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Sample records for stable dimer formation

  1. Species A rotavirus NSP3 acquires its translation inhibitory function prior to stable dimer formation.

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    Hugo I Contreras-Treviño

    Full Text Available Species A rotavirus non-structural protein 3 (NSP3 is a translational regulator that inhibits or, under some conditions, enhances host cell translation. NSP3 binds to the translation initiation factor eIF4G1 and evicts poly-(A binding protein (PABP from eIF4G1, thus inhibiting translation of polyadenylated mRNAs, presumably by disrupting the effect of PABP bound to their 3'-ends. NSP3 has a long coiled-coil region involved in dimerization that includes a chaperone Hsp90-binding domain (HS90BD. We aimed to study the role in NSP3 dimerization of a segment of the coiled-coil region adjoining the HS90BD. We used a vaccinia virus system to express NSP3 with point mutations in conserved amino acids in the coiled-coil region and determined the effects of these mutations on translation by metabolic labeling of proteins as well as on accumulation of stable NSP3 dimers by non-dissociating Western blot, a method that separates stable NSP3 dimers from the monomer/dimerization intermediate forms of the protein. Four of five mutations reduced the total yield of NSP3 and the formation of stable dimers (W170A, K171E, R173E and R187E:K191E, whereas one mutation had the opposite effects (Y192A. Treatment with the proteasome inhibitor MG132 revealed that stable NSP3 dimers and monomers/dimerization intermediates are susceptible to proteasome degradation. Surprisingly, mutants severely impaired in the formation of stable dimers were still able to inhibit host cell translation, suggesting that NSP3 dimerization intermediates are functional. Our results demonstrate that rotavirus NSP3 acquires its function prior to stable dimer formation and remain as a proteasome target throughout dimerization.

  2. Fibrillar dimer formation of islet amyloid polypeptides

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    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)

    2015-05-08

    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.

  3. Fibrillar dimer formation of islet amyloid polypeptides

    Science.gov (United States)

    Chiu, Chi-cheng; de Pablo, Juan J.

    2015-09-01

    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.

  4. Stability and Formation of Isobutylene Dimers.

    Science.gov (United States)

    Goldsmith, Robert H.

    1983-01-01

    Isobutylene is an important bulk chemical for the petroleum industry. Dimerization and hydrogenation reactions produce the standard fuel octane rating comparison. This classic chemistry is often misrepresented in modern texts, however, and this paper attempts to correlate the physical organic principles that apply. (Author)

  5. A potential new, stable state of the E-cadherin strand-swapped dimer in solution.

    Science.gov (United States)

    Schumann-Gillett, Alexandra; Mark, Alan E; Deplazes, Evelyne; O'Mara, Megan L

    2018-01-01

    E-cadherin is a transmembrane glycoprotein that facilitates inter-cellular adhesion in the epithelium. The ectodomain of the native structure is comprised of five repeated immunoglobulin-like domains. All E-cadherin crystal structures show the protein in one of three alternative conformations: a monomer, a strand-swapped trans homodimer and the so-called X-dimer, which is proposed to be a kinetic intermediate to forming the strand-swapped trans homodimer. However, previous studies have indicated that even once the trans strand-swapped dimer is formed, the complex is highly dynamic and the E-cadherin monomers may reorient relative to each other. Here, molecular dynamics simulations have been used to investigate the stability and conformational flexibility of the human E-cadherin trans strand-swapped dimer. In four independent, 100 ns simulations, the dimer moved away from the starting structure and converged to a previously unreported structure, which we call the Y-dimer. The Y-dimer was present for over 90% of the combined simulation time, suggesting that it represents a stable conformation of the E-cadherin dimer in solution. The Y-dimer conformation is stabilised by interactions present in both the trans strand-swapped dimer and X-dimer crystal structures, as well as additional interactions not found in any E-cadherin dimer crystal structures. The Y-dimer represents a previously unreported, stable conformation of the human E-cadherin trans strand-swapped dimer and suggests that the available crystal structures do not fully capture the conformations that the human E-cadherin trans homodimer adopts in solution.

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

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

    2017-02-21

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

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

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    Ayana Tagawa

    2017-09-01

    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

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

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    Tagawa, Ayana; Numata, Tomoko; Shikata, Toshiyuki

    2017-09-01

    Raman scattering and infrared (IR) absorption spectra of enantiopure (R)-propylene carbonate ((R)PC) 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. (R)PC 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 (R)PC 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 the pure

  9. Statistical analysis of dimer formation in supersaturated metal vapor based on molecular dynamics simulation

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    Korenchenko, Anna E.; Vorontsov, Alexander G.; Gelchinski, Boris R.; Sannikov, Grigorii P.

    2018-04-01

    We discuss the problem of dimer formation during the homogeneous nucleation of atomic metal vapor in an inert gas environment. We simulated nucleation with molecular dynamics and carried out the statistical analysis of double- and triple-atomic collisions as the two ways of long-lived diatomic complex formation. Close pair of atoms with lifetime greater than the mean time interval between atom-atom collisions is called a long-lived diatomic complex. We found that double- and triple-atomic collisions gave approximately the same probabilities of long-lived diatomic complex formation, but internal energy of the resulted state was essentially lower in the second case. Some diatomic complexes formed in three-particle collisions are stable enough to be a critical nucleus.

  10. Quantitative determination of cyclobutane thymine dimers in DNA by stable isotope-dilution mass spectrometry

    International Nuclear Information System (INIS)

    Podmore, I.D.; Cooke, M.S.; Herbert, K.E.; Lunec, J.

    1996-01-01

    In order to understand the role of UV-induced DNA lesions in biological processes such as mutagenesis and carcinogenesis, it is essential to detect and quantify DNA damage in cells. In this paper we present a novel and both highly selective and sensitive assay using capillary gas chromatography (GC) combined with mass spectrometry (MS) for the detection and accurate quantitation of a major product of UV-induced DNA damage (cis-syb cyclobutadithymine). Quantitation of the cyclobutane thymine dimer was achieved by the use of an internal standard in the form of a stable 2 H-labeled analogue. Both isotopically labeled and nonlabeled dimers were prepared directly from their corresponding monomers. Each was identified as their trimethylsilyl ether derivative by GC-MS. Calibration plots were obtained for known quantities of both nonlabeled and analyte and internal standard. Quantitation of cis-syn cyclobutadithymine was demonstrated in DNA exposed to UVC radiation over a dose range of 0 3500 J m -2 . Under the conditions used, the limit of detection was found to be 20-50 fmol on column (equivalent to 0.002-0.005 nmol dimer per mg DNA). The results of the present study indicate that capillary GC-MS is an ideally suited technique for selective and sensitive quantification of cis-syn cyclobutadithymine in DNA and hence UV-induced DNA damage. (author)

  11. Deciphering the kinetic binding mechanism of dimeric ligands using a potent plasma-stable dimeric inhibitor of postsynaptic density protein-95 as an example

    DEFF Research Database (Denmark)

    Chi, Celestine N; Bach, Anders; Gottschalk, Marie

    2010-01-01

    Dimeric ligands can be potent inhibitors of protein-protein or enzyme-substrate interactions. They have increased affinity and specificity toward their targets due to their ability to bind two binding sites simultaneously and are therefore attractive in drug design. However, few studies have...... 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...

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

    DEFF Research Database (Denmark)

    Smith, A. P.; Jonsson, Hannes

    1996-01-01

    We present theoretical results based on density functional theory and kinetic Monte Carlo simulations of silicon deposition and address observations made in recently reported low temperature scanning tunneling microscopy studies. A mechanism is presented which explains dimer formation on top...... of the substrate's dimer rows at 160 K and up to room temperature, while between-row dimers and longer strings of adatoms (''diluted dimer rows'') form at higher temperature. A crossover occurs at around room temperature between two different mechanisms for adatom diffusion in our model....

  13. Cooperative Formation of Icosahedral Proline Clusters from Dimers

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    Jacobs, Alexander D.; Jovan Jose, K. V.; Horness, Rachel; Raghavachari, Krishnan; Thielges, Megan C.; Clemmer, David E.

    2018-01-01

    Ion mobility spectrometry-mass spectrometry and Fourier transform infrared spectroscopy (FTIR) techniques were combined with quantum chemical calculations to examine the origin of icosahedral clusters of the amino acid proline. When enantiopure proline solutions are electrosprayed (using nanospray) from 100 mM ammonium acetate, only three peaks are observed in the mass spectrum across a concentration range of five orders of magnitude: a monomer [Pro+H]+ species, favored from 0.001 to 0.01 mM proline concentrations; a dimer [2Pro+H]+ species, the most abundant species for proline concentrations above 0.01 mM; and, the dimer and dodecamer [12Pro+2H]2+ for 1.0 mM and more concentrated proline solutions. Electrospraying racemic D/ L-proline solutions from 100 mM ammonium acetate leads to a monomer at low proline concentrations (0.001 to 0.1 mM), and a dimer at higher concentrations (>0.09 mM), as well as a very small population of 8 to 15 Pro clusters that comprise species from 2Pro. [Figure not available: see fulltext.

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

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    Yingzhi Xu

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

  15. A strategy for complex dimer formation when biomimicry fails: total synthesis of ten coccinellid alkaloids.

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    Sherwood, Trevor C; Trotta, Adam H; Snyder, Scott A

    2014-07-09

    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.

  16. Laser isotope separation using selective inhibition and encouragement of dimer formation

    International Nuclear Information System (INIS)

    Kivel, B.

    1979-01-01

    Method and apparatus for inhibiting dimer formation of molecules of a selected isotope type in a cooled flow of gas to enhance the effectiveness of mass difference isotope separation techniques are described. Molecules in the flow containing atoms of the selected isotope type are selectively excited by infrared radiation in order to inhibit the formation of dimers and larger clusters of such molecules, while the molecules not containing atoms of the selected, excited type are encouraged to form dimers and higher order aggregates by the cooling of the gaseous flow. The molecules with the excited isotope will predominate in monomers and will constitute the enriched product stream, while the aggregated group comprising molecules having the unexcited isotope will predominate in dimers and larger clusters of molecules, forming the tails stream. The difference in diffusion coefficientts between particles of the excited and unexcited isotopes is enhanced by the greater mass differences resulting from aggregation of unexcited particles into dimers and larger clusters. Prior art separation techniques which exploit differences in isotopic diffusion rates will consequently exhibit enhanced enrichment per stage by the utilization of the present invention

  17. Formation and detection of oxidant-generated tryptophan dimers in peptides and proteins

    DEFF Research Database (Denmark)

    Carroll, Luke; Pattison, David I; Davies, Justin B

    2017-01-01

    and function. Due to its low oxidation potential, the indole ring of tryptophan (Trp) is a major target, with this resulting in the formation of indolyl radicals (Trp•). These undergo multiple reactions including ring opening and dimerization which can result in protein aggregation. The factors that govern Trp...

  18. Dimers in nucleating vapors

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    Lushnikov, A. A.; Kulmala, M.

    1998-09-01

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

  19. Hsa-miR-1587 G-quadruplex formation and dimerization induced by NH4+, molecular crowding environment and jatrorrhizine derivatives.

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    Tan, Wei; Yi, Long; Zhu, Zhentao; Zhang, Lulu; Zhou, Jiang; Yuan, Gu

    2018-03-01

    A guanine-rich human mature microRNA, miR-1587, was discovered to form stable intramolecular G-quadruplexes in the presence of K + , Na + and low concentration of NH 4 + (25mM) by electrospray ionization mass spectrometry (ESI-MS) combined with circular dichroism (CD) spectroscopy. Furthermore, under high concentration of NH 4 + (100mM) or molecular crowding environments, miR-1587 formed a dimeric G-quadruplex through 3'-to-3' stacking of two monomeric G-quadruplex subunits with one ammonium ion sandwiched between the interfaces. Specifically, two synthesized jatrorrhizine derivatives with terminal amine groups could also induce the dimerization of miR-1587 G-quadruplex and formed 1:1 and 2:1 complexes with the dimeric G-quadruplex. In contrast, jatrorrhizine could bind with the dimeric miR-1587 G-quadruplex, but could not induce dimerization of miR-1587 G-quadruplex. These results provide a new strategy to regulate the functions of miR-1587 through induction of G-quadruplex formation and dimerization. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    DEFF Research Database (Denmark)

    Kristensen, K.; Enggrob, Kirsten; King, Stephanie Michelle

    2013-01-01

    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...... precursors. However, the sampling time resolution precluded conclusive evidence regarding formation from gas- or particle-phase processes. CCN activities of the particles formed in the smog chamber displayed a modest variation during the course of experiments, with kappa values in the range 0......-diaterpenyl ester was found at higher concentrations under higher temperature conditions, both in the smog-chamber study and in ambient air aerosol samples, and exhibited much higher concentrations at night relative to day-time in line with previous results. We conclude that analysis of pinyl dimer esters provides...

  1. Formation of covalent di-tyrosine dimers in recombinant α-synuclein

    DEFF Research Database (Denmark)

    van Maarschalkerweerd, A; Pedersen, MN; Peterson, H

    2015-01-01

    in standard recombinant protein preparations, induced without extrinsic oxidative or nitrative agents. The dimers exhibit no secondary structure but advanced SAXS studies reveal an increased structural definition, resulting in a more hydrophobic micro-environment than the highly disordered monomer......Parkinson's disease is associated with fibril deposition in the diseased brain. Misfolding events of the intrinsically disordered synaptic protein α-synuclein are suggested to lead to the formation of transient oligomeric and cytotoxic species. The etiology of Parkinson's disease is further...

  2. Formation of oxidative and non-oxidative dimers in metallothioneins: Implications for charge-state analysis for structural determination.

    Science.gov (United States)

    Irvine, Gordon W; Heinlein, Lina; Renaud, Justin B; Sumarah, Mark W; Stillman, Martin J

    2017-12-30

    Metallothioneins (MTs) are a class of dynamic proteins that have been investigated extensively using mass spectrometric methods due to their amenability to ionization. Here we detect the formation of oxidative and non-oxidative MT dimers using high-resolution mass spectrometry (HRMS) which has previously been overlooked with lower-resolution techniques. Recombinant human MT1a and its isolated domain fragments were analyzed by high-resolution Thermo Q-Exactive and Bruker time-of-flight (TOF) mass spectrometers. Covalent Cys modification was performed using N-ethylmalemide to probe the effect of Cys oxidation on dimer formation. Dimerization was detected in the analysis of select charge states of Zn 7 MT and apo-βMT. Specifically, high resolution (140 k) revealed the +6 dimer peaks overlapping with the +3 charge state, but not with the other charge states (+4, +5, +6). The proteins with covalently modified Cys did not show dimer formation in any of their charge states. Apo-α and apo-βαMT also did not form dimers under the conditions tested. Dimerization of MT was detected for zinc metalated and certain apo-MT forms with HRMS, which was not seen with lower-resolution techniques. These dimers appear overlapped only with certain charge states, confounding their analysis for structural characterization of MTs. The Zn-MT dimers appeared to be non-oxidative; however, the formation of dimers in the apo-protein is likely dependent on Cys oxidation. Copyright © 2017 John Wiley & Sons, Ltd.

  3. Photoinduced formation of an azobenzene-based CD-active supramolecular cyclic dimer.

    Science.gov (United States)

    Sogawa, Hiromitsu; Terada, Kayo; Miyagi, Yu; Shiotsuki, Masashi; Inai, Yoshihito; Masuda, Toshio; Sanda, Fumio

    2015-04-27

    A series of new photo-responsive amino acid-derived azobenzenedicarboxylic acid derivatives (S)-1 a-e were synthesized. Compound (S)-1 a in the trans form exhibited no circular dichroism (CD) signal in DMF under ambient conditions, whereas intense Cotton effects were observed upon UV irradiation, indicating the formation of a chiral supramolecular structure in the cis form. The CD signals disappeared when trifluoroacetic acid (TFA) was added to the solution. The ester counterpart [(S)-1 a'] showed no CD signal. Hydrogen bonding between the carboxy groups seemed necessary for constructing the supramolecular structure. The kinetic studies of cis to trans isomerization of (S)-1 a demonstrated that the formation of a chiral supramolecule enhances the stability of the cis-azobenzene structure. The ESI mass spectrum of stilbenedicarboxylic acid (S)-4, an analogue of (S)-1 b, confirmed the formation of a dimer. A theoretical CD study revealed that (S)-1 a in the cis form should be present as a cyclic chiral dimer. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Free radicals impair the anti-oxidative stress activity of DJ-1 through the formation of SDS-resistant dimer.

    Science.gov (United States)

    Yasuda, Tatsuki; Niki, Takeshi; Ariga, Hiroyoshi; Iguchi-Ariga, Sanae M M

    2017-04-01

    DJ-1 is a causative gene for familial Parkinson's disease (PD). Loss-of-function of DJ-1 protein is suggested to contribute to the onset of PD, but the causes of DJ-1 dysfunction remain insufficiently elucidated. In this study, we found that the SDS-resistant irreversible dimer of DJ-1 protein was formed in human dopaminergic neuroblastoma SH-SY5Y cells when the cells were exposed to massive superoxide inducers such as paraquat and diquat. The dimer was also formed in vitro by superoxide in PQ redox cycling system and hydroxyl radical produced in Fenton reaction. We, thus, found a novel phenomenon that free radicals directly affect DJ-1 to form SDS-resistant dimers. Moreover, the formation of the SDS-resistant dimer impaired anti-oxidative stress activity of DJ-1 both in cell viability assay and H 2 O 2 -elimination assay in vitro. Similar SDS-resistant dimers were steadily formed with several mutants of DJ-1 found in familial PD patients. These findings suggest that DJ-1 is impaired due to the formation of SDS-resistant dimer when the protein is directly attacked by free radicals yielded by external and internal stresses and that the DJ-1 impairment is one of the causes of sporadic PD.

  5. Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation.

    Science.gov (United States)

    Shore, Sabrina; Henderson, Jordana M; Lebedev, Alexandre; Salcedo, Michelle P; Zon, Gerald; McCaffrey, Anton P; Paul, Natasha; Hogrefe, Richard I

    2016-01-01

    For most sample types, the automation of RNA and DNA sample preparation workflows enables high throughput next-generation sequencing (NGS) library preparation. Greater adoption of small RNA (sRNA) sequencing has been hindered by high sample input requirements and inherent ligation side products formed during library preparation. These side products, known as adapter dimer, are very similar in size to the tagged library. Most sRNA library preparation strategies thus employ a gel purification step to isolate tagged library from adapter dimer contaminants. At very low sample inputs, adapter dimer side products dominate the reaction and limit the sensitivity of this technique. Here we address the need for improved specificity of sRNA library preparation workflows with a novel library preparation approach that uses modified adapters to suppress adapter dimer formation. This workflow allows for lower sample inputs and elimination of the gel purification step, which in turn allows for an automatable sRNA library preparation protocol.

  6. Influence of cytosine methylation on ultraviolet-induced cyclobutane pyrimidine dimer formation in genomic DNA

    Energy Technology Data Exchange (ETDEWEB)

    Rochette, Patrick J. [Division of Pathology, Department of Medical Biology, Universite Laval, Quebec, QC (Canada); Division of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Universite de Sherbrooke, Sherbrooke, QC (Canada); Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT (United States); Lacoste, Sandrine [Division of Pathology, Department of Medical Biology, Universite Laval, Quebec, QC (Canada); Division of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Universite de Sherbrooke, Sherbrooke, QC (Canada); Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB (Canada); Therrien, Jean-Philippe [Division of Pathology, Department of Medical Biology, Universite Laval, Quebec, QC (Canada); Bastien, Nathalie [Division of Pathology, Department of Medical Biology, Universite Laval, Quebec, QC (Canada); Division of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Universite de Sherbrooke, Sherbrooke, QC (Canada); Brash, Douglas E. [Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT (United States); Drouin, Regen, E-mail: Regen.Drouin@USherbrooke.ca [Division of Pathology, Department of Medical Biology, Universite Laval, Quebec, QC (Canada); Division of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Universite de Sherbrooke, Sherbrooke, QC (Canada)

    2009-06-01

    The ultraviolet (UV) component of sunlight is the main cause of skin cancer. More than 50% of all non-melanoma skin cancers and >90% of squamous cell carcinomas in the US carry a sunlight-induced mutation in the p53 tumor suppressor gene. These mutations have a strong tendency to occur at methylated cytosines. Ligation-mediated PCR (LMPCR) was used to compare at nucleotide resolution DNA photoproduct formation at dipyrimidine sites either containing or lacking a methylated cytosine. For this purpose, we exploited the fact that the X chromosome is methylated in females only on the inactive X chromosome, and that the FMR1 (fragile-X mental retardation 1) gene is methylated only in fragile-X syndrome male patients. Purified genomic DNA was irradiated with UVC (254 nm), UVB (290-320 nm) or monochromatic UVB (302 and 313 nm) to determine the effect of different wavelengths on cyclobutane pyrimidine dimer (CPD) formation along the X-linked PGK1 (phosphoglycerate kinase 1) and FMR1 genes. We show that constitutive methylation of cytosine increases the frequency of UVB-induced CPD formation by 1.7-fold, confirming that methylation per se is influencing the probability of damage formation. This was true for both UVB sources used, either broadband or monochromatic, but not for UVC. Our data prove unequivocally that following UVB exposure methylated cytosines are significantly more susceptible to CPD formation compared with unmethylated cytosines.

  7. Influence of cytosine methylation on ultraviolet-induced cyclobutane pyrimidine dimer formation in genomic DNA

    International Nuclear Information System (INIS)

    Rochette, Patrick J.; Lacoste, Sandrine; Therrien, Jean-Philippe; Bastien, Nathalie; Brash, Douglas E.; Drouin, Regen

    2009-01-01

    The ultraviolet (UV) component of sunlight is the main cause of skin cancer. More than 50% of all non-melanoma skin cancers and >90% of squamous cell carcinomas in the US carry a sunlight-induced mutation in the p53 tumor suppressor gene. These mutations have a strong tendency to occur at methylated cytosines. Ligation-mediated PCR (LMPCR) was used to compare at nucleotide resolution DNA photoproduct formation at dipyrimidine sites either containing or lacking a methylated cytosine. For this purpose, we exploited the fact that the X chromosome is methylated in females only on the inactive X chromosome, and that the FMR1 (fragile-X mental retardation 1) gene is methylated only in fragile-X syndrome male patients. Purified genomic DNA was irradiated with UVC (254 nm), UVB (290-320 nm) or monochromatic UVB (302 and 313 nm) to determine the effect of different wavelengths on cyclobutane pyrimidine dimer (CPD) formation along the X-linked PGK1 (phosphoglycerate kinase 1) and FMR1 genes. We show that constitutive methylation of cytosine increases the frequency of UVB-induced CPD formation by 1.7-fold, confirming that methylation per se is influencing the probability of damage formation. This was true for both UVB sources used, either broadband or monochromatic, but not for UVC. Our data prove unequivocally that following UVB exposure methylated cytosines are significantly more susceptible to CPD formation compared with unmethylated cytosines.

  8. A single β-octyl glucoside molecule induces HIV-1 Nef dimer formation in the absence of partner protein binding.

    Directory of Open Access Journals (Sweden)

    Mousheng Wu

    Full Text Available The HIV-1 Nef accessory protein is essential for viral pathogenicity and AIDS progression. Nef forms complexes with multiple host cell factors to facilitate viral replication and promote immune escape of HIV-infected cells. Previous X-ray crystal structures demonstrate that Nef forms homodimers, the orientation of which are influenced by host cell binding partners. In cell-based fluorescence complementation assays, Nef forms homodimers at the plasma membrane. However, recombinant Nef proteins often exist as monomers in solution, suggesting that membrane interaction may also trigger monomer to dimer transitions. In this study, we show that monomeric Nef core proteins can be induced to form dimers in the presence of low concentrations of the non-ionic surfactant, β-octyl glucoside (βOG. X-ray crystallography revealed that a single βOG molecule is present in the Nef dimer, with the 8-carbon acyl chain of the ligand binding to a hydrophobic pocket formed by the dimer interface. This Nef-βOG dimer interface involves helix αB, as observed in previous dimer structures, as well as a helix formed by N-terminal residues 54-66. Nef dimer formation is stabilized in solution by the addition of βOG, providing biochemical validation for the crystal structure. These observations together suggest that the interaction with host cell lipid mediators or other hydrophobic ligands may play a role in Nef dimerization, which has been previously linked to multiple Nef functions including host cell protein kinase activation, CD4 downregulation, and enhancement of HIV-1 replication.

  9. Ethanol water azeotrope Study. Molecular characterization of ethanol dimers, hetero dimers and hetero trimers of ethanol water

    International Nuclear Information System (INIS)

    Mejia, Sol M; Espinal, Juan F; Mondragon, Fanor

    2006-01-01

    In this investigation, as a first stage, we studied the structure and stability of the dimers,hetero dimers and hetero trimers like aggregates of ethanol and ethanol water respectively. Molecular modelling using hybrid B3LYP of the density functional theory (DFT) was used in this research. O-H bond lengths, hydrogen bond distances, CCOH dihedral angles, enthalpies and Gibbs free energies of dimerization and trimerization and vibrational frequencies of stretching O-H for the dimers and hetero dimers in function of the redshift undergone by proton donor molecules were analyzed. The results shows that the monomers arrange into aggregates which undergo geometric changes induced by the hydrogen bonds. For hetero dimers and hetero trimers the enhancement of the hydrogen bonds where the proton donor molecule corresponds to water was observed. In general, the dimers are more stable than the hetero dimers. We propose the formation of C-H-O hydrogen bonds in some hetero trimers

  10. Stable sheath formation in expanding magnetic field to divertor plate

    International Nuclear Information System (INIS)

    Tomita, Y.; Takayama, A.; Takamaru, H.; Sato, T.

    2002-01-01

    The stable sheath formation and the effects of charge exchange collisions of ions with cold neutrals for the stable presheath formation in an expanding magnetic field towards a divertor plate is studied by a one-dimensional analysis. The requirement for flow velocity of ions at a plasma-sheath boundary is more restricted than that of the uniform magnetic field, which should be greater than the ion sound speed. The difference, however, between both cases is an order of the Debye length to plasma radius, which is negligibly small. The requirement for ion flow velocity inside a quasi-neutral plasma is investigated by taking into account the effects of the charge exchange collisions. Without neutrals in the quasi-neutral plasma, the ion flow velocity at an injection point should be much greater than the ion sound speed. The unisotropic velocity distribution of injected ions with coupling the expanding magnetic field and the charge exchange collisions might mitigate this requirement. (orig.)

  11. Steroid dimer formation: metal reduction of methyl androst-4-ene-3, 17-dion-19-oate.

    Science.gov (United States)

    Templeton, J F; Majgier-Baranowska, H; Marat, K

    2000-04-01

    Two isomeric dimeric steroids, 3,3'-bis(methyl 3-hydroxyandrost-4-en-17-on-19-oate-3-yl), with symmetrical (alpha, alpha') and unsymmetrical structures (alpha,beta'), have been obtained by reduction of methyl androst-4-ene-3,17-dion-19-oate with zinc in aqueous acetic acid together with the major products, the isomeric methyl 5alpha- and 5beta-androst-3-en-17-on-19-oates. The structures of the dimers and unsaturated products are supported by spectroscopic methods. The symmetrical dimer was also obtained from treatment of the 4-en-3-on-19-oate ester with lithium in ammonia.

  12. Study Tranport Barrier Formation using Bi- Stable Sandpile Model

    International Nuclear Information System (INIS)

    Kitpitak, B.; Kanjanaput, W.; Poolyarat, N.; Picha, R; Onjun, T.

    2014-01-01

    The formation of plasma transport barrier in Tokamak is an important issue for achieving high energy confinement and sufficient fusion performance. The simulation using in this experiment simulates cycles of dropping grains in a sandpile with two stable and two unstable slope regimes which share the same characteristic as the formation of pedestal and there are several parameters used, including stable boundaries, grains in a toppling, relax process iterations per cycle, grains in a drop and number of drops per cycle. By using this simulation, the effects of the relaxation times and number of trooping grain (the number of collapsing grain in the relaxation process) can be investigated. It is found in the simulations that the pedestal region can be observed only when the number of deposited grain exceeds a critical value which is related to number of relaxation times and number of allowed trooping grain. In another words, the pedestal formation occurs when the particle deposition rate is higher than the average diffusion rate. In addition, altering amount of trooping grain can lead to remarkable effects on slope and height of the profiles. In order to achieve better energy confinement, further study of formation of plasma transport barrier is needed.

  13. Redox Activity of Oxo-Bridged Iridium Dimers in an N,O-Donor Environment: Characterization of Remarkably Stable Ir(IV,V) Complexes.

    Science.gov (United States)

    Sinha, Shashi Bhushan; Shopov, Dimitar Y; Sharninghausen, Liam S; Stein, Christopher J; Mercado, Brandon Q; Balcells, David; Pedersen, Thomas Bondo; Reiher, Markus; Brudvig, Gary W; Crabtree, Robert H

    2017-07-19

    Chemical and electrochemical oxidation or reduction of our recently reported Ir(IV,IV) mono-μ-oxo dimers results in the formation of fully characterized Ir(IV,V) and Ir(III,III) complexes. The Ir(IV,V) dimers are unprecedented and exhibit remarkable stability under ambient conditions. This stability and modest reduction potential of 0.99 V vs NHE is in part attributed to complete charge delocalization across both Ir centers. Trends in crystallographic bond lengths and angles shed light on the structural changes accompanying oxidation and reduction. The similarity of these mono-μ-oxo dimers to our Ir "blue solution" water-oxidation catalyst gives insight into potential reactive intermediates of this structurally elusive catalyst. Additionally, a highly reactive material, proposed to be a Ir(V,V) μ-oxo species, is formed on electrochemical oxidation of the Ir(IV,V) complex in organic solvents at 1.9 V vs NHE. Spectroelectrochemistry shows reversible conversion between the Ir(IV,V) and proposed Ir(V,V) species without any degradation, highlighting the exceptional oxidation resistance of the 2-(2-pyridinyl)-2-propanolate (pyalk) ligand and robustness of these dimers. The Ir(III,III), Ir(IV,IV) and Ir(IV,V) redox states have been computationally studied both with DFT and multiconfigurational calculations. The calculations support the stability of these complexes and provide further insight into their electronic structures.

  14. Biofilm formation and antibiotic production in Ruegeria mobilis are influenced by intracellular concentrations of cyclic dimeric guanosinmonophosphate

    DEFF Research Database (Denmark)

    D'Alvise, Paul; Magdenoska, Olivera; Melchiorsen, Jette

    2014-01-01

    species Ruegeria mobilis are associated with intracellular concentrations of the signal compound cyclic dimeric guanosinmonophosphate (c-di-GMP), which in bacteria regulates transitions between motile and sessile life stages. Genes for diguanylate cyclases and phosphodiesterases, which are involved in c...... formation and production of the potent antibiotic tropodithietic acid (TDA). An introduced phosphodiesterase gene decreased c-di-GMP and reduced biofilm formation and TDA production. tdaC, a key gene for TDA biosynthesis, was expressed only in attached or biofilm-forming cells, and expression was induced...

  15. Kinetic and hysteretic behavior of ATP hydrolysis of the highly stable dimeric ATP synthase of Polytomella sp.

    Science.gov (United States)

    Villavicencio-Queijeiro, Alexa; Pardo, Juan Pablo; González-Halphen, Diego

    2015-06-01

    The F1FO-ATP synthase of the colorless alga Polytomella sp. exhibits a robust peripheral arm constituted by nine atypical subunits only present in chlorophycean algae. The isolated dimeric enzyme exhibits a latent ATP hydrolytic activity which can be activated by some detergents. To date, the kinetic behavior of the algal ATPase has not been studied. Here we show that while the soluble F1 sector exhibits Michaelis-Menten kinetics, the dimer exhibits a more complex behavior. The kinetic parameters (Vmax and Km) were obtained for both the F1 sector and the dimeric enzyme as isolated or activated by detergent, and this activation was also seen on the enzyme reconstituted in liposomes. Unlike other ATP synthases, the algal dimer hydrolyzes ATP on a wide range of pH and temperature. The enzyme was inhibited by oligomycin, DCCD and Mg-ADP, although oligomycin induced a peculiar inhibition pattern that can be attributed to structural differences in the algal subunit-c. The hydrolytic activity was temperature-dependent and exhibited activation energy of 4 kcal/mol. The enzyme also exhibited a hysteretic behavior with a lag phase strongly dependent on temperature but not on pH, that may be related to a possible regulatory role in vivo. Copyright © 2015 Elsevier Inc. All rights reserved.

  16. Role of antioxidants in prevention of pyrimidine dimer formation in UVB irradiated human HaCaT keratinocytes.

    Science.gov (United States)

    Hochberg, Malka; Kohen, Ron; Enk, Claes D

    2006-06-01

    The objective of the present study was to study the role of reactive oxygen species (ROS) in UVB induced cyclobutane pyrimidine dimer (CPD) formation in human keratinocytes, and to examine the modulating activity of low molecular weight antioxidants. To demonstrate the involvement of ROS, we examined the protective capacity of alpha-tocopherol, tempamine, and diethyldithiocarbamate (DDC) on CPD formation in intact cells and naked DNA. HaCaT cells and naked DNA in water solution were irradiated with UVB in the presence of the antioxidants and CPD was determined by ELISA. We found that all three antioxidants provided protection against UVB induced CPD formation. The protection was observed in intact cells only and not in naked DNA. Since some of the tested antioxidants do not possess UV absorbing qualities, our findings suggest that in a cellular environment ROS play a role in CPD formation.

  17. Photoprotection by Cichorum endivia extracts: prevention of UVB-induced erythema, pyrimidine dimer formation and IL-6 expression.

    Science.gov (United States)

    Enk, C D; Hochberg, M; Torres, A; Lev, O; Dor, I; Srebnik, M; Dembitsky, V M

    2004-01-01

    In the gradual process of evolution, plants have developed natural sun protecting substances that enable continuous survival under direct and intense ultraviolet (UV) radiation. As part of our studies of plant-derived pigments that might constitute an alternative to conventional sunscreens, we have tested the ethanolic extracts of roots, stalks, and inflorescences of populations of wild Cichorum endivia subsp. Divaricatum (Asteraceae) in terms of protection against sunburn, and in prevention of UVB-induced pyrimidine dimer formation and IL-6 mRNA expression in the human keratinocyte cell line, HaCaT. Using ELISA technique for detection of pyrimidine dimers and RT-PCR for detection of IL-6, we found that the ethanolic extract of C. endivia roots absorbs radiation in the UVB spectrum and partially prevents induction of pyrimidine dimers and IL-6 expression. Application of the root extract on the skin prior to UVB irradiation totally prevented erythema. Our findings suggest that C. endivia extracts might possess sun-protective qualities that make them useful as sunscreens. Copyright 2004 S. Karger AG, Basel

  18. Stable sheath formation in expanding magnetic field to divertor plate

    International Nuclear Information System (INIS)

    Tomita, Y.; Takayama, A.; Takamaru, H.; Sato, T.

    2001-01-01

    The stable sheath formation in expanding magnetic field to a divertor plate was studied theoretically by one-dimensional analysis. In fusion devices the magnetic field is expanding in the direction of the plate, i.e. the magnitude of magnetic field is decreasing to the plate. In this configuration ions are accelerated to the plate due to the gradient of the magnetic field strength, so called a mirror force. The bombardment of accelerated ions to the plate may cause several severe problems to fusion plasmas, for example, release of large amount of impurities from the diverter plate. Limited research efforts have been carried out describing magnetic field effects on various potential formation and particle and heat fluxes to the divertor plate. The plasma-wall interaction in an oblique to the plate but uniform magnetic field has been studied by means of 1D-PIC numerical simulation. This analysis shows the formation of a quasi-neutral magnetic pre-sheath preceding the electrostatic Debye sheath, which scales to the ion gyroradius at the sound speed and to the incidence angle of the magnetic field. Sato clarifies this magnetic pre-sheath is attributed to the ion polarisation drift by the two dimensional kinetic analysis. None of effects, however, of non-uniformity of the magnetic field has been taken into account on the stable electrostatic potential and sheath formation. In this paper, we consider a collisionless sheath model between an infinite metal plate and a quasi-neutral plasma in the expanding magnetic field to the plate. One dimensional kinetic analysis leads that a condition for flow velocity of ions at a plasma-sheath boundary is more restricted than that of the uniform magnetic field, which should be larger than the ion sound speed. The difference, however, between both cases is an order of the Debye length to a plasma radius, which is negligible small. The requirement for the ion flow velocity inside the plasma is obtained from the condition of the quasi

  19. Fibroblast Growth Factor 2 Dimer with Superagonist In Vitro Activity Improves Granulation Tissue Formation During Wound Healing

    Science.gov (United States)

    Decker, Caitlin G.; Wang, Yu; Paluck, Samantha J.; Shen, Lu; Loo, Joseph A.; Levine, Alex J.; Miller, Lloyd S.; Maynard, Heather D.

    2015-01-01

    Site-specific chemical dimerization of fibroblast growth factor 2 (FGF2) with the optimal linker length resulted in a FGF2 homodimer with improved granulation tissue formation and blood vessel formation at exceptionally low concentrations. Homodimers of FGF2 were synthesized through site-specific linkages to both ends of different molecular weight poly(ethylene glycols) (PEGs). The optimal linker length was determined by screening dimer-induced metabolic activity of human dermal fibroblasts and found to be that closest to the inter-cysteine distance, 70 Å, corresponding to 2 kDa PEG. A straightforward analysis of the kinetics of second ligand binding as a function of tether length showed that, as the polymerization index (the number of monomer repeat units in the polymer, N) of the tether decreases, the mean time for second ligand capture decreases as ~N3/2, leading to an enhancement of the number of doubly bound ligands in steady-state for a given (tethered) ligand concentration. FGF2-PEG2k-FGF2 induced greater fibroblast metabolic activity than FGF2 alone, all other dimers, and all monoconjugates, at each concentration tested, with the greatest difference observed at low (0.1 ng/mL) concentration. FGF2-PEG2k-FGF2 further exhibited superior activity compared to FGF2 for both metabolic activity and migration in human umbilical vein endothelial cells, as well as improved angiogenesis in a coculture model in vitro. Efficacy in an in vivo wound healing model was assessed in diabetic mice. FGF2-PEG2k-FGF2 increased granulation tissue and blood vessel density in the wound bed compared to FGF2. The results suggest that this rationally designed construct may be useful for improving the fibroblast matrix formation and angiogenesis in chronic wound healing. PMID:26731578

  20. Nitrobenzene anti-parallel dimer formation in non-polar solvents

    Directory of Open Access Journals (Sweden)

    Toshiyuki Shikata

    2014-06-01

    Full Text Available We investigated the dielectric and depolarized Rayleigh scattering behaviors of nitrobenzene (NO2-Bz, which is a benzene mono-substituted with a planar molecular frame bearing the large electric dipole moment 4.0 D, in non-polar solvents solutions, such as tetrachloromethane and benzene, at up to 3 THz for the dielectric measurements and 8 THz for the scattering experiments at 20 °C. The dielectric relaxation strength of the system was substantially smaller than the proportionality to the concentration in a concentrated regime and showed a Kirkwood correlation factor markedly lower than unity; gK ∼ 0.65. This observation revealed that NO2-Bz has a tendency to form dimers, (NO2-Bz2, in anti-parallel configurations for the dipole moment with increasing concentration of the two solvents. Both the dielectric and scattering data exhibited fast and slow Debye-type relaxation modes with the characteristic time constants ∼7 and ∼50 ps in a concentrated regime (∼15 and ∼30 ps in a dilute regime, respectively. The fast mode was simply attributed to the rotational motion of the (monomeric NO2-Bz. However, the magnitude of the slow mode was proportional to the square of the concentration in the dilute regime; thus, the mode was assigned to the anti-parallel dimer, (NO2-Bz2, dissociation process, and the slow relaxation time was attributed to the anti-parallel dimer lifetime. The concentration dependencies of both the dielectric and scattering data show that the NO2-Bz molecular processes are controlled through a chemical equilibrium between monomers and anti-parallel dimers, 2NO2-Bz ↔ (NO2-Bz2, due to a strong dipole-dipole interaction between nitro groups.

  1. Functionalization with C-terminal cysteine enhances transfection efficiency of cell-penetrating peptides through dimer formation

    International Nuclear Information System (INIS)

    Åmand, Helene L.; Nordén, Bengt; Fant, Kristina

    2012-01-01

    Highlights: ► Reversible CPP dimerisation is a simple yet efficient strategy to improve delivery. ► Dimer formation enhances peptiplex stability, resulting in increased transfection. ► By dimerisation, the CPP EB1 even gain endosomal escape properties while lowering cytotoxicity. -- Abstract: Cell-penetrating peptides have the ability to stimulate uptake of macromolecular cargo in mammalian cells in a non-toxic manner and therefore hold promise as efficient and well tolerated gene delivery vectors. Non-covalent peptide-DNA complexes (“peptiplexes”) enter cells via endocytosis, but poor peptiplex stability and endosomal entrapment are considered as main barriers to peptide-mediated delivery. We explore a simple, yet highly efficient, strategy to improve the function of peptide-based vectors, by adding one terminal cysteine residue. This allows the peptide to dimerize by disulfide bond formation, increasing its affinity for nucleic acids by the “chelate effect” and, when the bond is reduced intracellularly, letting the complex dissociate to deliver the nucleic acid. By introducing a single C-terminal cysteine in the classical CPP penetratin and the penetratin analogs PenArg and EB1, we show that this minor modification greatly enhances the transfection capacity for plasmid DNA in HEK293T cells. We conclude that this effect is mainly due to enhanced thermodynamic stability of the peptiplexes as endosome-disruptive chloroquine is still required for transfection and the effect is more pronounced for peptides with lower inherent DNA condensation capacity. Interestingly, for EB1, addition of one cysteine makes the peptide able to mediate transfection in absence of chloroquine, indicating that dimerisation can also improve endosomal escape properties. Further, the cytotoxicity of EB1 peptiplexes is considerably reduced, possibly due to lower concentration of free peptide dimer resulting from its stronger binding to DNA.

  2. A disulfide-linked amyloid-beta peptide dimer forms a protofibril-like oligomer through a distinct pathway from amyloid fibril formation.

    Science.gov (United States)

    Yamaguchi, Takahiro; Yagi, Hisashi; Goto, Yuji; Matsuzaki, Katsumi; Hoshino, Masaru

    2010-08-24

    The conversion of the soluble, nontoxic amyloid-beta (Abeta) peptide into an aggregated, toxic form rich in beta-sheets is considered a key step in the development of Alzheimer's disease. Whereas growing evidence indicates that the Abeta amyloid fibrils consist of in-register parallel beta-sheets, little is known about the structure of soluble oligomeric intermediates because of their transient nature. To understand the mechanism by which amyloid fibrils form, especially the initial development of the "nucleus" oligomeric intermediates, we prepared covalently linked dimeric Abeta peptides and analyzed the kinetics of the fibril-forming process. A covalent bond introduced between two Abeta molecules dramatically facilitated the spontaneous formation of aggregates with a beta-sheet structure and affinity for thioflavin T. Transmission electron microscopy revealed, however, that these aggregates differed in morphology from amyloid fibrils, more closely resembling protofibrils. The protofibril-like aggregates were not the most thermodynamically stable state but were a kinetically trapped state. The results emphasize the importance of the conformational flexibility of the Abeta molecule and a balance in the association and dissociation rate for the formation of rigid amyloid fibrils.

  3. Spin singlet formation in MgTi2O4: evidence of a helical dimerization pattern.

    Science.gov (United States)

    Schmidt, M; Ratcliff, W; Radaelli, P G; Refson, K; Harrison, N M; Cheong, S W

    2004-02-06

    The transition-metal spinel MgTi2O4 undergoes a metal-insulator (M-I) transition on cooling below T(M-I)=260 K. A sharp reduction of the magnetic susceptibility below T(M-I) suggests the onset of a magnetic singlet state. Using high-resolution synchrotron and neutron powder diffraction, we have solved the low-temperature crystal structure of MgTi2O4, which is found to contain dimers with short Ti-Ti distances (the locations of the spin singlets) alternating with long bonds to form helices. Band structure calculations based on hybrid exchange density functional theory show that, at low temperatures, MgTi2O4 is an orbitally ordered band insulator.

  4. Selective amine catalysed steroidal dimerization

    Indian Academy of Sciences (India)

    steroid dimers in which carbon atoms comprise a ben- zene nucleus.6 A standard colour test for the presence of cholesterol is the formation of a green colour in concentrated sulphuric acid, and this was shown to be due to a polyenyl steroidal dimer carbocation.7–9 Many dimeric and oligomeric steroids exhibit interesting.

  5. 2-Ethynylpyridine dimers

    DEFF Research Database (Denmark)

    Bakarić, Danijela; Spanget-Larsen, Jens

    2018-01-01

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

  6. Ultraviolet-B-induced cyclobutane-pyrimidine dimer formation and repair in Arctic marine macrophytes.

    Science.gov (United States)

    van de Poll, Willem H; Hanelt, Dieter; Hoyer, Kirsten; Buma, Anita G J; Breeman, Anneke M

    2002-11-01

    The significance of ultraviolet-B radiation (UVBR: 280-315 nm)-induced DNA damage as a stress factor for Arctic marine macrophytes was examined in the Kongsfjord (Spitsbergen, 78 degrees 55.5'N, 11 degrees 56.0'E) in summer. UVBR penetration in the water column was monitored as accumulation of cyclobutane-pyrimidine dimers (CPD) in bare DNA. This showed that UVBR transparency of the fjord was variable, with 1% depths ranging between 4 and 8 m. In addition, induction and repair kinetics of CPD were studied in several subtidal macrophytes obtained from the Kongsfjord (5-15 m). Surface exposure experiments demonstrated CPD accumulation in Palmaria palmata, Devaleraea ramentacea, Phycodrys rubens, Coccotylus truncatus and Odonthalia dentata. In artificial light, field collected material of P. palmata, D. ramentacea, P. rubens and Laminaria saccharina showed efficient CPD repair, with only 10% of the artificially induced CPD remaining after 5 h. No significant differences in repair rate were observed among these species. CPD repair was slower or absent in O. dentata, C. truncatus and Monostroma arcticum, indicating that fast repair mechanisms such as photolyase were not continuously expressed in these species. CPD repair rates were not directly related to the vertical distribution of algae in the water column and to the reported UV sensitivity of the examined species. Dosimeter incubations showed that maximal exposure to DNA damaging wavelengths was low for all examined species. Furthermore, most species collected below the 1% depth for DNA damage displayed efficient CPD repair, suggesting that UVBR-induced CPD currently impose a minor threat for mature stages of these species growing in the Kongsfjord, Spitsbergen.

  7. How to link pyrene to its host lipid to minimize the extent of membrane perturbations and to optimize pyrene dimer formation

    DEFF Research Database (Denmark)

    Franova, M. D.; Repakova, J.; Holopainen, J. M.

    2014-01-01

    moiety is attached to the hydrocarbon chain. This is in contrast to saturated membranes, where pyrene-induced perturbations have been observed to be more prominent. Meanwhile, the formation of pyrene dimers depends on the linkage point between pyrene and its host lipid. Membrane-spanning dimers between......We study how lipid probes based on pyrene-labeling could be designed to minimize perturbations in lipid bilayers, and how the same design principles could be exploited to develop probes which gauge lipid dynamics primarily within a single lipid monolayer or between them. To this end, we use...... lipids in different membrane leaflets are observed only if the pyrene moiety is attached to the latter half of the acyl chain. A seemingly minor change to link pyrene to an acyl chain that is two carbons shorter leads to a situation where membrane-spanning dimers are no longer observed. Further...

  8. Formation of a stable oligomer of beta-2 microglobulin requires only transient encounter with Cu(II).

    Science.gov (United States)

    Calabrese, Matthew F; Miranker, Andrew D

    2007-03-16

    Beta-2 Microglobulin (beta2m) is a small, globular protein, with high solubility under conditions comparable to human serum. A complication of hemodialysis in renal failure patients is the deposition of unmodified beta2m as amyloid fibers. In vitro, exposure of beta2m to equimolar Cu(2+) under near-physiological conditions can result in self-association leading to amyloid fiber formation. Previously, we have shown that the early steps in this process involve a catalyzed structural rearrangement followed by formation of discrete oligomers. These oligomers, however, have a continued requirement for Cu(2+) while mature fibers are resistant to addition of metal chelate. Here, we report that the transition from Cu(2+) dependent to chelate resistant states occurs in the context of small oligomers, dimeric to hexameric in size. These species require Cu(2+) to form, but once generated, do not need metal cation for stability. Importantly, this transition occurs gradually over several days and the resulting oligomers are isolatable and kinetically stable on timescales exceeding weeks. In addition, formation is enhanced by levels of urea similar to those found in hemodialysis patients. Our results are consistent with our hypothesis that transient encounter of full-length wild-type beta2m with transition metal cation at the dialysis membrane interface is causal to dialysis related amyloidosis.

  9. Stable redox-cycling nitroxide Tempol inhibits NET formation

    Directory of Open Access Journals (Sweden)

    Ava eHosseinzadeh

    2012-12-01

    Full Text Available To prevent the spread of pathogens neutrophils as the first line of defence are able to release Neu-trophil Extracellular Traps (NETs, a recently discovered form of immune response. Reactive oxygen species (ROS have been shown to be essential for many different induction routes of NET formation. Therefore, pharmacological inhibition of ROS generation has implications for research and medicine related to NETs. The application of diphenylene iodonium (DPI, an inhibitor of NADPH oxidase activity, is limited due to its toxicity to host cells as well as microbes. Therefore, we investigated the effect of 4-Hydroxy-2,2,6,6-tetramethylpiperidine-1-oxyl (Tempol a mem-brane-permeable radical scavenger on NET formation triggered by phorbol esters and C. albicans. We quantified the amount of NETs with two complementary methods, using a microscopic analysis and an online fluorescence-based assay. In line with removal of ROS, Tempol reduced the amount of NET formation by neutrophils challenged with those stimuli significantly. Since Tempol effi-ciently blocks NET formation in vitro, it might be promising to test the effect of Tempol in experi-mental models of disorders in which NETs probably have hazardous effects.

  10. Even-odd alternation of the formation of dimer isomers in irradiated polycrystalline alkanes: evidence from product analysis

    International Nuclear Information System (INIS)

    Baudson, T.; Tilquin, B.

    1984-01-01

    Recent ESR studies on n-alkanes from n-C 11 to n-C 25 have shown that a prominent chain end (-CH 2 -CH 2 ) alkyl radical is formed in odd members of the series. In this preliminary discussion of our study, we shall report the capillary chromatogram in the dimer isomers range for n-alkanes ranging from n-C 11 to n-C 17 irradiated at 80 kGy. Dimer isomers, produced in part by the combination of chain end radicals, are eluted at the end chromatogram. The combination of two chain end radicals gives the dimer (D 11 ) isomer eluted at the last place. It is shown that dimers produced by the combination of chain end alkyl radicals are more important for the odd members of the series than for the even members. (author)

  11. Reactivity of paraquat with sodium salicylate: formation of stable complexes.

    Science.gov (United States)

    Dinis-Oliveira, Ricardo Jorge; de Pinho, Paula Guedes; Ferreira, António César Silva; Silva, Artur M S; Afonso, Carlos; Bastos, Maria de Lourdes; Remião, Fernando; Duarte, José Alberto; Carvalho, Félix

    2008-07-30

    Sodium salicylate (NaSAL) has been shown to be a promising antidote for the treatment of paraquat (PQ) poisonings. The modulation of the pro-oxidant and pro-inflammatory pathways, as well as the anti-thrombogenic properties of NaSAL are probably essential features for the healing effects provided by this drug. Nevertheless, a possible direct chemical reactivity between PQ and NaSAL is also a putative pathway to be considered, this hypothesis being the ground of the present study. In accordance, it is shown, for the first time that PQ and NaSAL react immediately in aqueous medium and within 2-3 min in the solid state. Photographs and scanning electron photomicrographs indicated that a new chemical entity is formed when both compounds are mixed. This assumption was corroborated by the evaluation of the melting point, and through several analytical techniques, namely ultraviolet/visible spectroscopy, nuclear magnetic resonance spectroscopy, gas chromatography/mass spectrometry/mass spectrometry (GC/MS/MS), liquid chromatography/electrospray ionization/mass spectrometry/mass spectrometry (LC/ESI/MS/MS) and infrared spectroscopy, which revealed that stable charge-transfer complexes are formed when PQ is mixed with NaSAL. LC/ESI/MS/MS allowed obtaining the stoichiometry of the charge-transfer complexes. In order to increase resolution, single value decomposition, acting as a filter, showed that the charge-transfer complexes with m/z 483, 643 and 803 correspond to the pseudo-molecular ions, respectively 1:2, 1:3 and 1:4 (PQ:NaSAL). In conclusion, these results provided a new and important mechanism of action of NaSAL against the toxicity mediated by PQ.

  12. Reactivity of paraquat with sodium salicylate: Formation of stable complexes

    International Nuclear Information System (INIS)

    Dinis-Oliveira, Ricardo Jorge; Guedes de Pinho, Paula; Ferreira, Antonio Cesar Silva; Silva, Artur M.S.; Afonso, Carlos; Bastos, Maria de Lourdes; Remiao, Fernando; Duarte, Jose Alberto; Carvalho, Felix

    2008-01-01

    Sodium salicylate (NaSAL) has been shown to be a promising antidote for the treatment of paraquat (PQ) poisonings. The modulation of the pro-oxidant and pro-inflammatory pathways, as well as the anti-thrombogenic properties of NaSAL are probably essential features for the healing effects provided by this drug. Nevertheless, a possible direct chemical reactivity between PQ and NaSAL is also a putative pathway to be considered, this hypothesis being the ground of the present study. In accordance, it is shown, for the first time that PQ and NaSAL react immediately in aqueous medium and within 2-3 min in the solid state. Photographs and scanning electron photomicrographs indicated that a new chemical entity is formed when both compounds are mixed. This assumption was corroborated by the evaluation of the melting point, and through several analytical techniques, namely ultraviolet/visible spectroscopy, nuclear magnetic resonance spectroscopy, gas chromatography/mass spectrometry/mass spectrometry (GC/MS/MS), liquid chromatography/electrospray ionization/mass spectrometry/mass spectrometry (LC/ESI/MS/MS) and infrared spectroscopy, which revealed that stable charge-transfer complexes are formed when PQ is mixed with NaSAL. LC/ESI/MS/MS allowed obtaining the stoichiometry of the charge-transfer complexes. In order to increase resolution, single value decomposition, acting as a filter, showed that the charge-transfer complexes with m/z 483, 643 and 803 correspond to the pseudo-molecular ions, respectively 1:2, 1:3 and 1:4 (PQ:NaSAL). In conclusion, these results provided a new and important mechanism of action of NaSAL against the toxicity mediated by PQ

  13. Dimeric form of peroxynitrite

    Science.gov (United States)

    Simon, K. V.; Tulub, A. V.

    2009-07-01

    The (ONOO)- anion, known as peroxynitrite, is characterized by a singlet spin state. A new stable dimer form of peroxynitrite [NO-O2]- in the triplet state at distances close to r(O-N) ≈ 2.885 Å between oxygen in the O2 structure and nitrogen has been established within the quantum-chemical CASSCF approximation. The vibrational motion of the dimer is significantly anharmonic; for the 16O and 14N isotopes, the differences in the energies of two neighboring levels correspond to frequencies of about 70-30 cm-1. The triplet dimer structure retains stability in the case of interaction with water molecules. The activation barriers caused by rearrangement of the peroxynitrite structure into the ground state of the NO{3/-} anion with the symmetry D 3 h are found.

  14. Stable, streamlined and helical cavity formation by the impact of Leidenfrost spheres

    Science.gov (United States)

    Mansoor, Mohammad; Vakarelski, Ivan; Marston, Jeremy; Truscott, Tadd; Thoroddsen, Sigurdur

    2016-11-01

    This work reports results from an experimental study on the formation of stable-streamlined and helical cavity wakes following the free-surface impact of Leidenfrost spheres. The Leidenfrost effect encapsulates the sphere by a vapor layer to prevent any physical contact with the surrounding liquid. This phenomenon is essential for the pacification of acoustic rippling along the cavity interface to result in a stable-streamlined cavity wake. Such a streamlined configuration experiences drag coefficients an order of magnitude lower than those acting on room temperature spheres. A striking observation is the formation of helical cavities which occur for impact Reynolds numbers Re0 >= 1 . 4 ×105 and are characterized by multiple interfacial ridges, stemming from and rotating synchronously about an evident contact line around the sphere equator. This helical configuration has 40 - 55 % smaller overall force coefficients than those obtained in the formation of stable cavity wakes.

  15. Selective amine catalysed steroidal dimerization

    Indian Academy of Sciences (India)

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

  16. Theoretical study of O2 adsorption and CO2 formation in bimetallic dimer clusters Au-M

    Science.gov (United States)

    Pacheco-Ortín, Sandy Maria; Agacino-Valdés, Esther; Mora, Pablo De La

    Cation, anion, and neutral states in Au-M dimer clusters have been calculated as a way to study in a small model, the Au-sites, and M-sites in a supported nanoparticle (NP). These charged states can be formed during a charge transfer process between certain atoms of the NP with the atoms of the support or simply with cationic or anionic defects. These results can be important to evaluate in a preliminary way, the relation between the activity of the Au-sites and M-sites because of its charge and the effectiveness of the adsorption of O2, and the subsequent interaction between adsorbed O2 and CO through a Langmuir-Rideal unimolecular mechanism. For the O2 adsorption over Au active site, the Au-Ir, Au-Au, Au-Ag, Au-Pd, and Au-Cu dimers yielded negative binding energies in all the charge states considered (anion, cation, and neutral); when M active site was considered, Au-Cu and Au-Ag dimers also gave negative values of binding energies in all the charged states. Furthermore, there was observed that electron rich Au-sites are essential in the O2 adsorption.

  17. Mechanistic Analysis and Thermochemical Kinetic Simulation of the Pathways for Volatile Product Formation from Pyrolysis of Polystyrene, Especially of the Dimer

    Energy Technology Data Exchange (ETDEWEB)

    Poutsma, Marvin L [ORNL

    2006-01-01

    Simulations of the initial distribution of volatiles from pyrolysis of polystyrene were based on propagation rate constants estimated by thermochemical kinetic procedures. The voluminous database exhibits a disturbing lack of consistency with respect to effects of conversion level, temperature, and reactor type. It therefore remains difficult to assign the true primary distribution of the major products, styrene, 2,4-diphenyl-1-butene (''dimer''), 2,4,6-triphenyl-1-hexene (''trimer''), 1,3-diphenylpropane, and toluene, and its dependence on conditions. Probable perturbations by secondary reactions and selective evaporation are considered. The rate constant for 1,3-hydrogen shift appears much too small to accommodate the commonly proposed ''back-biting'' mechanism for dimer formation. Dimer more likely arises by addition of benzyl radical to olefinic chain-ends, followed by {beta}-scission, although ambiguities remain in assigning rate constants for the addition and {beta}-scission steps. With this modification, the major products can be successfully associated with decay of the sec-benzylic chain-end radical. In contrast, the minimal formation of allylbenzene, 2,4-diphenyl-1-pentene, and 2,4,6-triphenyl-1-heptene suggests a minimal chain-propagating role for the prim chain-end radical. Compared with polyethylene, the much enhanced ''unzipping'' to form monomer from polystyrene and the more limited depth of ''back-biting'' into the chain arise from an enthalpy-driven acceleration of {beta}-scission coupled with a kinetically driven deceleration of intramolecular hydrogen transfer. In contrast, the greater ''unzipping'' of poly(isobutylene) compared with polyethylene is proposed to result from relief of steric strain.

  18. Protein body formation in stable transgenic tobacco expressing elastin-like polypeptide and hydrophobin fusion proteins.

    Science.gov (United States)

    Gutiérrez, Sonia P; Saberianfar, Reza; Kohalmi, Susanne E; Menassa, Rima

    2013-05-10

    Plants are recognized as an efficient and inexpensive system to produce valuable recombinant proteins. Two different strategies have been commonly used for the expression of recombinant proteins in plants: transient expression mediated by Agrobacterium; or stable transformation of the plant genome. However, the use of plants as bioreactors still faces two main limitations: low accumulation levels of some recombinant proteins and lack of efficient purification methods. Elastin-like polypeptide (ELP), hydrophobin I (HFBI) and Zera® are three fusion partners found to increase the accumulation levels of recombinant proteins and induce the formation of protein bodies (PBs) in leaves when targeted to the endoplasmic reticulum (ER) in transient expression assays. In this study the effects of ELP and HFBI fusion tags on recombinant protein accumulation levels and PB formation was examined in stable transgenic Nicotiana tabacum. The accumulation of recombinant protein and PB formation was evaluated in two cultivars of Nicotiana tabacum transformed with green fluorescent protein (GFP) fused to ELP or HFBI, both targeted and retrieved to the ER. The ELP and HFBI tags increased the accumulation of the recombinant protein and induced the formation of PBs in leaves of stable transgenic plants from both cultivars. Furthermore, these tags induced the formation of PBs in a concentration-dependent manner, where a specific level of recombinant protein accumulation was required for PBs to appear. Moreover, agro-infiltration of plants accumulating low levels of recombinant protein with p19, a suppressor of post-transcriptional gene silencing (PTGS), increased accumulation levels in four independent transgenic lines, suggesting that PTGS might have caused the low accumulation levels in these plants. The use of ELP and HFBI tags as fusion partners in stable transgenic plants of tobacco is feasible and promising. In a constitutive environment, these tags increase the accumulation levels

  19. Relative stabilities and the spectral signatures of stacked and hydrogen-bonded dimers of serotonin

    Science.gov (United States)

    Dev, S.; Giri, K.; Majumder, M.; Sathyamurthy, N.

    2015-10-01

    The O-HṡṡṡN hydrogen-bonded dimer of serotonin is shown to be more stable than the stacked dimer in its ground electronic state, by using the Møller-Plesset second-order perturbation theory (MP2) and the 6-31g** basis set. The vertical excitation energy for the lowest π → π* transition for the monomer as well as the dimer is predicted by time-dependent density functional theory. The experimentally observed red shift of excitation wavelength on oligomerisation is explained in terms of the change in the HOMO-LUMO energy gap due to complex formation. The impact of dimer formation on the proton magnetic resonance spectrum of serotonin monomer is also examined.

  20. Formation of stable bdelloplasts as a starvation-survival strategy of marine bdellovibrios

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez-Amat, A.; Torrella, F. (Universidad de Murcia (Spain))

    1990-09-01

    Bacteria belonging to the genus Bdellovibrio have been isolated from a variety of habitats, including soil (15), rivers (1), estuarine water, seawater, and solar salt concentration ponds. Several wild-type isolates of marine bdellovibrios formed stable bdelloplasts when they infected gram-negative bacterial prey under certain culture conditions. Synchronous predator-prey cultures and low nutrient concentrations increased the yield of stable bdelloplasts. The bdellovibrio cells retained in the stable bdelloplasts showed a high survival capacity in nutrient-depleted saline solution (10% viable Bdellovibrio cells after 3 months at 25{degrees}C), whereas Bdellovibrio attack-phase cells kept under the same starvation conditions lost viability more quickly (1% viable cells after 48 h). The addition of yeast extract to a stable bdelloplast suspension induced lysis of the bdelloplasts and release of motile infecting attack-phase Bdellovibrio cells. Other substances, such as free amino acids, protein hydrolysates, NH{sub 4}{sup +}, carbohydrates, and organic amines, did not induce such a release. Stable bdelloplasts were highly hydrophobic and had a lower endogenous respiration rate than attack-phase cells. In general, stable bdelloplasts were almost as sensitive to temperature changes, desiccation, sonication, tannic acid, and Triton X-100 treatment as attack-phase cells. Electron microscopy of stable bdelloplasts did not reveal any extra cell wall layer, either in the bdelloplast envelope or in the retained Bdellovibrio cells, unlike the bdellocysts of the soil bacterium Bdellovibrio sp. strain W. The authors propose that formation of stable bdelloplasts is a survival strategy of marine bdellovibrios which occurs in response to nutrient- and prey-poor seawater habitats.

  1. Sequence requirement for hand-in-hand interaction in formation of RNA dimers and hexamers to gear phi29 DNA translocation motor.

    Science.gov (United States)

    Chen, C; Zhang, C; Guo, P

    1999-06-01

    Translocation of DNA or RNA is a ubiquitous phenomenon. One intricate translocation process is viral DNA packaging. During maturation, the lengthy genome of dsDNA viruses is translocated with remarkable velocity into a limited space within the procapsid. We have revealed that phi29 DNA packaging is accomplished by a mechanism similar to driving a bolt with a hex nut, which consists of six DNA-packaging pRNAs. Four bases in each of the two pRNA loops are involved in RNA/RNA interactions to form a hexagonal complex that gears the DNA translocating machine. Without considering the tertiary interaction, in some cases only two G/C pairs between the interacting loops could provide certain pRNAs with activity. When all four bases were paired, at least one G/C pair was required for DNA packaging. The maximum number of base pairings between the two loops to allow pRNA to retain wild-type activity was five, whereas the minimum number was five for one loop and three for the other. The findings were supported by phylogenetic analysis of seven pRNAs from different phages. A 75-base RNA segment, bases 23-97, was able to form dimer, to interlock into the hexamer, to compete with full-length pRNA for procapsid binding, and therefore to inhibit phi29 assembly in vitro. Our result suggests that segment 23-97 is a self-folded, independent domain involved in procapsid binding and RNA/RNA interaction in dimer and hexamer formation, whereas bases 1-22 and 98-120 are involved in DNA translocation but dispensable for RNA/RNA interaction. Therefore, this 75-base RNA could be a model for structural studies in RNA dimerization.

  2. Study of structural stability and damaging effect on membrane for four Aβ42 dimers.

    Directory of Open Access Journals (Sweden)

    Wei Feng

    Full Text Available Increasing evidence shows that Aβ oligomers are key pathogenic molecules in Alzheimer's disease. Among Aβ oligomers, dimer is the smallest aggregate and toxic unit. Therefore, understanding its structural and dynamic properties is quite useful to prevent the formation and toxicity of the Aβ oligomers. In this study, we performed molecular dynamic simulations on four Aβ42 dimers, 2NCb, CNNC, NCNC and NCCN, within the hydrated DPPC membrane. Four Aβ42 dimers differ in the arrangements of two Aβ42 peptides. This study aims to investigate the impact of aggregation pattern of two Aβ peptides on the structural stability of the Aβ42 dimer and its disruption to the biological membrane. The MD results demonstrate that the NCCN, CNNC and NCNC have the larger structural fluctuation at the N-terminus of Aβ42 peptide, where the β-strand structure converts into the coil structure. The loss of the N-terminal β-strand further impairs the aggregate ability of Aβ42 dimer. In addition, inserting Aβ42 dimer into the membrane can considerably decrease the average APL of DPPC membrane. Moreover this decrease effect is largely dependent on the distance to the location of Aβ42 dimer and its secondary structure forms. Based on the results, the 2NCb is considered as a stable dimeric unit for aggregating the larger Aβ42 oligomer, and has a potent ability to disrupt the membrane.

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

    Directory of Open Access Journals (Sweden)

    Cowburn David

    2011-05-01

    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

  4. Symmetry of learning rate in synaptic plasticity modulates formation of flexible and stable memories.

    Science.gov (United States)

    Park, Youngjin; Choi, Woochul; Paik, Se-Bum

    2017-07-18

    Spike-timing-dependent plasticity (STDP) is considered critical to learning and memory functions in the human brain. Across various types of synapse, STDP is observed as different profiles of Hebbian and anti-Hebbian learning rules. However, the specific roles of diverse STDP profiles in memory formation still remain elusive. Here, we show that the symmetry of the learning rate profile in STDP is crucial to determining the character of stored memory. Using computer simulations, we found that an asymmetric learning rate generates flexible memory that is volatile and easily overwritten by newly appended information. Moreover, a symmetric learning rate generates stable memory that can coexist with newly appended information. In addition, by combining these two conditions, we could realize a hybrid memory type that operates in a way intermediate between stable and flexible memory. Our results demonstrate that various attributes of memory functions may originate from differences in the synaptic stability.

  5. Formation of magnetite nanoparticles at low temperature: from superparamagnetic to stable single domain particles.

    Directory of Open Access Journals (Sweden)

    Jens Baumgartner

    Full Text Available The room temperature co-precipitation of ferrous and ferric iron under alkaline conditions typically yields superparamagnetic magnetite nanoparticles below a size of 20 nm. We show that at pH  =  9 this method can be tuned to grow larger particles with single stable domain magnetic (> 20-30 nm or even multi-domain behavior (> 80 nm. The crystal growth kinetics resembles surprisingly observations of magnetite crystal formation in magnetotactic bacteria. The physicochemical parameters required for mineralization in these organisms are unknown, therefore this study provides insight into which conditions could possibly prevail in the biomineralizing vesicle compartments (magnetosomes of these bacteria.

  6. Fragmentation, auto-modification and post ionisation proton bound dimer ion formation: the differential mobility spectrometry of low molecular weight alcohols.

    Science.gov (United States)

    Ruszkiewicz, D M; Thomas, C L P; Eiceman, G A

    2016-08-07

    Differential mobility spectrometry (DMS) is currently being used for environmental monitoring of space craft atmospheres and has been proposed for the rapid assessment of patients at accident and emergency receptions. Three studies investigated hitherto undescribed complexity in the DMS spectra of methanol, ethanol, propan-1-ol and butan-1-ol product ions formed from a (63)Ni ionisation source. 54 000 DMS spectra obtained over a concentration range of 0.01 mg m(-3)(g) to 1.80 g m(-3)(g) revealed the phenomenon of auto-modification of the product ions. This occurred when the neutral vapour concentration exceeded the level required to induce a neutral-ion collision during the low field portion of the dispersion field waveform. Further, post-ionisation cluster-ion formation or protonated monomer/proton bound dimer inter-conversion within the ion-filter was indicated by apparent shifts in the values of the protonated monomer compensation field maximum; indicative of post-ionisation conversion of the protonated monomer to a proton-bound dimer. APCI-DMS-quadrupole mass spectrometry studies enabled the ion dissociation products from dispersion-field heating to be monitored and product ion fragmentation relationships to be proposed. Methanol was not observed to dissociate, while propan-1-ol and butan-1-ol underwent dissociation reactions consistent with dehydration processes that led ultimately to the generation of what is tentatively assigned as a cyclo-C3H3(+) ion (m/z 39) and hydrated protons. Studies of the interaction of ion filter temperature with dispersion-field heating of product ions isolated dissociation/fragmentation product ions that have not been previously described in DMS. The implications of these combined findings with regard to data sharing and data interpretation were highlighted.

  7. Meta-stable Solidification Created by the Detonation Method of Coating Formation

    Directory of Open Access Journals (Sweden)

    W. Wołczyński

    2012-04-01

    Full Text Available Particles of the Fe-Al type (less than 50m in diameter were sprayed onto the 045 steel substrate by means of the detonation method. The TEM, SAED and EDX analyses revealed that the Fe-Al particles have been partially melted in the experiment of coating formation. Particle undergone melting even within about 80% of its volume. Therefore, solidification of the melted part of particles was expected. Solidification differed significantly due to a large range of chemical composition of applied particles (from 15 at.% Al up to 63 at.% Al. A single particle containing 63 at.% Al was subjected to the detailed analysis, only. The TEM / SAED techniques revealed in the solidified part of particle three sub-layers: an amorphous phase,, periodically situated FeAl + Fe2Al5 phases, and a non-equilibrium phase,.A hypothesis dealing with the inter-metallic phases formation in such a single particle of the nominal composition N0 0.63 is presented. At first, the solid / liquid system is treated as an interconnection: substrate/liquid/nonmelted particle part. Therefore, it issuggested that the solidification occurs simultaneously in two directions: towards a substrate and towards a non-melted part of particle. The solidification mechanism is referred to the Fe-Al meta-stable phase diagram. It is shown that the melted part of particle solidifies rapidly according to the phase diagram of meta-stable equilibrium and at a significant deviation from the thermodynamic equilibrium.

  8. Pressure dependence of Ar.sup.+./sup..sub.2./sub., ArTi.sup.+./sup., and Ti.sup.+./sup..sub.2./sub. dimer formation in a magnetron sputtering discharge

    Czech Academy of Sciences Publication Activity Database

    Hippler, R.; Čada, Martin; Straňák, V.; Hubička, Zdeněk; Helm, C.A.

    2017-01-01

    Roč. 50, č. 44 (2017), s. 1-8, č. článku 445205. ISSN 0022-3727 R&D Projects: GA ČR GA17-08389S Institutional support: RVO:68378271 Keywords : magnetron sputtering * ion mass spectrometry * dimer formation * cluster formation Subject RIV: BL - Plasma and Gas Discharge Physics OBOR OECD: Fluids and plasma physics (including surface physics) Impact factor: 2.588, year: 2016

  9. submitter Thermodynamics of the formation of sulfuric acid dimers in the binary (H2SO4–H2O) and ternary (H2SO4–H2O–NH3) system

    CERN Document Server

    Kürten, A; Rondo, L; Bianchi, F; Duplissy, J; Jokinen, T; Junninen, H; Sarnela, N; Schobesberger, S; Simon, M; Sipilä, M; Almeida, J; Amorim, A; Dommen, J; Donahue, N M; Dunne, E M; Flagan, R C; Franchin, A; Kirkby, J; Kupc, A; Makhmutov, V; Petäjä, T; Praplan, A P; Riccobono, F; Steiner, G; Tomé, A; Tsagkogeorgas, G; Wagner, P E; Wimmer, D; Baltensperger, U; Kulmala, M; Worsnop, D R; Curtius, J

    2015-01-01

    Sulfuric acid is an important gas influencing atmospheric new particle formation (NPF). Both the binary $(H_2SO_4–H_2O)$ system and the ternary system involving ammonia $(H_2SO_4–H_2O–NH_3)$ may be important in the free troposphere. An essential step in the nucleation of aerosol particles from gas-phase precursors is the formation of a dimer, so an understanding of the thermodynamics of dimer formation over a wide range of atmospheric conditions is essential to describe NPF. We have used the CLOUD chamber to conduct nucleation experiments for these systems at temperatures from 208 to 248 K. Neutral monomer and dimer concentrations of sulfuric acid were measured using a chemical ionization mass spectrometer (CIMS). From these measurements, dimer evaporation rates in the binary system were derived for temperatures of 208 and 223 K. We compare these results to literature data from a previous study that was conducted at higher temperatures but is in good agreement with the present study. For the ternary sys...

  10. Standard Gibbs energies of formation and equilibrium constants from ab-initio calculations: Covalent dimerization of NO2 and synthesis of NH3

    International Nuclear Information System (INIS)

    Awasthi, Neha; Ritschel, Thomas; Lipowsky, Reinhard; Knecht, Volker

    2013-01-01

    Highlights: • ΔG and K eq for NO 2 dimerization and NH 3 synthesis calculated via ab-initio methods. • Vis-á-vis experiments, W1 and CCSD(T) are accurate and G3B3 also does quite well. • CBS-APNO most accurate for NH 3 reaction but shows limitations in modeling NO 2 . • Temperature dependence of ΔG and K eq is calculated for the NH 3 reaction. • Good agreement of calculated K eq with experiments and the van’t Hoff approximation. -- Abstract: Standard quantum chemical methods are used for accurate calculation of thermochemical properties such as enthalpies of formation, entropies and Gibbs energies of formation. Equilibrium reactions are widely investigated and experimental measurements often lead to a range of reaction Gibbs energies and equilibrium constants. It is useful to calculate these equilibrium properties from quantum chemical methods in order to address the experimental differences. Furthermore, most standard calculation methods differ in accuracy and feasibility of the system size. Hence, a systematic comparison of equilibrium properties calculated with different numerical algorithms would provide a useful reference. We select two well-known gas phase equilibrium reactions with small molecules: covalent dimer formation of NO 2 (2NO 2 ⇌ N 2 O 4 ) and the synthesis of NH 3 (N 2 + 3 H 2 ⇌ 2NH 3 ). We test four quantum chemical methods denoted by G3B3, CBS-APNO, W1 and CCSD(T) with aug-cc-pVXZ basis sets (X = 2, 3, and 4), to obtain thermochemical data for NO 2 , N 2 O 4 , and NH 3 . The calculated standard formation Gibbs energies Δ f G° are used to calculate standard reaction Gibbs energies Δ r G° and standard equilibrium constants K eq for the two reactions. Standard formation enthalpies Δ f H° are calculated in a more reliable way using high-level methods such as W1 and CCSD(T). Standard entropies S° for the molecules are calculated well within the range of experiments for all methods, however, the values of standard formation

  11. ON THE FORMATION OF A STABLE PENUMBRA IN A REGION OF FLUX EMERGENCE IN THE SUN

    Energy Technology Data Exchange (ETDEWEB)

    Murabito, M.; Guglielmino, S. L.; Zuccarello, F. [Dipartimento di Fisica e Astronomia—Sezione Astrofisica, Università degli Studi di Catania, Via S. Sofia 78, I-95123 Catania (Italy); Romano, P., E-mail: mmurabito@oact.inaf.it [INAF—Osservatorio Astrofisico di Catania, Via S. Sofia 78, I-95123 Catania (Italy)

    2017-01-01

    We studied the formation of the first penumbral sector around a pore in the following polarity of the NOAA Active Region (AR) 11490. We used a high spatial, spectral, and temporal resolution data set acquired by the Interferometric BIdimensional Spectrometer operating at the NSO/Dunn Solar Telescope, as well as data taken by the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory satellite. On the side toward the leading polarity, elongated granules in the photosphere and an arch filament system (AFS) in the chromosphere are present, while the magnetic field shows a sea-serpent configuration, indicating a region of magnetic flux emergence. We found that the formation of a stable penumbra in the following polarity of the AR begins in the area facing the opposite polarity located below the AFS in the flux emergence region, different from what was found by Schlichenmaier and colleagues. Moreover, during the formation of the first penumbral sector, the area characterized by magnetic flux density larger than 900 G and the area of the umbra increase.

  12. Condensed tannins: The formation of a diarylpropanol-catechinic acid dimer from base-catalyzed reactions of (+)-catechin

    Science.gov (United States)

    Seiji Ohara; Richard W. Hemingway

    1991-01-01

    Reaction of (+ )-catechin at pH 12 and 40 DC results in the stereoselective (if not stereospecific) formation of an enolic form of 1-[6-(3',4'-dihydroxyphenyl)-7-hydroxybicyclo[3.3.1]nonane-2,4,9-trione-3-yl]-1-(3,4-dihyroxyphenyl)-3-(2,-4,6-trihydroxyphenyl)-propan-2-ol. The n.m.r. chemical shift assignments determined by a variety of two-dimensional...

  13. Territorial dynamics and stable home range formation for central place foragers.

    Directory of Open Access Journals (Sweden)

    Jonathan R Potts

    Full Text Available Uncovering the mechanisms behind territory formation is a fundamental problem in behavioural ecology. The broad nature of the underlying conspecific avoidance processes are well documented across a wide range of taxa. Scent marking in particular is common to a large range of terrestrial mammals and is known to be fundamental for communication. However, despite its importance, exact quantification of the time-scales over which scent cues and messages persist remains elusive. Recent work by the present authors has begun to shed light on this problem by modelling animals as random walkers with scent-mediated interaction processes. Territories emerge as dynamic objects that continually change shape and slowly move without settling to a fixed location. As a consequence, the utilisation distribution of such an animal results in a slowly increasing home range, as shown for urban foxes (Vulpes vulpes. For certain other species, however, home ranges reach a stable state. The present work shows that stable home ranges arise when, in addition to scent-mediated conspecific avoidance, each animal moves as a central place forager. That is, the animal's movement has a random aspect but is also biased towards a fixed location, such as a den or nest site. Dynamic territories emerge but the probability distribution of the territory border locations reaches a steady state, causing stable home ranges to emerge from the territorial dynamics. Approximate analytic expressions for the animal's probability density function are derived. A programme is given for using these expressions to quantify both the strength of the animal's movement bias towards the central place and the time-scale over which scent messages persist. Comparisons are made with previous theoretical work modelling central place foragers with conspecific avoidance. Some insights into the mechanisms behind allometric scaling laws of animal space use are also given.

  14. Preservation of terrestrial plant biomarkers from Nachukui Formation sediments and their viability for stable isotope analysis

    Science.gov (United States)

    Kahle, E.; Uno, K. T.; Polissar, P. J.; Lepre, C. J.; deMenocal, P. B.

    2013-12-01

    Plio-Pleistocene sedimentary records from the Turkana Basin in eastern Africa provide a unique opportunity to compare a high-resolution record of climate and terrestrial vegetation with important changes in the record of human evolution. Molecular biomarkers from terrestrial vegetation can yield stable isotope ratios of hydrogen and carbon that reflect ancient climate and vegetation. However, the preservation of long-chain plant wax biomarkers in these paleosol, fluvial, and lacustrine sediments is not known, and this preservation must be studied to establish their utility for molecular stable isotope studies. We investigated leaf wax biomarkers in Nachukui Formation sediments deposited between 2.3 and 1.7 Ma to assess biomarker preservation. We analyzed n alkane and n alkanoic acid concentrations and, where suitable, molecular carbon and hydrogen isotope ratios. Molecular abundance distributions show a great deal of variance in biomarker preservation and plant-type source as indicated by the carbon preference index and average chain length. This variation suggests that some samples are suitable for isotopic analysis, while other samples lack primary terrestrial plant biomarker signatures. The biomarker signal in many samples contains significant additional material from unidentified sources. For example, the n-alkane distributions contain an unresolved complex mixture underlying the short and mid-chain n-alkanes. Samples from lacustrine intervals include long-chain diacids, hydroxy acids and (ω-1) ketoacids that suggest degradation of the original acids. Degradation of poorly preserved samples and the addition of non-terrestrial plant biomarkers may originate from a number of processes including forest fire or microbial alteration. Isotopic analysis of well-preserved terrestrial plant biomarkers will be presented along with examples where the original biomarker distribution has been altered.

  15. Comparative studies on the correlation between pyrimidine dimer formation and tyrosinase activity in Cloudman S91 melanoma cells after ultraviolet-irradiation

    International Nuclear Information System (INIS)

    Niggli, H.J.

    1990-01-01

    The authors compared the induction of pyrimidine dimer densities after UV-irradiation in mouse melanoma cells before and after treatment with cholera toxin. Treatment with cholera toxin stimulated tyrosinase activity up to 50-fold, leading to a marked, visually apparent increase in cellular melanin concentrations. Results indicate that de novo melanin pigmentation induced via the c-AMP pathway is not involved in protection against UV-induced thymine-containing pyrimidine dimers. In separate experiments, irradiation of toxin-treated and untreated mouse melanoma cells with UVC or UVB light produced a 20-30% lower dimer density compared to irradiated human skin fibroblasts. This finding suggests that melanin has some protection properties against UV-induced pyrimidine dimers, although the exact defense mechanism seems highly complex. (author)

  16. Substrate-Induced Dimerization of Engineered Monomeric Variants of Triosephosphate Isomerase from Trichomonas vaginalis.

    Directory of Open Access Journals (Sweden)

    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.

  17. 2-Ethynylpyridine dimers: IR spectroscopic and computational study

    Science.gov (United States)

    Bakarić, Danijela; Spanget-Larsen, Jens

    2018-04-01

    2-ethynylpyridine (2-EP) presents a multifunctional system capable of participation in hydrogen-bonded complexes utilizing hydrogen bond donating (tbnd Csbnd H, Aryl-H) and hydrogen bond accepting functions (N-atom, Ctbnd C and pyridine π-systems). In this work, IR spectroscopy and theoretical calculations are used to study possible 2-EP dimer structures as well as their distribution in an inert solvent such as tetrachloroethene. Experimentally, the tbnd Csbnd H stretching vibration of the 2-EP monomer absorbs close to 3300 cm-1, whereas a broad band with maximum around 3215 cm-1 emerges as the concentration rises, indicating the formation of hydrogen-bonded complexes involving the tbnd Csbnd H moiety. The Ctbnd C stretching vibration of monomer 2-EP close to 2120 cm-1 is, using derivative spectroscopy, resolved from the signals of the dimer complexes with maximum around 2112 cm-1. Quantum chemical calculations using the B3LYP + D3 model with counterpoise correction predict that the two most stable dimers are of the π-stacked variety, closely followed by dimers with intermolecular tbnd Csbnd H⋯N hydrogen bonding; the predicted red shifts of the tbnd Csbnd H stretching wavenumbers due to hydrogen bonding are in the range 54-120 cm-1. No species with obvious hydrogen bonding involving the Ctbnd C or pyridine π-systems as acceptors are predicted. Dimerization constant at 25 °C is estimated to be K2 = 0.13 ± 0.01 mol-1 dm3.

  18. TRIM28 epigenetic corepressor is indispensable for stable induced pluripotent stem cell formation

    Directory of Open Access Journals (Sweden)

    Marta Klimczak

    2017-08-01

    Full Text Available Cellular reprogramming proceeds in a stepwise pathway initiated by binding and transcription of pluripotency factors followed by genome-wide epigenetic changes. Priming events, such as erasure of DNA methylation and chromatin remodeling determines the success of pluripotency acquisition later. Therefore, growing efforts are made to understand epigenetic regulatory network that makes reprogramming possible and efficient. Here, we analyze the role of transcriptional corepressor TRIM28, involved in heterochromatin formation, during the process of reprogramming of mouse somatic cells into induced pluripotent stem cells (iPS cells. We demonstrate that Trim28 knockdown (Trim28 KD causes that emerging iPS cells differentiate immediately back into MEFs therefore they fail to yield stable iPS cell colonies. To better comprehend the mechanism of TRIM28 action in reprogramming, we performed a reverse-phase protein array (RPPA using in excess of 300 different antibodies and compared the proteomic profiles of wild-type and Trim28 KD cells during reprogramming. We revealed the differences in the dynamics of reprogramming of wild-type and Trim28 KD cells. Interestingly, proteomic profile of Trim28 KD cells at the final stage of reprogramming resembled differentiated state rather than maintenance of pluripotency and self-renewal, strongly suggesting spontaneous differentiation of Trim28 KD cells back to their parental cell type. We also observed that action of TRIM28 in reprogramming is accompanied by differential enrichment of proteins involved in cell cycle, adhesion and stemness. Collectively, these results suggest that regulation of epigenetic modifications coordinated by TRIM28 plays a crucial role in reprogramming process.

  19. The role of ring current O+ in the formation of stable auroral red arcs

    International Nuclear Information System (INIS)

    Kozyra, J.U.; Cravens, T.E.; Nagy, A.F.; Shelley, E.G.; Comfort, R.H.; Brace, L.H.

    1987-01-01

    Coulomb collisions between ring current protons and thermal electrons were first proposed by Cole (1965) as the energy source for stable auroral red (SAR) arcs. Recent observations have shown that the ring current and magnetospheric plasma contain significant amounts of heavy ions (Johnson et al., 1977; Young et al., 1977; Geiss et al., 1978; and others). In fact, the ring current is often dominated by heavy ions at those energies (E ≤ 17 keV) important for Coulomb collisions on SAR arc field lines (Kozyra et al., 1986a). Observations (during four SAR arcs in 1981) of thermal and energetic ion populations by the Dynamics Explorer 1 satellite in the magnetospheric energy source region and nearly simultaneous Langmuir probe measurements of enhanced electron temperatures by Dynamics Explorer 2 within the SAR arc at F region heights have allowed the authors to examine the role of heavy ions in the formation of SAR arcs. They find that (1) sufficient energy is transferred to the electron gas at high altitudes via Coulomb collisions between the observed ring current ions and thermal electrons to support the enhanced (SAR arc) F region electron temperatures measured on these field lines, (2) the latitudinal variation in the electron heating rates calculated using observed ion populations is consistent with the observed variation in electron temperature across the SAR arc, and (3) in all cases, ring current O + is the major source of energy for the SAR arcs. This implies a relationship between the heavy ion content of the magnetospheric plasma and the occurrence frequency and intensity of SAR arcs

  20. Globally Stable Microresonator Turing Pattern Formation for Coherent High-Power THz Radiation On-Chip

    Science.gov (United States)

    Huang, Shu-Wei; Yang, Jinghui; Yang, Shang-Hua; Yu, Mingbin; Kwong, Dim-Lee; Zelevinsky, T.; Jarrahi, Mona; Wong, Chee Wei

    2017-10-01

    In nonlinear microresonators driven by continuous-wave (cw) lasers, Turing patterns have been studied in the formalism of the Lugiato-Lefever equation with emphasis on their high coherence and exceptional robustness against perturbations. Destabilization of Turing patterns and the transition to spatiotemporal chaos, however, limit the available energy carried in the Turing rolls and prevent further harvest of their high coherence and robustness to noise. Here, we report a novel scheme to circumvent such destabilization, by incorporating the effect of local mode hybridizations, and we attain globally stable Turing pattern formation in chip-scale nonlinear oscillators with significantly enlarged parameter space, achieving a record-high power-conversion efficiency of 45% and an elevated peak-to-valley contrast of 100. The stationary Turing pattern is discretely tunable across 430 GHz on a THz carrier, with a fractional frequency sideband nonuniformity measured at 7.3 ×10-14 . We demonstrate the simultaneous microwave and optical coherence of the Turing rolls at different evolution stages through ultrafast optical correlation techniques. The free-running Turing-roll coherence, 9 kHz in 200 ms and 160 kHz in 20 minutes, is transferred onto a plasmonic photomixer for one of the highest-power THz coherent generations at room temperature, with 1.1% optical-to-THz power conversion. Its long-term stability can be further improved by more than 2 orders of magnitude, reaching an Allan deviation of 6 ×10-10 at 100 s, with a simple computer-aided slow feedback control. The demonstrated on-chip coherent high-power Turing-THz system is promising to find applications in astrophysics, medical imaging, and wireless communications.

  1. Liquid crystal dimers

    CERN Document Server

    Kumar Pal, Santanu

    2017-01-01

    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.

  2. Newcastle disease virus induces stable formation ofbona fidestress granules to facilitate viral replication through manipulating host protein translation.

    Science.gov (United States)

    Sun, Yingjie; Dong, Luna; Yu, Shengqing; Wang, Xiaoxu; Zheng, Hang; Zhang, Pin; Meng, Chunchun; Zhan, Yuan; Tan, Lei; Song, Cuiping; Qiu, Xusheng; Wang, Guijun; Liao, Ying; Ding, Chan

    2017-04-01

    Mammalian cells respond to various environmental stressors to form stress granules (SGs) by arresting cytoplasmic mRNA, protein translation element, and RNA binding proteins. Virus-induced SGs function in different ways, depending on the species of virus; however, the mechanism of SG regulation of virus replication is not well understood. In this study, Newcastle disease virus (NDV) triggered stable formation of bona fide SGs on HeLa cells through activating the protein kinase R (PKR)/eIF2α pathway. NDV-induced SGs contained classic SG markers T-cell internal antigen (TIA)-1, Ras GTPase-activating protein-binding protein (G3BP)-1, eukaryotic initiation factors, and small ribosomal subunit, which could be disassembled in the presence of cycloheximide. Treatment with nocodazole, a microtubule disruption drug, led to the formation of relatively small and circular granules, indicating that NDV infection induces canonical SGs. Furthermore, the role of SGs on NDV replication was investigated by knockdown of TIA-1 and TIA-1-related (TIAR) protein, the 2 critical components involved in SG formation from the HeLa cells, followed by NDV infection. Results showed that depletion of TIA-1 or TIAR inhibited viral protein synthesis, reduced extracellular virus yields, but increased global protein translation. FISH revealed that NDV-induced SGs contained predominantly cellular mRNA rather than viral mRNA. Deletion of TIA-1 or TIAR reduced NP mRNA levels in polysomes. These results demonstrate that NDV triggers stable formation of bona fide SGs, which benefit viral protein translation and virus replication by arresting cellular mRNA.-Sun, Y., Dong, L., Yu, S., Wang, X., Zheng, H., Zhang, P., Meng, C., Zhan, Y., Tan, L., Song, C., Qiu, X., Wang, G., Liao, Y., Ding, C. Newcastle disease virus induces stable formation of bona fide stress granules to facilitate viral replication through manipulating host protein translation. © FASEB.

  3. Biochemical, mutational and in silico structural evidence for a functional dimeric form of the ornithine decarboxylase from Entamoeba histolytica.

    Directory of Open Access Journals (Sweden)

    Preeti

    Full Text Available BACKGROUND: Entamoeba histolytica is responsible for causing amoebiasis. Polyamine biosynthesis pathway enzymes are potential drug targets in parasitic protozoan diseases. The first and rate-limiting step of this pathway is catalyzed by ornithine decarboxylase (ODC. ODC enzyme functions as an obligate dimer. However, partially purified ODC from E. histolytica (EhODC is reported to exist in a pentameric state. METHODOLOGY AND RESULTS: In present study, the oligomeric state of EhODC was re-investigated. The enzyme was over-expressed in Escherichia coli and purified. Pure protein was used for determination of secondary structure content using circular dichroism spectroscopy. The percentages of α-helix, β-sheets and random coils in EhODC were estimated to be 39%, 25% and 36% respectively. Size-exclusion chromatography and mass spectrophotometry analysis revealed that EhODC enzyme exists in dimeric form. Further, computational model of EhODC dimer was generated. The homodimer contains two separate active sites at the dimer interface with Lys57 and Cys334 residues of opposite monomers contributing to each active site. Molecular dynamic simulations were performed and the dimeric structure was found to be very stable with RMSD value ∼0.327 nm. To gain insight into the functional role, the interface residues critical for dimerization and active site formation were identified and mutated. Mutation of Lys57Ala or Cys334Ala completely abolished enzyme activity. Interestingly, partial restoration of the enzyme activity was observed when inactive Lys57Ala and Cys334Ala mutants were mixed confirming that the dimer is the active form. Furthermore, Gly361Tyr and Lys157Ala mutations at the dimer interface were found to abolish the enzyme activity and destabilize the dimer. CONCLUSION: To our knowledge, this is the first report which demonstrates that EhODC is functional in the dimeric form. These findings and availability of 3D structure model of EhODC dimer

  4. Impact of the Extended 1,1'-Bipyridinium Structure on the Electron Transfer and pi-Dimer Formation. Spectroelectrochemical and Computational Study

    Czech Academy of Sciences Publication Activity Database

    Tarábek, Ján; Kolivoška, Viliam; Gál, M.; Pospíšil, Lubomír; Valášek, M.; Kaminský, Jakub; Hromadová, Magdaléna

    2015-01-01

    Roč. 119, č. 32 (2015), s. 18056-18065 ISSN 1932-7447 R&D Projects: GA ČR(CZ) GA14-05180S; GA ČR GAP208/11/0105 Grant - others:GA AV ČR(CZ) M200401202; GA AV ČR(CZ) M200551205; GA MŠk(CZ) ED3.2.00/08.0144; GA MŠk(CZ) LM2010005 Program:M Institutional support: RVO:61388963 ; RVO:61388955 Keywords : EPR spectroelectrochemistry * extended bipyridinium * dimer Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.509, year: 2015

  5. Stable Formation Control of Multi-Robot System with Communication Delay

    Directory of Open Access Journals (Sweden)

    Limei Jiang

    2012-03-01

    Full Text Available In this paper, a distributed formation control algorithm with delayed information exchange is discussed. The algorithm, which is derived from the flocking behaviour of birds and consensus theory, enables robots to move in formation at a desired velocity. After a series of orthogonal transformations to the original formation system, the upper bound tolerable delay is obtained by using matrix theory and the Nyquist criterion. According to the results, the upper bound tolerable delay depends on the control parameters and eigenvalues of the Laplacian matrix. Therefore, the effect of the parameters on the maximum tolerable delay is analysed, obtaining the following conclusions: the upper bound tolerable delay is proportional to the parameters associated with the velocity, inversely proportional to the parameters associated with the position, and inversely proportional to the difference between the eigenvalue of Laplacian matrix and 1. The simulation results of a four-robot formation system with different communication delays verify the effectiveness of the formation control algorithm and the correctness of the theoretical analysis.

  6. Centriole triplet microtubules are required for stable centriole formation and inheritance in human cells.

    Science.gov (United States)

    Wang, Jennifer T; Kong, Dong; Hoerner, Christian R; Loncarek, Jadranka; Stearns, Tim

    2017-09-14

    Centrioles are composed of long-lived microtubules arranged in nine triplets. However, the contribution of triplet microtubules to mammalian centriole formation and stability is unknown. Little is known of the mechanism of triplet microtubule formation, but experiments in unicellular eukaryotes indicate that delta-tubulin and epsilon-tubulin, two less-studied tubulin family members, are required. Here, we report that centrioles in delta-tubulin and epsilon-tubulin null mutant human cells lack triplet microtubules and fail to undergo centriole maturation. These aberrant centrioles are formed de novo each cell cycle, but are unstable and do not persist to the next cell cycle, leading to a futile cycle of centriole formation and disintegration. Disintegration can be suppressed by paclitaxel treatment. Delta-tubulin and epsilon-tubulin physically interact, indicating that these tubulins act together to maintain triplet microtubules and that these are necessary for inheritance of centrioles from one cell cycle to the next.

  7. Neutron scattering in dimers

    DEFF Research Database (Denmark)

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

    1986-01-01

    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...... excitations are modulated by an interference term reflecting the distance between the magnetic ions within the dimers. The INS technique is particularly powerful for the study of effects like: temperature dependence of exchange, the role of biquadratic exchange, the combination of crystal-field and exchange...

  8. Adsorption of dimeric surfactants in lamellar silicates

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-12-01

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

  9. Retroviral RNA Dimerization: From Structure to Functions

    Directory of Open Access Journals (Sweden)

    Noé Dubois

    2018-03-01

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

  10. The role of stable α-synuclein oligomers in the molecular events underlying amyloid formation

    DEFF Research Database (Denmark)

    Lorenzen, Nikolai; Nielsen, Søren Bang; Buell, Alexander K.

    2014-01-01

    α-synuclein (αSN), whose aggregation is strongly implicated in the development of Parkinson’s disease (PD). The two types of oligomers are both formed under conditions where amyloid fibril formation is observed but differ in molecular weight by an order of magnitude. Both possess a degree of β......, either as precursors of fibrils or as species involved in the fibril elongation process or instead if they are associated with an aggregation process that is distinct from that generating mature fibrils. Here we describe and characterize in detail two well-defined oligomeric species formed by the protein...

  11. Utilizing Stable Isotopes and Isotopic Anomalies to Study Early Solar System Formation Processes

    Science.gov (United States)

    Simon, Justin

    2017-01-01

    Chondritic meteorites contain a diversity of particle components, i.e., chondrules and calcium-, aluminum-rich refractory inclusions (CAIs), that have survived since the formation of the Solar System. The chemical and isotopic compositions of these materials provide a record of the conditions present in the protoplanetary disk where they formed and can aid our understanding of the processes and reservoirs in which solids formed in the solar nebula, an important step leading to the accretion of planetesimals. Isotopic anomalies associated with nucleosynthetic processes are observed in these discrete materials, and can be compared to astronomical observations and astrophysical formation models of stars and more recently proplyds. The existence and size of these isotopic anomalies are typically thought to reflect a significant state of isotopic heterogeneity in the earliest Solar System, likely left over from molecular cloud heterogeneities on the grain scale, but some could also be due to late stellar injection. The homogenization of these isotopic anomalies towards planetary values can be used to track the efficiency and timescales of disk wide mixing,

  12. End binding proteins are obligatory dimers.

    Directory of Open Access Journals (Sweden)

    Indrani Sen

    Full Text Available End binding (EB proteins are responsible for the recruitment of an array of microtubule plus-end tracking proteins (+TIPs to growing microtubules ends. EBs encompass an N-terminal calponin homology domain that confers microtubule tip tracking activity to the protein. The C-terminal domain of EBs contains a coiled coil that mediates the parallel dimerization of EB monomers. This part of the protein is also responsible for partner binding. While dimerization is not essential for microtubule tip tracking by EBs it is a prerequisite for +TIP partner binding. The concentration of EBs in cells has been estimated to be in the range of hundreds of nanomoles. In contrast, in in vitro single molecule experiments EB concentrations of subnanomoles are employed. From a mechanistic point of view it is important to assess the oligomerization state of EBs at physiologically and experimentally relevant protein concentrations, in particular if the goal of a study is to model the behavior of EB-dependent dynamic +TIP networks. Here we have determined the stability of the EB1 and EB3 dimers using multi-angle light scattering and fluorescence analytical ultracentrifugation. We show that these EBs form stable dimers and do not dissociate even at very low nanomolar concentrations. The dimers remained stable at both room temperature as well as at the physiologically relevant temperature of 37°C. Together, our results reveal that EBs are obligatory dimers, a conclusion that has implications for the mechanistic understanding of these key proteins involved in the orchestration of dynamic protein networks at growing microtubule ends.

  13. Active thermochemical tables: water and water dimer.

    Science.gov (United States)

    Ruscic, Branko

    2013-11-21

    A new partition function for water dimer in the temperature range 200-500 K was developed by exploiting the equations of state for real water vapor, liquid water, and ice, and demonstrated to be significantly more accurate than any proposed so far in the literature. The new partition function allows the Active Thermochemical Tables (ATcT) approach to be applied on the available experimental and theoretical data relating to water dimer thermochemistry, leading to accurate water dimer enthalpies of formation of -499.115 ± 0.052 kJ mol(-1) at 298.15 K and -491.075 ± 0.080 kJ mol(-1) at 0 K. With the current ATcT enthalpy of formation of the water monomer, -241.831 ± 0.026 kJ mol(-1) at 298.15 K (-238.928 kJ mol(-1) at 0 K), this leads to the dimer bond dissociation enthalpy at 298.15 K of 15.454 ± 0.074 kJ mol(-1) and a 0 K bond dissociation energy of 13.220 ± 0.096 kJ mol(-1) (1105 ± 8 cm(-1)), the latter being in perfect agreement with recent experimental and theoretical determinations. The new partition function of water dimer allows the extraction and tabulation of heat capacity, entropy, enthalpy increment, reduced Gibbs energy, enthalpy of formation, and Gibbs energy of formation. Newly developed tabulations of analogous thermochemical properties for gas-phase water monomer and for water in condensed phases are also given, allowing the computations of accurate equilibria between the dimer and monomer in the 200-500 K range of temperatures.

  14. Ion beam induced surface pattern formation and stable travelling wave solutions.

    Science.gov (United States)

    Numazawa, Satoshi; Smith, Roger

    2013-03-06

    The formation of ripple structures on ion bombarded semiconductor surfaces is examined theoretically. Previous models are discussed and a new nonlinear model is formulated, based on the infinitesimal local atomic relocation induced by elastic nuclear collisions in the early stages of collision cascades and an associated density change in the near surface region. Within this framework ripple structures are shown to form without the necessity to invoke surface diffusion or large sputtering as important mechanisms. The model can also be extended to the case where sputtering is important, and it is shown that in this case certain 'magic' angles can occur at which the ripple patterns are most clearly defined. The results are in very good agreement with experimental observations.

  15. Formation of Hydroxymethyl DNA Adducts in Rats Orally Exposed to Stable Isotope Labeled Methanol

    Science.gov (United States)

    Lu, Kun; Gul, Husamettin; Upton, Patricia B.; Moeller, Benjamin C.; Swenberg, James A.

    2012-01-01

    Methanol is a large volume industrial chemical and widely used solvent and fuel additive. Methanol’s well known toxicity and use in a wide spectrum of applications has raised long-standing environmental issues over its safety, including its carcinogenicity. Methanol has not been listed as a carcinogen by any regulatory agency; however, there are debates about its carcinogenic potential. Formaldehyde, a metabolite of methanol, has been proposed to be responsible for the carcinogenesis of methanol. Formaldehyde is a known carcinogen and actively targets DNA and protein, causing diverse DNA and protein damage. However, formaldehyde-induced DNA adducts arising from the metabolism of methanol have not been reported previously, largely due to the absence of suitable DNA biomarkers and the inability to differentiate what was due to methanol compared with the substantial background of endogenous formaldehyde. Recently, we developed a unique approach combining highly sensitive liquid chromatography-mass spectrometry methods and exposure to stable isotope labeled chemicals to simultaneously quantify formaldehyde-specific endogenous and exogenous DNA adducts. In this study, rats were exposed daily to 500 or 2000 mg/kg [13CD4]-methanol by gavage for 5 days. Our data demonstrate that labeled formaldehyde arising from [13CD4]-methanol induced hydroxymethyl DNA adducts in multiple tissues in a dose-dependent manner. The results also demonstrated that the number of exogenous DNA adducts was lower than the number of endogenous hydroxymethyl DNA adducts in all tissues of rats administered 500 mg/kg per day for 5 days, a lethal dose to humans, even after incorporating an average factor of 4 for reduced metabolism due to isotope effects of deuterium-labeled methanol into account. PMID:22157354

  16. Stable silicon isotope signatures of marine pore waters - Biogenic opal dissolution versus authigenic clay mineral formation

    Science.gov (United States)

    Ehlert, Claudia; Doering, Kristin; Wallmann, Klaus; Scholz, Florian; Sommer, Stefan; Grasse, Patricia; Geilert, Sonja; Frank, Martin

    2016-10-01

    Dissolved silicon isotope compositions have been analysed for the first time in pore waters (δ30SiPW) of three short sediment cores from the Peruvian margin upwelling region with distinctly different biogenic opal content in order to investigate silicon isotope fractionation behaviour during early diagenetic turnover of biogenic opal in marine sediments. The δ30SiPW varies between +1.1‰ and +1.9‰ with the highest values occurring in the uppermost part close to the sediment-water interface. These values are of the same order or higher than the δ30Si of the biogenic opal extracted from the same sediments (+0.3‰ to +1.2‰) and of the overlying bottom waters (+1.1‰ to +1.5‰). Together with dissolved silicic acid concentrations well below biogenic opal saturation, our collective observations are consistent with the formation of authigenic alumino-silicates from the dissolving biogenic opal. Using a numerical transport-reaction model we find that approximately 24% of the dissolving biogenic opal is re-precipitated in the sediments in the form of these authigenic phases at a relatively low precipitation rate of 56 μmol Si cm-2 yr-1. The fractionation factor between the precipitates and the pore waters is estimated at -2.0‰. Dissolved and solid cation concentrations further indicate that off Peru, where biogenic opal concentrations in the sediments are high, the availability of reactive terrigenous material is the limiting factor for the formation of authigenic alumino-silicate phases.

  17. Integration of Stable Droplet Formation on a CD Microfluidic Device for Extreme Point of Care Applications

    Science.gov (United States)

    Ganesh, Shruthi Vatsyayani

    With the advent of microfluidic technologies for molecular diagnostics, a lot of emphasis has been placed on developing diagnostic tools for resource poor regions in the form of Extreme Point of Care devices. To ensure commercial viability of such a device there is a need to develop an accurate sample to answer system, which is robust, portable, isolated yet highly sensitive and cost effective. This need has been a driving force for research involving integration of different microsystems like droplet microfluidics, Compact-disc (CD)microfluidics along with sample preparation and detection modules on a single platform. This work attempts to develop a proof of concept prototype of one such device using existing CD microfluidics tools to generate stable droplets used in point of care diagnostics (POC diagnostics). Apart from using a fairly newer technique for droplet generation and stabilization, the work aims to develop this method focused towards diagnostics for rural healthcare. The motivation for this work is first described with an emphasis on the current need for diagnostic testing in rural health-care and the general guidelines prescribed by WHO for such a sample to answer system. Furthermore, a background on CD and droplet microfluidics is presented to understand the merits and de-merits of each system and the need for integrating the two. This phase of the thesis also includes different methods employed/demonstrated to generate droplets on a spinning platform. An overview on the detection platforms is also presented to understand the challenges involved in building an extreme point of care device. In the third phase of the thesis, general manufacturing techniques and materials used to accomplish this work is presented. Lastly, design trials for droplet generation is presented. The shortcomings of these trials are solved by investigating mechanisms pertaining to design modification and use of agarose based droplet generation to ensure a more robust sample

  18. When the dust settles: stable xenon isotope constraints on the formation of nuclear fallout.

    Science.gov (United States)

    Cassata, W S; Prussin, S G; Knight, K B; Hutcheon, I D; Isselhardt, B H; Renne, P R

    2014-11-01

    Nuclear weapons represent one of the most immediate threats of mass destruction. In the event that a procured or developed nuclear weapon is detonated in a populated metropolitan area, timely and accurate nuclear forensic analysis and fallout modeling would be needed to support attribution efforts and hazard assessments. Here we demonstrate that fissiogenic xenon isotopes retained in radioactive fallout generated by a nuclear explosion provide unique constraints on (1) the timescale of fallout formation, (2) chemical fractionation that occurs when fission products and nuclear fuel are incorporated into fallout, and (3) the speciation of fission products in the fireball. Our data suggest that, in near surface nuclear tests, the presence of a significant quantity of metal in a device assembly, combined with a short time allowed for mixing with the ambient atmosphere (seconds), may prevent complete oxidation of fission products prior to their incorporation into fallout. Xenon isotopes thus provide a window into the chemical composition of the fireball in the seconds that follow a nuclear explosion, thereby improving our understanding of the physical and thermo-chemical conditions under which fallout forms. Copyright © 2014 Elsevier Ltd. All rights reserved.

  19. Highly stable and reusable immobilized formate dehydrogenases: Promising biocatalysts for in situ regeneration of NADH

    Directory of Open Access Journals (Sweden)

    Barış Binay

    2016-02-01

    Full Text Available This study aimed to prepare robust immobilized formate dehydrogenase (FDH preparations which can be used as effective biocatalysts along with functional oxidoreductases, in which in situ regeneration of NADH is required. For this purpose, Candida methylica FDH was covalently immobilized onto Immobead 150 support (FDHI150, Immobead 150 support modified with ethylenediamine and then activated with glutaraldehyde (FDHIGLU, and Immobead 150 support functionalized with aldehyde groups (FDHIALD. The highest immobilization yield and activity yield were obtained as 90% and 132%, respectively when Immobead 150 functionalized with aldehyde groups was used as support. The half-life times (t1/2 of free FDH, FDHI150, FDHIGLU and FDHIALD were calculated as 10.6, 28.9, 22.4 and 38.5 h, respectively at 35 °C. FDHI150, FDHIGLU and FDHIALD retained 69, 38 and 51% of their initial activities, respectively after 10 reuses. The results show that the FDHI150, FDHIGLU and FDHIALD offer feasible potentials for in situ regeneration of NADH.

  20. Stable chromium isotopic composition of meteorites and metal-silicate experiments: Implications for fractionation during core formation

    Science.gov (United States)

    Bonnand, P.; Williams, H. M.; Parkinson, I. J.; Wood, B. J.; Halliday, A. N.

    2016-02-01

    We present new mass independent and mass dependent Cr isotope compositions for meteorites measured by double spike thermal ionisation mass spectrometry. Small differences in both mass independent 53Cr and 54Cr relative to the Bulk Silicate Earth are reported and are very similar to previously published values. Carbonaceous chondrites are characterised by an excess in 54Cr compared to ordinary and enstatite chondrites which make mass independent Cr isotopes a useful tool for distinguishing between meteoritic groups. Mass dependent stable Cr isotope compositions for the same samples are also reported. Carbonaceous and ordinary chondrites are identical within uncertainty with average δ53 Cr values of - 0.118 ± 0.040 ‰ and - 0.143 ± 0.074 ‰ respectively. The heaviest isotope compositions are recorded by an enstatite chondrite and a CO carbonaceous chondrite, both of which have relatively reduced chemical compositions implying some stable Cr isotope fractionation related to redox processes in the circumstellar disk. The average δ53 Cr values for chondrites are within error of the estimate for the Bulk Silicate Earth (BSE) also determined by double spiking. The lack of isotopic difference between chondritic material and the BSE provides evidence that Cr isotopes were not fractionated during core formation on Earth. A series of high-pressure experiments was also carried out to investigate stable Cr isotope fractionation between metal and silicate and no demonstrable fractionation was observed, consistent with our meteorites data. Mass dependent Cr isotope data for achondrites suggest that Cr isotopes are fractionated during magmatic differentiation and therefore further work is required to constrain the Cr isotopic compositions of the mantles of Vesta and Mars.

  1. Evidence from stable isotopes and10Be for solar system formation triggered by a low-mass supernova.

    Science.gov (United States)

    Banerjee, Projjwal; Qian, Yong-Zhong; Heger, Alexander; Haxton, W C

    2016-11-22

    About 4.6 billion years ago, some event disturbed a cloud of gas and dust, triggering the gravitational collapse that led to the formation of the solar system. A core-collapse supernova, whose shock wave is capable of compressing such a cloud, is an obvious candidate for the initiating event. This hypothesis can be tested because supernovae also produce telltale patterns of short-lived radionuclides, which would be preserved today as isotopic anomalies. Previous studies of the forensic evidence have been inconclusive, finding a pattern of isotopes differing from that produced in conventional supernova models. Here we argue that these difficulties either do not arise or are mitigated if the initiating supernova was a special type, low in mass and explosion energy. Key to our conclusion is the demonstration that short-lived 10 Be can be readily synthesized in such supernovae by neutrino interactions, while anomalies in stable isotopes are suppressed.

  2. Lidar Observation of Aerosol and Temperature Stratification over Urban Area During the Formation of a Stable Atmospheric PBL

    Science.gov (United States)

    Kolev, I.; Parvanov, O.; Kaprielov, B.; Mitev, V.; Simeonov, V.; Grigorov, I.

    1992-01-01

    In recent years, the processes in the atmospheric planetary boundary layer (PBL) over urban areas were intensely investigated, due to ecological problems related to the air, soil, and water pollution. New pollution sources in new residential districts, when in contradiction to the microclimate and topography requirements of that region, create a number of considerable hazards and problems. The present study is a continuation of our preceding investigations and aims at revealing the aerosol structure and stratification during the transition after sunset as measured by two lidars. Such observation of the nocturnal, stable PBL formation over an urban area in Bulgaria has not been reported before. The lidars' high time and spatial resolutions allow the changes of the internal structure of the PBL's part located above the surface layer to be observed.

  3. Evidence from stable isotopes and 10Be for solar system formation triggered by a low-mass supernova

    Science.gov (United States)

    Banerjee, Projjwal; Qian, Yong-Zhong; Heger, Alexander; Haxton, W. C.

    2016-11-01

    About 4.6 billion years ago, some event disturbed a cloud of gas and dust, triggering the gravitational collapse that led to the formation of the solar system. A core-collapse supernova, whose shock wave is capable of compressing such a cloud, is an obvious candidate for the initiating event. This hypothesis can be tested because supernovae also produce telltale patterns of short-lived radionuclides, which would be preserved today as isotopic anomalies. Previous studies of the forensic evidence have been inconclusive, finding a pattern of isotopes differing from that produced in conventional supernova models. Here we argue that these difficulties either do not arise or are mitigated if the initiating supernova was a special type, low in mass and explosion energy. Key to our conclusion is the demonstration that short-lived 10Be can be readily synthesized in such supernovae by neutrino interactions, while anomalies in stable isotopes are suppressed.

  4. Activation of Transcription Factor Nrf2 Signalling by the Sphingosine Kinase Inhibitor SKI-II Is Mediated by the Formation of Keap1 Dimers

    Science.gov (United States)

    Mercado, Nicolas; Kizawa, Yasuo; Ueda, Keitaro; Xiong, Yeping; Kimura, Genki; Moses, Audric; Curtis, Jonathan M.; Ito, Kazuhiro; Barnes, Peter J.

    2014-01-01

    Background Anti-oxidant capacity is crucial defence against environmental or endogenous oxidative stress. Nuclear factor erythroid 2-related factor 2 (Nrf2) is a redox-sensitive transcription factor that plays a key defensive role against oxidative and cytotoxic stress and cellular senescence. However, Nrf2 signalling is impaired in several aging-related diseases, such as chronic pulmonary obstructive disease (COPD), cancer, and neurodegenerative diseases. Thus, novel therapeutics that enhance Nrf2 signalling are an attractive approach to treat these diseases. Methodology/Principal Findings Nrf2 was stabilized by SKI-II (2-(p-hydroxyanilino)-4-(p-chlorophenyl) thiazole), which is a known sphingosine kinase inhibitor, in human bronchial epithelial cell line, BEAS2B, and in primary human bronchial epithelial cells, leading to enhancement of anti-oxidant proteins, such as HO-1, NQO1 and GCLM. The activation of Nrf2 was achieved by the generation of inactive dimerized form of Keap1, a negative regulator of Nrf2 expression, which was independent of sphingosine kinase inhibition. Using mice that were exposed to cigarette smoke, SKI-II induced Nrf2 expression together with HO-1 in their lungs. In addition, SKI-II reduced cigarette smoke mediated oxidative stress, macrophages and neutrophil infiltration and markers of inflammation in mice. Conclusions/Significance SKI-II appears to be a novel activator of Nrf2 signalling via the inactivation of Keap1. PMID:24505412

  5. Glycine Transporter Dimers

    Science.gov (United States)

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

    2015-01-01

    Different Na+/Cl−-dependent neurotransmitter transporters of the SLC6a family have been shown to form dimers or oligomers in both intracellular compartments and at the cell surface. In contrast, the glycine transporters (GlyTs) GlyT1 and -2 have been reported to exist as monomers in the plasma membrane based on hydrodynamic and native gel electrophoretic studies. Here, we used cysteine substitution and oxidative cross-linking to show that of GlyT1 and GlyT2 also form dimeric complexes within the plasma membrane. GlyT oligomerization at the cell surface was confirmed for both GlyT1 and GlyT2 by fluorescence resonance energy transfer microscopy. Endoglycosidase treatment and surface biotinylation further revealed that complex-glycosylated GlyTs form dimers located at the cell surface. Furthermore, substitution of tryptophan 469 of GlyT2 by an arginine generated a transporter deficient in dimerization that was retained intracellulary. Based on these results and GlyT structures modeled by using the crystal structure of the bacterial homolog LeuTAa, as a template, residues located within the extracellular loop 3 and at the beginning of transmembrane domain 6 are proposed to contribute to the dimerization interface of GlyTs. PMID:18252709

  6. Origin of dolomites in a downslope biostrome, Jefferson Formation (Frasnian), central Idaho: evidence from REE patterns, stable isotopes, and petrography

    Energy Technology Data Exchange (ETDEWEB)

    Dorobek, S.L.

    1987-08-01

    A completely dolomitized coral-stromatoporoid biostrome occurs at the top of the Dark Dolomite member of the Jefferson Formation (Frasnian) at Grandview Canyon, Lost River Range, central Idaho. The biostrome overlies a thick sequence of dolostones that were deposited in slope to deep ramp settings. The biostrome, therefore, formed in an open marine setting after shallowing of deep water environments. Zoned dolospar cement fills dissolution vugs and tectonic fractures. Stable isotopes for zoned dolospar are -13.1 to -6.5 per thousand delta/sup 18/O (average - 11.5) and -1.5 to -0.1 per thousand delta/sup 13/C (average -0.4). REE patterns for zoned dolospar have positive Ce anomalies, but total REE abundance is similar to REE abundance for replacive dolomites. Stratigraphic occurrence in an open marine setting, stable isotopes, and REE patterns suggest replacive dolomite phases formed during shallow burial diagenesis with significant involvement of nonevaporated sea water. More negative Ce anomalies near the top of the biostrome suggest a diagenetic overprint by oxidizing meteoric waters. Zoned dolospar probably formed from warmer, reducing burial fluids. Carbon for zoned dolospar probably was recycled from preexisting dolomite. These data may be useful for interpreting the origin of other anomalous platform dolostones.

  7. A Novel Dimer of α-Tocopherol

    Directory of Open Access Journals (Sweden)

    Anjan Patel

    2008-01-01

    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.

  8. Dimerization of Protegrin-1 in Different Environments

    Directory of Open Access Journals (Sweden)

    Yiannis N. Kaznessis

    2010-09-01

    Full Text Available The dimerization of the cationic β-hairpin antimicrobial peptide protegrin-1 (PG1 is investigated in three different environments: water, the surface of a lipid bilayer membrane, and the core of the membrane. PG1 is known to kill bacteria by forming oligomeric membrane pores, which permeabilize the cells. PG1 dimers are found in two distinct, parallel and antiparallel, conformations, known as important intermediate structural units of the active pore oligomers. What is not clear is the sequence of events from PG1 monomers in solution to pores inside membranes. The step we focus on in this work is the dimerization of PG1. In particular, we are interested in determining where PG1 dimerization is most favorable. We use extensive molecular dynamics simulations to determine the potential of mean force as a function of distance between two PG1 monomers in the aqueous subphase, the surface of model lipid bilayers and the interior of these bilayers. We investigate the two known distinct modes of dimerization that result in either a parallel or an antiparallel β-sheet orientation. The model bilayer membranes are composed of anionic palmitoyl-oleoyl-phosphatidylglycerol (POPG and palmitoyl-oleoyl-phosphatidylethanolamine (POPE in a 1:3 ratio (POPG:POPE. We find the parallel PG1 dimer association to be more favorable than the antiparallel one in water and inside the membrane. However, we observe that the antiparallel PG1 β-sheet dimer conformation is somewhat more stable than the parallel dimer association at the surface of the membrane. We explore the role of hydrogen bonds and ionic bridges in peptide dimerization in the three environments. Detailed knowledge of how networks of ionic bridges and hydrogen bonds contribute to peptide stability is essential for the purpose of understanding the mechanism of action for membrane-active peptides as well as for designing peptides which can modulate membrane properties. The findings are suggestive of the

  9. Role of cyclobutane dimers in UV-denaturation of DNA

    International Nuclear Information System (INIS)

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

    1978-01-01

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

  10. Mass dependent fractionation of stable chromium isotopes in mare basalts: Implications for the formation and the differentiation of the Moon

    Science.gov (United States)

    Bonnand, Pierre; Parkinson, Ian J.; Anand, Mahesh

    2016-02-01

    We present the first stable chromium isotopic data from mare basalts in order to investigate the similarity between the Moon and the Earth's mantle. A double spike technique coupled with MC-ICP-MS measurements was used to analyse 19 mare basalts, comprising high-Ti, low-Ti and KREEP-rich varieties. Chromium isotope ratios (δ53Cr) for mare basalts are positively correlated with indices of magmatic differentiation such as Mg# and Cr concentration which suggests that Cr isotopes were fractionated during magmatic differentiation. Modelling of the results provides evidence that spinel and pyroxene are the main phases controlling the Cr isotopic composition during fractional crystallisation. The most evolved samples have the lightest isotopic compositions, complemented by cumulates that are isotopically heavy. Two hypotheses are proposed to explain this fractionation: (i) equilibrium fractionation where heavy isotopes are preferentially incorporated into the spinel lattice and (ii) a difference in isotopic composition between Cr2+ and Cr3+ in the melt. However, both processes require magmatic temperatures below 1200 °C for appreciable Cr3+ to be present at the low oxygen fugacities found in the Moon (IW -1 to -2 log units). There is no isotopic difference between the most primitive high-Ti, low-Ti and KREEP basalts, which suggest that the sources of these basalts were homogeneous in terms of stable Cr isotopes. The least differentiated sample in our sample set is the low-Ti basalt 12016, characterised by a Cr isotopic composition of -0.222 ± 0.025‰, which is within error of the current BSE value (-0.124 ± 0.101‰). The similarity between the mantles of the Moon and Earth is consistent with a terrestrial origin for a major fraction of the lunar Cr. This similarity also suggests that Cr isotopes were not fractionated by core formation on the Moon.

  11. -CH2- lengthening of the internucleotide linkage in the ApA dimer can improve its conformational compatibility with its natural polynucleotide counterpart

    Science.gov (United States)

    Hanu, J.; Barvík, I.; Ruszová-Chmelová, K.; ŠtÆpánek, J.; Turpin, P.-Y.; Bok, J.; Rosenberg, I.; Petrová-Endová, M.

    2001-01-01

    The complete family of ApA phosphonate analogues with the internucleotide linkage elongated by insertion of a -CH2- group was prepared and the hybridisation and structural properties of its members in interaction with polyuridylic acid were investigated using an original 2D Raman approach. Except for the conformationally restricted ACHpA(2′3′endo-5′) modification, all of the isopolar, non-isosteric analogues form triplex-like complexes with poly(rU) at room temperature, in which two polymer strands are bound by Watson–Crick and Hoogsteen bonds to a central pseudostrand consisting of a ‘chain’ of A-dimers. For all of these dimers, the overall conformation of the triplexes was found to be similar according to their extracted Raman spectra. A simple semi-empirical model was introduced to explain the observed dependency of the efficiency of triplex formation on the adenine concentration. Apparently, for most of the modifications studied, the creation of a stable complex at room temperature requires the formation of a central pseudostrand, consisting of several adenine dimers. Molecular dynamics calculations were finally performed to interpret the differences in ‘cooperative’ behaviour between the different dimers studied. The results indicate that the exceptional properties of the ApCH2A(3′-5′) dimer could be caused by the 3D conformational compatibility of this modified linkage with the second (Hoogsteen) poly(rU) strand. PMID:11812852

  12. Radiation-induced apoptosis in human myeloma cell line increases BCL-2/BAX dimer formation and does not result in BAX/BAX homodimerization.

    Science.gov (United States)

    Filippovich, I V; Sorokina, N I; Lisbona, A; Chérel, M; Chatal, J F

    2001-06-01

    A popular model of BCL-2 and BAX involvement in apoptosis suggests that upon apoptosis induction cytosolic BAX translocates to the mitochondria, where it displays the pro-apoptotic function, which involves its homodimerization. BCL-2 exerts anti-apoptotic function by forming heterodimers with BAX, thus neutralizing the pro-apoptotic activity of the latter. We have shown that irradiation of the human myeloma cell line RPMI-8226 induced apoptosis as determined by DNA degradation, cytochrome c release into cytoplasm and BCL-2 caspase-mediated cleavage. BCL-2 protein was present only in the membrane fraction, whereas BAX was found both in cytosol and membranes isolated from non-irradiated cells. Radiation induced moderate redistribution of BAX from cytosol to membranes with a concomitant increase in BCL-2/BAX heterodimer formation. Rapid and transient BCL-2 phosphorylation in membrane fractions of irradiated cells did not affect BCL-2/BAX heterodimerization. We failed to detect any BAX/BAX homodimers in apoptotic cells. Our findings show that in irradiated RPMI-8226 cells the formation of BCL-2/BAX heterodimers correlates with apoptosis. We conclude that BCL-2/BAX heterodimers are negative regulators of death protection, and our data agree with those who propose that BCL-2 does not require BAX to exert its survival function. Copyright 2001 Wiley-Liss, Inc.

  13. Oxidative dimerization of (E)- and (Z)-2-propenylsesamol with O2 in the presence and absence of laccases and other catalysts: selective formation of carpanones and benzopyrans under different reaction conditions.

    Science.gov (United States)

    Constantin, Mihaela-Anca; Conrad, Jürgen; Merişor, Elena; Koschorreck, Katja; Urlacher, Vlada B; Beifuss, Uwe

    2012-05-18

    The oxidative dimerization of 2-propenylsesamol to carpanone with O(2) as the oxidant, which probably proceeds as a domino phenol oxidation/anti-β,β-radical coupling/intramolecular hetero Diels-Alder reaction, can be efficiently catalyzed by laccases. Experiments with laccases and other catalysts like a Co(salen) type catalyst and PdCl(2) clearly demonstrate that the diastereoselectivity of the carpanone formation does not depend on the catalyst but on the double-bond geometry of the substrate. With (E)-2-propenylsesamol as the substrate, carpanone and a so far unknown carpanone diastereoisomer are formed in a 9:1 ratio. When (Z)-2-propenylsesamol is used as starting material, carpanone is accompanied by two carpanone diastereoisomers unknown so far in a 5:1:4 ratio. All three carpanone diastereoisomers have been separated by HPLC, and their structures have been elucidated unambiguously by NMR spectroscopy, DFT calculations, and spin work analysis. When the oxidation of 2-propenylsesamol with O(2) is performed in the absence of any catalyst two diastereoisomeric benzopyrans are formed, probably as the result of a domino oxidation/intermolecular hetero Diels-Alder reaction. Under these conditions, carpanone is formed in trace amounts only.

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

    DEFF Research Database (Denmark)

    Petaja, Tuukka; Sipila, Mikko; Paasonen, Pauli

    2011-01-01

    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....

  15. Large shift and small broadening of Br2 valence band upon dimer formation with H2O: an ab initio study.

    Science.gov (United States)

    Franklin-Mergarejo, Ricardo; Rubayo-Soneira, Jesus; Halberstadt, Nadine; Ayed, Tahra; Bernal-Uruchurtu, Margarita I; Hernández-Lamoneda, Ramón; Janda, Kenneth C

    2011-06-16

    Valence electronic excitation spectra are calculated for the H(2)O···Br(2) complex using highly correlated ab initio potentials for both the ground and the valence electronic excited states and a 2-D approximation for vibrational motion. Due to the strong interaction between the O-Br and the Br-Br stretching motions, inclusion of these vibrations is the minimum necessary for the spectrum calculation. A basis set calculation is performed to determine the vibrational wave functions for the ground electronic state and a wave packet simulation is conducted for the nuclear dynamics on the excited state surfaces. The effects of both the spin-orbit interaction and temperature on the spectra are explored. The interaction of Br(2) with a single water molecule induces nearly as large a shift in the spectrum as is observed for an aqueous solution. In contrast, complex formation has a remarkably small effect on the T = 0 K width of the valence bands due to the fast dissociation of the dihalogen bond upon excitation. We therefore conclude that the widths of the spectra in aqueous solution are mostly due to inhomogeneous broadening. © 2011 American Chemical Society

  16. Thymine Dimerization in DNA is an Ultrafast Photoreaction

    OpenAIRE

    Schreier, Wolfgang J.; Schrader, Tobias E.; Koller, Florian O.; Gilch, Peter; Crespo-Hernández, Carlos E.; Swaminathan, Vijay N.; Carell, Thomas; Zinth, Wolfgang; Kohler, Bern

    2007-01-01

    Femtosecond time-resolved infrared spectroscopy is used to study the formation of cyclobutane dimers in the all-thymine oligonucleotide (dT)18 by ultraviolet light at 272 nanometers. The appearance of marker bands in time-resolved spectra indicate that dimers are fully formed ∼1 picosecond after ultraviolet excitation. The ultrafast appearance of this mutagenic photolesion points to an approximately barrierless excited-state reaction for bases that are properly oriented at the instant of ligh...

  17. Stable sulfur isotope partitioning during simulated petroleum formation as determined by hydrous pyrolysis of Ghareb Limestone, Israel

    Science.gov (United States)

    Amrani, Alon; Lewan, Michael D.; Aizenshtat, Zeev

    2005-11-01

    Hydrous pyrolysis experiments at 200 to 365°C were carried out on a thermally immature organic-rich limestone containing Type-IIS kerogen from the Ghareb Limestone in North Negev, Israel. This work focuses on the thermal behavior of both organic and inorganic sulfur species and the partitioning of their stable sulfur isotopes among organic and inorganic phases generated during hydrous pyrolyses. Most of the sulfur in the rock (85%) is organic sulfur. The most dominant sulfur transformation is cleavage of organic-bound sulfur to form H 2S (gas). Up to 70% of this organic sulfur is released as H 2S (gas) that is isotopically lighter than the sulfur in the kerogen. Organic sulfur is enriched by up to 2‰ in 34S during thermal maturation compared with the initial δ 34S values. The δ 34S values of the three main organic fractions (kerogen, bitumen and expelled oil) are within 1‰ of one another. No thermochemical sulfate reduction or sulfate formation was observed during the experiments. The early released sulfur reacted with available iron to form secondary pyrite and is the most 34S depleted phase, which is 21‰ lighter than the bulk organic sulfur. The large isotopic fractionation for the early formed H 2S is a result of the system not being in equilibrium. As partial pressure of H 2S (gas) increases, retro reactions with the organic sulfur in the closed system may cause isotope exchange and isotopic homogenization. Part of the δ 34S-enriched secondary pyrite decomposes above 300°C resulting in a corresponding decrease in the δ 34S of the remaining pyrite. These results are relevant to interpreting thermal maturation processes and their effect on kerogen-oil-H 2S-pyrite correlations. In particular, the use of pyrite-kerogen δ 34S relations in reconstructing diagenetic conditions of thermally mature rocks is questionable because formation of secondary pyrite during thermal maturation can mask the isotopic signature and quantity of the original diagenetic

  18. Alkane dimers interaction

    DEFF Research Database (Denmark)

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

    2010-01-01

    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...... values. The MGGA-M06-L density functional is a semi-local functional designed and has proven to provide accurate estimates of dispersion interactions for several systems at moderate computational cost. In the present application, it reproduces the trends obtained by the more expensive wavefunction...

  19. Formation of stable cell-cell contact without a solid/gel scaffold: Non-invasive manipulation by laser under depletion interaction with a polymer

    Science.gov (United States)

    Hashimoto, Shu; Yoshida, Aoi; Ohta, Taeko; Taniguchi, Hiroaki; Sadakane, Koichiro; Yoshikawa, Kenichi

    2016-07-01

    We report a novel method for constructing a stable three-dimensional cellular assembly in the absence of a solid or gel scaffold. A targeted cell was transferred to another cell, and the two were kept in contact for a few minutes by optical manipulation in an aqueous medium containing a hydrophilic polymer. Interestingly, this cell-cell adhesion was maintained even after elimination of the polymer. We discuss the mechanism of the formation of stable multi-cellular adhesion in terms of spontaneous rearrangement of the components embedded in the pair of facing membranes.

  20. Phosphorous dimerization in GaP high-pressure polymorph

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-06-01

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

  1. Dimerization inhibits the activity of receptor-like protein-tyrosine phosphatase-alpha

    DEFF Research Database (Denmark)

    Jiang, G; den Hertog, J; Su, J

    1999-01-01

    that dimerization can negatively regulate activity, through the interaction of an inhibitory 'wedge' on one monomer with the catalytic cleft of domain 1 in the other monomer. Here we show that dimerization inhibits the activity of a full-length RPTP in vivo. We generated stable disulphide-bonded full...

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

    DEFF Research Database (Denmark)

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

    2008-01-01

    . 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....

  3. Advances in Chemistry and Pharmacology of Triterpenoid Synthetic Dimers.

    Science.gov (United States)

    Bednarczyk-Cwynar, Barbara; Günther, Andrzej

    2017-01-01

    This review focuses on advances in chemistry and pharmacology of synthetic triterpenoid dimers, obtained from natural compounds. Synthetic triterpenoid dimers are divided into specific subgroups based on the structure of main triterpenoid monomeric skeleton. Synthetic triterpenoid derivatives of dimeric structure can be obtained through the covalent linkage of the C-3 hydroxyl or another group, via the C-2 atom or the C-17 carboxyl group (mainly anhydrides, amides or esters). Some triterpenes can undergo chemical transformations leading to the formation of cyclic dimers or other types of dimers. Most of the obtained triterpenoid dimers have been subjected to pharmacological tests evaluating their biological activity, mainly antiviral (HIV-1 RT, HCVpp, VSVpp, HIV-RT-C8166-CCR5), cytotoxic (against e.g. 388, MCF-7, SF-268, NCIH460, KM20L2, DU-145, Hep-G2, A549, BGC-823, PC-3), anti-inflammatory (iNOS, RAW 264.7) and antidiabetic (RMGPa inhibition). The authors also reported the ability of some of the obtained cyclic triterpenoid dimers to recognize anions and to form self-assembled structures. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  4. Dimerization and oligomerization of the chaperone calreticulin

    DEFF Research Database (Denmark)

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

    2003-01-01

    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...... that favour partial unfolding or an intramolecular local conformational change that allows oligomerization, resulting in a heterogeneous mixture of oligomers consisting of up to 10 calreticulin monomers. The oligomeric calreticulin was very stable, but oligomerization was partially reversed by addition of 8 m...

  5. Cold molecules: formation, trapping and spectroscopy. - Piling up of cesium dimers in a quadrupolar magnetic trap. - Spectroscopy by lack of photo-association; Molecules froides: formation, piegeage et spectroscopie. - Accumulation de dimeres de cesium dans un piege quadrupolaire magnetique. - Spectroscopie par frustration de photoassociation

    Energy Technology Data Exchange (ETDEWEB)

    Vanhaecke, N

    2003-10-15

    This thesis deals with the study of cold molecules obtained through the cold atom photo-association technique. Our study is focused both on manipulating external degrees of freedom of these Cs{sub 2} molecules and on studying their internal interactions. A quadrupolar magnetic trap of about 2.10{sup 5} cold Cs{sub 2} molecules is demonstrated. The trap lifetime is on the order of 600 ms, mainly limited by the background gas pressure. The trapped molecules are identified, which allows the determination of the trapped molecule cloud temperature, which is about 35 {mu}K. A dipolar trap is set up by the use of a focused CO{sub 2} laser beam. Moreover, this thesis describes a two-photon photo-association spectroscopy. We report the first study of two-photon photo-association line shapes, which exhibit typical Fano profiles. Taking advantage of the detailed understanding of these line shapes, we measure over one hundred high-lying level energies with an accuracy on the order of 10 MHz. Then we interpret theoretically these energies. The huge hyperfine structure of the Cesium atom binds us to solve a coupled channel Schroedinger equation for internuclear distances above 15 a{sub 0}. Hence we use an asymptotic theory to fit the potential parameters of the Cs{sub 2} dimer. We adjust those parameters by the mean of both evolutionary strategies and deterministic optimum seeking. This is followed by a careful statistics study, which leads to a very accurate determination of the Vander Waals coefficient. Moreover we report the first experimental determination of the exchange interaction amplitude. (author)

  6. Amyloid beta dimers/trimers potently induce cofilin-actin rods that are inhibited by maintaining cofilin-phosphorylation

    Directory of Open Access Journals (Sweden)

    Podlisny Marcia

    2011-01-01

    Full Text Available Abstract Background Previously we reported 1 μM synthetic human amyloid beta1-42 oligomers induced cofilin dephosphorylation (activation and formation of cofilin-actin rods within rat hippocampal neurons primarily localized to the dentate gyrus. Results Here we demonstrate that a gel filtration fraction of 7PA2 cell-secreted SDS-stable human Aβ dimers and trimers (Aβd/t induces maximal neuronal rod response at ~250 pM. This is 4,000-fold more active than traditionally prepared human Aβ oligomers, which contain SDS-stable trimers and tetramers, but are devoid of dimers. When incubated under tyrosine oxidizing conditions, synthetic human but not rodent Aβ1-42, the latter lacking tyrosine, acquires a marked increase (620 fold for EC50 in rod-inducing activity. Gel filtration of this preparation yielded two fractions containing SDS-stable dimers, trimers and tetramers. One, eluting at a similar volume to 7PA2 Aβd/t, had maximum activity at ~5 nM, whereas the other, eluting at the void volume (high-n state, lacked rod inducing activity at the same concentration. Fractions from 7PA2 medium containing Aβ monomers are not active, suggesting oxidized SDS-stable Aβ1-42 dimers in a low-n state are the most active rod-inducing species. Aβd/t-induced rods are predominantly localized to the dentate gyrus and mossy fiber tract, reach significance over controls within 2 h of treatment, and are reversible, disappearing by 24 h after Aβd/t washout. Overexpression of cofilin phosphatases increase rod formation when expressed alone and exacerbate rod formation when coupled with Aβd/t, whereas overexpression of a cofilin kinase inhibits Aβd/t-induced rod formation. Conclusions Together these data support a mechanism by which Aβd/t alters the actin cytoskeleton via effects on cofilin in neurons critical to learning and memory.

  7. Effect of Built-Up Edge Formation during Stable State of Wear in AISI 304 Stainless Steel on Machining Performance and Surface Integrity of the Machined Part.

    Science.gov (United States)

    Ahmed, Yassmin Seid; Fox-Rabinovich, German; Paiva, Jose Mario; Wagg, Terry; Veldhuis, Stephen Clarence

    2017-10-25

    During machining of stainless steels at low cutting -speeds, workpiece material tends to adhere to the cutting tool at the tool-chip interface, forming built-up edge (BUE). BUE has a great importance in machining processes; it can significantly modify the phenomenon in the cutting zone, directly affecting the workpiece surface integrity, cutting tool forces, and chip formation. The American Iron and Steel Institute (AISI) 304 stainless steel has a high tendency to form an unstable BUE, leading to deterioration of the surface quality. Therefore, it is necessary to understand the nature of the surface integrity induced during machining operations. Although many reports have been published on the effect of tool wear during machining of AISI 304 stainless steel on surface integrity, studies on the influence of the BUE phenomenon in the stable state of wear have not been investigated so far. The main goal of the present work is to investigate the close link between the BUE formation, surface integrity and cutting forces in the stable sate of wear for uncoated cutting tool during the cutting tests of AISI 304 stainless steel. The cutting parameters were chosen to induce BUE formation during machining. X-ray diffraction (XRD) method was used for measuring superficial residual stresses of the machined surface through the stable state of wear in the cutting and feed directions. In addition, surface roughness of the machined surface was investigated using the Alicona microscope and Scanning Electron Microscopy (SEM) was used to reveal the surface distortions created during the cutting process, combined with chip undersurface analyses. The investigated BUE formation during the stable state of wear showed that the BUE can cause a significant improvement in the surface integrity and cutting forces. Moreover, it can be used to compensate for tool wear through changing the tool geometry, leading to the protection of the cutting tool from wear.

  8. Effect of Built-Up Edge Formation during Stable State of Wear in AISI 304 Stainless Steel on Machining Performance and Surface Integrity of the Machined Part

    Science.gov (United States)

    Fox-Rabinovich, German; Wagg, Terry

    2017-01-01

    During machining of stainless steels at low cutting -speeds, workpiece material tends to adhere to the cutting tool at the tool–chip interface, forming built-up edge (BUE). BUE has a great importance in machining processes; it can significantly modify the phenomenon in the cutting zone, directly affecting the workpiece surface integrity, cutting tool forces, and chip formation. The American Iron and Steel Institute (AISI) 304 stainless steel has a high tendency to form an unstable BUE, leading to deterioration of the surface quality. Therefore, it is necessary to understand the nature of the surface integrity induced during machining operations. Although many reports have been published on the effect of tool wear during machining of AISI 304 stainless steel on surface integrity, studies on the influence of the BUE phenomenon in the stable state of wear have not been investigated so far. The main goal of the present work is to investigate the close link between the BUE formation, surface integrity and cutting forces in the stable sate of wear for uncoated cutting tool during the cutting tests of AISI 304 stainless steel. The cutting parameters were chosen to induce BUE formation during machining. X-ray diffraction (XRD) method was used for measuring superficial residual stresses of the machined surface through the stable state of wear in the cutting and feed directions. In addition, surface roughness of the machined surface was investigated using the Alicona microscope and Scanning Electron Microscopy (SEM) was used to reveal the surface distortions created during the cutting process, combined with chip undersurface analyses. The investigated BUE formation during the stable state of wear showed that the BUE can cause a significant improvement in the surface integrity and cutting forces. Moreover, it can be used to compensate for tool wear through changing the tool geometry, leading to the protection of the cutting tool from wear. PMID:29068405

  9. Effect of Built-Up Edge Formation during Stable State of Wear in AISI 304 Stainless Steel on Machining Performance and Surface Integrity of the Machined Part

    Directory of Open Access Journals (Sweden)

    Yassmin Seid Ahmed

    2017-10-01

    Full Text Available During machining of stainless steels at low cutting -speeds, workpiece material tends to adhere to the cutting tool at the tool–chip interface, forming built-up edge (BUE. BUE has a great importance in machining processes; it can significantly modify the phenomenon in the cutting zone, directly affecting the workpiece surface integrity, cutting tool forces, and chip formation. The American Iron and Steel Institute (AISI 304 stainless steel has a high tendency to form an unstable BUE, leading to deterioration of the surface quality. Therefore, it is necessary to understand the nature of the surface integrity induced during machining operations. Although many reports have been published on the effect of tool wear during machining of AISI 304 stainless steel on surface integrity, studies on the influence of the BUE phenomenon in the stable state of wear have not been investigated so far. The main goal of the present work is to investigate the close link between the BUE formation, surface integrity and cutting forces in the stable sate of wear for uncoated cutting tool during the cutting tests of AISI 304 stainless steel. The cutting parameters were chosen to induce BUE formation during machining. X-ray diffraction (XRD method was used for measuring superficial residual stresses of the machined surface through the stable state of wear in the cutting and feed directions. In addition, surface roughness of the machined surface was investigated using the Alicona microscope and Scanning Electron Microscopy (SEM was used to reveal the surface distortions created during the cutting process, combined with chip undersurface analyses. The investigated BUE formation during the stable state of wear showed that the BUE can cause a significant improvement in the surface integrity and cutting forces. Moreover, it can be used to compensate for tool wear through changing the tool geometry, leading to the protection of the cutting tool from wear.

  10. Theoretical investigation on the 2e/12c bond and second hyperpolarizability of azaphenalenyl radical dimers: Strength and effect of dimerization

    Science.gov (United States)

    Zhong, Rong-Lin; Xu, Hong-Liang; Sun, Shi-Ling; Qiu, Yong-Qing; Zhao, Liang; Su, Zhong-Min

    2013-09-01

    An increasing number of chemists have focused on the investigations of two-electron/multicenter bond (2e/mc) that was first introduced to describe the structure of radical dimers. In this work, the dimerization of two isoelectronic radicals, triazaphenalenyl (TAP) and hexaazaphenalenyl (HAP) has been investigated in theory. Results show TAP2 is a stable dimer with stronger 2e/12c bond and larger interaction energy, while HAP2 is a less stable dimer with larger diradical character. Interestingly, the ultraviolet-visible absorption spectra suggest that the dimerization induces a longer wavelength absorption in visible area, which is dependent on the strength of dimerization. Significantly, the amplitude of second hyperpolarizability (γyyyy) of HAP2 is 1.36 × 106 a.u. that is larger than 7.79 × 104 a.u. of TAP2 because of the larger diradical character of HAP2. Therefore, the results indicate that the strength of radical dimerization can be effectively detected by comparing the magnitude of third order non-linear optical response, which is beneficial for further theoretical and experimental studies on the properties of complexes formed by radical dimerization.

  11. Characterization of Hepatitis C Virus Core Protein Dimerization by Atomic Force Microscopy.

    Science.gov (United States)

    Li, Wenhui; Kou, Xiaolong; Xu, Jiachao; Zhou, Wei; Zhao, Rong; Zhang, Zhen; Fang, Xiaohong

    2018-03-14

    Dimerization of core protein is a crucial step in the formation of the hepatitis C virus (HCV) nucleocapsid, and inhibition of dimer formation is regarded as an attractive approach to design anti-HCV drugs. In this work, we developed the atomic force microscopy based single molecular force spectroscopy (AFM-SMFS) method for the characterization of core protein dimerization with the advantages of small amount of sample consumption and no need of labeling. Interaction force of the core protein with its antibody or aptamer was analyzed to investigate its stoichiometry and binding property. The two specific binding forces were detected due to the probing of dimeric and monomeric core protein, respectively. Moreover, the binding property of protein dimer was different from the monomer. Our work offers a new approach to study the dimerization of core protein, as well as other proteins, and to screen the HCV candidate inhibitors.

  12. Dimerization of 3He in 3He-4He mixture films

    International Nuclear Information System (INIS)

    Bashkin, E.

    1994-01-01

    3 He atoms dissolved in superfluid 4 He may form dimers ( 3 He) 2 in two-dimensional geometries. Dimer formation is studied in films of dilute 3 He- 4 He mixture. After designing a schematic 3 He- 3 He interaction potential, the dimer binding energy is calculated for various substrates. It is shown that 3 He impurity states localized near the substrate give rise to the highest magnitudes of the binding energy. (author). 32 refs., 6 figs.,; 1 tab

  13. X-ray crystallographic analysis and DFT calculations of three 'propylene linker' dimers linked by one polystep reaction

    Science.gov (United States)

    Shi, Yan; Tan, Xue-Jie; Xing, Dian-Xiang; Sui, Qi-Cheng; Liu, Bin; Feng, Wen-Quan; Liu, Yun

    2017-06-01

    In this manuscript, we report the synthesis, NMR and single-crystal structures of three propylene linking dimers related with the hydrolytic degradation of one 5,6-dehydronorcantharimide dimer. Special attention was paid to the conformation of propylene linkers in order to understand their changes in the reaction. Statistical analysis of CSD database revealed that a-a, g-a and g-g conformations may have similar stability in most cases and various complicated unpredictable non-covalent interactions may play important role in the formation of final rotamers. In order to reproduce all stable conformations and the energy barriers separating them, full range two-dimensional fully relaxed potential-energy surfaces (PES) scans of six 'propylene linker' dimers were calculated starting from the most stable crystal structures. The PES were scanned along both bridge Csbnd C single bond torsional angles (denoted as θ1 and θ2), while all other internal coordinates were optimized at the DFT/B3LYP/3-21G* level in gas phase. Then all energy minima were re-optimized again at the DFT/B3LYP/6-311 + G(d,p) level both in gas and ethanol solutions in order to evaluate the really stable rotamers. At last, 1D or 2D relaxed PES scans were performed between local stable rotamers to get reliable energy barriers. This method represents a less time-consuming and more reliable approach to the determination of conformational stability of propanediyl bridging chains. The combination of experimental, statistical and theoretical results shows that the observed conformation is jointly determined by the energy levels of the minima, energy barriers separating them, non-covalent interactions and somewhat randomness.

  14. Photo association in metastable helium in the vicinity of the Bose-Einstein condensation and production of giant dimers; Photo-association de l'helium metastable au voisinage de la condensation de Bose-Einstein et formation de dimeres geants

    Energy Technology Data Exchange (ETDEWEB)

    Leonard, J

    2003-11-15

    In the vicinity of Bose-Einstein condensation, the collisional properties of a dilute gas of metastable helium (He{sub 2}{sup 3}S) are governed by the rate of ionizing Penning collisions and the s-wave scattering length. In order to investigate these properties, we have carried out new photo-association experiments in which a pair of free atoms absorbs a photon to produce a molecule in an excited electronic state. In particular, we have observed 'giant dimers' for which the autoionizing process is inhibited. Accurate spectra have been acquired by the use of an original 'calorimetric' detection scheme. In addition, we have calculated long-range electronic potentials for the 2{sup 3} S + 2{sup 3} P system. Our asymptotic approach is described in detail, which reproduces the measured binding energies of the giant dimers with very good accuracy. (author)

  15. Dimerization Efficiency of Canine Distemper Virus Matrix Protein Regulates Membrane-Budding Activity.

    Science.gov (United States)

    Bringolf, Fanny; Herren, Michael; Wyss, Marianne; Vidondo, Beatriz; Langedijk, Johannes P; Zurbriggen, Andreas; Plattet, Philippe

    2017-08-15

    effective vaccines, both measles virus (MeV) and canine distemper virus (CDV) still lead to significant human and animal mortality worldwide. It is assumed that postexposure prophylaxis with specific antiviral compounds may synergize with vaccination campaigns to better control ongoing epidemics. Targeting the matrix (M) protein of MeV/CDV is attractive, because M coordinates viral assembly and egress through interaction with multiple cellular and viral components. However, the lack of basic molecular knowledge of how M orchestrates these functions precludes the rational design of antivirals. Here we combined structure-guided mutagenesis with cellular, biochemical, and functional assays to investigate a potential correlation between CDV M self-assembly and virus-like particle (VLP) formation. Altogether, our findings provide evidence that stable M dimers at the cell periphery are required to productively trigger VLPs. Such stabilized M dimeric units may facilitate further assembly into robust higher-order oligomers necessary to promote plasma membrane-budding activity. Copyright © 2017 American Society for Microbiology.

  16. Short lived maleimide triplet dimers. Kinetics and consequences

    International Nuclear Information System (INIS)

    Von Sonntag, J.

    2002-01-01

    Complete text of publication follows. The photochemistry of maleimide in non-aqueous solution is governed by the coexistence of two different triplet states, the keto triplet and a dimer triplet. This biradical is formed in the reaction of the keto triplet adding to the double bond of a ground state maleimide, in competition with electron transfer, (k 3 MI+MI = 2.6 x 10 9 dm 3 mol -1 s -1 ). Its spectrum is identical with that of the maleimide H-adduct radical (λ max = 370 ... 380 nm, broad, λ max = 255 nm, narrow, λ min = 290 nm). Its lifetime is 110 ns. While protolysis is confined to maleimide and aqueous solutions, the dimer triplet is found in acetonitrile as well. Dimer triplet formation is also observed with N-ethylmaleimide. Multi-wavelength 'global' analysis of the time profiles allowed us to separate the transient spectra and kinetics of the monomer and dimer triplet. The cyclobutane dimer yield (determined by GC) is independent of maleimide concentration. This proves that the dimer triplet does not contribute significantly to the initiation of a free-radical polymerisation. Time-dependent Hartree-Fock calculations agree with the experimental data and further confirm the proposed mechanisms

  17. Phosphorylcholine functionalized dendrimers for the formation of highly stable and reactive gold nanoparticles and their glucose conjugation for biosensing

    Energy Technology Data Exchange (ETDEWEB)

    Jia Lan; Lv Liping; Xu Jianping, E-mail: jianping_xu@zju.edu.cn; Ji Jian, E-mail: jijian@zju.edu.cn [Zhejiang University, Department of Polymer Science and Engineering, MOE Key Laboratory of Macromolecular Synthesis and Functionalization (China)

    2011-09-15

    Phosphorylcholine (PC)-functionalized poly(amido amine) (PAMAM) dendrimers were prepared and used as both reducing and stabilizing agents for synthesis of highly stable and reactive gold nanoparticles (Au NPs). Biomimetic PC-functionalized PAMAM dendrimers-stabilized gold nanoparticles (Au DSNPs) were formed by simply mixing the PC modified amine-terminated fifth-generation PAMAM dendrimers (G5-PC) with AuCl{sub 4}{sup -} ions by controlling the pH, no additional reducing agents or other stabilizers were needed. The obtained Au DSNPs were shown to be spherical, with particle diameters ranging from 5 to 12 nm, the sizes and growth kinetics of Au DSNPs could be tuned by changing the pH and the initial molar ratio of dendrimers to gold as indicated by transmission electron microscopy (TEM) and UV-Vis data. The prepared Au DSNPs showed excellent stability including: (1) stable at wide pH (7-13) values; (2) stable at high salt concentrations up to 2 M NaCl; (3) non-specific protein adsorption resistance. More importantly, surface functionalization could be performed by introducing desired functional groups onto the remained reactive amine groups. This was exemplified by the glucose conjugation. The glucose conjugated Au DSNPs showed bio-specific interaction with Concanavalin A (Con A), which induced aggregation of the Au NPs. Colorimetric detection of Con A based on the plasmon resonance of the glucose conjugated Au DSNPs was realized. A limit of detection (LOD) for Con A was 0.6 {mu}M, based on a signal-to-noise ratio (S/N) of 3. These findings demonstrated that the PC modified Au DSNPs could potentially serve as a versatile nano-platform for the biomedical applications.

  18. Fraction-specific controls on the trace element distribution in iron formations : Implications for trace metal stable isotope proxies

    NARCIS (Netherlands)

    Oonk, Paul B.H.; Tsikos, Harilaos; Mason, Paul R.D.; Henkel, Susann; Staubwasser, Michael; Fryer, Lindi; Poulton, Simon W.; Williams, Helen M.

    2017-01-01

    Iron formations (IFs) are important geochemical repositories that provide constraints on atmospheric and ocean chemistry, prior to and during the onset of the Great Oxidation Event. Trace metal abundances and their Mo-Cr-U isotopic ratios have been widely used for investigating ocean redox processes

  19. Quantitative evaluation of ruminal methane and carbon dioxide formation from formate through C-13 stable isotope analysis in a batch culture system.

    Science.gov (United States)

    He, Z X; Qiao, J Y; Yan, Q X; Tan, Z L; Wang, M

    2018-04-12

    Methane produced from formate is one of the important methanogensis pathways in the rumen. However, quantitative information of CH4 production from formate has been rarely reported. The aim of this study was to characterize the conversion rate (CR) of formic acid into CH4 and CO2 by rumen microorganisms. Ground lucerne hay was incubated with buffered ruminal fluid for 6, 12, 24 and 48 h. Before the incubation, 13C-labeled H13COOH was also supplied into the incubation bottle at a dose of 0, 1.5, 2.2 or 2.9 mg/g of DM substrate. There were no interactions (P>0.05) between dose and incubation time for all variables evaluated. When expressed as an absolute amount (ml in gas sample) or a relative CR (%), both 13CH4 and 13CO2 production quadratically increased (P<0.01) with the addition of H13COOH. The total 13C (13CH4 and 13CO2) CR was also quadratically increased (P<0.01) when H13COOH was added. Moreover, formate addition linearly decreased (P<0.031) the concentrations of NH3-N, total and individual volatile fatty acids (acetate, propionate and butyrate), and quadratically decreased (P<0.014) the populations of protozoa, total methanogens, Methanosphaera stadtmanae, Methanobrevibacter ruminantium M1, Methanobrevibacter smithii and Methanosarcina barkeri. In summary, formate affects ruminal fermentation and methanogenesis, as well as the rumen microbiome, in particular microorganisms which are directly or indirectly involved in ruminal methanogenesis. This study provides quantitative verification for the rapid dissimilation of formate into CH4 and CO2 by rumen microorganisms.

  20. Enhancing bio-availability of β-naphthoflavone by supramolecular complexation with 6,6'-thiobis(methylene)-β-cyclodextrin dimer.

    Science.gov (United States)

    Choi, Jae Min; Cho, Eunae; Lee, Benel; Jeong, Daham; Choi, Youngjin; Yu, Jae-Hyuk; Jung, Seunho

    2016-10-20

    The aryl hydrocarbon receptor (AhR) is a ligand activated transcriptional regulator, which governs key biological processes including detoxification of carcinogens. β-Naphthoflavone (β-NF) is a non-toxic flavonoid, and a potent AhR agonist. Thus, β-NF can induce the representative detoxifying enzyme cytochrome P4501A1, thereby enhancing the detoxification potential. However, its low water solubility hampers the use. We found that supramolecular complexation of β-NF with the synthetic 6,6'-thiobis(methylene)-β-cyclodextrin (β-CD-S) dimer significantly enhanced β-NF's role as an AhR agonist. The water solubility of β-NF was increased to 469 fold by effective supramolecular complexation with the β-CD-S dimer, and caused significant induction of cytochrome P4501A1. Stable formation of the supramolecular complex of β-NF with β-CD-S-dimer was verified by various analyses. In summary, supramolecular complexation of β-NF with β-CD-S dimer greatly enhanced bio-availability of β-NF as an AhR agonist. Our findings provide an easy, non-destructive, and alternative approach to enhance the bio-availability of therapeutics. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Highly stable triple helix formation by homopyrimidine (l)-acyclic threoninol nucleic acids with single stranded DNA and RNA

    DEFF Research Database (Denmark)

    Kumar, Vipin; Kesavan, Venkitasamy; Gothelf, Kurt Vesterager

    2015-01-01

    Acyclic (l)-threoninol nucleic acid (aTNA) containing thymine, cytosine and adenine nucleobases were synthesized and shown to form surprisingly stable triplexes with complementary single stranded homopurine DNA or RNA targets. The triplex structures consist of two (l)-aTNA strands and one DNA...... or RNA, and these triplexes are significantly stronger than the corresponding DNA or RNA duplexes as shown in competition experiments. As a unique property the (l)-aTNAs exclusively form triplex structures with DNA and RNA and no duplex structures are observed by gel electrophoresis. The results were...... compared to the known enantiomer (d)-aTNA, which forms much weaker triplexes depending upon temperature and time. It was demonstrated that (l)-aTNA triplexes are able to stop primer extension on a DNA template, showing the potential of (l)-aTNA for antisense applications....

  2. One-pot synthesis of polythiol ligand for highly bright and stable hydrophilic quantum dots toward bioconjugate formation

    Science.gov (United States)

    Dezhurov, Sergey V.; Krylsky, Dmitry V.; Rybakova, Anastasia V.; Ibragimova, Sagila A.; Gladyshev, Pavel P.; Vasiliev, Alexey A.; Morenkov, Oleg S.

    2018-03-01

    A fast and efficient one-pot synthesis of thiol-terminated poly(vinylpirrolidone-co-maleic anhydride-co-ethylene glycol dimethacrylate) based heterobifunctional polymer (PTVP) has been developed. The polymer was used for the modification of quantum dots (QDs) to prepare water soluble and stable QDs with emission quantum yield as high as 80%. Using carbodiimide method, PTVP-capped red light-emitting QDs were conjugated to model monoclonal antibodies specific to glycoprotein B (gB) of Aujeszky’s disease virus (ADV) and successfully used in the lateral flow assay (LFA) for the detection of ADV gB in biological fluids. A comparative analysis of the sensitivity of the method was carried out using three types of QDs emitting in the red and far-red region.

  3. Formation of stable direct current microhollow cathode discharge by venturi gas flow system for remote plasma source in atmosphere

    International Nuclear Information System (INIS)

    Park, Ki Wan; Lee, Tae Il; Hwang, Hyeon Seok; Noh, Joo Hyon; Baik, Hong Koo; Song, Kie Moon

    2008-01-01

    We introduce a microhollow cathode configuration with venturi gas flow to ambient air in order to obtain glow discharge at atmospheric pressure. Stable microhollow cathode discharge was formed in a 200 μm diameter at 9 mA and the optimum value of gas velocityxdiameter for hollow cathode effect was obtained in our system. In order to confirm hollow cathode effect, we measured the enhancement of E/N strength for 200 μm (0.31 m 2 /s) and 500 μm (0.78 m 2 /s) air discharge at 8 mA under the velocity of 156 m/s. As a result, an increase of 46.7% in E/N strength of the discharge of 200 μm hole was obtained compare to that of 500 μm

  4. Integrated high resolution stratigraphy of the Gurpi Formation (Late Cretaceous) in the Zagros Basin (Iran): Calcareous nannofossils, planktonic foraminifers, carbon and oxygen stable isotopes

    Science.gov (United States)

    Javad Razmjooei, Mohammad; Thibault, Nicolas; Kani, Anoshiravan; Dinarès-Turell, Jaume; Pucéat, Emmanuelle; Shahriari, Samira; Jamali, Amir Mohammad; Cocquerez, Théophile

    2017-04-01

    The Gurpi Formation (Fm.) consists of fossiliferous, alternating marls and marly limestones, spanning the Late Cretaceous to Paleocene in the NW to central part of the Zagros Basin. This formation was deposited in deep shelf to basin margin settings. A preliminary study of the calcareous nannofossil biostratigraphy and carbon and oxygen stable isotopes was already presented by Razmjooei et al. (2014) on the Shahneshin section (Shahneshin anticline) which corresponds to open marine, upper bathyal depositional environments. However this study was at a relatively low resolution and the section was not presented with a detailed sedimentology. The ca. 350 m long Gurpi Fm. of the Shahneshin section has been re-logged in detail in 2016 and a new high resolution study has been carried out, spanning the middle Coniacian to early Danian. Here, we present the result of this new investigation that integrates the biostratigraphy of calcareous nannofossils (based on 165 samples), that of planktonic foraminifers (62 samples) and carbon and oxygen stable isotopes (353 samples) along with a comprehensive panorama and detailed log of the section. A large number of carbon isotope excursions previously defined by Jarvis et al. (2006) and Thibault et al. (2016) have been identified in the section and can be correlated to the Gubbio record, which is the standard reference for the southwestern Tethys. Our new high resolution study constitutes a new reference for Late Cretaceous sediments of the eastern Tethys.

  5. The role of dimerization in prion replication.

    Science.gov (United States)

    Tompa, Peter; Tusnády, Gábor E; Friedrich, Peter; Simon, István

    2002-04-01

    The central theme in prion diseases is the conformational transition of a cellular protein from a physiologic to a pathologic (so-called scrapie) state. Currently, two alternative models exist for the mechanism of this autocatalytic process; in the template assistance model the prion is assumed to be a monomer of the scrapie conformer, whereas in the nucleated polymerization model it is thought to be an amyloid rod. A recent variation on the latter assumes disulfide reshuffling as the mechanism of polymerization. The existence of stable dimers, let alone their mechanistic role, is not taken into account in either of these models. In this paper we review evidence supporting that the dimerization of either the normal or the scrapie state, or both, has a decisive role in prion replication. The contribution of redox changes, i.e., the temporary opening and possible rearrangement of the intramolecular disulfide bridge is also considered. We present a model including these features largely ignored so far and show that it adheres satisfactorily to the observed phenomenology of prion replication.

  6. Experimental and Theoretical Study of the Rotation of Si Ad-dimers on the Si(100) Surface

    DEFF Research Database (Denmark)

    Swartzentruber, B. S.; Smith, A. P.; Jonsson, Hannes

    1996-01-01

    Scanning tunneling microscopy measurements and first principles density functional theory calculations are used to study the rate of the rotational transition of Si ad-dimers on top of the surface dimer rows of Si(100). The rotation rate and the relative population of the two stable orientations ...

  7. Comparative DFT study of van der Waals complexes: rare-gas dimers, alkaline-earth dimers, zinc dimer, and zinc-rare-gas dimers.

    Science.gov (United States)

    Zhao, Yan; Truhlar, Donald G

    2006-04-20

    Recent interest in the application of density functional theory prompted us to test various functionals for the van der Waals interactions in the rare-gas dimers, the alkaline-earth metal dimers, zinc dimer, and zinc-rare-gas dimers. In the present study, we report such tests for 18 DFT functionals, including both some very recent functionals and some well-established older ones. We draw the following conclusions based on the mean errors in binding energies and complex geometries: (1) B97-1 gives the best performance for predicting the geometry of rare-gas dimers, whereas M05-2X and B97-1 give the best energetics for rare-gas dimers. (2) PWB6K gives the best performance for the prediction of the geometry of the alkaline-earth metal dimers, zinc dimers, and zinc-rare-gas dimers. M05-2X gives the best energetics for the metal dimers, whereas B97-1 gives the best energetics for the zinc-rare-gas dimers. (3) The M05 functional is unique in providing good accuracy for both covalent transition-metal dimers and van der Waals metal dimers. (4) The combined mean percentage unsigned error in geometries and energetics shows that M05-2X and MPWB1K are the overall best methods for the prediction of van der Waals interactions in metal and rare-gas van der Waals dimers.

  8. THE FORMATION OF ECOLOGICAL AND ECONOMIC COMPETENCES IN THE CONTEXT OF THE STABLE DEVELOPMENT OF THE CARPATHIAN REGION

    Directory of Open Access Journals (Sweden)

    Volodymyr Khymynets

    2015-04-01

    Full Text Available The paper deals with the peculiarities of the formation of ecological and economic competences at modern school. The paper shows that ecological and economic education is continuous and uninterrupted psychological process which is directed towards the formation of knowledge, culture and consciousness of a person. Attention is paid to the problems of environmental and economic situation in the Carpathian region of Ukraine. Ecological and economic model of education can develop effectively only on the basis of humanistic orientation and innovation potential of the educational institution. The humanization provides increased attention to the individual as a whole, the promotion of its abilities, physical and moral qualities. Modern education aims to form environmentally and economically responsible person, that is ready for the conscious activity on the basis of the gained knowledge and formes behavioral norms and rules concerning the environment. Humanity has the ability to choose either the path of environmental and economic education, or the path of the global catastrophe and self-destruction. Civilized, cultured people are called to protect and multiply the good, by laws and authority to establish the highest spiritual values of the life in the society and public opinion. Only intelligence and environmental and economic culture, that is continuous educational training and educational activity, may generate culture of society, relevant to the permanent development, and transfer its relationships with the environment on the way of intelligent coexistence.

  9. Carbonate Mineral Formation on Mars: Clues from Stable Isotope Variation Seen in Cryogenic Laboratory Studies of Carbonate Salts

    Science.gov (United States)

    Socki, Richard; Niles, Paul B.; Sun, Tao; Fu, Qi; Romanek, Christopher S.; Gibson, Everett K.

    2013-01-01

    The geologic history of water on the planet Mars is intimately connected to the formation of carbonate minerals through atmospheric CO2 and its control of the climate history of Mars. Carbonate mineral formation under modern martian atmospheric conditions could be a critical factor in controlling the martian climate in a means similar to the rock weathering cycle on Earth. The combination of evidence for liquid water on the martian surface and cold surface conditions suggest fluid freezing could be very common on the surface of Mars. Cryogenic calcite forms readily when a rise in pH occurs as a result of carbon dioxide degassing quickly from freezing Ca-bicarbonate-rich water solutions. This is a process that has been observed in some terrestrial settings such as arctic permafrost cave deposits, lakebeds of the Dry Valleys of Antarctica, and in aufeis (river icings) from rivers of N.E. Alaska. We report here the results of a series of laboratory experiments that were conducted to simulate potential cryogenic carbonate formation on the planet Mars. These results indicate that carbonates grown under martian conditions (controlled atmospheric pressure and temperature) show enrichments from starting bicarbonate fluids in both carbon and oxygen isotopes beyond equilibrium values with average delta13C(DIC-CARB) values of 20.5%0 which exceed the expected equilibrium fractionation factor of [10(sup 3) ln alpha = 13%0] at 0 degC. Oxygen isotopes showed a smaller enrichment with delta18O(H2O-CARB) values of 35.5%0, slightly exceeding the equilibrium fractionation factor of [10(sup 3) ln alpha = 34%0 ] at 0degC. Large kinetic carbon isotope effects during carbonate precipitation could substantially affect the carbon isotope evolution of CO2 on Mars allowing for more efficient removal of 13C from the Noachian atmosphere enriched by atmospheric loss. This mechanism would be consistent with the observations of large carbon isotope variations in martian materials despite the

  10. Adventures in Holographic Dimer Models

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-08-12

    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.

  11. Dimerization in Highly Concentrated Solutions of Phosphoimidazolide Activated Monomucleotides

    Science.gov (United States)

    Kanavarioti, Anastassia

    1997-08-01

    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.

  12. Hydrogen spillover in Pt-single-walled carbon nanotube composites: formation of stable C-H bonds.

    Science.gov (United States)

    Bhowmick, Ranadeep; Rajasekaran, Srivats; Friebel, Daniel; Beasley, Cara; Jiao, Liying; Ogasawara, Hirohito; Dai, Hongjie; Clemens, Bruce; Nilsson, Anders

    2011-04-13

    Using in situ electrical conductivity and ex situ X-ray photoelectron spectroscopy (XPS) measurements, we have examined how the hydrogen uptake of single-walled carbon nanotubes (SWNTs) is influenced by the addition of Pt nanoparticles. The conductivity of platinum-sputtered single-walled carbon nanotubes (Pt-SWNTs) during molecular hydrogen exposure decreased more rapidly than that of the corresponding pure SWNTs, which supports a hydrogenation mechanism facilitated by "spillover" of dissociated hydrogen from the Pt nanoparticles. C 1s XPS spectra indicate that the Pt-SWNTs store hydrogen by means of chemisorption, that is, covalent C-H bond formation: molecular hydrogen charging at elevated pressure (8.27 bar) and room temperature yielded Pt-SWNTs with up to 16 ± 1.5 at. % sp(3)-hybridized carbon atoms, which corresponds to a hydrogen-storage capacity of 1.2 wt % (excluding the weight of Pt nanoparticles). Pt-SWNTs prepared by the Langmuir-Blodgett (LB) technique exhibited the highest Pt/SWNT ratio and also the best hydrogen uptake. © 2011 American Chemical Society

  13. New orientation formation and growth during primary recrystallization in stable single crystals of three face-centred cubic metals

    International Nuclear Information System (INIS)

    Miszczyk, M.; Paul, H.; Driver, J.H.; Maurice, C.

    2015-01-01

    Graphical abstract: For Ni, Cu and Cu-2%Al and (1 1 0)[0 0 −1] and (1 1 0)[1 −1 −2] initial orientations at the initial stages of recrystallization, the appearance of a specific number of new orientation groups of new grains has been demonstrated. The orientation relations across the recrystallization front are characterized by a high proportion of angles in the range 25–35° and 45–55° around axes mostly grouped about the 〈1 2 2〉, 〈1 1 1〉, 〈1 2 3〉 and 〈1 1 2〉 directions. A local minimum was noted for the disorientation angle densities close to 40° in all cases. For a single isolated nucleus of uniform orientation, the rotation axes are usually grouped around one of the normals of all four {1 1 1} planes but do not (or only rarely) coincide with them. The orientation of the growing new grain quickly transforms through the formation of a first generation twins. The most frequent situation occurs when the normal of the twinning face plane is situated near the rotation axis, around which the crystal lattice of the ‘primary nuclei’ rotates. Based on the anisotropy of grain growth a possible mechanism of orientation generation and grain growth by thermally activation movement of dislocation families, on {1 1 1} planes is proposed. - Abstract: The early stages of recrystallization have been systematically characterized in single crystal metals of medium and low stacking fault energy. Goss {1 1 0}〈0 0 1〉 and brass {1 1 0}〈1 1 2〉 oriented samples of Ni, Cu and Cu–2 wt.% Al alloy were deformed in a channel die to a logarithmic strain of 0.51 to develop a homogeneous structure composed of two sets of symmetrical primary microbands and then lightly annealed. Scanning electron microscopy/electron backscattered diffraction analyses demonstrate a strong relation between as-deformed orientations and the limited number of recrystallized grain orientations. The disorientation angles across the recrystallization front are mostly grouped in

  14. Kinetics of DNA tile dimerization.

    Science.gov (United States)

    Jiang, Shuoxing; Yan, Hao; Liu, Yan

    2014-06-24

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

  15. Dynamics and energetics of Ge(001) dimers

    NARCIS (Netherlands)

    van Houselt, Arie; van Gastel, Raoul; Poelsema, Bene; Zandvliet, Henricus J.W.

    2006-01-01

    The dynamic behavior of surface dimers on Ge(001) has been studied by positioning the tip of a scanning tunneling microscope over single flip-flopping dimers and measuring the tunneling current as a function of time. We observe that not just symmetric, but also asymmetric appearing dimers exhibit

  16. Interaction between Nbp35 and Cfd1 proteins of cytosolic Fe-S cluster assembly reveals a stable complex formation in Entamoeba histolytica.

    Directory of Open Access Journals (Sweden)

    Shadab Anwar

    Full Text Available Iron-Sulfur (Fe-S proteins are involved in many biological functions such as electron transport, photosynthesis, regulation of gene expression and enzymatic activities. Biosynthesis and transfer of Fe-S clusters depend on Fe-S clusters assembly processes such as ISC, SUF, NIF, and CIA systems. Unlike other eukaryotes which possess ISC and CIA systems, amitochondriate Entamoeba histolytica has retained NIF & CIA systems for Fe-S cluster assembly in the cytosol. In the present study, we have elucidated interaction between two proteins of E. histolytica CIA system, Cytosolic Fe-S cluster deficient 1 (Cfd1 protein and Nucleotide binding protein 35 (Nbp35. In-silico analysis showed that structural regions ranging from amino acid residues (P33-K35, G131-V135 and I147-E151 of Nbp35 and (G5-V6, M34-D39 and G46-A52 of Cfd1 are involved in the formation of protein-protein complex. Furthermore, Molecular dynamic (MD simulations study suggested that hydrophobic forces surpass over hydrophilic forces between Nbp35 and Cfd1 and Van-der-Waal interaction plays crucial role in the formation of stable complex. Both proteins were separately cloned, expressed as recombinant fusion proteins in E. coli and purified to homogeneity by affinity column chromatography. Physical interaction between Nbp35 and Cfd1 proteins was confirmed in vitro by co-purification of recombinant Nbp35 with thrombin digested Cfd1 and in vivo by pull down assay and immunoprecipitation. The insilico, in vitro as well as in vivo results prove a stable interaction between these two proteins, supporting the possibility of its involvement in Fe-S cluster transfer to target apo-proteins through CIA machinery in E. histolytica. Our study indicates that initial synthesis of a Fe-S precursor in mitochondria is not necessary for the formation of Cfd1-Nbp35 complex. Thus, Cfd1 and Nbp35 with the help of cytosolic NifS and NifU proteins can participate in the maturation of non-mitosomal Fe-S proteins

  17. Rubidium dimers in paraffin-coated cells

    International Nuclear Information System (INIS)

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

    2010-01-01

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

  18. Electron transfer reactions induced by the triplet state of thiacarbocyanine dimers

    International Nuclear Information System (INIS)

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

    2004-01-01

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

  19. Dynamic Trap Formation and Elimination in Colloidal Quantum Dots

    KAUST Repository

    Voznyy, O.

    2013-03-21

    Using first-principles simulations on PbS and CdSe colloidal quantum dots, we find that surface defects form in response to electronic doping and charging of the nanoparticles. We show that electronic trap states in nanocrystals are dynamic entities, in contrast with the conventional picture wherein traps are viewed as stable electronic states that can be filled or emptied, but not created or destroyed. These traps arise from the formation or breaking of atomic dimers at the nanoparticle surface. The dimers\\' energy levels can reside within the bandgap, in which case a trap is formed. Fortunately, we are also able to identify a number of shallow-electron-affinity cations that stabilize the surface, working to counter dynamic trap formation and allowing for trap-free doping. © 2013 American Chemical Society.

  20. Fiber optic D dimer biosensor

    Science.gov (United States)

    Glass, Robert S.; Grant, Sheila A.

    1999-01-01

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

  1. Competitive Energy and Electron Transfer in β-Functionalized Free-Base Porphyrin-Zinc Porphyrin Dimer Axially Coordinated to C60: Synthesis, Supramolecular Formation and Excited-State Processes.

    Science.gov (United States)

    Hu, Yi; Thomas, Michael B; Jinadasa, R G Waruna; Wang, Hong; D'Souza, Francis

    2017-09-18

    Simultaneous occurrence of energy and electron transfer events involving different acceptor sites in a newly assembled supramolecular triad comprised of covalently linked free-base porphyrin-zinc porphyrin dyad, H 2 P-ZnP axially coordinated to electron acceptor fullerene, has been successfully demonstrated. The dyad was connected through the β-pyrrole positions of the porphyrin macrocycle instead of the traditionally used meso-positions for better electronic communication. Interestingly, the β-pyrrole functionalization modulated the optical properties to such an extent that it was possible to almost exclusively excite the zinc porphyrin entity in the supramolecular triad. The measured binding constant for the complex with 1:1 molecular stoichiometry was in the order of 10 4  m -1 revealing moderately stable complex formation. An energy level diagram constructed using optical, electrochemical and computational results suggested that both the anticipated energy and electron events are thermodynamically feasible in the triad. Consequently, it was possible to demonstrate occurrence of excited state energy transfer to the covalently linked H 2 P, and electron transfer to the coordinated ImC 60 from studies involving steady-state and time-resolved emission, and femto- and nanosecond transient absorption studies. The estimated energy transfer was around 67 % in the dyad with a rate constant of 1.1×10 9  s -1 . In the supramolecular triad, the charge separated state was rather long-lived although it was difficult to arrive the exact lifetime of charge separated state from nanosecond transient spectral studies due to overlap of strong triplet excited signals of porphyrin in the monitoring wavelength window. Nevertheless, simultaneous occurrence of energy and electron transfer in the appropriately positioned energy and electron acceptor entities in a supramolecular triad was possible to demonstrate in the present study, a step forward to unraveling the complex

  2. Dissociative attachment to lithium dimers

    International Nuclear Information System (INIS)

    Wadehra, J.M.

    1987-01-01

    The cross sections and the rates of production of negative ions of atomic lithium by the process of dissociative electron attachment to lithium dimers are obtained by using the resonant scattering theory. Both the cross sections as well as the rates of attachment are enhanced if the lithium molecule is initially vibrationally excited. General expressions for approximately obtaining the rates of electron attachment to any vibrational level of Li 2 are presented

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

    Science.gov (United States)

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

    2016-08-01

    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.

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

    Science.gov (United States)

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

    2015-01-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Sarah N Ramsook

    Full Text Available Group E members of the SOX transcription factor family include SOX8, SOX9, and SOX10. Preceding the high mobility group (HMG domain in each of these proteins is a thirty-eight amino acid region that supports the formation of dimers on promoters containing tandemly inverted sites. The purpose of this study was to obtain new structural insights into how the dimerization region functions with the HMG domain. From a mutagenic scan of the dimerization region, the most essential amino acids of the dimerization region were clustered on the hydrophobic face of a single, predicted amphipathic helix. Consistent with our hypothesis that the dimerization region directly contacts the HMG domain, a peptide corresponding to the dimerization region bound a preassembled HMG-DNA complex. Sequence conservation among Group E members served as a basis to identify two surface exposed amino acids in the HMG domain of SOX9 that were necessary for dimerization. These data were combined to make a molecular model that places the dimerization region of one SOX9 protein onto the HMG domain of another SOX9 protein situated at the opposing site of a tandem promoter. The model provides a detailed foundation for assessing the impact of mutations on SOX Group E transcription factors.

  6. Mechanism of HIV reverse transcriptase inhibition by zinc: formation of a highly stable enzyme-(primer-template) complex with profoundly diminished catalytic activity.

    Science.gov (United States)

    Fenstermacher, Katherine J; DeStefano, Jeffrey J

    2011-11-25

    Several physiologically relevant cations including Ca(2+), Mn(2+), and Zn(2+) have been shown to inhibit HIV reverse transcriptase (RT), presumably by competitively displacing one or more Mg(2+) ions bound to RT. We analyzed the effects of Zn(2+) on reverse transcription and compared them to Ca(2+) and Mn(2+). Using nucleotide extension efficiency as a readout, Zn(2+) showed significant inhibition of reactions with 2 mM Mg(2+), even when present at only ∼5 μM. Mn(2+) and Ca(2+) were also inhibitory but at higher concentrations. Both Mn(2+) and Zn(2+) (but not Ca(2+)) supported RT incorporation in the absence of Mg(2+) with Mn(2+) being much more efficient. The maximum extension rates with Zn(2+), Mn(2+), and Mg(2+) were ∼0.1, 1, and 3.5 nucleotides per second, respectively. Zinc supported optimal RNase H activity at ∼25 μM, similar to the optimal for nucleotide addition in the presence of low dNTP concentrations. Surprisingly, processivity (average number of nucleotides incorporated in a single binding event with enzyme) during reverse transcription was comparable with Zn(2+) and Mg(2+), and single RT molecules were able to continue extension in the presence of Zn(2+) for several hours on the same template. Consistent with this result, the half-life for RT-Zn(2+)-(primer-template) complexes was 220 ± 60 min and only 1.7 ± 1 min with Mg(2+), indicating ∼130-fold more stable binding with Zn(2+). Essentially, the presence of Zn(2+) promotes the formation of a highly stable slowly progressing RT-(primer-template) complex.

  7. Structure of a Rabbit Muscle Fructose-1,6-Bisphosphate Aldolase A Dimer Variant

    Energy Technology Data Exchange (ETDEWEB)

    Sherawat,M.; Tolan, D.; Allen, K.

    2008-01-01

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

  8. Temporal and spatial variations in the diagenetic fabrics and stable isotopes of Pleistocene corals from the Ironshore Formation of Grand Cayman, British West Indies

    Science.gov (United States)

    Li, Rong; Jones, Brian

    2013-03-01

    On Grand Cayman, the unconformity bounded Units A to F in the Ironshore Formation represent repeated cycles of deposition and subaerial exposure that were associated with the dramatic oscillations in sea levels that characterized the Middle to Late Pleistocene. Montastrea annularis and Acropora palmata, the dominant corals found in Units A to F in the Rogers Wreck Point area and offshore George Town area, reflect these changes with their complex mosaics of marine (aragonite cements, bioerosion, internal sediments) and meteoric (calcitization of coral skeleton, dissolution) diagenetic features. The distribution of the diagenetic fabrics throughout this sequence, however, is not predictable. The randomness in the degree of skeletal calcitization is shown by the lack of systematic variation in calcitization from Units A to F, and the fact that the degree of skeletal calcification in M. annularis is higher than that in A. palmata in the Rogers Wreck Point area but less than in A. palmata in the George Town cores. The stable isotope compositions (δ13C, δ18O) of the corals from Units A to F plot along the same trend line with their positions on that trend reflecting the amount of meteoric diagenesis they have undergone. The variable styles and degrees of diagenesis evident in the corals from the Ironshore Formation reflect (1) the variable impact of intrinsic (e.g., skeletal architecture, porosity of coral) and extrinsic (e.g., sea level, climate) factors during each phase of diagenesis, and (2) temporal effects associated with the diagenetic overprinting that took place during each successive phase of diagenesis. This means that the diagenetic fabrics are not stratigraphically ordered and that it is impossible to correlate specific diagenetic phases with specific sea level lowstands or highstands.

  9. Designer interface peptide grafts target estrogen receptor alpha dimerization

    International Nuclear Information System (INIS)

    Chakraborty, S.; Asare, B.K.; Biswas, P.K.; Rajnarayanan, R.V.

    2016-01-01

    The nuclear transcription factor estrogen receptor alpha (ERα), triggered by its cognate ligand estrogen, regulates a variety of cellular signaling events. ERα is expressed in 70% of breast cancers and is a widely validated target for anti-breast cancer drug discovery. Administration of anti-estrogen to block estrogen receptor activation is still a viable anti-breast cancer treatment option but anti-estrogen resistance has been a significant bottle-neck. Dimerization of estrogen receptor is required for ER activation. Blocking ERα dimerization is therefore a complementary and alternative strategy to combat anti-estrogen resistance. Dimer interface peptide “I-box” derived from ER residues 503–518 specifically blocks ER dimerization. Recently using a comprehensive molecular simulation we studied the interaction dynamics of ERα LBDs in a homo-dimer. Based on this study, we identified three interface recognition peptide motifs LDKITDT (ERα residues 479–485), LQQQHQRLAQ (residues 497–506), and LSHIRHMSNK (residues 511–520) and reported the suitability of using LQQQHQRLAQ (ER 497–506) as a template to design inhibitors of ERα dimerization. Stability and self-aggregation of peptide based therapeutics poses a significant bottle-neck to proceed further. In this study utilizing peptide grafted to preserve their pharmacophoric recognition motif and assessed their stability and potential to block ERα mediated activity in silico and in vitro. The Grafted peptides blocked ERα mediated cell proliferation and viability of breast cancer cells but did not alter their apoptotic fate. We believe the structural clues identified in this study can be used to identify novel peptidometics and small molecules that specifically target ER dimer interface generating a new breed of anti-cancer agents. - Highlights: • Designer peptide grafts retain core molecular recognition motif during MD simulations. • Designer peptide grafts with Poly-ALA helix form stable

  10. Designer interface peptide grafts target estrogen receptor alpha dimerization

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, S. [Laboratory of Computational Biophysics & Bioengineering, Department of Physics, Tougaloo College, Tougaloo, MS 39174 (United States); Asare, B.K. [Department of Pharmacology and Toxicology, University of Buffalo, Buffalo, NY 14214 (United States); Biswas, P.K., E-mail: pbiswas@tougaloo.edu [Laboratory of Computational Biophysics & Bioengineering, Department of Physics, Tougaloo College, Tougaloo, MS 39174 (United States); Rajnarayanan, R.V., E-mail: rajendra@buffalo.edu [Department of Pharmacology and Toxicology, University of Buffalo, Buffalo, NY 14214 (United States)

    2016-09-09

    The nuclear transcription factor estrogen receptor alpha (ERα), triggered by its cognate ligand estrogen, regulates a variety of cellular signaling events. ERα is expressed in 70% of breast cancers and is a widely validated target for anti-breast cancer drug discovery. Administration of anti-estrogen to block estrogen receptor activation is still a viable anti-breast cancer treatment option but anti-estrogen resistance has been a significant bottle-neck. Dimerization of estrogen receptor is required for ER activation. Blocking ERα dimerization is therefore a complementary and alternative strategy to combat anti-estrogen resistance. Dimer interface peptide “I-box” derived from ER residues 503–518 specifically blocks ER dimerization. Recently using a comprehensive molecular simulation we studied the interaction dynamics of ERα LBDs in a homo-dimer. Based on this study, we identified three interface recognition peptide motifs LDKITDT (ERα residues 479–485), LQQQHQRLAQ (residues 497–506), and LSHIRHMSNK (residues 511–520) and reported the suitability of using LQQQHQRLAQ (ER 497–506) as a template to design inhibitors of ERα dimerization. Stability and self-aggregation of peptide based therapeutics poses a significant bottle-neck to proceed further. In this study utilizing peptide grafted to preserve their pharmacophoric recognition motif and assessed their stability and potential to block ERα mediated activity in silico and in vitro. The Grafted peptides blocked ERα mediated cell proliferation and viability of breast cancer cells but did not alter their apoptotic fate. We believe the structural clues identified in this study can be used to identify novel peptidometics and small molecules that specifically target ER dimer interface generating a new breed of anti-cancer agents. - Highlights: • Designer peptide grafts retain core molecular recognition motif during MD simulations. • Designer peptide grafts with Poly-ALA helix form stable

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

    DEFF Research Database (Denmark)

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

    2012-01-01

    An ingenious system evolved to facilitate insulin binding to the insulin receptor as a monomer and at the same time ensure sufficient stability of insulin during storage. Insulin dimer is the cornerstone of this system. Insulin dimer is relatively weak, which ensures dissociation into monomers...... 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...

  12. Fe65-PTB2 Dimerization Mimics Fe65-APP Interaction

    Directory of Open Access Journals (Sweden)

    Lukas P. Feilen

    2017-05-01

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

  13. Ortho and para hydrogen dimers on G/SiC(0001): combined STM and DFT study.

    Science.gov (United States)

    Merino, P; Švec, M; Martínez, J I; Mutombo, P; Gonzalez, C; Martín-Gago, J A; de Andres, P L; Jelinek, P

    2015-01-01

    The hydrogen (H) dimer structures formed upon room-temperature H adsorption on single layer graphene (SLG) grown on SiC(0001) are addressed using a combined theoretical-experimental approach. Our study includes density functional theory (DFT) calculations for the full (6√3 × 6√3)R30° unit cell of the SLG/SiC(0001) substrate and atomically resolved scanning tunneling microscopy images determining simultaneously the graphene lattice and the internal structure of the H adsorbates. We show that H atoms normally group in chemisorbed coupled structures of different sizes and orientations. We make an atomic scale determination of the most stable experimental geometries, the small dimers and ellipsoid-shaped features, and we assign them to hydrogen adsorbed in para dimers and ortho dimers configuration, respectively, through comparison with the theory.

  14. Modern rather than Mesoarchaean oxidative weathering responsible for the heavy stable Cr isotopic signatures of the 2.95 Ga old Ijzermijn iron formation (South Africa)

    Science.gov (United States)

    Albut, Gülüm; Babechuk, Michael G.; Kleinhanns, Ilka C.; Benger, Manuela; Beukes, Nicolas J.; Steinhilber, Bernd; Smith, Albertus J. B.; Kruger, Stephanus J.; Schoenberg, Ronny

    2018-05-01

    Previously reported stable Cr isotopic fractionation in Archaean paleosols and iron formations (IFs) have been interpreted as a signature of oxidative weathering of Cr(III) to Cr(VI) in soils, and delivery of isotopically heavy Cr(VI) into the oceans. One of the oldest reported fingerprints of this process is isotopically heavy Cr preserved in the 2.95 Ga old Ijzermijn IF, Sinqeni Formation of the Mozaan Group (Pongola Supergroup), South Africa and could suggest that atmospheric free oxygen was present ca. 600 million years earlier than the Great Oxidation Event (GOE). However, fractionated stable Cr isotopic signatures have only been found to date in surface outcrop samples of the White Mfolozi Inlier exposed along the White Mfolozi River Gorge. In this study, the latter outcrop was resampled along with two drill cores of the Ijzermijn IF and a drill core of the Scotts Hill IF to represent multiple exposures of Mozaan Group IFs with different states of preservation. A detailed geochemical comparison on bulk samples of different units was undertaken using stable Cr isotopes coupled with trace and major elements. Outcrop iron-rich mudstones (Fe - lutites) show very low LOI [wt] %, and very low Fe(II)/Fetot ratios, and lower Ca and Mg relative to equivalent facies in drill cores, indicating the effects that oxidative recent surface weathering had on Fe/Mn-rich carbonate minerals of the IF. Overall rare earth element and yttrium (REE + Y) mixing models agree well with previous studies, confirming that they were minimally disturbed by weathering and are consistent with a high magnitude of continental solutes delivered in a near-shore depositional environment, with a minor contribution of hydrothermally derived fluids that upwelled into shallower depositional setting. Importantly, all drill core samples of this study revealed δ53/52Cr values within the igneous inventory, despite variable amounts of detrital Cr input that includes nearly detritus-free, chert

  15. Stable carbon isotopes and lipid biomarkers provide new insight into the formation of calcite and siderite concretions in organic-matter rich deposits

    Science.gov (United States)

    Baumann, Lydia; Birgel, Daniel; Wagreich, Michael; Peckmann, Jörn

    2015-04-01

    Carbonate concretions from two distinct settings have been studied for their petrography, stable carbon and oxygen isotopes, and lipid biomarker content. Carbonate concretions are in large part products of microbial degradation of organic matter, as for example by sulfate-reducing bacteria, iron-reducing bacteria, and methanogenic archaea. For these prokaryotes certain lipid biomarkers such as hopanoids, terminally-branched fatty acids (bacteria) and isoprenoids (archaea) are characteristic. Two different types of concretions were studied: a) Upper Miocene septarian calcite concretions of the southern Vienna Basin embedded in brackish sediments represented by partly bituminous calcareous sands, silts and clays; b) Paleocene-Eocene siderite concretions enclosed in marine, sandy to silty turbidites with varying carbonate contents and marl layers from the Upper Gosau Subgroup in northern Styria. Calcite concretions consist of abundant calcite microspar (80-90 vol.%), as well as detrital minerals and iron oxyhydroxides. The septarian cracks show beginning cementation with dog-tooth calcite to varying degrees. Framboidal pyrite occurs in some of the calcite concretions, pointing to bacterial sulfate reduction. Siderite concretions consist of even finer carbonate crystals, mainly siderite (40-70 vol.%) but also abundant ferroan calcite, accompanied by iron oxyhydroxides and detrital minerals. The δ13C values of the calcite concretions (-6.8 to -4.1o ) most likely reflect a combination of bacterial organic matter oxidation and input of marine biodetrital carbonate. The δ18O values range from -8.9 to -7.8o agreeing with a formation within a meteoric environment. The surrounding host sediment shows about 1-2o higher δ13C and δ18O values. The siderite δ13C values (-11.1 to -7.5o ) point to microbial respiration of organic carbon and the δ18O values (-3.5 to +2.2o ) agree with a marine depositional environment. In contrast to the calcite concretions, the stable isotope

  16. Solitary waves in dimer binary collision model

    Science.gov (United States)

    Ahsan, Zaid; Jayaprakash, K. R.

    2017-01-01

    Solitary wave propagation in nonlinear diatomic (dimer) chains is a very interesting topic of research in the study of nonlinear lattices. Such waves were recently found to be supported by the essentially nonlinear granular lattice and Toda lattice. An interesting aspect of this discovery is attributed to the realization of a spectrum of the mass ratio (the only system parameter governing the dynamics) that supports the propagation of such waves corresponding to the considered interaction potential. The objective of this exposition is to explore solitary wave propagation in the dimer binary collision (BC) model. Interestingly, the dimer BC model supports solitary wave propagation at a discrete spectrum of mass ratios similar to those observed in granular and Toda dimers. Further, we report a qualitative and one-to-one correspondence between the spectrum of the mass ratio corresponding to the dimer BC model and those corresponding to granular and Toda dimer chains.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-05-01

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

  18. Energetics and structures of charged helium clusters: comparing stabilities of dimer and trimer cationic cores.

    Science.gov (United States)

    Marinetti, Fabio; Bodo, Enrico; Gianturco, Franco A; Yurtsever, Ersin

    2008-12-01

    We present accurate ab initio calculations of the most stable structures of He(n)(+) clusters in order to determine the more likely ionic core arrangements existing after reaching structural equilibrium of the clusters. Two potential energy surfaces are presented: one for the He(2)(+) and the other with the He(3)(+) linear ion, both interacting with one He atom. The two computed potentials are in turn employed within a classical structure optimization where the overall interaction forces are obtained within the sum-of-potentials approximation described in the main text. Because of the presence of many-body effects within the ionic core, we find that the arrangements with He(3)(+) as a core turn out to be energetically preferred, leading to the formation of He(3)(+)(He)(n-3) stable aggregates. Nanoscopic considerations about the relative stability of clusters with the two different cores are shown to give us new information on the dynamical processes observed in the impact ionization experiments of pure helium clusters and the importance of pre-equilibrium evaporation of the ionic dimers in the ionized clusters.

  19. Reactions between aromatic hydrocarbons and heterocycles: covalent and proton-bound dimer cations of benzene/pyridine.

    Science.gov (United States)

    El-Shall, M Samy; Ibrahim, Yehia M; Alsharaeh, Edreese H; Meot-Ner Mautner, Michael; Watson, Simon P

    2009-07-29

    negatively charged C atoms of the ring. In contrast, the more stable proton-bound PyH(+) x Py dimer contains a linear NH(+)...N hydrogen bond. The formation of the (benzene/pyridine)(*+) adduct may represent a general class of addition reactions that can form complex heterocyclic species in ionizing environments.

  20. Formation of new stable pigments from condensation reaction between malvidin 3-glucoside and (-)-epicatechin mediated by acetaldehyde: Effect of tartaric acid concentration.

    Science.gov (United States)

    Sun, Baoshan; Barradas, Tania; Leandro, Conceição; Santos, Cláudia; Spranger, Isabel

    2008-09-15

    The objective of this work was to study the effect of tartaric acid concentration on the condensation reaction between malvidin 3-glucoside (Mv-glc) and flavanols mediated by acetaldehyde in the model solution. The model wine solutions were prepared by 12% ethanol in water (v/v) with two different l-tartaric acid concentrations (5g/l and 25g/l, respectively) and at two different pH values (3.2 and 1.7, respectively). Four new pigments were detected in model wine solutions containing Mv-glc, (-)-epicatechin and acetaldehyde. By reverse-phase HPLC-DAD, ESI-MS and MS(n) fragmentation analysis, the four new pigments were tentatively identified as four isomers of hydroxyethyl malvidin-3-glucoside-ethyl-flavanol. The decrease in the concentration of Mv-glc and (-)-epicatechin and the increase in the concentration of the new identified pigments were more pronounced at higher tartaric acid concentration. At pH 1.7, although the two well-recognized ethyl-linked Mv-glc-flavanol isomers were quantitatively the major pigmented products in the reaction solution throughout the assay period, they appeared less stable than the four new pigments. At pH 3.2, the rate of formation of ethyl-linked Mv-glc-flavanol pigments was much slower than at pH 1.7, whereas the four new pigments were quantitatively the predominant pigmented products at the latter stage of the reaction. Copyright © 2008 Elsevier Ltd. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Jackie Penn

    2015-02-01

    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.

  2. Synergistic effect of signaling from receptors of soluble platelet agonists and outside-in signaling in formation of a stable fibrinogen-integrin αIIbβ3-actin cytoskeleton complex.

    Science.gov (United States)

    Budnik, Ivan; Shenkman, Boris; Savion, Naphtali

    2015-01-01

    Thrombus formation in the injured vessel wall is a highly complex process involving various blood-born components that go through specific temporal and spatial changes as observed by intravital videomicroscopy. Platelets bind transiently to the developing thrombus and may either become stably incorporated into or disengage from the thrombus. The aim of the present study was to reveal the processes involved in the formation of a stable thrombus. Platelet-rich plasma and washed platelets were studied by the aggregometer. The aggregate stability was challenged by eptifibatide. Platelet Triton-insoluble fraction was prepared and the actin and αIIb content in the cytoskeleton was analyzed by western blot. Maximal actin polymerization is achieved 1min after platelet activation while maximal αIIbβ3-actin cytoskeleton association requires 5 to 10min of activation and fibrinogen-mediated platelet-to-platelet bridging. Thus, actin polymerization is dependent on platelet activation and requires neither αIIbβ3 integrin occupation nor platelet aggregation. Formation of a stable aggregate requires platelet activation for more than 1min, complete increase in actin cytoskeleton fraction and partial association of αIIbβ3 with the actin cytoskeleton. However, direct αIIbβ3 activation is not sufficient for cytoskeleton complex formation. Thus, stable αIIbβ3-fibrinogen interaction, representing stable aggregate, is achieved after more than 1min agonist activation, involving inside-out and outside-in signaling but not after direct integrin activation, involving only outside-in signaling. Formation of a stable fibrinogen-αIIbβ3-actin cytoskeleton complex is the result of the combined effect of platelet stimulation by soluble agonists, activation of αIIbβ3, fibrinogen binding and platelet-to-platelet bridging. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-01-01

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

  4. Stable isotopes

    International Nuclear Information System (INIS)

    Evans, D.K.

    1986-01-01

    Seventy-five percent of the world's stable isotope supply comes from one producer, Oak Ridge Nuclear Laboratory (ORNL) in the US. Canadian concern is that foreign needs will be met only after domestic needs, thus creating a shortage of stable isotopes in Canada. This article describes the present situation in Canada (availability and cost) of stable isotopes, the isotope enrichment techniques, and related research programs at Chalk River Nuclear Laboratories (CRNL)

  5. Ultrabright Linearly Polarized Photon Generation from a Nitrogen Vacancy Center in a Nanocube Dimer Antenna

    DEFF Research Database (Denmark)

    Andersen, Sebastian Kim Hjælm; Kumar, Shailesh; Bozhevolnyi, Sergey I.

    2017-01-01

    We demonstrate an exceptionally bright photon source based on a single nitrogen-vacancy center (NV center) in a nanodiamond (ND) placed in the nanoscale gap between two monocrystalline silver cubes in a dimer configuration. The system is operated near saturation at a stable photon rate of 850 kcps...

  6. Enzymatic oxidative dimerization of silymarin flavonolignans

    Czech Academy of Sciences Publication Activity Database

    Gavezzotti, P.; Vavříková, Eva; Valentová, Kateřina; Fronza, G.; Kudanga, T.; Kuzma, Marek; Riva, S.; Biedermann, David; Křen, Vladimír

    2014-01-01

    Roč. 109, NOV 2014 (2014), s. 24-30 ISSN 1381-1177 R&D Projects: GA MŠk(CZ) LD13041; GA ČR(CZ) GP14-14373P Institutional support: RVO:61388971 Keywords : Silybin dimers * Silydianin dimer * Silymarin Subject RIV: CE - Biochemistry Impact factor: 2.128, year: 2014

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

    Energy Technology Data Exchange (ETDEWEB)

    Danielsen, E.M. (Univ. of Cophenhagen (Denmark))

    1990-01-09

    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.

  8. In vitro production of thymine dimer by ultroviolet irradiation of DNA from mesophilic and thermophilic bacteria

    International Nuclear Information System (INIS)

    Yein, F.S.; Stenesh, J.

    1989-01-01

    Thymine dimer was produced in vitro by ultraviolet irradiation of DNA, isolated from the mesophile Bacillus licheniformis and the thermophile B. stearothermophilus. Irradiation was performed at three different temperaturs (35, 45 and 55 C) and the thymine dimer was isolated and determined. An HPLC procedure was developed that permitted temperature was greater for the thermophile than for the mesophile. Formation of thymine dimer increased with temperature for both organisms but more so for the thermophile; over the temperature range of 35-55 C, the average increase in thymine dimer production for the themrophile was about 4-times that for the mesophile. The melting out temperature, as a function of increasing irradiation temperature, was essentially unchanged for the mesophilic DNA, but decreased progressively for the thermophilic DNA. These results are discussed in terms of the macromolecular theory of to the macromolecular theory of the thermophily. (author). 31 refs.; 4 figs.; 3 tabs

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

    DEFF Research Database (Denmark)

    Danielsen, E M

    1990-01-01

    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......The pig intestinal brush border enzymes aminopeptidase N (EC 3.4.11.2) and lactase-phlorizin hydrolase (EC 3.2.1.23-62) 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...

  10. Dimerization of the Glucan Phosphatase Laforin Requires the Participation of Cysteine 329

    Science.gov (United States)

    Sánchez-Martín, Pablo; Raththagala, Madushi; Bridges, Travis M.; Husodo, Satrio; Gentry, Matthew S.; Sanz, Pascual; Romá-Mateo, Carlos

    2013-01-01

    Laforin, encoded by a gene that is mutated in Lafora Disease (LD, OMIM 254780), is a modular protein composed of a carbohydrate-binding module and a dual-specificity phosphatase domain. Laforin is the founding member of the glucan-phosphatase family and regulates the levels of phosphate present in glycogen. Multiple reports have described the capability of laforin to form dimers, although the function of these dimers and their relationship with LD remains unclear. Recent evidence suggests that laforin dimerization depends on redox conditions, suggesting that disulfide bonds are involved in laforin dimerization. Using site-directed mutagenesis we constructed laforin mutants in which individual cysteine residues were replaced by serine and then tested the ability of each protein to dimerize using recombinant protein as well as a mammalian cell culture assay. Laforin-Cys329Ser was the only Cys/Ser mutant unable to form dimers in both assays. We also generated a laforin truncation lacking the last three amino acids, laforin-Cys329X, and this truncation also failed to dimerize. Interestingly, laforin-Cys329Ser and laforin-Cys329X were able to bind glucans, and maintained wild type phosphatase activity against both exogenous and biologically relevant substrates. Furthermore, laforin-Cys329Ser was fully capable of participating in the ubiquitination process driven by a laforin-malin complex. These results suggest that dimerization is not required for laforin phosphatase activity, glucan binding, or for the formation of a functional laforin-malin complex. Cumulatively, these results suggest that cysteine 329 is specifically involved in the dimerization process of laforin. Therefore, the C329S mutant constitutes a valuable tool to analyze the physiological implications of laforin’s oligomerization. PMID:23922729

  11. Directed diffusion of reconstituting dimers

    Energy Technology Data Exchange (ETDEWEB)

    Barma, Mustansir [Department of Theoretical Physics, Tata Institute of Fundamental Research, Mumbai 400005 (India); Grynberg, Marcelo D [Departamento de Fisica, Universidad Nacional de La Plata (1900) La Plata (Argentina); Stinchcombe, Robin B [Isaac Newton Institute for Mathematical Sciences, 20 Clarkson Road, Cambridge CB3 0EH (United Kingdom)

    2007-02-14

    We discuss the dynamical aspects of an asymmetric version of assisted diffusion of hard core particles on a ring studied by Menon et al (1997 J. Stat. Phys. 86 1237). The asymmetry brings in phenomena like kinematic waves and effects of the Kardar-Parisi-Zhang non-linearity, which combine with the feature of strongly broken ergodicity, a characteristic of the model. A central role is played by a single non-local invariant, the irreducible string, whose interplay with the driven motion of reconstituting dimers, arising from the assisted hopping, determines the asymptotic dynamics and scaling regimes. These are investigated both analytically and numerically through sector-dependent mappings to the asymmetric simple exclusion process.

  12. Structural and Vibrational Study on Monomer and Dimer Forms and Water Clusters of Acetazolamide

    Directory of Open Access Journals (Sweden)

    Aysen E. Ozel

    2013-01-01

    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.

  13. Neutral dipole-dipole dimers: A new field in science

    Science.gov (United States)

    Kosower, Edward M.; Borz, Galina

    2018-03-01

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

  14. Biocompatible Amphiphilic Hydrogel-Solid Dimer Particles as Colloidal Surfactants.

    Science.gov (United States)

    Chen, Dong; Amstad, Esther; Zhao, Chun-Xia; Cai, Liheng; Fan, Jing; Chen, Qiushui; Hai, Mingtan; Koehler, Stephan; Zhang, Huidan; Liang, Fuxin; Yang, Zhenzhong; Weitz, David A

    2017-12-26

    Emulsions of two immiscible liquids can slowly coalesce over time when stabilized by surfactant molecules. Pickering emulsions stabilized by colloidal particles can be much more stable. Here, we fabricate biocompatible amphiphilic dimer particles using a hydrogel, a strongly hydrophilic material, and achieve large contrast in the wetting properties of the two bulbs, resulting in enhanced stabilization of emulsions. We generate monodisperse single emulsions of alginate and shellac solution in oil using a flow-focusing microfluidics device. Shellac precipitates from water and forms a solid bulb at the periphery of the droplet when the emulsion is exposed to acid. Molecular interactions result in amphiphilic dimer particles that consist of two joined bulbs: one hydrogel bulb of alginate in water and the other hydrophobic bulb of shellac. Alginate in the hydrogel compartment can be cross-linked using calcium cations to obtain stable particles. Analogous to surfactant molecules at the interface, the resultant amphiphilic particles stand at the water/oil interface with the hydrogel bulb submerged in water and the hydrophobic bulb in oil and are thus able to stabilize both water-in-oil and oil-in-water emulsions, making these amphiphilic hydrogel-solid particles ideal colloidal surfactants for various applications.

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

    DEFF Research Database (Denmark)

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

    2005-01-01

    denaturing conditions at pH 2.3, helix conformations are still populated in 24% of the ensemble of molecules. The structure of HA4 at atomic resolution was assessed using nuclear magnetic resonance (NMR) spectroscopy. Long-range NOEs between remote residues at opposite peptide ends suggested the formation...... 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...

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

    Directory of Open Access Journals (Sweden)

    Ivana Biljan

    2017-12-01

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

  17. Effects of Cd{sup 2+} on cis-dimer structure of E-cadherin in living cells

    Energy Technology Data Exchange (ETDEWEB)

    Takeda, Hiroshi, E-mail: hirotake@sapmed.ac.jp

    2014-02-21

    Highlights: • The effects of Cd on the dimer of cadherin in living cells was analyzed. • Cd induced cadherin dimer formation was not detected in living cell with low Ca. • Ca mediated structural cooperativity and allostery in the native cadherin. • Ca concentration-dependent competitive displacement of Cd from cadherin is proposed. - Abstract: E-cadherin, a calcium (Ca{sup 2+})-dependent cell–cell adhesion molecule, plays a key role in the maintenance of tissue integrity. We have previously demonstrated that E-cadherin functions in vivo as a cis-dimer through chemical cross-linking reagents. Ca{sup 2+} plays an important role in the cis-dimer formation of cadherin. However, the molecular mechanisms by which Ca{sup 2+} interacts with the binding sites that regulate cis-dimer structures have not been completely elucidated. As expected for a Ca{sup 2+} antagonist, cadmium (Cd{sup 2+}) disrupts cadherin function by displacing Ca{sup 2+} from its binding sites on the cadherin molecules. We used Cd{sup 2+} as a probe for investigating the role of Ca{sup 2+} in the dynamics of the E-cadherin extracellular region that involve cis-dimer formation and adhesion. While cell–cell adhesion assembly was completely disrupted in the presence of Cd{sup 2+}, the amount of cis-dimers of E-cadherin that formed at the cell surface was not affected. In our “Cd{sup 2+}-switch” experiments, we did not find that Cd{sup 2+}-induced E-cadherin cis-dimer formation in EL cells when they were incubated in low-Ca{sup 2+} medium. In the present study, we demonstrated for the first time the effects of Cd{sup 2+} on the cis-dimer structure of E-cadherin in living cells using a chemical cross-link analysis.

  18. Biotransformation and Cytotoxic Activity of Guaiacol Dimer

    Directory of Open Access Journals (Sweden)

    Galuh Widiyarti

    2014-07-01

    Full Text Available Guaiacol, a phenolic compound is known as an anticancer. Dimerization of guaiacol has been done by biotransformation using peroxidase enzyme as biocatalyst. This enzyme was isolated from Indonesian plant, kailan (Brassica oleraceae var. alboglabra. Analysis of dimerization product was carried out by TLC, IR, LC-MS, and NMR. Whilst analysis of in-vitro cytotoxic activity was carried out by MTT method against breast cancer T47D and MCF7 cells. The result showed that the dimerization reaction gave O-para dehydroguaiacol. The in-vitro cytotoxic activity analysis showed that O-para dehydroguaiacol compound has potency as anti-breast cancer.

  19. Analysis of pyrimidine dimer content of isolated DNA by nuclease digestion

    International Nuclear Information System (INIS)

    Farland, W.H.; Sutherland, B.M.

    1980-01-01

    Isolated DNA is highly susceptible to degradation by exogenous nucleases. Complete digestion is possible with a number of well-characterized enzymes from a variety of sources. Treatment of DNA with a battery of enzymes including both phosphodiesterase and phosphatase activities yields a mixture of nucleosides and inorganic phosphate (P/sub i/) as a final product. Unlike native DNA, ultraviolet-irradiated DNA is resistant to complete digestion. Setlow et al. demonstrated that the structural changes in the DNA responsible for the nuclease resistance were the formation of cyclobutyl pyrimidine dimers, the major photoproduct in UV-irradiated DNA. Using venom phosphodiesterase, they demonstrated that UV irradiation of DNA affected both the rate and extent of enzymatic hydrolysis. In addition, it was demonstrated that the major nuclease-resistant product of this hydrolysis was an oligonucleotide containing dimerized pyrimidines. Treatment of the DNA to split the dimers, either photochemically or photoenzymatically, rendered the polymer more susceptible to hydrolysis by the phosphodiesterase. The specificity of photoreactivating enzyme for pyrimidine dimers lends support to the role of these structures in conferring nuclease resistance to UV-irradiated DNA. The nuclease resistance of DNA containing dimers has been the basis of several assays for the measurement of these photoproducts. Sutherland and Chamberlin reported the development of a rapid and sensitive assay for dimers in 32 P-labeled DNA

  20. Quantitation of pyrimidine dimers in DNA from UVB-irradiated alfalfa (Medicago sativa L.) seedlings

    International Nuclear Information System (INIS)

    Quaite, F.E.; Sutherland, B.M.; Sutherland, J.C.

    1991-01-01

    Depletion of stratospheric ozone will increase the solar ultraviolet radiation in the range from 290-320 nm (UVB) that reaches the surface of the earth, placing an increased UV burden on exposed organisms. One consequence of increased UVB may be decreased productivity of crop plants. A principal lesion caused by UV in DNA is the cyclobutyl pyrimidine dimer. We have adapted a method for measuring these dimers in nanogram quantities of non-radioactive DNA for use in UV-irradiated plants. We find that biologically relevant doses of broad band UVB radiation induce easily detectable frequencies of pyrimidine dimers in the DNA of irradiated alfalfa sprout leaves and that the dose response for dimer formation is linear up to doses of at least 690 J/m 2 . We also find easily measurable frequencies of dimers in the leaves of seedlings grown in glass filtered sunlight but not exposed to additional UVB, suggesting that significant number of dimers are formed in plants exposed to normal sunlight. 27 refs., 3 figs., 1 tab

  1. Elucidation of cladofulvin biosynthesis reveals a cytochrome P450 monooxygenase required for anthraquinone dimerization.

    Science.gov (United States)

    Griffiths, Scott; Mesarich, Carl H; Saccomanno, Benedetta; Vaisberg, Abraham; De Wit, Pierre J G M; Cox, Russell; Collemare, Jérôme

    2016-06-21

    Anthraquinones are a large family of secondary metabolites (SMs) that are extensively studied for their diverse biological activities. These activities are determined by functional group decorations and the formation of dimers from anthraquinone monomers. Despite their numerous medicinal qualities, very few anthraquinone biosynthetic pathways have been elucidated so far, including the enzymatic dimerization steps. In this study, we report the elucidation of the biosynthesis of cladofulvin, an asymmetrical homodimer of nataloe-emodin produced by the fungus Cladosporium fulvum A gene cluster of 10 genes controls cladofulvin biosynthesis, which begins with the production of atrochrysone carboxylic acid by the polyketide synthase ClaG and the β-lactamase ClaF. This compound is decarboxylated by ClaH to yield emodin, which is then converted to chrysophanol hydroquinone by the reductase ClaC and the dehydratase ClaB. We show that the predicted cytochrome P450 ClaM catalyzes the dimerization of nataloe-emodin to cladofulvin. Remarkably, such dimerization dramatically increases nataloe-emodin cytotoxicity against mammalian cell lines. These findings shed light on the enzymatic mechanisms involved in anthraquinone dimerization. Future characterization of the ClaM enzyme should facilitate engineering the biosynthesis of novel, potent, dimeric anthraquinones and structurally related compound families.

  2. Synthesis of new dimeric carvacrol compounds

    Directory of Open Access Journals (Sweden)

    Uttam B. More

    2008-12-01

    Full Text Available The polymer supported carvacrol anion was reacted with 1,2-dibromoethane, 1,4-dibromoethane, oxalyl dichloride, malonyl dichloride, succinyl dichloride, glutaroyl dichloride, and adipoyl dichloride to afford the corresponding dimeric carvacryl ethers or esters

  3. Laccase-mediated dimerization of the flavonolignan silybin

    Czech Academy of Sciences Publication Activity Database

    Gažák, Radek; Sedmera, Petr; Marzorati, M.; Riva, S.; Křen, Vladimír

    2008-01-01

    Roč. 50, 2-4 (2008), s. 87-92 ISSN 1381-1177 R&D Projects: GA AV ČR KJB400200701; GA MŠk OC D25.001; GA MŠk(CZ) LC06010; GA MŠk OC 170; GA MŠk ME 922 Grant - others:CZ(CZ) Bilateral Czech-Italian inter-academic projec Institutional research plan: CEZ:AV0Z50200510 Keywords : silybin * silymarin * dimer formation Subject RIV: EE - Microbiology, Virology Impact factor: 2.015, year: 2008

  4. Dimerization of Carboxylic Acids: An Equation of State Approach

    DEFF Research Database (Denmark)

    Tsivintzelis, Ioannis; Kontogeorgis, Georgios; Panayiotou, Costas

    2017-01-01

    The association term of the nonrandom hydrogen bonding theory, which is an equation of state model, is extended to describe the dimerization of carboxylic acids in binary mixtures with inert solvents and in systems of two different acids. Subsequently, the model is applied to describe the excess....... Consequently, the observed endothermic dissolution process is mainly attributed to the hindering of polar interactions. Furthermore, upon mixing of two carboxylic acids, the rearrangement of hydrogen bonds due to the formation of cross associating species results in an insignificant contribution to the heats...

  5. Dimerization of 3He in 3He-4He dilute mixtures filling narrow channels

    International Nuclear Information System (INIS)

    Bashkin, Eugene P.; Wojdylo, John

    2000-01-01

    We consider dimerization of 3 He in a dilute solution of 3 He in superfluid 4 He filling straight narrow channels that can be found in nanoscale porous media. Dimer formation is facilitated by the restricted geometry and occurs despite the fact that in bulk fluid the interparticle interaction is too weak to lead to a bound state. Dimerization results in the effective 'bosonization' of the system: a Bose quantum fluid of ( 3 He) 2 arises in place of the 3 He Fermi component. At high temperatures, when the 3 He impurity quasiparticles form a Maxwell-Boltzmann gas, a drastic change in the thermodynamics occurs due to the presence of dimers. The specific heat and magnetic susceptibility of the 3 He component, which we calculate at arbitrary degrees of dimerization, show a marked deviation from behavior expected of an undimerized 3 He component. We show that the binding energy--which depends on the channel width--is expected to be sufficiently high to make experimental observation feasible. The presence of ( 3 He) 2 dimers gives rise to an extra absorption mechanism for first sound propagating through the superfluid 4 He, due to resonant absorption and decay of dimers in the acoustic field. We have calculated the absorption coefficient. Several experiments suggest themselves, utilizing, perhaps, K-L zeolites or carbon nanotubes. If the dimers themselves turn out to be attractive, then quadrumers may appear: it may even be the case that a single 3 He polymer will form over the entire length of the channel

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

    Science.gov (United States)

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

    2006-06-01

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

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

    Science.gov (United States)

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

    2015-05-27

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

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

    Science.gov (United States)

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

    2015-01-01

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

  9. Counterions control whether self-assembly leads to formation of stable and well-defined unilamellar nanotubes or nanoribbons and nanorods

    DEFF Research Database (Denmark)

    Shi, Dong; Schwall, Christian; Sfintes, George

    2014-01-01

    Self-assembly of the amphiphilic π-conjugated carbenium ion ATOTA-1(+) in aqueous solution selectively leads to discrete and highly stable nanotubes or nanoribbons and nanorods, depending on the nature of the counterion (Cl(-) vs. PF6(-), respectively). The nanotubes formed by the Cl(-) salt...

  10. Eutectic Gallium-Indium (EGaIn) : A Liquid Metal Alloy for the Formation of Stable Structures in Microchannels at Room Temperature

    NARCIS (Netherlands)

    Dickey, Michael D.; Chiechi, Ryan C.; Larsen, Ryan J.; Weiss, Emily A.; Weitz, David A.; Whitesides, George M.

    2008-01-01

    This paper describes the rheological behavior of the liquid metal eutectic gallium-indium (EGaIn) as it is injected into microfluidic channels to form stable microstructures of liquid metal. EGaIn is well-suited for this application because of its rheological properties at room temperature: it

  11. Dimerization of HNO in aqueous solution: an interplay of solvation effects, fast acid-base equilibria, and intramolecular hydrogen bonding?

    Science.gov (United States)

    Fehling, Carsten; Friedrichs, Gernot

    2011-11-09

    The recent unraveling of the rather complex acid-base equilibrium of nitroxyl (HNO) has stimulated a renewed interest in the significance of HNO for biology and pharmacy. HNO plays an important role in enzymatic mechanisms and is discussed as a potential therapeutic agent against heart failure. A cumbersome property for studying HNO reactions, its fast dimerization leading to the rapid formation of N(2)O, is surprisingly far from being well understood. It prevents isolation and limits intermediate concentrations of nitroxyl in solution. In this study, a new mechanism for the HNO dimerization reaction in aqueous solution has been theoretically derived on the basis of DFT calculations. Detailed analysis of the initial reaction step suggests a reversal of the cis-trans isomer preference in solution compared to the corresponding gas phase reaction. In contrast to a gas phase derived model based on intramolecular rearrangement steps, an acid-base equilibrium model is in agreement with previous experimental findings and, moreover, explains the fundamental differences between the well studied gas phase reaction and the solvent reaction in terms of polarity, cis-trans isomerizations, and acidities of the intermediates. In the case of cis-hyponitrous acid, the calculated pK(a) values of the acid-base equilibria were found to be significantly different from the corresponding experimental value of the stable trans isomer. Under physiological conditions, N(2)O formation is dominated by the decomposition of the unstable monoanion cis-N(2)O(2)H(-) rather than that of the commonly stated cis-HONNOH.

  12. Theoretical analysis of the domain-swapped dimerization of cytochrome c: An MD and 3D-RISM approach

    Science.gov (United States)

    Yoshida, Norio; Higashi, Masahiro; Motoki, Hideyoshi; Hirota, Shun

    2018-01-01

    The structural stability of a cytochrome c domain-swapped dimer compared with that of the monomer was investigated by molecular dynamics (MD) simulations and by three-dimensional reference interaction site model (3D-RISM) theory. The structural fluctuation and structural energy of cytochrome c were treated by MD simulations, and the solvation thermodynamics was treated by 3D-RISM theory. The domain-swapped dimer state is slightly less stable than the monomer state, which is consistent with experimental observations; the total free energy difference is calculated as 25 kcal mol-1. The conformational change and translational/rotational entropy change contribute to the destabilization of the dimer, whereas the hydration and vibrational entropy contribute to the stabilization. Further analyses on the residues located at the hinge loop for swapping were conducted, and the results reveal details at the molecular level of the structural and interaction changes upon dimerization.

  13. Role of quaternary structure in muscle creatine kinase stability: tryptophan 210 is important for dimer cohesion.

    Science.gov (United States)

    Perraut, C; Clottes, E; Leydier, C; Vial, C; Marcillat, O

    1998-07-01

    A mutant of the dimeric rabbit muscle creatine kinase (MM-CK) in which tryptophan 210 was replaced has been studied to assess the role of this residue in dimer cohesion and the importance of the dimeric state for the native enzyme stability. Wild-type protein equilibrium unfolding induced by guanidine hydrochloride occurs through intermediate states with formation of a molten globule and a premolten globule. Unlike the wild-type enzyme, the mutant inactivates at lower denaturant concentration and the loss of enzymatic activity is accompanied by the dissociation of the dimer into two apparently compact monomers. However, the Stokes radius of the monomer increases with denaturant concentration as determined by size exclusion chromatography, indicating that, upon monomerization, the protein structure is destabilized. Binding of 8-anilinonaphthalene-1-sulfonate shows that the dissociated monomer exposes hydrophobic patches at its surface, suggesting that it could be a molten globule. At higher denaturant concentrations, both wild-type and mutant follow similar denaturation pathways with formation of a premolten globule around 1.5-M guanidine, indicating that tryptophan 210 does not contribute to a large extent to the monomer conformational stability, which may be ensured in the dimeric state through quaternary interactions.

  14. Characterization of human immunodeficiency virus type 2 envelope glycoproteins: Dimerization of the glycoprotein precursor during processing

    International Nuclear Information System (INIS)

    Rey, M.A.; Krust, B.; Laurent, A.G.; Montagnier, L.; Hovanessian, A.G.

    1989-01-01

    For glycoproteins with apparent molecular weights of 300,000, 140,000, 125,000, and 36,000 (gp300, gp140, gp125, and gp36) were detectable in human immunodeficiency virus type 2 (HIV-2)-infected cells. They have identical isoelectric points, suggesting that gp300 might be a dimeric form of the immature precursor, gp140. The purified gp300 can be dissociated in a slightly acidic buffer to give rise to monomers of 140,000 molecular weight. Such dissociated monomers and the purified gp140 showed identical patterns of polypeptides after partial proteolysis with Staphylococcus aureus V8 protease. Pulse-chase experiments indicated that gp300 is formed after synthesis of gp140 and before the detection of the mature external envelope glycoprotein, gp125. These results were confirmed by using various inhibitors of glycosylation and inhibitors of trimming enzymes. Dimer formation of the envelope glycoprotein precursor was also observed in cells infected with simian immunodeficiency virus (SIV), a virus closely related to HIV-2. On the other hand, the envelope glycoprotein precursor of HIV-1 did not form a dimer during its processing. Therefore, dimer formation seems to be a specific property of HIV-2 and SIV envelope gene expression. Such transient dimerization of the glycoprotein precursor might be required for its efficient transport to the Golgi apparatus and for its processing

  15. Cytotoxicity and radical intensity of eugenol, isoeugenol or related dimers.

    Science.gov (United States)

    Atsumi, T; Fujisawa, S; Satoh, K; Sakagami, H; Iwakura, I; Ueha, T; Sugita, Y; Yokoe, I

    2000-01-01

    To investigate the possible link between radicals and cytotoxicity of eugenol-related compounds, dimer compounds were synthesized from eugenol (4-allyl-2-methoxyphenol) or isoeugenol (4-propenyl-2-methoxyphenol): bis-eugenol (3,3'-dimethoxy-5,5'-di-2-propenyl-1,1'-biphenyl-2,2'-diol); dehydrodiisoeugenol (2-(3-methoxy-4-hydroxyphenyl)-3-methyl-5-(1-propenyl)-7-methoxy-2,3- dihydrobenzofuran) and alpha-di-isoeugenol (r-l-ethyl-5-hydroxy-t-3-(4-hydroxy-3-methoxyphenyl)-6-methoxy-c-2- methylindane). Both the cytotoxic activity and the DNA synthesis inhibitory activity of these compounds against a salivary gland tumor cell line (HSG) and normal human gingival fibroblast (HGF) were decreased in the order of: dehydrodiisoeugenol, alpha-di-isoeugenol > isoeugenol > eugenol > bis-eugenol. Electron spin resonance (ESR) spectroscopy showed that dehydrodiisoeugenol, alpha-di-isoeugenol and eugenol, but not isoeugenol and bis-eugenol, produced phenoxyl radicals under alkaline condition (pH > 9.5). However, benzyl radicals were produced during the dimerization of isoeugenol to dehydrodiisoeugenol. The radical intensity of alpha-di- and dehydrodiisoeugenol appeared at relatively later incubation time than eugenol, suggesting that their phenoxyl radical was more stable than that of eugenol. Such a phenoxyl radical is produced by scavenging free radicals, during the inhibition of lipid peroxidation. Higher cytotoxic activity of isoeugenol dimers was thought to be induced by interaction with cell membranes via the lipophilic radical. The present study supports the notion that relative cytotoxicity of chemicals can be evaluated by measuring the radical intensity using ESR.

  16. Stable configurations of graphene on silicon

    Energy Technology Data Exchange (ETDEWEB)

    Javvaji, Brahmanandam; Shenoy, Bhamy Maithry [Department of Aerospace Engineering, Indian Institute of Science, Bangalore 560012 (India); Mahapatra, D. Roy, E-mail: droymahapatra@aero.iisc.ernet.in [Department of Aerospace Engineering, Indian Institute of Science, Bangalore 560012 (India); Ravikumar, Abhilash [Department of Metallurgical and Materials Engineering, National Institute of Technology Karnataka, Surathkal 575025 (India); Hegde, G.M. [Center for Nano Science and Engineering, Indian Institute of Science, Bangalore 560012 (India); Rizwan, M.R. [Department of Metallurgical and Materials Engineering, National Institute of Technology Karnataka, Surathkal 575025 (India)

    2017-08-31

    Highlights: • Simulations of epitaxial growth process for silicon–graphene system is performed. • Identified the most favourable orientation of graphene sheet on silicon substrate. • Atomic local strain due to the silicon–carbon bond formation is analyzed. - Abstract: Integration of graphene on silicon-based nanostructures is crucial in advancing graphene based nanoelectronic device technologies. The present paper provides a new insight on the combined effect of graphene structure and silicon (001) substrate on their two-dimensional anisotropic interface. Molecular dynamics simulations involving the sub-nanoscale interface reveal a most favourable set of temperature independent orientations of the monolayer graphene sheet with an angle of ∽15° between its armchair direction and [010] axis of the silicon substrate. While computing the favorable stable orientations, both the translation and the rotational vibrations of graphene are included. The possible interactions between the graphene atoms and the silicon atoms are identified from their coordination. Graphene sheet shows maximum bonding density with bond length 0.195 nm and minimum bond energy when interfaced with silicon substrate at 15° orientation. Local deformation analysis reveals probability distribution with maximum strain levels of 0.134, 0.047 and 0.029 for 900 K, 300 K and 100 K, respectively in silicon surface for 15° oriented graphene whereas the maximum probable strain in graphene is about 0.041 irrespective of temperature. Silicon–silicon dimer formation is changed due to silicon–carbon bonding. These results may help further in band structure engineering of silicon–graphene lattice.

  17. Liposomes of dimeric artesunate phospholipid: A combination of dimerization and self-assembly to combat malaria.

    Science.gov (United States)

    Ismail, Muhammad; Ling, Longbing; Du, Yawei; Yao, Chen; Li, Xinsong

    2018-05-01

    Artemisinin and its derivatives are highly effective drugs in the treatment of P. falciparum malaria. However, their clinical applications face challenges because of short half-life, poor bioavailability and growing drug resistance. In this article, novel dimeric artesunate phospholipid (Di-ART-GPC) based liposomes were developed by combination of dimerization and self-assembly to address these shortcomings. Firstly, Di-ART-GPC conjugate was synthesized by a facile esterification of artesunate (ART) and glycerophosphorylcholine (GPC) and confirmed by MS, 1 H NMR and 13 C NMR. The conjugate was then assembled to form liposomes without excipient by thin film hydration method. The assembled Di-ART-GPC liposomes have typical multilamellar vesicle structure with bilayer morphology as determined by transmission electron microscopy (TEM) and cryogenic electron microscopy (cryo-EM). Moreover, the liposomes displayed an average hydrodynamic diameter of 190 nm and negative zeta potential at -20.35 mV as determined by Zetasizer. The loading capacity of ART was calculated approximately 77.6% by weight with this liposomal formulation after a simple calculation. In vitro drug release and degradation results showed that the Di-ART-GPC liposomes were stable in neutral physiological conditions but effectively degraded to release parent ART in simulated weakly acidic microenvironment. In vivo pharmacokinetics study revealed that Di-ART-GPC liposomes and conjugate have longer retention half-life in bloodstream. Importantly, Di-ART-GPC liposomes (IC 50 0.39 nM) and the conjugate (IC 50 1.90 nM) demonstrated excellent in vitro antiplasmodial activities without causing hemolysis of erythrocytes, which were superior to free ART (IC 50 5.17 nM) and conventional ART-loaded liposomes (IC 50 3.13 nM). Furthermore, the assembled liposomes resulted in enhanced parasites killing in P. berghei-infected mice in vivo with delayed recrudescence and improved survivability

  18. D-dimers (DD) in CVST.

    Science.gov (United States)

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

    2017-06-01

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

  19. Camelliin B and nobotanin I, macrocyclic ellagitannin dimers and related dimers, and their antitumor activity.

    Science.gov (United States)

    Yoshida, T; Chou, T; Haba, K; Okano, Y; Shingu, T; Miyamoto, K; Koshiura, R; Okuda, T

    1989-11-01

    Camelliin B and nobotanin I, dimeric hydrolyzable tannins of a new class having macrocyclic structures, were isolated from Camellia japonica and Heterocentron roseum, respectively. Nobotanin G and H of the structures related to nobotanin I, were also obtained from H. roseum. Camelliin B and also woodfordin C, a macrocyclic dimer from Woodfordia fruticosa, exhibited marked host-mediated antitumor activities.

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

    DEFF Research Database (Denmark)

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

    2011-01-01

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

  1. Stable particles

    International Nuclear Information System (INIS)

    Samios, N.P.

    1994-01-01

    I have been asked to review the subject of stable particles, essentially the particles that eventually comprised the meson and baryon octets, with a few more additions - with an emphasis on the contributions made by experiments utilizing the bubble chamber technique. In this activity, much work had been done by the photographic emulsion technique and cloud chambers - exposed to cosmic rays as well as accelerator based beams. In fact, many if not most of the stable particles were found by these latter two techniques, however, the foree of the bubble chamber (coupled with the newer and more powerful accelerators) was to verify, and reinforce with large statistics, the existence of these states, to find some of the more difficult ones, mainly neutrals and further to elucidate their properties, i.e., spin, parity, lifetimes, decay parameters, etc. (orig.)

  2. Stable particles

    International Nuclear Information System (INIS)

    Samios, N.P.

    1993-01-01

    I have been asked to review the subject of stable particles, essentially the particles that eventually comprised the meson and baryon octets. with a few more additions -- with an emphasis on the contributions made by experiments utilizing the bubble chamber technique. In this activity, much work had been done by the photographic emulsion technique and cloud chambers-exposed to cosmic rays as well as accelerator based beams. In fact, many if not most of the stable particles were found by these latter two techniques, however, the forte of the bubble chamber (coupled with the newer and more powerful accelerators) was to verify, and reinforce with large statistics, the existence of these states, to find some of the more difficult ones, mainly neutrals and further to elucidate their properties, i.e., spin, parity, lifetimes, decay parameters, etc

  3. The (6-4) Dimeric Lesion as a DNA Photosensitizer.

    Science.gov (United States)

    Vendrell-Criado, Victoria; Rodríguez-Muñiz, Gemma M; Lhiaubet-Vallet, Virginie; Cuquerella, M Consuelo; Miranda, Miguel A

    2016-07-04

    Based on our previous investigations into the photophysical properties of the 5-methyl-2-pyrimidone (Pyo) chromophore, we now extend our studies to the photobehavior of the dimeric (6-4) thymine photoproducts (6-4 PP) to evaluate their capability to act as instrinsic DNA photosensitizers. The lesion presents significant absorption in the UVB/UVA region, weak fluorescence emission, a singlet-excited-state energy of approximately 351 kJ mol(-1) , and a triplet-excited-state energy of 297 kJ mol(-1) . Its triplet transient absorption has a maximum at 420-440 nm, a lifetime of around 7 μs, and a high formation quantum yield, ΦISC =0.86. This species is efficiently quenched by thymidine. Its DNA photosensitizing properties are demonstrated by a series of experiments run on a pBR322 plasmid. The lesion photoinduces both single-strand breaks and the formation of cyclobutane thymine dimers. Altogether, these results show that, the substitution of the pyrimidone ring at C4 by a 5-hydroxy-5,6-dihydrothymine does not cancel out the photosensitization properties of the chromophore. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Plasmonic nanospherical dimers for color pixels

    KAUST Repository

    Alrasheed, Salma

    2018-04-20

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

  5. Multiply charged monopoles in cubic dimer model

    Science.gov (United States)

    Ganesh Jaya, Sreejith; Powell, Stephen

    2015-03-01

    The classical cubic dimer model is a 3D statistical mechanical system whose degrees of freedom are dimers that occupy the edges between nearest neighbour vertices of a cubic lattice. Dimer occupancies are subject to the local constraint that every vertex is associated with exactly one dimer. In the presence of an aligning interaction, it is known that the system exhibits an unconventional continuous thermal phase transition from a symmetry broken columnar phase to a Coulomb-phase. The transition is in the NCCP1 universality class, which also describes the Neel-VBS transition in the JQ model and the S =1/2 Heisenberg model with suppression of hedgehog defects. Using Monte-Carlo simulations of a pair of defects in a background of fluctuating dimers, we calculate the scaling exponents for fugacities of monopole defects of charge Q = 2 and 3 at this critical point. Our estimates suggest that Q = 3 monopoles are relevant and could therefore drive the JQ model away from the NCCP1 critical point on a hexagonal lattice.

  6. Catalytic Activity of μ-Carbido-Dimeric Iron(IV) Octapropylporphyrazinate in the 3,5,7,2',4'-Pentahydroxyflavone Oxidation Reaction with tert-Butyl Hydroperoxide

    Science.gov (United States)

    Tyurin, D. V.; Zaitseva, S. V.; Kudrik, E. V.

    2018-05-01

    It is found for the first time that μ-carbido-dimeric iron(IV) octapropylporphyrazinate displays catalytic activity in the oxidation reaction of natural flavonol morin with tert-butyl hydroperoxide, with the catalyst being stable under conditions of the reaction. The kinetics of this reaction are studied. It is shown the reaction proceeds via tentative formation of a complex between the catalyst and the oxidant, followed by O‒O bond homolytic cleavage. The kinetics of the reaction is described in the coordinates of the Michaelis-Menten equation. A linear dependence of the apparent reaction rate constant on the concentration of the catalyst is observed, testifying to its participation in the limiting reaction step. The equilibrium constants and rates of interaction are found. A mechanism is proposed for the reaction on the basis of the experimental data.

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

    DEFF Research Database (Denmark)

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

    2002-01-01

    E-cadherin, an adhesive transmembrane protein of epithelial adherens junctions, forms two types of detergent-resistant dimers: adhesive dimers consisting of cadherin molecules derived from two neighboring cells and lateral dimers incorporating cadherins of the same cell. Both dimers depend...... on the integrity of the same residue, Trp156. While the relative amounts of these complexes are not certain, we show here that in epithelial A-431 cells, adhesive dimers may be a prevalent form. Inactivation of the calcium-binding sites, located between successive cadherin ectodomains, drastically reduced...... the amount of adhesive dimers and concomitantly increased the amount of lateral dimers. A similar interdependence of adhesive and lateral dimers was observed in digitonin-permeabilized cells. In these cells, adhesive dimers immediately disassembled after lowering the Ca2+ concentration below 0.1 m...

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

    Directory of Open Access Journals (Sweden)

    Mariana Quesadas-Rojas

    2016-11-01

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

  9. Phosphorus Dimerization in Gallium Phosphide at High Pressure

    Energy Technology Data Exchange (ETDEWEB)

    Lavina, Barbara [High Pressure Science and Engineering Center, University of Nevada, Las Vegas, Nevada 89154, United States; Department of Physics and Astronomy, University of Nevada, Las Vegas, Nevada 89154, United States; Kim, Eunja [Department of Physics and Astronomy, University of Nevada, Las Vegas, Nevada 89154, United States; Cynn, Hyunchae [Lawrence Livermore National Laboratory, Livermore, California 94550, United States; Weck, Philippe F. [Sandia National Laboratories, Albuquerque, New Mexico 87185, United States; Seaborg, Kelly [High Pressure Science and Engineering Center, University of Nevada, Las Vegas, Nevada 89154, United States; Department of Physics and Astronomy, University of Nevada, Las Vegas, Nevada 89154, United States; Siska, Emily [High Pressure Science and Engineering Center, University of Nevada, Las Vegas, Nevada 89154, United States; Meng, Yue [HPCAT, Carnegie Institution of Washington, Argonne, Illinois 60439, United States; Evans, William [Lawrence Livermore National Laboratory, Livermore, California 94550, United States

    2018-02-09

    Using combined experimental and computational approaches, we show that at 43 GPa and 1300 K gallium phosphide adopts the super-Cmcm structure, here indicated with its Pearson notation oS24. First-principles enthalpy calculations demonstrate that this structure is more thermodynamically stable above ~20 GPa than previously proposed polymorphs. Here, in contrast to other polymorphs, the oS24 phase shows a strong bonding differentiation and distorted fivefold coordination geometries of both P atoms. The shortest bond of the phase is a single covalent P–P bond measuring 2.171(11) Å at synthesis pressure. Phosphorus dimerization in GaP sheds light on the nature of the super-Cmcm phase and provides critical new insights into the high-pressure polymorphism of octet semiconductors. Bond directionality and anisotropy explain the relatively low symmetry of this high-pressure phase.

  10. Photoionization of helium dimers; Photoionisation von Heliumdimeren

    Energy Technology Data Exchange (ETDEWEB)

    Havermeier, Tilo

    2010-06-09

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

  11. Dynamic reorganization of chromatin structure and selective DNA demethylation prior to stable enhancer complex formation during differentiation of primary hematopoietic cells in vitro.

    Science.gov (United States)

    Tagoh, Hiromi; Melnik, Svitlana; Lefevre, Pascal; Chong, Suyinn; Riggs, Arthur D; Bonifer, Constanze

    2004-04-15

    In order to gain insights in the true molecular mechanisms involved in cell fate decisions, it is important to study the molecular details of gene activation where such decisions occur, which is at the level of the chromatin structure of individual genes. In the study presented here we addressed this issue and examined the dynamic development of an active chromatin structure at the chicken lysozyme locus during the differentiation of primary myeloid cells from transgenic mouse bone marrow. Using in vivo footprinting we found that stable enhancer complex assembly and high-level gene expression are late events in cell differentiation. However, even before the onset of gene expression and stable transcription factor binding, specific chromatin alterations are observed. This includes changes in DNA topology and the selective demethylation of CpG dinucleotides located in the cores of critical transcription factor binding sites, but not in flanking DNA. These results firmly support the idea that epigenetic programs guiding blood cell differentiation are engraved into the chromatin of lineage-specific genes and that such chromatin changes are implemented before cell lineage specification.

  12. On the asymptotics of dimers on tori

    OpenAIRE

    Kenyon, Richard W.; Sun, Nike; Wilson, David B.

    2013-01-01

    We study asymptotics of the dimer model on large toric graphs. Let $\\mathbb L$ be a weighted $\\mathbb{Z}^2$-periodic planar graph, and let $\\mathbb{Z}^2 E$ be a large-index sublattice of $\\mathbb{Z}^2$. For $\\mathbb L$ bipartite we show that the dimer partition function on the quotient $\\mathbb{L}/(\\mathbb{Z}^2 E)$ has the asymptotic expansion $\\exp[A f_0 + \\text{fsc} + o(1)]$, where $A$ is the area of $\\mathbb{L}/(\\mathbb{Z}^2 E)$, $f_0$ is the free energy density in the bulk, and $\\text{fsc...

  13. Factorized ground state in dimerized spin chains

    Energy Technology Data Exchange (ETDEWEB)

    Giorgi, Gian Luca, E-mail: gianluca@ifisc.uib-csic.e [Institute for Cross-Disciplinary Physics and Complex Systems, IFISC (CSIC-UIB), Campus Universitat Illes Balears, E-07122 Palma de Mallorca (Spain)

    2010-09-01

    The possibility of observing factorized ground states in dimerized spin systems is studied. A set of sufficient conditions is derived which allows one to establish whether or not it is possible to have factorization both in nearest-neighbour and long-range Hamiltonians. These conditions can be derived by forcing factorization for each of the pairwise terms of the total Hamiltonian. Due to the peculiar structure of a dimerized chain, an antiferromagnetic factorized ground state of the kind |nearr), |nearr), |nwarr), |nwarr) (forbidden in regular chains) is possible.

  14. Stable beams

    CERN Multimedia

    2015-01-01

    Stable beams: two simple words that carry so much meaning at CERN. When LHC page one switched from "squeeze" to "stable beams" at 10.40 a.m. on Wednesday, 3 June, it triggered scenes of jubilation in control rooms around the CERN sites, as the LHC experiments started to record physics data for the first time in 27 months. This is what CERN is here for, and it’s great to be back in business after such a long period of preparation for the next stage in the LHC adventure.   I’ve said it before, but I’ll say it again. This was a great achievement, and testimony to the hard and dedicated work of so many people in the global CERN community. I could start to list the teams that have contributed, but that would be a mistake. Instead, I’d simply like to say that an achievement as impressive as running the LHC – a machine of superlatives in every respect – takes the combined effort and enthusiasm of everyone ...

  15. CT Findings of Disease with Elevated Serum D-Dimer Levels in an Emergency Room Setting

    Energy Technology Data Exchange (ETDEWEB)

    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)

    2012-01-15

    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.

  16. Live cell imaging unveils multiple domain requirements for in vivo dimerization of the glucocorticoid receptor.

    Directory of Open Access Journals (Sweden)

    Diego M Presman

    2014-03-01

    Full Text Available Glucocorticoids are essential for life, but are also implicated in disease pathogenesis and may produce unwanted effects when given in high doses. Glucocorticoid receptor (GR transcriptional activity and clinical outcome have been linked to its oligomerization state. Although a point mutation within the GR DNA-binding domain (GRdim mutant has been reported as crucial for receptor dimerization and DNA binding, this assumption has recently been challenged. Here we have analyzed the GR oligomerization state in vivo using the number and brightness assay. Our results suggest a complete, reversible, and DNA-independent ligand-induced model for GR dimerization. We demonstrate that the GRdim forms dimers in vivo whereas adding another mutation in the ligand-binding domain (I634A severely compromises homodimer formation. Contrary to dogma, no correlation between the GR monomeric/dimeric state and transcriptional activity was observed. Finally, the state of dimerization affected DNA binding only to a subset of GR binding sites. These results have major implications on future searches for therapeutic glucocorticoids with reduced side effects.

  17. Inhibition of Receptor Dimerization as a Novel Negative Feedback Mechanism of EGFR Signaling.

    Directory of Open Access Journals (Sweden)

    Malgorzata Kluba

    Full Text Available Dimerization of the epidermal growth factor receptor (EGFR is crucial for initiating signal transduction. We employed raster image correlation spectroscopy to continuously monitor the EGFR monomer-dimer equilibrium in living cells. EGFR dimer formation upon addition of EGF showed oscillatory behavior with a periodicity of about 2.5 min, suggesting the presence of a negative feedback loop to monomerize the receptor. We demonstrated that monomerization of EGFR relies on phospholipase Cγ, protein kinase C, and protein kinase D (PKD, while being independent of Ca2+ signaling and endocytosis. Phosphorylation of the juxtamembrane threonine residues of EGFR (T654/T669 by PKD was identified as the factor that shifts the monomer-dimer equilibrium of ligand bound EGFR towards the monomeric state. The dimerization state of the receptor correlated with the activity of an extracellular signal-regulated kinase, downstream of the EGFR. Based on these observations, we propose a novel, negative feedback mechanism that regulates EGFR signaling via receptor monomerization.

  18. Electrostatic Interactions at the Dimer Interface Stabilize the E. coli β Sliding Clamp.

    Science.gov (United States)

    Purohit, Anirban; England, Jennifer K; Douma, Lauren G; Tondnevis, Farzaneh; Bloom, Linda B; Levitus, Marcia

    2017-08-22

    Sliding clamps are ring-shaped oligomeric proteins that encircle DNA and associate with DNA polymerases for processive DNA replication. The dimeric Escherichia coli β-clamp is closed in solution but must adopt an open conformation to be assembled onto DNA by a clamp loader. To determine what factors contribute to the stability of the dimer interfaces in the closed conformation and how clamp dynamics contribute to formation of the open conformation, we identified conditions that destabilized the dimer and measured the effects of these conditions on clamp dynamics. We characterized the role of electrostatic interactions in stabilizing the β-clamp interface. Increasing salt concentration results in decreased dimer stability and faster subunit dissociation kinetics. The equilibrium dissociation constant of the dimeric clamp varies with salt concentration as predicted by simple charge-screening models, indicating that charged amino acids contribute to the remarkable stability of the interface at physiological salt concentrations. Mutation of a charged residue at the interface (Arg-103) weakens the interface significantly, whereas effects are negligible when a hydrophilic (Ser-109) or a hydrophobic (Ile-305) amino acid is mutated instead. It has been suggested that clamp opening by the clamp loader takes advantage of spontaneous opening-closing fluctuations at the clamp's interface, but our time-resolved fluorescence and fluorescence correlation experiments rule out conformational fluctuations that lead to a significant fraction of open states. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  19. Formation of Hierarchical In2S3-CdIn2S4Heterostructured Nanotubes for Efficient and Stable Visible Light CO2Reduction.

    Science.gov (United States)

    Wang, Sibo; Guan, Bu Yuan; Lu, Yan; Lou, Xiong Wen David

    2017-12-06

    We demonstrate rational design and fabrication of hierarchical In 2 S 3 -CdIn 2 S 4 heterostructured nanotubes as efficient and stable photocatalysts for visible light CO 2 reduction. The novel self-templated strategy, including sequential anion- and cation-exchange reactions, integrates two distinct sulfide semiconductors into hierarchical tubular hybrids with homogeneous interfacial contacts and ultrathin two-dimensional (2D) nanosheet subunits. Accordingly, the hierarchical heterostructured nanotubes facilitate separation and migration of photoinduced charge carriers, enhance the adsorption and concentration of CO 2 molecules, and offer rich active sites for surface redox reactions. Benefiting from these structural and compositional features, the optimized hierarchical In 2 S 3 -CdIn 2 S 4 nanotubes without employing noble metal cocatalysts in the catalytic system manifest remarkable performance for deoxygenative reduction of CO 2 with high CO generation rate (825 μmol h -1 g -1 ) and outstanding stability under visible light irradiation.

  20. Formation of stable and metastable phases in reciprocal systems PbSe + MI2 = MSe + PbI2 (M = Hg, Mn, Sn)

    International Nuclear Information System (INIS)

    Odin, I.N.; Grin'ko, V.V.; Kozlovskij, V.F.; Safronov, E.V.; Gapanovich, M.V.

    2004-01-01

    Using data of differential thermal, X-ray phase and microstructural analyses, phase diagrams of reciprocal systems PbSe + MI 2 = MSe + PbI 2 (M=Hg (1), Mn (2), Sn (3)) were constructed. It was ascertained that the HgSe-PbI 2 diagonal in system 1 is stable. Transformations leading to crystallization of metastable ternary compound formed in the system PbSe-PbI 2 and metastable polytypes of lead iodide in systems 1 and 2 in the range of temperatures from 620 to 685 K were studied. New intermediate metastable phases in systems 1, 2 and 3 were prepared by melt quenching. Crystal lattice parameters of the phases crystallizing in the CdCl 2 structural type were defined [ru

  1. Formation of Kokumi-Enhancing γ-Glutamyl Dipeptides in Parmesan Cheese by Means of γ-Glutamyltransferase Activity and Stable Isotope Double-Labeling Studies.

    Science.gov (United States)

    Hillmann, Hedda; Behr, Jürgen; Ehrmann, Matthias A; Vogel, Rudi F; Hofmann, Thomas

    2016-03-02

    Recently, γ-glutamyl dipeptides (γ-GPs) were found to be responsible for the attractive kokumi flavor of Parmesan cheese (PC). Quantitation of γ-GPs and their parent amino acids in 13-, 24-, and 30-month ripened PC samples by LC-MS/MS and stable isotope dilution analysis (SIDA), in-cheese (13)C-labeling studies, followed by analysis of the γ-glutamyl transferase (GGT) activity revealed γ-GPs to be generated most efficiently after 24 months of ripening by a GGT-catalyzed transfer of the γ-glutamyl moiety of L-glutamine onto various acceptor amino acids released upon casein proteolysis. Following the identification of milk as a potential GGT source in PC, the functionality of the milk's GGT to generate the target γ-GPs was validated by stable isotope double-labeling (SIDL) experiments. Therefore, raw and heat-treated milk samples were incubated with L-glutamine-[U-(13)C] and acceptor amino acids (X) and the hetero- (γ-Glu-[(13)C5]-X) and homotranspeptidation products (γ-Glu-Gln-[(13)C10]) were quantitated by LC-MS/MS-SIDA using γ-Glu-Ala-[(13)C3] as the internal standard. High GGT activity to generate the γ-GPs and preference for L-phenylalanine and L-methionine as acceptor amino acids were found in raw milk and milk samples heat-treated for 10 min up to a maximum of 65 °C. In comparison, GGT activity and SIDL studies performed with inoculated Lactobacillus strains, including Lactobacillus harbinensis and Lactobacillus casei identified in PC by means of 16S rRNA gene sequencing, did not show any significant GGT activity and unequivocally demonstrated unpasteurized cow's milk, rather than microorganisms, as a key factor in γ-glutamyl dipeptide generation in Parmesan cheese.

  2. Disruption of Rhodopsin Dimerization with Synthetic Peptides Targeting an Interaction Interface*

    Science.gov (United States)

    Jastrzebska, Beata; Chen, Yuanyuan; Orban, Tivadar; Jin, Hui; Hofmann, Lukas; Palczewski, Krzysztof

    2015-01-01

    Although homo- and heterodimerizations of G protein-coupled receptors (GPCRs) are well documented, GPCR monomers are able to assemble in different ways, thus causing variations in the interactive interface between receptor monomers among different GPCRs. Moreover, the functional consequences of this phenomenon, which remain to be clarified, could be specific for different GPCRs. Synthetic peptides derived from transmembrane (TM) domains can interact with a full-length GPCR, blocking dimer formation and affecting its function. Here we used peptides corresponding to TM helices of bovine rhodopsin (Rho) to investigate the Rho dimer interface and functional consequences of its disruption. Incubation of Rho with TM1, TM2, TM4, and TM5 peptides in rod outer segment (ROS) membranes shifted the resulting detergent-solubilized protein migration through a gel filtration column toward smaller molecular masses with a reduced propensity for dimer formation in a cross-linking reaction. Binding of these TM peptides to Rho was characterized by both mass spectrometry and a label-free assay from which dissociation constants were calculated. A BRET (bioluminescence resonance energy transfer) assay revealed that the physical interaction between Rho molecules expressed in membranes of living cells was blocked by the same four TM peptides identified in our in vitro experiments. Although disruption of the Rho dimer/oligomer had no effect on the rates of G protein activation, binding of Gt to the activated receptor stabilized the dimer. However, TM peptide-induced disruption of dimer/oligomer decreased receptor stability, suggesting that Rho supramolecular organization could be essential for ROS stabilization and receptor trafficking. PMID:26330551

  3. Disruption of Rhodopsin Dimerization with Synthetic Peptides Targeting an Interaction Interface.

    Science.gov (United States)

    Jastrzebska, Beata; Chen, Yuanyuan; Orban, Tivadar; Jin, Hui; Hofmann, Lukas; Palczewski, Krzysztof

    2015-10-16

    Although homo- and heterodimerizations of G protein-coupled receptors (GPCRs) are well documented, GPCR monomers are able to assemble in different ways, thus causing variations in the interactive interface between receptor monomers among different GPCRs. Moreover, the functional consequences of this phenomenon, which remain to be clarified, could be specific for different GPCRs. Synthetic peptides derived from transmembrane (TM) domains can interact with a full-length GPCR, blocking dimer formation and affecting its function. Here we used peptides corresponding to TM helices of bovine rhodopsin (Rho) to investigate the Rho dimer interface and functional consequences of its disruption. Incubation of Rho with TM1, TM2, TM4, and TM5 peptides in rod outer segment (ROS) membranes shifted the resulting detergent-solubilized protein migration through a gel filtration column toward smaller molecular masses with a reduced propensity for dimer formation in a cross-linking reaction. Binding of these TM peptides to Rho was characterized by both mass spectrometry and a label-free assay from which dissociation constants were calculated. A BRET (bioluminescence resonance energy transfer) assay revealed that the physical interaction between Rho molecules expressed in membranes of living cells was blocked by the same four TM peptides identified in our in vitro experiments. Although disruption of the Rho dimer/oligomer had no effect on the rates of G protein activation, binding of Gt to the activated receptor stabilized the dimer. However, TM peptide-induced disruption of dimer/oligomer decreased receptor stability, suggesting that Rho supramolecular organization could be essential for ROS stabilization and receptor trafficking. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  4. Effects of gold based dimers on structural and electronic properties of MoS{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Kadioglu, Yelda [Department of Physics, Adnan Menderes University, 09100 Aydın (Turkey); Gökoğlu, Gökhan [Department of Physics, Karabük University, 78050 Karabük (Turkey); Aktürk, Olcay Üzengi, E-mail: ouzengi@adu.edu.tr [Department of Electrical & Electronics Engineering, Adnan Menderes University, 09100 Aydın (Turkey); Nanotechnology Application and Research Center, Adnan Menderes University, 09100 Aydın (Turkey)

    2017-02-28

    Highlights: • Semiconductor MoS{sub 2} shows metallic character by AuPt and AuPd adsorption. • MoS{sub 2} maintains its semiconductor characteristics with a decrease in the band gap values after AuAg, AuCu, and AuAl adsorption. • AuPt adsorbed system is the most stable structure energetically. • AuAl exhibits the weakest adsorption to MoS{sub 2} among the considered dimers. - Abstract: In view of first principles calculations, we investigate the electronic structure redecoration of monolayer MoS{sub 2} upon adsorptions of AuAg, AuPt, AuPd, AuCu, and AuAl bimetallic dimers. Geometrical structure, band structures, electronic density of states, charge density differences of dimer adsorbed MoS{sub 2} systems are presented and discussed. All the systems studied have non-magnetic ground states. Charge transfers occur from dimer to surface except for AuPt adsorption. Our results indicate that the semiconductor MoS{sub 2} maintains its semiconductor character with decreased band gaps upon AuAg, AuCu, and AuAl adsorptions. However, MoS{sub 2} shows metallic behaviour by AuPt and AuPd adsorptions, so Pt-d and Pd-d states cross Fermi level yielding metallic character. AuPt adsorbed system has the highest E{sub ads} value of 3.15 eV indicating the most stable structure energetically among the dimer adsorbed MoS{sub 2} systems considered.

  5. PSD-95 uncoupling from NMDA receptors by Tat-N-dimer ameliorates neuronal depolarisation in cortical spreading depression

    DEFF Research Database (Denmark)

    Kucharz, Krzysztof; Søndergaard Rasmussen, Ida; Bach, Anders

    2017-01-01

    Cortical spreading depression is associated with activation of NMDA receptors, which interact with the postsynaptic density protein 95 (PSD-95) that binds to nitric oxide synthase (nNOS). Here, we tested whether inhibition of the nNOS/PSD-95/NMDA receptor complex formation by anti-ischemic compound......, UCCB01-144 (Tat-N-dimer) ameliorates the persistent effects of cortical spreading depression on cortical function. Using in vivo two-photon microscopy in somatosensory cortex in mice, we show that fluorescently labelled Tat-N-dimer readily crosses blood-brain barrier and accumulates in nerve cells...... during the first hour after i.v. injection. The Tat-N-dimer suppressed stimulation-evoked synaptic activity by 2-20%, while cortical blood flow and cerebral oxygen metabolic (CMRO2) responses were preserved. During cortical spreading depression, the Tat-N-dimer reduced the average amplitude...

  6. Formation of ZnO-Cd(OH){sub 2} core-shell nanoparticles by sol-gel method: An approach to modify surface chemistry for stable and enhanced green emission

    Energy Technology Data Exchange (ETDEWEB)

    Mishra, Rupali, E-mail: rupalimishra@rediffmail.co [Department of Physics, University of Allahabad, Allahabad-211002 (India); Nanophosphor Application Centre, University of Allahabad, Allahabad-211002 (India); Yadav, Raghvendra S.; Pandey, Avinash C. [Department of Physics, University of Allahabad, Allahabad-211002 (India); Nanophosphor Application Centre, University of Allahabad, Allahabad-211002 (India); Sanjay, Sharda. S. [Department of Chemistry, Ewing Christian College, Allahabad (India); Dar, Chitra [Department of Physics, University of Allahabad, Allahabad-211002 (India)

    2010-03-15

    We report the formation of highly stable and luminescent ZnO-Cd(OH){sub 2} core-shell nanoparticles by simple introduction of cadmium salt in the initial precursor solution, used to synthesize ZnO nanoparticles by sol-gel route. The cadmium to zinc salt concentration ratio has been also varied to control the growth of ZnO nanoparticles at the smaller particle size. Formation of ZnO-Cd(OH){sub 2} core-shell nanostructure has been confirmed by X-ray diffraction (XRD), energy dispersive analysis of X-rays (EDAX) and X-ray photoelectron spectroscopy (XPS). UV-vis absorption spectroscopy exhibits blue-shift in absorption edge on increasing cadmium concentrations. The photoluminescence emission spectra showed the remarkably stable and enhanced visible (green) emission from suspended ZnO-Cd(OH){sub 2} nanoparticles in comparison to bare ZnO nanoparticles. It is postulated that Cd(OH){sub 2} layer at the surface of ZnO nanoparticles prevents the agglomeration of nanoparticles and efficiently assists the trapping of hole at the surface site, a first step necessary for visible emission. The Fourier transform infrared spectroscopy (FTIR) also supports our assumption about surface chemistry.

  7. Biological consequences of cyclobutane pyrimidine dimers

    NARCIS (Netherlands)

    Vink, A.A.; Roza, L.

    2001-01-01

    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.

  8. Spectroscopic Observation of CS_2 Dimer

    Science.gov (United States)

    Rezaei, M.; Oliaee, J. Norooz; Moazzen-Ahmadi, N.; McKellar, A. R. W.

    2011-06-01

    Infrared spectra of the CS_2 dimer are observed in the region of the CS_2 ν_3 fundamental band (˜ 1535 Cm-1) using a tuneable diode laser spectrometer. The weakly-bound complex is formed in a pulsed supersonic slit-jet expansion of a dilute gas mixture of carbon disulfide in helium. Contrary to the planar slipped-parallel geometry previously observed for (CO_2)_2, (N_2O)_2 and (OCS)_2, the CS_2 dimer exhibits a cross-shaped structure with D2d symmetry. Two bands were observed and analyzed: the fundamental (C-S asymmetric stretch) and a combination involving this mode plus an intermolecular vibration. In both cases, the rotational structure corresponds to a perpendicular (Δ K = ± 1) band of a symmetric rotor molecule. The intermolecular center of mass separation (C-C distance) is determined to be 3.539(7) {Å}. Thanks to symmetry, this is the only parameter required to characterize the structure, if the monomer geometry is assumed to remain unchanged in the dimer. From the band centers of the fundamental and combination band an intermolecular frequency of 10.96 Cm-1 is obtained, which we assign as the torsional bending mode. This constitutes the first high resolution spectroscopic investigation of CS_2 dimer.

  9. Synthesis and characterization of monomeric and dimeric ...

    African Journals Online (AJOL)

    The two complexes are isostructural, with the central metal atom lying on a crystallographic 2-fold axis. Both complexes are approximately octahedral, the coordination being provided by two trans pyridine nitrogen atoms and two cis amine nitrogen atoms from the oxime ligands, and by two cis chlorides. The dimeric ...

  10. Analyses of stable isotopes in camelids collagen bones from Tulan Ravine, Atacama Puna, early formative period (CA 3,1000-2,400BP)

    International Nuclear Information System (INIS)

    Lopez, Patricio; Cartajena, Isabel; Nunez, Lautaro

    2013-01-01

    This paper presents the results of isotope analysis (δ 13 C y δ 15 N) conducted on bone collagen found in Lama guanicoe and Lama glama remains from Tulan-85 and Tulan-54 archaeological sites. Both sites have been dated to the Early Formative Period (ca. 3,100-2,400 ap) and are located southeast of the Atacama Puna basin. Faunal samples were selected using anatomical and morphometric criteria. The results indicate divergences in the diets of both species, reflecting vegetation variation in the Tulan Quebrada caused by altitude differences and linked to hunting and herding areas [es

  11. Structures of DNA containing psoralen crosslink and thymine dimer

    International Nuclear Information System (INIS)

    Kim, S.H.; Pearlman, D.A.; Holbrook, S.R.; Pirkle, D.

    1985-01-01

    UV irradiation by itself or in conjunction with other chemicals can cause covalent damages to DNA in living cells. To overcome the detrimental effect of DNA damage, cells developed a repair mechanism by which damaged DNA is repaired. In the absence of such repair, cell malfunction or cell death can occur. Two most studied radiation-induced DNA damage are thymine dimer formation by UV irradiation and psoralen crosslink by combination of psoralens and UV: In the former, two adjacent thymine bases on a strand of DNA are fused by forming cyclobutane ring, and in the latter, one pyrimidine on one DNA strand is crosslinked to another pyrimidine on the other strand via a psoralen. The authors' objective is to deduce the structure of DNA segment which contains a psoralen crosslink or a thymine dimer using the combination of results of X-ray crystallographic studies, molecular model building, and energy minimization. These structural features may be important for understanding the biological effects of such damages and for the recognition by the repair enzymes

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

    African Journals Online (AJOL)

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

  13. Stochastic optimization-based study of dimerization kinetics

    Indian Academy of Sciences (India)

    Keywords. Stochastic optimization; dimerization kinetics; sensitivity analysis; stochastic simulation algorithm; probability distribution function. ... 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 ...

  14. Ultraviolet Spectrum And Chemical Reactivity Of CIO Dimer

    Science.gov (United States)

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

    1992-01-01

    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.

  15. Structures and energetics of lithium adatom and its dimer on graphene–a DFT study

    International Nuclear Information System (INIS)

    Kaur, Gagandeep; Gupta, Shuchi; Dharamvir, Keya

    2015-01-01

    Highlights: • For single Li adatom adsorption on graphene, it prefers H-site followed by B-site. • By the examination of the calculated cohesive energies, it is possible to conclude that both Li/Li 2 binds strongly to graphene which corroborate previous results. • The calculations showed that the interaction between Li and graphene has minimal effects on the electronic states of the graphene sheet, in agreement with previous calculations. • Charge transfer (0.338e)upon adsorption also induces significant electric dipole moments and affect total magnetic moment at B-site and T-site. • For the Li dimer adsorption, we found that horizontal orientation is favored over the vertical. • Adsorption of lithium dimer to the HH-site alters graphene sheet only by small amount ∼0.0022 Å–0.0034 Å. • The methodology demonstrated in this paper maybe applied to larger lithium clusters on graphene sheet. - Abstract: We performed a systematic density functional theory (DFT) study of the adsorption of Lithium adatom and its dimer on graphene using SIESTA package [1], in the generalized gradient approximation (GGA). The adsorption energy, geometry, charge transfer and density of states of adatom/dimer-graphene system are calculated. The calculations showed that the interaction between Li adatom and graphene is strong (∼1.07 eV) and it prefers to adsorb on H-site. Further calculations of both horizontally and vertically aligned dimers show that the adsorption is also weak for the latter orientation. The preferred orientation of each dimer was found to be parallel to graphene sheet with the two atoms of the dimer occupying adjacent H-sites on the graphene. Significant charge transfer (∼0.388e) from Li adatom to graphene will induce electric dipole moments in the adatom/graphene system. We also calculated DOS for the stable Li -graphene system. The Fermi energy is seen to lie above the Dirac point inside the conduction band indicating that appreciable electrons

  16. Each protomer of a dimeric YidC functions as a single membrane insertase.

    Science.gov (United States)

    Spann, Dirk; Pross, Eva; Chen, Yuanyuan; Dalbey, Ross E; Kuhn, Andreas

    2018-01-12

    The membrane insertase YidC catalyzes the entrance of newly synthesized proteins into the lipid bilayer. As an integral membrane protein itself, YidC can be found as a monomer, a dimer or also as a member of the holotranslocase SecYEGDF-YajC-YidC. To investigate whether the dimeric YidC is functional and whether two copies cooperate to insert a single substrate, we constructed a fusion protein where two copies of YidC are connected by a short linker peptide. The 120 kDa protein is stable and functional as it supports the membrane insertion of the M13 procoat protein, the C-tailed protein SciP and the fusion protein Pf3-Lep. Mutations that inhibit either protomer do not inactivate the insertase and rather keep it functional. When both protomers are defective, the substrate proteins accumulate in the cytoplasm. This suggests that the dimeric YidC operates as two insertases. Consistent with this, we show that the dimeric YidC can bind two substrate proteins simultaneously, suggesting that YidC indeed functions as a monomer.

  17. A New Modular Approach to Nanoassembly: Stable and Addressable DNA Nanoconstructs via Orthogonal Click Chemistries

    KAUST Repository

    Gerrard, Simon R.

    2012-10-23

    Thermodynamic instability is a problem when assembling and purifying complex DNA nanostructures formed by hybridization alone. To address this issue, we have used photochemical fixation and orthogonal copper-free, ring-strain-promoted, click chemistry for the synthesis of dimeric, trimeric, and oligomeric modular DNA scaffolds from cyclic, double-stranded, 80-mer DNA nanoconstructs. This particular combination of orthogonal click reactions was more effective for nanoassembly than others explored. The complex nanostructures are stable to heat and denaturation agents and can therefore be purified and characterized. They are addressable in a sequence-specific manner by triplex formation, and they can be reversibly and selectively deconstructed. Nanostructures utilizing this orthogonal, chemical fixation methodology can be used as building blocks for nanomachines and functional DNA nanoarchitectures. © 2012 American Chemical Society.

  18. Neutral molecular cluster formation of sulfuric acid–dimethylamine observed in real time under atmospheric conditions

    Science.gov (United States)

    Kürten, Andreas; Jokinen, Tuija; Simon, Mario; Sipilä, Mikko; Sarnela, Nina; Junninen, Heikki; Adamov, Alexey; Almeida, João; Amorim, Antonio; Bianchi, Federico; Breitenlechner, Martin; Dommen, Josef; Donahue, Neil M.; Duplissy, Jonathan; Ehrhart, Sebastian; Flagan, Richard C.; Franchin, Alessandro; Hakala, Jani; Hansel, Armin; Heinritzi, Martin; Hutterli, Manuel; Kangasluoma, Juha; Kirkby, Jasper; Laaksonen, Ari; Lehtipalo, Katrianne; Leiminger, Markus; Makhmutov, Vladimir; Mathot, Serge; Onnela, Antti; Petäjä, Tuukka; Praplan, Arnaud P.; Riccobono, Francesco; Rissanen, Matti P.; Rondo, Linda; Schobesberger, Siegfried; Seinfeld, John H.; Steiner, Gerhard; Tomé, António; Tröstl, Jasmin; Winkler, Paul M.; Williamson, Christina; Wimmer, Daniela; Ye, Penglin; Baltensperger, Urs; Carslaw, Kenneth S.; Kulmala, Markku; Worsnop, Douglas R.; Curtius, Joachim

    2014-01-01

    For atmospheric sulfuric acid (SA) concentrations the presence of dimethylamine (DMA) at mixing ratios of several parts per trillion by volume can explain observed boundary layer new particle formation rates. However, the concentration and molecular composition of the neutral (uncharged) clusters have not been reported so far due to the lack of suitable instrumentation. Here we report on experiments from the Cosmics Leaving Outdoor Droplets chamber at the European Organization for Nuclear Research revealing the formation of neutral particles containing up to 14 SA and 16 DMA molecules, corresponding to a mobility diameter of about 2 nm, under atmospherically relevant conditions. These measurements bridge the gap between the molecular and particle perspectives of nucleation, revealing the fundamental processes involved in particle formation and growth. The neutral clusters are found to form at or close to the kinetic limit where particle formation is limited only by the collision rate of SA molecules. Even though the neutral particles are stable against evaporation from the SA dimer onward, the formation rates of particles at 1.7-nm size, which contain about 10 SA molecules, are up to 4 orders of magnitude smaller compared with those of the dimer due to coagulation and wall loss of particles before they reach 1.7 nm in diameter. This demonstrates that neither the atmospheric particle formation rate nor its dependence on SA can simply be interpreted in terms of cluster evaporation or the molecular composition of a critical nucleus. PMID:25288761

  19. Large D-Dimer Fluctuation in Normal Pregnancy

    DEFF Research Database (Denmark)

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

    2016-01-01

    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...... 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...... normal pregnancy, repeated D-dimer measurements are of no clinical use in the evaluation of thromboembolic events during pregnancy....

  20. The effects of LiBOB additive for stable SEI formation of PP13TFSI-organic mixed electrolyte in lithium ion batteries

    International Nuclear Information System (INIS)

    An Yongxin; Zuo Pengjian; Cheng Xinqun; Liao Lixia; Yin Geping

    2011-01-01

    Highlights: → LiBOB as the additive of SEI formation. → LiBOB containing mixed electrolyte shows well thermal stability and safety. → LiBOB improves the electrochemical performance of PP13TFSI-organic mixture. - Abstract: A safe electrolyte system is prepared from N-methyl-N-propylpiperidinium bis (trifluoromethanesulfonyl) imide (PP13TFSI), organic electrolyte (1 mol L -1 LiPF 6 /EC-DEC) and lithium bis (oxalato) borate (LiBOB). The additive of LiBOB enhances the stability of interface between electrolyte and anode. The LiBOB-containing mixed electrolytes show non-flammability and good compatibility with active materials. The performance of anode for lithium ion battery is successfully improved by LiBOB-containing mixed electrolytes, which shows 200 mA h g -1 reversible capacities at 0.3 C rate. The ionic conductivity and the lithium ion transference number in LiBOB-containing mixed electrolytes system also suits to application for lithium ion battery.

  1. Distinct Contributions of Tryptophan Residues within the Dimerization Domain to Nanog Function.

    Science.gov (United States)

    Mullin, Nicholas P; Gagliardi, Alessia; Khoa, Le Tran Phuc; Colby, Douglas; Hall-Ponsele, Elisa; Rowe, Arthur J; Chambers, Ian

    2017-05-19

    The level of the transcription factor Nanog directly determines the efficiency of mouse embryonic stem cell self-renewal. Nanog protein exists as a dimer with the dimerization domain composed of a simple repeat region in which every fifth residue is a tryptophan, the tryptophan repeat (WR). Although WR is necessary to enable Nanog to confer LIF-independent self-renewal, the mechanism of dimerization and the effect of modulating dimerization strength have been unclear. Here we couple mutagenesis with functional and dimerization assays to show that the number of tryptophans within the WR is linked to the strength of homodimerization, Sox2 heterodimerization and self-renewal activity. A reduction in the number of tryptophan residues leads initially to a gradual reduction in activity before a precipitous reduction in activity occurs upon reduction in tryptophan number below eight. Further functional attrition follows subsequent tryptophan number reduction with substitution of all tryptophan residues ablating dimerization and self-renewal function completely. A strong positional influence of tryptophans exists, with residues at the WR termini contributing more to Nanog function, particularly at the N-terminal end. Limited proteolysis demonstrates that a structural core of Nanog encompassing the homeodomain and the tryptophan repeat can support LIF-independent colony formation. These results increase understanding of the molecular interactions occurring between transcription factor subunits at the core of the pluripotency gene regulatory network and will enhance our ability to control pluripotent cell self-renewal and differentiation. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  2. Internal energy selection in vacuum ultraviolet photoionization of ethanol and ethanol dimers

    Science.gov (United States)

    Bodi, Andras

    2013-10-01

    Internal energy selected ethanol monomer and ethanol dimer ions were prepared by threshold photoionization of a supersonic molecular beam seeded with ethanol. The dissociative photoionization processes of the monomer, the lowest-energy CH3-loss channel of the dimer, and the fragmentation of larger clusters were found to be disjunct from the ionization onset to about 12 eV, which made it possible to determine the 0 K appearance energy of C-C bond breaking in the H-donor unit of the ethanol dimer cation as 9.719 ± 0.004 eV. This reaction energy is used together with ab initio calculations in a thermochemical cycle to determine the binding energy change from the neutral ethanol dimer to a protonated ethanol-formaldehyde adduct. The cycle also shows general agreement between experiment, theory, and previously published enthalpies of formation. The role of the initial ionization site, or rather the initial photoion state, is also discussed based on the dimer breakdown diagram and excited state calculations. There is no evidence for isolated state behavior, and the ethanol dimer dissociative photoionization processes appear to be governed by statistical theory and the ground electronic state of the ion. In the monomer breakdown diagram, the smoothly changing branching ratio between H and CH3 loss is at odds with rate theory predictions, and shows that none of the currently employed few-parameter rate models, appropriate for experimental rate curve fitting, yields a correct description for this process in the experimental energy range.

  3. Oligomerization state of photosynthetic core complexes is correlated with the dimerization affinity of a transmembrane helix.

    Science.gov (United States)

    Hsin, Jen; LaPointe, Loren M; Kazy, Alla; Chipot, Christophe; Senes, Alessandro; Schulten, Klaus

    2011-09-07

    In the Rhodobacter (Rba.) species of photosynthetic purple bacteria, a single transmembrane α-helix, PufX, is found within the core complex, an essential photosynthetic macromolecular assembly that performs the absorption and the initial processing of light energy. Despite its structural simplicity, many unresolved questions surround PufX, the most important of which is its location within the photosynthetic core complex. One proposed placement of PufX is at the center of a core complex dimer, where two PufX helices associate in the membrane and form a homodimer. Inability for PufX of certain Rba. species to form a homodimer is thought to lead to monomeric core complexes. In the present study, we employ a combination of computational and experimental techniques to test the hypothesized homodimerization of PufX. We carry out a systematic investigation to measure the dimerization affinity of PufX from four Rba. species, Rba. blasticus , Rba. capsulatus , Rba. sphaeroides , and Rba. veldkampii , using a molecular dynamics-based free-energy method, as well as experimental TOXCAT assays. We found that the four PufX helices have substantially different dimerization affinities. Both computational and experimental techniques demonstrate that species with dimeric core complexes have PufX that can potentially form a homodimer, whereas the one species with monomeric core complexes has a PufX with little to no dimerization propensity. Our analysis of the helix-helix interface revealed a number of positions that may be important for PufX dimerization and the formation of a hydrogen-bond network between these GxxxG-containing helices. Our results suggest that the different oligomerization states of core complexes in various Rba. species can be attributed, among other factors, to the different propensity of its PufX helix to homodimerize.

  4. Regioselective dimerization of ferulic acid in a micellar solution

    DEFF Research Database (Denmark)

    Larsen, E; Andreasen, Mette Findal; Christensen, L P

    2001-01-01

    -hydroxy-3-methoxyphenyl)-3,7-dioxabicyclo[3.3.0]octane-2,6-dione (18%) as the main product. The use of micelles appears to be not only a new way to synthesize regioisomeric ferulic acid dehydrodimers but may also help to understand the regiospecificity of dimeric hydroxycinnamate formation in vivo...... that regioisomeric ferulic acid dehydrodimers can be obtained in one step from trans-ferulic acid after attachment to these micelles and using the biomimetic peroxidase-H2O2 system. The surfactant hexadecyltrimethylammonium hydroxide yielded trans-4-(4-hydroxy-3-methoxybenzylidene)-2-(4-hydroxy-3-methoxyphenyl)-5......-oxotetrahydrofuran-3-carboxylic acid (25%), (E,E)-4,4'-dihydroxy-5,5'-dimethoxy-3,3'-bicinnamic acid (21%), and trans-5-[(E)-2-carboxyvinyl]-2-(4-hydroxy-3-methoxyphenyl)-7-methoxy-2,3-dihydrobenzofuran-3-carboxylic acid (14%), whereas the surfactant tetradecyltrimethylammonium bromide gave 4-cis, 8-cis-bis(4...

  5. Intermolecular potential energy surface for CS2 dimer.

    Science.gov (United States)

    Farrokhpour, Hossein; Mombeini, Zainab; Namazian, Mansoor; Coote, Michelle L

    2011-04-15

    A new four-dimensional intermolecular potential energy surface for CS(2) dimer is obtained by ab initio calculation of the interaction energies for a range of configurations and center-of-mass separation distances for the first time. The calculations were performed using the supermolecular approach at the Møller-Plesset second-order perturbation (MP2) level of theory with the augmented correlation consistent basis sets (aug-cc-pVxZ, x = D, T) and corrected for the basis-set superposition error using the full counterpoise correction method. A two-point extrapolation method was used to extrapolate the calculated energy points to the complete basis set limit. The effect of using the higher levels of theory, quadratic configuration interaction containing single, double, and perturbative triple excitations QCISD(T) and coupled cluster singles, doubles and perturbative triples excitations CCSD(T), on the shape of potential energy surface was investigated. It is shown that the MP2 level of theory apparently performs extremely poorly for describing the intermolecular potential energy surface, overestimating the total energy by a factor of nearly 1.73 in comparison with the QCISD(T) and CCSD(T) values. The value of isotropic dipole-dipole dispersion coefficient (C(6) ) of CS(2) fluid was obtained from the extrapolated MP2 potential energy surface. The MP2 extrapolated energy points were fitted to well-known analytical potential functions using two different methods to represent the potential energy surface analytically. The most stable configuration of the dimer was determined at R = 6.23 au, α = 90°, β = 90°, and γ = 90°, with a well depth of 3.980 kcal mol(-1) at the MP2 level of theory. Finally, the calculated second virial coefficients were compared with experimental values to test the quality of the presented potential energy surface. Copyright © 2010 Wiley Periodicals, Inc.

  6. Exploring the Stable Isotope Record of Lake Carpenter: A Lacustrine Sequence in the Aptian-Albian Cretaceous Cedar Mountain Formation, Utah, USA

    Science.gov (United States)

    Montgomery, E.; Al-Suwaidi, A. H.; Suarez, M. B.; Kirkland, J. I.; Suarez, C. A.

    2014-12-01

    The Cedar Mountain Formation (CMF) represents the earliest deposition of terrestrial Cretaceous strata in the USA, recording significant changes in biota and climate. Understanding these transitions requires improved time constraints and high-resolution proxy records. Here we present new δ13C (organic carbon & carbonate) chemostratigraphic record of a lacustrine sequence in a locality named "Lake Carpenter", near Moab, Utah. Lake Carpenter (LC) comprises interbedded limestone and mudstone units of the Ruby Ranch Member of the CMF. Results of the chemostratigraphy are constrained by detrital zircons from the section allowing correlation of the chemostratigraphy to the carbon isotope segments C9 to C11 (Bralower et al., 1999) spanning the Late Aptian to Early Albian, and supported by previous litho- and chemostratigraphic work in the CMF. δ13Corg values show a pronounced negative stepped excursion, of -6‰ with values reaching -32.3 ‰ occurring in conjunction with an increase in TOC. This negative excursion is followed by a positive recovery, with values of ~-25‰ and relatively low TOC. δ13Ccarb records positive values, up to +8‰, in the lowermost part of the section (changes in water supply to the lake, or climatic variability resulting in the lake drying out. δ13Corg values may be affected by local lake dynamics, including variations in organic carbon storage and changes in algal productivity, perhaps also indicative of changes in nutrient availability due to increased run off and/or fluctuations in atmospheric carbon particularly light δ13Corg. Both climatic and hydrological variation in the section may be due to the rise of the Sevier Mountains resulting in an orographic impact on the lake either as a result of increase in high altitude run off, or changes in the amount of precipitation.

  7. An introduction to the dimer model

    International Nuclear Information System (INIS)

    Kenyon, R.

    2004-01-01

    A perfect matching of a graph is a subset of edges which covers every vertex exactly once, that is, for every vertex there is exactly one edge in the set with that vertex as endpoint. The dimer model is the study of the set of perfect matchings of a (possibly infinite) graph. The most well-known example is when the graph is Z 2 , for which perfect matchings are equivalent (via a simple duality) to domino tilings, that is, tilings of the plane with 2 x 1 and 1 x 2 rectangles. In the first three sections we study domino tilings of the plane and of finite polygonal regions, or equivalently, perfect matchings on Z 2 and subgraphs of Z 2 . In the last two sections we study the FK-percolation model and the dimer model on a more general family of planar graphs

  8. PT -symmetric dimer of coupled nonlinear oscillators

    Indian Academy of Sciences (India)

    In this case there are three solutions of the coupled dimer eqs (1) and (2) out of which we present two solutions now and the third one (a novel superposed solution) in the next subsection. Solution I: It is easy to check that u(t) = ±v(t) = Adn[β(t + t0), m]. (22) is an exact solution provided. (ǫ + δ)β2 = −2β2, (2 − m)β2 = −1 ± k.

  9. Electronic structure of the water dimer cation

    Czech Academy of Sciences Publication Activity Database

    Pieniazek, P. A.; Vande Vondele, J.; Jungwirth, Pavel; Krylov, A. I.; Bradforth, S. E.

    2008-01-01

    Roč. 112, č. 27 (2008), s. 6159-6170 ISSN 1089-5639 R&D Projects: GA ČR(CZ) GA202/06/0286 Grant - others:NSF(US) CHE-0617060 Institutional research plan: CEZ:AV0Z40550506 Keywords : water dimer * ionization * proton transfer * ab initio Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.871, year: 2008

  10. On the dimerization of linear polymers

    International Nuclear Information System (INIS)

    Aragao Carvalho, C. de.

    1988-08-01

    We use the continuum limit of the Su-Schrieffer-Heeger model for linear polymers to construct its effective potential (Gibbs free energy) both at zero and finite temperature. We study both trans and cis-polymers. Our results show that, depending on a renormalization condition to be extracted from experiment, there are several possibilities for the minima of the dimerized ground state of cis-polymers. All calculations are done in the one-loop approximation. (author). 16 refs, 3 figs

  11. Chiroptical properties, binding affinity, and photostability of a conjugated zinc porphyrin dimer complexed with left-handed Z-DNA and right-handed B-DNA.

    Science.gov (United States)

    Choi, Jung Kyu; Reed, Aisha; Balaz, Milan

    2014-01-14

    We have studied the UV-vis absorption and chiroptical properties, binding affinity and photostability of a conjugated positively charged butadiyne-linked Zn(ii) porphyrin dimer bound to DNA sequence poly(dG-dC)2. Right-handed B-DNA, spermine-induced Z-DNA and Co(iii)-induced Z-DNA have been explored. Resonance light scattering (RLS) spectra showed formation of porphyrin aggregates in the presence of all DNA forms with the largest aggregates formed with B-DNA. The porphyrin dimer gave rise to induced bisignate circular dichroism (CD) signals in the presence of the left-handed Z-DNA conformations. On the other hand, the dimer stayed nearly chiroptically silent when complexed with the B-form of poly(dG-dC)2. Our results indicated that the conjugated Zn(ii) porphyrin dimer can be used as a sensor for the chiroptical detection of Z-DNA in the visible (400-500 nm) and near-infrared region of the electromagnetic spectrum (700-800 nm). The helicity of DNA had little effect on the dimer binding affinities. The photostability of the porphyrin dimer complexed with any form of DNA was higher than that of the free molecule. The porphyrin dimer bound to Z-DNA exhibited slower photobleaching than the B-DNA dimer complex.

  12. Palmitoylated APP Forms Dimers, Cleaved by BACE1

    Science.gov (United States)

    Fenn, Rebecca H.; Barren, Cory; Tanzi, Rudolph E.; Kovacs, Dora M.

    2016-01-01

    A major rate-limiting step for Aβ generation and deposition in Alzheimer’s disease brains is BACE1-mediated cleavage (β-cleavage) of the amyloid precursor protein (APP). We previously reported that APP undergoes palmitoylation at two cysteine residues (Cys186 and Cys187) in the E1-ectodomain. 8–10% of total APP is palmitoylated in vitro and in vivo. Palmitoylated APP (palAPP) shows greater preference for β-cleavage than total APP in detergent resistant lipid rafts. Protein palmitoylation is known to promote protein dimerization. Since dimerization of APP at its E1-ectodomain results in elevated BACE1-mediated cleavage of APP, we have now investigated whether palmitoylation of APP affects its dimerization and whether this leads to elevated β-cleavage of the protein. Here we report that over 90% of palAPP is dimerized while only ~20% of total APP forms dimers. PalAPP-dimers are predominantly cis-oriented while total APP dimerizes in both cis- and trans-orientation. PalAPP forms dimers 4.5-times more efficiently than total APP. Overexpression of the palmitoylating enzymes DHHC7 and DHHC21 that increase palAPP levels and Aβ release, also increased APP dimerization in cells. Conversely, inhibition of APP palmitoylation by pharmacological inhibitors reduced APP-dimerization in coimmunoprecipitation and FLIM/FRET assays. Finally, in vitro BACE1-activity assays demonstrate that palmitoylation-dependent dimerization of APP promotes β-cleavage of APP in lipid-rich detergent resistant cell membranes (DRMs), when compared to total APP. Most importantly, generation of sAPPβ-sAPPβ dimers is dependent on APP-palmitoylation while total sAPPβ generation is not. Since BACE1 shows preference for palAPP dimers over total APP, palAPP dimers may serve as novel targets for effective β-cleavage inhibitors of APP as opposed to BACE1 inhibitors. PMID:27875558

  13. Geochemical and stable isotopic data on barren and mineralized drill core in the Devonian Popovich Formation, Screamer sector of the Betze-Post gold deposit, northern Carlin trend, Nevada

    Science.gov (United States)

    Christiansen, William D.; Hofstra, Albert H.; Zohar, Pamela B.; Tousignant, Gilles

    2011-01-01

    The Devonian Popovich Formation is the major host for Carlin-type gold deposits in the northern Carlin trend of Nevada. The Popovich is composed of gray to black, thin-bedded, calcareous to dolomitic mudstone and limestone deposited near the carbonate platform margin. Carlin-type gold deposits are Eocene, disseminated, auriferous pyrite deposits characterized by acid leaching, sulfidation, and silicification that are typically hosted in Paleozoic calcareous sedimentary rocks exposed in windows through siliceous sedimentary rocks of the Roberts Mountains allochthon. The Carlin trend currently is the largest gold producer in the United States. The Screamer ore zone is a tabular body on the periphery of the huge Betze-Post gold deposit. Screamer is a good place to study both the original lithogeochemistry of the Popovich Formation and the effects of subsequent alteration and mineralization because it is below the level of supergene oxidation, mostly outside the contact metamorphic aureole of the Jurassic Goldstrike stock, has small, high-grade ore zones along fractures and Jurassic dikes, and has intervening areas with lower grade mineralization and barren rock. In 1997, prior to mining at Screamer, drill core intervals from barren and mineralized Popovich Formation were selected for geochemical and stable isotope analysis. The 332, five-foot core samples analyzed are from five holes separated by as much as 2000 feet (600 meters). The samples extend from the base of the Wispy unit up through the Planar and Soft sediment deformation units into the lower part of the upper Mud unit of the Popovich Formation.

  14. Thermodynamic origins of protein folding, allostery, and capsid formation in the human hepatitis B virus core protein.

    Science.gov (United States)

    Alexander, Crispin G; Jürgens, Maike C; Shepherd, Dale A; Freund, Stefan M V; Ashcroft, Alison E; Ferguson, Neil

    2013-07-23

    HBc, the capsid-forming "core protein" of human hepatitis B virus (HBV), is a multidomain, α-helical homodimer that aggressively forms human HBV capsids. Structural plasticity has been proposed to be important to the myriad functions HBc mediates during viral replication. Here, we report detailed thermodynamic analyses of the folding of the dimeric HBc protomer under conditions that prevented capsid formation. Central to our success was the use of ion mobility spectrometry-mass spectrometry and microscale thermophoresis, which allowed folding mechanisms to be characterized using just micrograms of protein. HBc folds in a three-state transition with a stable, dimeric, α-helical intermediate. Extensive protein engineering showed thermodynamic linkage between different structural domains. Unusual effects associated with mutating some residues suggest structural strain, arising from frustrated contacts, is present in the native dimer. We found evidence of structural gatekeepers that, when mutated, alleviated native strain and prevented (or significantly attenuated) capsid formation by tuning the population of alternative native conformations. This strain is likely an evolved feature that helps HBc access the different structures associated with its diverse essential functions. The subtle balance between native and strained contacts may provide the means to tune conformational properties of HBc by molecular interactions or mutations, thereby conferring allosteric regulation of structure and function. The ability to trap HBc conformers thermodynamically by mutation, and thereby ablate HBV capsid formation, provides proof of principle for designing antivirals that elicit similar effects.

  15. Interaction of the αβ dimers of the insulin-like growth factor I receptor required for receptor autophosphorylation

    International Nuclear Information System (INIS)

    Tollesfsen, S.E.; Stoszek, R.M.; Thompson, K.

    1991-01-01

    The authors have recently found that association of the two αβ dimers of the insulin-like growth factor I (IGF I) receptor is required for formation of a high-affinity binding site for IGF I. To determine the structural requirements for IGF I activated kinase activity, they have examined the effect of dissociation of the two αβ dimers of the IGF I receptor on β subunit autophosphorylation. The αβ dimers formed after treatment with 2 mM dithiothreitol (DTT) at pH 8.75 for 5 min were separated from IGF I receptor remaining as tetramers after DTT treatment by fast protein liquid chromatography on a Superose 6 gel filtration column. Purification of the αβ dimers was confirmed by Western blot analysis using 125 I-labeled αIR-3, a monoclonal antibody to the IGF I receptor. Autophosphorylation of the IGF I receptor (αβ) 2 tetramer, treated without DTT or remaining after DTT treatment, is stimulated 1.6-2.9-fold by IGF I. In contrast, autophosporylation of the αβ dimers incubated in the presence or absence of IGF I (100 ng/mL) does not occur. Both IGF I receptor dimers and tetramers exhibit similar kinase activities using the synthetic substrate Arg-Arg-Leu-Ile-Glu-Asp-Ala-Glu-Tyr-Ala-Ala-Arg-Gly, indicating that the failure to detect autophosphorylation of the IGF I receptor dimers does not result from inactivation of the kinase by DTT treatment. They conclude that autophosphorylation of the IGF I receptor depends upon the interaction of the two αβ dimers

  16. Dimerization of tri(4-bromophenyl)benzene by aryl-aryl coupling from solution on a gold surface.

    Science.gov (United States)

    Russell, James C; Blunt, Matthew O; Garfitt, Jason M; Scurr, David J; Alexander, Morgan; Champness, Neil R; Beton, Peter H

    2011-03-30

    Monolayers of monomer 1,3,5-tri(4-bromophenyl)benzene (TBPB) and the dimerized product 3,3''',5,5'''-tetra(4-bromophenyl)quaterphenyl (TBPQ) on a gold surface have been studied using ambient scanning tunneling microscopy and time-of-flight secondary ion mass spectrometry (ToF-SIMS). Molecular layers are prepared by allowing sessile drops of solution to dry on a gold substrate. For room-temperature deposition we observe ordered arrays of TBPB in three distinct packing arrangements. Deposition on a heated substrate leads to the formation of the dimerized product, TBPQ, through a surface-induced aryl-aryl coupling. Regions of TBPQ coexist with regions of disordered multiply linked molecules. The conversion of monomer TPBP to dimers is confirmed using ToF-SIMS. Our results demonstrate an alternative, solution-phase approach to the formation of large molecules and nanostructures by coupling reactions.

  17. Viscosity and sedimentation behaviors of the magnetorheological suspensions with oleic acid/dimer acid as surfactants

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Jianjian; Yan, Hua; Hu, Zhide; Ding, Ding

    2016-11-01

    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{sup −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. - Highlights: • Surfactants were employed to make adjustments of the hydrophobicity of particles. • Polar attractions between particles increased the viscosity considerably. • Loose and open flocculation was formed in CI/DA suspension. • The steric repulsion of oleic acid played a limited role in the stability.

  18. MspA nanopores from subunit dimers.

    Directory of Open Access Journals (Sweden)

    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

  19. Dimeric Building Blocks for Solid-Phase Synthesis of α-Peptide-β-Peptoid Chimeras

    DEFF Research Database (Denmark)

    Seigan, Gitte Bonke; Vedel, Line; Matthias, Witt,

    2008-01-01

    Recently, a novel type of antimicrobial and proteolytically stable peptidomimetic oligomers having an α-peptide-β-peptoid chimeric backbone was reported. The present paper describes efficient protocols for the preparation of a wide range of dimeric building blocks, displaying different types...... of side-chains, for use in solid-phase synthesis (SPS) of libraries of this type of oligomers. The β-peptoid monomers were obtained by microwave-assisted aza-Michael additions to acrylic esters. Subsequent solution-phase peptide coupling with suitably protected α-amino acids afforded dimeric intermediates....... Even sluggish peptide couplings, involving sterically hindered N-alkyl-β-alanines or amino acids with bulky side-chains, gave high yields on multigram-scale when using microwave (MW) irradiation. Protecting group and side-chain manipulations were performed as one-pot solution-phase procedures to afford...

  20. Easily processable highly ordered Langmuir-Blodgett films of quaterthiophene disiloxane dimer for monolayer organic field-effect transistors.

    Science.gov (United States)

    Sizov, Alexey S; Anisimov, Daniil S; Agina, Elena V; Borshchev, Oleg V; Bakirov, Artem V; Shcherbina, Maxim A; Grigorian, Souren; Bruevich, Vladimir V; Chvalun, Sergei N; Paraschuk, Dmitry Yu; Ponomarenko, Sergei A

    2014-12-23

    Self-assembly of highly soluble water-stable tetramethyldisiloxane-based dimer of α,α'-dialkylquaterthiophene on the water-air interface was investigated by Langmuir, grazing incidence X-ray diffraction, and X-ray reflectivity techniques. The conditions for formation of very homogeneous crystalline monolayer Langmuir-Blodgett (LB) films of the oligomer were found. Monolayer organic field-effect transistors (OFETs) based on these LB films as a semiconducting layer showed hole mobilities up to 3 × 10(-3) cm(2)/(V s), on-off ratio of 10(5), small hysteresis, and high long-term stability. The electrical performance of the LB films studied is close to that for the same material in the bulk or in the monolayer OFETs prepared from water vapor sensitive chlorosilyl derivatives of quaterthiophene by self-assembling from solution. These findings show high potential of disiloxane-based LB films in monolayer OFETs for large-area organic electronics.

  1. Van der Waals bond in dimers: H2Ne, H2Ar, H2Kr

    International Nuclear Information System (INIS)

    Waaijer, M.

    1981-01-01

    The H 2 -inert gas dimers H 2 X, and particularly H 2 Ne, H 2 Ar and H 2 Kr, form the subject of this thesis and are loosely bound van der Waals complexes, which is reflected in the low number of bound states and the small anisotropic interaction. The H 2 X dimers studied are formed in a supersonic nozzle expansion, in which the internal energy is converted into the macroscopic flow energy, establishing an internal temperature drop to 3 K, which favours dimer formation. Because of this cooling the H 2 X dimers relax to the lowest rotational states. The hyperfine transitions have been measured using magnetic beam resonance and yield information about the isotropic as well as the anisotropic intermolecular potential in the range between the classical turning points and in the adjacent part of the repulsive branch. The sensitivity of the method is very high and slight changes in the intermolecular potential cause significant effects. The analysis of the measured hyperfine transitions incorporates all interacting states of the molecule, bound as well as unbound (continuum) states. For H 2 Ne, which is the best studied H 2 -inert gas system from the experimental point of view, the author succeeded in establishing an intermolecular potential, that provides a solid ground for comparison with future ab initio calculations. (Auth.)

  2. Dimerization of DOCK2 is essential for DOCK2-mediated Rac activation and lymphocyte migration.

    Directory of Open Access Journals (Sweden)

    Masao Terasawa

    Full Text Available The migratory properties of lymphocytes depend on DOCK2, an atypical Rac activator predominantly expressed in hematopoietic cells. Although DOCK2 does not contain the Dbl homology domain typically found in guanine nucleotide exchange factors (GEFs, DOCK2 mediates the GTP-GDP exchange reaction for Rac via its DOCK homology region (DHR-2 (also known as CZH2 or Docker domain. DOCK2 DHR-2 domain is composed of three lobes, and Rac binding site and catalytic center are generated entirely from lobes B and C. On the other hand, lobe A has been implicated in dimer formation, yet its physiological significance remains unknown. Here, we report that lobe A-mediated DOCK2 dimerization is crucial for Rac activation and lymphocyte migration. We found that unlike wild-type DOCK2, DOCK2 mutant lacking lobe A failed to restore motility and polarity when expressed in thymoma cells and primary T cells lacking endogenous expression of DOCK2. Similar results were obtained with the DOCK2 point mutant having a defect in dimerization. Deletion of lobe A from the DHR-2 domain did not affect Rac GEF activity in vitro. However, fluorescence resonance energy transfer analyses revealed that lobe A is required for DOCK2 to activate Rac effectively during cell migration. Our results thus indicate that DOCK2 dimerization is functionally important under the physiological condition where only limited amounts of DOCK2 and Rac are localized to the plasma membrane.

  3. Effect of pigment on photomediated production of thymine dimers in cultured melanoma cells

    International Nuclear Information System (INIS)

    London, D.A.; Carter, D.M.; Condit, E.S.

    1976-01-01

    It was the aim of these studies to determine whether the presence of intracellular melanin quantitatively alters the rate of production of thymine dimers in DNA of irradiated cells in culture. Pigmented and nonpigmented Cloudman mouse melanoma cells were selected assuming that the two cell lines differ primarily in their content of melanin pigment. Cells were cultivated in tritiated thymine in order to label their DNA and were then exposed to ultraviolet (uv) irradiation (260 nm, 500-2000 ergs/mm 2 ). Neither cell line survived these doses of irradiation. DNA was extracted immediately following irradiation and was subjected to acid hydrolysis. The presence of thymine dimers was determined by two-dimensional paper chromatography. The percent of labeled thymine recovered as thymine dimer was calculated and was found to be a linear function of uv dose for both cell lines. The rate of formation of dimers in the nonpigmented cells was nearly twice that in the pigmented cells. These data demonstrate the photoprotective property of intracellular melanin in shielding isolated cells from one type of photomediated injury to DNA

  4. Dysprosium complexes with mono-/di-carboxylate ligands—From simple dimers to 2D and 3D frameworks

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yingjie, E-mail: yzx@ansto.gov.au [Australian Nuclear Science and Technology Organization, Locked Bag 2001, Kirrawee DC, NSW 2232 (Australia); Bhadbhade, Mohan [Mark Wainwright Analytical Centre, University of New South Wales, Kensington, NSW 2052 (Australia); Scales, Nicholas; Karatchevtseva, Inna [Australian Nuclear Science and Technology Organization, Locked Bag 2001, Kirrawee DC, NSW 2232 (Australia); Price, Jason R. [Australian Synchrotron, 800 Blackburn Road, Clayton, VIC 3168 (Australia); Lu, Kim; Lumpkin, Gregory R. [Australian Nuclear Science and Technology Organization, Locked Bag 2001, Kirrawee DC, NSW 2232 (Australia)

    2014-11-15

    Four dysprosium (Dy) single carboxylates, a formate, a propionate, a butyrate and an oxalate have been synthesized and structurally characterized. The structure of Dy(HCO{sub 2}){sub 3} (1) contains nine-fold coordinated Dy polyhedra in perfect tricapped trigonal prisms. They are linked through trigonal O atoms forming 1D pillars which are further linked together through tricapped O atoms into a 3D pillared metal organic framework. The network structure is stable up to 360 °C. The structure of [Dy{sub 2}(C{sub 2}O{sub 4}){sub 3}(H{sub 2}O){sub 6}]·2.5H{sub 2}O (2) contains nine-fold coordinated Dy polyhedra linking together through μ{sub 2}-bridging oxalate anions into a 2D hexagonal layered structure. Both [Dy{sub 2}(Pr){sub 6}(H{sub 2}O){sub 4}]·(HPr){sub 0.5} (3) [Pr=(C{sub 2}H{sub 5}CO{sub 2}){sup −1}] and [Dy{sub 2}(Bu){sub 6}(H{sub 2}O){sub 4}] (4) [Bu=(C{sub 3}H{sub 7}CO{sub 2}){sup −1}] have similar di-nuclear structures. The Raman vibration modes of the complexes have been investigated. - Graphical abstract: Four dysprosium (Dy) complexes with formate, propionate, butyrate and oxalate ligands have been synthesized and characterized. The Dy formato complex has a 3D pillared metal organic framework and the structure is stable up to 360 °C whilst the complexes with longer alkyl chained mono-carboxylates possess similar di-nuclear structures. The Dy oxalato complex has a 2D hexagonal (honeycomb-type) structure. Their Raman vibration modes have been investigated. - Highlights: • New Dysprosium complexes with formate, propionate, butyrate and oxalate ligands. • Crystal structures range from dimers to two and three dimensional frameworks. • Vibrational modes have been investigated and correlated to the structures. • The complexes are thermal robust and stable to over 300 °C.

  5. Study of dimerization reaction during cathodic splitting of halogen. Dimerization during reduction of butyl iodide

    International Nuclear Information System (INIS)

    Tomilov, A.P.

    2001-01-01

    The process of electrochemical reduction of butyl iodide in methanol in the presence of sodium methylate was studied. It was ascertained that the yield of dimer product, i. e. octane, depends essentially on the cathode material. Copper and iron (steel 3) proved the most active agents in dimerization process. Conditions (current density 0.03-0.10 A/cm 2 , 0 deg C, 0.005 M CH 3 ONa), under which octane yield amounts to 83-84% in matter, were found [ru

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

    Science.gov (United States)

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

    2018-03-01

    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.

  7. Serum D-dimer Levels Are Proportionally Associated with Left Atrial Enlargement in Patients with an Acute Ischemic Stroke due to Non-valvular Atrial Fibrillation.

    Science.gov (United States)

    Kim, Tae-Won; Song, In-Uk; Chung, Sung-Woo; Kim, Joong-Seok; Koo, Jaseong; Lee, Kwang-Soo

    2016-01-01

    Objective Left atrial enlargement (LAE) may predispose individuals to blood stasis in atrial fibrillation (AF), and thus play a crucial role in thrombogenesis. The D-dimer level is one of the surrogate markers for a hypercoagulable state and reflects thrombus formation in AF. Since the D-dimer level reflects hypercoagulability as well as thrombus and fibrin burdens, LAE could be associated with a D-dimer elevation. However, no studies have explored this association or which factors contribute to increases in the D-dimer levels in patients with AF. Therefore, we assessed whether the serum D-dimer levels are related to the left atrial volume index (LAVI) or other vascular risk factors and also evaluated the association between the D-dimer levels and the initial stroke severity. Methods Ninety-eight consecutive patients with an acute ischemic stroke and non-valvular AF (NVAF) who were anticoagulation-naïve were enrolled, and all patients were stratified into moderate-to-severe and mild neurologic deficit groups using the National Institutes of Health Stroke Scale on admission. The association between the initial serum D-dimer levels and the LAVI was evaluated in all enrolled patients, and the serum D-dimer levels were compared between the two groups. Results The patients were classified into two groups according to the severity of the neurologic deficit. In a partial correlation coefficient analysis adjusted for confounding factors, an increase in the initial serum D-dimer levels was significantly associated with LAVI (r=0.286; p=0.027). A linear regression analysis showed that a history of peripheral artery disease was the factor most strongly associated with the serum D-dimer level (t=3.90, pacute ischemic stroke and NVAF.

  8. Dimeric assembly of enterocyte brush border enzymes

    DEFF Research Database (Denmark)

    Danielsen, E M

    1994-01-01

    The noncovalent, dimeric assembly of small intestinal brush border enzymes was studied by sedimentation analysis in density gradients of extracts of pulse-labeled pig jejunal mucosal explants. Like aminopeptidase N (EC 3.4.11.2), sucrase-isomaltase (EC 3.2.1.48-10), aminopeptidase A (EC 3...... appearance of the liposome-reconstituted enzyme [Norén et al. (1986) J. Biol. Chem. 261, 12306-12309], showing only the inner, membrane-anchored domains of the monomers to be in close contact with one another while the outer domains are far apart. In contrast to the other brush border enzymes studied...

  9. Oncogenic TPM3-ALK activation requires dimerization through the coiled-coil structure of TPM3

    Energy Technology Data Exchange (ETDEWEB)

    Amano, Yosuke; Ishikawa, Rie; Sakatani, Toshio [Department of Respiratory Medicine, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655 (Japan); Ichinose, Junji [Department of Cardiothoracic Surgery, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655 (Japan); Sunohara, Mitsuhiro; Watanabe, Kousuke; Kage, Hidenori [Department of Respiratory Medicine, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655 (Japan); Nakajima, Jun [Department of Cardiothoracic Surgery, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655 (Japan); Nagase, Takahide; Ohishi, Nobuya [Department of Respiratory Medicine, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655 (Japan); Takai, Daiya, E-mail: dtakai-ind@umin.ac.jp [Department of Respiratory Medicine, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655 (Japan); Department of Clinical Laboratory, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655 (Japan)

    2015-02-13

    Inflammatory myofibroblastic tumor (IMT) is a mesenchymal tumor that can arise from anywhere in the body. Anaplastic lymphoma kinase (ALK) gene rearrangements, most often resulting in the tropomyosin 3 (TPM3)-ALK fusion gene, are the main causes of IMT. However, the mechanism of malignant transformation in IMT has yet to be elucidated. The purpose of this study was to clarify the role of the TPM3 region in the transformation of IMT via TPM3-ALK. Lentivirus vectors containing a TPM3-ALK fusion gene lacking various lengths of TPM3 were constructed and expressed in HEK293T and NIH3T3 cell lines. Focus formation assay revealed loss of contact inhibition in NIH3T3 cells transfected with full-length TPM3-ALK, but not with ALK alone. Blue-native polyacrylamide gel electrophoresis (BN-PAGE) revealed that TPM3-ALK dimerization increased in proportion to the length of TPM3. Western blot showed phosphorylation of ALK, ERK1/2, and STAT3 in HEK293T cells transfected with TPM3-ALK. Thus, the coiled-coil structure of TPM3 contributes to the transforming ability of the TPM3-ALK fusion protein, and longer TPM3 region leads to higher dimer formation. - Highlights: • TPM3-ALK fusion protein dimerizes through the coiled-coil structure of TPM3. • Longer coiled-coil structure of TPM3 leads to higher TPM3-ALK dimer formation. • Presence of TPM3-ALK dimer leads to ALK, STAT3, and ERK1/2 phosphorylation. • Presence of TPM3-ALK leads to loss of contact inhibition. • BN-PAGE is a simple technique for visualizing oncogenic dimerization.

  10. A stable analogue of thromboxane A2, 9,11-epithio-11,12-methanothromboxane A2, stimulates bone resorption in vitro and osteoclast-like cell formation in mouse marrow culture.

    Science.gov (United States)

    Saito, S; Yamasaki, K; Yamada, S; Matsumoto, A; Akatsu, T; Takahashi, N; Shibasaki, Y; Suda, T; Fukuhara, T

    1991-01-01

    Thromboxane A2 (TXA2) is a powerful promoter of platelet aggregation and smooth muscle contraction. However, this compound is highly unstable and is rapidly hydrated to a more stable metabolite, thromboxane B2 (TXB2). TXA2 has been considered to be involved in bone resorption, in particular bone loss caused by inflammatory diseases and by orthodontic treatment. However precise mechanisms of bone resorption caused by TXA2 have not yet been proved because of its highly unstable nature. Recently, a chemically stable analogue of TXA2, 9,11-epithio-11,12-methanothromboxane A2 (STA2), was successfully synthesized. Using this synthetic compound, we examined its in vitro bone resorbing activity and induction of osteoclast-like cells in a mouse marrow culture system in comparison with related compounds with bone resorbing activity. Like prostaglandin E2 (PGE2), a well-known bone resorbing agent, STA2 time- and dose-dependently stimulated the release of 45Ca from prelabelled mouse calvariae. Both STA2 and PGE2 induced the accumulation of cAMP in mouse calvariae. The TXA2 antagonist, ONO-3708, inhibited STA2-induced release of 45Ca. TXB2 induced neither bone resorption nor cAMP accumulation. When mouse marrow cells were cultured with STA2 for 8 days, osteoclast-like multinucleated cells appeared in parallel with the increase of the amount of STA2 added. Again TXB2 showed no effect on osteoclast-like cell formation. These results indicate a role for TXA2 in some form of bone resorption.

  11. Kinetics of the dimerization of retroviral proteases: The "fireman's grip" and dimerization

    Czech Academy of Sciences Publication Activity Database

    Ingr, Marek; Kondrová, Taťána; Stříšovský, Kvido; Majerová, E.; Konvalinka, Jan

    2003-01-01

    Roč. 12, - (2003), s. 2173-2182 ISSN 0961-8368 R&D Projects: GA MZd NI6339 Institutional research plan: CEZ:AV0Z4055905 Keywords : retroviral protease * dimerization * HIV protease Subject RIV: CE - Biochemistry Impact factor: 3.787, year: 2003

  12. Tunneling anisotropic magnetoresistance via molecular π orbitals of Pb dimers

    Science.gov (United States)

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

    2018-01-01

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

  13. Routes to new hafnium(IV) tetraaryl porphyrins and crystal structures of unusual phosphate-, sulfate-, and peroxide-bridged dimers.

    Science.gov (United States)

    Falber, Alexander; Todaro, Louis; Goldberg, Israel; Favilla, Michael V; Drain, Charles Michael

    2008-01-21

    New routes for the synthesis of mono tetraaryl porphyrinato hafnium(IV) complexes, Hf(IV)Por(L)(2), are reported, where the secondary ligands, L, are determined by the method of purification. These synthetic routes cater to the solubility of the macrocycles and provide access to Hf(IV) complexes of meso tetraaryl porphyrins bearing diverse functional groups such as phenyl, tolyl, pyridyl, pentafluorophenyl, and carboxyphenyl. The latter three derivatives significantly expand the repertoire of hafnium porphyrinates. One route refluxes the porphyrin with HfCl(4) in 1-chloronaphthalene or in a mixed solvent of 1-chloronaphthalene and o-cresol. A second, solventless method is also reported wherein the porphyrin is mixed with Hf(cp)(2)Cl(2) and heated to give the metalated porphyrin in good yields. Simultaneous purification and formation of stable porphyrinato hafnium(IV) diacetate complexes, Hf(Por)OAc(2), is accomplished by elution over silica gel using 3-5% acetic acid in the eluent. Exchange of the acetate ligands for other oxo-bearing ligands can be nearly quantitative, such as p-aminobenzoate (PABA), pentanoate (pent), or octanoate (oct). Notably, we find that two to three of a variety of small multitopic dianions such as peroxo (O(2)(-2)), SO(4)(-2), and HPO(4)(-2) serve to bridge between two Hf(Por) moieties to form stable dimers. The crystal structures of this library of Hf(Por) complexes are reported, and we note that careful analysis of crystallography data reveals (Por)Hf(micro-eta(2)-O(2))(2)Hf(Por) rather than four bridging oxo or hydroxy ions.

  14. Optical Fluoride Sensor Based on Monomer-Dimer Equilibrium of Scandium(III)-Octaethylporphyrin in a Plasticized Polymeric Film

    OpenAIRE

    Kang, Youngjea; Kampf, Jeff W.; Meyerhoff, Mark E.

    2007-01-01

    A fluoride-selective optical sensor based on scandium(III) octaethylporphyrin (Sc(III)OEP) as an ionophore within a plasticized PVC film is described. The presence of fluoride ion in the aqueous sample phase increases the formation of a difluoro-bridged Sc(III)OEP dimer species in the polymer film. The ability of the Sc(III) porphyrin to form the dimeric structure in the presence of fluoride is confirmed by UV-Vis spectroscopy and X-ray crystallography. For more practical sensing applications...

  15. 3D nanostar dimers with a sub-10-nm gap for single-/few-molecule surface-enhanced raman scattering

    KAUST Repository

    Chirumamilla, Manohar

    2014-01-22

    Plasmonic nanostar-dimers, decoupled from the substrate, have been fabricated by combining electron-beam lithography and reactive-ion etching techniques. The 3D architecture, the sharp tips of the nanostars and the sub-10 nm gap size promote the formation of giant electric-field in highly localized hot-spots. The single/few molecule detection capability of the 3D nanostar-dimers has been demonstrated by Surface-Enhanced Raman Scattering. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Directory of Open Access Journals (Sweden)

    Omar B. Kirikchi

    2016-01-01

    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.

  17. Rotational Spectrum of Propargyl Alcohol Dimer

    Science.gov (United States)

    Mani, Devendra; Arunan, E.

    2013-06-01

    Propargyl alcohol is a molecule of interest to astrophysics as well as combustion studies. Rotational-tunneling spectra of propargyl alcohol monomer is well known and shows that the molecule exists in gauche form. Recently we reported microwave spectra of Ar...propargyl alcohol complex. Propargyl alcochol exists in gauche form in the complex as well. In this study we have recorded pure rotational spectra of propargyl alcohol dimer between 4-13 GHz range.A total of 47 transitions, 24 a-type, 16 b-type and 7 c-type, have been observed and fitted with semi rigid rotor asymmetric top hamiltonian. The fitted rotational constants are: A = 2321.83323(47) MHz, B = 1150.47726(24) MHz and C = 1124.89000(20) MHz. The standard deviation for the fit is 2.5 kHz. The experimental rotational constants are very close to the structure predicted by ab-initio calculations in which two gauche-propargyl alcohol moieties are in three point contact stabilized by O-H...O, O-H...pi and C-H...pi interactions. Few transitions for duterated isotopologues of the dimer have also been observed and search for the remaining transitions is in progress. Details will be presented in the talk. E. Hirota,J. Mol. Spectrosc. 26 (1968) 335-350. J.C. Pearson, B.J. Drouin, J. Mol. Spectrosc. 234 (2005) 149-156. D. Mani, E. Arunan, ChemPhysChem 14 (2013) 754-763.

  18. Reinvestigation of the Structure of Protonated Lysine Dimer

    Science.gov (United States)

    Kong, Xianglei

    2014-03-01

    To better understand inconsistencies between the predicted infrared (IR) spectra of previously suggested isomers of Lys2H+ reported by Wu et al. (J. Am. Soc. Mass Spectrom. 22:1651-1659, 18) and the experimental IR photon dissociation (IRPD) spectrum obtained by Oh et al. (J. Am. Chem. Soc. 127:4076-4083, 4), the structure of Lys2H+ was reinvestigated using IRPD spectroscopy in the extended region 2700-3700 cm-1 and theoretical calculations. The new experimental IRPD spectrum is in good agreement with Oh's spectrum in the corresponding wavelength range. Based on calculations at the MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p) and MP2/6-31 + G(d,p)//MP2/6-31 + G(d,p) levels, a new salt-bridged isomer, ZW1, was found to be the most stable isomer; it is more energetically favored than the previously suggested charge-solvated isomer LL-CS01 by 10 or 26 kJ mol-1. Although the calculated IR spectrum of ZW1 is in good agreement with the experimental one in the range 2700-3700 cm-1, it is in poor agreement with the previous IRPD spectrum in the range 1000-1900 cm-1. This investigation shows that the intermolecular interactions inside the dimer are more complex than previously supposed. It is possible that both salt-bridged and charge-solvated isomers of Lys2H+ are stable in the gas phase, and the isomers generated during ionization are sensitive to the experimental conditions.

  19. Stable Isotope Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Tissue samples (skin, bone, blood, muscle) are analyzed for stable carbon, stable nitrogen, and stable sulfur analysis. Many samples are used in their entirety for...

  20. Explicit correlation treatment of the potential energy surface of CO{sub 2} dimer

    Energy Technology Data Exchange (ETDEWEB)

    Kalugina, Yulia N., E-mail: kalugina@phys.tsu.ru [Tomsk State University, 36 Lenin Ave., Tomsk 634050 (Russian Federation); Buryak, Ilya A. [Obukhov Institute of Atmospheric Physics, Russian Academy of Sciences, Moscow (Russian Federation); Chemistry Department, Lomonosov Moscow State University, Moscow (Russian Federation); Ajili, Yosra [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 Bd Descartes, 77454 Marne-La-Vallée (France); Laboratoire de Spectroscopie Atomique, Moléculaire et Applications - LSAMA Université de Tunis El Manar (Tunisia); Vigasin, Andrei A. [Obukhov Institute of Atmospheric Physics, Russian Academy of Sciences, Moscow (Russian Federation); Jaidane, Nejm Eddine [Laboratoire de Spectroscopie Atomique, Moléculaire et Applications - LSAMA Université de Tunis El Manar (Tunisia); Hochlaf, Majdi [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 Bd Descartes, 77454 Marne-La-Vallée (France)

    2014-06-21

    We present an extensive study of the four-dimensional potential energy surface (4D-PES) of the carbon dioxide dimer, (CO{sub 2}){sub 2}. This PES is developed over the set of intermolecular coordinates. The electronic computations are carried out at the explicitly correlated coupled cluster method with single, double, and perturbative triple excitations [CCSD(T)-F12] level of theory in connection with the augmented correlation-consistent aug-cc-pVTZ basis set. An analytic representation of the 4D-PES is derived. Our extensive calculations confirm that “Slipped Parallel” is the most stable form and that the T-shaped structure corresponds to a transition state. Later on, this PES is employed for the calculations of the vibrational energy levels of the dimer. Moreover, the temperature dependence of the dimer second virial coefficient and of the first spectral moment of rototranslational collision-induced absorption spectrum is derived. For both quantities, a good agreement is found between our values and the experimental data for a wide range of temperatures. This attests to the high quality of our PES. Generally, our PES and results can be used for modeling CO{sub 2} supercritical fluidity and examination of its role in planetary atmospheres. It can be also incorporated into dynamical computations of CO{sub 2} capture and sequestration. This allows deep understanding, at the microscopic level, of these processes.

  1. Acidic Residues Control the Dimerization of the N-terminal Domain of Black Widow Spiders’ Major Ampullate Spidroin 1

    Science.gov (United States)

    Bauer, Joschka; Schaal, Daniel; Eisoldt, Lukas; Schweimer, Kristian; Schwarzinger, Stephan; Scheibel, Thomas

    2016-09-01

    Dragline silk is the most prominent amongst spider silks and comprises two types of major ampullate spidroins (MaSp) differing in their proline content. In the natural spinning process, the conversion of soluble MaSp into a tough fiber is, amongst other factors, triggered by dimerization and conformational switching of their helical amino-terminal domains (NRN). Both processes are induced by protonation of acidic residues upon acidification along the spinning duct. Here, the structure and monomer-dimer-equilibrium of the domain NRN1 of Latrodectus hesperus MaSp1 and variants thereof have been investigated, and the key residues for both could be identified. Changes in ionic composition and strength within the spinning duct enable electrostatic interactions between the acidic and basic pole of two monomers which prearrange into an antiparallel dimer. Upon naturally occurring acidification this dimer is stabilized by protonation of residue E114. A conformational change is independently triggered by protonation of clustered acidic residues (D39, E76, E81). Such step-by-step mechanism allows a controlled spidroin assembly in a pH- and salt sensitive manner, preventing premature aggregation of spider silk proteins in the gland and at the same time ensuring fast and efficient dimer formation and stabilization on demand in the spinning duct.

  2. Acidic Residues Control the Dimerization of the N-terminal Domain of Black Widow Spiders' Major Ampullate Spidroin 1.

    Science.gov (United States)

    Bauer, Joschka; Schaal, Daniel; Eisoldt, Lukas; Schweimer, Kristian; Schwarzinger, Stephan; Scheibel, Thomas

    2016-09-29

    Dragline silk is the most prominent amongst spider silks and comprises two types of major ampullate spidroins (MaSp) differing in their proline content. In the natural spinning process, the conversion of soluble MaSp into a tough fiber is, amongst other factors, triggered by dimerization and conformational switching of their helical amino-terminal domains (NRN). Both processes are induced by protonation of acidic residues upon acidification along the spinning duct. Here, the structure and monomer-dimer-equilibrium of the domain NRN1 of Latrodectus hesperus MaSp1 and variants thereof have been investigated, and the key residues for both could be identified. Changes in ionic composition and strength within the spinning duct enable electrostatic interactions between the acidic and basic pole of two monomers which prearrange into an antiparallel dimer. Upon naturally occurring acidification this dimer is stabilized by protonation of residue E114. A conformational change is independently triggered by protonation of clustered acidic residues (D39, E76, E81). Such step-by-step mechanism allows a controlled spidroin assembly in a pH- and salt sensitive manner, preventing premature aggregation of spider silk proteins in the gland and at the same time ensuring fast and efficient dimer formation and stabilization on demand in the spinning duct.

  3. Excision repair of ultraviolet damage in mammalian cells: evidence for two steps in the excision of pyrimidine dimers

    International Nuclear Information System (INIS)

    Williams, J.I.; Cleaver, J.E.

    1978-01-01

    The incidence of pyrimidine dimer formation and the kinetics of DNA repair in African green monkey kidney CV-1 cells after ultraviolet (uv) irradiation were studied by measuring survival, T4 endonuclease V-sensitive sites, the fraction of pyrimidine dimers in acid-insoluble DNA as determined by thin layer chromatography (TLC), and repair replication. CV-1 cells exhibit a survival curve with extrapolation number n = 7.8 and D 0 = 2.5 J/m 2 . Pyrimidine dimers were lost from acid-insoluble DNA more slowly than endonuclease-sensitive sites were lost from or new bases were incorporated into high molecular weight DNA during the course of repair. Growth of CV-1 cultures in [ 3 H]thymidine or x irradiation (2 or 10 krads) 24 h before uv irradiation had no effect on repair replication induced by 25 J/m 2 of uv. These results suggest that pyrimidine dimer excision measurements by TLC are probably unaffected by radiation from high levels of incorporated radionuclides. The endonuclease-sensitive site and TLC measurements can be reconciled by the assumption that pyrimidine dimers are excised from high molecular weight DNA in acid-insoluble oligonucleotides that are slowly degraded to acid-soluble fragments

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-07-18

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

  5. Modeling the structure and vibrational spectra for oxouranium dichloride monomer and dimer

    Science.gov (United States)

    Umreiko, D. S.; Shundalau, M. B.; Trubina, O. V.

    2010-11-01

    Structural models are designed and spectral characteristics are computed for the monomer and dimer of the oxouranium dichloride (UOCl2) molecule based on ab initio calculations. The calculations were carried out in the LANL2DZ effective core potential approximation for the uranium atom and all-electron basis sets using DFT methods for oxygen and chlorine atoms (B3LYP/cc-pVDZ). A close-to-planar Y-shaped equilibrium configuration with Cs symmetry is obtained for the UOCl2 monomer. The formation of the dimer is accompanied by both significant changes in the structure of the monomeric fragments and the actual loss of their identities. The obtained spectral characteristics are analyzed and compared with experimental data. The adequacy of the proposed models and qualitative agreement between calculation and experiment are demonstrated.

  6. Aberrant phenotypes of transgenic mice expressing dimeric human erythropoietin

    Directory of Open Access Journals (Sweden)

    Yun Seong-Jo

    2012-01-01

    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

  7. Stochastic optimization-based study of dimerization kinetics

    Indian Academy of Sciences (India)

    Abstract. 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.

  8. Exact Solution of a Generalized Nonlinear Schrodinger Equation Dimer

    DEFF Research Database (Denmark)

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

    1998-01-01

    We present exact solutions for a nonlinear dimer system defined throught a discrete nonlinear Schrodinger equation that contains also an integrable Ablowitz-Ladik term. The solutions are obtained throught a transformation that maps the dimer into a double Sine-Gordon like ordinary nonlinear...

  9. Two Populations Mean-Field Monomer-Dimer Model

    Science.gov (United States)

    Alberici, Diego; Mingione, Emanuele

    2018-04-01

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

  10. Ab initio and matrix isolation study of the acetylene-furan dimer

    International Nuclear Information System (INIS)

    Sanchez-Garcia, Elsa; Mardyukov, Artur; Tekin, Adem; Crespo-Otero, Rachel; Montero, Luis A.; Sander, Wolfram; Jansen, Georg

    2008-01-01

    Five acetylene-furan dimer structures are identified using ab initio calculations at the second-order Moller-Plesset (MP2) level of theory. The structures are stabilized by two basic types of intermolecular interactions: the CH...O and the CH...π interaction. The CH...π interaction appears in two variants, depending on which molecule provides the hydrogen atom and which molecule the π system. The MP2 results indicate that the CH...π interaction between one of the hydrogen atoms of acetylene and the π system of furan as found in structure A is the strongest interaction, followed by the in-plane CH...O interaction in the second most stable acetylene-furan dimer structure B. A matrix isolation study shows the acetylene-furan dimer to exist in an argon matrix, but likely rather as structure B than as A. High level coupled cluster calculations with up to triple excitations (CCSD(T)) yield the interaction energy of structure A as about -2.4 kcal/mol in the complete basis set limit and find structure B to be nearly isoenergetic with -2.3 kcal/mol. This is confirmed in calculations employing the density functional theory combined with symmetry adapted intermolecular perturbation theory (DFT-SAPT) approach yielding interaction energies of -2.3 and -2.0 kcal/mol for A and B, respectively. DFT-SAPT also helps to understand the importance of the electrostatic, induction and dispersion interaction energies and their respective exchange counterparts for the stability of the various acetylene-furan dimer structures. The CH...O and CH...π interactions are furthermore analyzed with the help of the atoms in molecules (AIM) theory

  11. Global Structure of a Three-Way Junction in a Phi29 Packaging RNA Dimer Determined Using Site-Directed Spin Labeling

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Xiaojun; Tung, Chang-Shung; Sowa, Glenna; Hatmal, Ma' mon M.; Haworth, Ian S.; Qin, Peter Z.

    2012-02-08

    The condensation of bacteriophage phi29 genomic DNA into its preformed procapsid requires the DNA packaging motor, which is the strongest known biological motor. The packaging motor is an intricate ring-shaped protein/RNA complex, and its function requires an RNA component called packaging RNA (pRNA). Current structural information on pRNA is limited, which hinders studies of motor function. Here, we used site-directed spin labeling to map the conformation of a pRNA three-way junction that bridges binding sites for the motor ATPase and the procapsid. The studies were carried out on a pRNA dimer, which is the simplest ring-shaped pRNA complex and serves as a functional intermediate during motor assembly. Using a nucleotide-independent labeling scheme, stable nitroxide radicals were attached to eight specific pRNA sites without perturbing RNA folding and dimer formation, and a total of 17 internitroxide distances spanning the three-way junction were measured using Double Electron-Electron Resonance spectroscopy. The measured distances, together with steric chemical constraints, were used to select 3662 viable three-way junction models from a pool of 65 billion. The results reveal a similar conformation among the viable models, with two of the helices (HT and HL) adopting an acute bend. This is in contrast to a recently reported pRNA tetramer crystal structure, in which HT and HL stack onto each other linearly. The studies establish a new method for mapping global structures of complex RNA molecules, and provide information on pRNA conformation that aids investigations of phi29 packaging motor and developments of pRNA-based nanomedicine and nanomaterial.

  12. Palladium dimers adsorbed on graphene: A DFT study

    International Nuclear Information System (INIS)

    Kaur, Gagandeep; Gupta, Shuchi; Dharamvir, Keya

    2015-01-01

    The 2D structure of graphene shows a great promise for enhanced catalytic activity when adsorbed with palladium. We performed a systematic density functional theory (DFT) study of the adsorption of palladium dimer (Pd 2 ) on graphene using SIESTA package, in the generalized gradient approximation (GGA). The adsorption energy, geometry, and charge transfer of Pd 2 -graphene system are calculated. Both horizontal and vertical orientations of Pd 2 on graphene are studied. Our calculations revealed that the minimum energy configuration for Pd dimer is parallel to the graphene sheet with its two atoms occupying centre of adjacent hexagonal rings of graphene sheet. Magnetic moment is induced for Pd dimer adsorbed on graphene in vertical orientation while horizontal orientation of Pd dimer on graphene do not exhibit magnetism. Insignificant energy differences among adsorption sites means that dimer mobility on the graphene sheet is high. There is imperceptible distortion of graphene sheet perpendicular to its plane. However, some lateral displacements are seen

  13. Metal membrane with dimer slots as a universal polarizer

    DEFF Research Database (Denmark)

    Zhukovsky, Sergei; Zalkovskij, Maksim; Malureanu, Radu

    2014-01-01

    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......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...... 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...

  14. Family C 7TM receptor dimerization and activation

    DEFF Research Database (Denmark)

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

    2006-01-01

    The family C seven transmembrane (7TM) receptors constitutes a small and especially well characterized subfamily of the large 7TM receptor superfamily. Approximately 50% of current prescription drugs target 7TM receptors, this biologically important family represents the largest class of drug......-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...... changes that lead to receptor activation. Despite extensive studies of the receptor transmembrane domain, several key features, including the exact organization of the complete receptor dimer, the sequence of events leading to receptor activation, and the functional significance of dimerization, have yet...

  15. Effect of Substituents on the Bond Strength of Air-Stable Dicyanomethyl Radical Thermochromes.

    Science.gov (United States)

    Peterson, Joshua P; Geraskina, Margarita R; Zhang, Rui; Winter, Arthur H

    2017-06-16

    A series of substituted aryl dicyanomethyl radicals were synthesized, and the bonding thermodynamic parameters for self-dimerization were determined from van't Hoff plots obtained from variable-temperature electron paramagnetic resonance and ultraviolet-visible spectroscopy. At low temperatures, the radicals dimerize, but the colored, air-stable free radicals return upon heating. Heating and cooling cycles (5-95 °C) can be repeated without radical degradation and with striking thermochromic behavior. We find a linear free energy relationship between the Hammett para substituent parameter and the dimerization equilibrium constant, with para electron-donating substituents leading to a weaker bond and electron-withdrawing substituents leading to stronger bonds, following a captodative effect. Density functional theory investigations [B98D/6-31+G(d,p)] reveal that the dimers prefer a slip-stacked geometry and feature elongated bonds.

  16. A computational study of dimers and trimers of nitrosyl hydride: Blue shift of NH bonds that are involved in H-bond and orthogonal interactions

    International Nuclear Information System (INIS)

    Solimannejad, Mohammad; Massahi, Shokofeh; Alkorta, Ibon

    2009-01-01

    Ab initio calculations at MP2/aug-cc-pVTZ level were used to analyze the interactions between nitrosyl hydride (HNO) dimers and trimers. The structures obtained have been analyzed with the Atoms in Molecules (AIMs) and Natural Bond Orbital (NBO) methodologies. Four minima were located on the potential energy surface of the dimers. Nine different structures have been obtained for the trimers. Three types of interactions are observed, NH···N and NH···O hydrogen bonds and orthogonal interaction between the lone pair of the oxygen with the electron-deficient region of the nitrogen atom. Stabilization energies of dimers and trimers including BSSE and ZPE are in the range 4-8 kJ mol -1 and 12-19 kJ mol -1 , respectively. Blue shift of NH bond upon complex formation in the ranges between 30-80 and 14,114 cm -1 is predicted for dimers and trimers, respectively.

  17. Dimer Coverings on Random Polyomino Chains

    Science.gov (United States)

    Xiao, Chuanqi; Chen, Haiyan

    2015-06-01

    A polyomino chain is a planar square lattice that can be constructed by successively attaching squares to the previous one in two possible ways. A random polyomino chain is then generated by incorporating the Bernoulli distribution to the two types of attachment, which describes a zeroth-order Markov process. Let (ℜn, p) be the ensemble of random polyomino chains with n squares, where p∈[0,1] is a constant. Then, in this paper, we determine the explicit expression for the expectation of the number of dimer coverings over (ℜn, p). Our result shows that, with only one exception, i.e., p = 0, the average of the logarithm of this expectation is asymptotically nonzero when n → ∞.

  18. Dualism of Sensitivity and Selectivity of Porphyrin Dimers in Electroanalysis.

    Science.gov (United States)

    Lisak, Grzegorz; Tamaki, Takashi; Ogawa, Takuji

    2017-04-04

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

  19. Formation of amyloid fibers by monomeric light chain variable domains.

    Science.gov (United States)

    Brumshtein, Boris; Esswein, Shannon R; Landau, Meytal; Ryan, Christopher M; Whitelegge, Julian P; Phillips, Martin L; Cascio, Duilio; Sawaya, Michael R; Eisenberg, David S

    2014-10-03

    Systemic light chain amyloidosis is a lethal disease characterized by excess immunoglobulin light chains and light chain fragments composed of variable domains, which aggregate into amyloid fibers. These fibers accumulate and damage organs. Some light chains induce formation of amyloid fibers, whereas others do not, making it unclear what distinguishes amyloid formers from non-formers. One mechanism by which sequence variation may reduce propensity to form amyloid fibers is by shifting the equilibrium toward an amyloid-resistant quaternary structure. Here we identify the monomeric form of the Mcg immunoglobulin light chain variable domain as the quaternary unit required for amyloid fiber assembly. Dimers of Mcg variable domains remain stable and soluble, yet become prone to assemble into amyloid fibers upon disassociation into monomers. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  20. Efficient isolation of major procyanidin A-type dimers from peanut skins and B-type dimers from grape seeds

    NARCIS (Netherlands)

    Appeldoorn, M.M.; Sanders, M.B.; Vincken, J.P.; Cheynier, V.; Guerneve, Le C.; Gruppen, H.

    2009-01-01

    In order to fully explore the biofunctional potential of proanthocyanidins (PA), isolated and well-characterised PA dimers are of great importance. Current methods to obtain pure A- and B-type dimers are laborious, because they comprise multiple chromatographic steps, often yielding only one or two

  1. Stable convergence and stable limit theorems

    CERN Document Server

    Häusler, Erich

    2015-01-01

    The authors present a concise but complete exposition of the mathematical theory of stable convergence and give various applications in different areas of probability theory and mathematical statistics to illustrate the usefulness of this concept. Stable convergence holds in many limit theorems of probability theory and statistics – such as the classical central limit theorem – which are usually formulated in terms of convergence in distribution. Originated by Alfred Rényi, the notion of stable convergence is stronger than the classical weak convergence of probability measures. A variety of methods is described which can be used to establish this stronger stable convergence in many limit theorems which were originally formulated only in terms of weak convergence. Naturally, these stronger limit theorems have new and stronger consequences which should not be missed by neglecting the notion of stable convergence. The presentation will be accessible to researchers and advanced students at the master's level...

  2. Rotation and Negative Torque in Electrodynamically Bound Nanoparticle Dimers

    Energy Technology Data Exchange (ETDEWEB)

    Sule, Nishant [James; Yifat, Yuval [James; Gray, Stephen K. [Center; Scherer, Norbert F. [James; Department

    2017-10-16

    We examine the formation and concomitant rotation of electrodynamically bound dimers (EBD) of 150nm diameter Ag nanoparticles trapped in circularly polarized focused Gaussian beams. The rotation frequency of an EBD increases linearly with the incident beam power, reaching high mean values of ~ 4kHz for a relatively low incident power of 14mW. Using a coupled-dipole/effective polarizability model, we reveal that retardation of the scattered fields and electrodynamic interactions can lead to a “negative torque” causing rotation of the EBD in the direction opposite to that of the circular polarization. This intriguing opposite-handed rotation due to negative torque is clearly demonstrated using electrodynamics-Langevin dynamics simulations by changing particle separations and thus varying the retardation effects. Finally, negative torque is also demonstrated in experiments from statistical analysis of the EBD trajectories. These results demonstrate novel rotational dynamics of nanoparticles in optical matter using circular polarization and open a new avenue to control orientational dynamics through coupling to interparticle separation.

  3. Observation by flow 1H NMR and dimerization kinetics and products of reactive ortho-quinodimethanes and benzocyclobutadiene

    International Nuclear Information System (INIS)

    Fischer, D.

    1990-01-01

    The reactive o-quinodimethanes, 1,2-dimethylene-1,2-dihydronaphthalene (9) and o-xylylene (1) were observed by flow 1 H NMR spectroscopy at room temperature. The 1 H NMR spectrum of 9 was obtained in the absence of precursor and dimers. However, the 1 H NMR spectrum of the more reactive 1, generated in a similar manner from [o-((trimethylsilyl)methyl)benzyl]trimethylammonium iodide (5.) could be obtained only in the presence of its stable [4 + 2] and [4 + 4] dimers. The dimerization kinetics of 3-methyl- (5'), 3,6-dimethyl- (11), 3-isopropyl- (12), and 3,6-diisoproply-1,2-xylylene (13) in acetonitrile (CH 3 CN) were studied by stopped-flow UV-visible spectroscopy. Fluoride ion induced 1,2-elimination from 2-elimination from 2-trimethylsilylbenzocyclobutenyl-1 mesylate (26) was used to generate the reactive molecule benzocyclobutadiene (1') in CD 3 CN, which was observed by flow 1 H NMR spectroscopy at room temperature. The 1 H NMR spectrum (in CD 3 CN) of 1,2-dimethylene-1,2-dihydrothiophene (1 double-prime), obtained by fluoride ion induced 1,4-elimination from 3-(trimethylammoniummethyl)-2-(trimethylsilylmethyl)thiophene iodine was observed by flow 1 H NMR spectroscopy at room temperature. The dimerization rate of 1 double-prime in CH 3 CN, generated in the same manner, was measured by UV-visible spectroscopy. 166 refs., 7 figs., 7 tabs

  4. Dimerization of Smac is crucial for its mitochondrial retention by XIAP subsequent to mitochondrial outer membrane permeabilization.

    Science.gov (United States)

    Flanagan, Lorna; Sebastia, Jordi; Delgado, Maria Eugenia; Lennon, Jennifer C; Rehm, Markus

    2011-05-01

    Following the apoptotic permeabilization of the outer mitochondrial membrane, the inter-membrane space protein second mitochondria-derived activator of caspases (Smac) is released into the cytosol. Smac efficiently promotes apoptosis by antagonizing x-linked inhibitor of apoptosis protein (XIAP), an inhibitor of caspases-9, -3, and -7, via a short NH(2)-terminal inhibitor of apoptosis protein (IAP) binding motif (AVPI). Native Smac dimerizes to form a highly stable and inflexible elongated arch, however, a functional role for this outstretched structure so far remained unknown. Using time-lapse single-cell imaging of DLD-1 and HCT-116 colon cancer cells, we here demonstrate that upon mitochondrial outer membrane permeabilization physiological expression levels of XIAP are sufficient to selectively prolong the release of dimeric but not monomeric Smac. Elevating the expression of XIAP further extended the release duration of dimeric Smac and resulted in the mitochondrial retention of a significant proportion of the Smac pool. In contrast, monomeric Smac was always fully released and the release kinetics were not affected by altered XIAP expression. Our findings therefore indicate that the dimerization of Smac is critical for the XIAP-mediated retention of Smac at or inside the mitochondria. This article is part of a Special Issue entitled: 11th European Symposium on Calcium. 2010 Elsevier B.V. All rights reserved.

  5. Non-Covalent Interactions and Impact of Charge Penetration Effects in Linear Oligoacene Dimers and Single Crystals

    KAUST Repository

    Ryno, Sean

    2016-05-18

    Non-covalent interactions determine in large part the thermodynamic aspects of molecular packing in organic crystals. Using a combination of symmetry-adapted perturbation theory (SAPT) and classical multipole electrostatics, we describe the interaction potential energy surfaces for dimers of the oligoacene family, from benzene to hexacene. An analysis of these surfaces and a thorough assessment of dimers extracted from the reported crystal structures underline that high-order interactions (i.e., three-body non-additive interactions) must be considered in order to rationalize the details of the crystal structures. A comparison of the SAPT electrostatic energy with the multipole interaction energy demonstrates the importance of the contribution of charge penetration, which is shown to account for up to 50% of the total interaction energy in dimers extracted from the experimental single crystals; in the case of the most stable co-facial model dimers, this contribution is even larger than the total interaction energy. Our results highlight the importance of taking account of charge penetration in studies of the larger oligoacenes.

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

    KAUST Repository

    Han, Yu

    2016-03-31

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

  7. Dimer self-organization of impurity ytterbium ions in synthetic forsterite single crystals

    Science.gov (United States)

    Tarasov, V. F.; Sukhanov, A. A.; Dudnikova, V. B.; Zharikov, E. V.; Lis, D. A.; Subbotin, K. A.

    2017-07-01

    Paramagnetic centers formed by impurity Yb3+ ions in synthetic forsterite (Mg2SiO4) grown by the Czochralski technique are studied by X-band CW and pulsed EPR spectroscopy. These centers are single ions substituting magnesium in two different crystallographic positions denoted M1 and M2, and dimer associates formed by two Yb3+ ions in nearby positions M1. It is established that there is a pronounced mechanism favoring self-organization of ytterbium ions in dimer associates during the crystal growth, and the mechanism of the spin-spin coupling between ytterbium ions in the associate has predominantly a dipole-dipole character, which makes it possible to control the energy of the spin-spin interaction by changing the orientation of the external magnetic field. The structural computer simulation of cluster ytterbium centers in forsterite crystals is carried out by the method of interatomic potentials using the GULP 4.0.1 code (General Utility Lattice Program). It is established that the formation of dimer associates in the form of a chain parallel to the crystallographic axis consisting of two ytterbium ions with a magnesium vacancy between them is the most energetically favorable for ytterbium ions substituting magnesium in the position M1.

  8. Opening of the TAR hairpin in the HIV-1 genome causes aberrant RNA dimerization and packaging

    Directory of Open Access Journals (Sweden)

    Das Atze T

    2012-07-01

    Full Text Available Abstract Background The TAR hairpin is present at both the 5′ and 3′ end of the HIV-1 RNA genome. The 5′ element binds the viral Tat protein and is essential for Tat-mediated activation of transcription. We recently observed that complete TAR deletion is allowed in the context of an HIV-1 variant that does not depend on this Tat-TAR axis for transcription. Mutations that open the 5′ stem-loop structure did however affect the leader RNA conformation and resulted in a severe replication defect. In this study, we set out to analyze which step of the HIV-1 replication cycle is affected by this conformational change of the leader RNA. Results We demonstrate that opening the 5′ TAR structure through a deletion in either side of the stem region caused aberrant dimerization and reduced packaging of the unspliced viral RNA genome. In contrast, truncation of the TAR hairpin through deletions in both sides of the stem did not affect RNA dimer formation and packaging. Conclusions These results demonstrate that, although the TAR hairpin is not essential for RNA dimerization and packaging, mutations in TAR can significantly affect these processes through misfolding of the relevant RNA signals.

  9. Dominant negative actions of human prostacyclin receptor variant through dimerization: implications for cardiovascular disease.

    Science.gov (United States)

    Ibrahim, Salam; Tetruashvily, Mazell; Frey, Alex J; Wilson, Stephen J; Stitham, Jeremiah; Hwa, John; Smyth, Emer M

    2010-09-01

    Prostacyclin and thromboxane mediate opposing cardiovascular effects through their receptors, the prostacyclin receptor (IP) and thromboxane receptor (TP). Individuals heterozygous for an IP variant, IP(R212C), displayed exaggerated loss of platelet IP responsiveness and accelerated cardiovascular disease. We examined association of IP(R212C) into homo- and heterodimeric receptor complexes and the impact on prostacyclin and thromboxane biology. Dimerization of the IP, IP(R212C), and TPalpha was examined by bioluminesence resonance energy transfer in transfected HEK293 cells. We observed an equal propensity for formation of IPIP homodimers and IPTPalpha heterodimers. Compared with the IP alone, IP(R212C) displayed reduced cAMP generation and increased endoplasmic reticulum localization but underwent normal homo- and heterodimerization. When the IP(R212C) and IP were coexpressed, a dominant negative action of the variant was evident with enhanced wild-type IP localization to the endoplasmic reticulum and reduced agonist-dependent signaling. Further, the TPalpha activation response, which was shifted from inositol phosphate to cAMP generation following IPTPalpha heterodimerization, was normalized when the TPalpha instead dimerized with IP(R212C). IP(R212C) exerts a dominant action on the wild-type IP and TPalpha through dimerization. This likely contributes to accelerated cardiovascular disease in individuals carrying 1 copy of the variant allele.

  10. Vison excitations in near-critical quantum dimer models

    Science.gov (United States)

    Strübi, G.; Ivanov, D. A.

    2011-06-01

    We study vison excitations in a quantum dimer model interpolating between the Rokhsar-Kivelson models on the square and triangular lattices. In the square-lattice case, the model is known to be critical and characterized by U(1) topological quantum numbers. Introducing diagonal dimers brings the model to a Z2 resonating-valence-bond phase. We study variationally the emergence of vison excitations at low concentration of diagonal dimers, close to the critical point. We find that, in this regime, vison excitations are large in size and their structure resembles vortices in type-II superconductors.

  11. Family C 7TM receptor dimerization and activation

    DEFF Research Database (Denmark)

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

    2006-01-01

    changes that lead to receptor activation. Despite extensive studies of the receptor transmembrane domain, several key features, including the exact organization of the complete receptor dimer, the sequence of events leading to receptor activation, and the functional significance of dimerization, have yet...... 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....

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

    DEFF Research Database (Denmark)

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

    2008-01-01

    by fluorescence resonance energy transfer microscopy. Endoglycosidase treatment and surface biotinylation further revealed that complex-glycosylated GlyTs form dimers located at the cell surface. Furthermore, substitution of tryptophan 469 of GlyT2 by an arginine generated a transporter deficient in dimerization......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...

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

    DEFF Research Database (Denmark)

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

    2001-01-01

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

  14. Photoelectron Spectroscopy of 4-Bromochlorobenzene Dimer and Trimer Anions

    International Nuclear Information System (INIS)

    Kim, Namdoo

    2013-01-01

    I investigated the electron attachment to 4-BCB dimer and trimer anions using anion photoelectron spectroscopy and theoretical calculations. I found that an excess electron can be delocalized to these clusters through extended π-network. However, the nature of the ion core is different for the dimer and trimer. For the heterodimer anions, the geometry is determined by the differences in electronegativity of the molecules. Dimer anions with a large electronegativity difference have T-shaped geometries and those with a small electronegativity difference have PD geometries

  15. Combination Bands of the Nonpolar OCS Dimer Involving Intermolecular Modes

    Science.gov (United States)

    Rezaei, M.; Oliaee, J. Norooz; Moazzen-Ahmadi, N.; McKellar, A. R. W.

    2012-06-01

    Spectra of the nonpolar carbonyl sulfide in the region of the OCS ν_1 fundamental band were observed in a supersonic slit-jet apparatus. The expansion gas was probed using radiation from a tunable diode laser employed in a rapid-scan signal averaging mode. Three bands centered at 2085.906, 2103.504, and 2114.979 cm-1 were observed and anlysed. The rotational assignment and fitting of the bands were made by fixing the lower state parameters to those for the ground state of nonpolar (OCS)_2, thus confirming that they were indeed combination bands of the of the most stable isomer of OCS dimer. The band centered at 2085.906 cm-1 is a combination of the forbidden A_g intramolecular mode plus the geared bend intermolecular mode and that centered at 2114.979 cm-1 is a combination of the allowed B_u intramolecular mode plus the intermolecular van der Waals stretch. The combination at 2103.504 cm-1 can be assigned as a band whose upper state involves four quanta of the intramolecular bend or the B_u intramolecular mode plus two quanta of the intermolecular torsional mode. Isotopic work is needed to conclusively identify the vibrational assignment of this band. Our experimental frequencies for the geared bend and van der Waals modes are in good agreement with a recent high level ab initio calculation by Brown et al. J. Brown, Xiao-Gang Wang, T. Carrington Jr. and Richard Dawes, Journal of Chemical Physics, submitted.

  16. C-C bond formation and related reactions at the CNC backbone in (smif)FeX (smif = 1,3-di-(2-pyridyl)-2-azaallyl): dimerizations, 3 + 2 cyclization, and nucleophilic attack; transfer hydrogenations and alkyne trimerization (X = N(TMS)2, dpma = (di-(2-pyridyl-methyl)-amide)).

    Science.gov (United States)

    Frazier, Brenda A; Williams, Valerie A; Wolczanski, Peter T; Bart, Suzanne C; Meyer, Karsten; Cundari, Thomas R; Lobkovsky, Emil B

    2013-03-18

    Molecular orbital analysis depicts the CNC(nb) backbone of the smif (1,3-di-(2-pyridyl)-2-azaallyl) ligand as having singlet diradical and/or ionic character where electrophilic or nucleophilic attack is plausible. Reversible dimerization of (smif)Fe{N(SiMe3)2} (1) to [{(Me3Si)2N}Fe]2(μ-κ(3),κ(3)-N,py2-smif,smif) (2) may be construed as diradical coupling. A proton transfer within the backbone-methylated, and o-pyridine-methylated smif of putative ((b)Me2(o)Me2smif)FeN(SiMe3)2 (8) provides a route to [{(Me3Si)2N}Fe]2(μ-κ(4),κ(4)-N,py2,C-((b)Me,(b)CH2,(o)Me2(smif)H))2 (9). A 3 + 2 cyclization of ditolyl-acetylene occurs with 1, leading to the dimer [{2,5-di(pyridin-2-yl)-3,4-di-(p-tolyl-2,5-dihydropyrrol-1-ide)}FeN(SiMe3)2]2 (11), and the collateral discovery of alkyne cyclotrimerization led to a brief study that identified Fe(N(SiMe3)2(THF) as an effective catalyst. Nucleophilic attack by (smif)2Fe (13) on (t)BuNCO and (2,6-(i)Pr2C6H3)NCO afforded (RNHCO-smif)2Fe (14a, R = (t)Bu; 14b, 2,6-(i)PrC6H3). Calculations suggested that (dpma)2Fe (15) would favorably lose dihydrogen to afford (smif)2Fe (13). H2-transfer to alkynes, olefins, imines, PhN═NPh, and ketones was explored, but only stoichiometric reactions were affected. Some physical properties of the compounds were examined, and X-ray structural studies on several dinuclear species were conducted.

  17. Crystal Structure of a Dimerized Cockroach Allergen Bla g 2 Complexed with a Monoclonal Antibody

    Energy Technology Data Exchange (ETDEWEB)

    Li, Mi; Gustchina, Alla; Alexandratos, Jerry; Wlodawer, Alexander; Wünschmann, Sabina; Kepley, Christopher L.; Chapman, Martin D.; Pomes, Anna (INDOOR Bio.); (VCU); (NIH)

    2008-09-03

    The crystal structure of a 1:1 complex between the German cockroach allergen Bla g 2 and the Fab' fragment of a monoclonal antibody 7C11 was solved at 2.8-{angstrom} resolution. Bla g 2 binds to the antibody through four loops that include residues 60-70, 83-86, 98-100, and 129-132. Cation-{pi} interactions exist between Lys-65, Arg-83, and Lys-132 in Bla g 2 and several tyrosines in 7C11. In the complex with Fab', Bla g 2 forms a dimer, which is stabilized by a quasi-four-helix bundle comprised of an {alpha}-helix and a helical turn from each allergen monomer, exhibiting a novel dimerization mode for an aspartic protease. A disulfide bridge between C51a and C113, unique to the aspartic protease family, connects the two helical elements within each Bla g 2 monomer, thus facilitating formation of the bundle. Mutation of these cysteines, as well as the residues Asn-52, Gln-110, and Ile-114, involved in hydrophobic interactions within the bundle, resulted in a protein that did not dimerize. The mutant proteins induced less {beta}-hexosaminidase release from mast cells than the wild-type Bla g 2, suggesting a functional role of dimerization in allergenicity. Because 7C11 shares a binding epitope with IgE, the information gained by analysis of the crystal structure of its complex provided guidance for site-directed mutagenesis of the allergen epitope. We have now identified key residues involved in IgE antibody binding; this information will be useful for the design of vaccines for immunotherapy.

  18. stableGP

    Data.gov (United States)

    National Aeronautics and Space Administration — The code in the stableGP package implements Gaussian process calculations using efficient and numerically stable algorithms. Description of the algorithms is in the...

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

    Science.gov (United States)

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

    1996-11-01

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

  20. Dimer-based model for heptaspanning membrane receptors.

    Science.gov (United States)

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

    2005-07-01

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

  1. Dimers on Surface Graphs and Spin Structures. I

    DEFF Research Database (Denmark)

    Cimasoni, David; Reshetikhin, Nicolai

    2007-01-01

    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....

  2. Naturally Occurring Diterpenoid Dimers: Source, Biosynthesis, Chemistry and Bioactivities.

    Science.gov (United States)

    Lin, Li-Gen; Ung, Carolina Oi Lam; Feng, Zhe-Ling; Huang, Li; Hu, Hao

    2016-10-01

    Diterpenoid dimers are rare in nature and mainly found in higher plants including the families Acanthaceae, Annonaceae, Asteraceae, Calceolariaceae, Chrysobalanaceae, Cupressaceae, Euphorbiaceae, Fabaceae, Lamiaceae, Liliaceae, Meliaceae, Rhizophoraceae, Taxaceae, Velloziaceae, and Zingiberaceae. In addition, a few diterpenoid dimers have been also reported from fungi (Psathyrellaceae), liverworts (Scapaniaceae), and a gorgonian (Gorgoniidae). They feature a wide variety of structures due to different core skeletons, linkage patterns, substituents, and configurations. Accordingly, diterpenoid dimers exhibit a broad range of bioactivities, including cytotoxic, anti-inflammatory, antimicrobial, antimalarial, and antifouling properties, which have attracted more and more research interests in the past decades. This review with 176 metabolites from 109 references provides a comprehensive and up-to-date overview of the source, biosynthesis, structure, synthesis, and bioactivities of diterpenoid dimers. Georg Thieme Verlag KG Stuttgart · New York.

  3. Atomic model for the dimeric FOregion of mitochondrial ATP synthase.

    Science.gov (United States)

    Guo, Hui; Bueler, Stephanie A; Rubinstein, John L

    2017-11-17

    Mitochondrial adenosine triphosphate (ATP) synthase produces the majority of ATP in eukaryotic cells, and its dimerization is necessary to create the inner membrane folds, or cristae, characteristic of mitochondria. Proton translocation through the membrane-embedded F O region turns the rotor that drives ATP synthesis in the soluble F 1 region. Although crystal structures of the F 1 region have illustrated how this rotation leads to ATP synthesis, understanding how proton translocation produces the rotation has been impeded by the lack of an experimental atomic model for the F O region. Using cryo-electron microscopy, we determined the structure of the dimeric F O complex from Saccharomyces cerevisiae at a resolution of 3.6 angstroms. The structure clarifies how the protons travel through the complex, how the complex dimerizes, and how the dimers bend the membrane to produce cristae. Copyright © 2017, American Association for the Advancement of Science.

  4. Antiplasmodial dimeric chalcone derivatives from the roots of Uvaria siamensis.

    Science.gov (United States)

    Salae, Abdul-Wahab; Chairerk, Orapan; Sukkoet, Piyanut; Chairat, Therdsak; Prawat, Uma; Tuntiwachwuttikul, Pittaya; Chalermglin, Piya; Ruchirawat, Somsak

    2017-03-01

    Four dimeric chalcone derivatives, 8″,9″-dihydrowelwitschin H, uvarins A-C, a naphthalene derivative, 2-hydroxy-3-methoxy-6-(4'- hydroxyphenyl)naphthalene, and the known dimeric chalcones, dependensin and welwitschin E, flavonoids, a cyclohexane oxide derivative, an aromatic aldehyde were isolated from the roots of Uvaria siamensis (Annonaceae). The structures of the compounds were elucidated by spectroscopic analysis, as well as by comparison with literature data. The isolated compounds with a sufficient amount for biological assays were evaluated for their antimalarial, antimycobacterial, and cytotoxic activities. The dimeric chalcones 8″,9″-dihydrowelwitschin H, uvarins B and C, dependensin and welwitschin E showed strong antiplasmodial activity with IC 50 values of 3.10, 3.02, 3.09, 4.21 and 3.99 μg/mL, respectively. A possible biosynthesis pathway of the dimeric chalcones is discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Magnetic dimerization in the frustrated spin ladder Li2Cu2O (SO4)2

    Science.gov (United States)

    Vaccarelli, O.; Rousse, G.; Saúl, A.; Radtke, G.

    2017-11-01

    The magnetic properties of Li2Cu2O (SO4)2 are investigated in the framework of density functional theory. In its high-temperature tetragonal structure, this compound appears as a rare material realization of a frustrated spin-1/2 two-leg ladder, where magnetic frustration arises from competing nearest and next-nearest interactions along the legs. Through a large magnetoelastic coupling, the triclinic distortion occurring around 125 K is shown to induce the formation of a staggered dimer structure, lifting most of the magnetic frustration.

  6. The influence of strain on the diffusion of Si dimers on Si(001)

    NARCIS (Netherlands)

    Zoethout, E.; Zoethout, E.; Gurlu, O.; Gürlü, O.; Zandvliet, Henricus J.W.; Poelsema, Bene

    2000-01-01

    The influence of lattice mismatch-induced tensile strain on the diffusion of Si dimers on Si(001) has been studied. The rate of surface diffusion of a Si dimer along the substrate dimer rows is relatively insensitive to tensile strain, whereas the rate of diffusion for a Si dimer across the

  7. Potent immunosuppressive principles, dimeric sesquiterpene thioalkaloids, isolated from nupharis rhizoma, the rhizoma of Nuphar pumilum (nymphaeaceae): structure-requirement of nuphar-alkaloid for immunosuppressive activity.

    Science.gov (United States)

    Yamahara, J; Shimoda, H; Matsuda, H; Yoshikawa, M

    1996-09-01

    Potent immunosuppressants, the dimeric sesquiterpene thioalkaloids, 6-hydroxythiobinupharidine (2), 6,6'-dihydroxythiobinupharidine (3), 6-hydroxythionuphlutine B (5) and 6'-hydroxythionuphlutine B (6), were isolated from a natural medicine, Nupharis Rhizoma, the rhizoma of Nuphar pumilum (TIMM.) DC., through bioassay-guided separation together with five quinolizidine alkaloids (8, 9, 10, 11, 12). Dimeric sesquiterpene thioalkaloids (2, 3, 5, 6) were found to significantly inhibit anti-sheep erythrocyte plaque forming cell formation in mice spleen cells at 10(-6) M concentration. At this concentration, 2, 5 and 6 were found to exhibit no cytotoxicity to mice spleen cells, and 3 also showed only a little cytotoxicity. In addition, the inhibitory activity of several Nuphar alkaloids, dimeric sesquiterpene thioalkaloids (1, 4, 7, 8), and monomeric sesquiterpene alkaloids (9, 10, 11, 12) on anti-sheep erythrocyte plaque forming cell formation was examined and some structural requirement of Nuphar alkaloid for immunosuppressive activity was determined.

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

    Science.gov (United States)

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

    2017-01-01

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

  9. Hydrodynamic Torques and Rotations of Superparamagnetic Bead Dimers

    Science.gov (United States)

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

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

  10. Pair Interaction of Catalytical Sphere Dimers in Chemically Active Media

    Directory of Open Access Journals (Sweden)

    Jing-Min Shi

    2018-01-01

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

  11. VUV spectroscopy of rare gas van der Waals dimers

    International Nuclear Information System (INIS)

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

    1982-01-01

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

  12. Dimeric forms of cholinesterase in Sipunculus nudus.

    Science.gov (United States)

    Talesa, V; Principato, G B; Giovannini, E; Di Giovanni, M V; Rosi, G

    1993-07-15

    In developing a research on the cholinesterase (ChE) evolution in Invertebrata, this enzyme was studied in the unsegmented marine worm Sipunculus nudus. ChE activity was solubilized through three successive steps of extraction. These fractions are noted as low-salt (LSS), detergent (DS) and high-salt soluble (HSS) and represent 27%, 68% and 5% of total activity, respectively. LSS and DS ChE were purified to homogeneity by affinity chromatography on edrophonium-Sepharose gel. Purification factors of 1700 (LSS) and 1090 (DS) were obtained. The small amount of HSS ChE prevented a similar purification and an extensive characterization. Based on SDS/PAGE and density-gradient centrifugation, both LSS and DS enzymes show a M(r) value of about 130,000 and are likely G2 globular dimers of a 67,000 subunit. Moreover, LSS ChE seems to be an amphiphilic form including a hydrophobic domain, while DS ChE is probably linked to the cell membrane by a phosphatidylinositol anchor. Both LSS and DS enzymes hydrolyze at the highest rate propionylthiocholine. However, they also show a fairly high catalytic efficiency with other thiocholine esters as substrates, thus suggesting a wide and little-specialized conformation of the active site. Based on immunological cross-reactivity trials, LSS and DS ChE from S. nudus show a reduced structural affinity with a molluscan (Murex brandaris) enzyme. HSS ChE, an acetylcholinesterase, is also solubilized by heparin, like typical vertebrate HSS asymmetric enzymes. However, it lacks fast-sedimenting forms and an enzyme-anchoring collagenous structure.

  13. Woodfordin C, a macro-ring hydrolyzable tannin dimer with antitumor activity, and accompanying dimers from Woodfordia fruticosa flowers.

    Science.gov (United States)

    Yoshida, T; Chou, T; Nitta, A; Miyamoto, K; Koshiura, R; Okuda, T

    1990-05-01

    Three new dimeric hydrolyzable tannins, woodfordins A, B and C, along with seven known hydrolyzable tannins, including oenothein B, a dimer exhibiting marked host-mediated antitumor activity, were isolated from an Indonesian crude drug, Sidowayah [dried flowers of Woodfordia fruticosa (L.) Kurz (Lythraceae)]. The structures of the new tannins were elucidated based on chemical and spectral evidence. Woodfordin C, having a macro-ring structure, was also found to exhibit a significant antitumor activity.

  14. Structural basis of RNA recognition and dimerization by the STAR proteins T-STAR and Sam68.

    Science.gov (United States)

    Feracci, Mikael; Foot, Jaelle N; Grellscheid, Sushma N; Danilenko, Marina; Stehle, Ralf; Gonchar, Oksana; Kang, Hyun-Seo; Dalgliesh, Caroline; Meyer, N Helge; Liu, Yilei; Lahat, Albert; Sattler, Michael; Eperon, Ian C; Elliott, David J; Dominguez, Cyril

    2016-01-13

    Sam68 and T-STAR are members of the STAR family of proteins that directly link signal transduction with post-transcriptional gene regulation. Sam68 controls the alternative splicing of many oncogenic proteins. T-STAR is a tissue-specific paralogue that regulates the alternative splicing of neuronal pre-mRNAs. STAR proteins differ from most splicing factors, in that they contain a single RNA-binding domain. Their specificity of RNA recognition is thought to arise from their property to homodimerize, but how dimerization influences their function remains unknown. Here, we establish at atomic resolution how T-STAR and Sam68 bind to RNA, revealing an unexpected mode of dimerization different from other members of the STAR family. We further demonstrate that this unique dimerization interface is crucial for their biological activity in splicing regulation, and suggest that the increased RNA affinity through dimer formation is a crucial parameter enabling these proteins to select their functional targets within the transcriptome.

  15. Structural basis underlying CAC RNA recognition by the RRM domain of dimeric RNA-binding protein RBPMS

    Energy Technology Data Exchange (ETDEWEB)

    Teplova, Marianna; Farazi, Thalia A.; Tuschl, Thomas; Patel, Dinshaw J.

    2015-09-08

    Abstract

    RNA-binding protein with multiple splicing (designated RBPMS) is a higher vertebrate mRNA-binding protein containing a single RNA recognition motif (RRM). RBPMS has been shown to be involved in mRNA transport, localization and stability, with key roles in axon guidance, smooth muscle plasticity, as well as regulation of cancer cell proliferation and migration. We report on structure-function studies of the RRM domain of RBPMS bound to a CAC-containing single-stranded RNA. These results provide insights into potential topologies of complexes formed by the RBPMS RRM domain and the tandem CAC repeat binding sites as detected by photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation. These studies establish that the RRM domain of RBPMS forms a symmetrical dimer in the free state, with each monomer binding sequence-specifically to all three nucleotides of a CAC segment in the RNA bound state. Structure-guided mutations within the dimerization and RNA-binding interfaces of RBPMS RRM on RNA complex formation resulted in both disruption of dimerization and a decrease in RNA-binding affinity as observed by size exclusion chromatography and isothermal titration calorimetry. As anticipated from biochemical binding studies, over-expression of dimerization or RNA-binding mutants of Flag-HA-tagged RBPMS were no longer able to track with stress granules in HEK293 cells, thereby documenting the deleterious effects of such mutationsin vivo.

  16. Photo-physical properties of dimers formed by tri-aryl pyrylium salts: experimental and theoretical study

    International Nuclear Information System (INIS)

    Lampre, Isabelle

    1996-01-01

    This research thesis reports the study of dimers formed in solution by aggregation of tri-aryl pyrylium salts, in order to establish a direct correlation between properties and electronic structure of components, on the one hand, and molecular pattern, on the other hand. The author adopted a multidisciplinary approach by using experimental techniques and calculations based on the excitonic theory and methods of quantum chemistry. First, the properties of the first excited states of cationic chromophores have been studied (characterisation of electronic transitions, relaxation at the singlet excited state, formation of triplet state). Then, the author analysed dimerisation processes and showed that each dimer is formed by two pairs of ions. She discusses some original optical properties of dimers. The geometry of dimers is theoretically determined by minimising the system interaction potential energy. Electronic transitions are then determined as linear combinations of transitions of two monomers. Properties are thus calculated and are in agreement with those deduced from spectral analysis. The experimentally noticed polarisation change and large Stokes displacement are then explained in terms of emission for a localised state on a chromophore [fr

  17. Effects of a dimeric vs a monomeric nonionic contrast medium on renal function in patients with mild to moderate renal insufficiency: a double-blind, randomized clinical trial

    Energy Technology Data Exchange (ETDEWEB)

    Carraro, M.; Malalan, F.; Antonione, R.; Faccini, L. [Institute of Medicina Clinica, Ospedale di Cattinara, University of Trieste, Strada di Fiume 447, I-34 149 Trieste (Italy); Stacul, F.; Cova, M.; Petz, S.; Assante, M.; Dalla Palma, L. [Institute of Radiology, Ospedale di Cattinara, University of Trieste, Strada di Fiume 447, I-34 149 Trieste (Italy); Grynne, B.; Haider, T. [Nycomed Imaging AS, Nycoveien 1-2, N-0401 Oslo (Norway)

    1998-02-01

    The efficacy and safety of nonionic dimeric contrast media in subjects with impaired renal function is largely unknown. The present study was aimed at determining the risk of tubular nephrotoxicity in patients with mild to moderate renal insufficiency who underwent intravenous urography (IVU) with the nonionic dimeric contrast agent iodixanol (Visipaque, Nycomed Imaging, Oslo, Norway). In a double-blind protocol 64 patients (55 males; mean age 68.3 years) with serum creatinine between 135 and 265 {mu}mol/l who were to undergo IVU were randomized to receive iodixanol (a nonionic dimer) or iopromide (a nonionic monomer), 600 mg I/kg b. w. Renal function was evaluated before and 1 h, 6 h, 24 h, 48 h and 7 days after IVU with analysis of serum creatinine, urinary enzymes alanylaminopeptidase and N-acetyl-{beta}-glucosaminidase, and urinary microproteins {alpha}-1-microglobulin and albumin. Renal function remained stable in both contrast medium groups during the follow-up period. No statistically significant differences were observed between the monomer and the dimer in terms of urinary enzyme and microprotein excretion or serum creatinine. Transient radiocontrast-induced nephropathy developed in 1 patient who had received iodixanol. The administration of the nonionic dimeric contrast medium iodixanol, or of the nonionic monomer iopromide, entailed a low nephrotoxic potential in patients with mild to moderate renal insufficiency undergoing excretory urography. (orig.) With 2 figs., 1 tab., 13 refs.

  18. Energy Transfer in Supramolecular Heteronuclear Lanthanide Dimers and Application to Fluoride Sensing in Water.

    Science.gov (United States)

    Nonat, Aline; Liu, Tao; Jeannin, Olivier; Camerel, Franck; Charbonnière, Loïc J

    2018-03-12

    In the presence of fluoride anions, [LnL(H 2 O)] + complexes, based on the coordination of a lanthanide (Ln) cation into the cavity of a C 2v symmetrical cyclen-based ligand (L), self-assemble in water to form [(LnL) 2 F] + dimers. The crystal structures of the Yb hydrated monomer and of the fluorinated dimer are reported and analyzed to unravel the impact of the cumulative effect of weak hydrogen bonding and aromatic stacking interactions in the supramolecular assembly. The assembly is stable over a broad range of pH 3-8. A combination of equimolar amounts of Eu and Tb complexes led to a quasistatistical mixture of homo- and heterodimers, as observed by using electrospray mass spectrometry. In the heterodimers, selective excitation into the 7 F 6 → 5 D 4 absorption band of the Tb center at λ=488 nm allowed the observation of a Tb-to-Eu downshifting energy transfer, not observed in the absence of fluoride ions. Analysis of the excited-state lifetimes of the dimers within the frame of the Förster theory of energy transfer showed the transfer to have an efficiency of 34 %, with a corresponding Förster radius of 4.1 Å; thereby, unraveling the short Ln-Ln distance as a crucial parameter of the energy-transfer process. By using equimolar mixtures of the Tb and Eu complexes, the energy-transfer phenomenon was used for a ratiometric sensing of fluoride anions in water with a detection limit of 17.7 nm. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Engineering of Helicobacter pylori dimeric oxidoreductase DsbK (HP0231

    Directory of Open Access Journals (Sweden)

    Katarzyna Marta Bocian-Ostrzycka

    2016-07-01

    Full Text Available The formation of disulfide bonds that are catalyzed by proteins of the Dsb (disulfide bond family is crucial for the correct folding of many extracytoplasmic proteins. Thus, this formation plays an essential, pivotal role in the assembly of many virulence factors. The Helicobacter pylori disulfide bond-forming system is uncomplicated compared to the best-characterized Escherichia coli Dsb pathways. It possesses only two extracytoplasmic Dsb proteins named HP0377 and HP0231. As previously shown, HP0377 is a reductase involved in the process of cytochrome c maturation. Additionally, it also possesses disulfide isomerase activity. HP0231 was the first periplasmic dimeric oxidoreductase involved in disulfide generation to be described. Although HP0231 function is critical for oxidative protein folding, its structure resembles that of dimeric EcDsbG, which does not confer this activity. However, the HP0231 catalytic motifs (CXXC and the so-called cis-Pro loop are identical to that of monomeric EcDsbA. To understand the functioning of HP0231, we decided to study the relations between its sequence, structure and activity through an extensive analysis of various HP0231 point mutants, using in vivo and in vitro strategies. Our work shows the crucial role of the cis-Pro loop, as changing valine to threonine in this motif completely abolishes the protein function in vivo. Functioning of HP0231 is conditioned by the combination of CXXC and the cis-Pro loop, as replacing the HP0231 CXXC motif by the motif from EcDsbG or EcDsbC results in bifunctional protein, at least in E. coli. We also showed that the dimerization domain of HP0231 ensures contact with its substrates. Moreover, the activity of this oxidase is independent on the structure of the catalytic domain. Finally, we showed that HP0231 chaperone activity is independent of its redox function.

  20. Dimer coverings on random multiple chains of planar honeycomb lattices

    International Nuclear Information System (INIS)

    Ren, Haizhen; Zhang, Fuji; Qian, Jianguo

    2012-01-01

    We study dimer coverings on random multiple chains. A multiple chain is a planar honeycomb lattice constructed by successively fusing copies of a ‘straight’ condensed hexagonal chain at the bottom of the previous one in two possible ways. A random multiple chain is then generated by admitting the Bernoulli distribution on the two types of fusing, which describes a zeroth-order Markov process. We determine the expectation of the number of the pure dimer coverings (perfect matchings) over the ensemble of random multiple chains by the transfer matrix approach. Our result shows that, with only two exceptions, the average of the logarithm of this expectation (i.e., the annealed entropy per dimer) is asymptotically nonzero when the fusing process goes to infinity and the length of the hexagonal chain is fixed, though it is zero when the fusing process and the length of the hexagonal chain go to infinity simultaneously. Some numerical results are provided to support our conclusion, from which we can see that the asymptotic behavior fits well to the theoretical results. We also apply the transfer matrix approach to the quenched entropy and reveal that the quenched entropy of random multiple chains has a close connection with the well-known Lyapunov exponent of random matrices. Using the theory of Lyapunov exponents we show that, for some random multiple chains, the quenched entropy per dimer is strictly smaller than the annealed one when the fusing process goes to infinity. Finally, we determine the expectation of the free energy per dimer over the ensemble of the random multiple chains in which the three types of dimers in different orientations are distinguished, and specify a series of non-random multiple chains whose free energy per dimer is asymptotically equal to this expectation. (paper)

  1. Hydrogen Dimers in Giant-planet Infrared Spectra

    Science.gov (United States)

    Fletcher, Leigh N.; Gustafsson, Magnus; Orton, Glenn S.

    2018-03-01

    Despite being one of the weakest dimers in nature, low-spectral-resolution Voyager/IRIS observations revealed the presence of (H2)2 dimers on Jupiter and Saturn in the 1980s. However, the collision-induced H2–H2 opacity databases widely used in planetary science have thus far only included free-to-free transitions and have neglected the contributions of dimers. Dimer spectra have both fine-scale structure near the S(0) and S(1) quadrupole lines (354 and 587 cm‑1, respectively), and broad continuum absorption contributions up to ±50 cm‑1 from the line centers. We develop a new ab initio model for the free-to-bound, bound-to-free, and bound-to-bound transitions of the hydrogen dimer for a range of temperatures (40–400 K) and para-hydrogen fractions (0.25–1.0). The model is validated against low-temperature laboratory experiments, and used to simulate the spectra of the giant planets. The new collision-induced opacity database permits high-resolution (0.5–1.0 cm‑1) spectral modeling of dimer spectra near S(0) and S(1) in both Cassini Composite Infrared Spectrometer observations of Jupiter and Saturn, and in Spitzer Infrared Spectrometer (IRS) observations of Uranus and Neptune for the first time. Furthermore, the model reproduces the dimer signatures observed in Voyager/IRIS data near S(0) on Jupiter and Saturn, and generally lowers the amount of para-H2 (and the extent of disequilibrium) required to reproduce IRIS observations.

  2. Structural basis for the oligomerization-state switch from a dimer to a trimer of an engineered cortexillin-1 coiled-coil variant.

    Directory of Open Access Journals (Sweden)

    Saša Bjelić

    Full Text Available Coiled coils are well suited to drive subunit oligomerization and are widely used in applications ranging from basic research to medicine. The optimization of these applications requires a detailed understanding of the molecular determinants that control of coiled-coil formation. Although many of these determinants have been identified and characterized in great detail, a puzzling observation is that their presence does not necessarily correlate with the oligomerization state of a given coiled-coil structure. Thus, other determinants must play a key role. To address this issue, we recently investigated the unrelated coiled-coil domains from GCN4, ATF1 and cortexillin-1 as model systems. We found that well-known trimer-specific oligomerization-state determinants, such as the distribution of isoleucine residues at heptad-repeat core positions or the trimerization motif Arg-h-x-x-h-Glu (where h = hydrophobic amino acid; x = any amino acid, switch the peptide's topology from a dimer to a trimer only when inserted into the trigger sequence, a site indispensable for coiled-coil formation. Because high-resolution structural information could not be obtained for the full-length, three-stranded cortexillin-1 coiled coil, we here report the detailed biophysical and structural characterization of a shorter variant spanning the trigger sequence using circular dichroism, anatytical ultracentrifugation and x-ray crystallography. We show that the peptide forms a stable α-helical trimer in solution. We further determined the crystal structure of an optimised variant at a resolution of 1.65 Å, revealing that the peptide folds into a parallel, three-stranded coiled coil. The two complemented R-IxxIE trimerization motifs and the additional hydrophobic core isoleucine residue adopt the conformations seen in other extensively characterized parallel, three-stranded coiled coils. These findings not only confirm the structural basis for the switch in

  3. Structural basis for the oligomerization-state switch from a dimer to a trimer of an engineered cortexillin-1 coiled-coil variant.

    Science.gov (United States)

    Bjelić, Saša; Wieser, Mara; Frey, Daniel; Stirnimann, Christian U; Chance, Mark R; Jaussi, Rolf; Steinmetz, Michel O; Kammerer, Richard A

    2013-01-01

    Coiled coils are well suited to drive subunit oligomerization and are widely used in applications ranging from basic research to medicine. The optimization of these applications requires a detailed understanding of the molecular determinants that control of coiled-coil formation. Although many of these determinants have been identified and characterized in great detail, a puzzling observation is that their presence does not necessarily correlate with the oligomerization state of a given coiled-coil structure. Thus, other determinants must play a key role. To address this issue, we recently investigated the unrelated coiled-coil domains from GCN4, ATF1 and cortexillin-1 as model systems. We found that well-known trimer-specific oligomerization-state determinants, such as the distribution of isoleucine residues at heptad-repeat core positions or the trimerization motif Arg-h-x-x-h-Glu (where h = hydrophobic amino acid; x = any amino acid), switch the peptide's topology from a dimer to a trimer only when inserted into the trigger sequence, a site indispensable for coiled-coil formation. Because high-resolution structural information could not be obtained for the full-length, three-stranded cortexillin-1 coiled coil, we here report the detailed biophysical and structural characterization of a shorter variant spanning the trigger sequence using circular dichroism, anatytical ultracentrifugation and x-ray crystallography. We show that the peptide forms a stable α-helical trimer in solution. We further determined the crystal structure of an optimised variant at a resolution of 1.65 Å, revealing that the peptide folds into a parallel, three-stranded coiled coil. The two complemented R-IxxIE trimerization motifs and the additional hydrophobic core isoleucine residue adopt the conformations seen in other extensively characterized parallel, three-stranded coiled coils. These findings not only confirm the structural basis for the switch in oligomerization state from

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

    Directory of Open Access Journals (Sweden)

    Anders Allgardsson

    2017-08-01

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

  5. Surface damage in cystine, an amino acid dimer, induced by keV ions

    Science.gov (United States)

    Salles, R. C. M.; Coutinho, L. H.; da Veiga, A. G.; Sant'Anna, M. M.; de Souza, G. G. B.

    2018-01-01

    We have studied the interaction of an ion beam (17.6 keV F-) with cystine, a dimer formed by the binding of two cysteine residues. Cystine can be considered as an ideal prototype for the study of the relevance of the disulfide (—S—S—) chemical bond in biomolecules. For the sake of comparison, the amino acid cysteine has also been subjected to the same experimental conditions. Characterization of the samples by XPS and NEXAFS shows that both pristine cystine and pristine cysteine are found as a dipolar ion (zwitterion). Following irradiation, the dimer and the amino acid show a tendency to change from the dipole ion form to the normal uncharged form. The largest spectral modification was observed in the high resolution XPS spectra obtained at around the N 1s core level for the two biomolecules. The 2p sulfur edge spectra of cysteine and cystine were much less sensitive to radiation effects. We suggest that the disulfide bond (—S—S—) remains stable before and after irradiation, contributing to the larger radiation stability of cystine as compared to the amino acid cysteine.

  6. Double proton transfer reactions in the formic acid dimer in solution

    International Nuclear Information System (INIS)

    Kohanoff, J.; Estrin, D.A.; Laria, D.; Abashkin, Y.

    2000-06-01

    The issue of multiple proton transfer (PT) reactions in solution is addressed by performing molecular dynamics simulations for a formic acid dimer embedded in a water cluster. The reactant species is treated quantum mechanically, within a density functional approach, while the solvent is represented by a classical model. By constraining different distances within the dimer we analyze the PT process in a variety of situations representative of more complex environments. Free energy profiles are presented, and analyzed in terms of typical solvated configurations extracted from the simulations. A decrease in the PT barrier height upon solvation is rationalized in terms of a transition state which is more polarized than the stable states. The dynamics of the double PT process is studied in a low-barrier case and correlated with that of the polarization fluctuations of the solvent. Cooperative effects in the motion of the two protons are observed in two different situations: when the solvent polarization does not favor the transfer of one of the two protons and when the motion of the two protons is not synchronized. This body of observations is correlated with structural and dynamical local properties of the solvent in the vicinity of the reactant. (author)

  7. Are coiled-coils of dimeric kinesins unwound during their walking on microtubule?

    Science.gov (United States)

    Duan, Zhao-Wen; Xie, Ping; Li, Wei; Wang, Peng-Ye

    2012-01-01

    Dimeric kinesin motor proteins such as homodimeric kinesin-1, homodimeric Ncd and heterodimeric Kar3/Vik1are composed of two head domains which are connected together by a rod-shaped, coiled-coil stalk. Despite the extensive and intensive studies on structures, kinetics, dynamics and walking mechanism of the dimers, whether their coiled-coils are unwound or not during their walking on the microtubule is still an unclear issue. Here, we try to clarify this issue by using molecular dynamics simulations. Our simulation results showed that, for Ncd, a large change in potential of mean force is required to unwind the coiled-coil by only several pairs of residues. For both Ncd and kinesin-1, the force required to initiate the coiled-coil unwinding is larger than that required for unfolding of the single [Formula: see text]-helix that forms the coiled-coil or is larger than that required to unwind the DNA duplex, which is higher than the unbinding force of the kinesin head from the microtubule in strong microtubule-binding states. Based on these results and the comparison of the sequence between the coiled-coil of Kar3/Vik1 and those of Ncd and kinesin-1, it was deduced that the coiled-coil of the Kar3/Vik1 should also be very stable. Thus, we concluded that the coiled-coils of kinesin-1, Ncd and Kar3/Vik1 are almost impossible to unwind during their walking on the microtubule.

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

    Science.gov (United States)

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

    2008-04-18

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-02-15

    The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The dynamics and structure of Serratia marcescens endonuclease and its neighboring solvent are investigated by molecular dynamics (MD). Comparisons are made with structural and biochemical experiments. The dimer form is physiologic and functions more processively than the monomer. We previously found a channel formed by connected clusters of waters from the active site to the dimer interface. Here, we show that dimerization clearly changes correlations in the water structure and dynamics in the active site not seen in the monomer. Our results indicate that water at the active sites of the dimer is less affected compared with bulk solvent than in the monomer where it has much slower characteristic relaxation times. Given that water is a required participant in the reaction, this gives a clear advantage to dimerization in the absence of an apparent ability to use both active sites simultaneously.

  10. Stable Organic Neutral Diradical via Reversible Coordination.

    Science.gov (United States)

    Lu, Zhenpin; Quanz, Henrik; Burghaus, Olaf; Hofmann, Jonas; Logemann, Christian; Beeck, Sebastian; Schreiner, Peter R; Wegner, Hermann A

    2017-12-27

    We report the formation of a stable neutral diboron diradical simply by coordination of an aromatic dinitrogen compound to an ortho-phenyldiborane. This process is reversible upon addition of pyridine. The diradical species is stable above 200 °C. Computations are consistent with an open-shell triplet diradical with a very small open-shell singlet-triplet energy gap that is indicative of the electronic disjointness of the two radical sites. This opens a new way of generating stable radicals with fascinating electronic properties useful for a large variety of applications.

  11. High-level theoretical study of the NO dimer and tetramer: Has the tetramer been observed?

    Science.gov (United States)

    Ivanic, Joseph; Schmidt, Michael W.; Luke, Brian

    2012-12-01

    The ground-state properties of (NO)2 and (NO)4 have been investigated using multireference second-order perturbation theory (MRMP2) and include a two-tier extrapolation to the complete basis set (CBS) limit. For the NO dimer the MRMP2(18,14)/CBS predicted structure, binding energy (with respect to 2NO; De = 3.46 kcal/mol), and dipole moment (ue = 0.169 D) are in excellent agreement with experimental measurements (De = 2.8-3.8 kcal/mol; ue = 0.171 D). Additionally, three of four intermolecular anharmonic MRMP2(18,14)/CBS-estimated frequencies (143 cm-1, 238 cm-1, 421 cm-1) are in excellent agreement with recent gas-phase experimental measurements (135 cm-1, 239 cm-1, 429/428 cm-1); however, the predicted value of 151 cm-1 for the out-of-plane torsion (A2) is elevated compared to recent experimental estimates of 97-117 cm-1. Our finding that this infrared-forbidden vibration is also predicted to have an extremely low Raman activity (0.04 Å/amu at the MP2/QZ level of theory) conflicts with Raman measurements of a strong intensity for a low frequency band; however, these studies were performed for low temperature solid and liquid phases. Probing the possibility of the presence of higher order clusters we investigated the stability of (NO)4 and discovered three isomers, each resembling pairs of dimers, that were stable to dissociation to 2(NO)2, with the lowest-energy isomer (Ci structure) having a predicted binding energy almost identical to that of the dimer. Computed vibrational frequencies of the Ci isomer indicate that the 12 highest-frequency modes resemble barely shifted NO dimer-combined bands while the 13th highest-frequency mode at ˜100 cm-1 is exclusive to (NO)4. Moreover, this tetramer-unique vibration is infrared inactive but has a very high predicted Raman activity of some 24 Å/amu. Guided by the theoretical results, we reexamined and reassigned experimental Raman and infrared data going back to 1951 and determined that our best predictions of

  12. Participation of the extracellular domain in (pro)renin receptor dimerization

    Energy Technology Data Exchange (ETDEWEB)

    Suzuki-Nakagawa, Chiharu [The United Graduate School of Agricultural Sciences, Gifu University, Gifu (Japan); Nishimura, Misa; Tsukamoto, Tomoko; Aoyama, Sho [Department of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Gifu (Japan); Ebihara, Akio; Suzuki, Fumiaki [The United Graduate School of Agricultural Sciences, Gifu University, Gifu (Japan); Department of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Gifu (Japan); Nakagawa, Tsutomu, E-mail: nakagawa@gifu-u.ac.jp [The United Graduate School of Agricultural Sciences, Gifu University, Gifu (Japan); Department of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Gifu (Japan)

    2014-02-21

    Highlights: • The (pro)renin receptor [(P)RR] is a regulator of the renin–angiotensin system. • The region responsible for (P)RR dimerization was investigated. • (P)RR extracellular domain constructs were retained intracellularly. • The extracellular domain of (P)RR is responsible for its dimerization. • Novel insight into the regulatory mechanism of soluble (P)RR secretion is provided. - Abstract: The (pro)renin receptor [(P)RR] induces the catalytic activation of prorenin, as well as the activation of the mitogen-activated protein kinase (MAPK) signaling pathway; as such, it plays an important regulatory role in the renin–angiotensin system. (P)RR is known to form a homodimer, but the region participating in its dimerization is unknown. Using glutathione S-transferase (GST) as a carrier protein and a GST pull-down assay, we investigated the interaction of several (P)RR constructs with full-length (FL) (P)RR in mammalian cells. GST fusion proteins with FL (P)RR (GST-FL), the C-terminal M8-9 fragment (GST-M8-9), the extracellular domain (ECD) of (P)RR (GST-ECD), and the (P)RR ECD with a deletion of 32 amino acids encoded by exon 4 (GST-ECDd4) were retained intracellularly, whereas GST alone was efficiently secreted into the culture medium when transiently expressed in COS-7 cells. Immunofluorescence microscopy showed prominent localization of GST-ECD to the endoplasmic reticulum. The GST pull-down analysis revealed that GST-FL, GST-ECD, and GST-ECDd4 bound FLAG-tagged FL (P)RR, whereas GST-M8-9 showed little or no binding when transiently co-expressed in HEK293T cells. Furthermore, pull-down analysis using His-tag affinity resin showed co-precipitation of soluble (P)RR with FL (P)RR from a stable CHO cell line expressing FL h(P)RR with a C-terminal decahistidine tag. These results indicate that the (P)RR ECD participates in dimerization.

  13. In Search for Universal Models. Dimerization of Nitrosobenzenes and Investigation of Some Basic Chemical Concepts

    Directory of Open Access Journals (Sweden)

    Biljan, I.

    2012-09-01

    Full Text Available One of the most exploited approaches in scientific methodology is studying concepts by using a case study. In chemistry, a case study appears in finding a specific molecular and/or reaction system by which the investigated problem can be observed directly "on substance". Thus, the stu- died problem becomes a concrete system, rather than an abstract concept. Most case-study models are designed specifically to deepen one or another chemical problem. However, there exist (although rarely models, which afford their universality, i.e. could serve for modeling of qui- te different, and even epistemologically independent concepts. Systematic investigations of the chemistry of C-nitroso compounds performed in our Laboratory in last few years, have resulted in the discovery that such molecular system may be used as a model for studying a series of basic chemical concepts; selectivity, self-assembly, solid-state reaction mechanisms, photochromism and molecular logics. Since it is known that C-nitroso compounds under specific conditions dime- rize by forming new N=N bond (Scheme 1, the reaction can be used for studying selectivity in the formation of dimers between different nitroso monomers (Fig. 1 and Fig. 2. The system is very convenient for investigation of the structure-selectivity relations.6 It has already been established, especially in the work of Brian Gowenlock, that nitroso compounds in crystal form appear as di- mers. These discoveries inspired us to investigate the kinetics and mechanism of dimerization of nitroso monomers in solid state, because the freshly sublimed nitrosoaromatic compounds appear as crystals of monomers. Consequently, this molecular system is a perfect case-study model for concepts of solid-state reactions, self-organizations in the crystalline forms (Fig. 3, as well as for the8,13 Extending our research of self-organization of nitroso compounds to two-dimensional systems (Fig. 4, we have also de- monstrated the ability of

  14. Stable isotopes labelled compounds

    International Nuclear Information System (INIS)

    1982-09-01

    The catalogue on stable isotopes labelled compounds offers deuterium, nitrogen-15, and multiply labelled compounds. It includes: (1) conditions of sale and delivery, (2) the application of stable isotopes, (3) technical information, (4) product specifications, and (5) the complete delivery programme

  15. Stable Boundary Layer Issues

    NARCIS (Netherlands)

    Steeneveld, G.J.

    2012-01-01

    Understanding and prediction of the stable atmospheric boundary layer is a challenging task. Many physical processes are relevant in the stable boundary layer, i.e. turbulence, radiation, land surface coupling, orographic turbulent and gravity wave drag, and land surface heterogeneity. The

  16. Evolutionary Stable Strategy

    Indian Academy of Sciences (India)

    IAS Admin

    After Maynard-Smith and Price [1] mathematically derived why a given behaviour or strategy was adopted by a certain proportion of the population at a given time, it was shown that a strategy which is currently stable in a population need not be stable in evolutionary time (across generations). Additionally it was sug-.

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

    Energy Technology Data Exchange (ETDEWEB)

    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: benoit.cluzel@u-bourgogne.fr; 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)

    2014-10-27

    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.

  18. Sequential dimerization of human zipcode-binding protein IMP1 on RNA: a cooperative mechanism providing RNP stability

    DEFF Research Database (Denmark)

    Nielsen, J.; Kristensen, M. A.; Willemoes, Martin

    2004-01-01

    of low stability, whereas the second step was the discriminatory event that converted a putative RNA target into a ‘locked' stable RNP. The ability to dimerize was also observed between members of the IMP family of zipcode-binding proteins, providing a multitude of further interaction possibilities......Active cytoplasmic RNA localization depends on the attachment of RNA-binding proteins that dictate the destination of the RNA molecule. In this study, we used an electrophoretic mobility-shift assay in combination with equilibrium and kinetic analyses to characterize the assembly of the human...

  19. Activation of dimeric glucocorticoid receptors in osteoclast progenitors potentiates RANKL induced mature osteoclast bone resorbing activity.

    Science.gov (United States)

    Conaway, H Herschel; Henning, Petra; Lie, Anita; Tuckermann, Jan; Lerner, Ulf H

    2016-12-01

    Glucocorticoid (GC) therapy is the greatest risk factor for secondary osteoporosis. Pathogenic mechanisms involve an initial increase in bone resorption followed by decreased bone formation. To gain a better understanding of the resorptive activity of GCs, we have used mouse bone marrow macrophages (BMM) to determine if GCs can directly modulate RANKL stimulated osteoclast formation and/or activity. In agreement with previous studies, experiments performed in plastic wells showed that GCs (dexamethasone, hydrocortisone, and prednisolone) inhibited osteoclast number and size during the initial phases of RANKL stimulated osteoclastogenesis; however, in prolonged cultures, decreased apoptosis was observed and escape from GC induced inhibition occurred with an enhanced number of osteoclasts formed, many with an increased area. When BMM cells were seeded on bone slices, GCs robustly enhanced RANKL stimulated formation of resorption pits and release of CTX without affecting the number or size of osteoclasts formed and with no effect on apoptosis. Stimulation of pit formation was not associated with increased life span of osteoclasts or an effect on mRNA expression of several osteoclastic or osteoclastogenic genes. The potentiation of RANKL induced CTX release by dexamethasone was significantly less in BMM cells from mice with conditional knockout of the osteoclastic glucocorticoid receptor and completely absent in cells from GR dim mice, which carry a point mutation in one dimerizing interface of the GC receptor. These data suggest that: 1. Plastic is a poor medium to use for studying direct effects of GCs on osteoclasts 2. GCs can enhance bone resorption without decreasing apoptosis, and 3. A direct enhancement of RANKL mediated resorption is stimulated by the dimeric GC-receptor. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. Myosin VI Must Dimerize and Deploy Its Unusual Lever Arm in Order to Perform Its Cellular Roles

    Directory of Open Access Journals (Sweden)

    Monalisa Mukherjea

    2014-09-01

    Full Text Available It is unclear whether the reverse-direction myosin (myosin VI functions as a monomer or dimer in cells and how it generates large movements on actin. We deleted a stable, single-α-helix (SAH domain that has been proposed to function as part of a lever arm to amplify movements without impact on in vitro movement or in vivo functions. A myosin VI construct that used this SAH domain as part of its lever arm was able to take large steps in vitro but did not rescue in vivo functions. It was necessary for myosin VI to internally dimerize, triggering unfolding of a three-helix bundle and calmodulin binding in order to step normally in vitro and rescue endocytosis and Golgi morphology in myosin VI-null fibroblasts. A model for myosin VI emerges in which cargo binding triggers dimerization and unfolds the three-helix bundle to create a lever arm essential for in vivo functions.

  1. Phenyl-β-D-glucopyranoside and Phenyl-β-D-galactopyranoside Dimers: Small Structural Differences but Very Different Interactions

    Directory of Open Access Journals (Sweden)

    Imanol Usabiaga

    2018-02-01

    Full Text Available We report a combination of laser spectroscopy in molecular jets and quantum mechanical calculations to characterize the aggregation preferences of phenyl-β-D-glucopyranoside (β-PhGlc and phenyl-β-D-galactopyranoside (β-PhGal homodimers. At least two structures of β-PhGlc dimer were found maintaining the same intramolecular interactions of the monomers, but with additional intermolecular interactions between the hydroxyl groups. Several isomers were also found for the dimer of β-PhGal forming extensive hydrogen bond networks between the interacting molecules, of very different shape. All the species found present several CH•••π and OH•••π interactions that add stability to the aggregates. The results show how even the smallest change in a substituent, from axial to equatorial position, plays a decisive role in the formation of the dimers. These conclusions reinforce the idea that the small structural changes between sugar units are amplified by formation of intra and intermolecular hydrogen bond networks, helping other molecules (proteins, receptors to easily read the sugar code of glycans.

  2. Dimerization effect of sucrose octasulfate on rat FGF1

    DEFF Research Database (Denmark)

    Kulahin, Nikolaj; Kiselyov, Vladislav; Kochoyan, Artur

    2008-01-01

    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....

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

    DEFF Research Database (Denmark)

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

    2009-01-01

    -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...... for either of the protomers, which was not observed upon simple coexpression of the two receptors. It is concluded that covalently joined 7TM receptor dimers with surprisingly normal receptor properties can be constructed with use of an artificial transmembrane connector, which perhaps can be used to fuse...

  4. Dimer-flipping-assisted diffusion on a Si(001) surface

    International Nuclear Information System (INIS)

    Zi, J.; Min, B. J.; Lu, Y.; Wang, C. Z.; Ho, K. M.

    2000-01-01

    The binding sites and diffusion pathways of Si adatoms on a c(4x2) reconstructed Si(001) surface are investigated by a tight-binding method with an environment-dependent silicon potential in conjunction with ab initio calculations using the Car--Parrinello method. A new diffusion pathway along the trough edge driven by dimer flipping is found with a barrier of 0.74 eV, comparable to that of 0.68 eV along the top of the dimer rows

  5. Mutations of the kissing-loop dimerization sequence influence the site specificity of murine leukemia virus recombination in vivo

    DEFF Research Database (Denmark)

    Mikkelsen, J G; Lund, Anders Henrik; Duch, M

    2000-01-01

    synthesis in newly infected cells. We have previously shown that template shifts within the 5' leader of murine leukemia viruses occur preferentially within the kissing stem-loop motif, a cis element crucial for in vitro RNA dimer formation. By use of a forced recombination approach based on single......-cycle transfer of Akv murine leukemia virus-based vectors harboring defective primer binding site sequences, we now report that modifications of the kissing-loop structure, ranging from a deletion of the entire sequence to introduction of a single point mutation in the loop motif, significantly disturb site...... specificity of recombination within the highly structured 5' leader region. In addition, we find that an intact kissing-loop sequence favors optimal RNA encapsidation and vector transduction. Our data are consistent with the kissing-loop dimerization model and suggest that a direct intermolecular RNA...

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

    Science.gov (United States)

    Murugan, Sujithkumar; Hung, Hui-Chih

    2012-01-01

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  8. Normal modified stable processes

    DEFF Research Database (Denmark)

    Barndorff-Nielsen, Ole Eiler; Shephard, N.

    2002-01-01

    This paper discusses two classes of distributions, and stochastic processes derived from them: modified stable (MS) laws and normal modified stable (NMS) laws. This extends corresponding results for the generalised inverse Gaussian (GIG) and generalised hyperbolic (GH) or normal generalised inverse...... Gaussian (NGIG) laws. The wider framework thus established provides, in particular, for added flexibility in the modelling of the dynamics of financial time series, of importance especially as regards OU based stochastic volatility models for equities. In the special case of the tempered stable OU process...

  9. Applications of stable isotopes

    International Nuclear Information System (INIS)

    Letolle, R.; Mariotti, A.; Bariac, T.

    1991-06-01

    This report reviews the historical background and the properties of stable isotopes, the methods used for their measurement (mass spectrometry and others), the present technics for isotope enrichment and separation, and at last the various present and foreseeable application (in nuclear energy, physical and chemical research, materials industry and research; tracing in industrial, medical and agronomical tests; the use of natural isotope variations for environmental studies, agronomy, natural resources appraising: water, minerals, energy). Some new possibilities in the use of stable isotope are offered. A last chapter gives the present state and forecast development of stable isotope uses in France and Europe

  10. Molecular determinants of S100B oligomer formation.

    Directory of Open Access Journals (Sweden)

    Eva Thulin

    Full Text Available BACKGROUND: S100B is a dimeric protein that can form tetramers, hexamers and higher order oligomers. These forms have been suggested to play a role in RAGE activation. METHODOLOGY/PRINCIPAL FINDINGS: Oligomerization was found to require a low molecular weight trigger/cofactor and could not be detected for highly pure dimer, irrespective of handling. Imidazol was identified as a substance that can serve this role. Oligomerization is dependent on both the imidazol concentration and pH, with optima around 90 mM imidazol and pH 7, respectively. No oligomerization was observed above pH 8, thus the protonated form of imidazol is the active species in promoting assembly of dimers to higher species. However, disulfide bonds are not involved and the process is independent of redox potential. The process was also found to be independent of whether Ca(2+ is bound to the protein or not. Tetramers that are purified from dimers and imidazol by gel filtration are kinetically stable, but dissociate into dimers upon heating. Dimers do not revert to tetramer and higher oligomer unless imidazol is again added. Both tetramers and hexamers bind the target peptide from p53 with retained stoichiometry of one peptide per S100B monomer, and with high affinity (lgK = 7.3±0.2 and 7.2±0.2, respectively in 10 mM BisTris, 5 mM CaCl(2, pH 7.0, which is less than one order of magnitude reduced compared to dimer under the same buffer conditions. CONCLUSION/SIGNIFICANCE: S100B oligomerization requires protonated imidazol as a trigger/cofactor. Oligomers are kinetically stable after imidazol is removed but revert back to dimer if heated. The results underscore the importance of kinetic versus thermodynamic control of S100B protein aggregation.

  11. Observation by flow sup 1 H NMR and dimerization kinetics and products of reactive ortho-quinodimethanes and benzocyclobutadiene

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, D.

    1990-09-21

    The reactive o-quinodimethanes, 1,2-dimethylene-1,2-dihydronaphthalene (9) and o-xylylene (1) were observed by flow {sup 1}H NMR spectroscopy at room temperature. The {sup 1}H NMR spectrum of 9 was obtained in the absence of precursor and dimers. However, the {sup 1}H NMR spectrum of the more reactive 1, generated in a similar manner from (o-((trimethylsilyl)methyl)benzyl)trimethylammonium iodide (5.) could be obtained only in the presence of its stable (4 + 2) and (4 + 4) dimers. The dimerization kinetics of 3-methyl- (5{prime}), 3,6-dimethyl- (11), 3-isopropyl- (12), and 3,6-diisoproply-1,2-xylylene (13) in acetonitrile (CH{sub 3}CN) were studied by stopped-flow UV-visible spectroscopy. Fluoride ion induced 1,2-elimination from 2-elimination from 2-trimethylsilylbenzocyclobutenyl-1 mesylate (26) was used to generate the reactive molecule benzocyclobutadiene (1{prime}) in CD{sub 3}CN, which was observed by flow {sup 1}H NMR spectroscopy at room temperature. The {sup 1}H NMR spectrum (in CD{sub 3}CN) of 1,2-dimethylene-1,2-dihydrothiophene (1{double prime}), obtained by fluoride ion induced 1,4-elimination from 3-(trimethylammoniummethyl)-2-(trimethylsilylmethyl)thiophene iodine was observed by flow {sup 1}H NMR spectroscopy at room temperature. The dimerization rate of 1{double prime} in CH{sub 3}CN, generated in the same manner, was measured by UV-visible spectroscopy. 166 refs., 7 figs., 7 tabs.

  12. D-dimer to guide the duration of anticoagulation in patients with venous thromboembolism: a management study.

    Science.gov (United States)

    Palareti, Gualtiero; Cosmi, Benilde; Legnani, Cristina; Antonucci, Emilia; De Micheli, Valeria; Ghirarduzzi, Angelo; Poli, Daniela; Testa, Sophie; Tosetto, Alberto; Pengo, Vittorio; Prandoni, Paolo

    2014-07-10

    The optimal duration of anticoagulation in patients with venous thromboembolism (VTE) is uncertain. We investigated whether persistently negative D-dimers in patients with vein recanalization or stable thrombotic burden can identify subjects at low recurrence risk. Outpatients with a first VTE (unprovoked or associated with weak risk factors) were eligible after at least 3 months (12 in those with residual thrombosis) of anticoagulation. They received serial D-dimer measurements using commercial assays with predefined age/sex-specific cutoffs and were followed for up to 2 years. Of 1010 patients, anticoagulation was stopped in 528 (52.3%) with persistently negative D-dimer who subsequently experienced 25 recurrences (3.0% pt-y; 95% confidence interval [CI], 2.0-4.4%). Of the remaining 482 patients, 373 resumed anticoagulation and 109 refused it. Recurrent VTE developed in 15 patients (8.8% pt-y; 95% CI, 5.0-14.1) of the latter group and in 4 of the former (0.7% pt-y; 95% CI, 0.2-1.7; hazard ratio = 2.92; 95% CI, 1.87-9.72; P = .0006). Major bleeding occurred in 14 patients (2.3% pt-y; 95% CI, 1.3-3.9) who resumed anticoagulation. Serial D-dimer measurement is suitable in clinical practice for the identification of VTE patients in whom anticoagulation can be safely discontinued. This study was registered at clinicaltrials.gov as #NCT00954395. © 2014 by The American Society of Hematology.

  13. Analysing Stable Time Series

    National Research Council Canada - National Science Library

    Adler, Robert

    1997-01-01

    We describe how to take a stable, ARMA, time series through the various stages of model identification, parameter estimation, and diagnostic checking, and accompany the discussion with a goodly number...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-07-06

    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.

  15. On the Elusive Twelfth Vibrational State of Beryllium Dimer

    Czech Academy of Sciences Publication Activity Database

    Patkowski, K.; Špirko, Vladimír; Szalewicz, K.

    2009-01-01

    Roč. 326, č. 5958 (2009), s. 1382-1384 ISSN 0036-8075 Institutional research plan: CEZ:AV0Z40550506 Keywords : potential function * beryllium dimer * morphed potentials Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 29.747, year: 2009

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

    DEFF Research Database (Denmark)

    Gopalan, Aravind; Klærke, Benedikte; Rajput, Jyoti

    2012-01-01

    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...

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

    NARCIS (Netherlands)

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

    2011-01-01

    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

  18. Asymmetric electron capture in HCI collisions with rare gas dimers

    Science.gov (United States)

    Matsumoto, J.; Leredde, A.; Fléchard, X.; Shiromaru, H.; Rangama, J.; Zhou, C. L.; Iskandar, W.; Guillous, S.; Hennecart, D.; Mery, A.; Gervais, B.; Cassimi, A.

    2014-04-01

    Low-energy collisions between different rare gas dimers (Ar2, Ne2) and different projectiles (O3+, Ar9+, Xe20+) show that the weight of the different fragmentation processes, Coulomb explosion and Radiative Charge Transfer, strongly depends on the projectile charge state. This result is understood in term of impact parameter from which the electrons are captured on the projectile.

  19. DNAzyme-Controlled Cleavage of Dimer and Trimer Origami Tiles.

    Science.gov (United States)

    Wu, Na; Willner, Itamar

    2016-04-13

    Dimers of origami tiles are bridged by the Pb(2+)-dependent DNAzyme sequence and its substrate or by the histidine-dependent DNAzyme sequence and its substrate to yield the dimers T1-T2 and T3-T4, respectively. The dimers are cleaved to monomer tiles in the presence of Pb(2+)-ions or histidine as triggers. Similarly, trimers of origami tiles are constructed by bridging the tiles with the Pb(2+)-ion-dependent DNAzyme sequence and the histidine-dependent DNAzyme sequence and their substrates yielding the trimer T1-T5-T4. In the presence of Pb(2+)-ions and/or histidine as triggers, the programmed cleavage of trimer proceeds. Using Pb(2+) or histidine as trigger cleaves the trimer to yield T5-T4 and T1 or the dimer T1-T5 and T4, respectively. In the presence of Pb(2+)-ions and histidine as triggers, the cleavage products are the monomer tiles T1, T5, and T4. The different cleavage products are identified by labeling the tiles with 0, 1, or 2 streptavidin labels and AFM imaging.

  20. Dimeric Complexes of Tryptophan with M2+ Metal Ions

    NARCIS (Netherlands)

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

    2009-01-01

    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

  1. One-pot Solvent-free Catalytic Dimerization Reaction of ...

    Indian Academy of Sciences (India)

    Abstract. In this study, we report a smooth one-pot, solvent-free catalytic dimerization of phenylacetylene. (1) to 1-phenylnaphthalene (2) by Cu/C at room temperature in good yield (∼100%). In the computational study, the structure of the 1-phenylnaphthalene was optimized by DFT-B3LYP/6-31G* method. The rotation.

  2. Cationic zinc (II) dimers and one dimensional coordination polymer ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 126; Issue 5 ... Special issue on Chemical Crystallography Volume 126 Issue 5 September 2014 pp 1409-1415 ... These new molecules, dimers and polymer, were characterized by FT-IR, NMR, UV-vis, fluorescent and single crystal X-ray diffraction techniques.

  3. Spectroscopic observation and structure of CS2 dimer

    Science.gov (United States)

    Rezaei, M.; Norooz Oliaee, J.; Moazzen-Ahmadi, N.; McKellar, A. R. W.

    2011-04-01

    Infrared spectra of the CS2 dimer are observed in the region of the CS2 ν3 fundamental band (˜1535 cm-1) using a tunable diode laser spectrometer. The weakly bound complex is formed in a pulsed supersonic slit-jet expansion of a dilute gas mixture of carbon disulfide in helium. Contrary to the planar slipped-parallel geometry previously observed for (CO2)2, (N2O)2, and (OCS)2, the CS2 dimer exhibits a cross-shaped structure with D2d symmetry. Two bands were observed and analyzed: the fundamental (C-S asymmetric stretch) and a combination involving this mode plus an intermolecular vibration. In both cases, the rotational structure corresponds to a perpendicular (ΔK = ±1) band of a symmetric rotor molecule. The intermolecular center of mass separation (C-C distance) is determined to be 3.539(7) Å. Thanks to symmetry, this is the only parameter required to characterize the structure, if the monomer geometry is assumed to remain unchanged in the dimer. From the band centers of the fundamental and combination band an intermolecular frequency of 10.96 cm-1 is obtained, which we assign as the torsional bending mode. This constitutes the first high resolution spectroscopic investigation of CS2 dimer.

  4. Emergence of biaxial nematic phases in solutions of semiflexible dimers

    Science.gov (United States)

    Vaghela, Arvin; Teixeira, Paulo I. C.; Terentjev, Eugene M.

    2017-10-01

    We investigate the isotropic, uniaxial nematic and biaxial nematic phases, and the transitions between them, for a model lyotropic mixture of flexible molecules consisting of two rigid rods connected by a spacer with variable bending stiffness. We apply density-functional theory within the Onsager approximation to describe strictly excluded-volume interactions in this athermal model and to self-consistently find the orientational order parameters dictated by its complex symmetry, as functions of the density. Earlier work on lyotropic ordering of rigid bent-rod molecules is reproduced and extended to show explicitly the continuous phase transition at the Landau point, at a critical bend angle of 36∘. For flexible dimers with no intrinsic biaxiality, we find that a biaxial nematic phase can nevertheless form at a sufficiently high density and low bending stiffness. For bending stiffness κ >0.86 kBT , this biaxial phase manifests as dimer bending fluctuations occurring preferentially in one plane. When the dimers are more flexible, κ the modal shape of the fluctuating dimer is a V with an acute opening angle, and one of the biaxial order parameters changes sign, indicating a rotation of the directors. These two regions are separated by a narrow strip of uniaxial nematic in the phase diagram, which we generate in terms of the spacer stiffness and particle density.

  5. Characteristics of thymine dimer excision from xeroderma pigmentosum chromatin

    International Nuclear Information System (INIS)

    Fujiwara, Y.; Kano, Y.

    1983-01-01

    We investigated thymine dimer excision from xeroderma pigmentosum (XP) chromatin in the cell-free reconstruction system. The normal-cell extract performed specific dimer excision from native chromatin and DNA isolated from 100 J/m 2 -irradiated cells. Such an excision in vitro was rapid and required high concentrations of extract. The extracts of XP group A, C and G cells were unable to excise from their own native-chromatin, but capable of excising from chromatin deprived of loosely bound nonhistone proteins with 0.35 M NaCl, as were from purified DNA. Thus, group A, C and G cells are most likely to be defective in the specific XP factors facilitating the excising activity under multicomponent regulation at the chromatin level. Further, either of group A, C and G extracts successfully complemented the native chromatin of the alternative groups. Uniquely, the XP group D extract excised dimers from native chromatin in the normal fashion under the condition. These results suggest that XP group A, C, D and G cells examined may not be defective in the dimer specific endonuclease and exonuclease per se. 19 references, 3 figures, 2 tables

  6. Core-to-core dimers forming switchable mesophase

    Czech Academy of Sciences Publication Activity Database

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

    2017-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Montagnana Martina

    2006-01-01

    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.

  8. Identification of Trimer and Dimer of 4-hydroxy-3-methoxy ...

    African Journals Online (AJOL)

    The effect of intermolecular hydrogen bonding on the molecular structure of vanillin has been studied using negative ion chemical ionization (NICl) mass spectrometry methods. The [Trimer-H2O] and [Dimer-H2O] were observed at m/z 438 and 286 respectively in NICl (CH4) mass spectrum of vanillin. The NICl (Cl) mass ...

  9. Petrography, compositional characteristics and stable isotope ...

    African Journals Online (AJOL)

    Petrography, compositional characteristics and stable isotope geochemistry of the Ewekoro formation from Ibese Corehole, eastern Dahomey basin, southwestern Nigeria. ME Nton, MO ... Preserved pore types such as; intercrystaline, moldic and vuggy pores were observed as predominant conduits for fluids. The major ...

  10. petrography, compositional characteristics and stable isotope ...

    African Journals Online (AJOL)

    PROF EKWUEME

    Subsurface samples of the predominantly carbonate Ewekoro Formation, obtained from Ibese core hole within the Dahomey basin were used in this study. Investigations entail petrographic, elemental composition as well as stable isotopes (carbon and oxygen) geochemistry in order to deduce the different microfacies and ...

  11. Increasing stability of water-soluble PQQ glucose dehydrogenase by increasing hydrophobic interaction at dimeric interface

    Directory of Open Access Journals (Sweden)

    Ferri Stefano

    2005-02-01

    Full Text Available Abstract Background Water-soluble quinoprotein glucose dehydrogenase (PQQGDH-B from Acinetobacter calcoaceticus has a great potential for application as a glucose sensor constituent. Because this enzyme shows no activity in its monomeric form, correct quaternary structure is essential for the formation of active enzyme. We have previously reported on the increasing of the stability of PQQGDH-B by preventing the subunit dissociation. Previous studies were based on decreasing the entropy of quaternary structure dissociation but not on increasing the interaction between the two subunits. We therefore attempted to introduce a hydrophobic interaction in the dimeric interface to increase the stability of PQQGDH-B. Results Amino acid residues Asn340 and Tyr418 face each other at the dimer interface of PQQGDH-B, however no interaction exists between their side chains. We simultaneously substituted Asn340 to Phe and Tyr418 to Phe or Ile, to create the two mutants Asn340Phe/Tyr418Phe and Asn340Phe/Tyr418Ile. Furthermore, residues Leu280, Val282 and Val342 form a hydrophobic region that faces, on the other subunit, residues Thr416 and Thr417, again without any specific interaction. We simultaneously substituted Thr416 and Thr417 to Val, to create the mutant Thr416Val/Thr417Val. The temperatures resulting in lose of half of the initial activity of the constructed mutants were increased by 3–4°C higher over wild type. All mutants showed 2-fold higher thermal stability at 55°C than the wild-type enzyme, without decreasing their catalytic activities. From the 3D models of all the mutant enzymes, the predicted binding energies were found to be significantly greater that in the wild-type enzyme, consistent with the increases in thermal stabilities. Conclusions We have achieved via site-directed mutagenesis the improvement of the thermal stability of PQQGDH-B by increasing the dimer interface interaction. Through rational design based on the quaternary

  12. Structural analysis and dimerization profile of the SCAN domain of the pluripotency factor Zfp206

    KAUST Repository

    Liang, Yu

    2012-06-26

    Zfp206 (also named as Zscan10) belongs to the subfamily of C2H2 zinc finger transcription factors, which is characterized by the N-terminal SCAN domain. The SCAN domain mediates self-association and association between the members of SCAN family transcription factors, but the structural basis and selectivity determinants for complex formation is unknown. Zfp206 is important for maintaining the pluripotency of embryonic stem cells presumably by combinatorial assembly of itself or other SCAN family members on enhancer regions. To gain insights into the folding topology and selectivity determinants for SCAN dimerization, we solved the 1.85 crystal structure of the SCAN domain of Zfp206. In vitro binding studies using a panel of 20 SCAN proteins indicate that the SCAN domain Zfp206 can selectively associate with other members of SCAN family transcription factors. Deletion mutations showed that the N-terminal helix 1 is critical for heterodimerization. Double mutations and multiple mutations based on the Zfp206SCAN-Zfp110SCAN model suggested that domain swapped topology is a possible preference for Zfp206SCAN-Zfp110SCAN heterodimer. Together, we demonstrate that the Zfp206SCAN constitutes a protein module that enables C2H2 transcription factor dimerization in a highly selective manner using a domain-swapped interface architecture and identify novel partners for Zfp206 during embryonal development. 2012 The Author(s).

  13. Synthesis and Dimerization Studies of a Lipophilic Photoresponsive Aryl-Extended Tetraurea-Calix[4]pyrrole.

    Science.gov (United States)

    Sekiya, Ryo; Díaz-Moscoso, Alejandro; Ballester, Pablo

    2018-02-09

    We describe the syntheses of the lipophilic aryl-extended α,α,α,α-tetraurea-phenyl-calix[4]pyrrole 1, featuring four appended azo-phenyl groups with two tert-butoxy carbonyl meta-substituents and its photo-inactive counterpart 2. In CD 2 Cl 2 solutions, both tetraurea-calix[4]pyrroles self-assemble into dimeric capsules by encapsulating one molecule of a suitable bis-N-oxide or two molecules of a mono-N-oxide. The dimeric capsules are mainly stabilized by a cyclic array of sixteen hydrogen bonds established between the eight unidirectionally oriented urea groups. Photoirradiation experiments demonstrated the trans-to-cis isomerization of the azo-phenyl groups and the formation of a plethora of stereo isomeric cis-azo-enriched capsular assemblies. The highly cis-azo enriched capsular assemblies seem to show a reduced stability and their involvement in equilibria with non-capsular counterparts that also bind the N-oxides. The thermally induced cis-to-trans interconversion processes demonstrated the reversibility of the photoisomerization and the photostability of most binding partners. An equimolar mixture of the two tetraureas produced two homodimeric capsules and the heterodimeric counterpart in a ratio close to statistical distribution. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Glycolipid Biosurfactants Activate, Dimerize, and Stabilize Thermomyces lanuginosus Lipase in a pH-Dependent Fashion.

    Science.gov (United States)

    Madsen, Jens Kvist; Kaspersen, Jørn Døvling; Andersen, Camilla Bertel; Nedergaard Pedersen, Jannik; Andersen, Kell Kleiner; Pedersen, Jan Skov; Otzen, Daniel E

    2017-08-15

    We present a study of the interactions between the lipase from Thermomyces lanuginosus (TlL) and the two microbially produced biosurfactants (BSs), rhamnolipid (RL) and sophorolipid (SL). Both RL and SL are glycolipids; however, RL is anionic, while SL is a mixture of anionic and non-ionic species. We investigate the interactions of RL and SL with TlL at pH 6 and 8 and observe different effects at the two pH values. At pH 8, neither RL nor SL had any major effect on TlL stability or activity. At pH 6, in contrast, both surfactants increase TlL's thermal stability and fluorescence and activity measurements indicate interfacial activation of TlL, resulting in 3- and 6-fold improved activity in SL and RL, respectively. Nevertheless, isothermal titration calorimetry reveals binding of only a few BS molecules per lipase. Size-exclusion chromatography and small-angle X-ray scattering suggest formation of TlL dimers with binding of small amounts of either RL or SL at the dimeric interface, forming an elongated complex. We conclude that RL and SL are compatible with TlL and constitute promising green alternatives to traditional surfactants.

  15. Unprecedented solvent induced inter-conversion between monomeric and dimeric silylene-zinc iodide adducts.

    Science.gov (United States)

    Yadav, Sandeep; Sangtani, Ekta; Dhawan, Diksha; Gonnade, Rajesh G; Ghosh, Debashree; Sen, Sakya S

    2017-08-29

    Usually, when a silylene reacts with a transition metal Lewis acid, it forms an adduct which could be either monomeric or dimeric. However, we present here that a silylene, [PhC(NtBu) 2 SiN(SiMe 3 ) 2 ] can form both monomeric [PhC(NtBu) 2 Si{N(SiMe 3 ) 2 } → ZnI 2 ]·THF (1) and dimeric [{PhC(NtBu) 2 }(N(SiMe 3 ) 2 )SiZnI,(μ-I)] 2 (2) adducts upon reaction with ZnI 2 . The formation of 1 and 2 relies upon the solvent used for the reaction or crystallization. When the crystallization is carried out in THF complex 1 is formed, however, when the reaction and crystallization are performed in acetonitrile complex 2 is obtained. Both 1 and 2 were structurally authenticated and the nature of the Si-Zn bond in these complexes was determined by quantum chemical calculations. In addition, a spontaneous inter-conversion between 1 and 2 just by changing the solvents has been also observed; a feature presently not known for silylene-transition metal Lewis adducts.

  16. Biological activity and dimerization state of modified phytochrome A proteins.

    Directory of Open Access Journals (Sweden)

    Peng Liu

    Full Text Available To assess potential physical interactions of type I phyA with the type II phyB-phyE phytochromes in vivo, transgenes expressing fusion gene forms of phyA were introduced into the Arabidopsis phyA mutant background. When a single c-Myc (myc epitope is added to either the N- or C-terminus of phyA, the constructs completely complement phyA mutant phenotypes. However, addition of larger tags, such as six consecutive myc epitopes or the yellow fluorescent protein sequence, result in fusion proteins that show reduced activity. All the tagged phyA proteins migrate as dimers on native gels and co-immunoprecipitation reveals no binding interaction of phyA to any of the type II phys in the dark or under continuous far-red light. Dimers of the phyA 1-615 amino acid N-terminal photosensory domain (NphyA, generated in vivo with a yeast GAL4 dimerization domain and attached to a constitutive nuclear localization sequence, are expressed at a low level and, although they cause a cop phenotype in darkness and mediate a very low fluence response to pulses of FR, have no activity under continuous FR. It is concluded that type I phyA in its Pr form is present in plants predominantly or exclusively as a homodimer and does not stably interact with type II phys in a dimer-to-dimer manner. In addition, its activity in mediating response to continuous FR is sensitive to modification of its N- or C-terminus.

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

    DEFF Research Database (Denmark)

    Ahler-Toftehøj, Hans-Ulrik; Mikkelsen, Peter

    2009-01-01

    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...

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

    DEFF Research Database (Denmark)

    Haase, Christine; Joergensen, Maja; Ellervik, Christina

    2013-01-01

    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 of...... of different cut-off limits....

  19. Calcium stable isotope geochemistry

    Energy Technology Data Exchange (ETDEWEB)

    Gausonne, Nikolaus [Muenster Univ. (Germany). Inst. fuer Mineralogie; Schmitt, Anne-Desiree [Strasbourg Univ. (France). LHyGeS/EOST; Heuser, Alexander [Bonn Univ. (Germany). Steinmann-Inst. fuer Geologie, Mineralogie und Palaeontologie; Wombacher, Frank [Koeln Univ. (Germany). Inst. fuer Geologie und Mineralogie; Dietzel, Martin [Technische Univ. Graz (Austria). Inst. fuer Angewandte Geowissenschaften; Tipper, Edward [Cambridge Univ. (United Kingdom). Dept. of Earth Sciences; Schiller, Martin [Copenhagen Univ. (Denmark). Natural History Museum of Denmark

    2016-08-01

    This book provides an overview of the fundamentals and reference values for Ca stable isotope research, as well as current analytical methodologies including detailed instructions for sample preparation and isotope analysis. As such, it introduces readers to the different fields of application, including low-temperature mineral precipitation and biomineralisation, Earth surface processes and global cycling, high-temperature processes and cosmochemistry, and lastly human studies and biomedical applications. The current state of the art in these major areas is discussed, and open questions and possible future directions are identified. In terms of its depth and coverage, the current work extends and complements the previous reviews of Ca stable isotope geochemistry, addressing the needs of graduate students and advanced researchers who want to familiarize themselves with Ca stable isotope research.

  20. Optical fluoride sensor based on monomer-dimer equilibrium of scandium(III)-octaethylporphyrin in a plasticized polymeric film

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Youngjea; Kampf, Jeff W. [Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055 (United States); Meyerhoff, Mark E. [Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055 (United States)], E-mail: mmeyerho@umich.edu

    2007-08-29

    A fluoride-selective optical sensor based on scandium(III)-octaethylporphyrin (Sc(III)OEP) as an ionophore within a plasticized PVC film is described. The presence of fluoride ion in the aqueous sample phase increases the formation of a difluoro-bridged Sc(III)OEP dimer species in the polymer film. The ability of the Sc(III) porphyrin to form the dimeric structure in the presence of fluoride is confirmed by UV-vis spectroscopy and X-ray crystallography. For more practical sensing applications, a pH chromoionophore (ETH 7075) is added to the plasticized PVC film along with Sc(III)OEP and the observed optical response is based on coextraction of protons with sample phase fluoride to create the dimeric porphyrin and a protonated chromoionophore species. The selectivity pattern observed is F{sup -} >> ClO{sub 4}{sup -}, SCN{sup -}, NO{sub 3}{sup -} > Br{sup -}, Cl{sup -}. Only organic salicylate is a significant interferent. Fast and reversible fluoride response is observed over the range of 10{sup -4} to 10{sup -2} M fluoride, allowing use of the sensing film in a waveguide configuration for flow-injection measurements.

  1. Disulfide Bonds within the C2 Domain of RAGE Play Key Roles in Its Dimerization and Biogenesis

    Science.gov (United States)

    Wei, Wen; Lampe, Leonie; Park, Sungha; Vangara, Bhavana S.; Waldo, Geoffrey S.; Cabantous, Stephanie; Subaran, Sarah S.; Yang, Dongmei; Lakatta, Edward G.; Lin, Li

    2012-01-01

    Background The receptor for advanced glycation end products (RAGE) on the cell surface transmits inflammatory signals. A member of the immunoglobulin superfamily, RAGE possesses the V, C1, and C2 ectodomains that collectively constitute the receptor's extracellular structure. However, the molecular mechanism of RAGE biogenesis remains unclear, impeding efforts to control RAGE signaling through cellular regulation. Methodology and Result We used co-immunoprecipitation and crossing-linking to study RAGE oligomerization and found that RAGE forms dimer-based oligomers. Via non-reducing SDS-polyacrylamide gel electrophoresis and mutagenesis, we found that cysteines 259 and 301 within the C2 domain form intermolecular disulfide bonds. Using a modified tripartite split GFP complementation strategy and confocal microscopy, we also found that RAGE dimerization occurs in the endoplasmic reticulum (ER), and that RAGE mutant molecules without the double disulfide bridges are unstable, and are subjected to the ER-associated degradation. Conclusion Disulfide bond-mediated RAGE dimerization in the ER is the critical step of RAGE biogenesis. Without formation of intermolecular disulfide bonds in the C2 region, RAGE fails to reach cell surface. Significance This is the first report of RAGE intermolecular disulfide bond. PMID:23284645

  2. N-glycosylation and dimerization regulate the PtrMAN6 enzyme activity that may modulate generation of oligosaccharide signals.

    Science.gov (United States)

    Zhao, Yunjun; Zhang, Qian; Yuan, Luxia; Zhang, Rui; Li, Laigeng

    2013-11-01

    PtrMAN6 is a plant mannan endo-hydrolase involved in modulating cell expansion and cell wall thickening in Populus developing xylem. N-glycosylation and dimerization affect the PtrMAN6 enzymatic activity, which is crucial for production of the endogenous galactoglucomannan oligosaccharide signal molecule in plants. There are 5 potential N-glycosylation sites and 6 cysteines in PtrMAN6 sequence. Each of the N-glycosylation or cysteine sites was site-direct mutagenized individually as well as in combination to analyze their effects on the PtrMAN6 N-glycosylation or dimerization status and the enzyme activity. Our results demonstrated that all 5 potential N-glycosylation sites are involved in the N-glycosylation, which is essential for PtrMAN6 enzyme activity. Meanwhile, we found only 3 carboxyl-terminal cysteines are involved in formation of disulfide-linked dimer to regulate PtrMAN6 activity. The 3 carboxyl-terminal cysteines were conserved in the wall-bounded mannan endo-hydrolases, and this structure may play a role in regulating the PtrMAN6 activity through interaction with redox signals such as reactive oxygen species (ROS) and hydrogen sulfide (H2S) for GGMOs signal generation.

  3. DFT approach to (benzylthio)acetic acid: Conformational search, molecular (monomer and dimer) structure, vibrational spectroscopy and some electronic properties

    Science.gov (United States)

    Sienkiewicz-Gromiuk, Justyna

    2018-01-01

    The DFT studies were carried out with the B3LYP method utilizing the 6-31G and 6-311++G(d,p) basis sets depending on whether the aim of calculations was to gain the geometry at equilibrium, or to calculate the optimized molecular structure of (benzylthio)acetic acid (Hbta) in the forms of monomer and dimer. The minimum conformational energy search was followed by the potential energy surface (PES) scan of all rotary bonds existing in the acid molecule. The optimized geometrical monomeric and dimeric structures of the title compound were compared with the experimental structural data in the solid state. The detailed vibrational interpretation of experimental infrared and Raman bands was performed on the basis of theoretically simulated ESFF-scaled wavenumbers calculated for the monomer and dimer structures of Hbta. The electronic characteristics of Hbta is also presented in terms of Mulliken atomic charges, frontier molecular orbitals and global reactivity descriptors. Additionally, the MEP and ESP surfaces were computed to predict coordination sites for potential metal complex formation.

  4. Optical fluoride sensor based on monomer-dimer equilibrium of scandium(III)-octaethylporphyrin in a plasticized polymeric film.

    Science.gov (United States)

    Kang, Youngjea; Kampf, Jeff W; Meyerhoff, Mark E

    2007-08-29

    A fluoride-selective optical sensor based on scandium(III)-octaethylporphyrin (Sc(III)OEP) as an ionophore within a plasticized PVC film is described. The presence of fluoride ion in the aqueous sample phase increases the formation of a difluoro-bridged Sc(III)OEP dimer species in the polymer film. The ability of the Sc(III) porphyrin to form the dimeric structure in the presence of fluoride is confirmed by UV-vis spectroscopy and X-ray crystallography. For more practical sensing applications, a pH chromoionophore (ETH 7075) is added to the plasticized PVC film along with Sc(III)OEP and the observed optical response is based on coextraction of protons with sample phase fluoride to create the dimeric porphyrin and a protonated chromoionophore species. The selectivity pattern observed is F- > ClO4(-), SCN-, NO3(-) > Br-, Cl-. Only organic salicylate is a significant interferent. Fast and reversible fluoride response is observed over the range of 10(-4) to 10(-2) M fluoride, allowing use of the sensing film in a waveguide configuration for flow-injection measurements.

  5. Photoreactivation of pyrimidine dimers generated by a photosensitized reaction in RNA of the Smittia sp. embryos after UV-irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Kal' thoff, K.; Iekle, G. (Texas Univ., Austin (USA). Dept. of Zoology)

    1981-12-01

    Mechanisms of biological effects resulting from the irradiation of Smittia sp. embryos in an early stage of development with UV rays with the wave-length of 265, 285 and 295 nm are investigated. It is shown that the cessation of development, deceleration of protein synthesis and emergence of additional abdomens after the irradiation of embryos in early stages of development are not connected with the damage of the nucleus but with the formation of pyrimidine dimers in RNA in the cortical layer of ovum cytoplasm. At first, the energy of UV rays with the given wave-lengths is accepted in the cell by molecules-photosensitizers. It is shown for the first time that pyrimidine dimers generated in RNA can be photoreactivated on exposure of cells to light. Maternal RNA accumulated during oogenesis play an important role in the early embryogeny of insects and other animals ova developing in the sunlight. Therefore, the protection of embryo RNA from solar UV irradiation damage is provided for by the mechanisms of RNA pyrimidine dimers photoreactivation resulted from the sunlight long waves.

  6. Weak hydrogen bond topology in 1,1-difluoroethane dimer: A rotational study.

    Science.gov (United States)

    Chen, Junhua; Zheng, Yang; Wang, Juan; Feng, Gang; Xia, Zhining; Gou, Qian

    2017-09-07

    The rotational spectrum of the 1,1-difluoroethane dimer has been investigated by pulsed-jet Fourier transform microwave spectroscopy. Two most stable isomers have been detected, which are both stabilized by a network of three C-H⋯F-C weak hydrogen bonds: in the most stable isomer, two difluoromethyl C-H groups and one methyl C-H group act as the weak proton donors whilst in the second isomer, two methyl C-H groups and one difluoromethyl C-H group act as the weak proton donors. For the global minimum, the measurements have also been extended to its four 13 C isotopologues in natural abundance, allowing a precise, although partial, structural determination. Relative intensity measurements on a set of μ a -type transitions allowed estimating the relative population ratio of the two isomers as N I /N II ∼ 6/1 in the pulsed jet, indicating a much larger energy gap between these two isomers than that expected from ab initio calculation, consistent with the result from pseudo-diatomic dissociation energies estimation.

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    destructively with that from paths belonging to Fe(OH2)63+ monomers that coexist with the dimers, leading to a less apparent Fe shell in the EXAFS Fourier transform. This might be a reason why the characteristic Fe–Fe distance was not detected in previous EXAFS studies. The existence of μ-oxo dimers is further...... confirmed by Mössbauer analyses of analogous quick frozen solutions. This work also explores the electronic structure and the relative stability of the μ-oxo dimer in a comparison to the dihydroxo dimer using density function theory (DFT) calculations. The identification of such dimers in aqueous solutions...

  8. MALDI Mass Spectral Imaging of Bile Acids Observed as Deprotonated Molecules and Proton-Bound Dimers from Mouse Liver Sections

    Science.gov (United States)

    Rzagalinski, Ignacy; Hainz, Nadine; Meier, Carola; Tschernig, Thomas; Volmer, Dietrich A.

    2018-02-01

    Bile acids (BAs) play two vital roles in living organisms, as they are involved in (1) the secretion of cholesterol from liver, and (2) the lipid digestion/absorption in the intestine. Abnormal bile acid synthesis or secretion can lead to severe liver disorders. Even though there is extensive literature on the mass spectrometric determination of BAs in biofluids and tissue homogenates, there are no reports on the spatial distribution in the biliary network of the liver. Here, we demonstrate the application of high mass resolution/mass accuracy matrix-assisted laser desorption/ionization (MALDI)-Fourier-transform ion cyclotron resonance (FTICR) to MS imaging (MSI) of BAs at high spatial resolutions (pixel size, 25 μm). The results show chemical heterogeneity of the mouse liver sections with a number of branching biliary and blood ducts. In addition to ion signals from deprotonation of the BA molecules, MALDI-MSI generated several further intense signals at larger m/z for the BAs. These signals were spatially co-localized with the deprotonated molecules and easily misinterpreted as additional products of BA biotransformations. In-depth analysis of accurate mass shifts and additional electrospray ionization and MALDI-FTICR experiments, however, confirmed them as proton-bound dimers. Interestingly, dimers of bile acids, but also unusual mixed dimers of different taurine-conjugated bile acids and free taurine, were identified. Since formation of these complexes will negatively influence signal intensities of the desired [M - H]- ions and significantly complicate mass spectral interpretations, two simple broadband techniques were proposed for non-selective dissociation of dimers that lead to increased signals for the deprotonated BAs. [Figure not available: see fulltext.

  9. The structure of hyperthermophilic β-N-acetylglucosaminidase reveals a novel dimer architecture associated with the active site.

    Science.gov (United States)

    Mine, Shouhei; Kado, Yuji; Watanabe, Masahiro; Fukuda, Yohta; Abe, Yoshito; Ueda, Tadashi; Kawarabayasi, Yutaka; Inoue, Tsuyoshi; Ishikawa, Kazuhiko

    2014-11-01

    The β-N-acetylglucosaminidase from the hyperthermophilic bacteria Thermotoga maritima (NagA) hydrolyzes chitooligomers into monomer β-N-acetylglucosamine. Although NagA contains a highly conserved sequence motif found in glycoside hydrolase (GH) family 3, it can be distinguished from other GH family 3 β-N-acetylglucosaminidases by its substrate specificity and biological assembly. To investigate its unique structure around the active site, we determined the crystal structure of NagA at a resolution of 2.43 Å. The NagA forms a dimer structure in which the monomer structure consists of an N- and a C-terminal domain. The dimer structure exhibits high solvation free energy for dimer formation. From mutagenesis analyses, the catalytic nucleophile and general acid-base residues were supposed to be Asp245 and His173, respectively. The most striking characteristic of NagA was that it forms the active site cleft from the N-terminal domain and the C-terminal domain of the next polypeptide chain, whereas the other two-domain GH family 3 enzymes form the site within the same molecule. Another striking feature is that the loops located around the active site show high flexibility. One of the flexible loops contains the general acid-base His173 and was thought to be involved in substrate distortion during catalysis. In addition, a loop in close contact with the active site, which comes from the C-terminal domain of the next polypeptide chain, contains a region of high B-factor values, indicating the possibility that the C-terminal domain is involved in catalysis. These results suggest that the dimer structure of NagA is important for its activity and thermostability. Structural data are available in the Protein Data Bank under accession number 3WO8. © 2014 FEBS.

  10. Evolutionary Stable Strategy

    Indian Academy of Sciences (India)

    2016-08-26

    Aug 26, 2016 ... Home; Journals; Resonance – Journal of Science Education; Volume 21; Issue 9. Evolutionary Stable Strategy: Application of Nash Equilibrium in Biology. General ... Using some examples of classical games, we show how evolutionary game theory can help understand behavioural decisions of animals.

  11. The Stable Concordance Genus

    OpenAIRE

    Kearney, M. Kate

    2013-01-01

    The concordance genus of a knot is the least genus of any knot in its concordance class. Although difficult to compute, it is a useful invariant that highlights the distinction between the three-genus and four-genus. In this paper we define and discuss the stable concordance genus of a knot, which describes the behavior of the concordance genus under connected sum.

  12. Manifolds admitting stable forms

    Czech Academy of Sciences Publication Activity Database

    Le, Hong-Van; Panák, Martin; Vanžura, Jiří

    2008-01-01

    Roč. 49, č. 1 (2008), s. 101-11 ISSN 0010-2628 R&D Projects: GA ČR(CZ) GP201/05/P088 Institutional research plan: CEZ:AV0Z10190503 Keywords : stable forms * automorphism groups Subject RIV: BA - General Mathematics

  13. Stable isotope studies

    International Nuclear Information System (INIS)

    Ishida, T.

    1992-01-01

    The research has been in four general areas: (1) correlation of isotope effects with molecular forces and molecular structures, (2) correlation of zero-point energy and its isotope effects with molecular structure and molecular forces, (3) vapor pressure isotope effects, and (4) fractionation of stable isotopes. 73 refs, 38 figs, 29 tabs

  14. Interactive Stable Ray Tracing

    DEFF Research Database (Denmark)

    Dal Corso, Alessandro; Salvi, Marco; Kolb, Craig

    2017-01-01

    Interactive ray tracing applications running on commodity hardware can suffer from objectionable temporal artifacts due to a low sample count. We introduce stable ray tracing, a technique that improves temporal stability without the over-blurring and ghosting artifacts typical of temporal post-pr...

  15. The stable subgroup graph

    Directory of Open Access Journals (Sweden)

    Behnaz Tolue

    2018-07-01

    Full Text Available In this paper we introduce stable subgroup graph associated to the group $G$. It is a graph with vertex set all subgroups of $G$ and two distinct subgroups $H_1$ and $H_2$ are adjacent if $St_{G}(H_1\\cap H_2\

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

    International Nuclear Information System (INIS)

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

    2011-01-01

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

  17. Independent movement, dimerization and stability of tandem repeats of chicken brain alpha-spectrin

    Energy Technology Data Exchange (ETDEWEB)

    Kusunoki, H.; Minasov, G.; Macdonald, R.I.; Mondragon, A. (NWU)

    2010-03-08

    Previous X-ray crystal structures have shown that linkers of five amino acid residues connecting pairs of chicken brain {alpha}-spectrin and human erythroid {beta}-spectrin repeats can undergo bending without losing their {alpha}-helical structure. To test whether bending at one linker can influence bending at an adjacent linker, the structures of two and three repeat fragments of chicken brain {alpha}-spectrin have been determined by X-ray crystallography. The structure of the three-repeat fragment clearly shows that bending at one linker can occur independently of bending at an adjacent linker. This observation increases the possible trajectories of modeled chains of spectrin repeats. Furthermore, the three-repeat molecule crystallized as an antiparallel dimer with a significantly smaller buried interfacial area than that of {alpha}-actinin, a spectrin-related molecule, but large enough and of a type indicating biological specificity. Comparison of the structures of the spectrin and {alpha}-actinin dimers supports weak association of the former, which could not be detected by analytical ultracentrifugation, versus strong association of the latter, which has been observed by others. To correlate features of the structure with solution properties and to test a previous model of stable spectrin and dystrophin repeats, the number of inter-helical interactions in each repeat of several spectrin structures were counted and compared to their thermal stabilities. Inter-helical interactions, but not all interactions, increased in parallel with measured thermal stabilities of each repeat and in agreement with the thermal stabilities of two and three repeats and also partial repeats of spectrin.

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

    Science.gov (United States)

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

    2015-03-13

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

  19. Emergence of a Dimer-Dimer Interaction in the Low-Energy Effective Quantum-Dimer Model of a Diamond-Like-Decorated Square-Lattice Heisenberg Antiferromagnets with Further Neighbor Couplings

    Science.gov (United States)

    Hirose, Yuhei; Oguchi, Akihide; Fukumoto, Yoshiyuki

    2017-12-01

    We study spin-1/2 Heisenberg antiferromagnets on a diamond-like-decorated square lattice perturbed by two kinds of further neighbor couplings. In our previous study [https://doi.org/10.7566/JPSJ.85.094002" xlink:type="simple">J. Phys. Soc. Jpn. 85, 094002 (2016)], the second-order effective Hamiltonian for the Heisenberg model perturbed by a further neighbor coupling was found to be a square-lattice quantum-dimer model with a finite hopping amplitude, t > 0, and no dimer-dimer interaction, v = 0. In this study, we introduce another kind of further neighbor coupling and show that it leads to an attractive interaction between dimers, which suggests the stabilization of the columnar phase of the square-lattice quantum-dimer model. The calculated v/t is presented as a function of the ratio of the two exchange parameters in the Heisenberg model.

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

    DEFF Research Database (Denmark)

    Shin, J; Lee, W; Lee, D

    2001-01-01

    cytoplasmic domain is dependent on its oligomeric status, the conformation of the syndecan-4 cytoplasmic domain itself is important in the understanding of its biological roles. Gel filtration results show that the syndecan-4 cytoplasmic domain (4L) itself forms a dimer stabilized by ionic interactions......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...... 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...

  1. Dimers on two types of lattices on the Klein bottle

    Science.gov (United States)

    Lu, Fuliang; Zhang, Lianzhu

    2012-12-01

    The problem of enumerating close-packed dimers, or perfect matchings, on two types of lattices (the so-called 8.8.4 and 8.8.6 lattices) embedded on the Klein bottle is considered, and we obtain the explicit expression of the number of close-packed dimers and entropy. Our results imply that 8.8.4 lattices have the same entropy under three different boundary conditions (cylindrical, toroidal and Klein bottle) and 8.8.6 lattices have the same property. This article is part of ‘Lattice models and integrability’, a special issue of Journal of Physics A: Mathematical and Theoretical in honour of F Y Wu's 80th birthday.

  2. Stability of gold atoms and dimers adsorbed on graphene

    International Nuclear Information System (INIS)

    Varns, R; Strange, P

    2008-01-01

    We report density functional theory (DFT) calculations for gold atoms and dimers on the surface of graphene. The calculations were performed using the plane wave pseudopotential method. Calculations were performed for a variety of geometries, and both the graphene surface and gold atoms were allowed to fully relax. In agreement with experiment, our results show that the gold-gold interaction is considerably stronger than the gold-graphene interaction, implying that uniform coverage could not be attained. The minimum energy configuration for a single gold atom is found to be directly above a carbon atom, while for the dimer it is perpendicular to the surface and directly above a carbon-carbon bond. Our results are consistent with previous similar calculations

  3. Oxidative catalytic dimerization of methane: Syngas process alternative

    International Nuclear Information System (INIS)

    Salvi, G.

    1991-01-01

    A review of research progress relative to the direct conversion of methane into liquid hydrocarbons through oxidative catalytic dimerization indicates that high carbon (C 2 ) yields can be obtained in experimental conditions in which there is a high linear gas velocity, i.e., velocities greater than 0.45 m/s, at temperatures ranging between 800 and 850 degrees C, and with volumetric methane/oxygen ratios of 2 to 10. The high linear velocities have the function of preventing back-mixing phenomena and consequent product degradation. The suitable integration of dimerization (exothermic) with cracking (endothermic) of ethane to ethylene and higher olefins, as well as, oligomerization of the olefins to liquid hydrocarbons (synthesis fuels) can allow for the development of an very interesting process from both technical and economic points of view, especially for those countries with a mix of abundant natural gas reserves and scarce petroleum resources

  4. Différenciations dans les parcours de formation post-obligatoire en Suisse. Constantes et changements Pathways’ differentiations in post-compulsory education in Switzerland. Stable and changing features

    Directory of Open Access Journals (Sweden)

    Elisabetta Pagnossin

    2011-10-01

    Full Text Available Les décisions concernant la formation post-obligatoire des jeunes suisses sont toujours très influencées par le genre. La répartition des filles et des garçons dans les filières de formation post-obligatoire n’a pas beaucoup évolué durant la dernière décennie bien que le niveau d’éducation des filles ait augmenté de manière importante. Le modèle traditionnel de division du travail et des rôles sociaux défini par le genre est encore très présent dans le pays. Il se reflète naturellement sur les choix éducatifs et professionnels, surtout des jeunes de 15 ans. Non seulement le choix de la filière, mais surtout celui du domaine d’étude, reste très genré. Des changements sont pourtant décelables, surtout dans l’orientation des filles, qui sont plus nombreuses à s’investir dans des formations atypiques. Cette tendance devrait se poursuivre.Decisions on post-compulsory education for the young Swiss are always highly gendered. The distribution of girls and boys in post-compulsory pathways has not much evolved for a decade even if the level of education reached by girls has increased a lot. The traditional model of the gendered division of labour and of social roles is still very present in the country. It is obviously reflected in educational choices especially for the 15 year-olds. Choices of pathways and more particularly choices of educational fields remain very gendered. Nonetheless, some changes can be detected particularly regarding the orientation of girls as they are keener on investing themselves in atypical training courses. This trend should continue.

  5. A new phenylspirodrimane dimer from the fungus Stachybotrys chartarum.

    Science.gov (United States)

    Ding, Zhang-Gui; Ding, Jian-Hai; Zhao, Jiang-Yuan; Chunyu, Wei-Xun; Li, Ming-Gang; Gu, Shao-Jie; Wang, Fei; Wen, Meng-Liang

    2018-03-01

    A new phenylspirodrimane dimer, named stachartarin A (1), was isolated from cultures of the tin mine tailings-associated fungus Stachybotrys chartarum. Its structures were elucidated by means of spectroscopic methods. At the same time, the compound was tested for its cytotoxicity against HL-60, SMMC-7721, A-549, MCF-7, and SW480 cells. Copyright © 2018 Elsevier B.V. All rights reserved.

  6. A new dimeric anthraquinone from endophytic Talaromyces sp. YE3016.

    Science.gov (United States)

    Xie, Xiao-Song; Fang, Xiao-Wei; Huang, Rong; Zhang, Shou-Peng; Wei, Hong-Xia; Wu, Shao-Hua

    2016-08-01

    A new unsymmetrical dimeric anthraquinone, 3-demethyl-3-(2-hydroxypropyl)-skyrin (1) was isolated from the solid-state fermentation extract of an endophytic fungal strain Talaromyces sp. YE 3016, together with five known compounds, skyrin (2), oxyskyrin (3), emodin (4), 1,3,6-trihydroxy-8-methyl-anthraquinone (5) and ergosterol (6). The structure of the new compound was elucidated on the basis of spectroscopic analysis. Compounds 1-3 exhibited moderate cytotoxic activities against MCF-7 cell line.

  7. Plasmonic dimer antennas for surface enhanced Raman scattering.

    Science.gov (United States)

    Höflich, Katja; Becker, Michael; Leuchs, Gerd; Christiansen, Silke

    2012-05-11

    Electron beam induced deposition (EBID) has recently been developed into a method to directly write optically active three-dimensional nanostructures. For this purpose a metal-organic precursor gas (here dimethyl-gold(III)-acetylacetonate) is introduced into the vacuum chamber of a scanning electron microscope where it is cracked by the focused electron beam. Upon cracking the aforementioned precursor gas, 3D deposits are realized, consisting of gold nanocrystals embedded in a carbonaceous matrix. The carbon content in the deposits hinders direct plasmonic applications. However, it is possible to activate the deposited nanostructures for plasmonics by coating the EBID structures with a continuous silver layer of a few nanometers thickness. Within this silver layer collective motions of the free electron gas can be excited. In this way, EBID structures with their intriguing precision at the nanoscale have been arranged in arrays of free-standing dimer antenna structures with nanometer sized gaps between the antennas that face each other with an angle of 90°. These dimer antenna ensembles can constitute a reproducibly manufacturable substrate for exploiting the surface enhanced Raman effect (SERS). The achieved SERS enhancement factors are of the order of 10⁴ for the incident laser light polarized along the dimer axes. To prove the signal enhancement in a Raman experiment we used the dye methyl violet as a robust test molecule. In future applications the thickness of such a silver layer on the dimer antennas can easily be varied for tuning the plasmonic resonances of the SERS substrate to match the resonance structure of the analytes to be detected.

  8. Synthesis and anti-inflammatory activity of phenylbutenoid dimer analogs

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sung Soo; Fang, Yuan Ying; Park, Hae Eil [Kangwon National University, Chuncheon (Korea, Republic of)

    2015-06-15

    Several phenylbutenoid dimer (PBD) analogs were synthesized and evaluated for their inhibitory activities against nitric oxide (NO) production and TNF-α release. The PBD analogs were synthesized via Diels–Alder and subsequent Schlosser reactions as key steps. Among the tested compounds, two analogs (8c, 8f) exhibited much stronger inhibitory activity against LPS-stimulated NO production and TNF-α release in RAW 264.7 cells than that of wogonin.

  9. Antimicrobial Oligophenalenone Dimers from the Soil Fungus Talaromyces stipitatus

    OpenAIRE

    Zang , Yi; Genta-Jouve , Grégory; Escargueil , Alexandre E.; Larsen , Annette K.; Guedon , Laura; Nay , Bastien; Prado , Soizic

    2016-01-01

    International audience; New polyketide-derived oligophenalenone dimers, 9a-epi-bacillisporin E (1) and bacillisporins F–H (2–5), along with the known bacillisporin A (6), were isolated from the fungus Talaromyces stipitatus. Their structures and absolute configurations were determined on the basis of spectroscopic analyses, electronic circular dichroism, and GIAO NMR shift calculation followed by DP4 analysis. The antimicrobial activity of these compounds was evaluated against a panel of huma...

  10. Dimerization effect of sucrose octasulfate on rat FGF1

    International Nuclear Information System (INIS)

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

    2008-01-01

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

  11. On the photophysics and photochemistry of the water dimer

    Energy Technology Data Exchange (ETDEWEB)

    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)

    2012-12-28

    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.

  12. Correlative SEM SERS for quantitative analysis of dimer nanoparticles.

    Science.gov (United States)

    Timmermans, F J; Lenferink, A T M; van Wolferen, H A G M; Otto, C

    2016-11-14

    A Raman microscope integrated with a scanning electron microscope was used to investigate plasmonic structures by correlative SEM-SERS analysis. The integrated Raman-SEM microscope combines high-resolution electron microscopy information with SERS signal enhancement from selected nanostructures with adsorbed Raman reporter molecules. Correlative analysis is performed for dimers of two gold nanospheres. Dimers were selected on the basis of SEM images from multi aggregate samples. The effect of the orientation of the dimer with respect to the polarization state of the laser light and the effect of the particle gap size on the Raman signal intensity is observed. Additionally, calculations are performed to simulate the electric near field enhancement. These simulations are based on the morphologies observed by electron microscopy. In this way the experiments are compared with the enhancement factor calculated with near field simulations and are subsequently used to quantify the SERS enhancement factor. Large differences between experimentally observed and calculated enhancement factors are regularly detected, a phenomenon caused by nanoscale differences between the real and 'simplified' simulated structures. Quantitative SERS experiments reveal the structure induced enhancement factor, ranging from ∼200 to ∼20 000, averaged over the full nanostructure surface. The results demonstrate correlative Raman-SEM microscopy for the quantitative analysis of plasmonic particles and structures, thus enabling a new analytical method in the field of SERS and plasmonics.

  13. Dissociative Ionization of Argon Dimer by Intense Femtosecond Laser Pulses.

    Science.gov (United States)

    Cheng, Qian; Xie, Xiguo; Yuan, Zongqiang; Zhong, Xunqi; Liu, Yunquan; Gong, Qihuang; Wu, Chengyin

    2017-05-25

    We experimentally and theoretically studied dissociative ionization of argon dimer driven by intense femtosecond laser pulses. In the experiment, we measured the ion yield and the angular distribution of fragmental ions generated from the dissociative ionization channels of (1,1) (Ar 2 2+ → Ar + + Ar + ) and (2,1) (Ar 2 3+ → Ar 2+ + Ar + ) using a cold target recoil ion momentum spectroscopy. The channel ratio of (2,1)/(1,1) is 4.5-7.5 times of the yield ratio of double ionization to single ionization of argon monomer depending on the laser intensity. The measurement verified that the ionization of Ar + is greatly enhanced if there exists a neighboring Ar + separated by a critical distance. In addition, the fragmental ions exhibit an anisotropic angular distribution with the peak along the laser polarization direction and the full width at half maximum becomes broader with increasing laser intensity. Using a full three-dimensional classical ensemble model, we calculated the angle-dependent multiple ionization probability of argon dimer in intense laser fields. The results show that the experimentally observed anisotropic angular distribution of fragmental ions can be attributed to the angle-dependent enhanced ionization of the argon dimer in intense laser fields.

  14. Oligomerizations of deoxyadenosine bis-phosphates and of their 3-prime-5-prime, 3-prime-3-prime, and 5-prime-5-prime dimers - Effects of a pyrophosphate-linked, poly(T) analog

    Science.gov (United States)

    Visscher, J.; Bakker, C. G.; Schwartz, Alan W.

    1990-01-01

    The effect of a 3-prime-5-prime pyrophosphate-linked oligomer of pTp on oligomerizations of pdAp and of its 3-prime-5-prime, 3-prime-3-prime, and 5-prime-5-prime dimers was investigated, using HPLC to separate the reaction mixtures; peak detection was by absorbance monitoring at 254 nm. It was expected that the dimers would form stable complexes with the template, with the degree of stability depending upon the internal linkage of each dimer. It was found that, although the isomers differ substantially in their oligomerization behavior in the absence of template, the analog-template catalyzes the oligomerization to about the same extent in all three cases.

  15. Photochemical reaction mechanism of UV-B-induced monomerization of UVR8 dimers as the first signaling event in UV-B-regulated gene expression in plants.

    Science.gov (United States)

    Wu, Min; Strid, Åke; Eriksson, Leif A

    2014-01-30

    The Arabidopsis thaliana UV RESISTANCE LOCUS8 (UVR8) protein has been identified to specifically mediate photomorphogenic UV-B responses by acting as a UV-B photoreceptor. The dimeric structure of the UVR8 protein dissociates into signaling-active monomers upon UV-B exposure, and the monomers rapidly interact with downstream signaling components to regulate gene expression. UVR8 monomers revert to dimers in the absence of UV-B radiation, thereby reversing transcription activation. UVR8 amino acid residues W233 and W285 have been identified to play critical roles in the UVR8 dimer for the response to UV-B irradiation. In the present work, the photoreaction mechanism for UVR8 monomerization is explored with quantum chemical cluster calculations and evaluated by molecular dynamics simulations using the wild-type UVR8 dimer and novel force field parameters developed for intermediate radicals formed in the photochemical process. Three different models are investigated, which show that the preferred mechanism for UVR8 monomerization involves electron transfer from residue W233 to W285 and onward to R338 initiated by UV-B irradiation, coupled to simultaneous proton transfer from W233 to D129 leading to the formation of protonated D129, a deprotonated W233 radical, and a neutral R338 radical. Due to the formation of the neutral R338 radical, salt bridges involving this residue are disrupted together with the concomitant interruption of several other key salt bridges R286-D96, R286-D107, R338-D44, R354-E43, and R354-E53. The resulting large decrease in protein-protein interaction energy arising from this sequence of events leads to the monomerization of the UVR8 dimer. The mechanism presented is in accord with all experimental data available to date.

  16. Stable isotope analysis

    International Nuclear Information System (INIS)

    Tibari, Elghali; Taous, Fouad; Marah, Hamid

    2014-01-01

    This report presents results related to stable isotopes analysis carried out at the CNESTEN DASTE in Rabat (Morocco), on behalf of Senegal. These analyzes cover 127 samples. These results demonstrate that Oxygen-18 and Deuterium in water analysis were performed by infrared Laser spectroscopy using a LGR / DLT-100 with Autosampler. Also, the results are expressed in δ values (‰) relative to V-SMOW to ± 0.3 ‰ for oxygen-18 and ± 1 ‰ for deuterium.

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

    NARCIS (Netherlands)

    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.

    2015-01-01

    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

  18. Forensic Stable Isotope Biogeochemistry

    Science.gov (United States)

    Cerling, Thure E.; Barnette, Janet E.; Bowen, Gabriel J.; Chesson, Lesley A.; Ehleringer, James R.; Remien, Christopher H.; Shea, Patrick; Tipple, Brett J.; West, Jason B.

    2016-06-01

    Stable isotopes are being used for forensic science studies, with applications to both natural and manufactured products. In this review we discuss how scientific evidence can be used in the legal context and where the scientific progress of hypothesis revisions can be in tension with the legal expectations of widely used methods for measurements. Although this review is written in the context of US law, many of the considerations of scientific reproducibility and acceptance of relevant scientific data span other legal systems that might apply different legal principles and therefore reach different conclusions. Stable isotopes are used in legal situations for comparing samples for authenticity or evidentiary considerations, in understanding trade patterns of illegal materials, and in understanding the origins of unknown decedents. Isotope evidence is particularly useful when considered in the broad framework of physiochemical processes and in recognizing regional to global patterns found in many materials, including foods and food products, drugs, and humans. Stable isotopes considered in the larger spatial context add an important dimension to forensic science.

  19. The Krásná Hora, Milešov, and Příčovy Sb-Au ore deposits, Bohemian Massif: mineralogy, fluid inclusions, and stable isotope constraints on the deposit formation

    Science.gov (United States)

    Němec, Matěj; Zachariáš, Jiří

    2018-02-01

    The Krásná Hora-Milešov and Příčovy districts (Czech Republic) are the unique examples of Sb-Au subtype orogenic gold deposits in the Bohemian Massif. They are represented by quartz-stibnite veins and massive stibnite lenses grading into low-grade, disseminated ores in altered host rocks. Gold postdates the stibnite and is often replaced by aurostibite. The ore zones are hosted by hydrothermally altered dikes of lamprophyres (Krásná Hora-Milešov) or are associated with local strike-slip faults (Příčovy). Formation of Sb-Au deposits probably occurred shortly after the main gold-bearing event (348-338 Ma; Au-only deposits) in the central part of the Bohemian Massif. Fluid inclusion analyses suggest that stibnite precipitated at 250 to 130 °C and gold at 200 to 130 °C from low-salinity aqueous fluids. The main quartz gangue hosting the ore precipitated from the same type of fluid at about 300 °C. Early quartz-arsenopyrite veins are not associated with the Sb-Au deposition and formed from low-salinity, aqueous-carbonic fluid at higher pressure and temperature ( 250 MPa, 400 °C). The estimated oxygen isotope composition of the ore-bearing fluid (4 ± 1‰ SMOW; based on post-ore calcite) suggests its metamorphic or mixed magmatic-metamorphic origin and excludes the involvement of meteoric water. Rapid cooling of warm hydrothermal fluids reacting with "cold" host rock was probably the most important factor in the formation of both stibnite and gold.

  20. Acetic acid dimers in a nitrogen matrix: Observation of structures containing the higher-energy conformer

    Science.gov (United States)

    Lopes, Susy; Domanskaya, Alexandra V.; Räsänen, Markku; Khriachtchev, Leonid; Fausto, Rui

    2015-09-01

    Acetic acid (AA) dimers are studied experimentally by infrared spectroscopy in a N2 matrix and theoretically at the MP2/6-311++G(2d,2p) level of approximation. This work is focused on the first preparation and characterization of structures containing the higher-energy (cis) conformer of AA. Nine trans-trans, fourteen trans-cis, and six cis-cis dimers are theoretically predicted. Five trans-trans and a number of trans-cis dimers are identified in the experiments, but no indication of cis-cis dimers is found. Two trans-trans dimers and the trans-cis dimers are reported for the first time. One trans-cis dimer is prepared by selective vibrational excitation of the structurally related trans-trans dimer, which converts one of the trans subunits to the cis form. Several trans-cis dimers are obtained by annealing of a matrix containing both trans and cis monomers of AA. Tunneling-induced conversion of the trans-cis dimers into trans-trans forms (including two new trans-trans forms) is observed at low temperatures.

  1. Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions

    Science.gov (United States)

    Baltoumas, Fotis A.; Theodoropoulou, Margarita C.; Hamodrakas, Stavros J.

    2016-06-01

    A significant amount of experimental evidence suggests that G-protein coupled receptors (GPCRs) do not act exclusively as monomers but also form biologically relevant dimers and oligomers. However, the structural determinants, stoichiometry and functional importance of GPCR oligomerization remain topics of intense speculation. In this study we attempted to evaluate the nature and dynamics of GPCR oligomeric interactions. A representative set of GPCR homodimers were studied through Coarse-Grained Molecular Dynamics simulations, combined with interface analysis and concepts from network theory for the construction and analysis of dynamic structural networks. Our results highlight important structural determinants that seem to govern receptor dimer interactions. A conserved dynamic behavior was observed among different GPCRs, including receptors belonging in different GPCR classes. Specific GPCR regions were highlighted as the core of the interfaces. Finally, correlations of motion were observed between parts of the dimer interface and GPCR segments participating in ligand binding and receptor activation, suggesting the existence of mechanisms through which dimer formation may affect GPCR function. The results of this study can be used to drive experiments aimed at exploring GPCR oligomerization, as well as in the study of transmembrane protein-protein interactions in general.

  2. Coiled-coil motif in LBD16 and LBD18 transcription factors are critical for dimerization and biological function in arabidopsis.

    Science.gov (United States)

    Pandey, Shashank K; Kim, Jungmook

    2018-01-02

    The LATERAL ORGAN BOUNDARIES (LOB) DOMAIN (LBD) gene family members encode a class of plant-specific transcription factors that play important roles in many different aspects of plant growth and development. The LBD proteins contain a conserved LOB domain harboring a Leu zipper-like coiled-coil motif, which has been predicted to mediate protein-protein interactions among the LBD family members. Dimerization of transcription factors is crucial for the modulation of their DNA-binding affinity, specificity, and diversity, contributing to the transcriptional regulation of distinct cellular and biological responses. Our various molecular and biochemical experiments with genetic approaches on LBD16 and LBD18, which are known to control lateral root development in Arabidopsis, demonstrated that the conserved Leu or Val residues in the coiled-coil motifs of these transcription factors are critical for their dimerization as well as the transcriptional regulation to display their biological functions during lateral root formation. We further showed that beside the coiled-coil motif, the carboxyl-terminal region in LBD18 acts as an additional dimerization domain. These findings provide a molecular framework for the homo- and hetero-dimerization of the LBD family proteins for displaying their distinct and diverse biological functions in plants.

  3. Chemical and stable isotopic evidence for water/rock interaction and biogenic origin of coalbed methane, Fort Union Formation, Powder River Basin, Wyoming and Montana U.S.A

    Science.gov (United States)

    Rice, C.A.; Flores, R.M.; Stricker, G.D.; Ellis, M.S.

    2008-01-01

    Significant amounts (> 36??million m3/day) of coalbed methane (CBM) are currently being extracted from coal beds in the Paleocene Fort Union Formation of the Powder River Basin of Wyoming and Montana. Information on processes that generate methane in these coalbed reservoirs is important for developing methods that will stimulate additional production. The chemical and isotopic compositions of gas and ground water from CBM wells throughout the basin reflect generation processes as well as those that affect water/rock interaction. Our study included analyses of water samples collected from 228 CBM wells. Major cations and anions were measured for all samples, ??DH2O and ??18OH2O were measured for 199 of the samples, and ??DCH4 of gas co-produced with water was measured for 100 of the samples. Results show that (1) water from Fort Union Formation coal beds is exclusively Na-HCO3-type water with low dissolved SO4 content (median oxygen (< 0.15??mg/L), whereas shallow groundwater (depth generally < 120??m) is a mixed Ca-Mg-Na-SO4-HCO3 type; (2) water/rock interactions, such as cation exchange on clay minerals and precipitation/dissolution of CaCO3 and SO4 minerals, account for the accumulation of dissolved Na and depletion of Ca and Mg; (3) bacterially-mediated oxidation-reduction reactions account for high HCO3 (270-3310??mg/L) and low SO4 (median < 0.15??mg/L) values; (4) fractionation between ??DCH4 (- 283 to - 328 per mil) and ??DH2O (- 121 to - 167 per mil) indicates that the production of methane is primarily by biogenic CO2 reduction; and (5) values of ??DH2O and ??18OH2O (- 16 to - 22 per mil) have a wide range of values and plot near or above the global meteoric water line, indicating that the original meteoric water has been influenced by methanogenesis and by being mixed with surface and shallow groundwater.

  4. Chemical and stable isotopic composition of water and gas in the Fort Union Formation of the Powder River Basin, Wyoming and Montana: Evidence for water/rock interaction and the biogenic origin of coalbed natural gas

    Science.gov (United States)

    Rice, Cynthia A.; Flores, Romeo M.; Stricker, Gary D.; Ellis, Margaret S.

    2008-01-01

    Significant amounts (> 36 million m3/day) of coalbed methane (CBM) are currently being extracted from coal beds in the Paleocene Fort Union Formation of the Powder River Basin of Wyoming and Montana. Information on processes that generate methane in these coalbed reservoirs is important for developing methods that will stimulate additional production. The chemical and isotopic compositions of gas and ground water from CBM wells throughout the basin reflect generation processes as well as those that affect water/rock interaction. Our study included analyses of water samples collected from 228 CBM wells. Major cations and anions were measured for all samples, δDH2O and δ18OH2O were measured for 199 of the samples, and δDCH4 of gas co-produced with water was measured for 100 of the samples. Results show that (1) water from Fort Union Formation coal beds is exclusively Na–HCO3-type water with low dissolved SO4 content (median oxygen (< 0.15 mg/L), whereas shallow groundwater (depth generally < 120 m) is a mixed Ca–Mg–Na–SO4–HCO3 type; (2) water/rock interactions, such as cation exchange on clay minerals and precipitation/dissolution of CaCO3 and SO4 minerals, account for the accumulation of dissolved Na and depletion of Ca and Mg; (3) bacterially-mediated oxidation–reduction reactions account for high HCO3 (270–3310 mg/L) and low SO4 (median < 0.15 mg/L) values; (4) fractionation between δDCH4 (− 283 to − 328 per mil) and δDH2O (− 121 to − 167 per mil) indicates that the production of methane is primarily by biogenic CO2 reduction; and (5) values of δDH2O and δ18OH2O (− 16 to − 22 per mil) have a wide range of values and plot near or above the global meteoric water line, indicating that the original meteoric water has been influenced by methanogenesis and by being mixed with surface and shallow groundwater.

  5. Substrate-induced stable enzyme-inhibitor complex formation allows tight binding of novel 2-aminopyrimidin-4(3H)-ones to drug-resistant HIV-1 reverse transcriptase mutants.

    Science.gov (United States)

    Samuele, Alberta; Facchini, Marcella; Rotili, Dante; Mai, Antonello; Artico, Marino; Armand-Ugón, Mercedes; Esté, José A; Maga, Giovanni

    2008-09-01

    We recently reported the synthesis and biological evaluation of a novel series of 5-alkyl-2-(N,N-disubstituted)amino-6-(2,6-difluorophenylalkyl)-3,4-dihydropyrimidin-4(3H)-ones (F(2)-N,N-DABOs). These compounds are highly active against both wild-type HIV-1 and the K103N, Y181C, and Y188L mutant strains. Herein we present novel 6-(2-chloro-6-fluorophenylalkyl)-N,N-DABO (2-Cl-6-F-N,N-DABO) derivatives and investigate the molecular basis for their high-affinity binding to HIV-1 reverse transcriptase (RT). Our results show that the new compounds display higher association rates than the difluoro derivatives toward wild-type HIV-1 RT or drug-resistant RT mutant forms. We also show that they preferentially associate to either the free enzyme or the enzyme-nucleic acid binary complex, and that this binding is stabilized upon formation of the ternary complex between HIV-1 RT and both the nucleic acid and nucleotide substrates. Interestingly, one compound showed dissociation rates from the ternary complex with RT mutants K103N and Y181I 10-20-fold slower than from the corresponding complex with wild-type RT.

  6. Polyhydroxylated [60]fullerene binds specifically to functional recognition sites on a monomeric and a dimeric ubiquitin

    Science.gov (United States)

    Zanzoni, Serena; Ceccon, Alberto; Assfalg, Michael; Singh, Rajesh K.; Fushman, David; D'Onofrio, Mariapina

    2015-04-01

    The use of nanoparticles (NPs) in biomedical applications requires an in-depth understanding of the mechanisms by which NPs interact with biomolecules. NPs associating with proteins may interfere with protein-protein interactions and affect cellular communication pathways, however the impact of NPs on biomolecular recognition remains poorly characterized. In this respect, particularly relevant is the study of NP-induced functional perturbations of proteins implicated in the regulation of key biochemical pathways. Ubiquitin (Ub) is a prototypical protein post-translational modifier playing a central role in numerous essential biological processes. To contribute to the understanding of the interactions between this universally distributed biomacromolecule and NPs, we investigated the adsorption of polyhydroxylated [60]fullerene on monomeric Ub and on a minimal polyubiquitin chain in vitro at atomic resolution. Site-resolved chemical shift and intensity perturbations of Ub's NMR signals, together with 15N spin relaxation rate changes, exchange saturation transfer effects, and fluorescence quenching data were consistent with the reversible formation of soluble aggregates incorporating fullerenol clusters. The specific interaction epitopes were identified, coincident with functional recognition sites in a monomeric and lysine48-linked dimeric Ub. Fullerenol appeared to target the open state of the dynamic structure of a dimeric Ub according to a conformational selection mechanism. Importantly, the protein-NP association prevented the enzyme-catalyzed synthesis of polyubiquitin chains. Our findings provide an experiment-based insight into protein/fullerenol recognition, with implications in functional biomolecular communication, including regulatory protein turnover, and for the opportunity of therapeutic intervention in Ub-dependent cellular pathways.The use of nanoparticles (NPs) in biomedical applications requires an in-depth understanding of the mechanisms by which

  7. Repair of UV dimers in skin DNA of patients with basal cell carcinoma.

    Science.gov (United States)

    Segerbäck, Dan; Strozyk, Malgorzata; Snellman, Erna; Hemminki, Kari

    2008-09-01

    Epidemiologic studies suggest that exposure to sunlight is the primary etiologic agent for basal cell carcinoma. Formation of UV-induced DNA damage is believed to be a crucial event in the process leading to skin cancer. In this study, repair of photoproducts in DNA was followed in the skin of patients with basal cell carcinoma and control subjects. The subjects were exposed to 800 J/m(2) Commission Internationale de 1'Eclairag of solar-simulating radiation on buttock skin. Biopsies were taken at 0 hour, 24 hours, and 3 weeks after the exposure. Two cyclobutane pyrimidine dimers, TT=C and TT=T, were measured using a sensitive (32)P-postlabeling assay. Initial levels of both TT=C and TT=T differed between individuals in both groups. The levels of TT=T in patients with basal cell carcinoma and controls were similar (9.9 +/- 4.0 and 9.2 +/- 2.9 products per 10(6) normal nucleotides), whereas the level of TT=C was significantly lower in controls than in patients with basal cell carcinoma (6.2 +/- 3.1 versus 10.9 +/- 4.5 products per 10(6) normal nucleotides). The fractions of TT=T remaining after 24 hours and 3 weeks were significantly higher in patients with basal cell carcinoma (72% and 11%) compared with controls (48% and 5%). A slower removal in patients with basal cell carcinoma than in controls was indicated also for TT=C (52% versus 42% remaining at 24 hours); however, the difference between groups was not significant. When including data from our previously reported small-scale study, the fraction of dimers remaining at 24 hours was significantly higher in patients with basal cell carcinoma for both TT=C and TT=T. The data suggest that patients with basal cell carcinoma have a reduced capacity to repair UV-induced DNA lesions.

  8. Metabolism of strawberry mono- and dimeric ellagitannins in rats fed a diet containing fructo-oligosaccharides.

    Science.gov (United States)

    Jurgoński, Adam; Juśkiewicz, Jerzy; Fotschki, Bartosz; Kołodziejczyk, Krzysztof; Milala, Joanna; Kosmala, Monika; Grzelak-Błaszczyk, Katarzyna; Markiewicz, Lidia

    2017-03-01

    We investigated the effects of dietary supplementation with strawberry extracts rich in ETs and fructo-oligosaccharides (FOS) on the intestinal microbiota and the formation of bacterial metabolites in the distal intestine, as well as the absorption of ET metabolites and antioxidant status in rats. Rats were allocated into six groups of eight animals each and fed for 4 weeks with a control diet (group C), a control diet supplemented with FOS (group C + FOS) or modifications of these diets, in which a monomeric or dimeric ET-rich extract was added (groups ME and ME + FOS or DE and DE + FOS, respectively). The extract addition, the FOS addition and their interaction significantly affected the total and selected bacterial counts in the caecal digesta (all P bacterial count was the highest in group C + FOS, lower in group DE and the lowest in group ME + FOS (10.6, 10.3 and 8.52 log cells/g, respectively; P ≤ 0.05). The total caecal content of ET metabolites was higher in the ME and ME + FOS group than in the DE and DE + FOS group, respectively (67.8 and 89.5 vs. 13.0 and 18.0 µg/g, respectively; P < 0.001). The total plasma concentration of ET metabolites was higher in the ME + FOS and DE + FOS group than in the ME group (248 and 281 vs. 8.13 ng/mL, respectively; P < 0.001). ETs of the monomeric ET-rich extract are more prone to intestinal breakdown than those of the dimeric ET-rich extract, and absorption of their metabolites can be increased by dietary FOS; however, together, they evoke strong antibacterial activity.

  9. One pyrimidine dimer inactivates expression of a transfected gene in xeroderma pigmentosum cells

    International Nuclear Information System (INIS)

    Protic-Sabljic, M.; Kraemer, K.H.

    1985-01-01

    The authors have developed a host cell reactivation assay of DNA repair utilizing UV-treated plasmid vectors. The assay primarily reflects cellular repair of transcriptional activity of damaged DNA measured indirectly as enzyme activity of the transfected genes. They studied three plasmids (pSV2cat, 5020 base pairs; pSV2catSVgpt, 7268 base pairs; and pRSVcat, 5027 base pairs) with different sizes and promoters carrying the bacterial cat gene (CAT, chloramphenicol acetyltransferase) in a construction that permits cat expression in human cells. All human simian virus 40-transformed cells studied expressed high levels of the transfected cat gene. UV treatment of the plasmids prior to transfection resulted in differential decrease in CAT activity in different cell lines. With pSV2catSVgpt, UV inactivation of CAT expression was greater in the xeroderma pigmentosum group A and D lines than in the other human cell lines tested. The D 0 of the CAT inactivation curve was 50 J X m-2 for pSV2cat and for pRSVcat in the xeroderma pigmentosum group A cells. The similarity of the D0 data in the xeroderma pigmentosum group A cells for three plasmids of different size and promoters implies they all have similar UV-inactivation target size. UV-induced pyrimidine dimer formation in the plasmids was quantified by assay of the number of UV-induced T4 endonuclease V-sensitive sites. In the most sensitive xeroderma pigmentosum cells, with all three plasmids, one UV-induced pyrimidine dimer inactivates a target of about 2 kilobases, close to the size of the putative CAT mRNA

  10. Complex Relationship between Ligand Binding and Dimerization in the Epidermal Growth Factor Receptor

    Directory of Open Access Journals (Sweden)

    Nicholas J. Bessman

    2014-11-01

    Full Text Available The epidermal growth factor receptor (EGFR plays pivotal roles in development and is mutated or overexpressed in several cancers. Despite recent advances, the complex allosteric regulation of EGFR remains incompletely understood. Through efforts to understand why the negative cooperativity observed for intact EGFR is lost in studies of its isolated extracellular region (ECR, we uncovered unexpected relationships between ligand binding and receptor dimerization. The two processes appear to compete. Surprisingly, dimerization does not enhance ligand binding (although ligand binding promotes dimerization. We further show that simply forcing EGFR ECRs into preformed dimers without ligand yields ill-defined, heterogeneous structures. Finally, we demonstrate that extracellular EGFR-activating mutations in glioblastoma enhance ligand-binding affinity without directly promoting EGFR dimerization, suggesting that these oncogenic mutations alter the allosteric linkage between dimerization and ligand binding. Our findings have important implications for understanding how EGFR and its relatives are activated by specific ligands and pathological mutations.

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

    DEFF Research Database (Denmark)

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

    2011-01-01

    CTP synthase catalyzes the last committed step in de novo pyrimidine-nucleotide biosynthesis. Active CTP synthase is a tetrameric enzyme composed of a dimer of dimers. The tetramer is favoured in the presence of the substrate nucleotides ATP and UTP; when saturated with nucleotide, the tetramer c....... solfataricus CTP synthase according to a structural alignment with the E. coli enzyme all have large thermal parameters in the dimeric form. Furthermore, they are seen to undergo substantial movement upon tetramerization....

  12. Bethe Ansatz Solutions of the Bose-Hubbard Dimer

    Directory of Open Access Journals (Sweden)

    Jon Links

    2006-12-01

    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.

  13. Antimicrobial Oligophenalenone Dimers from the Soil Fungus Talaromyces stipitatus.

    Science.gov (United States)

    Zang, Yi; Genta-Jouve, Grégory; Escargueil, Alexandre E; Larsen, Annette K; Guedon, Laura; Nay, Bastien; Prado, Soizic

    2016-12-23

    New polyketide-derived oligophenalenone dimers, 9a-epi-bacillisporin E (1) and bacillisporins F-H (2-5), along with the known bacillisporin A (6), were isolated from the fungus Talaromyces stipitatus. Their structures and absolute configurations were determined on the basis of spectroscopic analyses, electronic circular dichroism, and GIAO NMR shift calculation followed by DP4 analysis. The antimicrobial activity of these compounds was evaluated against a panel of human pathogenic bacteria. Among them, bacillisporin H (5) exhibited antimicrobial activity together with modest cytotoxicity against HeLa cells.

  14. Improved Electron Transport with Reduced Contact Resistance in N-Doped Polymer Field-Effect Transistors with a Dimeric Dopant.

    Science.gov (United States)

    Wang, Rong; Guo, Yikun; Zhang, Di; Zhou, Huiqiong; Zhao, Dahui; Zhang, Yuan

    2018-01-15

    Attaining control on charge injection properties is significant for meaningful applications of organic field-effect transistors (OFETs). Here, molecular electron-doping is applied with an air-stable dimer dopant for n-type OFETs based on (naphthalene diimide-diketopyrrolopyrrole) polymer hosts. Through investigating the doping effect on contact and transport properties, it is found that the electron transport increases in n-doped OFETs at low doping regime with remaining large on/off ratios. These favorable meliorations are reconciled by the mitigated impacts of contact resistance and interfacial traps, as well as the surface morphology exhibiting features of increased ordering. The occurrence of doping in the presence of dimer dopants is evidenced by the observed shift of Fermi level toward vacuum level coupled with compositional analysis. Without applying vacuum-deposition-based contact doping, charge injection efficiencies are gained without losing OFET characteristics using the solution-based methodology. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    International Nuclear Information System (INIS)

    Goffinont, S.; Davidkova, M.; Spotheim-Maurizot, M.

    2009-01-01

    The wild type lactose repressor of Escherichia coli is a tetrameric protein formed by two identical dimers. They are associated via a C-terminal 4-helix bundle (called tetramerization domain) whose stability is ensured by the interaction of leucine zipper motifs. Upon in vitro γ-irradiation the repressor losses its ability to bind the operator DNA sequence due to damage of its DNA-binding domains. Using an engineered dimeric repressor for comparison, we show here that irradiation induces also the change of repressor oligomerisation state from tetramer to dimer. The splitting of the tetramer into dimers can result from the oxidation of the leucine residues of the tetramerization domain.

  16. Modified field enhancement and extinction by plasmonic nanowire dimers due to nonlocal response

    DEFF Research Database (Denmark)

    Toscano, Giuseppe; Raza, Søren; Jauho, Antti-Pekka

    2012-01-01

    it in a wide frequency range against analytical results for the extinction cross section of a cylindrical plasmonic nanowire. Our main results concern more complex geometries, namely cylindrical and bow-tie nanowire dimers that can strongly enhance optical fields. For both types of dimers we find that nonlocal...... response can strongly affect both the field enhancement in between the dimers and their respective extinction cross sections. In particular, we give examples of blueshifted maximal field enhancements near hybridized plasmonic dimer resonances that are still large but nearly two times smaller than...

  17. Observation of an aromatic radical anion dimer: (C10F8)2 sm-bullet -

    International Nuclear Information System (INIS)

    Werst, D.W.

    1994-01-01

    Radical cation dimers are observed for many alkenes and aromatic hydrocarbons as products of the reaction between monomer radical cation and neutral molecule. In most cases, the dimer radical anions, formed via reaction of the monomer radical anion with a neutral molecule, have not been observed. Here we report the observation of the dimer radical anion of octafluoronaphthalene, formed by reaction of C 10 F 8 ·- with the neutral parent molecules in nonpolar solvents following pulse radiolysis. Both monomer and dimer ions have been characterized by EPR spectra obtained by the time-resolved fluorescence-detected magnetic resonance

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-11-15

    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.

  19. Kinetic Stability May Determine the Interaction Dynamics of the Bifunctional Protein DCoH1, the Dimerization Cofactor of the Transcription Factor HNF-1[alpha

    Energy Technology Data Exchange (ETDEWEB)

    Rho, H.; Jones, C.N.; Rose, R.B. (NCSU)

    2010-12-07

    The two disparate functions of DCoH1 (dimerization cofactor of HNF-1)/PCD (pterin-4a-carbinolamine dehydratase) are associated with a change in oligomeric state. DCoH dimers enhance the activity of the diabetes-associated transcription factor HNF-1{alpha} (hepatocyte nuclear factor-1{alpha}), while the PCD activity of DCoH1 homotetramers aids in aromatic amino acid metabolism. These complexes compete for the same interface of the DCoH dimer. Formation of the DCoH1/HNF-1{alpha} complex requires cofolding. The homotetramer of the DCoH1 paralogue, DCoH2, interacts with HNF-1{alpha} through simple mixing. To further investigate regulation of DCoH/HNF-1{alpha} complex formation, we measured the stability of the DCoH1 homotetramer through unfolding studies by intrinsic tryptophan fluorescence. DCoH2 unfolding is reversible. Surprisingly, the DCoH1 homotetramer is resistant to guanidine unfolding but refolds at a much lower guanidine concentration. We show that a point mutation at the DCoH1 tetramer interface, Thr 51 Ser, overcomes the dissociation barrier of the homotetramer and increases the interaction with HNF-1{alpha}. The 1.8 {angstrom} resolution crystal structure of DCoH1 T51S shows the presence of an ordered water molecule at the tetramer interface, as in DCoH2, which may destabilize the homotetramer. The equilibrium unfolding data were fit to a two-state model with no apparent intermediate. Folding intermediates were detectable by size exclusion chromatography. For wild-type DCoH1 the intermediates changed with time, suggesting a kinetic origin for the unfolding barrier of the homotetramer. We propose an unfolding pathway in which the tetramer unfolds slowly, but the dimer folds reversibly. Implications for regulation of DCoH1/HNF-1{alpha} complex formation are discussed.

  20. Marginally Stable Nuclear Burning

    Science.gov (United States)

    Strohmayer, Tod E.; Altamirano, D.

    2012-01-01

    Thermonuclear X-ray bursts result from unstable nuclear burning of the material accreted on neutron stars in some low mass X-ray binaries (LMXBs). Theory predicts that close to the boundary of stability oscillatory burning can occur. This marginally stable regime has so far been identified in only a small number of sources. We present Rossi X-ray Timing Explorer (RXTE) observations of the bursting, high- inclination LMXB 4U 1323-619 that reveal for the first time in this source the signature of marginally stable burning. The source was observed during two successive RXTE orbits for approximately 5 ksec beginning at 10:14:01 UTC on March 28, 2011. Significant mHz quasi- periodic oscillations (QPO) at a frequency of 8.1 mHz are detected for approximately 1600 s from the beginning of the observation until the occurrence of a thermonuclear X-ray burst at 10:42:22 UTC. The mHz oscillations are not detected following the X-ray burst. The average fractional rms amplitude of the mHz QPOs is 6.4% (3 - 20 keV), and the amplitude increases to about 8% below 10 keV.This phenomenology is strikingly similar to that seen in the LMXB 4U 1636-53. Indeed, the frequency of the mHz QPOs in 4U 1323-619 prior to the X-ray burst is very similar to the transition frequency between mHz QPO and bursts found in 4U 1636-53 by Altamirano et al. (2008). These results strongly suggest that the observed QPOs in 4U 1323-619 are, like those in 4U 1636-53, due to marginally stable nuclear burning. We also explore the dependence of the energy spectrum on the oscillation phase, and we place the present observations within the context of the spectral evolution of the accretion-powered flux from the source.

  1. Advanced thermally stable jet fuels

    Energy Technology Data Exchange (ETDEWEB)

    Schobert, H.H.

    1999-01-31

    The Pennsylvania State University program in advanced thermally stable coal-based jet fuels has five broad objectives: (1) Development of mechanisms of degradation and solids formation; (2) Quantitative measurement of growth of sub-micrometer and micrometer-sized particles suspended in fuels during thermal stressing; (3) Characterization of carbonaceous deposits by various instrumental and microscopic methods; (4) Elucidation of the role of additives in retarding the formation of carbonaceous solids; (5) Assessment of the potential of production of high yields of cycloalkanes by direct liquefaction of coal. Future high-Mach aircraft will place severe thermal demands on jet fuels, requiring the development of novel, hybrid fuel mixtures capable of withstanding temperatures in the range of 400--500 C. In the new aircraft, jet fuel will serve as both an energy source and a heat sink for cooling the airframe, engine, and system components. The ultimate development of such advanced fuels requires a thorough understanding of the thermal decomposition behavior of jet fuels under supercritical conditions. Considering that jet fuels consist of hundreds of compounds, this task must begin with a study of the thermal degradation behavior of select model compounds under supercritical conditions. The research performed by The Pennsylvania State University was focused on five major tasks that reflect the objectives stated above: Task 1: Investigation of the Quantitative Degradation of Fuels; Task 2: Investigation of Incipient Deposition; Task 3: Characterization of Solid Gums, Sediments, and Carbonaceous Deposits; Task 4: Coal-Based Fuel Stabilization Studies; and Task 5: Exploratory Studies on the Direct Conversion of Coal to High Quality Jet Fuels. The major findings of each of these tasks are presented in this executive summary. A description of the sub-tasks performed under each of these tasks and the findings of those studies are provided in the remainder of this volume

  2. Formation and transformations of radical-cations of aliphatic ketones in freon matrices at low temperatures

    International Nuclear Information System (INIS)

    Belevskij, V.N.; Belopushkin, S.I.; Fel'dman, V.I.

    1987-01-01

    Monomeric and dimeric radical-cations of ketones as well as RCHCOMe radicals which yields depend on concentrations of CFCl 3 ketones are stabilized in γ-irradiated solutions of acetone and methyl ethyl ketone in CFCl 3 (0.1-22%) at 77 K. Under light action dimeric radical-cations are transformed into RCHCOMe, and monomeric ones disappear without radical formation. Different types of ion-molecular reactions in a solid phase with monomeric and dimeric radical-cation participation are shown

  3. Direct Observation of the Ultrafast Evolution of Open-Shell Biradical in Photochromic Radical Dimer.

    Science.gov (United States)

    Kobayashi, Yoichi; Okajima, Hajime; Sotome, Hikaru; Yanai, Takeshi; Mutoh, Katsuya; Yoneda, Yusuke; Shigeta, Yasuteru; Sakamoto, Akira; Miyasaka, Hiroshi; Abe, Jiro

    2017-05-10

    Delocalized biradicals have been extensively studied because of fundamental interests to singlet biradicals and several potential applications such as to two-photon absorption materials. However, many of the biradical studies only focus on the static properties of the rigid molecular structures. It is expected that the biradical properties of the delocalized biradicals are sensitive to the subtle changes of the molecular structures and their local environments. Therefore, the studies of the dynamic properties of the system will give further insight into stable radical chemistry. In this study, we directly probe the ultrafast dynamics of the delocalized biradical of a photochromic radical dimer, pentaarylbiimidazole (PABI), by time-resolved visible and infrared spectroscopies and quantum chemical calculations with the extended multistate complete active space second-order perturbation theory (XMS-CASPT2). While the photogenerated transient species was considered to be a single species of the biradical, the present ultrafast spectroscopic study revealed the existence of two transient isomers differing in the contributions of biradical character. The origin of the two metastable isomers is most probably due to the substantial van der Waals interaction between the phenyl rings substituted at the imidazole rings. Unraveling the temporal evolution of the biradical contribution will stimulate to explore novel delocalized biradicals and to develop biradical-based photofunctional materials utilizing the dynamic properties.

  4. Stabilization of dimeric β-glucosidase from Aspergillus niger via glutaraldehyde immobilization under different conditions.

    Science.gov (United States)

    Vazquez-Ortega, Perla Guadalupe; Alcaraz-Fructuoso, Maria Teresa; Rojas-Contreras, Juan A; López-Miranda, Javier; Fernandez-Lafuente, Roberto

    2018-03-01

    The dimeric enzyme β-glucosidase from Aspergillus niger has been immobilized on different amino-agarose beads at pH 5 and 7, exploiting the versatility of glutaraldehyde. The stability of the free enzyme depended on enzyme concentration. Immobilization via ion exchange improved enzyme stability/activity, depending on the immobilization pH. However, the enzyme was desorbed in 75 mM NaCl at pH 7 and some stability/enzyme concentration dependence still existed. of these biocatalysts with glutaraldehyde increased enzyme stability (e.g. at pH 5, after incubation under conditions where the enzyme just ionically exchanged was fully inactivated, the activity of the glutaraldehyde treated enzyme remained unaltered). Immobilization on glutaraldehyde pre-activated supports yielded a higher increase in enzyme activity, but the stabilization was lower. While when measuring the enzyme activity at pH 4 there were no changes after immobilization, all immobilized enzymes were more active than the free enzyme at pH 6 and 7 (2-3 times). The Ki/Km ratio did not significantly decrease in any immobilized biocatalysts, and in some cases it worsened in a significant way (by a 9 fold factor using preactivated supports). The new biocatalysts are significantly more stable and avoid enzyme subunit desorption, being the immobilization pH a key point in their design. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. A test on reactive force fields for the study of silica dimerization reactions

    Energy Technology Data Exchange (ETDEWEB)

    Moqadam, Mahmoud; Riccardi, Enrico; Trinh, Thuat T.; Åstrand, Per-Olof; Erp, Titus S. van, E-mail: titus.van.erp@ntnu.no [Department of Chemistry, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, Realfagbygget D3-117, 7491 Trondheim (Norway)

    2015-11-14

    We studied silica dimerization reactions in the gas and aqueous phase by density functional theory (DFT) and reactive force fields based on two parameterizations of ReaxFF. For each method (both ReaxFF force fields and DFT), we performed constrained geometry optimizations, which were subsequently evaluated in single point energy calculations using the other two methods. Standard fitting procedures typically compare the force field energies and geometries with those from quantum mechanical data after a geometry optimization. The initial configurations for the force field optimization are usually the minimum energy structures of the ab initio database. Hence, the ab initio method dictates which structures are being examined and force field parameters are being adjusted in order to minimize the differences with the ab initio data. As a result, this approach will not exclude the possibility that the force field predicts stable geometries or low transition states which are realistically very high in energy and, therefore, never considered by the ab initio method. Our analysis reveals the existence of such unphysical geometries even at unreactive conditions where the distance between the reactants is large. To test the effect of these discrepancies, we launched molecular dynamics simulations using DFT and ReaxFF and observed spurious reactions for both ReaxFF force fields. Our results suggest that the standard procedures for parameter fitting need to be improved by a mutual comparative method.

  6. Dimeric and different polymeric copper(II) salicylates - Crystal structure and spectral properties

    Science.gov (United States)

    Puchoňová, Miroslava; Mazúr, Milan; Moncol, Ján; Růžičková, Zdeňka; Valigura, Dušan

    2017-06-01

    The small differences in synthesis condition led to formation of four new copper(II) salicylatocomplexes - two differently polymeric [Cu(4-MeOSal)2(μ-H2O)2]n1, [Cu(μ-3,5-Br2Sal)2(H2O)2]n2 and two dimeric [Cu(5-MeSal)2(MeOH)]2ṡ2MeOH 3 [Cu(4-MeSal)2(EtOH)2]24 compounds, where 4-MeOSal = 4-methoxysalicylate, 3,5-Br2Sal = 3, 5-dibromsalicylate, 5-MeSal = 5-methylsalicylate, and 4-MeSal = 4-methoxysalicylate monoanion. Complexes were characterized by elemental analysis, UV-Vis, infrared, EPR spectra and single crystal X-ray analysis. Spectral properties are in good agreement with structural information. Intermolecular interactions are responsible for building supramolecular structure. The complexes 1 and 2 build up 2D supramolecular structures by the O-H⋯O hydrogen bonds formation while the complexes 3 and 4 are forming 1D supramolecular chain of paddle wheel units and coordinated solvent molecules.

  7. Strontium stable isotope behaviour accompanying basalt weathering

    Science.gov (United States)

    Burton, K. W.; Parkinson, I. J.; Gíslason, S. G. R.

    2016-12-01

    The strontium (Sr) stable isotope composition of rivers is strongly controlled by the balance of carbonate to silicate weathering (Krabbenhöft et al. 2010; Pearce et al. 2015). However, rivers draining silicate catchments possess distinctly heavier Sr stable isotope values than their bedrock compositions, pointing to significant fractionation during weathering. Some have argued for preferential release of heavy Sr from primary phases during chemical weathering, others for the formation of secondary weathering minerals that incorporate light isotopes. This study presents high-precision double-spike Sr stable isotope data for soils, rivers, ground waters and estuarine waters from Iceland, reflecting both natural weathering and societal impacts on those environments. The bedrock in Iceland is dominantly basaltic, d88/86Sr ≈ +0.27, extending to lighter values for rhyolites. Geothermal waters range from basaltic Sr stable compositions to those akin to seawater. Soil pore waters reflect a balance of input from primary mineral weathering, precipitation and litter recycling and removal into secondary phases and vegetation. Rivers and ground waters possess a wide range of d88/86Sr compositions from +0.101 to +0.858. Elemental and isotope data indicate that this fractionation primarily results from the formation or dissolution of secondary zeolite (d88/86Sr ≈ +0.10), but also carbonate (d88/86Sr ≈ +0.22) and sometimes anhydrite (d88/86Sr ≈ -0.73), driving the residual waters to heavier or lighter values, respectively. Estuarine waters largely reflect mixing with seawater, but are also be affected by adsorption onto particulates, again driving water to heavy values. Overall, these data indicate that the stability and nature of secondary weathering phases, exerts a strong control on the Sr stable isotope composition of silicate rivers. [1] Krabbenhöft et al. (2010) Geochim. Cosmochim. Acta 74, 4097-4109. [2] Pearce et al. (2015) Geochim. Cosmochim. Acta 157, 125-146.

  8. Modeling Transmembrane Domain Dimers/Trimers of Plexin Receptors: Implications for Mechanisms of Signal Transmission across the Membrane

    Science.gov (United States)

    Zhang, Liqun; Polyansky, Anton; Buck, Matthias

    2015-01-01

    Single-pass transmembrane (TM) receptors transmit signals across lipid bilayers by helix association or by configurational changes within preformed dimers. The structure determination for such TM regions is challenging and has mostly been accomplished by NMR spectroscopy. Recently, the computational prediction of TM dimer structures is becoming recognized for providing models, including alternate conformational states, which are important for receptor regulation. Here we pursued a strategy to predict helix oligomers that is based on packing considerations (using the PREDDIMER webserver) and is followed by a refinement of structures, utilizing microsecond all-atom molecular dynamics simulations. We applied this method to plexin TM receptors, a family of 9 human proteins, involved in the regulation of cell guidance and motility. The predicted models show that, overall, the preferences identified by PREDDIMER are preserved in the unrestrained simulations and that TM structures are likely to be diverse across the plexin family. Plexin-B1 and –B3 TM helices are regular and tend to associate, whereas plexin-A1, -A2, –A3, -A4, -C1 and –D1 contain sequence elements, such as poly-Glycine or aromatic residues that distort helix conformation and association. Plexin-B2 does not form stable dimers due to the presence of TM prolines. No experimental structural information on the TM region is available for these proteins, except for plexin-C1 dimeric and plexin-B1 – trimeric structures inferred from X-ray crystal structures of the intracellular regions. Plexin-B1 TM trimers utilize Ser and Thr sidechains for interhelical contacts. We also modeled the juxta-membrane (JM) region of plexin-C1 and plexin-B1 and show that it synergizes with the TM structures. The structure and dynamics of the JM region and TM-JM junction provide determinants for the distance and distribution of the intracellular domains, and for their binding partners relative to the membrane. The structures

  9. How Does Thymine DNA Survive Ultrafast Dimerization Damage?

    Directory of Open Access Journals (Sweden)

    Hongjuan Wang

    2016-12-01

    Full Text Available The photodimerization reaction between the two adjacent thymine bases within a single strand has been the subject of numerous studies due to its potential to induce DNA mutagenesis and possible tumorigenesis in human skin cells. It is well established that the cycloaddition photoreaction takes place on a picosecond time scale along barrierless or low barrier singlet/triplet pathways. However, the observed dimerization quantum yield in different thymine multimer is considerable lower than might be expected. A reasonable explanation is required to understand why thymine in DNA is able to survive ultrafast dimerization damage. In this work, accurate quantum calculations based on the combined CASPT2//CASSCF/AMBER method were conducted to map the excited state relaxation pathways of the thymine monomer in aqueous solution and of the thymine oligomer in DNA. A monomer-like decay pathway, induced by the twisting of the methyl group, is found to provide a bypass channel to ensure the photostability of thymine in single-stranded oligomers. This fast relaxation path is regulated by the conical intersection between the bright SCT(1ππ* state with the intra-base charge transfer character and the ground state to remove the excess excitation energy, thereby achieving the ground-state recovery with high efficiency.

  10. Identification of a dimeric KDG aldolase from Agrobacterium tumefaciens.

    Science.gov (United States)

    Soares da Costa, Tatiana P; Patel, Madhvi; Desbois, Sebastien; Gupta, Ruchi; Faou, Pierre; Perugini, Matthew A

    2017-11-01

    Agrobacterium tumefaciens is a Gram-negative bacterium and causative agent of Crown Gall disease that infects a variety of economically important plants. The annotated A. tumefaciens genome contains 10 putative dapA genes, which code for dihydrodipicolinate synthase (DHDPS). However, we have recently demonstrated that only one of these genes (dapA7) encodes a functional DHDPS. The function of the other nine putative dapA genes is yet to be determined. Here, we demonstrate using bioinformatics that the product of the dapA5 gene (DapA5) possesses all the catalytic residues canonical to 2-keto-3-deoxygluconate (KDG) aldolase, which is a class I aldolase involved in glucose metabolism. We therefore expressed, purified, and characterized recombinant DapA5 using mass spectrometry, circular dichroism spectroscopy, analytical ultracentrifugation, and enzyme kinetics. The results show that DapA5 (1) adopts an α/β structure consistent with the TIM-barrel fold of KDG aldolases, (2) possesses KDG aldolase enzyme activity, and (3) exists as a tight dimer in solution. This study shows for the first time that dapA5 from A. tumefaciens encodes a functional dimeric KDG aldolase. © 2017 Wiley Periodicals, Inc.

  11. Gossypolhemiquinone, a dimeric sesquiterpenoid identified in cotton (Gossypium).

    Science.gov (United States)

    Stipanovic, Robert; Puckhaber, Lorraine; Frelichowski, James; Esquivel, Jesus; Westbrook, John; O'Neil, Mike; Bell, Alois; Dowd, Michael; Hake, Kater; Duke, Sara

    2016-02-01

    The report that the cotton leaf perforator, Bucculatrix thurberiella, is one of the few insect herbivores to attack Gossypium thurberi prompted an investigation of the terpenoids present in the leaves of this wild species of cotton. Members of Gossypium produce subepidermal pigment glands in their leaves that contain the dimeric sesquiterpenoid gossypol as well as other biosynthetically related terpenoids. In addition to gossypol, a previously unknown dimeric sesquiterpenoid, gossypolhemiquinone (GHQ), was identified in trace amounts in G. thurberi, a member of the D genome. Other members of the D genome of Gossypium were subsequently found to contain this compound, but GHQ was not detected in commercial cotton cultivars. When fed to Helicoverpa zea in an artificial diet, GHQ delayed days-to-pupation, reduced pupal weights, and survival to adulthood to a lesser or equal extent than gossypol in comparison to the control diet. However, GHQ had a synergistic effect on survival and days-to-pupation when combined with gossypol at the highest dosage tested (0.18%; 15.5:84.5 GHQ:gossypol). Because gossypol exhibits anti-cancer activity, GHQ was also evaluated for its anti-cancer activity against the National Cancer Institute's 60-Human Tumor Cell Line Screen. Significant inhibitory activity against most of these cell lines was not observed, but the results may offer some promise against leukemia cancer cell lines. Published by Elsevier Ltd.

  12. Dimerization of a Viral SET Protein Endows its Function

    Energy Technology Data Exchange (ETDEWEB)

    H Wei; M Zhou

    2011-12-31

    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.

  13. Function of E-protein dimers expressed in catfish lymphocytes

    Science.gov (United States)

    Hikima, Jun-ichi; Lennard Richard, Mara L.; Wilson, Melanie R.; Miller, Norman W.; Warr, Gregory W.

    2007-01-01

    E-proteins are essential class I bHLH transcription factors that play a role in lymphocyte development. In catfish lymphocytes the predominant E-proteins expressed are CFEB (a homologue of HEB) and E2A1, which both strongly drive transcription. In this study the role of homodimerization versus heterodimerization in the function of these catfish E-proteins was addressed through the use of expression constructs encoding forced dimers. Constructs expressing homo- and heterodimers were transfected into catfish B cells and shown to drive transcription from the catfish IGH enhancer. Expression from an artificial promoter containing a trimer of μE5 motifs clearly demonstrated that the homodimer of E2A1 drove transcription more strongly (by a factor of 10–25) than the CFEB homodimer in catfish B and T cells, while the heterodimer showed intermediate levels of transcriptional activation. Both CFEB1 and E2A1 proteins dimerized in vitro, and the heterodimer CFEB1-E2A1 was shown to bind the canonical μE5 motif. PMID:17870169

  14. Intermolecular Coulombic Decay (ICD) Occuring in Triatomic Molecular Dimer

    Science.gov (United States)

    Iskandar, Wael; Gatton, Averell; Gaire, Bishwanath; Champenois, Elio; Larsen, Kirk; Shivaram, Niranjan; Moradmand, Ali; Severt, Travis; Williams, Joshua; Slaughter, Daniel; Weber, Thorsten

    2017-04-01

    For over two decades, the production of ICD process has been extensively investigated theoretically and experimentally in different systems bounded by a week force (ex. van-der-Waals or Hydrogen force). Furthermore, the ICD process has been demonstrated a strong implication in biological system (DNA damage and DNA repair mechanism) because of the production of genotoxic low energy electrons during the decay cascade. Studying large complex system such as triatomic molecular dimer may be helpful for further exploration of ``Auger electron driven cancer therapy''. The present experiment investigates the dissociation dynamics happened in collision between a photons and CO2 dimer. We will focus more specifically on the CO2++CO2+ fragmentation channel and the detection in coincidence of the two ionic fragments and the two electrons will be done using a COld Target Recoil Ion Momentum Spectroscopy (COLTRIMS). The measurements of the Kinetic Energy Release of the two fragments and the relative angular distribution of the electrons in the molecular frame reveal that the ICD is the only mechanism responsible for the production of this fragmentation channel.

  15. Cell-permeant and photocleavable chemical inducer of dimerization.

    Science.gov (United States)

    Zimmermann, Mirjam; Cal, Ruben; Janett, Elia; Hoffmann, Viktor; Bochet, Christian G; Constable, Edwin; Beaufils, Florent; Wymann, Matthias P

    2014-04-25

    Chemical inducers of dimerization (CIDs) have been developed to orchestrate protein dimerization and translocation. Here we present a novel photocleavable HaloTag- and SNAP-tag-reactive CID (MeNV-HaXS) with excellent selectivity and intracellular reactivity. Excitation at 360 nm cleaves the methyl-6-nitroveratryl core of MeNV-HaXS. MeNV-HaXS covalently links HaloTag- and SNAP-tag fusion proteins, and enables targeting of selected membranes and intracellular organelles. MeNV-HaXS-mediated translocation has been validated for plasma membrane, late endosomes, lysosomes, Golgi, mitochondria, and the actin cytoskeleton. Photocleavage of MeNV-HaXS liberates target proteins and provides access to optical manipulation of protein relocation with high spatiotemporal and subcellular precision. MeNV-HaXS supports kinetic studies of protein dynamics and the manipulation of subcellular enzyme activities, which is exemplified for Golgi-targeted cargo and the assessment of nuclear import kinetics. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Tuning Liposome Membrane Permeability by Competitive Peptide Dimerization and Partitioning-Folding Interactions Regulated by Proteolytic Activity

    Science.gov (United States)

    Lim, Seng Koon; Sandén, Camilla; Selegård, Robert; Liedberg, Bo; Aili, Daniel

    2016-02-01

    Membrane active peptides are of large interest for development of drug delivery vehicles and therapeutics for treatment of multiple drug resistant infections. Lack of specificity can be detrimental and finding routes to tune specificity and activity of membrane active peptides is vital for improving their therapeutic efficacy and minimize harmful side effects. We describe a de novo designed membrane active peptide that partition into lipid membranes only when specifically and covalently anchored to the membrane, resulting in pore-formation. Dimerization with a complementary peptide efficiently inhibits formation of pores. The effect can be regulated by proteolytic digestion of the inhibitory peptide by the matrix metalloproteinase MMP-7, an enzyme upregulated in many malignant tumors. This system thus provides a precise and specific route for tuning the permeability of lipid membranes and a novel strategy for development of recognition based membrane active peptides and indirect enzymatically controlled release of liposomal cargo.

  17. IR absorption spectrum (4200-3100 cm-1) of H2O and (H2O)2 in CCl4. Estimates of the equilibrium constant and evidence that the atmospheric water absorption continuum is due to the water dimer

    International Nuclear Information System (INIS)

    Nicolaisen, Flemming M.

    2009-01-01

    IR absorption spectra, 4200-3100 cm -1 , of water in CCl 4 solutions are presented. It is shown that for saturated solutions significant amounts of water are present as dimer (ca. 2%). The IR spectra of the monomer and dimer are retrieved. The integrated absorption coefficients of the monomer absorption are significantly enhanced relative to the gas phase values. The dimer spectrum consists of 5 bands, of which 4 were expected from data from cold beams and cold matrices. The origin of the 'extra' band is discussed. In addition it is argued that the dimer absorption bands intensities must be enhanced relative to the gas phase values. Based on recent calculations of band strengths, and observed frequency shifts relative to the gas phase, the intensity enhancement factors are estimated as well as the monomer/dimer equilibrium constant in CCl 4 solution at T=296 K (K c =1.29 mol -1 L). It is noted that the observed dimer spectrum has a striking resemblance with the water vapour continuum determined by Burch in 1985 which was recently remeasured by Paynter et al. and it is concluded that the atmospheric water absorption continuum in the investigated spectral region must be due to water dimer. Based on the newly published spectral data a revised value of the gas phase equilibrium constant is suggested (K p =0.035 atm -1 at T=296 K) as well as a value for the standard enthalpy of formation, ΔH 0 =15.4 kJ mol -1 .

  18. Regulation of CCR7-dependent cell migration through?CCR7 homodimer formation

    OpenAIRE

    Kobayashi, Daichi; Endo, Masataka; Ochi, Hirotaka; Hojo, Hironobu; Miyasaka, Masayuki; Hayasaka, Haruko

    2017-01-01

    The chemokine receptor CCR7 contributes to various physiological and pathological processes including T cell maturation, T cell migration from the blood into secondary lymphoid tissues, and tumor cell metastasis to lymph nodes. Although a previous study suggested that the efficacy of CCR7 ligand-dependent T cell migration correlates with CCR7 homo- and heterodimer formation, the exact extent of contribution of the CCR7 dimerization remains unclear. Here, by inducing or disrupting CCR7 dimers,...

  19. Ultraviolet-B-induced cyclobutane-pyrimidine dimer formation and repair in arctic marine macrophytes

    NARCIS (Netherlands)

    van de Poll, W.H.; Hanelt, D; Hoyer, K.; Buma, A.G.J.; Breeman, Arno

    2002-01-01

    The significance of ultraviolet-B radiation (UVBR: 280-315 nm)-induced DNA damage as a stress factor for Arctic marine macrophytes was examined in the Kongsfjord (Spitsbergen, 78degrees55.5'N, 11degrees56.0'E) in summer. UVBR penetration in the water column was monitored as accumulation of

  20. RecFOR Is Not Required for Pneumococcal Transformation but Together with XerS for Resolution of Chromosome Dimers Frequently Formed in the Process

    Science.gov (United States)

    Johnston, Calum; Mortier-Barrière, Isabelle; Granadel, Chantal; Polard, Patrice; Martin, Bernard; Claverys, Jean-Pierre

    2015-01-01

    Homologous recombination (HR) is required for both genome maintenance and generation of diversity in eukaryotes and prokaryotes. This process initiates from single-stranded (ss) DNA and is driven by a universal recombinase, which promotes strand exchange between homologous sequences. The bacterial recombinase, RecA, is loaded onto ssDNA by recombinase loaders, RecBCD and RecFOR for genome maintenance. DprA was recently proposed as a third loader dedicated to genetic transformation. Here we assessed the role of RecFOR in transformation of the human pathogen Streptococcus pneumoniae. We firstly established that RecFOR proteins are not required for plasmid transformation, strongly suggesting that DprA ensures annealing of plasmid single-strands internalized in the process. We then observed no reduction in chromosomal transformation using a PCR fragment as donor, contrasting with the 10,000-fold drop in dprA - cells and demonstrating that RecFOR play no role in transformation. However, a ∼1.45-fold drop in transformation was observed with total chromosomal DNA in recFOR mutants. To account for this limited deficit, we hypothesized that transformation with chromosomal DNA stimulated unexpectedly high frequency (>30% of cells) formation of chromosome dimers as an intermediate in the generation of tandem duplications, and that RecFOR were crucial for dimer resolution. We validated this hypothesis, showing that the site-specific recombinase XerS was also crucial for dimer resolution. An even higher frequency of dimer formation (>80% of cells) was promoted by interspecies transformation with Streptococcus mitis chromosomal DNA, which contains numerous inversions compared to pneumococcal chromosome, each potentially promoting dimerization. In the absence of RecFOR and XerS, dimers persist, as confirmed by DAPI staining, and can limit the efficiency of transformation, since resulting in loss of transformant chromosome. These findings strengthen the view that different HR