverse opals. The spherical shape of the template was retained. SEM observations indicated that the periodic ordered voids were surrounded by titanium dioxide. The optical reflectance spectra indicated that the optical properties of the spherical titanium dioxide inverse opals were due to Bragg diffractions from the ordered structure. Filling in the voids of the inverse opals with different solvents caused remarkable changes in the reflectance peak.

An Unusual Dimeric Inhibitor of Acetylcholinesterase: Cooperative Binding of Crystal Violet

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Anders Allgardsson

2017-08-01

Full Text Available Acetylcholinesterase (AChE is an essential enzyme that terminates cholinergic transmission by a rapid hydrolysis of the neurotransmitter acetylcholine. AChE is an important target for treatment of various cholinergic deficiencies, including Alzheimer’s disease and myasthenia gravis. In a previous high throughput screening campaign, we identified the dye crystal violet (CV as an inhibitor of AChE. Herein, we show that CV displays a significant cooperativity for binding to AChE, and the molecular basis for this observation has been investigated by X-ray crystallography. Two monomers of CV bind to residues at the entrance of the active site gorge of the enzyme. Notably, the two CV molecules have extensive intermolecular contacts with each other and with AChE. Computational analyses show that the observed CV dimer is not stable in solution, suggesting the sequential binding of two monomers. Guided by the structural analysis, we designed a set of single site substitutions, and investigated their effect on the binding of CV. Only moderate effects on the binding and the cooperativity were observed, suggesting a robustness in the interaction between CV and AChE. Taken together, we propose that the dimeric cooperative binding is due to a rare combination of chemical and structural properties of both CV and the AChE molecule itself.

Inverse gold photonic crystals and conjugated polymer coated opals for functional materials

Energy Technology Data Exchange (ETDEWEB)

Landon, P.B.; Gutierrez, Jose; Ferraris, John P.; Martinez, I.L.; Giridharagopal, Rajiv; Wu, Y.-C.; Lee, Sergey; Parikh, Kunjal; Gillespie, Jessica; Ussery, Geoffrey; Karimi, Behzad; Baughman, Ray; Zakhidov, Anvar; Glosser, R

2003-10-01

Inverse gold photonic crystals templated from synthetic opals with a face centered cubic (FCC) crystal lattice were constructed by heat converting gold chloride to metallic gold. Tetrahedral formations constructed of alternating large and small octahedrons oriented in the zinc sulfide structure were created by controlling the infiltration of gold chloride. Silica spheres were coated with polyanilinesulfonic acid, polypyrrole, poly[2-methoxy-5-(2'-ethylhexyloxy)-1,4-phenylenevinylene] (MEH-PPV) and 5 nm colloidal gold. Ordinary yeast cells were coated with polyanilinesulfonic acid, polypyrrole and 5 nm colloidal gold. Spheres coated with MEH-PPV were dispersed in H{sub 2}O and coated with polyelectrolytes which recharged and sterically stabilized the colloidal surfaces. The recharged spheres self-assembled by sedimentation with a FCC crystalline lattice possessing 500 {mu}m wide and 1 mm long crystallites. Silica spheres with diameters as large as 1500 {mu}m were self-assembled along the [1 0 0] direction of the FCC crystal lattice. Opals infiltrated with gold and opals constructed from polymer coated spheres were co-infiltrated with polypropylene yielding inverse polypropylene composite photonic crystals.

Crystal structure of 2-cyano-N-(furan-2-ylmethyl-3-(3-nitrophenylpropanamide

Directory of Open Access Journals (Sweden)

Shivanna Subhadramma

2015-08-01

Full Text Available In the title compound, C15H11N3O4, the acetamide group is inclined to the furan ring by 66.5 (1°. The dihedral angle between the furan ring and the benzene ring is 66.8 (1°. In the crystal, molecules are linked by pairs of N—H...N hydrogen bonds, forming inversion dimers with an R22(12 ring motif. The dimers are linked via two pairs of C—H...O hydrogen bonds to the same acceptor oxygen atom, enclosing R21(6 ring motifs, forming chains along the [101] direction.

Optimal enhancement in conversion efficiency of crystalline Si solar cells using inverse opal photonic crystals as back reflectors

International Nuclear Information System (INIS)

Chaouachi, A; M’nif, A; Hamzaoui, A H; Chtourou, R

2015-01-01

The effect of using inverse opal photonic crystals as back reflectors on the power conversion efficiency of c-Si solar cells is investigated. The reflection spectra of inverse opal photonic crystals with different diameters of air spheres are simulated using the finite difference time domain (FDTD) method. The reflection peaks are correlated with photonic band gaps present in the photonic band gap diagram. Significant improvement in the optical absorption of the crystalline silicon layer is recorded when inverse opal photonic crystals are considered. Physical mechanisms which may contribute to the enhancement of the light absorption are underlined. With higher short-circuit current enhancement possible, and with no corresponding degradation in open-circuit voltage V oc or the fill factor, the power conversion efficiency is increased significantly when inverse opal photonic crystals are used as back reflectors with optimized diameter of air spheres. (paper)

Tricriticality for dimeric Coulomb molecular crystals in ground state

Science.gov (United States)

Travěnec, Igor; Šamaj, Ladislav

2017-12-01

We study the ground-state properties of a system of dimers. Each dimer consists in a pair of equivalent charges at a fixed distance, immersed in a neutralizing homogeneous background. All charges interact pairwisely by Coulomb potential. The dimer centers form a two-dimensional rectangular lattice with the aspect ratio α\\in [0, 1] and each dimer is allowed to rotate around its center. The previous numerical simulations, made for the more general Yukawa interaction, indicate that only two basic dimer configurations can appear: either all dimers are parallel or they have two different angle orientations within alternating (checkerboard) sublattices. As the dimer size increases, two second-order phase transitions, related to two kinds of the symmetry breaking in dimer’s orientations, were reported. In this paper, we use a recent analytic method based on an expansion of the interaction energy in Misra functions which converges quickly and provides an analytic derivation of the critical behaviour. Our main result is that there exists a specific aspect ratio of the rectangular lattice α^*=0.714 106 840 000 71\\ldots which divides the space of model’s phases onto two distinct regions. If the lattice aspect ratio α>α* , we recover both types of the second-order phase transitions and find that they are of mean-field type with the critical exponent β = 1/2 . If 0.711 535≤slantα<α* , the phase transition associated with the discontinuity of dimer’s angles on alternating sublattices becomes of first order. For α=α* , the first- and second-order phase transitions meet at the tricritical point, characterized by the different critical index β = 1/4 . Such phenomenon is known from literature about the Landau theory of one-component fields, but in our two-component version the scenario is more complicated: the component which is already in the symmetry-broken state at the tricritical point also interferes and exhibits unexpectedly the mean-field singular

Structural insights into lipid-dependent reversible dimerization of human GLTP

International Nuclear Information System (INIS)

Samygina, Valeria R.; Ochoa-Lizarralde, Borja; Popov, Alexander N.; Cabo-Bilbao, Aintzane; Goni-de-Cerio, Felipe; Molotkovsky, Julian G.; Patel, Dinshaw J.; Brown, Rhoderick E.; Malinina, Lucy

2013-01-01

It is shown that dimerization is promoted by glycolipid binding to human GLTP. The importance of dimer flexibility in wild-type protein is manifested by point mutation that ‘locks’ the dimer while diversifying ligand/protein adaptations. Human glycolipid transfer protein (hsGLTP) forms the prototypical GLTP fold and is characterized by a broad transfer selectivity for glycosphingolipids (GSLs). The GLTP mutation D48V near the ‘portal entrance’ of the glycolipid binding site has recently been shown to enhance selectivity for sulfatides (SFs) containing a long acyl chain. Here, nine novel crystal structures of hsGLTP and the SF-selective mutant complexed with short-acyl-chain monoSF and diSF in different crystal forms are reported in order to elucidate the potential functional roles of lipid-mediated homodimerization. In all crystal forms, the hsGLTP–SF complexes displayed homodimeric structures supported by similarly organized intermolecular interactions. The dimerization interface always involved the lipid sphingosine chain, the protein C-terminus (C-end) and α-helices 6 and 2, but the D48V mutant displayed a ‘locked’ dimer conformation compared with the hinge-like flexibility of wild-type dimers. Differences in contact angles, areas and residues at the dimer interfaces in the ‘flexible’ and ‘locked’ dimers revealed a potentially important role of the dimeric structure in the C-end conformation of hsGLTP and in the precise positioning of the key residue of the glycolipid recognition centre, His140. ΔY207 and ΔC-end deletion mutants, in which the C-end is shifted or truncated, showed an almost complete loss of transfer activity. The new structural insights suggest that ligand-dependent reversible dimerization plays a role in the function of human GLTP

Growth, Faraday and inverse Faraday characteristics of Tb2Ti2O7 crystal.

Science.gov (United States)

Guo, Feiyun; Sun, Yilin; Yang, Xiongsheng; Chen, Xin; Zhao, Bin; Zhuang, Naifeng; Chen, Jianzhong

2016-03-21

Tb2Ti2O7 (TTO) single crystal with dimensions of 20 × 20 × 16 mm3 was grown by the Czochralski method. Rietveld structure refinement of X-ray diffraction (XRD) data confirms that the compound crystallizes in the cubic system with pyrochlore structure. Transmission spectra, Magnetic circular dichroism (MCD) spectra, Faraday and inverse Faraday characteristics of TTO crystal have been measured and analyzed in detail. The results demonstrate that TTO crystal has high transmittance at 700-1400 nm waveband and a larger Verdat constant than that of TGG reported. Magnetic circular dichroism (MCD) spectra showed that the 4f→4f transitions of Tb3+ have significant contributions to the magneto-optical activity (MOA). In the time-resolved pump-probe spectroscopy, the rotation signals of the probe beam based on the inverse Faraday effect in magneto-optical crystal were observed at zero time delay, the full width at half maximum of the rotation and ellipticity signals can be as fast as ~500 fs, which indicates that TTO crystal can be a promising material for ultrafast all-optical magnetic switching.

Crystal structure of 2-pentyloxybenzamide

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Bernhard Bugenhagen

2014-10-01

Full Text Available In the title molecule, C12H17NO2, the amide NH2 group is oriented toward the pentyloxy substituent and an intramolecular N—H...O hydrogen bond is formed with the pentyloxy O atom. The benzene ring forms dihedral angles of 2.93 (2 and 5.60 (2° with the amide group and the pentyloxy group mean planes, respectively. In the crystal, molecules are linked by pairs of N—H...O hydrogen bonds, forming inversion dimers with their molecular planes parallel, but at an offset of 0.45 (1 Å to each other. These dimers are ordered into two types of symmetry-related columns extended along the a axis, with the mean plane of one set of dimers in a column approximately parallel to (121 and the other in a column approximately parallel to (1-21. The two planes form a dihedral angle of 85.31 (2°, and are linked via C—H...O hydrogen bonds and C—H...π interactions, forming a three-dimensional framework structure.

Zak phase and band inversion in dimerized one-dimensional locally resonant metamaterials

Science.gov (United States)

Zhu, Weiwei; Ding, Ya-qiong; Ren, Jie; Sun, Yong; Li, Yunhui; Jiang, Haitao; Chen, Hong

2018-05-01

The Zak phase, which refers to Berry's phase picked up by a particle moving across the Brillouin zone, characterizes the topological properties of Bloch bands in a one-dimensional periodic system. Here the Zak phase in dimerized one-dimensional locally resonant metamaterials is investigated. It is found that there are some singular points in the bulk band across which the Bloch states contribute π to the Zak phase, whereas in the rest of the band the contribution is nearly zero. These singular points associated with zero reflection are caused by two different mechanisms: the dimerization-independent antiresonance of each branch and the dimerization-dependent destructive interference in multiple backscattering. The structure undergoes a topological phase-transition point in the band structure where the band inverts, and the Zak phase, which is determined by the numbers of singular points in the bulk band, changes following a shift in dimerization parameter. Finally, the interface state between two dimerized metamaterial structures with different topological properties in the first band gap is demonstrated experimentally. The quasi-one-dimensional configuration of the system allows one to explore topology-inspired new methods and applications on the subwavelength scale.

Adventures in holographic dimer models

International Nuclear Information System (INIS)

Kachru, Shamit; Karch, Andreas; Yaida, Sho

2011-01-01

We abstract the essential features of holographic dimer models, and develop several new applications of these models. Firstly, semi-holographically coupling free band fermions to holographic dimers, we uncover novel phase transitions between conventional Fermi liquids and non-Fermi liquids, accompanied by a change in the structure of the Fermi surface. Secondly, we make dimer vibrations propagate through the whole crystal by way of double trace deformations, obtaining nontrivial band structure. In a simple toy model, the topology of the band structure experiences an interesting reorganization as we vary the strength of the double trace deformations. Finally, we develop tools that would allow one to build, in a bottom-up fashion, a holographic avatar of the Hubbard model.

Color Tunable and Upconversion Luminescence in Yb-Tm Co-Doped Yttrium Phosphate Inverse Opal Photonic Crystals.

Science.gov (United States)

Wang, Siqin; Qiu, Jianbei; Wang, Qi; Zhou, Dacheng; Yang, Zhengwen

2016-04-01

For this paper, YPO4: Tm, Yb inverse opals with the photonic band gaps at 475 nm and 655 nm were prepared by polystyrene colloidal crystal templates. We investigated the influence of photonic band gaps on the Tm-Yb upconversion emission which was in the YPO4: Tm Yb inverse opal photonic crystals. Comparing with the reference sample, significant suppression of both the blue and red upconversion luminescence of Tm3+ ions were observed in the inverse opals. The color purity of the blue emission was improved in the inverse opal by the suppression of red upconversion emission. Additionally, mechanism of upconversion emission in the inverse opal was discussed. We believe that the present work will be valuable for not only the foundational study of upconversion emission modification but also the development of new optical devices in upconversion lighting and display.

Periodic order and defects in Ni-based inverse opal-like crystals on the mesoscopic and atomic scale

Science.gov (United States)

Chumakova, A. V.; Valkovskiy, G. A.; Mistonov, A. A.; Dyadkin, V. A.; Grigoryeva, N. A.; Sapoletova, N. A.; Napolskii, K. S.; Eliseev, A. A.; Petukhov, A. V.; Grigoriev, S. V.

2014-10-01

The structure of inverse opal crystals based on nickel was probed on the mesoscopic and atomic levels by a set of complementary techniques such as scanning electron microscopy and synchrotron microradian and wide-angle diffraction. The microradian diffraction revealed the mesoscopic-scale face-centered-cubic (fcc) ordering of spherical voids in the inverse opal-like structure with unit cell dimension of 750±10nm. The diffuse scattering data were used to map defects in the fcc structure as a function of the number of layers in the Ni inverse opal-like structure. The average lateral size of mesoscopic domains is found to be independent of the number of layers. 3D reconstruction of the reciprocal space for the inverse opal crystals with different thickness provided an indirect study of original opal templates in a depth-resolved way. The microstructure and thermal response of the framework of the porous inverse opal crystal was examined using wide-angle powder x-ray diffraction. This artificial porous structure is built from nickel crystallites possessing stacking faults and dislocations peculiar for the nickel thin films.

Dimer-based model for heptaspanning membrane receptors.

Science.gov (United States)

Franco, Rafael; Casadó, Vicent; Mallol, Josefa; Ferré, Sergi; Fuxe, Kjell; Cortés, Antonio; Ciruela, Francisco; Lluis, Carmen; Canela, Enric I

2005-07-01

The existence of intramembrane receptor-receptor interactions for heptaspanning membrane receptors is now fully accepted, but a model considering dimers as the basic unit that binds to two ligand molecules is lacking. Here, we propose a two-state-dimer model in which the ligand-induced conformational changes from one component of the dimer are communicated to the other. Our model predicts cooperativity in binding, which is relevant because the other current models fail to address this phenomenon satisfactorily. Our two-state-dimer model also predicts the variety of responses elicited by full or partial agonists, neutral antagonists and inverse agonists. This model can aid our understanding of the operation of heptaspanning receptors and receptor channels, and, potentially, be important for improving the treatment of cardiovascular, neurological and neuropsychyatric diseases.

Crystal structure of hyperthermophilic esterase EstE1 and the relationship between its dimerization and thermostability properties

Directory of Open Access Journals (Sweden)

Koh Eunhee

2007-07-01

Full Text Available Abstract Background EstE1 is a hyperthermophilic esterase belonging to the hormone-sensitive lipase family and was originally isolated by functional screening of a metagenomic library constructed from a thermal environmental sample. Dimers and oligomers may have been evolutionally selected in thermophiles because intersubunit interactions can confer thermostability on the proteins. The molecular mechanisms of thermostabilization of this extremely thermostable esterase are not well understood due to the lack of structural information. Results Here we report for the first time the 2.1-Å resolution crystal structure of EstE1. The three-dimensional structure of EstE1 exhibits a classic α/β hydrolase fold with a central parallel-stranded beta sheet surrounded by alpha helices on both sides. The residues Ser154, Asp251, and His281 form the catalytic triad motif commonly found in other α/β hydrolases. EstE1 exists as a dimer that is formed by hydrophobic interactions and salt bridges. Circular dichroism spectroscopy and heat inactivation kinetic analysis of EstE1 mutants, which were generated by structure-based site-directed mutagenesis of amino acid residues participating in EstE1 dimerization, revealed that hydrophobic interactions through Val274 and Phe276 on the β8 strand of each monomer play a major role in the dimerization of EstE1. In contrast, the intermolecular salt bridges contribute less significantly to the dimerization and thermostability of EstE1. Conclusion Our results suggest that intermolecular hydrophobic interactions are essential for the hyperthermostability of EstE1. The molecular mechanism that allows EstE1 to endure high temperature will provide guideline for rational design of a thermostable esterase/lipase using the lipolytic enzymes showing structural similarity to EstE1.

Crystal structure of 3-(4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacen-3-ylpropanoic acid

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Takuma Kato

2017-12-01

Full Text Available The crystal structure of the title compound, C14H15BF2N2O2, which comprises a boron–dipyrromethene (BODIPY backbone and a propionic acid group, has been determined at 100 K. The BODIPY fused-ring system is nearly planar, with a maximum deviation from the mean plane of 0.032 (2 Å. In the crystal, pairs of O—H...O hydrogen bonds connect the molecules, forming inversion dimers. The dimers are linked via C—H...O hydrogen bonds, forming a tape along the a axis. The tapes are stacked along the c axis through C—H...F hydrogen bonds and π–π interactions.

Crystal structure of (benzenecarbothioamide-κSchloridobis(triphenylphosphane-κPsilver(I

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Wattana Ruangwut

2014-09-01

Full Text Available In the mononuclear mixed-ligand title complex, [AgCl(C7H7NS(C18H15P2], the AgI ion is four coordinated by one S atom of a benzenecarbothioamide ligand, two P atoms of two triphenylphosphane ligands and one chloride ion, displaying a distorted tetrahedral coordination geometry. In the crystal, pairs of N—H...Cl hydrogen bonds form inversion dimers. An intramolecular N—H...Cl hydrogen bond is also observed.

Obtaining the crystal potential by inversion from electron scattering intensities

International Nuclear Information System (INIS)

Allen, L.T.; Josefsson, T.W.; Leeb, H.

1998-01-01

A method to obtain the crystal potential from the intensities of the diffracted beams in high energy electron diffraction is proposed. It is based on a series of measurements for specific well determined orientations of the incident beam which determine the moduli of all elements of the scattering matrix. Using unitarity and the specific form of the scattering matrix (including symmetries) an overdetermined set of non-linear equations is obtained from these data. Solution of these equations yields the required phase information and allows the determination of a (projected) crystal potential by inversion which is unique up to an arbitrary shift of the origin. The reconstruction of potentials from intensities is illustrated for two realistic examples, a [111] systematic row case in ZnS and a [110] zone axis orientation in GaAs (both noncentrosymmetric crystals)

Crystal structure of diethyl 2-amino-6-[(thiophen-3-ylethynyl]azulene-1,3-dicarboxylate

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Sebastian Förster

2015-03-01

Full Text Available The title compound, C22H19NO4S, has an almost planar geometry supported by intramolecular N—H...O and C—H...O hydrogen bonds. The thiophene ring is inclined to the azulene ring by 4.85 (16°, while the ethoxycarbonyl groups are inclined to the azulene ring by 7.0 (2 and 5.7 (2°. In the crystal, molecules are linked by pairs of N—H...O hydrogen bonds, forming inversion dimers with an R22(12 ring motif. The dimers are linked via C—H...π interactions, forming sheets parallel to (10-1.

Controllable synthesis, crystal structure and magnetic properties of Monomer-Dimer Cocrystallized MnIII Salen-type composite material

Science.gov (United States)

Wu, Qiong; Wu, Wei; Wu, Yongmei; Li, Weili; Qiao, Yongfeng; Wang, Ying; Wang, Baoling

2018-04-01

By the reaction of manganese-Schiff-base complexes with penta-anionic Anderson heteropolyanion, a new supramolecular architecture [Mn2(Salen)2(H2O)2][Mn(Salen)(H2O)2]2Na[IMo6O24]·8H2O (1) (salen = N,N‧-ethylene-bis (salicylideneiminate) has been isolated. Compound 1 was characterized by the single-crystal X-ray diffraction, elemental, IR and thermal gravimetric analyses. Structural analysis reveals that the unit cell simultaneously contains MnIII-Salen dimer and monomer cation fragments, for which the Anderson-type polyanions serve as counter anions. In the packing arrangement, all the MnIII dimers are well separated by polyoxometalate units and form tertiary structure together with MnIII monomers. Interestingly, different from the previous work, in the exact same reaction conditions, we are able to template MnIII-Salen complexes into different configurations by varying the charge state of polyanions. Besides, the magnetic properties of 1 were also examined by using both dc and ac magnetic field of the superconducting quantum interference devices. Most importantly, our fitting of the experimental data to a Heisenberg-type spin model shows that there exists a ferromagnetic exchange interaction ∼5 K between the spins (S = 2) on MnIII in the dimer, while antiferromagnetic ones exist among monomers and dimer (∼2 K). This meta-magnetic state could induce a slight spin frustration at low temperature, which would in turn affect the magnetic behavior. In addition, our ac field measurement of the susceptibilities suggests a typical signature for a single-molecule magnet.

Crystal structures of 2-[(4,6-diaminopyrimidin-2-ylsulfanyl]-N-(naphthalen-1-ylacetamide and 2-[(4,6-diaminopyrimidin-2-ylsulfanyl]-N-(4-fluorophenylacetamide

Directory of Open Access Journals (Sweden)

S. Subasri

2017-02-01

Full Text Available The title compounds, C16H15N5OS, (I, and C12H12FN5OS, (II, are [(diaminopyrimidinesulfanyl]acetamide derivatives. In (I, the pyrimidine ring is inclined to the naphthalene ring system by 55.5 (1°, while in (II, the pyrimidine ring is inclined to the benzene ring by 58.93 (8°. In (II, there is an intramolecular N—H...N hydrogen bond and a short C—H...O contact. In the crystals of (I and (II, molecules are linked by pairs of N—H...N hydrogen bonds, forming inversion dimers with R22(8 ring motifs. In the crystal of (I, the dimers are linked by bifurcated N—H...(O,O and C—H...O hydrogen bonds, forming layers parallel to (100. In the crystal of (II, the dimers are linked by N—H...O hydrogen bonds, also forming layers parallel to (100. The layers are linked by C—H...F hydrogen bonds, forming a three-dimensional architecture.

Different β-alanine dimeric forms in trifluoromethanesulfonic acid salts. XRD and vibrational studies

Science.gov (United States)

Wołoszyn, Łukasz; Ilczyszyn, Maria M.

2018-03-01

Two new crystalline salts: β-alaninium trifluoromethanesulfonate (β-AlaOTf) and bis(β-alanine) trifluoromethanesulfonate (β-2AlaOTf) were obtained. The former one contains diprotonated β-alanine dimer, the latter one monoprotonated β-alanine dimer. Both compounds were studied by single crystal XRD, vibrational (IR and Raman) spectroscopy and calorimetric method. The quantum-mechanical calculations (DFT/B3LYP/6-311 ++G(2d,2p)) for the diprotonated dimer were carried out. The β-AlaOTf salt crystallizes in the P 1 bar space group of triclinic system (Z = 2), the β-2AlaOTf in the P21/m space group of monoclinic system (Z = 2). The vibrational data for the studied compounds are discussed in relation to their crystal structure, and provide insight into the character of hydrogen bonds and β-alanine protonation. The studied crystals do not exhibit phase transitions in the solid state.

Inverse opal photonic crystals with photonic band gaps in the visible and near-infrared

Science.gov (United States)

Jarvis, Brandon C.; Gilleland, Cody L.; Renfro, Tim; Gutierrez, Jose; Parikh, Kunjal; Glosser, R.; Landon, Preston B.

2005-08-01

Colloidal silica spheres with 200nm, 250nm, and 290nm diameters were self-assembled with single crystal crystallites 4-5mm wide and 10-15mm long. Larger spheres with diameters between 1000-2300nm were self-assembled with single crystal crystallites up to 1.5mm wide and 2mm long. The silica opals self-assembled vertically along the [100] direction of the face centered cubic lattice resulting in self-templated opals. Inverse opal photonic crystals with a partial band gap possessing a maximum in the near infrared at 3.8μm were constructed from opal templates composed of 2300nm diameter spheres with chalcogenide Ge33As12Se55 (AMTIR-1), a transparent glass in the near infrared with high refractive index. Inverse gold and gold/ polypropylene composite photonic crystals were fabricated from synthetic opal templates composed of 200-290nm silica spheres. The reflectance spectra and electrical conductance of the resulting structures is presented. Gold was infiltrated into opal templates as gold chloride and heat converted to metallic gold. Opals partially infiltrated with gold were co-infiltrated with polypropylene plastic for mechanical support prior to removal of the silica template with hydrofluoric acid.

Different β-alanine dimeric forms in trifluoromethanesulfonic acid salts. XRD and vibrational studies.

Science.gov (United States)

Wołoszyn, Łukasz; Ilczyszyn, Maria M

2018-03-15

Two new crystalline salts: β-alaninium trifluoromethanesulfonate (β-AlaOTf) and bis(β-alanine) trifluoromethanesulfonate (β-2AlaOTf) were obtained. The former one contains diprotonated β-alanine dimer, the latter one monoprotonated β-alanine dimer. Both compounds were studied by single crystal XRD, vibrational (IR and Raman) spectroscopy and calorimetric method. The quantum-mechanical calculations (DFT/B3LYP/6-311++G(2d,2p)) for the diprotonated dimer were carried out. The β-AlaOTf salt crystallizes in the P1¯ space group of triclinic system (Z=2), the β-2AlaOTf in the P2 1 /m space group of monoclinic system (Z=2). The vibrational data for the studied compounds are discussed in relation to their crystal structure, and provide insight into the character of hydrogen bonds and β-alanine protonation. The studied crystals do not exhibit phase transitions in the solid state. Copyright © 2017 Elsevier B.V. All rights reserved.

Laser desorption single-conformation UV and IR spectroscopy of the sulfonamide drug sulfanilamide, the sulfanilamide-water complex, and the sulfanilamide dimer.

Science.gov (United States)

Uhlemann, Thomas; Seidel, Sebastian; Müller, Christian W

2017-06-07

We have studied the conformational preferences of the sulfonamide drug sulfanilamide, its dimer, and its monohydrated complex through laser desorption single-conformation UV and IR spectroscopy in a molecular beam. Based on potential energy curves for the inversion of the anilinic and the sulfonamide NH 2 groups calculated at DFT level, we suggest that the zero-point level wave function of the sulfanilamide monomer is appreciably delocalized over all four conformer wells. The sulfanilamide dimer, and the monohydrated complex each exhibit a single isomer in the molecular beam. The isomeric structures of the sulfanilamide dimer and the monohydrated sulfanilamide complex were assigned based on their conformer-specific IR spectra in the NH and OH stretch region. Quantum Theory of Atoms in Molecules (QTAIM) analysis of the calculated electron density in the water complex suggests that the water molecule is bound side-on in a hydrogen bonding pocket, donating one O-HO[double bond, length as m-dash]S hydrogen bond and accepting two hydrogen bonds, a NHO and a CHO hydrogen bond. QTAIM analysis of the dimer electron density suggests that the C i symmetry dimer structure exhibits two dominating N-HO[double bond, length as m-dash]S hydrogen bonds, and three weaker types of interactions: two CHO bonds, two CHN bonds, and a chalcogen OO interaction. Most interestingly, the molecular beam dimer structure closely resembles the R dimer unit - the dimer unit with the greatest interaction energy - of the α, γ, and δ crystal polymorphs. Interacting Quantum Atoms analysis provides evidence that the total intermolecular interaction in the dimer is dominated by the short-range exchange-correlation contribution.

Structural insights into the intertwined dimer of fyn SH2.

Science.gov (United States)

Huculeci, Radu; Garcia-Pino, Abel; Buts, Lieven; Lenaerts, Tom; van Nuland, Nico

2015-12-01

Src homology 2 domains are interaction modules dedicated to the recognition of phosphotyrosine sites incorporated in numerous proteins found in intracellular signaling pathways. Here we provide for the first time structural insight into the dimerization of Fyn SH2 both in solution and in crystalline conditions, providing novel crystal structures of both the dimer and peptide-bound structures of Fyn SH2. Using nuclear magnetic resonance chemical shift analysis, we show how the peptide is able to eradicate the dimerization, leading to monomeric SH2 in its bound state. Furthermore, we show that Fyn SH2's dimer form differs from other SH2 dimers reported earlier. Interestingly, the Fyn dimer can be used to construct a completed dimer model of Fyn without any steric clashes. Together these results extend our understanding of SH2 dimerization, giving structural details, on one hand, and suggesting a possible physiological relevance of such behavior, on the other hand. © 2015 The Protein Society.

Crystal structure and DFT study of (E-4-[({4-[(pyridin-2-ylmethylideneamino]phenyl}aminomethyl]phenol

Directory of Open Access Journals (Sweden)

Md. Serajul Haque Faizi

2018-03-01

Full Text Available In the title Schiff base compound, C19H17N3O, the configuration about the C=N bond is E. The molecule is non-planar, with the phenolic and pyridine rings being inclined to the central benzene ring by 56.59 (4 and 15.13 (14°, respectively. In the crystal, molecules are linked by pairs of O—H...N hydrogen bonds, forming inversion dimers. The dimers are connected to neighbouring dimers by N—H...O hydrogen bonds and C—H...π interactions, forming layers parallel to the bc plane. The layers are linked by offset π–π interactions [intercentroid distance = 3.779 (2 Å], forming a three-dimensional supramolecular structure. Quantum chemical calculations of the molecule are in good agreement with the solid-state structure.

Crystal structure of methyl 2-hydroxy-5-[(4-oxo-4,5-dihydro-1,3-thiazol-2-ylamino]benzoate

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Shaaban K. Mohamed

2015-05-01

Full Text Available The title compound, C11H10N2O4S, crystallized with two independent molecules (A and B in the asymmetric unit. They differ primarily in the rotational orientation of the five-membered heterocyclic ring. In molecule A this ring is inclined to the benzene ring by 48.17 (8°, while in molecule B the same dihedral angle is 23.07 (8°. In each molecule there is an intramolecular O—H...O hydrogen bond involving the adjacent hydroxyl group and the ester carbonyl O atom. In the crystal, the A molecules are linked via pairs of N—H...N hydrogen bonds, forming inversion dimers. These dimers are linked to the B molecules via N—H.·O, C—H...O and C—H...S hydrogen bonds forming corrugated sheets lying parallel to (102.

Preparation and photonic bandgap properties of Na1/2Bi1/2TiO3 inverse opal photonic crystals

International Nuclear Information System (INIS)

Yang Zhengwen; Zhou Ji; Huang Xueguang; Xie Qin; Fu Ming; Li Bo; Li Longtu

2009-01-01

The Na 1/2 Bi 1/2 TiO 3 (NBT) inverse opal photonic crystals were prepared by the self-assembly technique in combination with a sol-gel method. In the preparation process, NBT precursors were filled into the interstices of the opal template assembled by monodispersive polystyrene microspheres. The polystyrene template was then removed by calcination at 800 deg. C for 5 h, meanwhile, a perovskite NBT inverse opal photonic crystal was formed. An optical micrograph shows that the NBT inverse opals reflect green-yellow light strongly. Moreover, a photonic band gap was observed by reflective spectra of NBT sample

Dimerization effect of sucrose octasulfate on rat FGF1

International Nuclear Information System (INIS)

Kulahin, N.; Kiselyov, V.; Kochoyan, A.; Kristensen, O.; Kastrup, Jette S.; Berezin, V.; Bock, E.; Gajhede, M.

2008-01-01

The work describes the sucrose octasulfate-mediated dimerization of rat FGF1 by gel-filtration experiments and crystal structure determination. Fibroblast growth factors (FGFs) constitute a family of at least 23 structurally related heparin-binding proteins that are involved in regulation of cell growth, survival, differentiation and migration. Sucrose octasulfate (SOS), a chemical analogue of heparin, has been demonstrated to activate FGF signalling pathways. The structure of rat FGF1 crystallized in the presence of SOS has been determined at 2.2 Å resolution. SOS-mediated dimerization of FGF1 was observed, which was further supported by gel-filtration experiments. The major contributors to the sulfate-binding sites in rat FGF1 are Lys113, Lys118, Arg122 and Lys128. An arginine at position 116 is a consensus residue in mammalian FGF molecules; however, it is a serine in rat FGF1. This difference may be important for SOS-mediated FGF1 dimerization in rat

Ultrafast optical switching of three-dimensional Si inverse opal photonic band gap crystals

NARCIS (Netherlands)

Euser, T.G.; Wei, Hong; Kalkman, Jeroen; Jun, Yoonho; Polman, Albert; Norris, David J.; Vos, Willem L.

2007-01-01

We present ultrafast optical switching experiments on three-dimensional photonic band gap crystals. Switching the Si inverse opal is achieved by optically exciting free carriers by a two-photon process. We probe reflectivity in the frequency range of second order Bragg diffraction where the photonic

L-Cysteine halogenides: A new family of salts with an L-cysteine⋯L-cysteinium dimeric cation

Science.gov (United States)

Ghazaryan, V. V.; Minkov, V. S.; Boldyreva, E. V.; Petrosyan, A. M.

2016-10-01

Two L-cysteinium-halogenides with (L-cysteine···L-cysteinium) dimeric cations have been obtained, (L-Cys⋯L-Cys+)·Cl-, and (L-Cys⋯L-Cys+)·Br-. Both salts crystallize in monoclinic space group P21. Although these salts have the same dimeric cations and isotypical halogen anions, crystal packing is different. The main difference between the two salts rests in the conformation of (L-Cys⋯L-Cys+) dimeric cation, which also differs from that of the dimeric cation in the previously reported compound L-Cys+(L-Cys⋯L-Cys+)·F-·(F-⋯HF). The dimeric cation is formed by a very short O-H⋯O hydrogen bond with d(O···O) of 2.449(2) Å and 2.435(11) Å in the chloride and bromide, respectively. In addition to crystal structure analysis, Infrared and Raman spectra have been registered and discussed with a particular focus on intermolecular interactions. The L-Cys+·Br-·H2O salt with a simple L-cysteinium cation was also obtained and the crystal structure solved. It resembles its chloride analogue, L-Cys+·Cl-·H2O.

Inverse Opal Photonic Crystals as an Optofluidic Platform for Fast Analysis of Hydrocarbon Mixtures.

Science.gov (United States)

Xu, Qiwei; Mahpeykar, Seyed Milad; Burgess, Ian B; Wang, Xihua

2018-06-13

Most of the reported optofluidic devices analyze liquid by measuring its refractive index. Recently, the wettability of liquid on various substrates has also been used as a key sensing parameter in optofluidic sensors. However, the above-mentioned techniques face challenges in the analysis of the relative concentration of components in an alkane hydrocarbon mixture, as both refractive indices and wettabilities of alkane hydrocarbons are very close. Here, we propose to apply volatility of liquid as the key sensing parameter, correlate it to the optical property of liquid inside inverse opal photonic crystals, and construct powerful optofluidic sensors for alkane hydrocarbon identification and analysis. We have demonstrated that via evaporation of hydrocarbons inside the periodic structure of inverse opal photonic crystals and observation of their reflection spectra, an inverse opal film could be used as a fast-response optofluidic sensor to accurately differentiate pure hydrocarbon liquids and relative concentrations of their binary and ternary mixtures in tens of seconds. In these 3D photonic crystals, pure chemicals with different volatilities would have different evaporation rates and can be easily identified via the total drying time. For multicomponent mixtures, the same strategy is applied to determine the relative concentration of each component simply by measuring drying time under different temperatures. Using this optofluidic sensing platform, we have determined the relative concentrations of ternary hydrocarbon mixtures with the difference of only one carbon between alkane hydrocarbons, which is a big step toward detailed hydrocarbon analysis for practical use.

Light activation of the LOV protein vivid generates a rapidly exchanging dimer.

Science.gov (United States)

Zoltowski, Brian D; Crane, Brian R

2008-07-08

The fungal photoreceptor Vivid (VVD) plays an important role in the adaptation of blue-light responses in Neurospora crassa. VVD, an FAD-binding LOV (light, oxygen, voltage) protein, couples light-induced cysteinyl adduct formation at the flavin ring to conformational changes in the N-terminal cap (Ncap) of the VVD PAS domain. Size-exclusion chromatography (SEC), equilibrium ultracentrifugation, and static and dynamic light scattering show that these conformational changes generate a rapidly exchanging VVD dimer, with an expanded hydrodynamic radius. A three-residue N-terminal beta-turn that assumes two different conformations in a crystal structure of a VVD C71V variant is essential for light-state dimerization. Residue substitutions at a critical hinge between the Ncap and PAS core can inhibit or enhance dimerization, whereas a Tyr to Trp substitution at the Ncap-PAS interface stabilizes the light-state dimer. Cross-linking through engineered disulfides indicates that the light-state dimer differs considerably from the dark-state dimer found in VVD crystal structures. These results verify the role of Ncap conformational changes in gating the photic response of N. crassa and indicate that LOV-LOV homo- or heterodimerization may be a mechanism for regulating light-activated gene expression.

Monomers, dimers, and trimers of [Au(CN2]− in a Ba(diaza-18-crown-62+ coordination polymer

Directory of Open Access Journals (Sweden)

2009-03-01

Full Text Available The structure of the title compound, poly[triaquatetra-μ-cyanido-tetracyanidobis(1,4,10,13-tetraoxa-7,16-diazacyclooctadecanedibarium(IItetragold(I], [Au4Ba2(CN8(C12H26N2O42(H2O3]n, displays O—H...N hydrogen bonding between water molecules and cyano ligands and an unusual pattern of aurophilic interactions that yields a monomer, dimer, and trimer of [Au(CN2]− within the same crystal structure. In two of the five Au positions, the atom resides on a center of inversion. The overall arrangement is that of a coordination polymer assisted by aurophilic and hydrogen-bonded interactions.

Family C 7TM receptor dimerization and activation

DEFF Research Database (Denmark)

Bonde, Marie Mi; Sheikh, Søren P; Hansen, Jakob Lerche

2006-01-01

The family C seven transmembrane (7TM) receptors constitutes a small and especially well characterized subfamily of the large 7TM receptor superfamily. Approximately 50% of current prescription drugs target 7TM receptors, this biologically important family represents the largest class of drug...... to be fully defined. This review presents the biochemical support for family C 7TM receptor dimerization and discusses its importance for receptor biosynthesis, surface expression, ligand binding and activation, since lessons learnt here may well be applicable to the whole superfamily of 7TM receptors.......-targets today. It is well established that family C 7TM receptors form homo- or hetero-dimers on the cell surface of living cells. The large extra-cellular domains (ECD) have been crystallized as a dimer in the presence and absence of agonist. Upon agonist binding, the dimeric ECD undergoes large conformational...

New investigations of the guanine trichloro cuprate(II) complex crystal

Science.gov (United States)

Fabijanić, Ivana; Matković-Čalogović, Dubravka; Pilepić, Viktor; Ivanišević, Irena; Mohaček-Grošev, Vlasta; Sanković, Krešimir

2017-01-01

Crystals of the guanine trichloro cuprate(II) complex, (HGua)2[Cu2Cl6]·2H2O (HGua = protonated guanine), were prepared and analysed by spectroscopic (IR, Raman) and computational methods. A new single-crystal X-ray diffraction analysis was conducted to obtain data with lower standard uncertainties than those in the previously published structure. Raman and IR spectroscopy and quantum-mechanical analysis gave us new insight into the vibrational states of the (HGua)2[Cu2Cl6]·2H2O crystal. The vibrational spectra of the crystal were assigned by performing a normal coordinate analysis for a free dimer with a centre of inversion as the only symmetry element. The stretching vibration observed at 279 cm-1 in the infrared spectrum corresponds to the N-Cu bond. The noncovalent interaction (NCI) plots and quantum theory of atoms in molecules (QTAIM) analysis of the electron density obtained from periodic DFT calculations elucidated the interactions that exist within the crystal structure. Closed-shell ionic attractions, as well as weak and medium strength hydrogen bonds, prevailed in the crystal packing.

Revealing the Dimeric Crystal and Solution Structure of β-Lactoglobulin at pH 4 and Its pH and Salt Dependent Monomer–Dimer Equilibrium

DEFF Research Database (Denmark)

Khan, Sanaullah; Ipsen, Richard; Almdal, Kristoffer

2018-01-01

The dimeric structure of bovine β-lactoglobulin A (BLGA) at pH 4.0 was solved to 2.0 Å resolution. Fitting the BLGA pH 4.0 structure to SAXS data at low ionic strength (goodness of fit R-factor = 3.6%) verified the dimeric state in solution. Analysis of the monomer–dimer equilibrium at varying pH...... and ionic strength by SAXS and scattering modeling showed that BLGA is dimeric at pH 3.0 and 4.0, shifting toward a monomer at pH 2.2, 2.6, and 7.0 yielding monomer/dimer ratios of 80/20%, 50/50%, and 25/75%, respectively. BLGA remained a dimer at pH 3.0 and 4.0 in 50–150 mM NaCl, whereas the electrostatic...... shielding raised the dimer content at pH 2.2, 2.6, and 7.0, i.e., below and above the pI. Overall, the findings provide new insights into the molecular characteristics of BLGA relevant for dairy product formulations and for various biotechnological and pharmaceutical applications....

Crystal structure of 4-allylsulfanyl-1H-pyrazolo[3,4-d]pyrimidine

Directory of Open Access Journals (Sweden)

Mohammed El Fal

2014-09-01

Full Text Available In the title compound, C8H8N4S, the pyrazolo[3,4-d]pyrimidine ring system is essentially planar, with a maximum deviation from the mean plane of 0.025 (3 Å. The allyl group is disordered over two sites in a 0.512 (6:0.488 (6 ratio. In the crystal, molecules are linked by pairs of N—H...N hydrogen bonds, forming inversion dimers with an R22(8 graph-set motif.

Structure of an RNA dimer of a regulatory element from human thymidylate synthase mRNA

OpenAIRE

Dibrov, Sergey; McLean, Jaime; Hermann, Thomas

2011-01-01

An oligonucleotide representing a regulatory element of human thymidylate synthase mRNA has been crystallized as a dimer. The structure of the asymmetric dimer has been determined at 1.97 Å resolution.

Spin Quantum Tunneling via Entangled States in a Dimer of Exchange-Coupled Single-Molecule Magnets

Science.gov (United States)

Tiron, R.; Wernsdorfer, W.; Foguet-Albiol, D.; Aliaga-Alcalde, N.; Christou, G.

2003-11-01

A new family of supramolecular, antiferromagnetically exchange-coupled dimers of single-molecule magnets (SMMs) has recently been reported. Each SMM acts as a bias on its neighbor, shifting the quantum tunneling resonances of the individual SMMs. Hysteresis loop measurements on a single crystal of SMM dimers have now established quantum tunneling of the magnetization via entangled states of the dimer. This shows that the dimer really does behave as a quantum mechanically coupled dimer, and also allows the measurement of the longitudinal and transverse superexchange coupling constants.

Mechanism for Controlling the Dimer-Monomer Switch and Coupling Dimerization to Catalysis of the Severe Acute Respiratory Syndrome Coronavirus 3C-Like Protease

Energy Technology Data Exchange (ETDEWEB)

Shi,J.; Sivaraman, J.; Song, J.

2008-01-01

Unlike 3C protease, the severe acute respiratory syndrome coronavirus (SARS-CoV) 3C-like protease (3CLpro) is only enzymatically active as a homodimer and its catalysis is under extensive regulation by the unique extra domain. Despite intense studies, two puzzles still remain: (i) how the dimer-monomer switch is controlled and (ii) why dimerization is absolutely required for catalysis. Here we report the monomeric crystal structure of the SARS-CoV 3CLpro mutant R298A at a resolution of 1.75 Angstroms . Detailed analysis reveals that Arg298 serves as a key component for maintaining dimerization, and consequently, its mutation will trigger a cooperative switch from a dimer to a monomer. The monomeric enzyme is irreversibly inactivated because its catalytic machinery is frozen in the collapsed state, characteristic of the formation of a short 310-helix from an active-site loop. Remarkably, dimerization appears to be coupled to catalysis in 3CLpro through the use of overlapped residues for two networks, one for dimerization and another for the catalysis.

Two Glass Transitions Associated to Different Dynamic Disorders in the Nematic Glassy State of a Non-Symmetric Liquid Crystal Dimer Dopped with γ-Alumina Nanoparticles

Science.gov (United States)

Diez-Berart, Sergio; López, David O.; Salud, Josep; Diego, José Antonio; Sellarès, Jordi; Robles-Hernández, Beatriz; de la Fuente, María Rosario; Ros, María Blanca

2015-01-01

In the present work, the nematic glassy state of the non-symmetric LC dimer α-(4-cyanobiphenyl-4′-yloxy)-ω-(1-pyrenimine-benzylidene-4′-oxy) undecane is studied by means of calorimetric and dielectric measurements. The most striking result of the work is the presence of two different glass transition temperatures: one due to the freezing of the flip-flop motions of the bulkier unit of the dimer and the other, at a lower temperature, related to the freezing of the flip-flop and precessional motions of the cyanobiphenyl unit. This result shows the fact that glass transition is the consequence of the freezing of one or more coupled dynamic disorders and not of the disordered phase itself. In order to avoid crystallization when the bulk sample is cooled down, the LC dimer has been confined via the dispersion of γ-alumina nanoparticles, in several concentrations.

Tunneling dynamics of double proton transfer in formic acid and benzoic acid dimers

Science.gov (United States)

Smedarchina, Zorka; Fernández-Ramos, Antonio; Siebrand, Willem

2005-04-01

Direct dynamics calculations based on instanton techniques are reported of tunneling splittings due to double proton transfer in formic and benzoic acid dimers. The results are used to assign the observed splittings to levels for which the authors of the high-resolution spectra could not provide a definitive assignment. In both cases the splitting is shown to be due mainly to the zero-point level rather than to the vibrationally or electronically excited level whose spectrum was investigated. This leads to zero-point splittings of 375MHz for (DCOOH)2 and 1107MHz for the benzoic acid dimer. Thus, contrary to earlier calculations, it is found that the splitting is considerably larger in the benzoic than in the formic acid dimer. The calculations are extended to solid benzoic acid where the asymmetry of the proton-transfer potential induced by the crystal can be overcome by suitable doping. This has allowed direct measurement of the interactions responsible for double proton transfer, which were found to be much larger than those in the isolated dimer. To account for this observation both static and dynamic effects of the crystal forces on the intradimer hydrogen bonds are included in the calculations. The same methodology, extended to higher temperatures, is used to calculate rate constants for HH, HD, and DD transfers in neat benzoic acid crystals. The results are in good agreement with reported experimental rate constants measured by NMR relaxometry and, if allowance is made for small structural changes induced by doping, with the transfer matrix elements observed in doped crystals. Hence the method used allows a unified description of tunneling splittings in the gas phase and in doped crystals as well as of transfer rates in neat crystals.

Structure of the dimeric form of CTP synthase from Sulfolobus solfataricus

DEFF Research Database (Denmark)

Lauritsen, Iben; Willemoës, Martin; Jensen, Kaj Frank

2011-01-01

CTP synthase catalyzes the last committed step in de novo pyrimidine-nucleotide biosynthesis. Active CTP synthase is a tetrameric enzyme composed of a dimer of dimers. The tetramer is favoured in the presence of the substrate nucleotides ATP and UTP; when saturated with nucleotide, the tetramer...... completely dominates the oligomeric state of the enzyme. Furthermore, phosphorylation has been shown to regulate the oligomeric states of the enzymes from yeast and human. The crystal structure of a dimeric form of CTP synthase from Sulfolobus solfataricus has been determined at 2.5 Å resolution...

Atomic resolution crystal structure of VcLMWPTP-1 from Vibrio cholerae O395: Insights into a novel mode of dimerization in the low molecular weight protein tyrosine phosphatase family

Energy Technology Data Exchange (ETDEWEB)

Nath, Seema; Banerjee, Ramanuj; Sen, Udayaditya, E-mail: udayaditya.sen@saha.ac.in

2014-07-18

Highlights: • VcLMWPTP-1 forms dimer in solution. • The dimer is catalytically active unlike other reported dimeric LMWPTPs. • The formation of extended dimeric surface excludes the active site pocket. • The surface bears closer resemblance to eukaryotic LMWPTPs. - Abstract: Low molecular weight protein tyrosine phosphatase (LMWPTP) is a group of phosphotyrosine phosphatase ubiquitously found in a wide range of organisms ranging from bacteria to mammals. Dimerization in the LMWPTP family has been reported earlier which follows a common mechanism involving active site residues leading to an enzymatically inactive species. Here we report a novel form of dimerization in a LMWPTP from Vibrio cholera 0395 (VcLMWPTP-1). Studies in solution reveal the existence of the dimer in solution while kinetic study depicts the active form of the enzyme. This indicates that the mode of dimerization in VcLMWPTP-1 is different from others where active site residues are not involved in the process. A high resolution (1.45 Å) crystal structure of VcLMWPTP-1 confirms a different mode of dimerization where the active site is catalytically accessible as evident by a tightly bound substrate mimicking ligand, MOPS at the active site pocket. Although being a member of a prokaryotic protein family, VcLMWPTP-1 structure resembles very closely to LMWPTP from a eukaryote, Entamoeba histolytica. It also delineates the diverse surface properties around the active site of the enzyme.

The crystal structure of an intermediate dimer of aspergilloglutamic peptidase that mimics the enzyme-activation product complex produced upon autoproteolysis.

Science.gov (United States)

Sasaki, Hiroshi; Kubota, Keiko; Lee, Woo C; Ohtsuka, Jun; Kojima, Masaki; Iwata, So; Nakagawa, Atsushi; Takahashi, Kenji; Tanokura, Masaru

2012-07-01

Aspergilloglutamic peptidase from Aspergillus niger var. macrosporus (AGP) is one of the so-called pepstatin-insensitive acid endopeptidases, which are distinct from the well-studied aspartic peptidases. Among the known homologues of the glutamic peptidases, AGP is a unique two-chain enzyme with a light chain and a heavy chain bound non-covalently with each other, and thus is an interesting target for protein structure-function relationship studies. In this article, we report the crystal structure of a dimeric form of the enzyme at a resolution of 1.6 Å. This form has a unique structure in which the C-terminal region of the light chain of one of the molecules binds to the active site cleft of the other molecule like a part of a substrate. This form mimics the enzyme-activation product complex produced upon autoproteolysis, and provides a structural clue that could help to clarify the activation mechanism. This type of dimeric structure of a peptidase is here reported for the first time.

Crystal structure of 3-methoxy-2-[5-(naphthalen-1-yl-4,5-dihydro-1H-pyrazol-3-yl]phenol

Directory of Open Access Journals (Sweden)

Dongsoo Koh

2015-11-01

Full Text Available In the title compound, C20H18N2O2, the central pyrazoline ring has an envelope conformation with the atom substituted by the naphthalene ring as the flap. It bridges a benzene ring and a naphthalene ring system which are almost normal to one another, making a dihedral angle of 82.03 (6 °. There is an intramolecular O—H...N hydrogen bond forming an S(6 ring motif. In the crystal, molecules are linked by pairs of N—H...π interactions, forming inversion dimers. There are also C—H...π interactions present and the dimers are linked via C—H...O hydrogen bonds, forming ribbons propagating along the a-axis direction.

Photonic crystals based on opals and inverse opals: synthesis and structural features

International Nuclear Information System (INIS)

Klimonsky, S O; Abramova, Vera V; Sinitskii, Alexander S; Tretyakov, Yuri D

2011-01-01

Methods of synthesis of photonic crystals based on opals and inverse opals are considered. Their structural features are discussed. Data on different types of structural defects and their influence on the optical properties of opaline materials are systematized. The possibilities of investigation of structural defects by optical spectroscopy, electron microscopy, microradian X-ray diffraction, laser diffraction and using an analysis of Kossel ring patterns are described. The bibliography includes 253 references.

Crystal structures of 2-[(4,6-di-amino-pyrimidin-2-yl)sulfan-yl]-N-(naphthalen-1-yl)acetamide and 2-[(4,6-di-amino-pyrimidin-2-yl)sulfan-yl]-N-(4-fluoro-phen-yl)acetamide.

Science.gov (United States)

Subasri, S; Kumar, Timiri Ajay; Sinha, Barij Nayan; Jayaprakash, Venkatesan; Viswanathan, Vijayan; Velmurugan, Devadasan

2017-02-01

The title compounds, C 16 H 15 N 5 OS, (I), and C 12 H 12 FN 5 OS, (II), are [(di-amino-pyrimidine)-sulfan-yl]acetamide derivatives. In (I), the pyrimidine ring is inclined to the naphthalene ring system by 55.5 (1)°, while in (II), the pyrimidine ring is inclined to the benzene ring by 58.93 (8)°. In (II), there is an intra-molecular N-H⋯N hydrogen bond and a short C-H⋯O contact. In the crystals of (I) and (II), mol-ecules are linked by pairs of N-H⋯N hydrogen bonds, forming inversion dimers with R 2 2 (8) ring motifs. In the crystal of (I), the dimers are linked by bifurcated N-H⋯(O,O) and C-H⋯O hydrogen bonds, forming layers parallel to (100). In the crystal of (II), the dimers are linked by N-H⋯O hydrogen bonds, also forming layers parallel to (100). The layers are linked by C-H⋯F hydrogen bonds, forming a three-dimensional architecture.

Inverse regulation of two classic Hippo pathway target genes in Drosophila by the dimerization hub protein Ctp.

Science.gov (United States)

Barron, Daniel A; Moberg, Kenneth

2016-03-14

The LC8 family of small ~8 kD proteins are highly conserved and interact with multiple protein partners in eukaryotic cells. LC8-binding modulates target protein activity, often through induced dimerization via LC8:LC8 homodimers. Although many LC8-interactors have roles in signaling cascades, LC8's role in developing epithelia is poorly understood. Using the Drosophila wing as a developmental model, we find that the LC8 family member Cut up (Ctp) is primarily required to promote epithelial growth, which correlates with effects on the pro-growth factor dMyc and two genes, diap1 and bantam, that are classic targets of the Hippo pathway coactivator Yorkie. Genetic tests confirm that Ctp supports Yorkie-driven tissue overgrowth and indicate that Ctp acts through Yorkie to control bantam (ban) and diap1 transcription. Quite unexpectedly however, Ctp loss has inverse effects on ban and diap1: it elevates ban expression but reduces diap1 expression. In both cases these transcriptional changes map to small segments of these promoters that recruit Yorkie. Although LC8 complexes with Yap1, a Yorkie homolog, in human cells, an orthologous interaction was not detected in Drosophila cells. Collectively these findings reveal that that Drosophila Ctp is a required regulator of Yorkie-target genes in vivo and suggest that Ctp may interact with a Hippo pathway protein(s) to exert inverse transcriptional effects on Yorkie-target genes.

Energy transfer and visible-infrared quantum cutting photoluminescence modification in Tm-Yb codoped YPO(4) inverse opal photonic crystals.

Science.gov (United States)

Wang, Siqin; Qiu, Jianbei; Wang, Qi; Zhou, Dacheng; Yang, Zhengwen

2015-08-01

YPO4:  Tm, Yb inverse opal photonic crystals were successfully synthesized by the colloidal crystal templates method, and the visible-infrared quantum cutting (QC) photoluminescence properties of YPO4:  Tm, Yb inverse opal photonic crystals were investigated. We obtained tetragonal phase YPO4 in all the samples when the samples sintered at 950°C for 5 h. The visible emission intensity of Tm3+ decreased significantly when the photonic bandgap was located at 650 nm under 480 nm excitation. On the contrary, the QC emission intensity of Yb3+ was enhanced as compared with the no photonic bandgap sample. When the photonic bandgap was located at 480 nm, the Yb3+ and Tm3+ light-emitting intensity weakened at the same time. We demonstrated that the energy transfer between Tm3+ and Yb3+ is enhanced by the suppression of the red emission of Tm3+. Additionally, the mechanisms for the influence of the photonic bandgap on the energy transfer process of the Tm3+, Yb3+ codoped YPO4 inverse opal are discussed.

Two modifications of Y2Piv6(HPiv)6 crystals: synthesis and structures

International Nuclear Information System (INIS)

Kiseleva, E.A.; Troyanov, S.I.; Korenev, Yu.M.

2006-01-01

Crystal structure of solvate of yttrium pivalate YPiv 3 ·3HPiv is studied. Existing of two polymorphous modifications of the compound is detected. It is shown that α- and β-modifications of yttrium pivalate solvate have molecular crystal structures and are built of Y 2 Piv 6 (HPiv) 6 dimers. Difference of these two modifications is in package of dimer molecules and in center-symmetricity of dimers in α-modification structure. Molecular and crystal structure, crystal lattice parameters are determined [ru

Core-to-core dimers forming switchable mesophase

Czech Academy of Sciences Publication Activity Database

Horčic, M.; Svoboda, J.; Novotná, Vladimíra; Pociecha, D.; Gorecka, E.

2017-01-01

Roč. 53, č. 18 (2017), s. 2721-2724 ISSN 1359-7345 R&D Projects: GA ČR GA15-02843S Institutional support: RVO:68378271 Keywords : liquid crystals * bent- core mesogens * dimers Subject RIV: JJ - Other Materials OBOR OECD: Nano-materials (production and properties) Impact factor: 6.319, year: 2016

Crystal structure of 1-[(6-chloropyridin-3-ylsulfonyl]-1,2,3,4-tetrahydroquinoline

Directory of Open Access Journals (Sweden)

S. Jeyaseelan

2015-06-01

Full Text Available The tetrahydropyridine ring of the quinoline system in the title compound, C14H13ClN2O2S, adopts a half-chair conformation with the bond-angle sum at the N atom being 350.0°. The dihedral angle between the least-squares planes of the two aromatic rings is 50.13 (11°. In the crystal, inversion dimers linked by pairs of C—H...O hydrogen bonds generate R22(10 loops. Additional intermolecular C—H...O hydrogen bonds generate C(7 chains along [100].

Crystal structure of (E-4-{2-[4-(allyloxyphenyl]diazenyl}benzoic acid

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Md. Lutfor Rahman

2014-12-01

Full Text Available The title compound, C16H14N2O3, has an E conformation about the azobenzene [—N=N– = 1.2481 (16 Å] linkage. The benzene rings are almost coplanar [dihedral angle = 1.36 (7°]. The O atoms of the carboxylic acid group are disordered over two sets of sites and were refined with an occupancy ratio of 0.5:0.5. The two disordered components of the carboxylic acid group make dihedral angles of 1.5 (14 and 3.8 (12° with the benzene ring to which they are attached. In the crystal, molecules are linked via pairs of O—H...O hydrogen bonds, forming inversion dimers. The dimers are connected via C—H...O hydrogen bonds, forming ribbons lying parallel to [120]. These ribbons are linked via C—H...π interactions, forming slabs parallel to (001.

Analytical expressions for the correlation function of a hard sphere dimer fluid

Science.gov (United States)

Kim, Soonho; Chang, Jaeeon; Kim, Hwayong

A closed form expression is given for the correlation function of a hard sphere dimer fluid. A set of integral equations is obtained from Wertheim's multidensity Ornstein-Zernike integral equation theory with Percus-Yevick approximation. Applying the Laplace transformation method to the integral equations and then solving the resulting equations algebraically, the Laplace transforms of the individual correlation functions are obtained. By the inverse Laplace transformation, the radial distribution function (RDF) is obtained in closed form out to 3D (D is the segment diameter). The analytical expression for the RDF of the hard dimer should be useful in developing the perturbation theory of dimer fluids.

Crystal structure of 2-(4-chlorophenyl-3-(4-methoxyphenyl-3-(methylsulfanylacrylonitrile

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Shamantha Kumar

2014-11-01

Full Text Available In the title compound, C17H14ClNOS, the aromatic rings are inclined to one another by 64.22 (9°. The acrylonitrile group (C=C—C[triple-bond]N is planar to within 0.003 (2 Å, with the S atom and the methyl C atom displaced from this plane by 0.2317 (6 and −0.637 (2 Å, respectively. In the crystal, molecules are linked via pairs of C—H...π interactions, forming inversion dimers. There are no other significant intermolecular interactions present.

Crystal structure of inhibitor of growth 4 (ING4) dimerization domain reveals functional organization of ING family of chromatin-binding proteins.

Science.gov (United States)

Culurgioni, Simone; Muñoz, Inés G; Moreno, Alberto; Palacios, Alicia; Villate, Maider; Palmero, Ignacio; Montoya, Guillermo; Blanco, Francisco J

2012-03-30

The protein ING4 binds to histone H3 trimethylated at Lys-4 (H3K4me3) through its C-terminal plant homeodomain, thus recruiting the HBO1 histone acetyltransferase complex to target promoters. The structure of the plant homeodomain finger bound to an H3K4me3 peptide has been described, as well as the disorder and flexibility in the ING4 central region. We report the crystal structure of the ING4 N-terminal domain, which shows an antiparallel coiled-coil homodimer with each protomer folded into a helix-loop-helix structure. This arrangement suggests that ING4 can bind simultaneously two histone tails on the same or different nucleosomes. Dimerization has a direct impact on ING4 tumor suppressor activity because monomeric mutants lose the ability to induce apoptosis after genotoxic stress. Homology modeling based on the ING4 structure suggests that other ING dimers may also exist.

Crystal structure of 3-{5-[3-(4-fluorophenyl-1-isopropyl-1H-indol-2-yl]-1H-pyrazol-1-yl}indolin-2-one ethanol monosolvate

Directory of Open Access Journals (Sweden)

Md. Lutfor Rahman

2016-03-01

Full Text Available The title indolin-2-one compound, C28H23FN4O·C2H6O, crystallizes as a 1:1 ethanol solvate. The ethanol molecule is disordered over two positions with refined site occupancies of 0.560 (14 and 0.440 (14. The pyrazole ring makes dihedral angles of 84.16 (10 and 85.33 (9° with the indolin-2-one and indole rings, respectively, whereas the dihedral angle between indolin-2-one and indole rings is 57.30 (7°. In the crystal, the components are linked by N—H...O and O—H...O hydrogen bonds, forming an inversion molecule–solvate 2:2 dimer with R44(12 ring motifs. The crystal structure is consolidated by π–π interaction between pairs of inversion-related indolin-2-one rings [interplanar spacing = 3.599 (2 Å].

Crystal and molecular structure of N-(4-nitrophenyl)-β-alanine—Its vibrational spectra and theoretical calculations

Science.gov (United States)

Marchewka, M. K.; Drozd, M.; Janczak, J.

2011-08-01

The N-(4-nitrophenyl)-β-alanine in crystalline form directly by the addition of 4-nitroaniline to the acrylic acid in aqueous solution has been obtained. The title β-alanine derivative crystallizes in the P2 1/ c space group of monoclinic system with four molecules per unit cell. The X-ray geometry of β-alanine derivative molecule has been compared with those obtained by molecular orbital calculations corresponding to the gas phase. In the crystal the molecules related by an inversion center interact via symmetrically equivalent O-H⋯O hydrogen bonds with O⋯O distance of 2.656(2) Å forming a dimeric structure. The dimers of β-alanine derivative weakly interact via N-H⋯O hydrogen bonds between the H atom of β-amine groups and one of O atom of nitro groups. The room temperature powder vibrational (infrared and Raman) measurements are in accordance with the X-ray analysis. In aqueous solution of 4-nitroaniline and acrylic acid, the double C dbnd C bond of vinyl group of acrylic acid breaks as result of 4-nitroaniline addition.

Biochemical and Structural Analysis of Hormone-sensitive Lipase Homolog EstE7: Insight into the Stabilized Dimerization of HSL-Homolog Proteins

International Nuclear Information System (INIS)

Nam, Ki Hyun; Park, Sung Ha; Lee, Won Ho; Hwang, Kwang Yeon

2010-01-01

Hormone sensitive lipase (HSL) plays a major role in energy homeostasis and lipid metabolism. Several crystal structures of HSL-homolog proteins have been identified, which has led to a better understanding of its molecular function. HSLhomolog proteins exit as both monomer and dimer, but the biochemical and structural basis for such oligomeric states has not been successfully elucidated. Therefore, we determined the crystal structure of HSL-homolog protein EstE7 from a metagenome library at 2.2 A resolution and characterized the oligomeric states of EstE7 both structurally and biochemically. EstE7 protein prefers the dimeric state in solution, which is supported by its higher enzymatic activity in the dimeric state. In the crystal form, EstE7 protein shows two-types of dimeric interface. Specifically, dimerization via the external β8-strand occurred through tight association between two pseudosymmetric folds via salt bridges, hydrogen bonds and van der Waals interactions. This dimer formation was similar to that of other HSL-homolog protein structures such as AFEST, BEFA, and EstE1. We anticipate that our results will provide insight into the oligomeric state of HSLhomolog proteins

Facile route to magnetophotonic crystals by infiltration of 3D inverse opals with magnetic nanoparticles

International Nuclear Information System (INIS)

Caicedo, J.M.; Taboada, E.; Hrabovsky, D.; Lopez-Garcia, M.; Herranz, G.; Roig, A.; Blanco, A.; Lopez, C.; Fontcuberta, J.

2010-01-01

We report here on the fabrication and characterization of magnetophotonic crystals obtained by infiltrating magnetic nanoparticles (maghemite) into silica-based inverse opals. Good quality opals, with adjustable photonic and magnetic characteristics have been obtained by this method. Magnetic and magneto-optic measurements, performed by using SQUID magnetometry and Kerr and Faraday effects, have been used to monitor the magnetic filling of the opals. It is observed that the Kerr rotation is not proportional to the overall magnetization of the magnetophotonic crystal. Possible scenarios for this unexpected result are discussed.

Dimers of nineteen-electron sandwich compounds: Crystal and electronic structures, and comparison of reducing strengths

KAUST Repository

Mohapatra, Swagat Kumar

2014-10-03

The dimers of some Group 8 metal cyclopentadienyl/ arene complexes and Group 9 metallocenes can be handled in air, yet are strongly reducing, making them useful n-dopants in organic electronics. In this work, the Xray molecular structures are shown to resemble those of Group 8 metal cyclopentadienyl/pentadienyl or Group 9 metal cyclopentadienyl/diene model compounds. Compared to those of the model compounds, the DFT HOMOs of the dimers are significantly destabilized by interactions between the metal and the central C-C σ-bonding orbital, accounting for the facile oxidation of the dimers. The lengths of these C-C bonds (X-ray or DFT) do not correlate with DFT dissociation energies, the latter depending strongly on the monomer stabilities. Ru and Ir monomers are more reducing than their Fe and Rh analogues, but the corresponding dimers also exhibit much higher dissociation energies, so the estimated monomer cation/neutral dimer potentials are, with the exception of that of [RhCp2]2, rather similar (-1.97 to-2.15 V vs. FeCp2 +/0 in THF). The consequences of the variations in bond strength and redox potentials for the reactivity of the dimers are discussed.

Dimers of nineteen-electron sandwich compounds: Crystal and electronic structures, and comparison of reducing strengths

KAUST Repository

Mohapatra, Swagat Kumar; Fonari, Alexandr; Risko, Chad; Yesudas, Kada; Moudgil, Karttikay; Delcamp, Jared Heath; Timofeeva, Tatiana V.; Bredas, Jean-Luc; Marder, Seth R.; Barlow, Stephen J.

2014-01-01

The dimers of some Group 8 metal cyclopentadienyl/ arene complexes and Group 9 metallocenes can be handled in air, yet are strongly reducing, making them useful n-dopants in organic electronics. In this work, the Xray molecular structures are shown to resemble those of Group 8 metal cyclopentadienyl/pentadienyl or Group 9 metal cyclopentadienyl/diene model compounds. Compared to those of the model compounds, the DFT HOMOs of the dimers are significantly destabilized by interactions between the metal and the central C-C σ-bonding orbital, accounting for the facile oxidation of the dimers. The lengths of these C-C bonds (X-ray or DFT) do not correlate with DFT dissociation energies, the latter depending strongly on the monomer stabilities. Ru and Ir monomers are more reducing than their Fe and Rh analogues, but the corresponding dimers also exhibit much higher dissociation energies, so the estimated monomer cation/neutral dimer potentials are, with the exception of that of [RhCp2]2, rather similar (-1.97 to-2.15 V vs. FeCp2 +/0 in THF). The consequences of the variations in bond strength and redox potentials for the reactivity of the dimers are discussed.

Extracting dimer structures from simulations of organic-based materials using QM/MM methods

Energy Technology Data Exchange (ETDEWEB)

Pérez-Jiménez, A.J., E-mail: aj.perez@ua.es; Sancho-García, J.C., E-mail: jc.sancho@ua.es

2015-09-28

Highlights: • DFT geometries of isolated dimers in organic crystals differ from experimental ones. • This can be corrected using QM/MM geometry optimizations. • The QM = B3LYP–D3(ZD)/cc-pVDZ and MM = GAFF combination works reasonably well. - Abstract: The functionality of weakly bound organic materials, either in Nanoelectronics or in Materials Science, is known to be strongly affected by their morphology. Theoretical predictions of the underlying structure–property relationships are frequently based on calculations performed on isolated dimers, but the optimized structure of the latter may significantly differ from experimental data even when dispersion-corrected methods are used for it. Here, we address this problem on two organic crystals, namely coronene and 5,6,11,12-tetrachlorotetracene, concluding that it is caused by the absence of the surrounding monomers present in the crystal, and that it can be efficiently cured when the dimer is embedded into a general Quantum Mechanics/Molecular Mechanics (QM/MM) geometry optimization scheme. We also investigate how the size of the MM region affects the results. These findings may be helpful for the simulation of the morphology of active materials in crystalline or glassy samples.

Spontaneous emission of semiconductor quantum dots in inverse opal SiO2 photonic crystals at different temperatures.

Science.gov (United States)

Yang, Peng; Yang, Yingshu; Wang, Yinghui; Gao, Jiechao; Sui, Ning; Chi, Xiaochun; Zou, Lu; Zhang, Han-Zhuang

2016-02-01

The photoluminescence (PL) characteristics of CdSe quantum dots (QDs) infiltrated into inverse opal SiO2 photonic crystals (PCs) are systemically studied. The special porous structure of inverse opal PCs enhanced the thermal exchange rate between the CdSe QDs and their surrounding environment. Finally, inverse opal SiO2 PCs suppressed the nonlinear PL enhancement of CdSe QDs in PCs excited by a continuum laser and effectively modulated the PL characteristics of CdSe QDs in PCs at high temperatures in comparison with that of CdSe QDs out of PCs. The final results are of benefit in further understanding the role of inverse opal PCs on the PL characteristics of QDs. Copyright © 2015 John Wiley & Sons, Ltd.

Crystallization and preliminary x-ray crystallography data of the dimer of tetramer s (abcd)2 of extracellular hemoglobin from Glossoscolex paulistus in cyano met form

International Nuclear Information System (INIS)

Ferreira, Frederico M.; Oliveira, Paulo S.L. de; Oliva, Glaucius

1996-01-01

Full text. The extracellular hemoglobin from Glossoscolex paulistus has a molecular weight near to 3.1 x 10 6 Da and a structure organized in a double-layered hexagonal oligomer. The tertiary complex of dimer of tetramers (abcd) 2 was obtained by chromography in Sephadex G-200, in pH 9.0, as a result of alkaline dissociation. Aiming to obtain a better understanding of the oligomeric structure and specially for the inter subunit interactions the extracellular hemoglobins, we have obtained crystals of dimer of tetramers (abcd) 2 of hemoglobin from Glossoscolex and we are studying the in behavior in different conditions of precipitants and pH's. Our goal is to solve the crystal structure in order to characterize, at atomic level, the subunits contacts, heme environment and differences in residues involved in oxygenation in order to understand in this hemoglobin. The crystallization experiments the protein concentration in the cyanomet form was about 10 mg/ml and the experiments were carried out at 18 0 C. The optimal crystallization condition achieved from factorial assays was 10% (w/v). Polyethylene glycol (PEG) 8,000 and 8%(v/v) ethylene glycol in 100 mM HEPES pH 7.5. The optimization of this condition was carried out with the variation of PEG concentrations from 6% up to 10% (by 1% step) and pH between 7.0 and 8.0. A quite critical p-H-dependence has been observed on crystal nucleation, decreasing from pH 7.0, in which the number of microcrystals in higher, up to pH 8.0, in which crystals did not appear even at higher PEG 8,000 (10% w/v). As several structures of hemoglobin from different sources (vertebrate and invertebrates) are available, we hope to solve their structure of hemoglobin from Glossoscolex paulistus by Molecular Replacement, even though the tetramer organization may be different in the earthworm as compared related to other known tetrameric hemoglobin structures. (author)

Dimers of nineteen-electron sandwich compounds: crystal and electronic structures, and comparison of reducing strengths.

Science.gov (United States)

Mohapatra, Swagat K; Fonari, Alexandr; Risko, Chad; Yesudas, Kada; Moudgil, Karttikay; Delcamp, Jared H; Timofeeva, Tatiana V; Brédas, Jean-Luc; Marder, Seth R; Barlow, Stephen

2014-11-17

The dimers of some Group 8 metal cyclopentadienyl/arene complexes and Group 9 metallocenes can be handled in air, yet are strongly reducing, making them useful n-dopants in organic electronics. In this work, the X-ray molecular structures are shown to resemble those of Group 8 metal cyclopentadienyl/pentadienyl or Group 9 metal cyclopentadienyl/diene model compounds. Compared to those of the model compounds, the DFT HOMOs of the dimers are significantly destabilized by interactions between the metal and the central CC σ-bonding orbital, accounting for the facile oxidation of the dimers. The lengths of these CC bonds (X-ray or DFT) do not correlate with DFT dissociation energies, the latter depending strongly on the monomer stabilities. Ru and Ir monomers are more reducing than their Fe and Rh analogues, but the corresponding dimers also exhibit much higher dissociation energies, so the estimated monomer cation/neutral dimer potentials are, with the exception of that of [RhCp2 ]2 , rather similar (-1.97 to -2.15 V vs. FeCp2 (+/0) in THF). The consequences of the variations in bond strength and redox potentials for the reactivity of the dimers are discussed. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Study of Inverse Ni-based Photonic Crystal using the Microradian X-ray Diffraction

Science.gov (United States)

Vasilieva, A. V.; Grigoryeva, N. A.; Mistonov, A. A.; Sapoletova, N. A.; Napolskii, K. S.; Eliseev, A. A.; Lukashin, A. V.; Tretyakov, Yu D.; Petukhov, A. V.; Byelov, D.; Chernyshov, D.; Okorokov, A. I.; Bouwman, W. G.; Grigoriev, S. V.

2010-10-01

Inverse photonic nickel-based crystal films formed by electrocrystallization of metal inside the voids of polymer artificial opal have been studied using the microradian X-ray diffraction. Analysis of the diffraction images agrees with an face-centred cubic (FCC) structure with the lattice constant a0 = 650 ± 10 nm and indicates two types of stacking sequences coexisting in the crystal (twins of ABCABC... and ACBACB... ordering motifs), the ratio between them being 4:5 The transverse structural correlation length Ltran is 2.4 ± 0.1 μm, which corresponds to a sample thickness of 6 layers. The in-plane structural correlation length Llong is 3.4 ± 0.2 μm, and the structure mosaic is of order of 10°.

Study of Inverse Ni-based Photonic Crystal using the Microradian X-ray Diffraction

International Nuclear Information System (INIS)

Vasilieva, A V; Okorokov, A I; Grigoriev, S V; Grigoryeva, N A; Mistonov, A A; Sapoletova, N A; Napolskii, K S; Eliseev, A A; Lukashin, A V; Tretyakov, Yu D; Petukhov, A V; Byelov, D; Chernyshov, D; Bouwman, W G

2010-01-01

Inverse photonic nickel-based crystal films formed by electrocrystallization of metal inside the voids of polymer artificial opal have been studied using the microradian X-ray diffraction. Analysis of the diffraction images agrees with an face-centred cubic (FCC) structure with the lattice constant a 0 = 650 ± 10 nm and indicates two types of stacking sequences coexisting in the crystal (twins of ABCABC... and ACBACB... ordering motifs), the ratio between them being 4:5 The transverse structural correlation length L tran is 2.4 ± 0.1 μm, which corresponds to a sample thickness of 6 layers. The in-plane structural correlation length L long is 3.4 ± 0.2 μm, and the structure mosaic is of order of 10 0 .

Study of Inverse Ni-based Photonic Crystal using the Microradian X-ray Diffraction

Energy Technology Data Exchange (ETDEWEB)

Vasilieva, A V; Okorokov, A I; Grigoriev, S V [Petersburg Nuclear Physics Institute, Gatchina, 188350, St. Petersburg (Russian Federation); Grigoryeva, N A; Mistonov, A A [Department of Physics, St. Petersburg State University, 198504, St. Petersburg (Russian Federation); Sapoletova, N A; Napolskii, K S; Eliseev, A A; Lukashin, A V; Tretyakov, Yu D [Department of Materials Science, Moscow State University, 119899, Moscow (Russian Federation); Petukhov, A V; Byelov, D [Debye Institute, Utrecht University, 3584 CH Utrecht (Netherlands); Chernyshov, D [SNBL European Synchrotron Radiation Facility (ESRF), 38043 Grenoble (France); Bouwman, W G, E-mail: vasilieva@lns.pnpi.spb.r [Delft Technical University, 2629 JB Delft (Netherlands)

2010-10-01

Inverse photonic nickel-based crystal films formed by electrocrystallization of metal inside the voids of polymer artificial opal have been studied using the microradian X-ray diffraction. Analysis of the diffraction images agrees with an face-centred cubic (FCC) structure with the lattice constant a{sub 0} = 650 {+-} 10 nm and indicates two types of stacking sequences coexisting in the crystal (twins of ABCABC... and ACBACB... ordering motifs), the ratio between them being 4:5 The transverse structural correlation length L{sub tran} is 2.4 {+-} 0.1 {mu}m, which corresponds to a sample thickness of 6 layers. The in-plane structural correlation length L{sub long} is 3.4 {+-} 0.2 {mu}m, and the structure mosaic is of order of 10{sup 0}.

Crystal Structure of Ripk4 Reveals Dimerization-Dependent Kinase Activity.

Science.gov (United States)

Huang, Christine S; Oberbeck, Nina; Hsiao, Yi-Chun; Liu, Peter; Johnson, Adam R; Dixit, Vishva M; Hymowitz, Sarah G

2018-05-01

Receptor-interacting protein kinase 4 (RIPK4) is a highly conserved regulator of epidermal differentiation. Members of the RIPK family possess a common kinase domain as well as unique accessory domains that likely dictate subcellular localization and substrate preferences. Mutations in human RIPK4 manifest as Bartsocas-Papas syndrome (BPS), a genetic disorder characterized by severe craniofacial and limb abnormalities. We describe the structure of the murine Ripk4 (MmRipk4) kinase domain, in ATP- and inhibitor-bound forms. The crystallographic dimer of MmRipk4 is similar to those of RIPK2 and BRAF, and we show that the intact dimeric entity is required for MmRipk4 catalytic activity through a series of engineered mutations and cell-based assays. We also assess the impact of BPS mutations on protein structure and activity to elucidate the molecular origins of the disease. Copyright © 2018 Elsevier Ltd. All rights reserved.

Crystal structure of methyl 3′-benzamido-4′-(4-methoxyphenyl-1′-methylspiro[indeno[1,2-b]quinoxaline-11,2′-pyrrolidine]-3′-carboxylate

Directory of Open Access Journals (Sweden)

Kuppan Chandralekha

2016-09-01

Full Text Available In the title compound, C35H30N4O3, the spiro C atom connects the five-membered pyrrolidine ring and the indenoquinoxaline ring system. The pyrrolidine ring adopts a twist conformation. An intramolecular N—H...N interaction between the amino group and the pyrazine ring is observed. In the crystal, molecules are linked by a pairs of C—H...O hydrogen bonds, forming inversion dimers.

Crystal structure of the 500-kDa yeast acetyl-CoA carboxylase holoenzyme dimer

Energy Technology Data Exchange (ETDEWEB)

Wei, Jia; Tong, Liang

2015-10-12

Acetyl-CoA carboxylase (ACC) has crucial roles in fatty acid metabolism and is an attractive target for drug discovery against diabetes, cancer and other diseases1, 2, 3, 4, 5, 6. Saccharomyces cerevisiae ACC (ScACC) is crucial for the production of very-long-chain fatty acids and the maintenance of the nuclear envelope7, 8. ACC contains biotin carboxylase (BC) and carboxyltransferase (CT) activities, and its biotin is linked covalently to the biotin carboxyl carrier protein (BCCP). Most eukaryotic ACCs are 250-kilodalton (kDa), multi-domain enzymes and function as homodimers and higher oligomers. They contain a unique, 80-kDa central region that shares no homology with other proteins. Although the structures of the BC, CT and BCCP domains and other biotin-dependent carboxylase holoenzymes are known1, 9, 10, 11, 12, 13, 14, there is currently no structural information on the ACC holoenzyme. Here we report the crystal structure of the full-length, 500-kDa holoenzyme dimer of ScACC. The structure is remarkably different from that of the other biotin-dependent carboxylases. The central region contains five domains and is important for positioning the BC and CT domains for catalysis. The structure unexpectedly reveals a dimer of the BC domain and extensive conformational differences compared to the structure of the BC domain alone, which is a monomer. These structural changes reveal why the BC domain alone is catalytically inactive and define the molecular mechanism for the inhibition of eukaryotic ACC by the natural product soraphen A15, 16 and by phosphorylation of a Ser residue just before the BC domain core in mammalian ACC. The BC and CT active sites are separated by 80 Å, and the entire BCCP domain must translocate during catalysis.

Asymmetric monometallic nanorod nanoparticle dimer and related compositions and methods

KAUST Repository

Han, Yu

2016-03-31

The fabrication of asymmetric monometallic nanocrystals with novel properties for plasmonics, nanophotonics and nanoelectronics. Asymmetric monometallic plasmonic nanocrystals are of both fundamental synthetic challenge and practical significance. In an example, a thiol-ligand mediated growth strategy that enables the synthesis of unprecedented Au Nanorod-Au Nanoparticle (AuNR-AuNP) dimers from pre-synthesized AuNR seeds. Using high-resolution electron microscopy and tomography, crystal structure and three-dimensional morphology of the dimer, as well as the growth pathway of the AuNP on the AuNR seed, was investigated for this example. The dimer exhibits an extraordinary broadband optical extinction spectrum spanning the UV, visible, and near infrared regions (300 - 1300 nm). This unexpected property makes the AuNR-AuNP dimer example useful for many nanophotonic applications. In two experiments, the dimer example was tested as a surface- enhanced Raman scattering (SERS) substrate and a solar light harvester for photothermal conversion, in comparison with the mixture of AuNR and AuNP. In the SERS experiment, the dimer example showed an enhancement factor about 10 times higher than that of the mixture, when the excitation wavelength (660 nm) was off the two surface plasmon resonance (SPR) bands of the mixture. In the photothermal conversion experiment under simulated sunlight illumination, the dimer example exhibited an energy conversion efficiency about 1.4 times as high as that of the mixture.

Crystal structure of ethylenedioxytetrathiafulvalene-4,5-bis(thiolbenzoic acid 0.25-hydrate

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Yuanyuan Zhang

2017-09-01

Full Text Available In the title compound (systematic name: 4,4′-{[2-(5,6-dihydro-[1,3]dithiolo[4,5-b][1,4]dioxin-2-ylidene-1,3-dithiole-4,5-diyl]bis(sulfanediyl}dibenzoic acid 0.25-hydrate, C22H14O6S6·0.25H2O, the tetrathiafulvalene (TTF core adopts a boat conformation, where the central S2C=CS2 plane makes dihedral angles of 31.34 (4 and 26.83 (6°, respectively, with the peripheral S2C=CS2 and S2C2O2 planes. In the crystal, the benzoic acid molecules are linked via O—H...O hydrogen bonds, forming inversion dimers with R22(8 motifs. The dimers are linked through weak C—H...O hydrogen bonds into a chain structure along [-101]. The chains stack along the a axis through S...S and S...C short contacts, forming layers parallel to the ac plane.

Periodic order and defects in Ni-based inverse opal-like crystals on the mesoscopic and atomic scale

OpenAIRE

Chumakova, A. V.; Valkovskiy, G. A.; Mistonov, A. A.; Dyadkin, V. A.; Grigoryeva, N. A.; Sapoletova, N. A.; Napolskii, K. S.; Eliseev, A. A.; Petukhov, Andrei V.; Grigoriev, S. V.

2014-01-01

The structure of inverse opal crystals based on nickel was probed on the mesoscopic and atomic levels by a set of complementary techniques such as scanning electron microscopy and synchrotron microradian and wide-angle diffraction. The microradian diffraction revealed the mesoscopic-scale face-centered-cubic (fcc) ordering of spherical voids in the inverse opal-like structure with unit cell dimension of 750±10nm. The diffuse scattering data were used to map defects in the fcc structure as a f...

One-way propagation of bulk states and robust edge states in photonic crystals with broken inversion and time-reversal symmetries

Science.gov (United States)

Lu, Jin-Cheng; Chen, Xiao-Dong; Deng, Wei-Min; Chen, Min; Dong, Jian-Wen

2018-07-01

The valley is a flexible degree of freedom for light manipulation in photonic systems. In this work, we introduce the valley concept in magnetic photonic crystals with broken inversion symmetry. One-way propagation of bulk states is demonstrated by exploiting the pseudo-gap where bulk states only exist at one single valley. In addition, the transition between Hall and valley-Hall nontrivial topological phases is also studied in terms of the competition between the broken inversion and time-reversal symmetries. At the photonic boundary between two topologically distinct photonic crystals, we illustrate the one-way propagation of edge states and demonstrate their robustness against defects.

A nanolens-type enhancement in the linear and second harmonic response of a metallic dimer

International Nuclear Information System (INIS)

Pustovit, Vitaliy; Biswas, Sushmita; Vaia, Richard; Urbas, Augustine

2014-01-01

In this paper we explore the linear and second-order nonlinear response of gold nanoparticle pairs (dimers). Despite that even-order nonlinear processes are forbidden in bulk centrosymmetric media like metals, second order nonlinear response exhibits a high degree of sensitivity for spherical nanoparticles where inversion symmetry is broken at the surface. Recent experiments demonstrate significant dependence of linear response and second-harmonic surface nonlinear response arising from the local fundamental field distribution in a dimer configuration. Our calculations are carried out taking into account high order multipolar interactions between metal nanoparticles, and demonstrate that linear and nonlinear optical responses of the dimer exhibit periodic behavior dependent on the separation distance between nanoparticles. This response increases for dimers with a large difference between particle sizes. (paper)

Periodic order and defects in Ni-based inverse opal-like crystals on the mesoscopic and atomic scale

NARCIS (Netherlands)

Chumakova, A. V.; Valkovskiy, G. A.; Mistonov, A. A.; Dyadkin, V. A.; Grigoryeva, N. A.; Sapoletova, N. A.; Napolskii, K. S.; Eliseev, A. A.; Petukhov, Andrei V.; Grigoriev, S. V.

2014-01-01

The structure of inverse opal crystals based on nickel was probed on the mesoscopic and atomic levels by a set of complementary techniques such as scanning electron microscopy and synchrotron microradian and wide-angle diffraction. The microradian diffraction revealed the mesoscopic-scale

Dimerization interface of 3-hydroxyacyl-CoA dehydrogenase tunes the formation of its catalytic intermediate.

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Yingzhi Xu

Full Text Available 3-Hydroxyacyl-CoA dehydrogenase (HAD, EC 1.1.1.35 is a homodimeric enzyme localized in the mitochondrial matrix, which catalyzes the third step in fatty acid β-oxidation. The crystal structures of human HAD and subsequent complexes with cofactor/substrate enabled better understanding of HAD catalytic mechanism. However, numerous human diseases were found related to mutations at HAD dimerization interface that is away from the catalytic pocket. The role of HAD dimerization in its catalytic activity needs to be elucidated. Here, we solved the crystal structure of Caenorhabditis elegans HAD (cHAD that is highly conserved to human HAD. Even though the cHAD mutants (R204A, Y209A and R204A/Y209A with attenuated interactions on the dimerization interface still maintain a dimerization form, their enzymatic activities significantly decrease compared to that of the wild type. Such reduced activities are in consistency with the reduced ratios of the catalytic intermediate formation. Further molecular dynamics simulations results reveal that the alteration of the dimerization interface will increase the fluctuation of a distal region (a.a. 60-80 that plays an important role in the substrate binding. The increased fluctuation decreases the stability of the catalytic intermediate formation, and therefore the enzymatic activity is attenuated. Our study reveals the molecular mechanism about the essential role of the HAD dimerization interface in its catalytic activity via allosteric effects.

Coupling of Ag Nanoparticle with Inverse Opal Photonic Crystals as a Novel Strategy for Upconversion Emission Enhancement of NaYF4: Yb(3+), Er(3+) Nanoparticles.

Science.gov (United States)

Shao, Bo; Yang, Zhengwen; Wang, Yida; Li, Jun; Yang, Jianzhi; Qiu, Jianbei; Song, Zhiguo

2015-11-18

Rare-earth-ion-doped upconversion (UC) nanoparticles have generated considerable interest because of their potential application in solar cells, biological labeling, therapeutics, and imaging. However, the applications of UC nanoparticles were still limited because of their low emission efficiency. Photonic crystals and noble metal nanoparticles are applied extensively to enhance the UC emission of rare earth ions. In the present work, a novel substrate consisting of inverse opal photonic crystals and Ag nanoparticles was prepared by the template-assisted method, which was used to enhance the UC emission of NaYF4: Yb(3+), Er(3+) nanoparticles. The red or green UC emissions of NaYF4: Yb(3+), Er(3+) nanoparticles were selectively enhanced on the inverse opal substrates because of the Bragg reflection of the photonic band gap. Additionally, the UC emission enhancement of NaYF4: Yb(3+), Er(3+) nanoparticles induced by the coupling of metal nanoparticle plasmons and photonic crystal effects was realized on the Ag nanoparticles included in the inverse opal substrate. The present results demonstrated that coupling of Ag nanoparticle with inverse opal photonic crystals provides a useful strategy to enhance UC emission of rare-earth-ion-doped nanoparticles.

Crystal structures of two solvates of (18-crown-6potassium acetate

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Phil Liebing

2016-12-01

Full Text Available The crystal and molecular strutures of two solvated forms of [K(18c6]OAc (18c6 = 18-crown-6 = 1,4,7,10,13,16-hexaoxacyclooctadecane and OAc = acetate were determined by single-crystal X-ray diffraction, namely (acetato-κ2O,O′(1,4,7,10,13,16-hexaoxacyclooctadecane-κ6Opotassium dihydrate, [K(CH3COO(C12H24O6]·2H2O (1 and (acetato-κ2O,O′aqua(1,4,7,10,13,16-hexaoxacyclooctadecane-κ6Opotassium acetic acid monosolvate [K(CH3COO(C12H24O6(H2O]·CH3COOH (2. In both compounds, the acetate anion is bonded to the potassium ion in a chelating fashion and the metal atom is consequently slightly displaced from the O6 plane of the crown ether. In the crystals, O—H...O hydrogen bonds lead to a polymeric ladder structure in the dihydrate 1, while the acetic acid hydrate 2 features inversion dimers.

Crystal structure of ethyl 2-(diethoxyphosphoryl-2-(2,3,4-trimethoxyphenylacetate

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Moritz Schubert

2014-09-01

Full Text Available The title compound, C17H27O8P, was prepared by Michaelis–Arbuzov reaction of ethyl 2-bromo-2-(2,3,4-trimethoxyphenylacetate and triethyl phosphite. Such compounds rarely crystallize, but single crystals were recovered after the initial oil was left for approximately 10 years. The bond angle of the sp3-hybridized C atom connecting the benzene derivative with the phospho unit is widened marginally [112.5 (2°]. The terminal P—O bond length of 1.464 (2 Å clearly indicates a double bond, whereas the two O atoms of the ethoxy groups connected to the phosphorous atom have bond lengths of 1.580 (2 Å and 1.581 (3 Å. The three methoxy groups emerge out of the benzene-ring plane due to steric hindrance [C—C—O—C torsion angles = −179.9 (3°, −52.9 (4° and 115.3 (4°]. In the crystal, inversion dimers linked by pairs of C—H...O=P hydrogen bonds generate R22(14 loops. The chosen crystal was modelled as a non-merohedral twin.

Quantitative Experimental Determination of Primer-Dimer Formation Risk by Free-Solution Conjugate Electrophoresis

Science.gov (United States)

Desmarais, Samantha M.; Leitner, Thomas; Barron, Annelise E.

2012-01-01

DNA barcodes are short, unique ssDNA primers that “mark” individual biomolecules. To gain better understanding of biophysical parameters constraining primer-dimer formation between primers that incorporate barcode sequences, we have developed a capillary electrophoresis method that utilizes drag-tag-DNA conjugates to quantify dimerization risk between primer-barcode pairs. Results obtained with this unique free-solution conjugate electrophoresis (FSCE) approach are useful as quantitatively precise input data to parameterize computation models of dimerization risk. A set of fluorescently labeled, model primer-barcode conjugates were designed with complementary regions of differing lengths to quantify heterodimerization as a function of temperature. Primer-dimer cases comprised two 30-mer primers, one of which was covalently conjugated to a lab-made, chemically synthesized poly-N-methoxyethylglycine drag-tag, which reduced electrophoretic mobility of ssDNA to distinguish it from ds primer-dimers. The drag-tags also provided a shift in mobility for the dsDNA species, which allowed us to quantitate primer-dimer formation. In the experimental studies, pairs of oligonucleotide primer-barcodes with fully or partially complementary sequences were annealed, and then separated by free-solution conjugate CE at different temperatures, to assess effects on primer-dimer formation. When less than 30 out of 30 basepairs were bonded, dimerization was inversely correlated to temperature. Dimerization occurred when more than 15 consecutive basepairs formed, yet non-consecutive basepairs did not create stable dimers even when 20 out of 30 possible basepairs bonded. The use of free-solution electrophoresis in combination with a peptoid drag-tag and different fluorophores enabled precise separation of short DNA fragments to establish a new mobility shift assay for detection of primer-dimer formation. PMID:22331820

Crystal structures of two 1:2 dihydrate compounds of chloranilic acid with 2-carboxypyridine and 2-carboxyquinoline

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Kazuma Gotoh

2017-12-01

Full Text Available The crystal structure of the 1:2 dihydrate compound of chloranilic acid (systematic name: 2,5-dichloro-3,6-dihydroxy-1,4-benzoquinone with 2-carboxypyridine (another common name: picolinic acid; systematic name: pyridine-2-carboxylic acid, namely, 2C6H5.5NO20.5+·C6HCl2O4−·2H2O, (I, has been determined at 180 K, and the structure of the 1:2 dihydrate compound of chloranilic acid with 2-carboxyquinoline (another common name: quinaldic acid; systematic name: quinoline-2-carboxylic acid, namely, 2C10H7NO2·C6H2Cl2O4·2H2O, (II, has been redetermined at 200 K. This determination presents a higher precision crystal structure than the previously published structure [Marfo-Owusu & Thompson (2014. X-ray Struct. Anal. Online, 30, 55–56]. Compound (I was analysed as a disordered structure over two states, viz. salt and co-crystal. The salt is bis(2-carboxypyridinium chloranilate dihydrate, 2C6H6NO2+·C6Cl2O42−·2H2O, and the co-crystal is bis(pyridinium-2-carboxylate chloranilic acid dihydrate, 2C6H5NO2·C6H2Cl2O4·2H2O, including zwitterionic 2-carboxypyridine. In both salt and co-crystal, the water molecule links the chloranilic acid and 2-carboxypyridine molecules through O—H...O and N—H...O hydrogen bonds. The 2-carboxypyridine molecules are connected into a head-to-head inversion dimer by a short O—H...O hydrogen bond, in which the H atom is disordered over two positions. Compound (II is a 1:2 dihydrate co-crystal of chloranilic acid and zwitterionic 2-carboxyquinoline. The water molecule links the chloranilic acid and 2-carboxyquinoline molecules through O—H...O hydrogen bonds. The 2-carboxyquinoline molecules are connected into a head-to-tail inversion dimer by a pair of N—H...O hydrogen bonds.

Carbene supported dimer of heavier ketenimine analogue with p and si atoms.

Science.gov (United States)

Roy, Sudipta; Dittrich, Birger; Mondal, Totan; Koley, Debasis; Stückl, A Claudia; Schwederski, Brigitte; Kaim, Wolfgang; John, Michael; Vasa, Suresh Kumar; Linser, Rasmus; Roesky, Herbert W

2015-05-20

A cyclic alkyl(amino) carbene (cAAC) stabilized dimer [(cAAC)Si(P-Tip)]2 (2) (Tip = 2,4,6-triisopropylphenyl) is reported. 2 can be considered as a dimer of the heavier ketenimine (R2C═C═N-R) analogue. The dark-red rod-shaped crystals of 2 were synthesized by reduction of the precursor, cAAC-dichlorosilylene-stabilized phosphinidene (cAAC)SiCl2→P-Tip with sodium napthalenide. The crystals of 2 are storable at room temperature for several months and stable up to 215 °C under an inert atmosphere. X-ray single-crystal diffraction revealed that 2 contains a cyclic nonplanar four-membered SiPSiP ring. Magnetic susceptibility measurements confirmed the singlet spin ground state of 2. Cyclic voltammetry of 2 showed a quasi-reversible one-electron reduction indicating the formation of the corresponding radical anion 2(•-), which was further characterized by EPR measurements in solution. The electronic structure and bonding of 2 and 2(•-) were studied by theoretical calculations. The experimentally obtained data are in good agreement with the calculated values.

Glycine transporter dimers: evidence for occurrence in the plasma membrane.

Science.gov (United States)

Bartholomäus, Ingo; Milan-Lobo, Laura; Nicke, Annette; Dutertre, Sébastien; Hastrup, Hanne; Jha, Alok; Gether, Ulrik; Sitte, Harald H; Betz, Heinrich; Eulenburg, Volker

2008-04-18

Different Na(+)/Cl(-)-dependent neurotransmitter transporters of the SLC6a family have been shown to form dimers or oligomers in both intracellular compartments and at the cell surface. In contrast, the glycine transporters (GlyTs) GlyT1 and -2 have been reported to exist as monomers in the plasma membrane based on hydrodynamic and native gel electrophoretic studies. Here, we used cysteine substitution and oxidative cross-linking to show that of GlyT1 and GlyT2 also form dimeric complexes within the plasma membrane. GlyT oligomerization at the cell surface was confirmed for both GlyT1 and GlyT2 by fluorescence resonance energy transfer microscopy. Endoglycosidase treatment and surface biotinylation further revealed that complex-glycosylated GlyTs form dimers located at the cell surface. Furthermore, substitution of tryptophan 469 of GlyT2 by an arginine generated a transporter deficient in dimerization that was retained intracellulary. Based on these results and GlyT structures modeled by using the crystal structure of the bacterial homolog LeuT(Aa), as a template, residues located within the extracellular loop 3 and at the beginning of transmembrane domain 6 are proposed to contribute to the dimerization interface of GlyTs.

The crystal structure of 6-(4-chlorophenyl-2-(4-methylbenzylimidazo[2,1-b][1,3,4]thiadiazole-5-carbaldehyde

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A. Sowmya

2016-10-01

Full Text Available In the title imidazo[2,1-b][1,3,4]thiadiazole derivative, C19H14ClN3OS, the 4-methylbenzyl and chlorophenyl rings are inclined to the planar imidazo[2,1-b][1,3,4]thiadiazole moiety (r.m.s. deviation = 0.012 Å by 64.5 (1 and 3.7 (1°, respectively. The molecular structure is primarily stabilized by a strong intramolecular C—H...O hydrogen bond, leading to the formation of a pseudo-seven-membered S(7 ring motif, and a short intramolecular C—H...N contact forming an S(5 ring motif. In the crystal, molecules are linked by pairs of C—H...S hydrogen bonds, forming inversion dimers. The dimers are linked by C—H...O and C—H...π interactions, forming chains propagating along [110].

Spin quantum tunneling via entangled states in a dimer of exchange coupled single-molecule magnets

Science.gov (United States)

Tiron, R.; Wernsdorfer, W.; Aliaga-Alcalde, N.; Foguet-Albiol, D.; Christou, G.

2004-03-01

A new family of supramolecular, antiferromagnetically exchange-coupled dimers of single-molecule magnets (SMMs) has recently been reported [W. Wernsdorfer, N. Aliaga-Alcalde, D.N. Hendrickson, and G. Christou, Nature 416, 406 (2002)]. Each SMM acts as a bias on its neighbor, shifting the quantum tunneling resonances of the individual SMMs. Hysteresis loop measurements on a single crystal of SMM-dimers have now established quantum tunneling of the magnetization via entangled states of the dimer. This shows that the dimer really does behave as a quantum-mechanically coupled dimer. The transitions are well separated, suggesting long coherence times compared to the time scale of the energy splitting. This result is of great importance if such systems are to be used for quantum computing. It also allows the measurement of the longitudinal and transverse superexchange coupling constants [Phys. Rev. Lett. 91, 227203 (2003)].

Physical and chemical transformations of μ-oxo dimers and alkoxy complexes of Fe-octaethylporphyrins in solids and in solutions

Science.gov (United States)

Ivashin, N. V.; Shulga, A. M.; Terekhov, S. N.; Dzilinski, K.

1996-11-01

It has been found that relatively small changes in conditions of crystallization in the synthesis process of μ-oxo dimers can lead to quite different products with dimeric or monomeric structures. Molecular structures of these products, discussed on the basis of Fe-octaethylporphyrin (FeOEP) complexes, have been studied using IR, NMR, EPR, resonance Raman (RR), mass and Mössbauer spectroscopies. The use of chloroform with admixture of alcohols (methanol, deuteromethanol and ethanol) in place of pure chloroform for crystallization of the eluate obtained during synthesis of μ-oxo dimers leads to the formation of alkoxy complexes instead of the μ-oxo dimers. It has been also established that dissolution of the μ-oxo dimers in chloroform-ethanol or chloroform-methanol mixtures leads to conversion of the μ-oxo dimers into the alkoxy complexes after evaporation of the solvents. Methoxy and ethoxy ligands in Fe(OEP)OCH 3 and Fe(OEP)OC 2H 5 complexes can exchange the positions during addition of ethanol to the former and methanol to the latter complex in solution. The possibility of generation of doubly bridged structures of the type: OEP Fe< RRFe OEP where R is OCH 3 or OC 2H 5 is discussed.

Specific features of the crystal packing that enable styryl dyes of the pyridine series to undergo the solid-phase [2 + 2] photocycloaddition including the process with single crystal retention

International Nuclear Information System (INIS)

Kuz'mina, L. G.; Vedernikov, A. I.; Sazonov, S. K.; Lobova, N. A.; Loginov, P. S.; Howard, J. A. K.; Alfimov, M. V.; Gromov, S. P.

2008-01-01

The crystal packing of a number of styryl dyes of the pyridine series is analyzed. The structures of three dyes and three [2 + 2] photocycloaddition (PCA) products, 1,2,3,4-tetrasubstituted cyclobutanes, obtained in single crystals are determined by X-ray diffraction. Stacks of planar organic cations are characteristic of styryl dye packings. The proceeding of the PCA reaction as a single crystal-to-single crystal transformation in the syn head-to-head stacks is in principle impossible. The syn head-to-tail stacking packings are favorable for the PCA reactions resulting in the centrosymmetric rctt isomers of cyclobutane. The stacking packings, in which molecules are related by the twofold axes (the anti arrangement of molecules), are also favorable for PCA in single crystals. In this case, the products are the rtct isomers of cyclobutane. The presence of the I - counterions in a packing is a factor impeding the PCA reaction, because the secondary I-H-C bonds increase the rigidity of the crystal lattice. The conditions necessary for proceeding the PCA reactions in styryl dyes as single crystal-to-single crystal processes are as follows: (1) the stacks split into pairs of organic cations (dimers) with the d distances within 4.2 A in a dimer and d exceeding 4.2 A between the dimers; and (2) the dimers are surrounded by flexible shells consisting of anions, solvate molecules, or flexible moieties of the organic cations themselves.

CtBP1/BARS Gly172 → Glu mutant structure: Impairing NAD(H)-binding and dimerization

International Nuclear Information System (INIS)

Nardini, Marco; Valente, Carmen; Ricagno, Stefano; Luini, Alberto; Corda, Daniela; Bolognesi, Martino

2009-01-01

C-terminal binding proteins (CtBPs) are multi-functional proteins involved in nuclear transcriptional co-repression, Golgi membrane fission, and synaptic ribbon formation. Binding of NAD(H) to CtBPs promotes dimerization. CtBP dimers act as a scaffold for multimeric protein complex formation, thus bridging transcriptional repressors and their targets in the nucleus. Based on size-exclusion chromatography experiments and on the crystal structure of the NAD(H)-free G172E CtBP mutant, we show here that absence of NAD(H) induces flexibility/backbone conformational changes at the dimerization interface and at the CtBP interdomain region. The results presented shed first light on the correlation between NAD(H)-binding and functional CtBP dimerization.

Crystal structure of ethyl (4R-2-amino-7-hydroxy-4-phenyl-4H-chromene-3-carboxylate

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Joel T. Mague

2015-07-01

Full Text Available In the title compound, C18H17NO4, the dihedral angle between the phenyl ring and the fused six-membered ring is 77.65 (4°. The conformation of the molecule is determined in part by an intramolecular N—H...O hydrogen bond between the amino H atom and the carbonyl O atom, forming an S(6 motif. In the crystal, molecules are linked into N—H...O hydrogen-bonded inversion dimers which are then connected into chains along [001], forming a two-dimensional network parallel to (100 via O—H...O hydrogen bonds. C—H...O interactions further contribute to the crystal stability. The ethyl group is disordered over two sets of sites in a 0.801 (5:0.199 (5 ratio.

The Structure of the Poxvirus A33 Protein Reveals a Dimer of Unique C-Type Lectin-Like Domains

Energy Technology Data Exchange (ETDEWEB)

Su, Hua-Poo; Singh, Kavita; Gittis, Apostolos G.; Garboczi, David N. (NIH)

2010-11-03

The current vaccine against smallpox is an infectious form of vaccinia virus that has significant side effects. Alternative vaccine approaches using recombinant viral proteins are being developed. A target of subunit vaccine strategies is the poxvirus protein A33, a conserved protein in the Chordopoxvirinae subfamily of Poxviridae that is expressed on the outer viral envelope. Here we have determined the structure of the A33 ectodomain of vaccinia virus. The structure revealed C-type lectin-like domains (CTLDs) that occur as dimers in A33 crystals with five different crystal lattices. Comparison of the A33 dimer models shows that the A33 monomers have a degree of flexibility in position within the dimer. Structural comparisons show that the A33 monomer is a close match to the Link module class of CTLDs but that the A33 dimer is most similar to the natural killer (NK)-cell receptor class of CTLDs. Structural data on Link modules and NK-cell receptor-ligand complexes suggest a surface of A33 that could interact with viral or host ligands. The dimer interface is well conserved in all known A33 sequences, indicating an important role for the A33 dimer. The structure indicates how previously described A33 mutations disrupt protein folding and locates the positions of N-linked glycosylations and the epitope of a protective antibody.

Crystallization of purple nitrous oxide reductase from Pseudomonas stutzeri

International Nuclear Information System (INIS)

Pomowski, Anja; Zumft, Walter G.; Kroneck, Peter M. H.; Einsle, Oliver

2010-01-01

The physiologically active form of nitrous oxide reductase was isolated and crystallized under strict exclusion of dioxygen and diffraction data were collected from crystals belonging to two different space groups. Nitrous oxide reductase (N 2 OR) from Pseudomonas stutzeri catalyzes the final step in denitrification: the two-electron reduction of nitrous oxide to molecular dinitrogen. Crystals of the enzyme were grown under strict exclusion of dioxygen by sitting-drop vapour diffusion using 2R,3R-butanediol as a cryoprotectant. N 2 OR crystallized in either space group P1 or P6 5 . Interestingly, the key determinant for the resulting space group was the crystallization temperature. Crystals belonging to space group P1 contained four 130 kDa dimers in the asymmetric unit, while crystals belonging to space group P6 5 contained a single dimer in the asymmetric unit. Diffraction data were collected to resolutions better than 2 Å

The dynamics of molecular dimers in the crystals of m-aminobenzoic acid studied by inelastic neutron scattering (INS), Raman, IR spectroscopy and DFT calculations

Energy Technology Data Exchange (ETDEWEB)

Pawlukojc, A.; Leciejewicz, J

2004-03-29

Inelastic neutron scattering, Raman and IR spectra were measured for m-aminobenzoic acid (MABA). Optimized geometries and observed frequencies were assigned using DFT calculation on the B3LYP/6-311G** level using Gaussian 98 and Gamess programs. Experimental structural and spectroscopic data are in good agreement with computations assuming the presence in the crystals of molecular dimers composed of two MABA molecules linked by a pair of O-H...O hydrogen bonds each provided by the carboxylic group. INS frequencies have been identified for the O-H (out of plane) mod0008.

Dimerization of inositol monophosphatase Mycobacterium tuberculosis SuhB is not constitutive, but induced by binding of the activator Mg2+

Directory of Open Access Journals (Sweden)

Nigou Jérôme

2007-08-01

Full Text Available Abstract Background The cell wall of Mycobacterium tuberculosis contains a wide range of phosphatidyl inositol-based glycolipids that play critical structural roles and, in part, govern pathogen-host interactions. Synthesis of phosphatidyl inositol is dependent on free myo-inositol, generated through dephosphorylation of myo-inositol-1-phosphate by inositol monophosphatase (IMPase. Human IMPase, the putative target of lithium therapy, has been studied extensively, but the function of four IMPase-like genes in M. tuberculosis is unclear. Results We determined the crystal structure, to 2.6 Å resolution, of the IMPase M. tuberculosis SuhB in the apo form, and analysed self-assembly by analytical ultracentrifugation. Contrary to the paradigm of constitutive dimerization of IMPases, SuhB is predominantly monomeric in the absence of the physiological activator Mg2+, in spite of a conserved fold and apparent dimerization in the crystal. However, Mg2+ concentrations that result in enzymatic activation of SuhB decisively promote dimerization, with the inhibitor Li+ amplifying the effect of Mg2+, but failing to induce dimerization on its own. Conclusion The correlation of Mg2+-driven enzymatic activity with dimerization suggests that catalytic activity is linked to the dimer form. Current models of lithium inhibition of IMPases posit that Li+ competes for one of three catalytic Mg2+ sites in the active site, stabilized by a mobile loop at the dimer interface. Our data suggest that Mg2+/Li+-induced ordering of this loop may promote dimerization by expanding the dimer interface of SuhB. The dynamic nature of the monomer-dimer equilibrium may also explain the extended concentration range over which Mg2+ maintains SuhB activity.

Preparation and characterization of dimeric and tetrameric clusters of molybdenum and tungsten

Energy Technology Data Exchange (ETDEWEB)

Ryan, T.R.

1981-10-01

The cyclo-addition of two Mo/sub 2/Cl/sub 4/(P(C/sub 6/H/sub 5/)/sub 3/)/sub 2/(CH/sub 3/OH)/sub 2/ molecules has produced a new type of tetrameric molybdenum cluster, Mo/sub 4/Cl/sub 8/L/sub 4/. Structural characterization of this dimer revealed weak molybdenum-methanol bonding which was consistent with the observed reactivity of the compound. New synthetic methods were devised for the preparation of Mo/sub 4/X/sub 8/L/sub 4/ clusters where X = Cl, Br, I and L = PR/sub 3/, Po/sub 3/, RCN, CH/sub 3/OH. A scheme for the metal-metal bonding in these clusters was presented which was in agreement with the known structural features of Mo/sub 4/Cl/sub 8/(PR/sub 3/)/sub 4/, R = C/sub 2/H/sub 5/, n-C/sub 4/H/sub 9/. The preparation of the analogous W/sub 4/Cl/sub 8/(PR/sub 3/)/sub 4/ cluster from WCl/sub 4/ was accomplished by application of techniques used in the molybdenum syntheses. The single crystal x-ray structure revealed slight differences from the molybdenum analog which were rationalized in terms of the known behavior in dimeric tungsten and molybdenum species. The attempted preparation of a tetrameric tungsten cluster from W/sub 2/(mhp)/sub 4/ was unsuccessful (mhp = anion of 2-methyl-6-hydroxypyridine). Instead, the new tungsten dimer, W/sub 2/Cl/sub 2/(mhp)/sub 3/, was isolated which possessed a metal-metal bond order of 3.5. The x-ray crystal structure of the dimer revealed that the chlorine atoms were situated cis, one bound to each tungsten. Cyclic voltammetry showed that the compound could be reversibly reduced, presumably to a W/sub 2//sup 4 +/ dimer containing a quadruple metal-metal bond.

Fe65-PTB2 Dimerization Mimics Fe65-APP Interaction

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Lukas P. Feilen

2017-05-01

Full Text Available Physiological function and pathology of the Alzheimer’s disease causing amyloid precursor protein (APP are correlated with its cytosolic adaptor Fe65 encompassing a WW and two phosphotyrosine-binding domains (PTBs. The C-terminal Fe65-PTB2 binds a large portion of the APP intracellular domain (AICD including the GYENPTY internalization sequence fingerprint. AICD binding to Fe65-PTB2 opens an intra-molecular interaction causing a structural change and altering Fe65 activity. Here we show that in the absence of the AICD, Fe65-PTB2 forms a homodimer in solution and determine its crystal structure at 2.6 Å resolution. Dimerization involves the unwinding of a C-terminal α-helix that mimics binding of the AICD internalization sequence, thus shielding the hydrophobic binding pocket. Specific dimer formation is validated by nuclear magnetic resonance (NMR techniques and cell-based analyses reveal that Fe65-PTB2 together with the WW domain are necessary and sufficient for dimerization. Together, our data demonstrate that Fe65 dimerizes via its APP interaction site, suggesting that besides intra- also intermolecular interactions between Fe65 molecules contribute to homeostatic regulation of APP mediated signaling.

Fe65-PTB2 Dimerization Mimics Fe65-APP Interaction.

Science.gov (United States)

Feilen, Lukas P; Haubrich, Kevin; Strecker, Paul; Probst, Sabine; Eggert, Simone; Stier, Gunter; Sinning, Irmgard; Konietzko, Uwe; Kins, Stefan; Simon, Bernd; Wild, Klemens

2017-01-01

Physiological function and pathology of the Alzheimer's disease causing amyloid precursor protein (APP) are correlated with its cytosolic adaptor Fe65 encompassing a WW and two phosphotyrosine-binding domains (PTBs). The C-terminal Fe65-PTB2 binds a large portion of the APP intracellular domain (AICD) including the GYENPTY internalization sequence fingerprint. AICD binding to Fe65-PTB2 opens an intra-molecular interaction causing a structural change and altering Fe65 activity. Here we show that in the absence of the AICD, Fe65-PTB2 forms a homodimer in solution and determine its crystal structure at 2.6 Å resolution. Dimerization involves the unwinding of a C-terminal α-helix that mimics binding of the AICD internalization sequence, thus shielding the hydrophobic binding pocket. Specific dimer formation is validated by nuclear magnetic resonance (NMR) techniques and cell-based analyses reveal that Fe65-PTB2 together with the WW domain are necessary and sufficient for dimerization. Together, our data demonstrate that Fe65 dimerizes via its APP interaction site, suggesting that besides intra- also intermolecular interactions between Fe65 molecules contribute to homeostatic regulation of APP mediated signaling.

Proteolysis of truncated hemolysin A yields a stable dimerization interface

Energy Technology Data Exchange (ETDEWEB)

Novak, Walter R.P.; Bhattacharyya, Basudeb; Grilley, Daniel P.; Weaver, Todd M. (Wabash); (UW)

2017-02-21

Wild-type and variant forms of HpmA265 (truncated hemolysin A) fromProteus mirabilisreveal a right-handed, parallel β-helix capped and flanked by segments of antiparallel β-strands. The low-salt crystal structures form a dimeric structureviathe implementation of on-edge main-chain hydrogen bonds donated by residues 243–263 of adjacent monomers. Surprisingly, in the high-salt structures of two variants, Y134A and Q125A-Y134A, a new dimeric interface is formedviamain-chain hydrogen bonds donated by residues 203–215 of adjacent monomers, and a previously unobserved tetramer is formed. In addition, an eight-stranded antiparallel β-sheet is formed from the flap regions of crystallographically related monomers in the high-salt structures. This new interface is possible owing to additional proteolysis of these variants after Tyr240. The interface formed in the high-salt crystal forms of hemolysin A variants may mimic the on-edge β-strand positioning used in template-assisted hemolytic activity.

Crystal structure of 2-amino-4-(4-chlorophenyl-1-(4-methylphenyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carbonitrile

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Shaaban K. Mohamed

2015-12-01

Full Text Available In the title compound, C23H20ClN3O, each of the cyclohexene and 1,4-dihydropyridine rings of the 1,4,5,6,7,8-hexahydroquinoline ring system adopts a twisted-boat conformation. The dihedral angle between the two benzene rings is 11.52 (7°. In the crystal, molecules are linked through a pair of amino–nitrile N—H...N hydrogen bonds, forming inversion dimers. These assemble into a three-dimensional network via C—H...O and C—H...π interactions.

Crystal structure of 2-hydroxyimino-2-(pyridin-2-yl-N′-[1-(pyridin-2-ylethylidene]acetohydrazide

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Maxym O. Plutenko

2014-12-01

Full Text Available The molecule of the title compound, C14H13N5O2, is approximately planar (r.m.s deviation for all non-H atoms = 0.093 Å, with the planes of the two pyridine rings inclined to one another by 5.51 (7°. The oxime group is syn to the amide group, probably due to the formation of an intramolecular N—H...N hydrogen bond that forms an S(6 ring motif. In the crystal, molecules are linked by pairs of bifurcated O—H...(O,N hydrogen bonds, forming inversion dimers. The latter are linked via C—H...O and C—H...N hydrogen bonds, forming sheets lying parallel to (502. The sheets are linked via π–π stacking interactions [inter-centroid distance = 3.7588 (9 Å], involving the pyridine rings of inversion-related molecules, forming a three-dimensional structure.

Synthesis, Crystal Structure and Luminescence Property of a New Silver(I) Dimer with Isonicotinic Acid

International Nuclear Information System (INIS)

Yuan, Qi; Liu, Bing

2005-01-01

The absorption spectrum was calculated from reflection spectrum by the Kubelka.Munk function. The energy gap of the title compound determined by extrapolation from the linear portion of the absorption edge in a (α/S) versus energy plot is 1.91 eV, which suggests that the title compound behaves as semiconductor. Isonicotinic acid (Iso), namely 4.pyridinecarboxylate, a multi.functional chelating and/or bridging ligand, has proved to be very powerful for the construction of multi. dimensional metal.organic coordination networks. Furthermore, The isonicotinic acid complexes has raised many interests in fluorescence probing with numerous potential applications for studies of microsecond diffusion and dynamics of membranes. Metal centers are potential carriers of electrochemical, magnetic, catalytic, or optical properties that may be introduced into the inorganic.organic hybrid materials. d"1"0 metals with rich photophysical and photochemical character have focused attentions to synthesize polynuclear complexes. Considering the versatile coordination abilities of Iso, we employ the ligand to coordinate with silver nitrate to fabricate a coordination complex with excellent fluorescence property. Herein we report the synthesis, crystal structure and fluorescence property of a new d"1"0 coordination dimer [Ag_2(Iso)_2(NO_3)_2

Diffusion and adsorption of dimers on reconstructed Pt(1 1 0) surfaces: First principle and EAM studies

Science.gov (United States)

Matrane, I.; Mazroui, M.; Sbiaai, K.

2018-03-01

We present a density functional theory (DFT) and embedded atom method (EAM) studies of Pt2 , Au2 and AuPt dimers adsorption and diffusion on the clean Pt (1 1 0) (1 × 1) surface and (1 × 2) (1 × 3) and (1 × 4) missing row reconstructed geometries. As a first step, adsorption energies are calculated for all considered dimers, and their stability is checked by computing the binding energies. Furthermore, the energy barriers for the elementary diffusion mechanisms (concerted jump, dissociation-reassociation and leapfrog) are calculated for dimers diffusion on all considered geometries. The potential energy profile for the leapfrog mechanism is provided for dimers diffusion on the (1 × 2) (1 × 3) and (1 × 4) missing row reconstructed geometries. Our results show that each of the three dimers exhibits a qualitatively different behaviours. In addition, the obtained results provide interesting atomistic information about dimers stability and mobility, which is required for understanding the macroscopic kinetics of crystal growth.

Crystal structure of 5,5′-bis(dimethylamino-N,N′-(3-methyl-3-azapentane-1,5-diyldi(naphthalene-1-sulfonamide

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Toyketa V. Horne

2015-12-01

Full Text Available In the title compound, C29H37N5O4S2, two arms substituted with dansyl derivatives are connected to a central tertiary amine, where the dihedral angle between the planes of two dansyl units is 56.39 (4°. Each arm contains a sulfonamide functional group and both N—H groups in the compound are pointed to the same side. The central part of the molecule is disordered over three sets of sites with a refined occupancy ratio of 0.547 (4:0.328 (4:0.125 (3. No intramolecular π–π or hydrogen-bonding interactions are observed. In the crystal, molecules are linked via pairs of N—H...O interactions involving the same acceptor atom, forming inversion dimers. In addition, C—H...O interactions exist between molecules, providing further stabilization of dimers.

Aromatic C-Nitroso Compounds and Their Dimers: A Model for Probing the Reaction Mechanisms in Crystalline Molecular Solids

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Ivana Biljan

2017-12-01

Full Text Available This review is focused on the dimerization and dissociation of aromatic C-nitroso compounds and their dimers, the reactions that could be used as a convenient model for studying the thermal organic solid-state reaction mechanisms. This molecular model is simple because it includes formation or breaking of only one covalent bond between two nitrogen atoms. The crystalline molecular solids of nitroso dimers (azodioxides dissociate by photolysis under the cryogenic conditions, and re-dimerize by slow warming. The thermal re-dimerization reaction is examined under the different topotactic conditions in crystals: disordering, surface defects, and phase transformations. Depending on the conditions, and on the molecular structure, aromatic C-nitroso compounds can associate to form one-dimensional polymeric structures and are able to self-assemble on gold surfaces.

Crystallization of bi-functional ligand protein complexes.

Science.gov (United States)

Antoni, Claudia; Vera, Laura; Devel, Laurent; Catalani, Maria Pia; Czarny, Bertrand; Cassar-Lajeunesse, Evelyn; Nuti, Elisa; Rossello, Armando; Dive, Vincent; Stura, Enrico Adriano

2013-06-01

Homodimerization is important in signal transduction and can play a crucial role in many other biological systems. To obtaining structural information for the design of molecules able to control the signalization pathways, the proteins involved will have to be crystallized in complex with ligands that induce dimerization. Bi-functional drugs have been generated by linking two ligands together chemically and the relative crystallizability of complexes with mono-functional and bi-functional ligands has been evaluated. There are problems associated with crystallization with such ligands, but overall, the advantages appear to be greater than the drawbacks. The study involves two matrix metalloproteinases, MMP-12 and MMP-9. Using flexible and rigid linkers we show that it is possible to control the crystal packing and that by changing the ligand-enzyme stoichiometric ratio, one can toggle between having one bi-functional ligand binding to two enzymes and having the same ligand bound to each enzyme. The nature of linker and its point of attachment on the ligand can be varied to aid crystallization, and such variations can also provide valuable structural information about the interactions made by the linker with the protein. We report here the crystallization and structure determination of seven ligand-dimerized complexes. These results suggest that the use of bi-functional drugs can be extended beyond the realm of protein dimerization to include all drug design projects. Copyright © 2013 Elsevier Inc. All rights reserved.

Non-additive non-interacting kinetic energy of rare gas dimers

Science.gov (United States)

Jiang, Kaili; Nafziger, Jonathan; Wasserman, Adam

2018-03-01

Approximations of the non-additive non-interacting kinetic energy (NAKE) as an explicit functional of the density are the basis of several electronic structure methods that provide improved computational efficiency over standard Kohn-Sham calculations. However, within most fragment-based formalisms, there is no unique exact NAKE, making it difficult to develop general, robust approximations for it. When adjustments are made to the embedding formalisms to guarantee uniqueness, approximate functionals may be more meaningfully compared to the exact unique NAKE. We use numerically accurate inversions to study the exact NAKE of several rare-gas dimers within partition density functional theory, a method that provides the uniqueness for the exact NAKE. We find that the NAKE decreases nearly exponentially with atomic separation for the rare-gas dimers. We compute the logarithmic derivative of the NAKE with respect to the bond length for our numerically accurate inversions as well as for several approximate NAKE functionals. We show that standard approximate NAKE functionals do not reproduce the correct behavior for this logarithmic derivative and propose two new NAKE functionals that do. The first of these is based on a re-parametrization of a conjoint Perdew-Burke-Ernzerhof (PBE) functional. The second is a simple, physically motivated non-decomposable NAKE functional that matches the asymptotic decay constant without fitting.

Crystals structure of Na3Li(TiF6)2

International Nuclear Information System (INIS)

Popov, D.Yu.; Antokhina, T.F.; Gerasimenko, A.V.; Kajdalova, T.A.; Sergienko, V.I.

2004-01-01

Crystals of Na 3 Li(TiF 6 ) 2 (1) were synthesized in aqueous solution and characterized by the elementary and X-ray phase analysis methods. According to X-ray diffraction analysis data compound 1 is crystallized in a tetragonal crystal system with the following parameters: a=5.130(1), c=18.046(4) A, Z=2, space group P4-bar2 1 c. Alternating layers on the basis of dimers made up by octahedrons of TiF 6 and Na(1)F 6 constitute the frame of compound 1 crystal structure. The dimer layers are joined in a continuous frame by Na(2) and Li cations. Coordination polyhedron of Li atom is tetrahedron (Li-F 1.898(3) A) [ru

Crystal structure of ethyl (E-2-cyano-3-(thiophen-2-ylacrylate: two conformers forming a discrete disorder

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Brian Castro Agudelo

2017-09-01

Full Text Available In the title compound, C10H9NO2S, all the non-H atoms, except for the ethyl fragment, lie nearly in the same plane. Despite the molecular planarity, the ethyl fragment presents more than one conformation, giving rise to a discrete disorder, which was modelled with two different crystallographic sites for the ethoxy O and ethoxy α-C atoms, with occupancy values of 0.5. In the crystal, the three-dimensional array is mainly directed by C—H...(O,N interactions, giving rise to inversion dimers with R22(10 and R22(14 motifs and infinite chains running along the [100] direction.

Crystal structure of 26-(4-methylphenyl-8,11,14,17-tetraoxa-28-azatetracyclo[22.3.1.02,7.018,23]hexacosa-2,4,6,18(23,19,21,24(1,25,27-nonaene

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T. Thanh Van Tran

2016-05-01

Full Text Available The title compound, C30H29NO4, is a tetracyclic system containing a 4-arylpyridine fragment, two benzene rings and an aza-17-crown-5 ether moiety, in a bowl-like arrangement. The pyridine ring is inclined to the 4-methylphenyl ring by 26.64 (6°, and by 57.43 (6 and 56.81 (6° to the benzene rings. The benzene rings are inclined to one another by 88.32 (6°. In the crystal, molecules are linked by pairs of C—H...N hydrogen bonds, forming inversion dimers with an R22(14 ring motif. The dimers are linked via a number of C—H...π interactions, forming a three-dimensional architecture.

Biogenesis of Triterpene Dimers from Orthoquinones Related to Quinonemethides: Theoretical Study on the Reaction Mechanism

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Mariana Quesadas-Rojas

2016-11-01

Full Text Available The biogenetic origin of triterpene dimers from the Celastraceae family has been proposed as assisted hetero-Diels-Alder reaction (HDA. In this work, computational calculation of HDA between natural quinonemethides (tingenone and isopristimerol and hypothetical orthoquinones has been performed at the M06-2X/6-31G(d level of theory. We have located all the HDA transition states supporting the biogenetic route via HDA cycloadditions. We found that all reactions take place through a concerted inverse electron demand and asynchronous mechanism. The enzymatic assistance for dimer formation was analyzed in terms of the calculated transition state energy barrier.

Crystal structure of (E-2-benzylidene-4-[(3-phenyl-4,5-dihydroisoxazol-5-ylmethyl]-2H-benzo[b][1,4]thiazin-3(4H-one

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Nada Kheira Sebbar

2015-06-01

Full Text Available In the title compound, C25H20N2O2S, the dihydroisoxazole ring exhibits an envelope conformation with the methine atom being the flap, while the 1,4-thiazine ring displays a screw-boat conformation. The six-membered ring fused to the 1,4-thiazine ring makes dihedral angles of 63.04 (2 and 54.7 (2° with the mean planes through the five-membered heterocycle and the attached phenyl ring, respectively. The phenyl group connected to the 1,4-thiazine ring is disordered over two sites [major component = 0.57 (2]. The most prominent interactions in the crystal structure are C—H...O hydrogen bonds that link molecules, forming inversion dimers, and C—H...N hydrogen bonds that link the dimers into columns parallel to the b axis.

Thermo-, photo-, and mechano-responsive liquid crystal networks enable tunable photonic crystals.

Science.gov (United States)

Akamatsu, N; Hisano, K; Tatsumi, R; Aizawa, M; Barrett, C J; Shishido, A

2017-10-25

Tunable photonic crystals exhibiting optical properties that respond reversibly to external stimuli have been developed using liquid crystal networks (LCNs) and liquid crystal elastomers (LCEs). These tunable photonic crystals possess an inverse opal structure and are photo-responsive, but circumvent the usual requirement to contain dye molecules in the structure that often limit their applicability and cause optical degradation. Herein, we report tunable photonic crystal films that reversibly tune the reflection peak wavelength under thermo-, photo- and mechano-stimuli, through bilayering a stimuli-responsive LCN including azobenzene units with a colourless inverse opal film composed of non-responsive, flexible durable polymers. By mechanically deforming the azobenzene containing LCN via various stimuli, the reflection peak wavelength from the bilayered film assembly could be shifted on demand. We confirm that the reflection peak shift occurs due to the deformation of the stimuli-responsive layer propagating towards and into the inverse opal layer to change its shape in response, and this shift behaviour is repeatable without optical degradation.

Novel covalently linked insulin dimer engineered to investigate the function of insulin dimerization

DEFF Research Database (Denmark)

Vinther, Tine N.; Norrman, Mathias; Strauss, Holger M.

2012-01-01

An ingenious system evolved to facilitate insulin binding to the insulin receptor as a monomer and at the same time ensure sufficient stability of insulin during storage. Insulin dimer is the cornerstone of this system. Insulin dimer is relatively weak, which ensures dissociation into monomers...... in the circulation, and it is stabilized by hexamer formation in the presence of zinc ions during storage in the pancreatic ß-cell. Due to the transient nature of insulin dimer, direct investigation of this important form is inherently difficult. To address the relationship between insulin oligomerization...... and insulin stability and function, we engineered a covalently linked insulin dimer in which two monomers were linked by a disulfide bond. The structure of this covalent dimer was identical to the self-association dimer of human insulin. Importantly, this covalent dimer was capable of further oligomerization...

The two-state dimer receptor model: a general model for receptor dimers.

Science.gov (United States)

Franco, Rafael; Casadó, Vicent; Mallol, Josefa; Ferrada, Carla; Ferré, Sergi; Fuxe, Kjell; Cortés, Antoni; Ciruela, Francisco; Lluis, Carmen; Canela, Enric I

2006-06-01

Nonlinear Scatchard plots are often found for agonist binding to G-protein-coupled receptors. Because there is clear evidence of receptor dimerization, these nonlinear Scatchard plots can reflect cooperativity on agonist binding to the two binding sites in the dimer. According to this, the "two-state dimer receptor model" has been recently derived. In this article, the performance of the model has been analyzed in fitting data of agonist binding to A(1) adenosine receptors, which are an example of receptor displaying concave downward Scatchard plots. Analysis of agonist/antagonist competition data for dopamine D(1) receptors using the two-state dimer receptor model has also been performed. Although fitting to the two-state dimer receptor model was similar to the fitting to the "two-independent-site receptor model", the former is simpler, and a discrimination test selects the two-state dimer receptor model as the best. This model was also very robust in fitting data of estrogen binding to the estrogen receptor, for which Scatchard plots are concave upward. On the one hand, the model would predict the already demonstrated existence of estrogen receptor dimers. On the other hand, the model would predict that concave upward Scatchard plots reflect positive cooperativity, which can be neither predicted nor explained by assuming the existence of two different affinity states. In summary, the two-state dimer receptor model is good for fitting data of binding to dimeric receptors displaying either linear, concave upward, or concave downward Scatchard plots.

Synthesis, Crystal Structure and Luminescence Property of a New Silver(I) Dimer with Isonicotinic Acid

Energy Technology Data Exchange (ETDEWEB)

Yuan, Qi [Pharmacy College of Henan University, Kaifeng (China); Liu, Bing [Chinese Academy of Sciences, Fuzhou (China)

2005-10-15

The absorption spectrum was calculated from reflection spectrum by the Kubelka.Munk function. The energy gap of the title compound determined by extrapolation from the linear portion of the absorption edge in a (α/S) versus energy plot is 1.91 eV, which suggests that the title compound behaves as semiconductor. Isonicotinic acid (Iso), namely 4.pyridinecarboxylate, a multi.functional chelating and/or bridging ligand, has proved to be very powerful for the construction of multi. dimensional metal.organic coordination networks. Furthermore, The isonicotinic acid complexes has raised many interests in fluorescence probing with numerous potential applications for studies of microsecond diffusion and dynamics of membranes. Metal centers are potential carriers of electrochemical, magnetic, catalytic, or optical properties that may be introduced into the inorganic.organic hybrid materials. d{sup 10} metals with rich photophysical and photochemical character have focused attentions to synthesize polynuclear complexes. Considering the versatile coordination abilities of Iso, we employ the ligand to coordinate with silver nitrate to fabricate a coordination complex with excellent fluorescence property. Herein we report the synthesis, crystal structure and fluorescence property of a new d{sup 10} coordination dimer [Ag{sub 2}(Iso){sub 2}(NO{sub 3}){sub 2}].

Hydrogen atom trapping in a self-organized one-dimensional dimer

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Tsuyoshi Takami

2014-09-01

Full Text Available Metal–organic frameworks (MOFs have attracted widespread attention owing to their unusual structure and properties produced by their nanospaces. However, many MOFs possess the similar three-dimensional frameworks, limiting their structural variety and operating capacity for hydrogen storage under ambient conditions. Here we report the synthesis and structural characterization of a single-crystal one-dimensional dimer whose structure, operating capacity, and physical mechanism contrast with those of existing MOFs. The hydrogen storage capacity of 2.6 wt.% is comparable to the highest capacity achieved by existing MOFs at room temperature. This exceptional storage capacity is realized by self-organization during crystal growth using a weak base.

Arm-in-Arm Response Regulator Dimers Promote Intermolecular Signal Transduction

Energy Technology Data Exchange (ETDEWEB)

Baker, Anna W.; Satyshur, Kenneth A.; Morales, Neydis Moreno; Forest, Katrina T. (UW)

2016-02-01

Bacteriophytochrome photoreceptors (BphPs) and their cognate response regulators make up two-component signal transduction systems which direct bacteria to mount phenotypic responses to changes in environmental light quality. Most of these systems utilize single-domain response regulators to transduce signals through unknown pathways and mechanisms. Here we describe the photocycle and autophosphorylation kinetics of RtBphP1, a red light-regulated histidine kinase from the desert bacteriumRamlibacter tataouinensis. RtBphP1 undergoes red to far-red photoconversion with rapid thermal reversion to the dark state. RtBphP1 is autophosphorylated in the dark; this activity is inhibited under red light. The RtBphP1 cognate response regulator, theR. tataouinensisbacteriophytochrome response regulator (RtBRR), and a homolog, AtBRR fromAgrobacterium tumefaciens, crystallize unexpectedly as arm-in-arm dimers, reliant on a conserved hydrophobic motif, hFWAhL (where h is a hydrophobic M, V, L, or I residue). RtBRR and AtBRR dimerize distinctly from four structurally characterized phytochrome response regulators found in photosynthetic organisms and from all other receiver domain homodimers in the Protein Data Bank. A unique cacodylate-zinc-histidine tag metal organic framework yielded single-wavelength anomalous diffraction phases and may be of general interest. Examination of the effect of the BRR stoichiometry on signal transduction showed that phosphorylated RtBRR is accumulated more efficiently than the engineered monomeric RtBRR (RtBRR_mon) in phosphotransfer reactions. Thus, we conclude that arm-in-arm dimers are a relevant signaling intermediate in this class of two-component regulatory systems.

Crystal structures of 2-benzylamino-4-(4-bromophenyl-6,7,8,9-tetrahydro-5H-cyclohepta[b]pyridine-3-carbonitrile and 2-benzylamino-4-(4-chlorophenyl-6,7,8,9-tetrahydro-5H-cyclohepta[b]pyridine-3-carbonitrile

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R. A. Nagalakshmi

2015-01-01

Full Text Available In the title compounds, C24H22BrN3, (I, and C24H22ClN3, (II, the 2-aminopyridine ring is fused with a cycloheptane ring, which adopts a half-chair conformation. The planes of the phenyl and benzene rings are inclined to that of the central pyridine ring [r.m.s. deviations = 0.0083 (1 and 0.0093 (1 Å for (I and (II, respectively] by 62.47 (17 and 72.51 (14°, respectively, in (I, and by 71.44 (9 and 54.90 (8°, respectively, in (II. The planes of the aromatic rings are inclined to one another by 53.82 (17° in (I and by 58.04 (9° in (II. In the crystals of both (I and (II, pairs of N—H...Nnitrile hydrogen bonds link the molecules, forming inversion dimers with R22(12 ring motifs. In (I, the resulting dimers are connected through C—H...Br hydrogen bonds, forming sheets parallel to (10-1, and π–π interactions [inter-centroid distance = 3.7821 (16 Å] involving inversion-related pyridine rings, forming a three-dimensional network. In (II, the resulting dimers are connected through π–π interactions [inter-centroid distance = 3.771 (2 Å] involving inversion-related pyridine rings, forming a two-dimensional network lying parallel to (001.

Crystal structure of rac-3-[2,3-bis(phenylsulfanyl-3H-indol-3-yl]propanoic acid

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Wayland E. Noland

2015-11-01

Full Text Available The title compound, C23H19NO2S2, was obtained as an unexpected regioisomer from an attempted synthesis of an intermediate for a substituent-effect study on ergot alkaloids. This is the first report of a 1H-indole monothioating at the 2- and 3-positions to give a 3H-indole. In the crystal, the acid H atom is twisted roughly 180° from the typical carboxy conformation and forms centrosymmetric O—H...N hydrogen-bonded dimers with the indole N atom of an inversion-related molecule. Together with a weak C—H...O hydrogen bond involving the carbonyl O atom, chains are formed along [100].

Crystal structures of N-(4-chlorophenyl-2-[(4,6-diaminopyrimidin-2-ylsulfanyl]acetamide and N-(3-chlorophenyl-2-[(4,6-diaminopyrimidin-2-ylsulfanyl]acetamide

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S. Subasri

2017-04-01

Full Text Available The title compounds, C12H12ClN5OS, (I, and C12H12ClN5OS, (II, are 2-[(diaminopyrimidin-2-ylsulfanyl]acetamides. Compound (II, crystallizes with two independent molecules (A and B in the asymmetric unit. In each of the molecules, in both (I and (II, an intramolecular N—H...N hydrogen bond forms an S(7 ring motif. The pyrimidine ring is inclined to the benzene ring by 42.25 (14° in (I, and by 59.70 (16 and 62.18 (15° in molecules A and B, respectively, of compound (II. In the crystal of (I, molecules are linked by pairs of N—H...N hydrogen bonds, forming inversion dimers with an R22(8 ring motif. The dimers are linked via bifurcated N—H...O and C—H...O hydrogen bonds, forming corrugated layers parallel to the ac plane. In the crystal of (II, the A molecules are linked through N—H...O and N—H...Cl hydrogen bonds, forming layers parallel to (100. The B molecules are also linked by N—H...O and N—H...Cl hydrogen bonds, also forming layers parallel to (100. The parallel layers of A and B molecules are linked via N—H...N hydrogen bonds, forming a three-dimensional structure.

Novel covalently linked insulin dimer engineered to investigate the function of insulin dimerization.

Directory of Open Access Journals (Sweden)

Tine N Vinther

Full Text Available An ingenious system evolved to facilitate insulin binding to the insulin receptor as a monomer and at the same time ensure sufficient stability of insulin during storage. Insulin dimer is the cornerstone of this system. Insulin dimer is relatively weak, which ensures dissociation into monomers in the circulation, and it is stabilized by hexamer formation in the presence of zinc ions during storage in the pancreatic β-cell. Due to the transient nature of insulin dimer, direct investigation of this important form is inherently difficult. To address the relationship between insulin oligomerization and insulin stability and function, we engineered a covalently linked insulin dimer in which two monomers were linked by a disulfide bond. The structure of this covalent dimer was identical to the self-association dimer of human insulin. Importantly, this covalent dimer was capable of further oligomerization to form the structural equivalent of the classical hexamer. The covalently linked dimer neither bound to the insulin receptor, nor induced a metabolic response in vitro. However, it was extremely thermodynamically stable and did not form amyloid fibrils when subjected to mechanical stress, underlining the importance of oligomerization for insulin stability.

Role of local assembly in the hierarchical crystallization of associating colloidal hard hemispheres

Science.gov (United States)

Lei, Qun-li; Hadinoto, Kunn; Ni, Ran

2017-10-01

Hierarchical self-assembly consisting of local associations of simple building blocks for the formation of complex structures widely exists in nature, while the essential role of local assembly remains unknown. In this work, by using computer simulations, we study a simple model system consisting of associating colloidal hemispheres crystallizing into face-centered-cubic crystals comprised of spherical dimers of hemispheres, focusing on the effect of dimer formation on the hierarchical crystallization. We found that besides assisting the crystal nucleation because of increasing the symmetry of building blocks, the association between hemispheres can also induce both reentrant melting and reentrant crystallization depending on the range of interaction. Especially when the interaction is highly sticky, we observe a novel reentrant crystallization of identical crystals, which melt only in a certain temperature range. This offers another axis in fabricating responsive crystalline materials by tuning the fluctuation of local association.

1.8 Å structure of murine GITR ligand dimer expressed in Drosophila melanogaster S2 cells

International Nuclear Information System (INIS)

Chattopadhyay, Kausik; Ramagopal, Udupi A.; Nathenson, Stanley G.; Almo, Steven C.

2009-01-01

1.8 Å X-ray crystal structure of mouse GITRL expressed in D. melanogaster S2 cells shows an identical ‘strand-exchanged’ dimeric assembly similar to that observed previously for the E. coli-expressed protein. Glucocorticoid-induced TNF receptor ligand (GITRL), a prominent member of the TNF superfamily, activates its receptor on both effector and regulatory T cells to generate critical costimulatory signals that have been implicated in a wide range of T-cell immune functions. The crystal structures of murine and human orthologs of GITRL recombinantly expressed in Escherichia coli have previously been determined. In contrast to all classical TNF structures, including the human GITRL structure, murine GITRL demonstrated a unique ‘strand-exchanged’ dimeric organization. Such a novel assembly behavior indicated a dramatic impact on receptor activation as well as on the signaling mechanism associated with the murine GITRL costimulatory system. In this present work, the 1.8 Å resolution crystal structure of murine GITRL expressed in Drosophila melanogaster S2 cells is reported. The eukaryotic protein-expression system allows transport of the recombinant protein into the extracellular culture medium, thus maximizing the possibility of obtaining correctly folded material devoid of any folding/assembly artifacts that are often suspected with E. coli-expressed proteins. The S2 cell-expressed murine GITRL adopts an identical ‘strand-exchanged’ dimeric structure to that observed for the E. coli-expressed protein, thus conclusively demonstrating the novel quaternary structure assembly behavior of murine GITRL

1.8 Å structure of murine GITR ligand dimer expressed in Drosophila melanogaster S2 cells

Energy Technology Data Exchange (ETDEWEB)

Chattopadhyay, Kausik [Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461 (United States); Ramagopal, Udupi A. [Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461 (United States); Nathenson, Stanley G., E-mail: nathenso@aecom.yu.edu [Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461 (United States); Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461 (United States); Almo, Steven C., E-mail: nathenso@aecom.yu.edu [Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461 (United States); Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461 (United States); Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461 (United States)

2009-05-01

1.8 Å X-ray crystal structure of mouse GITRL expressed in D. melanogaster S2 cells shows an identical ‘strand-exchanged’ dimeric assembly similar to that observed previously for the E. coli-expressed protein. Glucocorticoid-induced TNF receptor ligand (GITRL), a prominent member of the TNF superfamily, activates its receptor on both effector and regulatory T cells to generate critical costimulatory signals that have been implicated in a wide range of T-cell immune functions. The crystal structures of murine and human orthologs of GITRL recombinantly expressed in Escherichia coli have previously been determined. In contrast to all classical TNF structures, including the human GITRL structure, murine GITRL demonstrated a unique ‘strand-exchanged’ dimeric organization. Such a novel assembly behavior indicated a dramatic impact on receptor activation as well as on the signaling mechanism associated with the murine GITRL costimulatory system. In this present work, the 1.8 Å resolution crystal structure of murine GITRL expressed in Drosophila melanogaster S2 cells is reported. The eukaryotic protein-expression system allows transport of the recombinant protein into the extracellular culture medium, thus maximizing the possibility of obtaining correctly folded material devoid of any folding/assembly artifacts that are often suspected with E. coli-expressed proteins. The S2 cell-expressed murine GITRL adopts an identical ‘strand-exchanged’ dimeric structure to that observed for the E. coli-expressed protein, thus conclusively demonstrating the novel quaternary structure assembly behavior of murine GITRL.

2-(5-Fluoro-3-isopropylsulfanyl-7-methyl-1-benzofuran-2-ylacetic acid

Directory of Open Access Journals (Sweden)

Hong Dae Choi

2012-04-01

Full Text Available The title compound, C14H15FO3S, was prepared by alkaline hydrolysis of ethyl 2-(5-fluoro-3-isopropylsulfanyl-7-methyl-1-benzofuran-2-ylacetate. In the crystal, molecules are linked via pairs of O—H...O hydrogen bonds, forming inversion dimers. These dimers are connected by weak C—H...O hydrogen bonds.

Study of DNA Origami Dimerization and Dimer Dissociation Dynamics and of the Factors that Limit Dimerization.

Science.gov (United States)

Liber, Miran; Tomov, Toma E; Tsukanov, Roman; Berger, Yaron; Popov, Mary; Khara, Dinesh C; Nir, Eyal

2018-06-01

Organizing DNA origami building blocks into higher order structures is essential for fabrication of large structurally and functionally diverse devices and molecular machines. Unfortunately, the yields of origami building block attachment reactions are typically not sufficient to allow programed assembly of DNA devices made from more than a few origami building blocks. To investigate possible reasons for these low yields, a detailed single-molecule fluorescence study of the dynamics of rectangular origami dimerization and origami dimer dissociation reactions is conducted. Reactions kinetics and yields are investigated at different origami and ion concentrations, for different ion types, for different lengths of bridging strands, and for the "sticky end" and "weaving welding" attachment techniques. Dimerization yields are never higher than 86%, which is typical for such systems. Analysis of the dynamic data shows that the low yield cannot be explained by thermodynamic instability or structural imperfections of the origami constructs. Atomic force microscopy and gel electrophoresis evidence reveal self-dimerization of the origami monomers, likely via blunt-end interactions made possible by the presence of bridging strands. It is suggested that this mechanism is the major factor that inhibits correct dimerization and means to overcome it are discussed. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of Molecular Flexibility on the Nematic-to-Isotropic Phase Transition for Highly Biaxial Molecular Non-Symmetric Liquid Crystal Dimers

Science.gov (United States)

Sebastián, Nerea; López, David Orencio; Diez-Berart, Sergio; de la Fuente, María Rosario; Salud, Josep; Pérez-Jubindo, Miguel Angel; Ros, María Blanca

2011-01-01

In this work, a study of the nematic (N)–isotropic (I) phase transition has been made in a series of odd non-symmetric liquid crystal dimers, the α-(4-cyanobiphenyl-4’-yloxy)-ω-(1-pyrenimine-benzylidene-4’-oxy) alkanes, by means of accurate calorimetric and dielectric measurements. These materials are potential candidates to present the elusive biaxial nematic (NB) phase, as they exhibit both molecular biaxiality and flexibility. According to the theory, the uniaxial nematic (NU)–isotropic (I) phase transition is first-order in nature, whereas the NB–I phase transition is second-order. Thus, a fine analysis of the critical behavior of the N–I phase transition would allow us to determine the presence or not of the biaxial nematic phase and understand how the molecular biaxiality and flexibility of these compounds influences the critical behavior of the N–I phase transition. PMID:28824100

The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.

Science.gov (United States)

Schulte, Kathrin; Pawlowski, Nikolaus; Faelber, Katja; Fröhlich, Chris; Howard, Jonathan; Daumke, Oliver

2016-03-02

The immunity-related GTPases (IRGs) constitute a powerful cell-autonomous resistance system against several intracellular pathogens. Irga6 is a dynamin-like protein that oligomerizes at the parasitophorous vacuolar membrane (PVM) of Toxoplasma gondii leading to its vesiculation. Based on a previous biochemical analysis, it has been proposed that the GTPase domains of Irga6 dimerize in an antiparallel fashion during oligomerization. We determined the crystal structure of an oligomerization-impaired Irga6 mutant bound to a non-hydrolyzable GTP analog. Contrary to the previous model, the structure shows that the GTPase domains dimerize in a parallel fashion. The nucleotides in the center of the interface participate in dimerization by forming symmetric contacts with each other and with the switch I region of the opposing Irga6 molecule. The latter contact appears to activate GTP hydrolysis by stabilizing the position of the catalytic glutamate 106 in switch I close to the active site. Further dimerization contacts involve switch II, the G4 helix and the trans stabilizing loop. The Irga6 structure features a parallel GTPase domain dimer, which appears to be a unifying feature of all dynamin and septin superfamily members. This study contributes important insights into the assembly and catalytic mechanisms of IRG proteins as prerequisite to understand their anti-microbial action.

Structure of a rabbit muscle fructose-1, 6-bisphosphate aldolase A dimer variant

Energy Technology Data Exchange (ETDEWEB)

Sherawat, Manashi [Department of Physiology and Biophysics, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118-2394 (United States); Tolan, Dean R., E-mail: tolan@bu.edu [Department of Biology, Boston University, 5 Cummington Street, Boston, MA 02215 (United States); Allen, Karen N., E-mail: tolan@bu.edu [Department of Physiology and Biophysics, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118-2394 (United States)

2008-05-01

The X-ray crystallographic structure of a dimer variant of fructose-1, 6-bisphosphate aldolase demonstrates a stable oligomer that mirrors half of the native tetramer. The presence of product demonstrates that this is an active form. Fructose-1, 6-bisphosphate aldolase (aldolase) is an essential enzyme in glycolysis and gluconeogenesis. In addition to this primary function, aldolase is also known to bind to a variety of other proteins, a property that may allow it to perform ‘moonlighting’ roles in the cell. Although monomeric and dimeric aldolases possess full catalytic activity, the enzyme occurs as an unusually stable tetramer, suggesting a possible link between the oligomeric state and these noncatalytic cellular roles. Here, the first high-resolution X-ray crystal structure of rabbit muscle D128V aldolase, a dimeric form of aldolase mimicking the clinically important D128G mutation in humans associated with hemolytic anemia, is presented. The structure of the dimer was determined to 1.7 Å resolution with the product DHAP bound in the active site. The turnover of substrate to produce the product ligand demonstrates the retention of catalytic activity by the dimeric aldolase. The D128V mutation causes aldolase to lose intermolecular contacts with the neighboring subunit at one of the two interfaces of the tetramer. The tertiary structure of the dimer does not significantly differ from the structure of half of the tetramer. Analytical ultracentrifugation confirms the occurrence of the enzyme as a dimer in solution. The highly stable structure of aldolase with an independent active site is consistent with a model in which aldolase has evolved as a multimeric scaffold to perform other noncatalytic functions.

Crystal structure of the Japanese encephalitis virus envelope protein.

Science.gov (United States)

Luca, Vincent C; AbiMansour, Jad; Nelson, Christopher A; Fremont, Daved H

2012-02-01

Japanese encephalitis virus (JEV) is the leading global cause of viral encephalitis. The JEV envelope protein (E) facilitates cellular attachment and membrane fusion and is the primary target of neutralizing antibodies. We have determined the 2.1-Å resolution crystal structure of the JEV E ectodomain refolded from bacterial inclusion bodies. The E protein possesses the three domains characteristic of flavivirus envelopes and epitope mapping of neutralizing antibodies onto the structure reveals determinants that correspond to the domain I lateral ridge, fusion loop, domain III lateral ridge, and domain I-II hinge. While monomeric in solution, JEV E assembles as an antiparallel dimer in the crystal lattice organized in a highly similar fashion as seen in cryo-electron microscopy models of mature flavivirus virions. The dimer interface, however, is remarkably small and lacks many of the domain II contacts observed in other flavivirus E homodimers. In addition, uniquely conserved histidines within the JEV serocomplex suggest that pH-mediated structural transitions may be aided by lateral interactions outside the dimer interface in the icosahedral virion. Our results suggest that variation in dimer structure and stability may significantly influence the assembly, receptor interaction, and uncoating of virions.

Expression, purification, crystallization and preliminary X-ray crystallographic studies of hepatitis B virus core fusion protein corresponding to octahedral particles

International Nuclear Information System (INIS)

Kikuchi, Masaki; Iwabuchi, Shinichiro; Kikkou, Tatsuhiko; Noguchi, Keiichi; Odaka, Masafumi; Yohda, Masafumi; Kawata, Masaaki; Sato, Chikara; Matsumoto, Osamu

2013-01-01

Novel hepatitis B virus-like particles of recombinant dimeric core–GFP fusion protein were expressed, purified and crystallized. The crystals diffracted to 2.15 Å resolution and belonged to space group F432, with unit-cell parameters a = b = c = 219.7 Å. Recombinant hepatitis B virus core proteins dimerize to form building blocks that are capable of self-assembly into a capsid. A core capsid protein dimer (CPD) linked to a green fluorescent protein variant, EGFP, at the C-terminus has been designed. The recombinant fusion CPD was expressed in Escherichia coli, assembled into virus-like particles (VLPs), purified and crystallized. The single crystal diffracted to 2.15 Å resolution and belonged to the cubic space group F432, with unit-cell parameters a = b = c = 219.7 Å. The fusion proteins assembled into icosahedral VLPs in aqueous solution, but were rearranged into octahedral symmetry through the crystal-packing process under the crystallization conditions

Structure of a second crystal form of Bence-Jones protein Loc: Strikingly different domain associations in two crystal forms of a single protein

International Nuclear Information System (INIS)

Schiffer, M.; Ainsworth, C.; Xu, Z.B.; Carperos, W.; Olsen, K.; Solomon, A.; Stevens, F.J.; Chang, C.H.

1989-01-01

The authors have determined the structure of the immunoglobulin light-chain dimer Loc in a second crystal form that was grown from distilled water. The crystal structure was determined to 2.8-angstrom resolution; the R factor is 0.22. The two variable domains are related by local 2-fold axes and form an antigen binding pocket. The variable domain-variable domain interaction observed in this crystal form differs from the one exhibited by the protein when crystallized from ammonium sulfate in which the two variable domains formed a protrusion. The structure attained in the distilled water crystals is similar to, but not identical with, the one observed for the Mcg light-chain dimer in crystals grown from ammonium sulfate. Thus, two strikingly different structures were attained by this multisubunit protein in crystals grown under two different, commonly used, crystallization techniques. The quaternary interactions exhibited by the protein in the two crystal forms are sufficiently different to suggest fundamentally different interpretations of the structural basis for the function of this protein. This observation may have general implications regarding the use of single crystallographic determinations for detailed identification of structural and functional relationships. On the other hand, proteins whose structures can be altered by manipulation of crystallization conditions may provide useful systems for study of fundamental structural chemistry

Electrical conduction studies in ferric-doped KHSO 4 single crystals

Science.gov (United States)

Sharon, M.; Kalia, A. K.

1980-03-01

Direct-current conductivity of ferric-doped (138, 267, and 490 ppm) single crystals of KHSO 4 has been studied. The mechanism for the dc conduction process is discussed. It is observed that the ferric ion forms a (Fe 3+-two vacancies) complex and the enthaply for its formation is 0.09 ± 0.01 eV. It is proposed that each ferric ion removes two protons from each HSO 4 dimer. The conductivity plot shows the presence of intrinsic and extrinsic regions. It is proposed that in the intrinsic region the dimer of HSO -4 breaks reversibly to form a long-chain monomer-type structure. The conductivity in the KHSO 4 crystal is proposed to be controlled by the rotation of HSO -4 tetrahedra along the axis which contains no hydrogen atom. Isotherm calculation for the trivalent-doped system is applied to this crystal and the results are compared with Co 2+-doped KHSO 4 crystal. The distribution coefficient of ferric ion in the KHSO 4 single crystal is calculated to be 4.5 × 10 -1. Ferric ion causes tapering in the crystal growth habit of KHSO 4 and it is believed to be due to the presence of (Fe 3+-two vacancies) complex. The enthalpy values for the various other processes are as follows: enthalpy for the breakage of HSO -4 dimer ( Hi) = 1.28 ± 0.01 eV; enthalpy for the rotation of HSO -4 tetrahedron ( Hm) = 0.58 ± 0.01 eV.

Dimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tengcongensis solved ab initio

Energy Technology Data Exchange (ETDEWEB)

Liebschner, Dorothee [National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439 (United States); Brzezinski, Krzysztof [National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439 (United States); University of Bialystok, 15-399 Bialystok (Poland); Dauter, Miroslawa [Argonne National Laboratory, Argonne, IL 60439 (United States); Dauter, Zbigniew, E-mail: dauter@anl.gov [National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439 (United States); Nowak, Marta; Kur, Józef; Olszewski, Marcin, E-mail: dauter@anl.gov [Gdansk University of Technology, 80-952 Gdansk (Poland); National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439 (United States)

2012-12-01

The N-terminal domain of the PriB protein from the thermophilic bacterium T. tengcongensis (TtePriB) was expressed and its crystal structure has been solved at the atomic resolution of 1.09 Å by direct methods. PriB is one of the components of the bacterial primosome, which catalyzes the reactivation of stalled replication forks at sites of DNA damage. The N-terminal domain of the PriB protein from the thermophilic bacterium Thermoanaerobacter tengcongensis (TtePriB) was expressed and its crystal structure was solved at the atomic resolution of 1.09 Å by direct methods. The protein chain, which encompasses the first 104 residues of the full 220-residue protein, adopts the characteristic oligonucleotide/oligosaccharide-binding (OB) structure consisting of a five-stranded β-barrel filled with hydrophobic residues and equipped with four loops extending from the barrel. In the crystal two protomers dimerize, forming a six-stranded antiparallel β-sheet. The structure of the N-terminal OB domain of T. tengcongensis shows significant differences compared with mesophile PriBs. While in all other known structures of PriB a dimer is formed by two identical OB domains in separate chains, TtePriB contains two consecutive OB domains in one chain. However, sequence comparison of both the N-terminal and the C-terminal domains of TtePriB suggests that they have analogous structures and that the natural protein possesses a structure similar to a dimer of two N-terminal domains.

Unravelling Thiol’s Role in Directing Asymmetric Growth of Au Nanorod–Au Nanoparticle Dimers

KAUST Repository

Huang, Jianfeng

2015-12-15

Asymmetric nanocrystals have practical significance in nanotechnologies but present fundamental synthetic challenges. Thiol ligands have proven effective in breaking the symmetric growth of metallic nanocrystals but their exact roles in the synthesis remain elusive. Here, we synthesized an unprecedented Au nanorod-Au nanoparticle (AuNR-AuNP) dimer structure with the assistance of a thiol ligand. On the basis of our experimental observations, we unraveled for the first time that the thiol could cause an inhomogeneous distribution of surface strains on the seed crystals as well as a modulated reduction rate of metal precursors, which jointly induced the asymmetric growth of monometallic dimers. © 2015 American Chemical Society.

Pyroelectric field assisted ion migration induced by ultraviolet laser irradiation and its impact on ferroelectric domain inversion in lithium niobate crystals

International Nuclear Information System (INIS)

Ying, C. Y. J.; Mailis, S.; Daniell, G. J.; Steigerwald, H.; Soergel, E.

2013-01-01

The impact of UV laser irradiation on the distribution of lithium ions in ferroelectric lithium niobate single crystals has been numerically modelled. Strongly absorbed UV radiation at wavelengths of 244–305 nm produces steep temperature gradients which cause lithium ions to migrate and result in a local variation of the lithium concentration. In addition to the diffusion, here the pyroelectric effect is also taken into account which predicts a complex distribution of lithium concentration along the c-axis of the crystal: two separated lithium deficient regions on the surface and in depth. The modelling on the local lithium concentration and the subsequent variation of the coercive field are used to explain experimental results on the domain inversion of such UV treated lithium niobate crystals

Dimer monomer transition and dimer re-formation play important role for ATM cellular function during DNA repair

International Nuclear Information System (INIS)

Du, Fengxia; Zhang, Minjie; Li, Xiaohua; Yang, Caiyun; Meng, Hao; Wang, Dong; Chang, Shuang; Xu, Ye; Price, Brendan; Sun, Yingli

2014-01-01

Highlights: • ATM phosphorylates the opposite strand of the dimer in response to DNA damage. • The PETPVFRLT box of ATM plays a key role in its dimer dissociation in DNA repair. • The dephosphorylation of ATM is critical for dimer re-formation after DNA repair. - Abstract: The ATM protein kinase, is a serine/threonine protein kinase that is recruited and activated by DNA double-strand breaks, mediates responses to ionizing radiation in mammalian cells. Here we show that ATM is held inactive in unirradiated cells as a dimer and phosphorylates the opposite strand of the dimer in response to DNA damage. Cellular irradiation induces rapid intermolecular autophosphorylation of serine 1981 that causes dimer dissociation and initiates cellular ATM kinase activity. ATM cannot phosphorylate the substrates when it could not undergo dimer monomer transition. After DNA repair, the active monomer will undergo dephosphorylation to form dimer again and dephosphorylation is critical for dimer re-formation. Our work reveals novel function of ATM dimer monomer transition and explains why ATM dimer monomer transition plays such important role for ATM cellular activity during DNA repair

Crystal structure of 2-hy-droxy-imino-2-(pyridin-2-yl)-N'-[1-(pyridin-2-yl)ethyl-idene]acetohydrazide.

Science.gov (United States)

Plutenko, Maxym O; Lampeka, Rostislav D; Haukka, Matti; Nordlander, Ebbe

2014-12-01

The mol-ecule of the title compound, C14H13N5O2, is approximately planar (r.m.s deviation for all non-H atoms = 0.093 Å), with the planes of the two pyridine rings inclined to one another by 5.51 (7)°. The oxime group is syn to the amide group, probably due to the formation of an intra-molecular N-H⋯N hydrogen bond that forms an S(6) ring motif. In the crystal, mol-ecules are linked by pairs of bifurcated O-H⋯(O,N) hydrogen bonds, forming inversion dimers. The latter are linked via C-H⋯O and C-H⋯N hydrogen bonds, forming sheets lying parallel to (502). The sheets are linked via π-π stacking inter-actions [inter-centroid distance = 3.7588 (9) Å], involving the pyridine rings of inversion-related mol-ecules, forming a three-dimensional structure.

Purification, crystal structure determination and functional characterization of type III antifreeze proteins from the European eelpout Zoarces viviparus

DEFF Research Database (Denmark)

Wilkens, Casper; Poulsen, Jens-Christian Navarro; Ramløv, Hans

2014-01-01

Antifreeze proteins (AFPs) are essential components of many organisms adaptation to cold temperatures. Fish type III AFPs are divided into two groups, SP isoforms being much less active than QAE1 isoforms. Two type III AFPs from Zoarces viviparus, a QAE1 (ZvAFP13) and an SP (ZvAFP6) isoform......, are here characterized and their crystal structures determined. We conclude that the higher activity of the QAE1 isoforms cannot be attributed to single residues, but rather a combination of structural effects. Furthermore both ZvAFP6 and ZvAFP13 crystal structures have water molecules around T18...... equivalent to the tetrahedral-like waters previously identified in a neutron crystal structure. Interestingly, ZvAFP6 forms dimers in the crystal, with a significant dimer interface. The presence of ZvAFP6 dimers was confirmed in solution by native electrophoresis and gel filtration. To our knowledge...

Crystallization of the class IV adenylyl cyclase from Yersinia pestis

International Nuclear Information System (INIS)

Smith, Natasha; Kim, Sook-Kyung; Reddy, Prasad T.; Gallagher, D. Travis

2006-01-01

The class IV adenylyl cyclase from Y. pestis has been crystallized in an orthorhombic form suitable for structure determination. The class IV adenylyl cyclase from Yersinia pestis has been cloned and crystallized in both a triclinic and an orthorhombic form. An amino-terminal His-tagged construct, from which the tag was removed by thrombin, crystallized in a triclinic form diffracting to 1.9 Å, with one dimer per asymmetric unit and unit-cell parameters a = 33.5, b = 35.5, c = 71.8 Å, α = 88.7, β = 82.5, γ = 65.5°. Several mutants of this construct crystallized but diffracted poorly. A non-His-tagged native construct (179 amino acids, MW = 20.5 kDa) was purified by conventional chromatography and crystallized in space group P2 1 2 1 2 1 . These crystals have unit-cell parameters a = 56.8, b = 118.6, c = 144.5 Å, diffract to 3 Å and probably have two dimers per asymmetric unit and V M = 3.0 Å 3 Da −1 . Both crystal forms appear to require pH below 5, complicating attempts to incorporate nucleotide ligands into the structure. The native construct has been produced as a selenomethionine derivative and crystallized for phasing and structure determination

Development of β-linked quaterthiophene and tetrathiafulvalene dimers as new organic semiconductors

International Nuclear Information System (INIS)

Ashizawa, Minoru; Yu, Yan; Niimura, Takuro; Tsuboi, Kazuma; Matsumoto, Hidetoshi; Tanioka, Akihiko; Mori, Takehiko

2010-01-01

A series of β-linked quaterthiophene and tetrathiafulvalene dimers 1-4 has been prepared. Their redox and optical properties are almost the same as the parent monomers indicative of very little interaction between the monomers. Crystal structures of 1, 2, and 4 are highly one-dimensional, in which molecular structure of 1 is planar whereas those of 2 and 4 are in a bent form.

Revealing stacking sequences in inverse opals by microradian X-ray diffraction

NARCIS (Netherlands)

Sinitskii, A.; Abramova, V.; Grigorieva, N.; Grigoriev, S.; Snigirev, A.; Byelov, D.; Petukhov, A.V.

2010-01-01

We present the results of the structural analysis of inverse opal photonic crystals by microradian X-ray diffraction. Inverse opals based on different oxide materials (TiO2, SiO2 and Fe2O3) were fabricated by templating polystyrene colloidal crystal films grown by the vertical deposition technique.

Magnetic feature and near-infrared absorption of a [Pt(mnt)2]-based H-bond supramolecular crystal

International Nuclear Information System (INIS)

Li, Cui-Ping; Nie, Li; Pei, Wen-Bo; Li, Li; Tian, Zheng-Fang; Liu, Jian-Lan; Gao, Xu-Sheng; Ren, Xiao-Ming

2016-01-01

A new salt [H 2 DABCO][Pt(mnt) 2 ] 2 (1) (mnt 2- =maleonitriledithiolate and H 2 DABCO 2+ is diprotonated 1,4-diazabicyclo[2.2.2]octane) has been synthesized; its crystal structure, magnetic and near-IR absorption properties have been investigated. Two different [Pt(mnt) 2 ] - anions form the strong π-dimers, labeled as Pt(1)-dimer and Pt(2)-dimer, with quite shorter Pt…Pt and S…S distances and molecular plane-to-plane distance (<3.5 Å) within a dimer. The [Pt(mnt) 2 ] 2 2- π-dimers are connected through the cations in the strong H-bond manner to form three-dimensional H-bond supramolecular crystal. The salt shows weak paramagnetism in 1.99–300 K and this is due to the existence of strong antiferromagnetic coupling within a π-dimer. In addition, a small thermal hysteresis loop is observed at ca. 120 K, indicating that a phase transition probably occurs that is further confirmed by variable-temperature IR spectra. Another fascinating functionality of 1 is the intense near-IR absorption in the region of 750–2500 nm, and this near-IR absorption feature makes it to be a promising optical material. - Graphical abstract: A H-bond supramolecular crystal of [H 2 DABCO][Pt(mnt) 2 ] 2 shows a magnetic phase transition at ca. 120 K with sizable thermal hysteresis loop and intense near-IR absorption in the region of 750–2500 nm.

Sigma- versus Pi-Dimerization Modes of Triangulene.

Science.gov (United States)

Mou, Zhongyu; Kertesz, Miklos

2018-04-20

We show that the diradicaloid triangulene, a graphene nano-flake molecule, can aggregate in a variety of dimerization modes. We found by density functional theory modeling a number of triangulene dimers including six doubly bonded σ-dimers in addition to the previously reported six pancake bonded π-dimer isomers. The σ-dimers display a wide range of stabilities: the interaction energy of the most stable σ-dimer is -25.17 kcal mol -1 . Besides the doubly bonded σ-dimers with closed shell ground states, we also found an open-shell singly σ-bonded diradicaloid dimer. We found an interesting isomerization route between a doubly bonded σ-dimer, a singly bonded σ-dimer with a low-lying triplet state and two π-bonded dimers with low-lying quintet states. Derivatives of triangulene, trioxo-triangulenes (TOTs) have been previously characterized experimentally. Here, we show the reasons why so far only the π-dimer but not the σ-dimer was experimentally observed for all TOTs. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure of the cold-shock domain protein from Neisseria meningitidis reveals a strand-exchanged dimer

Energy Technology Data Exchange (ETDEWEB)

Ren, Jingshan [The Oxford Protein Production Facility, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Nettleship, Joanne E.; Sainsbury, Sarah [The Oxford Protein Production Facility, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Saunders, Nigel J. [Bacterial Pathogenesis and Functional Genomics Group, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE (United Kingdom); Owens, Raymond J., E-mail: ray@strubi.ox.ac.uk [The Oxford Protein Production Facility, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom)

2008-04-01

The X-ray crystal structure of the cold-shock domain protein from N. meningitidis reveals a strand-exchanged dimer. The structure of the cold-shock domain protein from Neisseria meningitidis has been solved to 2.6 Å resolution and shown to comprise a dimer formed by the exchange of two β-strands between protein monomers. The overall fold of the monomer closely resembles those of other bacterial cold-shock proteins. The neisserial protein behaved as a monomer in solution and was shown to bind to a hexathymidine oligonucleotide with a stoichiometry of 1:1 and a K{sub d} of 1.25 µM.

Biophysical characterization and crystal structure of the Feline Immunodeficiency Virus p15 matrix protein.

Science.gov (United States)

Serrière, Jennifer; Robert, Xavier; Perez, Magali; Gouet, Patrice; Guillon, Christophe

2013-06-24

Feline Immunodeficiency Virus (FIV) is a viral pathogen that infects domestic cats and wild felids. During the viral replication cycle, the FIV p15 matrix protein oligomerizes to form a closed matrix that underlies the lipidic envelope of the virion. Because of its crucial role in the early and late stages of viral morphogenesis, especially in viral assembly, FIV p15 is an interesting target in the development of potential new therapeutic strategies. Our biochemical study of FIV p15 revealed that it forms a stable dimer in solution under acidic conditions and at high concentration, unlike other retroviral matrix proteins. We determined the crystal structure of full-length FIV p15 to 2 Å resolution and observed a helical organization of the protein, typical for retroviral matrix proteins. A hydrophobic pocket that could accommodate a myristoyl group was identified, and the C-terminal end of FIV p15, which is mainly unstructured, was visible in electron density maps. As FIV p15 crystallizes in acidic conditions but with one monomer in the asymmetric unit, we searched for the presence of a biological dimer in the crystal. No biological assembly was detected by the PISA server, but the three most buried crystallographic interfaces have interesting features: the first one displays a highly conserved tryptophan acting as a binding platform, the second one is located along a 2-fold symmetry axis and the third one resembles the dimeric interface of EIAV p15. Because the C-terminal end of p15 is involved in two of these three interfaces, we investigated the structure and assembly of a C-terminal-truncated form of p15 lacking 14 residues. The truncated FIV p15 dimerizes in solution at a lower concentration and crystallizes with two molecules in the asymmetric unit. The EIAV-like dimeric interface is the only one to be retained in the new crystal form. The dimeric form of FIV p15 in solution and its extended C-terminal end are characteristic among lentiviral matrix proteins

Crystallization of Spätzle, a cystine-knot protein involved in embryonic development and innate immunity in Drosophila melanogaster

Energy Technology Data Exchange (ETDEWEB)

Hoffmann, Anita; Neumann, Piotr [Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Abteilung Physikalische Biotechnologie, Kurt-Mothes-Strasse 3, 06120 Halle (Saale) (Germany); Schierhorn, Angelika [Max-Planck-Institut für Proteinfaltung, Abteilung Massenspektrometrie, Kurt-Mothes-Strasse 3, 06120 Halle (Saale) (Germany); Stubbs, Milton T., E-mail: stubbs@biochemtech.uni-halle.de [Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Abteilung Physikalische Biotechnologie, Kurt-Mothes-Strasse 3, 06120 Halle (Saale) (Germany); Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg (Germany)

2008-08-01

Crystallization of the cystine-knot protein Spätzle occurred following serendipitous limited degradation of the pro-Spätzle propeptide during the crystallization experiment. The Spätzle protein is involved in both the definition of the dorsal–ventral axis during embryonic development and in the adult innate immune response. The disulfide-linked dimeric cystine-knot protein has been expressed as a proprotein in inclusion bodies in Escherichia coli and refolded in vitro by rapid dilution. Initial orthorhombic crystals that diffracted to 7 Å resolution were obtained after three months by the sitting-drop vapour-diffusion method. Optimization of the crystallization conditions resulted in orthorhombic crystals (space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 53.0, b = 59.2, c = 62.5 Å) that diffracted to 2.8 Å resolution in-house. The small volume of the asymmetric unit indicated that it was not possible for the crystals to contain the complete pro-Spätzle dimer. Mass spectrometry, N-terminal sequencing and Western-blot analysis revealed that the crystals contained the C-terminal disulfide-linked cystine-knot dimer. Comparison of various crystallization experiments indicated that degradation of the N-terminal prodomain was dependent on the buffer conditions.

High-quality photonic crystals with a nearly complete band gap obtained by direct inversion of woodpile templates with titanium dioxide.

Science.gov (United States)

Marichy, Catherine; Muller, Nicolas; Froufe-Pérez, Luis S; Scheffold, Frank

2016-02-25

Photonic crystal materials are based on a periodic modulation of the dielectric constant on length scales comparable to the wavelength of light. These materials can exhibit photonic band gaps; frequency regions for which the propagation of electromagnetic radiation is forbidden due to the depletion of the density of states. In order to exhibit a full band gap, 3D PCs must present a threshold refractive index contrast that depends on the crystal structure. In the case of the so-called woodpile photonic crystals this threshold is comparably low, approximately 1.9 for the direct structure. Therefore direct or inverted woodpiles made of high refractive index materials like silicon, germanium or titanium dioxide are sought after. Here we show that, by combining multiphoton lithography and atomic layer deposition, we can achieve a direct inversion of polymer templates into TiO2 based photonic crystals. The obtained structures show remarkable optical properties in the near-infrared region with almost perfect specular reflectance, a transmission dip close to the detection limit and a Bragg length comparable to the lattice constant.

Control activity of yeast geranylgeranyl diphosphate synthase from dimer interface through H-bonds and hydrophobic interaction.

Science.gov (United States)

Chang, Chih-Kang; Teng, Kuo-Hsun; Lin, Sheng-Wei; Chang, Tao-Hsin; Liang, Po-Huang

2013-04-23

Previously we showed that yeast geranylgeranyl diphosphate synthase (GGPPS) becomes an inactive monomer when the first N-terminal helix involved in dimerization is deleted. This raises questions regarding why dimerization is required for GGPPS activity and which amino acids in the dimer interface are essential for dimerization-mediated activity. According to the GGPPS crystal structure, three amino acids (N101, N104, and Y105) located in the helix F of one subunit are near the active site of the other subunit. As presented here, when these residues were replaced individually with Ala caused insignificant activity changes, N101A/Y105A and N101A/N104A but not N104A/Y105A showed remarkably decreased k(cat) values (200-250-fold). The triple mutant N101A/N104A/Y105A displayed no detectable activity, although dimer was retained in these mutants. Because N101 and Y105 form H-bonds with H139 and R140 in the other subunit, respectively, we generated H139A/R140A double mutant and found it was inactive and became monomeric. Therefore, the multiple mutations apparently influence the integrity of the catalytic site due to the missing H-bonding network. Moreover, Met111, also on the highly conserved helix F, was necessary for dimer formation and enzyme activity. When Met111 was replaced with Glu, the negative-charged repulsion converted half of the dimer into a monomer. In conclusion, the H-bonds mainly through N101 for maintaining substrate binding stability and the hydrophobic interaction of M111 in dimer interface are essential for activity of yeast GGPPS.

2-Ethynylpyridine dimers

DEFF Research Database (Denmark)

Bakarić, Danijela; Spanget-Larsen, Jens

2018-01-01

are used to study possible 2-EP dimer structures as well as their distribution in an inert solvent such as tetrachloroethene. Experimentally, the ≡C–H stretching vibration of the 2-EPmonomer absorbs close to 3300 cm−1, whereas a broad band withmaximum around 3215 cm−1 emerges as the concentration rises...... model with counterpoise correction predict that the two most stable dimers are of the pi-stacked variety, closely followed by dimers with intermolecular ≡C–H···N hydrogen bonding; the predicted red shifts of the ≡C–H stretching wavenumbers due to hydrogen bonding are in the range 54 – 120 cm–1...

Crystal structure of 4-(1H-indol-3-yl-2-(4-methoxyphenyl-6-phenylpyridine-3-carbonitrile

Directory of Open Access Journals (Sweden)

R. Vishnupriya

2014-10-01

Full Text Available In the title compound, C27H19N3O, the dihedral angles between the plane of the pyridine ring and those of the indole (r.m.s. deviation = 0.018 Å, phenyl and methoxybenzene substituents are 33.60 (6, 25.28 (7 and 49.31 (7°, respectively. The N atom of the carbonitrile group is significantly displaced [0.288 (2 Å] from the plane of the pyridine ring, perhaps due to steric crowding. In the crystal, inversion dimers linked by pairs of N—H...Nn (n = nitrile hydrogen bonds generate R22(16 loops. Aromatic π–π stacking [centroid–centroid separation = 3.6906 (7 Å] and very weak C—H...π interactions are also observed".

Phosphorous dimerization in GaP high-pressure polymorph

Energy Technology Data Exchange (ETDEWEB)

Lavina, Barbara [Univ. of Nevada, Las Vegas, NV (United States). High Pressure Science and Engineering Center (HiPSEC), Dept. of Physics and Astronomy; Kim, Eunja [Univ. of Nevada, Las Vegas, NV (United States). Dept. of Physics and Astronomy; Cynn, Hyunchae [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Weck, Philippe F [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Seaborg, Kelly [Univ. of Nevada, Las Vegas, NV (United States). High Pressure Science and Engineering Center (HiPSEC), Dept. of Physics and Astronomy; Siska, Emily [Univ. of Nevada, Las Vegas, NV (United States). High Pressure Science and Engineering Center (HiPSEC); Meng, Yue [Carnegie Inst. of Washington, Argonne, IL (United States). Geophysical Lab., High Pressure Collaborative Access Team (HPCAT); Evans, Williams [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2016-06-01

We report on the experimental and theoretical characterization of a novel GaP polymorph formed by laser heating of a single crystal of GaP-II in its stable region near 43 GPa. Thereby formed unstrained multigrain sample at 43 GPa and 1300 K, allowed high-resolution crystallographic analysis. We find an oS24 as an energetically optimized crystal structure contrary to oS8 reported by Nelmes et al. (1997). Our DFT calculation confirms a stable existence of oS24 between 18 – 50 GPa. The emergence of the oS24 structure is related to the differentiation of phosphorous atoms between those forming P-P dimers and those forming P-Ga bonds only. Bonding anisotropy explains the symmetry lowering with respect to what is generally expected for semiconductors high-pressure polymorphs. The metallization of GaP does not occur through a uniform change of the nature of its bonds but through the formation of an anisotropic phase containing different bond types.

Crystal structure of 2-hy­droxy­imino-2-(pyridin-2-yl)-N′-[1-(pyridin-2-yl)ethyl­idene]acetohydrazide

Science.gov (United States)

Plutenko, Maxym O.; Lampeka, Rostislav D.; Haukka, Matti; Nordlander, Ebbe

2014-01-01

The mol­ecule of the title compound, C14H13N5O2, is approximately planar (r.m.s deviation for all non-H atoms = 0.093 Å), with the planes of the two pyridine rings inclined to one another by 5.51 (7)°. The oxime group is syn to the amide group, probably due to the formation of an intra­molecular N—H⋯N hydrogen bond that forms an S(6) ring motif. In the crystal, mol­ecules are linked by pairs of bifurcated O—H⋯(O,N) hydrogen bonds, forming inversion dimers. The latter are linked via C—H⋯O and C—H⋯N hydrogen bonds, forming sheets lying parallel to (502). The sheets are linked via π–π stacking inter­actions [inter-centroid distance = 3.7588 (9) Å], involving the pyridine rings of inversion-related mol­ecules, forming a three-dimensional structure. PMID:25552998

Packing motifs as predictors of the propensity of antibody fragments to crystallize

Science.gov (United States)

Edmundson, Allen B.; DeWitt, Christina R.; Goldsteen, Benjamin Z.; Ramsland, Paul A.

1999-01-01

A recurring theme in the crystallization of antibody fragments in our laboratory has been a packing pattern involving formation of intermolecular, antiparallel β-pleated sheets across two-fold axes. The most common motif is the antiparallel stacking of constant (C) domains of light (L) chain dimers or Fab molecules. Here, cross-molecule six-stranded sheets are produced by hydrogen-bonding interactions of three-residue polypeptide segments (triads), in the i, i+2 and i+4 positions of the final strands (designated 3-3) of the three-chain layers from two adjacent molecules. In the variable (V) domains the triads are supplied by the first strands (4-1) of the four-chain layers and the resulting cross-molecule sheets contain eight strands. The latter type of packing is more likely to be seen in crystals of Fv fragments (V domains only) than in those of L chain dimers or Fabs. Amongst the triads from either the V or C domains, there are on average four sets of backbone carbonyl and amide groups within hydrogen bonding distance (chain dimers, Fab and Fvs are likely to crystallize in these packing patterns.

Residue conservation and dimer-interface analysis of olfactory receptor molecular models

Directory of Open Access Journals (Sweden)

Ramanathan Sowdhamini

2012-10-01

Full Text Available Olfactory Receptors (ORs are members of the Class A rhodopsin like G-protein coupled receptors (GPCRs which are the initial players in the signal transduction cascade, leading to the generation of nerve impulses transmitted to the brain and resulting in the detection of odorant molecules. Despite the accumulation of thousands of olfactory receptor sequences, no crystal structures of ORs are known tο date. However, the recent availability of crystallographic models of a few GPCRs allows us to generate homology models of ORs and analyze their amino acid patterns, as there is a huge diversity in OR sequences. In this study, we have generated three-dimensional models of 100 representative ORs from Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans and Sacharomyces cerevisiae which were selected on the basis of a composite classification scheme and phylogenetic analysis. The crystal structure of bovine rhodopsin was used as a template and it was found that the full-length models have more than 90% of their residues in allowed regions of the Ramachandran plot. The structures were further used for analysis of conserved residues in the transmembrane and extracellular loop regions in order to identify functionally important residues. Several ORs are known to be functional as dimers and hence dimer interfaces were predicted for OR models to analyse their oligomeric functional state.

Dimeric Structure of the Blue Light Sensor Protein Photozipper in the Active State.

Science.gov (United States)

Ozeki, Kohei; Tsukuno, Hiroyuki; Nagashima, Hiroki; Hisatomi, Osamu; Mino, Hiroyuki

2018-02-06

The light oxygen voltage-sensing (LOV) domain plays a crucial role in blue light (BL) sensing in plants and microorganisms. LOV domains are usually associated with the effector domains and regulate the activities of effector domains in a BL-dependent manner. Photozipper (PZ) is monomeric in the dark state. BL induces reversible dimerization of PZ and subsequently increases its affinity for the target DNA sequence. In this study, we report the analyses of PZ by pulsed electron-electron double resonance (PELDOR). The neutral flavin radical was formed by BL illumination in the presence of dithiothreitol in the LOV-C254S (without the bZIP domain) and PZ-C254S mutants, where the cysteine residue responsible for adduct formation was replaced with serine. The magnetic dipole interactions of 3 MHz between the neutral radicals were detected in both LOV-C254S and PZ-C254S, indicating that these mutants are dimeric in the radical state. The PELDOR simulation showed that the distance between the radical pair is close to that estimated from the dimeric crystal structure in the "light state" [Heintz, U., and Schlichting, I. (2016) eLife 5, e11860], suggesting that in the radical state, LOV domains in PZ-C254S form a dimer similar to that of LOV-C254S, which lacks the bZIP domain.

Crystal structure of 2-methylamino-4-(6-methyl-4-oxo-4H-chromen-3-yl-3-nitropyrano[3,2-c]chromen-5(4H-one with an unknown solvate

Directory of Open Access Journals (Sweden)

Rajamani Raja

2015-09-01

Full Text Available In the title compound, C23H16N2O7, the mean planes of the two chromene units (r.m.s. deviations = 0.031 and 0.064 Å are almost normal to one another with a dihedral angle of 85.59 (6°. The central six-membered pyran ring has a distorted envelope conformation, with the methine C atom at the flap. There is an intramolecular N—H...O hydrogen bond, which generates an S(6 ring motif. In the crystal, molecules are linked by pairs of N—H...O hydrogen bonds, forming inversion dimers with an R22(12 ring motif. The dimers are linked by pairs of C—H...O hydrogen bonds, enclosing R22(6 ring motifs, forming zigzag chains along [001]. The chains are linked by a second pair of C—H...O hydrogen bonds, forming slabs parallel to (110. Within the slabs there are C—H...π interactions present. A region of disordered electron density was treated with the SQUEEZE procedure in PLATON [Spek (2015. Acta Cryst. C71, 9–18] following unsuccessful attempts to model it as plausible solvent molecule(s. The given chemical formula and other crystal data do not take into account the unknown solvent molecule(s.

Synthesis and characterization of monomeric and dimeric manganese(II and zinc(II complexes of pyridine-2-carbaldoxime

Directory of Open Access Journals (Sweden)

Jørgen Glerup

2000-12-01

Full Text Available The syntheses and characterization of two complexes of manganese(II and one complex of zinc(II with the ligand pyridine-2-carbaldoxime, C6H6N2O, are described. The monomeric manganese(II complex cis-[Mn(C6H6N2O 2Cl2] (1 crystallizes in the orthorhombic space group Pbcn with 4 formula units in a cell of dimensions a = 12.479(3 Å, b = 10.348(2 Å, and c = 11. 974(2 Å. The structure has been refined to a final value of the conventional R-factor of 0.0330 based on 1513 observed independent reflections. The analogous zinc(II complex, cis-[Zn(C6H6N2O2Cl2] (2 also crystallizes in the orthorhombic space group Pbcn with 4 formula units in a cell of dimensions a = 12.215(2 Å, b = 10.383(2 Å, and c = 12. 016(2 Å. The structure has been refined to a final value of the conventional R-factor of 0.0377 based on 1117 observed independent reflections. The two complexes are isostructural, with the central metal atom lying on a crystallographic 2-fold axis. Both complexes are approximately octahedral, the coordination being provided by two trans pyridine nitrogen atoms and two cis amine nitrogen atoms from the oxime ligands, and by two cis chlorides. The dimeric manganese(II complex [(C6H6N2O(CH3OHClMnCl2MnCl(CH3OH(C6H6N2O] (3 crystallizes in the monoclinic space group P21/n with 2 formula units in a cell of dimensions a = 7.895(2 Å, b = 11.196(3 Å, and c = 12. 544(2 Å, and b = 98.39(2o. The structure has been refined to a final value of the conventional R-factor of 0.0312 based on 1568 observed independent reflections. There is a crystallographic inversion center in the middle of the dimer relating one manganese center to the other. The geometry at each manganese(II center is again roughly octahedral, coordination being provided by two nitrogen atoms from the oxime ligand, a terminal chloride ion trans to the amine nitrogen, the oxygen atom of the coordinated methanol molecule, and two bridging chlorides that link the two halves of the dimer. The Mn

Rubidium dimers in paraffin-coated cells

International Nuclear Information System (INIS)

Acosta, V M; Windes, D; Corsini, E; Ledbetter, M P; Karaulanov, T; Budker, D; Jarmola, A; Auzinsh, M; Rangwala, S A; Jackson Kimball, D F

2010-01-01

Measurements were made to determine the density of rubidium dimer vapor in paraffin-coated cells. The number density of dimers and atoms in similar paraffin-coated and uncoated cells was measured by optical spectroscopy. Due to the relatively low melting point of paraffin, a limited temperature range of 43-80 0 C was explored, with the lower end corresponding to a dimer density of less than 10 7 cm -3 . With 1 min integration time, a sensitivity to dimer number density of better than 10 6 cm -3 was achieved. No significant difference in dimer density between the cells was observed.

Dimers in nucleating vapors

Science.gov (United States)

Lushnikov, A. A.; Kulmala, M.

1998-09-01

The dimer stage of nucleation may affect considerably the rate of the nucleation process at high supersaturation of the nucleating vapor. Assuming that the dimer formation limits the nucleation rate, the kinetics of the particle formation-growth process is studied starting with the definition of dimers as bound states of two associating molecules. The partition function of dimer states is calculated by summing the Boltzmann factor over all classical bound states, and the equilibrium population of dimers is found for two types of intermolecular forces: the Lennard-Jones (LJ) and rectangular well+hard core (RW) potentials. The principle of detailed balance is used for calculating the evaporation rate of dimers. The kinetics of the particle formation-growth process is then investigated under the assumption that the trimers are stable with respect to evaporation and that the condensation rate is a power function of the particle mass. If the power exponent λ=n/(n+1) (n is a non-negative integer), the kinetics of the process is described by a finite set of moments of particle mass distribution. When the characteristic time of the particle formation by nucleation is much shorter than that of the condensational growth, n+2 universal functions of a nondimensional time define the kinetic process. These functions are calculated for λ=2/3 (gas-to-particle conversion in the free molecular regime) and λ=1/2 (formation of islands on surfaces).

Investigation of the antiferromagnetic - ferromagnetic dimer chain compound BaCu{sub 2}V{sub 2}O{sub 8} at zero and finite temperatures

Energy Technology Data Exchange (ETDEWEB)

Klyushina, Ekaterina; Lake, Bella [Helmholtz-Zentrum Berlin fuer Materialien und Energie (Germany); Institut fuer Festkoerperphysik, Technische Universitaet Berlin (Germany); Tiegel, Alexander; Manmana, Salvatore [Georg-August-Universitaet Goettingen (Germany); Islam, Nazmul; Klemke, Bastian [Helmholtz-Zentrum Berlin fuer Materialien und Energie (Germany); Park, Jitae [Heinz Maier-Leibnitz Zentrum, TU Muenchen, Garching (Germany); Honecker, Andreas [Universite de Cergy-Pontoise (France)

2016-07-01

Highly dimerized quantum magnets have attracted a great deal of attention in the recently due to the unconventional temperature behavior of their magnetic excitations. Here we present our investigations of the highly dimerized antiferromagnet-ferromagnetic 1D chain BaCu{sub 2}V{sub 2}O{sub 8} both at base and at finite temperatures. The single crystal inelastic neutron scattering measurements at base temperature reveal that there are two excitation branches which disperse along the L direction over the energy range of 36-46 meV. The comparison with DMRG simulations indicates that the antiferromagnetic dimers are coupled ferromagnetically along the c axis. The line shape of the excitations at the dispersion minima was found to become asymmetry with increasing temperature. Thus unconventional thermal behavior also exists in dimer compounds with ferromagnetic interdimer coupling.

QM/MM studies of cisplatin complexes with DNA dimer and octamer

KAUST Repository

Gkionis, Konstantinos

2012-08-01

Hybrid QM/MM calculations on adducts of cisplatin with DNA dimer and octamer are reported. Starting from the crystal structure of a cisplatin-DNA dimer complex and an NMR structure of a cisplatin-DNA octamer complex, several variants of the ONIOM approach are tested, all employing BHandH for the QM part and AMBER for MM. We demonstrate that a generic set of molecular mechanics parameters for description of Pt-coordination can be used within the subtractive ONIOM scheme without loss of accuracy, such that dedicated parameters for new platinum complexes may not be required. Comparison of optimised structures obtained with different strategies indicates that electrostatic embedding is vital for proper description of the complex, while inclusion of water molecules as explicit solvent further improves performance. The resulting DNA structural parameters are in good general agreement with the experimental structure obtained, particularly when the inherent variability in NMR-derived parameters is taken into account. © 2012 Elsevier B.V.

Modulation of Bacillus thuringiensis Phosphatidylinositol-Specific Phospholipase C Activity by Mutations in the Putative Dimerization Interface

Energy Technology Data Exchange (ETDEWEB)

Shi, X.; Shao, C; Zhang, X; Zambonelli, C; Redfield, A; Head, J; Seaton, B; Roberts, M

2009-01-01

Cleavage of phosphatidylinositol (PI) to inositol 1,2-(cyclic)-phosphate (cIP) and cIP hydrolysis to inositol 1-phosphate by Bacillus thuringiensis phosphatidylinositol-specific phospholipase C are activated by the enzyme binding to phosphatidylcholine (PC) surfaces. Part of this reflects improved binding of the protein to interfaces. However, crystallographic analysis of an interfacially impaired phosphatidylinositol-specific phospholipase (W47A/W242A) suggested protein dimerization might occur on the membrane. In the W47A/W242A dimer, four tyrosine residues from one monomer interact with the same tyrosine cluster of the other, forming a tight dimer interface close to the membrane binding regions. We have constructed mutant proteins in which two or more of these tyrosine residues have been replaced with serine. Phospholipid binding and enzymatic activity of these mutants have been examined to assess the importance of these residues to enzyme function. Replacing two tyrosines had small effects on enzyme activity. However, removal of three or four tyrosine residues weakened PC binding and reduced PI cleavage by the enzyme as well as PC activation of cIP hydrolysis. Crystal structures of Y247S/Y251S in the absence and presence of myo-inositol as well as Y246S/Y247S/Y248S/Y251S indicate that both mutant proteins crystallized as monomers, were very similar to one another, and had no change in the active site region. Kinetic assays, lipid binding, and structural results indicate that either (i) a specific PC binding site, critical for vesicle activities and cIP activation, has been impaired, or (ii) the reduced dimerization potential for Y246S/Y247S/Y248S and Y246S/Y247S/Y248S/Y251S is responsible for their reduced catalytic activity in all assay systems.

Crystal structure of 4-aminobenzoic acid–4-methylpyridine (1/1

Directory of Open Access Journals (Sweden)

M. Krishna Kumar

2015-02-01

Full Text Available In the title 1:1 adduct, C6H7N·C7H7NO2, the carboxylic acid group is twisted at an angle of 4.32 (18° with respect to the attached benzene ring. In the crystal, the carboxylic acid group is linked to the pyridine ring by an O—H...N hydrogen bond, forming a dimer. The dimers are linked by N—H...O hydrogen bonds, generating (010 sheets.

Collisional properties of weakly bound heteronuclear dimers

NARCIS (Netherlands)

Marcelis, B.; Kokkelmans, S.J.J.M.F.; Shlyapnikov, G.V.; Petrov, D.S.

2008-01-01

We consider collisional properties of weakly bound heteronuclear molecules (dimers) formed in a two-species mixture of atoms with a large mass difference. We focus on dimers containing light fermionic atoms as they manifest collisional stability due to an effective dimer-dimer repulsion originating

Ultrasmall-angle X-ray scattering analysis of photonic crystal structure

International Nuclear Information System (INIS)

Abramova, V. V.; Sinitskii, A. S.; Grigor'eva, N. A.; Grigor'ev, S. V.; Belov, D. V.; Petukhov, A. V.; Mistonov, A. A.; Vasil'eva, A. V.; Tret'yakov, Yu. D.

2009-01-01

The results of an ultrasmall-angle X-ray scattering study of iron(III) oxide inverse opal thin films are presented. The photonic crystals examined are shown to have fcc structure with amount of stacking faults varying among the samples. The method used in this study makes it possible to easily distinguish between samples with predominantly twinned fcc structure and nearly perfect fcc stacking. The difference observed between samples fabricated under identical conditions is attributed to random layer stacking in the self-assembled colloidal crystals used as templates for fabricating the inverse opals. The present method provides a versatile tool for analyzing photonic crystal structure in studies of inverse opals made of various materials, colloidal crystals, and three-dimensional photonic crystals of other types.

The biochemistry of the protein crystal toxin of Bacillus thuringiensis

Science.gov (United States)

Paul G. Fast

1985-01-01

The crystal consists of dimeric protein subunits. The monomer peptide chains are held together in the subunit and the subunit in the crystal by disulfide and non-covalent bonds. The monomer peptide has a molecular weight of about 130 kdaltons which, in the presence of proteases, is hydrolyzed to a protease-resistant-protein of 65 kda that is toxic both to larvae by...

Mixed dimers, ch. 7

International Nuclear Information System (INIS)

Deursen, A.P.J. van; Reuss, J.

1976-01-01

An attempt has been made to detect mixed dimers in nozzle beams of mixtures; NeAr and HeNe dimers were observed with sufficient intensity to determine the total collision cross section. A similar attempt for H 2 Ar was partially hampered by the circumstance that the corresponding HAr + ion must be detected on the wing of the thousand times larger Ar + peak. The search for H 2 He, H 2 Ne and HeAr dimers was not successful, due to masking ion peaks, H 5 + for HHe + , 21 Ne + for H 20 Ne + , and CO 2 + for HeAr + . (Auth.)

Electron-nuclear corellations for photoinduced dynamics in molecular dimers

Science.gov (United States)

Kilin, Dmitri S.; Pereversev, Yuryi V.; Prezhdo, Oleg V.

2003-03-01

Ultrafast photoinduced dynamics of electronic excitation in molecular dimers is drastically affected by dynamic reorganization of of inter- and intra- molecular nuclear configuration modelled by quantized nuclear degree of freedom [1]. The dynamics of the electronic population and nuclear coherence is analyzed with help of both numerical solution of the chain of coupled differential equations for mean coordinate, population inversion, electronic-vibrational correlation etc.[2] and by propagating the Gaussian wavepackets in relevant adiabatic potentials. Intriguing results were obtained in the approximation of small energy difference and small change of nuclear equilibrium configuration for excited electronic states. In the limiting case of resonance between electronic states energy difference and frequency of the nuclear mode these results have been justified by comparison to exactly solvable Jaynes-Cummings model. It has been found that the photoinduced processes in dimer are arranged according to their time scales:(i) fast scale of nuclear motion,(ii) intermediate scale of dynamical redistribution of electronic population between excited states as well as growth and dynamics of electronic -nuclear correlation,(iii) slow scale of electronic population approaching to the quasiequilibrium distribution, decay of electronic-nuclear correlation, and diminishing the amplitude of mean coordinate oscillations, accompanied by essential growth of the nuclear coordinate dispersion associated with the overall nuclear wavepacket width. Demonstrated quantum-relaxational features of photoinduced vibronic dinamical processess in molecular dimers are obtained by simple method, applicable to large biological systems with many degrees of freedom. [1] J. A. Cina, D. S. Kilin, T. S. Humble, J. Chem. Phys. (2003) in press. [2] O. V. Prezhdo, J. Chem. Phys. 117, 2995 (2002).

2-(4-Fluorophenyl-2H-chromen-4(3H-one

Directory of Open Access Journals (Sweden)

Michał Wera

2012-02-01

Full Text Available In the crystal structure of the title compound, C15H11FO2, molecules form inversion dimers through pairs of weak C—H...O hydrogen bonds. Dimers oriented in parallel, linked by C—H...π contacts, are arranged in columns along the b axis. The fluorophenyl ring and the benzene ring of the 2H-chromen-4(3H-one unit are inclined to one another by 70.41 (16°. They are respectively parallel in a given column or almost perpendicular [oriented at an angle of 87.8 (1°] in neighbouring (inversely oriented columns, forming a herringbone pattern.

Neutral dipole-dipole dimers: A new field in science

Science.gov (United States)

Kosower, Edward M.; Borz, Galina

2018-03-01

Dimer formation with dipole neutralization produces species such as low polarity water (LPW) compatible with hydrophobic surfaces (Phys. Chem. Chem. Phys. 2015, 17, 24895-24900) Dimerization and dipole neutralization occurs for N-methylacetamide on polyethylene, a behavior drastically different from its contortions in acetonitrile on AgBr:AgCl planar crystals (AgX) (ChemPhysChem 2014, 15, 3598-3607). The weak infrared absorption of the amide dimer on polyethylene is shown experimentally. Dimerization of palmitic acid is shown along with some of the many ramifications for intracellular systems. Polyoligomers of water are present on polyethylene surfaces. Some high resolution spectra of three of the polyoligomers of water are shown along with a mechanistic scheme for polyoligomer formation and dissolution. The structures of some of the oligomers are known from spectroscopic studies of water on AgX. The scope of the article begins with PE, generally accepted as hydrophobic. The IR of PE revealed not only that water was present but that it appeared in two forms, oligomers (O) and polyoligomers (PO). How did we recognize what they were? These species had been observed as especially strong "marker" peaks in the spectra1 of water placed on planar AgX, a platform developed by Katzir and his coworkers [6]. But there was a problem: the proximity to PE of oligomers with substantial (calculated) dipole moments and thus polarity, including cyclic hexamers of water (chair and boat forms), the cyclic pentamer, the books I and II, and the cyclic trimer [7a]. Another link was needed, a role perfectly fit by the already cited low polarity water (LPW). The choice was experimentally supported by the detection of low intensity absorption in the bending region.Some important generalities flow from these results. What other dimers might be present in the biological or chemical world? Palmitic acid dimer (PAD) would be a candidate for decreasing the polarity of the acid (PA). Another

Crystal structure of ethyl 2-({[(4Z-3,5-dioxo-1-phenylpyrazolidin-4-ylidene]methyl}aminoacetate

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Shaaban K. Mohamed

2014-09-01

Full Text Available The title compound, C14H15N3O4, is nearly planar, the dihedral angle between the planes of the phenyl and pyrazolidine rings being 1.13 (7 Å, and that between the plane of the pyrazolidine ring and the mean plane of the side chain [C—N—C–C(=O—O; r.m.s. deviation = 0.024 Å] being 2.52 (7°. This is due in large part to the presence of the intramolecular N—H...O and C—H...O hydrogen bonds. In the crystal, pairwise N—H...O hydrogen bonds form inversion dimers, which are further associated into layers, lying very close to plane (-120, via pairwise C—H...O hydrogen bonds. The layers are then weakly connected through C—H...O hydrogen bonds, forming a three-dimensional structure.

Dimers at Ge/Si(001) surfaces: Ge coverage dependent quenching, reactivation of flip-flop motion, and interaction with dimer vacancy lines

International Nuclear Information System (INIS)

Hirayama, H.; Mizuno, H.; Yoshida, R.

2002-01-01

We studied Ge coverage (θ Ge ) dependent quenching, reactivation of the flip-flop motion, and interaction with dimer vacancy lines (DVLs) of dimers on Ge/Si(001) surfaces using a scanning tunneling microscope (STM) combined with a molecular beam epitaxy apparatus. Deposition of ∼0.3 ML (monolayer) Ge quenched the flip-flop motion, making all dimers asymmetric. Further deposition introduced DVLs at θ Ge ≥∼0.5 ML, and symmetric dimer domains appeared again locally at θ≥1.5 ML. High-resolution STM images indicated that asymmetric dimer rows always invert their phase in alternation with buckled dimer's up-end at the DVLs. Low-temperature STM images indicated that the symmetric dimer domains were due to flip-flopping of asymmetric dimers activated by large θ Ge at room temperature. The symmetric dimer domains extended along the dimer rows over the DVLs due to the phase correlation

Comparison of clinical probability-adjusted D-dimer and age-adjusted D-dimer interpretation to exclude venous thromboembolism.

Science.gov (United States)

Takach Lapner, Sarah; Julian, Jim A; Linkins, Lori-Ann; Bates, Shannon; Kearon, Clive

2017-10-05

Two new strategies for interpreting D-dimer results have been proposed: i) using a progressively higher D-dimer threshold with increasing age (age-adjusted strategy) and ii) using a D-dimer threshold in patients with low clinical probability that is twice the threshold used in patients with moderate clinical probability (clinical probability-adjusted strategy). Our objective was to compare the diagnostic accuracy of age-adjusted and clinical probability-adjusted D-dimer interpretation in patients with a low or moderate clinical probability of venous thromboembolism (VTE). We performed a retrospective analysis of clinical data and blood samples from two prospective studies. We compared the negative predictive value (NPV) for VTE, and the proportion of patients with a negative D-dimer result, using two D-dimer interpretation strategies: the age-adjusted strategy, which uses a progressively higher D-dimer threshold with increasing age over 50 years (age in years × 10 µg/L FEU); and the clinical probability-adjusted strategy which uses a D-dimer threshold of 1000 µg/L FEU in patients with low clinical probability and 500 µg/L FEU in patients with moderate clinical probability. A total of 1649 outpatients with low or moderate clinical probability for a first suspected deep vein thrombosis or pulmonary embolism were included. The NPV of both the clinical probability-adjusted strategy (99.7 %) and the age-adjusted strategy (99.6 %) were similar. However, the proportion of patients with a negative result was greater with the clinical probability-adjusted strategy (56.1 % vs, 50.9 %; difference 5.2 %; 95 % CI 3.5 % to 6.8 %). These findings suggest that clinical probability-adjusted D-dimer interpretation is a better way of interpreting D-dimer results compared to age-adjusted interpretation.

Crystallization of Ulex europaeus lectin I.

Science.gov (United States)

Vandonselaar, M; Delbaere, L T

1994-10-21

The lectin I from Ulex europaeus (UEAI) has a strong affinity for the H-type 2 human blood group determinant. Single crystals of UEAI have been grown in the monoclinic crystal system. Initial crystals were obtained after 11 months from a solution of 10 mg/ml protein, 40% 2,4-methylpentanediol and 0.1 N acetate buffer at pH 5.2. The technique of washing and reseeding was used to generate large suitable crystals. The space group is C2 with a = 78.84 A, b = 69.85 A, c = 120.62 A, beta = 108.74 degrees and Z = 4; there is one molecular dimer per asymmetric unit and the solvent content is estimated to be 58%. The crystals diffract to at least 2.8 A d spacings and are stable in the X-ray beam for more than three days.

I222 crystal form of despentapeptide (B26-B30) insulin provides new insights into the properties of monomeric insulin.

Science.gov (United States)

Whittingham, Jean L; Youshang, Zhang; Záková, Lenka; Dodson, Eleanor J; Turkenburg, Johan P; Brange, Jens; Dodson, G Guy

2006-05-01

Despentapeptide (des-B26-B30) insulin (DPI), an active modified insulin, has been crystallized in the presence of 20% acetic acid pH 2. A crystal structure analysis to 1.8 A spacing (space group I222) revealed that the DPI molecule, which is unable to make beta-strand interactions for physiological dimer formation and is apparently monomeric in solution, formed an alternative lattice-generated dimer. The formation of this dimer involved interactions between surfaces which included the B9-B19 alpha-helices (usually buried by the dimer-dimer contacts within the native hexamer). The two crystallographically independent molecules within the dimer were essentially identical and were similar in conformation to T-state insulin as seen in the T(6) insulin hexamer. An unusual feature of each molecule in the dimer was the presence of two independent conformations at the B-chain C-terminus (residues B20-B25). Both conformations were different from that of native insulin, involving a 3.5 A displacement of the B20-B23 beta-turn and a repositioning of residue PheB25 such that it made close van der Waals contact with the main body of the molecule, appearing to stabilize the B-chain C-terminus.

Near-Infrared and Optical Beam Steering and Frequency Splitting in Air-Holes-in-Silicon Inverse Photonic Crystals

Science.gov (United States)

2017-01-01

We present the design of a dielectric inverse photonic crystal structure that couples line-defect waveguide propagating modes into highly directional beams of controllable directionality. The structure utilizes a triangular lattice made of air holes drilled in an infinitely thick Si slab, and it is designed for operation in the near-infrared and optical regime. The structure operation is based on the excitation and manipulation of dark dielectric surface states, in particular on the tailoring of the dark states’ coupling to outgoing radiation. This coupling is achieved with the use of properly designed external corrugations. The structure adapts and matches modes that travel through the photonic crystal and the free space. Moreover it facilitates the steering of the outgoing waves, is found to generate well-defined, spatially and spectrally isolated beams, and may serve as a frequency splitting component designed for operation in the near-infrared regime and in particular the telecom optical wavelength band. The design complies with the state-of-the-art Si nanofabrication technology and can be directly scaled for operation in the optical regime. PMID:29541653

Self-association of an indole based guanidinium-carboxylate-zwitterion: formation of stable dimers in solution and the solid state

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Carolin Rether

2010-01-01

Full Text Available The indole based zwitterion 2 forms stable dimers held together by H-bond assisted ion pairs. Dimerisation was confirmed in the solid state and studied in solution using dilution NMR experiments. Even though zwitterion 2 forms very stable dimers even in DMSO, their stability is lower than of an analogous pyrrole based zwitterion 1. As revealed by the X-ray crystal structure the two binding sites in 2 cannot be planar due to steric interactions between the guanidinium group and a neighbouring aromatic CH. Hence the guanidinium moiety is twisted out of planarity from the rest of the molecule forcing the two monomers in dimer 2·2 to interact in a non-ideal orientation. Furthermore, the acidity of the NHs is lower than in 1 (as determined by UV-pH-titration also leading to less efficient binding interactions.

Formic acid dimers in a nitrogen matrix

Science.gov (United States)

Lopes, Susy; Fausto, Rui; Khriachtchev, Leonid

2018-01-01

Formic acid (HCOOH) dimers are studied by infrared spectroscopy in a nitrogen matrix and by ab initio calculations. We benefit from the use of a nitrogen matrix where the lifetime of the higher-energy (cis) conformer is very long (˜11 h vs. 7 min in an argon matrix). As a result, in a nitrogen matrix, a large proportion of the cis conformer can be produced by vibrational excitation of the lower-energy (trans) conformer. Three trans-trans, four trans-cis, and three cis-cis dimers are found in the experiments. The spectroscopic information on most of these dimers is enriched compared to the previous studies in an argon matrix. The cis-cis dimers of ordinary formic acid (without deuteration) are reported here for the first time. Several conformational processes are obtained using selective excitation by infrared light, some of them also for the first time. In particular, we report on the formation of cis-cis dimers upon vibrational excitation of trans-cis dimers. Tunneling decays of several dimers have been detected in the dark. The tunneling decay of cis-cis dimers of formic acid as well as the stabilization of cis units in cis-cis dimers is also observed for the first time.

Inversion symmetry and local vs. dispersive interactions in the nucleation of hydrogen bonded cyclic n-mer and tape of imidazolecarboxamidines

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2008-07-01

Full Text Available Substitutional changes to imidazolecarboxamidine that preserved intermolecular hydrogen bonding in the solid state were used to study the relationship between packing and the hydrogen bond motif. Various motifs competed, but the most common imidazolecarboxamidine crystalline phase was a Ci symmetric dimer that established inversion centers by associating enantiomeric tautomers. Counter to intuition, the calculated gas-phase energies per molecule of the solid state atomic coordinates of the Ci dimer motifs were higher than those of the C1 dimer, trimer, tetramer and tape motifs, while the packing densities of Ci dimers were found to be higher. This result was interpreted as an enhanced ability of the Ci dimers to pack. If other motifs competed, the hydrogen bonds and conformations should be lower in energy than the Ci dimer. The results detail the effect of packing on the conformation in these molecules. The results are interpreted as a rough measure of the energetic compromise between packing and the energies related to the coordinates involving one dihedral angle and hydrogen bonding. The results establish a connection between solution and solid phase conformation.

Crystal structure of human protein kinase CK2

DEFF Research Database (Denmark)

Niefind, K; Guerra, B; Ermakowa, I

2001-01-01

The crystal structure of a fully active form of human protein kinase CK2 (casein kinase 2) consisting of two C-terminally truncated catalytic and two regulatory subunits has been determined at 3.1 A resolution. In the CK2 complex the regulatory subunits form a stable dimer linking the two catalyt...... as a docking partner for various protein kinases. Furthermore it shows an inter-domain mobility in the catalytic subunit known to be functionally important in protein kinases and detected here for the first time directly within one crystal structure.......The crystal structure of a fully active form of human protein kinase CK2 (casein kinase 2) consisting of two C-terminally truncated catalytic and two regulatory subunits has been determined at 3.1 A resolution. In the CK2 complex the regulatory subunits form a stable dimer linking the two catalytic...... subunits, which make no direct contact with one another. Each catalytic subunit interacts with both regulatory chains, predominantly via an extended C-terminal tail of the regulatory subunit. The CK2 structure is consistent with its constitutive activity and with a flexible role of the regulatory subunit...

Discrimination between biological interfaces and crystal-packing contacts

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Yuko Tsuchiya

2008-11-01

Full Text Available Yuko Tsuchiya1, Haruki Nakamura2, Kengo Kinoshita1,31Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo, 108-8639, Japan; 2Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan; 3Bioinformatics Research and Development, JST, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, JapanAbstract: A discrimination method between biologically relevant interfaces and artificial crystal-packing contacts in crystal structures was constructed. The method evaluates protein-protein interfaces in terms of complementarities for hydrophobicity, electrostatic potential and shape on the protein surfaces, and chooses the most probable biological interfaces among all possible contacts in the crystal. The method uses a discriminator named as “COMP”, which is a linear combination of the complementarities for the above three surface features and does not correlate with the contact area. The discrimination of homo-dimer interfaces from symmetry-related crystal-packing contacts based on the COMP value achieved the modest success rate. Subsequent detailed review of the discrimination results raised the success rate to about 88.8%. In addition, our discrimination method yielded some clues for understanding the interaction patterns in several examples in the PDB. Thus, the COMP discriminator can also be used as an indicator of the “biological-ness” of protein-protein interfaces.Keywords: protein-protein interaction, complementarity analysis, homo-dimer interface, crystal-packing contact, biological interfaces

D-dimers (DD) in CVST.

Science.gov (United States)

Wang, Hui Fang; Pu, Chuan Qiang; Yin, Xi; Tian, Cheng Lin; Chen, Ting; Guo, Jun Hong; Shi, Qiang

2017-06-01

We were interested in further confirming whether D-dimers (DD) are indeed elevated in cerebral venous sinus thrombosis (CVST) as reported in those studies. CVST patients who had a plasma D-dimer test (139 cases) were included and divided into two groups: elevated D-dimer group (EDG) (>0.5 μg/mL; 65 cases) and normal D-dimer group (NDG) (≤0.5 μg/mL; 74 cases). The two groups were compared in terms of demographic data, clinical manifestation, laboratory and imaging data, using inferential statistical methods. The chi-squared and Fisher exact test showed that, compared to the NDG (74 cases), patients with elevated D-dimer levels were more likely to have a shorter symptom duration (SD) (30 ± 83.9 versus 90 ± 58.9 d, p = 0.003), more risk factors (75.4% versus 52.7%, p = 0.006), higher multiple venous sinus involvement (75.4% versus 59.5%, p = 0.037), increased fibrinogen (43.1% versus 18.9%, p = 0.037) and higher levels of blood glucose (18.3% versus 11%, p = 0.037). According to correlation analyses, D-dimer levels were positively correlated with number of venous sinuses involvement (NVS) (r = 0.321, p = 0.009) in the EDG. Multivariate logistic regression analysis showed that SD (OR, 0.025; 95% CI, 1.324-6.043; p = 0.000), NVS (OR, 1.573; 95% CI, 1.15-2.151; p = 0.005) and risk factors (OR, 3.321; 95% CI, 1.451-7.564; p = 0.004) were significantly different between the two groups. D-dimer is elevated in patients with acute/subacute CVST.

Palmitoylated APP Forms Dimers, Cleaved by BACE1.

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Raja Bhattacharyya

Full Text Available A major rate-limiting step for Aβ generation and deposition in Alzheimer's disease brains is BACE1-mediated cleavage (β-cleavage of the amyloid precursor protein (APP. We previously reported that APP undergoes palmitoylation at two cysteine residues (Cys186 and Cys187 in the E1-ectodomain. 8-10% of total APP is palmitoylated in vitro and in vivo. Palmitoylated APP (palAPP shows greater preference for β-cleavage than total APP in detergent resistant lipid rafts. Protein palmitoylation is known to promote protein dimerization. Since dimerization of APP at its E1-ectodomain results in elevated BACE1-mediated cleavage of APP, we have now investigated whether palmitoylation of APP affects its dimerization and whether this leads to elevated β-cleavage of the protein. Here we report that over 90% of palAPP is dimerized while only ~20% of total APP forms dimers. PalAPP-dimers are predominantly cis-oriented while total APP dimerizes in both cis- and trans-orientation. PalAPP forms dimers 4.5-times more efficiently than total APP. Overexpression of the palmitoylating enzymes DHHC7 and DHHC21 that increase palAPP levels and Aβ release, also increased APP dimerization in cells. Conversely, inhibition of APP palmitoylation by pharmacological inhibitors reduced APP-dimerization in coimmunoprecipitation and FLIM/FRET assays. Finally, in vitro BACE1-activity assays demonstrate that palmitoylation-dependent dimerization of APP promotes β-cleavage of APP in lipid-rich detergent resistant cell membranes (DRMs, when compared to total APP. Most importantly, generation of sAPPβ-sAPPβ dimers is dependent on APP-palmitoylation while total sAPPβ generation is not. Since BACE1 shows preference for palAPP dimers over total APP, palAPP dimers may serve as novel targets for effective β-cleavage inhibitors of APP as opposed to BACE1 inhibitors.

Solvothermal syntheses, crystal structures, optical and thermal ...

Indian Academy of Sciences (India)

compounds 1–3 exhibit optical band gaps between 2.06 and 2.35 eV. Keywords. .... under a nitrogen stream of 100 mL min. −1 . 2.3 X-ray diffraction. Single-crystal ..... Liu G N, Guo G C, Wang M S, Cai L Z and Huang J S. 2010 Five dimeric ...

Chemically Patterned Inverse Opal Created by a Selective Photolysis Modification Process.

Science.gov (United States)

Tian, Tian; Gao, Ning; Gu, Chen; Li, Jian; Wang, Hui; Lan, Yue; Yin, Xianpeng; Li, Guangtao

2015-09-02

Anisotropic photonic crystal materials have long been pursued for their broad applications. A novel method for creating chemically patterned inverse opals is proposed here. The patterning technique is based on selective photolysis of a photolabile polymer together with postmodification on released amine groups. The patterning method allows regioselective modification within an inverse opal structure, taking advantage of selective chemical reaction. Moreover, combined with the unique signal self-reporting feature of the photonic crystal, the fabricated structure is capable of various applications, including gradient photonic bandgap and dynamic chemical patterns. The proposed method provides the ability to extend the structural and chemical complexity of the photonic crystal, as well as its potential applications.

Stochastic optimization-based study of dimerization kinetics

Indian Academy of Sciences (India)

To this end, we study dimerization kinetics of protein as a model system. We follow the dimerization kinetics using a stochastic simulation algorithm and ... optimization; dimerization kinetics; sensitivity analysis; stochastic simulation ... tion in large molecules and clusters, or the design ..... An unbiased strategy of allocating.

Role of the EHD2 unstructured loop in dimerization, protein binding and subcellular localization.

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Kriti Bahl

Full Text Available The C-terminal Eps 15 Homology Domain proteins (EHD1-4 play important roles in regulating endocytic trafficking. EHD2 is the only family member whose crystal structure has been solved, and it contains an unstructured loop consisting of two proline-phenylalanine (PF motifs: KPFRKLNPF. In contrast, despite EHD2 having nearly 70% amino acid identity with its paralogs, EHD1, EHD3 and EHD4, the latter proteins contain a single KPF or RPF motif, but no NPF motif. In this study, we sought to define the precise role of each PF motif in EHD2's homo-dimerization, binding with the protein partners, and subcellular localization. To test the role of the NPF motif, we generated an EHD2 NPF-to-NAF mutant to mimic the homologous sequences of EHD1 and EHD3. We demonstrated that this mutant lost both its ability to dimerize and bind to Syndapin2. However, it continued to localize primarily to the cytosolic face of the plasma membrane. On the other hand, EHD2 NPF-to-APA mutants displayed normal dimerization and Syndapin2 binding, but exhibited markedly increased nuclear localization and reduced association with the plasma membrane. We then hypothesized that the single PF motif of EHD1 (that aligns with the KPF of EHD2 might be responsible for both binding and localization functions of EHD1. Indeed, the EHD1 RPF motif was required for dimerization, interaction with MICAL-L1 and Syndapin2, as well as localization to tubular recycling endosomes. Moreover, recycling assays demonstrated that EHD1 RPF-to-APA was incapable of supporting normal receptor recycling. Overall, our data suggest that the EHD2 NPF phenylalanine residue is crucial for EHD2 localization to the plasma membrane, whereas the proline residue is essential for EHD2 dimerization and binding. These studies support the recently proposed model in which the EHD2 N-terminal region may regulate the availability of the unstructured loop for interactions with neighboring EHD2 dimers, thus promoting

Crystal structure of (E-pent-2-enoic acid

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Tim Peppel

2015-05-01

Full Text Available The molecule of the title compound, C5H8O2, a low-melting α,β-unsaturated carboxylic acid, is essentially planar [maximum displacement = 0.0239 (13 Å]. In the crystal, molecules are linked into centrosymmetric dimers via pairs of O—H...O hydrogen bonds.

Retroviral RNA Dimerization: From Structure to Functions

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Noé Dubois

2018-03-01

Full Text Available The genome of the retroviruses is a dimer composed by two homologous copies of genomic RNA (gRNA molecules of positive polarity. The dimerization process allows two gRNA molecules to be non-covalently linked together through intermolecular base-pairing. This step is critical for the viral life cycle and is highly conserved among retroviruses with the exception of spumaretroviruses. Furthermore, packaging of two gRNA copies into viral particles presents an important evolutionary advantage for immune system evasion and drug resistance. Recent studies reported RNA switches models regulating not only gRNA dimerization, but also translation and packaging, and a spatio-temporal characterization of viral gRNA dimerization within cells are now at hand. This review summarizes our current understanding on the structural features of the dimerization signals for a variety of retroviruses (HIVs, MLV, RSV, BLV, MMTV, MPMV…, the mechanisms of RNA dimer formation and functional implications in the retroviral cycle.

9-Benzyl-6-benzylsulfanyl-9H-purin-2-amine

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Maywan Hariono

2014-03-01

Full Text Available In the title compound, C19H17N5S, the dihedral angles between the purine ring system (r.m.s. deviation = 0.009 Å and the S-bound and methylene-bound phenyl rings are 74.67 (8 and 71.28 (7°, respectively. In the crystal, inversion dimers linked by pairs of N—H...N hydrogen bonds generate R22(8 loops. C—H...N interactions link the dimers into (100 sheets.

In situ detection of estrogen receptor dimers in breast carcinoma cells in archival materials using proximity ligation assay (PLA).

Science.gov (United States)

Iwabuchi, Erina; Miki, Yasuhiro; Ono, Katsuhiko; Onodera, Yoshiaki; Suzuki, Takashi; Hirakawa, Hisashi; Ishida, Takanori; Ohuchi, Noriaki; Sasano, Hironobu

2017-01-01

Estrogen receptor (ER) is required for carcinoma cell proliferation in the great majority of breast cancer and also functions as a dimer. ER dimeric proteins have been largely identified by BRET/FRET analyses but their in situ visualization have not yet been reported. Recently, in situ Proximity Ligation Assay (PLA) has been developed as the methods detecting protein interactions in situ. Therefore, in this study we firstly demonstrated the dimerization of ERα in breast carcinoma cell lines and tissues using PLA. The human breast carcinoma cell lines MCF-7, T-47D and MDA-MB-231 were used in this study. Cells were treated with ER agonist or antagonist and fixed in 4% PFA, and ER dimers were subsequently detected using PLA. The evaluation of ER dimers in breast carcinoma cell lines were quantified by measuring the area of dots localized in the nuclei using image analysis. We also firstly demonstrated the visualization of ER dimer patterns in 10% formalin-fixed paraffin-embedded tissues of breast cancer using PLA technique. Estradiol (E2) administration induced ERα homodimers in the nuclei of MCF-7 and T-47D but not in ER-negative MDA-MB-231. 4-OH tamoxifen also induced ERα homodimers but the subcellular localization of these ERα homodimers was predominant in cytoplasm instead of the nuclei induced by E2 treatment. ICI182,780 treatment did decrease the number of formation of ERα homodimers in MCF-7. In breast cancer patients, ERα PLA score was significantly correlated positively with ERα- or PgR (progesterone receptor) immunohistochemical scores and inversely with Ki-67-labeling index, respectively. We also demonstrated the ERα/β heterodimer as well as ERα homodimers in both breast carcinoma cell lines and surgical pathology specimens. In summary, we did firstly succeed in the visualization of ER dimeric proteins using PLA method. The evaluation of ER dimer patterns could provide pivotal information as to the prediction of response to endocrine therapy of

Statistical transmutation in doped quantum dimer models.

Science.gov (United States)

Lamas, C A; Ralko, A; Cabra, D C; Poilblanc, D; Pujol, P

2012-07-06

We prove a "statistical transmutation" symmetry of doped quantum dimer models on the square, triangular, and kagome lattices: the energy spectrum is invariant under a simultaneous change of statistics (i.e., bosonic into fermionic or vice versa) of the holes and of the signs of all the dimer resonance loops. This exact transformation enables us to define the duality equivalence between doped quantum dimer Hamiltonians and provides the analytic framework to analyze dynamical statistical transmutations. We investigate numerically the doping of the triangular quantum dimer model with special focus on the topological Z(2) dimer liquid. Doping leads to four (instead of two for the square lattice) inequivalent families of Hamiltonians. Competition between phase separation, superfluidity, supersolidity, and fermionic phases is investigated in the four families.

Strain mediated interaction of adatom dimers

OpenAIRE

Kappus, Wolfgang

2013-01-01

An earlier model for substrate strain mediated interactions between monomer adatoms is extended to the interaction of monomers with dimers and the interaction of dimers. While monomers (sitting on high symmetric sites) are supposed to create isotropic stress on the substrate, dimers would create anisotropic stress caused by stretching their bond. Resulting interactions are strongly angle dependent and also reflect the elastic anisotropy of the substrate. The applicability of a continuum elast...

Crystallization and preliminary X-ray analysis of Leishmania major glyoxalase I

Energy Technology Data Exchange (ETDEWEB)

Ariza, Antonio; Vickers, Tim J.; Greig, Neil; Fairlamb, Alan H.; Bond, Charles S., E-mail: c.s.bond@dundee.ac.uk [Division of Biological Chemistry and Molecular Microbiology, Wellcome Trust Biocentre, School of Life Sciences, University of Dundee, Dundee DD1 5EH,Scotland (United Kingdom)

2005-08-01

The detoxification enzyme glyoxalase I from L. major has been crystallized. Preliminary molecular-replacement calculations indicate the presence of three glyoxalase I dimers in the asymmetric unit. Glyoxalase I (GLO1) is a putative drug target for trypanosomatids, which are pathogenic protozoa that include the causative agents of leishmaniasis. Significant sequence and functional differences between Leishmania major and human GLO1 suggest that it may make a suitable template for rational inhibitor design. L. major GLO1 was crystallized in two forms: the first is extremely disordered and does not diffract, while the second, an orthorhombic form, produces diffraction to 2.0 Å. Molecular-replacement calculations indicate that there are three GLO1 dimers in the asymmetric unit, which take up a helical arrangement with their molecular dyads arranged approximately perpendicular to the c axis. Further analysis of these data are under way.

Beta2-adrenergic receptor homodimers: Role of transmembrane domain 1 and helix 8 in dimerization and cell surface expression.

Science.gov (United States)

Parmar, Vikas K; Grinde, Ellinor; Mazurkiewicz, Joseph E; Herrick-Davis, Katharine

2017-09-01

Even though there are hundreds of reports in the published literature supporting the hypothesis that G protein-coupled receptors (GPCR) form and function as dimers this remains a highly controversial area of research and mechanisms governing homodimer formation are poorly understood. Crystal structures revealing homodimers have been reported for many different GPCR. For adrenergic receptors, a potential dimer interface involving transmembrane domain 1 (TMD1) and helix 8 (H8) was identified in crystal structures of the beta 1 -adrenergic (β 1 -AR) and β 2 -AR. The purpose of this study was to investigate a potential role for TMD1 and H8 in dimerization and plasma membrane expression of functional β 2 -AR. Charged residues at the base of TMD1 and in the distal portion of H8 were replaced, singly and in combination, with non-polar residues or residues of opposite charge. Wild type and mutant β 2 -AR, tagged with YFP and expressed in HEK293 cells, were evaluated for plasma membrane expression and function. Homodimer formation was evaluated using bioluminescence resonance energy transfer, bimolecular fluorescence complementation, and fluorescence correlation spectroscopy. Amino acid substitutions at the base of TMD1 and in the distal portion of H8 disrupted homodimer formation and caused receptors to be retained in the endoplasmic reticulum. Mutations in the proximal region of H8 did not disrupt dimerization but did interfere with plasma membrane expression. This study provides biophysical evidence linking a potential TMD1/H8 interface with ER export and the expression of functional β 2 -AR on the plasma membrane. This article is part of a Special Issue entitled: Interactions between membrane receptors in cellular membranes edited by Kalina Hristova. Copyright © 2016 Elsevier B.V. All rights reserved.

Nucleation of rotating crystals by Thiovulum majus bacteria

Science.gov (United States)

Petroff, A. P.; Libchaber, A.

2018-01-01

Thiovulum majus self-organize on glass surfaces into active two-dimensional crystals of rotating cells. Unlike classical crystals, these bacterial crystallites continuously rotate and reorganize as the power of rotating cells is dissipated by the surrounding flow. In this article, we describe the earliest stage of crystallization, the attraction of two bacteria into a hydrodynamically-bound dimer. This process occurs in three steps. First a free-swimming cell collides with the wall and becomes hydrodynamically bound to the two-dimensional surface. We present a simple model to understand how viscous forces localize cells near the chamber walls. Next, the cell diffuses over the surface for an average of 63+/- 6 s before escaping to the bulk fluid. The diffusion coefficient {D}{{eff}}=7.98 +/- 0.1 μ {{{m}}}2 {{{s}}}-1 of these 8.5 μ {{m}} diameter cells corresponds to a temperature of (4.16+/- 0.05)× {10}4 K, and thus cannot be explained by equilibrium fluctuations. Finally, two cells coalesce into a rotating dimer when the convergent flow created by each cell overwhelms their active Brownian motion. This occurs when cells diffuse to within a distance of 13.3 ± 0.2 μm of each other.

1,5-Bis(1-phenyl-ethyl-idene)thio-carbono-hydrazide.

Science.gov (United States)

Feng, Lei; Ji, Haiwei; Wang, Renliang; Ge, Haiyan; Li, Li

2011-06-01

The title mol-ecule, C(17)H(18)N(4)S, is not planar, as indicated by the dihedral angle of 27.24 (9)° between the two benzene rings. In the crystal, inter-molecular N-H⋯S hydrogen bonds link pairs of mol-ecules into inversion dimers.

Origin and effective reduction of inversion domains in aluminum nitride grown by a sublimation method

Science.gov (United States)

Shigetoh, Keisuke; Horibuchi, Kayo; Nakamura, Daisuke

2017-11-01

Owing to the large differences in the chemical properties between Al and N polarities in aluminum nitride (AlN), the choice of the polar direction for crystal growth strongly affects not only the quality but also the shape (facet formation) of the grown crystal. In particular, N-polar (0 0 0 -1) has been considered to be a more preferable direction than Al-polar (0 0 0 1) for sublimation growth because compared to Al-polar (0 0 0 1), N-polar (0 0 0 -1) exhibits better stability at high growth rate (high supersaturation) conditions and enables easier lateral enlargement of the crystal. However, some critical growth conditions induce polarity inversion and hinder stable N-polar growth. Furthermore, the origin of the polarity inversion in AlN growth by the sublimation method is still unclear. To ensure stable N-polar growth without polarity inversion, the formation mechanism of the inversion domain during AlN sublimation growth must be elucidated. Therefore, herein, we demonstrate homoepitaxial growth on an N-polar seed and carefully investigate the obtained crystal that shows polarity inversion. Annular bright-field scanning transmission electron microscopy reveals that polarity is completely converted to the Al polarity via the formation of a 30 nm thick mixed polar layer (MPL) just above the seed. Moreover, three-dimensional atom probe tomography shows the segregation of the oxygen impurities in the MPL with a high concentration of about 3 atom%. Finally, by avoiding the incorporation of oxygen impurity into the crystal at the initial stage of the growth, we demonstrate an effective reduction (seven orders of magnitude) of the inversion domain boundary formation.

Interaction with the Src homology (SH3-SH2) region of the Src-family kinase Hck structures the HIV-1 Nef dimer for kinase activation and effector recruitment.

Science.gov (United States)

Alvarado, John Jeff; Tarafdar, Sreya; Yeh, Joanne I; Smithgall, Thomas E

2014-10-10

HIV-1 Nef supports high titer viral replication in vivo and is essential for AIDS progression. Nef function depends on interactions with multiple host cell effectors, including Hck and other Src-family kinases. Here we describe the x-ray crystal structure of Nef in complex with the Hck SH3-SH2 regulatory region to a resolution of 1.86 Å. The complex crystallized as a dimer of complexes, with the conserved Nef PXXPXR motif engaging the Hck SH3 domain. A new intercomplex contact was found between SH3 Glu-93, and Nef Arg-105. Mutagenesis of Hck SH3 Glu-93 interfered with Nef·Hck complex formation and kinase activation in cells. The Hck SH2 domains impinge on the N-terminal region of Nef to stabilize a dimer conformation that exposes Asp-123, a residue critical for Nef function. Our results suggest that in addition to serving as a kinase effector for Nef, Hck binding may reorganize the Nef dimer for functional interaction with other signaling partners. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Interaction with the Src Homology (SH3-SH2) Region of the Src-family Kinase Hck Structures the HIV-1 Nef Dimer for Kinase Activation and Effector Recruitment*

Science.gov (United States)

Alvarado, John Jeff; Tarafdar, Sreya; Yeh, Joanne I.; Smithgall, Thomas E.

2014-01-01

HIV-1 Nef supports high titer viral replication in vivo and is essential for AIDS progression. Nef function depends on interactions with multiple host cell effectors, including Hck and other Src-family kinases. Here we describe the x-ray crystal structure of Nef in complex with the Hck SH3-SH2 regulatory region to a resolution of 1.86 Å. The complex crystallized as a dimer of complexes, with the conserved Nef PXXPXR motif engaging the Hck SH3 domain. A new intercomplex contact was found between SH3 Glu-93, and Nef Arg-105. Mutagenesis of Hck SH3 Glu-93 interfered with Nef·Hck complex formation and kinase activation in cells. The Hck SH2 domains impinge on the N-terminal region of Nef to stabilize a dimer conformation that exposes Asp-123, a residue critical for Nef function. Our results suggest that in addition to serving as a kinase effector for Nef, Hck binding may reorganize the Nef dimer for functional interaction with other signaling partners. PMID:25122770

Crystal structure and dimerization equilibria of PcoC, a methionine-rich copper resistance protein from Escherichia coli

Energy Technology Data Exchange (ETDEWEB)

Wernimont, A.K.; Huffman, D.L.; Finney, L.A.; Demeler, B.; O' Halloran, T.V.; Rosenzweig, A.C.

2010-03-08

PcoC is a soluble periplasmic protein encoded by the plasmid-born pco copper resistance operon of Escherichia coli. Like PcoA, a multicopper oxidase encoded in the same locus and its chromosomal homolog CueO, PcoC contains unusual methionine rich sequences. Although essential for copper resistance, the functions of PcoC, PcoA, and their conserved methionine-rich sequences are not known. Similar methionine motifs observed in eukaryotic copper transporters have been proposed to bind copper, but there are no precedents for such metal binding sites in structurally characterized proteins. The high-resolution structures of apo PcoC, determined for both the native and selenomethionine-containing proteins, reveal a seven-stranded barrel with the methionines unexpectedly housed on a solvent-exposed loop. Several potential metal-binding sites can be discerned by comparing the structures to spectroscopic data reported for copper-loaded PcoC. In the native structure, the methionine loop interacts with the same loop on a second molecule in the asymmetric unit. In the selenomethionine structure, the methionine loops are more exposed, forming hydrophobic patches on the protein surface. These two arrangements suggest that the methionine motifs might function in protein-protein interactions between PcoC molecules or with other methionine-rich proteins such as PcoA. Analytical ultracentrifugation data indicate that a weak monomer-dimer equilibrium exists in solution for the apo protein. Dimerization is significantly enhanced upon binding Cu(I) with a measured {Delta}({Delta}G{sup o}) {le} -8.0 kJ/mole, suggesting that copper might bind at the dimer interface.

Thermal properties of carbon inverse opal photonic crystals

International Nuclear Information System (INIS)

Aliev, Ali E.; Lee, Sergey B.; Baughman, Ray H.; Zakhidov, Anvar A.

2007-01-01

The thermal conductivity of thin-wall glassy carbon and graphitic carbon inverse opals, fabricated by templating of silica opal has been measured in the temperature range 10-400 K using transient pulse method. The heat flow through 100 A-thick layers of graphite sheets tiled on spherical surfaces of empty overlapping spheres arrayed in face-centered-cubic lattices has been analyzed in term of anisotropy factor. Taking into account high anisotropy factor in graphite, γ=342, we found that the thermal conductivity of inverse opal prepared by chemical vapor deposition infiltration is limited by heat flow across the graphitic layers in bottleneck, κ-perpendicular =3.95 W/m K. The electronic contribution to the thermal conductivity, κ e(300K) =3.7x10 -3 W/m K is negligible comparing to the measured value, κ (300K) =0.33 W/m K. The obtained phonon mean free path, l=90 nm is comparable with the graphite segments between hexagonal array of interconnections

Structural basis for the cooperative DNA recognition by Smad4 MH1 dimers

Science.gov (United States)

Baburajendran, Nithya; Jauch, Ralf; Tan, Clara Yueh Zhen; Narasimhan, Kamesh; Kolatkar, Prasanna R.

2011-01-01

Smad proteins form multimeric complexes consisting of the ‘common partner’ Smad4 and receptor regulated R-Smads on clustered DNA binding sites. Deciphering how pathway specific Smad complexes multimerize on DNA to regulate gene expression is critical for a better understanding of the cis-regulatory logic of TGF-β and BMP signaling. To this end, we solved the crystal structure of the dimeric Smad4 MH1 domain bound to a palindromic Smad binding element. Surprisingly, the Smad4 MH1 forms a constitutive dimer on the SBE DNA without exhibiting any direct protein–protein interactions suggesting a DNA mediated indirect readout mechanism. However, the R-Smads Smad1, Smad2 and Smad3 homodimerize with substantially decreased efficiency despite pronounced structural similarities to Smad4. Therefore, intricate variations in the DNA structure induced by different Smads and/or variant energetic profiles likely contribute to their propensity to dimerize on DNA. Indeed, competitive binding assays revealed that the Smad4/R-Smad heterodimers predominate under equilibrium conditions while R-Smad homodimers are least favored. Together, we present the structural basis for DNA recognition by Smad4 and demonstrate that Smad4 constitutively homo- and heterodimerizes on DNA in contrast to its R-Smad partner proteins by a mechanism independent of direct protein contacts. PMID:21724602

Purification, crystallization and preliminary X-ray structure analysis of the banana lectin from Musa paradisiaca.

Science.gov (United States)

Singh, D D; Saikrishnan, K; Kumar, Prashant; Dauter, Z; Sekar, K; Surolia, A; Vijayan, M

2004-11-01

The banana lectin from Musa paradisiaca, MW 29.4 kDa, has been isolated, purified and crystallized. The trigonal crystals contain one dimeric molecule in the asymmetric unit. The structure has been solved using molecular replacement to a resolution of 3 A. The structure of the subunit is similar to that of jacalin-like lectins.

Crystal structure of enolase from Drosophila melanogaster.

Science.gov (United States)

Sun, Congcong; Xu, Baokui; Liu, Xueyan; Zhang, Zhen; Su, Zhongliang

2017-04-01

Enolase is an important enzyme in glycolysis and various biological processes. Its dysfunction is closely associated with diseases. Here, the enolase from Drosophila melanogaster (DmENO) was purified and crystallized. A crystal of DmENO diffracted to 2.0 Å resolution and belonged to space group R32. The structure was solved by molecular replacement. Like most enolases, DmENO forms a homodimer with conserved residues in the dimer interface. DmENO possesses an open conformation in this structure and contains conserved elements for catalytic activity. This work provides a structural basis for further functional and evolutionary studies of enolase.

Photoionization of helium dimers

International Nuclear Information System (INIS)

Havermeier, Tilo

2010-01-01

The helium dimer is one of the most weakly bound systems in the universe. This makes it an interesting quantum mechanical object for investigation. These Van der Waals Clusters can be produced in an expansion of a cryogenic gas jet through a small nozzle into vacuum. In the present experiment we examine the interaction of He dimers with synchrotron radiation at an energy range from 64 to 78 eV. We observed different pathways leading to single ionization of both He atoms of the dimer compound. This two close standing ions begin now to dissociate in cause of their coulomb potential. All charged fragments were detected in coincidence with a COLTRIMS system. Especially Interatomic Coulombic Decay (ICD) and the two step process (TS1) were clearly identified. Furthermore a distribution of the internuclear distance was obtained from the measured Kinetic Energy Release (KER). (orig.)

Pyrimidine dimer formation and repair in human skin

International Nuclear Information System (INIS)

Sutherland, B.M.; Harber, L.C.; Kochevar, I.E.

1980-01-01

Cyclobutyl pyrimidine dimers have been detected in the DNA of human skin following in vivo irradiation with suberythermal doses of ultraviolet (UV) radiation from FS-20 sun lamp fluorescent tubes. Dimers were assayed by treatment of extracted DNA with Micrococus luteus UV-specific endonuclease, alkaline agarose electrophoresis, and ethidum bromide staining. This technique, in contrast to conventional dimer assays, can be used with nonradioactive DNA and is optimal at low UV light doses. These data suggest that some dimer disappearance by excision repair occurs within 20 min of UV irradiation and that photoreactivation of dimers can make a contribution to the total repair process

2-Methyl-1-(3-methylphenylsulfonylnaphtho[2,1-b]furan

Directory of Open Access Journals (Sweden)

Hong Dae Choi

2014-04-01

Full Text Available In the title compound, C20H16O3S, the dihedral angle between the mean planes of the naphthofuran and 3-methylphenyl fragments is 88.56 (2°. In the crystal, molecules are linked via pairs of C—H...O hydrogen bonds, forming inversion dimers. These dimers are linked by π–π interactions between the furan rings of neighbouring molecules [centroid–centroid distance = 3.701 (2 Å] into supramolecular chains running along the a-axis direction.

(E-3-[5-(Diphenylaminothiophen-2-yl]-1-(pyridin-3-ylprop-2-en-1-one

Directory of Open Access Journals (Sweden)

Rui Li

2013-09-01

Full Text Available In the title compound, C24H18N2OS, the pyridine and the two phenyl rings are oriented at dihedral angles of 10.1 (5, 71.7 (6 and 68.7 (5°, respectively, to the central thiophene ring. In the crystal, pairs of weak C—H...O hydrogen bonds link inversion-related molecules, forming dimers. The dimers are linked by further weak C—H...O hydrogen bonds, forming chains running along the a-axis direction.

N,N′-Bis(4-aminobenzyloxalamide

Directory of Open Access Journals (Sweden)

Juan Saulo Gonzalez-Gonzalez

2011-02-01

Full Text Available In the title compound, C16H18N4O2, the two carbonyl groups are in an antiperiplanar conformation with an O=C—C=O torsion angle of 173.86 (17°. In the crystal, a pair of intermolecular N—H...O hydrogen bonds, forming an R22(10 ring motif, connect the molecules into an inversion dimer. The dimers are further linked by N—H...N and C—H...π interactions, forming a zigzag chain along the b axis.

Dimerization-Induced Allosteric Changes of the Oxyanion-Hole Loop Activate the Pseudorabies Virus Assemblin pUL26N, a Herpesvirus Serine Protease.

Directory of Open Access Journals (Sweden)

Martin Zühlsdorf

2015-07-01

Full Text Available Herpesviruses encode a characteristic serine protease with a unique fold and an active site that comprises the unusual triad Ser-His-His. The protease is essential for viral replication and as such constitutes a promising drug target. In solution, a dynamic equilibrium exists between an inactive monomeric and an active dimeric form of the enzyme, which is believed to play a key regulatory role in the orchestration of proteolysis and capsid assembly. Currently available crystal structures of herpesvirus proteases correspond either to the dimeric state or to complexes with peptide mimetics that alter the dimerization interface. In contrast, the structure of the native monomeric state has remained elusive. Here, we present the three-dimensional structures of native monomeric, active dimeric, and diisopropyl fluorophosphate-inhibited dimeric protease derived from pseudorabies virus, an alphaherpesvirus of swine. These structures, solved by X-ray crystallography to respective resolutions of 2.05, 2.10 and 2.03 Å, allow a direct comparison of the main conformational states of the protease. In the dimeric form, a functional oxyanion hole is formed by a loop of 10 amino-acid residues encompassing two consecutive arginine residues (Arg136 and Arg137; both are strictly conserved throughout the herpesviruses. In the monomeric form, the top of the loop is shifted by approximately 11 Å, resulting in a complete disruption of the oxyanion hole and loss of activity. The dimerization-induced allosteric changes described here form the physical basis for the concentration-dependent activation of the protease, which is essential for proper virus replication. Small-angle X-ray scattering experiments confirmed a concentration-dependent equilibrium of monomeric and dimeric protease in solution.

CH3NH3PbCl3 Single Crystals: Inverse Temperature Crystallization and Visible-Blind UV-Photodetector

KAUST Repository

Maculan, Giacomo

2015-09-02

Single crystals of hybrid perovskites have shown remarkably improved physical properties compared to their polycrystalline film counterparts, underscoring their importance in the further development of advanced semiconductor devices. Here we present a new method of sizeable CH3NH3PbCl3 single crystal growth based on retrograde solubility behavior of hybrid perovskites. We show, for the first time, the energy band structure, charge-carrier recombination and transport properties of single crystal CH3NH3PbCl3. The chloride-based perovskite crystals exhibit trap-state density, charge carriers concentration, mobility and diffusion length comparable with the best quality crystals of methylammonium lead iodide or bromide perovskites reported so far. The high quality of the crystal along with its suitable optical bandgap enabled us to design and build an efficient visible-blind UV-photodetector, demonstrating the potential of this material to be employed in optoelectronic applications.

Dynamic interplay between adhesive and lateral E-cadherin dimers

DEFF Research Database (Denmark)

Klingelhöfer, Jörg; Laur, Oscar Y; Troyanovsky, Regina B

2002-01-01

M. The disappearance of adhesive dimers was counterbalanced by an increase in Trp156-dependent lateral dimers. Increasing the calcium concentration to a normal level rapidly restored the original balance between adhesive and lateral dimers. We also present evidence that E-cadherin dimers in vivo have a short lifetime...

Up-conversion nanoparticles sensitized inverse opal photonic crystals enable efficient water purification under NIR irradiation

Science.gov (United States)

Zhang, Yuanyuan; Wang, Lili; Ma, Xiumei; Ren, Junfeng; Sun, Qinxing; Shi, Yongsheng; Li, Lin; Shi, Jinsheng

2018-03-01

A novel porous monolayer inverse opal (IO) structure was prepared by a simple sol-gel method combined with a self-assembly PS photonic crystal (PC) as template. By prolonging deposition time of PS spheres, three-dimensional multilayer TiO2 IOPC was also fabricated. Up-conversion nanoparticles (UCNPs) were selected to sensitize TiO2 IOPCs. Photocatalytic activity of as-prepared materials was investigated by disinfection of bacteria and organic pollutant degradation. Under NIR light irradiation, a large improvement in bacterial inactivation and photodegradation efficiency could be seen for NYF/TiO2 composites in comparison with other samples. As for monolayer NYF/TiO2, water disinfection of 100% inactivation of bacteria is realized within 11 h and kinetic constant of RhB degradation is 0.133 h-1, which is about 10 times higher than that of pure TiO2 IOPCs. Reasons of enhanced photocatalytic activity were systematically investigated and a possible mechanism for NIR-driven photocatalysis was reasonably proposed.

Plasmonic nanospherical dimers for color pixels

KAUST Repository

Alrasheed, Salma

2018-04-20

Display technologies are evolving more toward higher resolution and miniaturization. Plasmonic color pixels can offer solutions to realize such technologies due to their sharp resonances and selective scattering and absorption at particular wavelengths. Metal nanosphere dimers are capable of supporting plasmon resonances that can be tuned to span the entire visible spectrum. In this article, we demonstrate numerically bright color pixels that are highly polarized and broadly tuned using periodic arrays of metal nanosphere dimers on a glass substrate. We show that it is possible to obtain RGB pixels in the reflection mode. The longitudinal plasmon resonance of nanosphere dimers along the axis of the dimer is the main contributor to the color of the pixel, while far-field diffractive coupling further enhances and tunes the plasmon resonance. The computational method used is the finite-difference time-domain method. The advantages of this approach include simplicity of the design, bright coloration, and highly polarized function. In addition, we show that it is possible to obtain different colors by varying the angle of incidence, the periodicity, the size of the dimer, the gap, and the substrate thickness.

The Crystal Structures of the N-terminal Photosensory Core Module of Agrobacterium Phytochrome Agp1 as Parallel and Anti-parallel Dimers*

Science.gov (United States)

Nagano, Soshichiro; Scheerer, Patrick; Zubow, Kristina; Michael, Norbert; Inomata, Katsuhiko; Lamparter, Tilman; Krauß, Norbert

2016-01-01

Agp1 is a canonical biliverdin-binding bacteriophytochrome from the soil bacterium Agrobacterium fabrum that acts as a light-regulated histidine kinase. Crystal structures of the photosensory core modules (PCMs) of homologous phytochromes have provided a consistent picture of the structural changes that these proteins undergo during photoconversion between the parent red light-absorbing state (Pr) and the far-red light-absorbing state (Pfr). These changes include secondary structure rearrangements in the so-called tongue of the phytochrome-specific (PHY) domain and structural rearrangements within the long α-helix that connects the cGMP-specific phosphodiesterase, adenylyl cyclase, and FhlA (GAF) and the PHY domains. We present the crystal structures of the PCM of Agp1 at 2.70 Å resolution and of a surface-engineered mutant of this PCM at 1.85 Å resolution in the dark-adapted Pr states. Whereas in the mutant structure the dimer subunits are in anti-parallel orientation, the wild-type structure contains parallel subunits. The relative orientations between the PAS-GAF bidomain and the PHY domain are different in the two structures, due to movement involving two hinge regions in the GAF-PHY connecting α-helix and the tongue, indicating pronounced structural flexibility that may give rise to a dynamic Pr state. The resolution of the mutant structure enabled us to detect a sterically strained conformation of the chromophore at ring A that we attribute to the tight interaction with Pro-461 of the conserved PRXSF motif in the tongue. Based on this observation and on data from mutants where residues in the tongue region were replaced by alanine, we discuss the crucial roles of those residues in Pr-to-Pfr photoconversion. PMID:27466363

The Crystal Structures of the N-terminal Photosensory Core Module of Agrobacterium Phytochrome Agp1 as Parallel and Anti-parallel Dimers.

Science.gov (United States)

Nagano, Soshichiro; Scheerer, Patrick; Zubow, Kristina; Michael, Norbert; Inomata, Katsuhiko; Lamparter, Tilman; Krauß, Norbert

2016-09-23

Agp1 is a canonical biliverdin-binding bacteriophytochrome from the soil bacterium Agrobacterium fabrum that acts as a light-regulated histidine kinase. Crystal structures of the photosensory core modules (PCMs) of homologous phytochromes have provided a consistent picture of the structural changes that these proteins undergo during photoconversion between the parent red light-absorbing state (Pr) and the far-red light-absorbing state (Pfr). These changes include secondary structure rearrangements in the so-called tongue of the phytochrome-specific (PHY) domain and structural rearrangements within the long α-helix that connects the cGMP-specific phosphodiesterase, adenylyl cyclase, and FhlA (GAF) and the PHY domains. We present the crystal structures of the PCM of Agp1 at 2.70 Å resolution and of a surface-engineered mutant of this PCM at 1.85 Å resolution in the dark-adapted Pr states. Whereas in the mutant structure the dimer subunits are in anti-parallel orientation, the wild-type structure contains parallel subunits. The relative orientations between the PAS-GAF bidomain and the PHY domain are different in the two structures, due to movement involving two hinge regions in the GAF-PHY connecting α-helix and the tongue, indicating pronounced structural flexibility that may give rise to a dynamic Pr state. The resolution of the mutant structure enabled us to detect a sterically strained conformation of the chromophore at ring A that we attribute to the tight interaction with Pro-461 of the conserved PRXSF motif in the tongue. Based on this observation and on data from mutants where residues in the tongue region were replaced by alanine, we discuss the crucial roles of those residues in Pr-to-Pfr photoconversion. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Reversible dimer formation and stability of the anti-tumour single-chain Fv antibody MFE-23 by neutron scattering, analytical ultracentrifugation, and NMR and FT-IR spectroscopy.

Science.gov (United States)

Lee, Yie Chia; Boehm, Mark K; Chester, Kerry A; Begent, Richard H J; Perkins, Stephen J

2002-06-28

MFE-23 is a single chain Fv (scFv) antibody molecule used to target colorectal cancer through its high affinity for the tumour marker carcinoembryonic antigen (CEA). ScFv molecules are formed from peptide-linked antibody V(H) and V(L) domains, and many of these form dimers. Our recent crystal structure for MFE-23 showed that this formed an unusual symmetric back-to-back association of two monomers that is consistent with a domain-swapped diabody structure. Neutron scattering and modelling fits showed that MFE-23 existed as compact V(H)-V(L)-linked monomers at therapeutically relevant concentrations below 1 mg/ml. Size-exclusion gel chromatography showed that the monomeric and dimeric forms of MFE-23 could be separated, and that the proportions of these two forms depended on the starting MFE-23 concentration. Sedimentation equilibrium experiments by analytical ultracentrifugation at nine concentrations of MFE-23 indicated a reversible monomer-dimer self-association equilibrium with an association constant of 1.9x10(3)-2.2x10(3) M(-1). Sedimentation velocity experiments using the time derivative g(s(*)) method showed that MFE-23-His has a concentration-dependent weight average sedimentation coefficient that increased from 1.8 S for the monomer to about 3-6 S for the dimer. Both values agreed with those calculated from the MFE-23 crystal structure. In relation to the thermal stability of MFE-23, denaturation experiments by (1)H NMR and FT-IR spectroscopy showed that the molecule is stable up to 47 degrees C, after which denaturation was irreversible. MFE-23 dimerisation is discussed in terms of a new model for diabody structures, in which the V(H) and V(L) domains in the monomer are able to dissociate and reassociate to form a dimer, or diabody, but in which symmetric back-to-back contacts between the two monomers are formed. This dimerisation in solution is attributed to the complementary nature of the C-terminal surface of the MFE-23 monomer. Crystal structures for

Simulations of the polarisation-dependent Raman intensity of β-carotene in photosystem II crystals

International Nuclear Information System (INIS)

Brose, K.; Zouni, A.; Müh, F.; Mroginski, M.A.; Maultzsch, J.

2013-01-01

Highlights: • First polarisation-dependent Raman spectroscopy on photosystem II crystals. • Orientation-dependent Raman intensity simulations for di- and monomeric crystals. • Simulations account for all β-carotenes (β-Car) in the unit cell for the first time. • Prediction for identificationy of the β-Car cation in side-path electron transport. - Abstract: In order to clarify possibilities to identify the β-carotene (β-Car) radicals in secondary electron transfer (ET) reactions in the photosystem II core complex (PSIIcc), Raman intensities of all 96 β-Car cofactors in the unit cell of PSIIcc-dimer crystals as a function of polarisation and crystal orientation were simulated based on the 2.9 Å resolution structure. The Raman-active symmetry A g in the C 2h group is assigned to the β-Car modes ν 66 and ν 67 . Simulations are in agreement with experiment for off-resonant excitation at 1064 nm. Resonant measurements at 476 and 532 nm excitation can not be explained, which is attributed to mode mixing in the excited state and the existence of different spectral pools. The identity of the β-Car oxidised in secondary ET can not be resolved by Raman measurements on PSIIcc-dimer crystals. Additional simulations show that similar measurements on PSIIcc-monomer crystals could provide a possible route to solve this issue

Simulations of the polarisation-dependent Raman intensity of β-carotene in photosystem II crystals

Energy Technology Data Exchange (ETDEWEB)

Brose, K., E-mail: katharina.brose@gmx.net [Institut für Festkörperphysik, Technische Universität Berlin, Hardenbergstraße 36, 10623 Berlin (Germany); Zouni, A. [Institut für Chemie, Max-Volmer-Laboratorium, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin (Germany); Müh, F. [Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Straße 69, 4040 Linz (Austria); Mroginski, M.A. [Institut für Chemie, Max-Volmer-Laboratorium, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin (Germany); Maultzsch, J. [Institut für Festkörperphysik, Technische Universität Berlin, Hardenbergstraße 36, 10623 Berlin (Germany)

2013-06-03

Highlights: • First polarisation-dependent Raman spectroscopy on photosystem II crystals. • Orientation-dependent Raman intensity simulations for di- and monomeric crystals. • Simulations account for all β-carotenes (β-Car) in the unit cell for the first time. • Prediction for identificationy of the β-Car cation in side-path electron transport. - Abstract: In order to clarify possibilities to identify the β-carotene (β-Car) radicals in secondary electron transfer (ET) reactions in the photosystem II core complex (PSIIcc), Raman intensities of all 96 β-Car cofactors in the unit cell of PSIIcc-dimer crystals as a function of polarisation and crystal orientation were simulated based on the 2.9 Å resolution structure. The Raman-active symmetry A{sub g} in the C{sub 2h} group is assigned to the β-Car modes ν{sub 66} and ν{sub 67}. Simulations are in agreement with experiment for off-resonant excitation at 1064 nm. Resonant measurements at 476 and 532 nm excitation can not be explained, which is attributed to mode mixing in the excited state and the existence of different spectral pools. The identity of the β-Car oxidised in secondary ET can not be resolved by Raman measurements on PSIIcc-dimer crystals. Additional simulations show that similar measurements on PSIIcc-monomer crystals could provide a possible route to solve this issue.

Age-Adjusted D-Dimer in the Prediction of Pulmonary Embolism: Does a Normal Age-Adjusted D-Dimer Rule Out PE?

Directory of Open Access Journals (Sweden)

Jacob Ortiz

2017-01-01

Full Text Available Risk assessment for pulmonary embolism (PE currently relies on physician judgment, clinical decision rules (CDR, and D-dimer testing. There is still controversy regarding the role of D-dimer testing in low or intermediate risk patients. The objective of the study was to define the role of clinical decision rules and D-dimer testing in patients suspected of having a PE. Records of 894 patients referred for computed tomography pulmonary angiography (CTPA at a University medical center were analyzed. The clinical decision rules overall had an ROC of approximately 0.70, while signs of DVT had the highest ROC (0.80. A low probability CDR coupled with a negative age-adjusted D-dimer largely excluded PE. The negative predictive value (NPV of an intermediate CDR was 86–89%, while the addition of a negative D-dimer resulted in NPVs of 94%. Thus, in patients suspected of having a PE, a low or intermediate CDR does not exclude PE; however, in patients with an intermediate CDR, a normal age-adjusted D-dimer increases the NPV.

Peptides Interfering 3A Protein Dimerization Decrease FMDV Multiplication.

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Mónica González-Magaldi

Full Text Available Nonstructural protein 3A is involved in relevant functions in foot-and-mouth disease virus (FMDV replication. FMDV 3A can form homodimers and preservation of the two hydrophobic α-helices (α1 and α2 that stabilize the dimer interface is essential for virus replication. In this work, small peptides mimicking residues involved in the dimer interface were used to interfere with dimerization and thus gain insight on its biological function. The dimer interface peptides α1, α2 and that spanning the two hydrophobic α-helices, α12, impaired in vitro dimer formation of a peptide containing the two α-helices, this effect being higher with peptide α12. To assess the effect of dimer inhibition in cultured cells, the interfering peptides were N-terminally fused to a heptaarginine (R7 sequence to favor their intracellular translocation. Thus, when fused to R7, interference peptides (100 μM were able to inhibit dimerization of transiently expressed 3A, the higher inhibitions being found with peptides α1 and α12. The 3A dimerization impairment exerted by the peptides correlated with significant, specific reductions in the viral yield recovered from peptide-treated FMDV infected cells. In this case, α2 was the only peptide producing significant reductions at concentrations lower than 100 μM. Thus, dimer interface peptides constitute a tool to understand the structure-function relationship of this viral protein and point to 3A dimerization as a potential antiviral target.

Methyl 4-[N-(5-bromopyrimidin-2-ylcarbamoyl]benzoate

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Hui-Ling Hu

2012-08-01

Full Text Available In the title compound, C13H10BrN3O3, the pyrimidine and benzene rings are twisted with an interplanar angle of 58.4 (1°. The secondary amide group adopts a cis conformation with an H—N—C—O torsion angle of 14.8 (1°. In the crystal, molecules are connected into inversion dimers via pairs of N—H...N hydrogen bonds, generating an R22(8 motif. The dimers are further connected through a C—Br...O interaction [3.136 (1 Å and 169.31 (1°] into a chain along [110]. Weak C—H...N hydrogen bonds between the methyl benzoate groups and pyrimidine rings are also observed in the crystal structure.

Magnetic topology of Co-based inverse opal-like structures

OpenAIRE

Grigoryeva, N.A.; Mistonov, A.A.; Napolskii, K.S.; Sapoletova, N.A.; Eliseev, A.A.; Bouwman, W.; Byelov, D.; Petukhov, A.V.; Chernyshov, D.Y.; Eckerlebe, H.; Vasilieva, A.V.; Grigoriev, S.V.

2011-01-01

The magnetic and structural properties of a cobalt inverse opal-like crystal have been studied by a combination of complementary techniques ranging from polarized neutron scattering and superconducting quantum interference device (SQUID) magnetometry to x-ray diffraction. Microradian small-angle x-ray diffraction shows that the inverse opal-like structure (OLS) synthesized by the electrochemical method fully duplicates the three-dimensional net of voids of the template artificial opal. The in...

Chlorido{(E-1-[(2-methoxyphenyldiazenyl]naphthalen-2-olato}palladium(II

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Assia Mili

2016-04-01

Full Text Available In the title complex, [Pd(C17H13N2O2Cl], the PdII atom is tetracoordinated by an N and two O atoms of an (E-1-[(2-methoxyphenyldiazenyl]naphthalen-2-olate ligand and by a Cl atom, and has a square-planar coordination. In the crystal, molecules are linked by pairs of C—H...Cl hydrogen bonds, forming inversion dimers. The dimers are linked via offset π–π interactions [intercentroid distance = 3.546 (3 Å], forming chains running parallel to [100].

Ethyl 2-[(5Z-5-(4-methylbenzylidene-2,4-dioxo-1,3-thiazolidin-3-yl]acetate

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Karrouchi Khalid

2016-06-01

Full Text Available In the title molecule, C15H15NO4S, the dihedral angle between the almost planar heterocyclic ring (r.m.s. deviation = 0.027 Å and the benzene ring is 5.33 (8°. The chain of the ester group adopts an extended conformation [C—O—C—C = −174.80 (14°]. In the crystal, inversion dimers linked by pairs of C—H...O hydrogen bonds generate R22(10 loops and further such bonds connect the dimers into `stair-step' chains propagating in [100].

(E-2-(4-Chlorophenoxy-N′-(pyridin-4-ylmethylideneacetohydrazide

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Xiao-jin Rao

2013-01-01

Full Text Available In the title compound, C14H12ClN3O2, the acylhydrazone base [C(=O—N—N=C] is essentially planar, with an r.m.s. deviation of 0.0095 Å, and makes a dihedral angle of 12.52 (10°with the pyridine ring. In the crystal, molecules are linked via pairs of N—H...O hydrogen bonds, forming inversion dimers with an R22(8 graph-set motif. The dimers are linked via C—H...π interactions forming chains along [101].

Fractional decay of quantum dots in real photonic crystals

DEFF Research Database (Denmark)

Kristensen, Philip Trøst; Koenderink, A. Femius; Lodahl, Peter

2008-01-01

We show that fractional decay may be observable in experiments using quantum dots and photonic crystals with parameters that are currently achievable. We focus on the case of inverse opal photonic crystals and locate the position in the crystal where the effect is most pronounced. Furthermore, we...

Mahler Measure, Eisenstein Series and Dimers

NARCIS (Netherlands)

Stienstra, J.

2007-01-01

This note reveals a mysterious link between the partition function of certain dimer models on 2-dimensional tori and the L-function of their spectral curves. It also relates the partition function in certain families of dimer models to Eisenstein series. http://www.arxiv.org/abs/math.NT/0502197

4-[(E-(4-Fluorobenzylideneamino]benzoic acid

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Blanca M. Muñoz-Flores

2012-01-01

Full Text Available In the title compound, C14H10FNO2, the benzene rings make a dihedral angle of 57.50 (13°, and the molecule has an E configuration about the C=N bond. In the crystal, molecules are linked via pairs of O—H...O hydrogen bonds, forming inversion dimers.

1,5-Bis(1-phenyl­ethyl­idene)thio­carbono­hydrazide

Science.gov (United States)

Feng, Lei; Ji, Haiwei; Wang, Renliang; Ge, Haiyan; Li, Li

2011-01-01

The title mol­ecule, C17H18N4S, is not planar, as indicated by the dihedral angle of 27.24 (9)° between the two benzene rings. In the crystal, inter­molecular N—H⋯S hydrogen bonds link pairs of mol­ecules into inversion dimers. PMID:21754879

Effects of Dimers on Cooperation in the Spatial Prisoner's Dilemma Game

International Nuclear Information System (INIS)

Li Haihong; Cheng Hongyan; Dai Qionglin; Ju Ping; Yang Junzhong; Zhang Mei

2011-01-01

We investigate the evolutionary prisoner's dilemma game in structured populations by introducing dimers, which are defined as that two players in each dimer always hold a same strategy. We find that influences of dimers on cooperation depend on the type of dimers and the population structure. For those dimers in which players interact with each other, the cooperation level increases with the number of dimers though the cooperation improvement level depends on the type of network structures. On the other hand, the dimers, in which there are not mutual interactions, will not do any good to the cooperation level in a single community, but interestingly, will improve the cooperation level in a population with two communities. We explore the relationship between dimers and self-interactions and find that the effects of dimers are similar to that of self-interactions. Also, we find that the dimers, which are established over two communities in a multi-community network, act as one type of interaction through which information between communities is communicated by the requirement that two players in a dimer hold a same strategy. (general)

Fabrication of colloidal crystal heterostructures by a room temperature floating self-assembly method

International Nuclear Information System (INIS)

Wang Aijun; Chen Shengli; Dong Peng

2011-01-01

Highlights: → Opal colloidal crystal heterostructure of several square centimeters in area was fabricated within only tens of minutes. → A fabricated colloidal crystal heterostructure was composed of a PS opal and a TiO 2 inverse opal crystal films. → The photonic heterostructure had two photonic-band gaps. → The relative position of the two photonic-band gaps can be controlled by the size of PS microspheres used to fabricate the photonic heterostructure. - Abstract: Photonic crystal heterostructures were fabricated through a room temperature floating self-assembly (RTFSA) method recently developed by our research group. Applying this method, opal colloidal crystal heterostructures of several square centimeters in area were fabricated within tens of minutes without special facilities, and a heterostructure composed of a PS opal and a TiO 2 inverse opal crystal films was fabricated. SEM image of the PS opal-TiO 2 inverse opal heterostructure showed the ordered growth of the top opal film of the heterostructure was hardly disturbed by the cracks in the TiO 2 inverse opal film. The UV-vis transmission spectra indicated that the photonic heterostructures had two photonic-band gaps, and the relative position of two photonic-band gaps can be controlled by the size of PS microspheres used to fabricated the photonic heterostructures.

Enzymatic Inverse Opal Hydrogel Particles for Biocatalyst.

Science.gov (United States)

Wang, Huan; Gu, Hongcheng; Chen, Zhuoyue; Shang, Luoran; Zhao, Ze; Gu, Zhongze; Zhao, Yuanjin

2017-04-19

Enzymatic carriers have a demonstrated value for chemical reactions and industrial applications. Here, we present a novel kind of inverse opal hydrogel particles as the enzymatic carriers. The particles were negatively replicated from spherical colloidal crystal templates by using magnetic nanoparticles tagged acrylamide hydrogel. Thus, they were endowed with the features of monodispersity, small volume, complete penetrating structure, and controllable motion, which are all beneficial for improving the efficiency of biocatalysis. In addition, due to the ordered porous nanostructure, the inverse opal hydrogel particles were imparted with unique photonic band gaps (PBGs) and vivid structural colors for encoding varieties of immobilized enzymes and for constructing a multienzymes biocatalysis system. These features of the inverse opal hydrogel particles indicate that they are ideal enzymatic carriers for biocatalysis.

Kinetics of DNA tile dimerization.

Science.gov (United States)

Jiang, Shuoxing; Yan, Hao; Liu, Yan

2014-06-24

Investigating how individual molecular components interact with one another within DNA nanoarchitectures, both in terms of their spatial and temporal interactions, is fundamentally important for a better understanding of their physical behaviors. This will provide researchers with valuable insight for designing more complex higher-order structures that can be assembled more efficiently. In this report, we examined several spatial factors that affect the kinetics of bivalent, double-helical (DH) tile dimerization, including the orientation and number of sticky ends (SEs), the flexibility of the double helical domains, and the size of the tiles. The rate constants we obtained confirm our hypothesis that increased nucleation opportunities and well-aligned SEs accelerate tile-tile dimerization. Increased flexibility in the tiles causes slower dimerization rates, an effect that can be reversed by introducing restrictions to the tile flexibility. The higher dimerization rates of more rigid tiles results from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. We believe that the results presented here will assist in improved implementation of DNA tile based algorithmic self-assembly, DNA based molecular robotics, and other specific nucleic acid systems, and will provide guidance to design and assembly processes to improve overall yield and efficiency.

Dimers in Piecewise Temperleyan Domains

Science.gov (United States)

Russkikh, Marianna

2018-03-01

We study the large-scale behavior of the height function in the dimer model on the square lattice. Richard Kenyon has shown that the fluctuations of the height function on Temperleyan discretizations of a planar domain converge in the scaling limit (as the mesh size tends to zero) to the Gaussian Free Field with Dirichlet boundary conditions. We extend Kenyon's result to a more general class of discretizations. Moreover, we introduce a new factorization of the coupling function of the double-dimer model into two discrete holomorphic functions, which are similar to discrete fermions defined in Smirnov (Proceedings of the international congress of mathematicians (ICM), Madrid, Spain, 2006; Ann Math (2) 172:1435-1467, 2010). For Temperleyan discretizations with appropriate boundary modifications, the results of Kenyon imply that the expectation of the double-dimer height function converges to a harmonic function in the scaling limit. We use the above factorization to extend this result to the class of all polygonal discretizations, that are not necessarily Temperleyan. Furthermore, we show that, quite surprisingly, the expectation of the double-dimer height function in the Temperleyan case is exactly discrete harmonic (for an appropriate choice of Laplacian) even before taking the scaling limit.

Detection of cyclobutane thymine dimers in DNA of human cells with monoclonal antibodies raised against a thymine dimer-containing tetranucleotide

Energy Technology Data Exchange (ETDEWEB)

Roza, L; Wulp, K.J.M. van der; MacFarlane, S J; Lohman, P H.M.; Baan, R A

1988-11-01

A hybrid cell line (hybridoma) has been isolated after fusion between mouse-plasmacytoma cells and spleen cells from mice immunized with a thymine dimer-containing tetranucleotide coupled to a carrier protein. Monoclonal antibodies produced by this hybridoma were characterized by testing the effect of various inhibitors in a competitive enzyme-linked immunosorbent assay (ELISA). The antibodies have a high specificity for thymine dimers in single-stranded DNA or poly(dT), but do not bind UV-irradiated d(TpC)/sub 5/. Less binding is observed with short thymine dimer-containing sequences. In vitro treatment of UV-irradiated DNA with photoreactivating enzyme in the presence of light, or with Micrococcus luteus UV-endonuclease results in disappearance of antigenicity. Antibody-binding to DNA isolated from UV-irradiated human fibroblasts (at 254 nm) is linear with dose. Removal of thymine dimers in these cells during a post-irradiation incubation, as detected with the antibodies, is fast initially but the rate rapidly decreases (about 50% residual dimers at 20 h after 10 J/m/sup 2/). The induction of thymine dimers in human skin irradiated with low doses of UV-B, too, was demonstrated immunochemically, by ELISA as well as by quantitative immunofluorescence microscopy.

Hydrodynamic Torques and Rotations of Superparamagnetic Bead Dimers

Science.gov (United States)

Pease, Christopher; Etheridge, J.; Wijesinghe, H. S.; Pierce, C. J.; Prikockis, M. V.; Sooryakumar, R.

Chains of micro-magnetic particles are often rotated with external magnetic fields for many lab-on-a-chip technologies such as transporting beads or mixing fluids. These applications benefit from faster responses of the actuated particles. In a rotating magnetic field, the magnetization of superparamagnetic beads, created from embedded magnetic nano-particles within a polymer matrix, is largely characterized by induced dipoles mip along the direction of the field. In addition there is often a weak dipole mop that orients out-of-phase with the external rotating field. On a two-bead dimer, the simplest chain of beads, mop contributes a torque Γm in addition to the torque from mip. For dimers with beads unbound to each other, mop rotates individual beads which generate an additional hydrodynamic torque on the dimer. Whereas, mop directly torques bound dimers. Our results show that Γm significantly alters the average frequency-dependent dimer rotation rate for both bound and unbound monomers and, when mop exceeds a critical value, increases the maximum dimer rotation frequency. Models that include magnetic and hydrodynamics torques provide good agreement with the experimental findings over a range of field frequencies.

(1S*,2S*,4R*,5R*-Cyclohexane-1,2,4,5-tetracarboxylic acid

Directory of Open Access Journals (Sweden)

Akira Uchida

2014-01-01

Full Text Available The title compound, C10H12O8, a prospective raw material for colourless polyimides which are applied to electronic and microelectronic devices, lies about an inversion centre and the cyclohexane ring adopts a chair conformation. Two crystallographycally independent carboxylic acid groups on adjacent C atoms are in equatorial positions, resulting in a mutually trans conformation. In the crystal, O—H...O hydrogen bonds around an inversion centre and a threefold rotoinversion axis, respectively, form an inversion dimer with an R22(8 motif and a trimer with an R33(12 motif.

Perturbation of the dimer interface of triosephosphate isomerase and its effect on Trypanosoma cruzi.

Directory of Open Access Journals (Sweden)

Vanesa Olivares-Illana

2007-10-01

Full Text Available Chagas disease affects around 18 million people in the American continent. Unfortunately, there is no satisfactory treatment for the disease. The drugs currently used are not specific and exert serious toxic effects. Thus, there is an urgent need for drugs that are effective. Looking for molecules to eliminate the parasite, we have targeted a central enzyme of the glycolytic pathway: triosephosphate isomerase (TIM. The homodimeric enzyme is catalytically active only as a dimer. Because there are significant differences in the interface of the enzymes from the parasite and humans, we searched for small molecules that specifically disrupt contact between the two subunits of the enzyme from Trypanosoma cruzi but not those of TIM from Homo sapiens (HTIM, and tested if they kill the parasite.Dithiodianiline (DTDA at nanomolar concentrations completely inactivates recombinant TIM of T. cruzi (TcTIM. It also inactivated HTIM, but at concentrations around 400 times higher. DTDA was also tested on four TcTIM mutants with each of its four cysteines replaced with either valine or alanine. The sensitivity of the mutants to DTDA was markedly similar to that of the wild type. The crystal structure of the TcTIM soaked in DTDA at 2.15 A resolution, and the data on the mutants showed that inactivation resulted from alterations of the dimer interface. DTDA also prevented the growth of Escherichia coli cells transformed with TcTIM, had no effect on normal E. coli, and also killed T. cruzi epimastigotes in culture.By targeting on the dimer interface of oligomeric enzymes from parasites, it is possible to discover small molecules that selectively thwart the life of the parasite. Also, the conformational changes that DTDA induces in the dimer interface of the trypanosomal enzyme are unique and identify a region of the interface that could be targeted for drug discovery.

Adsorption of dimeric surfactants in lamellar silicates

Energy Technology Data Exchange (ETDEWEB)

Balcerzak, Mateusz; Pietralik, Zuzanna [Department of Macromolecular Physics, Faculty of Physics, A. Mickiewicz University, Umultowska 85, 61-614 Poznań (Poland); Domka, Ludwik [Department of Metalorganic Chemistry, Faculty of Chemistry, A. Mickiewicz University, Grunwaldzka 6, 60-780 Poznań (Poland); Skrzypczak, Andrzej [Institute of Chemical Technology, Poznań University of Technology, Berdychowo 4, 60-965 Poznań (Poland); Kozak, Maciej, E-mail: mkozak@amu.edu.pl [Department of Macromolecular Physics, Faculty of Physics, A. Mickiewicz University, Umultowska 85, 61-614 Poznań (Poland)

2015-12-01

Highlights: • The intercalation of dimeric surfactants changed the morphology of MMT samples. • XRD indicated structures formed by surfactant molecules in interlayer space. • The four-step thermal decomposition of dimeric surfactant, confirms intercalation. - Abstract: The adsorption of different types of cationic surfactants in lamellar silicates changes their surface character from hydrophilic to hydrophobic. This study was undertaken to obtain lamellar silicates modified by a series of novel dimeric (gemini) surfactants of different length alkyl chains and to characterise these organophilised materials. Synthetic sodium montmorillonite SOMASIF® ME 100 (M) and enriched bentonite of natural origin (Nanoclay – hydrophilic bentonite®) were organophilised with dimeric (gemini) surfactants (1,1′-(1,4-butanediyl)bis(alkoxymethyl)imidazolium dichlorides). As a result of surfactant molecule adsorption in interlamellar space, the d-spacing (d{sub 001}) increased from 0.97 nm (for the anhydrous structure) to 2.04 nm. A Fourier transform infrared spectroscopy (FTIR) analysis of the modified systems reveals bands assigned to the stretching vibrations of the CH{sub 2} and CH{sub 3} groups and the scissoring vibrations of the NH group from the structure of the dimeric surfactants. Thermogravimetric (TG) and derivative thermogravimetric (DTG) studies imply a four-stage process of surfactant decomposition. Scanning electron microscopy (SEM) images provide information on the influence of dimeric surfactant intercalation into the silicate structures. Particles of the modified systems show a tendency toward the formation of irregularly shaped agglomerates.

c -Axis Dimer and Its Electronic Breakup: The Insulator-to-Metal Transition in Ti2 O3

Science.gov (United States)

Chang, C. F.; Koethe, T. C.; Hu, Z.; Weinen, J.; Agrestini, S.; Zhao, L.; Gegner, J.; Ott, H.; Panaccione, G.; Wu, Hua; Haverkort, M. W.; Roth, H.; Komarek, A. C.; Offi, F.; Monaco, G.; Liao, Y.-F.; Tsuei, K.-D.; Lin, H.-J.; Chen, C. T.; Tanaka, A.; Tjeng, L. H.

2018-04-01

We report on our investigation of the electronic structure of Ti2 O3 using (hard) x-ray photoelectron and soft x-ray absorption spectroscopy. From the distinct satellite structures in the spectra, we have been able to establish unambiguously that the Ti-Ti c -axis dimer in the corundum crystal structure is electronically present and forms an a1 ga1 g molecular singlet in the low-temperature insulating phase. Upon heating, we observe a considerable spectral weight transfer to lower energies with orbital reconstruction. The insulator-metal transition may be viewed as a transition from a solid of isolated Ti-Ti molecules into a solid of electronically partially broken dimers, where the Ti ions acquire additional hopping in the a -b plane via the egπ channel, the opening of which requires consideration of the multiplet structure of the on-site Coulomb interaction.

Magnetostructural relationship for μ2-phenoxido bridged ferric dimers.

Science.gov (United States)

Yu, Fei; Cao, Zi-Heng; Ge, Jing-Yuan; Sun, Yi-Chen; Ouyang, Zhong-Wen; Zuo, Jing-Lin; Wang, Zhenxing; Kurmoo, Mohamedally

2017-03-27

Three Fe(iii) dimers, [Fe 2 (L-H) 2 ]·2CH 3 CN (1), [Fe 2 (L-OCH 3 ) 2 ] (2) and [Fe 2 (L-OC 2 H 5 ) 2 ]·2CH 3 CN (3), containing the pentadentate O,N,N,O,O-donor Schiff-base ligands with variable size pendants, were synthesized and structurally characterized. The three ligands were generated in situ from 2-(iminomethyl)phenol, 2-methoxy-6-(iminomethyl)phenol and 2-ethoxy-6-(iminomethyl)phenol, respectively. All three crystal structures contain centrosymmetric dimers of edge-sharing octahedra of Fe(iii) ions through a pair of μ 2 -phenoxido bridges. The exchange coupling is ferromagnetic for 1 (J = +0.47(1) cm -1 , ∠Fe-O-Fe = 98.02°) and 2 (J = +0.86(1) cm -1 , ∠Fe-O-Fe = 97.17°), but antiferromagnetic for 3 (J = -0.72(1) cm -1 , ∠Fe-O-Fe = 98.53°), which are correlated by high-field electron paramagnetic resonance revealing moderate magneto-anisotropy of D = -0.24(3) cm -1 , E = 0.08(1) cm -1 for 1, D = -0.38(1) cm -1 , E = 0.11(1) cm -1 for 2, and D = 0.30(3) cm -1 , E = 0.02(1) cm -1 for 3. The exchange couplings were further estimated by DFT calculations, which gave the finest Fe-O-Fe angle of 97.83° for the ferromagnetic-antiferromagnetic crossover.

D-dimer Test

Science.gov (United States)

... 1997). Taber's Cyclopedic Medical Dictionary. F.A. Davis Company, Philadelphia, PA [18th Edition]. Pagana, Kathleen D. & Pagana, ... www.itxm.org . Titus, K. (2003 January). Identity crisis persists: which D-dimer? CAP Today , In the ...

Investigation of optical properties of PMMA opals and inverse opals with YVO4-Eu nano-phosphors

International Nuclear Information System (INIS)

Thakur, Shashi; Gathania, Arvind K.

2015-01-01

In recent years, opals and inverse opals have attracted the attention of researchers because of their potential applications in photonic devices. The idea of the periodic photonic crystal was proposed by Yablonovitch and John. The photonic crystals are in analogy with crystalline solid: electromagnetic waves propagating in the photonic crystal experienced periodic spatial variation of dielectric constant, as the de Broglie wave propagation in crystalline solids experienced periodic variation of the atomic potential. In the present work we synthesized the PMMA spheres using colloidal crystallization method and PMMA colloidal multilayer crystal were developed on the quartz substrate by self-assembly vertical deposition method. Afterward PMMA microspheres were infiltrated with YVO 4 -Eu nano-phosphors followed by heating at 500 °C and above to form the inverse opals. Transmission spectra for pure PMMA, infiltrated PMMA and inverse opal of PMMA are obtained. The colloidal crystal multilayer shows a stop band at 596nm, which arises from the Bragg reflection of the (111) planes. The central position of this band gap is shifted to 608nm because of the change in the refractive index of the structure after infiltration. As the calcination was carried out at 500 °C and 600 °C, the central position of the band shifted to 483nm and 500nm respectively, because of the change in the effective refractive index of the structure and shrinkage in the direction perpendicular to the film. The resulting structure still exhibits a band gap, as the crystalline ordering is kept after the crystal is inverted. The intensity of inverse opals of PMMA is very small as compared to the bulk powder briefing the application of microstructures for the low voltage light emitting diodes (LEDs). The results show band gap and luminescent characteristics strongly depend upon infiltration. (author)

High-quality bulk hybrid perovskite single crystals within minutes by inverse temperature crystallization

KAUST Repository

Saidaminov, Makhsud I.; Abdelhady, Ahmed L.; Banavoth, Murali; Alarousu, Erkki; Burlakov, Victor M.; Peng, Wei; Dursun, Ibrahim; Wang, Lingfei; He, Yao; Maculan, Giacomo; Goriely, Alain; Wu, Tao; Mohammed, Omar F.; Bakr, Osman

2015-01-01

Single crystals of methylammonium lead trihalide perovskites (MAPbX3; MA=CH3NH3+, X=Br− or I−) have shown remarkably low trap density and charge transport properties; however, growth of such high-quality semiconductors is a time-consuming process

Molecular mechanics calculations on cobalt phthalocyanine dimers

NARCIS (Netherlands)

Heuts, J.P.A.; Schipper, E.T.W.M.; Piet, P.; German, A.L.

1995-01-01

In order to obtain insight into the structure of cobalt phthalocyanine dimers, molecular mechanics calculations were performed on dimeric cobalt phthalocyanine species. Molecular mechanics calculations are first presented on monomeric cobalt(II) phthalocyanine. Using the Tripos force field for the

Crystallization and preliminary X-ray diffraction analysis of three myotoxic phospholipases A2 from Bothrops brazili venom

International Nuclear Information System (INIS)

Fernandes, Carlos A. H.; Gartuzo, Elaine C. G.; Pagotto, Ivan; Comparetti, Edson J.; Huancahuire-Vega, Salomón; Ponce-Soto, Luis Alberto; Costa, Tássia R.; Marangoni, Sergio; Soares, Andreimar M.; Fontes, Marcos R. M.

2012-01-01

Two myotoxic and noncatalytic Lys49-phospholipases A 2 (braziliantoxin-II and MT-II) and a myotoxic and catalytic phospholipase A 2 (braziliantoxin-III) from B. brazili were crystallized. X-ray diffraction data sets were collected and molecular-replacement solutions were obtained. Two myotoxic and noncatalytic Lys49-phospholipases A 2 (braziliantoxin-II and MT-II) and a myotoxic and catalytic phospholipase A 2 (braziliantoxin-III) from the venom of the Amazonian snake Bothrops brazili were crystallized. The crystals diffracted to resolutions in the range 2.56–2.05 Å and belonged to space groups P3 1 21 (braziliantoxin-II), P6 5 22 (braziliantoxin-III) and P2 1 (MT-II). The structures were solved by molecular-replacement techniques. Both of the Lys49-phospholipases A 2 (braziliantoxin-II and MT-II) contained a dimer in the asymmetric unit, while the Asp49-phospholipase A 2 braziliantoxin-III contained a monomer in its asymmetric unit. Analysis of the quaternary assemblies of the braziliantoxin-II and MT-II structures using the PISA program indicated that both models have a dimeric conformation in solution. The same analysis of the braziliantoxin-III structure indicated that this protein does not dimerize in solution and probably acts as a monomer in vivo, similar to other snake-venom Asp49-phospholipases A 2

Structure and dimerization of the catalytic domain of the protein phosphatase Cdc14p, a key regulator of mitotic exit in Saccharomyces cerevisiae.

Science.gov (United States)

Kobayashi, Junya; Matsuura, Yoshiyuki

2017-10-01

In the budding yeast Saccharomyces cerevisiae, the protein phosphatase Cdc14p orchestrates various events essential for mitotic exit. We have determined the X-ray crystal structures at 1.85 Å resolution of the catalytic domain of Cdc14p in both the apo state, and as a complex with S160-phosphorylated Swi6p peptide. Each asymmetric unit contains two Cdc14p chains arranged in an intimately associated homodimer, consistent with its oligomeric state in solution. The dimerization interface is located on the backside of the substrate-binding cleft. Structure-based mutational analyses indicate that the dimerization of Cdc14p is required for normal growth of yeast cells. © 2017 The Protein Society.

Dynamics of the water dimer + nitric oxide collision

Energy Technology Data Exchange (ETDEWEB)

Ree, Jong Baik [Dept. of Chemistry Education, Chonnam National University, Gwangju (Korea, Republic of); Kim, Yoo Hang [Dept. of Chemistry, Inha University, Incheon (Korea, Republic of); Shin, Hyung Kyu [Dept. of Chemistry, University of Nevada, Nevada (Korea, Republic of)

2017-02-15

Collision-induced intermolecular energy transfer and intramolecular vibrational redistribution in the collision of a water dimer and nitric oxide are studied by use of quasiclassical procedures. Intermolecular energy flow is shown to occur mainly through a direct-mode mechanism transferring relatively large amounts in strong collisions. About a quarter of the energy initially deposited in the dimer transfers to the ground state NO, while the rest redistributes among internal motions of the collision system. The main portion of initial energy deposited in the dimer redistributes in the stretches of the donor monomer through the 1:1 resonance followed by in the bend through the 1:2 resonance. Energy transfer from the excited NO to the ground-state dimer is equally efficient, transferring more than half the initial excitation to the donor monomer, the efficiency that is attributed to the internal modes operating as energy reservoirs. The hydrogen bond shares about 15% of the initial excitation stored in both dimer-to-NO and NO-to-dimer processes as a result of strong coupling of the hydrogen bond with the proton-donor OH bond of the monomer. A small fraction of collisions proceeds through a complex-mode mechanism and lead to NO dissociation, the dissociated O atom showing a propensity to form a new hydrogen bond.

Tah1 helix-swap dimerization prevents mixed Hsp90 co-chaperone complexes

International Nuclear Information System (INIS)

Morgan, Rhodri M. L.; Pal, Mohinder; Roe, S. Mark; Pearl, Laurence H.; Prodromou, Chrisostomos

2015-01-01

A helix swap involving the fifth helix between two adjacently bound Tah1 molecules restores the normal binding environment of the conserved MEEVD peptide of Hsp90. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes with Hsp90 and Tah1. Specific co-chaperone adaptors facilitate the recruitment of client proteins to the Hsp90 system. Tah1 binds the C-terminal conserved MEEVD motif of Hsp90, thus linking an eclectic set of client proteins to the R2TP complex for their assembly and regulation by Hsp90. Rather than the normal complement of seven α-helices seen in other tetratricopeptide repeat (TPR) domains, Tah1 unusually consists of the first five only. Consequently, the methionine of the MEEVD peptide remains exposed to solvent when bound by Tah1. In solution Tah1 appears to be predominantly monomeric, and recent structures have failed to explain how Tah1 appears to prevent the formation of mixed TPR domain-containing complexes such as Cpr6–(Hsp90) 2 –Tah1. To understand this further, the crystal structure of Tah1 in complex with the MEEVD peptide of Hsp90 was determined, which shows a helix swap involving the fifth α-helix between two adjacently bound Tah1 molecules. Dimerization of Tah1 restores the normal binding environment of the bound Hsp90 methionine residue by reconstituting a TPR binding site similar to that in seven-helix-containing TPR domain proteins. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes

Tah1 helix-swap dimerization prevents mixed Hsp90 co-chaperone complexes

Energy Technology Data Exchange (ETDEWEB)

Morgan, Rhodri M. L.; Pal, Mohinder; Roe, S. Mark; Pearl, Laurence H., E-mail: laurence.pearl@sussex.ac.uk; Prodromou, Chrisostomos, E-mail: laurence.pearl@sussex.ac.uk [University of Sussex, Falmer, Brighton BN1 9RQ (United Kingdom)

2015-05-01

A helix swap involving the fifth helix between two adjacently bound Tah1 molecules restores the normal binding environment of the conserved MEEVD peptide of Hsp90. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes with Hsp90 and Tah1. Specific co-chaperone adaptors facilitate the recruitment of client proteins to the Hsp90 system. Tah1 binds the C-terminal conserved MEEVD motif of Hsp90, thus linking an eclectic set of client proteins to the R2TP complex for their assembly and regulation by Hsp90. Rather than the normal complement of seven α-helices seen in other tetratricopeptide repeat (TPR) domains, Tah1 unusually consists of the first five only. Consequently, the methionine of the MEEVD peptide remains exposed to solvent when bound by Tah1. In solution Tah1 appears to be predominantly monomeric, and recent structures have failed to explain how Tah1 appears to prevent the formation of mixed TPR domain-containing complexes such as Cpr6–(Hsp90){sub 2}–Tah1. To understand this further, the crystal structure of Tah1 in complex with the MEEVD peptide of Hsp90 was determined, which shows a helix swap involving the fifth α-helix between two adjacently bound Tah1 molecules. Dimerization of Tah1 restores the normal binding environment of the bound Hsp90 methionine residue by reconstituting a TPR binding site similar to that in seven-helix-containing TPR domain proteins. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes.

Frequency dependent steering with backward leaky waves via photonic crystal interface layer.

Science.gov (United States)

Colak, Evrim; Caglayan, Humeyra; Cakmak, Atilla O; Villa, Alessandro D; Capolino, Filippo; Ozbay, Ekmel

2009-06-08

A Photonic Crystal (PC) with a surface defect layer (made of dimers) is studied in the microwave regime. The dispersion diagram is obtained with the Plane Wave Expansion Method. The dispersion diagram reveals that the dimer-layer supports a surface mode with negative slope. Two facts are noted: First, a guided (bounded) wave is present, propagating along the surface of the dimer-layer. Second, above the light line, the fast traveling mode couple to the propagating spectra and as a result a directive (narrow beam) radiation with backward characteristics is observed and measured. In this leaky mode regime, symmetrical radiation patterns with respect to the normal to the PC surface are attained. Beam steering is observed and measured in a 70 degrees angular range when frequency ranges in the 11.88-13.69 GHz interval. Thus, a PC based surface wave structure that acts as a frequency dependent leaky wave antenna is presented. Angular radiation pattern measurements are in agreement with those obtained via numerical simulations that employ the Finite Difference Time Domain Method (FDTD). Finally, the backward radiation characteristics that in turn suggest the existence of a backward leaky mode in the dimer-layer are experimentally verified using a halved dimer-layer structure.

Magnetic topology of Co-based inverse opal-like structures

NARCIS (Netherlands)

Grigoryeva, N.A.; Mistonov, A.A.; Napolskii, K.S.; Sapoletova, N.A.; Eliseev, A.A.; Bouwman, W.; Byelov, D.; Petukhov, A.V.; Chernyshov, D.Y.; Eckerlebe, H.; Vasilieva, A.V.; Grigoriev, S.V.

2011-01-01

Themagnetic and structural properties of a cobalt inverse opal-like crystal have been studied by a combination of complementary techniques ranging from polarized neutron scattering and superconducting quantum interference device (SQUID) magnetometry to x-ray diffraction. Microradian small-angle

Determination of the Tetramer-Dimer Equilibrium Constant of Rabbit ...

African Journals Online (AJOL)

Hemoglobin is a tetrameric protein which is able to dissociate into dimers. The dimers can in turn dissociate into tetramers. It has been found that dimers are more reactive than tetramers. The difference in the reactivity of these two species has been used to determine the tetramerdimer dissociation constant of various ...

CH3NH3PbCl3 Single Crystals: Inverse Temperature Crystallization and Visible-Blind UV-Photodetector

KAUST Repository

Maculan, Giacomo; Sheikh, Arif D.; Abdelhady, Ahmed L.; Saidaminov, Makhsud I.; Haque, Mohammed; Banavoth, Murali; Alarousu, Erkki; Mohammed, Omar F.; Wu, Tao; Bakr, Osman

2015-01-01

a new method of sizeable CH3NH3PbCl3 single crystal growth based on retrograde solubility behavior of hybrid perovskites. We show, for the first time, the energy band structure, charge-carrier recombination and transport properties of single crystal

The influence of fabrication deviations on the photonic band gap of three-dimensional inverse woodpile nanostructures

NARCIS (Netherlands)

Woldering, L.A.; Mosk, Allard; Tjerkstra, R.W.; Vos, Willem L.

2009-01-01

The effects of unintended deviations from ideal inverse woodpile photonic crystals on the photonic band gap are discussed. Such deviations occur during the nanofabrication of the crystal. By computational analyses it is shown that the band gap of this type of crystal is robust to most types of

Glycosylation Alters Dimerization Properties of a Cell-surface Signaling Protein, Carcinoembryonic Antigen-related Cell Adhesion Molecule 1 (CEACAM1)*

Science.gov (United States)

Zhuo, You; Yang, Jeong-Yeh; Moremen, Kelley W.; Prestegard, James H.

2016-01-01

Human carcinoembryonic antigen-related cell adhesion molecule 1 (C?/Au: EACAM1) is a cell-surface signaling molecule involved in cell adhesion, proliferation, and immune response. It is also implicated in cancer angiogenesis, progression, and metastasis. This diverse set of effects likely arises as a result of the numerous homophilic and heterophilic interactions that CEACAM1 can have with itself and other molecules. Its N-terminal Ig variable (IgV) domain has been suggested to be a principal player in these interactions. Previous crystal structures of the β-sandwich-like IgV domain have been produced using Escherichia coli-expressed material, which lacks native glycosylation. These have led to distinctly different proposals for dimer interfaces, one involving interactions of ABED β-strands and the other involving GFCC′C″ β-strands, with the former burying one prominent glycosylation site. These structures raise questions as to which form may exist in solution and what the effect of glycosylation may have on this form. Here, we use NMR cross-correlation measurements to examine the effect of glycosylation on CEACAM1-IgV dimerization and use residual dipolar coupling (RDC) measurements to characterize the solution structure of the non-glycosylated form. Our findings demonstrate that even addition of a single N-linked GlcNAc at potential glycosylation sites inhibits dimer formation. Surprisingly, RDC data collected on E. coli expressed material in solution indicate that a dimer using the non-glycosylated GFCC′C″ interface is preferred even in the absence of glycosylation. The results open new questions about what other factors may facilitate dimerization of CEACAM1 in vivo, and what roles glycosylation may play in heterophylic interactions. PMID:27471271

π–π-Induced aggregation and single-crystal fluorescence anisotropy of 5,6,10b-triazaacephenanthrylene

Directory of Open Access Journals (Sweden)

Katarzyna Ostrowska

2018-05-01

Full Text Available The structural origin of absorption and fluorescence anisotropy of the single crystal of the π-conjugated heterocyclic system 5,6,10b-triazaacephenanthrylene, TAAP, is presented in this study. X-ray analysis shows that the crystal framework in the space group P\\overline{1} is formed by centrosymmetric dimers of face-to-face mutually oriented TAAP molecules joined by π–π non-covalent interactions. The conformation of the TAAP molecule is stabilized by intramolecular C—H...N(sp2, N(sp2H...π(CN, and C—H...O(sp2 hydrogen bonds. The presence of weak π–π interactions is confirmed by quantum theory of atoms in molecules (QTAIM and non-covalent interaction (NCI analysis. The analysis of the optical spectra of TAAP in solution and in the solid state does not allow the specification of the aggregation type. DFT calculations for the dimer in the gas phase indicate that the lowest singlet excitation is forbidden by symmetry, suggesting H-type aggregation, even though the overall absorption spectrum is bathochromically shifted as for the J-type. The experimental determination of the permanent dipole moment of a TAAP molecule in 1,4-dioxane solution indicates the presence of the monomer form. The calculated absorption and emission spectra of the crystal in a simple approximation are consistent with the experimentally determined orientation of the absorption and emission transition dipole moments in TAAP single crystals. The electrostatic interaction between monomers with a permanent dipole moment (ca 4 D each could result in the unusual spectroscopic JH-aggregate behaviour of the TAAP dimer.

Magnetic topology of Co-based inverse opal-like structures

NARCIS (Netherlands)

Grigoryeva, N.A.; Mistonov, A.A.; Napolskii, K.S.; Sapoletova, N.A.; Eliseev, A.A.; Bouwman, W.G.; Byelov, D.V.; Petukhov, A.V.; Chernyshov, D.Y.; Eckerlebe, H.; Vasilieva, A.V.; Grigoriev, S.V.

2011-01-01

The magnetic and structural properties of a cobalt inverse opal-like crystal have been studied by a combination of complementary techniques ranging from polarized neutron scattering and superconducting quantum interference device (SQUID) magnetometry to x-ray diffraction. Microradian small-angle

Theoretical modeling of infrared spectra of the hydrogen and deuterium bond in aspirin crystal

Science.gov (United States)

Ghalla, Houcine; Rekik, Najeh; Michta, Anna; Oujia, Brahim; Flakus, Henryk T.

2010-01-01

An extended quantum theoretical approach of the ν IR lineshape of cyclic dimers of weakly H-bonded species is proposed. We have extended a previous approach [M.E.-A. Benmalti, P. Blaise, H.T. Flakus, O. Henri-Rousseau, Chem. Phys. 320 (2006) 267] by accounting for the anharmonicity of the slow mode which is described by a "Morse" potential in order to reproduce the polarized infrared spectra of the hydrogen and deuterium bond in acetylsalicylic acid (aspirin) crystals. From comparison of polarized IR spectra of isotopically neat and isotopically diluted aspirin crystals it resulted that centrosymmetric aspirin dimer was the bearer of the crystal main spectral properties. In this approach, the adiabatic approximation is performed for each separate H-bond bridge of the dimer and a strong non-adiabatic correction is introduced into the model via the resonant exchange between the fast mode excited states of the two moieties. Within the strong anharmonic coupling theory, according to which the X-H→⋯Y high-frequency mode is anharmonically coupled to the H-bond bridge, this model incorporated the Davydov coupling between the excited states of the two moieties, the quantum direct and indirect dampings and the anharmonicity for the H-bond bridge. The spectral density is obtained within the linear response theory by Fourier transform of the damped autocorrelation functions. The evaluated spectra are in fairly good agreement with the experimental ones by using a minimum number of independent parameters. The effect of deuteration has been well reproduced by reducing simply the angular frequency of the fast mode and the anharmonic coupling parameter.

(E-2-(5-Chloro-2-hydroxybenzylidene-N-cyclohexylhydrazine-1-carbothioamide

Directory of Open Access Journals (Sweden)

Md. Azharul Arafath

2017-01-01

Full Text Available In the title compound, C14H18ClN3OS, the phenol ring is almost coplanar with the hydrazinecarbothioamide moiety, making a dihedral angle of 6.92 (8°. The cyclohexane ring has a chair conformation and the conformation about the C=N bond is E. In the crystal, molecules are linked by N—H...O and O—H...S hydrogen bonds, forming inversion dimers with an R22(14 ring motif flanked by two R22(6 ring motifs. The dimers are linked by short Cl...Cl interactions, forming layers parallel to the ab plane.

Dualism of Sensitivity and Selectivity of Porphyrin Dimers in Electroanalysis.

Science.gov (United States)

Lisak, Grzegorz; Tamaki, Takashi; Ogawa, Takuji

2017-04-04

This work uncovers the application of porphyrin dimers for the use in electroanalysis, such as potentiometric determination of ions. It also puts in question a current perception of an occurrence of the super-Nernstian response, as a result of the possible dimerization of single porphyrins within an ion-selective membrane. To study that, four various porphyrin dimers were used as ionophores, namely, freebase-freebase, Zn-Zn, Zn-freebase, and freebase-Zn. Since the Zn-freebase and freebase-Zn porphyrin dimers carried both anion- and cation-sensitive porphyrin units, their application in ISEs was utilized in both anion- and cation-sensitive sensors. With respect to the lipophilic salt added, both porphyrins dimers were found anion- and cation-sensitive. This allowed using a single molecule as novel type of versatile ionophore (anion- and cation-selective), simply by varying the membrane composition. All anion-sensitive sensors were perchlorate-sensitive, while the cation-selective sensors were silver-sensitive. The selectivity of the sensors depended primarily on the porphyrin dimers in the ion-selective membrane. Furthermore, the selectivity of cation-sensitive dimer based sensors was found significantly superior to the ones measured for the single porphyrin unit based sensors (precursors of the porphyrin dimers). Thus, the dimerization of single porphyrins may actually be a factor to increase or modulate porphyrin selectivity. Moreover, in the case of cation-sensitive sensors, the selectivity vastly depended on the order of porphyrin units in the dimer. This opens a new approach of regulating and adjusting sensitivity and selectivity of the sensor through the application of complex porphyrin systems with more than one porphyrin units with mix sensitive porphyrins.

Her4 and Her2/neu tyrosine kinase domains dimerize and activate in a reconstituted in vitro system.

Science.gov (United States)

Monsey, John; Shen, Wei; Schlesinger, Paul; Bose, Ron

2010-03-05

Her4 (ErbB-4) and Her2/neu (ErbB-2) are receptor-tyrosine kinases belonging to the epidermal growth factor receptor (EGFR) family. Crystal structures of EGFR and Her4 kinase domains demonstrate kinase dimerization and activation through an allosteric mechanism. The kinase domains form an asymmetric dimer, where the C-lobe surface of one monomer contacts the N-lobe of the other monomer. EGFR kinase dimerization and activation in vitro was previously reported using a nickel-chelating lipid-liposome system, and we now apply this system to all other members of the EGFR family. Polyhistidine-tagged Her4, Her2/neu, and Her3 kinase domains are bound to these nickel-liposomes and are brought to high local concentration, mimicking what happens to full-length receptors in vivo following ligand binding. Addition of nickel-liposomes to Her4 kinase domain results in 40-fold activation in kinase activity and marked enhancement of C-terminal tail autophosphorylation. Activation of Her4 shows a sigmoidal dependence on kinase concentration, consistent with a cooperative process requiring kinase dimerization. Her2/neu kinase activity is also activated by nickel-liposomes, and is increased further by heterodimerization with Her3 or Her4. The ability of Her3 and Her4 to heterodimerize and activate other family members is studied in vitro. Her3 kinase domain readily activates Her2/neu but is a poor activator of Her4, which differs from the prediction made by the asymmetric dimer model. Mutation of Her3 residues (952)ENI(954) to the corresponding sequence in Her4 enhanced the ability of Her3 to activate Her4, demonstrating that sequence differences on the C-lobe surface influence the heterodimerization and activation of ErbB kinase domains.

β-lactoglobulin's conformational requirements for ligand binding at the calyx and the dimer interphase: a flexible docking study.

Directory of Open Access Journals (Sweden)

Lenin Domínguez-Ramírez

Full Text Available β-lactoglobulin (BLG is an abundant milk protein relevant for industry and biotechnology, due significantly to its ability to bind a wide range of polar and apolar ligands. While hydrophobic ligand sites are known, sites for hydrophilic ligands such as the prevalent milk sugar, lactose, remain undetermined. Through the use of molecular docking we first, analyzed the known fatty acid binding sites in order to dissect their atomistic determinants and second, predicted the interaction sites for lactose with monomeric and dimeric BLG. We validated our approach against BLG structures co-crystallized with ligands and report a computational setup with a reduced number of flexible residues that is able to reproduce experimental results with high precision. Blind dockings with and without flexible side chains on BLG showed that: i 13 experimentally-determined ligands fit the calyx requiring minimal movement of up to 7 residues out of the 23 that constitute this binding site. ii Lactose does not bind the calyx despite conformational flexibility, but binds the dimer interface and an alternate Site C. iii Results point to a probable lactolation site in the BLG dimer interface, at K141, consistent with previous biochemical findings. In contrast, no accessible lysines are found near Site C. iv lactose forms hydrogen bonds with residues from both monomers stabilizing the dimer through a claw-like structure. Overall, these results improve our understanding of BLG's binding sites, importantly narrowing down the calyx residues that control ligand binding. Moreover, our results emphasize the importance of the dimer interface as an insufficiently explored, biologically relevant binding site of particular importance for hydrophilic ligands. Furthermore our analyses suggest that BLG is a robust scaffold for multiple ligand-binding, suitable for protein design, and advance our molecular understanding of its ligand sites to a point that allows manipulation to control

Antiphase inversion domains in lithium cobaltite thin films deposited on single-crystal sapphire substrates

International Nuclear Information System (INIS)

Zheng, S.J.; Fisher, C.A.J.; Hitosugi, T.; Kumatani, A.; Shiraki, S.; Ikuhara, Y.H.; Kuwabara, A.; Moriwake, H.; Oki, H.; Ikuhara, Y.

2013-01-01

Antiphase inversion domains in LiCoO 2 thin films prepared by pulsed laser deposition on sapphire single-crystal substrates are analyzed using a combination of (scanning) transmission electron microscopy and first-principles calculations. Domains form epitaxially on the substrates with orientation relationships of [112 ¯ 0] LiCoO 2 (0001) LiCoO 2 //[11 ¯ 00] α-Al 2 O 3 (0001) α-Al 2 O 3 and [1 ¯ 1 ¯ 20] LiCoO 2 (0001) LiCoO 2 //[11 ¯ 00] α-Al 2 O 3 (0001) α-Al 2 O 3 . In addition, substrate/film interfaces with the above orientation relationships always have the same stacking sequence of Al–O–Co–O–Li–O. This is confirmed to be the most energetically stable stacking arrangement according to first-principles calculations. Individual domains form as a result of steps one (0 0 0 1) O–Al–O spacing in height on the otherwise flat substrate surface. Because the orientation of adjacent (0 0 0 1) AlO 6 octahedra in Al 2 O 3 are rotated by 180°, while LiO 6 and CoO 6 octahedra in LiCoO 2 are all aligned in the same direction, substrate steps produce LiCoO 2 domains rotated 180° relative to their neighbors. The similar size of oxygen octahedra in the two materials also means that the step height is close to the layer spacing in LiCoO 2 , so that (0 0 0 1) Li and Co layers of adjacent domains are shifted by one layer relative to each other at each domain boundary, aligning Li layers with Co layers across the boundary. The combination of these two effects generates antiphase inversion domains. The domain boundaries effectively sever Li-ion diffusion pathways in the (0 0 0 1) planes between domains and thus are expected to have a detrimental effect on Li-ion conductivity

Factors associated with D-dimer levels in HIV-infected individuals

DEFF Research Database (Denmark)

Borges, Alvaro H; O'Connor, Jemma L; Phillips, Andrew N

2014-01-01

BACKGROUND: Higher plasma D-dimer levels are strong predictors of mortality in HIV+ individuals. The factors associated with D-dimer levels during HIV infection, however, remain poorly understood. METHODS: In this cross-sectional study, participants in three randomized controlled trials...... with measured D-dimer levels were included (N = 9,848). Factors associated with D-dimer were identified by linear regression. Covariates investigated were: age, gender, race, body mass index, nadir and baseline CD4+ count, plasma HIV RNA levels, markers of inflammation (C-reactive protein [CRP], interleukin-6...... viruses, was positively correlated with D-dimer. Other factors independently associated with higher D-dimer levels were black race, higher plasma HIV RNA levels, being off ART at baseline, and increased levels of CRP, IL-6 and cystatin C. In contrast, higher baseline CD4+ counts and higher high...

Purification, crystallization and crystallographic analysis of Clostridium thermocellum endo-1,4-β-d-xylanase 10B in complex with xylohexaose

Energy Technology Data Exchange (ETDEWEB)

Najmudin, Shabir, E-mail: shabir@dq.fct.unl.pt [REQUIMTE, Departamento de Química, FCT-UNL, 2829-516 Caparica (Portugal); Pinheiro, Benedita A. [CIISA - Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa (Portugal); Romão, Maria J. [REQUIMTE, Departamento de Química, FCT-UNL, 2829-516 Caparica (Portugal); Prates, José A. M.; Fontes, Carlos M. G. A., E-mail: shabir@dq.fct.unl.pt [CIISA - Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa (Portugal); REQUIMTE, Departamento de Química, FCT-UNL, 2829-516 Caparica (Portugal)

2008-08-01

The N-terminal moiety of C. thermocellum endo-1,4-β-d-xylanase 10B, comprising a carbohydrate-binding module (CBM22-1) and a GH10 E337A mutant domain, has been crystallized in complex with xylohexaose. The crystals belong to the trigonal space group P3{sub 2}21, contain a dimer in the asymmetric unit and diffract to beyond 2.0 Å resolution. The cellulosome of Clostridium thermocellum is a highly organized multi-enzyme complex of cellulases and hemicellulases involved in the hydrolysis of plant cell-wall polysaccharides. The bifunctional multi-modular xylanase Xyn10B is one of the hemicellulase components of the C. thermocellum cellulosome. The enzyme contains an internal glycoside hydrolase family 10 catalytic domain (GH10) and a C-terminal family 1 carbohydrate esterase domain (CE1). The N-terminal moiety of Xyn10B (residues 32–551), comprising a carbohydrate-binding module (CBM22-1) and the GH10 E337A mutant, was crystallized in complex with xylohexaose. The crystals belong to the trigonal space group P3{sub 2}21 and contain a dimer in the asymmetric unit. The crystals diffracted to beyond 2.0 Å resolution.

On the Sensitivity of Peptide Nucleic Acid Duplex Formation and Crystal Dissolution to a Variation of Force-Field Parameters.

Science.gov (United States)

Bachmann, Stephan J; Lin, Zhixiong; Stafforst, Thorsten; van Gunsteren, Wilfred F; Dolenc, Jožica

2014-01-14

The technique of one-step perturbation to explore the relation between particular force-field parameters on the one hand and particular properties of a biomolecular system on the other hand from one or a few molecular dynamics simulations is applied to investigate the dependence of the free enthalpy of dimer formation and of crystal dissolution of a self-complementary fragment (H-CGTACG-NH2) of peptide nucleic acid, PNA, a mimic of DNA. The simulations show that PNA dimer formation in aqueous solution is favored by a decrease in the base charges with respect to values of the GROMOS 45A4 force field, while it is disfavored by a decrease in the backbone charges. In contrast, crystal dissolution of the PNA dimer is favored by a decrease in base charges, while a variation of backbone charges has a minor effect on this free enthalpy change. These opposite effects in a crystalline versus aqueous solution environment can be understood from the different water contents for these systems and have consequences for biomolecular force-field development.

Study of molybdenum(VI) dimerization equilibrium in strongly acidic medium

International Nuclear Information System (INIS)

Esbelin, E.

2000-01-01

Molybdenum (VI) was investigated spectro-photometrically in non complexing and strongly acidic medium for the first time by Krumenacker. Cationic species of molybdenum were identified by electrophoresis on cellulose paper in highly acidic solutions. From these early results using absorption spectrophotometry, Krumenacker postulated the condensation of molybdenum in this medium. He studied the polymeric species by measuring diffusion coefficients and identified the polymeric form as a dimer. He described the system by equations (1) and (2). Cruywagen later added two equations (3) and (4) to supplement the description of the system. The aim of this work was to re-examine the conditional dimerization equilibrium between the various species of molybdenum(VI) in strongly acid medium by focussing on the influence of the medium. All Mo solution concentrations were analyzed by ICP-AES. Absorbance of the solutions were measured with a VARIAN model CARY5 spectrophotometer in double beam mode with air as reference; blank solutions contained all reagents except molybdenum. The quartz cell path length was 1 mm. The dimerization of monomeric molybdenum(VI) was investigated spectro-photometrically at perchloric acid concentrations of 0.5, 1.0, 2.0 and 3 M at 25 deg C. Two absorption bands at 215 and 245 nm were observed and attributed to monomeric and dimeric forms respectively. The variations in the conditional molar absorption coefficient of molybdenum with total molybdenum(VI) concentration is indicative of several molybdenum forms involved in the total absorbance. Dimerization equilibrium is defined by equation (5). By using the additivity of absorbance and mass conservation of molybdenum, a descriptive equation of the 'spectrochemical' system is developed. This equation is linearized into two forms (6) et (7). From them, two refinement methods were used to estimate the conditional dimerization constant K' d for various medium concentrations. This numerical procedure offers

Mechanochemical synthesis of N-salicylideneaniline: thermosalient effect of polymorphic crystals

Directory of Open Access Journals (Sweden)

Sudhir Mittapalli

2017-05-01

Full Text Available Polymorphs of the dichloro derivative of N-salicylideneaniline exhibit mechanical responses such as jumping (Forms I and III and exploding (Form II in its three polymorphs. The molecules are connected via the amide N—H...O dimer synthon and C—Cl...O halogen bond in the three crystal structures. A fourth high-temperature Form IV was confirmed by variable-temperature single-crystal X-ray diffraction at 180°C. The behaviour of jumping exhibited by the polymorphic crystals of Forms I and III is due to the layered sheet morphology and the transmission of thermal stress in a single direction, compared with the corrugated sheet structure of Form II such that heat dissipation is more isotropic causing blasting. The role of weak C—Cl...O interactions in the thermal response of molecular crystals is discussed.

Gold nanoparticle incorporated inverse opal photonic crystal capillaries for optofluidic surface enhanced Raman spectroscopy.

Science.gov (United States)

Zhao, Xiangwei; Xue, Jiangyang; Mu, Zhongde; Huang, Yin; Lu, Meng; Gu, Zhongze

2015-10-15

Novel transducers are needed for point of care testing (POCT) devices which aim at facile, sensitive and quick acquisition of health related information. Recent advances in optofluidics offer tremendous opportunities for biological/chemical analysis using extremely small sample volumes. This paper demonstrates nanostructured capillary tubes for surface enhanced Raman spectroscopy (SERS) analysis in a flow-through fashion. The capillary tube integrates the SERS sensor and the nanofluidic structure to synergistically offer sample delivery and analysis functions. Inside the capillary tube, inverse opal photonic crystal (IO PhC) was fabricated using the co-assembly approach to form nanoscale liquid pathways. In the nano-voids of the IO PhC, gold nanoparticles were in situ synthesized and functioned as the SERS hotspots. The advantages of the flow-through SERS sensor are multifold. The capillary effect facilities the sample delivery process, the nanofluidic channels boosts the interaction of analyte and gold nanoparticles, and the PhC structure strengthens the optical field near the SERS hotspots and results in enhanced SERS signals from analytes. As an exemplary demonstration, the sensor was used to measure creatinein spiked in artificial urine samples with detection limit of 0.9 mg/dL. Copyright © 2015 Elsevier B.V. All rights reserved.

Ferroelectric inverse opals with electrically tunable photonic band gap

International Nuclear Information System (INIS)

Li Bo; Zhou Ji; Li Longtu; Wang Xingjun; Liu Xiaohan; Zi Jian

2003-01-01

We present a scheme for tuning the photonic band gap (PBG) by an external electric field in a ferroelectric inverse opal structure. The inverse opals, consisting of ferroelectric (Pb,La)(Zr,Ti)O 3 (PLZT) ceramics, were synthesized by a sol-gel process. Optical reflection spectra show that the PBG of the PLZT inverse opals shifts continuously with the change in the applied electric field. As the photonic crystals (PCs) consist of the high-refractive-index constituent and possess an 'all-solid' structure, it should supply a more reliable mode to tune the PBG by the electric field for the superprism effect in PCs. It should be of high interest in device applications

Synthesis and crystal structures of three new benzotriazolylpropanamides

Directory of Open Access Journals (Sweden)

Donna S. Amenta

2017-06-01

Full Text Available The base-catalyzed Michael addition of 2-methylacrylamide to benzotriazole afforded 3-(1H-benzotriazol-1-yl-2-methylpropanamide, C10H12N4O (1, in 32% yield in addition to small amounts of isomeric 3-(2H-benzotriazol-2-yl-2-methylpropanamide, C10H12N4O (2. In a similar manner, 3-(1H-benzotriazol-1-yl-N,N-dimethylpropanamide, C11H14N4O (3, was prepared from benzotriazole and N,N-dimethylacrylamide. All three products have been structurally characterized by single-crystal X-ray diffraction. The crystal structures of 1 and 2 comprise infinite arrays formed by N—H...O and N—H...N bridges, as well as π–π interactions, while the molecules of 3 are aggregated to simple π-dimers in the crystal.

Constraining the Magmatic System at Mount St. Helens (2004-2008) Using Bayesian Inversion With Physics-Based Models Including Gas Escape and Crystallization

International Nuclear Information System (INIS)

Wong, Ying-Qi; Segall, Paul; Bradley, Andrew; Anderson, Kyle

2017-01-01

Physics-based models of volcanic eruptions track conduit processes as functions of depth and time. When used in inversions, these models permit integration of diverse geological and geophysical data sets to constrain important parameters of magmatic systems. We develop a 1-D steady state conduit model for effusive eruptions including equilibrium crystallization and gas transport through the conduit and compare with the quasi-steady dome growth phase of Mount St. Helens in 2005. Viscosity increase resulting from pressure-dependent crystallization leads to a natural transition from viscous flow to frictional sliding on the conduit margin. Erupted mass flux depends strongly on wall rock and magma permeabilities due to their impact on magma density. Including both lateral and vertical gas transport reveals competing effects that produce nonmonotonic behavior in the mass flux when increasing magma permeability. Using this physics-based model in a Bayesian inversion, we link data sets from Mount St. Helens such as extrusion flux and earthquake depths with petrological data to estimate unknown model parameters, including magma chamber pressure and water content, magma permeability constants, conduit radius, and friction along the conduit walls. Even with this relatively simple model and limited data, we obtain improved constraints on important model parameters. We find that the magma chamber had low (<5 wt %) total volatiles and that the magma permeability scale is well constrained at ~10 –11.4 m 2 to reproduce observed dome rock porosities. Here, compared with previous results, higher magma overpressure and lower wall friction are required to compensate for increased viscous resistance while keeping extrusion rate at the observed value.

X-ray yields from high-energy heavy ions channeled through a crystal: their crystal thickness and projectile dependences

International Nuclear Information System (INIS)

Kondo, C.; Takabayashi, Y.; Muranaka, T.; Masugi, S.; Azuma, T.; Komaki, K.; Hatakeyama, A.; Yamazaki, Y.; Takada, E.; Murakami, T.

2005-01-01

X-rays emitted from Ar 17+ , Fe 24+ and Kr 35+ ions of about 400 MeV/u transmitting through a thin Si crystal of about 20 μm thickness have been measured in a planar channeling condition and compared with those in a random incident condition. We have found that the X-ray yield from Ar 17+ ions is larger for the channeling condition than for the random incidence, while those from Fe 24+ and Kr 35+ ions are rather smaller. Such tendencies are explained by considering the projectile dependences of excitation and ionization probabilities together with X-ray emission rates. A crude simulation has qualitatively reproduced these experimental results. When the crystal thickness is small, the X-ray yield is smaller in the channeling condition than in the random incident condition, because excitation is depressed. However, for thicker crystals, the X-ray yield is larger, since the survived population of projectile-bound electrons is larger due to small ionization probabilities under the channeling condition. This inversion occurs at a specific crystal thickness depending on projectile species. Whether the thickness of the used crystal is smaller or larger than the inversion thickness determines enhancement or depression of the X-ray yield in the channeling condition

Association of atoms into universal dimers using an oscillating magnetic field.

Science.gov (United States)

Langmack, Christian; Smith, D Hudson; Braaten, Eric

2015-03-13

In a system of ultracold atoms near a Feshbach resonance, pairs of atoms can be associated into universal dimers by an oscillating magnetic field with a frequency near that determined by the dimer binding energy. We present a simple expression for the transition rate that takes into account many-body effects through a transition matrix element of the contact. In a thermal gas, the width of the peak in the transition rate as a function of the frequency is determined by the temperature. In a dilute Bose-Einstein condensate of atoms, the width is determined by the inelastic scattering rates of a dimer with zero-energy atoms. Near an atom-dimer resonance, there is a dramatic increase in the width from inelastic atom-dimer scattering and from atom-atom-dimer recombination. The recombination contribution provides a signature for universal tetramers that are Efimov states consisting of two atoms and a dimer.

Multiple regions of Harvey sarcoma virus RNA can dimerize in vitro.

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Feng, Y X; Fu, W; Winter, A J; Levin, J G; Rein, A

1995-04-01

Retroviruses contain a dimeric RNA consisting of two identical molecules of plus-strand genomic RNA. The structure of the linkage between the two monomers is not known, but they are believed to be joined near their 5' ends. Darlix and coworkers have reported that transcripts of retroviral RNA sequences can dimerize spontaneously in vitro (see, for example, E. Bieth, C. Gabus, and J. L. Darlix, Nucleic Acids Res. 18:119-127, 1990). As one approach to identification of sequences which might participate in the linkage, we have mapped sequences derived from the 5' 378 bases of Harvey sarcoma virus (HaSV) RNA which can dimerize in vitro. We found that at least three distinct regions, consisting of nucleotides 37 to 229, 205 to 272, and 271 to 378, can form these dimers. Two of these regions contain nucleotides 205 to 226; computer analysis suggests that this region can form a stem-loop with an inverted repeat in the loop. We propose that this hypothetical structure is involved in dimer formation by these two transcripts. We also compared the thermal stabilities of each of these dimers with that of HaSV viral RNA. Dimers of nucleotides 37 to 229 and 205 to 272 both exhibited melting temperatures near that of viral RNA, while dimers of nucleotides 271 to 378 are quite unstable. We also found that dimers of nucleotides 37 to 378 formed at 37 degrees C are less thermostable than dimers of the same RNA formed at 55 degrees C. It seems possible that bases from all of these regions participate in the dimer linkage present in viral RNA.

Dimerization of nitrophorin 4 at low pH and comparison to the K1A mutant of nitrophorin 1.

Science.gov (United States)

Berry, Robert E; Yang, Fei; Shokhireva, Tatiana K; Amoia, Angela M; Garrett, Sarah A; Goren, Allena M; Korte, Stephanie R; Zhang, Hongjun; Weichsel, Andrzej; Montfort, William R; Walker, F Ann

2015-01-20

Nitrophorin 4, one of the four NO-carrying heme proteins from the salivary glands of Rhodnius prolixus, forms a homodimer at pH 5.0 with a Kd of ∼8 μM. This dimer begins to dissociate at pH 5.5 and is completely dissociated to monomer at pH 7.3, even at 3.7 mM. The dimer is significantly stabilized by binding NO to the heme and at pH 7.3 would require dilution to well below 0.2 mM to completely dissociate the NP4-NO homodimer. The primary techniques used for investigating the homodimer and the monomer-dimer equilibrium were size-exclusion fast protein liquid chromatography at pH 5.0 and (1)H{(15)N} heteronuclear single-quantum coherence spectroscopy as a function of pH and concentration. Preparation of site-directed mutants of NP4 (A1K, D30A, D30N, V36A/D129A/L130A, K38A, R39A, K125A, K125E, D132A, L133V, and K38Q/R39Q/K125Q) showed that the N-terminus, D30, D129, D132, at least one heme propionate, and, by association, likely also E32 and D35 are involved in the dimerization. The "closed loop" form of the A-B and G-H flexible loops of monomeric NP4, which predominates in crystal structures of the monomeric protein reported at pH 5.6 but not at pH 7.5 and which involves all of the residues listed above except D132, is required for dimer formation. Wild-type NP1 does not form a homodimer, but NP1(K1A) and native N-terminal NP1 form dimers in the presence of NO. The homodimer of NP1, however, is considerably less stable than that of NP4 in the absence of NO. This suggests that additional aspartate or glutamate residues present in the C-terminal region of NP4, but not NP1, are also involved in stabilizing the dimer.

Kinetics of thymine dimer excision in ultraviolet-irradiated human cells

International Nuclear Information System (INIS)

Ehmann, U.K.; Cook, K.H.; Friedberg, E.C.

1978-01-01

We have investigated the kinetics of the loss of thymine dimers from the acid-insoluble fraction of several ultraviolet (uv)-irradiated cultured human cell lines. Our results show that uv fluences between 10 and 40 J/m 2 produce an average of 21 to 85 x 10 5 thymine dimers per cell and an eventual maximal loss per cell of 12 to 20 x 10 5 thymine dimers. The time for half-maximal loss of dimers ranged from 12 to 22 h after uv irradiation. In contrast, the time for half-maximal repair synthesis of DNA measured by autoradiography was 4.5 h. This figure agrees well with reported half-maximal repair synthesis times, which range from 0.5 to 3.6 h based on our analysis. The discrepancy in the kinetics of the loss of thymine dimers from DNA and repair synthesis is discussed in terms of possible molecular mechanisms of thymine dimer excision in vivo and in terms of possible experimental artifacts

Role of cyclobutane dimers in UV-denaturation of DNA

International Nuclear Information System (INIS)

Zavil'gel'skij, G.B.; Zuev, A.V.

1978-01-01

UV irradiation of double-stranded DNA produces local denatured regions. The evidence presented indicates that these single-stranded regions arise from photoproducts other than pyrimidine dimers. The irradiation of T2 DNA at 8x10 4 erg/mm 2 (254 nm) produces 6-8% thymine dimers, amd Tsub(mel) drops by 12-14 deg C, accompanied by a significant broadening of the transition profile. The kinetics of denatured region formation and lowering Tsub(mel) corresponds to that of formation of crosslinkages and differs markedly from the kinetics of formation of cyclobutane pyrimidine dimers. Treatment of UV-irradiated DNA with light in the presence of yeast photoreactivating enzyme monomerizes almost all thymine dimers but does not change the Tsub(mel). Local denatured regions are detected in UV-irradiated DNA and are absent from AcPhM-sensibilized DNA, which contains 20-25% thymine dimers, as determined by the accridine orange fluorescence technique. S1 nuclease from Aspergillis oryzae produces single-strand breaks in UV-irradiated DNA of phage PM2 but is not active on AcPhM-treated PM2 DNA, which contains about 50 thymine dimers. It is supposed that the formation of a cyclobutane dimer only weakens the hydrogen bonds in the AT base pair rather than breaks them. Local denatured regions are thought to arise from the accumulation in UV-irradiated DNA (254 nm) of the sufficient number of photoproducts with impaired ability to base pairing

Opal shell structures: direct assembly versus inversion approach.

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Deng, Tian-Song; Sharifi, Parvin; Marlow, Frank

2013-09-16

Opal shell structures can be fabricated in two ways: By direct assembly from hollow spheres (hs-opal) or by infiltration of precursors into opal templates and inversion. The resulting lattice disturbances were characterized by scanning electron microscopy (SEM), optical microscopy, and transmission spectra. The hs-opal system shows much lower disturbances, for example, a lower number of cracks and lattice deformations. The strong suppression of crack formation in one of these inverse opal structures can be considered as promising candidates for the fabrication of more perfect photonic crystals. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Characterization of oxygen dimer-enriched silicon detectors

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Boisvert, V; Moll, M; Murin, L I; Pintilie, I

2005-01-01

Various types of silicon material and silicon p+n diodes have been treated to increase the concentration of the oxygen dimer (O2i) defect. This was done by exposing the bulk material and the diodes to 6 MeV electrons at a temperature of about 350 °C. FTIR spectroscopy has been performed on the processed material confirming the formation of oxygen dimer defects in Czochralski silicon pieces. We also show results from TSC characterization on processed diodes. Finally, we investigated the influence of the dimer enrichment process on the depletion voltage of silicon diodes and performed 24 GeV/c proton irradiations to study the evolution of the macroscopic diode characteristics as a function of fluence.

Dimeric Surfactants: Promising Ingredients of Cosmetics and Toiletries

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Naveen Kumar

2013-11-01

Full Text Available Surfactants are an essential ingredient for cosmetic, toiletries and personal care products for enhancing their performance. Dimeric surfactants demonstrate superiority compared to conventional surfactants in all areas of application. Dimeric surfactants are extremely promising for utilization in various cosmetic formulations viz. shampoo, lotions, creams, conditioners etc. These surfactants possess extremely unique surface properties viz. lower surface tension, unique micellization, low critical micelle concentration (CMC and antimicrobial activity, higher solubilization etc. Dimerics enhance the performances of cosmetics in an extraordinary manner and provide eco-friendly preparations for human epidermis.

Controlling chirality with helix inversion in cholesteric liquid crystals

NARCIS (Netherlands)

Katsonis, Nathalie Hélène; Lacaze, E.; Ferrarini, A.

2012-01-01

The helical organization of cholesteric liquid crystals is omnipresent in living matter. Achieving control over the structure of the cholesteric helix consequently holds great potential for developing stimuli-responsive materials matching the level of sophistication of biological systems. In

Tunable photoluminescent materials based on two phenylcarbazole-based dimers through the substituent groups

Energy Technology Data Exchange (ETDEWEB)

Tang, Gui-Mei, E-mail: meiguit@163.com; Chi, Rui-Hai; Wan, Wen-Zhu; Chen, Zhi-Qiang; Yan, Ting-Xiang; Dong, Yan-Ping; Wang, Yong-Tao, E-mail: ceswyt@qlu.edu.cn; Cui, Yue-Zhi

2017-05-15

Two phenylcarbazole-based dimers, namely, 9,9'-diphenyl-9H,9'H−3,3'-bicarbazole (1) and 9,9'-bis(4-bromophenyl)−9H,9'H−3,3'-bicarbazole (2), have been obtained through the oxidation of 9-phenylcarbazole and 9-(4’-bromophenyl) in the presence of FeCl{sub 3}, respectively, which show strong photoluminescent properties with the fluorescence quantum yields of 0.2 and 0.21 based on the reference of Quinin sulfate, respectively. The maximal emission peak of compounds 1 and 2 were observed at 465 and 413 nm in the solid state, respectively, revealing that the luminescent properties were tuned by the substituent group. The title compounds were characterized by FI-IR, UV–vis, {sup 1}H-NMR, {sup 13}C-NMR, {sup 1}H−{sup 13}C NMR, mass spectra, elemental analysis (EA) and single-crystal X-ray diffraction. Both compounds 1 and 2 crystallize in space group P-1, and supramolecular hydrogen bondings and stacking interactions between aromatic rings are observed. Compounds 1 and 2 display trans- and cis-formation structures, respectively. Two compounds show high thermal stabilities, in which the decomposition temperature is 414 and 363 °C for 1 and 2, respectively. - Graphical abstract: Two phenylcarbazole-based dimers have been obtained through the oxidation of 9-phenylcarbazole and 9-(4’-bromophenyl) in the presence of FeCl{sub 3}, respectively. The maximal emission peaks of compounds 1 and 2 were observed at 465 and 413 nm, respectively, revealing that the luminescent properties were tuned by the substituent group. Compounds 1 and 2 display trans- and cis-formation structures, respectively, and they show high thermal stabilities.

Two Populations Mean-Field Monomer-Dimer Model

Science.gov (United States)

Alberici, Diego; Mingione, Emanuele

2018-04-01

A two populations mean-field monomer-dimer model including both hard-core and attractive interactions between dimers is considered. The pressure density in the thermodynamic limit is proved to satisfy a variational principle. A detailed analysis is made in the limit of one population is much smaller than the other and a ferromagnetic mean-field phase transition is found.

The nature of the [TTF]˙+···[TTF]˙+ interactions in the [TTF]2(2+) dimers embedded in charged [3]catenanes: room-temperature multicenter long bonds.

Science.gov (United States)

Capdevila-Cortada, Marçal; Novoa, Juan J

2012-04-23

The properties of tetrathiafulvalene dimers ([TTF](2)(2+)) and the functionalized ring-shaped bispropargyl (BPP)-functionalized TTF dimers, [BPP-TTF](2)(2+), found at room temperature in charged [3]catenanes, were evaluated by M06L calculations. The results showed that their isolated [TTF](2)(2+) and [BPP-TTF](2)(2+) dimers are energetically unstable towards dissociation. When enclosed in the 4(+)-charged central cyclophane ring of charged [3]catenanes (CBPQT(4+)), [TTF](2)(2+) and [BPP-TTF](2)(2+) dimers are also energetically unstable with respect to leaving the CBPQT(4+) ring; since the barrier for the exiting process is only about 3 kcal mol(-1), that is, within the reach of thermal energies at room temperature (neutral [TTF](2)(0) dimers are stable within the CBPQT(4+) ring). However, the [BPP-TTF](2)(2+) dimers in charged [3]catenanes cannot exit, because this would imply breaking the covalent bonds of the BPP-TTF(+) macrocycle. Finally, it was shown that the [TTF](2)(2+), [BPP-TTF](2)(2+) dimers, and charged [3]catenanes are energetically stable in solution and in crystals of their salts, in the first case due to the interactions with the solvent, and in the second case mostly due to cation-anion interactions. In these environmental conditions at room temperature the TTF units of the [BPP-TTF](2)(2+) dimers make short contacts, thus allowing their SOMO orbitals to overlap: a room-temperature multicenter long bond is formed, similar to those previously found in other [TTF](2)(2+) salts and their solutions. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Crystallization and preliminary X-ray characterization of prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis

International Nuclear Information System (INIS)

Nakajima, Yoshitaka; Ito, Kiyoshi; Xu, Yue; Yamada, Nozomi; Onohara, Yuko; Ito, Takashi; Yoshimoto, Tadashi

2005-01-01

P. gingivalis prolyl tripeptidyl aminopeptidase has been crystallized by the vapour-diffusion method. Diffraction data have been collected and processed to 2.1 Å resolution. A recombinant form of prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis has been crystallized by the hanging-drop vapour-diffusion method using potassium sodium tartrate as a precipitating agent. The crystals belong to the hexagonal space group P6 3 22, with unit-cell parameters a = b = 149.4, c = 159.7 Å. The crystals are most likely to contain one subunit of a dimer in the asymmetric unit, with a V M value of 3.14 Å 3 Da −1 . Diffraction data were collected to 2.1 Å resolution using synchrotron radiation at the BL5 station of the Photon Factory

Evaluation of Serum D-dimer Levels in Children with Pneumonia

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Nilgün Selçuk Duru

2016-03-01

Full Text Available Aim: The aim of this study was to investigate the relationship of plasma D-dimer levels with duration of hospitalization and radiological and laboratory findings in patients with pneumonia. Methods: Forty-seven patients with pneumonia (31 boys and 16 girls, mean age: 4.2±4.7 years were included in the study. The patients were divided into two groups according to duration of hospitalization and three groups according to radiological findings. D-dimer and other laboratory findings were compared between the groups. Results: The mean serum D-dimer level was 1333.5±1364.4 ng/L. There was no statistically significant difference in D-dimer, leukocyte, erythrocyte sedimentation rate (ESR and C-reactive protein (CRP between the groups divided according to duration of hospitalization. In addition, there was no statistically difference in D-dimer levels between the groups divided according to radiological findings. Age, percentage of neutrophils, ESR and fibrinogen levels were higher in patients with lobar pneumonia when compared with the other groups and CRP level was higher in lobar pneumonia group when compared to interstitial pneumonia group. D-dimer levels were negatively correlated with age and positively correlated with ESR, CRP, and fibrinogen. Conclusion: In our study, D-dimer levels were high in patient with pneumonia. Further studies with a larger number of patients are necessary to determine the role of D-dimer levels as an acutephase reactant in patients with pneumonia

Electron transfer reactions induced by the triplet state of thiacarbocyanine dimers

International Nuclear Information System (INIS)

Chibisov, Alexander K.; Slavnova, Tatyana D.; Goerner, Helmut

2004-01-01

The photoinduced electron transfer between either cationic 5,5 ' -dichloro-3,3 ' ,9-triethylthiacarbocyanine (1) or a structurally similar anionic dye (2) and appropriate donors, e.g. ascorbic acid, and acceptors, e.g. methyl viologen, was studied by ns-laser photolysis. In aqueous solution the dyes in the ground state are present as an equilibrated mixture of dimers and monomers, whereas the triplet state is mainly populated from dimers. The triplet states of both dimers and monomers are quenched by electron donors or acceptors and the rate constant for quenching is generally 2-4 times higher for dimers than for monomers. The kinetics of triplet decay and radical formation and decay as a result of primary and secondary electron transfer were analyzed. While the one-electron reduced dimer decays due to back reactions, the one-electron oxidized dimer rapidly dissociates into the monomer and the monomeric dye radical. For the dimeric dye/donor/acceptor systems the primary photoinduced electron transfer occurs either from the donor or to the acceptor yielding the dimeric dye radicals. The one-electron reduced dimer can be efficiently oxidized by acceptors, e.g. the rate constant for reaction of the dimeric dye radical of 1 with methyl viologen (photoreductive pathway of sensitization) is 1.6x10 9 M -1 s -1 . The photooxidative pathway of sensitization is more complicated; after dissociation of the dimeric dye radical, the monomeric dye radical is reduced in a secondary electron transfer from ascorbic acid, e.g. with a rate constant of 1x10 9 M -1 s -1 for 2, yielding the monomer. On increasing the donor concentration the photooxidative pathway of sensitization is switched to a photoreductive one

Structure and interactions of a dimeric variant of sHIP, a novel virulence determinant of Streptococcus pyogenes

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Carl eDiehl

2016-02-01

Full Text Available Streptococcus pyogenes is one of the most significant bacterial pathogens in the human population mostly causing superficial and uncomplicated infections (pharyngitis and impetigo but also invasive and life-threatening disease. We have previously identified a virulence determinant, protein sHIP, which is secreted at higher levels by an invasive compared to a non-invasive strain of S. pyogenes. The present work presents a further characterization of the structural and functional properties of this bacterial protein. Biophysical and structural studies have shown that protein sHIP forms stable tetramers both in the crystal and in solution. The tetramers are composed of four helix-loop-helix motifs with the loop regions connecting the helices displaying a high degree of flexibility. Owing to interactions at the tetramer interface, the observed tetramer can be described as a dimer of dimers. We identified three residues at the tetramer interface (Leu84, Leu88, Tyr95, which due to largely non-polar side-chains, could be important determinants for protein oligomerization. Based on these observations, we produced a sHIP variant in which these residues were mutated to alanines. Biophysical experiments clearly indicated that the sHIP mutant appear only as dimers in solution confirming the importance of the interfacial residues for protein oligomerisation. Furthermore, we could show that the sHIP mutant interacts with intact histidine-rich glycoprotein (HRG and the histidine-rich repeats in HRG, and inhibits their antibacterial activity to the same or even higher extent as compared to the wild type protein sHIP. We determined the crystal structure of the sHIP mutant, which, as a result of the high quality of the data, allowed us to improve the existing structural model of the protein. Finally, by employing NMR spectroscopy in solution, we generated a model for the complex between the sHIP mutant and an HRG-derived heparin-binding peptide, providing further

The crystal structure of the regulatory domain of the human sodium-driven chloride/bicarbonate exchanger.

Science.gov (United States)

Alvadia, Carolina M; Sommer, Theis; Bjerregaard-Andersen, Kaare; Damkier, Helle Hasager; Montrasio, Michele; Aalkjaer, Christian; Morth, J Preben

2017-09-21

The sodium-driven chloride/bicarbonate exchanger (NDCBE) is essential for maintaining homeostatic pH in neurons. The crystal structure at 2.8 Å resolution of the regulatory N-terminal domain of human NDCBE represents the first crystal structure of an electroneutral sodium-bicarbonate cotransporter. The crystal structure forms an equivalent dimeric interface as observed for the cytoplasmic domain of Band 3, and thus establishes that the consensus motif VTVLP is the key minimal dimerization motif. The VTVLP motif is highly conserved and likely to be the physiologically relevant interface for all other members of the SLC4 family. A novel conserved Zn 2+ -binding motif present in the N-terminal domain of NDCBE is identified and characterized in vitro. Cellular studies confirm the Zn 2+ dependent transport of two electroneutral bicarbonate transporters, NCBE and NBCn1. The Zn 2+ site is mapped to a cluster of histidines close to the conserved ETARWLKFEE motif and likely plays a role in the regulation of this important motif. The combined structural and bioinformatics analysis provides a model that predicts with additional confidence the physiologically relevant interface between the cytoplasmic domain and the transmembrane domain.

Tunneling anisotropic magnetoresistance via molecular π orbitals of Pb dimers

Science.gov (United States)

Schöneberg, Johannes; Ferriani, Paolo; Heinze, Stefan; Weismann, Alexander; Berndt, Richard

2018-01-01

Pb dimers on a ferromagnetic surface are shown to exhibit large tunneling anisotropic magnetoresistance (TAMR) due to molecular π orbitals. Dimers oriented differently with respect to the magnetization directions of a ferromagnetic Fe double layer on W(110) were made with a scanning tunneling microscope. Depending on the dimer orientations, TAMR is absent or as large as 20% at the Fermi level. General arguments and first-principles calculations show that mixing of molecular orbitals due to spin-orbit coupling, which leads to TAMR, is maximal when the magnetization is oriented parallel to the dimer axis.

VUV spectroscopy of rare gas van der Waals dimers

International Nuclear Information System (INIS)

Dehmer, P.M.; Pratt, S.T.

1982-01-01

We have undertaken a systematic study of the photoionization spectra of the homonuclear and heteronuclear rare gas dimers in order to better understand the nature of the bonding in the Rydberg states adnd ions of these molecules. We have obtained results for Ar 2 , Kr 2 , Xe 2 , NeAr, NeKr, NeXe, ArKr, ArXe, and KrXe. Of the remaining dimer species (Ne 2 and the Herare gas dimers), only Ne 2 has been studied using photoionization mass spectrometry. The results of the present series of experiments provide information both on the excited states of the neutral dimers and on the ground and excited states of the dimer ions. Using the data obtained in these measurements, we are able to compile for the first time a nearly complete list of ground state dissociation energies for the homonuclear and heteronuclear rare gas dimer ions. Somewhat less complete results are obtained for the excited states of these species. The observed trends in binding energy provide an excellent example of the systematic changes that occur as a result of changes in atomic orbital energies, polarizability, and internuclear distance, and these trends can be explained qualitatively in terms of simple molecular orbital theory

The Role of Antisymmetric Exchange on the Quantum Interference between States of Different Spin Length in a dimeric Molecular Nanomagnet.

Science.gov (United States)

Del Barco, Enrique

2009-03-01

We report direct evidence of quantum oscillations of the total spin length of a dimeric molecular nanomagnet through the observation of quantum interference associated with tunneling trajectories between states having different spin quantum numbers. As we outline, this is a consequence of the unique characteristics of a molecular Mn12 wheel which behaves as a (weak) ferromagnetic exchange-coupled molecular dimer: each half of the molecule acts as a single-molecule magnet (SMM), while the weak coupling between the two halves gives rise to an additional internal spin degree of freedom within the molecule, namely that its total spin may fluctuate. This extra degree of freedom accounts for several magnetization tunneling resonances that cannot be explained within the usual giant spin approximation. More importantly, the observation of quantum interference provides unambiguous evidence for the quantum mechanical superposition involving entangled states of both halves of the wheel. Magnetization results obtained in two other versions of this compound, in which the ligands have been modified, show that slight variations of the relative distance between the Mn ions determine whether the molecule behaves as a rigid magnetic unit of spin S = 7 or as two exchange-coupled halves of spin S = 7/2. We analyze the effect of the Dzyaloshinskii-Moriya antisymmetric exchange interaction in a molecule with a centre of inversion symmetry and propose a formal model to account for the observed broken degeneracy that preserves the molecular inversion symmetry.

Structure and spectroscopic properties of N,S-coordinating 2-methyl-sulfanyl-N-[(1H-pyrrol-2-yl)methyl-idene]aniline methanol monosolvate.

Science.gov (United States)

Richards, D Douglas; Ang, M Trisha C; McDonald, Robert; Bierenstiel, Matthias

2015-10-01

The reaction of pyrrole-2-carboxaldehyde and 2-(methyl-sulfan-yl)aniline in refluxing methanol gave an olive-green residue in which yellow crystals of the title compound, C12H12N2S·CH3OH, were grown from slow evaporation of methanol at 263 K. In the crystal, hydrogen-bonding inter-actions link the aniline mol-ecule and a nearby methanol solvent mol-ecule. These units are linked by a pair of weak C-H⋯Omethanol interactions, forming inversion dimers consisting of two main molecules and two solvent molecules.

Methyl (2Z-2-{[N-(2-formylphenyl-4-methylbenzenesulfonamido]methyl}-3-(naphthalen-1-ylprop-2-enoate

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R. Madhanraj

2012-02-01

Full Text Available In the title compound, C29H25NO5S, the sulfonyl-bound benzene ring forms dihedral angles of 42.1 (1 and 48.5 (1°, respectively, with the formyl-substituted benzene ring and the naphthalene residue. In the crystal, pairs of C—H...O interactions lead to the formation of R22(10 inversion dimers, which are linked by further C—H...O interactions into supramolecular tapes running along [100]. The crystal packing is further stabilized by C—H...π interactions.

Structure and spectroscopic properties of N,S-coordinating 2-methylsulfanyl-N-[(1H-pyrrol-2-ylmethylidene]aniline methanol monosolvate

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D. Douglas Richards

2015-10-01

Full Text Available The reaction of pyrrole-2-carboxaldehyde and 2-(methylsulfanylaniline in refluxing methanol gave an olive-green residue in which yellow crystals of the title compound, C12H12N2S·CH3OH, were grown from slow evaporation of methanol at 263 K. In the crystal, hydrogen-bonding interactions link the aniline molecule and a nearby methanol solvent molecule. These units are linked by a pair of weak C—H...Omethanol interactions, forming inversion dimers consisting of two main molecules and two solvent molecules.

Pair Interaction of Catalytical Sphere Dimers in Chemically Active Media

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Jing-Min Shi

2018-01-01

Full Text Available We study the pair dynamics of two self-propelled sphere dimers in the chemically active medium in which a cubic autocatalytic chemical reaction takes place. Concentration gradient around the dimer, created by reactions occurring on the catalytic sphere surface and responsible for the self-propulsion, is greatly influenced by the chemical activities of the environment. Consequently, the pair dynamics of two dimers mediated by the concentration field are affected. In the particle-based mesoscopic simulation, we combine molecular dynamics (MD for potential interactions and reactive multiparticle collision dynamics (RMPC for solvent flow and bulk reactions. Our results indicate three different configurations between a pair of dimers after the collision, i.e., two possible scenarios of bound dimer pairs and one unbound dimer pair. A phase diagram is sketched as a function of the rate coefficients of the environment reactions. Since the pair interactions are the basic elements of larger scale systems, we believe the results may shed light on the understanding of the collective dynamics.

Subsurface dimerization in III-V semiconductor (001) surfaces

DEFF Research Database (Denmark)

Kumpf, C.; Marks, L.D.; Ellis, D.

2001-01-01

We present the atomic structure of the c(8 X 2) reconstructions of InSb-, InAs-, and GaAs-(001) surfaces as determined by surface x-ray diffraction using direct methods. Contrary to common belief, group III dimers are not prominent on the surface, instead subsurface dimerization of group m atoms ...... takes place in the second bilayer, accompanied by a major rearrangement of the surface atoms above the dimers to form linear arrays. By varying the occupancies of four surface sites the (001)-c(8 X 2) reconstructions of III-V semiconductors can be described in a unified model....

The water dimer II: Theoretical investigations

Energy Technology Data Exchange (ETDEWEB)

Mukhopadhyay, Anamika; Xantheas, Sotiris S.; Saykally, Richard J.

2018-03-29

As the archetype of hydrogen bonding between water molecules, the water dimer has been extensively studied by both theory and experiment for nearly seven decades. In this article, we present a detailed chronological review of the theoretical advances using electronic structure methods pertaining to the structure, hydrogen bonding and vibrational spectroscopy of the water dimer as well as the role of its potential energy surface in the development of classical force fields to describe intermolecular interaction in clusters and liquid water.

In Situ Structural Characterization of Ferric Iron Dimers in Aqueous Solutions

DEFF Research Database (Denmark)

Zhu, Mengqiang; Puls, Brendan W.; Frandsen, Cathrine

2013-01-01

The structure of ferric iron (Fe3+) dimers in aqueous solutions has long been debated. In this work, we have determined the dimer structure in situ in aqueous solutions using extended X-ray absorption fine structure (EXAFS) spectroscopy. An Fe K-edge EXAFS analysis of 0.2 M ferric nitrate solutions...... at pH 1.28–1.81 identified a Fe–Fe distance at ∼3.6 Å, strongly indicating that the dimers take the μ-oxo form. The EXAFS analysis also indicates two short Fe–O bonds at ∼1.80 Å and ten long Fe–O bonds at ∼2.08 Å, consistent with the μ-oxo dimer structure. The scattering from the Fe–Fe paths interferes...... confirmed by Mössbauer analyses of analogous quick frozen solutions. This work also explores the electronic structure and the relative stability of the μ-oxo dimer in a comparison to the dihydroxo dimer using density function theory (DFT) calculations. The identification of such dimers in aqueous solutions...

The purification, crystallization and preliminary structural characterization of PhzM, a phenazine-modifying methyltransferase from Pseudomonas aeruginosa

International Nuclear Information System (INIS)

Gohain, Neelakshi; Thomashow, Linda S.; Mavrodi, Dmitri V.; Blankenfeldt, Wulf

2006-01-01

PhzM, an S-adenosylmethionine-dependent methyltransferase enzyme that catalyzes a reaction involved in the biosynthesis of pyocyanin in P. aeruginosa, was cloned, overexpressed and crystallized. Data collection from native and selenomethionine-labelled crystals is reported. Pyocyanin, phenazine-1-carboxylic acid and more than 70 related compounds collectively known as phenazines are produced by various species of Pseudomonas, including the fluorescent pseudomonad P. aeruginosa, a Gram-negative opportunistic pathogen in humans and animals. P. aeruginosa synthesizes a characteristic blue water-soluble compound called pyocyanin (1-hydroxy-5-methyl-phenazine). Two enzymes designated PhzM and PhzS are involved in the terminal steps of its synthesis and very little is known about these enzymes. In this study, PhzM, a dimeric S-adenosylmethionine-dependent methyltransferase, was purified and crystallized from PEG 3350/sodium cacodylate/sodium citrate pH 6.5. The crystals belong to space group P1, with unit-cell parameters a = 46.1, b = 61.8, c = 69.6 Å, α = 96.3, β = 106.6, γ = 106.9°. They contain one dimer in the asymmetric unit and diffract to a resolution of 1.8 Å. Anomalous data to 2.3 Å resolution have been collected from seleno-l-methionine-labelled PhzM

3-Ethyl-4-[(E-(4-fluorobenzylideneamino]-1H-1,2,4-triazole-5(4H-thione

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Alphonsus D'souza

2012-05-01

Full Text Available In the title compound, C11H11FN4S, the dihedral angle between the 1,2,4-triazole ring and the benzene ring is 25.04 (12° and an intramoleuclar C—H...S interaction leads to an S(6 ring. In the crystal, inversion dimers linked by pairs of N—H...S hydrogen bonds generate R22(8 loops.

Crystal structures of a manganese(I and a rhenium(I complex of a bipyridine ligand with a non-coordinating benzoic acid moiety

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Sheri Lense

2018-05-01

Full Text Available The structures of two facially coordinated Group VII metal complexes are reported, namely: fac-bromido[2-(2,2′-bipyridin-6-ylbenzoic acid-κ2N,N′]tricarbonylmanganese(I tetrahydrofuran monosolvate, [MnBr(C17H12N2O2(CO3]·C4H8O, I, and fac-[2-(2,2′-bipyridin-6-ylbenzoic acid-κ2N,N′]tricarbonylchloridorhenium(I tetrahydrofuran monosolvate, [ReCl(C17H12N2O2(CO3]·C4H8O, II. In both complexes, the metal ion is coordinated by three carbonyl ligands, a halide ion, and a 2-(2,2′-bipyridin-6-ylbenzoic acid ligand, in a distorted octahedral geometry. In manganese complex I, the tetrahydrofuran (THF solvent molecule could not be refined due to disorder. The benzoic acid fragment is also disordered over two positions, such that the carboxylic acid group is either positioned near to the bromide ligand or to the axial carbonyl ligand. In the crystal of I, the complex molecules are linked by a pair of C—H...Br hydrogen bonds, forming inversion dimers that stack up the a-axis direction. In the rhenium complex II, there is hydrogen bonding between the benzoic acid moiety and a disordered co-crystallized THF molecule. In the crystal, the molecules are linked by C—H...Cl hydrogen bonds, forming layers parallel to (100 separated by layers of THF solvent molecules.

Purification, crystallization and preliminary crystallographic studies of plant S-adenosyl-l-homocysteine hydrolase (Lupinus luteus)

Energy Technology Data Exchange (ETDEWEB)

Brzezinski, Krzysztof [Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan (Poland); Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan (Poland); Bujacz, Grzegorz [Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan (Poland); Faculty of Food Chemistry and Biotechnology, Technical University of Lodz (Poland); Jaskolski, Mariusz, E-mail: mariuszj@amu.edu.pl [Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan (Poland); Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan (Poland)

2008-07-01

Single crystals of recombinant S-adenosyl-l-homocysteine hydrolase from L. luteus in complex with adenosine diffract X-rays to 1.17 Å resolution at 100 K. The crystals are tetragonal, space group P4{sub 3}2{sub 1}2, and contain one copy of the dimeric enzyme in the asymmetric unit. By degrading S-adenosyl-l-homocysteine, which is a byproduct of S-adenosyl-l-methionine-dependent methylation reactions, S-adenosyl-l-homocysteine hydrolase (SAHase) acts as a regulator of cellular methylation processes. S-Adenosyl-l-homocysteine hydrolase from the leguminose plant yellow lupin (Lupinus luteus), LlSAHase, which is composed of 485 amino acids and has a molecular weight of 55 kDa, has been cloned, expressed in Escherichia coli and purified. Crystals of LlSAHase in complex with adenosine were obtained by the hanging-drop vapour-diffusion method using 20%(w/v) PEG 4000 and 10%(v/v) 2-propanol as precipitants in 0.1 M Tris–HCl buffer pH 8.0. The crystals were tetragonal, space group P4{sub 3}2{sub 1}2, with unit-cell parameters a = 122.4, c = 126.5 Å and contained two protein molecules in the asymmetric unit, corresponding to the functional dimeric form of the enzyme. Atomic resolution (1.17 Å) X-ray diffraction data have been collected using synchrotron radiation.

Purification, crystallization and preliminary crystallographic studies of plant S-adenosyl-l-homocysteine hydrolase (Lupinus luteus)

International Nuclear Information System (INIS)

Brzezinski, Krzysztof; Bujacz, Grzegorz; Jaskolski, Mariusz

2008-01-01

Single crystals of recombinant S-adenosyl-l-homocysteine hydrolase from L. luteus in complex with adenosine diffract X-rays to 1.17 Å resolution at 100 K. The crystals are tetragonal, space group P4 3 2 1 2, and contain one copy of the dimeric enzyme in the asymmetric unit. By degrading S-adenosyl-l-homocysteine, which is a byproduct of S-adenosyl-l-methionine-dependent methylation reactions, S-adenosyl-l-homocysteine hydrolase (SAHase) acts as a regulator of cellular methylation processes. S-Adenosyl-l-homocysteine hydrolase from the leguminose plant yellow lupin (Lupinus luteus), LlSAHase, which is composed of 485 amino acids and has a molecular weight of 55 kDa, has been cloned, expressed in Escherichia coli and purified. Crystals of LlSAHase in complex with adenosine were obtained by the hanging-drop vapour-diffusion method using 20%(w/v) PEG 4000 and 10%(v/v) 2-propanol as precipitants in 0.1 M Tris–HCl buffer pH 8.0. The crystals were tetragonal, space group P4 3 2 1 2, with unit-cell parameters a = 122.4, c = 126.5 Å and contained two protein molecules in the asymmetric unit, corresponding to the functional dimeric form of the enzyme. Atomic resolution (1.17 Å) X-ray diffraction data have been collected using synchrotron radiation

Investigations of interhydrogen bond dynamical coupling effects in the polarized IR spectra of acetanilide crystals.

Science.gov (United States)

Flakus, Henryk T; Michta, Anna

2010-02-04

This Article presents the investigation results of the polarized IR spectra of the hydrogen bond in acetanilide (ACN) crystals measured in the frequency range of the proton and deuteron stretching vibration bands, nu(N-H) and nu(N-D). The basic spectral properties of the crystals were interpreted quantitatively in terms of the "strong-coupling" theory. The model of the centrosymmetric dimer of hydrogen bonds postulated by us facilitated the explanation of the well-developed, two-branch structure of the nu(N-H) and nu(N-D) bands as well as the isotopic dilution effects in the spectra. On the basis of the linear dichroic and temperature effects in the polarized IR spectra of ACN crystals, the H/D isotopic "self-organization" effects were revealed. A nonrandom distribution of hydrogen isotope atoms (H or D) in the lattice was deduced from the spectra of isotopically diluted ACN crystals. It was also determined that identical hydrogen isotope atoms occupy both hydrogen bonds in the dimeric systems, where each hydrogen bond belongs to a different chain. A more complex fine structure pattern of nu(N-H) and nu(N-D) bands in ACN spectra in comparison with the spectra of other secondary amides (e.g., N-methylacetamide) can be explained in terms of the "relaxation" theory of the IR spectra of hydrogen-bonded systems.

Crystal structure of 4,6-diamino-2,2-dimethyl-3-[3-(2,4,5-trichlorophenoxypropoxy]-2,3-dihydro-1,3,5-triazin-1-ium chloride methanol monosolvate

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Pattarapol Khongsuk

2015-08-01

Full Text Available In the title methanol-solvated salt, C14H19Cl3N5O2+·Cl−·CH3OH, the triazine molecule is protonated at one of the triazine N atoms. In the crystal, the triazine cations are linked through a pair of N—H...N hydrogen bonds, with graph-set R22(8, forming an inversion dimer. The protonated N atom and the 2- and 4-amino groups of the triazine cation interact with the chloride anion through N—H...Cl hydrogen bonds, leading to the formation of a tape structure running along the b-axis direction. A short Cl...Cl contact [3.2937 (9 Å] is observed in the tape. The methanol molecule is linked to the chloride anion and the triazine cation, respectively, by an O—H...Cl hydrogen bond and a C—H...O interaction.

Structure of a novel shoulder-to-shoulder p24 dimer in complex with the broad-spectrum antibody A10F9 and its implication in capsid assembly.

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Ying Gu

Full Text Available Mature HIV-1 viral particles assemble as a fullerene configuration comprising p24 capsid hexamers, pentamers and dimers. In this paper, we report the X-ray crystal structures of the p24 protein from natural HIV-1 strain (BMJ4 in complex with Fab A10F9, which recognizes a conserved epitope in the C-terminal domain of the BMJ4 p24 protein. Our structures reveal a novel shoulder-to-shoulder p24 dimerization mode that is mediated by an S-S bridge at C177. Consistent with these structures, the shoulder-to-shoulder dimer that was obtained from the BMJ4 strain was also observed in p24 proteins from other strains by the introduction of a cysteine residue at position 177. The potential biological significance was further validated by the introduction of a C177A mutation in the BMJ4 strain, which then displays a low infectivity. Our data suggest that this novel shoulder-to-shoulder dimer interface trapped by this unique S-S bridge could represent a physiologically relevant mode of HIV-1 capsid assembly during virus maturation, although Cys residue itself may not be critical for HIV-I replication.

SOXE transcription factors form selective dimers on non-compact DNA motifs through multifaceted interactions between dimerization and high-mobility group domains.

Science.gov (United States)

Huang, Yong-Heng; Jankowski, Aleksander; Cheah, Kathryn S E; Prabhakar, Shyam; Jauch, Ralf

2015-05-27

The SOXE transcription factors SOX8, SOX9 and SOX10 are master regulators of mammalian development directing sex determination, gliogenesis, pancreas specification and neural crest development. We identified a set of palindromic SOX binding sites specifically enriched in regulatory regions of melanoma cells. SOXE proteins homodimerize on these sequences with high cooperativity. In contrast to other transcription factor dimers, which are typically rigidly spaced, SOXE group proteins can bind cooperatively at a wide range of dimer spacings. Using truncated forms of SOXE proteins, we show that a single dimerization (DIM) domain, that precedes the DNA binding high mobility group (HMG) domain, is sufficient for dimer formation, suggesting that DIM : HMG rather than DIM:DIM interactions mediate the dimerization. All SOXE members can also heterodimerize in this fashion, whereas SOXE heterodimers with SOX2, SOX4, SOX6 and SOX18 are not supported. We propose a structural model where SOXE-specific intramolecular DIM:HMG interactions are allosterically communicated to the HMG of juxtaposed molecules. Collectively, SOXE factors evolved a unique mode to combinatorially regulate their target genes that relies on a multifaceted interplay between the HMG and DIM domains. This property potentially extends further the diversity of target genes and cell-specific functions that are regulated by SOXE proteins.

SOXE transcription factors form selective dimers on non-compact DNA motifs through multifaceted interactions between dimerization and high-mobility group domains

Science.gov (United States)

Huang, Yong-Heng; Jankowski, Aleksander; Cheah, Kathryn S. E.; Prabhakar, Shyam; Jauch, Ralf

2015-01-01

The SOXE transcription factors SOX8, SOX9 and SOX10 are master regulators of mammalian development directing sex determination, gliogenesis, pancreas specification and neural crest development. We identified a set of palindromic SOX binding sites specifically enriched in regulatory regions of melanoma cells. SOXE proteins homodimerize on these sequences with high cooperativity. In contrast to other transcription factor dimers, which are typically rigidly spaced, SOXE group proteins can bind cooperatively at a wide range of dimer spacings. Using truncated forms of SOXE proteins, we show that a single dimerization (DIM) domain, that precedes the DNA binding high mobility group (HMG) domain, is sufficient for dimer formation, suggesting that DIM : HMG rather than DIM:DIM interactions mediate the dimerization. All SOXE members can also heterodimerize in this fashion, whereas SOXE heterodimers with SOX2, SOX4, SOX6 and SOX18 are not supported. We propose a structural model where SOXE-specific intramolecular DIM:HMG interactions are allosterically communicated to the HMG of juxtaposed molecules. Collectively, SOXE factors evolved a unique mode to combinatorially regulate their target genes that relies on a multifaceted interplay between the HMG and DIM domains. This property potentially extends further the diversity of target genes and cell-specific functions that are regulated by SOXE proteins. PMID:26013289

Three-Dimensional Inverse Opal Photonic Crystal Substrates toward Efficient Capture of Circulating Tumor Cells.

Science.gov (United States)

Xu, Hongwei; Dong, Biao; Xiao, Qiaoqin; Sun, Xueke; Zhang, Xinran; Lyu, Jiekai; Yang, Yudan; Xu, Lin; Bai, Xue; Zhang, Shuang; Song, Hongwei

2017-09-13

Artificial fractal structures have attracted considerable scientific interest in circulating tumor cells (CTCs) detection and capture, which plays a pivotal role in the diagnosis and prognosis of cancer. Herein, we designed a bionic TiO 2 inverse opal photonic crystal (IOPC) structure for highly efficient immunocapture of CTCs by combination of a magnetic Fe 3 O 4 @C6@silane nanoparticles with anti-EpCAM (antiepithelial cell adhesion molecule) and microchannel structure. Porous structure and dimension of IOPC TiO 2 can be precisely controlled for mimicking cellular components, and anti-EpCAM antibody was further modified on IOPC interface by conjugating with polydopamine (PDA). The improvement of CTCs capture efficiency reaches a surprising factor of 20 for the IOPC interface compared to that on flat glass, suggesting that the IOPCs are responsible for the dramatic enhancement of the capture efficiency of MCF-7 cells. IOPC substrate with pore size of 415 nm leads to the optimal CTCs capture efficiency of 92% with 1 mL/h. Besides the cell affinity, IOPCs also have the advantage of light scattering property which can enhance the excitation and emission light of fluorescence labels, facilitating the real-time monitoring of CTCs capture. The IOPC-based platform demonstrates excellent performance in CTCs capture, which will take an important step toward specific recognition of disease-related rare cells.

Toxicological Evaluation of a Potential Immunosensitizer for Use as a Mucosal Adjuvant—Bacillus thuringiensis Cry1Ac Spore-Crystals: A Possible Inverse Agonist that Deserves Further Investigation

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Bélin Poletto Mezzomo

2015-12-01

Full Text Available In addition to their applicability as biopesticides, Bacillus thuringiensis (Bt Cry1Ac spore-crystals are being researched in the immunology field for their potential as adjuvants in mucosal and parenteral immunizations. We aimed to investigate the hematotoxicity and genotoxicity of Bt spore-crystals genetically modified to express Cry1Ac individually, administered orally (p.o. or with a single intraperitoneal (i.p. injection 24 h before euthanasia, to simulate the routes of mucosal and parenteral immunizations in Swiss mice. Blood samples were used to perform hemogram, and bone marrow was used for the micronucleus test. Cry1Ac presented cytotoxic effects on erythroid lineage in both routes, being more severe in the i.p. route, which also showed genotoxic effects. The greater severity noted in this route, mainly at 6.75 mg/kg, as well as the intermediate effects at 13.5 mg/kg, and the very low hematotoxicity at 27 mg/kg, suggested a possible inverse agonism. The higher immunogenicity for the p.o. route, particularly at 27 mg/kg, suggested that at this dose, Cry 1Ac could potentially be used as a mucosal adjuvant (but not in parenteral immunizations, due to the genotoxic effects observed. This potential should be investigated further, including making an evaluation of the proposed inverse agonism and carrying out cytokine profiling.

Piezooptical constants of Rochelle salt crystals

OpenAIRE

V.Yo. Stadnyk; M.O. Romanyuk; V.Yu. Kurlyak; V.F.Vachulovych

2000-01-01

The influence of uniaxial mechanical pressure applied along the principal axes and the corresponding bisectors on the birefringent properties of Rochelle salt (RS) crystals are studied. The temperature (77-300 K) and spectral (300-700 nm) dependencies of the effective and absolute piezooptical constants of the RS crystals are calculated. The intercept of dispersion curves of is revealed in the region of the birefringence sign inversion. This testifies that the anizotropy of the piezooptical ...

Nanomechanical resonant structures in single-crystal diamond

OpenAIRE

Burek, Michael J.; Ramos, Daniel; Patel, Parth; Frank, Ian W.; Lončar, Marko

2013-01-01

With its host of outstanding material properties, single-crystal diamond is an attractive material for nanomechanical systems. Here, the mechanical resonance characteristics of freestanding, single-crystal diamond nanobeams fabricated by an angled-etching methodology are reported. Resonance frequencies displayed evidence of significant compressive stress in doubly clamped diamond nanobeams, while cantilever resonance modes followed the expected inverse-length-squared trend. Q-factors on the o...

Lipovitellin-phosvitin crystals with orthorhombic features: thin-section electron microscopy, gel electrophoresis, and microanalysis in teleost and amphibian yolk platelets and a comparison with other vertebrates

International Nuclear Information System (INIS)

Lange, R.H.; Richter, H.P.; Riehl, R.; Zierold, K.; Trandaburu, T.; Magdowski, G.

1983-01-01

Yolk-platelet crystals in the teleosts Pelvicachromis pulcher and Noemacheilus barbatulus and the amphibians Xenopus laevis, Rana temporaria, R. esculenta, and Triturus sp. have been studied by electron diffraction and imaging using a standardized processing (glutaraldehyde-osmium tetroxide fixation, glutaraldehyde-urea embedding, thin-section staining), by X-ray microanalysis, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis of their constituents. The crystal lattice is orthorhombic having. Crystal images in the three axial projections point to the presence of space group P212121 (or an approximation of it since the lipovitellin dimers cannot be fully equivalent in some cases), to differences between the phosvitins of the two teleosts, and to a highly unusual stain exclusion from large crystal constituents interpreted as representing lipovitellin dimers. Microanalysis in ultrathin cryosections and other preparations revealed K and Cl to be the prominent ions in the crystals (and in the superficial layer of the platelet). Gel electrophoresis (including data of cyclostomes) showed considerable molecular variations despite a closely similar crystal architecture, emphasizing a physiological significance of the architecture, which may have remained conserved for nearly 400 million years according to paleontologic views

5-Bromo-4-(3,4-dimethoxyphenylthiazol-2-amine

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Hazem A. Ghabbour

2012-06-01

Full Text Available In the title compound, C11H11BrN2O2S, the thiazole ring makes a dihedral angle of 53.16 (11° with the adjacent benzene ring. The two methoxy groups are slightly twisted from the attached benzene ring with C—O—C—C torsion angles of −9.2 (3 and −5.5 (3°. In the crystal, molecules are linked by a pair of N—H...N hydrogen bonds into an inversion dimer with an R22(8 ring motif. The dimers are further connected by N—H...O hydrogen bonds into a tape along [-110].

2-Oxo-2H-chromen-3-yl 4-tert-butylbenzoate

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Konan René Kambo

2016-10-01

Full Text Available In the title coumarin derivative, C20H18O4, the benzene ring of the benzoate group is oriented at a dihedral angle of 57.55 (9° with respect to the planar chromene ring system [maximum deviation from plane is 0.027 (2 Å]. In the crystal, inversion-related molecules are linked into dimers via C—H...O hydrogen bonds, generating R22(12 loops. The dimers are linked by further C—H...O hydrogen bonds forming layers, parallel to the bc plane, which are linked via C—H...π interactions, forming a three-dimensional framework

4-({[6-(4-Chlorobenzyl-4-methyl-5-oxo-4,5-dihydro-1,2,4-triazin-3-yl]sulfanyl}acetyl-3-phenylsydnone

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Hoong-Kun Fun

2011-04-01

Full Text Available In the title syndone (1,2,3-oxadiazol-3-ylium-5-olate compound, C21H16ClN5O4S, the dihedral angle between the benzene and oxadiazole rings is 55.62 (11° and that between the triazine and the chloro-substituted phenyl rings is 82.45 (9°. There is an intramolecular C—H...S hydrogen bond, which generates an S(5 ring motif. In the crystal, inversion dimers linked by pairs of C—H...O hydrogen bonds generate R22(20 loops. The dimers are connected by C—H...N and C—H...O hydrogen bonds.

Radiation chemistry of aromatic dimer radical cations

International Nuclear Information System (INIS)

Okamoto, Kazumasa; Tagawa, Seiichi

2009-01-01

π-π Interactions of aromatic molecules are paid attention much in many fields, especially biology, chemistry, and applied physics, represented as protein, DNA, electron donor-accepter complexes, charge transfers, and self assembly molecules. Aromatic molecules including benzene rings are the simplest case to study the π-π interactions. To interpret the charge resonance (CR) structure in the dimer radical cations, spectroscopic and ESR methods have been carried out. The spectroscopic study on the dimer radical ion of molecules with two chromophores would be profitable to identify the electronic and configurational properties. In this article, dynamics of the dimer radical cation of benzenes, polystyrenes, and resist polymers is described on the basis of direct observation of CR band by the nanosecond pulse radiolysis and low temperature γ-radiolysis methods. (author)

Analysis of hepatitis C virus RNA dimerization and core–RNA interactions

Science.gov (United States)

Ivanyi-Nagy, Roland; Kanevsky, Igor; Gabus, Caroline; Lavergne, Jean-Pierre; Ficheux, Damien; Penin, François; Fossé, Philippe; Darlix, Jean-Luc

2006-01-01

The core protein of hepatitis C virus (HCV) has been shown previously to act as a potent nucleic acid chaperone in vitro, promoting the dimerization of the 3′-untranslated region (3′-UTR) of the HCV genomic RNA, a process probably mediated by a small, highly conserved palindromic RNA motif, named DLS (dimer linkage sequence) [G. Cristofari, R. Ivanyi-Nagy, C. Gabus, S. Boulant, J. P. Lavergne, F. Penin and J. L. Darlix (2004) Nucleic Acids Res., 32, 2623–2631]. To investigate in depth HCV RNA dimerization, we generated a series of point mutations in the DLS region. We find that both the plus-strand 3′-UTR and the complementary minus-strand RNA can dimerize in the presence of core protein, while mutations in the DLS (among them a single point mutation that abolished RNA replication in a HCV subgenomic replicon system) completely abrogate dimerization. Structural probing of plus- and minus-strand RNAs, in their monomeric and dimeric forms, indicate that the DLS is the major if not the sole determinant of UTR RNA dimerization. Furthermore, the N-terminal basic amino acid clusters of core protein were found to be sufficient to induce dimerization, suggesting that they retain full RNA chaperone activity. These findings may have important consequences for understanding the HCV replicative cycle and the genetic variability of the virus. PMID:16707664

Analysis of hepatitis C virus RNA dimerization and core-RNA interactions.

Science.gov (United States)

Ivanyi-Nagy, Roland; Kanevsky, Igor; Gabus, Caroline; Lavergne, Jean-Pierre; Ficheux, Damien; Penin, François; Fossé, Philippe; Darlix, Jean-Luc

2006-01-01

The core protein of hepatitis C virus (HCV) has been shown previously to act as a potent nucleic acid chaperone in vitro, promoting the dimerization of the 3'-untranslated region (3'-UTR) of the HCV genomic RNA, a process probably mediated by a small, highly conserved palindromic RNA motif, named DLS (dimer linkage sequence) [G. Cristofari, R. Ivanyi-Nagy, C. Gabus, S. Boulant, J. P. Lavergne, F. Penin and J. L. Darlix (2004) Nucleic Acids Res., 32, 2623-2631]. To investigate in depth HCV RNA dimerization, we generated a series of point mutations in the DLS region. We find that both the plus-strand 3'-UTR and the complementary minus-strand RNA can dimerize in the presence of core protein, while mutations in the DLS (among them a single point mutation that abolished RNA replication in a HCV subgenomic replicon system) completely abrogate dimerization. Structural probing of plus- and minus-strand RNAs, in their monomeric and dimeric forms, indicate that the DLS is the major if not the sole determinant of UTR RNA dimerization. Furthermore, the N-terminal basic amino acid clusters of core protein were found to be sufficient to induce dimerization, suggesting that they retain full RNA chaperone activity. These findings may have important consequences for understanding the HCV replicative cycle and the genetic variability of the virus.

1-(Furan-2-yl-2-(2H-indazol-2-ylethanone

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Özden Özel Güven

2014-04-01

Full Text Available The asymmetric unit of the title compound, C13H10N2O2, contains two crystallographically independent molecules (A and B. The indazole ring systems are approximately planar [maximum deviations = 0.0037 (15 and −0.0198 (15 Å], and their mean planes are oriented at 80.10 (5 and 65.97 (4° with respect to the furan rings in molecules A and B, respectively. In the crystal, pairs of C—H...N hydrogen bonds link the B molecules, forming inversion dimers. These dimers are bridged by the A molecules via C—H...O hydrogen bonds, forming sheets parallel to (011. There are also C—H...π interactions present, and π–π interactions between neighbouring furan and the indazole rings [centroid–centroid distance = 3.8708 (9 Å] of inversion-related molecules, forming a three-dimensional structure.

Ab initio interionic potentials for NaCl by multiple lattice inversion

International Nuclear Information System (INIS)

Zhang Shuo; Chen Nanxian

2002-01-01

Based on the Chen-Moebius lattice inversion and a series of pseudopotential total-energy curves, a different method is presented to derive the ab initio interionic pair potentials for B1-type ionic crystals. Comparing with the experimental data, the static properties of B1- and B2-type NaCl are well reproduced by the interionic potentials. Moreover, the phase stability of B1-NaCl has been described by the energy minimizations from the global deformed and disturbed states. The molecular-dynamics simulations for the molten NaCl indicate that the calculated mean-square displacements, radial distribution function, and diffusion coefficients gain good agreements with the experimental results. It can be concluded that the inversion pair potentials are valid over a wide range of interionic separations for describing the structural properties of B1-type ionic crystals

Crystallization and preliminary X-ray characterization of prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis

Energy Technology Data Exchange (ETDEWEB)

Nakajima, Yoshitaka; Ito, Kiyoshi; Xu, Yue; Yamada, Nozomi; Onohara, Yuko; Ito, Takashi; Yoshimoto, Tadashi [Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521 (Japan)

2005-12-01

P. gingivalis prolyl tripeptidyl aminopeptidase has been crystallized by the vapour-diffusion method. Diffraction data have been collected and processed to 2.1 Å resolution. A recombinant form of prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis has been crystallized by the hanging-drop vapour-diffusion method using potassium sodium tartrate as a precipitating agent. The crystals belong to the hexagonal space group P6{sub 3}22, with unit-cell parameters a = b = 149.4, c = 159.7 Å. The crystals are most likely to contain one subunit of a dimer in the asymmetric unit, with a V{sub M} value of 3.14 Å{sup 3} Da{sup −1}. Diffraction data were collected to 2.1 Å resolution using synchrotron radiation at the BL5 station of the Photon Factory.

Quantum dissipative dynamics and decoherence of dimers on helium droplets

International Nuclear Information System (INIS)

Schlesinger, Martin

2011-01-01

In this thesis, quantum dynamical simulations are performed in order to describe the vibrational motion of diatomic molecules in a highly quantum environment, so-called helium droplets. We aim to reproduce and explain experimental findings which were obtained from dimers on helium droplets. Nanometer-sized helium droplets contain several thousands of 4 He atoms. They serve as a host for embedded atoms or molecules and provide an ultracold ''refrigerator'' for them. Spectroscopy of molecules in or on these droplets reveals information on both the molecule and the helium environment. The droplets are known to be in the superfluid He II phase. Superfluidity in nanoscale systems is a steadily growing field of research. Spectra obtained from full quantum simulations for the unperturbed dimer show deviations from measurements with dimers on helium droplets. These deviations result from the influence of the helium environment on the dimer dynamics. In this work, a well-established quantum optical master equation is used in order to describe the dimer dynamics effectively. The master equation allows to describe damping fully quantum mechanically. By employing that equation in the quantum dynamical simulation, one can study the role of dissipation and decoherence in dimers on helium droplets. The effective description allows to explain experiments with Rb 2 dimers on helium droplets. Here, we identify vibrational damping and associated decoherence as the main explanation for the experimental results. The relation between decoherence and dissipation in Morse-like systems at zero temperature is studied in more detail. The dissipative model is also used to investigate experiments with K 2 dimers on helium droplets. However, by comparing numerical simulations with experimental data, one finds that further mechanisms are active. Here, a good agreement is obtained through accounting for rapid desorption of dimers. We find that decoherence occurs in the electronic manifold of the

Photon Propagation through Linearly Active Dimers

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José Delfino Huerta Morales

2017-06-01

Full Text Available We provide an analytic propagator for non-Hermitian dimers showing linear gain or losses in the quantum regime. In particular, we focus on experimentally feasible realizations of the PT -symmetric dimer and provide their mean photon number and second order two-point correlation. We study the propagation of vacuum, single photon spatially-separable, and two-photon spatially-entangled states. We show that each configuration produces a particular signature that might signal their possible uses as photon switches, semi-classical intensity-tunable sources, or spatially entangled sources to mention a few possible applications.

Mutability of bacteriophage M13 by ultraviolet light: role of pyrimidine dimers

International Nuclear Information System (INIS)

Schaaper, R.M.; Glickman, B.W.

1982-01-01

The role of pyrimidine dimers in mutagenesis by ultraviolet light was examined by measuring the UV-induced reversion of six different bacteriophage M13 amber mutants for which the neighboring DNA sequences are known. The mutational response at amber (TAG) codons preceded by a guanine or adenine (where no pyrimidine dimer can be formed) were compared with those preceded by thymine or cytosine (where dimer formation is possible). Equivalent levels of UV-induced mutagenesis were observed at both kinds of sites. This observation demonstrates that there is no requirement for a pyrimidine dimer directly at the site of UV-induced mutation in this single-stranded DNA phage. UV irradiation of the phage was also performed in the presence of Ag + ions, which specifically sensitize the DNA to dimer formation. The two methods of irradiation, when compared at equal survival levels (and presumably equal dimer frequencies), produced equivalent frequencies of reversion of the amber phage. We believe these results indicate that while the presence of pyrimidine dimers may be a prerequisite for UV mutagenesis, the actual mutagenic event can occur at a site some distance removed from a dimer. (orig.)

Crystal structure of human importin-α1 (Rch1, revealing a potential autoinhibition mode involving homodimerization.

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Hideyuki Miyatake

Full Text Available In this study, we determined the crystal structure of N-terminal importin-β-binding domain (IBB-truncated human importin-α1 (ΔIBB-h-importin-α1 at 2.63 Å resolution. The crystal structure of ΔIBB-h-importin-α1 reveals a novel closed homodimer. The homodimer exists in an autoinhibited state in which both the major and minor nuclear localization signal (NLS binding sites are completely buried in the homodimerization interface, an arrangement that restricts NLS binding. Analytical ultracentrifugation studies revealed that ΔIBB-h-importin-α1 is in equilibrium between monomers and dimers and that NLS peptides shifted the equilibrium toward the monomer side. This finding suggests that the NLS binding sites are also involved in the dimer interface in solution. These results show that when the IBB domain dissociates from the internal NLS binding sites, e.g., by binding to importin-β, homodimerization possibly occurs as an autoinhibition state.

Fabrication of Au- and Ag–SiO{sub 2} inverse opals having both localized surface plasmon resonance and Bragg diffraction

Energy Technology Data Exchange (ETDEWEB)

Erola, Markus O.A.; Philip, Anish; Ahmed, Tanzir; Suvanto, Sari; Pakkanen, Tuula T., E-mail: Tuula.Pakkanen@uef.fi

2015-10-15

The inverse opal films of SiO{sub 2} containing metal nanoparticles can have both the localized surface plasmon resonance (LSPR) of metal nanoparticles and the Bragg diffraction of inverse opal crystals of SiO{sub 2}, which are very useful properties for applications, such as tunable photonic structures, catalysts and sensors. However, effective processes for fabrication of these films from colloidal particles have rarely been reported. In our study, two methods for preparation of inverse opal films of SiO{sub 2} with three different crystal sizes and containing gold or silver nanoparticles (NPs) via self-assembly using electrostatic interactions and capillary forces are reported. The Bragg diffraction of inverse opal films of SiO{sub 2} in the presence and absence of the template was measured and predicted on the basis of with UV–vis spectroscopy and scanning electron microscopy. The preparation methods used provided good-quality inverse opal SiO{sub 2} films containing highly dispersed, plasmonic AuNPs or AgNPs and having both Bragg diffractions and LSPRs. - Graphical abstract: For syntheses of SiO{sub 2} inverse opals containing Au/Ag nanoparticles two approaches and three template sizes were employed. Self-assembly of template molecules and metal nanoparticles occurred using electrostatic interactions and capillary forces. Both the Bragg diffraction of the photonic crystal and the localized surface plasmon resonance of Au/Ag nanoparticles were detected. - Highlights: • Fabrication methods of silica inverse opals containing metal nanoparticles studied. • Three template sizes used to produce SiO{sub 2} inverse opals with Au/Ag nanoparticles. • PS templates with Au nanoparticles adsorbed used in formation of inverse opals. • Ag particles infiltrated in inverse opals with capillary and electrostatic forces. • Bragg diffractions of IOs and surface plasmon resonances of nanoparticles observed.

Synthesis and spectral characterization of mono- and binuclear copper(II) complexes derived from 2-benzoylpyridine-N4-methyl-3-thiosemicarbazone: Crystal structure of a novel sulfur bridged copper(II) box-dimer

Science.gov (United States)

Jayakumar, K.; Sithambaresan, M.; Aiswarya, N.; Kurup, M. R. Prathapachandra

2015-03-01

Mononuclear and binuclear copper(II) complexes of 2-benzoylpyridine-N4-methyl thiosemicarbazone (HL) were prepared and characterized by a variety of spectroscopic techniques. Structural evidence for the novel sulfur bridged copper(II) iodo binuclear complex is obtained by single crystal X-ray diffraction analysis. The complex [Cu2L2I2], a non-centrosymmetric box dimer, crystallizes in monoclinic C2/c space group and it was found to have distorted square pyramidal geometry (Addison parameter, τ = 0.238) with the square basal plane occupied by the thiosemicarbazone moiety and iodine atom whereas the sulfur atom from the other coordinated thiosemicarbazone moiety occupies the apical position. This is the first crystallographically studied system having non-centrosymmetrical entities bridged via thiolate S atoms with Cu(II)sbnd I bond. The tridentate thiosemicarbazone coordinates in mono deprotonated thionic tautomeric form in all complexes except in sulfato complex, [Cu(HL)(SO4)]·H2O (1) where it binds to the metal centre in neutral form. The magnetic moment values and the EPR spectral studies reflect the binuclearity of some of the complexes. The spin Hamiltonian and bonding parameters are calculated based on EPR studies. In all the complexes g|| > g⊥ > 2.0023 and the g values in frozen DMF are consistent with the dx2-y2 ground state. The thermal stabilities of some of the complexes were also determined.

Fiber optic D dimer biosensor

Science.gov (United States)

Glass, Robert S.; Grant, Sheila A.

1999-01-01

A fiber optic sensor for D dimer (a fibrinolytic product) can be used in vivo (e.g., in catheter-based procedures) for the diagnosis and treatment of stroke-related conditions in humans. Stroke is the third leading cause of death in the United States. It has been estimated that strokes and stroke-related disorders cost Americans between $15-30 billion annually. Relatively recently, new medical procedures have been developed for the treatment of stroke. These endovascular procedures rely upon the use of microcatheters. These procedures could be facilitated with this sensor for D dimer integrated with a microcatheter for the diagnosis of clot type, and as an indicator of the effectiveness, or end-point of thrombolytic therapy.

Singlet fission in pentacene dimers

Science.gov (United States)

Zirzlmeier, Johannes; Lehnherr, Dan; Coto, Pedro B.; Chernick, Erin T.; Casillas, Rubén; Basel, Bettina S.; Thoss, Michael; Tykwinski, Rik R.; Guldi, Dirk M.

2015-01-01

Singlet fission (SF) has the potential to supersede the traditional solar energy conversion scheme by means of boosting the photon-to-current conversion efficiencies beyond the 30% Shockley–Queisser limit. Here, we show unambiguous and compelling evidence for unprecedented intramolecular SF within regioisomeric pentacene dimers in room-temperature solutions, with observed triplet quantum yields reaching as high as 156 ± 5%. Whereas previous studies have shown that the collision of a photoexcited chromophore with a ground-state chromophore can give rise to SF, here we demonstrate that the proximity and sufficient coupling through bond or space in pentacene dimers is enough to induce intramolecular SF where two triplets are generated on one molecule. PMID:25858954

Optical properties of electrically connected plasmonic nanoantenna dimer arrays

Science.gov (United States)

Zimmerman, Darin T.; Borst, Benjamin D.; Carrick, Cassandra J.; Lent, Joseph M.; Wambold, Raymond A.; Weisel, Gary J.; Willis, Brian G.

2018-02-01

We fabricate electrically connected gold nanoantenna arrays of homodimers and heterodimers on silica substrates and present a systematic study of their optical properties. Electrically connected arrays of plasmonic nanoantennas make possible the realization of novel photonic devices, including optical sensors and rectifiers. Although the plasmonic response of unconnected arrays has been studied extensively, the present study shows that the inclusion of nanowire connections modifies the device response significantly. After presenting experimental measurements of optical extinction for unconnected dimer arrays, we compare these to measurements of dimers that are interconnected by gold nanowire "busbars." The connected devices show the familiar dipole response associated with the unconnected dimers but also show a second localized surface plasmon resonance (LSPR) that we refer to as the "coupled-busbar mode." Our experimental study also demonstrates that the placement of the nanowire along the antenna modifies the LSPR. Using finite-difference time-domain simulations, we confirm the experimental results and investigate the variation of dimer gap and spacing. Changing the dimer gap in connected devices has a significantly smaller effect on the dipole response than it does in unconnected devices. On the other hand, both LSPR modes respond strongly to changing the spacing between devices in the direction along the interconnecting wires. We also give results for the variation of E-field strength in the dimer gap, which will be important for any working sensor or rectenna device.

Metal membrane with dimer slots as a universal polarizer

Science.gov (United States)

Zhukovsky, Sergej; Zalkovskij, Maksim; Malureanu, Radu; Kremers, Christian; Chigrin, Dmitry; Tang, Peter T.; Jepsen, Peter U.; Lavrinenko, Andrei V.

2014-03-01

In this work, we show theoretically and confirm experimentally that thin metal membranes patterned with an array of slot dimers (or their Babinet analogue with metal rods) can function as a versatile spectral and polarization filter. We present a detailed covariant multipole theory for the electromagnetic response of an arbitrary dimer based on the Green functions approach. The theory confirms that a great variety of polarization properties, such as birefringence, chirality and elliptical dichroism, can be achieved in a metal layer with such slot-dimer patterning (i.e. in a metasurface). Optical properties of the metasurface can be extensively tuned by varying the geometry (shape and dimensions) of the dimer, for example, by adjusting the sizes and mutual placement of the slots (e.g. inter-slot distance and alignment angle). Three basic shapes of dimers are analyzed: II-shaped (parallel slots), V-shaped, and T-shaped. These particular shapes of dimers are found to be sensitive to variations of the slots lengths and orientation of elements. Theoretical results are well supported by full-wave three-dimensional simulations. Our findings were verified experimentally on the metal membranes fabricated using UV lithography with subsequent Ni growth. Such metasurfaces were characterized using time-domain THz spectroscopy. The samples exhibit pronounced optical activity (500 degrees per wavelength) and high transmission: even though the slots cover only 4.3 % of the total membrane area the amplitude transmission reaches 0.67 at the resonance frequency 0.56 THz.

Crystal structure of strontium dinickel iron orthophosphate

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Said Ouaatta

2015-10-01

Full Text Available The title compound, SrNi2Fe(PO43, synthesized by solid-state reaction, crystallizes in an ordered variant of the α-CrPO4 structure. In the asymmetric unit, two O atoms are in general positions, whereas all others atoms are in special positions of the space group Imma: the Sr cation and one P atom occupy the Wyckoff position 4e (mm2, Fe is on 4b (2/m, Ni and the other P atom are on 8g (2, one O atom is on 8h (m and the other on 8i (m. The three-dimensional framework of the crystal structure is built up by [PO4] tetrahedra, [FeO6] octahedra and [Ni2O10] dimers of edge-sharing octahedra, linked through common corners or edges. This structure comprises two types of layers stacked alternately along the [100] direction. The first layer is formed by edge-sharing octahedra ([Ni2O10] dimer linked to [PO4] tetrahedra via common edges while the second layer is built up from a strontium row followed by infinite chains of alternating [PO4] tetrahedra and FeO6 octahedra sharing apices. The layers are held together through vertices of [PO4] tetrahedra and [FeO6] octahedra, leading to the appearance of two types of tunnels parallel to the a- and b-axis directions in which the Sr cations are located. Each Sr cation is surrounded by eight O atoms.

Structure of the dimeric N-glycosylated form of fungal β-N-acetylhexosaminidase revealed by computer modeling, vibrational spectroscopy, and biochemical studies

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Sklenář Jan

2007-05-01

Full Text Available Abstract Background Fungal β-N-acetylhexosaminidases catalyze the hydrolysis of chitobiose into its constituent monosaccharides. These enzymes are physiologically important during the life cycle of the fungus for the formation of septa, germ tubes and fruit-bodies. Crystal structures are known for two monomeric bacterial enzymes and the dimeric human lysosomal β-N-acetylhexosaminidase. The fungal β-N-acetylhexosaminidases are robust enzymes commonly used in chemoenzymatic syntheses of oligosaccharides. The enzyme from Aspergillus oryzae was purified and its sequence was determined. Results The complete primary structure of the fungal β-N-acetylhexosaminidase from Aspergillus oryzae CCF1066 was used to construct molecular models of the catalytic subunit of the enzyme, the enzyme dimer, and the N-glycosylated dimer. Experimental data were obtained from infrared and Raman spectroscopy, and biochemical studies of the native and deglycosylated enzyme, and are in good agreement with the models. Enzyme deglycosylated under native conditions displays identical kinetic parameters but is significantly less stable in acidic conditions, consistent with model predictions. The molecular model of the deglycosylated enzyme was solvated and a molecular dynamics simulation was run over 20 ns. The molecular model is able to bind the natural substrate – chitobiose with a stable value of binding energy during the molecular dynamics simulation. Conclusion Whereas the intracellular bacterial β-N-acetylhexosaminidases are monomeric, the extracellular secreted enzymes of fungi and humans occur as dimers. Dimerization of the fungal β-N-acetylhexosaminidase appears to be a reversible process that is strictly pH dependent. Oligosaccharide moieties may also participate in the dimerization process that might represent a unique feature of the exclusively extracellular enzymes. Deglycosylation had only limited effect on enzyme activity, but it significantly affected

Solid state NMR sequential resonance assignments and conformational analysis of the 2x10.4 kDa dimeric form of the Bacillus subtilis protein Crh

Energy Technology Data Exchange (ETDEWEB)

Boeckmann, Anja [Institut de Biologie et Chimie des Proteines, C.N.R.S UMR 5086 (France)], E-mail: a.bockmann@ibcp.fr; Lange, Adam [Max-Planck-Institute for Biophysical Chemistry, Solid-state NMR (Germany); Galinier, Anne [Institut de Biologie Structurale et Microbiologie, C.N.R.S UPR 9043 (France); Luca, Sorin [Max-Planck-Institute for Biophysical Chemistry, Solid-state NMR (Germany); Giraud, Nicolas; Juy, Michel [Institut de Biologie et Chimie des Proteines, C.N.R.S UMR 5086 (France); Heise, Henrike [Max-Planck-Institute for Biophysical Chemistry, Solid-state NMR (Germany); Montserret, Roland; Penin, Francois [Institut de Biologie et Chimie des Proteines, C.N.R.S UMR 5086 (France); Baldus, Marc [Max-Planck-Institute for Biophysical Chemistry, Solid-state NMR (Germany)], E-mail: maba@mpibpc.mpg.de

2003-12-15

Solid state NMR sample preparation and resonance assignments of the U-[{sup 13}C,{sup 15}N] 2x10.4 kDa dimeric form of the regulatory protein Crh in microcrystalline, PEG precipitated form are presented. Intra- and interresidue correlations using dipolar polarization transfer methods led to nearly complete sequential assignments of the protein, and to 88% of all {sup 15}N, {sup 13}C chemical shifts. For several residues, the resonance assignments differ significantly from those reported for the monomeric form analyzed by solution state NMR. Dihedral angles obtained from a TALOS-based statistical analysis suggest that the microcrystalline arrangement of Crh must be similar to the domain-swapped dimeric structure of a single crystal form recently solved using X-ray crystallography. For a limited number of protein residues, a remarkable doubling of the observed NMR resonances is observed indicative of local static or dynamic conformational disorder. Our study reports resonance assignments for the largest protein investigated by solid state NMR so far and describes the conformational dimeric variant of Crh with previously unknown chemical shifts.

RecFOR Is Not Required for Pneumococcal Transformation but Together with XerS for Resolution of Chromosome Dimers Frequently Formed in the Process

Science.gov (United States)

Johnston, Calum; Mortier-Barrière, Isabelle; Granadel, Chantal; Polard, Patrice; Martin, Bernard; Claverys, Jean-Pierre

2015-01-01

Homologous recombination (HR) is required for both genome maintenance and generation of diversity in eukaryotes and prokaryotes. This process initiates from single-stranded (ss) DNA and is driven by a universal recombinase, which promotes strand exchange between homologous sequences. The bacterial recombinase, RecA, is loaded onto ssDNA by recombinase loaders, RecBCD and RecFOR for genome maintenance. DprA was recently proposed as a third loader dedicated to genetic transformation. Here we assessed the role of RecFOR in transformation of the human pathogen Streptococcus pneumoniae. We firstly established that RecFOR proteins are not required for plasmid transformation, strongly suggesting that DprA ensures annealing of plasmid single-strands internalized in the process. We then observed no reduction in chromosomal transformation using a PCR fragment as donor, contrasting with the 10,000-fold drop in dprA - cells and demonstrating that RecFOR play no role in transformation. However, a ∼1.45-fold drop in transformation was observed with total chromosomal DNA in recFOR mutants. To account for this limited deficit, we hypothesized that transformation with chromosomal DNA stimulated unexpectedly high frequency (>30% of cells) formation of chromosome dimers as an intermediate in the generation of tandem duplications, and that RecFOR were crucial for dimer resolution. We validated this hypothesis, showing that the site-specific recombinase XerS was also crucial for dimer resolution. An even higher frequency of dimer formation (>80% of cells) was promoted by interspecies transformation with Streptococcus mitis chromosomal DNA, which contains numerous inversions compared to pneumococcal chromosome, each potentially promoting dimerization. In the absence of RecFOR and XerS, dimers persist, as confirmed by DAPI staining, and can limit the efficiency of transformation, since resulting in loss of transformant chromosome. These findings strengthen the view that different HR

RecFOR is not required for pneumococcal transformation but together with XerS for resolution of chromosome dimers frequently formed in the process.

Directory of Open Access Journals (Sweden)

Calum Johnston

2015-01-01

Full Text Available Homologous recombination (HR is required for both genome maintenance and generation of diversity in eukaryotes and prokaryotes. This process initiates from single-stranded (ss DNA and is driven by a universal recombinase, which promotes strand exchange between homologous sequences. The bacterial recombinase, RecA, is loaded onto ssDNA by recombinase loaders, RecBCD and RecFOR for genome maintenance. DprA was recently proposed as a third loader dedicated to genetic transformation. Here we assessed the role of RecFOR in transformation of the human pathogen Streptococcus pneumoniae. We firstly established that RecFOR proteins are not required for plasmid transformation, strongly suggesting that DprA ensures annealing of plasmid single-strands internalized in the process. We then observed no reduction in chromosomal transformation using a PCR fragment as donor, contrasting with the 10,000-fold drop in dprA- cells and demonstrating that RecFOR play no role in transformation. However, a ∼1.45-fold drop in transformation was observed with total chromosomal DNA in recFOR mutants. To account for this limited deficit, we hypothesized that transformation with chromosomal DNA stimulated unexpectedly high frequency (>30% of cells formation of chromosome dimers as an intermediate in the generation of tandem duplications, and that RecFOR were crucial for dimer resolution. We validated this hypothesis, showing that the site-specific recombinase XerS was also crucial for dimer resolution. An even higher frequency of dimer formation (>80% of cells was promoted by interspecies transformation with Streptococcus mitis chromosomal DNA, which contains numerous inversions compared to pneumococcal chromosome, each potentially promoting dimerization. In the absence of RecFOR and XerS, dimers persist, as confirmed by DAPI staining, and can limit the efficiency of transformation, since resulting in loss of transformant chromosome. These findings strengthen the view that

Analytical study of avian reticuloendotheliosis virus dimeric RNA generated in vivo and in vitro.

Science.gov (United States)

Darlix, J L; Gabus, C; Allain, B

1992-12-01

The retroviral genome consists of two identical RNA molecules associated at their 5' ends by a stable structure called the dimer linkage structure. The dimer linkage structure, while maintaining the dimer state of the retroviral genome, might also be involved in packaging and reverse transcription, as well as recombination during proviral DNA synthesis. To study the dimer structure of the retroviral genome and the mechanism of dimerization, we analyzed features of the dimeric genome of reticuloendotheliosis virus (REV) type A and identified elements required for its dimerization. Here we report that the REV dimeric genome extracted from virions and infected cells, as well as that synthesized in vitro, is more resistant to heat denaturation than avian sarcoma and leukemia virus, murine leukemia virus, or human immunodeficiency virus type 1 dimeric RNA. The minimal domain required to form a stable REV RNA dimer in vitro was found to map between positions 268 and 452 (KpnI and SalI sites), thus corresponding to the E encapsidation sequence (J. E. Embretson and H. M. Temin, J. Virol. 61:2675-2683, 1987). In addition, both the 5' and 3' halves of E are necessary in cis for RNA dimerization and the extent of RNA dimerization is influenced by viral sequences flanking E. Rapid and efficient dimerization of REV RNA containing gag sequences in addition to the E sequences and annealing of replication primer tRNA(Pro) to the primer-binding site necessitate the nucleocapsid protein.

Structural, electrical, magnetic, and optical properties of bis-benzene-1,2-dithiolato-Au(IV) crystals

DEFF Research Database (Denmark)

Schiødt, Niels Christian; Bjørnholm, Thomas; Bechgaard, Klaus

1996-01-01

Analysis of x-ray diffraction from a single crystal of bis-benzene-1,2-dithiolato-Au(IV) [Au(bdt)(2)] at 125 K reveals a superstructure along the stacks of Au(bdt)(2) molecules corresponding to a dimerization of the molecules along the stack. Within a dimer, intermolecular sulfur-sulfur contacts...... pressure is 0.11 Omega(-1) m(-1) rising smoothly to 0.67 Omega(-1) m(-1) at 0.55 GPa isotropic pressure. The magnetic susceptibility chi is low compared to the spin susceptibility of a system with one free spin per molecule. An activated behavior of chi is observed, which gives rise to a monotonic increase...

Dimerization of human immunodeficiency virus (type 1) RNA: stimulation by cations and possible mechanism.

Science.gov (United States)

Marquet, R; Baudin, F; Gabus, C; Darlix, J L; Mougel, M; Ehresmann, C; Ehresmann, B

1991-05-11

The retroviral genome consists of two identical RNA molecules joined close to their 5' ends by the dimer linkage structure. Recent findings indicated that retroviral RNA dimerization and encapsidation are probably related events during virion assembly. We studied the cation-induced dimerization of HIV-1 RNA and results indicate that all in vitro generated HIV-1 RNAs containing a 100 nucleotide domain downstream from the 5' splice site are able to dimerize. RNA dimerization depends on the concentration of RNA, mono- and multivalent cations, the size of the monovalent cation, temperature, and pH. Up to 75% of HIV-1 RNA is dimeric in the presence of spermidine. HIV-1 RNA dimer is fairly resistant to denaturing agents and unaffected by intercalating drugs. Antisense HIV-1 RNA does not dimerize but heterodimers can be formed between HIV-1 RNA and either MoMuLV or RSV RNA. Therefore retroviral RNA dimerization probably does not simply proceed through mechanisms involving Watson-Crick base-pairing. Neither adenine and cytosine protonation, nor quartets containing only guanines appear to determine the stability of the HIV-1 RNA dimer, while quartets involving both adenine(s) and guanine(s) could account for our results. A consensus sequence PuGGAPuA found in the putative dimerization-encapsidation region of all retroviral genomes examined may participate in the dimerization process.

Competition between spin-orbit coupling, magnetism, and dimerization in the honeycomb iridates: α -Li2IrO3 under pressure

Science.gov (United States)

Hermann, V.; Altmeyer, M.; Ebad-Allah, J.; Freund, F.; Jesche, A.; Tsirlin, A. A.; Hanfland, M.; Gegenwart, P.; Mazin, I. I.; Khomskii, D. I.; Valentí, R.; Kuntscher, C. A.

2018-02-01

Single-crystal x-ray diffraction studies with synchrotron radiation on the honeycomb iridate α -Li2IrO3 reveal a pressure-induced structural phase transition with symmetry lowering from monoclinic to triclinic at a critical pressure of Pc=3.8 GPa. According to the evolution of the lattice parameters with pressure, the transition mainly affects the a b plane and thereby the Ir hexagon network, leading to the formation of Ir-Ir dimers. These observations are independently predicted and corroborated by our ab initio density functional theory calculations where we find that the appearance of Ir-Ir dimers at finite pressure is a consequence of a subtle interplay between magnetism, correlation, spin-orbit coupling, and covalent bonding. Our results further suggest that at Pc the system undergoes a magnetic collapse. Finally we provide a general picture of competing interactions for the honeycomb lattices A2M O3 with A =Li , Na and M =Ir , Ru.

A Model for Dimerization of the SOX Group E Transcription Factor Family.

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Sarah N Ramsook

Full Text Available Group E members of the SOX transcription factor family include SOX8, SOX9, and SOX10. Preceding the high mobility group (HMG domain in each of these proteins is a thirty-eight amino acid region that supports the formation of dimers on promoters containing tandemly inverted sites. The purpose of this study was to obtain new structural insights into how the dimerization region functions with the HMG domain. From a mutagenic scan of the dimerization region, the most essential amino acids of the dimerization region were clustered on the hydrophobic face of a single, predicted amphipathic helix. Consistent with our hypothesis that the dimerization region directly contacts the HMG domain, a peptide corresponding to the dimerization region bound a preassembled HMG-DNA complex. Sequence conservation among Group E members served as a basis to identify two surface exposed amino acids in the HMG domain of SOX9 that were necessary for dimerization. These data were combined to make a molecular model that places the dimerization region of one SOX9 protein onto the HMG domain of another SOX9 protein situated at the opposing site of a tandem promoter. The model provides a detailed foundation for assessing the impact of mutations on SOX Group E transcription factors.

3-Chloro-4-methyl­quinolin-2(1H)-one

Science.gov (United States)

Kassem, Mohamed G.; Ghabbour, Hazem A.; Abdel-Aziz, Hatem A.; Fun, Hoong-Kun; Ooi, Chin Wei

2012-01-01

The title compound, C10H8ClNO, is almost planar (r.m.s. deviation for the 13 non-H atoms = 0.023 Å). In the crystal, inversion dimers linked by pairs of N—H⋯O hydrogen bonds generate R 2 2(8) rings. Weak aromatic π–π stacking inter­actions [centroid–centroid distance = 3.7622 (12) Å] also occur. PMID:22589913

(3R,4Z-1,3-Diethyl-4-(2-oxopropylidene-2,3,4,5-tetrahydro-1H-1,5-benzodiazepin-2-one

Directory of Open Access Journals (Sweden)

Laila El Foujji

2018-04-01

Full Text Available In the title compound, C16H20N2O2, the seven-membered ring adopts a bowl-shaped conformation while the orientation of the 2-oxopropylidene substituent is determined by an intramolecular N—H...O hydrogen bond, which generates an S(6 ring. In the crystal, inversion dimers linked by pairs of very weak C—H...O interactions occur, which generate R22(8 loops.

Excitonic Behavior of Rhodamine Dimers: A Single-Molecule Study

NARCIS (Netherlands)

Hernando Campos, J.; van der Schaaf, Martijn; van Dijk, E.M.H.P.; Sauer, Markus; Garcia Parajo, M.F.; van Hulst, N.F.

2003-01-01

The optical behavior of a dimer of tetramethylrhodamine-5-isothiocyanate has been investigated by means of single-molecule measurements. Bulk absorption and fluorescence spectra show the existence of two populations of the dimer molecule that exhibit distinct excitonic interactions (strong and weak

2-Ethynylpyridine dimers: IR spectroscopic and computational study

Science.gov (United States)

Bakarić, Danijela; Spanget-Larsen, Jens

2018-04-01

2-ethynylpyridine (2-EP) presents a multifunctional system capable of participation in hydrogen-bonded complexes utilizing hydrogen bond donating (tbnd Csbnd H, Aryl-H) and hydrogen bond accepting functions (N-atom, Ctbnd C and pyridine π-systems). In this work, IR spectroscopy and theoretical calculations are used to study possible 2-EP dimer structures as well as their distribution in an inert solvent such as tetrachloroethene. Experimentally, the tbnd Csbnd H stretching vibration of the 2-EP monomer absorbs close to 3300 cm-1, whereas a broad band with maximum around 3215 cm-1 emerges as the concentration rises, indicating the formation of hydrogen-bonded complexes involving the tbnd Csbnd H moiety. The Ctbnd C stretching vibration of monomer 2-EP close to 2120 cm-1 is, using derivative spectroscopy, resolved from the signals of the dimer complexes with maximum around 2112 cm-1. Quantum chemical calculations using the B3LYP + D3 model with counterpoise correction predict that the two most stable dimers are of the π-stacked variety, closely followed by dimers with intermolecular tbnd Csbnd H⋯N hydrogen bonding; the predicted red shifts of the tbnd Csbnd H stretching wavenumbers due to hydrogen bonding are in the range 54-120 cm-1. No species with obvious hydrogen bonding involving the Ctbnd C or pyridine π-systems as acceptors are predicted. Dimerization constant at 25 °C is estimated to be K2 = 0.13 ± 0.01 mol-1 dm3.

Arithmetic crystal classes of magnetic symmetries

International Nuclear Information System (INIS)

Angelova, M.N.; Boyle, L.L.

1993-01-01

The symmetries and properties of a broad class of magnetic crystals are described by magnetic space groups which contain both (unitary) spatial symmetry operations and their combinations with the (anti-unitary operation of) time inversion, 0. The spatial symmetry operations form a halving, non-magnetic, space group H of the magnetic group M such that M=H+aH. As an abstract group the magnetic group M is isomorphic to a non-magnetic group G. The anti-unitary operator a is simply the time inversion 0 when M is a grey group but a product of time inversion with some spatial operation belonging to the coset G-H when M is a black-and-white group. (Author)

DAXX envelops a histone H3.3-H4 dimer for H3.3-specific recognition

Energy Technology Data Exchange (ETDEWEB)

Elsässer, Simon J; Huang, Hongda; Lewis, Peter W; Chin, Jason W; Allis, C David; Patel, Dinshaw J [MSKCC; (Rockefeller); (MRC)

2013-01-24

Histone chaperones represent a structurally and functionally diverse family of histone-binding proteins that prevent promiscuous interactions of histones before their assembly into chromatin. DAXX is a metazoan histone chaperone specific to the evolutionarily conserved histone variant H3.3. Here we report the crystal structures of the DAXX histone-binding domain with a histone H3.3–H4 dimer, including mutants within DAXX and H3.3, together with in vitro and in vivo functional studies that elucidate the principles underlying H3.3 recognition specificity. Occupying 40% of the histone surface-accessible area, DAXX wraps around the H3.3–H4 dimer, with complex formation accompanied by structural transitions in the H3.3–H4 histone fold. DAXX uses an extended α-helical conformation to compete with major inter-histone, DNA and ASF1 interaction sites. Our structural studies identify recognition elements that read out H3.3-specific residues, and functional studies address the contributions of Gly90 in H3.3 and Glu225 in DAXX to chaperone-mediated H3.3 variant recognition specificity.

Synthesis and spectral characterization of mono- and binuclear copper(II) complexes derived from 2-benzoylpyridine-N⁴-methyl-3-thiosemicarbazone: crystal structure of a novel sulfur bridged copper(II) box-dimer.

Science.gov (United States)

Jayakumar, K; Sithambaresan, M; Aiswarya, N; Kurup, M R Prathapachandra

2015-03-15

Mononuclear and binuclear copper(II) complexes of 2-benzoylpyridine-N(4)-methyl thiosemicarbazone (HL) were prepared and characterized by a variety of spectroscopic techniques. Structural evidence for the novel sulfur bridged copper(II) iodo binuclear complex is obtained by single crystal X-ray diffraction analysis. The complex [Cu2L2I2], a non-centrosymmetric box dimer, crystallizes in monoclinic C2/c space group and it was found to have distorted square pyramidal geometry (Addison parameter, τ=0.238) with the square basal plane occupied by the thiosemicarbazone moiety and iodine atom whereas the sulfur atom from the other coordinated thiosemicarbazone moiety occupies the apical position. This is the first crystallographically studied system having non-centrosymmetrical entities bridged via thiolate S atoms with Cu(II)I bond. The tridentate thiosemicarbazone coordinates in mono deprotonated thionic tautomeric form in all complexes except in sulfato complex, [Cu(HL)(SO4)]·H2O (1) where it binds to the metal centre in neutral form. The magnetic moment values and the EPR spectral studies reflect the binuclearity of some of the complexes. The spin Hamiltonian and bonding parameters are calculated based on EPR studies. In all the complexes g||>g⊥>2.0023 and the g values in frozen DMF are consistent with the d(x2-y2) ground state. The thermal stabilities of some of the complexes were also determined. Copyright © 2014 Elsevier B.V. All rights reserved.

Photoionization of helium dimers; Photoionisation von Heliumdimeren

Energy Technology Data Exchange (ETDEWEB)

Havermeier, Tilo

2010-06-09

The helium dimer is one of the most weakly bound systems in the universe. This makes it an interesting quantum mechanical object for investigation. These Van der Waals Clusters can be produced in an expansion of a cryogenic gas jet through a small nozzle into vacuum. In the present experiment we examine the interaction of He dimers with synchrotron radiation at an energy range from 64 to 78 eV. We observed different pathways leading to single ionization of both He atoms of the dimer compound. This two close standing ions begin now to dissociate in cause of their coulomb potential. All charged fragments were detected in coincidence with a COLTRIMS system. Especially Interatomic Coulombic Decay (ICD) and the two step process (TS1) were clearly identified. Furthermore a distribution of the internuclear distance was obtained from the measured Kinetic Energy Release (KER). (orig.)

Blue light-induced LOV domain dimerization enhances the affinity of Aureochrome 1a for its target DNA sequence

Science.gov (United States)

Heintz, Udo; Schlichting, Ilme

2016-01-01

The design of synthetic optogenetic tools that allow precise spatiotemporal control of biological processes previously inaccessible to optogenetic control has developed rapidly over the last years. Rational design of such tools requires detailed knowledge of allosteric light signaling in natural photoreceptors. To understand allosteric communication between sensor and effector domains, characterization of all relevant signaling states is required. Here, we describe the mechanism of light-dependent DNA binding of the light-oxygen-voltage (LOV) transcription factor Aureochrome 1a from Phaeodactylum tricornutum (PtAu1a) and present crystal structures of a dark state LOV monomer and a fully light-adapted LOV dimer. In combination with hydrogen/deuterium-exchange, solution scattering data and DNA-binding experiments, our studies reveal a light-sensitive interaction between the LOV and basic region leucine zipper DNA-binding domain that together with LOV dimerization results in modulation of the DNA affinity of PtAu1a. We discuss the implications of these results for the design of synthetic LOV-based photosensors with application in optogenetics. DOI: http://dx.doi.org/10.7554/eLife.11860.001 PMID:26754770

Electrical conductivity of high-purity germanium crystals at low temperature

Science.gov (United States)

Yang, Gang; Kooi, Kyler; Wang, Guojian; Mei, Hao; Li, Yangyang; Mei, Dongming

2018-05-01

The temperature dependence of electrical conductivity of single-crystal and polycrystalline high-purity germanium (HPGe) samples has been investigated in the temperature range from 7 to 100 K. The conductivity versus inverse of temperature curves for three single-crystal samples consist of two distinct temperature ranges: a high-temperature range where the conductivity increases to a maximum with decreasing temperature, and a low-temperature range where the conductivity continues decreasing slowly with decreasing temperature. In contrast, the conductivity versus inverse of temperature curves for three polycrystalline samples, in addition to a high- and a low-temperature range where a similar conductive behavior is shown, have a medium-temperature range where the conductivity decreases dramatically with decreasing temperature. The turning point temperature ({Tm}) which corresponds to the maximum values of the conductivity on the conductivity versus inverse of temperature curves are higher for the polycrystalline samples than for the single-crystal samples. Additionally, the net carrier concentrations of all samples have been calculated based on measured conductivity in the whole measurement temperature range. The calculated results show that the ionized carrier concentration increases with increasing temperature due to thermal excitation, but it reaches saturation around 40 K for the single-crystal samples and 70 K for the polycrystalline samples. All these differences between the single-crystal samples and the polycrystalline samples could be attributed to trapping and scattering effects of the grain boundaries on the charge carriers. The relevant physical models have been proposed to explain these differences in the conductive behaviors between two kinds of samples.

Two inorganic-organic hybrid materials based on polyoxometalate anions and methylene blue: Preparations, crystal structures and properties

International Nuclear Information System (INIS)

Nie Shanshan; Zhang Yaobin; Liu Bin; Li Zuoxi; Hu Huaiming; Xue Ganglin; Fu Feng; Wang Jiwu

2010-01-01

Two novel inorganic-organic hybrid materials based on an organic dye cation methylene blue (MB) and Lindqvist-type POM polyanions, [C 22 H 18 N 3 S] 2 Mo 6 O 19 2DMF (1) and [C 22 H 18 N 3 S] 2 W 6 O 19 2DMF (2) were synthesized under ambient conditions and characterized by CV, IR spectroscopy, solid diffuse reflectance spectrum, UV-vis spectra in DMF solution, luminescent spectrum and single crystal X-ray diffraction. Crystallographic data reveal that compounds 1 and 2 are isostructural and both crystallize in the triclinic space group P1-bar . Their crystal structures present that the layers of organic molecules and inorganic anions array alternatively, and there exist strong π...π stacking interactions between dimeric MB cations and near distance interactions among organic dye cations, Lindqvist-type POM polyanions and DMF molecules. The solid diffuse reflectance spectra and UV-vis spectra in DMF solution appear new absorption bands ascribed to the charge-transfer transition between the cationic MB donor and the POM acceptors. Studies of the photoluminescent properties show that the formation of 1 and 2 lead to the fluorescence quenching of starting materials. -- Graphical abstract: Their crystal structures present that the layers of organic molecules and inorganic anions array alternatively, and there exist strong π...π stacking interactions between dimeric MB cations. Display Omitted

Exact Solution of a Generalized Nonlinear Schrodinger Equation Dimer

DEFF Research Database (Denmark)

Christiansen, Peter Leth; Maniadis, P.; Tsironis, G.P.

1998-01-01

We present exact solutions for a nonlinear dimer system defined throught a discrete nonlinear Schrodinger equation that contains also an integrable Ablowitz-Ladik term. The solutions are obtained throught a transformation that maps the dimer into a double Sine-Gordon like ordinary nonlinear...... differential equation....

Quantum-statistical mechanics of an atom-dimer mixture: Lee-Yang cluster expansion approach

International Nuclear Information System (INIS)

Ohkuma, Takahiro; Ueda, Masahito

2006-01-01

We use the Lee-Yang cluster expansion method to study quantum-statistical properties of a mixture of interconvertible atoms and dimers, where the dimers form in a two-body bound state of the atoms. We point out an infinite series of cluster diagrams whose summation leads to the Bose-Einstein condensation of the dimers below a critical temperature. Our theory captures some important features of a cold atom-dimer mixture such as interconversion of atoms and dimers and properties of the mixture at the unitarity limit

Crystallization and preliminary X-ray diffraction analysis of the fructofuranosidase from Xanthophyllomyces dendrorhous

International Nuclear Information System (INIS)

Polo, Aitana; Linde, Dolores; Estévez, Marta; Fernández-Lobato, María; Sanz-Aparicio, Julia

2010-01-01

The invertase from X. dendrorhous has been purified, deglycosylated and crystallized and diffraction data have been collected to 2.3 Å resolution. Xanthophyllomyces dendrorhous invertase is an extracellular enzyme that releases β-fructose from the nonreducing termini of various β-d-fructofuranoside substrates. Its ability to produce neokestose by transglycosylation makes this enzyme an interesting research target for applications in industrial biotechnology. The native enzyme, which is highly glycosylated, failed to crystallize. Therefore, it was submitted to EndoH deglycosylating treatment and crystals were grown by vapour-diffusion methods. The crystals belonged to space group P2 1 2 1 2, with unit-cell parameters a = 75.29, b = 204.93, c = 146.25 Å. Several diffraction data sets were collected using a synchrotron source. Self-rotation function and gel-filtration experiments suggested that the enzyme is a dimer with twofold symmetry

Formation of thymine containing dimers in skin exposed to ultraviolet radiation

Energy Technology Data Exchange (ETDEWEB)

Johnson, B E [Dundee Univ. (UK)

1978-01-01

Nuclear DNA appears to be the major molecular target for the inhibitory, mutagenic and lethal effects of ultraviolet radiation on cells in culture. Cyclobutyl dimers between adjacent pyrimidine bases, the major photochemical lesions for these effects in prokaryotes, also play a part in UVR effects on eukaryotes cells. Pyrimidine dimers have been isolated from in vivo UV-irradiated guinea pig and mouse skin. The wavelength dependence for dimer induction is similar to that for acute skin reactions but no direct causal relationship has been established. Sunlight UVR may induce dimers in skin DNA. Excision of dimers from mouse skin in vivo is deficient as it is for most rodent cells in culture; human cell excision is efficient and the difficulties in interpretation of UV-carcinogenesis results with mice in terms of human skin cancer are therefore increased.

Artificial light harvesting by dimerized Möbius ring

Science.gov (United States)

Xu, Lei; Gong, Z. R.; Tao, Ming-Jie; Ai, Qing

2018-04-01

We theoretically study artificial light harvesting by a Möbius ring. When the donors in the ring are dimerized, the energies of the donor ring are split into two subbands. Because of the nontrivial Möbius boundary condition, both the photon and acceptor are coupled to all collective-excitation modes in the donor ring. Therefore, the quantum dynamics in the light harvesting is subtly influenced by dimerization in the Möbius ring. It is discovered that energy transfer is more efficient in a dimerized ring than that in an equally spaced ring. This discovery is also confirmed by a calculation with the perturbation theory, which is equivalent to the Wigner-Weisskopf approximation. Our findings may be beneficial to the optimal design of artificial light harvesting.

The induction and repair of cyclobutane thymidine dimers in human skin

International Nuclear Information System (INIS)

Roza, L.; Erasmus Univ., Rotterdam; Vermeulen, W.; Schans, G.P. van der; Lohman, P.H.M.

1987-01-01

The most important detrimental effect of ultraviolet radiation (UV) on the living cell, so far known, is the induction of damage in the DNA. The major photoproducts induced in DNA by UV-C (200-280 nm) and UV-B (280-315 nm) are the cyclobutane-type pyrimidine dimers, which have been implicated in UV-induced mutagenesis and carcinogenesis. Dimer lesions in DNA of cells may be repaired in the dark by a multi-enzyme process (excision repair), or via a light dependent enzymatic reaction known as photoreactivation (phr) which is specific for pyrimidine dimers. Although phr has been found to occur in a wide range of organisms, studies on the presence of phr in mammalian cells have yielded conflicting results. To investigate repair of pyrimidine dimers in human skin cells irradiated in vivo, a specific and sensitive detection method was developed based on a monoclonal antibody directed against thymidine dimers. Application together with a fluorescent immunostaining permits the direct detection of thymidine dimers in human skin cells. The method is used in studies aimed at a better understanding of the role of these lesions in the process of carcinogenesis. A report is given on the isolation and characterization of the antibodies, and their application in a study on the induction of pyrimidine dimers in human skin and on photorepair in cultured cells. 10 refs.; 2 figs

Effects of Dimerization of Serratia marcescens Endonuclease on Water Dynamics.

Energy Technology Data Exchange (ETDEWEB)

Chen, Chuanying; Beck, Brian W.; Krause, Kurt; Weksberg, Tiffany E.; Pettitt, Bernard M.

2007-02-15

The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The dynamics and structure of Serratia marcescens endonuclease and its neighboring solvent are investigated by molecular dynamics (MD). Comparisons are made with structural and biochemical experiments. The dimer form is physiologic and functions more processively than the monomer. We previously found a channel formed by connected clusters of waters from the active site to the dimer interface. Here, we show that dimerization clearly changes correlations in the water structure and dynamics in the active site not seen in the monomer. Our results indicate that water at the active sites of the dimer is less affected compared with bulk solvent than in the monomer where it has much slower characteristic relaxation times. Given that water is a required participant in the reaction, this gives a clear advantage to dimerization in the absence of an apparent ability to use both active sites simultaneously.

Crystallization and preliminary characterization of dihydropteridine reductase from Dictyostelium discoideum

International Nuclear Information System (INIS)

Chen, Cong; Seo, Kyung Hye; Kim, Hye Lim; Zhuang, Ningning; Park, Young Shik; Lee, Kon Ho

2008-01-01

The dihydropteridine reductase from D. discoideum has been crystallized. Diffraction data were collected from a rectangular-shaped crystal to 2.16 Å resolution. Dihydropteridine reductase from Dictyostelium discoideum (dicDHPR) can produce d-threo-BH 4 [6R-(1′R,2′R)-5,6,7,8-tetrahydrobiopterin], a stereoisomer of l-erythro-BH 4 , in the last step of tetrahydrobiopterin (BH 4 ) recycling. In this reaction, DHPR uses NADH as a cofactor to reduce quinonoid dihydrobiopterin back to BH 4 . To date, the enzyme has been purified to homogeneity from many sources. In this report, the dicDHPR–NAD complex has been crystallized using the hanging-drop vapour-diffusion method with PEG 3350 as a precipitant. Rectangular-shaped crystals were obtained. Crystals grew to maximum dimensions of 0.4 × 0.6 × 0.1 mm. The crystal belonged to space group P2 1 , with unit-cell parameters a = 49.81, b = 129.90, c = 78.76 Å, β = 100.00°, and contained four molecules in the asymmetric unit, forming two closely interacting dicDHPR–NAD dimers. Diffraction data were collected to 2.16 Å resolution using synchrotron radiation. The crystal structure has been determined using the molecular-replacement method

Interatomic potentials for PuC by Chen–Möbius multiple lattice inversion

International Nuclear Information System (INIS)

Huang, H.; Meng, D.Q.; Lai, X.C.; Li, G.; Long, Y.

2013-01-01

The atomic interactions of PuC with B1 structure were described by Chen–Möbius lattice inversion combined with first-principle calculations. In order to obtain the inversion potential parameters of PuC, three different structures including two virtual crystals were built and the Morse function plus a modified term was adopted to fit the pair-potential curves. The reliability of the inversion potential was tested by checking the stability of the transition of PuC from disordered to ordered state and comparing the calculated and experimental physical and thermal properties of PuC. All the results show that the inversion potential could give a stable and accurate description of the atomic interactions in PuC and the physical and thermal properties of PuC are well reproduced by the potential

Designer interface peptide grafts target estrogen receptor alpha dimerization

International Nuclear Information System (INIS)

Chakraborty, S.; Asare, B.K.; Biswas, P.K.; Rajnarayanan, R.V.

2016-01-01

The nuclear transcription factor estrogen receptor alpha (ERα), triggered by its cognate ligand estrogen, regulates a variety of cellular signaling events. ERα is expressed in 70% of breast cancers and is a widely validated target for anti-breast cancer drug discovery. Administration of anti-estrogen to block estrogen receptor activation is still a viable anti-breast cancer treatment option but anti-estrogen resistance has been a significant bottle-neck. Dimerization of estrogen receptor is required for ER activation. Blocking ERα dimerization is therefore a complementary and alternative strategy to combat anti-estrogen resistance. Dimer interface peptide “I-box” derived from ER residues 503–518 specifically blocks ER dimerization. Recently using a comprehensive molecular simulation we studied the interaction dynamics of ERα LBDs in a homo-dimer. Based on this study, we identified three interface recognition peptide motifs LDKITDT (ERα residues 479–485), LQQQHQRLAQ (residues 497–506), and LSHIRHMSNK (residues 511–520) and reported the suitability of using LQQQHQRLAQ (ER 497–506) as a template to design inhibitors of ERα dimerization. Stability and self-aggregation of peptide based therapeutics poses a significant bottle-neck to proceed further. In this study utilizing peptide grafted to preserve their pharmacophoric recognition motif and assessed their stability and potential to block ERα mediated activity in silico and in vitro. The Grafted peptides blocked ERα mediated cell proliferation and viability of breast cancer cells but did not alter their apoptotic fate. We believe the structural clues identified in this study can be used to identify novel peptidometics and small molecules that specifically target ER dimer interface generating a new breed of anti-cancer agents. - Highlights: • Designer peptide grafts retain core molecular recognition motif during MD simulations. • Designer peptide grafts with Poly-ALA helix form stable

Designer interface peptide grafts target estrogen receptor alpha dimerization

Energy Technology Data Exchange (ETDEWEB)

Chakraborty, S. [Laboratory of Computational Biophysics & Bioengineering, Department of Physics, Tougaloo College, Tougaloo, MS 39174 (United States); Asare, B.K. [Department of Pharmacology and Toxicology, University of Buffalo, Buffalo, NY 14214 (United States); Biswas, P.K., E-mail: pbiswas@tougaloo.edu [Laboratory of Computational Biophysics & Bioengineering, Department of Physics, Tougaloo College, Tougaloo, MS 39174 (United States); Rajnarayanan, R.V., E-mail: rajendra@buffalo.edu [Department of Pharmacology and Toxicology, University of Buffalo, Buffalo, NY 14214 (United States)

2016-09-09

The nuclear transcription factor estrogen receptor alpha (ERα), triggered by its cognate ligand estrogen, regulates a variety of cellular signaling events. ERα is expressed in 70% of breast cancers and is a widely validated target for anti-breast cancer drug discovery. Administration of anti-estrogen to block estrogen receptor activation is still a viable anti-breast cancer treatment option but anti-estrogen resistance has been a significant bottle-neck. Dimerization of estrogen receptor is required for ER activation. Blocking ERα dimerization is therefore a complementary and alternative strategy to combat anti-estrogen resistance. Dimer interface peptide “I-box” derived from ER residues 503–518 specifically blocks ER dimerization. Recently using a comprehensive molecular simulation we studied the interaction dynamics of ERα LBDs in a homo-dimer. Based on this study, we identified three interface recognition peptide motifs LDKITDT (ERα residues 479–485), LQQQHQRLAQ (residues 497–506), and LSHIRHMSNK (residues 511–520) and reported the suitability of using LQQQHQRLAQ (ER 497–506) as a template to design inhibitors of ERα dimerization. Stability and self-aggregation of peptide based therapeutics poses a significant bottle-neck to proceed further. In this study utilizing peptide grafted to preserve their pharmacophoric recognition motif and assessed their stability and potential to block ERα mediated activity in silico and in vitro. The Grafted peptides blocked ERα mediated cell proliferation and viability of breast cancer cells but did not alter their apoptotic fate. We believe the structural clues identified in this study can be used to identify novel peptidometics and small molecules that specifically target ER dimer interface generating a new breed of anti-cancer agents. - Highlights: • Designer peptide grafts retain core molecular recognition motif during MD simulations. • Designer peptide grafts with Poly-ALA helix form stable

Dihydroxo-bridged dimeric Cu(II) system containing sandwiched non-coordinating phenylacetate anion: Crystal structure, spectroscopic, anti-bacterial, anti-fungal and DNA-binding studies of [(phen)(H2O)Cu(OH)2Cu(H2O)(phen)]2L.6H2O: (HL = phenylacetic acid; phen = 1,10-phenanthroline)

Science.gov (United States)

Iqbal, Muhammad; Ali, Saqib; Tahir, Muhammad Nawaz; Shah, Naseer Ali

2017-09-01

This paper reports the synthesis, X-ray crystal structure, DNA-binding, antibacterial and antifungal studies of a rare dihydroxo-bridged dinuclear copper(II) complex including 1,10-phenanthroline (Phen) ligands and phenylacetate (L) anions, [Cu2(Phen)2(OH)2(H2O)2].2L.6H2O. Structural data revealed distorted square-pyramidal geometry for each copper(II) atom with the basal plane formed by the two nitrogen atoms of the phenantroline ligand and the oxygen atoms of two bridging hydroxyl groups. The apical positions are filled by the oxygen atom from a water molecule. This forms a centrosymmetric cationic dimer where the uncoordinated phenylacetate ligands serve to balance the electrical charge. The dimers interact by means of hydrogen bonds aided by the coordinated as well as uncoordinated water molecules and phenyl-acetate moieties in the crystal lattice. The binding ability of the complex with salmon sperm DNA was determined using cyclic voltammetry and absorption spectroscopy yielding binding constants 2.426 × 104 M-1 and 1.399 × 104 M-1, respectively. The complex was screened against two Gram-positive (Micrococcus luteus and Bacillus subtilis) and one Gram-negative (Escherichia coli) bacterial strains exhibiting significant activity against all the three strains. The complex exhibited significant, moderate and no activity against fungal strains Mucor piriformis, Helminthosporium solani and Aspergillus Niger, respectively. These preliminary tests indicate the competence of the complex towards the development of a potent biological drug.

Expression, purification, crystallization and preliminary X-ray analysis of tannase from Lactobacillus plantarum

International Nuclear Information System (INIS)

Wu, Mingbo; Peng, Xiaohong; Wen, Hua; Wang, Qin; Chen, Qianming; McKinstry, William J.; Ren, Bin

2013-01-01

A recombinant form of tannase from L. plantarum was purified and crystallized. A native data set has been collected to 1.65 Å resolution. Tannase catalyses the hydrolysis of the galloyl ester bond of tannins to release gallic acid. It belongs to the serine esterases and has wide applications in the food, feed, beverage, pharmaceutical and chemical industries. The tannase from Lactobacillus plantarum was cloned, expressed and purified. The protein was crystallized by the sitting-drop vapour-diffusion method with microseeding. The crystals belonged to space group P1, with unit-cell paramters a = 46.5, b = 62.8, c = 83.8 Å, α = 70.4, β = 86.0, γ = 79.4°. Although the enzyme exists mainly as a monomer in solution, it forms a dimer in the asymmetric unit of the crystal. The crystals diffracted to beyond 1.60 Å resolution using synchrotron radiation and a complete data set was collected to 1.65 Å resolution

Spatial filters on demand based on aperiodic Photonic Crystals

Energy Technology Data Exchange (ETDEWEB)

Gailevicius, Darius; Purlys, Vytautas; Peckus, Martynas; Gadonas, Roaldas [Laser Research Center, Department of Quantum Electronics, Vilnius University (Lithuania); Staliunas, Kestutis [DONLL, Departament de Fisica, Universitat Politecnica de Catalunya (UPC), Terrassa (Spain); Institucio Catalana de Recerca i Estudis Avancats (ICREA), Barcelona (Spain)

2017-08-15

Photonic Crystal spatial filters, apart from stand-alone spatial filtering function, can also suppress multi-transverse-mode operation in laser resonators. Here it is shown that such photonic crystals can be designed by solving the inverse problem: for a given spatial filtering profile. Optimized Photonic Crystal filters were fabricated in photosensitive glass. Experiments have shown that such filters provide a more pronounced filtering effect for total and partial transmissivity conditions. (copyright 2017 by WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

N-(2,5-Dimethylphenyl-4-methylbenzenesulfonamide

Directory of Open Access Journals (Sweden)

B. Thimme Gowda

2010-01-01

Full Text Available In the crystal structure of the title compound, C15H17NO2S, the conformation of the N—C bond in the C—SO2—NH—C segment has gauche torsions with respect to the S=O bonds. The molecule is bent at the S atom with a C—SO2—NH—C torsion angle of −61.0 (2°. The dihedral angle between the two aromatic rings is 49.4 (1°. The crystal structure features inversion-related dimers linked by pairs of N—H...O hydrogen bonds.

2-Amino-5-fluorobenzoic acid

Directory of Open Access Journals (Sweden)

K. Gunasekaran

2013-03-01

Full Text Available In the title compound, C7H6FNO2, the molecule is almost planar (r.m.s. deviation for the non-H atoms = 0.015 Å and an intramolecular N—H...O hydrogen bond closes an S(6 ring. In the crystal, inversion dimers linked by pairs of O—H...O hydrogen bonds generate R22(8 loops. Weak N—H...F hydrogen bonds, short F...F contacts [2.763 (2 Å] and aromatic π–π stacking interactions [centroid–centroid separation = 3.5570 (11 Å] are also observed in the crystal structure.

Mixed-valence, layered, cation radical salts of the ethane-bridged dimeric tetrathiafulvalene [(EDT-TTF-CH2-)2#centre dot#+] [X-][THF]0.5, X-=FeCl4-, GaCl4-

DEFF Research Database (Denmark)

Mézière, C.; Fourmigué, M.; Canadell, E.

2000-01-01

The synthesis and X-ray crystal structure of the ethane-linked dimeric tetrathiafulvalene [(EDT-TTF-CH2)(2)], 1,2-bis(ethylenedithiotetrathiafulvalenyl)ethane (1), is reported. It oxidizes reversibly at 0.45 and 0.90 V vs SCE. Electrocrystallization in the presence of [n-Bu4N][FeCl4] or [n-Bu4N...

Dimerization of the voltage-sensing phosphatase controls its voltage-sensing and catalytic activity.

Science.gov (United States)

Rayaprolu, Vamseedhar; Royal, Perrine; Stengel, Karen; Sandoz, Guillaume; Kohout, Susy C

2018-05-07

Multimerization is a key characteristic of most voltage-sensing proteins. The main exception was thought to be the Ciona intestinalis voltage-sensing phosphatase (Ci-VSP). In this study, we show that multimerization is also critical for Ci-VSP function. Using coimmunoprecipitation and single-molecule pull-down, we find that Ci-VSP stoichiometry is flexible. It exists as both monomers and dimers, with dimers favored at higher concentrations. We show strong dimerization via the voltage-sensing domain (VSD) and weak dimerization via the phosphatase domain. Using voltage-clamp fluorometry, we also find that VSDs cooperate to lower the voltage dependence of activation, thus favoring the activation of Ci-VSP. Finally, using activity assays, we find that dimerization alters Ci-VSP substrate specificity such that only dimeric Ci-VSP is able to dephosphorylate the 3-phosphate from PI(3,4,5)P 3 or PI(3,4)P 2 Our results indicate that dimerization plays a significant role in Ci-VSP function. © 2018 Rayaprolu et al.

Changes in fibrin D-dimer, fibrinogen, and protein S during pregnancy

DEFF Research Database (Denmark)

Hansen, Anette Tarp; Andreasen, Birgitte Horst; Salvig, Jannie Dalby

2010-01-01

Background. Pregnancy is a hypercoagulable state with a 5- to 10- fold higher risk of venous thromboembolism. Existing reference intervals for fibrin D-dimer (D-dimer), functional fibrinogen (fibrinogen) and protein S, free antigen (protein S) are based on non-pregnant patients and reference...... intervals for pregnant patients are warranted. Objectives. The aim of the present study was to contribute to the establishment of reference intervals for D-dimer, fibrinogen and protein S during pregnancy and to discuss the use of the analyses during pregnancy. Methods. We included 55 healthy pregnant women...... in gestational week 11–17, with normal current pregnancy. Blood samples were collected in gestational weeks 11–17, 21–27 and 34–37. The three plasma parameters D-dimer, fibrinogen and protein S were analysed by STA-R Evolution®. Results. A significant rise in D-dimer was found from first to second trimester (p...

Radiation-induced tetramer-to-dimer transition of Escherichia coli lactose repressor

International Nuclear Information System (INIS)

Goffinont, S.; Davidkova, M.; Spotheim-Maurizot, M.

2009-01-01

The wild type lactose repressor of Escherichia coli is a tetrameric protein formed by two identical dimers. They are associated via a C-terminal 4-helix bundle (called tetramerization domain) whose stability is ensured by the interaction of leucine zipper motifs. Upon in vitro γ-irradiation the repressor losses its ability to bind the operator DNA sequence due to damage of its DNA-binding domains. Using an engineered dimeric repressor for comparison, we show here that irradiation induces also the change of repressor oligomerisation state from tetramer to dimer. The splitting of the tetramer into dimers can result from the oxidation of the leucine residues of the tetramerization domain.

From Soil to Structure, a Novel Dimeric β-Glucosidase Belonging to Glycoside Hydrolase Family 3 Isolated from Compost Using Metagenomic Analysis

Science.gov (United States)

McAndrew, Ryan P.; Park, Joshua I.; Heins, Richard A.; Reindl, Wolfgang; Friedland, Gregory D.; D'haeseleer, Patrik; Northen, Trent; Sale, Kenneth L.; Simmons, Blake A.; Adams, Paul D.

2013-01-01

A recent metagenomic analysis sequenced a switchgrass-adapted compost community to identify enzymes from microorganisms that were specifically adapted to switchgrass under thermophilic conditions. These enzymes are being examined as part of the pretreatment process for the production of “second-generation” biofuels. Among the enzymes discovered was JMB19063, a novel three-domain β-glucosidase that belongs to the GH3 (glycoside hydrolase 3) family. Here, we report the structure of JMB19063 in complex with glucose and the catalytic variant D261N crystallized in the presence of cellopentaose. JMB19063 is first structure of a dimeric member of the GH3 family, and we demonstrate that dimerization is required for catalytic activity. Arg-587 and Phe-598 from the C-terminal domain of the opposing monomer are shown to interact with bound ligands in the D261N structure. Enzyme assays confirmed that these residues are absolutely essential for full catalytic activity. PMID:23580647

Crystal Structures of Apo and Metal-Bound Forms of the UreE Protein from Helicobacter pylori: Role of Multiple Metal Binding Sites

Energy Technology Data Exchange (ETDEWEB)

Shi, Rong; Munger, Christine; Asinas, Abdalin; Benoit, Stephane L.; Miller, Erica; Matte, Allan; Maier, Robert J.; Cygler, Miroslaw (McGill); (Georgia); (Biotech Res.)

2010-10-22

The crystal structure of the urease maturation protein UreE from Helicobacter pylori has been determined in its apo form at 2.1 {angstrom} resolution, bound to Cu{sup 2+} at 2.7 {angstrom} resolution, and bound to Ni{sup 2+} at 3.1 {angstrom} resolution. Apo UreE forms dimers, while the metal-bound enzymes are arranged as tetramers that consist of a dimer of dimers associated around the metal ion through coordination by His102 residues from each subunit of the tetramer. Comparison of independent subunits from different crystal forms indicates changes in the relative arrangement of the N- and C-terminal domains in response to metal binding. The improved ability of engineered versions of UreE containing hexahistidine sequences at either the N-terminal or C-terminal end to provide Ni{sup 2+} for the final metal sink (urease) is eliminated in the H102A version. Therefore, the ability of the improved Ni{sup 2+}-binding versions to deliver more nickel is likely an effect of an increased local concentration of metal ions that can rapidly replenish transferred ions bound to His102.

D-dimer: a useful tool in gauging optimal duration of oral anticoagulant therapy?

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M. Silingardi

2013-05-01

Full Text Available BACKGROUND AND AIM OF THE STUDY Optimal duration of oral anticoagulant therapy (OAT in idiopathic venous thromboembolism (VTE is unknown. Indefinite OAT carries an unacceptable risk of major bleeding and prospective studies have demonstrated that OAT is no longer protective after its withdrawal. How to identify the patients at risk for recurrence? D-dimer is a marker of thrombin activity. Early prospective studies showed that elevated D-dimer levels after anticoagulation had a highly predictive value for a recurrent episode. Does D-dimer assay have a role in gauging the appropriate duration of anticoagulant therapy? The PROLONG study tries to answer this question. METHOD D-dimer assay was performed one month after stopping anticoagulation. Patiens with normal D-dimer levels did not resume anticoagulation while patients with elevated D-dimer levels were randomized to discontinue or resume anticoagulation. Study end-points was the composite of recurrent VTE and major bleeding during an average follow-up of 1.4 years. RESULTS The rate of recurrence is significantly higher in patients with elevated D-dimer levels who discontinued anticoagulation. Resuming anticoagulation in this cohort of patients markedly reduces recurrent events without increasing major bleeding. DISCUSSION AND CONCLUSIONS PROLONG study is provocative, because D-dimer assay is simple, thus not requiring dedicated laboratory facilities. D-dimer test has otherwise high sensitivity but low specificity in VTE diagnosis. Aspecifically elevated D-dimer levels are available in the elderly and the majority of patients included in the study were > 65 years old, thus introducing a possible selection bias. Nonetheless the results of the study are useful for the clinician. Prolongation of vitamin K antagonists in patients with elevated D-dimer levels one month after discontinuation of OAT for a first unprovoked episode of VTE results in a favourable risk-benefit relationship. Probably this

Dimer and String Formation during Low Temperature Silicon Deposition on Si(100)

DEFF Research Database (Denmark)

Smith, A. P.; Jonsson, Hannes

1996-01-01

We present theoretical results based on density functional theory and kinetic Monte Carlo simulations of silicon deposition and address observations made in recently reported low temperature scanning tunneling microscopy studies. A mechanism is presented which explains dimer formation on top...... of the substrate's dimer rows at 160 K and up to room temperature, while between-row dimers and longer strings of adatoms (''diluted dimer rows'') form at higher temperature. A crossover occurs at around room temperature between two different mechanisms for adatom diffusion in our model....

Crystal structures of (E-4-[1-(2-carbamothioylhydrazinylideneethyl]phenyl acetate and (E-4-[1-(2-carbamothioylhydrazinylideneethyl]phenyl benzoate

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Vijayan Viswanathan

2017-01-01

Full Text Available In the title compounds, C11H13N3O2S, (I, and C16H15N3O2S, (II, the thiosemicarbazone group adopts an extended conformation. The acetate ester (I crystallizes with two independent molecules in the asymmetric unit. In the benzoate ester (II, the planes of the two aryl rings are inclined to one another by 46.70 (7°. In both compounds, there is a short intramolecular N—H...N contact present, forming an S(5 ring motif. In the crystals of both compounds, molecules are linked via pairs of N—H...S hydrogen bonds, forming dimers with R22(8 ring motifs. The dimers are linked by N—H...S and N—H...O hydrogen bonds, forming slabs parallel to (01-1. In (I, there are N—H...π and C—H...π interactions present within the slabs, while in (II, there are only N—H...π interactions present.

A discotic triphenylene dimer as organic hole transporting material for electroluminescence devices

International Nuclear Information System (INIS)

Mao Huaxiang; He Zhiqun; Wang Junling; Zhang Chunxiu; Xie, Ping; Zhang Rongben

2007-01-01

A triphenylene dimer, an intermediate between a discotic triphenylene molecule and the macromolecule, had been prepared by linking together two triphenylene units via phenylene carbamate linkages, which was formed through a reaction between one 1,4-phenylene diisocyanate and two hydroxyl end groups on flexible substituents of triphenylenes. The dimer exhibited good film-forming property. Its temperature-dependent phase transitions were investigated using differential scanning calorimetry and polarized optical microscopy. Room temperature microstructure of the dimer was analyzed by X-ray diffraction. Charge mobility of the triphenylene dimer was also measured. Our preliminary result using the materials in a sandwich light-emitting device is reported here. It demonstrates that the triphenylene dimer is a promising candidate as a hole transporting material

D-dimer as marker for microcirculatory failure: correlation with LOD and APACHE II scores.

Science.gov (United States)

Angstwurm, Matthias W A; Reininger, Armin J; Spannagl, Michael

2004-01-01

The relevance of plasma d-dimer levels as marker for morbidity and organ dysfunction in severely ill patients is largely unknown. In a prospective study we determined d-dimer plasma levels of 800 unselected patients at admission to our intensive care unit. In 91% of the patients' samples d-dimer levels were elevated, in some patients up to several hundredfold as compared to normal values. The highest mean d-dimer values were present in the patient group with thromboembolic diseases, and particularly in non-survivors of pulmonary embolism. In patients with circulatory impairment (r=0.794) and in patients with infections (r=0.487) a statistically significant correlation was present between d-dimer levels and the APACHE II score (P<0.001). The logistic organ dysfunction score (LOD, P<0.001) correlated with d-dimer levels only in patients with circulatory impairment (r=0.474). On the contrary, patients without circulatory impairment demonstrated no correlation of d-dimer levels to the APACHE II or LOD score. Taking all patients together, no correlations of d-dimer levels with single organ failure or with indicators of infection could be detected. In conclusion, d-dimer plasma levels strongly correlated with the severity of the disease and organ dysfunction in patients with circulatory impairment or infections suggesting that elevated d-dimer levels may reflect the extent of microcirculatory failure. Thus, a therapeutic strategy to improve the microcirculation in such patients may be monitored using d-dimer plasma levels.

Dimerization of the Glucan Phosphatase Laforin Requires the Participation of Cysteine 329

Science.gov (United States)

Sánchez-Martín, Pablo; Raththagala, Madushi; Bridges, Travis M.; Husodo, Satrio; Gentry, Matthew S.; Sanz, Pascual; Romá-Mateo, Carlos

2013-01-01

Laforin, encoded by a gene that is mutated in Lafora Disease (LD, OMIM 254780), is a modular protein composed of a carbohydrate-binding module and a dual-specificity phosphatase domain. Laforin is the founding member of the glucan-phosphatase family and regulates the levels of phosphate present in glycogen. Multiple reports have described the capability of laforin to form dimers, although the function of these dimers and their relationship with LD remains unclear. Recent evidence suggests that laforin dimerization depends on redox conditions, suggesting that disulfide bonds are involved in laforin dimerization. Using site-directed mutagenesis we constructed laforin mutants in which individual cysteine residues were replaced by serine and then tested the ability of each protein to dimerize using recombinant protein as well as a mammalian cell culture assay. Laforin-Cys329Ser was the only Cys/Ser mutant unable to form dimers in both assays. We also generated a laforin truncation lacking the last three amino acids, laforin-Cys329X, and this truncation also failed to dimerize. Interestingly, laforin-Cys329Ser and laforin-Cys329X were able to bind glucans, and maintained wild type phosphatase activity against both exogenous and biologically relevant substrates. Furthermore, laforin-Cys329Ser was fully capable of participating in the ubiquitination process driven by a laforin-malin complex. These results suggest that dimerization is not required for laforin phosphatase activity, glucan binding, or for the formation of a functional laforin-malin complex. Cumulatively, these results suggest that cysteine 329 is specifically involved in the dimerization process of laforin. Therefore, the C329S mutant constitutes a valuable tool to analyze the physiological implications of laforin’s oligomerization. PMID:23922729

Crystallization and preliminary X-ray diffraction analysis of alanine racemase from Pseudomonas putida YZ-26

International Nuclear Information System (INIS)

Liu, Junlin; Feng, Lei; Shi, Yawei; Feng, Wei

2012-01-01

A recombinant alanine racemase from the Pseudomonas putida YZ-26, has been crystallized by the sitting-drop vapor-diffusion method and X-ray diffraction data were collected to 2.4 Å. A recombinant form of alanine racemase (Alr) from Pseudomonas putida YZ-26 has been crystallized by the sitting-drop vapour diffusion method. X-ray diffraction data were collected to 2.4 Å resolution. The crystals belong to the space group C222 1 , with unit-cell parameters a = 118.08, b = 141.86, c = 113.83 Å, and contain an Alr dimer in the asymmetric unit. The Matthews coefficient and the solvent content were calculated to be 2.8 Å 3 Da −1 and approximately 50%, respectively

4-[(3-Phenyl-4,5-dihydroisoxazol-5-ylmethyl]-2H-benzo[b][1,4]thiazin-3(4H-one

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Nada Kheira Sebbar

2016-06-01

Full Text Available In the title compound, C18H16N2O2S, the 5-dihydroisoxazol-5-yl ring and its phenyl substituent are nearly coplanar, with the largest deviation from the mean plane being 0.0184 (16 Å. The thiomorpholin-3-one ring adopts a screw-boat conformation and the attached benzene ring makes a dihedral angle of 42.26 (7° with the mean plane through the 3-phenyl-4,5-dihydroisoxazol-5-yl ring system. In the crystal, molecules are linked by pairs of C—H...N hydrogen bonds, forming inversion dimers. These dimers are linked via C—H...O hydrogen bonds, generating a three-dimensional network.

Expression, purification, crystallization and preliminary X-ray analysis of a nucleoside kinase from the hyperthermophile Methanocaldococcus jannaschii

International Nuclear Information System (INIS)

Arnfors, Linda; Hansen, Thomas; Meining, Winfried; Schönheit, Peter; Ladenstein, Rudolf

2005-01-01

Nucleoside kinase from the hyperthermophilic archaeon M. jannaschii is a member of the PFK-B family which belongs to the ribokinase superfamily. Here, its expression, purification, crystallization and preliminary X-ray analysis are described. Methanocaldococcus jannaschii nucleoside kinase (MjNK) is an ATP-dependent non-allosteric phosphotransferase that shows high catalytic activity for guanosine, inosine and cytidine. MjNK is a member of the phosphofructokinase B family, but participates in the biosynthesis of nucleoside monophosphates rather than in glycolysis. MjNK was crystallized as the apoenzyme as well as in complex with an ATP analogue and Mg 2+ . The latter crystal form was also soaked with fructose-6-phosphate. Synchrotron-radiation data were collected to 1.70 Å for the apoenzyme crystals and 1.93 Å for the complex crystals. All crystals exhibit orthorhombic symmetry; however, the apoenzyme crystals contain one monomer per asymmetric unit whereas the complex crystals contain a dimer

Dimer coverings on random multiple chains of planar honeycomb lattices

International Nuclear Information System (INIS)

Ren, Haizhen; Zhang, Fuji; Qian, Jianguo

2012-01-01

We study dimer coverings on random multiple chains. A multiple chain is a planar honeycomb lattice constructed by successively fusing copies of a ‘straight’ condensed hexagonal chain at the bottom of the previous one in two possible ways. A random multiple chain is then generated by admitting the Bernoulli distribution on the two types of fusing, which describes a zeroth-order Markov process. We determine the expectation of the number of the pure dimer coverings (perfect matchings) over the ensemble of random multiple chains by the transfer matrix approach. Our result shows that, with only two exceptions, the average of the logarithm of this expectation (i.e., the annealed entropy per dimer) is asymptotically nonzero when the fusing process goes to infinity and the length of the hexagonal chain is fixed, though it is zero when the fusing process and the length of the hexagonal chain go to infinity simultaneously. Some numerical results are provided to support our conclusion, from which we can see that the asymptotic behavior fits well to the theoretical results. We also apply the transfer matrix approach to the quenched entropy and reveal that the quenched entropy of random multiple chains has a close connection with the well-known Lyapunov exponent of random matrices. Using the theory of Lyapunov exponents we show that, for some random multiple chains, the quenched entropy per dimer is strictly smaller than the annealed one when the fusing process goes to infinity. Finally, we determine the expectation of the free energy per dimer over the ensemble of the random multiple chains in which the three types of dimers in different orientations are distinguished, and specify a series of non-random multiple chains whose free energy per dimer is asymptotically equal to this expectation. (paper)

A new D-dimer cutoff in bedridden hospitalized elderly patients.

Science.gov (United States)

Granziera, Serena; Rechichi, Alfonsina; De Rui, Marina; De Carlo, Paola; Bertozzo, Giulia; Marigo, Lucia; Nante, Giovanni; Manzato, Enzo

2013-03-01

Asymptomatic deep vein thrombosis (DVT) and pulmonary embolism are leading causes of morbidity following the hospitalization of elderly people. The diagnosis of DVT is supported by the D-dimer laboratory assay. The concentration of D-dimer increases in patients with DVT, but may be high in other conditions too (i.e. cancer, infections and inflammation). Old age coincides with a physiological increase in D-dimer values, and that is why D-dimer assay in the elderly is characteristically highly sensitive but scarcely specific. The aim of our study was to explore the reliability of different D-dimer cutoffs for the diagnosis of asymptomatic DVT in a population of bedridden hospitalized elderly patients. We studied 199 patients who were a mean 86.3 ± 6.7 years old. All participants underwent lower limb Doppler ultrasound (DUS) and D-dimer venous blood sampling on admission. In our cohort, the usual cutoff proved highly sensitive (100%), but its specificity was very poor (20.1%). To find a higher cutoff that could improve the method's specificity, we analyzed our data using a receiver operating characteristic curve analysis. The resulting D-dimer cutoff of 492 μg/l enabled us to retain the same sensitivity while improving the test's specificity to 39.1%, with a consequent improvement in its positive predictive value and accuracy. In addition to improving the method's reliability, this result may be helpful in clinical practice, in both medical wards and nursing homes. By adopting a cutoff of 492 μg/l, clinicians could significantly increase the proportion of older patients in whom DVT can be safely ruled out, reducing referrals for DUS and administration of heparin, with consequent clinical, practical and economic advantages.

Kinetics of the monomer-dimer reaction of yeast hexokinase PI.

Science.gov (United States)

Hoggett, J G; Kellett, G L

1992-10-15

Kinetic studies of the glucose-dependent monomer-dimer reaction of yeast hexokinase PI at pH 8.0 in the presence of 0.1 M-KCl have been carried out using the fluorescence temperature-jump technique. A slow-relaxation effect was observed which was attributed from its dependence on enzyme concentration to the monomer-dimer reaction; the reciprocal relaxation times tau-1 varied from 3 s-1 at low concentrations of glucose to 42 s-1 at saturating concentrations. Rate constants for association (kass.) and dissociation (kdiss.) were determined as a function of glucose concentration using values of the equilibrium association constant of the monomer-dimer reaction derived from sedimentation ultracentrifugation studies under similar conditions, and also from the dependence of tau-2 on enzyme concentration. kass. was almost independent of glucose concentration and its value (2 x 10(5) M-1.s-1) was close to that expected for a diffusion-controlled process. The influence of glucose on the monomer-dimer reaction is entirely due to effects on kdiss., which increases from 0.21 s-1 in the absence of glucose to 25 s-1 at saturating concentrations. The monomer and dimer forms of hexokinase have different affinities and Km values for glucose, and the results reported here imply that there may be a significant lag in the response of the monomer-dimer reaction to changes in glucose concentrations in vivo with consequent hysteretic effects on the hexokinase activity.

Crystal Structure of AGR_C_4470p from Agrobacterium tumefaciens

Energy Technology Data Exchange (ETDEWEB)

Vorobiev,S.; Neely, H.; Seetharaman, J.; Ma, L.; Xiao, R.; Acton, T.; Montelione, G.; Tong, L.

2007-01-01

We report here the crystal structure at 2.0 {angstrom} resolution of the AGR{_}C{_}4470p protein from the Gram-negative bacterium Agrobacterium tumefaciens. The protein is a tightly associated dimer, each subunit of which bears strong structural homology with the two domains of the heme utilization protein ChuS from Escherichia coli and HemS from Yersinia enterocolitica. Remarkably, the organization of the AGR{_}C{_}4470p dimer is the same as that of the two domains in ChuS and HemS, providing structural evidence that these two proteins evolved by gene duplication. However, the binding site for heme, while conserved in HemS and ChuS, is not conserved in AGR{_}C{_}4470p, suggesting that it probably has a different function. This is supported by the presence of two homologs of AGR{_}C{_}4470p in E. coli, in addition to the ChuS protein.

Crystallization and preliminary X-ray diffraction analysis of the fructofuranosidase from Schwanniomyces occidentalis

International Nuclear Information System (INIS)

Polo, Aitana; Álvaro-Benito, Miguel; Fernández-Lobato, María; Sanz-Aparicio, Julia

2009-01-01

The invertase from Schwanniomyces occidentalis has been expressed in Saccharomyces cerevisiae, purified and crystallized. The wild-type enzyme was also purified and crystallized and diffraction data were collected to 2.9 Å resolution. Schwanniomyces occidentalis invertase is an extracellular enzyme that releases β-fructose from the nonreducing termini of various β-d-fructofuranoside substrates. Its ability to produce 6-kestose by transglycosylation makes this enzyme an interesting research target for applications in industrial biotechnology. The enzyme has been expressed in Saccharomyces cerevisiae. Recombinant and wild-type forms, which showed different glycosylation patterns, were crystallized by vapour-diffusion methods. Although crystallization trials were conducted on both forms of the protein, crystals suitable for X-ray crystallographic analyses were only obtained from the wild-type enzyme. The crystals belonged to space group P2 1 2 1 2 1 , with unit-cell parameters a = 105.78, b = 119.49, c = 137.68 Å. A diffraction data set was collected using a synchrotron source. Self-rotation function and sedimentation-velocity experiments suggested that the enzyme was dimeric with twofold symmetry

Structural features of the KPI domain control APP dimerization, trafficking, and processing.

Science.gov (United States)

Ben Khalifa, Naouel; Tyteca, Donatienne; Marinangeli, Claudia; Depuydt, Mathieu; Collet, Jean-François; Courtoy, Pierre J; Renauld, Jean-Christophe; Constantinescu, Stefan; Octave, Jean-Noël; Kienlen-Campard, Pascal

2012-02-01

The two major isoforms of human APP, APP695 and APP751, differ by the presence of a Kunitz-type protease inhibitor (KPI) domain in the extracellular region. APP processing and function is thought to be regulated by homodimerization. We used bimolecular fluorescence complementation (BiFC) to study dimerization of different APP isoforms and mutants. APP751 was found to form significantly more homodimers than APP695. Mutation of dimerization motifs in the TM domain did not affect fluorescence complementation, but native folding of KPI is critical for APP751 homodimerization. APP751 and APP695 dimers were mostly localized at steady state in the Golgi region, suggesting that most of the APP751 and 695 dimers are in the secretory pathway. Mutation of the KPI led to the retention of the APP homodimers in the endoplasmic reticulum. We finally showed that APP751 is more efficiently processed through the nonamyloidogenic pathway than APP695. These findings provide new insight on the particular role of KPI domain in APP dimerization. The correlation observed between dimerization, subcellular localization, and processing suggests that dimerization acts as an efficient regulator of APP trafficking in the secretory compartments that has major consequences on its processing.

(2E-3-Phenylprop-2-en-1-yl thiocyanate

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Ezzat Khan

2017-04-01

Full Text Available In the title compound, C10H9NS, the C—S—C bond angle is 99.41 (9° and the dihedral angle between the trans-alkene fragment and the benzene ring is 16.49 (19°. In the crystal, inversion dimers linked by pairs of extremely weak C—H...N interactions occur, as does a short S...N contact [3.2258 (19 Å].

N,N′-Bis(2-hydroxy-3-ethoxybenzylidenebutane-1,4-diamine

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Hoong-Kun Fun

2009-04-01

Full Text Available The title Schiff base compound, C22H28N2O4, lies across a crystallographic inversion centre and adopts an E configuration with respect to the C=N bond. Pairs of weak intermolecular C—H...O interactions link neighbouring molecules into dimers with an R22(28 ring motif. The crystal structure is stabilized by intermolecular C—H...π interactions. An intramolecular O—H...N hydrogen bond occurs.

4,5-Bis(isopropylsulfanylbenzene-1,2-dicarbonitrile

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Xingcui Wu

2010-04-01

Full Text Available In the title compound, C14H16N2S2, the C atoms of the aromatic ring, the two cyanide groups and the two S atoms of the isopropylsulfanyl groups are almost coplanar [maximum deviation from the mean plane = 0.042 (7 Å]. In the crystal, inversion dimers linked by aromatic π–π stacking occur, with a centroid–centroid separation of 3.7543 (8 Å.

3-[(E-(2,4-Dichloropbenzylideneamino]benzoic acid

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Adnan Ashraf

2011-01-01

Full Text Available In the crystal of the title compound, C14H9Cl2NO2, inversion-related dimers with R22(8 ring motifs are formed by intermolecular O—H...O hydrogen bonding. The 3-aminobenzoic acid group and the 2,4-dichlobenzaldehyde moiety subtend a dihedral angle of 55.10 (2°. The H atom of the carboxyl group is disordered over two sites with equal occupancies.

2′-Hydroxymethyl-1′-(4-methylphenyl-2′-nitro-1′,2′,5′,6′,7′,7a′-hexahydrospiro[indoline-3,3′-pyrrolizin]-2-one

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S. Sathya

2012-02-01

Full Text Available In the title compound, C22H23N3O4, the tolyl ring is almost perpendicular [83.86 (7°] to the best plane through the eight atoms of the pyrrolizidine ring system. The molecular conformation is stabilized by an intramolecular O—H...O hydrogen bond. The crystal packing features inversion dimers with R22(8 motifs linked by pairs of N—H...O hydrogen bonds.

On the asymptotics of dimers on tori

OpenAIRE

Kenyon, Richard W.; Sun, Nike; Wilson, David B.

2013-01-01

We study asymptotics of the dimer model on large toric graphs. Let $\\mathbb L$ be a weighted $\\mathbb{Z}^2$-periodic planar graph, and let $\\mathbb{Z}^2 E$ be a large-index sublattice of $\\mathbb{Z}^2$. For $\\mathbb L$ bipartite we show that the dimer partition function on the quotient $\\mathbb{L}/(\\mathbb{Z}^2 E)$ has the asymptotic expansion $\\exp[A f_0 + \\text{fsc} + o(1)]$, where $A$ is the area of $\\mathbb{L}/(\\mathbb{Z}^2 E)$, $f_0$ is the free energy density in the bulk, and $\\text{fsc...

On the diffusion and self-trapping of surface dimers

Science.gov (United States)

Kappus, W.

1982-03-01

The theory of elastic interactions between surface atoms which are caused by substrate strains is applied to the interaction of dimers on the (211) surface of tungsten. From the comparison of theoretical and experimental interactions which were derived from the diffusion behaviour of dimers, conclusions are drawn on the nature of the adatom-substrate bond.

Crystallization and preliminary X-ray analysis of CooA from Carboxydothermus hydrogenoformans

International Nuclear Information System (INIS)

Komori, Hirofumi; Satomoto, Kensuke; Ueda, Yasufumi; Shibata, Naoki; Inagaki, Sayaka; Yoshioka, Shiro; Aono, Shigetoshi; Higuchi, Yoshiki

2006-01-01

CooA from C. hydrogenoformans has been crystallized by the vapour-diffusion method using polyethylene glycol as a precipitant. The crystal diffracted to 2.3 Å resolution. CooA, a homodimeric haem-containing protein, is responsible for transcriptional regulation in response to carbon monoxide (CO). It has a b-type haem as a CO sensor. Upon binding CO to the haem, CooA binds promoter DNA and activates expression of genes for CO metabolism. CooA from Carboxydothermus hydrogenoformans has been overexpressed in Escherichia coli, purified and crystallized by the vapour-diffusion method. The crystal belongs to space group P2 1 , with unit-cell parameters a = 61.8, b = 94.7, c = 92.8 Å, β = 104.8°. The native and anomalous difference Patterson maps indicated that two CooA dimers are contained in the asymmetric unit and are related by a translational symmetry almost parallel to the c axis

Egg Component-Composited Inverse Opal Particles for Synergistic Drug Delivery.

Science.gov (United States)

Liu, Yuxiao; Shao, Changmin; Bian, Feika; Yu, Yunru; Wang, Huan; Zhao, Yuanjin

2018-05-23

Microparticles have a demonstrated value in drug delivery systems. The attempts to develop this technology focus on the generation of functional microparticles by using innovative but accessible materials. Here, we present egg component-composited microparticles with a hybrid inverse opal structure for synergistic drug delivery. The egg component inverse opal particles were produced by using egg yolk to negatively replicate colloid crystal bead templates. Because of their huge specific surface areas, abundant nanopores, and complex nanochannels of the inverse opal structure, the resultant egg yolk particles could be loaded with different kinds of drugs, such as hydrophobic camptothecin (CPT), by simply immersing them into the corresponding drug solutions. Attractively, additional drugs, such as the hydrophilic doxorubicin (DOX), could also be encapsulated into the particles through the secondary filling of the drug-doped egg white hydrogel into the egg yolk inverse opal scaffolds, which realized the synergistic drug delivery for the particles. It was demonstrated that the egg-derived inverse opal particles were with large quantity and lasting releasing for the CPT and DOX codelivery, and thus could significantly reduce cell viability, and enhance therapeutic efficacy in treating cancer cells. These features of the egg component-composited inverse opal microparticles indicated that they are ideal microcarriers for drug delivery.

Soaking suggests "alternative facts": Only co-crystallization discloses major ligand-induced interface rearrangements of a homodimeric tRNA-binding protein indicating a novel mode-of-inhibition.

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Frederik Rainer Ehrmann

Full Text Available For the efficient pathogenesis of Shigella, the causative agent of bacillary dysentery, full functionality of tRNA-guanine transglycosylase (TGT is mandatory. TGT performs post-transcriptional modifications of tRNAs in the anticodon loop taking impact on virulence development. This suggests TGT as a putative target for selective anti-shigellosis drug therapy. Since bacterial TGT is only functional as homodimer, its activity can be inhibited either by blocking its active site or by preventing dimerization. Recently, we discovered that in some crystal structures obtained by soaking the full conformational adaptation most likely induced in solution upon ligand binding is not displayed. Thus, soaked structures may be misleading and suggest irrelevant binding modes. Accordingly, we re-investigated these complexes by co-crystallization. The obtained structures revealed large conformational rearrangements not visible in the soaked complexes. They result from spatial perturbations in the ribose-34/phosphate-35 recognition pocket and, consequently, an extended loop-helix motif required to prevent access of water molecules into the dimer interface loses its geometric integrity. Thermodynamic profiles of ligand binding in solution indicate favorable entropic contributions to complex formation when large conformational adaptations in the dimer interface are involved. Native MS titration experiments reveal the extent to which the homodimer is destabilized in the presence of each inhibitor. Unexpectedly, one ligand causes a complete rearrangement of subunit packing within the homodimer, never observed in any other TGT crystal structure before. Likely, this novel twisted dimer is catalytically inactive and, therefore, suggests that stabilizing this non-productive subunit arrangement may be used as a further strategy for TGT inhibition.

Giant Lamb shift in photonic crystals

International Nuclear Information System (INIS)

Wang Xuehua; Kivshar, Yuri S.; Gu Benyuan

2004-01-01

We obtain a general result for the Lamb shift of excited states of multilevel atoms in inhomogeneous electromagnetic structures and apply it to study atomic hydrogen in inverse-opal photonic crystals. We find that the photonic-crystal environment can lead to very large values of the Lamb shift, as compared to the case of vacuum. We also suggest that the position-dependent Lamb shift should extend from a single level to a miniband for an assembly of atoms with random distribution in space, similar to the velocity-dependent Doppler effect in atomic/molecular gases

Asymmetric monometallic nanorod nanoparticle dimer and related compositions and methods

KAUST Repository

Han, Yu; Huang, Jianfeng; Zhu, Yihan

2016-01-01

and three-dimensional morphology of the dimer, as well as the growth pathway of the AuNP on the AuNR seed, was investigated for this example. The dimer exhibits an extraordinary broadband optical extinction spectrum spanning the UV, visible, and near

Theoretical analysis of the influence of flexoelectric effect on the defect site in nematic inversion walls

International Nuclear Information System (INIS)

Zheng Gui-Li; Xuan Li; Zhang Hui; Ye Wen-Jiang; Zhang Zhi-Dong; Song Hong-Wei

2016-01-01

Based on the experimental phenomena of flexoelectric response at defect sites in nematic inversion walls conducted by Kumar et al., we gave the theoretical analysis using the Frank elastic theory. When a direct-current electric field normal to the plane of the substrate is applied to the parallel aligned nematic liquid crystal cell with weak anchoring, the rotation of ±1 defects in the narrow inversion walls can be exhibited. The free energy of liquid crystal molecules around the +1 and –1 defect sites in the nematic inversion walls under the electric field was formulated and the electric-field-driven structural changes at the defect site characterized by polar and azimuthal angles of the local director were simulated. The results reveal that the deviation of azimuthal angle induced by flexoelectric effect are consistent with the switching of extinction brushes at the +1 and −1 defects obtained in the experiment conducted by Kumar et al. (paper)

DFT Study of dimers of dimethyl sulfoxide in gas phase

Directory of Open Access Journals (Sweden)

Reza Fazaeli

2014-10-01

Full Text Available Density functional (DFT calculations at M05-2x/aug-cc-pVDZ level were used to analyze the interactions between dimethyl sulfoxide (DMSO dimers. The structures obtained have been ana-lyzed with the Atoms in Molecules (AIMs and Natural Bond Orbital (NBO methodologies. Four minima were located on the potential energy surface of the dimers. Three types of interac-tions are observed, CH•••O, CH•••S hydrogen bonds and orthogonal interaction between the lone pair of the oxygen with the electron-deficient region of the sulfur atom. Stabilization energies of dimers including BSSE and ZPE are in the range 27–40 kJmol-1. The most stable conformers of dimers at DFT level is cyclic structure with antiparallel orientation of S=O groups pairing with three C–H∙∙∙O and a S∙∙∙O interactions.

Synthesis, characterization, crystal structure, and thermal analysis of 2-chloro-N-(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl) acetamide

Energy Technology Data Exchange (ETDEWEB)

Sharma, R. [University of Jammu, X-ray Crystallography Laboratory, Post-Graduate Department of Physics & Electronics (India); Nayak, P. S.; Narayana, B. [Mangalore University, Mangalagangotri, Department of Studies in Chemistry (India); Kant, R., E-mail: rkvk.paper11@gmail.com [University of Jammu, X-ray Crystallography Laboratory, Post-Graduate Department of Physics & Electronics (India)

2015-12-15

The title compound, C{sub 13}H{sub 14}O{sub 2}N{sub 3}Cl, has been synthesized by the reaction of chloroacetyl chloride with 4-aminoantipyrine in basic media and characterized by FT-IR, CHN elemental analysis, UV-Vis, TGA, DTA, DSC and single crystal X-ray diffraction. crystals are monoclinic, sp. gr. P2{sub 1}/c, a = 6.9994(6), b = 12.4035(13), c = 15.836(2) Å, β = 100.367(9)°, Z = 4. The crystal structure is stabilized by N–H···O and C–H···O interactions, the former interactions result in the formation of dimers corresponding to R{sub 2}{sup 2} (10) graphset motif and the dimers are further connected by C–H···O hydrogen bonding forming chains. In addition, the thermal stability of the compound was determined by TGA, DTA, DSC analysis, and absorption at λ{sub max} = 298 nm was determined by UV-Vis spectrophotometer.

Photoreactivation of pyrimidine dimers in the DNA of normal and xeroderma pigmentosum cells

International Nuclear Information System (INIS)

Sutherland, B.M.; Oliver, R.; Fuselier, C.O.; Sutherland, J.C.

1976-01-01

Photoproducts formed in the DNA of human cells irradiated with ultraviolet light (uv) were identified as cyclobutyl pyrimidine dimers by their chromatographic mobility, reversibility to monomers upon short wavelength uv irradiation, and comparison of the kinetics of this monomerization with that of authentic cis--syn thymine--thymine dimers prepared by irradiation of thymine in ice. The level of cellular photoreactivation of these dimers reflects the level of photoreactivating enzyme measured in cell extracts. Action spectra for cellular dimer photoreactivation in the xeroderma pigmentosum line XP12BE agree in range (300 nm to at least 577 nm) and maximum (near 400 nm) with that for photoreactivation by purified human photoreactivating enzyme. Normal human cells can also photoreactivate dimers in their DNA. The action spectrum for the cellular monomerization of dimers is similar to that for photoreactivation by the photoreactivating enzyme in extracts of normal human fibroblasts

Visualization of multipolar longitudinal and transversal surface plasmon modes in nanowire dimers.

Science.gov (United States)

Alber, Ina; Sigle, Wilfried; Müller, Sven; Neumann, Reinhard; Picht, Oliver; Rauber, Markus; van Aken, Peter A; Toimil-Molares, Maria Eugenia

2011-12-27

We study the transversal and longitudinal localized surface plasmon resonances in single nanowires and nanowire dimers excited by the fast traveling electron beam in a transmission electron microscope equipped with high-resolution electron energy-loss spectroscopy. Bright and dark longitudinal modes up to the fifth order are resolved on individual metallic nanowires. On nanowire dimers, mode splitting into bonding and antibonding is measured up to the third order for several dimers with various aspect ratio and controlled gap size. We observe that the electric field maxima of the bonding modes are shifted toward the gap, while the electric field maxima of the antibonding modes are shifted toward the dimer ends. Finally, we observe that the transversal mode is not detected in the region of the dimer gap and decays away from the rod more rapidly than the longitudinal modes.

Purification, crystallization and preliminary X-ray crystallographic analysis of the archaeal phosphoglycerate mutase PH0037 from Pyrococcus horikoshii OT3

Energy Technology Data Exchange (ETDEWEB)

Lokanath, Neratur K.; Kunishima, Naoki, E-mail: kunisima@spring8.or.jp [Advanced Protein Crystallography Research Group, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148 (Japan)

2006-08-01

The archaeal phosphoglycerate mutase PH0037 from P. horikoshii OT3 has been crystallized in space group R32, with unit-cell parameters a = 155.62, c = 230.35 Å. A 2.2 Å resolution data was collected at SPring-8 beamline BL26B1. Phosphoglycerate mutases catalyze the interconversion of 2-phosphoglycerate and 3-phosphoglycerate in glycolysis and gluconeogenesis pathways. The archaeal phosphoglycerate mutase PH0037 from Pyrococcus horikoshii OT3 has been overexpressed in Escherichia coli and purified. Crystals were obtained using the oil-microbatch method at 291 K. A native data set extending to a resolution of 2.2 Å has been collected and processed in space group R32. Assuming the presence of a dimer in the asymmetric unit, the V{sub M} value is calculated to be 3.0 Å{sup 3} Da{sup −1}, consistent with the dynamic light-scattering experiment result, which shows a dimeric state of the protein in solution. Molecular-replacement trials using the crystal structure of Bacilllus stearothermophilus phosphoglycerate mutase as a search model did not provide a satisfactory solution, indicating substantially different structures of these two phophoglycerate mutases.

Thermal expansion of crystals of the N2 type

International Nuclear Information System (INIS)

Tolkachev, A.M.; Manzhelii, V.G.; Azarenkov, V.P.; Jezowski, A.; Kosobutskaya, E.A.

1981-01-01

Linear expansion coefficients of low temperature crystals with linear molecules and Pa3 lattice N 2 (2-21 K), CO(2-28 K), CO 2 (2-25 K), N 2 O(2-90 K) were measured. A version of the law of corresponding states to describe the translational component of the thermal expansion of the substances studied and other low temperature crystals with close-packed lattices is proposed. In the thermal properties of crystals consisting of molecules without inversion centre, we have found anomalies interpreted as the evidence of a partial dipole ordering. (orig.)

Dimerization of 3He in 3He-4He mixture films

International Nuclear Information System (INIS)

Bashkin, E.

1994-01-01

3 He atoms dissolved in superfluid 4 He may form dimers ( 3 He) 2 in two-dimensional geometries. Dimer formation is studied in films of dilute 3 He- 4 He mixture. After designing a schematic 3 He- 3 He interaction potential, the dimer binding energy is calculated for various substrates. It is shown that 3 He impurity states localized near the substrate give rise to the highest magnitudes of the binding energy. (author). 32 refs., 6 figs.,; 1 tab

cis elements and trans-acting factors involved in dimer formation of murine leukemia virus RNA.

Science.gov (United States)

Prats, A C; Roy, C; Wang, P A; Erard, M; Housset, V; Gabus, C; Paoletti, C; Darlix, J L

1990-02-01

The genetic material of all retroviruses examined so far consists of two identical RNA molecules joined at their 5' ends by the dimer linkage structure (DLS). Since the precise location of the DLS as well as the mechanism and role(s) of RNA dimerization remain unclear, we analyzed the dimerization process of Moloney murine leukemia virus (MoMuLV) genomic RNA. For this purpose we derived an in vitro model for RNA dimerization. By using this model, murine leukemia virus RNA was shown to form dimeric molecules. Deletion mutagenesis in the 620-nucleotide leader of MoMuLV RNA showed that the dimer promoting sequences are located within the encapsidation element Psi between positions 215 and 420. Furthermore, hybridization assays in which DNA oligomers were used to probe monomer and dimer forms of MoMuLV RNA indicated that the DLS probably maps between positions 280 and 330 from the RNA 5' end. Also, retroviral nucleocapsid protein was shown to catalyze dimerization of MoMuLV RNA and to be tightly bound to genomic dimer RNA in virions. These results suggest that MoMuLV RNA dimerization and encapsidation are probably controlled by the same cis element, Psi, and trans-acting factor, nucleocapsid protein, and thus might be linked during virion formation.

Accuracy of D-Dimers to Rule Out Venous Thromboembolism Events across Age Categories

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G. Der Sahakian

2010-01-01

Full Text Available Background. Strategies combining pretest clinical assessment and D-dimers measurement efficiently and safely rule out venous thromboembolism events (VTE in low- and intermediate-risk patients. Objectives. As process of ageing is associated with altered concentrations of coagulation markers including an increase in D-dimers levels, we investigated whether D-dimers could reliably rule out VTE across age categories. Method. We prospectively assessed the test performance in 1,004 patients visiting the emergency department during the 6-month period with low or intermediate risk of VTE who also received additional diagnostic procedures. Results. 67 patients had VTE with D-dimers levels above the threshold, and 3 patients displayed D-dimers levels below the threshold. We observed that specificity of D-dimers test decreased in an age-dependent manner. However, sensitivity and negative predictive value remained at very high level in each age category including older patients. Conclusion. We conclude that, even though D-dimers level could provide numerous false positive results in elderly patients, its high sensitivity could reliably help physicians to exclude the diagnosis of VTE in every low- and intermediate-risk patient.

4,4-Difluoro-2,3;5,6-bis(tetramethylene-4-bora-3a,4a-diaza-s-indacene (LD540

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Kirsi Salorinne

2014-01-01

Full Text Available The title compound, C18H21BF2N2, is a lipophilic dye based on a BODIPY fluorophore backbone, which was developed for microscopic imaging of lipid droplets; the molecule has a planar BODIPY core [dihedral angle between the pyrrole rings = 2.3 (3°] and two tetramethylene substituents at the 2,3- and 5,6-positions in a half-chair conformation. One of the tetramethylene substituents is disordered over two two sets of sites with site occupancies of 0.5. In the crystal, pairs of C—H...F interactions link the molecules into inversion dimers. Neighbouring dimers are linked by further C—H...F interactions, forming an infinite array. C—H...π and π–π [centroid–centroid distance = 4.360 (3 Å] interactions are observed between the BODIPY core and the tetramethylene substituents of neighbouring dimer pairs.

Analysis of pyrimidine dimer content of isolated DNA by nuclease digestion

International Nuclear Information System (INIS)

Farland, W.H.; Sutherland, B.M.

1980-01-01

Isolated DNA is highly susceptible to degradation by exogenous nucleases. Complete digestion is possible with a number of well-characterized enzymes from a variety of sources. Treatment of DNA with a battery of enzymes including both phosphodiesterase and phosphatase activities yields a mixture of nucleosides and inorganic phosphate (P/sub i/) as a final product. Unlike native DNA, ultraviolet-irradiated DNA is resistant to complete digestion. Setlow et al. demonstrated that the structural changes in the DNA responsible for the nuclease resistance were the formation of cyclobutyl pyrimidine dimers, the major photoproduct in UV-irradiated DNA. Using venom phosphodiesterase, they demonstrated that UV irradiation of DNA affected both the rate and extent of enzymatic hydrolysis. In addition, it was demonstrated that the major nuclease-resistant product of this hydrolysis was an oligonucleotide containing dimerized pyrimidines. Treatment of the DNA to split the dimers, either photochemically or photoenzymatically, rendered the polymer more susceptible to hydrolysis by the phosphodiesterase. The specificity of photoreactivating enzyme for pyrimidine dimers lends support to the role of these structures in conferring nuclease resistance to UV-irradiated DNA. The nuclease resistance of DNA containing dimers has been the basis of several assays for the measurement of these photoproducts. Sutherland and Chamberlin reported the development of a rapid and sensitive assay for dimers in 32 P-labeled DNA

Inverse design of multicomponent assemblies

Science.gov (United States)

Piñeros, William D.; Lindquist, Beth A.; Jadrich, Ryan B.; Truskett, Thomas M.

2018-03-01

Inverse design can be a useful strategy for discovering interactions that drive particles to spontaneously self-assemble into a desired structure. Here, we extend an inverse design methodology—relative entropy optimization—to determine isotropic interactions that promote assembly of targeted multicomponent phases, and we apply this extension to design interactions for a variety of binary crystals ranging from compact triangular and square architectures to highly open structures with dodecagonal and octadecagonal motifs. We compare the resulting optimized (self- and cross) interactions for the binary assemblies to those obtained from optimization of analogous single-component systems. This comparison reveals that self-interactions act as a "primer" to position particles at approximately correct coordination shell distances, while cross interactions act as the "binder" that refines and locks the system into the desired configuration. For simpler binary targets, it is possible to successfully design self-assembling systems while restricting one of these interaction types to be a hard-core-like potential. However, optimization of both self- and cross interaction types appears necessary to design for assembly of more complex or open structures.

1,1,2,2-Tetrakis[2,4-dichloro-6-(diethoxymethylphenoxymethyl]ethene

Directory of Open Access Journals (Sweden)

Yavuz Köysal

2012-10-01

Full Text Available In the title compound, C50H60Cl8O12, the molecules are disordered about an inversion center located at the mid-point of the central C=C bond. These atoms show disorder and were modelled with two different orientations with site occupancies of 0.828 (3 and 0.172 (3. The dihedral angle between the two benzene rings in the asymmetric unit is 52.80 (6°. Intramolecular C—H...O and C—H...Cl interactions occur and the crystal packing features inversion dimers linked by pairs of C—H...O bonds, generating R22(10 loops.