Sample records for dimers

  1. Universality in bosonic dimer-dimer scattering

    Deltuva, A. [Centro de Fisica Nuclear, Universidade de Lisboa, P-1649-003 Lisboa (Portugal)


    Bosonic dimer-dimer scattering is studied near the unitary limit using momentum-space equations for the four-particle transition operators. The impact of the Efimov effect on the dimer-dimer scattering observables is explored, and a number of universal relations is established with high accuracy. The rate for the creation of Efimov trimers via dimer-dimer collisions is calculated.

  2. Neutron scattering in dimers

    Gudel, H. U.; Furrer, A.; Kjems, Jørgen


    Insulating compounds containing dimers of transition metal and rare earth ions have been studied by inelastic neutron scattering (INS). Energy splittings can be directly determined, and the corresponding parameters are easily extracted from the experimental data. The intensities of dimer excitati......Insulating compounds containing dimers of transition metal and rare earth ions have been studied by inelastic neutron scattering (INS). Energy splittings can be directly determined, and the corresponding parameters are easily extracted from the experimental data. The intensities of dimer...

  3. Liquid crystal dimers

    Kumar Pal, Santanu


    This book covers in-depth discussion of design principles, synthesis and thermal behavior of all types of liquid crystal (LC) dimers. The text presents recent advances in the field of LC dimers consisting of different mesogenic units such as calamitic, discotic and bent-core molecules. It starts with a chapter on the introduction of liquid crystal dimers, including their odd-even behavior, basic classification of dimers and common mesophases in dimers. The text shows how the molecular architectures are being used to develop new materials to study a range of interesting phenomena such as the biaxial nematic phase containing rod-like and disc-like mesogenic units. Finally, the text presents perspectives related to technological relevance of these dimers such as dopants in LC display mixtures exhibiting faster relaxation time, strong flexoelectric coupling and others to effect control over the properties of these materials.

  4. Protein dimerization. Inside job.

    Metzger, H


    In a sophisticated combination of genetic engineering and organic synthesis, a general method for dimerizing recombinant intracellular proteins has been devised; the usefulness of the method should now be testable.

  5. Superbackscattering nanoparticle dimers.

    Liberal, Iñigo; Ederra, Iñigo; Gonzalo, Ramón; Ziolkowski, Richard W


    The theory and design of superbackscattering nanoparticle dimers are presented. We analytically derive the optimal configurations and the upper bound of their backscattering cross-sections. In particular, it is demonstrated that electrically small nanoparticle dimers can enhance the backscattering by a factor of 6.25 with respect to single dipolar particles. We demonstrate that optimal designs approaching this theoretical limit can be found by using a simple circuit model. The study of practical implementations based on plasmonic and high-permittivity particles has been also addressed. Moreover, the numerical examples reveal that the dimers can attain close to a fourfold enhancement of the single nanoparticle response even in the presence of high losses.

  6. Superbackscattering Nanoparticle Dimers

    Liberal, Iñigo; Gonzalo, Ramón; Ziolkoski, Richard W


    The theory and design of superbackscattering nanoparticle dimers are presented. We analytically derive the optimal configurations and the upper bound of their backscattering cross-sections. In particular, it is demonstrated that electrically small nanoparticle dimers can enhance the backscattering by a factor of 6.25 with respect to single dipolar particles. We demonstrate that optimal designs approaching this theoretical limit can be found by using a simple circuit model. The study of practical implementations based on plasmonic and high-permittivity particles reveal that fourfold enhancement factors might be attainable even with realistic losses.

  7. Alkane dimers interaction

    Ferrighi, Lara; Madsen, Georg Kent Hellerup; Hammer, Bjørk


    The interaction energies of a series of n-alkane dimers, from methane to decane, have been investigated with Density Functional Theory (DFT), using the MGGA-M06-L density functional. The results are compared both to the available wavefunction-based values as well as to dispersion corrected DFT...

  8. The acrylonitrile dimer ion

    Ervasti, Henri K.; Jobst, Karl J.; Burgers, Peter C.; Ruttink, Paul J. Ae; Terlouw, Johan K.


    Large energy barriers prohibit the rearrangement of solitary acrylonitrile ions, CH2CHCN+, into their more stable hydrogen-shift isomers CH2CCNH+ or CHCH-CNH+. This prompted us to examine if these isomerizations occur by self-catalysis in acrylonitrile dimer ions. Such ions, generated by chemical ionization experiments of acrylonitrile with an excess of carbon dioxide, undergo five dissociations in the [mu]s time frame, as witnessed by peaks at m/z 53, 54, 79, 80 and 105 in their metastable ion mass spectrum. Collision experiments on these product ions, deuterium labeling, and a detailed computational analysis using the CBS-QB3 model chemistry lead to the following conclusions: (i) the m/z 54 ions are ions CH2CHCNH+ generated by self-protonation in ion-dipole stabilized hydrogen-bridged dimer ions [CH2CHCN...H-C(CN)CH2]+ and [CH2CHCN...H-C(H)C(H)CN]+; the proton shifts in these ions are associated with a small reverse barrier; (ii) dissociation of the H-bridged ions into CH2CCNH+ or CHCH-CNH+ by self-catalysis is energetically feasible but kinetically improbable: experiment shows that the m/z 53 ions are CH2CHCN+ ions, generated by back dissociation; (iii) the peaks at m/z 79, 80 and 105 correspond with the losses of HCN, C2H2 and H, respectively. The calculations indicate that these ions are generated from dimer ions that have adopted the (much more stable) covalently bound "head-to-tail" structure [CH2CHCN-C(H2)C(H)CN]+; experiments indicate that the m/z 79 (C5H5N) and m/z 105 (C6H6N2) ions have linear structures but the m/z 80 (C4H4N2) ions consist of ionized pyrimidine in admixture with its stable pyrimidine-2-ylidene isomer. Acrylonitrile is a confirmed species in interstellar space and our study provides experimental and computational evidence that its dimer radical cation yields the ionized prebiotic pyrimidine molecule.

  9. Dynamics of a bouncing dimer

    Dorbolo, S; Tsimring, L S; Kudrolli, A


    We investigate the dynamics of a dimer bouncing on a vertically oscillated plate. The dimer, composed of two spheres rigidly connected by a light rod, exhibits several modes depending on initial and driving conditions. The first excited mode has a novel horizontal drift in which one end of the dimer stays on the plate during most of the cycle, while the other end bounces in phase with the plate. The speed and direction of the drift depend on the aspect ratio of the dimer. We employ event-driven simulations based on a detailed treatment of frictional interactions between the dimer and the plate in order to elucidate the nature of the transport mechanism in the drift mode.

  10. Universal dimer-dimer scattering in lattice effective field theory

    Elhatisari, Serdar; Lee, Dean; Meißner, Ulf-G; Rupak, Gautam


    We consider two-component fermions with short-range interactions and large scattering length. This system has universal properties that are realized in many different fields including atomic, nuclear and particle physics. In the limit of large fermion-fermion scattering length $a_\\mathrm{ff}$ and zero range interaction, all properties of the system scale proportionally with the only length scale $a_\\mathrm{ff}$. We consider the case where there are bound dimers and calculate the scattering phase shifts for the two-dimer system near threshold using lattice effective field theory. From the scattering phase shifts, we extract the universal dimer-dimer scattering length $a_\\mathrm{dd}/a_\\mathrm{ff}=0.645(89)$ and effective range $r_\\mathrm{dd}/a_\\mathrm{ff}=-0.413(79)$.

  11. Collisional properties of weakly bound heteronuclear dimers

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


    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

  12. Adventures in Holographic Dimer Models

    Kachru, Shamit; /Stanford U., Phys. Dept. /SLAC; Karch, Andreas; /Washington U., Seattle; Yaida, Sho; /Stanford U., Phys. Dept.


    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.

  13. Kinetics of DNA tile dimerization.

    Jiang, Shuoxing; Yan, Hao; Liu, Yan


    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.

  14. NMR Structural Studies on Alamethicin Dimers



    15N labeled alamethicin dimer was synthesized. The structure and dynamics of alamethicin dimers were studied with nuclear magnetic resonance (NMR) spectroscopy. The data from 15N-labeled alamethicin dimer suggest little differences in conformation between the dimer and monomer in the Aib1-Pro14 region. Significant difference in the conformation of the C-terminus are manifest in the NH chemical shifts in the Val15-Pho20 region.

  15. Rubidium dimers in paraffin-coated cells

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


    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 deg C was explored, with the lower end corresponding to a dimer density of less than 10^7 cm^(-3). With one-minute integration time, a sensitivity to dimer number density of better than 10^6 cm^(-3) was achieved. No significant difference in dimer density was observed between the cells.

  16. Fiber optic D dimer biosensor

    Glass, Robert S.; Grant, Sheila A.


    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.

  17. Mechanism of FGF receptor dimerization and activation

    Sarabipour, Sarvenaz; Hristova, Kalina


    Fibroblast growth factors (fgfs) are widely believed to activate their receptors by mediating receptor dimerization. Here we show, however, that the FGF receptors form dimers in the absence of ligand, and that these unliganded dimers are phosphorylated. We further show that ligand binding triggers structural changes in the FGFR dimers, which increase FGFR phosphorylation. The observed effects due to the ligands fgf1 and fgf2 are very different. The fgf2-bound dimer structure ensures the smallest separation between the transmembrane (TM) domains and the highest possible phosphorylation, a conclusion that is supported by a strong correlation between TM helix separation in the dimer and kinase phosphorylation. The pathogenic A391E mutation in FGFR3 TM domain emulates the action of fgf2, trapping the FGFR3 dimer in its most active state. This study establishes the existence of multiple active ligand-bound states, and uncovers a novel molecular mechanism through which FGFR-linked pathologies can arise.

  18. Synthesis of steroidal dimers: Selective amine catalysed steroidal dimerization

    Shamsuzzaman; Mohd Gulfam Aalam; Tabassum Siddiqui


    Some new dimeric steroids namely cholest-5-en-3-spiro-[6',5'-oxa]-5'-cholest-3'-one (2), cholest-5-en-7-spiro-[4',5'-oxa]-5'-cholest-7'-one (4a) and 3-substitutedcholest-5-en-7-spiro-[4',5'-oxa]-3'-substituted-5'-cholestan-7'-ones (4b, c) are synthesized starting from cholest-5-en-3-one (1), cholest-5-en-7-one (3a) and 3-substituted-cholest-5-en-7-ones (3b, c) respectively by using DMAP and xylene. All the synthesized compounds were characterized by using IR, MS and 1H, 13C NMR spectral and elemental analysis.

  19. Dimerization of Human Growth Hormone by Zinc

    Cunningham, Brian C.; Mulkerrin, Michael G.; Wells, James A.


    Size-exclusion chromatography and sedimentation equilibrium studies demonstrated that zinc ion (Zn2+) induced the dimerization of human growth hormone (hGH). Scatchard analysis of 65Zn2+ binding to hGH showed that two Zn2+ ions associate per dimer of hGH in a cooperative fashion. Cobalt (II) can substitute for Zn2+ in the hormone dimer and gives a visible spectrum characteristic of cobalt coordinated in a tetrahedral fashion by oxygen- and nitrogen-containing ligands. Replacement of potential Zn2+ ligands (His18, His21, and Glu174) in hGH with alanine weakened both Zn2+ binding and hGH dimer formation. The Zn2+-hGH dimer was more stable than monomeric hGH to denaturation in guanidine-HCl. Formation of a Zn2+-hGH dimeric complex may be important for storage of hGH in secretory granules.

  20. Dimer models and Calabi-Yau algebras

    Broomhead, Nathan


    In this thesis we study dimer models, as introduced in string theory, which give a way of writing down a class of non-commutative `superpotential' algebras. Some examples are 3-dimensional Calabi-Yau algebras, as defined by Ginzburg, and some are not. We consider two types of `consistency' condition on dimer models, and show that a `geometrically consistent' model is `algebraically consistent'. Finally we prove that the algebras obtained from algebraically consistent dimer models are 3-dimensional Calabi-Yau algebras.

  1. On Dimer Models and Closed String Theories

    Sarkar, Tapobrata


    We study some aspects of the recently discovered connection between dimer models and D-brane gauge theories. We argue that dimer models are also naturally related to closed string theories on non compact orbifolds of $\\BC^2$ and $\\BC^3$, via their twisted sector R charges, and show that perfect matchings in dimer models correspond to twisted sector states in the closed string theory. We also use this formalism to study the combinatorics of some unstable orbifolds of $\\BC^2$.

  2. Dimerization of norbornene on zeolite catalysts

    N. G. Grigor’eva; S. V. Bubennov; L. M. Khalilov; B. I. Kutepov


    The high activity and selectivity of H‐Beta and H‐ZSM‐12 zeolites in the dimerization of norbornene was established. The norbornene conversion reached 100%in chlorinated paraffin and argon gas medium, with a selectivity of dimer formation of 88%–98%. Four stereo‐isomers of the bis‐2,2’‐norbornylidene structure were identified in the dimer fraction, with the (Z)‐anti‐bis‐2,2’‐norbornylidene prevailing over the others.

  3. Enhanced Chiral Recognition by Cyclodextrin Dimers

    Bart Jan Ravoo


    Full Text Available In this article we investigate the effect of multivalency in chiral recognition. To this end, we measured the host-guest interaction of a β-cyclodextrin dimer with divalent chiral guests. We report the synthesis of carbohydrate-based water soluble chiral guests functionalized with two borneol, menthol, or isopinocampheol units in either (+ or (– configuration. We determined the interaction of these divalent guests with a β-cyclodextrin dimer using isothermal titration calorimetry. It was found that—in spite of a highly unfavorable conformation—the cyclodextrin dimer binds to guest dimers with an increased enantioselectivity, which clearly reflects the effect of multivalency.

  4. Sputtering of dimers off a silicon surface

    Nietiadi, Maureen L. [Physics Department, University Kaiserslautern, Erwin-Schroedinger-Strasse, D-67663 Kaiserslautern (Germany); Research Center OPTIMAS, University Kaiserslautern, Erwin-Schroedinger-Strasse, D-67663 Kaiserslautern (Germany); Rosandi, Yudi [Physics Department, University Kaiserslautern, Erwin-Schroedinger-Strasse, D-67663 Kaiserslautern (Germany); Research Center OPTIMAS, University Kaiserslautern, Erwin-Schroedinger-Strasse, D-67663 Kaiserslautern (Germany); Department of Physics, Universitas Padjadjaran, Jatinangor, Sumedang 45363 (Indonesia); Kopnarski, Michael [Physics Department, University Kaiserslautern, Erwin-Schroedinger-Strasse, D-67663 Kaiserslautern (Germany); Research Center OPTIMAS, University Kaiserslautern, Erwin-Schroedinger-Strasse, D-67663 Kaiserslautern (Germany); Institut fuer Oberflaechen- und Schichtanalytik IFOS GmbH, Trippstadter Strasse 120, D-67663 Kaiserslautern (Germany); Urbassek, Herbert M., E-mail: [Physics Department, University Kaiserslautern, Erwin-Schroedinger-Strasse, D-67663 Kaiserslautern (Germany); Research Center OPTIMAS, University Kaiserslautern, Erwin-Schroedinger-Strasse, D-67663 Kaiserslautern (Germany)


    We present experimental and molecular-dynamics simulation results of the sputtering of a Si surface by 2 keV Ar ions. Results on both the monomer and dimer distributions are presented. In simulation, these distributions follow a generalized Thompson law with power exponent n=2 and n=3, respectively. The experimental data, obtained via plasma post-ionization in an SNMS (secondary neutral mass spectrometry) apparatus, show good agreement with respect to the dimer fraction, and the relative energy distributions of dimers and monomers. The consequences for the dimer sputtering mechanism are discussed.

  5. Mahler Measure, Eisenstein Series and Dimers

    Stienstra, J.


    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.

  6. Dimeric assembly of enterocyte brush border enzymes

    Danielsen, E M


    temperature (20 degrees C) reduced the rate of, but did not prevent, dimerization. Maltase-glucoamylase (EC only appeared as a dimer when extracted and analyzed under low salt conditions, suggesting a weak association between the two subunits. This finding is consistent with the electronmicroscopic...

  7. Potassium Hexacyanoferrate (III-Catalyzed Dimerization of Hydroxystilbene: Biomimetic Synthesis of Indane Stilbene Dimers

    Jing-Shan Xie


    Full Text Available Using potassium hexacyanoferrate (III–sodium acetate as oxidant, the oxidative coupling reaction of isorhapontigenin and resveratrol in aqueous acetone resulted in the isolation of three new indane dimers 4, 6, and 7, together with six known stilbene dimers. Indane dimer 5 was obtained for the first time by direct transformation from isorhapontigenin. The structures and relative configurations of the dimers were elucidated using spectral analysis, and their possible formation mechanisms were discussed. The results indicate that this reaction could be used as a convenient method for the semi-synthesis of indane dimers because of the mild conditions and simple reaction products.

  8. Statistical transmutation in doped quantum dimer models.

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


    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.

  9. Universal four-Boson states in ultracold molecular gases: resonant effects in dimer-dimer collisions.

    D'Incao, J P; von Stecher, J; Greene, Chris H


    We study the manifestations of universal four-body physics in ultracold dimer-dimer collisions. We show that resonant features associated with three-body Efimov physics and dimer-dimer scattering lengths are universally related. The emergence of universal four-boson states allows for the tunability of the dimer-dimer interaction, thus enabling the future study of ultracold molecular gases with both attractive and repulsive interactions. Moreover, our study of the interconversion between dimers and Efimov trimers shows that B2+B2-->B3+B rearrangement reactions can provide an efficient trimer formation mechanism. Our analysis of the temperature dependence of this reaction provides an interpretation of the available experimental data and sheds light on the possible experimental realization of rearrangement processes in ultracold gases.

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

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


    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...

  11. Quantum dimer model for the pseudogap metal

    Punk, Matthias; Allais, Andrea; Sachdev, Subir


    We propose a quantum dimer model for the metallic state of the hole-doped cuprates at low hole density, p. The Hilbert space is spanned by spinless, neutral, bosonic dimers and spin S=1/2, charge +e fermionic dimers. The model realizes a “fractionalized Fermi liquid” with no symmetry breaking and small hole pocket Fermi surfaces enclosing a total area determined by p. Exact diagonalization, on lattices of sizes up to 8×8, shows anisotropic quasiparticle residue around the pocket Fermi surfaces. We discuss the relationship to experiments. PMID:26195771

  12. Quantum dimer model for the pseudogap metal.

    Punk, Matthias; Allais, Andrea; Sachdev, Subir


    We propose a quantum dimer model for the metallic state of the hole-doped cuprates at low hole density, p. The Hilbert space is spanned by spinless, neutral, bosonic dimers and spin S = 1/2, charge +e fermionic dimers. The model realizes a "fractionalized Fermi liquid" with no symmetry breaking and small hole pocket Fermi surfaces enclosing a total area determined by p. Exact diagonalization, on lattices of sizes up to 8 × 8, shows anisotropic quasiparticle residue around the pocket Fermi surfaces. We discuss the relationship to experiments.

  13. Quantitative analysis of cyclic dimer fatty acid content in the dimerization product by proton NMR spectroscopy.

    Park, Kyun Joo; Kim, Minyoung; Seok, Seunghwan; Kim, Young-Wun; Kim, Do Hyun


    In this work, (1)H NMR is utilized for the quantitative analysis of a specific cyclic dimer fatty acid in a dimer acid mixture using the pseudo-standard material of mesitylene on the basis of its structural similarity. Mesitylene and cyclic dimer acid levels were determined using the signal of the proton on the cyclic ring (δ=6.8) referenced to the signal of maleic acid (δ=6.2). The content of the cyclic dimer fatty acid was successfully determined through the standard curve of mesitylene and the reported equation. Using the linearity of the mesitylene curve, the cyclic dimer fatty acid in the oil mixture was quantified. The results suggest that the proposed method can be used to quantify cyclic compounds in mixtures to optimize the dimerization process.

  14. Formation of cystine slipknots in dimeric proteins.

    Mateusz Sikora

    Full Text Available We consider mechanical stability of dimeric and monomeric proteins with the cystine knot motif. A structure based dynamical model is used to demonstrate that all dimeric and some monomeric proteins of this kind should have considerable resistance to stretching that is significantly larger than that of titin. The mechanisms of the large mechanostability are elucidated. In most cases, it originates from the induced formation of one or two cystine slipknots. Since there are four termini in a dimer, there are several ways of selecting two of them to pull by. We show that in the cystine knot systems, there is strong anisotropy in mechanostability and force patterns related to the selection. We show that the thermodynamic stability of the dimers is enhanced compared to the constituting monomers whereas machanostability is either lower or higher.

  15. A New Dimeric Phthalide from Angelica sinensis

    Ling YI; Ping LI; Zhi Ming BI


    A new dimeric phthalide named Z, Z'-3.3'a, 7.7'a-diligustilide was isolated from the roots of Angelica sinensis. Its structure was determined using spectroscopic methods and X-ray crystallographic diffraction analysis.

  16. Designing Stable Antiparallel Coiled Coil Dimers

    曾宪纲; 周海梦


    The history of antiparallel coiled coil dimer design is briefly reviewed and the main principles governing the successful designs are explained. They include analysis of the inter-subunit electrostatic repulsion for determining partners for dimerization and of the buried polar interaction for determining the relative orientation of the partners. A theory is proposed to explain the lack of antiparallel coiled coil homodimers in nature.

  17. Formation of Cystine Slipknots in Dimeric Proteins

    Mateusz Sikora; Marek Cieplak


    We consider mechanical stability of dimeric and monomeric proteins with the cystine knot motif. A structure based dynamical model is used to demonstrate that all dimeric and some monomeric proteins of this kind should have considerable resistance to stretching that is significantly larger than that of titin. The mechanisms of the large mechanostability are elucidated. In most cases, it originates from the induced formation of one or two cystine slipknots. Since there are four termini in a dim...

  18. Role of Rydberg states in the photostability of heterocyclic dimers: the case of pyrazole dimer.

    Zilberg, Shmuel; Haas, Yehuda


    A new route for the nonradiative decay of photoexcited, H-bonded, nitrogen-containing, heterocyclic dimers is offered and exemplified by a study of the pyrazole dimer. In some of these systems the N(3s) Rydberg state is the lowest excited singlet state. This state is formed by direct light absorption or by nonradiative transition from the allowed ππ* state. An isomer of this Rydberg state is formed by H atom transfer to the other component of the dimer. The newly formed H-bonded radical pair is composed of two radicals (a H-adduct of pyrazole, a heterocyclic analogue of the NH(4) radical) and the pyrazolium π-radical. It is calculated to have a shallow local minimum and is the lowest point on the PES of the H-pyrazole/pyrazolium radical pair. This species can cross back to the ground state of the original dimer through a relatively small energy gap and compete with the H-atom loss channel, known for the monomer. In both Rydberg dimers, an electron occupies a Rydberg orbital centered mostly on one of the two components of the dimer. This Rydberg Center Shift (RCS) mechanism, proposed earlier (Zilberg, S.; Kahan, A.; Haas, Y. Phys. Chem. Chem. Phys. 2012, 14, 8836), leads to deactivation of the electronically excited dimer while keeping it intact. It, thus, may explain the high photostability of the pyrazole dimer as well as other heterocyclic dimers.

  19. Dynamic interplay between adhesive and lateral E-cadherin dimers

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


    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...

  20. Adsorption of dimeric surfactants in lamellar silicates

    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: [Department of Macromolecular Physics, Faculty of Physics, A. Mickiewicz University, Umultowska 85, 61-614 Poznań (Poland)


    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.

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

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


    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...

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

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


    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....

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

    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.

  4. Geometric Reid's recipe for dimer models

    Bocklandt, Raf; Velez, Alexander Quintero


    Crepant resolutions of three-dimensional toric Gorenstein singularities are derived equivalent to noncommutative algebras arising from consistent dimer models. By choosing a special stability parameter and hence a distinguished crepant resolution $Y$, this derived equivalence generalises the Fourier-Mukai transform relating the $G$-Hilbert scheme and the skew group algebra $\\CC[x,y,z]\\ast G$ for a finite abelian subgroup of $\\SL(3,\\CC)$. We show that this equivalence sends the vertex simples to pure sheaves, except for the zero vertex which is mapped to the dualising complex of the compact exceptional locus. This generalises results of Cautis-Logvinenko and Cautis-Craw-Logvinenko to the dimer setting, though our approach is different in each case. We also describe some of these pure sheaves explicitly and compute the support of the remainder, providing a dimer model analogue of results from Logvinenko.

  5. Partition-DFT on the Water Dimer

    Gómez, Sara; Restrepo, Albeiro; Wasserman, Adam


    As is well known, the ground-state symmetry group of the water dimer switches from its equilibrium $C_{s}$-character to $C_{2h}$-character as the distance between the two oxygen atoms of the dimer decreases below $R_{\\rm O-O}\\sim 2.5$ \\AA{}. For a range of $R_{\\rm O-O}$ between 1 and 5 \\AA{}, and for both symmetries, we apply Partition Density Functional Theory (PDFT) to find the unique monomer densities that sum to the correct dimer densities while minimizing the sum of the monomer energies. We calculate the work involved in deforming the isolated monomer densities and find that it is slightly larger for the $C_s$ geometry for all $R_{\\rm O-O}$. We discuss how the PDFT densities and the corresponding partition potentials support the orbital-interaction picture of hydrogen-bond formation.

  6. Photoionization of helium dimers; Photoionisation von Heliumdimeren

    Havermeier, Tilo


    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.)

  7. Kosterlitz Thouless Universality in Dimer Models

    Chandrasekharan, S; Chandrasekharan, Shailesh; Strouthos, Costas G.


    Using the monomer-dimer representation of strongly coupled U(N) lattice gauge theories with staggered fermions, we study finite temperature chiral phase transitions in (2+1) dimensions. A new cluster algorithm allows us to compute monomer-monomer and dimer-dimer correlations at zero monomer density (chiral limit) accurately on large lattices. This makes it possible to show convincingly, for the first time, that these models undergo a finite temperature phase transition which belongs to the Kosterlitz-Thouless universality class. We find that this universality class is unaffected even in the large N limit. This shows that the mean field analysis often used in this limit breaks down in the critical region.

  8. A Novel Dimer of α-Tocopherol

    Anjan Patel


    Full Text Available Decomposition of the complex 4, formed between the α-tocopherol ortho-quinone methide (2 and NMMO, by fast heating from −78∘C to 70∘C in inert solvents produces a novel α-tocopherol dimer with 6H,12H-dibenzo[b,f][1,5]dioxocine structure (5 which—in contrast to the well-known spiro-dimer of α-tocopherol (3—is symmetrical. This is the first example of a direct reaction of the highly transient zwitterionic, aromatic precursor 2a in the formation of the ortho-quinone methide 2.

  9. Synthesis of Methoxyethyl Nucleoside Dimer Phosphoramidates

    Yu, Gi Weon; Kang, Yong Han [Hanyang University, Ansan (Korea, Republic of)


    Four types of methoxyethyl (MOE) nucleoside phosphoramidites, which are categorized as second-generation building blocks of antisense oligonucleotide drugs, were synthesized. Also, three types of MOE nucleoside dimer phosphoramidites were synthesized to increase the efficiency and oligomer purity in solid phase synthesis. The block-like dimer phosphoramidites can prevent or minimize the formation of the (N-1) mer impurity, thereby affording the fabrication of pure oligonucleotides and reducing the synthesis time by performing coupling reactions in the order of 2 + 2 + 2.

  10. Photon Propagation through Linearly Active Dimers

    José Delfino Huerta Morales


    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.

  11. Refined conformal spectra in the dimer model

    Rasmussen, Jorgen


    Working with Lieb's transfer matrix for the dimer model, we point out that the full set of dimer configurations may be partitioned into disjoint subsets (sectors) closed under the action of the transfer matrix. These sectors are labelled by an integer or half-integer quantum number we call the variation index. In the continuum scaling limit, each sector gives rise to a representation of the Virasoro algebra. We determine the corresponding conformal partition functions and their finitizations, and observe an intriguing link to the Ramond and Neveu-Schwarz sectors of the critical dense polymer model as described by a conformal field theory with central charge c=-2.

  12. A p-quinodimethane-bridged porphyrin dimer.

    Zeng, Wangdong; Ishida, Masatoshi; Lee, Sangsu; Sung, Young Mo; Zeng, Zebing; Ni, Yong; Chi, Chunyan; Kim, Dongho; Wu, Jishan


    A p-quinodimethane (p-QDM)-bridged porphyrin dimer 1 has been prepared for the first time. An unexpected Michael addition reaction took place when we attempted to synthesize compound 1 by reaction of the cross-conjugated keto-linked porphyrin dimers 8a and 8b with alkynyl/aryl Grignard reagents. Alternatively, compound 1 could be successfully prepared by intramolecular Friedel-Crafts alkylation of the diol-linked porphyrin dimer 14 with concomitant oxidation in air. Compound 1 shows intense one-photon absorption (OPA, λ(max)=955 nm, ε=45400 M(-1) cm(-1)) and a large two-photon absorption (TPA) cross-section (σ((2))(max)=2080 GM at 1800 nm) in the near-infrared (NIR) region due to its extended π-conjugation and quinoidal character. It also exhibits a short singlet excited-state lifetime of 25 ps. The cyclic voltammogram of 1 displays multiple redox waves with a small electrochemical energy gap of 0.86 eV. The ground-state geometry, electronic structure, and optical properties of 1 have been further studied by density functional theory (DFT) calculations and compared with those of the keto-linked dimer 8b. This research has revealed that incorporation of a p-QDM unit into the porphyrin framework had a significant impact on its optical and electronic properties, leading to a novel NIR OPA and TPA chromophore.

  13. Geometric Reid's recipe for dimer models

    Bocklandt, R.; Craw, A.; Quintero Vélez, A.


    Crepant resolutions of three-dimensional toric Gorenstein singularities are derived equivalent to noncommutative algebras arising from consistent dimer models. By choosing a special stability parameter and hence a distinguished crepant resolution Y, this derived equivalence generalises the Fourier-M

  14. The Diamagnetic Susceptibility of the Tubulin Dimer

    Wim Bras


    Full Text Available An approximate value of the diamagnetic anisotropy of the tubulin dimer, Δχdimer, has been determined assuming axial symmetry and that only the α-helices and β-sheets contribute to the anisotropy. Two approaches have been utilized: (a using the value for the Δχα for an α-helical peptide bond given by Pauling (1979 and (b using the previously determined anisotropy of fibrinogen as a calibration standard. The Δχdimer≈4×10-27 JT−2 obtained from these measurements are similar to within 20%. Although Cotton-Mouton measurements alone cannot be used to estimate Δχ directly, the value we measured, CMdimer=1.41±0.03×10-8 T−2cm2mg−1, is consistent with the above estimate for Δχdimer. The method utilized for the determination of the tubulin dimer diamagnetic susceptibility is applicable to other proteins and macromolecular assemblies as well.

  15. A new lignan dimer from Mallotus philippensis.

    Mai, Nguyen Thi; Cuong, Nguyen Xuan; Thao, Nguyen Phuong; Nam, Nguyen Hoai; Khoi, Nguyen Huu; Minh, Chau Van; Heyden, Yvan Vander; Thuan, Ngo Thi; Tuyen, Nguyen Van; Quetin-Leclercq, Joëlle; Kiem, Phan Van


    A new lignan dimer, bilariciresinol (1), was isolated from the leaves of Mallotus philippensis, along with platanoside (2), isovitexin (3), dihydromyricetin (4), bergenin (5), 4-O-galloylbergenin (6), and pachysandiol A (7). Their structures were elucidated by spectroscopic experiments including 1D and 2D NMR and FTICR-MS.

  16. Biological consequences of cyclobutane pyrimidine dimers

    Vink, A.A.; Roza, L.


    In the skin many molecules may absorb ultraviolet (UV) radiation upon exposure. In particular, cellular DNA strongly absorbs shorter wavelength solar UV radiation, resulting in various types of DNA damage. Among the DNA photoproducts produced the cyclobutane pyrimidine dimers (CPDs) are predominant.

  17. Synthesis of novel 15-membered macrolide dimers

    Shu Tao Ma; Rui Xin Ma; Rui Qing Xian; Bo Jiao


    A series of novel dimers of 15-memhered macrolides was synthesized and evaluated. The directs exhibited excellent activity against erythromycin-susceptible S. pneumonia, but did not show any improved activity against erythromycin-resistant S. pneumoniae encoded by erm gene.

  18. Amplitude enhancement by a gold dimer

    Hong, Xin; Wang, Jingxin; Jin, Zheng


    The unique optical properties such as brightness, non-bleaching, good bio-compatibility make gold particles ideal label candidates for molecular probes. Due to the strongly enhanced field, aggregation of gold nanoparticles finds themselves plenty of applications in bio-imaging. But limited by its small cross-section associated with nanometer sized particle, it is a big challenge to employ it in a single molecular detection. The field enhancement results from the effect of plasmonic coupling between two closely attached gold nanoparticle under the right excitation condition. With the aim to apply the gold dimer probe to find the molecules in our recently established optical detection method, we compared of the amplitude enhancement by the dimer relative to a single particle. The amplitude distribution under a highly focused illumination objective was calculated, whose results suggest that at the optimized excitation condition, the local field can be enhanced 190 fold. In consequence, experimental detection was carried out. Gold dimers were linked together by the hybridization of two single chain DNAs. Dimer and single particle probes were mixed together in one detection. Overwhelming contrast between these two kinds of probes were clearly exhibited in the experimental detection image. This method can provide a way to a high specific detection in early diagnosis.

  19. Universal bosonic tetramers of dimer-atom-atom structure

    Deltuva, A.


    Unstable four-boson states having an approximate dimer-atom-atom structure are studied using momentum-space integral equations for the four-particle transition operators. For a given Efimov trimer the universal properties of the lowest associated tetramer are determined. The impact of this tetramer on the atom-trimer and dimer-dimer collisions is analyzed. The reliability of the three-body dimer-atom-atom model is studied.

  20. Ultraviolet Spectrum And Chemical Reactivity Of CIO Dimer

    Demore, William B.; Tschuikow-Roux, E.


    Report describes experimental study of ultraviolet spectrum and chemical reactivity of dimer of chlorine monoxide (CIO). Objectives are to measure absorption cross sections of dimer at near-ultraviolet wavelengths; determine whether asymmetrical isomer (CIOCIO) exists at temperatures relevant to Antarctic stratosphere; and test for certain chemical reactions of dimer. Important in photochemistry of Antarctic stratosphere.

  1. A Nove Asymmetric ent—Kauranoid Dimer from Isodon enanderianus

    纳智; 黎胜红; 等


    Further investigation on the aerial parts of Isodon enanderianus afforded a novel asymmetric ent-kauranoid dimer,enanderi-nanin J(1).The structure of the dimer was elucidated by means of spectroscopic methods (including 2D NMR tecniques ),Enanderinanin J was a dimer of xerophilusin A and probably formed by [4+2] cycloaddition.

  2. A Novel Asymmetric ent-Kauranoid Dimer from Isodon enanderianus

    NA,Zhi(纳智); LI,Sheng-Hong(黎胜红); XIANG,Wei(项伟); ZHAO,Ai-Hua(赵爱华); LI,Chao-Ming(李朝明); SUN,Han-Dong(孙汉董)


    Further investigation on the aerial parts of Isodon enanderianus afforded a novel asymmetric ent-kauranoid dimer, enanuderinaninJ (1). The structure of the dimer was elucidated by means of spectroscopic methods (including 2D NMR techniques ). Enanderinanin J was a dimer of xerophilusin A and probably formed by [ 4 + 2] cycloaddition.

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

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


    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.

  4. Construction of a ferritin dimer by breaking its symmetry

    Zheng, B; Uenuma, M; Uraoka, Y; Yamashita, I [Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192 (Japan); CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012 (Japan)


    Ferritin has a mono-dispersed structure and biomineralization properties that allow it to form various kinds of nanoparticles and play an important role in modern nanotechnology. Independent nanoparticles synthesized in ferritin are valuable, but moreover a pair of nanoparticles can bring new properties different from those of the independent nanoparticles. In this study, by breaking ferritin's symmetry, we successfully produced ferritin dimers which provide real protein frameworks for nanoparticle dimer formation. Identical nickel hydro-oxide nanoparticle dimers were produced by simply biomineralizing ferritin dimers. The method presented here can produce multi-functional ferritin dimers with different kinds of nanoparticles.

  5. Large D-Dimer Fluctuation in Normal Pregnancy

    Hedengran, Katrine K; Andersen, Malene R; Stender, Steen


    pregnancies were recruited. D-dimer was repeatedly measured during pregnancy, at active labor, and on the first and second postpartum days. Percentiles for each gestational week were calculated. Each individual D-dimer was normalized by transformation into percentiles for the relevant gestational age......Introduction. D-dimer levels increase throughout pregnancy, hampering the usefulness of the conventional threshold for dismissing thromboembolism. This study investigates the biological fluctuation of D-dimer in normal pregnancy. Methods. A total of 801 healthy women with expected normal...... normal pregnancy, repeated D-dimer measurements are of no clinical use in the evaluation of thromboembolic events during pregnancy....

  6. Plasmonic rod dimers as elementary planar chiral meta-atoms

    Zhukovsky, Sergei V; Chigrin, Dmitry N


    Electromagnetic response of metallic rod dimers is theoretically calculated for arbitrary planar arrangement of rods in the dimer. It is shown that dimers without an in-plane symmetry axis exhibit elliptical dichroism and act as "atoms" in planar chiral metamaterials. Due to a very simple geometry of the rod dimer, such planar metamaterials are much easier in fabrication than conventional split-ring or gammadion-type structures, and lend themselves to a simple analytical treatment based on coupled dipole model. Dependencies of metamaterial's directional asymmetry on the dimer's geometry are established analytically and confirmed in numerical simulations.

  7. Calcium-dependent Dimerization of Human Soluble Calcium Activated Nucleotidase: Characterization of the Dimer Interface

    Yang,M.; Horii, K.; Herr, A.; Kirley, T.


    Mammals express a protein homologous to soluble nucleotidases used by blood-sucking insects to inhibit host blood clotting. These vertebrate nucleotidases may play a role in protein glycosylation. The activity of this enzyme family is strictly dependent on calcium, which induces a conformational change in the secreted, soluble human nucleotidase. The crystal structure of this human enzyme was recently solved; however, the mechanism of calcium activation and the basis for the calcium-induced changes remain unclear. In this study, using analytical ultracentrifugation and chemical cross-linking, we show that calcium or strontium induce noncovalent dimerization of the soluble human enzyme. The location and nature of the dimer interface was elucidated using a combination of site-directed mutagenesis and chemical cross-linking, coupled with crystallographic analyses. Replacement of Ile{sup 170}, Ser{sup 172}, and Ser{sup 226} with cysteine residues resulted in calcium-dependent, sulfhydryl-specific intermolecular cross-linking, which was not observed after cysteine introduction at other surface locations. Analysis of a super-active mutant, E130Y, revealed that this mutant dimerized more readily than the wild-type enzyme. The crystal structure of the E130Y mutant revealed that the mutated residue is found in the dimer interface. In addition, expression of the full-length nucleotidase revealed that this membrane-bound form can also dimerize and that these dimers are stabilized by spontaneous oxidative cross-linking of Cys{sup 30}, located between the single transmembrane helix and the start of the soluble sequence. Thus, calcium-mediated dimerization may also represent a mechanism for regulation of the activity of this nucleotidase in the physiological setting of the endoplasmic reticulum or Golgi.

  8. Revisiting the Optical PT-Symmetric Dimer

    José Delfino Huerta Morales


    Full Text Available Optics has proved a fertile ground for the experimental simulation of quantum mechanics. Most recently, optical realizations of PT -symmetric quantum mechanics have been shown, both theoretically and experimentally, opening the door to international efforts aiming at the design of practical optical devices exploiting this symmetry. Here, we focus on the optical PT -symmetric dimer, a two-waveguide coupler where the materials show symmetric effective gain and loss, and provide a review of the linear and nonlinear optical realizations from a symmetry-based point of view. We go beyond a simple review of the literature and show that the dimer is just the smallest of a class of planar N-waveguide couplers that are the optical realization of the Lorentz group in 2 + 1 dimensions. Furthermore, we provide a formulation to describe light propagation through waveguide couplers described by non-Hermitian mode coupling matrices based on a non-Hermitian generalization of the Ehrenfest theorem.

  9. Revisiting the optical $PT$-symmetric dimer

    Morales, J D Huerta; López-Aguayo, S; Rodríguez-Lara, B M


    Optics has proved a fertile ground for the experimental simulation of quantum mechanics. Most recently, optical realizations of $\\mathcal{PT}$-symmetric quantum mechanics have been shown, both theoretically and experimentally, opening the door to international efforts aiming at the design of practical optical devices exploiting this symmetry. Here, we focus on the optical $\\mathcal{PT}$-symmetric dimer, a two-waveguide coupler were the materials show symmetric effective gain and loss, and provide a review of the linear and nonlinear optical realizations from a symmetry based point of view. We go beyond a simple review of the literature and show that the dimer is just the smallest of a class of planar $N$-waveguide couplers that are the optical realization of Lorentz group in 2+1 dimensions. Furthermore, we provide a formulation to describe light propagation through waveguide couplers described by non-Hermitian mode coupling matrices based on a non-Hermitian generalization of Ehrenfest theorem.

  10. Fibrillar dimer formation of islet amyloid polypeptides

    Chiu, Chi-cheng [Univ. of Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States); de Pablo, Juan J. [Univ. of Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States)


    Amyloid deposits of human islet amyloid polypeptide (hIAPP), a 37-residue hormone co-produced with insulin, have been implicated in the development of type 2 diabetes. Residues 20 – 29 of hIAPP have been proposed to constitute the amyloidogenic core for the aggregation process, yet the segment is mostly unstructured in the mature fibril, according to solid-state NMR data. Here we use molecular simulations combined with bias-exchange metadynamics to characterize the conformational free energies of hIAPP fibrillar dimer and its derivative, pramlintide. We show that residues 20 – 29 are involved in an intermediate that exhibits transient β-sheets, consistent with recent experimental and simulation results. By comparing the aggregation of hIAPP and pramlintide, we illustrate the effects of proline residues on inhibition of the dimerization of IAPP. The mechanistic insights presented here could be useful for development of therapeutic inhibitors of hIAPP amyloid formation.

  11. Immunoglobulin Free Light Chain Dimers in Human Diseases

    Batia Kaplan


    Full Text Available Immunoglobulin free light chain (FLC kappa (κ and lambda (λ isotypes exist mainly in monomeric and dimeric forms. Under pathological conditions, the level of FLCs as well as the structure of monomeric and dimeric FLCs and their dimerization properties might be significantly altered. The abnormally high fractions of dimeric FLCs were demonstrated in the serum of patients with multiple myeloma (MM and primary systemic amyloidosis (AL, as well as in the serum of anephric patients. The presence of tetra- and trimolecular complexes formed due to dimer-dimer and dimer-monomer interactions was detected in the myeloma serum. Analysis of the amyloidogenic light chains demonstrated mutations within the dimer interface, thus raising the possibility that these mutations are responsible for amyloidogenicity. Increased κ monomer and dimer levels, as well as a high κ/λ monomer ratio, were typically found in the cerebrospinal fluid from patients with multiple sclerosis (MS. In many MS cases, the elevation of κ FLCs was accompanied by an abnormally high proportion of λ dimers. This review focuses on the disease-related changes of the structure and level of dimeric FLCs, and raises the questions regarding their formation, function, and role in the pathogenesis and diagnosis of human diseases.

  12. Entanglement and decoherence in a quantum dimer

    Hou Xi-Wen; Hui Zi; Ding Rui-Min; Chen Xiao-Yang; Gao Yu


    The dynamical properties of quantum entanglement in an integrable quantum dimer are studied in terms of the reduced-density linear entropy with various coupling parameters and total boson numbers. The characteristic time of decoherence process in the early-time evolution of the linear entropy is obtained, indicating that the characteristic time and the corresponding entropy exhibit a maximum near the position of the corresponding classical separatrix energy.

  13. Path integrals for dimerized quantum spin systems

    Foussats, Adriana, E-mail: [Facultad de Ciencias Exactas, Ingenieria y Agrimensura and Instituto de Fisica Rosario (UNR-CONICET), Av. Pellegrini 250, 2000 Rosario (Argentina); Greco, Andres [Facultad de Ciencias Exactas, Ingenieria y Agrimensura and Instituto de Fisica Rosario (UNR-CONICET), Av. Pellegrini 250, 2000 Rosario (Argentina); Muramatsu, Alejandro [Institut fuer Theoretische Physik III, Universitaet Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart (Germany)


    Dimerized quantum spin systems may appear under several circumstances, e.g. by a modulation of the antiferromagnetic exchange coupling in space, or in frustrated quantum antiferromagnets. In general, such systems display a quantum phase transition to a Neel state as a function of a suitable coupling constant. We present here two path-integral formulations appropriate for spin S=1/2 dimerized systems. The first one deals with a description of the dimers degrees of freedom in an SO(4) manifold, while the second one provides a path-integral for the bond-operators introduced by Sachdev and Bhatt. The path-integral quantization is performed using the Faddeev-Jackiw symplectic formalism for constrained systems, such that the measures and constraints that result from the algebra of the operators is provided in both cases. As an example we consider a spin-Peierls chain, and show how to arrive at the corresponding field-theory, starting with both an SO(4) formulation and bond-operators.

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

    Du, Fengxia [Laboratory of Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101 (China); Zhang, Minjie [Laboratory of Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Li, Xiaohua; Yang, Caiyun [Laboratory of Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101 (China); Meng, Hao; Wang, Dong; Chang, Shuang [Laboratory of Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Xu, Ye [Department of Radiation Oncology, Division of Genomic Stability, Dana Farber Cancer Institute, Harvard Medical School, MA 02134 (United States); Price, Brendan, E-mail: [Department of Radiation Oncology, Division of Genomic Stability, Dana Farber Cancer Institute, Harvard Medical School, MA 02134 (United States); Sun, Yingli, E-mail: [Laboratory of Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101 (China)


    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.

  15. MspA nanopores from subunit dimers.

    Mikhail Pavlenok

    Full Text Available Mycobacterium smegmatis porin A (MspA forms an octameric channel and represents the founding member of a new family of pore proteins. Control of subunit stoichiometry is important to tailor MspA for nanotechnological applications. In this study, two MspA monomers were connected by linkers ranging from 17 to 62 amino acids in length. The oligomeric pore proteins were purified from M. smegmatis and were shown to form functional channels in lipid bilayer experiments. These results indicated that the peptide linkers did not prohibit correct folding and localization of MspA. However, expression levels were reduced by 10-fold compared to wild-type MspA. MspA is ideal for nanopore sequencing due to its unique pore geometry and its robustness. To assess the usefulness of MspA made from dimeric subunits for DNA sequencing, we linked two M1-MspA monomers, whose constriction zones were modified to enable DNA translocation. Lipid bilayer experiments demonstrated that this construct also formed functional channels. Voltage gating of MspA pores made from M1 monomers and M1-M1 dimers was identical indicating similar structural and dynamic channel properties. Glucose uptake in M. smegmatis cells lacking porins was restored by expressing the dimeric mspA M1 gene indicating correct folding and localization of M1-M1 pores in their native membrane. Single-stranded DNA hairpins produced identical ionic current blockades in pores made from monomers and subunit dimers demonstrating that M1-M1 pores are suitable for DNA sequencing. This study provides the proof of principle that production of single-chain MspA pores in M. smegmatis is feasible and paves the way for generating MspA pores with altered stoichiometries. Subunit dimers enable better control of the chemical and physical properties of the constriction zone of MspA. This approach will be valuable both in understanding transport across the outer membrane in mycobacteria and in tailoring MspA for nanopore

  16. Metal enhanced fluorescence of Ag-nanoshell dimer

    Liaw, Jiunn-Woei; Chen, Huang-Chih; Chen, Bae-Renn; Kuo, Mao-Kuen


    The plasmon modes of Ag-nanoshell dimer on metal enhanced fluorescence (MEF) are studied theoretically. The amplified excitation rate of a dimer (two identical Ag nanoshells) illuminated by a plane wave for exciting a molecule located at the gap center is calculated. Subsequently, the apparent quantum yield of the emission of the excited molecule affected by the dimer is investigated. The multiple multipole method is used for the both simulations. Finally, the enhancement factor of the dimer on the overall photoluminescence of the molecule in terms of the two parameters is evaluated. Our results show that Ag-nanoshell dimer is a dual-band photoluminescence enhancer for MEF at the bonding dipole and quadrupole modes. The former is broadband, and the latter narrowband. Both bands depend on the gap size. Moreover, the average enhancement factor of Ag-nanoshell dimer for MEF with a Stokes shift is discussed.

  17. Cytochrome P450 as dimerization catalyst in diketopiperazine alkaloid biosynthesis.

    Saruwatari, Takayoshi; Yagishita, Fumitoshi; Mino, Takashi; Noguchi, Hiroshi; Hotta, Kinya; Watanabe, Kenji


    As dimeric natural products frequently exhibit useful biological activities, identifying and understanding their mechanisms of dimerization is of great interest. One such compound is (−)-ditryptophenaline, isolated from Aspergillus flavus, which inhibits substance P receptor for potential analgesic and anti-inflammatory activity. Through targeted gene knockout in A. flavus and heterologous yeast gene expression, we determined for the first time the gene cluster and pathway for the biosynthesis of a dimeric diketopiperazine alkaloid. We also determined that a single cytochrome P450, DtpC, is responsible not only for pyrroloindole ring formation but also for concurrent dimerization of N-methylphenylalanyltryptophanyl diketopiperazine monomers into a homodimeric product. Furthermore, DtpC exhibits relaxed substrate specificity, allowing the formation of two new dimeric compounds from a non-native monomeric precursor, brevianamide F. A radical-mediated mechanism of dimerization is proposed.

  18. Thermodynamic properties for the sodium dimer

    Song, Xiao-Qin; Wang, Chao-Wen; Jia, Chun-Sheng


    We present a closed-form expression of the classical vibrational partition function for the improved Rosen-Morse potential energy model. We give explicit expressions for the vibrational mean energy, vibrational specific heat, vibrational free energy, and vibrational entropy for diatomic molecule systems. The properties of these thermodynamic functions for the Na2 dimer are discussed in detail. We find that the improved Rosen-Morse potential model is superior to the harmonic oscillator in calculating the heat capacity for the Na2 molecules.

  19. Thermodynamics of acetylene van der Waals dimerization

    Colussi, A. J.; Sander, S. P.; Friedl, R. R.


    Integrated band intensities of the 620/cm absorption in (C2H2)2 are measured by FTIR spectroscopy at constant acetylene pressure between 198 and 273 K. These data, in conjunction with ab initio results for (C2H2)2, are used for the statistical evaluation of the equilibrium constant Kp(T) for acetylene-cluster dimerization. The present results are used to clarify the role of molecular clusters in chemical systems at or near equilibrium, in particular in Titan's stratosphere.

  20. The properties of dimers confined between two charged plates.

    Hatlo, Marius M; Bohinc, Klemen; Lue, Leo


    We consider two like-charged planar surfaces immersed in solution of oppositely charged dimer counterions with a bond length l. To analyze this system, we extend and employ a self-consistent field theory that has been shown to be accurate from the weak to the intermediate through to the strong coupling regimes. In the limit of very short dimers, the results converge to the results for pointlike divalent ions. Near the surfaces, the dimers lie parallel to the charged plates. In the intermediate coupling regime, the dimers are aligned perpendicularly to the surface when they are a distance l from a surface. In the weak coupling regime, the interactions are only repulsive. At slightly higher couplings, there is a minimum in the variation of the free energy with distance at approximately the bond length of the dimers, which arises from bridging conformations of the dimers. In the intermediate coupling regime, an additional minimum in the free energy is observed at much smaller distances, which is due to the correlations between the dimers. For large dimer bond lengths, this minimum is metastable with respect to the previous minimum. However, as the bond length decreases, this minimum becomes the stable, while the minimum associated with the dimer bond length becomes metastable and eventually disappears. For shorter dimer bond length the attractive interaction is the result of correlations between counterions and charges on the surfaces. We find that dimers can mediate attractive interaction between like-charged surfaces in the intermediate coupling regime. The analysis of orientations confirms the bridging mechanism for sufficiently long dimers, whereas at high electrostatic couplings charge correlations contribute to the attraction.

  1. Rotational spectra of propargyl alcohol dimer: A dimer bound with three different types of hydrogen bonds

    Mani, Devendra; Arunan, E., E-mail: [Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012 (India)


    Pure rotational spectra of the propargyl alcohol dimer and its three deuterium isotopologues have been observed in the 4 to 13 GHz range using a pulsed-nozzle Fourier transform microwave spectrometer. For the parent dimer, a total of 51 transitions could be observed and fitted within experimental uncertainty. For two mono-substituted and one bi-substituted deuterium isotopologues, a total of 14, 17, and 19 transitions were observed, respectively. The observed rotational constants for the parent dimer [A = 2321.8335(4) MHz, B = 1150.4774(2) MHz, and C = 1124.8898(2) MHz] are close to those of the most stable structure predicted by ab initio calculations. Spectra of the three deuterated isotopologues and Kraitchman analysis positively confirm this structure. Geometrical parameters and “Atoms in Molecules” analysis on the observed structure reveal that the two propargyl alcohol units in the dimer are bound by three different types of hydrogen bonds: O–H⋯O, O–H⋯π, and C–H⋯π. To the best of our knowledge, propargyl alcohol seems to be the smallest molecule forming a homodimer with three different points of contact.

  2. Synthesis of Symmetrical Biaryls via Rhodium Catalyzed Dimerization of Arylmercurials and Mechanism of the Dimerization


    A series of symmetrical biaryls was synthesized from arylmercuric chlorides and biarylmercurials in the presence of [ClRh(CO)2]2 in hexamethylphosphoramide(HMPA). The mechanism of the [ClRh(CO)2]2 catalyzed dimerization of biarylmercurials was studied, and shown to be mainly intermolecular reaction.

  3. Assembly of Drosophila centromeric nucleosomes requires CID dimerization.

    Zhang, Weiguo; Colmenares, Serafin U; Karpen, Gary H


    Centromeres are essential chromosomal regions required for kinetochore assembly and chromosome segregation. The composition and organization of centromeric nucleosomes containing the essential histone H3 variant CENP-A (CID in Drosophila) is a fundamental, unresolved issue. Using immunoprecipitation of CID mononucleosomes and cysteine crosslinking, we demonstrate that centromeric nucleosomes contain CID dimers in vivo. Furthermore, CID dimerization and centromeric targeting require a residue implicated in formation of the four-helix bundle, which mediates intranucleosomal H3 dimerization and nucleosome integrity. Taken together, our findings suggest that CID nucleosomes are octameric in vivo and that CID dimerization is essential for correct centromere assembly.

  4. Disordered clusters of Bak dimers rupture mitochondria during apoptosis

    Uren, Rachel T; O’Hely, Martin; Iyer, Sweta; Bartolo, Ray; Shi, Melissa X; Brouwer, Jason M; Alsop, Amber E; Dewson, Grant; Kluck, Ruth M


    During apoptosis, Bak and Bax undergo major conformational change and form symmetric dimers that coalesce to perforate the mitochondrial outer membrane via an unknown mechanism. We have employed cysteine labelling and linkage analysis to the full length of Bak in mitochondria. This comprehensive survey showed that in each Bak dimer the N-termini are fully solvent-exposed and mobile, the core is highly structured, and the C-termini are flexible but restrained by their contact with the membrane. Dimer-dimer interactions were more labile than the BH3:groove interaction within dimers, suggesting there is no extensive protein interface between dimers. In addition, linkage in the mobile Bak N-terminus (V61C) specifically quantified association between dimers, allowing mathematical simulations of dimer arrangement. Together, our data show that Bak dimers form disordered clusters to generate lipidic pores. These findings provide a molecular explanation for the observed structural heterogeneity of the apoptotic pore. DOI: PMID:28182867

  5. Pathogenic Cysteine Removal Mutations in FGFR Extracellular Domains Stabilize Receptor Dimers and Perturb the TM Dimer Structure.

    Sarabipour, Sarvenaz; Hristova, Kalina


    Missense mutations that introduce or remove cysteine residues in receptor tyrosine kinases are believed to cause pathologies by stabilizing the active receptor tyrosine kinase dimers. However, the magnitude of this stabilizing effect has not been measured for full-length receptors. Here, we characterize the dimer stabilities of three full-length fibroblast growth factor receptor (FGFR) mutants harboring pathogenic cysteine substitutions: the C178S FGFR1 mutant, the C342R FGFR2 mutant, and the C228R FGFR3 mutant. We find that the three mutations stabilize the FGFR dimers. We further see that the mutations alter the configuration of the FGFR transmembrane dimers. Thus, both aberrant dimerization and perturbed dimer structure likely contribute to the pathological phenotypes arising due to these mutations.

  6. Dimeric Labdane Diterpenes: Synthesis and Antiproliferative Effects

    Guillermo Schmeda-Hirschmann


    Full Text Available Several diterpenes with the labdane skeleton show biological activity, including antiproliferative effects. Most of the research work on bioactive labdanes has been carried out on naturally occurring diterpenes and semisynthetic derivatives, but much less is known on the effects of diterpene dimers. The aim of the present work was to synthesize dimeric diterpenes from the labdane imbricatolic acid using esters, ethers and the triazole ring as linkers. Some 18 new derivatives were prepared and the compounds were evaluated for antiproliferative activity on human normal fibroblasts (MRC-5 and the following human tumor cell lines: AGS, SK-MES-1, J82 and HL-60. The diethers 8–10, differing in the number of CH2 units in the linker, presented better antiproliferative activity with a maximum effect for the derivative 9. The best antiproliferative effect against HL-60 cells was found for compounds 3 and 17, with IC50 values of 22.3 and 23.2 μM, lower than that found for the reference compound etoposide (2.23 μM. The compounds 9, 17 and 11 were the most active derivatives towards AGS cells with IC50 values of 17.8, 23.4 and 26.1 μM. A free carboxylic acid function seems relevant for the effect as several of the compounds showed less antiproliferative effect after methylation.

  7. Water dimer absorption of visible light

    J. Hargrove


    Full Text Available Laboratory measurements of water vapor absorption using cavity ring-down spectroscopy revealed a broad absorption at 405 nm with a quadratic dependence on water monomer concentration, a similar absorption with a linear component at 532 nm, and only linear absorption at 570 nm in the vicinity of water monomer peaks. D2O absorption is weaker and linear at 405 nm. Van't Hoff plots constructed at 405.26 nm suggest that for dimerization, Keq=0.056±0.02 atm−1, ΔH°301 K=−16.6±2 kJ mol−1 and ΔS°301 K=−80±10 J mol−1 K−1. This transition peaks at 409.5 nm, could be attributed to the 8th overtone of water dimer and the 532 nm absorption to the 6th overtone. It is possible that some lower overtones previously searched for are less enhanced. These absorptions could increase water vapor feed back calculations leading to higher global temperature projections with currently projected greenhouse gas levels or greater cooling from greenhouse gas reductions.

  8. Modelling study of dimerization in mammalian defensins

    Verma Chandra


    Full Text Available Abstract Background Defensins are antimicrobial peptides of innate immunity functioning by non-specific binding to anionic phospholipids in bacterial membranes. Their cationicity, amphipathicity and ability to oligomerize are considered key factors for their action. Based on structural information on human β-defensin 2, we examine homologous defensins from various mammalian species for conserved functional physico-chemical characteristics. Results Based on homology greater than 40%, structural models of 8 homologs of HBD-2 were constructed. A conserved pattern of electrostatics and dynamics was observed across 6 of the examined defensins; models backed by energetics suggest that the defensins in these 6 organisms are characterized by dimerization-linked enhanced functional potentials. In contrast, dimerization is not energetically favoured in the sheep, goat and mouse defensins, suggesting that they function efficiently as monomers. Conclusion β-defensin 2 from some mammals may work as monomers while those in others, including humans, work as oligomers. This could potentially be used to design human defensins that may be effective at lower concentrations and hence have therapeutic benefits.

  9. Exact Solution of a Generalized Nonlinear Schrodinger Equation Dimer

    Christiansen, Peter Leth; Maniadis, P.; Tsironis, G.P.


    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....

  10. Synthesis of novel organo-phosphorus C60 dimers


    Carbon bridged organophosphorus C60 dimers were obtained by the reaction of aminome- thylenebisphosphonate anion with C60 and fully characterized by 1HNMR, 31PNMR, 13CNMR, FT- MALDI-MS, FT-IR, UV-Vis, DEPT and HMBC, and the dimeric compounds undergo hydrolysis by using TMSI.

  11. Local field enhancement: comparing self-similar and dimer nanoantennas

    Pellegrini, Giovanni; Finazzi, Marco; Biagioni, Paolo


    We study the local field enhancement properties of self-similar nanolenses and compare the obtained results with the performance of standard dimer nanoantennas. We report that, despite the additional structural complexity, self-similar nanolenses are unable to provide significant improvements over the field enhancement performance of standard plasmonic dimers.

  12. Synthesis,Characterization,and Electrochemical Property of Nanometer Porphyrin Dimer


    A nanometer porphyrin dimer was synthesized with fumaryl chloride as a bridge-linked reagent. The characterization was carried out with elemental analyses, 1H NMR, UV-Vis, and IR spectrometries, and then the electrochemical properties of the porphyrins were studied. The authors found that there was moderate electronic communication between the two porphyrin rings in the nanometer porphyrin dimer.

  13. Loop groups, Clusters, Dimers and Integrable systems

    Fock, V V


    We describe a class of integrable systems on Poisson submanifolds of the affine Poisson-Lie groups $\\widehat{PGL}(N)$, which can be enumerated by cyclically irreducible elements the co-extended affine Weyl groups $(\\widehat{W}\\times \\widehat{W})^\\sharp$. Their phase spaces admit cluster coordinates, whereas the integrals of motion are cluster functions. We show, that this class of integrable systems coincides with the constructed by Goncharov and Kenyon out of dimer models on a two-dimensional torus and classified by the Newton polygons. We construct the correspondence between the Weyl group elements and polygons, demonstrating that each particular integrable model admits infinitely many realisations on the Poisson-Lie groups. We also discuss the particular examples, including the relativistic Toda chains and the Schwartz-Ovsienko-Tabachnikov pentagram map.

  14. Pseudo-two-dimensional random dimer lattices

    Naether, U., E-mail: [Instituto de Ciencia de Materiales de Aragón and Departamento de Física de la Materia Condensada, CSIC – Universidad de Zaragoza, 50009 Zaragoza (Spain); Mejía-Cortés, C.; Vicencio, R.A. [Departamento de Física and MSI – Nucleus for Advanced Optics, Center for Optics and Photonics (CEFOP), Facultad de Ciencias, Universidad de Chile, Santiago (Chile)


    We study the long-time wave transport in correlated and uncorrelated disordered 2D arrays. When a separation of dimensions is applied to the model, we find that the previously predicted 1D random dimer phenomenology also appears in so-called pseudo-2D arrays. Therefore, a threshold behavior is observed in terms of the effective size for eigenmodes, as well as in long-time dynamics. A minimum system size is required to observe this threshold, which is very important when considering a possible experimental realization. For the long-time evolution, we find that for correlated lattices a super-diffusive long-range transport is observed. For completely uncorrelated disorder 2D transport becomes sub-diffusive within the localization length and for random binary pseudo-2D arrays localization is observed.

  15. Dimerization and oligomerization of the chaperone calreticulin

    Jørgensen, Charlotte S; Ryder, L Rebekka; Steinø, Anne;


    protein. Using PAGE, urea gradient gel electrophoresis, capillary electrophoresis and MS, we show that dimerization through the SH group can be induced by lowering the pH to 5-6, heating, or under conditions that favour partial unfolding such as urea concentrations above 2.6 m or SDS concentrations above...... 0.025%. Moreover, we show that calreticulin also has the ability to self-oligomerize through noncovalent interactions at urea concentrations above 2.6 m at pH below 4.6 or above pH 10, at temperatures above 40 degrees C, or in the presence of high concentrations of organic solvents (25%), conditions...... urea or 1% SDS, and heat-induced oligomerization could be inhibited by 8 m urea or 1% SDS when present during heating. Comparison of the binding properties of monomeric and oligomeric calreticulin in solid-phase assays showed increased binding to peptides and denatured proteins when calreticulin...

  16. Edge Magnon Excitation in Spin Dimer Systems

    Sakaguchi, Ryo; Matsumoto, Masashige


    Magnetic excitation in a spin dimer system on a bilayer honeycomb lattice is investigated in the presence of a zigzag edge, where disordered and ordered phases can be controlled by a quantum phase transition. In analogy with the case of graphene with a zigzag edge, a flat edge magnon mode appears in the disordered phase. In an ordered phase, a finite magnetic moment generates a mean-field potential to the magnon. Since the potential is nonuniform on the edge and bulk sites, it affects the excitation, and the dispersion of the edge mode deviates from the flat shape. We investigate how the edge magnon mode evolves when the phase changes through the quantum phase transition and discuss the similarities to ordered spin systems on a monolayer honeycomb lattice.

  17. Molecular Dynamics Simulation of Amyloid Beta Dimer Formation

    Urbanc, B; Ding, F; Sammond, D; Khare, S; Buldyrev, S V; Stanley, H E; Dokholyan, N V


    Recent experiments with amyloid-beta (Abeta) peptide suggest that formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of Abeta oligomers depends on their structure, which is governed by assembly dynamics. Due to limitations of current experimental techniques, a detailed knowledge of oligomer structure at the atomic level is missing. We introduce a molecular dynamics approach to study Abeta dimer formation: (1) we use discrete molecular dynamics simulations of a coarse-grained model to identify a variety of dimer conformations, and (2) we employ all-atom molecular mechanics simulations to estimate the thermodynamic stability of all dimer conformations. Our simulations of a coarse-grained Abeta peptide model predicts ten different planar beta-strand dimer conformations. We then estimate the free energies of all dimer conformations in all-atom molecular mechanics simulations with explicit water. We compare the free energies of Abeta(1-42) and Abeta(1-40...

  18. Metal membrane with dimer slots as a universal polarizer

    Zhukovsky, Sergei; Zalkovskij, Maksim; Malureanu, Radu


    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...

  19. Three types of couplings between asymmetric plasmonic dimers.

    Chao, Yen-Chun; Tseng, Hsuan-Chi; Chang, Kao-Der; Chang, Chih-Wei


    We report extensive numerical studies on plasmonic dimers of different configurations and find that their coupling effects can be categorized into three types of phenomena. First, like ordinary mechanical systems, the plasmonic dimers can exhibit positive couplings that show anti-crossing behavior. Second, they can also be arranged to exhibit negative couplings that display opposite trends in resonant frequency shifts. Third, when there are surface currents in proximity to each other, the resonance frequencies of the dimers exhibit unusual redshifts that do not have any analogies in conventional systems. Our work suggests that in addition to the well-known electric and magnetic dipolar interactions, contributions from the inductance of displacement currents in the near field cannot be ignored. Overall, asymmetric plasmonic dimers exhibit better sensitivities than the symmetric counterparts and our extensive studies also enable us to identify the plasmonic dimer with the highest sensing capabilities.

  20. Threshold electron attachment and electron impact ionization involving oxygen dimers

    Kreil, J.; Ruf, M.-W.; Hotop, H.; Ettischer, I.; Buck, U.


    Using two different crossed-beams machines we have carried out the first quantitative study of threshold electron attachment and electron impact-induced ionization and fragmentation involving oxygen dimers (O 2) 2. In the electron attachment experiment we study electron transfer from state-selected Ar **(20d) Rydberg atoms to O 2 molecules and dimers in a skimmed supersonic beam at variable nozzle temperatures ( T0) and stagnation pressures ( p0). The relative dimer density is determined through measurements of Penning ionization by metastable Ne *(3s 3P2,0) atoms and used to estimate the absolute cross-section for O 2- formation in collisions of Ar **(20d) Rydberg atoms with O 2 dimers to be nearly 10 -17 m 2, almost four orders of magnitude larger than that for O 2- formation in collisions of Ar **(20d) Rydberg atoms with O 2 monomers. The fragmentation of the oxygen cluster beam is quantitatively characterized by the transverse helium beam scattering method which allows us to spatially separate different clusters. It is shown that in 70 eV electron impact of (O 2) 2 only 3.6(4)% of the dimers are detected as dimer ions (O 2) 2+. In additional experiments involving SF 6 clusters we show that SF 6 dimers fragment nearly completely upon 70 eV electron impact, yielding SF 5+ ions (probability for (SF 6)·SF 5+ production at most 0.3%).

  1. Asymmetric monometallic nanorod nanoparticle dimer and related compositions and methods

    Han, Yu


    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.

  2. Stochastic optimization-based study of dimerization kinetics

    Srijeeta Talukder; Shrabani Sen; Ralf Metzler; Suman K Banik; Pinaki Chaudhury


    We investigate the potential of numerical algorithms to decipher the kinetic parameters involved in multi-step chemical reactions. To this end, we study dimerization kinetics of protein as a model system. We follow the dimerization kinetics using a stochastic simulation algorithm and combine it with three different optimization techniques (genetic algorithm, simulated annealing and parallel tempering) to obtain the rate constants involved in each reaction step. We find good convergence of the numerical scheme to the rate constants of the process. We also perform a sensitivity test on the reaction kinetic parameters to see the relative effects of the parameters for the associated profile of the monomer/dimer distribution.

  3. Subsurface dimerization in III-V semiconductor (001) surfaces

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


    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....

  4. Circular dimers of lambda DNA in infected, nonlysogenic Escherichia coli

    Freifelder, D.; Baran, N.; Folkmanis, A.; Freifelder, D.L.R.


    Covalently closed circular dimerss of phage lambda DNA have been found in Escherichia coli infected with lambda. These dimers can be formed by either the lambda Red or Int systems, by a nonrecombinational replicative mechanism requiring the activity of the lambda O and P genes or by joining of the cohesive ends. Dimers mediated by the E. coli Rec system have not been observed. Those formed by the Int system often result from recombination between different DNA molecules; however, the Red-mediated dimer may be a result of replicative extension of a single DNA molecule. Trimers have also been observed but studied only briefly.

  5. Time resolved structural dynamics of butadiyne-linked porphyrin dimers.

    Camargo, Franco V A; Hall, Christopher R; Anderson, Harry L; Meech, Stephen R; Heisler, Ismael A


    In this work, the timescales and mechanisms associated with the structural dynamics of butadiyne-linked porphyrin dimers are investigated through time resolved narrowband pump/broadband probe transient absorption spectroscopy. Our results confirm previous findings that the broadening is partly due to a distribution of structures with different (dihedral) angular conformations. Comparison of measurements with excitations on the red and blue sides of the Q-band unravel the ground and excited state conformational re-equilibration timescales. Further comparison to a planarized dimer, through the addition of a ligand, provides conclusive evidence for the twisting motion performed by the porphyrin dimer in solution.

  6. Time resolved structural dynamics of butadiyne-linked porphyrin dimers

    Franco V. A. Camargo


    Full Text Available In this work, the timescales and mechanisms associated with the structural dynamics of butadiyne-linked porphyrin dimers are investigated through time resolved narrowband pump/broadband probe transient absorption spectroscopy. Our results confirm previous findings that the broadening is partly due to a distribution of structures with different (dihedral angular conformations. Comparison of measurements with excitations on the red and blue sides of the Q-band unravel the ground and excited state conformational re-equilibration timescales. Further comparison to a planarized dimer, through the addition of a ligand, provides conclusive evidence for the twisting motion performed by the porphyrin dimer in solution.

  7. Multicritical tensor models and hard dimers on spherical random lattices

    Bonzom, Valentin


    Random tensor models which display multicritical behaviors in a remarkably simple fashion are presented. They come with entropy exponents \\gamma = (m-1)/m, similarly to multicritical random branched polymers. Moreover, they are interpreted as models of hard dimers on a set of random lattices for the sphere in dimension three and higher. Dimers with their exclusion rules are generated by the different interactions between tensors, whose coupling constants are dimer activities. As an illustration, we describe one multicritical point, which is interpreted as a transition between the dilute phase and a crystallized phase, though with negative activities.

  8. How to use D-dimer in acute cardiovascular care

    Giannitsis, Evangelos; Mair, Johannes; Christersson, Christina


    D-dimer testing is important to aid in the exclusion of venous thromboembolic events (VTEs), including deep venous thrombosis and pulmonary embolism, and it may be used to evaluate suspected aortic dissection. D-dimer is produced upon activation of the coagulation system with the generation and s...... testing. For the exclusion of pulmonary embolism/deep vein thrombosis, age-adjusted cut-offs are recommend. Clinicians must be aware of the validated use of their hospital's D-dimer assay to avoid inappropriate use of this biomarker in routine care....

  9. Third-Order Optical Nonlinearity in Novel Porphyrin Dimers

    PEI Song-Hao; ZHAO Da-Peng; ZHANG Wei; ZHENG Wen-Qi; WANG Xing-Qiao; PENG Wei-Xian; SHI Guang; SONG Ying-Lin


    @@ We investigate the third-order optical nonlinearities in four novel porphyrin dimers (directs A to I)) and a monomeric porphyrin H2 CPTPP measured by using the single-beam z-scan technique with a pulsed Q-switched Nd:YAG nanosecond laser at 532nm.All the samples show strong excited state absorption (ESA) and high value of X(3) in the ns domain at this wavelength.We perform a comparison between dimer A and its monomer H2 CPTPP in their third-order optical nonlinearity, and discuss the relationships between the values of X(3) and the different bridging groups for all the dimers.

  10. Dimeric Surfactants: Promising Ingredients of Cosmetics and Toiletries

    Naveen Kumar


    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.

  11. Smectic Phase Formed by DNA Dimers

    Salamonczyk, Miroslaw; Gleeson, James; Jakli, Antal; Sprunt, Samuel; Dhont, Jan; Stiakakis, Emmanuel

    The rapidly expanding bio market is driving the development and characterization of new multifunctional materials. In particular, nucleic acids are under intense study for gene therapy, drug delivery and other bio-safe applications [1,2,3]. DNA is well-known to form a cholesteric nematic liquid crystal in its native form; however, much recent research has focused on self-assembly and mesomorphic behavior in concentrated solutions of short DNA helices [4]. Our work focuses on DNA dimers, consisting of 48 base-pair double-stranded helices connected by a 5 to 20 base flexible single strand, and suspended in a natural buffer. Depending on temperature, concentration and length of the flexible spacer, polarizing optical microscopy and small angle x-ray scattering reveal cholesteric nematic and, remarkably, smectic liquid crystalline phases. A model for smectic phase formation in this system will be presented. 1] J.-L. Lim et al., Int. J. of. Pharm. 490 (2015) 2652] D.-H. Kim et al., Nature Biotech. 23 (2005) 2223] K. Liu et al., Chem. Eur. J. 21 (2015) 48984] M. Nakata et al., Science 318 (2007) 1276 NSF DMR 1307674.

  12. Vibrations of the carbon dioxide dimer

    Chen, Hua; Light, J. C.


    Fully coupled four-dimensional quantum-mechanical calculations are presented for intermolecular vibrational states of rigid carbon dioxide dimer for J=0. The Hamiltonian operator is given in collision coordinates. The Hamiltonian matrix elements are evaluated using symmetrized products of spherical harmonics for angles and a potential optimized discrete variable representation (PO-DVR) for the intermolecular distance. The lowest ten or so states of each symmetry are reported for the potential energy surface (PES) given by Bukowski et al. [J. Chem. Phys. 110, 3785 (1999)]. Due to symmetries, there is no interconversion tunneling splitting for the ground state. Our calculations show that there is no tunneling shift of the ground state within our computation precision (0.01 cm-1). Analysis of the wave functions shows that only the ground states of each symmetry are nearly harmonic. The van der Waals frequencies and symmetry adapted force constants are found and compared to available experimental values. Strong coupling between the stretching coordinates and the bending coordinates are found for vibrationally excited states. The interconversion tunneling shifts are discussed for the vibrationally excited states.

  13. Family C 7TM receptor dimerization and activation

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


    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......-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...... 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....

  14. Metallothionein dimers studied by nano-spray mass spectrometry.

    Hathout, Yetrib; Reynolds, Kristy J; Szilagyi, Zoltan; Fenselau, Catherine


    Both transient and stable dimers of metallothionein have been characterized, based on earlier studies using NMR, circular dichroism and size-exclusion chromatography. Here additional characterization is provided by nanospray mass spectrometry. Rapid redistribution of metal ions between monomeric Cd7- and Zn7-metallothionein 2a is monitored by nanospray. An experiment in which theses two forms of the monomeric protein are separated by a dialysis membrane, which will pass metal ions but not proteins, confirms that a transient dimer must form for metal ions to be redistributed. On the other hand, size-exclusion chromatography of reconstituted Zn7- or Cd7-metallothionein revealed the presence of monomeric and dimeric species. These dimers do not equilibrate readily to form monomers and they are shown to be covalent.

  15. 21 CFR 176.120 - Alkyl ketene dimers.


    ... derived from the fatty acids of animal or vegetable fats and oils. (b) The alkyl ketene dimers are used as... HUMAN CONSUMPTION (CONTINUED) INDIRECT FOOD ADDITIVES: PAPER AND PAPERBOARD COMPONENTS Substances...

  16. [Antioxidant and antibacterial activities of dimeric phenol compounds].

    Ogata, Masahiro


    We studied the antioxidant and antibacterial activities of monomeric and dimeric phenol compounds. Dimeric compounds had higher antioxidant activities than monomeric compounds. Electron spin resonance spin-trapping experiments showed that phenol compounds with an allyl substituent on their aromatic rings directly scavenged superoxide, and that only eugenol trapped hydroxyl radicals. We developed a generation system of the hydroxyl radical without using any metals by adding L-DOPA and DMPO to PBS or MiliQ water in vitro. We found that eugenol trapped hydroxyl radicals directly and is metabolized to a dimer. On the other hand, dipropofol, a dimer of propofol, has strong antibacterial activity against Gram-positive bacteria. However, it lacks solubility in water and this property is assumed to limit its efficacy. We tried to improve the solubility and found a new solubilization method of dipropofol in water with the addition of a monosaccharide or ascorbic acid.

  17. Gnetuhainin S, a New Resveratrol Dimer from Gnetum hainanense


    Gnetuhainin S, a new resveratrol dimer, was isolated from the lianas of Gnetum hainanense C. Y. Cheng. Its structure and relative configuration were established on the basis of spectroscopic evidence.

  18. UV spectra of benzene isotopomers and dimers in helium nanodroplets

    Schmied, Roman; ćarçabal, Pierre; Dokter, Adriaan M.; Lonij, Vincent P. A.; Lehmann, Kevin K.; Scoles, Giacinto


    We report spectra of various benzene isotopomers and their dimers in helium nanodroplets in the region of the first Herzberg-Teller allowed vibronic transition 601 1B2u←1A1g (the A00 transition) at ˜260 nm. Excitation spectra have been recorded using both beam depletion detection and laser-induced fluorescence. Unlike for many larger aromatic molecules, the monomer spectra consist of a single "zero-phonon" line, blueshifted by ˜30 cm-1 from the gas phase position. Rotational band simulations show that the moments of inertia of C6H6 in the nanodroplets are at least six-times larger than in the gas phase. The dimer spectra present the same vibronic fine structure (though modestly compressed) as previously observed in the gas phase. The fluorescence lifetime and quantum yield of the dimer are found to be equal to those of the monomer, implying substantial inhibition of excimer formation in the dimer in helium.

  19. DLTS study of the oxygen dimer formation kinetics in silicon

    Yarykin, Nikolai; Weber, Jörg


    The introduction rates of radiation defects, in particular the X- and M-centers for which the oxygen dimer is a precursor, are investigated as a function of duration of the pre-irradiation heat treatment at 480∘ C in Czochralski-grown silicon both of n- and p-types. The characteristic annealing time to grow the X-center concentration in the n-type crystal is found to be about 1 h in accordance with the model which implies no significant barrier for the dimer formation. The M-center concentration in the p-type crystal is found to be nearly independent of duration of the pre-irradiation annealing after a few minutes transient period. This behavior is ascribed to the stabilization of dimer concentration due to an effective dimer trapping in these samples.

  20. DLTS study of the oxygen dimer formation kinetics in silicon

    Yarykin, Nikolai, E-mail: nay@iptm.r [Institute of Microelectronics Technology RAS, 142432 Chernogolovka, Moscow Region (Russian Federation); Weber, Joerg [Technische Universitaet Dresden, 01062 Dresden (Germany)


    The introduction rates of radiation defects, in particular the X- and M-centers for which the oxygen dimer is a precursor, are investigated as a function of duration of the pre-irradiation heat treatment at 480 deg. C in Czochralski-grown silicon both of n- and p-types. The characteristic annealing time to grow the X-center concentration in the n-type crystal is found to be about 1 h in accordance with the model which implies no significant barrier for the dimer formation. The M-center concentration in the p-type crystal is found to be nearly independent of duration of the pre-irradiation annealing after a few minutes transient period. This behavior is ascribed to the stabilization of dimer concentration due to an effective dimer trapping in these samples.

  1. Dimer representations of the Temperley-Lieb algebra

    Morin-Duchesne, Alexi; Ruelle, Philippe


    A new spin-chain representation of the Temperley-Lieb algebra $TL_n(\\beta=0)$ is introduced and related to the dimer model. Unlike the usual XXZ spin-chain representations of dimension $2^n$, this dimer representation is of dimension $2^{n-1}$. A detailed analysis of its structure is presented and found to yield indecomposable zigzag modules not appearing in traditional spin-chain scenarios.

  2. Theoretical Study on the Intermolecular Interactions of Tetrazole Dimers


    Tetrazole monomers (Ⅰ,Ⅱ) and all of their possible stable dimers (1, 2, 3, 4, 5, 6, 7and 8) were fully optimized by DFT method at the B3LYP/6-311++G** level. Among the eight dimers, there were two 1H-tetrazole dimers, three 2H-tetrazole dimers and three hetero dimers of 1H-tetrazole and 2H-tetrazole. Vibrational frequencies were calculated to ascertain that each structure was stable (no imaginary frequencies). The basis set superposition errors (BSSE) are 2.78,2.28, 2.97, 2.75, 2.74, 2.18, 1.23 and 3.10 kJ/mol, and the zero point energy (ZPE) corrections for the interaction energies are 4.88, 4.18, 3.87, 3.65, 3.54, 3.22, 2.87 and 4.34 kJ/mol for 1, 2, 3, 4, 5, 6,7 and 8, respectively. After BSSE and ZPE corrections, the greatest corrected intermolecular interaction energy ofthe dimers is -43.71 kJ/mol. The charge redistribution mainly occurs on the very small. Natural bond orbital (NBO) analysis was performed to reveal the origin of the interaction. Based on the statistical thermodynamic method, the standard thermodynamic functions, heat capacities (C0p), entropies (S0T) and thermal corrections to enthalpy (H0T), and the changes of thermodynamic properties from monomer to dimer in the temperature range of 200.00 K to 700 K have been obtained. 1H-tetrazole monomer can spontaneously tum into two stable dimers at 298.15 K.

  3. Dimers on Surface Graphs and Spin Structures. I

    Cimasoni, David; Reshetikhin, Nicolai


    Partition functions for dimers on closed oriented surfaces are known to be alternating sums of Pfaffians of Kasteleyn matrices. In this paper, we obtain the formula for the coefficients in terms of discrete spin structures.......Partition functions for dimers on closed oriented surfaces are known to be alternating sums of Pfaffians of Kasteleyn matrices. In this paper, we obtain the formula for the coefficients in terms of discrete spin structures....

  4. Quantum Phase Transitions and Dimerized Phases in Frustrated Spin Ladder

    WEN Rui; LIU Guang-Hua; TIAN Guang-Shan


    In this paper, we study the phase diagram of a frustrated spin ladder model by applying the bosonization technique and the density-matrix renormalization-group (DMRG) algorithm. Effect of the intra-chain next-nearestneighbor (NNN) super-exchange interaction is investigated in detail and the order parameters are calculated to detect the emergence of the dimerized phases. We find that the intra-chain NNN interaction plays a key role in inducing dimerized phases.

  5. Dimer representations of the Temperley–Lieb algebra

    Morin-Duchesne, Alexi, E-mail: [Institut de Recherche en Mathématique et Physique, Université Catholique de Louvain, Louvain-la-Neuve, B-1348 (Belgium); Rasmussen, Jørgen, E-mail: [School of Mathematics and Physics, University of Queensland St Lucia, Brisbane, Queensland 4072 (Australia); Ruelle, Philippe, E-mail: [Institut de Recherche en Mathématique et Physique, Université Catholique de Louvain, Louvain-la-Neuve, B-1348 (Belgium)


    A new spin-chain representation of the Temperley–Lieb algebra TL{sub n}(β=0) is introduced and related to the dimer model. Unlike the usual XXZ spin-chain representations of dimension 2{sup n}, this dimer representation is of dimension 2{sup n−1}. A detailed analysis of its structure is presented and found to yield indecomposable zigzag modules.


    Xiao-chun Qin; Chun-lai Ren


    Combining self-consistent-field theory and density-functional theory,we systematically study the deformation of copolymer micelles induced by the presence of amphiphilic dimer particles.Due to the amphiphilic nature,dimer particles tend to accumulate onto the interface of the copolymer micelle.With increasing concentration of the symmetric dimer particles,which are made of two identical spherical particles,the micelle deforms from the initial sphere to ellipse,dumbbell,and finally separates into two micelles.Furthermore,asymmetric dimer particles,composed by two particles with different sizes,are considered to investigate the influence of geometry of dimer particles on the deformation of the micelle.It is found that the micelle inclines to deform into dumbbell due to the additional curvature originating in the gathering of asymmetric dimer particles onto the interface of the micelle.The present study on the deformation of micelles is useful to understand the possible shape variation in the course of cell division/fusion.

  7. Tetramerization reinforces the dimer interface of MnSOD.

    Yuewei Sheng

    Full Text Available Two yeast manganese superoxide dismutases (MnSOD, one from Saccharomyces cerevisiae mitochondria (ScMnSOD and the other from Candida albicans cytosol (CaMnSODc, have most biochemical and biophysical properties in common, yet ScMnSOD is a tetramer and CaMnSODc is a dimer or "loose tetramer" in solution. Although CaMnSODc was found to crystallize as a tetramer, there is no indication from the solution properties that the functionality of CaMnSODc in vivo depends upon the formation of the tetrameric structure. To elucidate further the functional significance of MnSOD quaternary structure, wild-type and mutant forms of ScMnSOD (K182R, A183P mutant and CaMnSODc (K184R, L185P mutant with the substitutions at dimer interfaces were analyzed with respect to their oligomeric states and resistance to pH, heat, and denaturant. Dimeric CaMnSODc was found to be significantly more subject to thermal or denaturant-induced unfolding than tetrameric ScMnSOD. The residue substitutions at dimer interfaces caused dimeric CaMnSODc but not tetrameric ScMnSOD to dissociate into monomers. We conclude that the tetrameric assembly strongly reinforces the dimer interface, which is critical for MnSOD activity.

  8. Dimeric interactions and complex formation using direct coevolutionary couplings.

    dos Santos, Ricardo N; Morcos, Faruck; Jana, Biman; Andricopulo, Adriano D; Onuchic, José N


    We develop a procedure to characterize the association of protein structures into homodimers using coevolutionary couplings extracted from Direct Coupling Analysis (DCA) in combination with Structure Based Models (SBM). Identification of dimerization contacts using DCA is more challenging than intradomain contacts since direct couplings are mixed with monomeric contacts. Therefore a systematic way to extract dimerization signals has been elusive. We provide evidence that the prediction of homodimeric complexes is possible with high accuracy for all the cases we studied which have rich sequence information. For the most accurate conformations of the structurally diverse dimeric complexes studied the mean and interfacial RMSDs are 1.95Å and 1.44Å, respectively. This methodology is also able to identify distinct dimerization conformations as for the case of the family of response regulators, which dimerize upon activation. The identification of dimeric complexes can provide interesting molecular insights in the construction of large oligomeric complexes and be useful in the study of aggregation related diseases like Alzheimer's or Parkinson's.

  9. Determining equilibrium constants for dimerization reactions from molecular dynamics simulations.

    De Jong, Djurre H; Schäfer, Lars V; De Vries, Alex H; Marrink, Siewert J; Berendsen, Herman J C; Grubmüller, Helmut


    With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices covers sufficiently many dimerization and dissociation events, their binding free energy is readily derived from the fraction of time during which the two helices are observed in dimeric form. Exactly how the correct value for the free energy is to be calculated, however, is unclear, and indeed several different and contradictory approaches have been used. In particular, results obtained via Boltzmann statistics differ from those determined via the law of mass action. Here, we develop a theory that resolves this discrepancy. We show that for simulation systems containing two molecules, the dimerization free energy is given by a formula of the form ΔG ∝ ln(P(1) /P(0) ). Our theory is also applicable to high concentrations that typically have to be used in molecular dynamics simulations to keep the simulation system small, where the textbook dilute approximations fail. It also covers simulations with an arbitrary number of monomers and dimers and provides rigorous error estimates. Comparison with test simulations of a simple Lennard Jones system with various particle numbers as well as with reference free energy values obtained from radial distribution functions show full agreement for both binding free energies and dimerization statistics.

  10. Products and mechanism of acene dimerization. A computational study.

    Zade, Sanjio S; Zamoshchik, Natalia; Reddy, A Ravikumar; Fridman-Marueli, Galit; Sheberla, Dennis; Bendikov, Michael


    The high reactivity of acenes can reduce their potential applications in the field of molecular electronics. Although pentacene is an important material for use in organic field-effect transistors because of its high charge mobility, its reactivity is a major disadvantage hindering the development of pentacene applications. In this study, several reaction pathways for the thermal dimerization of acenes were considered computationally. The formation of acene dimers via a central benzene ring and the formation of acene-based polymers were found to be the preferred pathways, depending on the length of the monomer. Interestingly, starting from hexacene, acene dimers are thermodynamically disfavored products, and the reaction pathway is predicted to proceed instead via a double cycloaddition reaction (polymerization) to yield acene-based polymers. A concerted asynchronous reaction mechanism was found for benzene and naphthalene dimerization, while a stepwise biradical mechanism was predicted for the dimerization of anthracene, pentacene, and heptacene. The biradical mechanism for dimerization of anthracene and pentacene proceeds via syn or anti transition states and biradical minima through stepwise biradical pathways, while dimerization of heptacene proceeds via asynchronous ring closure of the complex formed by two heptacene molecules. The activation barriers for thermal dimerization decrease rapidly with increasing acene chain length and are calculated (at M06-2X/6-31G(d)+ZPVE) to be 77.9, 57.1, 33.3, -0.3, and -12.1 kcal/mol vs two isolated acene molecules for benzene, naphthalene, anthracene, pentacene, and heptacene, respectively. If activation energy is calculated vs the initially formed complex of two acene molecules, then the calculated barriers are 80.5, 63.2, 43.7, 16.7, and 12.3 kcal/mol. Dimerization is exothermic from anthracene onward, but it is endothermic at the terminal rings, even for heptacene. Phenyl substitution at the most reactive meso

  11. Dimer-atom-atom recombination in the universal four-boson system

    Deltuva, A.


    The dimer-atom-atom recombination process in the system of four identical bosons with resonant interactions is studied. The description uses the exact Alt, Grassberger and Sandhas equations for the four-particle transition operators that are solved in the momentum-space framework. The dimer-dimer and atom-trimer channel contributions to the ultracold dimer-atom-atom recombination rate are calculated. The dimer-atom-atom recombination rate greatly exceeds the three-atom recombination rate.

  12. Intermolecular disulfide bond influences unphosphorylated STAT3 dimerization and function.

    Butturini, Elena; Gotte, Giovanni; Dell'Orco, Daniele; Chiavegato, Giulia; Marino, Valerio; Canetti, Diana; Cozzolino, Flora; Monti, Maria; Pucci, Piero; Mariotto, Sofia


    Signal transducer and activator of transcription 3 (STAT3) is a transcription factor activated by the phosphorylation of tyrosine 705 in response to many cytokines and growth factors. Recently, the roles for unphosphorylated STAT3 (U-STAT3) have been described in response to cytokine stimulation, in cancers, and in the maintenance of heterochromatin stability. It has been reported that U-STAT3 dimerizes, shuttles between the cytoplasm and nucleus, and binds to DNA, thereby driving genes transcription. Although many reports describe the active role of U-STAT3 in oncogenesis in addition to phosphorylated STAT3, the U-STAT3 functional pathway remains elusive.In this report, we describe the molecular mechanism of U-STAT3 dimerization, and we identify the presence of two intermolecular disulfide bridges between Cys367 and Cys542 and Cys418 and Cys426, respectively. Recently, we reported that the same cysteines contribute to the redox regulation of STAT3 signaling pathway both in vitro and in vivo The presence of these disulfides is here demonstrated to largely contribute to the structure and the stability of U-STAT3 dimer as the dimeric form rapidly dissociates upon reduction in the S-S bonds. In particular, the Cys367-Cys542 disulfide bridge is shown to be critical for U-STAT3 DNA-binding activity. Mutation of the two Cys residues completely abolishes the DNA-binding capability of U-STAT3. Spectroscopic investigations confirm that the noncovalent interactions are sufficient for proper folding and dimer formation, but that the interchain disulfide bonds are crucial to preserve the functional dimer. Finally, we propose a reaction scheme of U-STAT3 dimerization with a first common step followed by stabilization through the formation of interchain disulfide bonds. © 2016 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

  13. Threshold electron attachment and electron impact ionization involving oxygen dimers

    Kreil, J.; Ruf, M.-W.; Hotop, H. [Fachbereich Physik, Universitaet Kaiserslautern, D-67653 Kaiserslautern (Germany); Ettischer, I.; Buck, U. [Max-Planck-Institut fuer Stroemungsforschung, Bunsenstrasse 10, D-37073 Goettingen (Germany)


    Using two different crossed-beams machines we have carried out the first quantitative study of threshold electron attachment and electron impact-induced ionization and fragmentation involving oxygen dimers (O{sub 2}){sub 2}. In the electron attachment experiment we study electron transfer from state-selected Ar{sup **}(20d) Rydberg atoms to O{sub 2} molecules and dimers in a skimmed supersonic beam at variable nozzle temperatures (T{sub 0}) and stagnation pressures (p{sub 0}). The relative dimer density is determined through measurements of Penning ionization by metastable Ne{sup *}(3s {sup 3}P{sub 2,0}) atoms and used to estimate the absolute cross-section for O{sub 2}{sup -} formation in collisions of Ar{sup **}(20d) Rydberg atoms with O{sub 2} dimers to be nearly 10{sup -17} m{sup 2}, almost four orders of magnitude larger than that for O{sub 2}{sup -} formation in collisions of Ar{sup **}(20d) Rydberg atoms with O{sub 2} monomers. The fragmentation of the oxygen cluster beam is quantitatively characterized by the transverse helium beam scattering method which allows us to spatially separate different clusters. It is shown that in 70 eV electron impact of (O{sub 2}){sub 2} only 3.6(4)% of the dimers are detected as dimer ions (O{sub 2}){sub 2}{sup +}. In additional experiments involving SF{sub 6} clusters we show that SF{sub 6} dimers fragment nearly completely upon 70 eV electron impact, yielding SF{sub 5}{sup +} ions (probability for (SF{sub 6}){center_dot}SF{sub 5}{sup +} production at most 0.3%). (Copyright (c) 1998 Elsevier Science B.V., Amsterdam. All rights reserved.)

  14. Integrability and conformal data of the dimer model

    Morin-Duchesne, Alexi; Rasmussen, Jørgen; Ruelle, Philippe


    The central charge of the dimer model on the square lattice is still being debated in the literature. In this paper, we provide evidence supporting the consistency of a c=-2 description. Using Lieb’s transfer matrix and its description in terms of the Temperley-Lieb algebra {{TL}}n at β =0, we provide a new solution of the dimer model in terms of the model of critical dense polymers on a tilted lattice and offer an understanding of the lattice integrability of the dimer model. The dimer transfer matrix is analyzed in the scaling limit, and the result for {L}0-\\frac{c}{24} is expressed in terms of fermions. Higher Virasoro modes are likewise constructed as limits of elements of {{TL}}n and are found to yield a c=-2 realization of the Virasoro algebra, familiar from fermionic bc ghost systems. In this realization, the dimer Fock spaces are shown to decompose, as Virasoro modules, into direct sums of Feigin-Fuchs modules, themselves exhibiting reducible yet indecomposable structures. In the scaling limit, the eigenvalues of the lattice integrals of motion are found to agree exactly with those of the c=-2 conformal integrals of motion. Consistent with the expression for {L}0-\\frac{c}{24} obtained from the transfer matrix, we also construct higher Virasoro modes with c = 1 and find that the dimer Fock space is completely reducible under their action. However, the transfer matrix is found not to be a generating function for the c = 1 integrals of motion. Although this indicates that Lieb’s transfer matrix description is incompatible with the c = 1 interpretation, it does not rule out the existence of an alternative, c = 1 compatible, transfer matrix description of the dimer model.

  15. Monitoring of receptor dimerization using plasmonic coupling of gold nanoparticles.

    Crow, Matthew J; Seekell, Kevin; Ostrander, Julie H; Wax, Adam


    The dimerization of receptors on the cell membrane is an important step in the activation of cell signaling pathways. Several methods exist for observing receptor dimerization, including coimmunoprecipitation, chemical cross-linking, and fluorescence resonance energy transfer (FRET). These techniques are limited in that only FRET is appropriate for live cells, but even that method suffers from photobleaching and bleed-through effects. In this study, we implement an alternative method for the targeting of HER-2 homodimer formation based on the plasmonic coupling of gold nanoparticles functionalized with HER-2 Ab. In the presented studies, SK-BR-3 cells, known to overexpress HER-2, are labeled with these nanoparticles and receptor colocalization is observed using plasmonic coupling. HER-2 targeted nanoparticles bound to these cells exhibit a peak resonance that is significantly red-shifted relative to those bound to similar receptors on A549 cells, which have significantly lower levels of HER-2 expression. This significant red shift indicates plasmonic coupling is occurring and points to a new avenue for assessing dimerization by monitoring their colocalization. To determine that dimerization is occurring, the refractive index of the nanoenvironment of the labels is assessed using a theoretical analysis based on the Mie coated sphere model. The results indicate scattering by single, isolated nanoparticles for the low HER-2 expressing A549 cell line, but the scattering observed for the HER-2 overexpressing SK-BR-3 cell line may only be explained by plasmonic-coupling of proximal nanoparticle pairs. To validate the conformation of nanoparticles bound to HER-2 receptors undergoing dimerization, discrete dipole approximation (DDA) models are used to assess spectra of scattering by coupled nanoparticles. Comparison of the experimental results with theoretical models indicates that NP dimers are formed for the labeling of SK-BR-3 cells, suggesting that receptor

  16. Dimerization in Highly Concentrated Solutions of Phosphoimidazolide Activated Monomucleotides

    Kanavarioti, Anastassia


    Phosphoimidazolide activated ribomononucleotides (*pN) are useful substrates for the non-enzymatic synthesis of polynucleotides. However, dilute neutral aqueous solutions of *pN typically yield small amounts of dimers and traces of polymers; most of *pN hydrolyzes to yield nucleoside 5'-monophosphate. Here we report the self-condensation of nucleoside 5'-phosphate 2-methylimidazolide (2-MeImpN with N = cytidine, uridine or guanosine) in the presence of Mg2+ in concentrated solutions, such as might have been found in an evaporating lagoon on prebiotic Earth. The product distribution indicates that oligomerization is favored at the expense of hydrolysis. At 1.0 M, 2-MeImpU and 2-MeImpC produce about 65% of oligomers including 4% of the 3',5'-linked dimer. Examination of the product distribution of the three isomeric dimers in a self-condensation allows identification of reaction pathways that lead to dimer formation. Condensations in a concentrated mixture of all three nucleotides (U,C,G mixtures) is made possible by the enhanced solubility of 2-MeImpG in such mixtures. Although percent yield of internucleotide linked dimers is enhanced as a function of initial monomer concentration, pyrophosphate dimer yields remain practically unchanged at about 20% for 2-MeImpU, 16% for 2-MeImpC and 25% of the total pyrophosphate in the U,C,G mixtures. The efficiency by which oligomers are produced in these concentrated solutions makes the evaporating lagoon scenario a potentially interesting medium for the prebiotic synthesis of dimers and short RNAs.

  17. Synthesis and Applications of Non-spherical Dimer Colloids

    Yoon, Kisun

    Colloids are promising building blocks in material synthesis because of their controllability of size and surface properties. The synthesis of chemically and/or geometrically anisotropic colloidal particles has received attentions with the expectation of building blocks for complex structures. However, the synthesis of anisotropic colloidal particles is by far more difficult than the synthesis of spherical colloidal particles. Lack of monodispersity and productivity of many anisotropic particles often limits their applications as a building block for complex structures. Thus, it is highly desirable to develop methods which can produce a large amount of monodisperse non-spherical particles with controllable asymmetric surface properties. This dissertation details the work for developing such a method. The major result of this dissertation is a synthetic method to produce monodisperse non-spherical colloids with anisotropic surface property in a large quantity. The anisotropic colloid, which we call it as Dimer particle, has two fused lobes like a dumbbell and each lobe's size can be independently controlled. We present a novel method to synthesize sub-micron size Dimer particles. This method can produce a large amount of submicron-sized Dimer particles with good monodispersity and well-controlled shape. Submicron-sized Dimer particles have been highly desired since they can be used as a building block for self assembly using Brownian motion, colloidal surfactant for Pickering emulsion, and photonic materials. To fully take advantage of the anisotropy of the particles, we develop a facile method to tailor the surface property of each lobe independently by asymmetrically coating the particles with gold nanoparticles. This method doesn't need the arrangement of particles onto any type of interfaces. Asymmetric coating of gold nanoparticles can be carried out simply by mixing Dimer particles with gold nanoparticles. The formation mechanism of the submicron-sized Dimer

  18. Mechanism of ubiquitylation by dimeric RING ligase RNF4

    Plechanovová, Anna; Jaffray, Ellis G.; McMahon, Stephen A.; Johnson, Kenneth A.; Navrátilová, Iva; Naismith, James H.; Hay, Ronald T.


    Mammalian RNF4 is a dimeric RING ubiquitin E3 ligase that ubiquitylates poly-SUMOylated proteins. We found that RNF4 bound ubiquitin-charged UbcH5a tightly but free UbcH5a weakly. To provide insight into the mechanism of RING-mediated ubiquitylation we docked the UbcH5~ubiquitin thioester onto the RNF4 RING structure. This revealed that with E2 bound to one monomer of RNF4, the thioester-linked ubiquitin could reach across the dimer to engage the other monomer. In this model the “Ile44 hydrophobic patch” of ubiquitin is predicted to engage a conserved tyrosine located at the dimer interface of the RING and mutation of these residues blocked ubiquitylation activity. Thus, dimeric RING ligases are not simply inert scaffolds that bring substrate and E2-loaded ubiquitin into close proximity. Instead, they facilitate ubiquitin transfer by preferentially binding the E2~ubiquitin thioester across the dimer and activating the thioester bond for catalysis. PMID:21857666

  19. Synthesis of a distinct water dimer inside fullerene C70

    Zhang, Rui; Murata, Michihisa; Aharen, Tomoko; Wakamiya, Atsushi; Shimoaka, Takafumi; Hasegawa, Takeshi; Murata, Yasujiro


    The water dimer is an ideal chemical species with which to study hydrogen bonds. Owing to the equilibrium between the monomer and oligomer structure, however, selective generation and separation of a genuine water dimer has not yet been achieved. Here, we report a synthetic strategy that leads to the successful encapsulation of one or two water molecules inside fullerene C70. These endohedral C70 compounds offer the opportunity to study the intrinsic properties of a single water molecule without any hydrogen bonding, as well as an isolated water dimer with a single hydrogen bond between the two molecules. The unambiguously determined off-centre position of water in (H2O)2@C70 by X-ray diffraction provides insights into the formation of (H2O)2@C70. Subsequently, the 1H NMR spectroscopic measurements for (H2O)2@C70 confirmed the formation of a single hydrogen bond rapidly interchanging between the encapsulated water dimer. Our theoretical calculations revealed a peculiar cis-linear conformation of the dimer resulting from confinement effects inside C70.

  20. Integrability and conformal data of the dimer model

    Morin-Duchesne, Alexi; Ruelle, Philippe


    The central charge of the dimer model on the square lattice is still being debated in the literature. In this paper, we provide evidence supporting the consistency of a $c=-2$ description. Using Lieb's transfer matrix and its description in terms of the Temperley-Lieb algebra $TL_n$ at $\\beta = 0$, we provide a new solution of the dimer model in terms of the model of critical dense polymers on a tilted lattice and offer an understanding of the lattice integrability of the dimer model. The dimer transfer matrix is analysed in the scaling limit and the result for $L_0-\\frac c{24}$ is expressed in terms of fermions. Higher Virasoro modes are likewise constructed as limits of elements of $TL_n$ and are found to yield a $c=-2$ realisation of the Virasoro algebra, familiar from fermionic $bc$ ghost systems. In this realisation, the dimer Fock spaces are shown to decompose, as Virasoro modules, into direct sums of Feigin-Fuchs modules, themselves exhibiting reducible yet indecomposable structures. In the scaling lim...

  1. Recognition of HIV TAR RNA by triazole linked neomycin dimers.

    Kumar, Sunil; Arya, Dev P


    A series of neomycin dimers have been synthesized using 'click chemistry' with varying linker functionality and length to target the TAR RNA region of HIV virus. TAR (trans activation response) RNA region, a 59 base pair stem loop structure located at 5'-end of all nascent HIV-1 transcripts interacts with a key regulatory protein, Tat, and necessitates the replication of HIV-1 virus. Neomycin, an aminosugar, has been shown to exhibit more than one binding site with HIV TAR RNA. Multiple TAR binding sites of neomycin prompted us to design and synthesize a small library of neomycin dimers using click chemistry. The binding between neomycin dimers and HIV TAR RNA was characterized using spectroscopic techniques including FID (Fluorescent Intercalator Displacement) titration and UV-thermal denaturation. UV thermal denaturation studies demonstrate that neomycin dimer binding increase the melting temperature (T(m)) of the HIV TAR RNA up to 10°C. Ethidium bromide displacement titrations revealed nanomolar IC(50) between neomycin dimers and HIV TAR RNA, whereas with neomycin, a much higher IC(50) in the micromolar range is observed.

  2. Regulation of primate lentiviral RNA dimerization by structural entrapment

    Lodmell J Stephen


    Full Text Available Abstract Background Genomic RNA dimerization is an important process in the formation of an infectious lentiviral particle. One of the signals involved is the stem-loop 1 (SL1 element located in the leader region of lentiviral genomic RNAs which also plays a role in encapsidation and reverse transcription. Recent studies revealed that HIV types 1 and 2 leader RNAs adopt different conformations that influence the presentation of RNA signals such as SL1. To determine whether common mechanisms of SL1 regulation exist among divergent lentiviral leader RNAs, here we compare the dimerization properties of SIVmac239, HIV-1, and HIV-2 leader RNA fragments using homologous constructs and experimental conditions. Prior studies from several groups have employed a variety of constructs and experimental conditions. Results Although some idiosyncratic differences in the dimerization details were observed, we find unifying principles in the regulation strategies of the three viral RNAs through long- and short-range base pairing interactions. Presentation and efficacy of dimerization through SL1 depends strongly upon the formation or dissolution of the lower stem of SL1 called stem B. SL1 usage may also be down-regulated by long-range interactions involving sequences between SL1 and the first codons of the gag gene. Conclusion Despite their sequence differences, all three lentiviral RNAs tested in this study showed a local regulation of dimerization through the stabilization of SL1.

  3. Dimer-tetramer transition controls RUNX1/ETO leukemogenic activity.

    Wichmann, Christian; Becker, Yvonne; Chen-Wichmann, Linping; Vogel, Vitali; Vojtkova, Anna; Herglotz, Julia; Moore, Sandra; Koch, Joachim; Lausen, Jörn; Mäntele, Werner; Gohlke, Holger; Grez, Manuel


    RUNX1/ETO, the fusion protein resulting from the chromosomal translocation t(8;21), is one of the most frequent translocation products in acute myeloid leukemia. Several in vitro and in vivo studies have shown that the homo-tetramerization domain of ETO, the nervy homology region 2 (NHR2), is essential for RUNX1/ETO oncogenic activity. We analyzed the energetic contribution of individual amino acids within the NHR2 to RUNX1/ETO dimer-tetramer transition and found a clustered area of 5 distinct amino acids with strong contribution to the stability of tetramers. Substitution of these amino acids abolishes tetramer formation without affecting dimer formation. Similar to RUNX1/ETO monomers, dimers failed to bind efficiently to DNA and to alter expression of RUNX1-dependent genes. RUNX1/ETO dimers do not block myeloid differentiation, are unable to enhance the self-renewal capacity of hematopoietic progenitors, and fail to induce leukemia in a murine transplantation model. Our data reveal the existence of an essential structural motif (hot spot) at the NHR2 dimer-tetramer interface, suitable for a molecular intervention in t(8;21) leukemias.

  4. Effects of Dimerization of Serratia marcescens Endonuclease on Water Dynamics.

    Chen, Chuanying; Beck, Brian W.; Krause, Kurt; Weksberg, Tiffany E.; Pettitt, Bernard M.


    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.

  5. Photodissociation pathways and lifetimes of protonated peptides and their dimers

    Gopalan, Aravind; Klærke, Benedikte; Rajput, Jyoti


    Photodissociation lifetimes and fragment channels of gas-phase, protonated YAn (n = 1,2) peptides and their dimers were measured with 266 nm photons. The protonated monomers were found to have a fast dissociation channel with an exponential lifetime of ∼200 ns while the protonated dimers show...... rate constants also confirmed a statistical nature of the photodissociation processes in the dipeptide monomers and dimers. The classical RRKM expression gives a rate constant as an analytical function of the number of active vibrational modes in the system, estimated separately on the basis...... of the equipartition theorem. It demonstrates encouraging results in predicting fragmentation lifetimes of protonated peptides. Finally, we present the first experimental evidence for a photo-induced conversion of tyrosine-containing peptides into monocyclic aromatic hydrocarbon along with a formamide molecule both...

  6. Self-deactivation of water vapor - Role of the dimer

    Zuckerwar, A. J.


    A phenomenological multiple-relaxation theory of the deactivation rate constant for the nu-2 (1 - 0) bending mode of water vapor is presented which incorporates the role not only of the excited monomer but also of the bound molecular complex, in particular the dimer. The deactivation takes place by means of three parallel processes: (1) collisional deexcitation of the excited monomer, (2) a two-step reaction involving association and spontaneous redissociation of an H2O collision complex, and (3) spontaneous dissociation of the stably bound H2O dimer. Oxygen, but not nitrogen or argon, serves as an effective chaperon for the formation of the activated complex. This observation explains the impurity dependence of the self-deactivation rate constant of water vapor. Analysis of an ultrasonic absorption peak based on the third process yields values for the standard entropy and enthalpy of dissociation of the stably bound H2O dimer.

  7. Characterization of oxygen dimer-enriched silicon detectors

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


    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.

  8. Dimer Models from Mirror Symmetry and Quivering Amoebae

    Feng, B; Kennaway, K D; Vafa, C; Feng, Bo; He, Yang-Hui; Kennaway, Kristian D.; Vafa, Cumrun


    Dimer models are 2-dimensional combinatorial systems that have been shown to encode the gauge groups, matter content and tree-level superpotential of the world-volume quiver gauge theories obtained by placing D3-branes at the tip of a singular toric Calabi-Yau cone. In particular the dimer graph is dual to the quiver graph. However, the string theoretic explanation of this was unclear. In this paper we use mirror symmetry to shed light on this: the dimer models live on a T^2 subspace of the T^3 fiber that is involved in mirror symmetry and is wrapped by D6-branes. These D6-branes are mirror to the D3-branes at the singular point, and geometrically encode the same quiver theory on their world-volume.

  9. Inequivalent models of irreversible dimer filling: ``Transition state'' dependence

    Nord, R. S.; Evans, J. W.


    Irreversible adsorption of diatomics on crystalline surfaces is sometimes modeled as random dimer filling of adjacent pairs of sites on a lattice. We note that this process can be implemented in two distinct ways: (i) randomly pick adjacent pairs of sites, jj', and fill jj' only if both are empty (horizontal transition state); or (ii) randomly pick a single site, j, and if j and at least one neighbor are empty, then fill j and a randomly chosen empty neighbor (vertical transition state). Here it is instructive to consider processes which also include competitive random monomer filling of single sites. We find that although saturation (partial) coverages differ little between the models for pure dimer filling, there is a significant difference for comparable monomer and dimer filling rates. We present exact results for saturation coverage behavior for a linear lattice, and estimates for a square lattice. Ramifications for simple models of CO oxidation on surfaces are indicated.

  10. Intrinsic Kinetic Modeling of Thermal Dimerization of C5 Fraction

    Guo Liang; Wang Tiefeng; Li Dongfeng; Wang Jinfu


    This work aims to investigate the intrinsic kinetics of thermal dimerization of C5 fraction in the reactive distilla-tion process. Experiments are conducted in an 1000-mL stainless steel autoclave under some selected design conditions. By means of the weighted least squares method, the intrinsic kinetics of thermal dimerization of C5 fraction is established, and the corresponding pre-exponential factor as well as the activation energy are determined. For example, the pre-exponential factor A is equal to 4.39×105 and the activation energy Ea is equal to 6.58×104 J/mol for the cyclopentadiene dimerization re-action. The comparison between the experimental and calculated results shows that the kinetics model derived in this work is accurate and reliable, which can be used in the design of reactive distillation columns.

  11. Ultrafast Dissociation of Metastable CO2 + in a Dimer

    Ding, Xiaoyan; Haertelt, M.; Schlauderer, S.; Schuurman, M. S.; Naumov, A. Yu.; Villeneuve, D. M.; McKellar, A. R. W.; Corkum, P. B.; Staudte, A.


    We triply ionize the van der Waals bound carbon monoxide dimer with intense ultrashort pulses and study the breakup channel (CO )23 +→C++O++CO+ . The fragments are recorded in a cold target recoil ion momentum spectrometer. We observe a fast CO2 + dissociation channel in the dimer, which does not exist for the monomer. We found that a nearby charge breaks the symmetry of a X3Π state of CO2 + and induces an avoided crossing that allows a fast dissociation. Calculation on the full dimer complex shows the coupling of different charge states, as predicted from excimer theory, gives rise to electronic state components not present in the monomer, thereby enabling fast dissociation with higher kinetic energy release. These results demonstrate that the electronic structure of molecular cluster complexes can give rise to dynamics that is qualitatively different from that observed in the component monomers.

  12. Optofluidic taming of a colloidal dimer with a silicon nanocavity

    Pin, C.; Renaut, C. [Groupe d' Optique de Champ Proche - LRC CEA n°DSM-08-36, Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR CNRS n°6303- Université de Bourgogne, Dijon (France); University Grenoble Alpes, INAC-SP2M-SINAPS, F-38000 Grenoble, France and CEA, INAC-SP2M-SINAPS, F-38000 Grenoble (France); University Grenoble Alpes, CNRS, CEA-Leti Minatec, LTM, F-38054 Grenoble Cedex (France); Cluzel, B., E-mail:; Fornel, F. de [Groupe d' Optique de Champ Proche - LRC CEA n°DSM-08-36, Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR CNRS n°6303- Université de Bourgogne, Dijon (France); Peyrade, D. [University Grenoble Alpes, CNRS, CEA-Leti Minatec, LTM, F-38054 Grenoble Cedex (France); Picard, E.; Hadji, E. [University Grenoble Alpes, INAC-SP2M-SINAPS, F-38000 Grenoble, France and CEA, INAC-SP2M-SINAPS, F-38000 Grenoble (France)


    We report here the optical trapping of a heterogeneous colloidal dimer above a photonic crystal nanocavity used as an on-chip optical tweezer. The trapped dimer consists of a cluster of two dielectric microbeads of different sizes linked by van der Waals forces. The smallest bead, 1 μm in diameter, is observed to be preferentially trapped by the nanotweezer, leaving the second bead untrapped. The rotational nature of the trapped dimer Brownian motion is first evidenced. Then, in the presence of a fluid flow, control of its orientation and rotation is achieved. The whole system is found to show high rotational degrees of freedom, thereby acting as an effective flow-sensitive microscopic optical ball joint.

  13. Photodissociation pathways and lifetimes of protonated peptides and their dimers

    Gopalan, Aravind; Klærke, Benedikte; Rajput, Jyoti


    channel in the dimer was found to result in cleavage of the H-bonds after energy transfer through these H-bonds. In general, the dissociation of these protonated peptides is non-prompt and the decay time was found to increase with the size of the peptides. Quantum RRKM calculations of the microcanonical......Photodissociation lifetimes and fragment channels of gas-phase, protonated YAn (n = 1,2) peptides and their dimers were measured with 266 nm photons. The protonated monomers were found to have a fast dissociation channel with an exponential lifetime of ∼200 ns while the protonated dimers show...... of the equipartition theorem. It demonstrates encouraging results in predicting fragmentation lifetimes of protonated peptides. Finally, we present the first experimental evidence for a photo-induced conversion of tyrosine-containing peptides into monocyclic aromatic hydrocarbon along with a formamide molecule both...

  14. Micellisation and immunoreactivities of dimeric beta-caseins.

    Yousefi, Reza; Gaudin, Jean-Charles; Chobert, Jean-Marc; Pourpak, Zahra; Moin, Mostafa; Moosavi-Movahedi, Ali Akbar; Haertle, Thomas


    Bovine beta-casein (beta-CN) is a highly amphiphilic micellising phospho-protein showing chaperone-like activity in vitro. Recently, existence of multiple sequential epitopes on beta-CN polypeptide chain in both hydrophilic-polar (psi) and hydrophobic-apolar domains (phi) has been evidenced. In order to clarify specific contribution of polar and apolar domains in micellisation process and in shaping immunoreactivity of beta-CN, its dimeric/bi-amphiphilic "quasi palindromic" forms covalently connected by a disulfide bond linking either N-terminal (C4 beta-CND) or C-terminal domain (C208 beta-CND) were produced and studied. Depending on the C- or N-terminal position of inserted cysteine, each dimeric beta-CN contains one polar/apolar region at the centre and two external hydrophobic/hydrophilic ends. Consequently, such casein dimers have radically different polarities/hydrophobicities on their outside surfaces. Dynamic light scattering (DLS) measurements indicate that these dimeric casein molecules form micelles of different sizes depending on arrangement of polar fragments of the beta-CN mutants in their constrained dimers. Non-aggregated dimers have different hydrodynamic diameters that could be explained by their different geometries. Measurements of fluorescence showed more hydrophobic environment of Trp residues of C208 beta-CND, while in similar experimental conditions Trp residues of C4 beta-CND and native beta-CN were more exposed to the polar medium. Both fluorescence and DLS studies showed greater propensity for micellisation of the dimeric beta-CNs, suggesting that the factors inducing the formation of micelles are stronger in the bi-amphiphilic dimers. 1-anilino-naphthalene-8-sulfonate (ANS) binding studies showed different binding of ANS by these dimers as well as different exposition of ANS binding (hydrophobic) regions in the micellar states. The differences in fluorescence resonance energy transfer (FRET) profiles of C4 beta-CND and C208 beta-CND can


    Jia-huai eWang


    Full Text Available Despite major advances in T cell receptor (TCR biology and structure, how peptide-MHC complex (pMHC ligands trigger αβ TCR activation remains unresolved. Two views exist. One model postulates that monomeric TCR-pMHC ligation events are sufficient while a second proposes that TCR-TCR dimerization in cis via Cα domain interaction plus pMHC binding is critical. We scrutinized 22 known TCR/pMHC complex crystal structures, and did not find any predicted molecular Cα-Cα contacts in these crystals that would allow for physiological TCR dimerization. Moreover, the presence of conserved glycan adducts on the outer face of the Cα domain preclude the hypothesized TCR dimerization through the Cα domain. Observed functional consequences of Cα mutations are likely indirect, with TCR microclusters at the immunological synapse driven by TCR transmembrane/cytoplasmic interactions via signaling molecules, scaffold proteins and/or cytoskeletal elements.

  16. Microwave Spectrum of the Isopropanol-Water Dimer

    Mead, Griffin; Finneran, Ian A.; Carroll, Brandon; Blake, Geoffrey


    Microwave spectroscopy provides a unique opportunity to study model non-covalent interactions. Of particular interest is the hydrogen bonding of water, whose various molecular properties are influenced by both strong and weak intermolecular forces. More specifically, measuring the hydrogen bonded structures of water-alcohol dimers investigates both strong (OH ··· OH) and weak (CH ··· OH) hydrogen bond interactions. Recently, we have measured the pure rotational spectrum of the isopropanol-water dimer using chirped-pulse Fourier transform microwave spectroscopy (CP-FTMW) between 8-18 GHz. Here, we present the spectrum of this dimer and elaborate on the structure's strong and weak hydrogen bonding.

  17. Dimeric α-Cobratoxin X-ray Structure

    Osipov, Alexey V.; Rucktooa, Prakash; Kasheverov, Igor E.; Filkin, Sergey Yu.; Starkov, Vladislav G.; Andreeva, Tatyana V.; Sixma, Titia K.; Bertrand, Daniel; Utkin, Yuri N.; Tsetlin, Victor I.


    In Naja kaouthia cobra venom, we have earlier discovered a covalent dimeric form of α-cobratoxin (αCT-αCT) with two intermolecular disulfides, but we could not determine their positions. Here, we report the αCT-αCT crystal structure at 1.94 Å where intermolecular disulfides are identified between Cys3 in one protomer and Cys20 of the second, and vice versa. All remaining intramolecular disulfides, including the additional bridge between Cys26 and Cys30 in the central loops II, have the same positions as in monomeric α-cobratoxin. The three-finger fold is essentially preserved in each protomer, but the arrangement of the αCT-αCT dimer differs from those of noncovalent crystallographic dimers of three-finger toxins (TFT) or from the κ-bungarotoxin solution structure. Selective reduction of Cys26-Cys30 in one protomer does not affect the activity against the α7 nicotinic acetylcholine receptor (nAChR), whereas its reduction in both protomers almost prevents α7 nAChR recognition. On the contrary, reduction of one or both Cys26-Cys30 disulfides in αCT-αCT considerably potentiates inhibition of the α3β2 nAChR by the toxin. The heteromeric dimer of α-cobratoxin and cytotoxin has an activity similar to that of αCT-αCT against the α7 nAChR and is more active against α3β2 nAChRs. Our results demonstrate that at least one Cys26-Cys30 disulfide in covalent TFT dimers, similar to the monomeric TFTs, is essential for their recognition by α7 nAChR, although it is less important for interaction of covalent TFT dimers with the α3β2 nAChR. PMID:22223648

  18. Simulations of coherent nonlinear optical response of molecular vibronic dimers

    Perlík, Václav


    We have implemented vibronic dynamics for simulations of the third order coherent response of electronic dimers. In the present communication we provide the full and detailed description of the dynamical model, recently used for simulations of chlorophyll-carotenoid dyads, terylene dimers, or hypericin. We allow for explicit vibronic level structure, by including selected vibrational modes into a "system". Bath dynamics include the Landau-Teller vibrational relaxation, electronic dephasing, and nonlinear vibronic (to bath) coupling. Simulations combine effects of transport and dephasing between vibronic levels. Transport is described by master equation within secular approximation, phase is accumulated in cumulants and its calculation follows the transport pathways during waiting time period.

  19. Dimerization of argon and the properties of its small clusters

    Titov, S. V.; Serov, S. A.; Ostrovskii, G. M.


    Statistical thermodynamic means are used to study the bound state of a small cluster AN (2 ≤ N ≤ 5) of Lennard-Jones particles in a spherical cavity. The statistical sum is calculated by the Monte Carlo method. For the dimer, integration is reduced to quadratures. The integration region contains only phase space points corresponding to the bound cluster state. Dimerization constant 2A = A2 is calculated via the probability of finding a molecule in the bound state using the example of argon.

  20. Synthesis and polarized photoluminescence of novel phosphorescent cyclometalated platinum dimer

    Shi Ping Jiang; Kai Jun Luo; Ying Han Wang; Xin Wang; Ying Jiang; Yan Yan Wei


    A novel phosphorescent cyclometalated platinum dimer with bis-[2-(p-dodecyloxyphenyl) pyridyl]-hexane-l,6-diol as ligand and 1,3-( 1-n-hexyl,3-n-heptadecyl) diketone as ancillary ligand was synthesized. The chemical structure and liquid crystal property of the dimer were characterized by 1H NMR, ESI-MS, polarizing optical microscopy (POM) and differential scanning calorimetry (DSC). The aligned film of title compound on the rubbed polyimide film is intensely emissive at room temperature with emission maximum at 516 nm. The luminescence dichroic ratio (I∥/ IL) at 516 nm is 3.1.

  1. Biophysical characterization of the dimer and tetramer interface interactions of the human cytosolic malic enzyme.

    Sujithkumar Murugan

    Full Text Available The cytosolic NADP(+-dependent malic enzyme (c-NADP-ME has a dimer-dimer quaternary structure in which the dimer interface associates more tightly than the tetramer interface. In this study, the urea-induced unfolding process of the c-NADP-ME interface mutants was monitored using fluorescence and circular dichroism spectroscopy, analytical ultracentrifugation and enzyme activities. Here, we demonstrate the differential protein stability between dimer and tetramer interface interactions of human c-NADP-ME. Our data clearly demonstrate that the protein stability of c-NADP-ME is affected predominantly by disruptions at the dimer interface rather than at the tetramer interface. First, during thermal stability experiments, the melting temperatures of the wild-type and tetramer interface mutants are 8-10°C higher than those of the dimer interface mutants. Second, during urea denaturation experiments, the thermodynamic parameters of the wild-type and tetramer interface mutants are almost identical. However, for the dimer interface mutants, the first transition of the urea unfolding curves shift towards a lower urea concentration, and the unfolding intermediate exist at a lower urea concentration. Third, for tetrameric WT c-NADP-ME, the enzyme is first dissociated from a tetramer to dimers before the 2 M urea treatment, and the dimers then dissociated into monomers before the 2.5 M urea treatment. With a dimeric tetramer interface mutant (H142A/D568A, the dimer completely dissociated into monomers after a 2.5 M urea treatment, while for a dimeric dimer interface mutant (H51A/D90A, the dimer completely dissociated into monomers after a 1.5 M urea treatment, indicating that the interactions of c-NADP-ME at the dimer interface are truly stronger than at the tetramer interface. Thus, this study provides a reasonable explanation for why malic enzymes need to assemble as a dimer of dimers.

  2. Plasma D-dimer concentration in patients with systemic sclerosis

    Montagnana Martina


    Full Text Available Abstract Background Systemic sclerosis (SSc is an autoimmune disorder of the connective tissue characterized by widespread vascular lesions and fibrosis. Little is known so far on the activation of the hemostatic and fibrinolytic systems in SSc, and most preliminary evidences are discordant. Methods To verify whether SSc patients might display a prothrombotic condition, plasma D-dimer was assessed in 28 consecutive SSc patients and in 33 control subjects, matched for age, sex and environmental habit. Results and discussion When compared to healthy controls, geometric mean and 95% confidence interval (IC95% of plasma D-dimer were significantly increased in SSc patients (362 ng/mL, IC 95%: 361–363 ng/mL vs 229 ng/mL, IC95%: 228–231 ng/mL, p = 0.005. After stratifying SSc patients according to disease subset, no significant differences were observed between those with limited cutaneous pattern and controls, whereas patients with diffuse cutaneous pattern displayed substantially increased values. No correlation was found between plasma D-dimer concentration and age, sex, autoantibody pattern, serum creatinine, erythrosedimentation rate, nailfold videocapillaroscopic pattern and pulmonary involvement. Conclusion We demonstrated that SSc patients with diffuse subset are characterized by increased plasma D-dimer values, reflecting a potential activation of both the hemostatic and fibrinolytic cascades, which might finally predispose these patients to thrombotic complications.

  3. Two-Dimensional Electronic Spectroscopy of a Model Dimer System

    Prokhorenko V.I.


    Full Text Available Two-dimensional spectra of a dimer were measured to determine the timescale for electronic decoherence at room temperature. Anti-correlated beats in the crosspeaks were observed only during the period corresponding to the measured homogeneous lifetime.

  4. Weakly Stabilized Primary Borenium Cations and their Dicationic Dimers

    Prokofjevs, Aleksandrs; Kampf, Jeff W.; Solovyev, Andrey; Curran, Dennis P.; Vedejs, Edwin


    Hydride abstraction from monocationic hydride bridged salts [H(H2B–L)2]+ [B(C6F5)4]− (L = Lewis base) generates an observable primary borenium cation for L = iPr2NEt, but with L = Me3N, Me2NPr, or several N-heterocyclic carbenes, highly reactive dicationic dimers are formed. PMID:24087933

  5. Dimeric Complexes of Tryptophan with M2+ Metal Ions

    Dunbar, R. C.; Steill, J. D.; Polfer, N. C.; Oomens, J.


    IRMPD spectroscopy using the FELIX free electron laser and a Fourier transform ICR mass spectrometer was used to characterize the structures of electrosprayed dimer complexes M(2+)Trp(2) of tryptophan with a series of eight doubly charged metal ions, including alkaline earths Ca, Sr, and Ba, and tra




    Four new stilbene dimers, gnetuhainins P (1), Q (2), K (3) and L (4), were isolated from the lianas of Gnetum hainanense C. Y. Cheng. Their structures and relative configurations were determined on the basis of spectroscopic evidence, especially 2D NMR techniques.

  7. Dispersion Interactions and the Stability of Amine Dimers

    Guttmann, Robin


    Abstract Weak, intermolecular interactions in amine dimers were studied by using the combination of a dispersionless density functional and a function that describes the dispersion contribution to the interaction energy. The validity of this method was shown by comparison of structural and energetic properties with data obtained with a conventional density functional and the coupled cluster method. The stability of amine dimers was shown to depend on the size, the shape, and the relative orientation of the alkyl substituents, and it was shown that the stabilization energy for large substituents is dominated by dispersion interactions. In contrast to traditional chemical explanations that attribute stability and condensed matter properties solely to hydrogen bonding and, thus, to the properties of the atoms forming the hydrogen bridge, we show that without dispersion interactions not even the stability and structure of the ammonia dimer can be correctly described. The stability of amine dimers depends crucially on the interaction between the non‐polar alkyl groups, which is dominated by dispersion interactions. This interaction is also responsible for the energetic part of the free energy interaction used to describe hydrophobic interactions in liquid alkanes. The entropic part has its origin in the high degeneracy of the interaction energy for complexes of alkane molecules, which exist in a great variety of conformers, having their origin in internal rotations of the alkane chains. PMID:28794953

  8. A Novel Dimeric Eremophilane from Ligularia virgaurea spp. Oligocephala

    Quan Xiang WU; Xia LIU; Yan Ping SHI


    A novel dimeric eremophilane, ligulolide B, was isolated from the alcoholic extract of the whole plant of Ligularia virgaurea spp. oligocephala. The structure was elucidated by various spectroscopic methods including intensive 2D NMR techniques (1H-1H COSY, gHMQC,gHMBC and 1H-1H NOESY) and HR-ESI-MS.

  9. Centrosymmetric dimer of quinuclidine betaine and squaric acid complex

    Dega-Szafran, Z.; Katrusiak, A.; Szafran, M.


    The complex of squaric acid (3,4-dihydroxy-3-cyclobuten-1,2-dion, H2SQ) with quinuclidine betaine (1-carboxymethyl-1-azabicyclo[2.2.2]octane inner salt, QNB), 1, has been characterized by single-crystal X-ray analysis, FTIR and NMR spectroscopies and by DFT calculations. In the crystal of 1, monoclinic space group P21/n, one proton from H2SQ is transferred to QNB. QNBH+ and HSQ- are linked together by a Osbnd H⋯O hydrogen bond of 2.553(2) Å. Two such QNBH+·HSQ- complexes form a centrosymmetric dimer bridged by two Osbnd H⋯O bonds of 2.536(2) Å. The FTIR spectrum is consistent with the X-ray results. The structures of monomer QNBH+·HSQ- (1a) and dimer [QNB·H2SQ]2 (2) have been optimized at the B3LYP/6-311++G(d,p) level of theory. Isolated dimer 2 optimized back to a molecular aggregate of H2SQ and QNB. The calculated frequencies for the optimized structure of dimer 2 have been used to explain the frequencies of the experimental FTIR spectrum. The interpretation of 1H and 13C NMR spectra has been based on the calculated GIAO/B3LYP/6-311++G(d,p) magnetic isotropic shielding constants for monomer 1a.

  10. Entanglement Transfer in a Four-Qubit Dimerized Heisenberg System

    SHAO Bin; HUANG Min; WANG Zhao-ming; ZOU Jian


    Entanglement transfer is investigated in a dimerized Heisenberg system.Coneurrence as the measure of entanglement is calculated by the time-evolved state starting from an initially entangled state of spin pair.It is shown that perfect entanglement transfer can be realized at 80me special time and suitable interacting.

  11. Dimers of Azurin as model systems for electron transfer

    Jongh, Thyra Estrid de


    This thesis describes the investigation of crosslinked complexes of the blue copper protein azurin by means of spectroscopic techniques such as Uv-Vis and NMR as well as by X-ray crystallography. These non-physiological dimers serve as model systems for interprotein electron transfer (ET) and allow

  12. Gnapholide: a new guaiac-dimer from Pulicaria gnaphalodes (Asteraceae).

    Ali, Muhammad Shaiq; Jahangir, Muhammad; Uzair, Syed Shah; Erian, Ayman Wahba; Tareen, Rasool Bakhsh


    The ethyl acetate soluble part of the chloroform extract of Pulicaria gnaphalodes belonging to the family Asteraceae afforded a new sesquiterpene-dimer of guaiane class named as gnapholide and anabsinthin of the same skeleton. The structures of both the compounds were elucidated with the aid of spectroscopic techniques including 2D NMR.

  13. Synthesis and Dimerization Behavior of Five Metallophthalocyanines in Different Solvents

    Zhenhua Cheng


    Full Text Available Metallophthalocyanine (MPc has become one of the metal organic compounds with the largest production and the most widely application, because of its excellent performance in catalytic oxidation. However, aggregation of the MPc in solution, resulting in decreased solubility, greatly limits the performance of application. Studying the behavior of dimerization of MPcs can provide a theoretical basis for solving the problem of the low solubility. So five metallophthalocyanines (FePc, CoPc, NiPc, CuPc, and ZnPc were prepared with improved method and characterized. Dimerization of the five MPcs was measured by UV-Vis spectroscopy separately in N,N-dimethyl formamide (DMF and dimethylsulfoxide (DMSO. The red-shift of maximum absorption wavelength and deviations from Lambert-Beer law with increasing the concentration were observed for all the five MPcs. The dimerization equilibrium constants (K of the five MPcs in DMF were arranged in order of CoPc > ZnPc > CuPc > FePc > NiPc, while in DMSO they were arranged in order of ZnPc > CoPc > FePc > CuPc > NiPc. The type of the central metal and nature of the solvent affect the dimerization of the MPcs.

  14. A novel dimeric procyanidin glucoside from Polygonum aviculare

    Hai Jian Cong; Shu Wei Zhang; Chong Zhang; Yu Jie Huang; Li Jiang Xuan


    A novel dimeric procyanidin glucoside,catechin 3-O-acetate-(4α→8)-catechin 3-O-acetate-3′-O-β-D-glucopyranoside (1),along with five flavonoids and one lignan were isolated from the aerial parts of Polygonum aviculare.Their structures were elucidated by spectroscopic analyses including 1D,2D NMR,MS and CD methods.

  15. Angle-Resolved Plasmonic Properties of Single Gold Nanorod Dimers

    Jian Wu; Xuxing Lu; Qiannan Zhu; Junwei Zhao; Qishun Shen; Li Zhan; Weihai Ni


    Through wet-chemical assembly methods, gold nanorods were placed close to each other and formed a dimer with a gap distance*1 nm, and hence degenerated plasmonic dipole modes of individual nanorods coupled together to produce hybridized bonding and antibonding resonance modes. Previous studies using a condenser for illumination result in averaged signals over all excitation angles. By exciting an individual dimer obliquely at different angles, we demonstrate that these two new resonance modes are highly tunable and sensitive to the angle between the excitation polarization and the dimer orientation, which follows cos2u dependence. Moreover, for dimer structures with various structure angles, the resonance wavelengths as well as the refractive index sensitivities were found independent of the structure angle. Cal-culated angle-resolved plasmonic properties are in good agreement with the measurements. The assembled nanostructures investigated here are important for fundamental researches as well as potential applications when they are used as building blocks in plasmon-based optical and optoelectronic devices.

  16. Entanglement in spin-1/2 dimerized Heisenberg systems

    Sun, Z; Hu, A Z; Li, Y Q; Sun, Zhe; Wang, XiaoGuang; Hu, AnZi; Li, You-Quan


    We study entanglement in dimerized Heisenberg systems. In particular, we give exact results of ground-state pairwise entanglement for the four-qubit model by identifying a Z_2 symmetry. Although the entanglements cannot identify the critical point of the system, the mean entanglement of nearest-neighbor qubits really does, namely, it reaches a maximum at the critical point.

  17. Entanglement in Spin-1/2 Dimerized Heisenberg Systems

    SUN Zhe; WANG Xiao-Guang; HU An-Zi; LI You-Quan


    We study entanglement in dimerized Heisenberg systems. In particular, we give exact results of groundstate pairwise entanglement for the four-qubit model by identifying a Z2 symmetry. Although the entanglements cannot identify the critical point of the system, the mean entanglement of the nearest-neighbor qubits really does, namely, it reaches a maximum at the critical point.

  18. Determining Equilibrium Constants for Dimerization Reactions from Molecular Dynamics Simulations

    De Jong, Djurre H.; Schafer, Lars V.; De Vries, Alex H.; Marrink, Siewert J.; Berendsen, Herman J. C.; Grubmueller, Helmut


    With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices c

  19. Construction of covalently coupled, concatameric dimers of 7TM receptors

    Terpager, Marie; Scholl, D Jason; Kubale, Valentina;


    -Ala repeats flanked by flexible spacers and positively charged residues to ensure correct inside-out orientation plus an extracellular HA-tag to construct covalently coupled dimers of 7TM receptors. Such 15 TM concatameric homo- and heterodimers of the beta(2)-adrenergic and the NK(1) receptors, which...

  20. Ising anyons in frustration-free Majorana-dimer models

    Ware, Brayden; Son, Jun Ho; Cheng, Meng; Mishmash, Ryan V.; Alicea, Jason; Bauer, Bela


    Dimer models have long been a fruitful playground for understanding topological physics. Here, we introduce a class, termed Majorana-dimer models, wherein bosonic dimers are decorated with pairs of Majorana modes. We find that the simplest examples of such systems realize an intriguing, intrinsically fermionic phase of matter that can be viewed as the product of a chiral Ising theory, which hosts deconfined non-Abelian quasiparticles, and a topological px-i py superconductor. While the bulk anyons are described by a single copy of the Ising theory, the edge remains fully gapped. Consequently, this phase can arise in exactly solvable, frustration-free models. We describe two parent Hamiltonians: one generalizes the well-known dimer model on the triangular lattice, while the other is most naturally understood as a model of decorated fluctuating loops on a honeycomb lattice. Using modular transformations, we show that the ground-state manifold of the latter model unambiguously exhibits all properties of the Ising×(px-i py) theory. We also discuss generalizations with more than one Majorana mode per site, which realize phases related to Kitaev's 16-fold way in a similar fashion.

  1. Facile synthesis of dimer phase of coronene and its optical properties

    Hayakawa, T.; Song, H.; Ishii, Y.; Kawasaki, S., E-mail: [Nagoya Institute of Technology, Gokiso, Showa, Nagoya, Aichi (Japan)


    We synthesized very pure dimer phase of coronene by simple heat-treatment and subsequent sublimation purification. It was found that the dimer phase emits very bright red light under the irradiation of low energy ultra-violet light.

  2. Structural proof of a dimeric positive modulator bridging two identical AMPA receptor-binding sites

    Kaae, Birgitte Høiriis; Harpsøe, Kasper; Kastrup, Jette Sandholm Jensen;


    Dimeric positive allosteric modulators of ionotropic glutamate receptors were designed, synthesized, and characterized pharmacologically in electrophysiological experiments. The designed compounds are dimers of arylpropylsulfonamides and have been constructed without a linker. The monomeric...

  3. Designer interface peptide grafts target estrogen receptor alpha dimerization

    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: [Laboratory of Computational Biophysics & Bioengineering, Department of Physics, Tougaloo College, Tougaloo, MS 39174 (United States); Rajnarayanan, R.V., E-mail: [Department of Pharmacology and Toxicology, University of Buffalo, Buffalo, NY 14214 (United States)


    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

  4. Radiation-enhanced optical antenna based on nonperiodic metallic nanoparticle dimer chain

    Chen, Xiaolin; Yu, Wenhai; Yue, Wencheng; Yao, Peijun; Liu, Wen


    With the aid of multi-sphere dyadic Green's function, we present a design of optical nanoantenna which is composed of a nonperiodic nanoparticle dimer chain. By breaking the periodicity of the dimer chain, the radiative emission of the dimer chain is significantly enhanced because the strong coupling which limits radiation enhancement is inhibited when the separations between dimers are reduced. Our work clearly shows the crucial role of nonperiodicity in the design of the Yagi-Uda nanoantenna.

  5. Stereo- and regio-selectivity in the photosensitized dimerization of 1, 3-dimethylthymine in solution

    HEI Xiaoming; SONG Qinhua; TANG Wenjian; WANG Hongbo; GUO Qingxiang; YU Shuqin


    The effects of reaction pathway and temperature on stereo- and regio-selectivity of photocycloaddition of 1, 3-dimethylthymine (DMT) which gives four cyclobutane type dimers in solution using acetone as the photosensitizer, are investigated by measuring the product distribution. It is demonstrated that the ground-state aggregation between DMT molecules mainly leads to (h-t)dimers, and the diffusion-controlled triplet dimerization is favorable to the formation of (h-h) dimers.

  6. Higher order expansions for the entropy of a dimer or a monomer-dimer system on d-dimensional lattices

    Butera, Paolo; Pernici, Mario


    Recently an expansion as a power series in 1/d has been presented for the specific entropy of a complete dimer covering of a d-dimensional hypercubic lattice. This paper extends from 3 to 10 the number of terms known in the series. Likewise an expansion for the entropy, dependent on the dimer-density p, of a monomer-dimer system, involving a sum sum_k a_k(d) p^k, has been recently offered. We herein extend the number of the known expansion coefficients from 6 to 20 for the hyper-cubic lattices of general dimension d and from 6 to 24 for the hyper-cubic lattices of dimensions d 2. The computations of this paper have led us to make the following marvelous conjecture: "In the case of the hyper-cubic lattices, all the expansion coefficients, a_k(d), are positive"! This paper results from a simple melding of two disparate research programs: one computing to high orders the Mayer series coefficients of a dimer gas, the other studying the development of entropy from these coefficients. An effort is made to make thi...

  7. Synthesis of β,β'-Porphyrin Dimer Linked by Vinylene

    Jiang, Xuliang; Li, Panli; Wang, Yucheng; Shen, Qi; Tao, Jingchao; Shi, Weimin


    Synthesis of a novel β,β'-tetraalkylporphyrin dimer linked by vinylene was discribed, in which the dimer was readily prepared from a porphyrin-derived Wittig reagent and a mono-formylated porphyrin via Wittig reaction. No π-conjugation between the two porphyrin rings was obserbed, and the dimer was in trans form.

  8. A Large Conformational Change of a Bridged β-Cyclodextrin Dimer in Aqueous Solution

    Xiao Qi ZHENG; Yong Hui WANG; Qing Xiang GUO; Li YANG; You Cheng LIU


    A novel bridged β-CD dimer in which two β-cyclodextrins were linked by a naphthalene at positions 2 and 7 has been synthesized. 1H and 13CNMR measurements showed that a large change in the conformation of the dimer occurred in aqueous solution. The dimer interacted with methyl and ethyl orange to form stable inclusion complexes via "induced fit" mechanism.

  9. Age- and sex-dependent reference intervals for D-dimer

    Haase, Christine; Joergensen, Maja; Ellervik, Christina;


    A low D-dimer is commonly used to exclude venous thromboembolism in low risk patients. However, the reference intervals are poorly defined and D-dimer has been shown to increase by patient age. We aimed to establish age- and sex-dependent D-dimer reference intervals and to test the consequence...

  10. Sublattice signatures of transitions in a $\\mathcal{PT}$-symmetric dimer lattice

    Harter, Andrew K


    Lattice models with non-hermitian, parity and time-reversal ($\\mathcal{PT}$) symmetric Hamiltonians, realized most readily in coupled optical systems, have been intensely studied in the past few years. A $\\mathcal{PT}$-symmetric dimer lattice consists of dimers with intra-dimer coupling $\

  11. Evaluation of stability difference between asymmetric homochiral dimer in (S)-thalidomide crystal and symmetric heterochiral dimer in (RS)-thalidomide crystal

    Suzuki, Toshiya; Tanaka, Masahito; Shiro, Motoo; Shibata, Norio; Osaka, Tetsuya; Asahi, Toru


    This article discusses differences in physicochemical properties such as solubility and melting point between (S)-thalidomide and (RS)-thalidomide based on crystal structures determined by X-ray diffraction experiments. Investigation of such differences is of great importance because thalidomide has attracted considerable attention again due to its wide-range bioactivity for intractable diseases. In this article, structures of hydrogen-bonded rings were compared between asymmetric homochiral dimers in (S)-thalidomide crystal and symmetric heterochiral dimers in (RS)-thalidomide crystal. The heterochiral dimer was evaluated to be more stable than the homochiral dimer by the energy calculations for hydrogen-bonded rings in those dimers. These results indicate that differences in physicochemical properties between enantiomeric and racemic thalidomides originate from the difference of structural stability between homochiral and heterochiral dimers.

  12. Solution structure of the dimeric cytoplasmic domain of syndecan-4

    Shin, J; Lee, W; Lee, D


    The syndecans, transmembrane proteoglycans which are involved in the organization of cytoskeleton and/or actin microfilaments, have important roles as cell surface receptors during cell-cell and/or cell-matrix interactions. Since previous studies indicate that the function of the syndecan-4...... between peptides at physiological pH. Commensurately, the NMR structures demonstrate that syndecan-4L is a compact intertwined dimer with a symmetric clamp shape in the central variable V region with a root-mean-square deviation between backbone atom coordinates of 0.95 A for residues Leu(186)-Ala(195...... in the center of the dimeric twist similar to our previously reported 4V structure. The overall topology of the central variable region within the 4L structure is very similar to that of 4V complexed with the phosphatidylinositol 4,5-bisphosphate; however, the intersubunit interaction mode is affected...

  13. Acylphenols and dimeric acylphenols from Myristica maxima Warb.

    Othman, Muhamad Aqmal; Sivasothy, Yasodha; Looi, Chung Yeng; Ablat, Abdulwali; Mohamad, Jamaludin; Litaudon, Marc; Awang, Khalijah


    Giganteone E (1), a new dimeric acylphenol was isolated as a minor constituent from the bark of Myristica maxima Warb. The structure of 1 was established on the basis of 1D and 2D NMR techniques and LCMS-IT-TOF analysis. Malabaricones A-C (2-4), giganteones A and C (5 and 6), maingayones A and B (7 and 8), maingayic acid B (9) and β-sitosteryl oleate (10) were also characterized in this plant for the first time. Compound 10 was identified for the first time in the Myristicaceae. Compounds 2 and 5 were active against human prostate cancer cell-lines, thus making this the first report on the prostate cancer inhibiting potential of acylphenols and dimeric acylphenols. Compounds 1, 4, 5, 7 and 8 exhibited potent DPPH free radical scavenging activity. This is the first report on their free radical scavenging capacity.

  14. Antioxidant Properties of Aminoethylcysteine Ketimine Decarboxylated Dimer: A Review

    Rosa Marina Matarese


    Full Text Available Aminoethylcysteine ketimine decarboxylated dimer is a natural sulfur-containing compound detected in human plasma and urine, in mammalian brain and in many common edible vegetables. Over the past decade many studies have been undertaken to identify its metabolic role. Attention has been focused on its antioxidant properties and on its reactivity against oxygen and nitrogen reactive species. These properties have been studied in different model systems starting from plasma lipoproteins to specific cellular lines. All these studies report that aminoethylcysteine ketimine decarboxylated dimer is able to interact both with reactive oxygen and nitrogen species (hydrogen peroxide, superoxide anion, hydroxyl radical, peroxynitrite and its derivatives. Its antioxidant activity is similar to that of Vitamin E while higher than other hydrophilic antioxidants, such as trolox and N-acetylcysteine.

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

    Bartholomäus, Ingo; Milan-Lobo, Laura; Nicke, Annette


    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......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...

  16. Probing quantum discord in a Heisenberg dimer compound.

    Chakraborty, Tanmoy; Singh, Harkirat; Singh, Sourabh; Gopal, Radha Krishna; Mitra, Chiranjib


    A quantitative estimation of quantum discord is performed for a Heisenberg spin 1/2 dimer compound (NH4CuPO4, H2O) by means of experimental magnetic and thermal measurements. Magnetic susceptibility and specific heat data were collected for NH4CuPO4, H2O and analyzed within the framework of the Heisenberg isolated dimer model. Internal energy as a function of temperature is obtained by integrating the specific heat versus temperature data. Subsequently, quantum discord, total correlations and spin-spin correlation function are quantified from susceptibility and internal energy and plotted as a function of temperature. Violation of Bell's inequality is also tested for NH4CuPO4, H2O via both experimental susceptibility and specific heat data signifying the presence of entanglement.


    Woods, Paul M.; Viti, Serena [Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT (United Kingdom); Slater, Ben; Raza, Zamaan; Brown, Wendy A.; Burke, Daren J., E-mail: [Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ (United Kingdom)


    Glycolaldehyde, the simplest monosaccharide sugar, has recently been detected in low- and high-mass star-forming cores. Following our previous investigation into glycolaldehyde formation, we now consider a further mechanism for the formation of glycolaldehyde that involves the dimerization of the formyl radical, HCO. Quantum mechanical investigation of the HCO dimerization process upon an ice surface is predicted to be barrierless and therefore fast. In an astrophysical context, we show that this mechanism can be very efficient in star-forming cores. It is limited by the availability of the formyl radical, but models suggest that only very small amounts of CO are required to be converted to HCO to meet the observational constraints.

  18. Glycolaldehyde Formation via the Dimerization of the Formyl Radical

    Woods, Paul M.; Slater, Ben; Raza, Zamaan; Viti, Serena; Brown, Wendy A.; Burke, Daren J.


    Glycolaldehyde, the simplest monosaccharide sugar, has recently been detected in low- and high-mass star-forming cores. Following our previous investigation into glycolaldehyde formation, we now consider a further mechanism for the formation of glycolaldehyde that involves the dimerization of the formyl radical, HCO. Quantum mechanical investigation of the HCO dimerization process upon an ice surface is predicted to be barrierless and therefore fast. In an astrophysical context, we show that this mechanism can be very efficient in star-forming cores. It is limited by the availability of the formyl radical, but models suggest that only very small amounts of CO are required to be converted to HCO to meet the observational constraints.

  19. Dimerization effect of sucrose octasulfate on rat FGF1

    Kulahin, Nikolaj; Kiselyov, Vladislav; Kochoyan, Artur


    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 A 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....

  20. Solitons in a chain of PT-invariant dimers

    Suchkov, Sergey V; Dmitriev, Sergey V; Kivshar, Yuri S


    Dynamics of a chain of interacting parity-time invariant nonlinear dimers is investigated. A dimer is built as a pair of coupled elements with equal gain and loss. A relation between stationary soliton solutions of the model and solitons of the discrete nonlinear Schrodinger (DNLS) equation is demonstrated. Approximate solutions for solitons whose width is large in comparison to the lattice spacing are derived, using a continuum counterpart of the discrete equations. These solitons are mobile, featuring nearly elastic collisions. Stationary solutions for narrow solitons, which are immobile due to the pinning by the effective Peierls-Nabarro potential, are constructed numerically, starting from the anti-continuum limit. The solitons with the amplitude exceeding a certain critical value suffer an instability leading to blowup, which is a specific feature of the nonlinear PT-symmetric chain, making it dynamically different from DNLS lattices. A qualitative explanation of this feature is proposed. The instability...

  1. Inhibition of HIV-1 Reverse Transcriptase Dimerization by Small Molecules.

    Tintori, Cristina; Corona, Angela; Esposito, Francesca; Brai, Annalaura; Grandi, Nicole; Ceresola, Elisa Rita; Clementi, Massimo; Canducci, Filippo; Tramontano, Enzo; Botta, Maurizio


    Because HIV-1 reverse transcriptase is an enzyme whose catalytic activity depends on its heterodimeric structure, this system could be a target for inhibitors that perturb the interactions between the protein subunits, p51 and p66. We previously demonstrated that the small molecule MAS0 reduced the association of the two RT subunits and simultaneously inhibited both the polymerase and ribonuclease H activities. In this study, some analogues of MAS0 were rationally selected by docking studies and evaluated in vitro for their ability to disrupt dimeric assembly. Two inhibitors were identified with improved activity compared to MAS0. This study lays the basis for the rational design of more potent inhibitors of RT dimerization.

  2. Intramolecular hydrophobic interactions are critical mediators of STAT5 dimerization

    Fahrenkamp, Dirk; Li, Jinyu; Ernst, Sabrina; Schmitz-van de Leur, Hildegard; Chatain, Nicolas; Küster, Andrea; Koschmieder, Steffen; Lüscher, Bernhard; Rossetti, Giulia; Müller-Newen, Gerhard


    STAT5 is an essential transcription factor in hematopoiesis, which is activated through tyrosine phosphorylation in response to cytokine stimulation. Constitutive activation of STAT5 is a hallmark of myeloid and lymphoblastic leukemia. Using homology modeling and molecular dynamics simulations, a model of the STAT5 phosphotyrosine-SH2 domain interface was generated providing first structural information on the activated STAT5 dimer including a sequence, for which no structural information is available for any of the STAT proteins. We identified a novel intramolecular interaction mediated through F706, adjacent to the phosphotyrosine motif, and a unique hydrophobic interface on the surface of the SH2 domain. Analysis of corresponding STAT5 mutants revealed that this interaction is dispensable for Epo receptor-mediated phosphorylation of STAT5 but essential for dimer formation and subsequent nuclear accumulation. Moreover, the herein presented model clarifies molecular mechanisms of recently discovered leukemic STAT5 mutants and will help to guide future drug development.

  3. UV resonance Raman analysis of trishomocubane and diamondoid dimers

    Meinke, Reinhard, E-mail:; Thomsen, Christian; Maultzsch, Janina [Institut für Festkörperphysik, Technische Universität Berlin, Hardenbergstr. 36, D-10623 Berlin (Germany); Richter, Robert; Merli, Andrea [Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, D-10623 Berlin (Germany); Fokin, Andrey A. [Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 58, D-35392 Giessen (Germany); Department of Organic Chemistry, Kiev Polytechnic Institute, pr. Pobedy 37, 03056 Kiev (Ukraine); Koso, Tetyana V.; Schreiner, Peter R. [Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 58, D-35392 Giessen (Germany); Rodionov, Vladimir N. [Department of Organic Chemistry, Kiev Polytechnic Institute, pr. Pobedy 37, 03056 Kiev (Ukraine)


    We present resonance Raman measurements of crystalline trishomocubane and diamantane dimers containing a C=C double bond. Raman spectra were recorded with excitation energies between 2.33 eV and 5.42 eV. The strongest enhancement is observed for the C=C stretch vibration and a bending mode involving the two carbon atoms of the C=C bond, corresponding to the B{sub 2g} wagging mode of ethylene. This is associated with the localization of the π-HOMO and LUMO and the elongation of the C=C bond length and a pyramidalization of the two sp{sup 2}-hybridized carbon atoms at the optical excitation. The observed Raman resonance energies of the trishomocubane and diamantane dimers are significantly lower than the HOMO-LUMO gaps of the corresponding unmodified diamondoids.

  4. Role of the Chlorophyll Dimer in Bacterial Photosynthesis

    Warshel, Arieh


    The role of a special dimer (D) of bacterio-chlorophyll molecules in bacterial photosynthesis was examined by calculations of the rates of electron transfer reactions in a system of the dimer and a bacteriopheophytin (BPh) molecule. It was found that the dependence of the potential surfaces of D on the distance between the monomers allows a fast light-induced electron transfer from D to BPh but only a slow back reaction (reduction of D+ by BPh-). The same potential surfaces allow efficient reduction of D+ by cytochrome c. Possible advantages of greatly different values of the electronic matrix elements for the forward and back reactions are pointed out. It is suggested that the electrostatic interaction between D+ and an ionized group of the protein might play an important role in the photosynthetic reaction.

  5. Dimers on surface graphs and spin structures. II

    Cimasoni, David; Reshetikhin, Nicolai


    In a previous paper [3], we showed how certain orientations of the edges of a graph Γ embedded in a closed oriented surface Σ can be understood as discrete spin structures on Σ. We then used this correspondence to give a geometric proof of the Pfaffian formula for the partition function of the di......In a previous paper [3], we showed how certain orientations of the edges of a graph Γ embedded in a closed oriented surface Σ can be understood as discrete spin structures on Σ. We then used this correspondence to give a geometric proof of the Pfaffian formula for the partition function...... of the dimer model on Γ. In the present article, we generalize these results to the case of compact oriented surfaces with boundary. We also show how the operations of cutting and gluing act on discrete spin structures and how they change the partition function. These operations allow to reformulate the dimer...

  6. Mechanism of Processive Movement of Monomeric and Dimeric Kinesin Molecules

    Ping Xie


    Full Text Available Kinesin molecules are motor proteins capable of moving along microtubule by hydrolyzing ATP. They generally have several forms of construct. This review focuses on two of the most studied forms: monomers such as KIF1A (kinesin-3 family and dimers such as conventional kinesin (kinesin-1 family, both of which can move processively towards the microtubule plus end. There now exist numerous models that try to explain how the kinesin molecules convert the chemical energy of ATP hydrolysis into the mechanical energy to “power” their proceesive movement along microtubule. Here, we attempt to present a comprehensive review of these models. We further propose a new hybrid model for the dimeric kinesin by combining the existing models and provide a framework for future studies in this subject.

  7. Dimerization-assisted energy transport in light-harvesting complexes.

    Yang, S; Xu, D Z; Song, Z; Sun, C P


    We study the role of the dimer structure of light-harvesting complex II (LH2) in excitation transfer from the LH2 [without a reaction center (RC)] to the LH1 (surrounding the RC) or from the LH2 to another LH2. The excited and unexcited states of a bacteriochlorophyll (BChl) are modeled by a quasispin. In the framework of quantum open system theory, we represent the excitation transfer as the total leakage of the LH2 system and then calculate the transfer efficiency and average transfer time. For different initial states with various quantum superposition properties, we study how the dimerization of the B850 BChl ring can enhance the transfer efficiency and shorten the average transfer time.

  8. Dimerization-assisted energy transport in light-harvesting complexes

    Yang, S; Song, Z; Sun, C P


    We study the role of the dimer structure of light-harvesting complex II (LH2) in excitation transfer from the LH2 (without a reaction center (RC)) to the LH1 (surrounding the RC), or from the LH2 to another LH2. The excited and un-excited states of a bacteriochlorophyll (BChl) are modeled by quasi-spin. In the framework of quantum open system theory, we represent the excitation transfer as the total leakage of the LH2 system, and then calculate the transfer efficiency and average transfer time at a low enough temperature. For different initial states with various quantum superposition properties, we study how the dimerization of the B850 BChl ring can enhance the transfer efficiency and shorten the average transfer time.

  9. Conformational Heterogeneity of Bax Helix 9 Dimer for Apoptotic Pore Formation

    Liao, Chenyi; Zhang, Zhi; Kale, Justin; Andrews, David W.; Lin, Jialing; Li, Jianing


    Helix α9 of Bax protein can dimerize in the mitochondrial outer membrane (MOM) and lead to apoptotic pores. However, it remains unclear how different conformations of the dimer contribute to the pore formation on the molecular level. Thus we have investigated various conformational states of the α9 dimer in a MOM model — using computer simulations supplemented with site-specific mutagenesis and crosslinking of the α9 helices. Our data not only confirmed the critical membrane environment for the α9 stability and dimerization, but also revealed the distinct lipid-binding preference of the dimer in different conformational states. In our proposed pathway, a crucial iso-parallel dimer that mediates the conformational transition was discovered computationally and validated experimentally. The corroborating evidence from simulations and experiments suggests that, helix α9 assists Bax activation via the dimer heterogeneity and interactions with specific MOM lipids, which eventually facilitate proteolipidic pore formation in apoptosis regulation.

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

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


    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.

  11. Plasmon excitations in the dimers formed by atom chains

    Xue, Hong-jie; Hao, Da-peng; Zhang, Ming; Wang, Xiao-mei


    Based on the linear response theory in the random-phase approximation and the free-electron gas model, we study the plasmon excitations in the dimers formed by atom chains. With the help of energy absorption spectrum and charge distribution, the evolutions of longitudinal and transverse plasmon, and the effect of the system parameters such as size, atomic separation and electron filling on plasmon are obtained. In addition, the dipole, quadrupole, end and central plasmon are observed.

  12. Multiple-charge transfer and trapping in DNA dimers

    Tornow, Sabine; Bulla, Ralf; Anders, Frithjof B.; Zwicknagl, Gertrud


    We investigate the charge transfer characteristics of one and two excess charges in a DNA base-pair dimer using a model Hamiltonian approach. The electron part comprises diagonal and off-diagonal Coulomb matrix elements such a correlated hopping and the bond-bond interaction, which were recently calculated by Starikov [E. B. Starikov, Philos. Mag. Lett. 83, 699 (2003)10.1080/0950083031000151374] for different DNA dimers. The electronic degrees of freedom are coupled to an ohmic or a superohmic bath serving as dissipative environment. We employ the numerical renormalization group method in the nuclear tunneling regime and compare the results to Marcus theory for the thermal activation regime. For realistic parameters, the rate that at least one charge is transferred from the donor to the acceptor in the subspace of two excess electrons significantly exceeds the rate in the single charge sector. Moreover, the dynamics is strongly influenced by the Coulomb matrix elements. We find sequential and pair transfer as well as a regime where both charges remain self-trapped. The transfer rate reaches its maximum when the difference of the on-site and intersite Coulomb matrix element is equal to the reorganization energy which is the case in a guanine/cytosine (GC)-dimer. Charge transfer is completely suppressed for two excess electrons in adenine/thymine (AT)-dimer in an ohmic bath and replaced by damped coherent electron-pair oscillations in a superohmic bath. A finite bond-bond interaction W alters the transfer rate: it increases as function of W when the effective Coulomb repulsion exceeds the reorganization energy (inverted regime) and decreases for smaller Coulomb repulsion.

  13. Wave packet dynamics of potassium dimers attached to helium nanodroplets

    Claas, P.; Droppelmann, G.; Schulz, C. P.; Mudrich, M.; Stienkemeier, F.


    The dynamics of vibrational wave packets excited in K$_2$ dimers attached to superfluid helium nanodroplets is investigated by means of femtosecond pump-probe spectroscopy. The employed resonant three-photon-ionization scheme is studied in a wide wavelength range and different pathways leading to K$^+_2$-formation are identified. While the wave packet dynamics of the electronic ground state is not influenced by the helium environment, perturbations of the electronically excited states are obs...

  14. A New Hydroxychavicol Dimer from the Roots of Piper betle

    Huei-Yu Tu; Horng-Liang Lay; Chun-Chien Chien; Chwan-Fwu Lin; Tsong-Long Hwang


    A new hydroxychavicol dimer, 2-(g'-hydroxychavicol)-hydroxychavicol (1), was isolated from the roots of Piper betle Linn. along with five known compounds, hydroxychavicol (2), aristololactam A II (3), aristololactam B II (4), piperolactam A (5) and cepharadione A (6). The structures of these isolated compounds were elucidated by spectroscopic methods. Compounds 1 and 2 exhibited inhibitory effects on the generation of superoxide anion and the release of elastase by human neutrophils.

  15. A New Hydroxychavicol Dimer from the Roots of Piper betle

    Huei-Yu Tu


    Full Text Available A new hydroxychavicol dimer, 2-(g'-hydroxychavicol-hydroxychavicol (1, was isolated from the roots of Piper betle Linn. along with five known compounds, hydroxychavicol (2, aristololactam A II (3, aristololactam B II (4, piperolactam A (5 and cepharadione A (6. The structures of these isolated compounds were elucidated by spectroscopic methods. Compounds 1 and 2 exhibited inhibitory effects on the generation of superoxide anion and the release of elastase by human neutrophils.

  16. A new hydroxychavicol dimer from the roots of Piper betle.

    Lin, Chwan-Fwu; Hwang, Tsong-Long; Chien, Chun-Chien; Tu, Huei-Yu; Lay, Horng-Liang


    A new hydroxychavicol dimer, 2-(g'-hydroxychavicol)-hydroxychavicol (1), was isolated from the roots of Piper betle Linn. along with five known compounds, hydroxychavicol (2), aristololactam A II (3), aristololactam B II (4), piperolactam A (5) and cepharadione A (6). The structures of these isolated compounds were elucidated by spectroscopic methods. Compounds 1 and 2 exhibited inhibitory effects on the generation of superoxide anion and the release of elastase by human neutrophils.

  17. Naturally occurring pentaoxygenated, hexaoxygenated and dimeric xanthones: a literature survey

    V. Peres


    Full Text Available This review gives information on the chemical study of 71 pentaoxygenated, 11 hexaoxygenated and 9 dimeric and more complex xanthones naturally occurring in 7 families, 29 genus and 62 species of higher plants, and 11 described as fern and fungal metabolites. The value of these groups of substances in the connection with the pharmacological activity and the therapeutic use of some species is shown. The structural formulas of 23 isolated compounds and their distribution in the species studied are given.

  18. Excited State Pathways Leading to Formation of Adenine Dimers.

    Banyasz, Akos; Martinez-Fernandez, Lara; Ketola, Tiia-Maaria; Muñoz-Losa, Aurora; Esposito, Luciana; Markovitsi, Dimitra; Improta, Roberto


    The reaction intermediate in the path leading to UV-induced formation of adenine dimers A═A and AA* is identified for the first time quantum mechanically, using PCM/TD-DFT calculations on (dA)2 (dA: 2'deoxyadenosine). In parallel, its fingerprint is detected in the absorption spectra recorded on the millisecond time-scale for the single strand (dA)20 (dA: 2'deoxyadenosine).

  19. A DFT study of substituent effects in corannulene dimers.

    Josa, Daniela; Rodríguez Otero, Jesús; Cabaleiro Lago, Enrique M


    Corannulene dimers made up of corannulene monomers with different curvature and substituents were studied using M06-2X, B97D and ωB97XD functionals and 6-31+G* basis set. Corannulene molecules were substituted with five alternating Br, Cl, CH(3), C(2)H or CN units. Geometric results showed that substituents gave rise to small changes in the curvature of corannulene bowls. So, there was not a clear relationship between the curvature of bowls and the changes on interaction energy generated by addition of substituents in the bowl. Electron withdrawing substituents gave rise to a more positive molecular electrostatic potential (MEP) of the bowl, which was able to get a strong interaction with the negative MEP at the surface of a fullerene. Substitution with CN caused the largest effect, giving rise to the most positive MEP and to a large interaction energy of -24.64 kcal mol(-1), at the ωB97XD/6-31+G* level. Dispersive effects must be taken into account to explain the catching ability of the different substituted corannulenes. For unsubstituted dimers, calculations with DFT-D methods employing ωB97XD and B97D functionals led to similar results to those previously reported at the SCS-MP2/cc-pVTZ level for corannulene dimers (A. Sygula and S. Saebø, Int. J. Quant. Chem., 2009, 109, 65). In particular, the ωB97XD functional led to a difference of only 0.35 kcal mol(-1), regarding MP2 interaction energy for corannulene dimers. On the other hand, the M06-2X functional showed a general considerable underestimation of interaction energies. This functional worked quite well to study trends, but not to obtain absolute interaction energies.

  20. Dimer Models, Free Fermions and Super Quantum Mechanics

    Dijkgraaf, R; Reffert, S


    This note relates topics in statistical mechanics, graph theory and combinatorics, lattice quantum field theory, super quantum mechanics and string theory. We give a precise relation between the dimer model on a graph embedded on a torus and the massless free Majorana fermion living on the same lattice. A loop expansion of the fermion determinant is performed, where the loops turn out to be compositions of two perfect matchings. These loop states are sorted into co-chain groups using categorification techniques similar to the ones used for categorifying knot polynomials. The Euler characteristic of the resulting co-chain complex recovers the Newton polynomial of the dimer model. We re-interpret this system as supersymmetric quantum mechanics, where configurations with vanishing net winding number form the ground states. Finally, we make use of the quiver gauge theory - dimer model correspondence to obtain an interpretation of the loops in terms of the physics of D-branes probing a toric Calabi-Yau singularity...

  1. On the photophysics and photochemistry of the water dimer

    Segarra-Marti, Javier; Merchan, Manuela [Instituto de Ciencia Molecular, Universitat de Valencia, P.O. Box 22085, 46071 Valencia (Spain); Roca-Sanjuan, Daniel; Lindh, Roland [Department of Chemistry - Angstroem, Theoretical Chemistry Program, Uppsala University, Box 518, 75120 Uppsala (Sweden)


    The photochemistry of the water dimer irradiated by UV light is studied by means of the complete active space perturbation theory//complete active space self-consistent field (CASPT2//CASSCF) method and accurate computational approaches like as minimum energy paths. Both electronic structure computations and ab initio molecular dynamics simulations are carried out. The results obtained show small shifts relative to a single water molecule on the vertical excitation energies of the dimer due to the hydrogen bond placed between the water donor (W{sub D}) and the water acceptor (W{sub A}). A red-shift and a blue-shift are predicted for the W{sub D} and W{sub A}, respectively, supporting previous theoretical and experimental results. The photoinduced chemistry of the water dimer is described as a process occurring between two single water molecules in which the effect of the hydrogen bond plays a minor role. Thus, the photoinduced decay routes correspond to two photodissociation processes, one for each water molecule. The proposed mechanism for the decay channels of the lowest-lying excited states of the system is established as the photochemical production of a hydrogen-bonded H{sub 2}O Horizontal-Ellipsis HO species plus a hydrogen H atom.

  2. Assembly and separation of semiconductor quantum dot dimers and trimers.

    Xu, Xiangxing; Stöttinger, Sven; Battagliarin, Glauco; Hinze, Gerald; Mugnaioli, Enrico; Li, Chen; Müllen, Klaus; Basché, Thomas


    Repeated precipitation of colloidal semiconductor quantum dots (QD) from a good solvent by adding a poor solvent leads to an increasing number of QD oligomers after redispersion in the good solvent. By using density gradient ultracentrifugation we have been able to separate QD monomer, dimer, and trimer fractions from higher oligomers in such solutions. In the corresponding fractions QD dimers and trimers have been enriched up to 90% and 64%, respectively. Besides directly coupled oligomers, QD dimers and trimers were also assembled by linkage with a rigid terrylene diimide dye (TDI) and separated again by ultracentrifugation. High-resolution transmission electron micrographs show that the interparticle distances are clearly larger than those for directly coupled dots proving that the QDs indeed are cross-linked by the dye. Moreover, energy transfer from the QDs to the TDI "bridge" has been observed. Individual oligomers (directly coupled or dye-linked) can be readily deposited on a substrate and studied simultaneously by scanning force and optical microscopy. Our simple and effective scheme is applicable to a wide range of ligand stabilized colloidal nanoparticles and opens the way to a detailed study of electronic coupling in, e.g., QD molecules.

  3. Nonlinearity and trapping in excitation transfer Dimers and Trimers.

    Barvik, I; Schanz, H; Barvik, Ivan; Esser, Bernd; Schanz, Holger


    We study the interplay between nonlinearity in exciton transport and trapping due to a sink site for the dimer and the trimer with chain configuration by a numerical integration of the discrete nonlinear Schroedinger equation. Our results for the dimer show, that the formation of a self trapped state due to the nonlinear coupling increases the life time of the exciton substantially. Self trapping can be enhanced by the sink for short times, but for long times it disappears. In the trimer consisting of a subdimer extended by a sink site exists a transition between states localized on the two sites of the subdimer before for larger nonlinear coupling self trapping on one site of the subdimer is observed. For large trapping rates the fear of death effect leads to an increasing life time of the excitation on both, the dimer and the trimer. The sink site is then effectively decoupled. We explain this effect using an asymptotic theory for strong trapping and demonstrate it by direct numerical computation.

  4. Benchmark calculations for elastic fermion-dimer scattering

    Bour, Shahin; Lee, Dean; Meißner, Ulf-G


    We present continuum and lattice calculations for elastic scattering between a fermion and a bound dimer in the shallow binding limit. For the continuum calculation we use the Skorniakov-Ter-Martirosian (STM) integral equation to determine the scattering length and effective range parameter to high precision. For the lattice calculation we use the finite-volume method of L\\"uscher. We take into account topological finite-volume corrections to the dimer binding energy which depend on the momentum of the dimer. After subtracting these effects, we find from the lattice calculation kappa a_fd = 1.174(9) and kappa r_fd = -0.029(13). These results agree well with the continuum values kappa a_fd = 1.17907(1) and kappa r_fd = -0.0383(3) obtained from the STM equation. We discuss applications to cold atomic Fermi gases, deuteron-neutron scattering in the spin-quartet channel, and lattice calculations of scattering for nuclei and hadronic molecules at finite volume.

  5. Quantum Monte Carlo calculations of the dimerization energy of borane.

    Fracchia, Francesco; Bressanini, Dario; Morosi, Gabriele


    Accurate thermodynamic data are required to improve the performance of chemical hydrides that are potential hydrogen storage materials. Boron compounds are among the most interesting candidates. However, different experimental measurements of the borane dimerization energy resulted in a rather wide range (-34.3 to -39.1) ± 2 kcal/mol. Diffusion Monte Carlo (DMC) simulations usually recover more than 95% of the correlation energy, so energy differences rely less on error cancellation than other methods. DMC energies of BH(3), B(2)H(6), BH(3)CO, CO, and BH(2)(+) allowed us to predict the borane dimerization energy, both via the direct process and indirect processes such as the dissociation of BH(3)CO. Our D(e) = -43.12(8) kcal/mol, corrected for the zero point energy evaluated by considering the anharmonic contributions, results in a borane dimerization energy of -36.59(8) kcal/mol. The process via the dissociation of BH(3)CO gives -34.5(2) kcal/mol. Overall, our values suggest a slightly less D(e) than the most recent W4 estimate D(e) = -44.47 kcal/mol [A. Karton and J. M. L. Martin, J. Phys. Chem. A 111, 5936 (2007)]. Our results show that reliable thermochemical data for boranes can be predicted by fixed node (FN)-DMC calculations.

  6. Effects of dimers on cooperation in the spatial prisoner's dilemma game

    Li, Haihong; Dai, Qionglin; Ju, Ping; Zhang, Mei; Yang, Junzhong


    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 ...

  7. Synthesis and photophysical properties of a single bond linked tetracene dimer

    Sun, Tingting; Shen, Li; Liu, Heyuan; Sun, Xuan; Li, Xiyou


    A tetracene dimer linked directly by a single bond has been successfully prepared by using electron withdrawing groups to improve the stability. The molecular structure of this dimer is characterized by 1H NMR, MALDI-TOF mass spectroscopy, and elemental analysis. The minimized molecular structure and X-ray crystallography reveal that the tetracene subunits of this dimer adopt an orthogonal configuration. Its absorption spectrum differs significantly from that of its monomeric counterpart, suggesting the presence of strong interactions between the two tetracene subunits. The excited state of this dimer is delocalized on both two tetracene subunits, which is significantly different from that of orthogonal anthracene dimers, but similar with that observed for orthogonal pentacene dimer. Most of the excited states of this dimer decay by radioactive channels, which is different from the localized twisted charge transfer state (LTCT) channel of anthracene dimers and the singlet fission (SF) channel of pentacene dimers. The results of this research suggest that similar orthogonal configurations caused different propertied for acene dimers with different conjugation length.

  8. Correlation analysis between plasma D-dimer levels and orthopedic trauma severity

    ZHANG Li-dan; LIU Hong-bo; LI Yu-neng; MA Hai-mei; LIU Ya-bo; WANG Man-yi


    Background The correlation between the plasma D-dimer level and deep vein thrombosis has not been conclusive in various studies.The aim of this research was to study the relationship between plasma D-dimer levels and the severity of orthopedic trauma by retrospective examination of orthopedic trauma cases.Methods Clinically acute trauma and non-acute trauma patients were selected and their plasma D-dimer levels were measured.Plasma D-dimer levels in patients of these two groups were compared.The relationship between the plasma D-dimer level and the severity of the trauma was also studied.Results There were 548 cases in the acute trauma group and 501 cases in the non-acute trauma group.The levels of plasma D-dimer were significantly higher in the acute trauma group than in the non-acute trauma group (P <0.01).In the acute trauma group,the correlation between the D-dimer level and the number of fractures was a positive linear correlation (r=0.9532).Conclusions Elevated plasma D-dimer is common in trauma patients.The D-dimer level and the number of fractures in the trauma patients are closely correlated.D-dimer is not only an indicator for the diagnosis of deep vein thrombosis and pulmonary embolus,but also an indicator of the severity of trauma in acute trauma patients.

  9. Magnetic properties of transition metal Mn, Fe and Co dimers on monolayer phosphorene

    Khan, Imran; Hong, Jisang


    We studied the geometries, electronic structure and magnetic properties of substitutional doping and adsorption of transition metal (Mn, Fe and Co) dimers on phosphorene monolayer in the framework of the generalized gradient approximation (GGA) and GGA + U. Electronic band structures and magnetic properties were dependent on the doping type and dopant materials. For Mn and Fe substitutional and adsorption dimers, we obtained semiconducting band structures with spin polarization. However, we found a half-metallic feature in Co substitutional dimer while the Co adsorption dimer showed a semiconducting behavior without any spin polarization. With GGA + U, all the systems showed spin polarized semiconducting band structures except Co adsorption dimer which remained unaffected. The hybridization between transition metal (TM) and phosphorene sheet contributed to suppressing the magnetic moment of TM dimers. For instance, the total magnetic moments of -2.0, 4.24 and 1.28 μ B/cell for Mn, Fe and Co substitutional dimers were obtained while the Mn and Fe adsorption dimers showed magnetic moments of -1.69 and 0.46 μ B/cell. These magnetic moments were enhanced with GGA + U. The same magnetic ground states were obtained both from GGA and GGA + U approaches except for the Mn dimers. We observed that the Mn and Fe substitutional dimers showed an out-of-plane magnetization while an in-plane magnetization was observed in Co substitutional dimer. The Mn adsorption dimer still displayed a perpendicular magnetization whereas the Fe adsorption dimer had an in-plane magnetization. We found that the both GGA and GGA + U showed the same magnetization direction in all the systems.

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

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


    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.

  11. Dynamically configurable hybridization of plasmon modes in nanoring dimer arrays

    Zhang, Lei; Dong, Zhaogang; Wang, Ying Min; Liu, Yan Jun; Zhang, Shuang; Yang, Joel Kwang Wei; Qiu, Cheng-Wei


    We present a novel strategy capable of dynamically configuring the plasmon-induced transparency (PIT) effect with a polarization-dependent controllability based on a nanoring dimer array. The controllable coupling strength between the superradiant and subradiant modes is due to the polarization-dependent field distributions. It is shown that this dynamically controlled PIT is realized with a modulation depth as high as 95%, and a linear dependence of the coupling strength on polarization angle is deduced using a coupled-oscillator model. We believe that our results will inspire further exciting achievements that utilize various polarization states of the electromagnetic wave and pave a way towards applications using PIT with dynamic controllability such as slow light, optical nonlinearities and chemical/bio-sensing.We present a novel strategy capable of dynamically configuring the plasmon-induced transparency (PIT) effect with a polarization-dependent controllability based on a nanoring dimer array. The controllable coupling strength between the superradiant and subradiant modes is due to the polarization-dependent field distributions. It is shown that this dynamically controlled PIT is realized with a modulation depth as high as 95%, and a linear dependence of the coupling strength on polarization angle is deduced using a coupled-oscillator model. We believe that our results will inspire further exciting achievements that utilize various polarization states of the electromagnetic wave and pave a way towards applications using PIT with dynamic controllability such as slow light, optical nonlinearities and chemical/bio-sensing. Electronic supplementary information (ESI) available: Method, mode supported by single nanoring, transmittance spectrum of single nanoring, comparison of transmittance spectra simulated under different illumination angles, diffraction coupling in the proposed nanoring dimer system, and the coupled Lorentz oscillator model and parameters

  12. Integral equation study of soft-repulsive dimeric fluids

    Munaò, Gianmarco; Saija, Franz


    We study fluid structure and water-like anomalies of a system constituted by dimeric particles interacting via a purely repulsive core-softened potential by means of integral equation theories. In our model, dimers interact through a repulsive pair potential of inverse-power form with a softened repulsion strength. By employing the Ornstein–Zernike approach and the reference interaction site model (RISM) theory, we study the behavior of water-like anomalies upon progressively increasing the elongation λ of the dimers from the monomeric case (λ =0 ) to the tangent configuration (λ =1 ). For each value of the elongation we consider two different values of the interaction potential, corresponding to one and two length scales, with the aim to provide a comprehensive description of the possible fluid scenarios of this model. Our theoretical results are systematically compared with already existing or newly generated Monte Carlo data: we find that theories and simulations agree in providing the picture of a fluid exhibiting density and structural anomalies for low values of λ and for both the two values of the interaction potential. Integral equation theories give accurate predictions for pressure and radial distribution functions, whereas the temperatures where anomalies occur are underestimated. Upon increasing the elongation, the RISM theory still predicts the existence of anomalies; the latter are no longer observed in simulations, since their development is likely precluded by the onset of crystallization. We discuss our results in terms of the reliability of integral equation theories in predicting the existence of water-like anomalies in core-softened fluids.

  13. Dimerization and DNA recognition rules of mithramycin and its analogues.

    Weidenbach, Stevi; Hou, Caixia; Chen, Jhong-Min; Tsodikov, Oleg V; Rohr, Jürgen


    The antineoplastic and antibiotic natural product mithramycin (MTM) is used against cancer-related hypercalcemia and, experimentally, against Ewing sarcoma and lung cancers. MTM exerts its cytotoxic effect by binding DNA as a divalent metal ion (Me(2+))-coordinated dimer and disrupting the function of transcription factors. A precise molecular mechanism of action of MTM, needed to develop MTM analogues selective against desired transcription factors, is lacking. Although it is known that MTM binds G/C-rich DNA, the exact DNA recognition rules that would allow one to map MTM binding sites remain incompletely understood. Towards this goal, we quantitatively investigated dimerization of MTM and several of its analogues, MTM SDK (for Short side chain, DiKeto), MTM SA-Trp (for Short side chain and Acid), MTM SA-Ala, and a biosynthetic precursor premithramycin B (PreMTM B), and measured the binding affinities of these molecules to DNA oligomers of different sequences and structural forms at physiological salt concentrations. We show that MTM and its analogues form stable dimers even in the absence of DNA. All molecules, except for PreMTM B, can bind DNA with the following rank order of affinities (strong to weak): MTM=MTM SDK>MTM SA-Trp>MTM SA-Ala. An X(G/C)(G/C)X motif, where X is any base, is necessary and sufficient for MTM binding to DNA, without a strong dependence on DNA conformation. These recognition rules will aid in mapping MTM sites across different promoters towards development of MTM analogues as useful anticancer agents.

  14. Bethe Ansatz Solutions of the Bose-Hubbard Dimer

    Jon Links


    Full Text Available The Bose-Hubbard dimer Hamiltonian is a simple yet effective model for describing tunneling phenomena of Bose-Einstein condensates. One of the significant mathematical properties of the model is that it can be exactly solved by Bethe ansatz methods. Here we review the known exact solutions, highlighting the contributions of V.B. Kuznetsov to this field. Two of the exact solutions arise in the context of the Quantum Inverse Scattering Method, while the third solution uses a differential operator realisation of the su(2 Lie algebra.

  15. Bis(triphenylphosphine)silver(i) perrhenate, a cyclic dimer.

    Deiser, F; Kraus, F; Schmidbaur, H


    The 1 : 4 and 1 : 2 complexes of silver perrhenate and triphenylphosphine, [(Ph3P)4Ag](+) ReO4(-) and [(Ph3P)2AgReO4]2, have been prepared and their structures determined in the solid state by X-ray diffraction. The former is composed of independent ions, while in the latter the ions are aggregated into cyclic dimers. The silver centers are tetracoordinated including contact with two bridging perrhenate anions, setting this structure apart from that of its gold analogue [(Ph3P)2Au](+) ReO4(-) where the gold centers are strictly two-coordinate.

  16. It takes two to flirt with a dimeric RNase.

    D'Alessio, Giuseppe


    In my long RNase-life-time I have had the fortune to entertain with Lelio Mazzarella what I have called special interactions, which not only advanced my knowledge of proteins but also gave pleasure, as one obtains by reading a beautiful book, an inspiring poem, or watching a very good movie. In this article, I recall the more than 30-year long story of these interactions in which "it took two," a structural biologist with his coworkers and a biochemist with his coworkers, to flirt with an unusual, dimeric RNase.

  17. Novel modulated Hexatic Phases in Symmetric Liquid Crystal Dimers

    Date, R; Luckhurst, G.; Shuman, M.; Seddon, J


    Homologues of the dimeric α,ω-bis(4-n-alkylanilinebenzylidene-4'-oxy)alkanes (m.OnO.m) have been synthesised with spacer lengths n ranging from 9 to 12 methylene units and with terminal alkyl chain lengths m of 10, 12 and 14. Characterisation of these materials has been carried out by X-ray diffraction, differential scanning calorimetry and optical microscopy. In six of these compounds a novel modulated tilted hexatic phase, denoted S1, has been identified, in which the smectic layers have a ...

  18. Multiple gold-dimer detection from large scattering background

    Hong, Xin; Jin, Zheng


    Gold nanoparticles exhibit unique plasmonic optical properties in visible to near infrared band. Especially the coupling effect existing at the gap between a closely linked particle pair can make the local field strongly enhanced. These properties make gold particles more attractive to be employed as molecular probes in biomedical related fundamental and clinical researches. However in the bio-system exist many large molecules or groups, whose optical signals can strongly depress the gold particles without detectable. In this paper, we proposed a method to extract the targets which are labelled by gold dimer pairs from large scattering background.

  19. Structure of dimeric, recombinant Sulfolobus solfataricus phosphoribosyl diphosphate synthase

    Andersen, Rune W.; Lo Leggio, Leila; Hove-Jensen, Bjarne


    The enzyme 5-phosphoribosyl-1-α-diphosphate (PRPP) synthase (EC catalyses the Mg2+-dependent transfer of a diphosphoryl group from ATP to the C1 hydroxyl group of ribose 5-phosphate resulting in the production of PRPP and AMP. A nucleotide sequence specifying Sulfolobus solfataricus PRPP...... PRPP synthase as a search model. The two amino acid sequences share 35 % identity. The resulting asymmetric unit consists of three separated dimers. The protein was co-crystallised in the presence of AMP and ribose 5-phosphate, but in the electron density map of the active site only AMP and a sulphate...

  20. On the integrability of PT-symmetric dimers

    Pickton, J


    The coupled discrete linear and Kerr nonlinear Schrodinger equations with gain and loss describing transport on dimers with parity-time (PT) symmetric potentials are considered. The model is relevant among others to experiments in optical couplers and proposals on Bose-Einstein condensates in PT symmetric double-well potentials. It is shown that the models are integrable. A pendulum equation with a linear potential and a constant force for the phase-difference between the fields is obtained, which explains the presence of unbounded solutions above a critical threshold parameter.

  1. Transport properties of a ladder with two random dimer chains

    Hu Donng-Sheng; Zhu Chen-Ping; Zhang Yong-Mei


    We investigate the transport properties of a ladder with two random dimer (RD) chains. It is found that there are two extended states in the ladder with identical RD chains and a critical state regarded as an extended state in the ladder with pairing RD chains. Such a critical state is caused by the chiral symmetry. The ladder with identical RD chains can be decoupled into two isolated RD chains and the ladder with pairing RD chains can not. The analytic expressions of the extended states are presented for the ladder with identical RD chains.

  2. DNA melting properties of the dityrosine cross-linked dimer of Ribonuclease A.

    Dinda, Amit Kumar; Chattaraj, Saparya; Ghosh, Sudeshna; Tripathy, Debi Ranjan; Dasgupta, Swagata


    Several DNA binding proteins exist in dimeric form when bound with DNA to be able to exhibit various biological processes such as DNA repair, DNA replication and gene expression. Various dimeric forms of Ribonuclease A (RNase A) and other members of the ribonuclease A superfamily are endowed with a multitude of biological activities such as antitumor and antiviral activity. In the present study, we have compared the DNA binding properties between the RNase A monomer and the dityrosine (DT) cross-linked RNase A dimer, and checked the inhibitory effect of DNA on the ribonucleolytic activity of the dimeric protein. An agarose gel based assay shows that like the monomer, the dimer also binds with DNA. The number of nucleotides bound per monomer unit of the dimer is higher than the number of nucleotides that bind with the each monomer. From fluorescence measurements, the association constant (Ka) values for complexation of the monomer and the dimer with ct-DNA are (4.95±0.45)×10(4)M(-1) and (1.29±0.05)×10(6)M(-1) respectively. Binding constant (Kb) values for the binding of the monomer and the dimer with ct-DNA were determined using UV-vis spectroscopy and were found to be (4.96±1.67)×10(4)M(-1) and (4.32±0.31)×10(5)M(-1) respectively. Circular dichroism studies shows that the dimer possesses significant effect on DNA conformation. The melting profile for the ct-DNA-dimer indicated that the melting temperature (Tm) for the ct-DNA-dimer complex is lower compared to the ct-DNA-monomer complex. The ribonucleolytic activity of the dimer, like the monomer, diminishes upon binding with DNA.

  3. Dimeric boronates derived from the reaction of schiff bases and boronic acids

    Barba, Victor [Universidad Autonoma del Estado de Morelos, Cuernavaca, Morelos (Mexico). Centro de Investigaciones Quimicas; Santillan, Rosa; Farfan, Norberto [Instituto Politecnico Nacional (IPN), Mexico, D.F. (Mexico). Centro de Investigacion y de Estudios Avanzados. Dept. de Quimica]. E-mail:


    The one-pot synthesis of dimeric boron complexes is reported. The compounds were obtained by reaction of Schiff bases (tridentate ligands) with trans-{beta}-phenylvinylboronic acid, 3-thiopheneboronic acid and methylboronic acid. Building of the dimeric structures is favored by the presence of intramolecular N{yields}B coordination bonds, resulting in the formation of ten-membered ring heterocycles. An X-ray crystallographic analysis for one of them confirmed the dimeric nature of these compounds. (author)

  4. Circular dimers of a lambda DNA in infected, nonlysogenic Escherichia coli.

    Freifelder, D; Baran, N; Folkmanis, A; Freifelder, D L


    Covalently closed circular dimers of phage lambda DNA have been found in Escherichia coli infected with lambda. These dimers can be formed by either the lambda Red or Int systems, by a nonrecombinational replicative mechanism requiring the activity of the lambda O and P genes or by joining of the cohesive ends. Dimers mediated by the E. coli Rec system have not been observed. Those formed by the Int system often result from recombination between different DNA molecules; however, the Red-mediated dimers may be a result of replicative extension of a single DNA molecule. Trimers have also been observed but studied only briefly.

  5. Dimer and String Formation during Low Temperature Silicon Deposition on Si(100)

    Smith, A. P.; Jonsson, Hannes


    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....

  6. Radiation-induced tetramer-to-dimer transition of Escherichia coli lactose repressor

    Goffinont, S. [Centre de Biophysique Moleculaire, CNRS, rue C. Sadron, 45071 Orleans (France); Davidkova, M. [Department of Radiation Dosimetry, Nuclear Physics Institute AS CR, Na Truhlarce 39/64, 18086, Prague 8 (Czech Republic); Spotheim-Maurizot, M., E-mail: [Centre de Biophysique Moleculaire, CNRS, rue C. Sadron, 45071 Orleans (France)


    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 {gamma}-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.

  7. An Analytical Analysis of CDT Coupled to Dimer-like Matter

    Atkin, Max R


    We consider a model of restricted dimers coupled to two-dimensional causal dynamical triangulations (CDT), where the dimer configurations are restricted in the sense that they do not include dimers in regions of high curvature. It is shown how the model can be solved analytically using bijections with decorated trees. At a negative critical value for the dimer fugacity the model undergoes a phase transition at which the critical exponent associated to the geometry changes. This represents the first account of an analytical study of a matter model with two-dimensional interactions coupled to CDT.

  8. Dimerization of a flocculent protein from Moringa oleifera: experimental evidence and in silico interpretation.

    Pavankumar, Asalapuram R; Kayathri, Rajarathinam; Murugan, Natarajan A; Zhang, Qiong; Srivastava, Vaibhav; Okoli, Chuka; Bulone, Vincent; Rajarao, Gunaratna K; Ågren, Hans


    Many proteins exist in dimeric and other oligomeric forms to gain stability and functional advantages. In this study, the dimerization property of a coagulant protein (MO2.1) from Moringa oleifera seeds was addressed through laboratory experiments, protein-protein docking studies and binding free energy calculations. The structure of MO2.1 was predicted by homology modelling, while binding free energy and residues-distance profile analyses provided insight into the energetics and structural factors for dimer formation. Since the coagulation activities of the monomeric and dimeric forms of MO2.1 were comparable, it was concluded that oligomerization does not affect the biological activity of the protein.

  9. Experimental Observation of Strongly Bound Dimers of Sulfuric Acid: Application to Nucleation in the Atmosphere

    Petaja, Tuukka; Sipila, Mikko; Paasonen, Pauli


    Sulfuric acid is a key compound in atmospheric nucleation. Here we report on the observation of a close-to-collision-limited sulfuric acid dimer formation in atmospherically relevant laboratory conditions in the absence of measurable quantities of ammonia or organics. The observed dimer formation...... compound(s) with (a) concentration(s) high enough to prevent the dimer evaporation. Such a stabilizing compound should be abundant enough in any natural environment and would therefore not limit the formation of sulfuric acid dimers in the atmosphere....

  10. Solid-phase synthesis of 2{sup '}-O-methoxyethyl oligonucleotides using dimeric phosphoramidate blocks

    Yu, Gi Weon; Kang, Yong Han [Dept. of Applied Chemistry, Hanyang University, Ansan (Korea, Republic of)


    This research focused on the method of using dimeric phosphoramidite blocks to synthesize oligonucleotides for development as oligonucleotide drugs. A 16-mer oligonucleotide with the randomly selected sequence of C*C*T*C*G*C *T*C*T*C*G*C*C* C*G*C was synthesized using CC, GC, and TC dimers, a combination of monomers and dimers, or only monomers as building blocks. Using dimer blocks in this synthetic method provided a significant decrease in critical impurities that had similar properties to the main product, which was confirmed by LC-MS and HPLC analysis.

  11. Diagnostic implication of fibrin degradation products and D-dimer in aortic dissection

    Dong, Jian; Duan, Xianli; Feng, Rui; Zhao, Zhiqing; Feng, Xiang; Lu, Qingsheng; Jing, Qing; Zhou, Jian; Bao, Junmin; Jing, Zaiping


    Fibrin degradation products (FDP) and D-dimer have been considered to be involved in many vascular diseases. In this study we aimed to explore the diagnostic implication of FDP and D-dimer in aortic dissection patients. 202 aortic dissection patients were collected as the case group, 150 patients with other cardiovascular diseases, including myocardial infarction (MI, n = 45), pulmonary infarction (n = 51) and abdominal aortic aneurysm (n = 54) were collected as non-dissection group, and 27 healthy people were in the blank control group. The FDP and D-dimer levels were detected with immune nephelometry. Logist regression analysis was performed to evaluate the influence of FDP and D-dimer for the aortic dissection patients. ROC curve was used to determine the diagnostic value of FDP and D-dimer. The FDP and D-dimer levels were significantly higher in aortic dissection patients than in non-dissection patients and the healthy controls. FDP and D-dimer were both the risk factors for patients with aortic dissection. From the ROC analysis, diagnostic value of FDP and D-dimer were not high to distinguish aortic dissection patients from the non-dissection patients. However FDP and D-dimer could be valuable diagnostic marker to differentiate aortic dissection patients and healthy controls with both AUC 0.863. PMID:28262748

  12. Vortexlike topological defects in nematic colloids: chiral colloidal dimers and 2D crystals.

    Tkalec, U; Ravnik, M; Zumer, S; Musevic, I


    We show that chiral ordering of the underlying complex fluid strongly influences defect formation and colloidal interactions. Nonsingular defect loops with a topological charge -2 are observed, with a cross section identical to hyperbolic vortices in magnetic systems. These loops are binding spontaneously formed pairs of colloidal particles and dimers, which are chiral objects. Chiral dimer-dimer interaction weakly depends on the chirality of dimers and leads to the assembly of 2D nematic colloidal crystals of pure or "mixed" chirality, intercalated with a lattice of nonsingular vortexlike defects.

  13. Brug af D-dimer til at udelukke dyb venøs trombose i overekstremiteterne

    Ahler-Toftehøj, Hans-Ulrik; Mikkelsen, Peter


    D-dimer is often used to exclude deep venous thrombosis, primarily in the lower extremities. We describe a 38-year-old man who had deep venous thrombosis in the left vena subclavia in spite of a normal D-dimer. Only one inconclusive survey compares the value of D-dimer and upper extremity deep...... venous thrombosis. We conclude that where deep venous thrombosis of the upper extremities is suspected, you cannot rely on the D-dimer value, but should examine the patient using other modalities such as colour Doppler ultrasound. Udgivelsesdato: 2009-Sep...

  14. Cooperative binding mode of the inhibitors of R6K replication, pi dimers.

    Bowers, Lisa M; Filutowicz, Marcin


    The replication initiator protein, pi, plays an essential role in the initiation of plasmid R6K replication. Both monomers and dimers of pi bind to iterons in the gamma origin of plasmid R6K, yet monomers facilitate open complex formation, while dimers, the predominant form in the cell, do not. Consequently, pi monomers activate replication, while pi dimers inhibit replication. Recently, it was shown that the monomeric form of pi binds multiple tandem iterons in a strongly cooperative fashion, which might explain how monomers outcompete dimers for replication initiation when plasmid copy number and pi supply are low. Here, we examine cooperative binding of pi dimers and explore the role that these interactions may have in the inactivation of gamma origin. To examine pi dimer/iteron interactions in the absence of competing pi monomer/iteron interactions using wild-type pi, constructs were made with key base changes to each iteron that eliminate pi monomer binding yet have no impact on pi dimer binding. Our results indicate that, in the absence of pi monomers, pi dimers bind with greater cooperativity to alternate iterons than to adjacent iterons, thus preferentially leaving intervening iterons unbound and the origin unsaturated. We discuss new insights into plasmid replication control by pi dimers.

  15. High performance absorber structure using subwavelength multi-branch dimers

    He, Kebo; Su, Guangyao; Liu, Chuanhong; Gou, Fangwang; Zhang, Zhaoyu


    As the desire growing of the thin film absorption structure for various sub-wavelength applications such as photo detector, thin-film thermal emitters, thermo photovoltaic cells, and multi-color filters, we proposed a type of subwavelength multi-branch dimers which exhibit several tunable dipole-dipole-like plasmonic resonances and integrated it into metal-insulator-metal structure as the top layer. The structures are studied through numerical calculation by finite element method. When normal incident is considered, the novel structure shows three absorption peaks in the considered wavelength range. One peak has near-perfect absorption and the other two also show excellent absorption.. When different angle oblique incident is considered, the absorption only has slight change, which is useful to an ultrathin absorber structure. In addition, we find that the thickness of the dielectric layer can tune the absorption rates for each absorption peak. In general, the multi-branch dimers can easily tune its absorption rates and spectrum via the change of their geometric parameters such as branch lengths, branch angles, and dielectric layer thickness.

  16. Condensin Smc2-Smc4 Dimers Are Flexible and Dynamic.

    Eeftens, Jorine M; Katan, Allard J; Kschonsak, Marc; Hassler, Markus; de Wilde, Liza; Dief, Essam M; Haering, Christian H; Dekker, Cees


    Structural maintenance of chromosomes (SMC) protein complexes, including cohesin and condensin, play key roles in the regulation of higher-order chromosome organization. Even though SMC proteins are thought to mechanistically determine the function of the complexes, their native conformations and dynamics have remained unclear. Here, we probe the topology of Smc2-Smc4 dimers of the S. cerevisiae condensin complex with high-speed atomic force microscopy (AFM) in liquid. We show that the Smc2-Smc4 coiled coils are highly flexible polymers with a persistence length of only ∼ 4 nm. Moreover, we demonstrate that the SMC dimers can adopt various architectures that interconvert dynamically over time, and we find that the SMC head domains engage not only with each other, but also with the hinge domain situated at the other end of the ∼ 45-nm-long coiled coil. Our findings reveal structural properties that provide insights into the molecular mechanics of condensin complexes. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  17. [Retarded excision of pyrimidine dimers in human unstimulated lymphocytes].

    Snopov, S A; Roza, L; de Gruijl, F R


    Using immuno-labelling of cyclobutane pyrimidine dimers (CPDs) in nuclei of peripheral lymphocytes after their UVC-irradiation and cultivation, we have found that within the first four hours of cultivation the CPD-specific fluorescent signal from cell nuclei increased. Earlier, a similar increase in binding of antibody specific for pyrimidine (6-4) pyrimidone photoproducts to undenatured DNA isolated from UV-irradiated Chinese hamster ovary cells was reported (Mitchell et al., 1986). Our experiments showed that nucleotide excision repair enzyme might induce such of DNA modification in lymphocyte nuclei that increased specific antibody binding to DNA fragments with lesions. We suggest that enzymatic formation of open structures in DNA predominated qualitatively over dual-incision and excision of these fragments, and resulted in the enhanced exposure of the pyrimidine dimers in nuclei to specific antibodies. The results evidence that nucleotid excision repair in unstimualted human lymphocytes being deficient in dual incision and removal of UV-induced DNA lesions appear to be capable of performing chromatin relaxation and pre-incision uncoiling of DNA fragments with lesions.

  18. Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes

    Arakawa Kazuharu


    Full Text Available Abstract Background During the replication process of bacteria with circular chromosomes, an odd number of homologous recombination events results in concatenated dimer chromosomes that cannot be partitioned into daughter cells. However, many bacteria harbor a conserved dimer resolution machinery consisting of one or two tyrosine recombinases, XerC and XerD, and their 28-bp target site, dif. Results To study the evolution of the dif/XerCD system and its relationship with replication termination, we report the comprehensive prediction of dif sequences in silico using a phylogenetic prediction approach based on iterated hidden Markov modeling. Using this method, dif sites were identified in 641 organisms among 16 phyla, with a 97.64% identification rate for single-chromosome strains. The dif sequence positions were shown to be strongly correlated with the GC skew shift-point that is induced by replicational mutation/selection pressures, but the difference in the positions of the predicted dif sites and the GC skew shift-points did not correlate with the degree of replicational mutation/selection pressures. Conclusions The sequence of dif sites is widely conserved among many bacterial phyla, and they can be computationally identified using our method. The lack of correlation between dif position and the degree of GC skew suggests that replication termination does not occur strictly at dif sites.

  19. Ankyrin-G Inhibits Endocytosis of Cadherin Dimers.

    Cadwell, Chantel M; Jenkins, Paul M; Bennett, Vann; Kowalczyk, Andrew P


    Dynamic regulation of endothelial cell adhesion is central to vascular development and maintenance. Furthermore, altered endothelial adhesion is implicated in numerous diseases. Therefore, normal vascular patterning and maintenance require tight regulation of endothelial cell adhesion dynamics. However, the mechanisms that control junctional plasticity are not fully understood. Vascular endothelial cadherin (VE-cadherin) is an adhesive protein found in adherens junctions of endothelial cells. VE-cadherin mediates adhesion through trans interactions formed by its extracellular domain. Trans binding is followed by cis interactions that laterally cluster the cadherin in junctions. VE-cadherin is linked to the actin cytoskeleton through cytoplasmic interactions with β- and α-catenin, which serve to increase adhesive strength. Furthermore, p120-catenin binds to the cytoplasmic tail of cadherin and stabilizes it at the plasma membrane. Here we report that induced cis dimerization of VE-cadherin inhibits endocytosis independent of both p120 binding and trans interactions. However, we find that ankyrin-G, a protein that links membrane proteins to the spectrin-actin cytoskeleton, associates with VE-cadherin and inhibits its endocytosis. Ankyrin-G inhibits VE-cadherin endocytosis independent of p120 binding. We propose a model in which ankyrin-G associates with and inhibits the endocytosis of VE-cadherin cis dimers. Our findings support a novel mechanism for regulation of VE-cadherin endocytosis through ankyrin association with cadherin engaged in lateral interactions.

  20. Dimerization of a Viral SET Protein Endows its Function

    H Wei; M Zhou


    Histone modifications are regarded as the most indispensible phenomena in epigenetics. Of these modifications, lysine methylation is of the greatest complexity and importance as site- and state-specific lysine methylation exerts a plethora of effects on chromatin structure and gene transcription. Notably, paramecium bursaria chlorella viruses encode a conserved SET domain methyltransferase, termed vSET, that functions to suppress host transcription by methylating histone H3 at lysine 27 (H3K27), a mark for eukaryotic gene silencing. Unlike mammalian lysine methyltransferases (KMTs), vSET functions only as a dimer, but the underlying mechanism has remained elusive. In this study, we demonstrate that dimeric vSET operates with negative cooperativity between the two active sites and engages in H3K27 methylation one site at a time. New atomic structures of vSET in the free form and a ternary complex with S-adenosyl homocysteine and a histone H3 peptide and biochemical analyses reveal the molecular origin for the negative cooperativity and explain the substrate specificity of H3K27 methyltransferases. Our study suggests a 'walking' mechanism, by which vSET acts all by itself to globally methylate host H3K27, which is accomplished by the mammalian EZH2 KMT only in the context of the Polycomb repressive complex.

  1. Proteolysis of truncated hemolysin A yields a stable dimerization interface

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


    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.

  2. Dimerization deficiency of enigmatic retinitis pigmentosa-linked rhodopsin mutants

    Ploier, Birgit; Caro, Lydia N.; Morizumi, Takefumi; Pandey, Kalpana; Pearring, Jillian N.; Goren, Michael A.; Finnemann, Silvia C.; Graumann, Johannes; Arshavsky, Vadim Y.; Dittman, Jeremy S.; Ernst, Oliver P.; Menon, Anant K.


    Retinitis pigmentosa (RP) is a blinding disease often associated with mutations in rhodopsin, a light-sensing G protein-coupled receptor and phospholipid scramblase. Most RP-associated mutations affect rhodopsin's activity or transport to disc membranes. Intriguingly, some mutations produce apparently normal rhodopsins that nevertheless cause disease. Here we show that three such enigmatic mutations--F45L, V209M and F220C--yield fully functional visual pigments that bind the 11-cis retinal chromophore, activate the G protein transducin, traffic to the light-sensitive photoreceptor compartment and scramble phospholipids. However, tests of scramblase activity show that unlike wild-type rhodopsin that functionally reconstitutes into liposomes as dimers or multimers, F45L, V209M and F220C rhodopsins behave as monomers. This result was confirmed in pull-down experiments. Our data suggest that the photoreceptor pathology associated with expression of these enigmatic RP-associated pigments arises from their unexpected inability to dimerize via transmembrane helices 1 and 5.

  3. DNA targeting and cleavage by an engineered metalloprotein dimer.

    Wong-Deyrup, Siu Wah; Prasannan, Charulata; Dupureur, Cynthia M; Franklin, Sonya J


    Nature has illustrated through numerous examples that protein dimerization has structural and functional advantages. We previously reported the design and characterization of an engineered "metallohomeodomain" protein (C2) based on a chimera of the EF-hand Ca-binding motif and the helix-turn-helix motif of homeodomains (Lim and Franklin in Protein Sci. 15:2159-2165, 2004). This small metalloprotein binds the hard metal ions Ca(II) and Ln(III) and interacts with DNA with modest sequence preference and affinity, yet exhibits only residual DNA cleavage activity. Here we have achieved substantial improvement in function by constructing a covalent dimer of this C2 module (F2) to create a larger multidomain protein. As assayed via fluorescence spectroscopy, this F2 protein binds Ca(II) more avidly (25-fold) than C2 on a per-domain basis; in gel shift selection experiments, metallated F2 exhibits a specificity toward 5'-TAATTA-3' sequences. Finally, Ca(2)F2 cleaves plasmid DNA and generates a linear product in a Ca(II)-dependent way, unlike the CaC2 monomer. To the best of our knowledge this activation of Ca(II) in the context of an EF-hand binding motif is unique and represents a significant step forward in the design of artificial metallonucleases by utilizing biologically significant metal ions.

  4. Ionization satellites of the ArHe dimer

    Miteva, Tsveta; Klaiman, Shachar; Gokhberg, Kirill [Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 229, D-69120 Heidelberg (Germany); Gromov, Evgeniy V., E-mail: [Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 229, D-69120 Heidelberg (Germany); Laboratory of Quantum Chemistry, Computer Center, Irkutsk State University, K. Marks 1, 664003 Irkutsk (Russian Federation)


    Ionization satellites are key ingredients in the control of post ionization processes such as molecular dissociation and interatomic Coulombic decay. Here, using the high-level ab initio method of multi-reference configuration interaction up to triple excitations, we study the potential energy curves (PECs) of the ionization satellites of the ArHe dimer. With this model system, we demonstrate that the simple model used in alkaline earth metal and rare gas complexes to describe the satellites as a Rydberg electron moving on top of a dicationic core does not fully hold for the rare gas clusters. The more complex valence structure in the rare gas atom leads to the mixing of different electronic configurations of the dimer. This prevents one from assigning a single dicationic parent state to some of the ionization satellites. We further analyze the structure of the different PECs, demonstrating how the density of the Rydberg electron is reflected in the structure of the PEC wherever the simple model is applicable.

  5. Structure of dimeric, recombinant Sulfolobus solfataricus phosphoribosyl diphosphate synthase: a bent dimer defining the adenine specificity of the substrate ATP.

    Andersen, Rune W; Leggio, Leila Lo; Hove-Jensen, Bjarne; Kadziola, Anders


    The enzyme 5-phosphoribosyl-1-α-diphosphate (PRPP) synthase (EC catalyses the Mg(2+)-dependent transfer of a diphosphoryl group from ATP to the C1 hydroxyl group of ribose 5-phosphate resulting in the production of PRPP and AMP. A nucleotide sequence specifying Sulfolobus solfataricus PRPP synthase was synthesised in vitro with optimised codon usage for expression in Escherichia coli. Following expression of the gene in E. coli PRPP synthase was purified by heat treatment and ammonium sulphate precipitation and the structure of S. solfataricus PRPP synthase was determined at 2.8 Å resolution. A bent dimer oligomerisation was revealed, which seems to be an abundant feature among PRPP synthases for defining the adenine specificity of the substrate ATP. Molecular replacement was used to determine the S. solfataricus PRPP synthase structure with a monomer subunit of Methanocaldococcus jannaschii PRPP synthase as a search model. The two amino acid sequences share 35 % identity. The resulting asymmetric unit consists of three separated dimers. The protein was co-crystallised in the presence of AMP and ribose 5-phosphate, but in the electron density map of the active site only AMP and a sulphate ion were observed. Sulphate ion, reminiscent of the ammonium sulphate precipitation step of the purification, seems to bind tightly and, therefore, presumably occupies and blocks the ribose 5-phosphate binding site. The activity of S. solfataricus PRPP synthase is independent of phosphate ion.

  6. Trans-dimerization of JAM-A regulates Rap2 and is mediated by a domain that is distinct from the cis-dimerization interface.

    Monteiro, Ana C; Luissint, Anny-Claude; Sumagin, Ronen; Lai, Caroline; Vielmuth, Franziska; Wolf, Mattie F; Laur, Oskar; Reiss, Kerstin; Spindler, Volker; Stehle, Thilo; Dermody, Terence S; Nusrat, Asma; Parkos, Charles A


    Junctional adhesion molecule-A (JAM-A) is a tight junction-associated signaling protein that regulates epithelial cell proliferation, migration, and barrier function. JAM-A dimerization on a common cell surface (in cis) has been shown to regulate cell migration, and evidence suggests that JAM-A may form homodimers between cells (in trans). Indeed, transfection experiments revealed accumulation of JAM-A at sites between transfected cells, which was lost in cells expressing cis- or predicted trans-dimerization null mutants. Of importance, microspheres coated with JAM-A containing alanine substitutions to residues 43NNP45 (NNP-JAM-A) within the predicted trans-dimerization site did not aggregate. In contrast, beads coated with cis-null JAM-A demonstrated enhanced clustering similar to that observed with wild-type (WT) JAM-A. In addition, atomic force microscopy revealed decreased association forces in NNP-JAM-A compared with WT and cis-null JAM-A. Assessment of effects of JAM-A dimerization on cell signaling revealed that expression of trans- but not cis-null JAM-A mutants decreased Rap2 activity. Furthermore, confluent cells, which enable trans-dimerization, had enhanced Rap2 activity. Taken together, these results suggest that trans-dimerization of JAM-A occurs at a unique site and with different affinity compared with dimerization in cis. Trans-dimerization of JAM-A may thus act as a barrier-inducing molecular switch that is activated when cells become confluent.

  7. Elevated d-dimer cut-off values for computed tomography pulmonary angiography—d-dimer correlates with location of embolism

    Kubak, Mateuzs Piotr; Borthne, Arne; Ruud, Espen Asak; Ashraf, Haseem


    Background Acute pulmonary embolism (APE) is a potentially fatal condition, and making a timely diagnosis can be challenging. Computed tomography pulmonary angiography (CTPA) has become the modality of choice, and this contributes to the increasing load on emergency room CT scanners. Our purpose was to investigate whether an elevated d-dimer cut-off could reduce the demand for CTPA while maintaining a high sensitivity and negative predictive value (NPV). Methods We retrospectively reviewed all patients referred for CTPA with suspicion of APE in 2012, and collected d-dimer values and CTPA results. We investigated the diagnostic performance of d-dimer using a 0.5 mg/L cut-off and an age adjusted cut-off. We also evaluated a new and elevated cut-off. Cases were categorized according to their CTPA result into: no embolism, peripheral embolism, lobar embolism and central embolism. Finally we investigated a possible correlation between d-dimer values and location of embolism. Results We included 1,051 CTPAs, from which 216 (21%) showed pulmonary embolism. There were concomitant d-dimer analyses in 822 CTPA examinations. The current 0.5 mg/L cut-off achieved a sensitivity and NPV of 99%. The age-adjusted cut-off achieved a sensitivity and NPV of 98%, and our suggested cut-off of 0.9 mg/L achieved a sensitivity and NPV of 97%. Conclusions We conclude that the elevated d-dimer cut-off of 0.9 mg/L achieved a high sensitivity and NPV, while reducing the number of CTPA by 27%. The correlation between d-dimer values and location of embolisms supports the suggestion of an elevated d-dimer value. PMID:27386486

  8. Anti-parallel dimer and tetramer formation of propylene carbonate

    Ayana Tagawa


    Full Text Available Raman scattering and infrared (IR absorption spectra of enantiopure (R-propylene carbonate ((RPC and racemic propylene carbonate (PC were recorded at room temperature, 25 °C, in benzene (Bz solution and in the pure liquid state to investigate the presence of dimers and other higher order intermolecular associations. (RPC and PC both demonstrated a strong C=O stretching vibrational band. The band exhibited changes in its shape and resonance wavenumber highly dependent on the concentrations of PCs, whereas a difference between the chirality of (RPC and PC had little influence. In an extremely dilute condition, doubly split bands were observed at 1807 and 1820 cm-1 in both Raman and IR spectra, which are assigned to the characteristic bands of isolated monomeric PCs. An additional band appeared at 1795 cm-1 in a dilute to concentrated regime, and its magnitude strengthened with increasing concentrations accompanied with slight increasing in the magnitude of 1807 cm-1 band in Raman spectra, while an increase in the magnitude of 1807 cm-1 band was clearly greater than that of 1795 cm-1 band in IR spectra. The spectrum changes at 1795 and 1807 cm-1 were attributed to characteristics of anti-parallel dimer formation of PCs caused by strong dipole-dipole interactions between C=O groups. Moreover, another additional signal was clearly observed at 1780-1790 cm-1 in a concentrated regime, and became the primary signal in the pure liquid state with slight increasing in the intensity of 1795 cm-1 band in Raman spectra. On the other hand, in IR spectra the observed increasing of 1780-1790 cm-1 band was much less than that of 1795 cm-1 band. These newly found spectrum changes in the concentrated regime are attributed to the formation of anti-parallel tetramers of PCs based on the characteristics of band selection rule found in Raman and IR spectra. Equilibrium constants for the anti-parallel dimer (KD and tetramer formation (KT of PCs in Bz solution and in

  9. Multi-Component Protein - Protein Docking Based Protocol with External Scoring for Modeling Dimers of G Protein-Coupled Receptors.

    Kaczor, Agnieszka A; Guixà-González, Ramon; Carrió, Pau; Poso, Antti; Dove, Stefan; Pastor, Manuel; Selent, Jana


    In order to apply structure-based drug design techniques to GPCR complexes, it is essential to model their 3D structure. For this purpose, a multi-component protocol was derived based on protein-protein docking which generates populations of dimers compatible with membrane integration, considering all reasonable interfaces. At the next stage, we applied a scoring procedure based on up to eleven different parameters including shape or electrostatics complementarity. Two methods of consensus scoring were performed: (i) average scores of 100 best scored dimers with respect to each interface, and (ii) frequencies of interfaces among 100 best scored dimers. In general, our multi-component protocol gives correct indications for dimer interfaces that have been observed in X-ray crystal structures of GPCR dimers (opsin dimer, chemokine CXCR4 and CCR5 dimers, κ opioid receptor dimer, β1 adrenergic receptor dimer and smoothened receptor dimer) but also suggests alternative dimerization interfaces. Interestingly, at times these alternative interfaces are scored higher than the experimentally observed ones suggesting them to be also relevant in the life cycle of studied GPCR dimers. Further results indicate that GPCR dimer and higher-order oligomer formation may involve transmembrane helices (TMs) TM1-TM2-TM7, TM3-TM4-TM5 or TM4-TM5-TM6 but not TM1-TM2-TM3 or TM2-TM3-TM4 which is in general agreement with available experimental and computational data.

  10. A Model for Dimerization of the SOX Group E Transcription Factor Family.

    Ramsook, Sarah N; Ni, Joyce; Shahangian, Shokofeh; Vakiloroayaei, Ana; Khan, Naveen; Kwan, Jamie J; Donaldson, Logan W


    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.

  11. Genetic predictors of fibrin D-dimer levels in healthy adults

    N.L. Smith (Nicholas); J.E. Huffman (Jennifer E.); D.P. Strachan (David); J. Huang (Jian); A. Dehghan (Abbas); S. Trompet (Stella); L.M. Lopez (Lorna M.); S.Y. Shin (So Youn); J. Baumert (Jens); V. Vitart (Veronique); J.C. Bis (Joshua); S.H. Wild (Sarah); A. Rumley (Ann); Q. Yang (Qiong Fang); A.G. Uitterlinden (André); D.J. Stott (David. J.); G. Davies (Gareth); A.M. Carter (Angela M.); B. Thorand (Barbara); O. Polašek (Ozren); B. McKnight (Barbara); H. Campbell (Harry); A.R. Rudnicka (Alicja); M.H. Chen (Min-hsin); B.M. Buckley (Brendan M.); S.E. Harris (Sarah); A. Peters (Annette); D. Pulanic (Drazen); T. Lumley (Thomas); A.J.M. de Craen (Anton J.M.); D.C. Liewald (David C.); C. Gieger (Christian); I. Ford (Ian); A.J. Gow (Alan J.); M. Luciano (Michelle); D.J. Porteous (David J.); X. Guo (Xiuqing); N. Sattar (Naveed); A. Tenesa (Albert); M. Cushman (Mary Ann); P.E. Slagboom (Eline); P.M. Visscher (Peter M.); T.D. Spector (Tim); T. Illig (Thomas); I. Rudan (Igor); E.G. Bovill (Edwin G.); A.F. Wright (Alan); W.L. McArdle (Wendy); G.H. Tofler (Geoffrey); A. Hofman (Albert); R.G.J. Westendorp (Rudi); J.M. Starr (John); P.J. Grant (Peter J.); M. Karakas (Mahir); N.D. Hastie (Nicholas D.); B.M. Psaty (Bruce); J.F. Wilson (James); G.D.O. Lowe (Gordon); C.J. O'Donnell (Christopher); J.C.M. Witteman (Jacqueline); J.W. Jukema (Jan Wouter); I.J. Deary (Ian); N. Soranzo (Nicole); W. Koenig (Wolfgang); C. Hayward (Caroline)


    textabstractBACKGROUND: Fibrin fragment D-dimer, one of several peptides produced when crosslinked fibrin is degraded by plasmin, is the most widely used clinical marker of activated blood coagulation. To identity genetic loci influencing D-dimer levels, we performed the first large-scale, genome-wi

  12. D-dimer concentration outliers are not rare in at-term pregnant women.

    Wang, Yu; Gao, Jie; Du, Juan


    To determine the D-dimer levels in pregnant women at term and the differences between pregnant women with different D-dimer levels. The plasma D-dimer concentrations in pregnant women at term were identified in a cross-sectional study. The clinical indicators that are potentially relevant to D-dimer levels were compared between the pregnant women with different D-dimer levels (i.e., normal, mildly increased, and severely increased). There were always some D-dimer concentration outliers in the pregnant women at term regardless of the presence or absence of complications, and there were no significant differences in maternal age, gestational age, gravidity, parity, blood count, blood coagulation, or liver function between the pregnant women with different D-dimer levels. D-dimer levels may vary significantly during pregnancy for unknown reasons. This variation, particularly in pregnant women at term, might lead to questionable diagnostic information regarding coagulation. Copyright © 2016 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  13. Evidence for the dimerization-mediated catalysis of methionine sulfoxide reductase A from Clostridium oremlandii.

    Lee, Eun Hye; Lee, Kitaik; Kwak, Geun-Hee; Park, Yeon Seung; Lee, Kong-Joo; Hwang, Kwang Yeon; Kim, Hwa-Young


    Clostridium oremlandii MsrA (CoMsrA) is a natively selenocysteine-containing methionine-S-sulfoxide reductase and classified into a 1-Cys type MsrA. CoMsrA exists as a monomer in solution. Herein, we report evidence that CoMsrA can undergo homodimerization during catalysis. The monomeric CoMsrA dimerizes in the presence of its substrate methionine sulfoxide via an intermolecular disulfide bond between catalytic Cys16 residues. The dimeric CoMsrA is resolved by the reductant glutaredoxin, suggesting the relevance of dimerization in catalysis. The dimerization reaction occurs in a concentration- and time-dependent manner. In addition, the occurrence of homodimer formation in the native selenoprotein CoMsrA is confirmed. We also determine the crystal structure of the dimeric CoMsrA, having the dimer interface around the two catalytic Cys16 residues. A central cone-shaped hole is present in the surface model of dimeric structure, and the two Cys16 residues constitute the base of the hole. Collectively, our biochemical and structural analyses suggest a novel dimerization-mediated mechanism for CoMsrA catalysis that is additionally involved in CoMsrA regeneration by glutaredoxin.

  14. Variations in the heterogeneity of the decay of the fluorescence in six procyanidin dimers

    Donghwan Cho; Rujiang Tian; Lawrence J. Porter; Richard W. Hemingway; Wayne L. Mattice


    The decay of the fluorescence has been measured in 1,4-dioxane for six dimers of (2R,3R)-(-)-epicatechin and (2R,3S)-(+)-catechin, hereafter denoted simply epicatechin and catechin. The dimers are epicatechin-(4β→8)-catechin, epicatechin-(4β→8)-epicatechin...

  15. Random sampling for the monomer-dimer model on a lattice

    J. van den Berg (Rob); R.M. Brouwer (Rachel)


    textabstractIn the monomer-dimer model on a graph, each matching (collection of non-overlapping edges) ${M$ has a probability proportional to $lambda^{|M|$, where $lambda > 0$ is the model parameter, and $|M|$ denotes the number of edges in $M$. An approximate random sample from the monomer-dimer

  16. Synchronized oscillations of dimers in biphasic charged fd-virus suspensions

    Kang, K.; Piao, S. H.; Choi, H. J.


    Micron-sized colloidal spheres that are dispersed in an isotropic-nematic biphasic host suspension of charged rods (fd-virus particles) are shown to spontaneously form dimers, which exhibit a synchronized oscillatory motion. Dimer formation is not observed in the monophase of isotropic and nematic suspensions. The synchronized oscillations of dimers are connected to the inhomogeneous state of the host suspension of charged rods (fd viruses) where nematic domains are in coexistence with isotropic regions. The synchronization of oscillations occurs in bulk states, in the absence of an external field. With a low field strength of an applied electric field, the synchronization is rather reduced, but it recovers again when the field is turned off. In this Rapid Communication, we report this observation as an example of the strange attractor, occurring in the mixture of PS (polystyrene) dimers in an isotropic-nematic coexistence biphasic fd-virus network. Furthermore, we highlight that the synchronization of PS-dimer oscillations is the result of a global bifurcation diagram, driven by a delicate balance between the short-attractive "twisted" interaction of PS dimers and long-ranged electrostatic repulsive interactions of charged fd rods. The interest is then in the local enhancement of "twist-nematic" elasticity in reorientation of the dimer oscillations. An analysis of image-time correlations is provided with the data movies and Fourier transforms of averaged orientations for the synchronized oscillations of dimers in the biphasic I -N coexistence concentration of charged fd-virus suspensions.

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

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


    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...

  18. The intrinsically disordered RNR inhibitor Sml1 is a dynamic dimer

    Danielsson, Jens; Liljedahl, Leena; Ba´ra´ny-Wallje, Elsa


    . Sml1 belongs to the class of intrinsically disordered proteins with a high degree of dynamics and very little stable structure. Earlier suggestions for a dimeric structure of Sml1 were confirmed, and from translation diffusion NMR measurements, a dimerization dissociation constant of 0.1 mM at 4...... natively disordered proteins....

  19. DFT molecular simulations of solvated glucose dimers: explicit vs. implicit water

    The behavior of Glucose dimers in solution is investigated at the DFT level of theory via optimization and constant energy DFT molecular dynamics. The effect of the solvent on the dimer is treated two different ways: using the implicit solvation method COSMO alone to treat the bulk water behavior an...

  20. Dimer interface of bovine cytochrome c oxidase is influenced by local posttranslational modifications and lipid binding.

    Liko, Idlir; Degiacomi, Matteo T; Mohammed, Shabaz; Yoshikawa, Shinya; Schmidt, Carla; Robinson, Carol V


    Bovine cytochrome c oxidase is an integral membrane protein complex comprising 13 protein subunits and associated lipids. Dimerization of the complex has been proposed; however, definitive evidence for the dimer is lacking. We used advanced mass spectrometry methods to investigate the oligomeric state of cytochrome c oxidase and the potential role of lipids and posttranslational modifications in its subunit interfaces. Mass spectrometry of the intact protein complex revealed that both the monomer and the dimer are stabilized by large lipid entities. We identified these lipid species from the purified protein complex, thus implying that they interact specifically with the enzyme. We further identified phosphorylation and acetylation sites of cytochrome c oxidase, located in the peripheral subunits and in the dimer interface, respectively. Comparing our phosphorylation and acetylation sites with those found in previous studies of bovine, mouse, rat, and human cytochrome c oxidase, we found that whereas some acetylation sites within the dimer interface are conserved, suggesting a role for regulation and stabilization of the dimer, phosphorylation sites were less conserved and more transient. Our results therefore provide insights into the locations and interactions of lipids with acetylated residues within the dimer interface of this enzyme, and thereby contribute to a better understanding of its structure in the natural membrane. Moreover dimeric cytochrome c oxidase, comprising 20 transmembrane, six extramembrane subunits, and associated lipids, represents the largest integral membrane protein complex that has been transferred via electrospray intact into the gas phase of a mass spectrometer, representing a significant technological advance.

  1. Fourier transform infrared spectroscopy and theoretical study of dimethylamine dimer in the gas phase.

    Du, Lin; Kjaergaard, Henrik G


    Dimethylamine (DMA) has been studied by gas-phase Fourier transform infrared (FTIR) spectroscopy. We have identified a spectral transition that is assigned to the DMA dimer. The IR spectra of the dimer in the gas phase are obtained by spectral subtraction of spectra recorded at different pressures. The enthalpy of hydrogen bond formation was obtained for the DMA dimer by temperature-dependence measurements. We complement the experimental results with ab initio and anharmonic local mode model calculations of monomer and dimer. Compared to the monomer, our calculations show that in the dimer the N-H bond is elongated, and the NH-stretching fundamental shifts to a lower wavenumber. More importantly, the weak NH-stretching fundamental transition has a pronounced intensity increase upon complexation. However, the first NH-stretching overtone transition is not favored by the same intensity enhancement, and we do not observe the first NH-stretching overtone of the dimer. On the basis of the measured and calculated intensity of the NH-stretching transition of the dimer, the equilibrium constant for dimerization at room temperature was determined.

  2. Self-assembly of Asymmetric Dimer Particles in Supported Copolymer Bilayer

    Xiao-chun Qin; Chun-lai Ren


    Using self-consistent field and density functional theories, we investigate the self-assembly behavior of asymmetric dimer particles in a supported AB block copolymer bilayer. Asymmetric dimer particles are amphiphilic molecules composed by two different spheres. One prefers to A block of copolymers and the other likes B block when they are introduced into the copolymer bilayer. The two layer structure of the dimer particles is formed within the bilayer.Due to the presence of the substrate surface, the symmetry of the two leaflets of the bilayer is broken, which may lead to two different layer structures of dimer particles within each leaflet of the bilayer. With the increasing concentration of the asymmetric dimer particles,in-plane structure of the dimer particles undergoes sparse square, hexagonal, dense square, and cylindrical structures. In a further condensed packing, a bending cylindrical structure comes into being. Here we verify that the entropic effect of copolymers, the enthalpy of the system and the steric repulsion of the dimer particles are three important factors determing the self-assembly of dimer particles within the supported copolymer bilayer.

  3. Reversible Dimerization of Acid-Denatured ACBP Controlled by Helix A4

    Fieber, Wolfgang; Kragelund, Birthe Brandt; Meldal, Morten Peter;


    of dimers and revealed a cooperative stabilization of helix A4 in this process. This emphasizes its special role in the structure formation in the denatured state of ACBP. No dimers are formed in the presence of guanidine hydrochloride, which underlines the fundamental difference between the nature...

  4. Complexation of fisetin with novel cyclosophoroase dimer to improve solubility and bioavailability.

    Jeong, Daham; Choi, Jae Min; Choi, Youngjin; Jeong, Karpjoo; Cho, Eunae; Jung, Seunho


    Rhizobium species produce cyclosophoraose (Cys), which is an unbranched cyclic β-(1,2)-glucan. We synthesized novel cationic cyclosophoraose dimer (Cys dimer) and its structure was confirmed via NMR spectroscopy and MALDI-TOF mass spectrometry analysis. In this study, we investigated the complexation of hardly soluble drug fisetin (3,3',4',7-tetrahydroxyflavone) with Cys dimer to improve the solubility of fisetin, and its solubility was increased up to 6.5-fold. The solubility of fisetin with Cys dimer showed 2.4-fold better than with β-cyclodextrin. The fisetin-Cys dimer complex was characterized by using, phase solubility diagram, 2D NMR, FT-IR spectroscopy, SEM, DSC analysis and molecular modeling. Through the molecular docking simulations, complexation ability of fisetin with host molecules were in the following order: Cys dimer>Cys monomer>β-CD. The fisetin-Cys dimer complex showed also higher cytotoxicity to HeLa cells than free fisetin, indicating that the Cys dimer to improve bioavailability of fisetin. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. Evaluation of Serum D-dimer Levels in Children with Pneumonia

    Nilgün Selçuk Duru


    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

  6. Programmed dissociation of dimer and trimer origami structures by aptamer-ligand complexes.

    Wu, Na; Willner, Itamar


    Dimer- and trimer-origami frames are bridged by duplexes that include caged, sequence-specific, anti-ATP and/or anti-cocaine aptamer sequences. The programmed dissociation of the origami dimers or trimers in the presence of ATP and/or cocaine ligands is demonstrated. The processes are followed by AFM imaging and by electrophoretic experiments.

  7. Structure of the dimeric form of CTP synthase from Sulfolobus solfataricus

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


    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 c...

  8. In Situ Structural Characterization of Ferric Iron Dimers in Aqueous Solutions

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


    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 solutio...

  9. Genetic predictors of fibrin D-dimer levels in healthy adults

    N.L. Smith (Nicholas); J.E. Huffman (Jennifer E.); D.P. Strachan (David); J. Huang (Jian); A. Dehghan (Abbas); S. Trompet (Stella); L.M. Lopez (Lorna M.); S.Y. Shin (So Youn); J. Baumert (Jens); V. Vitart (Veronique); J.C. Bis (Joshua); S.H. Wild (Sarah); A. Rumley (Ann); Q. Yang (Qiong Fang); A.G. Uitterlinden (André); D.J. Stott (David. J.); G. Davies (Gareth); A.M. Carter (Angela M.); B. Thorand (Barbara); O. Polašek (Ozren); B. McKnight (Barbara); H. Campbell (Harry); A.R. Rudnicka (Alicja); M.H. Chen (Min-hsin); B.M. Buckley (Brendan M.); S.E. Harris (Sarah); A. Peters (Annette); D. Pulanic (Drazen); T. Lumley (Thomas); A.J.M. de Craen (Anton J.M.); D.C. Liewald (David C.); C. Gieger (Christian); I. Ford (Ian); A.J. Gow (Alan J.); M. Luciano (Michelle); D.J. Porteous (David J.); X. Guo (Xiuqing); N. Sattar (Naveed); A. Tenesa (Albert); M. Cushman (Mary Ann); P.E. Slagboom (Eline); P.M. Visscher (Peter M.); T.D. Spector (Tim); T. Illig (Thomas); I. Rudan (Igor); E.G. Bovill (Edwin G.); A.F. Wright (Alan); W.L. McArdle (Wendy); G.H. Tofler (Geoffrey); A. Hofman (Albert); R.G.J. Westendorp (Rudi); J.M. Starr (John); P.J. Grant (Peter J.); M. Karakas (Mahir); N.D. Hastie (Nicholas D.); B.M. Psaty (Bruce); J.F. Wilson (James); G.D.O. Lowe (Gordon); C.J. O'Donnell (Christopher); J.C.M. Witteman (Jacqueline); J.W. Jukema (Jan Wouter); I.J. Deary (Ian); N. Soranzo (Nicole); W. Koenig (Wolfgang); C. Hayward (Caroline)


    textabstractBACKGROUND: Fibrin fragment D-dimer, one of several peptides produced when crosslinked fibrin is degraded by plasmin, is the most widely used clinical marker of activated blood coagulation. To identity genetic loci influencing D-dimer levels, we performed the first large-scale, genome-wi

  10. Synthesis and antiviral activity of new dimeric inhibitors against HIV-1

    Danel, Krzysztof; Larsen, Louise M.; Pedersen, Erik Bjerreg.


    by Sonogashira reaction, ‘click' chemistry or Pd-catalyzed oxidative coupling. The iodo precursor 5 turned out as a potent compound against wild type and mutated HIV-1 virus. All dimeric compounds showed lower activity against HIV-1 than MKC-442, except the asymmetric dimer of AZT and 1a which showed an activity...

  11. Dimerization of Indanedioneketene to Spiro-oextanone: A Theoretical Study

    Bakalbassis, Evangelos G; Malamidou-Xenikaki, Elizabeth; Spyroudis, Spyros; Xantheas, Sotiris S


    Indanedioneketene, a compound resulting from the thermal degradation of the phenyliodonium ylide of lawsone, dimerises quantitatively to a spiro-oxetanone derivative, a key compound for further transformations. A theoretical DFT study of this unusual for α-oxoketenes [2+2] cyclization reaction both in the gas phase and in dichloromethane solution, provides support for a) a single-step, transitionstate (involving a four-membered cyclic ring) charge controlled, concerted mechanism, and b) a [4+2] cyclization reaction, not observed but studied theoretically in this study. A parallel study of an open chain α,α'-dioxoketene dimerization explains the difference in the stability and reactivity observed experimentally between the cyclic and open chain products.

  12. Monomer-dimer tatami tilings of square regions

    Erickson, Alejandro


    We prove that the number of monomer-dimer tilings of an $n\\times n$ square grid, with $m

  13. Entanglement in the supermolecular dimer [Mn4]2

    Xu Chang-Tan; Chen Gang; He Ming-Ming; Liang Jiu-Qing


    This paper investigates the entanglement in the supermolecular dimer [Mn4]2 consisting of a pair of single molecular magnets with antiferromagnetic exchange-coupling J. The conventional von Neumann entropy as a function of the exchange-coupling is calculated explicitly for all eigenstates with the quantum number range from M = M1 + M2 = -9to 0. It is shown that the yon Neumann entropy is not a monotonic function of the coupling strength. However, it is significant that the entropy of entanglement has the maximum values and the minimum values for most eigenstates,which is extremely useful in the quantum computing. It also presents the time-evolution of entanglement from various initial states. The results are useful in the design of devices based on the entanglement of two molecular magnets.

  14. [Clinical use of D-dimer in patients with cancer].

    Lecumberri, Ramón; Pegenaute, Carlota; Páramo, José A


    There is a well-known close relationship between cancer and the haemostatic system. Plasma D-dimer (DD) is a marker of fibrin generation and lysis. In the clinical practice, its main use is in the diagnostic algorithms of venous thromboembolism (VTE), and it is one of the diagnostic criteria of disseminated intravacular coagulation. In patients with cancer, the specificity of DD is lower than in the general population, reducing its usefulness. However, there is a growing evidence that points out a possible application of DD in the clinical management of cancer patients as a predictor of VTE, marker of hidden cancer in patients with idiopathic VTE, or even as an independent prognostic factor of response to chemotherapy and survival. In this review, the current evidence supporting the use of DD in cancer patients is critically exposed and discussed.

  15. Theoretical Investigation on Triplet Excitation Energy Transfer in Fluorene Dimer

    Yu-bing Si; Xin-xin Zhong; Wei-wei Zhang; Yi Zhao


    Triplet-triplet energy transfer in fluorene dimer is investigated by combining rate theories with electronic structure calculations.The two key parameters for the control of energy transfer,electronic conpling and reorganization energy,are calculated based on the diabatic states constructed by the constrained density functional theory.The fluctuation of the electronic coupling is further revealed by molecular dynamics simulation.Succeedingly,the diagonal and off-diagonal fluctuations of thc Hamiltonian are mapped from the correlation functions of those parameters,and the rate is then estimated both from the perturbation theory and wavepacket diffusion method.The results manifest that both the static and dynamic fluctuations enhance the rate significantly,but the rate from the dynamic fluctuation is smaller than that from the static fluctuation.

  16. Analysis of Photoassociation Spectra for Giant Helium Dimers

    Léonard, J; Walhout, M; Van der Straten, P; Leduc, M


    We perform a theoretical analysis to interpret the spectra of purely long-range helium dimers produced by photoassociation (PA) in an ultra-cold gas of metastable helium atoms. The experimental spectrum obtained with the PA laser tuned closed to the $2^3S_1\\leftrightarrow 2^3P_0$ atomic line has been reported in a previous Letter. Here, we first focus on the corrections to be applied to the measured resonance frequencies in order to infer the molecular binding energies. We then present a calculation of the vibrational spectra for the purely long-range molecular states, using adiabatic potentials obtained from perturbation theory. With retardation effects taken into account, the agreement between experimental and theoretical determinations of the spectrum for the $0_u^+$ purely long-range potential well is very good. The results yield a determination of the lifetime of the $2^3P$ atomic state.

  17. The infrared spectrum of the 12C 18O dimer

    McKellar, A. R. W.


    The infrared spectrum of ( 12C 18O) 2 has been studied for the first time using a tunable diode laser spectrometer in the 2095 cm -1 region to probe a pulsed supersonic jet expansion. Very dilute gas mixtures of CO in He were used, resulting in small consumption of 12C 18O sample gas, as well as cold and simple spectra. The results were analyzed using a term value scheme to obtain model-independent energies for 7 rotational levels belonging to 2 stacks in the lower state, vCO=0, and 22 levels belonging to 7 stacks in the upper state, vCO=1. The two ground state isomers of the CO dimer were found to be separated by only 0.639 cm -1 for ( 12C 18O) 2. These results provide a foundation for future studies of the millimeter wave spectrum.

  18. Collective plasmon modes in a compositionally asymmetric nanoparticle dimer

    Fuyi Chen


    Full Text Available The plasmon coupling phenomenon of heterodimers composed of silver, gold and copper nanoparticles of 60 nm in size and spherical in shape were studied theoretically within the scattered field formulation framework. In-phase dipole coupled σ-modes were observed for the Ag-Au and Ag-Cu heterodimers, and an antiphase dipole coupled π-mode was observed for the Ag-Au heterodimer. These observations agree well with the plasmon hybridization theory. However, quadrupole coupled modes dominate the high energy wavelength range from 357-443 nm in the scattering cross section of the D=60 nm Ag-Au and Ag-Cu heterodimer. We demonstrate for the first time that collective plasmon modes in a compositionally asymmetric nanoparticle dimer have to be predicted from the dipole-dipole approximation of plasmon hybridization theory together with the interband transition effect of the constitutive metals and the retardation effect of the nanoparticle size.

  19. Beryllium dimer: a bond based on non-dynamical correlation.

    El Khatib, Muammar; Bendazzoli, Gian Luigi; Evangelisti, Stefano; Helal, Wissam; Leininger, Thierry; Tenti, Lorenzo; Angeli, Celestino


    The bond nature in beryllium dimer has been theoretically investigated using high-level ab initio methods. A series of ANO basis sets of increasing quality, going from sp to spdf ghi contractions, has been employed, combined with HF, CAS-SCF, CISD, and MRCI calculations with several different active spaces. The quality of these calculations has been checked by comparing the results with valence Full-CI calculations, performed with the same basis sets. It is shown that two quasi-degenerated partly occupied orbitals play a crucial role to give a qualitatively correct description of the bond. Their nature is similar to that of the edge orbitals that give rise to the quasi-degenerated singlet-triplet states in longer beryllium chains.

  20. Twists of Pl\\"ucker coordinates as dimer partition functions

    Scott, Jeanne


    The homogeneous coordinate ring of the Grassmannian Gr(k,n) has a cluster structure defined in terms of planar diagrams known as Postnikov diagrams. The cluster corresponding to such a diagram consists entirely of Pl\\"ucker coordinates. We introduce a twist map on Gr(k,n) related to the BZ-twist, and give an explicit Laurent expansion for the twist of an arbitrary Pl\\"ucker coordinate, in terms of the cluster variables associated with a fixed Postnikov diagram. The expansion arises as a (scaled) dimer partition function of a weighted version of the bipartite graph dual to the Postnikov diagram, modified by a boundary condition determined by the Pl\\"ucker coordinate.

  1. Dimerous Electron and Quantum Interference beyond the Probability Amplitude Paradigm

    Kassandrov, Vladimir V


    We generalize the formerly proposed relationship between a special complex geometry (originating from the structure of biquaternion algebra) and induced real geometry of (extended) space-time. The primordial dynamics in complex space allows for a new realization of the "one electron Universe" of Wheeler-Feynman (the so called "ensemble of duplicons") and leads to a radical concept of "dimerous" (consisting of two identical matter pre-elements, "duplicons") electron. Using this concept, together with an additional phase-like invariant (arising from the complex pre-geometry), we manage to give a visual classical explanation for quantum interference phenomena and, in particular, for the canonical two-slit experiment. Fundamental relativistic condition of quantum interference generalizing the de Broglie relationship is obtained, and an experimentally verifiable distinction in predictions of quantum theory and presented algebrodynamical scheme is established.

  2. Environment-assisted quantum transport and trapping in dimers

    Muelken, Oliver


    We study the dynamics and trapping of excitations for a dimer with an energy off-set $\\Delta$ coupled to an external environment. Using a Lindblad quantum master equation approach, we calculate the survival probability $\\Pi(t)$ of the excitation and define different lifetimes $\\tau_s$ of the excitation, corresponding to the duration of the decay of $\\Pi(t)$ in between two predefined values. We show that it is not possible to always enhance the overall decay to the trap. However, it is possible, even for not too small environmental couplings and for values of $\\Delta$ of the order ${\\cal O}(1)$, to decrease certain lifetimes $\\tau_s$, leading to faster decay of $\\Pi(t)$ in these time intervals: There is an optimal environmental coupling, leading to a maximal decay for fixed $\\Delta$.

  3. Computational Study of Monosubstituted Azo(tetrazolepentazolium)-Based Ionic Dimers.

    Pimienta, Ian S O


    The structures of monosubstituted azo(tetrazolepentazolium) cations (N11CHR(+)), oxygen-rich anions such as N(NO2)2(-), NO3(-), and ClO4(-), and the corresponding ion pairs are investigated using ab initio quantum chemistry calculations. The substituents (R) used are H, F, CH3, CN, NH2, OH, OCH3, N3, NF2, and C2H3. The stability of the protonated cation is explored by examining the decomposition pathway of the protonated cation (N11CH2(+)) to yield molecular N2 fragments. The heats of formation of these cations, which are based on isodesmic (bond type conserving) reactions, are dependent on the nature of the substituents. Ionic dimer structures are obtained, but side reactions including proton transfer, binding, and hydrogen bonding are observed in the gas phase. Implicit solvation studies are performed to determine the solution properties of the ion pairs.

  4. An alternative RNA polymerase I structure reveals a dimer hinge.

    Kostrewa, Dirk; Kuhn, Claus-D; Engel, Christoph; Cramer, Patrick


    RNA polymerase I (Pol I) is the central, 14-subunit enzyme that synthesizes the ribosomal RNA (rRNA) precursor in eukaryotic cells. The recent crystal structure of Pol I at 2.8 Å resolution revealed two novel elements: the `expander' in the active-centre cleft and the `connector' that mediates Pol I dimerization [Engel et al. (2013), Nature (London), 502, 650-655]. Here, a Pol I structure in an alternative crystal form that was solved by molecular replacement using the original atomic Pol I structure is reported. The resulting alternative structure lacks the expander but still shows an expanded active-centre cleft. The neighbouring Pol I monomers form a homodimer with a relative orientation distinct from that observed previously, establishing the connector as a hinge between Pol I monomers.

  5. Quantum Monte Carlo study of the protonated water dimer

    Dagrada, Mario; Saitta, Antonino M; Sorella, Sandro; Mauri, Francesco


    We report an extensive theoretical study of the protonated water dimer (Zundel ion) by means of the highly correlated variational Monte Carlo and lattice regularized Monte Carlo approaches. This system represents the simplest model for proton transfer (PT) and a correct description of its properties is essential in order to understand the PT mechanism in more complex acqueous systems. Our Jastrow correlated AGP wave function ensures an accurate treatment of electron correlations. Exploiting the advantages of contracting the primitive basis set over atomic hybrid orbitals, we are able to limit dramatically the number of variational parameters with a systematic control on the numerical precision, crucial in order to simulate larger systems. We investigate energetics and geometrical properties of the Zundel ion as a function of the oxygen-oxygen distance, taken as reaction coordinate. In both cases, our QMC results are found in excellent agreement with coupled cluster CCSD(T) technique, the quantum chemistry "go...

  6. Charge transfer excitons in C60-dimers and polymers

    Harigaya, K


    Charge-transfer (CT) exciton effects are investigated for the optical absorption spectra of crosslinked C60 systems by using the intermediate exciton theory. We consider the C60-dimers, and the two (and three) molecule systems of the C60-polymers. We use a tight-binding model with long-range Coulomb interactions among electrons, and the model is treated by the Hartree-Fock approximation followed by the single-excitation configuration interaction method. We discuss the variations in the optical spectra by changing the conjugation parameter between molecules. We find that the total CT-component increases in smaller conjugations, and saturates at the intermediate conjugations. It decreases in the large conjugations. We also find that the CT-components of the doped systems are smaller than those of the neutral systems, indicating that the electron-hole distance becomes shorter in the doped C60-polymers.

  7. Dimer site-bond percolation on a triangular lattice

    Ramirez, L. S.; De la Cruz Félix, N.; Centres, P. M.; Ramirez-Pastor, A. J.


    A generalization of the site-percolation problem, in which pairs of neighbor sites (site dimers) and bonds are independently and randomly occupied on a triangular lattice, has been studied by means of numerical simulations. Motivated by considerations of cluster connectivity, two distinct schemes (denoted as S{\\cap}B and S{\\cup}B ) have been considered. In S{\\cap}B (S{\\cup}B ), two points are said to be connected if a sequence of occupied sites and (or) bonds joins them. Numerical data, supplemented by analysis using finite-size scaling theory, were used to determine (i) the complete phase diagram of the system (phase boundary between the percolating and nonpercolating regions), and (ii) the values of the critical exponents (and universality) characterizing the phase transition occurring in the system.

  8. A New Asymmetric ent-Kauranoid Dimer from Rabdosia rubescens

    LU Hai-ying; LIANG Jing-yu


    Objective To study the ent-kaurane diterpenoids from Rabdosia rubescens.Methods The compounds were isolated by chromatographies and their structures were identified by spectral analyses.Results Four compounds were isolated,and they were identified as bisrubescensin E (1),2α,3α,24-trihydroxyurs-12-en-28-oic acid (2),2α,3α,24-trihydroxyurs-12,20-(30)-dien-28-oic acid (3),and 6,7-dihydroxycoumarin (4).Conclusion Compound 1 is a new asymmetric ent-kauranoid dimer.Compound 2 is isolated from the plant for the first time.Compounds 3 and 4 are isolated from the plants ofRabdosia (B1.) Hassk for the first time.

  9. Bright solitons in a PT-symmetric chain of dimers

    Kirikchi, Omar B; Susanto, Hadi


    We study the existence and stability of fundamental bright discrete solitons in a parity-time (PT)-symmetric coupler composed by a chain of dimers, that is modelled by linearly coupled discrete nonlinear Schrodinger equations with gain and loss terms. We use a perturbation theory for small coupling between the lattices to perform the analysis, which is then confirmed by numerical calculations. Such analysis is based on the concept of the so-called anti-continuum limit approach. We consider the fundamental onsite and intersite bright solitons. Each solution has symmetric and antisymmetric configurations between the arms. The stability of the solutions is then determined by solving the corresponding eigenvalue problem. We obtain that both symmetric and antisymmetric onsite mode can be stable for small coupling, on the contrary of the reported continuum limit where the antisymmetric solutions are always unstable. The instability is either due to the internal modes crossing the origin or the appearance of a quart...

  10. Formation and occurrence of dimer esters of pinene oxidation products in atmospheric aerosols

    Kristensen, Kasper; Enggrob, Kirsten L.; King, S. M.


    The formation of carboxylic acids and dimer esters from alpha-pinene oxidation was investigated in a smog chamber and in ambient aerosol samples collected during the Biosphere Effects on Aerosols and Photochemistry Experiment (BEARPEX). Chamber experiments of alpha-pinene ozonolysis in dry air...... and at low NOx concentrations demonstrated formation of two dimer esters, pinyl-diaterpenyl (MW 358) and pinonyl-pinyl dimer ester (MW 368), under both low- and high-temperature conditions. Concentration levels of the pinyl-diaterpenyl dimer ester were lower than the assumed first-generation oxidation...... products cis-pinic and terpenylic acids, but similar to the second-generation oxidation products 3-methyl-1,2,3-butane tricarboxylic acid (MBTCA) and diaterpenylic acid acetate (DTAA). Dimer esters were observed within the first 30 min, indicating rapid production simultaneous to their structural...

  11. Dimerization of the yeast eukaryotic translation initiation factor 5A requires hypusine and is RNA dependent.

    Gentz, Petra M; Blatch, Gregory L; Dorrington, Rosemary A


    Post-translational modification of the highly conserved K51 residue of the Saccharomyces cerevisiae eukaryotic translation initiation factor 5A (eIF5A) to form hypusine, is essential for its many functions including the binding of specific mRNAs. We characterized hypusinated yeast eIF5A by size-exclusion chromatography and native PAGE, showing that the protein exists as a homodimer. A K51R mutant, which was not functional in vivo eluted as a monomer and inhibition of hypusination abolished dimerization. Furthermore, treatment of dimeric eIF5A with RNase A resulted in disruption of the dimer, leading us to conclude that RNA binding is also required for dimerization of eIF5A. We present a model of dimerization, based on the Neurospora crassa structural analogue, HEX-1.

  12. Microwave Measurements of Maleimide and its Doubly Hydrogen Bonded Dimer with Formic ACID*

    Pejlovas, Aaron M.; Kang, Lu; Kukolich, Stephen G.


    The microwave spectra were measured for the maleimide monomer and the maleimide-formic acid doubly hydrogen bonded dimer using a pulsed-beam Fourier transform microwave spectrometer. Many previously studied doubly hydrogen bonded dimers are formed between oxygen containing species, so it is important to also characterize and study other dimers containing nitrogen, as hydrogen bonding interactions with nitrogen are found in biological systems such as in DNA. The transition state of the dimer does not exhibit C_2_V symmetry, so the tunneling motion was not expected to be observed based on the symmetry, but it would be very important to also observe the tunneling process for an asymmetric dimer. Single-line b-type transitions were observed, so the tunneling motion was not observed in our microwave spectra. The hydrogen bond lengths were determined using a nonlinear least squares fitting program. *Supported by the NSF CHE-1057796

  13. Changes in fibrin D-dimer, fibrinogen, and protein S during pregnancy

    Hansen, Anette Tarp; Andreasen, Birgitte Horst; Salvig, Jannie Dalby


    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....... Changes during pregnancy in plasma D-dimer, protein S and fibrinogen were confirmed. Further clinical studies are needed to clarify a clinical useful cut-off point for D-dimer in pregnancy. We suggest careful attention to a low peripartum fibrinogen, since it indicates an increased bleeding risk. We...

  14. Application of Bruggeman and Maxwell Garnett homogenization formalisms to random composite materials containing dimers

    Mackay, Tom G


    The homogenization of a composite material comprising three isotropic dielectric materials was investigated. The component materials were randomly distributed as spherical particles, with the particles of two of the component materials being coupled to form dimers. The Bruggeman and Maxwell Garnett formalisms were developed to estimate the permittivity dyadic of the homogenized composite material (HCM), under the quasi-electrostatic approximation. Both randomly oriented and identically oriented dimers were accommodated; in the former case the HCM is isotropic, whereas in the latter case the HCM is uniaxial. Representative numerical results for composite materials containing dielectric--dielectric dimers demonstrate close agreement between the estimates delivered by the Bruggeman and Maxwell Garnett formalisms. For composite materials containing metal--dielectric dimers with moderate degrees of dissipation, the estimates of the two formalisms are in broad agreement, provided that the dimer volume fractions are...

  15. Stabilization of the dimeric birch pollen allergen Bet v 1 impacts its immunological properties.

    Kofler, Stefan; Ackaert, Chloé; Samonig, Martin; Asam, Claudia; Briza, Peter; Horejs-Hoeck, Jutta; Cabrele, Chiara; Ferreira, Fatima; Duschl, Albert; Huber, Christian; Brandstetter, Hans


    Many allergens share several biophysical characteristics, including the capability to undergo oligomerization. The dimerization mechanism in Bet v 1 and its allergenic properties are so far poorly understood. Here, we report crystal structures of dimeric Bet v 1, revealing a noncanonical incorporation of cysteine at position 5 instead of genetically encoded tyrosine. Cysteine polysulfide bridging stabilized different dimeric assemblies, depending on the polysulfide linker length. These dimers represent quaternary arrangements that are frequently observed in related proteins, reflecting their prevalence in unmodified Bet v 1. These conclusions were corroborated by characteristic immunologic properties of monomeric and dimeric allergen variants. Hereby, residue 5 could be identified as an allergenic hot spot in Bet v 1. The presented results refine fundamental principles in protein chemistry and emphasize the importance of protein modifications in understanding the molecular basis of allergenicity.

  16. Amphiphile dependency of the monomeric and dimeric forms of acetylcholinesterase from human erythrocyte membrane.

    Ott, P; Brodbeck, U


    Human erythrocyte membrane-bound acetylcholinesterase was converted to a monomeric species by treatment of ghosts with 2-mercaptoethanol and iodoacetic acid. After solubilization with Triton X-100, the reduced and alkylated enzyme was partially purified by affinity chromatography and separated from residual dimeric enzyme by sucrose density gradient centrifugation in a zonal rotor. Monomeric and dimeric acetylcholinesterase showed full enzymatic activity in presence of Triton X-100 whereas in the absence of detergent, activity was decreased to approx. 20% and 15%, respectively. Preformed egg phosphatidylcholine vesicles fully sustained activity of the monomeric species whereas the dimer was only 80% active. The results suggest that a dimeric structure is not required for manifestation of amphiphile dependency of membrane-bound acetylcholinesterase from human erythrocytes. Furthermore, monomeric enzyme appears to be more easily inserted into phospholipid bilayers than the dimeric species.

  17. Amorphous Silica-Promoted Lysine Dimerization: a Thermodynamic Prediction

    Kitadai, Norio; Nishiuchi, Kumiko; Nishii, Akari; Fukushi, Keisuke


    It has long been suggested that mineral surfaces played a crucial role in the abiotic polymerization of amino acids that preceded the origin of life. Nevertheless, it remains unclear where the prebiotic process took place on the primitive Earth, because the amino acid-mineral interaction and its dependence on environmental conditions have yet to be understood adequately. Here we examined experimentally the adsorption of L-lysine (Lys) and its dimer (LysLys) on amorphous silica over a wide range of pH, ionic strength, adsorbate concentration, and the solid/water ratio, and determined the reaction stoichiometries and the equilibrium constants based on the extended triple-layer model (ETLM). The retrieved ETLM parameters were then used, in combination with the equilibrium constant for the peptide bond formation in bulk water, to calculate the Lys-LysLys equilibrium in the presence of amorphous silica under various aqueous conditions. Results showed that the silica surface favors Lys dimerization, and the influence varies greatly with changing environmental parameters. At slightly alkaline pH (pH 9) in the presence of a dilute NaCl (1 mM), the thermodynamically attainable LysLys from 0.1 mM Lys reached a concentration around 50 times larger than that calculated without silica. Because of the versatility of the ETLM, which has been applied to describe a wide variety of biomolecule-mineral interactions, future experiments with the reported methodology are expected to provide a significant constraint on the plausible geological settings for the condensation of monomers to polymers, and the subsequent chemical evolution of life.

  18. Ionization dynamics of water dimer on ice surface

    Tachikawa, Hiroto


    The solid surface provides an effective two-dimensional reaction field because the surface increases the encounter probability of bi-molecular collision reactions. Also, the solid surface stabilizes a reaction intermediate because the excess energy generated by the reaction dissipates into the bath modes of surface. The ice surface in the universe is one of the two dimensional reaction fields. However, it is still unknown how the ice surface affects to the reaction mechanism. In the present study, to elucidate the specific property of the ice surface reaction, ionization dynamics of water dimer adsorbed on the ice surface was theoretically investigated by means of direct ab-initio molecular dynamics (AIMD) method combined with ONIOM (our own n-layered integrated molecular orbital and molecular mechanics) technique, and the result was compared with that of gas phase reaction. It was found that a proton is transferred from H2O+ to H2O within the dimer and the intermediate complex H3O+(OH) is formed in both cases. However, the dynamic features were different from each other. The reaction rate of the proton transfer on the ice surface was three times faster than that in the gas phase. The intermediate complex H3O+(OH) was easily dissociated to H3O+ and OH radical on the ice surface, and the lifetime of the complex was significantly shorter than that of gas phase (100 fs vs. infinite). The reason why the ice surface accelerates the reaction was discussed in the present study.

  19. Structural insights into lipid-dependent reversible dimerization of human GLTP

    Samygina, Valeria R.; Ochoa-Lizarralde, Borja [CIC bioGUNE, Technology Park of Bizkaia, 48160 Derio (Spain); Popov, Alexander N. [European Synchrotron Radiation Facility, 38043 Grenoble (France); Cabo-Bilbao, Aintzane; Goni-de-Cerio, Felipe [CIC bioGUNE, Technology Park of Bizkaia, 48160 Derio (Spain); Molotkovsky, Julian G. [Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow 117997 (Russian Federation); Patel, Dinshaw J. [Memorial Sloan–Kettering Cancer Center, New York, NY 10021 (United States); Brown, Rhoderick E., E-mail: [University of Minnesota, Austin, MN 55912 (United States); Malinina, Lucy, E-mail: [CIC bioGUNE, Technology Park of Bizkaia, 48160 Derio (Spain)


    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.

  20. Resolution of DL-Pantolactone with Ethyldiamine Bridged Dimer Permethyβ-Cyclodextrin as GC Stationary Phase


    Ethyldiamine bridged dimer permethy-β-CD and other cyclodextrins were used as GC stationary phase to resolute DL-pantolactone.It is found that this CD dimer has a good selectivity for DL-pantolactone.

  1. Novel Air Stable Organic Radical Semiconductor of Dimers of Dithienothiophene, Single Crystals, and Field-Effect Transistors.

    Zhang, Hantang; Dong, Huanli; Li, Yang; Jiang, Wei; Zhen, Yonggang; Jiang, Lang; Wang, Zhaohui; Chen, Wei; Wittmann, Angela; Hu, Wenping


    Singly linked and vinyl-linked dimers of dithienothiophenes exhibit different electronic behaviors. Single crystals of the singly linked dimer show a high conductivity of 0.265 S cm(-1) , five orders of magnitude higher than that of the vinyl-linked dimer. The huge increase in the hole density of singly linked dimers results from the formation of radicals, which can be reversibly tuned by facile thermal de-doping.

  2. A redox-dependent dimerization switch regulates activity and tolerance for reactive oxygen species of barley seed glutathione peroxidase

    Navrot, Nicolas; Skjoldager, Nicklas; Bunkenborg, Jakob


    Monomeric and dimeric forms of recombinant barley (Hordeum vulgare subsp. vulgare) glutathione peroxidase 2 (HvGpx2) are demonstrated to display distinctly different functional properties in vitro. Monomeric HvGpx2 thus has five fold higher catalytic efficiency than the dimer towards tert-butyl h...... active, but more oxidation-resistant dimer. ...

  3. Structural features of piperazinyl-linked ciprofloxacin dimers required for activity against drug-resistant strains of Staphylococcus aureus.

    Kerns, Robert J; Rybak, Michael J; Kaatz, Glenn W; Vaka, Flamur; Cha, Raymond; Grucz, Richard G; Diwadkar, Veena U


    We previously demonstrated that piperazinyl-linked fluoroquinolone dimers possess potent antibacterial activity against drug-resistant strains of Staphylococcus aureus. In this study, we report the preparation and evaluation of a series of incomplete dimers toward ascertaining structural features of piperazinyl-linked ciprofloxacin dimers that render these agents refractory to fluoroquinolone-resistance mechanisms in Staphylococcus aureus.

  4. [Negative D-dimers and exclusion of venous thromboembolism--own experience].

    Dworakowska, Dorota; Kazimierska, Ewa; Weyer-Hepka, Jolanta; Skibowska-Bielińska, Anna; Swiatkowska-Stodulska, Renata; Lubińska, Monika; Czestochowska, Eugenia


    The assessment of D-dimer concentration has become essential step during diagnostic algorithm of venous thromboembolism (VTE). This test characterizes high sensitivity but limited specificity. Negative D-dimer with high probability excludes VTE. The aim of this study was to assess the percentage of patients treated in Department of Internal Medicine, Endocrinology and Haemostatic Disorders, Medical University of Gdańisk, who in spite of clinical signs of VTE showed normal D-dimer level. Between 2000 and 2004 in our department 57 cases with recent deep vein thrombosis (DVT) were diagnosed, in 2 cases with co-existence of pulmonary embolism (PE). The D-dimer concentration was assessed in patients' plasma with the use of immunoturbidometry. Between 57 cases with VTE, 7 patients (12%) showed normal D-dimer level (<500 microg/ml). This group consisted of 4 men and 3 women, aged from 40 to 82 years (the mean age of 58 years). In all 7 cases DVT was diagnosed, in 2 patients with concomitent PE. The final diagnosis was confirmed by compression ultrasonography and pulmonary scintigraphy. Our analysis underlines the observation that occurrence of VTE and negative d-dimer concentration is possible and may probably be related to methodological limitations. However, the lack of increase of D-dimer could also be caused by fibrinolysis alteration.

  5. Domain-Swapped Dimers of Intracellular Lipid-Binding Proteins: Evidence for Ordered Folding Intermediates.

    Assar, Zahra; Nossoni, Zahra; Wang, Wenjing; Santos, Elizabeth M; Kramer, Kevin; McCornack, Colin; Vasileiou, Chrysoula; Borhan, Babak; Geiger, James H


    Human Cellular Retinol Binding Protein II (hCRBPII), a member of the intracellular lipid-binding protein family, is a monomeric protein responsible for the intracellular transport of retinol and retinal. Herein we report that hCRBPII forms an extensive domain-swapped dimer during bacterial expression. The domain-swapped region encompasses almost half of the protein. The dimer represents a novel structural architecture with the mouths of the two binding cavities facing each other, producing a new binding cavity that spans the length of the protein complex. Although wild-type hCRBPII forms the dimer, the propensity for dimerization can be substantially increased via mutation at Tyr60. The monomeric form of the wild-type protein represents the thermodynamically more stable species, making the domain-swapped dimer a kinetically trapped entity. Hypothetically, the wild-type protein has evolved to minimize dimerization of the folding intermediate through a critical hydrogen bond (Tyr60-Glu72) that disfavors the dimeric form.

  6. The E2 Domains of APP and APLP1 Share a Conserved Mode of Dimerization

    S Lee; Y Xue; J Hulbert; Y Wang; X Liu; B Demeler; Y Ha


    Amyloid precursor protein (APP) is genetically linked to Alzheimer's disease. APP is a type I membrane protein, and its oligomeric structure is potentially important because this property may play a role in its function or affect the processing of the precursor by the secretases to generate amyloid {beta}-peptide. Several independent studies have shown that APP can form dimers in the cell, but how it dimerizes remains controversial. At least three regions of the precursor, including a centrally located and conserved domain called E2, have been proposed to contribute to dimerization. Here we report two new crystal structures of E2, one from APP and the other from APLP1, a mammalian APP homologue. Comparison with an earlier APP structure, which was determined in a different space group, shows that the E2 domains share a conserved and antiparallel mode of dimerization. Biophysical measurements in solution show that heparin binding induces E2 dimerization. The 2.1 {angstrom} resolution electron density map also reveals phosphate ions that are bound to the protein surface. Mutational analysis shows that protein residues interacting with the phosphate ions are also involved in heparin binding. The locations of two of these residues, Arg-369 and His-433, at the dimeric interface suggest a mechanism for heparin-induced protein dimerization.

  7. Thermal entanglement in an orthogonal dimer-plaquette chain with alternating Ising-Heisenberg coupling.

    Paulinelli, H G; de Souza, S M; Rojas, Onofre


    In this paper we explore the entanglement in an orthogonal dimer-plaquette Ising-Heisenberg chain, assembled between plaquette edges, also known as orthogonal dimer plaquettes. The quantum entanglement properties involving an infinite chain structure are quite important, not only because the mathematical calculation is cumbersome but also because real materials are well represented by infinite chains. Using the local gauge symmetry of this model, we are able to map onto a simple spin-1 like Ising and spin-1/2 Heisenberg dimer model with single effective ion anisotropy. Thereafter this model can be solved using the decoration transformation and transfer matrix approach. First, we discuss the phase diagram at zero temperature of this model, where we find five ground states, one ferromagnetic, one antiferromagnetic, one triplet-triplet disordered and one triplet-singlet disordered phase, beside a dimer ferromagnetic-antiferromagnetic phase. In addition, we discuss the thermodynamic properties such as entropy, where we display the residual entropy. Furthermore, using the nearest site correlation function it is possible also to analyze the pairwise thermal entanglement for both orthogonal dimers. Additionally, we discuss the threshold temperature of the entangled region as a function of Hamiltonian parameters. We find a quite interesting thin reentrance threshold temperature for one of the dimers, and we also discuss the differences and similarities for both dimers.

  8. Influence of linker length and composition on enzymatic activity and ribosomal binding of neomycin dimers.

    Watkins, Derrick; Kumar, Sunil; Green, Keith D; Arya, Dev P; Garneau-Tsodikova, Sylvie


    The human and bacterial A site rRNA binding as well as the aminoglycoside-modifying enzyme (AME) activity against a series of neomycin B (NEO) dimers is presented. The data indicate that by simple modifications of linker length and composition, substantial differences in rRNA selectivity and AME activity can be obtained. We tested five different AMEs with dimeric NEO dimers that were tethered via triazole, urea, and thiourea linkages. We show that triazole-linked dimers were the worst substrates for most AMEs, with those containing the longer linkers showing the largest decrease in activity. Thiourea-linked dimers that showed a decrease in activity by AMEs also showed increased bacterial A site binding, with one compound (compound 14) even showing substantially reduced human A site binding. The urea-linked dimers showed a substantial decrease in activity by AMEs when a conformationally restrictive phenyl linker was introduced. The information learned herein advances our understanding of the importance of the linker length and composition for the generation of dimeric aminoglycoside antibiotics capable of avoiding the action of AMEs and selective binding to the bacterial rRNA over binding to the human rRNA.

  9. Structural features of the KPI domain control APP dimerization, trafficking, and processing.

    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


    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.

  10. STIM1 dimers undergo unimolecular coupling to activate Orai1 channels

    Zhou, Yandong; Wang, Xizhuo; Wang, Xianming; Loktionova, Natalia A.; Cai, Xiangyu; Nwokonko, Robert M.; Vrana, Erin; Wang, Youjun; Rothberg, Brad S.; Gill, Donald L.


    The endoplasmic reticulum (ER) Ca2+ sensor, STIM1, becomes activated when ER-stored Ca2+ is depleted and translocates into ER-plasma membrane junctions where it tethers and activates Orai1 Ca2+ entry channels. The dimeric STIM1 protein contains a small STIM-Orai-activating region (SOAR)--the minimal sequence sufficient to activate Orai1 channels. Since SOAR itself is a dimer, we constructed SOAR concatemer-dimers and introduced mutations at F394, which is critical for Orai1 coupling and activation. The F394H mutation in both SOAR monomers completely blocks dimer function, but F394H introduced in only one of the dimeric SOAR monomers has no effect on Orai1 binding or activation. This reveals an unexpected unimolecular coupling between STIM1 and Orai1 and argues against recent evidence suggesting dimeric interaction between STIM1 and two adjacent Orai1 channel subunits. The model predicts that STIM1 dimers may be involved in crosslinking between Orai1 channels with implications for the kinetics and localization of Orai1 channel opening.

  11. Morphological and physiological retinal degeneration induced by intravenous delivery of vitamin A dimers in rabbits

    Jackie Penn


    Full Text Available The eye uses vitamin A as a cofactor to sense light and, during this process, some vitamin A molecules dimerize, forming vitamin A dimers. A striking chemical signature of retinas undergoing degeneration in major eye diseases such as age-related macular degeneration (AMD and Stargardt disease is the accumulation of these dimers in the retinal pigment epithelium (RPE and Bruch’s membrane (BM. However, it is not known whether dimers of vitamin A are secondary symptoms or primary insults that drive degeneration. Here, we present a chromatography-free method to prepare gram quantities of the vitamin A dimer, A2E, and show that intravenous administration of A2E to the rabbit results in retinal degeneration. A2E-damaged photoreceptors and RPE cells triggered inflammation, induced remolding of the choroidal vasculature and triggered a decline in the retina’s response to light. Data suggest that vitamin A dimers are not bystanders, but can be primary drivers of retinal degeneration. Thus, preventing dimer formation could be a preemptive strategy to address serious forms of blindness.

  12. The Dimer Interface of the Membrane Type 1 Matrix Metalloproteinase Hemopexin Domain

    Tochowicz, Anna; Goettig, Peter; Evans, Richard; Visse, Robert; Shitomi, Yasuyuki; Palmisano, Ralf; Ito, Noriko; Richter, Klaus; Maskos, Klaus; Franke, Daniel; Svergun, Dmitri; Nagase, Hideaki; Bode, Wolfram; Itoh, Yoshifumi


    Homodimerization is an essential step for membrane type 1 matrix metalloproteinase (MT1-MMP) to activate proMMP-2 and to degrade collagen on the cell surface. To uncover the molecular basis of the hemopexin (Hpx) domain-driven dimerization of MT1-MMP, a crystal structure of the Hpx domain was solved at 1.7 Å resolution. Two interactions were identified as potential biological dimer interfaces in the crystal structure, and mutagenesis studies revealed that the biological dimer possesses a symmetrical interaction where blades II and III of molecule A interact with blades III and II of molecule B. The mutations of amino acids involved in the interaction weakened the dimer interaction of Hpx domains in solution, and incorporation of these mutations into the full-length enzyme significantly inhibited dimer-dependent functions on the cell surface, including proMMP-2 activation, collagen degradation, and invasion into the three-dimensional collagen matrix, whereas dimer-independent functions, including gelatin film degradation and two-dimensional cell migration, were not affected. These results shed light on the structural basis of MT1-MMP dimerization that is crucial to promote cellular invasion. PMID:21193411

  13. The monomer-dimer problem and moment Lyapunov exponents of homogeneous Gaussian random fields

    Vladimirov, Igor G


    We consider an "elastic" version of the statistical mechanical monomer-dimer problem on the n-dimensional integer lattice. Our setting includes the classical "rigid" formulation as a special case and extends it by allowing each dimer to consist of particles at arbitrarily distant sites of the lattice, with the energy of interaction between the particles in a dimer depending on their relative position. We reduce the free energy of the elastic dimer-monomer (EDM) system per lattice site in the thermodynamic limit to the moment Lyapunov exponent (MLE) of a homogeneous Gaussian random field (GRF) whose mean value and covariance function are the Boltzmann factors associated with the monomer energy and dimer potential. In particular, the classical monomer-dimer problem becomes related to the MLE of a moving average GRF. We outline an approach to recursive computation of the partition function for "Manhattan" EDM systems where the dimer potential is a weighted l1-distance and the auxiliary GRF is a Markov random fie...

  14. Dynamic Cholesterol-Conditioned Dimerization of the G Protein Coupled Chemokine Receptor Type 4.

    Kristyna Pluhackova


    Full Text Available G protein coupled receptors (GPCRs allow for the transmission of signals across biological membranes. For a number of GPCRs, this signaling was shown to be coupled to prior dimerization of the receptor. The chemokine receptor type 4 (CXCR4 was reported before to form dimers and their functionality was shown to depend on membrane cholesterol. Here, we address the dimerization pattern of CXCR4 in pure phospholipid bilayers and in cholesterol-rich membranes. Using ensembles of molecular dynamics simulations, we show that CXCR4 dimerizes promiscuously in phospholipid membranes. Addition of cholesterol dramatically affects the dimerization pattern: cholesterol binding largely abolishes the preferred dimer motif observed for pure phospholipid bilayers formed mainly by transmembrane helices 1 and 7 (TM1/TM5-7 at the dimer interface. In turn, the symmetric TM3,4/TM3,4 interface is enabled first by intercalating cholesterol molecules. These data provide a molecular basis for the modulation of GPCR activity by its lipid environment.

  15. Accuracy of D-Dimers to Rule Out Venous Thromboembolism Events across Age Categories

    G. Der Sahakian


    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.

  16. Structure and stability of RNA/RNA kissing complex: with application to HIV dimerization initiation signal.

    Cao, Song; Chen, Shi-Jie


    We develop a statistical mechanical model to predict the structure and folding stability of the RNA/RNA kissing-loop complex. One of the key ingredients of the theory is the conformational entropy for the RNA/RNA kissing complex. We employ the recently developed virtual bond-based RNA folding model (Vfold model) to evaluate the entropy parameters for the different types of kissing loops. A benchmark test against experiments suggests that the entropy calculation is reliable. As an application of the model, we apply the model to investigate the structure and folding thermodynamics for the kissing complex of the HIV-1 dimerization initiation signal. With the physics-based energetic parameters, we compute the free energy landscape for the HIV-1 dimer. From the energy landscape, we identify two minimal free energy structures, which correspond to the kissing-loop dimer and the extended-duplex dimer, respectively. The results support the two-step dimerization process for the HIV-1 replication cycle. Furthermore, based on the Vfold model and energy minimization, the theory can predict the native structure as well as the local minima in the free energy landscape. The root-mean-square deviations (RMSDs) for the predicted kissing-loop dimer and extended-duplex dimer are ~3.0 Å. The method developed here provides a new method to study the RNA/RNA kissing complex.

  17. pi-pi Stacking of curved carbon networks: The corannulene dimer

    Sygula, Andrzej; Saebø, Svein

    Dimers of corannulene, a curved, saucer shaped molecule, were studied by theoretical calculations using second order Møller-Plesset perturbation theory and a large polarized triple zeta basis set. Three dimer motifs were investigated: the "native" dimer is the concave-convex stacking of two monomers with the geometries of both monomers conserved; the ldquoplanarrdquo motif with both monomers forced to be planar; and the ldquoC60-likerdquo dimer where the outer monomer has the native geometry while the inner one has the curvature of buckminsterfullerene C60. Both staggered and eclipsed conformations of the dimers were investigated. Our calculations show that the binding energy of the native concave-convex corannulene dimer is quite substantial (17.2 kcal/mole at the ldquobestrdquo SCS-MP2/cc-pvtz level of theory) with an equilibrium distance of about 3.64 Å. Surprisingly, there are only minor differences in both binding energies and equilibrium distances between the three different dimer motifs. This suggests that the curvature of the conjugated carbon networks does not disable their ability to form pi-pi stacked assemblies similar to the planar systems. However, in contrast to the planar systems, at least part of the binding energies in the stacked curved systems can be attributed to attractive electrostatic dipole-dipole contributions since buckybowls exhibit significant dipole moments. For the ldquoplanarrdquo dimer, a staggered arrangement of the two monomers is preferred, while eclipsed conformations are the most stable for all curved dimers. For all systems, the basis set superposition errors are large (ca. 7 kcal/mol) at the equilibrium distance even with our largest basis sets.

  18. Antiviral activity of α-helical stapled peptides designed from the HIV-1 capsid dimerization domain

    Cowburn David


    Full Text Available Abstract Background The C-terminal domain (CTD of HIV-1 capsid (CA, like full-length CA, forms dimers in solution and CTD dimerization is a major driving force in Gag assembly and maturation. Mutations of the residues at the CTD dimer interface impair virus assembly and render the virus non-infectious. Therefore, the CTD represents a potential target for designing anti-HIV-1 drugs. Results Due to the pivotal role of the dimer interface, we reasoned that peptides from the α-helical region of the dimer interface might be effective as decoys to prevent CTD dimer formation. However, these small peptides do not have any structure in solution and they do not penetrate cells. Therefore, we used the hydrocarbon stapling technique to stabilize the α-helical structure and confirmed by confocal microscopy that this modification also made these peptides cell-penetrating. We also confirmed by using isothermal titration calorimetry (ITC, sedimentation equilibrium and NMR that these peptides indeed disrupt dimer formation. In in vitro assembly assays, the peptides inhibited mature-like virus particle formation and specifically inhibited HIV-1 production in cell-based assays. These peptides also showed potent antiviral activity against a large panel of laboratory-adapted and primary isolates, including viral strains resistant to inhibitors of reverse transcriptase and protease. Conclusions These preliminary data serve as the foundation for designing small, stable, α-helical peptides and small-molecule inhibitors targeted against the CTD dimer interface. The observation that relatively weak CA binders, such as NYAD-201 and NYAD-202, showed specificity and are able to disrupt the CTD dimer is encouraging for further exploration of a much broader class of antiviral compounds targeting CA. We cannot exclude the possibility that the CA-based peptides described here could elicit additional effects on virus replication not directly linked to their ability to bind

  19. Vibrational relaxation of hydrogen fluoride by HF dimers in a laser excited nozzle beam

    Knuth, E.L.; Rubahn, H.; Toennies, J.P.; Wanner, J.


    An HF nozzle beam and a cw HF laser beam in a coaxial and antiparallel arrangement facilitated exciting HF molecules vibrationally in v-italic = 1,J-italic up to the saturation limit. A beam consisting exclusively of monomeric HF was generated by heating the beam source to 600 K and was confirmed using a mass spectrometer. Energy-flux measurements made using a bolometer indicate that the vibrational energy distribution initiated by the laser is conserved, confirming that V--T energy transfer to monomers is slow. The maximum measured flux of HF(v-italic = 1,J-italic) molecules was 1.5 x 10/sup 17/ molecules s/sup -1/ sr/sup -1/ at 670 mbar stagnation pressure. Beams consisting of a mixture of monomeric and polymeric HF were generated using appropriate combinations of source temperature and pressure. In the presence of dimers, the excited monomers relax rapidly by a fast V--V transfer and subsequent predissociation of the metastable dimers. The loss of beam energy due to energy transport by the departing dimer fragments was detected bolometrically. The laser-induced depletion of dimers was determined over a wide source pressure range at T-italic/sub 0/ = 300 K using a mass spectrometer. From a kinetic model of these dimer-depletion data, the product of cross section and transfer probability for V--V energy transfer from HF (v-italic = 1) monomers to dimers was deduced to be 14 A-circle/sup 2/. The terminal-dimer-concentration equation for HF nozzle beams was refined. An analysis of the energy fluxes measured by the bolometer with no laser excitation of the beam revealed that, for an HF nozzle beam, the flow from the source to the detector is, in general, nonisenthalpic due to the onset of dimerization. Mach-number focusing enriches the dimer mole fractions detected by the bolometer.

  20. D-dimer levels and cerebral infarction in critically ill cancer patients.

    Ryu, Jeong-Am; Bang, Oh Young; Lee, Geun-Ho


    D-dimer levels have been used in the diagnosis of a variety of thrombosis-related diseases. In this study, we evaluated whether measuring D-dimer levels can help to diagnose cerebral infarction (CI) in critically ill cancer patients. We retrospectively evaluated all cancer patients who underwent brain magnetic resonance imaging (MRI) between March 2010 and February 2014 at the medical oncology intensive care unit (ICU) of Samsung Medical Center. Brain MRI scanning was performed when CI was suspected due to acute neurological deficits. We compared D-dimer levels between patients ultimately diagnosed as having or not having CI and analyzed diffusion-weighted imaging (DWI) lesion patterns. A total of 88 patients underwent brain MRI scanning due to clinical suspicion of CI; altered mental status and unilateral hemiparesis were the most common neurological deficits. CI was ultimately diagnosed in 43 (49%) patients. According to the DWI patterns, multiple arterial infarctions (40%) were more common than single arterial infarctions (9%). Cryptogenic stroke etiologies were more common (63%) than determined etiologies. There was no significant difference in D-dimer levels between patients with and without CI (P = 0.319). Although D-dimer levels were not helpful in diagnosing CI, D-dimer levels were associated with cryptogenic etiologies in critically ill cancer patients; D-dimer levels were higher in the cryptogenic etiology group than in the determined etiology group or the non-infarction group (P = 0.001). In multivariate analysis, elevated D-dimer levels (> 8.89 μg/mL) were only associated with cryptogenic stroke (adjusted OR 5.46; 95% confidence interval, 1.876-15.857). Abnormal D-dimer levels may support the diagnosis of cryptogenic stroke in critically ill cancer patients.

  1. Spontaneous dimerization, critical lines, and short-range correlations in a frustrated spin-1 chain

    Chepiga, Natalia; Affleck, Ian; Mila, Frédéric


    We report on a detailed investigation of the spin-1 J1-J2-J3 Heisenberg model, a frustrated model with nearest-neighbor coupling J1, next-nearest neighbor coupling J2, and a three-site interaction J3[(Si -1.Si) (Si.Si +1) +H .c . ] previously studied in [Phys. Rev. B 93, 241108(R) (2016), 10.1103/PhysRevB.93.241108]. Using density matrix renormalization group (DMRG) and exact diagonalizations, we show that the phase boundaries between the Haldane phase, the next-nearest neighbor Haldane phase, and the dimerized phase can be very accurately determined by combining the information deduced from the dimerization, the ground-state energy, the entanglement spectrum and the Berry phase. By a careful investigation of the finite-size spectrum, we also show that the transition between the next-nearest neighbor Haldane phase and the dimerized phase is in the Ising universality class all along the critical line. Furthermore, we justify the conformal embedding of the SU (2) 2 Wess-Zumino-Witten conformal field theory in terms of a boson and an Ising field, and we explicitly derive a number of consequences of this embedding for the spectrum along the SU (2) 2 transition line between the Haldane phase and the dimerized phase. We also show that the solitons along the first-order transition line between the Haldane phase and the dimerized phase carry a spin-1/2, while the domain walls between different dimerization domains inside the dimerized phase carry a spin 1. Finally, we show that short-range correlations change character in the Haldane and dimerized phases through disorder and Lifshitz lines, as well as through the development of short-range dimer correlations in the Haldane phase, leading to a remarkably rich phase diagram.

  2. Dimerization of the glucan phosphatase laforin requires the participation of cysteine 329.

    Pablo Sánchez-Martín

    Full Text Available 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.

  3. An artemisinin-derived dimer has highly potent anti-cytomegalovirus (CMV and anti-cancer activities.

    Ran He

    Full Text Available We recently reported that two artemisinin-derived dimers (dimer primary alcohol 606 and dimer sulfone 4-carbamate 832-4 are significantly more potent in inhibiting human cytomegalovirus (CMV replication than artemisinin-derived monomers. In our continued evaluation of the activities of artemisinins in CMV inhibition, twelve artemisinin-derived dimers and five artemisinin-derived monomers were used. Dimers as a group were found to be potent inhibitors of CMV replication. Comparison of CMV inhibition and the slope parameter of dimers and monomers suggest that dimers are distinct in their anti-CMV activities. A deoxy dimer (574, lacking the endoperoxide bridge, did not have any effect on CMV replication, suggesting a role for the endoperoxide bridge in CMV inhibition. Differences in anti-CMV activity were observed among three structural analogs of dimer sulfone 4-carbamate 832-4 indicating that the exact placement and oxidation state of the sulfur atom may contribute to its anti-CMV activity. Of all tested dimers, artemisinin-derived diphenyl phosphate dimer 838 proved to be the most potent inhibitor of CMV replication, with a selectivity index of approximately 1500, compared to our previously reported dimer sulfone 4-carbamate 832-4 with a selectivity index of about 900. Diphenyl phosphate dimer 838 was highly active against a Ganciclovir-resistant CMV strain and was also the most active dimer in inhibition of cancer cell growth. Thus, diphenyl phosphate dimer 838 may represent a lead for development of a highly potent and safe anti-CMV compound.

  4. Monomer and dimer radical cations of benzene, toluene, and naphthalene.

    Das, Tomi Nath


    Pulse radiolytic generation of monomeric and dimeric cations of benzene, toluene, and naphthalene in aqueous acid media at room temperature and their spectrophotometric characterization is discussed. Results presented include measurements of each aromatic's solubility in H(2)O-H(2)SO(4) and H(2)O-HClO(4) media over the acidity range pH 1 to H(0) -7.0, facile oxidative generation, and real-time identification of appropriate cationic transients with respective lambda(max) (nm) and epsilon (M(-1) cm(-1)) values measured as follows: C(6)H(6)(*+) (443, 1145 +/- 75), C(6)H(5)CH(3)(*+) (428, 1230 +/- 90), C(10)H(8)(*+) (381, 3650 +/- 225, and 687, 2210 +/- 160), (C(6)H(6))(2)(*+) (860, 2835 +/- 235), (C(6)H(5)CH(3))(2)(*+) (950, 1685 +/- 155), and (C(10)H(8))(2)(*+) (1040, 4170 +/- 320). Kinetic measurements reveal the respective formation rates of monomeric cations to be near-diffusion controlled, while the forward rate values for the dimeric species generation are marginally slower. The proton activity corrected pK(a) values are found to remain between -2.6 and -1.3 for the ArH(*+) species (C(6)H(6)(*+) most acidic, C(10)H(8)(*+) least acidic), while the pK(a) values of (ArH)(2)(*+) species vary from -5.0 to -3.0 ((C(6)H(6))(2)(*+) most acidic, (C(10)H(8))(2)(*+) least acidic). In H(0) -5 in aqueous H(2)SO(4), the respective stabilization energy of (C(6)H(6))(2)(*+), (C(6)H(5)CH(3))(2)(*+), and (C(10)H(8))(2)(*+) is estimated to be 16.6, 15.0, and 13.7 kcal mol(-1). Thus, the aqueous acid solution emerges as an alternative medium for typical radical-cationic studies, while offering compatibility for the deprotonated radical characterization near neutral pH.

  5. Aberrant phenotypes of transgenic mice expressing dimeric human erythropoietin

    Yun Seong-Jo


    Full Text Available Abstract Background Dimeric human erythropoietin (dHuEPO peptides are reported to exhibit significantly higher biological activity than the monomeric form of recombinant EPO. The objective of this study was to produce transgenic (tg mice expressing dHuEPO and to investigate the characteristics of these mice. Methods A dHuEPO-expressing vector under the control of the goat beta-casein promoter, which produced a dimer of human EPO molecules linked by a 2-amino acid peptide linker (Asp-Ile, was constructed and injected into 1-cell fertilized embryos by microinjection. Mice were screened using genomic DNA samples obtained from tail biopsies. Blood samples were obtained by heart puncture using heparinized tubes, and hematologic parameters were assessed. Using the microarray analysis tool, we analyzed differences in gene expression in the spleens of tg and control mice. Results A high rate of spontaneous abortion or death of the offspring was observed in the recipients of dHuEPO embryos. We obtained 3 founder lines (#4, #11, and #47 of tg mice expressing the dHuEPO gene. However, only one founder line showed stable germline integration and transmission, subsequently establishing the only transgenic line (#11. We obtained 2 F1 mice and 3 F2 mice from line #11. The dHuEPO protein could not be obtained because of repeated spontaneous abortions in the tg mice. Tg mice exhibited symptoms such as short lifespan and abnormal blood composition. The red blood cell count, white blood cell count, and hematocrit levels in the tg mice were remarkably higher than those in the control mice. The spleens of the tg mice (F1 and F2 females were 11- and -21-fold larger than those of the control mice. Microarray analysis revealed 2,672 spleen-derived candidate genes; more genes were downregulated than upregulated (849/764. Reverse transcriptase-polymerase chain reaction (RT-PCR and quantitative real-time PCR (qRT-PCR were used for validating the results of the microarray

  6. Excitation Localization/Delocalization Isomerism in a Strongly Coupled Covalent Dimer of 1,3-Diphenylisobenzofuran

    Schrauben, Joel N.; Akdag, Akin; Wen, Jin; Havlas, Zdenek; Ryerson, Joseph L.; Smith, Millie B.; Michl, Josef; Johnson, Justin C.


    Two isomers of both the lowest excited singlet (S1) and triplet (T1) states of the directly para, para'-connected covalent dimer of the singlet-fission chromophore 1,3-diphenylisobenzofuran have been observed. In one isomer, excitation is delocalized over both halves of the dimer, and in the other, it is localized on one or the other half. For a covalent dimer in solution, such 'excitation isomerism' is extremely rare. The vibrationally relaxed isomers do not interconvert, and their photophysical properties, including singlet fission, differ significantly.

  7. Cationic zinc (II) dimers and one dimensional coordination polymer from ionic carboxylic acid

    Paladugu Suresh; Ganesan Prabusankar


    A rare example of chelating two tetra cationic paddle-wheel zinc dimers were synthesized from the reaction between flexible imidazolium carboxylate (LH2Br2) and corresponding zinc precursors. A zinc coordination polymer was synthesised by treating in situ generation of 2 in the presence of 4,4′-bipyridine. These new molecules, dimers and polymer, were characterized by FT-IR, NMR, UV-vis, fluorescent and single crystal X-ray diffraction techniques. Zinc polymer is the first example of 1D coordination polymer constructed by tetra cationic zinc dimer as a secondary building unit in coordination polymer.

  8. Na + concentration dependence of intermolecular distance in 3,4,9,10-perylenetetracarboxylic dianhydride dimer

    Fujii, Kazuhito


    We have discussed the Na + concentration dependence of the intermolecular distance of 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) dimers in aqueous solution of NaOH. We have particularly focused on the S10-S00 transition of the PTCDA dimers which is sensitive to the intermolecular distance and we have found that the S10 state is split for the higher lying sublevel and the lower lying sublevel with the increase of the Na + concentrations. From the energy shift of the lower lying sublevel, we have estimated the intermolecular distance of the PTCDA dimer, that changes from 7.5 to 4.9 Å by the Na + concentration.

  9. Formation and diffusion of water dimers on rutile TiO2(110).

    Matthiesen, J; Hansen, J O; Wendt, S; Lira, E; Schaub, R; Laegsgaard, E; Besenbacher, F; Hammer, B


    From an interplay of time-lapsed high resolution scanning tunneling microscopy and density functional theory calculations we reveal the formation and diffusion of water dimers on hydrated rutile TiO2(110)-(1x1) surfaces, i.e., surfaces containing OH_{br} groups. At temperatures between approximately 150 and approximately 210 K water monomers diffusing along the Ti troughs were found to form stable water dimers that diffuse faster than the water monomers. An H bond mediated rollover mechanism operating for the water dimers explains the experimental findings.

  10. ERIS, an endoplasmic reticulum IFN stimulator, activates innate immune signaling through dimerization.

    Sun, Wenxiang; Li, Yang; Chen, Lu; Chen, Huihui; You, Fuping; Zhou, Xiang; Zhou, Yi; Zhai, Zhonghe; Chen, Danying; Jiang, Zhengfan


    We report here the identification and characterization of a protein, ERIS, an endoplasmic reticulum (ER) IFN stimulator, which is a strong type I IFN stimulator and plays a pivotal role in response to both non-self-cytosolic RNA and dsDNA. ERIS (also known as STING or MITA) resided exclusively on ER membrane. The ER retention/retrieval sequence RIR was found to be critical to retain the protein on ER membrane and to maintain its integrity. ERIS was dimerized on innate immune challenges. Coumermycin-induced ERIS dimerization led to strong and fast IFN induction, suggesting that dimerization of ERIS was critical for self-activation and subsequent downstream signaling.

  11. Propagation of light in serially coupled plasmonic nanowire dimer: Geometry dependence and polarization control

    Singh, Danveer; Raghuwanshi, Mohit; Pavan Kumar, G. V. [Photonics and Optical Nanoscopy Laboratory, Department of Physics and Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune 411008 (India)


    We experimentally studied plasmon-polariton-assisted light propagation in serially coupled silver nanowire (Ag-NW) dimers and probed their dependence on bending-angle between the nanowires and polarization of incident light. From the angle-dependence study, we observed that obtuse angles between the nanowires resulted in better transmission than acute angles. From the polarization studies, we inferred that light emission from junction and distal ends of Ag-NW dimers can be systematically controlled. Further, we applied this property to show light routing and polarization beam splitting in obtuse-angled Ag-NW dimer. The studied geometry can be an excellent test-bed for plasmonic circuitry.

  12. Evaluation of D-dimer test in patients on chronic hemodialysis

    Vurusic Branimir


    Full Text Available Determining the value of D-Dimer is a routine test in case of suspecting thromboembolic event. In patients on chronic dialysis, baseline concentrations for biomarkers have changed in widespread clinical use, which prompted us to measure the concentration of D-dimer, due to disorders of hemostasis in chronic kidney failure. From the evaluation of the findings of D-dimer in 67 patients and the available literature we can conclude that the value of the test in the diagnosis of thromboembolic events has significantly decreased.

  13. Altered Specificity of DNA-Binding Proteins with Transition Metal Dimerization Domains

    Cuenoud, Bernard; Schepartz, Alanna


    The bZIP motif is characterized by a leucine zipper domain that mediates dimerization and a basic domain that contacts DNA. A series of transition metal dimerization domains were used to alter systematically the relative orientation of basic domain peptides. Both the affinity and the specificity of the peptide-DNA interaction depend on domain orientation. These results indicate that the precise configuration linking the domains is important; dimerization is not always sufficient for DNA binding. This approach to studying the effect of orientation on protein function complements mutagenesis and could be used in many systems.

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

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


    [IL-6]), antiretroviral therapy (ART) use, ART regimens, co-morbidities (hepatitis B/C, diabetes mellitus, prior cardiovascular disease), smoking, renal function (estimated glomerular filtration rate [eGFR] and cystatin C) and cholesterol. RESULTS: Women from all age groups had higher D-dimer levels...... 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...

  15. Phenylalanine binding is linked to dimerization of the regulatory domain of phenylalanine hydroxylase.

    Zhang, Shengnan; Roberts, Kenneth M; Fitzpatrick, Paul F


    Analytical ultracentrifugation has been used to analyze the oligomeric structure of the isolated regulatory domain of phenylalanine hydroxylase. The protein exhibits a monomer-dimer equilibrium with a dissociation constant of ~46 μM; this value is unaffected by the removal of the 24 N-terminal residues or by phosphorylation of Ser16. In contrast, phenylalanine binding (Kd = 8 μM) stabilizes the dimer. These results suggest that dimerization of the regulatory domain of phenylalanine hydroxylase is linked to allosteric activation of the enzyme.

  16. Scaling of the Surface Plasmon Resonance in Gold and Silver Dimers Probed by EELS

    Kadkhodazadeh, Shima; de Lasson, Jakob Rosenkrantz; Beleggia, Marco


    with distance. Here, we have applied electron energy-loss spectroscopy (EELS) and scanning transmission electron microscopy (STEM) imaging to investigate the relationship between the SPR wavelength of gold and silver nanosphere dimers (radius R) and interparticle distance (d) in the range 0.1R .... Instead, within the range 0.1R gold and silver dimers. Despite this common power dependence, consistently larger SPR wavelength shifts are registered for silver for a given change in d, implying...... silver dimers to be more sensitive plasmon rulers than their gold counterparts....

  17. D-dimer is useful in assessing the vulnerable blood in elderly patients with coronary disease

    Yansong Zheng; Qiang Zeng; Liping Zhang; Liufa Duan; Kunlun He; Qiufu Zheng


    Background and objective The value of D-dimer in the risk stratification of patients with coronary artery diseas(CAD)and the relationship between D-dimer and the diseased coronary arteries remains controversial or unclear.especially in the elderly.Thisstudy was to evaluate the usefulness of D-djmer as a biomarker in assessing the vuinerable blood in the elderly patients with coronarydisease.Methods Sixty elderly (≥60 years old)male patients with suspected CAD were enrolled in this prospective study.Patients were divided into CAD group(n=41,10 with stable angina and 31 with unstable angina)and control group(n=19)according to their coronary angiography Results Clinicalinformation including age,body mass index(BMI),smoking index,and thecomplications of Primary hypertension or diabetes.and CAD family history was collected.Venous blood was sampled serially for thedetermination of total cholesterol,HDL cholesterol,LDL cholesterol,triglycerides,apoAl,apoB,glucose,uric acid,homocysteine(Hey),hs-CRP,soluble thrombomodulin(sTM),and marker of fibrinolytic system and hypercoagulability,such as D-dimer,fibrinogen,etc.The extent of coronary atherosclerosis was assessed.using the Gensini scoring system on the basis of coronary angiography.Results Compared with the controls.the patients with CAD had significantly higher levels of D-dimer.D-dimer level wassignificantly correlated to age.hs-CR P.Hcy,and PAI-1.Patients with D-dimer levels in the top triplicate of D-dimer level hadsignificantly higher prevalence of unstable angina compared with patients in the lowest triplicate(OR=4.8,Z=3.28,P=0.001).In anordinal logistic regression.the OR value ofdeveloping more serious CAD augmented 3.1-foid with each increasing triplicate of D-dimer.Patients with unstable angina had a significantly higher level of D-dimer than the controls(P=0.005),and an increasing trend comparedwith patients with stable angina (P=0.059).whereas there was no difference between the patients with stable angina and

  18. A 4% efficient organic solar cell using a fluorinated fused subphthalocyanine dimer as an electron acceptor

    Verreet, Bregt; Heremans, Paul [IMEC, Kapeldreef 75, B-3001 Leuven (Belgium); ESAT, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Leuven (Belgium); Rand, Barry P.; Cheyns, David; Hadipour, Afshin; Aernouts, Tom [IMEC, Kapeldreef 75, B-3001 Leuven (Belgium); Medina, Anais; Claessens, Christian G. [Departamento de Quimica Organica, Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid (Spain); Torres, Tomas [Departamento de Quimica Organica, Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid (Spain); IMDEA-Nanociencia, Facultad de Ciencias, Ciudad Universitaria de Cantoblanco, 28049 Madrid (Spain)


    Planar bilayer organic solar cells with a fluorinated fused subphthalocyanine dimer (FSubPcDimer) as an acceptor and chloroboron (III) subphthalocyanine (SubPc) as a donor obtain a 60% higher J{sub sc} compared to cells using C{sub 60} as an acceptor, resulting in a power conversion efficiency of 4%. This is obtained thanks to the important contribution to the photocurrent of the low-bandgap FSubPcDimer. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  19. Theoretical Studies on the Hydrogen-bonding and π-Stacking Interactions in the m-Nisoldipine Polymorphism Dimers%Theoretical Studies on the Hydrogen-bonding and π-Stacking Interactions in the m-Nisoldipine Polymorphism Dimers

    Zhu, Min; Meng, Lingpeng; Zheng, Shijun; Wang, Jing; Zeng, Yanli


    The intermolecular interactions in the dimers of m-nisoldipine polymorphism were studied by B3LYP calculations and quantum theory of "atoms in molecules" (QTAIM) studies. Four geometries of dimers were obtained: dimer I (a:dimer, O…H--N), dimer II (b-dimer, O…H--N), dimer III (b-dimer, n-stacking-c), and dimer IV (b-dimer, n-stacking-p). The interaction energies of the four dimers are along the sequence of II〉I〉III〉IV. The intermolecular distance of the interactions follows the order: I (O…H--N)〈II (O…H--N), and III (n-stacking)〈 IV (n-stacking). Both the O…H--N hydrogen-bonding and n-stacking interactions belong to weak non-covalent interactions. The O…H--N hydrogen-bonding interactions with more electrostatic characters are stronger than the n-stacking interactions. The strength of the weak interactions decreases in the order: I〉II〉III〉IV, and the electrostatic character decreases along the sequence: I〉II〉III〉IV.

  20. Acoustic Type-II Weyl Nodes from Stacking Dimerized Chains

    Yang, Zhaoju; Zhang, Baile


    Lorentz-violating type-II Weyl fermions, which were missed in Weyl's prediction of nowadays classified type-I Weyl fermions in quantum field theory, have recently been proposed in condensed matter systems. The semimetals hosting type-II Weyl fermions offer a rare platform for realizing many exotic physical phenomena that are different from type-I Weyl systems. Here we construct the acoustic version of a type-II Weyl Hamiltonian by stacking one-dimensional dimerized chains of acoustic resonators. This acoustic type-II Weyl system exhibits distinct features in a finite density of states and unique transport properties of Fermi-arc-like surface states. In a certain momentum space direction, the velocity of these surface states is determined by the tilting direction of the type-II Weyl nodes rather than the chirality dictated by the Chern number. Our study also provides an approach of constructing acoustic topological phases at different dimensions with the same building blocks.

  1. Bright Solitons in a PT-Symmetric Chain of Dimers

    Omar B. Kirikchi


    Full Text Available We study the existence and stability of fundamental bright discrete solitons in a parity-time- (PT- symmetric coupler composed by a chain of dimers that is modelled by linearly coupled discrete nonlinear Schrödinger equations with gain and loss terms. We use a perturbation theory for small coupling between the lattices to perform the analysis, which is then confirmed by numerical calculations. Such analysis is based on the concept of the so-called anticontinuum limit approach. We consider the fundamental onsite and intersite bright solitons. Each solution has symmetric and antisymmetric configurations between the arms. The stability of the solutions is then determined by solving the corresponding eigenvalue problem. We obtain that both symmetric and antisymmetric onsite mode can be stable for small coupling, in contrast to the reported continuum limit where the antisymmetric solutions are always unstable. The instability is either due to the internal modes crossing the origin or the appearance of a quartet of complex eigenvalues. In general, the gain-loss term can be considered parasitic as it reduces the stability region of the onsite solitons. Additionally, we analyse the dynamic behaviour of the onsite and intersite solitons when unstable, where typically it is either in the form of travelling solitons or soliton blow-ups.

  2. Polarization State of Light Scattered from Quantum Plasmonic Dimer Antennas.

    Yang, Longkun; Wang, Hancong; Fang, Yan; Li, Zhipeng


    Plasmonic antennas are able to concentrate and re-emit light in a controllable manner through strong coupling between metallic nanostructures. Only recently has it found that quantum mechanical effects can drastically change the coupling strength as the feature size approaches atomic scales. Here, we present a comprehensive experimental and theoretical study of the evolution of the resonance peak and its polarization state as the dimer-antenna gap narrows to subnanometer scale. We clearly can identify the classical plasmonic regime, a crossover regime where nonlocal screening plays an important role, and the quantum regime where a charge transfer plasmon appears due to interparticle electron tunneling. Moreover, as the gap decreases from tens of to a few nanometers, the bonding dipole mode tends to emit photons with increasing polarizability. When the gap narrows to quantum regime, a significant depolarization of the mode emission is observed due to the reduction of the charge density of coupled quantum plasmons. These results would be beneficial for the understanding of quantum effects on emitting-polarization of nanoantennas and the development of quantum-based photonic nanodevices.

  3. Photoionization spectroscopy of excited states of cold cesium dimers

    Bouloufa, Nadia; Viteau, Matthieu; Chotia, Amodsen; Fioretti, Andrea; Gabbanini, Carlo; Allegrini, Maria; Aymar, Mireille; Comparat, Daniel; Dulieu, Olivier; Pillet, Pierre


    Photoionization spectroscopy of cold cesium dimers obtained by photoassociation of cold atoms in a magneto-optical trap is reported here. In particular, we report on the observation and on the spectroscopic analysis of all the excited states that have actually been used for efficient detection of cold molecules stabilized in the triplet a^3Sigma_u^+ ground state. They are: the (1)^3Sigma_g^+ state connected to the 6s+6p asymptote, the (2)^3Sigma_g^+ and (2)^3Pi_g states connected to the 6s+5d asymptote and finally the (3)^3Sigma_g^+ state connected to the 6s + 7s asymptote. The detection through these states spans a wide range of laser energies, from 8000 to 16500 cm-1, obtained with different laser dyes and techniques. Information on the initial distribution of cold molecules among the different vibrational levels of the a^3Sigma_u^+ ground state is also provided. This spectroscopic knowledge is important when conceiving schemes for quantum manipulation, population transfer and optical detection of cold cesi...

  4. Ultraviolet light-induced cyclobutane pyrimidine dimers in rabbit eyes.

    Mallet, Justin D; Rochette, Patrick J


    Sunlight exposure of the eye leads to pathologies including photokeratitis, cortical cataracts, pterygium, actinic conjunctivitis and age-related macular degeneration. It is well established that exposure to ultraviolet (UV) radiations leads to DNA damage, mainly cyclobutane pyrimidine dimers (CPDs). CPD formation is the principal factor involved in skin cancer. However, the exact mechanism by which sunlight induces ocular pathologies is not well understood. To shed light on this issue, we quantified the CPD formation onto DNA of rabbit ocular cells following UVB exposure. We found that CPDs were induced only in the structures of the ocular anterior chamber (cornea, iris and lens) and were more concentrated in the corneal epithelium. Residual UVB that pass through the cornea are completely absorbed by the anterior layers of the iris. CPDs were also detected in the central portion of the lens that is not protected by the iris (pupil). By determining the UV-induced DNA damage formation in eyes, we showed that anterior ocular structures are a reliable physical barrier that protects the subjacent structures from the toxic effects of UV. Although the corneal epithelium is the structure where most of the CPDs were detected, no cancer is related to solar exposure.

  5. Autoregulation of MARCH1 expression by dimerization and autoubiquitination.

    Bourgeois-Daigneault, Marie-Claude; Thibodeau, Jacques


    Some members of the membrane-associated RING-CH family of E3 ubiquitin ligases (MARCHs) are membrane-bound and target major players of the immune response. MARCH1 ubiquitinates and downregulates MHC class II expression in APCs. It is induced by IL-10 and despite a strong increase in mRNA expression in human primary monocytes, the protein remains hardly detectable. To gain insights into the posttranslational regulation of MARCH1, we investigated whether its expression is itself regulated by ubiquitination. Our results demonstrate that MARCH1 is ubiquitinated in transfected human cell lines. Polyubiquitin chain-specific Abs revealed the presence of K48-linked polyubiquitin chains. A mutant devoid of lysine residues in the N- and C-terminal regions was less ubiquitinated and had a prolonged half-life. Reduced ubiquitination was also observed for an inactive mutated form of the molecule (M1WI), suggesting that MARCH1 is capable of autoubiquitination. Immunoprecipitation and energy transfer experiments demonstrated that MARCH1 homodimerizes and also forms heterodimers with others family members. Coexpression of MARCH1 decreased the protein levels of the inactive M1WI, suggesting a transubiquitination process. Taken together, our results suggest that MARCH1 may regulate its own expression through dimerization and autoubiquitination.

  6. Self-Assembling Multifunctional Peptide Dimers for Gene Delivery Systems

    Kitae Ryu


    Full Text Available Self-assembling multifunctional peptide was designed for gene delivery systems. The multifunctional peptide (MP consists of cellular penetrating peptide moiety (R8, matrix metalloproteinase-2 (MMP-2 specific sequence (GPLGV, pH-responsive moiety (H5, and hydrophobic moiety (palmitic acid (CR8GPLGVH5-Pal. MP was oxidized to form multifunctional peptide dimer (MPD by DMSO oxidation of thiols in terminal cysteine residues. MPD could condense pDNA successfully at a weight ratio of 5. MPD itself could self-assemble into submicron micelle particles via hydrophobic interaction, of which critical micelle concentration is about 0.01 mM. MPD showed concentration-dependent but low cytotoxicity in comparison with PEI25k. MPD polyplexes showed low transfection efficiency in HEK293 cells expressing low level of MMP-2 but high transfection efficiency in A549 and C2C12 cells expressing high level of MMP-2, meaning the enhanced transfection efficiency probably due to MMP-induced structural change of polyplexes. Bafilomycin A1-treated transfection results suggest that the transfection of MPD is mediated via endosomal escape by endosome buffering ability. These results show the potential of MPD for MMP-2 targeted gene delivery systems due to its multifunctionality.

  7. Active control of nano dimers response using piezoelectric effect

    Mekkawy, Ahmed A.; Ali, Tamer A.; Badawi, Ashraf H.


    Nano devices can be used as building blocks for Internet of Nano-Things network devices, such as sensors/actuators, transceivers, and routers. Although nano particles response can be engineered to fit in different regimes, for such a nano particle to be used as an active nano device, its properties should be dynamically controlled. This controllability is a challenge, and there are many proposed techniques to tune nanoparticle response on the spot through a sort of control signal, wither that signal is optical (for all-optical systems) or electronic (for opto-electronic systems). This will allow the use of nano particles as nano-switches or as dynamic sensors that can pick different frequencies depending on surrounding conditions or depending on a smart decisions. In this work, we propose a piezoelectric substrate as an active control mediator to control plasmonic gaps in nano dimers. This method allows for integrating nano devices with regular electronics while communicating control signals to nano devices through applying electric signals to a piezoelectric material, in order to control the gaps between nano particles in a nano cluster. We do a full numerical study to the system, analyzing the piezoelectric control resolution (minimum gap change step) and its effect on a nanodimer response as a nanoantenna. This analysis considers the dielectric functions of materials within the visible frequencies range. The effects of different parameters, such as the piezoelectric geometrical structure and materials, on the gap control resolution and the operating frequency are studied.

  8. Preparation of gold nanoparticle dimers via streptavidin-induced interlinking

    Zon, Vera B.; Sachsenhauser, Matthias; Rant, Ulrich, E-mail: [Technische Universitaet Muenchen, Walter Schottky Institut (Germany)


    There is great interest in establishing efficient means of organizing nanoparticles into complex structures, especially in fields like nano-optical devices. One of the demonstrated routes uses biomolecular scaffolds, like the streptavidin-biotin system, to deterministically separate and structure particle complexes. However, controlled formation of streptavidin-linked nanoparticle dimers or trimers is challenging, and large aggregates are often formed under conditions that are difficult to regulate. Here, we studied the aggregates and interlinking kinetics of biotin-functionalized 20 nm gold nanoparticles in the presence of the interlinking protein, streptavidin. We found two different protein-linker concentration regions where small stable particle aggregates are formed: when the protein and nanoparticle concentrations are similar and when the protein to nanoparticle concentration ratio exceeds intermediate concentrations (10:1-100:1) that promote precipitation of large aggregates. We attribute this behavior to the limited availability of free-linker molecules and the limited availability of free ligand (biotin) on the particle surface for low and high protein concentrations, respectively. Furthermore, we show that the product can be additionally enriched up to 25 % through either centrifugation in sucrose or size-exclusion chromatography. These results provide additional understanding into the assembly of ligand-functionalized nanoparticles with water-soluble linkers and provide a facile way to produce well-defined small aggregates for potential use in, for instance, surface-enhanced spectroscopy.

  9. New ent-kaurane diterpenoid dimer from Pulicaria inuloides.

    Galala, Amal A; Sallam, Amal; Abdel-Halim, Osama B; Gedara, Sahar R


    A new naturally occurring ent-kaurane diterpenoid dimer, 15β, 15'β-oxybis (ent-kaur-16-en-19-oic acid) (1) along with six known compounds, 15β-hydroxy-ent-kaur-16-en-19-oic acid (2), 15β-hydroxy-ent-kaur-16-en-19-oate-β-d-glucopyranoside (3), 6-hydroxykaempferol-3, 7-dimethyl ether (4), quercetagetin 3, 7, 3'-trimethyl ether (5), β-sitosterol (6) and β-sitosterol glucoside (daucosterol) (7) were isolated from the aerial parts of Pulicaria inuloides DC. Compounds 2-5 were isolated for the first time from genus Pulicaria. The structures of compounds 1-7 were established on the basis of extensive 1D and 2D NMR spectroscopic techniques in combination with ESI-MS. The antimicrobial activity of the isolated compounds was evaluated against Staphylococcus aureus, Escherichia coli and Candida albicans. Sulphorhodamine B cytotoxic assay against HepG2 (liver cancer) cell line and ABTS antioxidant assay were carried out.

  10. Polymeric architectures of bismuth citrate based on dimeric building blocks


    Four bismuth complexes, (H2En)[Bi2(cit)2(H2O)4/3]·(H2O)x (1), (H2En)3[Bi2(cit)2Cl4]·(H2O)x (2), (HPy)2[Bi2(cit)2(H2O)8/5]·(H2O)x (3) and (H2En)[Bi2(cit)2](H2O)x (4) [cit = citrate4-; En = ethylenediamine; Py = pyridine] have been synthesized and crystallized. The crystal structures reveal that the basic building blocks in all of these complexes are bismuth citrate dimeric units which combine to form polymeric architectures. The embedded protonated ethylenediamine and pyridine moieties in the polymeric frameworks have been identified by X-ray crystallography and solid-state cross polarization/magic angle spinning (CP/MAS) 13C NMR. Based on the framework of complex 1, a structural model of a clinically used antiulcer drug, ranitidine bismuth citrate (RBC) was generated. The behavior of the protonated amine-bismuth citrate complexes in acidic aqueous solution has been studied by electrospray ionization-mass spectrometry (ESI-MS).

  11. Roughness effect on the efficiency of dimer antenna based biosensor

    Dominique Barchiesi


    Full Text Available The fabrication process of nanodevices is continually improved. However, most of the nanodevices, such as biosensors present rough surfaces with mean roughness of some nanometers even if the deposition rate of material is more controlled. The effect of roughness on performance of biosensors was fully addressed for plane biosensors and gratings, but rarely addressed for biosensors based on Local Plasmon Resonance. The purpose of this paper is to evaluate numerically the influence of nanometric roughness on the efficiency of a dimer nano-biosensor (two levels of roughness are considered. Therefore, we propose a general numerical method, that can be applied to any other nanometric shape, to take into account the roughness in a three dimensional model. The study focuses on both the far-field, which corresponds to the experimental detected data, and the near-field, responsible for exciting and then detecting biological molecules. The results suggest that the biosensor efficiency is highly sensitive to the surface roughness. The roughness can produce important shifts of the extinction efficiency peak and a decrease of its amplitude resulting from changes in the distribution of near-field and absorbed electric field intensities.

  12. Antifungal dimeric chalcone derivative kamalachalcone E from Mallotus philippinensis.

    Kulkarni, Roshan R; Tupe, Santosh G; Gample, Suwarna P; Chandgude, Macchindra G; Sarkar, Dhiman; Deshpande, Mukund V; Joshi, Swati P


    From the red coloured extract (Kamala) prepared through acetone extraction of the fresh whole uncrushed fruits of Mallotus philippinensis, one new dimeric chalcone (1) along with three known compounds 1-(5,7-dihydroxy-2,2,6-trimethyl-2H-1-benzopyran-8-yl)-3-phenyl-2-propen-1-one (2), rottlerin (3) and 4'-hydroxyrottlerin (4) were isolated. The structure of compound 1 was elucidated by 1D and 2D NMR analyses that included HSQC, HMBC, COSY and ROESY experiments along with the literature comparison. Compounds 1-4 were evaluated for antifungal activity against different human pathogenic yeasts and filamentous fungi. The antiproliferative activity of the compounds was evaluated against Thp-1 cell lines. Compounds 1 and 2 both exhibited IC50 of 8, 4 and 16 μg/mL against Cryptococcus neoformans PRL518, C. neoformans ATCC32045 and Aspergillus fumigatus, respectively. Compound 4, at 100 μg/mL, showed 54% growth inhibition of Thp-1 cell lines.

  13. Alcohol dimers--how much diagonal OH anharmonicity?

    Kollipost, Franz; Papendorf, Kim; Lee, Yu-Fang; Lee, Yuan-Pern; Suhm, Martin A


    The OH bond of methanol, ethanol and t-butyl alcohol becomes more anharmonic upon hydrogen bonding and the infrared intensity ratio between the overtone and the fundamental transition of the bridging OH stretching mode decreases drastically. FTIR spectroscopy of supersonic slit jet expansions allows to quantify these effects for isolated alcohol dimers, enabling a direct comparison to anharmonic vibrational predictions. The diagonal anharmonicity increase amounts to 15-18%, growing with increasing alkyl substitution. The overtone/fundamental IR intensity ratio, which is on the order of 0.1 or more for isolated alcohols, drops to 0.004-0.001 in the hydrogen-bonded OH group, making overtone detection very challenging. Again, alkyl substitution enhances the intensity suppression. Vibrational second order perturbation theory appears to capture these effects in a semiquantitative way. Harmonic quantum chemistry predictions for the hydrogen bond-induced OH stretching frequency shift (the widely used infrared signature of hydrogen bonding) are insufficient, and diagonal anharmonicity corrections from experiment make the agreement between theory and experiment worse. Inclusion of anharmonic cross terms between hydrogen bond modes and the OH stretching mode is thus essential, as is a high level electronic structure theory. The isolated molecule results are compared to matrix isolation data, complementing earlier studies in N2 and Ar by the more weakly interacting Ne and p-H2 matrices. Matrix effects on the hydrogen bond donor vibration are quantified.

  14. Qualitative point-of-care D-dimer testing compared with quantitative D-dimer testing in excluding pulmonary embolism in primary care.

    Lucassen, W A M; Erkens, P M G; Geersing, G J; Büller, H R; Moons, K G M; Stoffers, H E J H; van Weert, H C P M


    General practitioners can safely exclude pulmonary embolism (PE) by using the Wells PE rule combined with D-dimer testing. To compare the accuracy of a strategy using the Wells rule combined with either a qualitative point-of-care (POC) D-dimer test performed in primary care or a quantitative laboratory-based D-dimer test. We used data from a prospective cohort study including 598 adults suspected of PE in primary care in the Netherlands. General practitioners scored the Wells rule and carried out a qualitative POC test. All patients were referred to hospital for reference testing. We obtained quantitative D-dimer test results as performed in hospital laboratories. The primary outcome was the prevalence of venous thromboembolism in low-risk patients. Prevalence of PE was 12.2%. POC D-dimer test results were available in 582 patients (97%). Quantitative test results were available in 401 patients (67%). We imputed results in 197 patients. The quantitative test and POC test missed one (0.4%) and four patients (1.5%), respectively, with a negative strategy (Wells ≤ 4 points and D-dimer test negative) (P = 0.20). The POC test could exclude 23 more patients (4%) (P = 0.05). The sensitivity and specificity of the Wells rule combined with a POC test were 94.5% and 51.0% and, combined with a quantitative test, 98.6% and 47.2%, respectively. Combined with the Wells PE rule, both tests are safe to use in excluding PE. The quantitative test seemed to be safer than the POC test, albeit not statistically significant. The specificity of the POC test was higher, resulting in more patients in whom PE could be excluded. © 2015 International Society on Thrombosis and Haemostasis.

  15. Diagnostic Accuracy of a New d-Dimer Assay (Sclavo Auto d-Dimer) for Exclusion of Deep Vein Thrombosis in Symptomatic Outpatients.

    Legnani, Cristina; Cini, Michela; Frascaro, Mirella; Rodorigo, Giuseppina; Sartori, Michelangelo; Cosmi, Benilde


    In patients presenting non-high clinical pretest probability (PTP), a negative d-dimer can exclude venous thromboembolism without imaging tests. However, each d-dimer assay should be validated in prospective studies. We evaluated an automated d-dimer immunoassay using the Sclavo Auto d-dimer (Sclavo Diagnostics Int, Sovicille, Italy) provided by Dasit Diagnostica (Cornaredo, Milan, Italy). Three hundred two consecutive outpatients suspected of leg deep vein thrombosis (DVT) with non-high PTP were included. The Sclavo Auto d-dimer assay was evaluated on 2 analyzers (Sysmex CA-7000 and Sysmex CS-2100; Sysmex Corporation, Kobe, Japan, provided by Dasit). The cutoff value (200 ng/mL) was established a priori. Prevalence of DVT was 11.9%. Since no false-negative patients were detected, the sensitivity and negative predictive values (NPVs) were 100% (sensitivity = CA-7000: 100% [95% confidence interval, CI: 93.3-100], CS-2100: 100% [95% CI: 93.3-100]; NPV = CA-7000: 100% [95% CI: 97.9-100], CS-2100: 100% [95% CI: 98.0-100]). Specificity was 65.4% (95% CI: 59.4-71.1) and 69.2% (95% CI: 63.3-74.7) for CA-7000 and CS-2100, respectively. Specificity increased when a higher cutoff value (234 ng/mL) was used for patients aged ≥60 years without compromising the safety. Assay reproducibility was satisfactory at concentrations near the cutoff value (total coefficient of variations d-dimer assay was accurate when used for DVT diagnostic workup in outpatients with non-high PTP. Based on its high sensitivity and NPV, it can be used as a stand-alone test in outpatients with non-high PTP. Given its high specificity, the number of patients in whom further imaging techniques can be avoided increased, improving the yield of the test.

  16. Van der Waals potential and vibrational energy levels of the ground state radon dimer

    Sheng, Xiaowei; Qian, Shifeng; Hu, Fengfei


    In the present paper, the ground state van der Waals potential of the Radon dimer is described by the Tang-Toennies potential model, which requires five essential parameters. Among them, the two dispersion coefficients C6 and C8 are estimated from the well determined dispersion coefficients C6 and C8 of Xe2. C10 is estimated by using the approximation equation that C6C10 / C82 has an average value of 1.221 for all the rare gas dimers. With these estimated dispersion coefficients and the well determined well depth De and Re the Born-Mayer parameters A and b are derived. Then the vibrational energy levels of the ground state radon dimer are calculated. 40 vibrational energy levels are observed in the ground state of Rn2 dimer. The last vibrational energy level is bound by only 0.0012 cm-1.

  17. Human cystatin C forms an inactive dimer during intracellular trafficking in transfected CHO cells

    Merz, G S; Benedikz, Eirikur; Schwenk, V


    To define the cellular processing of human cystatin C as well as to lay the groundwork for investigating its contribution to lcelandic Hereditary Cerebral Hemorrhage with Amyloidosis (HCHWA-I), we have characterized the trafficking, secretion, and extracellular fate of human cystatin C...... that the cystatin C dimer, formed during intracellular trafficking, is converted to monomer at or before secretion. Cells in which exit from the endoplasmic reticulum (ER) was blocked with brefeldin A contained the 33 kDa species, indicating that cystatin C dimerization occurs in the ER. After removal of brefeldin......, presumably as a consequence of the low pH of late endosome/lysosomes. As a dimer, cystatin C would be prevented from inhibiting the lysosomal cysteine proteases. These results reveal a novel mechanism, transient dimerization, by which cystatin C is inactivated during the early part of its trafficking through...

  18. Nonlinear optical properties of porphyrin and chlorophyll dimers studied by degenerated four wave mixing

    Chen, L.X.Q.


    As one of the important elements in natural and artificial electron transfer and energy transfer processes, porphyrin and its derivatives have received much attention in photoelectronics and photoelectronic materials. As our first attempt to relate the {pi}-{pi} electronic couplings between porphyrin macrocycles to apparent third order nonlinear susceptibilities, we measured {chi}({sup 3}) for several porphyrin and chlorophyll a derivatives, including dimers with different configurations. Our preliminary results show that the dimers have enhanced {chi}({sup 3}) compared to those of the monomer. This enhancement is related to the relative orientations between the two macrocycles in the dimers. The parallel dimers with close face-to-face distances seem to have the highest enhancement in {chi}({sup 3}). Thus, we believe that {chi}({sup 3}) is strongly related to the {pi}-{pi} electronic coupling between the two conjugated ring systems.

  19. Nonlinear optical properties of porphyrin and chlorophyll dimers studied by degenerated four wave mixing

    Chen, L.X.Q.


    As one of the important elements in natural and artificial electron transfer and energy transfer processes, porphyrin and its derivatives have received much attention in photoelectronics and photoelectronic materials. As our first attempt to relate the [pi]-[pi] electronic couplings between porphyrin macrocycles to apparent third order nonlinear susceptibilities, we measured [chi]([sup 3]) for several porphyrin and chlorophyll a derivatives, including dimers with different configurations. Our preliminary results show that the dimers have enhanced [chi]([sup 3]) compared to those of the monomer. This enhancement is related to the relative orientations between the two macrocycles in the dimers. The parallel dimers with close face-to-face distances seem to have the highest enhancement in [chi]([sup 3]). Thus, we believe that [chi]([sup 3]) is strongly related to the [pi]-[pi] electronic coupling between the two conjugated ring systems.

  20. Biosynthesis of intestinal microvillar proteins. Dimerization of aminopeptidase N and lactase-phlorizin hydrolase

    Danielsen, E M


    The pig intestinal brush border enzymes aminopeptidase N (EC and lactase-phlorizin hydrolase (EC are present in the microvillar membrane as homodimers. Dimethyl adipimidate was used to cross-link the two [35S]methionine-labeled brush border enzymes from cultured mucosal...... explants. For aminopeptidase N, dimerization did not begin until 5-10 min after synthesis, and maximal dimerization by cross-linking of the transient form of the enzyme required 1 h, whereas the mature form of aminopeptidase N cross-linked with unchanged efficiency from 45 min to 3 h of labeling. Formation...... of dimers of this enzyme therefore occurs prior to the Golgi-associated processing, and the slow rate of dimerization may be the rate-limiting step in the transport from the endoplasmic reticulum to the Golgi complex. For lactase-phlorizin hydrolase, the posttranslational processing includes a proteolytic...

  1. Design of dimerization inhibitors of HIV-1 aspartic proteinase: A computer-based combinatorial approach

    Caflisch, Amedeo; Schramm, Hans J.; Karplus, Martin


    Inhibition of dimerization to the active form of the HIV-1 aspartic proteinase (HIV-1 PR) may be a way to decrease the probability of escape mutations for this viral protein. The Multiple Copy Simultaneous Search (MCSS) methodology was used to generate functionality maps for the dimerization interface of HIV-1 PR. The positions of the MCSS minima of 19 organic fragments, once postprocessed to take into account solvation effects, are in good agreement with experimental data on peptides that bind to the interface. The MCSS minima combined with an approach for computational combinatorial ligand design yielded a set of modified HIV-1 PR C-terminal peptides that are similar to known nanomolar inhibitors of HIV-1 PR dimerization. A number of N-substituted 2,5-diketopiperazines are predicted to be potential dimerization inhibitors of HIV-1 PR.

  2. Transition metal dimers as potential molecular magnets: A challenge to computational chemistry

    Fritsch, Daniel; Richter, Manuel; Eschrig, Helmut


    Dimers are the smallest chemical objects that show magnetic anisotropy. We focus on 3$d$ and 4$d$ transition metal dimers that have magnetic ground states in most cases. Some of these magnetic dimers have a considerable barrier against re-orientation of their magnetization, the so-called magnetic anisotropy energy, MAE. The height of this barrier is important for technological applications, as it determines, e.g., the stability of information stored in magnetic memory devices. It can be estimated by means of relativistic density functional calculations. Our approach is based on a full-potential local-orbital method (FPLO) in a four-component Dirac-Kohn-Sham implementation. Orbital polarization corrections to the local density approximation are employed. They are discussed in the broader context of orbital dependent density functionals. Ground state properties (spin multiplicity, bond length, harmonic vibrational frequency, spin- and orbital magnetic moment, and MAE) of the 3$d$ and 4$d$ transition metal dimer...

  3. Theoretical Studies on Intermolecular Interactions of 4-Amino-5-nitro-1,2,3-triazole Dimers

    LU Ya-Lin; GONG Xue-Dong; JU Xue-Hai; MA Xiu-Fang; XIAO He-Ming


    Seven optimized configurations and their electronic structures of 4-amino-5-nitro-1,2,3-triazole dimers on their potential energy surface have been obtained by using density functional theory (DFT) method at the B3LYP/6-311++G** level. The maximum intermolecular interaction energy is -35.42 kJ/mol via the basis set superposition error-correction (BSSE) and zero point energy-correction (ZPE). Charge transfers between the two subsystems are small. The vibration analysis of optimized configurations was performed, and the thermodynamic property changes from monomer to dimer have been obtained with the temperature ranging from 200 to 800 K on the basis of statistical thermodynamics. It is found that the hydrogen bonds contribute to the dimers dominantly, and the extent of intermolecular interaction is mainly determined by the hydrogen bonds' strength rather than their number. The dimerization processes of Ⅳ, Ⅴ and Ⅵ can occur spontaneously at 200 K.

  4. A theoretical study on the intermolecular interaction of energetic system-itromethane dimer

    李金山; 董海山; 肖鹤鸣


    Three optimized geometries of nitromethane dimer have been obtained at the HF/6-31G* level. Dimer binding energies have been corrected for the basis set superposition error (BSSE) and the zero point energy. Computed results indicate that the cyclic structure cf (CH3NO2)2 is the most stable of three optimized geometries, whose corrected binding energyis 17.29 kJ·mo1-1 at the MP4SDTQ/6-31G*//HF/6-31G* level. In the optimized structures of nitromethane dimer, the intermolecular hydrogen bond has not been found; and the chargetransfer interaction between CH3NO2 subsystems is weak; and the correlation interaction energy makes a little contribution to the intermolecular interaction energy of the dimer.

  5. Dimeric ligands for GPCRs involved in human reproduction : synthesis and biological evaluation

    Bonger, Kimberly Michelle


    Dimeric ligands for G-protein coupled receptors that are involved in human reproduction, namely the gonadotropin releasing hormone receptor, the luteinizing hormone receptor and the follicle-stimulating hormone receptor, were synthesized and biologically evaluated.

  6. Gnetupendin C, a New Stilbene Dimer from the Lianas of Gnetum Pendulum


    Gnetupendin C, a new dimer coupled by a resveratrol and an oxyresveratrol unit, was isolated from the lianas of Gnetum pendulum C.Y. Cheng (Gnetaceae). Its structure was established on the basis of spectroscopic evidence, especially 2D techniques.

  7. A Note on Dimer Models and D-brane Gauge Theories

    Agarwal, Prarit; Sarkar, Tapobrata


    The connection between quiver gauge theories and dimer models has been well studied. It is known that the matter fields of the quiver gauge theories can be represented using the perfect matchings of the dimer model. We conjecture that the perfect matchings give information about the charge matrix of the quiver gauge theory. Further, we perform explicit computations on some aspects of partial resolutions of toric singularities using dimer models. We analyse these with graph theory techniques, using the perfect matchings of orbifolds of the form $\\BC^3/\\Gamma$, where the orbifolding group $\\Gamma$ may be noncyclic. Using these, we study the construction of the superpotential of gauge theories living on D-branes which probe these singularities, including the case where one or more adjoint fields are present upon partial resolution. Applying a combination of open and closed string techniques to dimer models, we also study some aspects of their symmetries.

  8. A strategy for complex dimer formation when biomimicry fails: total synthesis of ten coccinellid alkaloids.

    Sherwood, Trevor C; Trotta, Adam H; Snyder, Scott A


    Although dimeric natural products can often be synthesized in the laboratory by directly merging advanced monomers, these approaches sometimes fail, leading instead to non-natural architectures via incorrect unions. Such a situation arose during our studies of the coccinellid alkaloids, when attempts to directly dimerize Nature's presumed monomeric precursors in a putative biomimetic sequence afforded only a non-natural analogue through improper regiocontrol. Herein, we outline a unique strategy for dimer formation that obviates these difficulties, one which rapidly constructs the coccinellid dimers psylloborine A and isopsylloborine A through a terminating sequence of two reaction cascades that generate five bonds, five rings, and four stereocenters. In addition, a common synthetic intermediate is identified which allows for the rapid, asymmetric formal or complete total syntheses of eight monomeric members of the class.

  9. Robust Discrimination between Single Gold Nanoparticles and Their Dimers in Aqueous Solution for Ultrasensitive Homogeneous Bioassays

    Jun Kobayashi


    Full Text Available We propose a robust method to distinguish isolated single gold nanoparticles (AuNP monomers and their dimers under Brownian motion, a key for ultrasensitive homogeneous bioassays, including AuNP sandwich assays. To detect dimers and distinguish them from a larger number of monomers in aqueous solution, single-particle polarization microscopy was performed. For the accurate detection of individual particles, the optical anisotropy and rotational diffusion time are measured because a dimer is much more anisotropic than the nearly spherical monomer and the rotational diffusion time of a dimer is four times that of a monomer. By employing an autocorrelation analysis, we defined a measure of distinguishing that simultaneously enables high detection probability and low error probability. The detection platform offers homogeneous DNA hybridization assays and immunoassays at the subpicomolar level.

  10. Dimers of cyclic carbonates: chirality recognition in battery solvents and energy storage.

    Kollipost, Franz; Hesse, Susanne; Lee, Juhyon J; Suhm, Martin A


    Dimers of ethylene carbonate and propylene carbonate are created in supersonic jet expansions and characterized by FTIR spectroscopy. Fermi resonances are switched on and off by dimerization. There is a unique centrosymmetric dimer of ethylene carbonate in a pronounced case of complementary chirality synchronization, contributing to its energy storage capacity at melting. Two chiral propylene carbonate molecules combine in more intricate ways. If they have the same handedness, one of them is forced into an axial conformation and the binding partner stays in the more stable equatorial structure. If they have opposite handedness, centrosymmetric dimers of either axial or equatorial conformations are formed. This suggests the usefulness of chirality control in elucidating ionic transport mechanisms in battery solvents and asymmetric catalysis in such solvents.

  11. Synthesis and properties of a covalently linked angular perylene imide dimer.

    Thorley, Karl J; Würthner, Frank


    Utilizing the unexplored chemistry of a monocarbon analog to perylene bisimide, a covalently linked angular perylene dimer was synthesized. On the basis of measured optical properties and molecular modeling, the spectral changes relative to a monomeric reference perylene can be explained by an angle-dependent oblique exciton coupling model. With a roughly trigonal interchromophore arrangement, the dimer building block is promising for larger, cyclic assemblies to mimic naturally occurring light harvesting complexes.

  12. Plasmonic nanoparticle dimers for optical sensing of DNA in complex media.

    Chen, Jennifer I L; Chen, Yeechi; Ginger, David S


    We introduce a new sensing modality based on the actuation of discrete gold nanoparticle dimers. Binding of the target DNA leads to a geometrical extension of the dimer, thereby yielding a spectral blue shift in the hybridized plasmon mode as detected by single nanostructure scattering spectroscopy. The magnitude and opposite direction of this shift enabled us to spectroscopically distinguish the target from nonspecific binding and to detect the target in complex media like serum.

  13. Structure and Stability of a Dimeric G-Quadruplex Formed by Cyclic Oligonucleotides

    Joan Casals


    containing two copies of the human telomeric repeat. In the presence of sodium, NMR data are consistent with a dimeric structure of the molecule in which two cycles self-associate forming a quadruplex with three guanine tetrads connected by edgewise loops. The two macrocycles are arranged in a parallel way, and the dimeric structure exhibits a high melting temperature. These results indicate that cyclization of the phosphodiester chain does not prevent quadruplex formation, although it affects the global topology of the quadruplex.

  14. Photoreactivation of pyrimidine dimers in DNA from thyroid cells of the teleost, Poecilia formosa

    Achey, P.M.; Woodhead, A.D.; Setlow, R.B.


    We have developed and used a simple technique to estimate the quantity of pyrimidine dimers in unlabeled cellular DNA. DNA is extracted from cells, treated with an endonuclease specific for dimers, and its molecular weight estimated by its electrophoretic mobility on alkaline agarose slab gels. The technique is used to show that cells from thyroid tissue of the fish Poecilia formosa have photoreactivating activity towards dimmers in the cellular DNA.

  15. CDT coupled to dimer matter: An analytical approach via tree bijections

    Atkin, Max R


    We review a recently obtained analytical solution of a restricted so-called hard dimers model coupled to two-dimensional CDT. The combinatorial solution is obtained via bijections of causal triangulations with dimers and decorated trees. We show that the scaling limit of this model can also be obtained from a multi-critical point of the transfer matrix for dynamical triangulations of triangles and squares when one disallows for spatial topology changes to occur.

  16. Stabilization of Tryptophan Hydroxylase 2 by L-Phenylalanine Induced Dimerization

    Tidemand, Kasper Damgaard; Christensen, Hans Erik Mølager; Hoeck, Niclas


    fluorimetry, the unfolding transitions of rchTPH2 and NΔ47-rchTPH2 are found to shift from polyphasic to apparent two-state by the addition of L-Trp or L-Phe. Analytical gel filtration revealed that rchTPH2 and NΔ47-rchTPH2 reside in a monomer-dimer equilibrium which is significantly shifted towards dimer...

  17. Functional role of dimerization of human peptidylarginine deiminase 4 (PAD4.

    Yi-Liang Liu

    Full Text Available Peptidylarginine deiminase 4 (PAD4 is a homodimeric enzyme that catalyzes Ca²⁺-dependent protein citrullination, which results in the conversion of arginine to citrulline. This paper demonstrates the functional role of dimerization in the regulation of PAD4 activity. To address this question, we created a series of dimer interface mutants of PAD4. The residues Arg8, Tyr237, Asp273, Glu281, Tyr435, Arg544 and Asp547, which are located at the dimer interface, were mutated to disturb the dimer organization of PAD4. Sedimentation velocity experiments were performed to investigate the changes in the quaternary structures and the dissociation constants (K(d between wild-type and mutant PAD4 monomers and dimers. The kinetic data indicated that disrupting the dimer interface of the enzyme decreases its enzymatic activity and calcium-binding cooperativity. The K(d values of some PAD4 mutants were much higher than that of the wild-type (WT protein (0.45 µM and were concomitant with lower k(cat values than that of WT (13.4 s⁻¹. The K(d values of the monomeric PAD4 mutants ranged from 16.8 to 45.6 µM, and the k(cat values of the monomeric mutants ranged from 3.3 to 7.3 s⁻¹. The k(cat values of these interface mutants decreased as the K(d values increased, which suggests that the dissociation of dimers to monomers considerably influences the activity of the enzyme. Although dissociation of the enzyme reduces the activity of the enzyme, monomeric PAD4 is still active but does not display cooperative calcium binding. The ionic interaction between Arg8 and Asp547 and the Tyr435-mediated hydrophobic interaction are determinants of PAD4 dimer formation.

  18. New 3,4-seco-ent-kaurene dimers from Croton micans.

    Mateu, Elsa; Chavez, Katiuska; Riina, Ricarda; Compagnone, Reinaldo S; Delle Monache, Franco; Suárez, Alírica I


    From the stems of Croton micans Sw., five new 3,4-seco-ent-kaurene dimers: micansinoic acid (1), isomicansinoic acid (2), and the dimethyl (3), monomethyl (4) and monoethyl ester (5) of micansinoic acid were isolated. The structures of the new compounds were elucidated by spectroscopic data interpretation, mainly 1D and 2D NMR experiments and MS. These compounds are the first 3,4-seco-ent-kaurene dimers from a Croton species.

  19. On the gas-phase dimerization of negatively charged closo-dodecaborates: a theoretical study.

    Zeonjuk, Lei Liu; Vankova, Nina; Knapp, Carsten; Gabel, Detlef; Heine, Thomas


    We have studied the intriguing gas-phase dimerization of the B12In(-) (n = 9, 8) anions to B24I2n(2-) dianions by means of density functional theory calculations. The dimerization of B12I9(-) to B24I18(2-) has been detected experimentally in a previous study (Phys. Chem. Chem. Phys., 2011, 13, 5712) utilizing electrospray ionization ion trap mass spectrometry (ESI-IT-MS), whereas the formation of B24I16(2-) from B12I8(-) is modeled here prior to experiment. Calculations are carried out to determine the molecular and electronic structures, the bonding situation and the stability of the dimers relative to the respective monomers. The dimerization process is found to be thermodynamically favorable, and the stability of the lowest-energy structures is substantiated by molecular dynamics simulations. The calculations imply that the experimentally observed B24I18(2-) and the hypothetical B24I16(2-) species are formed through dimerization of the respective B12In(-) (n = 9, 8) monomers, rather than through loss of two I radicals from B24I2n+2(2-) dimers. Electronic properties such as natural charges, vertical detachment energies (VDEs), frontier molecular orbitals (FMOs), and HOMO-LUMO gaps are computed and analyzed in detail for all monomers and dimers. The analysis shows that the most stable B24I2n(2-) dimers are formed through two 2c-2e B-B and two 3c-2e B-I-B bridges between the parent B12In(-) (n = 9, 8) monomers. These new bridging bonds engage the deiodinated (bare) faces of the two B12 icosahedra, as well as one (per monomer) of the nearest boron neighbors and its iodine substituent.

  20. N-glycosylation of the β2 adrenergic receptor regulates receptor function by modulating dimerization.

    Li, Xiaona; Zhou, Mang; Huang, Wei; Yang, Huaiyu


    N-glycosylation is a common post-translational modification of G-protein-coupled receptors (GPCRs). However, it remains unknown how N-glycosylation affects GPCR signaling. β2 adrenergic receptor (β2 AR) has three N-glycosylation sites: Asn6, Asn15 at the N-terminus, and Asn187 at the second extracellular loop (ECL2). Here, we show that deletion of the N-glycan did not affect receptor expression and ligand binding. Deletion of the N-glycan at the N-terminus rather than Asn187 showed decreased effects on isoproterenol-promoted G-protein-dependent signaling, β-arrestin2 recruitment, and receptor internalization. Both N6Q and N15Q showed decreased receptor dimerization, while N187Q did not influence receptor dimerization. As decreased β2 AR homodimer accompanied with reduced efficiency for receptor function, we proposed that the N-glycosylation of β2 AR regulated receptor function by influencing receptor dimerization. To verify this hypothesis, we further paid attention to the residues at the dimerization interface. Studies of Lys60 and Glu338, two residues at the receptor dimerization interface, exhibited that the K60A/E338A showed decreased β2 AR dimerization and its effects on receptor signaling were similar to N6Q and N15Q, which further supported the importance of receptor dimerization for receptor function. This work provides new insights into the relationship among glycosylation, dimerization, and function of GPCRs. Peptide-N-glycosidase F (PNGase F, EC; endo-β-N-acetylglucosaminidase A (Endo-A, EC © 2017 Federation of European Biochemical Societies.

  1. Mutational Analysis and Allosteric Effects in the HIV-1 Capsid Protein Carboxyl-Terminal Dimerization Domain


    The carboxyl-terminal domain (CTD, residues 146−231) of the HIV-1 capsid (CA) protein plays an important role in the CA−CA dimerization and viral assembly of the human immunodeficiency virus type 1. Disrupting the native conformation of the CA is essential for blocking viral capsid formation and viral replication. Thus, it is important to identify the exact nature of the structural changes and driving forces of the CTD dimerization that take place in mutant forms. Here, we compare the structural stability, conformational dynamics, and association force of the CTD dimers for both wild-type and mutated sequences using all-atom explicit-solvent molecular dynamics (MD). The simulations show that Q155N and E159D at the major homology region (MHR) and W184A and M185A at the helix 2 region are energetically less favorable than the wild-type, imposing profound negative effects on intermolecular CA−CA dimerization. Detailed structural analysis shows that three mutants (Q155N, E159D, and W184A) display much more flexible local structures and weaker CA−CA association than the wild-type, primarily due to the loss of interactions (hydrogen bonds, side chain hydrophobic contacts, and π-stacking) with their neighboring residues. Most interestingly, the MHR that is far from the interacting dimeric interface is more sensitive to the mutations than the helix 2 region that is located at the CA−CA dimeric interface, indicating that structural changes in the distinct motif of the CA could similarly allosterically prevent the CA capsid formation. In addition, the structural and free energy comparison of the five residues shorter CA (151−231) dimer with the CA (146−231) dimer further indicates that hydrophobic interactions, side chain packing, and hydrogen bonds are the major, dominant driving forces in stabilizing the CA interface. PMID:19199580

  2. Substrate-Induced Dimerization of Engineered Monomeric Variants of Triosephosphate Isomerase from Trichomonas vaginalis.

    Samuel Lara-Gonzalez

    Full Text Available The dimeric nature of triosephosphate isomerases (TIMs is maintained by an extensive surface area interface of more than 1600 Å2. TIMs from Trichomonas vaginalis (TvTIM are held in their dimeric state by two mechanisms: a ball and socket interaction of residue 45 of one subunit that fits into the hydrophobic pocket of the complementary subunit and by swapping of loop 3 between subunits. TvTIMs differ from other TIMs in their unfolding energetics. In TvTIMs the energy necessary to unfold a monomer is greater than the energy necessary to dissociate the dimer. Herein we found that the character of residue I45 controls the dimer-monomer equilibrium in TvTIMs. Unfolding experiments employing monomeric and dimeric mutants led us to conclude that dimeric TvTIMs unfold following a four state model denaturation process whereas monomeric TvTIMs follow a three state model. In contrast to other monomeric TIMs, monomeric variants of TvTIM1 are stable and unexpectedly one of them (I45A is only 29-fold less active than wild-type TvTIM1. The high enzymatic activity of monomeric TvTIMs contrast with the marginal catalytic activity of diverse monomeric TIMs variants. The stability of the monomeric variants of TvTIM1 and the use of cross-linking and analytical ultracentrifugation experiments permit us to understand the differences between the catalytic activities of TvTIMs and other marginally active monomeric TIMs. As TvTIMs do not unfold upon dimer dissociation, herein we found that the high enzymatic activity of monomeric TvTIM variants is explained by the formation of catalytic dimeric competent species assisted by substrate binding.

  3. Molecular Insight into Affinities of Gallated and Nongallated Proanthocyanidins Dimers to Lipid Bilayers

    Zhu, Wei; Xiong, Le; Peng, Jinming; Deng, Xiangyi; Gao, Jun; Li, Chun-Mei


    Experimental studies have proved the beneficial effects of proanthocyanidins (Pas) relating to interaction with the cell membrane. But the detailed mechanisms and structure-function relationship was unclear. In present study, molecular dynamics (MD) simulations were used to study the interactions of four PA dimers with a lipid bilayer composed of 1:1 mixed 1-palmitoyl-2-oleoyl phosphatidylcholine (POPC) and 1-palmitoyl-2-oleoyl phosphatidylethanolamine (POPE). The results showed that the gallated PA dimers had much higher affinities to the bilayer with lower binding free energies compared with nongallated PA dimers. The gallated PA dimers penetrated deeper into the bilayer and formed more hydrogen bonds (H-bonds) with bilayer oxygen atoms, especially the deeper oxygen atoms of the lipids simultaneously, thus inducing stronger lateral expansion of the membrane and lipid tails disorder. The present results provided molecular insights into the interactions between PA dimers and bio-membranes and agreed with our experimental results well. These molecular interactions helped to elucidate the structure-function relationship of the PA dimers and provided a foundation for a better understanding of the underlying mechanisms of the bioactivities of PA oligomers.

  4. Complete Structure of an Epithelial Keratin Dimer: Implications for Intermediate Filament Assembly.

    David J Bray

    Full Text Available Keratins are cytoskeletal proteins that hierarchically arrange into filaments, starting with the dimer sub-unit. They are integral to the structural support of cells, in skin, hair and nails. In skin, keratin is thought to play a critical role in conferring the barrier properties and elasticity of skin. In general, the keratin dimer is broadly described by a tri-domain structure: a head, a central rod and a tail. As yet, no atomistic-scale picture of the entire dimer structure exists; this information is pivotal for establishing molecular-level connections between structure and function in intermediate filament proteins. The roles of the head and tail domains in facilitating keratin filament assembly and function remain as open questions. To address these, we report results of molecular dynamics simulations of the entire epithelial human K1/K10 keratin dimer. Our findings comprise: (1 the first three-dimensional structural models of the complete dimer unit, comprising of the head, rod and tail domains; (2 new insights into the chirality of the rod-domain twist gained from analysis of the full domain structure; (3 evidence for tri-subdomain partitioning in the head and tail domains; and, (4 identification of the residue characteristics that mediate non-covalent contact between the chains in the dimer. Our findings are immediately applicable to other epithelial keratins, such as K8/K18 and K5/K14, and to intermediate filament proteins in general.

  5. Investigation of the hydrated 7-hydroxy-4-methylcoumarin dimer by combined IR/UV spectroscopy.

    Stamm, A; Schwing, K; Gerhards, M


    The first molecular beam investigations on a coumarin dimer and clusters of a coumarin dimer with water both in the neutral (S0) and cationic (D0) electronic ground state are performed. The structure and structural changes due to ionization of the isolated 7-hydroxy-4-methylcoumarin dimer (7H4MC)2 as well as its mono- and dihydrate (7H4MC)2(H2O)1-2 are analyzed by applying combined IR/UV spectroscopy compared with density functional theory calculations. In case of the neutral dimer of 7H4MC a doubly hydrogen-bonded structure is formed. This doubly hydrogen-bonded arrangement opens to a singly hydrogen-bonded structure in the ion presenting a rearrangement reaction within an isolated dimer. By attaching one or two water molecules to the neutral 7H4MC dimer water is inserted into the hydrogen bonds. In contrast to the non-hydrated species this general binding motif with water in a bridging function does not change via ionization but especially for the dihydrate the spatial arrangement of the two 7H4MC units changes strengthening the interaction between the aromatic chromophores. The presented analyses illustrate the strong dependence of binding motifs as a function of successive hydration and charge including a rearrangement reaction.

  6. Theoretical Study on Intermolecular Interactions and Thermodynamic Properties of Nitroamine Dimers

    JU,Xue-Hai(居学海); XIAO,He-Ming(肖鹤鸣)


    Ab initio self-consistent field (SCF) and Moller-Plesset correlation correction methods emplo ying 6-31G * * basis set have been applied to the optimizations of nitroamine dimers. The binding energies have been corrected for the basis set superposition error (BSSE) and the zero-point energy. Three optimized dimers have been obtained. The BSSE corrected binding energy of the most stable dimer is predicted to be -31.85k J/mol at the MP4/6-31G* *//MP2/6-31G* * level. The energy barriers of the Walden conversion for - NH2 group are 19.7 kJ/mol and 18.3 kJ/mol for monomer and the most stable dimer, respectively. The molecular interaction makes the internal rotation around N1 - N2 even more difficult. The thermodynamic properties of nitroamine and its dimers at different temperatures have been calculated on the basis of vibrational analyses. The change of the Gibbs free energy for the aggregation from monomer to the most stable dimer at standard pressure and 298.2 K is predicted to be 14.05 kJ/mol.

  7. Dimerization of tetherin is not essential for its antiviral activity against Lassa and Marburg viruses.

    Toshie Sakuma

    Full Text Available Tetherin (also known as BST2, CD317 or HM1.24 has recently been reported to inhibit a wide range of viruses. However, the antiviral mechanism of action of tetherin has not been determined. Both ends of the tetherin molecule are associated with the plasma membrane and it forms a homodimer. Therefore, a model in which progeny virions are retained on the cell surface by dimer formation between tetherin molecules on the viral envelope and plasma membrane has been proposed as the antiviral mechanism of action of this molecule. To investigate this possibility, we examined the correlation between dimerization and antiviral activity of tetherin in Lassa and Marburg virus-like particle production systems using tetherin mutants deficient in dimer formation. However, the tetherin mutant with complete loss of dimerization activity still showed apparent antiviral activity, indicating that dimerization of tetherin is not essential for its antiviral activity. This suggests that tetherin retains progeny virions on the cell surface by a mechanism other than dimerization.

  8. Influence of mechanical hemolysis of blood on two D-dimer immunoassays.

    Lippi, Giuseppe; Avanzini, Paola; Zobbi, Valentina; Ippolito, Luigi


    Although there is broad information about the influence of spurious hemolysis on several laboratory tests, less is known on the bias produced on D-dimer testing. Four different pools were obtained from primary blood tubes, and each of them was divided into four aliquots. The first nonhemolyzed was centrifuged, the plasma was separated and then tested for hemolysis index and D-dimer. The second (hemolyzed aliquot A), third (hemolyzed aliquot B) and fourth (hemolyzed aliquot C) aliquots were mechanically hemolyzed by aspirating whole blood one, two and three times through a fine needle. The plasma was then separated and tested for hemolysis index and D-dimer. D-dimer was quantified by HemosIL AcuStar D-dimer and HemosIL D-dimer HS for ACL TOP. Undetectable hemolysis was present in aliquot nonhemolyzed (hemolysis interference is more likely to be biological than analytical. The modest bias observed in samples with frank hemolysis (i.e. cell-free hemoglobin of 11.5 g/l) confirms that both methods are robust against this type of interference, so that test results might be released in the majority of mildly hemolyzed samples.

  9. Role of Human DNA Polymerase kappa in Extension Opposite from a cis-syn Thymine Dimer

    R Vasquez-Del Carpio; T Silverstein; S Lone; R Johnson; L Prakash; S Prakash; A Aggarwal


    Exposure of DNA to UV radiation causes covalent linkages between adjacent pyrimidines. The most common lesion found in DNA from these UV-induced linkages is the cis-syn cyclobutane pyrimidine dimer. Human DNA polymerase {Kappa} (Pol{Kappa}), a member of the Y-family of DNA polymerases, is unable to insert nucleotides opposite the 3'T of a cis-syn T-T dimer, but it can efficiently extend from a nucleotide inserted opposite the 3'T of the dimer by another DNA polymerase. We present here the structure of human Pol{Kappa} in the act of inserting a nucleotide opposite the 5'T of the cis-syn T-T dimer. The structure reveals a constrained active-site cleft that is unable to accommodate the 3'T of a cis-syn T-T dimer but is remarkably well adapted to accommodate the 5'T via Watson-Crick base pairing, in accord with a proposed role for Pol{Kappa} in the extension reaction opposite from cyclobutane pyrimidine dimers in vivo.

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

    Yingzhi Xu

    Full Text Available 3-Hydroxyacyl-CoA dehydrogenase (HAD, EC 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.

  11. Biosynthesis of intestinal microvillar proteins. Dimerization of aminopeptidase N and lactase-phlorizin hydrolase

    Danielsen, E.M. (Univ. of Cophenhagen (Denmark))


    The pig intestinal brush border enzymes aminopeptidase and lactase-phlorizin hydrolase are present in the microvilla membrane as homodimers. Dimethyl adipimidate was used to cross-link the two ({sup 35}S)methionine-labeled brush border enzymes from cultured mucosal explants. For aminopeptidase N, dimerization did not begin until 5-10 min after synthesis, and maximal dimerization by cross-linking of the transient form of the enzyme required 1 h, whereas the mature form of aminopeptidase N cross-linked with unchanged efficiency from 45 min to 3 h of labeling. Formation of dimers of this enzyme therefore occurs prior to the Golgi-associated processing, and the slow rate of dimerization may be the rate-limiting step in the transport from the endoplasmic reticulum to the Golgi complex. For lactase-phlorizin hydrolase, the posttranslational processing includes a proteolytic cleavage of its high molecular weight precursor. Since only the mature form and not the precursor of this enzyme could be cross-linked, formation of tightly associated dimers only takes place after transport out of the endoplasmic reticulum. Dimerization of the two brush border enzymes therefore seems to occur in different organelles of the enterocyte.

  12. Dislocations and vacancies in two-dimensional mixed crystals of spheres and dimers

    Gerbode, Sharon J.


    In colloidal crystals of spheres, dislocation motion is unrestricted. On the other hand, recent studies of relaxation in crystals of colloidal dimer particles have demonstrated that the dislocation dynamics in such crystals are reminiscent of glassy systems. The observed glassy dynamics arise as a result of dislocation cages formed by certain dimer orientations. In the current study, we use experiments and simulations to investigate the transition that arises when a pure sphere crystal is doped with an increasing concentration of dimers. Specifically, we focus on both dislocation caging and vacancy motion. Interestingly, we find that any nonzero fraction of dimers introduces finite dislocation cages, suggesting that glassy dynamics are present for any mixed crystal. However, we have also identified a vacancy-mediated uncaging mechanism for releasing dislocations from their cages. This mechanism is dependent on vacancy diffusion, which slows by orders of magnitude as the dimer concentration is increased. We propose that in mixed crystals with low dimer concentrations vacancy diffusion is fast enough to uncage dislocations and delay the onset of glassy dislocation dynamics. © 2010 The American Physical Society.

  13. Surface characterization and orientation interaction between diamond- like carbon layer structure and dimeric liquid crystals

    Naradikian, H.; Petrov, M.; Katranchev, B.; Milenov, T.; Tinchev, S.


    Diamond-like carbon (DLC) and amorphous carbon films are very promising type of semiconductor materials. Depending on the hybridization sp2/sp3 ratio, the material’s band gap varies between 0.8 and 3 eV. Moreover carbon films possess different interesting for practice properties: comparable to the Silicon, Diamond like structure has 22-time better thermal conductivity etc. Here we present one type of implementation of such type nanostructure. That is one attempt for orientation of dimeric LC by using of pre-deposited DLC layer with different ratio of sp2/sp3 hybridized carbon content. It could be expected a pronounced π1-π2interaction between s and p orbital levels on the surface and the dimeric ring of LC. We present comparison of surface anchoring strengths of both orientation inter-surfaces DLC/dimeric LC and single wall carbon nanotubes (SWCNT)/dimeric LC. The mechanism of interaction of dimeric LC and activated surfaces with DLC or SWCNT will be discussed. In both cases we have π-π interaction, which in combination with hydrogen bonding, typical for the dimeric LCs, influence the LC alignment. The Raman spectroscopy data evidenced the presence of charge transfer between contacting hexagonal rings of DLC and the C = O groups of the LC molecules.

  14. Structural relaxation of acridine orange dimer in bulk water and inside a single live lung cell

    Chowdhury, Rajdeep; Nandi, Somen; Halder, Ritaban; Jana, Biman; Bhattacharyya, Kankan


    Structural relaxation of the acridine orange (AO) dimer in bulk water and inside a single live lung cell is studied using time resolved confocal microscopy and molecular dynamics (MD) simulations. The emission maxima ( λem max ˜ 630 nm) of AO in a lung cancer cell (A549) and a non-cancer lung fibroblast cell (WI38) suggest that AO exists as a dimer inside the cell. Time-dependent red shift in emission maximum indicates dynamic relaxation of the AO dimer (in the excited state) with a time constant of 500-600 ps, both in bulk water and inside the cell. We have calculated the equilibrium relaxation dynamics of the AO dimer in the ground state using MD simulations and found a slow component of time scale ˜350 ps. The intra- and inter-molecular components of the total relaxation dynamics of the AO dimer reveal the presence of a slow component of the order of a few hundred picoseconds. Upon restricting intra-molecular dye dynamics by harmonic constraint between AO monomers, the slow component vanishes. Combining the experimental observations and MD simulation results, we ascribe the slow component of the dynamic relaxation of the AO dimer to the structural relaxation, namely, fluctuations in the distance between the two monomers and associated fluctuation in the number of water molecules.

  15. Dimerization of the transmembrane domain of amyloid precursor proteins and familial Alzheimer's disease mutants

    Fraser Paul E


    Full Text Available Abstract Background Amyloid precursor protein (APP is enzymatically cleaved by γ-secretase to form two peptide products, either Aβ40 or the more neurotoxic Aβ42. The Aβ42/40 ratio is increased in many cases of familial Alzheimer's disease (FAD. The transmembrane domain (TM of APP contains the known dimerization motif GXXXA. We have investigated the dimerization of both wild type and FAD mutant APP transmembrane domains. Results Using synthetic peptides derived from the APP-TM domain, we show that this segment is capable of forming stable transmembrane dimers. A model of a dimeric APP-TM domain reveals a putative dimerization interface, and interestingly, majority of FAD mutations in APP are localized to this interface region. We find that FAD-APP mutations destabilize the APP-TM dimer and increase the population of APP peptide monomers. Conclusion The dissociation constants are correlated to both the Aβ42/Aβ40 ratio and the mean age of disease onset in AD patients. We also show that these TM-peptides reduce Aβ production and Aβ42/Aβ40 ratios when added to HEK293 cells overexpressing the Swedish FAD mutation and γ-secretase components, potentially revealing a new class of γ-secretase inhibitors.

  16. Monomer-dimer model on a scale-free small-world network

    Zhang, Zhongzhi; Sheng, Yibin; Jiang, Qiang


    The explicit determination of the number of monomer-dimer arrangements on a network is a theoretical challenge, and exact solutions to monomer-dimer problem are available only for few limiting graphs with a single monomer on the boundary, e.g., rectangular lattice and quartic lattice; however, analytical research (even numerical result) for monomer-dimer problem on scale-free small-world networks is still missing despite the fact that a vast variety of real systems display simultaneously scale-free and small-world structures. In this paper, we address the monomer-dimer problem defined on a scale-free small-world network and obtain the exact formula for the number of all possible monomer-dimer arrangements on the network, based on which we also determine the asymptotic growth constant of the number of monomer-dimer arrangements in the network. We show that the obtained asymptotic growth constant is much less than its counterparts corresponding to two-dimensional lattice and Sierpinski fractal having the same average degree as the studied network, which indicates from another aspect that scale-free networks have a fundamentally distinct architecture as opposed to regular lattices and fractals without power-law behavior.

  17. Quaternary organization of a phytochrome dimer as revealed by cryoelectron microscopy

    Li, H.; Li, H.; Zhang, J.; Vierstra, R. D.


    Phytochromes are a collection of dimeric photoreceptors that direct a diverse array of responses in plants and microorganisms through photoconversion between a red light-absorbing ground state Pr, and a far-red light-absorbing photoactivated state Pfr. Photoconversion from Pr to Pfr is initiated by a light-driven rotation within the covalently attached bilin, which then triggers a series of protein conformational changes in the binding pocket. These movements ultimately affect an appended output module, which often has reversible protein kinase activity. Propagation of the light signal from the bilin to the output module likely depends on the dimerization interface but its architecture and response to phototransformation remain unclear. Here, we used single particle cryoelectron microscopy to determine the quaternary arrangement of the phytochrome dimer as Pr, using the bacteriophytochrome (BphP) from Deinococcus radiodurans. Contrary to the long-standing view that the two monomers are held together solely via their C-terminal region, we provide unambiguous evidence that the N-terminal bilin-binding region of BphP also provides a dimerization interface with the C-terminal kinase domain appearing as a more flexible appendage. The BphP monomers dimerize in parallel with the polypeptides intimately twisting around each other in a right-handed fashion. Based on this electron microscopic picture, we propose that the light-driven conformational changes transmitted from the chromophore to the output module along the spine of this extensive dimer interface is the central feature underpinning phytochrome signaling.

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

    Mohapatra, Swagat Kumar


    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.

  19. Role of antibodies in developing drugs that target G-protein-coupled receptor dimers.

    Hipser, Chris; Bushlin, Ittai; Gupta, Achla; Gomes, Ivone; Devi, Lakshmi A


    G-protein-coupled receptors are important molecular targets in drug discovery. These receptors play a pivotal role in physiological signaling pathways and are targeted by nearly 50% of currently available drugs. Mounting evidence suggests that G-protein-coupled receptors form dimers, and various studies have shown that dimerization is necessary for receptor maturation, signaling, and trafficking. However, the physiological implications of dimerization in vivo have not been well explored because detection of GPCR dimers in endogenous systems has been a challenging task. One exciting new approach to this challenge is the generation of antibodies against specific G-protein-coupled receptor dimers. Such antibodies could be used as tools for characterization of heteromer-specific function; as reagents for their purification, tissue localization, and regulation in vivo; and as probes for mapping their functional domains. In addition, such antibodies could serve as alternative ligands for G-protein-coupled receptor heteromers. Thus, heteromer-specific antibodies represent novel tools for the exploration and manipulation of G-protein-coupled receptor-dimer pharmacology.

  20. Cholesterol modulates the dimer interface of the β₂-adrenergic receptor via cholesterol occupancy sites.

    Prasanna, Xavier; Chattopadhyay, Amitabha; Sengupta, Durba


    The β2-adrenergic receptor is an important member of the G-protein-coupled receptor (GPCR) superfamily, whose stability and function are modulated by membrane cholesterol. The recent high-resolution crystal structure of the β2-adrenergic receptor revealed the presence of possible cholesterol-binding sites in the receptor. However, the functional relevance of cholesterol binding to the receptor remains unexplored. We used MARTINI coarse-grained molecular-dynamics simulations to explore dimerization of the β2-adrenergic receptor in lipid bilayers containing cholesterol. A novel (to our knowledge) aspect of our results is that receptor dimerization is modulated by membrane cholesterol. We show that cholesterol binds to transmembrane helix IV, and cholesterol occupancy at this site restricts its involvement at the dimer interface. With increasing cholesterol concentration, an increased presence of transmembrane helices I and II, but a reduced presence of transmembrane helix IV, is observed at the dimer interface. To our knowledge, this study is one of the first to explore the correlation between cholesterol occupancy and GPCR organization. Our results indicate that dimer plasticity is relevant not just as an organizational principle but also as a subtle regulatory principle for GPCR function. We believe these results constitute an important step toward designing better drugs for GPCR dimer targets.

  1. Investigation of the hydrated 7-hydroxy-4-methylcoumarin dimer by combined IR/UV spectroscopy

    Stamm, A.; Schwing, K.; Gerhards, M., E-mail: [TU Kaiserslautern, Fachbereich Chemie and Research Center Optimas, Erwin-Schroedinger-Straße 52, D-67663 Kaiserslautern (Germany)


    The first molecular beam investigations on a coumarin dimer and clusters of a coumarin dimer with water both in the neutral (S{sub 0}) and cationic (D{sub 0}) electronic ground state are performed. The structure and structural changes due to ionization of the isolated 7-hydroxy-4-methylcoumarin dimer (7H4MC){sub 2} as well as its mono- and dihydrate (7H4MC){sub 2}(H{sub 2}O){sub 1-2} are analyzed by applying combined IR/UV spectroscopy compared with density functional theory calculations. In case of the neutral dimer of 7H4MC a doubly hydrogen-bonded structure is formed. This doubly hydrogen-bonded arrangement opens to a singly hydrogen-bonded structure in the ion presenting a rearrangement reaction within an isolated dimer. By attaching one or two water molecules to the neutral 7H4MC dimer water is inserted into the hydrogen bonds. In contrast to the non-hydrated species this general binding motif with water in a bridging function does not change via ionization but especially for the dihydrate the spatial arrangement of the two 7H4MC units changes strengthening the interaction between the aromatic chromophores. The presented analyses illustrate the strong dependence of binding motifs as a function of successive hydration and charge including a rearrangement reaction.

  2. Complete Structure of an Epithelial Keratin Dimer: Implications for Intermediate Filament Assembly

    Bray, David J.; Walsh, Tiffany R.; Noro, Massimo G.; Notman, Rebecca


    Keratins are cytoskeletal proteins that hierarchically arrange into filaments, starting with the dimer sub-unit. They are integral to the structural support of cells, in skin, hair and nails. In skin, keratin is thought to play a critical role in conferring the barrier properties and elasticity of skin. In general, the keratin dimer is broadly described by a tri-domain structure: a head, a central rod and a tail. As yet, no atomistic-scale picture of the entire dimer structure exists; this information is pivotal for establishing molecular-level connections between structure and function in intermediate filament proteins. The roles of the head and tail domains in facilitating keratin filament assembly and function remain as open questions. To address these, we report results of molecular dynamics simulations of the entire epithelial human K1/K10 keratin dimer. Our findings comprise: (1) the first three-dimensional structural models of the complete dimer unit, comprising of the head, rod and tail domains; (2) new insights into the chirality of the rod-domain twist gained from analysis of the full domain structure; (3) evidence for tri-subdomain partitioning in the head and tail domains; and, (4) identification of the residue characteristics that mediate non-covalent contact between the chains in the dimer. Our findings are immediately applicable to other epithelial keratins, such as K8/K18 and K5/K14, and to intermediate filament proteins in general. PMID:26181054

  3. NMR detection of intermolecular interaction sites in the dimeric 5'-leader of the HIV-1 genome.

    Keane, Sarah C; Van, Verna; Frank, Heather M; Sciandra, Carly A; McCowin, Sayo; Santos, Justin; Heng, Xiao; Summers, Michael F


    HIV type-1 (HIV-1) contains a pseudodiploid RNA genome that is selected for packaging and maintained in virions as a noncovalently linked dimer. Genome dimerization is mediated by conserved elements within the 5'-leader of the RNA, including a palindromic dimer initiation signal (DIS) that has been proposed to form kissing hairpin and/or extended duplex intermolecular contacts. Here, we have applied a (2)H-edited NMR approach to directly probe for intermolecular interactions in the full-length, dimeric HIV-1 5'-leader (688 nucleotides; 230 kDa). The interface is extensive and includes DIS:DIS base pairing in an extended duplex state as well as intermolecular pairing between elements of the upstream Unique-5' (U5) sequence and those near the gag start site (AUG). Other pseudopalindromic regions of the leader, including the transcription activation (TAR), polyadenylation (PolyA), and primer binding (PBS) elements, do not participate in intermolecular base pairing. Using a (2)H-edited one-dimensional NMR approach, we also show that the extended interface structure forms on a time scale similar to that of overall RNA dimerization. Our studies indicate that a kissing dimer-mediated structure, if formed, exists only transiently and readily converts to the extended interface structure, even in the absence of the HIV-1 nucleocapsid protein or other RNA chaperones.

  4. Origin of Symmetric Dimer Images of Si(001) Observed by Low-Temperature Scanning Tunneling Microscopy

    Ren, Xiao-Yan; Kim, Hyun-Jung; Niu, Chun-Yao; Jia, Yu; Cho, Jun-Hyung


    It has been a long-standing puzzle why buckled dimers of the Si(001) surface appeared symmetric below ~20 K in scanning tunneling microscopy (STM) experiments. Although such symmetric dimer images were concluded to be due to an artifact induced by STM measurements, its underlying mechanism is still veiled. Here, we demonstrate, based on a first-principles density-functional theory calculation, that the symmetric dimer images are originated from the flip-flop motion of buckled dimers, driven by quantum tunneling (QT). It is revealed that at low temperature the tunneling-induced surface charging with holes reduces the energy barrier for the flipping of buckled dimers, thereby giving rise to a sizable QT-driven frequency of the flip-flop motion. However, such a QT phenomenon becomes marginal in the tunneling-induced surface charging with electrons. Our findings provide an explanation for low-temperature STM data that exhibits apparent symmetric (buckled) dimer structure in the filled-state (empty-state) images.

  5. HLA-G Dimers in the Prolongation of Kidney Allograft Survival

    Maureen Ezeakile


    Full Text Available Human leukocyte antigen-G (HLA-G contributes to acceptance of allografts in solid organ/tissue transplantation. Most studies have determined that soluble HLA-G isoforms are systematically detected in serum/plasma of transplanted patients with significantly fewer episodes of acute and/or chronic rejection of allogeneic tissue/organ. Current models of the interactions of HLA-G and its specific receptors explain it as functioning in a monomeric form. However, in recent years, new data has revealed the ability of HLA-G to form disulfide-linked dimeric complexes with high preferential binding and functional activities. Limited data are available on the role of soluble HLA-G dimers in clinical pathological conditions. We describe here the presence of soluble HLA-G dimers in kidney transplant patients. Our study showed that a high level of HLA-G dimers in plasma and increased expression of the membrane-bound form of HLA-G on monocytes are associated with prolongation of kidney allograft survival. We also determined that the presence of soluble HLA-G dimers links to the lower levels of proinflammatory cytokines, suggesting a potential role of HLA-G dimers in controlling the accompanying inflammatory state.

  6. Non-Ligand-Induced Dimerization is Sufficient to Initiate the Signalling and Endocytosis of EGF Receptor

    George Kourouniotis


    Full Text Available The binding of epidermal growth factor (EGF to EGF receptor (EGFR stimulates cell mitogenesis and survival through various signalling cascades. EGF also stimulates rapid EGFR endocytosis and its eventual degradation in lysosomes. The immediate events induced by ligand binding include receptor dimerization, activation of intrinsic tyrosine kinase and autophosphorylation. However, in spite of intensified efforts, the results regarding the roles of these events in EGFR signalling and internalization is still very controversial. In this study, we constructed a chimeric EGFR by replacing its extracellular domain with leucine zipper (LZ and tagged a green fluorescent protein (GFP at its C-terminus. We showed that the chimeric LZ-EGFR-GFP was constitutively dimerized. The LZ-EGFR-GFP dimer autophosphorylated each of its five well-defined C-terminal tyrosine residues as the ligand-induced EGFR dimer does. Phosphorylated LZ-EGFR-GFP was localized to both the plasma membrane and endosomes, suggesting it is capable of endocytosis. We also showed that LZ-EGFR-GFP activated major signalling proteins including Src homology collagen-like (Shc, extracellular signal-regulated kinase (ERK and Akt. Moreover, LZ-EGFR-GFP was able to stimulate cell proliferation. These results indicate that non-ligand induced dimerization is sufficient to activate EGFR and initiate cell signalling and EGFR endocytosis. We conclude that receptor dimerization is a critical event in EGF-induced cell signalling and EGFR endocytosis.

  7. Microwave Measurements of the Tropolone-Formic Acid Doubly Hydrogen Bonded DIMER*

    Pejlovas, Aaron M.; Serrato, Agapito, III; Lin, Wei; Kukolich, Stephen G.


    The microwave spectrum was measured for the tropolone-formic acid doubly hydrogen bonded dimer using a pulsed-beam Fourier transform microwave spectrometer in order to search for the concerted double proton tunneling motion. The tunneling motion was expected for the dimer, as the transition state of this motion exhibits C_2_V symmetry, which has been thought to be a requirement to observe the concerted double proton tunneling. The tunneling motion was not observed for this dimer, as the transitions measured did not show observable splittings into doublets. The barrier height calculated of the dimer using B3LYP/aug-cc-pVTZ was about 15000 cm^-^1, significantly larger than the value determined for the propiolic acid-formic acid dimer (3800 cm^-^1),^a which showed the tunneling motion. The estimated separation of the minima in the potential energy surface is estimated to be very similar to that of propiolic acid-formic acid (about 0.8 Å),^a so the large barrier height may be why the tunneling process was not observed. ^aDaly, A. M.; Bunker, P. R.; Kukolich, S. G. Communications: Evidence for Proton Tunneling from the Microwave Spectrum of the Formic Acid-Propiolic Acid Dimer. J. Chem. Phys. 132, 2010, 201101/1. *Supported by the NSF CHE-1057796

  8. Adapting the D-dimer cutoff for thrombosis detection in elderly outpatients.

    Andro, Marion; Righini, Marc; Le Gal, Grégoire


    D-dimer measurement is an important step in diagnostic strategies for venous thromboembolism. It allows the safe ruling out of the diagnosis with no need for imaging tests in approximately 30% of outpatients. However, the usefulness of d-dimer is limited in elderly patients; the likelihood of a negative d-dimer strongly decreases with age, making physicians reluctant to order the test. Several attempts to improve the performance of D-dimer in elderly patients have been pursued. Recently, an age-adjusted cutoff was derived; the optimal cutoff value (in µg/l) appears to be equal to the patient's age (in years) multiplied by ten in patients over 50 years of age with a low pretest clinical risk of venous thromboembolism. This age-adjusted cutoff value has been extensively and externally validated in retrospective studies that included mostly outpatients with suspected deep vein thrombosis or pulmonary embolism and used various quantitative D-dimer assays. All available studies confirmed the increased usefulness and similar safety of the age-adjusted cutoff compared with the conventional cutoff, the most important benefit being obtained in elderly patients. However, before any recommendation for clinical practice can be made, a prospective diagnostic management outcome study is lacking, in which all low clinical risk patients with D-dimer levels below their age-adjusted cutoff would be left untreated with no further diagnostic testing.

  9. Kinetics of endophilin N-BAR domain dimerization and membrane interactions.

    Capraro, Benjamin R; Shi, Zheng; Wu, Tingting; Chen, Zhiming; Dunn, Joanna M; Rhoades, Elizabeth; Baumgart, Tobias


    The recruitment to plasma membrane invaginations of the protein endophilin is a temporally regulated step in clathrin-mediated endocytosis. Endophilin is believed to sense or stabilize membrane curvature, which in turn likely depends on the dimeric structure of the protein. The dynamic nature of the membrane association and dimerization of endophilin is thus functionally important and is illuminated herein. Using subunit exchange Förster resonance energy transfer (FRET), we determine dimer dissociation kinetics and find a dimerization equilibrium constant orders of magnitude lower than previously published values. We characterize N-BAR domain membrane association kinetics under conditions where the dimeric species predominates, by stopped flow, observing prominent electrostatic sensitivity of membrane interaction kinetics. Relative to membrane binding, we find that protein monomer/dimer species equilibrate with far slower kinetics. Complementary optical microscopy studies reveal strikingly slow membrane dissociation and an increase of dissociation rate constant for a construct lacking the amphipathic segment helix 0 (H0). We attribute the slow dissociation kinetics to higher-order protein oligomerization on the membrane. We incorporate our findings into a kinetic scheme for endophilin N-BAR membrane binding and find a significant separation of time scales for endophilin membrane binding and subsequent oligomerization. This separation may facilitate the regulation of membrane trafficking phenomena.

  10. Trihydroxybenzoic Acid Dimer-induced Apoptosis Effects in vitro

    NIU Feng-lan; WANG Xue-dong; WANG Ying-li; SONG Lian-sheng


    The in vitro inhibitory effect of trihydroxybenzoic acid dimer(TAD) extracted from Trapabispinosd roxb on HeLa cell growth was investigated via the MTT[3-(4,5-dimethylthiazol-2-yl)-2,5-diophenyl-tetrazolium bromide] reduction method. The morphological changes of HeLa cells were observed by means of an optical microscope and a transmission electron microscope(TEM); the cell circles and apoptosis were detected by a flow cytometer. It was found that TAD can significantly inhibit the growth of Hela cells and can induce the apoptosis of HeLa cells. It was also found that the inhibition to the growth of Hela cells and the induction to the apoptosis of HeLa cells have a dosage-dependent feature. The inhibiting rates of TAD with mass concentrations of 25.000, 12.500 and 6.250 mg/L to the HeLa cell growth were 52.04%, 34.44% and 23.72% after 30 h, respectively, while those with TAD mass concentrations of 100.000, 50.000, 25.000, 12.500, 6.250 and 3.125 mg/L showed positive correlation with a correlation coefficient value of r=0.9859(P<0.01) and a IC50 value of 10.90 mg/L. Observed by means of TEM, the HeLa cells exposed to 25.000, 12.500 and 6.250 mg/L TAD showed apoptosis to various extents, shrinkage of the cell nuclei, condensation and margination of chromatin, and cavitation of mitochondrion. An apoptosis peak was detected via a flow cytometer. It can be drawn from the results that TAD extracted from Trapabispinosd roxb has an evident inhibitory effect on the proliferation of and an inductive effect on the apoptosis of HeLa cells, but has no obvious arrest action towards the cell circles of HeLa cells.

  11. Naturally-occurring dimers of flavonoids as anticarcinogens.

    Mercader, Andrew G; Pomilio, Alicia B


    Biflavonoids are dimers of flavonoid moieties linked by a C-C or C-O-C bond. Simple, complex, rearranged, natural and ketalized Diels-Alder adducts, benzofuran derivatives, and spirobiflavonoids are some of the structural groups of biflavonoids. These compounds are mainly distributed in the Gymnosperms, Angiosperms (monocots and dicots), ferns (Pteridophyta), and mosses (Bryophyta). Biflavonoids have shown a variety of biological activities, including anticancer, antibacterial, antifungal, antiviral, antiinflammatory, analgesic, antioxidant, vasorelaxant, anticlotting, among others. This work is focused on probably the most potentially relevant biological activity of biflavonoids, the anticancer activity and the involved mechanisms of action, such as induction of apoptosis [inhibition of cyclic nucleotide phosphodiesterases; effects on NF-κB family of transcription factors; activation of caspase(s); inhibition effects on bcl-2 expression, and upregulation of p53 and caspase-3 gene expression]; inhibition of angiogenesis [anti-proliferative effects; activation of Rho-GTPases and ERK signaling pathways; inhibition of FASN activity]; inhibition of pre-mRNA splicing; inhibition of human DNA topoisomerases I and II-α; anti-inflammatory/ immunoregulatory effects [inhibition of XO; inhibition of proinflammatory enzymes, such as PLA2 and COX; effects on cytokines mediated COX-2 and iNOS expression]; modulation of immune response; inhibition of protein tyrosine phosphorylation; antioxidant and analgesic activities in relation to the anticarcinogen behavior. For that reason the structures and anticarcinogenic activities of 83 biflavonoids are thoroughly discussed. The results of this work indicate that biflavonoids strongly affect the cancer cells with little effect on normal cell proliferation, suggesting a therapeutic potential against cancer.

  12. New approach to IR study of monomer-dimer self-association: 2,2-dimethyl-3-ethyl-3-pentanol in tetrachloroethylene as an example.

    Chen, Jenn-Shing; Wu, Cheng-Chang; Kao, Dah-Yu


    The dimerization of 2,2-dimethyl-3-ethyl-3-pentanol in tetrachloroethylene in the diluted region has been studied at four temperatures by IR spectroscopy. The aforementioned solute compound is chosen because self-association beyond dimerization is hampered by the steric hindrance generated by the bulky sidechains. The integrated absorbances of the monomer bands were treated based on Eq. (9) to obtain its molar absorptivity and dimerization constant. The same dimerization constant as well as the molar absorptivity of dimer band can be obtained based on Eq. (13) from the data treatment of the integrated absorbances of the dimer band. The disparity between two values of dimerization constant determined by two independent sources offers an opportunity to check the consistency of the determination. The standard enthalpy and entropy of dimerization have also been calculated by means of van't Hoff plot, respectively, from the data of temperature-dependent dimerization constants obtained from the monomer bands and dimer bands.

  13. Deciphering the kinetic binding mechanism of dimeric ligands using a potent plasma-stable dimeric inhibitor of postsynaptic density protein-95 as an example

    Chi, Celestine N; Bach, Anders; Gottschalk, Marie


    addressed the kinetic mechanism of interaction of such bivalent ligands. We have investigated the binding interaction of a recently identified potent plasma-stable dimeric pentapeptide and PDZ1-2 of postsynaptic density protein-95 (PSD-95) using protein engineering in combination with fluorescence...

  14. Structure and dimerization of translation initiation factor aIF5B in solution

    Rasmussen, Louise Caroe Vohlander [Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C (Denmark); Oliveira, Cristiano Luis Pinto [Department of Chemistry, Centre for mRNP Biogenesis and Metabolism, and iNANO Interdisciplinary Nanoscience Center, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C (Denmark); Byron, Olwyn [Glasgow Biomedical Research Center, University of Glasgow, Glasgow G12 8QQ, Scotland (United Kingdom); Jensen, Janni Mosgaard [Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C (Denmark); Pedersen, Jan Skov [Department of Chemistry, Centre for mRNP Biogenesis and Metabolism, and iNANO Interdisciplinary Nanoscience Center, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C (Denmark); Sperling-Petersen, Hans Uffe [Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C (Denmark); Mortensen, Kim Kusk, E-mail: [Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C (Denmark)


    Highlights: Black-Right-Pointing-Pointer aIF5B forms maximum 5.0-6.8% irreversible dimers in solution. Black-Right-Pointing-Pointer Sedimentation coefficients for monomer and dimer are 3.64 and 5.51 {+-} 0.29 S. Black-Right-Pointing-Pointer Adding only 2% glycerol prevents dimerization. Black-Right-Pointing-Pointer SAXS on aIF5B monomer gave an R{sub g} of 37.5 {+-} 0.2 A and a D{sub max} of {approx}130 A. Black-Right-Pointing-Pointer There are universal structural differences between aIF5B and Escherichia coli IF2. -- Abstract: Translation initiation factor 5B (IF5B) is required for initiation of protein synthesis. The solution structure of archaeal IF5B (aIF5B) was analysed by small-angle X-ray scattering (SAXS) and dynamic light scattering (DLS) and was indicated to be in both monomeric and dimeric form. Sedimentation equilibrium (SE) analytical ultracentrifugation (AUC) of aIF5B indicated that aIF5B forms irreversible dimers in solution but only to a maximum of 5.0-6.8% dimer. Sedimentation velocity (SV) AUC at higher speed also indicated the presence of two species, and the sedimentation coefficients s{sub 20,w}{sup 0} were determined to be 3.64 and 5.51 {+-} 0.29 S for monomer and dimer, respectively. The atomic resolution (crystallographic) structure of aIF5B (Roll-Mecak et al. ) was used to model monomer and dimer, and theoretical sedimentation coefficients for these models were computed (3.89 and 5.63 S, respectively) in good agreement with the sedimentation coefficients obtained from SV analysis. Thus, the structure of aIF5B in solution must be very similar to the atomic resolution structure of aIF5B. SAXS data were acquired in the same buffer with the addition of 2% glycerol to inhibit dimerization, and the resultant monomeric aIF5B in solution did indeed adopt a structure very similar to the one reported earlier for the protein in crystalline form. The p(r) function indicated an elongated conformation supported by a radius of gyration of 37.5 {+-} 0.2 A

  15. The stability of the acetic acid dimer in microhydrated environments and in aqueous solution.

    Pašalić, Hasan; Tunega, Daniel; Aquino, Adélia J A; Haberhauer, Georg; Gerzabek, Martin H; Lischka, Hans


    The thermodynamic stability of the acetic acid dimer conformers in microhydrated environments and in aqueous solution was studied by means of molecular dynamics simulations using the density functional based tight binding (DFTB) method. To confirm the reliability of this method for the system studied, density functional theory (DFT) and second order Møller-Plesset perturbation theory (MP2) calculations were performed for comparison. Classical optimized potentials for liquid simulations (OPLS) force field dynamics was used as well. One focus of this work was laid on the study of the capabilities of water molecules to break the hydrogen bonds of the acetic acid dimer. The barrier for insertion of one water molecule into the most stable cyclic dimer is found to lie between 3.25 and 4.8 kcal mol(-1) for the quantum mechanical methods, but only at 1.2 kcal mol(-1) for OPLS. Starting from different acetic acid dimer structures optimized in gas phase, DFTB dynamics simulations give a different picture of the stability in the microhydrated environment (4 to 12 water molecules) as compared to aqueous solution. In the former case all conformers are converted to the hydrated cyclic dimer, which remains stable over the entire simulation time of 1 ns. These results demonstrate that the considered microhydrated environment is not sufficient to dissociate the acetic acid dimer. In aqueous solution, however, the DFTB dynamics shows dissociation of all dimer structures (or processes leading thereto) starting after about 50 ps, demonstrating the capability of the water environment to break up the relatively strong hydrogen bridges. The OPLS dynamics in the aqueous environment shows--in contrast to the DFTB results--immediate dissociation, but a similar long-term behavior.

  16. Dimerization of green sensitizing cyanines in solution. A spectroscopic and theoretical study of the bonding nature

    Baraldi, I.; Caselli, M.; Momicchioli, F.; Ponterini, G.; Vanossi, D.


    The bonding nature in cyanine-dye aggregates has been investigated by studying dimerization in solution of 3,3 '-disulfopropyl-4,5,4 ',5 '-dibenzo-9-ethyloxacarbocyanine (D) and three other oxacarbocyanine analogues (E, F, G) used as photographic sensitizers in the green spectral region. Quantitative information on the monomer-dimer equilibrium of dye D in different solvents and of its analogues (E, F, G) in water was obtained by measurement of the absorption spectrum as a function of dye concentration and of temperature. Dimerization was found to be generally driven by enthalpic factors traceable to strong attractive van der Waals interactions between the two large and highly polarizable dye molecules. Entropic contributions to ΔG0 usually favour dissociation but are smaller than the enthalpic ones. The visible absorption spectrum of the dimer consists in a classic two-branched exciton band with a marked splitting ( 1600 cm-1 in water). The experimental observations were the subject of a theoretical study including classical molecular dynamics (MD) and Monte Carlo (MC) calculations of the dimer structure and comparative analysis of monomer and dimer spectra by the CS INDO CI method. Computer simulations led to three similar H-type structures, the most stable of which is characterized by a distance of 4.7 Å between the planes of the chromophores and an endo-endo configuration of the sulfopropyl substituents. The calculated dimer spectrum was clearly interpreted in terms of exciton model but a quantitative agreement with the two-maximum exciton band could be obtained only by assuming substantial deviation of the long molecular axes from parallelism. On the basis of normal coordinate calculations it is suggested that such configurations may occur with a high probability in virtue of twisting vibrational motions of extremely low frequency.

  17. D-dimer assay in Egyptian patients with Gaucher disease: correlation with bone and lung involvement.

    Sherif, Eman M; Tantawy, Azza A G; Adly, Amira A M; Kader, Hossam A; Ismail, Eman A R


    Gaucher disease is the most frequent lysosomal storage disorder. Bone and lung involvement are two major causes of morbidity in this disease. D-dimer is a reliable indicator of active microvascular thrombosis, even in patients without overt hypercoagulation. This study aimed to assess D-dimer levels in Gaucher disease, correlating this marker to clinical characteristics and radiological parameters to investigate its role as a potential predictor for the occurrence and severity of skeletal and pulmonary manifestations. The study population consisted of 56 Egyptian patients with Gaucher disease, 36 had type 1 Gaucher disease (64.3%) and 20 had type 3 Gaucher disease (35.7%). Thirty healthy individuals were enrolled as a control group. D-dimer levels were significantly higher in all patients with Gaucher disease compared with controls (P < 0.001). Patients with type 3 showed significantly higher D-dimer concentrations compared with type 1 (P < 0.001). Pulmonary involvement was present in a significant proportion among type 3 Gaucher patients (P < 0.05), whereas bone changes were present in a higher percentage in type 1 compared with type 3 Gaucher patients. D-dimers were significantly higher in patients with abnormal MRI findings of the long bones and in those with ground glass appearance on high-resolution computerized tomography of the chest compared with patients with normal radiology (P < 0.001). Splenectomized patients displayed significantly higher D-dimer levels compared with nonsplenectomized patients (P < 0.001). Our results suggest that D-dimer is significantly elevated in Gaucher disease, particularly type 3, and may be considered as a potential marker of risk prediction of bone and lung involvement that could be used to monitor treatment response.

  18. Ionization of cytosine monomer and dimer studied by VUV photoionization and electronic structure calculations

    Kostko, Oleg; Bravaya, Ksenia; Krylov, Anna; Ahmed, Musahid


    We report a combined theoretical and experimental study of ionization of cytosine monomers and dimers. Gas-phase molecules are generated by thermal vaporization of cytosine followed by expansion of the vapor in a continuous supersonic jet seeded in Ar. The resulting species are investigated by single photon ionization with tunable vacuum-ultraviolet (VUV) synchrotron radiation and mass analyzed using reflectron mass spectrometry. Energy onsets for the measured photoionization efficiency (PIE) spectra are 8.60+-0.05 eV and 7.6+-0.1 eV for the monomer and the dimer, respectively, and provide an estimate for the adiabatic ionization energies (AIE). The first AIE and the ten lowest vertical ionization energies (VIEs) for selected isomers of cytosine dimer computed using equation-of-motion coupled-cluster (EOM-IP-CCSD) method are reported. The comparison of the computed VIEs with the derivative of the PIE spectra, suggests that multiple isomers of the cytosine dimer are present in the molecular beam. The calculations reveal that the large red shift (0.7 eV) of the first IE of the lowest-energy cytosine dimer is due to strong inter-fragment electrostatic interactions, i.e., the hole localized on one of the fragments is stabilized by the dipole moment of the other. A sharp rise in the CH+ signal at 9.20+-0.05 eV is ascribed to the formation of protonated cytosine by dissociation of the ionized dimers. The dominant role of this channel is supported by the computed energy thresholds for the CH+ appearance and the barrierless or nearly barrierless ionization-induced proton transfer observed for five isomers of the dimer.

  19. FtsK-dependent dimer resolution on multiple chromosomes in the pathogen Vibrio cholerae.

    Marie-Eve Val

    Full Text Available Unlike most bacteria, Vibrio cholerae harbors two distinct, nonhomologous circular chromosomes (chromosome I and II. Many features of chromosome II are plasmid-like, which raised questions concerning its chromosomal nature. Plasmid replication and segregation are generally not coordinated with the bacterial cell cycle, further calling into question the mechanisms ensuring the synchronous management of chromosome I and II. Maintenance of circular replicons requires the resolution of dimers created by homologous recombination events. In Escherichia coli, chromosome dimers are resolved by the addition of a crossover at a specific site, dif, by two tyrosine recombinases, XerC and XerD. The process is coordinated with cell division through the activity of a DNA translocase, FtsK. Many E. coli plasmids also use XerCD for dimer resolution. However, the process is FtsK-independent. The two chromosomes of the V. cholerae N16961 strain carry divergent dimer resolution sites, dif1 and dif2. Here, we show that V. cholerae FtsK controls the addition of a crossover at dif1 and dif2 by a common pair of Xer recombinases. In addition, we show that specific DNA motifs dictate its orientation of translocation, the distribution of these motifs on chromosome I and chromosome II supporting the idea that FtsK translocation serves to bring together the resolution sites carried by a dimer at the time of cell division. Taken together, these results suggest that the same FtsK-dependent mechanism coordinates dimer resolution with cell division for each of the two V. cholerae chromosomes. Chromosome II dimer resolution thus stands as a bona fide chromosomal process.

  20. Collective dark states controlled transmission in plasmonic slot waveguide with a stub coupled to a cavity dimer

    Liu, Zhenzhen; Zhang, Qiang; Zhang, Xiaoming; Tao, Keyu


    We report collective dark states controlled transmission in metal-dielectric-metal waveguides with a stub coupled to two twin cavities, namely, plasmonic waveguide-stub-dimer systems. In absence of one individual cavity in the dimer, plasmon induced transparency (PIT) is possible when the cavity and the stub have the same resonance frequency. However, it is shown that the hybridized modes in the dimer collectively generate two dark states which make the stub-dimer "invisible" to the straight waveguide, splitting the original PIT peak into two in the transmission spectrum. Simultaneously, the original PIT peak becomes a dip due to dark state interaction, yielding anti-PIT-like modulation of the transmission. With full-wave electromagnetic simulation, we demonstrate that this transition is controlled by the dimer-stub separation and the dimer-stub relative position. All results are analytically described by the temporal coupled mode theory. Our results may be useful in designing densely integrated optical circu...

  1. Pair density wave superconducting states and statistical mechanics of dimers

    Soto Garrido, Rodrigo Andres

    The following thesis is divided in two main parts. Chapters 2, 3 and 4 are devoted to the study of the so called pair-density-wave (PDW) superconducting state and some of its connections to electronic liquid crystal (ELC) phases, its topological aspects in a one dimensional model and its appearance in a quasi-one dimensional system. On the other hand, chapter 5 is focused on the investigation of the classical statistical mechanics properties of dimers, in particular, the dimer model on the Aztec diamond graph and its relation with the octahedron equation. In chapter 2 we present a theory of superconducting states where the Cooper pairs have a nonzero center-of-mass momentum, inhomogeneous superconducting states known as a pair-density-waves (PDWs) states. We show that in a system of spin-1/2 fermions in two dimensions in an electronic nematic spin-triplet phase where rotational symmetry is broken in both real and spin space PDW phases arise naturally in a theory that can be analysed using controlled approximations. We show that several superfluid phases that may arise in this phase can be treated within a controlled BCS mean field theory, with the strength of the spin-triplet nematic order parameter playing the role of the small parameter of this theory. We find that in a spin-triplet nematic phase, in addition to a triplet p-wave and spin-singlet d-wave (or s depending on the nematic phase) uniform superconducting states, it is also possible to have a d-wave (or s) PDW superconductor. The PDW phases found here can be either unidirectional, bidirectional, or tridirectional depending on the spin-triplet nematic phase and which superconducting channel is dominant. In addition, a triple-helix state is found in a particular channel. We show that these PDW phases are present in the weak-coupling limit, in contrast to the usual Fulde-Ferrell-Larkin-Ovchinnikov phases, which require strong coupling physics in addition to a large magnetic field (and often both). In chapter

  2. CT Findings of Disease with Elevated Serum D-Dimer Levels in an Emergency Room Setting

    Choi, Ji Youn; Kwon, Woo Cheol; Kim, Young Ju [Dept. of Radiology, Wonju Christian Hospital, Yensei University Wonju College of Medicine, Wonju (Korea, Republic of)


    Pulmonary embolism and deep vein thrombosis are the leading causes of elevated serum D-dimer levels in the emergency room. Although D-dimer is a useful screening test because of its high sensitivity and negative predictive value, it has a low specificity. In addition, D-dimer can be elevated in various diseases. Therefore, information on the various diseases with elevated D-dimer levels and their radiologic findings may allow for accurate diagnosis and proper management. Herein, we report the CT findings of various diseases with elevated D-dimer levels in an emergency room setting, including an intravascular contrast filling defect with associated findings in a venous thromboembolism, fracture with soft tissue swelling and hematoma formation in a trauma patient, enlargement with contrast enhancement in the infected organ of a patient, coronary artery stenosis with a perfusion defect of the myocardium in a patient with acute myocardial infarction, high density of acute thrombus in a cerebral vessel with a low density of affected brain parenchyma in an acute cerebral infarction, intimal flap with two separated lumens in a case of aortic dissection, organ involvement of malignancy in a cancer patient, and atrophy of a liver with a dilated portal vein and associated findings.

  3. Ab initio Studies on Intermolecular Interaction of Formamide and Hydroxyacetonitrile Dimers

    JU Xue-hai; XIE Lun-jia; XIA Qi-ying; XIAO He-ming


    The structures, the binding energies and the thermodynamic properties of formamide and hydroxyacetonitrile(HAN) dimers have been studied by means of the self-consistent ab initio Hartree-Fock and the second-order Mφller-Plesset correlation energy correction methods. The counterpoise procedure was used to check the basis set superposition error(BSSE) of the binding energies. There exist cyclic structures in a formamide dimer(Ⅰ), a HAN dimer(Ⅱ) and their heterodimer(Ⅲ). The corrected binding energies for dimers Ⅰ, Ⅱ and Ⅲ are respectively -45.53, -45.83 and -43.89 kJ/mol at the MP2/aug-cc-p VDZ//HF/aug-cc-p VDZ level. The change of the Gibbs free energies(ΔG) in the process of Ⅰ+Ⅱ→2Ⅲ was predicted to be -2.74 kJ/mol at 298.15 K. Dimer Ⅲ can be spontaneously produced in the mixture of formamide and HAN, which is in agreement with the experimental fact that most cyanohydrins are capable of interacting with dipeptide cyclo-His-Phe(CHP).

  4. Plasmid control of 6-aminohexanoic acid cyclic dimer degradation enzymes of Flavobacterium sp. KI72.

    Negoro, S; Shinagawa, H; Nakata, A; Kinoshita, S; Hatozaki, T; Okada, H


    Flavobacterium sp. K172, which is able to grow on 6-aminohexanoic acid cyclic dimer as the sole source of carbon and nitrogen, and plasmid control of the responsible enzymes, 6-aminohexanoic acid cyclic dimer hydrolase and 6-aminohexanoic acid linear oligomer hydrolase, were studied. The wild strain of K172 harbors three kinds of plasmid, pOAD1 (26.2 megadaltons), pOAD2 (28.8 megadaltons), and pOAD3 (37.2 megadaltons). The wild strain K172 was readily cured of its ability to grow on the cyclic dimer by mitomycin C, and the cyclic dimer hydrolase could not be detected either as catalytic activity or by antibody precipitation. No reversion of the cured strains was detected. pOAD2 was not detected in every cured strain tested but was restored in a transformant. The transformant recovered both of the enzyme activities, and the cyclic dimer hydrolase of the transformant was immunologically identical with that of the wild strain. All of the strains tested, including the wild, cured, and transformant ones, possessed identical pOAD3 irrespective of the metabolizing activity. Some of the cured strains possessed pOAD1 identical with the wild strain, but the others harbored plasmids with partially altered structures which were likely to be derived from pOAD1 by genetic rearrangements such as deletion, insertion, or substitution. These results suggested that the genes of the enzymes were borne on pOAD2.

  5. Chiral and Achiral Nanodumbbell Dimers: The Effect of Geometry on Plasmonic Properties.

    Smith, Kyle W; Zhao, Hangqi; Zhang, Hui; Sánchez-Iglesias, Ana; Grzelczak, Marek; Wang, Yumin; Chang, Wei-Shun; Nordlander, Peter; Liz-Marzán, Luis M; Link, Stephan


    Metal nanoparticles with a dumbbell-like geometry have plasmonic properties similar to those of their nanorod counterparts, but the unique steric constraints induced by their enlarged tips result in distinct geometries when self-assembled. Here, we investigate gold dumbbells that are assembled into dimers within polymeric micelles. A single-particle approach with correlated scanning electron microscopy and dark-field scattering spectroscopy reveals the effects of dimer geometry variation on the scattering properties. The dimers are prepared using exclusively achiral reagents, and the resulting dimer solution produces no detectable ensemble circular dichroism response. However, single-particle circular differential scattering measurements uncover that this dimer sample is a racemic mixture of individual nanostructures with significant positive and negative chiroptical signals. These measurements are complemented with detailed simulations that confirm the influence of various symmetry elements on the overall peak resonance energy, spectral line shape, and circular differential scattering response. This work expands the current understanding of the influence self-assembled geometries have on plasmonic properties, particularly with regard to chiral and/or racemic samples which may have significant optical activity that may be overlooked when using exclusively ensemble characterization techniques.

  6. Pharmaceutical aspects of the recombinant human serum albumin dimer: structural characteristics, biological properties, and medical applications.

    Taguchi, Kazuaki; Chuang, Victor Tuan Giam; Maruyama, Toru; Otagiri, Masaki


    Human serum albumin is the most abundant protein in the blood. It is clinically used in the treatment of severe hypoalbuminemia and as a plasma expander. The use of albumins as a carrier for drugs is currently being developed, and some are now in the preclinical and clinical trial stages. The main technologies for utilizing an albumin as a drug carrier are protein fusion, polymerization and surface modification, and so on. Among these technologies, albumin dimerization has wide clinical applications as a plasma expander as well as a drug carrier. Despite the fact that many reports have appeared on drugs using an albumin dimer as a carrier, our knowledge of the characteristics of the albumin dimer itself is incomplete. In this review, we summarize the structural characteristics of recombinant albumin dimers produced by two methods, namely, chemical linkage with 1,6-bis(maleimido)hexane and genetically linked with an amino acid linker, and the physicochemical characteristics and biological properties of these preparations. Finally, the potential for pharmaceutical applications of albumin dimers in clinical situations is discussed.

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

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


    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.

  8. Viscosity and sedimentation behaviors of the magnetorheological suspensions with oleic acid/dimer acid as surfactants

    Yang, Jianjian; Yan, Hua; Hu, Zhide; Ding, Ding


    This work deals with the role of polar interactions on the viscosity and sedimentation behaviors of magnetorheological suspensions with micro-sized magnetic particles dispersed in oil carriers. The oleic acid and dimer acid were employed to make an adjustment of the hydrophobicity of iron particles, in the interest of performing a comparative evaluation of the contributions of the surface polarity. The viscosity tests show that the adsorbed surfactant layer may impose a hindrance to the movement of iron particles in the oil medium. The polar attractions between dimer acid covered particles gave rise to a considerable increase in viscosity, indicating flocculation structure developed in the suspensions. The observed plateau-like region in the vicinity of 0.1 s-1 for MRF containing dimer acid is possibly due to the flocculation provoked by the carboxylic polar attraction, in which the structure is stable against fragmentation. Moreover, a quick recovery of the viscosity and a higher viscosity-temperature index also suggest the existence of particle-particle polar interaction in the suspensions containing dimer acid. The sedimentation measurements reveal that the steric repulsion of oleic acid plays a limited role in the stability of suspensions only if a large quantity of surfactant was used. The sedimentation results observed in the dimer acid covered particles confirm that loose and open flocculation was formed and enhanced sedimentation stability.

  9. Using Dimers to Measure Biosignatures and Atmospheric Pressure for Terrestrial Exoplanets

    Misra, Amit; Claire, Mark; Crisp, Dave


    We present a new method to probe atmospheric pressure on Earthlike planets using (O2-O2) dimers in the near-infrared. We also show that dimer features could be the most readily detectable biosignatures for Earthlike atmospheres, and may even be detectable in transit transmission with the James Webb Space Telescope (JWST). The absorption by dimers changes more rapidly with pressure and density than that of monomers, and can therefore provide additional information about atmospheric pressures. By comparing the absorption strengths of rotational and vibrational features to the absorption strengths of dimer features, we show that in some cases it may be possible to estimate the pressure at the reflecting surface of a planet. This method is demonstrated by using the O2 A band and the 1.06 $\\mu$m dimer feature, either in transmission or reflected spectra. It works best for planets around M dwarfs with atmospheric pressures between 0.1 and 10 bars, and for O2 volume mixing ratios above 50% of Earth's present day lev...

  10. Synthesis and mesomorphism of diacetylene-bridged triphenylene discotic liquid crystal dimers


    Connecting two discotic mesogens via a spacer not only stabilizes the columnar mesophase but also leads to the formation of glass columnar phase, and therefore improves the physical properties of discotic liquid crystals as organic semiconductor. Here, we report the synthesis of eight diacetylene-bridged triphenylene discotic liquid crystal dimers, [C18H6(OCnH2n+1)4(OMe)O2C-C8H16-C≡≡ C-]2, 3(n), (n = 4-8), [C18H6(OC6H13)5O2C-C8H16-C≡≡ C-]2, 6 and [C18H6(OC6H13)5O-(CH2)m-C≡≡ C-]2, 8(m), (m = 1, 3) by Eglinton coupling reaction. The thermotropic liquid crystal properties were studied by differential scanning calorimetry and polarized optical microscopy. The results are showed as follows: the length of peripheral alkyl chains of triphenylene influenced properties of liquid crystal dimers; dimers 3(n) (n = 5-8) and 6 had glass columnar phase, and no crystallization was observed above -50℃ for all the triphenylene dimers; compared with 3(6), 6 showed higher molecular symmetry, more stable columnar mesophase and wider mesophase range. The connecting group, length and rigidity of spacer had important influence on the mesomorphism of diacetylene-bridged triphenylene discotic liquid crystal dimers.

  11. Overexpression and characterization of dimeric and tetrameric forms of recombinant serine hydroxymethyltransferase from Bacillus stearothermophilus

    Venkatakrishna R Jala; V Prakash; N Appaji Rao; H S Savithri


    Serine hydroxymethyltransferase (SHMT), a pyridoxal-5′-phosphate (PLP) dependent enzyme catalyzes the interconversion of L-Ser and Gly using tetrahydrofolate as a substrate. The gene encoding for SHMT was amplified by PCR from genomic DNA of Bacillus stearothermophilus and the PCR product was cloned and overexpressed in Escherichia coli. The purified recombinant enzyme was isolated as a mixture of dimer (90%) and tetramer (10%). This is the first report demonstrating the existence of SHMT as a dimer and tetramer in the same organism. The specific activities at 37°C of the dimeric and tetrameric forms were 6.7 U/mg and 4.1 U/mg, respectively. The purified dimer was extremely thermostable with a m of 85°C in the presence of PLP and L-Ser. The temperature optimum of the dimer was 80°C with a specific activity of 32.4 U/mg at this temperature. The enzyme catalyzed tetrahydrofolate-independent reactions at a slower rate compared to the tetrahydrofolate-dependent retro-aldol cleavage of L-Ser. The interaction with substrates and their analogues indicated that the orientation of PLP ring of B. stearothermophilus SHMT was probably different from sheep liver cytosolic recombinant SHMT (scSHMT).

  12. Activation of NF-κB signalling by fusicoccin-induced dimerization.

    Skwarczynska, Malgorzata; Molzan, Manuela; Ottmann, Christian


    Chemically induced dimerization is an important tool in chemical biology for the analysis of protein function in cells. Here we report the use of the natural product fusicoccin (FC) to induce dimerization of 14-3-3-fused target proteins with proteins tagged to the C terminus (CT) of the H(+)-ATPase PMA2. To prevent nonproductive or detrimental interactions of the 14-3-3 proteins and CT fusions with endogenous cell proteins, their interaction surface was engineered to facilitate FC-induced dimerization exclusively between the introduced protein constructs. Live-cell imaging documented the reversible FC-induced translocation of 14-3-3 and CT to different cell compartments depending on localization sequences fused to their dimerization partner protein. The functionality of this system was demonstrated by the FC-induced importation of the NF-κB-CT into the nucleus. In HeLa cells, FC-mediated dimerization of the NF-κB-CT with a constitutively nuclear-localized 14-3-3 protein led to an NF-κB-specific cellular response by inducing IL-8 secretion.

  13. Stability of functionalized C{sub 60} paramagnetic dimers and monomers

    Miller, Michael [Armament Research Development and Engineering Center, Picatinny, NJ 07806-5000 (United States); Owens, Frank J., E-mail: [Department of Physics, Hunter College, City University of New York, 695 Park Ave., NY 10065 (United States)


    Highlights: Black-Right-Pointing-Pointer DFT is used to calculate the bond dissociation energy of functionalized C{sub 60} dimers. Black-Right-Pointing-Pointer The results show the dimers would not be stable above room temperature. Black-Right-Pointing-Pointer The calculations indicate the observed magnetism cannot be due to C{sub 60} dimers. Black-Right-Pointing-Pointer Because of their higher stability the ferromagnetism is likely due to X-C{sub 60} monomers. - Abstract: Density functional theory is used to calculate the bond dissociation energy to cleave the C{sub 60}=C{sub 60} bond of the paramagnetic X-C{sub 60}=C{sub 60}-X and X-C{sub 60}=C{sub 60} dimers where X is F, OH, O and H. The results show that these dimers would not be stable much above room temperature and therefore cannot constitute the paramagnetic phase needed to form the observed ferromagnetism which has been shown to be stable up to 800 K. The calculated bond dissociation energies to remove an F, OH or H from a single C{sub 60} are large suggesting that they could be the source of the unpaired spin needed for the high temperature ferromagnetism.

  14. Interplay of Specific Trans- and Juxtamembrane Interfaces in Plexin A3 Dimerization and Signal Transduction.

    Barton, Rachael; Khakbaz, Pouyan; Bera, Indrani; Klauda, Jeffery B; Iovine, M Kathryn; Berger, Bryan W


    Plexins are transmembrane proteins that serve as guidance receptors during angiogenesis, lymphangiogenesis, neuronal development, and zebrafish fin regeneration, with a putative role in cancer metastasis. Receptor dimerization or clustering, induced by extracellular ligand binding but modulated in part by the plexin transmembrane (TM) and juxtamembrane (JM) domains, is thought to drive plexin activity. Previous studies indicate that isolated plexin TM domains interact through a conserved, small-x3-small packing motif, and the cytosolic JM region interacts through a hydrophobic heptad repeat; however, the roles and interplay of these regions in plexin signal transduction remain unclear. Using an integrated experimental and simulation approach, we find disruption of the small-x3-small motifs in the Danio rerio Plexin A3 TM domain enhances dimerization of the TM-JM domain by enhancing JM-mediated dimerization. Furthermore, mutations of the cytosolic JM heptad repeat that disrupt dimerization do so even in the presence of TM domain mutations. However, mutations to the small-x3-small TM interfaces also disrupt Plexin A3 signaling in a zebrafish axonal guidance assay, indicating the importance of this TM interface in signal transduction. Collectively, our experimental and simulation results demonstrate that multiple TM and JM interfaces exist in the Plexin A3 homodimer, and these interfaces independently regulate dimerization that is important in Plexin A3 signal transduction.

  15. Copper dimer interactions on a thermomechanical superfluid {sup 4}He fountain

    Popov, Evgeny; Eloranta, Jussi, E-mail: [Department of Chemistry and Biochemistry, California State University at Northridge, 18111 Nordhoff St., Northridge, California 91330 (United States)


    Laser induced fluorescence imaging and frequency domain excitation spectroscopy of the copper dimer (B{sup 1}Σ{sub g}{sup +}←X{sup 1}Σ{sub u}{sup +}) in thermomechanical helium fountain at 1.7 K are demonstrated. The dimers penetrate into the fountain provided that their average propagation velocity is ca. 15 m/s. This energy threshold is interpreted in terms of an imperfect fountain liquid-gas interface, which acts as a trap for low velocity dimers. Orsay-Trento density functional theory calculations for superfluid {sup 4}He are used to characterize the dynamics of the dimer solvation process into the fountain. The dimers first accelerate towards the fountain surface and once the surface layer is crossed, they penetrate into the liquid and further slow down to Landau critical velocity by creating a vortex ring. Theoretical lineshape calculations support the assignment of the experimentally observed bands to Cu{sub 2} solvated in the bulk liquid. The vibronic progressions are decomposed of a zero-phonon line and two types of phonon bands, which correlate with solvent cavity interface compression (t < 200 fs) and expansion (200 < t < 500 fs) driven by the electronic excitation. The presented experimental method allows to perform molecular spectroscopy in bulk superfluid helium where the temperature and pressure can be varied.

  16. Effect of testosterone and its aliphatic and aromatic dimers on DNA morphology.

    Chanphai, P; Agudelo, D; Vesper, A R; Bérubé, G; Tajmir-Riahi, H A


    Conjugation of DNA with testosterone and it aliphatic dimer (alip) and aromatic dimer (arom) was investigated in aqueous solution at pH 7.4. Multiple spectroscopic methods, transmission electron microscopy (TEM) and molecular modeling were used to characterize steroid-DNA binding and DNA morphology. Spectroscopic analysis showed that testosterone binds DNA via A7, A16, A17, T8, T15 and T18 nucleobases with overall binding constants Ktest-DNA=1.8 (±0.4)×10(4)M(-1), Ktest-dimeralip-DNA=5.7 (±0.7)×10(4)M(-1) and Ktest-dimer-arom-DNA=7.3 (±0.9)×10(4)M(-1). The binding affinity increases in this order: testosterone dimer-aromatic>testosterone dimer-aliphatic>testosterone. The steroid loading efficacy was 40-50%. Transmission electron microscopy showed major changes in DNA morphology as testosterone-DNA interaction occurred with increase in the diameter of the DNA aggregate, indicating encapsulation of testosterone by DNA. Modeling showed the presence of several nucleobases attached to testosterone with the free binding energy of -4.93Kcal/mol.

  17. Kinetic analysis of histamine release due to covalently linked IgE dimers

    Dembo, M. (Los Alamos Scientific Lab., NM); Kagey-Sobotka, A.; Lichtenstein, L.M.; Goldstein, B.


    We present a kinetic model of histamine release from human basophils due to covalently linked IgE dimers. Comparison of theory with experiment shows that the model gives a good description of histamine release by IgE dimers and allows a number of the parameters of the model to be determined. Comparison with previous models of release by conventional antigens indicates that despite their covalent structure, IgE dimers are subject to the same laws governing inactivation as are antigen produced crosslinks. In addition, the kinetic equation which relates the rate of histamine release to the number of crosslinked Fc/sub e/ receptors per cell is the same for crosslinks formed by IgE dimers as for antigen induced crosslinks. Quantitative fitting of histamine release data also yields a value for the rate constant for crosslink formation by IgE dimer on the cell surface (r/sub x/ approx. = to 5 x 10/sup -10/ cm/sup 2//sec). This rate constant is remarkably high and indicates that the reaction is diffusion controlled.

  18. Stabilization of sulfuric acid dimers by ammonia, methylamine, dimethylamine, and trimethylamine

    Jen, Coty N.; McMurry, Peter H.; Hanson, David R.


    This study experimentally explores how ammonia (NH3), methylamine (MA), dimethylamine (DMA), and trimethylamine (TMA) affect the chemical formation mechanisms of electrically neutral clusters that contain two sulfuric acid molecules (dimers). Dimers may also contain undetectable compounds, such as water or bases, that evaporate upon ionization and sampling. Measurements were conducted using a glass flow reactor which contained a steady flow of humidified nitrogen with sulfuric acid concentrations of 107 to 109 cm-3. A known molar flow rate of a basic gas was injected into the flow reactor. The University of Minnesota Cluster Chemical Ionization Mass Spectrometer was used to measure the resulting sulfuric acid vapor and cluster concentrations. It was found that, for a given concentration of sulfuric acid vapor, the dimer concentration increases with increasing concentration of the basic gas, eventually reaching a plateau. The base concentrations at which the dimer concentrations saturate suggest NH3 < MA < TMA ≲ DMA in forming stabilized sulfuric acid dimers. Two heuristic models for cluster formation by acid-base reactions are developed to interpret the data. The models provide ranges of evaporation rate constants that are consistent with observations and leads to an analytic expression for nucleation rates that is consistent with atmospheric observations.

  19. Monoubiquitination and activity of the paracaspase MALT1 requires glutamate 549 in the dimerization interface.

    Katrin Cabalzar

    Full Text Available The mucosa-associated lymphoid tissue protein-1 (MALT1, also known as paracaspase is a protease whose activity is essential for the activation of lymphocytes and the growth of cells derived from human diffuse large B-cell lymphomas of the activated B-cell subtype (ABC DLBCL. Crystallographic approaches have shown that MALT1 can form dimers via its protease domain, but why dimerization is relevant for the biological activity of MALT1 remains largely unknown. Using a molecular modeling approach, we predicted Glu 549 (E549 to be localized within the MALT1 dimer interface and thus potentially relevant. Experimental mutation of this residue into alanine (E549A led to a complete impairment of MALT1 proteolytic activity. This correlated with an impaired capacity of the mutant to form dimers of the protease domain in vitro, and a reduced capacity to promote NF-κB activation and transcription of the growth-promoting cytokine interleukin-2 in antigen receptor-stimulated lymphocytes. Moreover, this mutant could not rescue the growth of ABC DLBCL cell lines upon MALT1 silencing. Interestingly, the MALT1 mutant E549A was unable to undergo monoubiquitination, which we identified previously as a critical step in MALT1 activation. Collectively, these findings suggest a model in which E549 at the dimerization interface is required for the formation of the enzymatically active, monoubiquitinated form of MALT1.

  20. Monoubiquitination and activity of the paracaspase MALT1 requires glutamate 549 in the dimerization interface.

    Cabalzar, Katrin; Pelzer, Christiane; Wolf, Annette; Lenz, Georg; Iwaszkiewicz, Justyna; Zoete, Vincent; Hailfinger, Stephan; Thome, Margot


    The mucosa-associated lymphoid tissue protein-1 (MALT1, also known as paracaspase) is a protease whose activity is essential for the activation of lymphocytes and the growth of cells derived from human diffuse large B-cell lymphomas of the activated B-cell subtype (ABC DLBCL). Crystallographic approaches have shown that MALT1 can form dimers via its protease domain, but why dimerization is relevant for the biological activity of MALT1 remains largely unknown. Using a molecular modeling approach, we predicted Glu 549 (E549) to be localized within the MALT1 dimer interface and thus potentially relevant. Experimental mutation of this residue into alanine (E549A) led to a complete impairment of MALT1 proteolytic activity. This correlated with an impaired capacity of the mutant to form dimers of the protease domain in vitro, and a reduced capacity to promote NF-κB activation and transcription of the growth-promoting cytokine interleukin-2 in antigen receptor-stimulated lymphocytes. Moreover, this mutant could not rescue the growth of ABC DLBCL cell lines upon MALT1 silencing. Interestingly, the MALT1 mutant E549A was unable to undergo monoubiquitination, which we identified previously as a critical step in MALT1 activation. Collectively, these findings suggest a model in which E549 at the dimerization interface is required for the formation of the enzymatically active, monoubiquitinated form of MALT1.

  1. Effect of Dimerization on the Dynamics of Neurotransmitter:Sodium Symporters.

    Gur, Mert; Cheng, Mary Hongying; Zomot, Elia; Bahar, Ivet


    Dimerization is a common feature among the members of the neurotransmitter:sodium symporter (NSS) family of membrane proteins. Yet, the effect of dimerization on the mechanism of action of NSS members is not fully understood. In this study, we examined the collective dynamics of two members of the family, leucine transporter (LeuT) and dopamine transporter (DAT), to assess the significance of dimerization in modulating the functional motions of the monomers. We used to this aim the anisotropic network model (ANM), an efficient and robust method for modeling the intrinsic motions of proteins and their complexes. Transporters belonging to the NSS family are known to alternate between outward-facing (OF) and inward-facing (IF) states, which enables the uptake and release of their substrate (neurotransmitter) respectively, as the substrate is transported from the exterior to the interior of the cell. In both LeuT and DAT, dimerization is found to alter the collective motions intrinsically accessible to the individual monomers in favor of the functional transitions (OF ↔ IF), suggesting that dimerization may play a role in facilitating transport.

  2. Dimerization drives EGFR endocytosis through two sets of compatible endocytic codes.

    Wang, Qian; Chen, Xinmei; Wang, Zhixiang


    We have shown previously that epidermal growth factor (EGF) receptor (EGFR) endocytosis is controlled by EGFR dimerization. However, it is not clear how the dimerization drives receptor internalization. We propose that EGFR endocytosis is driven by dimerization, bringing two sets of endocytic codes, one contained in each receptor monomer, in close proximity. Here, we tested this hypothesis by generating specific homo- or hetero-dimers of various receptors and their mutants. We show that ErbB2 and ErbB3 homodimers are endocytosis deficient owing to the lack of endocytic codes. Interestingly, EGFR-ErbB2 or EGFR-ErbB3 heterodimers are also endocytosis deficient. Moreover, the heterodimer of EGFR and the endocytosis-deficient mutant EGFRΔ1005-1017 is also impaired in endocytosis. These results indicate that two sets of endocytic codes are required for receptor endocytosis. We found that an EGFR-PDGFRβ heterodimer is endocytosis deficient, although both EGFR and PDGFRβ homodimers are endocytosis-competent, indicating that two compatible sets of endocytic codes are required. Finally, we found that to mediate the endocytosis of the receptor dimer, the two sets of compatible endocytic codes, one contained in each receptor molecule, have to be spatially coordinated.


    Abreu C.R.A.


    Full Text Available The effect of surface topography upon the adsorption of dimer molecules is analyzed by means of grand canonical ensemble Monte Carlo simulations. Heterogeneous surfaces were assumed to consist of a square lattice containing active sites with two different energies. These were distributed in three different configurations: a random distribution of isolated sites; a random distribution of grains with four high-energy sites; and a random distribution of grains with nine high-energy sites. For the random distribution of isolated sites, the results are in good agreement with the molecular simulations performed by Nitta et al. (1997. In general, the comparison with theoretical models shows that the Nitta et al. (1984 isotherm presents good predictions of dimer adsorption both on homogeneous and heterogeneous surfaces with sites having small differences in characteristic energies. The molecular simulation results also show that the energy topology of the solid surfaces plays an important role in the adsorption of dimers on solids with large differences in site energies. For these cases, the Nitta et al. model does not describe well the data on dimer adsorption on random heterogeneous surfaces (grains with one acid site, but does describe reasonably well the adsorption of dimers on more patchwise heterogeneous surfaces (grains with nine acid sites.

  4. Structure of the dimerization domain of DiGeorge critical region 8

    Senturia, R.; Faller, M.; Yin, S.; Loo, J.A.; Cascio, D.; Sawaya, M.R.; Hwang, D.; Clubb, R.T.; Guo, F. (UCLA)


    Maturation of microRNAs (miRNAs, {approx}22nt) from long primary transcripts [primary miRNAs (pri-miRNAs)] is regulated during development and is altered in diseases such as cancer. The first processing step is a cleavage mediated by the Microprocessor complex containing the Drosha nuclease and the RNA-binding protein DiGeorge critical region 8 (DGCR8). We previously reported that dimeric DGCR8 binds heme and that the heme-bound DGCR8 is more active than the heme-free form. Here, we identified a conserved dimerization domain in DGCR8. Our crystal structure of this domain (residues 298-352) at 1.7 {angstrom} resolution demonstrates a previously unknown use of a WW motif as a platform for extensive dimerization interactions. The dimerization domain of DGCR8 is embedded in an independently folded heme-binding domain and directly contributes to association with heme. Heme-binding-deficient DGCR8 mutants have reduced pri-miRNA processing activity in vitro. Our study provides structural and biochemical bases for understanding how dimerization and heme binding of DGCR8 may contribute to regulation of miRNA biogenesis.

  5. Resonance hybridization and near field properties of strongly coupled plasmonic ring dimer-rod nanosystem

    Koya, Alemayehu Nana; Ji, Boyu; Hao, Zuoqiang; Lin, Jingquan, E-mail: [School of Science, Changchun University of Science and Technology, Changchun 130022 (China)


    Combined effects of polarization, split gap, and rod width on the resonance hybridization and near field properties of strongly coupled gold dimer-rod nanosystem are comparatively investigated in the light of the constituent nanostructures. By aligning polarization of the incident light parallel to the long axis of the nanorod, introducing small split gaps to the dimer walls, and varying width of the nanorod, we have simultaneously achieved resonance mode coupling, huge near field enhancement, and prolonged plasmon lifetime. As a result of strong coupling between the nanostructures and due to an intense confinement of near fields at the split and dimer-rod gaps, the extinction spectrum of the coupled nanosystem shows an increase in intensity and blueshift in wavelength. Consequently, the near field lifespan of the split-nanosystem is prolonged in contrast to the constituent nanostructures and unsplit-nanosystem. On the other hand, for polarization of the light perpendicular to the long axis of the nanorod, the effect of split gap on the optical responses of the coupled nanosystem is found to be insignificant compared to the parallel polarization. These findings and such geometries suggest that coupling an array of metallic split-ring dimer with long nanorod can resolve the huge radiative loss problem of plasmonic waveguide. In addition, the Fano-like resonances and immense near field enhancements at the split and dimer-rod gaps imply the potentials of the nanosystem for practical applications in localized surface plasmon resonance spectroscopy and sensing.

  6. Self-assembly in a model colloidal mixture of dimers and spherical particles

    Prestipino, Santi; Munaò, Gianmarco; Costa, Dino; Caccamo, Carlo


    We investigate the structure of a dilute mixture of amphiphilic dimers and spherical particles, a model relevant to the problem of encapsulating globular "guest" molecules in a dispersion. Dimers and spheres are taken to be hard particles, with an additional attraction between spheres and the smaller monomers in a dimer. Using the Monte Carlo simulation, we document the low-temperature formation of aggregates of guests (clusters) held together by dimers, whose typical size and shape depend on the guest concentration χ. For low χ (less than 10%), most guests are isolated and coated with a layer of dimers. As χ progressively increases, clusters grow in size becoming more and more elongated and polydisperse; after reaching a shallow maximum for χ ≈50 % , the size of clusters again reduces upon increasing χ further. In one case only (χ =50 % and moderately low temperature) the mixture relaxed to a fluid of lamellae, suggesting that in this case clusters are metastable with respect to crystal-vapor separation. On heating, clusters shrink until eventually the system becomes homogeneous on all scales. On the other hand, as the mixture is made denser and denser at low temperature, clusters get increasingly larger until a percolating network is formed.

  7. Ligand binding by the tandem glycine riboswitch depends on aptamer dimerization but not double ligand occupancy.

    Ruff, Karen M; Strobel, Scott A


    The glycine riboswitch predominantly exists as a tandem structure, with two adjacent, homologous ligand-binding domains (aptamers), followed by a single expression platform. The recent identification of a leader helix, the inclusion of which eliminates cooperativity between the aptamers, has reopened the debate over the purpose of the tandem structure of the glycine riboswitch. An equilibrium dialysis-based assay was combined with binding-site mutations to monitor glycine binding in each ligand-binding site independently to understand the role of each aptamer in glycine binding and riboswitch tertiary interactions. A series of mutations disrupting the dimer interface was used to probe how dimerization impacts ligand binding by the tandem glycine riboswitch. While the wild-type tandem riboswitch binds two glycine equivalents, one for each aptamer, both individual aptamers are capable of binding glycine when the other aptamer is unoccupied. Intriguingly, glycine binding by aptamer-1 is more sensitive to dimerization than glycine binding by aptamer-2 in the context of the tandem riboswitch. However, monomeric aptamer-2 shows dramatically weakened glycine-binding affinity. In addition, dimerization of the two aptamers in trans is dependent on glycine binding in at least one aptamer. We propose a revised model for tandem riboswitch function that is consistent with these results, wherein ligand binding in aptamer-1 is linked to aptamer dimerization and stabilizes the P1 stem of aptamer-2, which controls the expression platform.

  8. Structural and Vibrational Study on Monomer and Dimer Forms and Water Clusters of Acetazolamide

    Aysen E. Ozel


    Full Text Available Experimental IR and Raman spectra of solid acetazolamide have been analysed by computing the molecular structures and vibrational spectra of monomer and dimer forms and water clusters of acetazolamide. The possible stable conformers of free acetazolamide molecule in the ground state were obtained by scanning the potential energy surface through the dihedral angles, D1 (1S-2C-6S-9N, D2 (4N-5C-12N-14C, and D3 (5C-12N-14C-16C. The final geometry parameters for the obtained stable conformers were determined by means of geometry optimization, carried out at DFT/B3LYP/6-31G++(d,p theory level. Afterwards the possible dimer forms of the molecule and acetazolamide-H2O clusters were formed and their energetically preferred conformations were investigated using the same method and the same level of theory. The effect of BSSE on the structure and energy of acetazolamide dimer has been investigated. The assignment of the vibrational modes was performed based on the potential energy distribution of the vibrational modes, calculated by using GAR2PED program. The experimental vibrational wavenumbers of solid acetazolamide are found to be in better agreement with the calculated wavenumbers of dimer form of acetazolamide than those of its monomeric form. NBO analysis has been performed on both monomer and dimer geometries.

  9. Design, synthesis and biological studies of survivin dimerization modulators that prolong mitotic cycle.

    Chettiar, Somsundaram N; Cooley, James V; Park, In-Hee; Bhasin, Deepak; Chakravarti, Arnab; Li, Pui-Kai; Li, Chenglong; Jacob, Naduparambil Korah


    Survivin, a member of the inhibitor of apoptosis protein (IAP) family proteins, has essential roles in cell division and inhibition of apoptosis. Several clinical studies in cancer patients have shown that the elevated levels of survivin correlate with aggressiveness of the disease and resistance to radiation and chemotherapeutic treatments. Survivin is an integral component of chromosomal passenger complex (CPC) where it binds to borealin and INCENP through its dimerization interface. Thus, disruption of functional survivin along its dimer interface with a small molecule is hypothesized to inhibit the proliferation of cancer cells and sensitize them to therapeutic agents and radiation. Recently, a small molecule (Abbott8) was reported to bind at the dimerization interface of survivin. Further development of this compound was accomplished by computational modeling of the molecular interactions along the dimerization interface, which has led to the design of promising survivin dimerization modulators. Two of the most potent survivin modulators, LLP3 and LLP9 at concentrations between 50 and 100nM, caused delay in mitotic progression and major mitotic defects in proliferating human umbilical vein endothelial cells (HUVEC) and prostate cancer cells (PC3).

  10. Structure of FGFR3 transmembrane domain dimer: implications for signaling and human pathologies.

    Bocharov, Eduard V; Lesovoy, Dmitry M; Goncharuk, Sergey A; Goncharuk, Marina V; Hristova, Kalina; Arseniev, Alexander S


    Fibroblast growth factor receptor 3 (FGFR3) transduces biochemical signals via lateral dimerization in the plasma membrane, and plays an important role in human development and disease. Eight different pathogenic mutations, implicated in cancers and growth disorders, have been identified in the FGFR3 transmembrane segment. Here, we describe the dimerization of the FGFR3 transmembrane domain in membrane-mimicking DPC/SDS (9/1) micelles. In the solved NMR structure, the two transmembrane helices pack into a symmetric left-handed dimer, with intermolecular stacking interactions occurring in the dimer central region. Some pathogenic mutations fall within the helix-helix interface, whereas others are located within a putative alternative interface. This implies that although the observed dimer structure is important for FGFR3 signaling, the mechanism of FGFR3-mediated transduction across the membrane is complex. We propose an FGFR3 signaling mechanism that is based on the solved structure, available structures of isolated soluble FGFR domains, and published biochemical and biophysical data.

  11. Dimerization capacities of FGF2 purified with or without heparin-affinity chromatography.

    Natalia Platonova

    Full Text Available Fibroblast growth factor-2 (FGF2 is a pleiotropic growth factor exhibiting a variety of biological activities. In this article, we studied the capacity of FGF2 purified with or without heparin affinity chromatography to self-associate. Analyzing the NMR HSQC spectra for different FGF2 concentrations, heparin-affinity purified FGF2 showed perturbations that indicate dimerization and are a higher-order oligomerization state. HSQC perturbation observed with different FGF2 concentrations revealed a heparin-binding site and two dimer interfaces. Thus, with increasing protein concentrations, FGF2 monomers make contacts with each other and form dimers or higher order oligomers. On the contrary, FGF2 purified with ion-exchange chromatography did not show similar perturbation indicating that self-association of FGF2 is eliminated if purification is done without heparin-affinity chromatography. The HSQC spectra of heparin-affinity purified FGF2 can be reproduced to some extent by adding heparin tetra-saccharide to ion exchange chromatography purified FGF2. Heparin-affinity purified FGF2 bound to acceptor and donor beads in a tagged form using His-tagged or GST-tagged proteins, also dimerized in the AlphaScreen™ assay. This assay was further validated using different experimental conditions and competitors. The assay constitutes an interesting tool to study dimerization of other FGF forms as well.

  12. Clinical applicability of D-dimer assay in the diagnosis of pulmonary embolism reduces with aging

    Luca Masotti


    Full Text Available Despite modern algorithms have been proposed for diagnosis of pulmonary embolism (PE, it remains understimed and often missed in clinical practice, especially in elderly patients, resulting in high morbidity and mortality when early and correctly untreated. One of the main controversial issue is represented by the role and applicability of D-dimer in the diagnostic work up of geriatric patients. Most recent guidelines in young-adult patients suggest to perform D-dimer assay by ELISA or immunoturbidimetric methods only in non high pre-test clinical probability (PTP patients; in these patients negative D-dimer can safely rule out the diagnosis of PE. This strategy is safe also in elderly patients; however the percentage of patients with non high PTP and negative D-dimer reduces progressively with age, making difficult its clinical applicability. The Authors, starting from two case reports, up date the diagnostic management of PE underling the limitations of D-dimer assay in elderly patients.

  13. Synthesis and mesomorphism of diacetylene-bridged triphenylene discotic liquid crystal dimers

    JI Hong; ZHAO KeQing; YU WenHao; WANG BiQin; HU Pin


    Connecting two discotic mesogens via a spacer not only stabilizes the columnar mesophase but also leads to the formation of glass columnar phase,and therefore improves the physical properties of discotic liquid crystals as organic semiconductor.Here,we report the synthesis of eight diacetylene-bridged triphenylene discotic liquid crystal dimers,[C18H6(OCnH2n+1)4(OMe)O2C-CsH16-C≡C-]2,3(n),(n=4-8),[C18H6(OC6H13)5O2C-C8H16-C≡C-]2,6 and [C18H6(OC6H13)5O-(CH2)m-C≡C-]2,8(m),(m=1,3) by Eglinton coupling reaction.The thermotropic liquid crystal properties were studied by differential scanning calorimetry and polarized optical microscopy.The results are showed as follows:the length of peripheral alkyl chains of triphenylene influenced properties of liquid crystal dimers;dimers 3(n) (n=5-8) and 6 had glass columnar phase,and no crystallization was observed above -50℃ for all the triphenylene dimers;compared with 3(6),6 showed higher molecular symmetry,more stable columnar mesophase and wider mesophase range.The connecting group,length and rigidity of spacer had important influence on the mesomorphism of diacetylene-bridged triphenylene discotic liquid crystal dimers.

  14. Hepatitis C virus genomic RNA dimerization is mediated via a kissing complex intermediate

    Shetty, Sumangala; Kim, Seungtaek; Shimakami, Tetsuro; Lemon, Stanley M.; Mihailescu, Mihaela-Rita


    With over 200 million people infected with hepatitis C virus (HCV) worldwide, there is a need for more effective and better-tolerated therapeutic strategies. The HCV genome is a positive-sense; single-stranded RNA encoding a large polyprotein cleaved at multiple sites to produce at least ten proteins, among them an error-prone RNA polymerase that confers a high mutation rate. Despite considerable overall sequence diversity, in the 3′-untranslated region of the HCV genomic RNA there is a 98-nucleotide (nt) sequence named X RNA, the first 55 nt of which (X55 RNA) are 100% conserved among all HCV strains. The X55 region has been suggested to be responsible for in vitro dimerization of the genomic RNA in the presence of the viral core protein, although the mechanism by which this occurs is unknown. In this study, we analyzed the X55 region and characterized the mechanism by which it mediates HCV genomic RNA dimerization. Similar to a mechanism proposed previously for the human immunodeficiency 1 virus (HIV-1) genome, we show that dimerization of the HCV genome involves formation of a kissing complex intermediate, which is converted to a more stable extended duplex conformation in the presence of the core protein. Mutations in the dimer linkage sequence loop sequence that prevent RNA dimerization in vitro significantly reduced but did not completely ablate the ability of HCV RNA to replicate or produce infectious virus in transfected cells. PMID:20360391

  15. Antimicrobial peptide protegrin-3 adopt an antiparallel dimer in the presence of DPC micelles: a high-resolution NMR study

    Usachev, K. S., E-mail:; Efimov, S. V.; Kolosova, O. A.; Klochkova, E. A.; Aganov, A. V.; Klochkov, V. V. [Kazan Federal University, NMR Laboratory, Institute of Physics (Russian Federation)


    A tendency to dimerize in the presence of lipids was found for the protegrin. The dimer formation by the protegrin-1 (PG-1) is the first step for further oligomeric membrane pore formation. Generally there are two distinct model of PG-1 dimerization in either a parallel or antiparallel β-sheet. But despite the wealth of data available today, protegrin dimer structure and pore formation is still not completely understood. In order to investigate a more detailed dimerization process of PG-1 and if it will be the same for another type of protegrins, in this work we used a high-resolution NMR spectroscopy for structure determination of protegrin-3 (RGGGL-CYCRR-RFCVC-VGR) in the presence of perdeuterated DPC micelles and demonstrate that PG-3 forms an antiparallel NCCN dimer with a possible association of these dimers. This structural study complements previously published solution, solid state and computational studies of PG-1 in various environments and validate the potential of mean force simulations of PG-1 dimers and association of dimers to form octameric or decameric β-barrels.

  16. External electric field effects on the mechanical properties of the αβ-tubulin dimer of microtubules: a molecular dynamics study.

    Saeidi, H R; Lohrasebi, A; Mahnam, K


    The mechanical properties of the αβ-tubulin dimer of microtubules was modeled by using the molecular dynamics (MD) simulation method. The effect on the mechanical properties of the dimer of the existence and nonexistence of an applied electric field, either constant or periodic, was studied. Since there are charged or polar groups in the dimer structure, the electric field can interact with the dimer. The elastic constant and Young's modulus of the dimer were decreased when the dimer was exposed to a constant electric field of 0.03 V/nm. Furthermore, applying an oscillating electric field in the 1 GHz range to the dimer increased the elastic constant and Young's modulus of the dimer. These parameters were related to dimer rigidity and, consequently, in this frequency range, the application of electric fields may affect the function of microtubules.

  17. Plasmonic Dimer-Like Nanoassemblies for Surface-Enhanced Raman Spectroscop

    Rigo, Maria; Seo, Jaetae; Kim, Wan-Joong; Jung, Sungsoo; Hampton University Team; Etri Collaboration; Kriss Collaboration


    We report on the preparation of gold dimers in which the near-field coupling in their subwavelength gap is influenced by the individual gold nanoparticles size and the molecule's length used to assemble the dimers. The nano assemblies display plasmonic modes similar to those observed in rod-like nanoparticles. The longitudinal mode of the gold dimers shift as a function of gold nanoparticles size and concentration and it is influenced by the concentration of Rhodamine 6G (R6G), the molecule used as nanoparticle linker. We report large surface enhanced Raman scattering (SERS) enhancements for R6G when using linked-gold nano-assemblies as a SERS substrate. A discussion about the main origins for the large enhancement of molecular vibrational modes is presented. This work at Hampton University was supported by the National Science Foundation (HRD-0734635 and HRD-0630372).

  18. Dimeric (isoquinoline)(N-salicylidene-D,L-glutamato)copper(II) ethanol solvate.

    Langer, Vratislav; Gyepesová, Dalma; Kohútová, Mária; Valent, Aladár


    The title racemic complex, bis[mu-N-(2-oxidobenzylidene)-D,L-glutamato(2-)]bis[(isoquinoline)copper(II)] ethanol disolvate, [Cu(2)(C(12)H(11)NO(5))(2)(C(9)H(7)N)(2)].2C(2)H(6)O, adopts a square-pyramidal Cu(II) coordination mode with a tridentate N-salicylideneglutamato Schiff base dianion and an isoquinoline ligand bound in the basal plane. The apex of the pyramid is occupied by a phenolic O atom from the adjacent chelate molecule at an apical distance of 2.487 (3) A, building a dimer located on the crystallographic inversion center. The Cu...Cu spacing within the dimers is 3.3264 (12) A. The ethanol solvent molecules are hydrogen bonded to the dimeric complex molecules, forming infinite chains in the a direction. The biological activity of the title complex has been studied.

  19. Properties of the Lennard-Jones dimeric fluid in two dimensions: an integral equation study.

    Urbic, Tomaz; Dias, Cristiano L


    The thermodynamic and structural properties of the planar soft-sites dumbbell fluid are examined by Monte Carlo simulations and integral equation theory. The dimers are built of two Lennard-Jones segments. Site-site integral equation theory in two dimensions is used to calculate the site-site radial distribution functions for a range of elongations and densities and the results are compared with Monte Carlo simulations. The critical parameters for selected types of dimers were also estimated. We analyze the influence of the bond length on critical point as well as tested correctness of site-site integral equation theory with different closures. The integral equations can be used to predict the phase diagram of dimers whose molecular parameters are known.

  20. Mapping key interactions in the dimerization process of HBHA from Mycobacterium tuberculosis, insights into bacterial agglutination.

    Esposito, Carla; Cantisani, Marco; D'Auria, Gabriella; Falcigno, Lucia; Pedone, Emilia; Galdiero, Stefania; Berisio, Rita


    HBHA is a cell-surface protein implicated in the dissemination of Mycobacterium tuberculosis (Mtb) from the site of primary infection. Its N-terminal coiled-coil region is also involved in bacterial agglutination. However, despite the importance of HBHA dimerization in agglutination, protein regions involved in dimerization are hitherto not known. Here, we mapped these regions by coupling peptide synthesis, biochemical and computational analyses, and identified structural determinants for HBHA monomer-monomer recognition. Importantly, we obtained the first molecule able to induce HBHA dimer disaggregation at 37°C, the typical growth temperature of Mtb. This result provides new opportunities towards the development of Mtb anti-aggregation molecules with therapeutic interest.

  1. Structure of isothiocyanic acid dimers. Theoretical and FTIR matrix isolation studies

    Krupa, Justyna; Wierzejewska, Maria


    A quantum mechanical study of the potential energy surface for the HNCS dimer is reported. The calculations were performed using DFT and ab initio MP2 methods. The most stable is a cyclic form with a double N-H⋯S interaction and the interaction energy in the range of 16.91-18.92 kJ mol-1. An open HNCS dimer bound by the N-H⋯N hydrogen bond is by ca 3.3-5.1 kJ mol-1 less stable. Experimental FTIR matrix isolation studies of HNCS/N2 system show that exclusively less stable open dimer is formed in solid nitrogen. Possible reasons for the observed discrepancy between theory and experiment are discussed.

  2. Pressure effects on the radical-radical recombination reaction of photochromic bridged imidazole dimers.

    Mutoh, Katsuya; Abe, Jiro


    The bridged imidazole dimers are some of the attractive fast photochromic compounds which have potential applications to the ophthalmic lenses, real-time hologram and molecular machines. The strategy for expanding their photochromic properties such as the colour variation and tuning the decolouration rates has been vigorously investigated, but the insight into the structural changes along the photochromic reactions has not been demonstrated in detail. Here, we demonstrated the pressure dependence of the radical-radical recombination reaction of the bridged imidazole dimers. The radical-radical interaction can be controlled by applying high pressure. Our results give fundamental information about the molecular dynamics of the bridged imidazole dimers, leading to the development of new functional photochromic machines and pressure-sensitive photochromic materials.

  3. Elevation in D-dimer concentrations is positively correlated with gestation in normal uncomplicated pregnancy

    Jeremiah ZA


    Full Text Available Zaccheaus A Jeremiah,1 Teddy C Adias,2 Margaret Opiah,3 Siyeoforiye P George,4 Osaro Mgbere,5 Ekere J Essien61Department of Medical Laboratory Sciences, Niger Delta University, Wilberforce Island, Nigeria; 2Bayelsa State College of Health Technology, Ogbia-Town, Nigeria; 3Department of Maternal and Child Health, Faculty of Nursing, Niger Delta University, Wilberforce Island, Nigeria; 4Postgraduate Hematology Unit, Rivers State University of Science and Technology, Port Harcourt, Nigeria; 5Houston Department of Health and Human Services, Houston, TX, USA; 6Institute of Community Health, University of Houston, Houston, TX, USABackground: D-dimer levels have been reported to increase progressively during pregnancy, but how this affects Nigerian women is not well known.Objective: This study aims to determine the D-dimer concentration and its relationship to other coagulation parameters among pregnant women in Port Harcourt, Nigeria.Method: In a cross-sectional observational study conducted in Port Harcourt, Nigeria, 120 pregnant women and 60 nonpregnant controls, drawn from a tertiary health institution in the Niger Delta, Nigeria, were assessed, using the standard procedures, for the following parameters: D-dimer concentration, prothrombin time, activated partial thromboplastin time, platelet count, hemoglobin, and packed cell volume.Results: The median D-dimer concentration of 153.1 ng/mL in the pregnant group was found to be significantly elevated when compared with the control value of 118.5 ng/mL (t = 2.348, P = 0.021. Conversely, there was a marked depression in the platelet count among pregnant women (193.5 × 109/L when compared with 229.0 × 109/L in the control group (t = 3.424; P = 0.001. There was no statistically significant difference in the values for the prothrombin time and the activated partial thromboplastin time between pregnant and nonpregnant women. D-dimer values correlated positively and significantly with gestation (r = 0

  4. Gold dimer nanoantenna with slanted gap for tunable LSPR and improved SERS

    Kessentini, Sameh


    We focus on improving the surface-enhanced Raman scattering (SERS) of dimer nanoantenna by tailoring the shape of the coupled nanoantennas extremities from rounded to straight or slanted ones. A numerical model based on the discrete dipole approximation method-taking into account periodicity, adhesion layer, and roughness-is first validated by comparison with localized surface plasmon resonance (LSPR) and SERS experiments on round-edged dimer nanoantennas and then used to investigate the effect of the straight or slanted gap in the dimer antenna. Simulations show that both LSPR and SERS can be tuned by changing the gap slanting angle. The SERS enhancement factor can also be improved by 2 orders of magnitude compared to the one reached using a rounded gap. Therefore, the slanting angle can be used as a new control parameter in the design of SERS substrates to guarantee stronger field confinement and higher sensitivity, especially as its feasibility is demonstrated. © 2014 American Chemical Society.

  5. Finite size effects on the electromagnetic field enhancement from low-dimensional silver nanoshell dimer arrays

    Song, Youlin [Zhengzhou University, China; Zhao, Ke [ORNL; Jia, Yu [Zhengzhou University, China; Hu, Xing [Zhengzhou University, China; Zhang, Zhenyu [ORNL


    Finite size effects on the optical properties of one-dimensional 1D and two-dimensional 2D nanoshell dimer arrays are investigated using generalized Mie theory and coupled dipole approximation within the context of surface-enhanced Raman spectroscopy SERS. It is shown that the huge enhancement in the electromagnetic EM field at the center of a given dimer oscillates with the length of the 1D array. For an array of fixed length, the EM enhancement also oscillates along the array, but with a different period. Both types of oscillations can be attributed to the interference of the dynamic dipole fields from different dimers in the array. When generalized to 2D arrays, EM enhancement higher than that of the 1D arrays can be gained with a constant magnitude, a salient feature advantageous to experimental realization of single-molecule SERS. 2008 American Institute of Physics. DOI: 10.1063/1.3009293

  6. Finite Size Effects on the Electromagnetic Field Enhancement from Low-dimensional Silver Nanoshell Dimer Arrays

    Song, Youlin; Zhao, Ke; Jia, Yu; Hu, Xing; Zhang, Zhenyu


    Finite size effects on the optical properties of one-dimensional (1D) and 2D nanoshell dimer arrays are investigated using generalized Mie theory and coupled dipole approximation within the context of surface-enhanced Raman spectroscopy (SERS). It is shown that the huge enhancement in the electromagnetic (EM) field at the center of a given dimer oscillates with the length of the 1D array. For an array of fixed length, the EM enhancement also oscillates along the array, but with a different period. Both types of oscillations can be attributed to the interference of the dynamic dipole fields from different dimers in the array. When generalized to 2D arrays, EM enhancement higher than that of the 1D arrays can be gained with a constant magnitude, a salient feature advantageous to experimental realization of single-molecule SERS. [K. Zhao et al, J. Chem. Phys. 125, 081102 (2005); Y. L. Song et al, accepted by J. Chem. Phys.

  7. Longiberine and O-methyllongiberine, dimeric protoberberine-benzyl tetrahydroisoquinoline alkaloids from Thalictrum longistylum(1).

    Lee, S S; Wu, W N; Wilton, J H; Beal, J L; Doskotch, R W


    Two benzyltetrahydroisoquinoline-protoberberine dimers, longiberine (1) and O-methyllongiberine (2), were isolated from the roots of Thalictrum longistylum and represent a new class of dimeric alkaloids. The structure of longiberine (1) was established by spectral and chemical methods. Reductive cleavage of O-ethyllongiberine (4) with Na/liquid NH(3) yielded (+)-(S)-N-methylcoclaurine (5), which determined one-half of the dimer, and 1D and 2D NMR studies arranged the substituents on the protoberberine nucleus. Chemical conversion of thalidezine (6) to 1 via the O-acetyl N,N-didemethyl derivative 9, which was methylenated in the Mannich reaction and N-methylated by the Eschweiler-Clarke procedure, established the second asymmetric center as S and confirmed the ring size and the order of the substituents for 1. Methylation of 1 with diazomethane formed the O-methyl derivative 2, identical with the natural product.

  8. Dichroism, chirality, and polarization eigenstates in Babinet nanoslot-dimer membrane metamaterials

    Zhukovsky, Sergei; Chigrin, Dmitry N.; Kremers, Christian


    We present a detailed theoretical description of the optical properties of planar metamaterials comprising a metal membrane patterned with openings (microslots) arranged in closely located couples (dimers). Using the covariant coupled-dipole approach, the effective material tensors of such a meta......We present a detailed theoretical description of the optical properties of planar metamaterials comprising a metal membrane patterned with openings (microslots) arranged in closely located couples (dimers). Using the covariant coupled-dipole approach, the effective material tensors...... of such a metamaterial are recovered, and contributions responsible for elliptical dichroism and optical activity are identified. Polarization conversion properties of II-shaped and V-shaped dimers are determined and explained in terms of elliptically polarized eigenmodes of the metamaterial. Good agreement with direct...

  9. Critical behavior in the cubic dimer model at nonzero monomer density

    Sreejith, G. J.; Powell, Stephen


    We study critical behavior in the classical cubic dimer model (CDM) in the presence of a finite density of monomers. With attractive interactions between parallel dimers, the monomer-free CDM exhibits an unconventional transition from a Coulomb phase to a dimer crystal. Monomers act as charges (or monopoles) in the Coulomb phase and, at nonzero density, lead to a standard Landau-type transition. We use large-scale Monte Carlo simulations to study the system in the neighborhood of the critical point, and find results in agreement with detailed predictions of scaling theory. Going beyond previous studies of the transition in the absence of monomers, we explicitly confirm the distinction between conventional and unconventional criticality, and quantitatively demonstrate the crossover between the two. Our results also provide additional evidence for the theoretical claim that the transition in the CDM belongs in the same universality class as the deconfined quantum critical point in the SU (2) JQ model.

  10. Suppression of electroreductive dimerization of benzaldehyde by addition of. cap alpha. -cyclodextrin

    Matsue, T.; Tasaki, C.; Fujihira, M.; Osa, T.


    Electrochemical reduction of carbonyl compounds to the corresponding alcohols is an important subject in organic electrochemistry. The effect of ..cap alpha..-cyclodextrin (..cap alpha..-CD) on the electroreduction of benzaldehyde was investigated. The reduction in aqueous system produces benzyl alcohol and 1,2-diphenyl-1,2-ethanediol (hydrobenzoin, dimerization product). The addition of ..cap alpha..-CD caused the decrease in the yield of hydrobenzoin. This suppression effect was observed both in the controlled potential and controlled current electrolyses. This is accounted for by the retardation of the dimerization rate between the neutral radicals, since inclusion of substrate provides severe steric hindrance around the reaction site. The addition had only a small influence on the stereochemistry of hydrobenzoin formed by the dimerization.

  11. Excision of pyrimidine dimers from nuclear deoxyribonucleic acid in ultraviolet-irradiated Dictyostelium discoideum

    Clark, J.M.; Deering, R.A.


    A sensitive endonuclease assay was used to study the fate of pyrimidine dimers introduced by ultraviolet irradiation into the nuclear deoxyribonucleic acid of the cellular slime mold Dictyostellium discoideum. Analysis of the frequency of T4 endonuclease V-induced single-strand breaks by alkaline sucrose gradient sedimentation showed that strain NC4 (rad/sup +/) removed >98% of the dimers induced by irradiation at 40 J/m/sup 2/ (254 nm) within 215 min after irradiation. HPS104 (radC44), a mutant sensitive to ultraviolet irradiation, removed 91% under these conditions, although at a significantly slower rate than NC4: only 8% were removed during the 10- to 15- min period immediately after irradiation, whereas NC4 excised 64% during this interval. HPS104 thus appears to be deficient in the activity(ies) responsible for rapidly incising ultraviolet-irradiated nuclear deoxyribonucleic acid at the sites of pyrimidine dimers.

  12. Dimers of heavy p-elements of groups IV-VI: Electronic, vibrational, and magnetic properties

    Borisova, S. D.; Rusina, G. G.; Eremeev, S. V.; Chulkov, E. V.


    Equilibrium lengths and binding energies, vibrational frequencies, width of the HOMO-LUMO gap, and the magnetic anisotropy energies for one- and two-component dimers of heavy p elements of Groups IV (Sn, Pb), V (Sb, Bi), and VI (Se, Te) with a pronounced relativistic effect have been calculated with the use of the formalism of the density functional theory. It has been shown that it is necessary to take into account the spin-orbit coupling, which significantly affects the energy parameters of clusters. The analysis of the data obtained has revealed that the Pb-Te, Pb-Se, Sn-Te, and Sn-Se dimers have the widest gap at the Fermi level and the lowest reactivity. The magnetic anisotropy energy has been calculated for all single- and doublecomponent dimers and the direction of the easy magnetization axis has been determined.

  13. Model for growth hormone receptor activation based on subunit rotation within a receptor dimer

    Brown, Richard J.; Adams, Julian J.; Pelekanos, Rebecca A.; Wan, Yu; McKinstry, William J.; Palethorpe, Kathryn; Seeber, Ruth M.; Monks, Thea A.; Eidne, Karin A.; Parker, Michael W.; Waters, Michael J. (UWA); (St. Vincent); (Queensland)


    Growth hormone is believed to activate the growth hormone receptor (GHR) by dimerizing two identical receptor subunits, leading to activation of JAK2 kinase associated with the cytoplasmic domain. However, we have reported previously that dimerization alone is insufficient to activate full-length GHR. By comparing the crystal structure of the liganded and unliganded human GHR extracellular domain, we show here that there is no substantial change in its conformation on ligand binding. However, the receptor can be activated by rotation without ligand by inserting a defined number of alanine residues within the transmembrane domain. Fluorescence resonance energy transfer (FRET), bioluminescence resonance energy transfer (BRET) and coimmunoprecipitation studies suggest that receptor subunits undergo specific transmembrane interactions independent of hormone binding. We propose an activation mechanism involving a relative rotation of subunits within a dimeric receptor as a result of asymmetric placement of the receptor-binding sites on the ligand.

  14. Analytic expression for three-body recombination rates into deep dimers

    Fedorov, D V; Jensen, A S; Zinner, N T


    We investigate three-body recombination rates into deep dimers in cold atomic gases with large scattering length within hyper-spherical adiabatic zero-range approach. We derive closed analytic expressions for the rates for one- and two-species gases. Although the deep dimers are beyond the zero-range theory the latter can still describe the recombination into deep dimers by use of one additional short-range absorption parameter. The recombination rate, as function of the scattering length, retains the known universal behavior --- the fourth power trend with characteristic log-periodic peaks --- however increasing the short-range absorption broadens the peaks until they are eventually completely smeared out. Increasing the heavy-to-light mass ratio in a two-species system decreases the distance between the peaks and increases the overal scale of the recombination rate.

  15. Van der Waals interactions in rare-gas dimers: The role of interparticle interactions

    Chen, Yu-Ting; Chai, Jeng-Da


    We investigate the potential energy curves of rare-gas dimers with various ranges and strengths of interparticle interactions (nuclear-electron, electron-electron, and nuclear-nuclear interactions). Our investigation is based on the highly accurate coupled-cluster theory associated with those interparticle interactions. For comparison, the performance of the corresponding Hartree-Fock theory, second-order Moller-Plesset perturbation theory, and density functional theory is also investigated. Our results reveal that when the interparticle interactions retain the long-range Coulomb tails, the nature of van der Waals interactions in the rare-gas dimers remains similar. By contrast, when the interparticle interactions are sufficiently short-range, the conventional van der Waals interactions in the rare-gas dimers completely disappear, yielding purely repulsive potential energy curves.

  16. Computational studies of the structural properties of the monomer and dimer of Aβ(1-28)

    Dong, Xiao; Chen, Wei; Mousseau, Normand; Derreumaux, Philippe


    Neurodegenerative diseases are linked with the self-assembly of normally soluble proteins into amyloid fibrils. In this work, in silico characterization of the structures of the monomer and dimer of Aβ(1-28) are studied with the coarse-grained OPEP model using the activation-relaxation technique (ART nouveau). We find a dominant anti-parallel β-sheet structure present for both the monomer and dimer. While the monomer does not adopt a stable conformation, it fluctuates around a well-defined structure: starting from the end point, the monomer wraps a first time around, producing a β-hairpin and returns on the other side of the N-terminal, forming a three-strand β-sheet. The dimer assembles in a similar fashion, but with the two strands interlocking. The thermodynamics of the molecular assemblies and various folding path-ways are further studied using molecular dynamics.

  17. The Nature of Binding in the Phenalenyl Dimer and its Derivatives

    Kolb, Brian; Thonhauser, Timo; Kertesz, Miklos


    The biradical phenalenyl (π)-dimer and its derivatives have attracted interest recently because of their potentially useful electrical, optical, and magnetic properties. These properties can be tuned by adjusting the binding characteristics between the monomers within the dimer. Typically, this is done by substituting electron withdrawing or donating groups onto the (α) or (β)-site carbons. An understanding of this binding lies at the heart of useful application of these materials. In this work, the binding characteristics of phenalenyl dimers were investigated using density functional theory. In particular, the vdW-DF functional was used to explore the role of van der Waals interactions in the binding within this system. A comparison of the binding curves with those of the closed shell derivatives wherein the central carbons have been replaced by either nitrogen or boron sheds light into the nature of the interactions between the monomers.

  18. Dynamics of a Chlorophyll Dimer in Collective and Local Thermal Environments

    Merkli, M; Sayre, R T; Gnanakaran, S; Könenberg, M; Nesterov, A I; Song, H


    We present a theoretical analysis of exciton transfer and decoherence effects in a photosynthetic dimer interacting with collective (correlated) and local (uncorrelated) protein-solvent environments. Our approach is based on the framework of the spin-boson model. We derive explicitly the thermal relaxation and decoherence rates of the exciton transfer process, valid for arbitrary temperatures and for arbitrary (in particular, large) interaction constants between the dimer and the environments. We establish a generalization of the Marcus formula, giving reaction rates for dimer levels possibly individually and asymmetrically coupled to environments. We identify rigorously parameter regimes for the validity of the generalized Marcus formula. The existence of long living quantum coherences at ambient temperatures emerges naturally from our approach.

  19. Synthesis and Characterization of Tetrahydrofurfurylcyclopentadienyl Molybdenum Tricarbonyl Dimer: Evidence for 19-Electron Intramolecular "Solvento" Interactions.

    Gallagher, Michelle; Dougherty, Pat; Tanner, Pamela S.; Barbini, Denis C.; Schulte, Jurgen; Jones, Wayne E.


    The synthesis and characterization of a THF pendant, dimeric Mo cyclopentadienyl complex is reported and the structure characterized by NMR, FTIR, and UV-vis spectroscopies. The dimer was found to undergo metal-metal bond homolysis under either photochemical or electrochemical conditions to yield an odd-electron complex. Cyclic voltammetry under varying scan rate conditions from 25 to 10 000 mV/s demonstrates a dynamic equilibrium process that we assign to the formation of either an intramolecular 19-electron (18 + delta) complex or a bare 17-electron complex. Photolysis of the dimer in room temperature solution could be monitored as a loss of the dpi-dsigma transition at 503 nm by transient absorption spectroscopy. The recovery of the transient absorption signal at 410 nm follows first-order kinetics at a rate of 5 x 10(3) s(-1).

  20. Van der Waals universality in homonuclear atom-dimer elastic collisions

    Giannakeas, P


    The universal aspects of atom-dimer elastic collisions are investigated within the framework of Faddeev equations. The two-body interactions between the neutral atoms are approximated by the separable potential approach. Our analysis considers a pure van der Waals potential tail as well as soft-core van der Waals interactions permitting us in this manner to address the universally general features of atom-dimer resonant spectra. In particular, we show that the atom-dimer resonances are solely associated with the {\\it excited} Efimov states. Furthermore, the positions of the corresponding resonances for a soft-core potentials with more than 5 bound states are in good agreement with the corresponding results from an infinitely deep pure van der Waals tail potential.