Science.gov

Sample records for 3-phospho-d-glycerate carboxy-lyase dimerizing

  1. Demonstration of transcriptional regulation of specific genes by phytochrome action

    PubMed Central

    Silverthorne, Jane; Tobin, Elaine M.

    1984-01-01

    We have developed an in vitro transcription system that uses nuclei isolated from Lemna gibba G-3. The in vitro transcripts include sequences homologous to hybridization probes for the small subunit of ribulose-1,5-bisphosphate carboxylase [3-phospho-D-glycerate carboxy-lyase (dimerizing), EC 4.1.1.39], the light-harvesting chlorophyll a/b-protein, and rRNA. Light-harvesting chlorophyll a/b-protein sequences are transcribed to a greater extent in nuclei isolated from plants grown in darkness with 2 min of red light every 8 hr than in nuclei isolated from dark-treated plants. Furthermore, the amount of these transcripts measured in plants given a single minute of red light after dark treatment is increased over the amount measured in dark-treated plants. The effect of red light is at least partially reversible by 10 min of far-red light given immediately after the red light pulse. Transcription of both rRNA and small subunit sequences is also stimulated by a single minute of red light as compared to dark-treated tissue. However, the relative magnitudes of the increases compared to the dark levels are smaller than the increase seen for the chlorophyll a/b-protein, possibly because of the higher level of transcription of these sequences in the dark. The effect of red light on the transcription of small subunit and rRNA sequences is also reversible by immediate treatment with 10 min of far-red light. Pulse chase studies of dark-treated nuclei for up to 110 min do not show substantial turnover of in vitro labeled small subunit and chlorophyll a/b-protein transcripts. We therefore conclude that phytochrome action has induced specific changes in transcription of these genes. Images PMID:16593420

  2. Dimeric Sesquiterpenoids.

    PubMed

    Liao, Shang-Gao; Yue, Jian-Min

    2016-01-01

    It is widely accepted that a large number of proteins that are responsible for cellular function exist as dimers or need to be activated by dimerization before mediating certain signaling pathways. Simultaneously targeting both monomeric moieties of the dimeric proteins has shown potential in the development of various therapeutic agents. As dimeric molecules might be able to act on both moieties of a dimeric protein, dimeric sesquiterpenoids (DSs), which are generated biogenetically from coupling of two sesquiterpenoid molecules, are in essence potential biologically active molecules, and have attracted in recent years great attention for their peculiar structures and biological activities. In fact, a number of DSs are more potent than their monomeric precursors for some activities such as anti-inflammatory, anti-tumor, immunosuppressive, potassium channel blocking, antimalarial, anti-virus, and neurotrophic activities.The complex and diversified structures of DSs also attracted attention of chemists in their isolation, structural elucidation, and synthetic construction.In the contribution, a general view of the classification and distribution of DSs will be provided. Strategies for the structural elucidation of DSs and their analogues is presented. Chemical strategies for the convergence of the two sesquiterpenoid units is reviewed. Biological activities are discussed under each type of activity. PMID:26659108

  3. D-dimer test

    MedlinePlus

    D-dimer tests are used to check for blood clotting problems. Blood clots can cause health problems, such ... that you probably do not have problems with blood clotting. If you are getting the D-dimer test ...

  4. Dimeric Cinchona alkaloids.

    PubMed

    Boratyński, Przemysław J

    2015-05-01

    Nature is full of dimeric alkaloids of various types from many plant families, some of them with interesting biological properties. However, dimeric Cinchona alkaloids were not isolated from any species but were products of designed partial chemical synthesis. Although the Cinchona bark is amongst the sources of oldest efficient medicines, the synthetic dimers found most use in the field of asymmetric synthesis. Prominent examples include the Sharpless dihydroxylation and aminohydroxylation ligands, and dimeric phase transfer catalysts. In this article the syntheses of Cinchona alkaloid dimers and oligomers are reviewed, and their structure and applications are outlined. Various synthetic routes exploit reactivity of the alkaloids at the central 9-hydroxyl group, quinuclidine, and quinoline rings, as well as 3-vinyl group. This availability of reactive sites, in combination with a plethora of linker molecules, contributes to the diversity of the products obtained. PMID:25586655

  5. Dimerization of lipocalin allergens

    PubMed Central

    Niemi, Merja H.; Rytkönen-Nissinen, Marja; Miettinen, Ilja; Jänis, Janne; Virtanen, Tuomas; Rouvinen, Juha

    2015-01-01

    Lipocalins are one of the most important groups of inhalant animal allergens. The analysis of structural features of these proteins is important to get insights into their allergenicity. We have determined two different dimeric crystal structures for bovine dander lipocalin Bos d 2, which was earlier described as a monomeric allergen. The crystal structure analysis of all other determined lipocalin allergens also revealed oligomeric structures which broadly utilize inherent structural features of the β-sheet in dimer formation. According to the moderate size of monomer-monomer interfaces, most of these dimers would be transient in solution. Native mass spectrometry was employed to characterize quantitatively transient dimerization of two lipocalin allergens, Bos d 2 and Bos d 5, in solution. PMID:26346541

  6. Metalloporphines: Dimers and Trimers.

    PubMed

    Jentzen, Walter; Shelnutt, John A; Scheidt, W Robert

    2016-06-20

    Procedures for the purification and subsequent crystallization of the slightly soluble four-coordinate metallporphines, the simplest possible porphyrin derivatives, are described. Crystals of the porphine derivatives of cobalt(II), copper(II), platinum(II), and two polymorphs of zinc(II) were obtained. Analysis of the crystal and molecular structures shows that all except the platinum(II) derivative form an unusual trimeric species in the solid state. The isomorphous cobalt(II), copper(II), and one zinc(II) polymorph pack in the unit cell to form dimers as well as the trimers. Interplanar spacings between porphine rings are similar in both the dimers and trimers and range between 3.24 and 3.37 Å. Porphine rings are strongly overlapped with lateral shifts between ring centers in both the dimers and trimers with values between 1.52 and 1.70 Å or in Category S as originally defined by Scheidt and Lee. Periodic trends in the M-Np bond distances parallel those observed previously for tetraphenyl- and octaethylporphyrin derivatives. PMID:27276239

  7. Inhibiting EGFR Dimerization Using Triazolyl-Bridged Dimerization Arm Mimics

    PubMed Central

    Hanold, Laura E.; Oruganty, Krishnadev; Ton, Norman T.; Beedle, Aaron M.; Kannan, Natarajan; Kennedy, Eileen J.

    2015-01-01

    The epidermal growth factor receptor (EGFR) is overexpressed in multiple carcinomas and is the focus of a variety of targeted therapies. Here we report the design of peptide-based compounds that mimic the EGFR dimerization arm and inhibit allosteric activation of EGFR. These peptides are modified to contain a triazolyl bridge between the peptide strands to constrain the EGFR dimerization arm β-loop. In this study, we demonstrate that these peptides have significantly improved proteolytic stability over the non-modified peptide sequence, and their inhibitory effects are dependent on the number of the methylene units and orientation of the introduced triazolyl bridge. We identified a peptide, EDA2, which downregulates receptor phosphorylation and dimerization and reduces cell viability. This is the first example of a biologically active triazolyl-bridged peptide targeting the EGFR dimerization interface that effectively downregulates EGFR activation. PMID:25790232

  8. Mechanically Stabilized Tetrathiafulvalene Radical Dimers

    SciTech Connect

    Coskun, Ali; Spruell, Jason M.; Barin, Gokhan; Fahrenbach, Albert C.; Forgan, Ross S.; Colvin, Michael T.; Carmieli, Raanan; Benitez, Diego; Tkatchouk, Ekaterina; Friedman, Douglas C.; Sarjeant, Amy A.; Wasielewski, Michael R.; Goddard, William A.; Stoddart, J. Fraser

    2011-01-01

    Two donor-acceptor [3]catenanes—composed of a tetracationic molecular square, cyclobis(paraquat-4,4'-biphenylene), as the π-electron deficient ring and either two tetrathiafulvalene (TTF) and 1,5-dioxynaphthalene (DNP) containing macrocycles or two TTF-butadiyne-containing macrocycles as the π-electron rich components—have been investigated in order to study their ability to form TTF radical dimers. It has been proven that the mechanically interlocked nature of the [3]catenanes facilitates the formation of the TTF radical dimers under redox control, allowing an investigation to be performed on these intermolecular interactions in a so-called “molecular flask” under ambient conditions in considerable detail. In addition, it has also been shown that the stability of the TTF radical-cation dimers can be tuned by varying the secondary binding motifs in the [3]catenanes. By replacing the DNP station with a butadiyne group, the distribution of the TTF radical-cation dimer can be changed from 60% to 100%. These findings have been established by several techniques including cyclic voltammetry, spectroelectrochemistry and UV-vis-NIR and EPR spectroscopies, as well as with X-ray diffraction analysis which has provided a range of solid-state crystal structures. The experimental data are also supported by high-level DFT calculations. The results contribute significantly to our fundamental understanding of the interactions within the TTF radical dimers.

  9. Adventures in Holographic Dimer Models

    SciTech Connect

    Kachru, Shamit; Karch, Andreas; 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.

  10. Benchmarking of optical dimerizer systems.

    PubMed

    Pathak, Gopal P; Strickland, Devin; Vrana, Justin D; Tucker, Chandra L

    2014-11-21

    Optical dimerizers are a powerful new class of optogenetic tools that allow light-inducible control of protein-protein interactions. Such tools have been useful for regulating cellular pathways and processes with high spatiotemporal resolution in live cells, and a growing number of dimerizer systems are available. As these systems have been characterized by different groups using different methods, it has been difficult for users to compare their properties. Here, we set about to systematically benchmark the properties of four optical dimerizer systems, CRY2/CIB1, TULIPs, phyB/PIF3, and phyB/PIF6. Using a yeast transcriptional assay, we find significant differences in light sensitivity and fold-activation levels between the red light regulated systems but similar responses between the CRY2/CIB and TULIP systems. Further comparison of the ability of the CRY2/CIB1 and TULIP systems to regulate a yeast MAPK signaling pathway also showed similar responses, with slightly less background activity in the dark observed with CRY2/CIB. In the process of developing this work, we also generated an improved blue-light-regulated transcriptional system using CRY2/CIB in yeast. In addition, we demonstrate successful application of the CRY2/CIB dimerizers using a membrane-tethered CRY2, which may allow for better local control of protein interactions. Taken together, this work allows for a better understanding of the capacities of these different dimerization systems and demonstrates new uses of these dimerizers to control signaling and transcription in yeast. PMID:25350266

  11. The dimer of unsubstituted silole

    SciTech Connect

    Lei, Deqing; Chen, Yue-Shen; Gaspar, P.P.

    1992-02-01

    Gas-phase flow pyrolysis of 1-(trimethylsilyl)-1-silacyclopent-3-ene and 1-methoxy-1-(trimethylsilyl)-1-silacyclopent-3-ene leads to the formation of the dimer of silole, 3,8-disila-3a, 4,7,7a-tetrahydro-4,7-methano-1H-indene. Attempts to isolate or trap the silole monomer by means other than self-reaction have failed. It is suggested that the initially formed intermediate silylene, 1-silacyclopent-3-enylidene, undergoes rearrangement to silole and that silole is not very reactive in 2 + 4 cycloadditions, but does undergo dimerization. 19 refs., 1 fig.

  12. Photochemical dimerization of organic compounds

    SciTech Connect

    Crabtree, R.H.; Brown, S.H.; Muedas, C.A.; Ferguson, R.R.

    1992-04-14

    This patent describes improvement in a Group IIb photosensitized vapor phase dimerization of an organic compound in which a gaseous mixture of a Group IIB metal and the organic compound is irradiated in a reaction zone with a photosensitizing amount of radiant energy. The improvement comprises: a continuous stream of the gaseous mixture is passed as a vapor phase in a single pass through the reaction zone at a temperature at which the thus-produced dimer condenses immediately upon the formation thereof; the starting gaseous mixture comprises hydrogen and two ethylenically unsaturated compounds selected from the group consisting of alkenes of at least six carbon atoms, unsaturated nitriles, unsaturated epoxides, unsaturated silanes, unsaturated amines, unsaturated phosphines, and fluorinated alkenes; the gaseous mixture comprises nitrous oxide and the organic compound is a saturated compound with C-H bond strengths greater than 100 kcal/mol or a mixture of the saturated compound and an alkene; or the starting gaseous comprises an activating amount of hydrogen and the dimerization is a dehydrodimerization or cross-dimerization of a saturated hydrocarbon.

  13. Kinetics of DNA tile dimerization.

    PubMed

    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. PMID:24794259

  14. Single residue modification of only one dimer within the hemoglobin tetramer reveals autonomous dimer function

    NASA Astrophysics Data System (ADS)

    Ackers, Gary K.; Dalessio, Paula M.; Lew, George H.; Daugherty, Margaret A.; Holt, Jo M.

    2002-07-01

    The mechanism of cooperativity in the human hemoglobin tetramer (a dimer of dimers) has historically been modeled as a simple two-state system in which a low-affinity structural form (T) switches, on ligation, to a high-affinity form (R), yielding a net loss of hydrogen bonds and salt bridges in the dimer-dimer interface. Modifications that weaken these cross-dimer contacts destabilize the quaternary T tetramer, leading to decreased cooperativity and enhanced ligand affinity, as demonstrated in many studies on symmetric double modifications, i.e., a residue site modified in both - or both -subunits. In this work, hybrid tetramers have been prepared with only one modified residue, yielding molecules composed of a wild-type dimer and a modified dimer. It is observed that the cooperative free energy of ligation to the modified dimer is perturbed to the same extent whether in the hybrid tetramer or in the doubly modified tetramer. The cooperative free energy of ligation to the wild-type dimer is unperturbed, even in the hybrid tetramer, and despite the overall destabilization of the T tetramer by the modification. This asymmetric response by the two dimers within the same tetramer shows that loss of dimer-dimer contacts is not communicated across the dimer-dimer interface, but is transmitted through the dimer that bears the modified residue. These observations are interpreted in terms of a previously proposed dimer-based model of cooperativity with an additional quaternary (T/R) component.

  15. Characterization of mAb dimers reveals predominant dimer forms common in therapeutic mAbs.

    PubMed

    Plath, Friederike; Ringler, Philippe; Graff-Meyer, Alexandra; Stahlberg, Henning; Lauer, Matthias E; Rufer, Arne C; Graewert, Melissa A; Svergun, Dmitri; Gellermann, Gerald; Finkler, Christof; Stracke, Jan O; Koulov, Atanas; Schnaible, Volker

    2016-07-01

    The formation of undesired high molecular weight species such as dimers is an important quality attribute for therapeutic monoclonal antibody formulations. Therefore, the thorough understanding of mAb dimerization and the detailed characterization mAb dimers is of great interest for future pharmaceutical development of therapeutic antibodies. In this work, we focused on the analyses of different mAb dimers regarding size, surface properties, chemical identity, overall structure and localization of possible dimerization sites. Dimer fractions of different mAbs were isolated to a satisfactory purity from bulk material and revealed 2 predominant overall structures, namely elongated and compact dimer forms. The elongated dimers displayed one dimerization site involving the tip of the Fab domain. Depending on the stress applied, these elongated dimers are connected either covalently or non-covalently. In contrast, the compact dimers exhibited non-covalent association. Several interaction points were detected for the compact dimers involving the hinge region or the base of the Fab domain. These results indicate that mAb dimer fractions are rather complex and may contain more than one kind of dimer. Nevertheless, the overall appearance of mAb dimers suggests the existence of 2 predominant dimeric structures, elongated and compact, which are commonly present in preparations of therapeutic mAbs. PMID:27031922

  16. Mechanism of FGF receptor dimerization and activation

    NASA Astrophysics Data System (ADS)

    Sarabipour, Sarvenaz; Hristova, Kalina

    2016-01-01

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

  17. Mechanism of FGF receptor dimerization and activation.

    PubMed

    Sarabipour, Sarvenaz; Hristova, Kalina

    2016-01-01

    Fibroblast growth factors (fgfs) are widely believed to activate their receptors by mediating receptor dimerization. Here we show, however, that the FGF receptors form dimers in the absence of ligand, and that these unliganded dimers are phosphorylated. We further show that ligand binding triggers structural changes in the FGFR dimers, which increase FGFR phosphorylation. The observed effects due to the ligands fgf1 and fgf2 are very different. The fgf2-bound dimer structure ensures the smallest separation between the transmembrane (TM) domains and the highest possible phosphorylation, a conclusion that is supported by a strong correlation between TM helix separation in the dimer and kinase phosphorylation. The pathogenic A391E mutation in FGFR3 TM domain emulates the action of fgf2, trapping the FGFR3 dimer in its most active state. This study establishes the existence of multiple active ligand-bound states, and uncovers a novel molecular mechanism through which FGFR-linked pathologies can arise. PMID:26725515

  18. Mechanism of FGF receptor dimerization and activation

    PubMed Central

    Sarabipour, Sarvenaz; Hristova, Kalina

    2016-01-01

    Fibroblast growth factors (fgfs) are widely believed to activate their receptors by mediating receptor dimerization. Here we show, however, that the FGF receptors form dimers in the absence of ligand, and that these unliganded dimers are phosphorylated. We further show that ligand binding triggers structural changes in the FGFR dimers, which increase FGFR phosphorylation. The observed effects due to the ligands fgf1 and fgf2 are very different. The fgf2-bound dimer structure ensures the smallest separation between the transmembrane (TM) domains and the highest possible phosphorylation, a conclusion that is supported by a strong correlation between TM helix separation in the dimer and kinase phosphorylation. The pathogenic A391E mutation in FGFR3 TM domain emulates the action of fgf2, trapping the FGFR3 dimer in its most active state. This study establishes the existence of multiple active ligand-bound states, and uncovers a novel molecular mechanism through which FGFR-linked pathologies can arise. PMID:26725515

  19. Singlet fission in pentacene dimers.

    PubMed

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

    2015-04-28

    Singlet fission (SF) has the potential to supersede the traditional solar energy conversion scheme by means of boosting the photon-to-current conversion efficiencies beyond the 30% Shockley-Queisser limit. Here, we show unambiguous and compelling evidence for unprecedented intramolecular SF within regioisomeric pentacene dimers in room-temperature solutions, with observed triplet quantum yields reaching as high as 156 ± 5%. Whereas previous studies have shown that the collision of a photoexcited chromophore with a ground-state chromophore can give rise to SF, here we demonstrate that the proximity and sufficient coupling through bond or space in pentacene dimers is enough to induce intramolecular SF where two triplets are generated on one molecule. PMID:25858954

  20. Singlet fission in pentacene dimers

    PubMed Central

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

    2015-01-01

    Singlet fission (SF) has the potential to supersede the traditional solar energy conversion scheme by means of boosting the photon-to-current conversion efficiencies beyond the 30% Shockley–Queisser limit. Here, we show unambiguous and compelling evidence for unprecedented intramolecular SF within regioisomeric pentacene dimers in room-temperature solutions, with observed triplet quantum yields reaching as high as 156 ± 5%. Whereas previous studies have shown that the collision of a photoexcited chromophore with a ground-state chromophore can give rise to SF, here we demonstrate that the proximity and sufficient coupling through bond or space in pentacene dimers is enough to induce intramolecular SF where two triplets are generated on one molecule. PMID:25858954

  1. Fiber optic D dimer biosensor

    DOEpatents

    Glass, R.S.; Grant, S.A.

    1999-08-17

    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. 4 figs.

  2. Fiber optic D dimer biosensor

    DOEpatents

    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.

  3. An RSA study of dimers

    NASA Astrophysics Data System (ADS)

    Ciesla, Michal; Barbasz, Jakub

    2012-03-01

    The first theoretical study of a dimer adsorption process at a homogeneous surface is presented. By using the RSA algorithm, we show example monolayers, discuss estimations of random jamming coverages and measure the surface blocking function, which could be used for calculating real systems kinetics. We also find the correlation function for coverages generated and analyse the orientational ordering inside the adsorbed monolayer. The results are compared with theoretical and experimental data.

  4. Redox properties of metalloporphyrin dimers

    SciTech Connect

    Collman, J.P.; Prodolliet, J.W.; Leidner, C.R.

    1986-05-28

    Cyclic and rotated disk voltammetry of two metalloporphyrin dimers, (Ru(OEP))/sub 2/ and (Os(OEP))/sub 2/, exhibit four oxidations and two reductions for each compound which are all chemically and electrochemically reversible on the voltammetric time scale. Comparison of the formal potentials of the six couples suggests that the first two oxidations are metal-centered redox processes; the remaining four couples are likely to be ligand centered. Controlled chemical oxidations using ferricinium hexafluorophosphate, silver tetrafluoroborate, and tris(4-bromophenyl)ammonium hexachloroantimonate cleanly generate the monocations (M(OEP))/sub 2//sup +/ and the dications (M(OEP))/sub 2//sup 2 +/. NMR, ESR, and electronic spectroscopy of these dimeric, cationic products support the assignment of the two oxidations as metal centered. These oxidations permit the preparation of the two series of metalloporphyrin dimers: paramagnetic (M(OEP))/sub 2/ with bond order = 2, paramagnetic (M(OEP))/sub 2//sup +/ with bond order = 2.5, and diamagnetic (M(OEP))/sub 2//sup 2 +/ with bond order = 3.

  5. Dimerization of Human Growth Hormone by Zinc

    NASA Astrophysics Data System (ADS)

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

    1991-08-01

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

  6. Functional Significance of Serotonin Receptor Dimerization

    PubMed Central

    Herrick-Davis, Katharine

    2013-01-01

    The original model of G protein activation by a single G-protein-coupled receptor (GPCR) is giving way to a new model wherein two protomers of a GPCR dimer interact with a single G protein. This article will review the evidence suggesting that 5-HT receptors form dimers/oligomers and will compare the findings with results obtained from studies with other biogenic amine receptors. Topics to be covered include the origin or biogenesis of dimer formation, potential dimer interface(s), and oligomer size (dimer versus tetramer or higher order). The functional significance will be discussed in terms of G-protein activation following ligand binding to one or two protomers in a dimeric structure, the formation of heterodimers and the development of bivalent ligands. PMID:23811735

  7. Quantum criticality in dimerized spin ladders

    NASA Astrophysics Data System (ADS)

    Chitov, Gennady Y.; Ramakko, Brandon W.; Azzouz, Mohamed

    2008-06-01

    We analyze the possibility of quantum criticality (gaplessness) in dimerized antiferromagnetic two- and three-leg spin- (1)/(2) ladders. Contrary to earlier studies of these models, we examine different dimerization patterns in the ladder. We find that ladders with the columnar dimerization order have lower zero-temperature energies, and they are always gapped. For the staggered dimerization order, we find the quantum critical lines, in agreement with earlier analyses. The bond mean-field theory we apply demonstrates its quantitative accuracy and agrees with available numerical results. We conclude that unless some mechanism for locking dimerization into the energetically less favorable staggered configuration is provided, the dimerized ladders do not order into the phase where the quantum criticality occurs.

  8. Monomer-dimer problem on some networks

    NASA Astrophysics Data System (ADS)

    Wu, Ruijuan; Yan, Weigen

    2016-09-01

    Zhang et al. (2012) obtained the exact formula for the number of all possible monomer-dimer arrangements and the asymptotic growth constant on a scale-free small-world network. In this note, we generalize this result and obtain the exact solution on the monomer-dimer model on many networks. Particularly, we prove that these networks have the same asymptotic growth constant of the number of monomer-dimer arrangements.

  9. Free Energy Landscapes for Amyloidogenic Tetrapeptides Dimerization

    PubMed Central

    Baumketner, A.; Shea, J.-E.

    2005-01-01

    The oligomerization of four peptide sequences, KFFE, KVVE, KLLE, and KAAE is studied using replica-exchange molecular dynamics simulations with an atomically detailed peptide model. Previous experimental studies reported that of these four peptides, only those containing phenylalanine and valine residues form fibrils. We show that the fibrillogenic propensities of these peptides can be rationalized in terms of the equilibrium thermodynamics of their early oligomers. Thermodynamic stability of dimers, as measured by the temperature of monomer association, is seen to be higher for those peptides that are able to form fibrils. Although the relative high and low stabilities of the KFFE and KAAE dimers arise from their respective high and low interpeptide interaction energies, the higher stability of the KVVE dimer over the KLLE system results from the smaller loss of configurational entropy accompanying the dimerization of KVVE. Free energy landscapes for dimerization are found to be strongly sequence-dependent, with a high free energy barrier separating the monomeric and dimeric states for KVVE, KLLE, and KAAE sequences. In contrast, the most fibrillogenic peptide, KFFE, displayed downhill assembly, indicating enhanced kinetic accessibility of its dimeric states. The dimeric phase for all peptide sequences is found to be heterogeneous, containing both antiparallel β-sheet structures that can grow into full fibrils as well as disordered dimers acting as on- or off-pathway intermediates for fibrillation. PMID:16127168

  10. Sputtering of dimers off a silicon surface

    NASA Astrophysics Data System (ADS)

    Nietiadi, Maureen L.; Rosandi, Yudi; Kopnarski, Michael; Urbassek, Herbert M.

    2012-10-01

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

  11. Dithiothreitol causes HIV-1 integrase dimer dissociation while agents interacting with the integrase dimer interface promote dimer formation.

    PubMed

    Tsiang, Manuel; Jones, Gregg S; Hung, Magdeleine; Samuel, Dharmaraj; Novikov, Nikolai; Mukund, Susmith; Brendza, Katherine M; Niedziela-Majka, Anita; Jin, Debi; Liu, Xiaohong; Mitchell, Michael; Sakowicz, Roman; Geleziunas, Romas

    2011-03-15

    We have developed a homogeneous time-resolved fluorescence resonance energy transfer (FRET)-based assay that detects the formation of HIV-1 integrase (IN) dimers. The assay utilizes IN monomers that express two different epitope tags that are recognized by their respective antibodies, coupled to distinct fluorophores. Surprisingly, we found that dithiothreitol (DTT), a reducing agent essential for in vitro enzymatic activity of IN, weakened the interaction between IN monomers. This effect of DTT on IN is dependent on its thiol groups, since the related chemical threitol, which contains hydroxyls in place of thiols, had no effect on IN dimer formation. By studying mutants of IN, we determined that cysteines in IN appear to be dispensable for the dimer dissociation effect of DTT. Peptides derived from the IN binding domain (IBD) of lens epithelium derived growth factor/transcriptional coactivator p75 (LEDGF), a cellular cofactor that interacts with the IN dimer interface, were tested in this IN dimerization assay. These peptides, which compete with LEDGF for binding to IN, displayed an intriguing equilibrium binding dose-response curve characterized by a plateau rising to a peak, then descending to a second plateau. Mathematical modeling of this binding system revealed that these LEDGF-derived peptides promote IN dimerization and block subunit exchange between IN dimers. This dose-response behavior was also observed with a small molecule that interacts with the IN dimer interface and inhibits LEDGF binding to IN. In conclusion, this novel IN dimerization assay revealed that peptide and small molecule inhibitors of the IN-LEDGF interaction also stabilize IN dimers and promote their formation. PMID:21222490

  12. The water dimer I: Experimental characterization

    NASA Astrophysics Data System (ADS)

    Mukhopadhyay, Anamika; Cole, William T. S.; Saykally, Richard J.

    2015-07-01

    As the archetype of water hydrogen bonding, the water dimer has been studied extensively by both theory and experiment for nearly seven decades. In this article, we present a detailed chronological review of the experimental dimer studies and the insights into the complex nature of water and hydrogen bonding gained from them. A subsequent letter will review the corresponding theoretical advances.

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

    PubMed

    Xie, Jing-Shan; Wen, Jin; Wang, Xian-Fen; Zhang, Jian-Qiao; Zhang, Ji-Fa; Kang, Yu-Long; Hui, You-Wei; Zheng, Wen-Sheng; Yao, Chun-Suo

    2015-01-01

    Using potassium hexacyanoferrate (III)-sodium acetate as oxidant, the oxidative coupling reaction of isorhapontigenin and resveratrol in aqueous acetone resulted in the isolation of three new indane dimers 4, 6, and 7, together with six known stilbene dimers. Indane dimer 5 was obtained for the first time by direct transformation from isorhapontigenin. The structures and relative configurations of the dimers were elucidated using spectral analysis, and their possible formation mechanisms were discussed. The results indicate that this reaction could be used as a convenient method for the semi-synthesis of indane dimers because of the mild conditions and simple reaction products. PMID:26694345

  14. Statistical transmutation in doped quantum dimer models.

    PubMed

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

    2012-07-01

    We prove a "statistical transmutation" symmetry of doped quantum dimer models on the square, triangular, and kagome lattices: the energy spectrum is invariant under a simultaneous change of statistics (i.e., bosonic into fermionic or vice versa) of the holes and of the signs of all the dimer resonance loops. This exact transformation enables us to define the duality equivalence between doped quantum dimer Hamiltonians and provides the analytic framework to analyze dynamical statistical transmutations. We investigate numerically the doping of the triangular quantum dimer model with special focus on the topological Z(2) dimer liquid. Doping leads to four (instead of two for the square lattice) inequivalent families of Hamiltonians. Competition between phase separation, superfluidity, supersolidity, and fermionic phases is investigated in the four families. PMID:23031119

  15. Electronic transitions of palladium dimer

    SciTech Connect

    Qian, Yue; Ng, Y. W.; Chen, Zhihua; Cheung, A. S.-C.

    2013-11-21

    The laser induced fluorescence spectrum of palladium dimer (Pd{sub 2}) in the visible region between 480 and 700 nm has been observed and analyzed. The gas-phase Pd{sub 2} molecule was produced by laser ablation of palladium metal rod. Eleven vibrational bands were observed and assigned to the [17.1] {sup 3}II{sub g} - X{sup 3}Σ{sub u}{sup +} transition system. The bond length (r{sub o}) and vibrational frequency (ΔG{sub 1/2}) of the ground X{sup 3}Σ{sub u}{sup +} state were determined to be 2.47(4) Å and 211.4(5) cm{sup −1}, respectively. A molecular orbital energy level diagram was used to understand the observed ground and excited electronic states. This is the first gas-phase experimental investigation of the electronic transitions of Pd{sub 2}.

  16. Single residue modification of only one dimer within the hemoglobin tetramer reveals autonomous dimer function

    PubMed Central

    Ackers, Gary K.; Dalessio, Paula M.; Lew, George H.; Daugherty, Margaret A.; Holt, Jo M.

    2002-01-01

    The mechanism of cooperativity in the human hemoglobin tetramer (a dimer of αβ dimers) has historically been modeled as a simple two-state system in which a low-affinity structural form (T) switches, on ligation, to a high-affinity form (R), yielding a net loss of hydrogen bonds and salt bridges in the dimer–dimer interface. Modifications that weaken these cross-dimer contacts destabilize the quaternary T tetramer, leading to decreased cooperativity and enhanced ligand affinity, as demonstrated in many studies on symmetric double modifications, i.e., a residue site modified in both α- or both β-subunits. In this work, hybrid tetramers have been prepared with only one modified residue, yielding molecules composed of a wild-type dimer and a modified dimer. It is observed that the cooperative free energy of ligation to the modified dimer is perturbed to the same extent whether in the hybrid tetramer or in the doubly modified tetramer. The cooperative free energy of ligation to the wild-type dimer is unperturbed, even in the hybrid tetramer, and despite the overall destabilization of the T tetramer by the modification. This asymmetric response by the two dimers within the same tetramer shows that loss of dimer–dimer contacts is not communicated across the dimer–dimer interface, but is transmitted through the dimer that bears the modified residue. These observations are interpreted in terms of a previously proposed dimer-based model of cooperativity with an additional quaternary (T/R) component. PMID:12119405

  17. Quantum dimer model for the pseudogap metal

    PubMed Central

    Punk, Matthias; Allais, Andrea; Sachdev, Subir

    2015-01-01

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

  18. Biomimetic synthesis: discovery of xanthanolide dimers.

    PubMed

    Shang, Hai; Liu, Junhua; Bao, Ruiyang; Cao, Yu; Zhao, Kun; Xiao, Chengqian; Zhou, Bing; Hu, Lihong; Tang, Yefeng

    2014-12-22

    Starting from xanthatin, the biomimetic synthesis of 4β,5β-epoxyxanthatin-1α,4α-endoperoxide, a novel monomeric xanthanolide, has been achieved. Moreover, four unprecedented xanthanolide dimers were synthesized by three different dimerizations of xanthatin, either in a head-to-head or head-to-tail fashion. Notably, these dimeric compounds were firstly identified as artifacts in the laboratory, and two of them, mogolides A and B, proved to be natural products present in the Xanthium mogolium Kitag plant. PMID:25430055

  19. Spin 3/2 dimer model

    NASA Astrophysics Data System (ADS)

    Rachel, S.

    2009-05-01

    We present a parent Hamiltonian for weakly dimerized valence bond solid states for arbitrary half-integral S. While the model reduces for S=1/2 to the Majumdar-Ghosh Hamiltonian, we discuss this model and its properties for S=3/2. Its degenerate ground state is the most popular toy model state for discussing dimerization in spin 3/2 chains. In particular, it describes the impurity-induced dimer phase in Cr8Ni as proposed recently. We point out that the explicit construction of the Hamiltonian and its main features apply to arbitrary half-integral spin S.

  20. Environment assisted energy transfer in dimer system

    SciTech Connect

    Khan, Salman; Ibrahim, M.; Khan, M.K.

    2014-02-15

    The influence of collective and multilocal environments on the energy transfer between the levels of a dimer is studied. The dynamics of energy transfer are investigated by considering coupling of collective environment with the levels of the dimer in the presence of both two individuals and mutually correlated multilocal environments. It is shown that every way of coupling we consider assists, though differently, the probability of transition between the levels of dimer. The probability of transition is strongly enhanced when the two local environments are mutually correlated. -- Highlights: • The dynamics of energy transfer between the levels of a dimer are studied. • Coupling of collective as well as individual environments are considered. • The environments are in spin star configurations. • The environment assists the energy transfer between the levels. • For correlated multilocal environments, the transition probability is almost 100%.

  1. Formation of cystine slipknots in dimeric proteins.

    PubMed

    Sikora, Mateusz; Cieplak, Marek

    2013-01-01

    We consider mechanical stability of dimeric and monomeric proteins with the cystine knot motif. A structure based dynamical model is used to demonstrate that all dimeric and some monomeric proteins of this kind should have considerable resistance to stretching that is significantly larger than that of titin. The mechanisms of the large mechanostability are elucidated. In most cases, it originates from the induced formation of one or two cystine slipknots. Since there are four termini in a dimer, there are several ways of selecting two of them to pull by. We show that in the cystine knot systems, there is strong anisotropy in mechanostability and force patterns related to the selection. We show that the thermodynamic stability of the dimers is enhanced compared to the constituting monomers whereas machanostability is either lower or higher. PMID:23520470

  2. Formation of Cystine Slipknots in Dimeric Proteins

    PubMed Central

    Sikora, Mateusz; Cieplak, Marek

    2013-01-01

    We consider mechanical stability of dimeric and monomeric proteins with the cystine knot motif. A structure based dynamical model is used to demonstrate that all dimeric and some monomeric proteins of this kind should have considerable resistance to stretching that is significantly larger than that of titin. The mechanisms of the large mechanostability are elucidated. In most cases, it originates from the induced formation of one or two cystine slipknots. Since there are four termini in a dimer, there are several ways of selecting two of them to pull by. We show that in the cystine knot systems, there is strong anisotropy in mechanostability and force patterns related to the selection. We show that the thermodynamic stability of the dimers is enhanced compared to the constituting monomers whereas machanostability is either lower or higher. PMID:23520470

  3. Multiply charged monopoles in cubic dimer model

    NASA Astrophysics Data System (ADS)

    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.

  4. Slab photonic crystals with dimer colloid bases

    SciTech Connect

    Riley, Erin K.; Liddell Watson, Chekesha M.

    2014-06-14

    The photonic band gap properties for centered rectangular monolayers of asymmetric dimers are reported. Colloids in suspension have been organized into the phase under confinement. The theoretical model is inspired by the range of asymmetric dimers synthesized via seeded emulsion polymerization and explores, in particular, the band structures as a function of degree of lobe symmetry and degree of lobe fusion. These parameters are varied incrementally from spheres to lobe-tangent dimers over morphologies yielding physically realizable particles. The work addresses the relative scarcity of theoretical studies on photonic crystal slabs with vertical variation that is consistent with colloidal self-assembly. Odd, even and polarization independent gaps in the guided modes are determined for direct slab structures. A wide range of lobe symmetry and degree of lobe fusion combinations having Brillouin zones with moderate to high isotropy support gaps between odd mode band indices 3-4 and even mode band indices 1-2 and 2-3.

  5. Structure of the human dimeric ATM kinase.

    PubMed

    Lau, Wilson C Y; Li, Yinyin; Liu, Zhe; Gao, Yuanzhu; Zhang, Qinfen; Huen, Michael S Y

    2016-01-01

    DNA-double strand breaks activate the serine/threonine protein kinase ataxia-telangiectasia mutated (ATM) to initiate DNA damage signal transduction. This activation process involves autophosphorylation and dissociation of inert ATM dimers into monomers that are catalytically active. Using single-particle electron microscopy (EM), we determined the structure of dimeric ATM in its resting state. The EM map could accommodate the crystal structure of the N-terminal truncated mammalian target of rapamycin (mTOR), a closely related enzyme of the phosphatidylinositol 3-kinase-related protein kinase (PIKK) family, allowing for the localization of the N- and the C-terminal regions of ATM. In the dimeric structure, the actives sites are buried, restricting the access of the substrates to these sites. The unanticipated domain organization of ATM provides a basis for understanding its mechanism of inhibition. PMID:27097373

  6. Structure of the human dimeric ATM kinase

    PubMed Central

    Lau, Wilson C. Y.; Li, Yinyin; Liu, Zhe; Gao, Yuanzhu; Zhang, Qinfen; Huen, Michael S. Y.

    2016-01-01

    ABSTRACT DNA-double strand breaks activate the serine/threonine protein kinase ataxia-telangiectasia mutated (ATM) to initiate DNA damage signal transduction. This activation process involves autophosphorylation and dissociation of inert ATM dimers into monomers that are catalytically active. Using single-particle electron microscopy (EM), we determined the structure of dimeric ATM in its resting state. The EM map could accommodate the crystal structure of the N-terminal truncated mammalian target of rapamycin (mTOR), a closely related enzyme of the phosphatidylinositol 3-kinase-related protein kinase (PIKK) family, allowing for the localization of the N- and the C-terminal regions of ATM. In the dimeric structure, the actives sites are buried, restricting the access of the substrates to these sites. The unanticipated domain organization of ATM provides a basis for understanding its mechanism of inhibition. PMID:27097373

  7. Thermodynamics of porphyrin dimerization in aqueous solutions.

    PubMed Central

    Margalit, R; Rotenberg, M

    1984-01-01

    The dimerization equilibrium of deuteroporphyrin IX and of mesoporphyrin IX in aqueous solutions were studied by fluorimetric techniques over the 0.01-1 microM concentration range, where dimerization is the dominant aggregation process. Deuteroporphyrin IX was studied at several temperatures over the range 22-37 degrees C, and mesoporphyrin at 25 and 37 degrees C. The magnitudes determined for the dimerization equilibrium constants (25 degrees C, neutral pH, phosphate-buffered saline) are 2.3 X 10(6)M-1 and 5.4 X 10(6)M-1 for the deutero and meso derivatives respectively. The meso, deutero and haemato species tested show a similar temperature effect, namely dimerization decreasing with increasing temperature, indicating the involvement of a negative enthalpy change. Van't Hoff isochore of the dimerization constants determined for deuteroporphyrin IX was linear within the temperature range of 22-37 degrees C, allowing the calculation of the thermodynamic parameters. For deuteroporphyrin dimerization, those were found to be delta G0 = -36. 4kJ X mol-1; delta H0 = -46. 0kJ X mol-1 and delta S0 = -32.2J X K-1 X mol-1 (at neutral pH, 25 degrees C, phosphate-buffered saline), showing the process to be enthalpy-driven. Similar trends have been found for porphyrin species other than those studied here. Our data fit with a hypothesis giving a major role to the solvent in driving porphyrins to aggregate in aqueous solution. The magnitudes and directions of the energetic changes fit better with the expectation of the ' solvophobic force' theory predicting enthalpy-driven association, than with the classic hydrophobic bonding, predicting the association to be entropy-driven. PMID:6743228

  8. Rubidium dimer destruction by a diode laser

    SciTech Connect

    Ban, T.; Aumiler, D.; Pichler, G.

    2005-02-01

    We observed rubidium dimer destruction by excitation of rubidium vapor with diode laser light tuned across the Rb D{sub 2} resonance line in a 2400 GHz tuning interval. The destruction was measured for rubidium atom concentrations in the (1-9)x10{sup 16} cm{sup -3} range, pump beam power up to 43 mW, and with a 5 Torr of the helium buffer gas. We discuss the physical mechanisms involved and specify the molecular pathways which may effectively lead to the observed dimer destruction.

  9. Temperature measurement of sputtered metal dimers

    SciTech Connect

    Fayet, P.; Wolf, J.P.; Woeste, L.

    1986-05-15

    The temperatures of sputtered alkali-metal dimers have been measured using one- and two-photon ionization spectroscopy. They are estimated to be 1470 +- 300 K, 1025 +- 200 K, and 1000 +- 200 K for Cs/sub 2/, K/sub 2/, and Na/sub 2/, respectively. The vibrational and rotational temperatures are found to be very similar. No dependence of the dimer excitation is found, neither on target temperature nor on the primary-ion energy. The results are compared with some currently used models to explain cluster formation in sputtering experiments.

  10. Molecular mechanisms of asymmetric RAF dimer activation.

    PubMed

    Jambrina, Pablo G; Bohuszewicz, Olga; Buchete, Nicolae-Viorel; Kolch, Walter; Rosta, Edina

    2014-08-01

    Protein phosphorylation is one of the most common post-translational modifications in cell regulatory mechanisms. Dimerization plays also a crucial role in the kinase activity of many kinases, including RAF, CDK2 (cyclin-dependent kinase 2) and EGFR (epidermal growth factor receptor), with heterodimers often being the most active forms. However, the structural and mechanistic details of how phosphorylation affects the activity of homo- and hetero-dimers are largely unknown. Experimentally, synthesizing protein samples with fully specified and homogeneous phosphorylation states remains a challenge for structural biology and biochemical studies. Typically, multiple changes in phosphorylation lead to activation of the same protein, which makes structural determination methods particularly difficult. It is also not well understood how the occurrence of phosphorylation and dimerization processes synergize to affect kinase activities. In the present article, we review available structural data and discuss how MD simulations can be used to model conformational transitions of RAF kinase dimers, in both their phosphorylated and unphosphorylated forms. PMID:25109958

  11. Dimers on the 33 .42 lattice

    NASA Astrophysics Data System (ADS)

    Li, Shuli; Yan, Weigen

    2016-06-01

    In this work, we obtain explicit expression of the number of close-packed dimers (perfect matchings) of the 33 .42 lattice with cylindrical boundary condition. Particularly, we show that the entropy of 33 .42 lattice is the same for cylindrical and toroidal boundary conditions.

  12. Adsorption of dimeric surfactants in lamellar silicates

    NASA Astrophysics Data System (ADS)

    Balcerzak, Mateusz; Pietralik, Zuzanna; Domka, Ludwik; Skrzypczak, Andrzej; Kozak, Maciej

    2015-12-01

    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 (d001) 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 CH2 and CH3 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.

  13. Ligand regulation of a constitutively dimeric EGF receptor.

    PubMed

    Freed, Daniel M; Alvarado, Diego; Lemmon, Mark A

    2015-01-01

    Ligand-induced receptor dimerization has traditionally been viewed as the key event in transmembrane signalling by epidermal growth factor receptors (EGFRs). Here we show that the Caenorhabditis elegans EGFR orthologue LET-23 is constitutively dimeric, yet responds to its ligand LIN-3 without changing oligomerization state. SAXS and mutational analyses further reveal that the preformed dimer of the LET-23 extracellular region is mediated by its domain II dimerization arm and resembles other EGFR extracellular dimers seen in structural studies. Binding of LIN-3 induces only minor structural rearrangements in the LET-23 dimer to promote signalling. Our results therefore argue that EGFR can be regulated by allosteric changes within an existing receptor dimer--resembling signalling by insulin receptor family members, which share similar extracellular domain compositions but form covalent dimers. PMID:26060020

  14. Thymine Dimer Formation probed by Time-Resolved Vibrational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Schreier, Wolfgang J.; Schrader, Tobias E.; Roller, Florian O.; Gilch, Peter; Zinth, Wolfgang; Kohler, Bern

    Cyclobutane pyrimidine dimers are the major photoproducts formed when DNA is exposed to UV light. Femtosecond time-resolved vibrational spectroscopy reveals that thymine dimers are formed in thymidine oligonucleotides in an ultrafast photoreaction.

  15. Ligand regulation of a constitutively dimeric EGF receptor

    NASA Astrophysics Data System (ADS)

    Freed, Daniel M.; Alvarado, Diego; Lemmon, Mark A.

    2015-06-01

    Ligand-induced receptor dimerization has traditionally been viewed as the key event in transmembrane signalling by epidermal growth factor receptors (EGFRs). Here we show that the Caenorhabditis elegans EGFR orthologue LET-23 is constitutively dimeric, yet responds to its ligand LIN-3 without changing oligomerization state. SAXS and mutational analyses further reveal that the preformed dimer of the LET-23 extracellular region is mediated by its domain II dimerization arm and resembles other EGFR extracellular dimers seen in structural studies. Binding of LIN-3 induces only minor structural rearrangements in the LET-23 dimer to promote signalling. Our results therefore argue that EGFR can be regulated by allosteric changes within an existing receptor dimer--resembling signalling by insulin receptor family members, which share similar extracellular domain compositions but form covalent dimers.

  16. Localized light-induced protein dimerization in living cells using a photocaged dimerizer

    PubMed Central

    Ballister, Edward R.; Aonbangkhen, Chanat; Mayo, Alyssa M.; Lampson, Michael A.; Chenoweth, David M.

    2015-01-01

    Regulated protein localization is critical for many cellular processes. Several techniques have been developed for experimental control over protein localization, including chemically induced and light-induced dimerization, which both provide temporal control. Light-induced dimerization offers the distinct advantage of spatial precision within subcellular length scales. A number of elegant systems have been reported that utilize natural light-sensitive proteins to induce dimerization via direct protein–protein binding interactions, but the application of these systems at cellular locations beyond the plasma membrane has been limited. Here we present a new technique to rapidly and reversibly control protein localization in living cells with subcellular spatial resolution using a cell-permeable, photoactivatable chemical inducer of dimerization. We demonstrate light-induced recruitment of a cytosolic protein to individual centromeres, kinetochores, mitochondria and centrosomes in human cells, indicating that our system is widely applicable to many cellular locations. PMID:25400104

  17. Dimerization of visual pigments in vivo.

    PubMed

    Zhang, Tao; Cao, Li-Hui; Kumar, Sandeep; Enemchukwu, Nduka O; Zhang, Ning; Lambert, Alyssia; Zhao, Xuchen; Jones, Alex; Wang, Shixian; Dennis, Emily M; Fnu, Amrita; Ham, Sam; Rainier, Jon; Yau, King-Wai; Fu, Yingbin

    2016-08-01

    It is a deeply engrained notion that the visual pigment rhodopsin signals light as a monomer, even though many G protein-coupled receptors are now known to exist and function as dimers. Nonetheless, recent studies (albeit all in vitro) have suggested that rhodopsin and its chromophore-free apoprotein, R-opsin, may indeed exist as a homodimer in rod disk membranes. Given the overwhelmingly strong historical context, the crucial remaining question, therefore, is whether pigment dimerization truly exists naturally and what function this dimerization may serve. We addressed this question in vivo with a unique mouse line (S-opsin(+)Lrat(-/-)) expressing, transgenically, short-wavelength-sensitive cone opsin (S-opsin) in rods and also lacking chromophore to exploit the fact that cone opsins, but not R-opsin, require chromophore for proper folding and trafficking to the photoreceptor's outer segment. In R-opsin's absence, S-opsin in these transgenic rods without chromophore was mislocalized; in R-opsin's presence, however, S-opsin trafficked normally to the rod outer segment and produced functional S-pigment upon subsequent chromophore restoration. Introducing a competing R-opsin transmembrane helix H1 or helix H8 peptide, but not helix H4 or helix H5 peptide, into these transgenic rods caused mislocalization of R-opsin and S-opsin to the perinuclear endoplasmic reticulum. Importantly, a similar peptide-competition effect was observed even in WT rods. Our work provides convincing evidence for visual pigment dimerization in vivo under physiological conditions and for its role in pigment maturation and targeting. Our work raises new questions regarding a potential mechanistic role of dimerization in rhodopsin signaling. PMID:27462111

  18. Path Forward for RAF Therapies: Inhibition of Monomers and Dimers.

    PubMed

    Kortum, Robert L; Morrison, Deborah K

    2015-09-14

    Current BRAF inhibitors block signaling from monomeric BRAF(V600E), but not from oncogenic RAS, which requires RAF dimerization. In this issue of Cancer Cell, Yao and colleagues investigate why current drugs are ineffective against RAF dimers, while Peng and colleagues describe a pan-RAF inhibitor targeting both monomeric and dimeric RAF. PMID:26373275

  19. Four-wave mixing spectroscopy of molecular dimers. Application to dimers of pentacene in p-terphenyl

    NASA Astrophysics Data System (ADS)

    Levinsky, Howard; Wiersma, Douwe A.

    1982-10-01

    Dispersive coherent Stokes-Raman scattering (CSRS) experiments on pentacene dimers in p-terphenyl were performed to locate the corresponding singly excited, delocalized, dimer levels. In addition the CNRS technique was used to locate the doubly excited dimer state. Future experiments exploring the dynamics of this novel state are discussed.

  20. Epidermal Growth Factor Receptor Dimerization and Activation Require Ligand-Induced Conformational Changes in the Dimer Interface

    PubMed Central

    Dawson, Jessica P.; Berger, Mitchell B.; Lin, Chun-Chi; Schlessinger, Joseph; Lemmon, Mark A.; Ferguson, Kathryn M.

    2005-01-01

    Structural studies have shown that ligand-induced epidermal growth factor receptor (EGFR) dimerization involves major domain rearrangements that expose a critical dimerization arm. However, simply exposing this arm is not sufficient for receptor dimerization, suggesting that additional ligand-induced dimer contacts are required. To map these contributions to the dimer interface, we individually mutated each contact suggested by crystallographic studies and analyzed the effects on receptor dimerization, activation, and ligand binding. We find that domain II contributes >90% of the driving energy for dimerization of the extracellular region, with domain IV adding little. Within domain II, the dimerization arm forms much of the dimer interface, as expected. However, a loop from the sixth disulfide-bonded module (immediately C-terminal to the dimerization arm) also makes a critical contribution. Specific ligand-induced conformational changes in domain II are required for this loop to contribute to receptor dimerization, and we identify a set of ligand-induced intramolecular interactions that appear to be important in driving these changes, effectively “buttressing” the dimer interface. Our data also suggest that similar conformational changes may determine the specificity of ErbB receptor homo- versus heterodimerization. PMID:16107719

  1. Pyrimidine dimer formation and repair in human skin

    SciTech Connect

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

    1980-09-01

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

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

    SciTech Connect

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

    2006-01-01

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

  3. Soluble Epoxide Hydrolase Dimerization Is Required for Hydrolase Activity*

    PubMed Central

    Nelson, Jonathan W.; Subrahmanyan, Rishi M.; Summers, Sol A.; Xiao, Xiangshu; Alkayed, Nabil J.

    2013-01-01

    Soluble epoxide hydrolase (sEH) plays a key role in the metabolic conversion of the protective eicosanoid 14,15-epoxyeicosatrienoic acid to 14,15-dihydroxyeicosatrienoic acid. Accordingly, inhibition of sEH hydrolase activity has been shown to be beneficial in multiple models of cardiovascular diseases, thus identifying sEH as a valuable therapeutic target. Recently, a common human polymorphism (R287Q) was identified that reduces sEH hydrolase activity and is localized to the dimerization interface of the protein, suggesting a relationship between sEH dimerization and activity. To directly test the hypothesis that dimerization is essential for the proper function of sEH, we generated mutations within the sEH protein that would either disrupt or stabilize dimerization. We quantified the dimerization state of each mutant using a split firefly luciferase protein fragment-assisted complementation system. The hydrolase activity of each mutant was determined using a fluorescence-based substrate conversion assay. We found that mutations that disrupted dimerization also eliminated hydrolase enzymatic activity. In contrast, a mutation that stabilized dimerization restored hydrolase activity. Finally, we investigated the kinetics of sEH dimerization and found that the human R287Q polymorphism was metastable and capable of swapping dimer partners faster than the WT enzyme. These results indicate that dimerization is required for sEH hydrolase activity. Disrupting sEH dimerization may therefore serve as a novel therapeutic strategy for reducing sEH hydrolase activity. PMID:23362272

  4. Soluble epoxide hydrolase dimerization is required for hydrolase activity.

    PubMed

    Nelson, Jonathan W; Subrahmanyan, Rishi M; Summers, Sol A; Xiao, Xiangshu; Alkayed, Nabil J

    2013-03-15

    Soluble epoxide hydrolase (sEH) plays a key role in the metabolic conversion of the protective eicosanoid 14,15-epoxyeicosatrienoic acid to 14,15-dihydroxyeicosatrienoic acid. Accordingly, inhibition of sEH hydrolase activity has been shown to be beneficial in multiple models of cardiovascular diseases, thus identifying sEH as a valuable therapeutic target. Recently, a common human polymorphism (R287Q) was identified that reduces sEH hydrolase activity and is localized to the dimerization interface of the protein, suggesting a relationship between sEH dimerization and activity. To directly test the hypothesis that dimerization is essential for the proper function of sEH, we generated mutations within the sEH protein that would either disrupt or stabilize dimerization. We quantified the dimerization state of each mutant using a split firefly luciferase protein fragment-assisted complementation system. The hydrolase activity of each mutant was determined using a fluorescence-based substrate conversion assay. We found that mutations that disrupted dimerization also eliminated hydrolase enzymatic activity. In contrast, a mutation that stabilized dimerization restored hydrolase activity. Finally, we investigated the kinetics of sEH dimerization and found that the human R287Q polymorphism was metastable and capable of swapping dimer partners faster than the WT enzyme. These results indicate that dimerization is required for sEH hydrolase activity. Disrupting sEH dimerization may therefore serve as a novel therapeutic strategy for reducing sEH hydrolase activity. PMID:23362272

  5. Fibrillar dimer formation of islet amyloid polypeptides

    NASA Astrophysics Data System (ADS)

    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.

  6. Fibrillar dimer formation of islet amyloid polypeptides

    SciTech Connect

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

    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.

  7. Potential energy studies on silane dimers

    NASA Astrophysics Data System (ADS)

    Mahlanen, Riina; Pakkanen, Tapani A.

    2011-04-01

    Intermolecular interactions and parameters for use in MD studies of large molecule systems have earlier been determined for hydrocarbons, carbon tetrahalides and sulfur. The paper reports a model representing nonbonding interactions between silane molecules, which were examined in the same way as hydrocarbons in an earlier (neopentane, isopropane, propane, and ethane) study. Intermolecular potentials were determined for 11 combinations of silane compound pairs (silane SiH 4, disilane Si 2H 6, trisilane Si 3H 8, isotetrasilane Si 4H 10 and neopentasilane Si 5H 12) with MP2/aug(df)-6-311G ∗ab initio calculations. The most stable dimer configurations were identified. With use of the modified Morse potential model to represent the interactions, 276 new potential energy surfaces were generated for silane dimers. Separate and generic pair potentials were calculated for the silanes. The pair potentials can be used in MD studies of silanes.

  8. Repair of DNA-containing pyrimidine dimers

    SciTech Connect

    Grossman, L.; Caron, P.R.; Mazur, S.J.; Oh, E.Y.

    1988-08-01

    Ultraviolet light-induced pyrimidine dimers in DNA are recognized and repaired by a number of unique cellular surveillance systems. The most direct biochemical mechanism responding to this kind of genotoxicity involves direct photoreversal by flavin enzymes that specifically monomerize pyrimidine:pyrimidine dimers monophotonically in the presence of visible light. Incision reactions are catalyzed by a combined pyrimidine dimer DNA-glycosylase:apyrimidinic endonuclease found in some highly UV-resistant organisms. At a higher level of complexity, Escherichia coli has a uvr DNA repair system comprising the UvrA, UvrB, and UvrC proteins responsible for incision. There are several preincision steps governed by this pathway, which includes an ATP-dependent UvrA dimerization reaction required for UvrAB nucleoprotein formation. This complex formation driven by ATP binding is associated with localized topological unwinding of DNA. This same protein complex can catalyze an ATPase-dependent 5'----3'-directed strand displacement of D-loop DNA or short single strands annealed to a single-stranded circular or linear DNA. This putative translocational process is arrested when damaged sites are encountered. The complex is now primed for dual incision catalyzed by UvrC. The remainder of the repair process involves UvrD (helicase II) and DNA polymerase I for a coordinately controlled excision-resynthesis step accompanied by UvrABC turnover. Furthermore, it is proposed that levels of repair proteins can be regulated by proteolysis. UvrB is converted to truncated UvrB* by a stress-induced protease that also acts at similar sites on the E. coli Ada protein. Although UvrB* can bind with UvrA to DNA, it cannot participate in helicase or incision reactions. It is also a DNA-dependent ATPase.21 references.

  9. Nanoradar based on nonlinear dimer nanoantenna.

    PubMed

    Lapshina, Nadezhda; Noskov, Roman; Kivshar, Yuri

    2012-09-15

    We introduce the concept of a nanoradar based on the operation of a nonlinear plasmonic nanoantenna. The nanoradar action originates from modulational instability occurring in a dimer nanoantenna consisting of two subwavelength nonlinear nanoparticles. Modulation instability causes a dynamical energy exchange between the nanoantenna eigenmodes resulting in periodic scanning of the nanoantenna scattering pattern. Such nanoradar demonstrates a wide scanning sector, low operation threshold, and ultrafast time response being potentially useful for many applications in nanophotonics circuitry. PMID:23041904

  10. Plasmomechanical Resonators Based on Dimer Nanoantennas.

    PubMed

    Thijssen, Rutger; Kippenberg, Tobias J; Polman, Albert; Verhagen, Ewold

    2015-06-10

    Nanomechanical resonators are highly suitable as sensors of minute forces, displacements, or masses. We realize a single plasmonic dimer antenna of subwavelength size, integrated with silicon nitride nanobeams. The sensitive dependence of the antenna response on the beam displacement creates a plasmomechanical system of deeply subwavelength size in all dimensions. We use it to demonstrate transduction of thermal vibrations to scattered light fields and discuss the noise properties and achievable coupling strengths in these systems. PMID:25938170

  11. Dimer models and quiver gauge theories

    NASA Astrophysics Data System (ADS)

    Pichai, Ramadevi

    2013-12-01

    = 1 quiver gauge theories on coincident D3 branes placed at a tip of a Calabi-Yau singularity C are dual to string theories on AdS5×X5 where X5 are Sasaki-Einstein spaces. We present a neat combinatorial approach called dimer model to understand interrelations between toric quiver gauge theories and toric data representing the Calabi-Yau singularities.

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

    SciTech Connect

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

    2014-10-03

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

  13. MspA Nanopores from Subunit Dimers

    PubMed Central

    Pavlenok, Mikhail; Derrington, Ian M.; Gundlach, Jens H.; Niederweis, Michael

    2012-01-01

    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 sequencing of DNA. PMID

  14. MspA nanopores from subunit dimers.

    PubMed

    Pavlenok, Mikhail; Derrington, Ian M; Gundlach, Jens H; Niederweis, Michael

    2012-01-01

    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 sequencing of DNA. PMID

  15. Peptides Interfering 3A Protein Dimerization Decrease FMDV Multiplication

    PubMed Central

    de la Torre, Beatriz G.; Valle, Javier; Andreu, David; Sobrino, Francisco

    2015-01-01

    Nonstructural protein 3A is involved in relevant functions in foot-and-mouth disease virus (FMDV) replication. FMDV 3A can form homodimers and preservation of the two hydrophobic α-helices (α1 and α2) that stabilize the dimer interface is essential for virus replication. In this work, small peptides mimicking residues involved in the dimer interface were used to interfere with dimerization and thus gain insight on its biological function. The dimer interface peptides α1, α2 and that spanning the two hydrophobic α-helices, α12, impaired in vitro dimer formation of a peptide containing the two α-helices, this effect being higher with peptide α12. To assess the effect of dimer inhibition in cultured cells, the interfering peptides were N-terminally fused to a heptaarginine (R7) sequence to favor their intracellular translocation. Thus, when fused to R7, interference peptides (100 μM) were able to inhibit dimerization of transiently expressed 3A, the higher inhibitions being found with peptides α1 and α12. The 3A dimerization impairment exerted by the peptides correlated with significant, specific reductions in the viral yield recovered from peptide-treated FMDV infected cells. In this case, α2 was the only peptide producing significant reductions at concentrations lower than 100 μM. Thus, dimer interface peptides constitute a tool to understand the structure-function relationship of this viral protein and point to 3A dimerization as a potential antiviral target. PMID:26505190

  16. Absolute Ligand Discrimination by Dimeric Signaling Receptors.

    PubMed

    Fathi, Sepehr; Nayak, Chitra R; Feld, Jordan J; Zilman, Anton G

    2016-09-01

    Many signaling pathways act through shared components, where different ligand molecules bind the same receptors or activate overlapping sets of response regulators downstream. Nevertheless, different ligands acting through cross-wired pathways often lead to different outcomes in terms of the target cell behavior and function. Although a number of mechanisms have been proposed, it still largely remains unclear how cells can reliably discriminate different molecular ligands under such circumstances. Here we show that signaling via ligand-induced receptor dimerization-a very common motif in cellular signaling-naturally incorporates a mechanism for the discrimination of ligands acting through the same receptor. PMID:27602720

  17. Equivalence between XY and dimerized models

    NASA Astrophysics Data System (ADS)

    Campos Venuti, Lorenzo; Roncaglia, Marco

    2010-06-01

    The spin-1/2 chain with XY anisotropic coupling in the plane and the XX isotropic dimerized chain are shown to be equivalent in the bulk. For finite systems, we prove that the equivalence is exact in given parity sectors, after taking care of the precise boundary conditions. The proof is given constructively by finding unitary transformations that map the models onto each other. Moreover, we considerably generalized our mapping and showed that even in the case of fully site-dependent couplings the XY chain can be mapped onto an XX model. This result has potential application in the study of disordered systems.

  18. Critical Factors Determining Dimerization of Human Antizyme Inhibitor*

    PubMed Central

    Su, Kuo-Liang; Liao, Ya-Fan; Hung, Hui-Chih; Liu, Guang-Yaw

    2009-01-01

    Ornithine decarboxylase (ODC) is the first enzyme involved in polyamine biosynthesis, and it catalyzes the decarboxylation of ornithine to putrescine. ODC is a dimeric enzyme, whereas antizyme inhibitor (AZI), a positive regulator of ODC that is homologous to ODC, exists predominantly as a monomer and lacks decarboxylase activity. The goal of this paper was to identify the essential amino acid residues that determine the dimerization of AZI. The nonconserved amino acid residues in the putative dimer interface of AZI (Ser-277, Ser-331, Glu-332, and Asp-389) were substituted with the corresponding residues in the putative dimer interface of ODC (Arg-277, Tyr-331, Asp-332, and Tyr-389, respectively). Analytical ultracentrifugation analysis was used to determine the size distribution of these AZI mutants. The size-distribution analysis data suggest that residue 331 may play a major role in the dimerization of AZI. Mutating Ser-331 to Tyr in AZI (AZI-S331Y) caused a shift from a monomer configuration to a dimer. Furthermore, in comparison with the single mutant AZI-S331Y, the AZI-S331Y/D389Y double mutant displayed a further reduction in the monomer-dimer Kd, suggesting that residue 389 is also crucial for AZI dimerization. Analysis of the triple mutant AZI-S331Y/D389Y/S277R showed that it formed a stable dimer (Kd value = 1.3 μm). Finally, a quadruple mutant, S331Y/D389Y/S277R/E332D, behaved as a dimer with a Kd value of ∼0.1 μm, which is very close to that of the human ODC enzyme. The quadruple mutant, although forming a dimer, could still be disrupted by antizyme (AZ), further forming a heterodimer, and it could rescue the AZ-inhibited ODC activity, suggesting that the AZ-binding ability of the AZI dimer was retained. PMID:19635796

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

    PubMed

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

    2010-03-21

    We consider two like-charged planar surfaces immersed in solution of oppositely charged dimer counterions with a bond length l. To analyze this system, we extend and employ a self-consistent field theory that has been shown to be accurate from the weak to the intermediate through to the strong coupling regimes. In the limit of very short dimers, the results converge to the results for pointlike divalent ions. Near the surfaces, the dimers lie parallel to the charged plates. In the intermediate coupling regime, the dimers are aligned perpendicularly to the surface when they are a distance l from a surface. In the weak coupling regime, the interactions are only repulsive. At slightly higher couplings, there is a minimum in the variation of the free energy with distance at approximately the bond length of the dimers, which arises from bridging conformations of the dimers. In the intermediate coupling regime, an additional minimum in the free energy is observed at much smaller distances, which is due to the correlations between the dimers. For large dimer bond lengths, this minimum is metastable with respect to the previous minimum. However, as the bond length decreases, this minimum becomes the stable, while the minimum associated with the dimer bond length becomes metastable and eventually disappears. For shorter dimer bond length the attractive interaction is the result of correlations between counterions and charges on the surfaces. We find that dimers can mediate attractive interaction between like-charged surfaces in the intermediate coupling regime. The analysis of orientations confirms the bridging mechanism for sufficiently long dimers, whereas at high electrostatic couplings charge correlations contribute to the attraction. PMID:20331276

  20. RING domain dimerization is essential for RNF4 function.

    PubMed

    Liew, Chu Wai; Sun, Huaiyu; Hunter, Tony; Day, Catherine L

    2010-10-01

    RNF4 [RING (really interesting new gene) finger protein 4] family ubiquitin ligases are RING E3 ligases that regulate the homoeostasis of SUMOylated proteins by promoting their ubiquitylation. In the present paper we report that the RING domain of RNF4 forms a stable dimer, and that dimerization is required for ubiquitin transfer. Our results suggest that the stability of the E2~ubiquitin thioester bond is regulated by RING domain dimerization. PMID:20681948

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

    SciTech Connect

    Mani, Devendra; Arunan, E.

    2014-10-28

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

  2. On the correlation factor of pure polar fluids whose molecules dimerize to nonpolar dimers

    NASA Astrophysics Data System (ADS)

    Mognaschi, E. R.; Laboranti, L. M.; Chierico, A.

    The dipolar correlation of pure polar fluids whose molecules undergo dimerization, resulting in the formation of nonpolar ring dimers and polar monomers in statistical equilibrium, has been studied. Such a system has been treated as a solution of polar molecules (monomers) in an apolar solvent (dimers). This approach allowed us to introduce a new parameter that accounts for the correlation among polar monomers, besides the well known Kirkwood-Fröhlich correlation factor. A relation between the two correlation factors, involving the degree of association, has been established. The above summarized model was applied to the case of five monocarboxylic fatty acids: propionic, n-butyric, n-valeric, caprylic, and pelargonic. On going from high to low molecular mass terms the room temperature static dielectric constant of the considered series of acids increases together with the degree of association, obtained from adiabatic compressibility data on the hypothesis that only dimerization occurs. This behaviour of the static dielectric constant, unexpected on the basis of the decrease of polar monomer density due to the increase of the degree of association, has been interpreted taking into account the dipolar correlation among monomers.

  3. Structural Basis of p75 Transmembrane Domain Dimerization.

    PubMed

    Nadezhdin, Kirill D; García-Carpio, Irmina; Goncharuk, Sergey A; Mineev, Konstantin S; Arseniev, Alexander S; Vilar, Marçal

    2016-06-01

    Dimerization of single span transmembrane receptors underlies their mechanism of activation. p75 neurotrophin receptor plays an important role in the nervous system, but the understanding of p75 activation mechanism is still incomplete. The transmembrane (TM) domain of p75 stabilizes the receptor dimers through a disulfide bond, essential for the NGF signaling. Here we solved by NMR the three-dimensional structure of the p75-TM-WT and the functionally inactive p75-TM-C257A dimers. Upon reconstitution in lipid micelles, p75-TM-WT forms the disulfide-linked dimers spontaneously. Under reducing conditions, p75-TM-WT is in a monomer-dimer equilibrium with the Cys(257) residue located on the dimer interface. In contrast, p75-TM-C257A forms dimers through the AXXXG motif on the opposite face of the α-helix. Biochemical and cross-linking experiments indicate that AXXXG motif is not on the dimer interface of p75-TM-WT, suggesting that the conformation of p75-TM-C257A may be not functionally relevant. However, rather than mediating p75 homodimerization, mutagenesis of the AXXXG motif reveals its functional role in the regulated intramembrane proteolysis of p75 catalyzed by the γ-secretase complex. Our structural data provide an insight into the key role of the Cys(257) in stabilization of the weak transmembrane dimer in a conformation required for the NGF signaling. PMID:27056327

  4. Kinase-mediated quasi-dimers of EGFR

    PubMed Central

    Bublil, Erez M.; Pines, Gur; Patel, Gargi; Fruhwirth, Gilbert; Ng, Tony; Yarden, Yosef

    2010-01-01

    Ligand-induced dimerization of the epidermal growth factor receptor (ErbB-1/EGFR) involves conformational changes that expose an extracellular dimerization interface. Subsequent alterations within the cytoplasmic kinase domain, which culminate in tyrosine phosphorylation, are less understood. Our study addressed this question by using two strategies: a chimeric receptor approach employed ErbB-3, whose defective kinase domain was replaced by the respective part of EGFR. The implanted full-length kinase, unlike its subdomains, conferred dimerization and catalysis. The data infer that the kinase function of EGFR is restrained by the carboxyl tail; once grafted distally to the ectopic tail of ErbB-3, the kinase domain acquires quasi-dimerization and activation. In an attempt to alternatively refold the cytoplasmic tail, our other approach employed kinase inhibitors. Biophysical measurements and covalent cross-linking analyses showed that inhibitors targeting the active conformation of EGFR, in contrast to a compound recognizing the inactive conformation, induce quasi-dimers in a manner similar to the chimeric ErbB-3 molecule. Collectively, these observations unveil kinase domain-mediated quasi-dimers, which are regulated by an autoinhibitory carboxyl tail. On the basis of these observations, we propose that quasi-dimers precede formation of ligand-induced, fully active dimers, which are stabilized by both extracellular and intracellular receptor-receptor interactions.—Bublil, E. M., Pines, G., Patel, G., Fruhwirth, G., Ng, T., Yosef Yarden. Kinase-mediated quasi-dimers of EGFR. PMID:20682838

  5. Villain transformation for ferrimagnetic spin chain with dimerization

    NASA Astrophysics Data System (ADS)

    Yang, Ge; Chen, Yuge; Chen, Bin

    2015-10-01

    The dimerized ferrimagnetic spin chain has been approached both in the presence and absence of the external magnetic field by using the Villain transformation. Two branches of the low-lying energy modes have been presented and the upper branch of the mode demonstrates the exotic omega-shape when the dimerization parameter is greater than 0.6. We also find that the competition between magnetic field and the dimerization parameter also contribute the omega-shape in lower branch mode. Thermodynamic quantities like free energy, specific heat, magnetization, and susceptibility in finite temperature and magnetic field with different dimerization parameters have also been presented.

  6. A Directly Fused Subporphyrin Dimer with a Wavelike Structure.

    PubMed

    Okuda, Yasuhiro; Tsurumaki, Eiji; Oh, Juwon; Sung, Jooyoung; Kim, Dongho; Osuka, Atsuhiro

    2016-08-01

    [Ni(cod)2 ]-mediated intramolecular reductive coupling of β-β' linked meso,meso'-dibromosubporphyrin dimer gave the anti-isomer of meso-meso', β-β' doubly linked subporphyrin dimer as the first example of a fused subporphyrin dimer. The fused dimer 3anti displays an wavelike coplanar structure, a perturbed and red-shifted absorption spectrum, reversible redox behaviors with a decreased electrochemical HOMO-LUMO band gap, and a short S1 -state lifetime owing to the delocalized π-electronic network. PMID:27325499

  7. Dimer-dimer interaction of the bacterial selenocysteine synthase SelA promotes functional active site formation and catalytic specificity

    PubMed Central

    Itoh, Yuzuru; Bröcker, Markus J.; Sekine, Shun-ichi; Söll, Dieter; Yokoyama, Shigeyuki

    2015-01-01

    The 21st amino acid, selenocysteine (Sec), is incorporated translationally into proteins, and is synthesized on its specific tRNA (tRNASec). In Bacteria, the selenocysteine synthase SelA converts Ser-tRNASec, formed by seryl-tRNA synthetase, to Sec-tRNASec. SelA, a member of the fold-type-I pyridoxal 5′-phosphate (PLP)-dependent enzyme superfamily, has an exceptional homodecameric quaternary structure with a molecular mass of about 500 kDa. Our previously determined crystal structures of Aquifex aeolicus SelA complexed with tRNASec revealed that the ring-shaped decamer is composed of pentamerized SelA dimers, with two SelA dimers arranged to collaboratively interact with one Ser-tRNASec. The SelA catalytic site is close to the dimer-dimer interface, but the significance of the dimer-pentamerization in the catalytic site formation remained elusive. In the present study, we examined the quaternary interactions, and demonstrated their importance for SelA activity by systematic mutagenesis. Furthermore, we determined the crystal structures of “depentamerized” SelA variants with mutations at the dimer-dimer interface that prevent pentamerization. These dimeric SelA variants formed a distorted and inactivated catalytic site, and confirmed that the pentamer interactions are essential for productive catalytic site formation. Intriguingly, the conformation of the non-functional active site of dimeric SelA shares structural features with other fold-type-I PLP-dependent enzymes with native dimer or tetramer (dimer-of-dimers) quaternary structures. PMID:24456689

  8. Glassy dislocation dynamics in colloidal dimer crystals

    NASA Astrophysics Data System (ADS)

    Gerbode, Sharon

    2012-02-01

    Dislocation mobility is central to both the mechanical response and the relaxation mechanisms of crystalline materials. Recent experiments have explored the role of novel particle anisotropies in affecting the rules of defect motion in crystals. ``Peanut-shaped'' colloidal dimer particles consisting of two connected spherical lobes form densely packed crystals in 2D. In these ``degenerate crystals,'' the particle lobes occupy triangular lattice sites while the particle axes are randomly oriented among the three crystalline directions. One consequence of the random orientations of the dimers is that dislocation glide is severely limited by certain particle arrangements in the degenerate crystals. Using optical tweezers to manipulate single lobe-sized spherical intruder particles, we locally deform the crystal, creating defects. During subsequent relaxation, the dislocations formed during the deformation leave the crystal grain, either via annihilation with other dislocations or by moving to a grain boundary. Interestingly, in large crystalline grains this dislocation relaxation occurs through a two-stage process reminiscent of slow relaxations in glassy systems, suggesting the novel concept that glassy phenomena may be introduced to certain kinds of colloidal crystals via simple anisotropic constituents.

  9. Rotational Spectrum of Propargyl Alcohol Dimer

    NASA Astrophysics Data System (ADS)

    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.

  10. Fibrillar dimer formation of islet amyloid polypeptides

    DOE PAGESBeta

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

    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 experimentalmore » 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.« less

  11. Salt bridge residues between I-Ak dimer of dimers alpha-chains modulate antigen presentation.

    PubMed

    Yadati, S; Nydam, T; Demian, D; Wade, T K; Gabriel, J L; Barisas, B G; Wade, W F

    1999-03-15

    Class II dimers of dimers are predicted to have functional significance in antigen presentation. The putative contact amino acids of the I-Ak class II dimer of dimers have been identified by molecular modeling based on the DR1 crystal structure (Nydam et al., Int. Immunol. 10, 1237,1998). We have previously reported the role in antigen presentation of dimer of dimers contact amino acids located in the C-terminal domains of the alpha- and beta-chains of class II. Our calculations show that residues Ealpha89 and Ralpha145 in the alpha2-domain form an inter alpha-chain salt bridge between pairs of alphabeta-heterodimers. Other residues, Qalpha92 and Nalpha115, may be involved in close association in that part of the alpha-chain. We investigated the role of these amino acids on class II expression and antigen presentation. Class II composed of an Ealpha89K substituted alpha-chain paired with a wt beta-chain exhibited inhibited antigen presentation and expression of alpha-chain serologic epitopes. In contrast, mutation of Ralpha145E had less affect on antigen presentation and did not affect I-Ak serologic epitopes. Interchanging charges of the salt bridge residues by expressing both Ralpha145E and Ealpha89K on the same chain obviated the large negative effect of the Ealpha89K mutation on antigen presentation but not on the serologic epitopes. Our results are similar for those reported for mutation of DR3's inter-chain salt bridge with the exception that double mutants did not moderate the DR3 defect. Interestingly, the amino acids differences between I-A and DR change the location of the inter-chain salt bridges. In DR1 these residues are located at positions Ealpha88 and Kalpha111; in I-Ak these residues are located at position Ealpha89 and Ralpha145. Inter alpha-chain salt bridges are thus maintained in various class II molecules by amino acids located in different parts of the alpha2-domain. This conservation of structure suggests that considerable functional

  12. Photophysics of rhodamine dimers in Langmuir-Blodgett films

    NASA Astrophysics Data System (ADS)

    Vuorimaa, E.; Ikonen, M.; Lemmetyinen, H.

    1994-11-01

    Temperature dependent dimerization processes of octadecylrhodamine B (RB) and octadecylrhodamine 6G (R6G) in Langmuir-Blodgett (LB) films were studied by steady-state and time-resolved fluorescence methods. The geometry of the dimers in LB films is equal for both dyes, but different to the geometry of the dimers found in solutions. The sandwich-type dimers with lifetimes of 710 ps for RB and 620 ps for R6G have their fluorescence maxima at 635 and 620 nm for RB and R6G, respectively. The dimer with an oblique geometry has its fluorescence maximum at 675 nm for both dyes, and its fluorescence lifetime is 4.6 ns for RB and 4.9 ns for R6G. The proportion of fluorescent dimers increases with decreasing temperature, when the nonfluorescent H dimers reorganize to fluorescent J dimers. The activation energy for this temperature induced process is 1.4 and 2.6 kJ mol -1 for RB and R6G, respectively.

  13. Photophysics of rhodamine dimers in Langmuir-Blodgett films

    NASA Astrophysics Data System (ADS)

    Vuorimaa, E.; Ikonen, M.; Lemmetyinen, H.

    1994-11-01

    Temperature dependent dimerization processes of octadecylrhodamine B (RB) and octadecylrhodamine 6G (R6G) in Langmuir-Blodgett (LB) films were studied by steady-state and time-resolved fluorescence methods. The geometry of the dimers in LB films is equal for both dyes, but different to the geometry of the dimers found in solutions. The sandwich-type dimers with lifetimes of 710 ps for RB and 620 ps for R6G have their fluorescence maxima at 635 and 620 nm for RB and R6G, respectively. The dimer with an oblique geometry has its fluorescence maximum at 675 nm for both dyes, and its fluorescence lifetime is 4.6 ns for RB and 4.9 ns for R6G. The proportion of fluorescent dimers increases with decreasing temperature, when the nonfluorescent H dimers reorganize to fluorescent J dimers. The activation energy for this temperature induced process is 1.4 and 2.6 kJ/mol for RB and R6G, respectively.

  14. 21 CFR 176.120 - Alkyl ketene dimers.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Alkyl ketene dimers. 176.120 Section 176.120 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) INDIRECT FOOD ADDITIVES: PAPER AND PAPERBOARD COMPONENTS Substances for Use Only as Components of Paper and Paperboard § 176.120 Alkyl ketene dimers....

  15. Advantage of Being a Dimer for Serratia marcescens Endonuclease?

    PubMed Central

    Chen, Chuanying; Krause, Kurt; Pettitt, B. Montgomery

    2009-01-01

    The monomer and dimer of the bacterium Serratia marcescens endonuclease (SMnase) are each catalytically active and the two subunits of the dimer function independently of each other. Nature however chooses the dimer form instead of the monomer. In order to explain this, we performed molecular dynamics (MD) simulations of both model built complexes of a subunit of SMnase and the dimer with DNA in aqueous solution. We estimated the electrostatic binding energy, analyzed the distribution and dynamics of water around the complexes, identified water clusters in the protein, and related dynamics of water to the protein's function. We find that the dimer form has an electrostatic advantage over the monomer to associate with DNA. Although Mg2+ remains hexa-coordinated during the simulation, the binding pathway of DNA to Mg2+ changes from inner-sphere binding in the monomer to outer-sphere in the dimer, which may be more energetically favorable. In addition, two water clusters in the active site of each monomer and in the dimer complex were identified and localized in two regions, named ‘stabilizing’ and ‘working’ region. Water in the ‘working’ region in the dimer complex has larger fluctuations than that in the monomer. PMID:19053714

  16. 21 CFR 176.120 - Alkyl ketene dimers.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... HUMAN CONSUMPTION (CONTINUED) INDIRECT FOOD ADDITIVES: PAPER AND PAPERBOARD COMPONENTS Substances for Use Only as Components of Paper and Paperboard § 176.120 Alkyl ketene dimers. Alkyl ketene dimers may be safely used as a component of articles intended for use in producing, manufacturing,...

  17. 21 CFR 176.120 - Alkyl ketene dimers.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... HUMAN CONSUMPTION (CONTINUED) INDIRECT FOOD ADDITIVES: PAPER AND PAPERBOARD COMPONENTS Substances for Use Only as Components of Paper and Paperboard § 176.120 Alkyl ketene dimers. Alkyl ketene dimers may be safely used as a component of articles intended for use in producing, manufacturing,...

  18. Ising and dimer models in two and three dimensions

    NASA Astrophysics Data System (ADS)

    Moessner, R.; Sondhi, S. L.

    2003-08-01

    Motivated by recent interest in 2+1 dimensional quantum dimer models, we revisit Fisher’s mapping of two-dimensional Ising models to hardcore dimer models. First, we note that the symmetry breaking transition of the ferromagnetic Ising model maps onto a non-symmetry breaking transition in dimer language—instead it becomes a deconfinement transition for test monomers. Next, we introduce a modification of Fisher’s mapping in which a second dimer model, also equivalent to the Ising model, is defined on a generically different lattice derived from the dual. In contrast to Fisher’s original mapping, this enables us to reformulate frustrated Ising models as dimer models with positive weights and we illustrate this by providing a new solution of the fully frustrated Ising model on the square lattice. Finally, by means of the modified mapping we show that a large class of three-dimensional Ising models are precisely equivalent, in the time continuum limit, to particular quantum dimer models. As Ising models in three dimensions are dual to Ising gauge theories, this further yields an exact map between the latter and the quantum dimer models. The paramagnetic phase in Ising language maps onto a deconfined, topologically ordered phase in the dimer models. Using this set of ideas, we also construct an exactly soluble quantum eight vertex model.

  19. Disrupting Dimerization Translocates Soluble Epoxide Hydrolase to Peroxisomes

    PubMed Central

    Nelson, Jonathan W.; Das, Anjali J.; Barnes, Anthony P.; Alkayed, Nabil J.

    2016-01-01

    The epoxyeicosatrienoic acid (EET) neutralizing enzyme soluble epoxide hydrolase (sEH) is a neuronal enzyme, which has been localized in both the cytosol and peroxisomes. The molecular basis for its dual localization remains unclear as sEH contains a functional peroxisomal targeting sequence (PTS). Recently, a missense polymorphism was identified in human sEH (R287Q) that enhances its peroxisomal localization. This same polymorphism has also been shown to generate weaker sEH homo-dimers. Taken together, these observations suggest that dimerization may mask the sEH PTS and prevent peroxisome translocation. In the current study, we test the hypothesis that dimerization is a key regulator of sEH subcellular localization. Specifically, we altered the dimerization state of sEH by introducing substitutions in amino acids responsible for the dimer-stabilizing salt-bridge. Green Fluorescent Protein (GFP) fusions of each of mutants were co-transfected into mouse primary cultured cortical neurons together with a PTS-linked red fluorescent protein to constitutively label peroxisomes. Labeled neurons were analyzed using confocal microscopy and co-localization of sEH with peroxisomes was quantified using Pearson’s correlation coefficient. We find that dimer-competent sEH constructs preferentially localize to the cytosol, whereas constructs with weakened or disrupted dimerization were preferentially targeted to peroxisomes. We conclude that the sEH dimerization status is a key regulator of its peroxisomal localization. PMID:27203283

  20. Vertically-oriented nanoparticle dimer based on focused plasmonic trapping.

    PubMed

    Shen, Zhe; Su, Lei; Shen, Yao-Chun

    2016-07-11

    We proposed a vertically-oriented dimer structure based on focused plasmonic trapping of metallic nanoparticle. Quantitative FDTD calculations and qualitative analysis by simplified dipole approximation revealed that localized surface plasmon coupling dominates in the plasmon hybridization, and the vertically-oriented dimer can effectively make use of the dominant longitudinal component of the surface plasmon virtual probe thus providing much stronger electric field in the gap. Furthermore, for practical application the top nanoparticle of the dimer can be replaced with an atomic force microscope tip which enables the precise control of the gap distance of the dimer. Therefore the proposed vertically-oriented dimer structure provides both the scanning capability and the extremely-high electrical field necessary for the high sensitivity Raman imaging. PMID:27410874

  1. Rovibrationally Inelastic Collisions of Ultracold Lithium Dimer

    NASA Astrophysics Data System (ADS)

    Jasmine, William; Stewart, Brian

    2016-05-01

    We have calculated cross sections for rovibrationally inelastic collisions of Li2 A(1) 1Σu+ colliding with neon and xenon on ab initio potentials. We find that the inelastic cross section can be very large and increasing at low collision velocity. This behavior is very well modeled as a Langevin process. The total inelastic cross section is a sizable fraction of the total capture cross section, typically about a third. For Li2 - Xe, the total inelastic rate constants are several thousand square angstroms, and level-to-level rate constants are several hundred square angstroms at collision speeds below 1000 cm/s, implying that such collisions might be observable in photoassociated lithium dimer.

  2. Entanglement and bifurcation in the integrable dimer

    SciTech Connect

    Hou Xiwen; Chen Jinghua; Hu Bambi

    2005-03-01

    In this Brief Report the properties of both dynamical and static entanglement in the integrable quantum dimer are studied in terms of the reduced-density linear entropy and von Neumann entropy with various coupling parameters, total boson numbers, and initial states. The mean entanglement, which is defined to be averaged over time, is used to describe the influence of the classical separatrix on the behavior of entanglement. It is shown that the mean entanglement exhibits a maximum near the position of the corresponding classical separatrix energy and that the static entanglement of the state with the largest eigenvalue of the quantum spectrum displays a maximum near the bifurcation point. For weak coupling and larger total boson number the maximum entanglement state is exactly at the position of the classical separatrix and bifurcation. In strong coupling all initial states have nearly the same mean entanglement.

  3. Integrability of PT-symmetric dimers

    NASA Astrophysics Data System (ADS)

    Pickton, J.; Susanto, H.

    2013-12-01

    The coupled discrete linear and Kerr nonlinear Schrödinger equations with gain and loss describing transport on dimers with parity-time (PT)-symmetric potentials are considered. The model is relevant among others to experiments in optical couplers and proposals on Bose-Einstein condensates in PT-symmetric double-well potentials. It is known that the models are integrable. Here, the integrability is exploited further to construct the phase portraits of the system. A pendulum equation with a linear potential and a constant force for the phase difference between the fields is obtained, which explains the presence of unbounded solutions above a critical threshold parameter. The behavior of all solutions of the system, including changes in the topological structure of the phase plane, is then discussed.

  4. Long- and short-term in vitro D-dimer stability measured with INNOVANCE D-Dimer.

    PubMed

    Böhm-Weigert, M; Wissel, T; Muth, H; Kemkes-Matthes, B; Peetz, D

    2010-02-01

    In vitro D-dimer stability in plasma is widely assumed, but has not yet been documented by systematic studies using samples covering a wide range of D-dimer. We investigated the short- and long-term stability of D-dimer in clinical citrated plasma samples with normal and pathological levels. The short-term stability was analysed by measuring D-dimer fresh, after storage of plasma for 4 hours at room temperature (RT) and after an additional 24 h storage at +2 to +8 degrees C (n=40). Long-term stability samples (n=40) were measured fresh and after storage for 19, 25 and 36 months at < or =-60 degrees C. The effect of repeated freezing was analysed by measuring samples (n=50) fresh and after four consecutive freeze-thaw cycles. D-dimer was measured on the BCS System using the INNOVANCE D-Dimer assay (Siemens Healthcare Diagnostics Products GmbH, Marburg, Germany). D-dimer values at baseline ranged from 0.23-22.2 mg/l FEU. The mean percentage change after storage for 4 hours at RT and additional 24 hours at +2 to +8 degrees C was +3.8% and +2.7%, respectively. The mean percentage change after frozen storage for 19, 25 and 36 months at < or =-60 degrees C was -11.7%, -4.8% and -9.3%, respectively. The small decrease of D-dimer values after frozen storage was not time-dependent. Repeated freezing did not significantly alter D-dimer values (mean change < or =5%). The data demonstrate stability of D-dimer in plasma prior to freezing for up to 4 hours at RT and for up to 24 hours at +2 to +8 degrees C as well as in plasma stored for up to three years at < or =-60 degrees C. PMID:20126827

  5. Dimeric phenalenyl-based neutral radical molecular conductors.

    PubMed

    Chi, X; Itkis, M E; Kirschbaum, K; Pinkerton, A A; Oakley, R T; Cordes, A W; Haddon, R C

    2001-05-01

    We report the preparation, crystallization, and solid-state characterization of ethyl (3)- and butyl (4)-substituted spiro-biphenalenyl radicals. Both of these compounds are found to be conducting face-to-face pi-dimers in the solid state but with different room-temperature magnetic ground states. At room temperature, 4 exists as a diamagnetic pi-dimer (interplanar separation of approximately 3.1 A), whereas 3 is a paramagnetic pi-dimer (interplanar separation of approximately 3.3 A), and both compounds show phase transitions between the paramagnetic and diamagnetic forms. Electrical resistivity measurements of single crystals of 3 and 4 show that the transition from the high-temperature paramagnetic pi-dimer form to the low-temperature diamagnetic pi-dimer structure is accompanied by an increase in conductivity by about 2 orders of magnitude. This behavior is unprecedented and is very difficult to reconcile with the usual understanding of a Peierls dimerization, which inevitably leads to an insulating ground state. We tentatively assign the enhancement in the conductivity to a decrease in the on-site Coulombic correlation energy (U), as the dimers form a super-molecule with twice the amount of conjugation. PMID:11457155

  6. The Talin Dimer Structure Orientation Is Mechanically Regulated

    PubMed Central

    Golji, Javad; Mofrad, Mohammad R.K.

    2014-01-01

    Formation of a stable cell-substrate contact can be regulated by mechanical force, especially at the focal adhesion. Individual proteins that make up the focal adhesions, such as talin, can exhibit mechanosensing. We previously described one mode of talin mechanosensing in which the vinculin-binding site of talin is exposed after force-induced stretch of a single talin rod domain. Here, we describe a second mode of talin mechanosensing in which the talin dimer itself can adopt different orientations in response to mechanical stimulation. Using molecular dynamics models, we demonstrate that the C-terminus region of the talin dimer is flexible mainly at the linker between the dimerization helices and the nearby actin-binding helical bundle. Our molecular dynamics simulations reveal two possible orientations of the talin dimer at its C-terminus. The extracellular matrix (ECM)-bound integrins cross-linked by talin can be forced apart leading to an elongated orientation of the talin dimer, and the ECM-bound integrins can be forced together by the ECM producing a collapsed orientation of the talin dimer. Formation of the elongated orientation is shown to be more favorable. Switching between the two talin dimer orientations constitutes a mode of mechanosensing. PMID:25418161

  7. A dimeric form of prothrombin on membrane surfaces.

    PubMed Central

    Anderson, P J

    1998-01-01

    Blood coagulation requires the conversion of zymogens to active enzymes. These reactions are facilitated by Ca2+-dependent protein binding to membrane surfaces containing anionic phospholipids. Here it is shown that only in the presence of both Ca2+ and phospholipid vesicles composed of phosphatidylcholine and phosphatidylserine can a prothrombin dimer be chemically cross-linked. A cross-linker containing evenly spaced reactive groups was prepared by activating the carboxy groups of a ten-residue glutamic acid peptide and allowed to react with physiological concentrations of prothrombin. When Ca2+ and anionic phospholipids were both present during exposure to the cross-linker, it was found that more than 50% of the prothrombin was trapped as a chemically defined dimer with reaction times of the order of 1 min. The dimer yield remained high even when reactions were performed at high phospholipid-to-protein ratios at protein concentrations an order of magnitude less than physiological. Amino acid sequencing of a CNBr peptide produced from the purified dimer localized the cross-link to residues Lys341 and Lys427 of prothrombin. The specificity and high yield under mild conditions of the cross-linking suggest that dimeric membrane bound prothrombin might be a physiologically relevant substrate for the formation of thrombin. Prothrombinase converts this modified protein to an enzyme that catalyses the hydrolysis of a thrombin chromogenic substrate as efficiently as thrombin and is inhibited by a thrombin active-site directed inhibitor, but is a thrombin dimer. The thrombin dimer has impaired activity compared with thrombin with respect to physiological functions requiring binding to exosite I. A model based on the known structure of thrombin is presented that can account for the prothrombin dimer and the properties of the dimeric thrombin formed from it. PMID:9841875

  8. Electric and magnetic hotspots in dielectric nanowire dimers.

    PubMed

    Mirzaei, Ali; Miroshnichenko, Andrey E

    2015-04-14

    We study the formation of the electric and magnetic near-field hotspots in dielectric cylindrical dimers. We compare dielectric and metallic dimers by using experimental data for all materials and consider both TM and TE polarizations of light. We demonstrate that dielectric dimers allow us to simultaneously achieve pure magnetic and electric near-field hotspots for both polarizations in contrast to plasmonic structures. This offers new approaches for near-field engineering such as sensing, control of spontaneous emission, and enhanced Raman scattering. PMID:25773044

  9. Dynamic combinatorial enrichment of polyconformational D-/L-peptide dimers.

    PubMed

    Jadhav, Kirtikumar B; Lichtenecker, Roman J; Bullach, Anke; Mandal, Bhubaneswar; Arndt, Hans-Dieter

    2015-04-01

    D-/L-peptides such as gramicidin A (gA) adopt unique dimeric β-helical structures of different topologies. To overcome their conformational promiscuity and enrich individual components, a dynamic combinatorial approach assisted by thiol tags was developed. This method led to identification of the preferential formation of antiparallel dimers under a broad range of conditions, which was independent of peptide side-chain polarity. Exclusive formation of an antiparallel cyclic dimer was achieved in the presence of cesium ions. PMID:25711604

  10. Asymmetric and connected graphene dimers for a tunable plasmonic response

    NASA Astrophysics Data System (ADS)

    Rosolen, G.; Maes, B.

    2015-11-01

    We investigate the infrared response of graphene dimers with various doping and polarization configurations. The interaction between the plasmonic resonances of graphene nanodisks leads to a rich, tunable behavior. The hybridization of the nanodisk modes enables the excitation of resonances that would be invisible or dark in a single disk. The simulation results show various anticrossings that depend on dark-bright or bright-bright mode coupling, which we can describe via a simple Hamiltonian model. In addition, we determine the response of a dimer bridged by a tunable graphene junction. This structure leads to charge transfer plasmons, with an even higher absorption efficiency and tunability than nonbridged dimers.

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

    PubMed Central

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

    2016-01-01

    In this work, the timescales and mechanisms associated with the structural dynamics of butadiyne-linked porphyrin dimers are investigated through time resolved narrowband pump/broadband probe transient absorption spectroscopy. Our results confirm previous findings that the broadening is partly due to a distribution of structures with different (dihedral) angular conformations. Comparison of measurements with excitations on the red and blue sides of the Q-band unravel the ground and excited state conformational re-equilibration timescales. Further comparison to a planarized dimer, through the addition of a ligand, provides conclusive evidence for the twisting motion performed by the porphyrin dimer in solution. PMID:26798839

  12. Adsorption of silver dimer on graphene - A DFT study

    SciTech Connect

    Kaur, Gagandeep; Gupta, Shuchi; Rani, Pooja; Dharamvir, Keya

    2014-04-24

    We performed a systematic density functional theory (DFT) study of the adsorption of silver dimer (Ag{sub 2}) on graphene using SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) package, in the generalized gradient approximation (GGA). The adsorption energy, geometry, and charge transfer of Ag2-graphene system are calculated. The minimum energy configuration for a silver dimer is parallel to the graphene sheet with its two atoms directly above the centre of carbon-carbon bond. The negligible charge transfer between the dimer and the surface is also indicative of a weak bond. The methodology demonstrated in this paper may be applied to larger silver clusters on graphene sheet.

  13. Anisotropic dynamics in a shaken granular dimer gas experiment

    NASA Astrophysics Data System (ADS)

    Atwell, J.; Olafsen, J. S.

    2005-06-01

    The dynamics, velocity fluctuations, and particle-plate interactions for a two-dimensional granular gas of shaken, nonspherical particles are studied experimentally. The experiment consists of a horizontal plate that is vertically oscillated to drive the dynamics of macroscopic dimers, spherical pairs that are loosely connected by a rod that couple the interaction each of the spheres has with the shaking plate. The extended nature of the particles results in more than one energy-momentum transfer between the plate and each dimer per shaking cycle. This complex interaction results in anisotropic behavior for the dimer that is a function of the shaking parameters.

  14. Human white blood cells contain cyclobutyl pyrimidine dimer photolyase

    SciTech Connect

    Sutherland, B.M.; Bennett, P.V.

    1995-10-10

    Although enzymatic photoreactivation of cyclobutyl pyrimidine dimers in DNA is present in almost all organisms, its presence in placental mammals is controversial. We tested human white blood cells for photolyase by using three defined DNAs (suprecoiled pET-2, nonsupercoiled bacteriphage {lambda}, and a defined-sequence 287-bp oligonucleotide), two dimer-specific endonucleases (T4 endonuclease V and UV endonuclease from Micrococcus luteus), and three assay methods. We show that human white blood cells contain photolyase that can photorepair pyrimidine dimers in defined supercoiled and linear DNAs and in a 287-bp oligonucleotide and that human photolyase is active on genomic DNA in intact human cells. 44 refs., 3 figs.

  15. BH3-in-groove dimerization initiates and helix 9 dimerization expands Bax pore assembly in membranes.

    PubMed

    Zhang, Zhi; Subramaniam, Sabareesh; Kale, Justin; Liao, Chenyi; Huang, Bo; Brahmbhatt, Hetal; Condon, Samson G F; Lapolla, Suzanne M; Hays, Franklin A; Ding, Jingzhen; He, Feng; Zhang, Xuejun C; Li, Jianing; Senes, Alessandro; Andrews, David W; Lin, Jialing

    2016-01-18

    Pro-apoptotic Bax induces mitochondrial outer membrane permeabilization (MOMP) by forming oligomers through a largely undefined process. Using site-specific disulfide crosslinking, compartment-specific chemical labeling, and mutational analysis, we found that activated integral membrane Bax proteins form a BH3-in-groove dimer interface on the MOM surface similar to that observed in crystals. However, after the α5 helix was released into the MOM, the remaining interface with α2, α3, and α4 helices was rearranged. Another dimer interface was formed inside the MOM by two intersected or parallel α9 helices. Combinations of these interfaces generated oligomers in the MOM. Oligomerization was initiated by BH3-in-groove dimerization, without which neither the other dimerizations nor MOMP occurred. In contrast, α9 dimerization occurred downstream and was required for release of large but not small proteins from mitochondria. Moreover, the release of large proteins was facilitated by α9 insertion into the MOM and localization to the pore rim. Therefore, the BH3-in-groove dimerization on the MOM nucleates the assembly of an oligomeric Bax pore that is enlarged by α9 dimerization at the rim. PMID:26702098

  16. CLEC-2 activates Syk through dimerization.

    PubMed

    Hughes, Craig E; Pollitt, Alice Y; Mori, Jun; Eble, Johannes A; Tomlinson, Michael G; Hartwig, John H; O'Callaghan, Christopher A; Fütterer, Klaus; Watson, Steve P

    2010-04-01

    The C-type lectin receptor CLEC-2 activates platelets through Src and Syk tyrosine kinases, leading to tyrosine phosphorylation of downstream adapter proteins and effector enzymes, including phospholipase-C gamma2. Signaling is initiated through phosphorylation of a single conserved tyrosine located in a YxxL sequence in the CLEC-2 cytosolic tail. The signaling pathway used by CLEC-2 shares many similarities with that used by receptors that have 1 or more copies of an immunoreceptor tyrosine-based activation motif, defined by the sequence Yxx(L/I)x(6-12)Yxx(L/I), in their cytosolic tails or associated receptor chains. Phosphorylation of the conserved immunoreceptor tyrosine-based activation motif tyrosines promotes Syk binding and activation through binding of the Syk tandem SH2 domains. In this report, we present evidence using peptide pull-down studies, surface plasmon resonance, quantitative Western blotting, tryptophan fluorescence measurements, and competition experiments that Syk activation by CLEC-2 is mediated by the cross-linking through the tandem SH2 domains with a stoichiometry of 2:1. In support of this model, cross-linking and electron microscopy demonstrate that CLEC-2 is present as a dimer in resting platelets and converted to larger complexes on activation. This is a unique mode of activation of Syk by a single YxxL-containing receptor. PMID:20154219

  17. Smectic Phase Formed by DNA Dimers

    NASA Astrophysics Data System (ADS)

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

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

  18. Spin Dimers: from BEC to Luttinger liquids

    NASA Astrophysics Data System (ADS)

    Giamarchi, Thierry

    2011-03-01

    Localized spin systems, and in particular dimer systems, provide a fantastic laboratory to study the interplay between quantum effects and the interaction between excitations. Magnetic field and temperature allow an excellent control on the density of excitations and various very efficient probes such as neutrons and NMR are available. They can thus be used as ``quantum simulators'' to tackle with great success questions that one would normally search in itinerant interacting quantum systems. In particular they have provided excellent realizations of Bose-Einstein condensates [1,2]. This allowed not only to probe the properties of interacting bosons in a variety of dimensions but also to study in a controlled way additional effects such as disorder. If the dimensionality is reduced they also allow to test in a quantitative way Luttinger liquid physics [3,4,5]. I will discuss these various cases, and show that we have now good theoretical tools to make quantitative comparisons with the experiments. Finally, how to go from this low dimensional case where the spins behave essentially as fermions, to the higher dimensional case where they behave as (essentially free) bosons, is a very challenging, and experimentally relevant issue. This work was supported in part by the Swiss SNF under MaNEP and division II.

  19. Tensor renormalization group approach to classical dimer models

    NASA Astrophysics Data System (ADS)

    Roychowdhury, Krishanu; Huang, Ching-Yu

    2015-05-01

    We analyze classical dimer models on a square and a triangular lattice using a tensor network representation of the dimers. The correlation functions are numerically calculated using the recently developed "tensor renormalization group" (TRG) technique. The partition function for the dimer problem can be calculated exactly by the Pfaffian method, which is used here as a platform for comparing the numerical results. The TRG approach turns out to be a powerful tool for describing gapped systems with exponentially decaying correlations very efficiently due to its fast convergence. This is the case for the dimer model on the triangular lattice. However, the convergence becomes very slow and unstable in the case of the square lattice where the model has algebraically decaying correlations. We highlight these aspects with numerical simulations and critically appraise the robustness of the TRG approach by contrasting the results for small and large system sizes against the exact calculations. Furthermore, we benchmark our TRG results with the classical Monte Carlo method.

  20. Sodium dimers on the surface of liquid {sup 4}He

    SciTech Connect

    Ancilotto, F.; DeToffol, G.; Toigo, F.

    1995-12-01

    We have studied the structure of a sodium dimer interacting with liquid {sup 4}He. We calculated the equilibrium configuration and binding energy of a Na{sub 2} molecule solvated in a bulk liquid {sup 4}He ``bubble`` and near the liquid-vapor interface ``dimple`` by using a density-functional approach. We find that the solvated molecule is a metastable state, while the the lowest energy bound state occurs when the molecule lies flat on the surface of the liquid. The binding energy for the ``erect`` dimer is only {similar_to}1 K higher than the flat dimer, with no potential energy barrier between the two orientations, implying relatively free rotations of the molecule on the surface. The small effects of the liquid environment on the vibrational properties of the dimer are investigated.

  1. Non-stripe charge order in dimerized organic conductors

    NASA Astrophysics Data System (ADS)

    Mori, Takehiko

    2016-06-01

    This paper demonstrates charge order is important in dimerized β - and κ -phase organic conductors similar to the uniform θ - and α -phase conductors. Here the magnitude of the dimerization represents the deviation from the ideal triangular lattice in analogy with the anisotropy in the θ phase. Since the ratio of the intradimer transfer integral to the interdimer transfer integral is as large as ˜2.6 , these dimerized phases lead to a dimer Mott insulator, whereas the Coulomb repulsion is closer to the triangular lattice because the ratio of the intradimer Coulomb repulsion to the interdimer Coulomb repulsion is comparatively small (˜1.7 ). Accordingly, in the static-limit calculation, non-stripe charge order with threefold periodicity appears between the uniform and the stripe phases, and the analogy with the θ phase suggests the first-order nature of the metal-insulator transition.

  2. Emission of dimers from a free surface of heated water

    NASA Astrophysics Data System (ADS)

    Bochkarev, A. A.; Polyakova, V. I.

    2014-09-01

    The emission rate of water dimers from a free surface and a wetted solid surface in various cases was calculated by a simplified Monte Carlo method with the use of the binding energy of water molecules. The binding energy of water molecules obtained numerically assuming equilibrium between the free surface of water and vapor in the temperature range of 298-438 K corresponds to the coordination number for liquid water equal to 4.956 and is close to the reference value. The calculation results show that as the water temperature increases, the free surface of water and the wetted solid surface become sources of free water dimers. At a temperature of 438 K, the proportion of dimers in the total flow of water molecules on its surface reaches 1%. It is found that in the film boiling mode, the emission rate of dimers decreases with decreasing saturation vapor. Two mechanisms of the emission are described.

  3. Glassy dislocation dynamics in 2D colloidal dimer crystals.

    PubMed

    Gerbode, Sharon J; Agarwal, Umang; Ong, Desmond C; Liddell, Chekesha M; Escobedo, Fernando; Cohen, Itai

    2010-08-13

    Although glassy relaxation is typically associated with disorder, here we report on a new type of glassy dynamics relating to dislocations within 2D crystals of colloidal dimers. Previous studies have demonstrated that dislocation motion in dimer crystals is restricted by certain particle orientations. Here, we drag an optically trapped particle through such dimer crystals, creating dislocations. We find a two-stage relaxation response where initially dislocations glide until encountering particles that cage their motion. Subsequent relaxation occurs logarithmically slowly through a second process where dislocations hop between caged configurations. Finally, in simulations of sheared dimer crystals, the dislocation mean squared displacement displays a caging plateau typical of glassy dynamics. Together, these results reveal a novel glassy system within a colloidal crystal. PMID:20868079

  4. Highly tunable gold nanorod dimer resonances mediated through conductive junctions

    NASA Astrophysics Data System (ADS)

    Fontana, Jake; Ratna, Banahalli

    2015-03-01

    Tailoring the resonant frequency in plasmonic nanostructures is critical to developing disruptive metamaterial technologies. Here we numerically study the optical properties of gold nanorod dimers connected end-to-end by a thin metallic bridge. We find the resonant frequency along the long axis of the dimer shifts linearly with the nanorod aspect ratio behaving as it was a single nanorod with an aspect ratio nearly an order of magnitude larger. We show by controlling the material and geometry of the connecting bridge the effective depolarization factor of the dimer is significantly modulated tuning the resonant frequency over a decade, from 1 to 10 μm. We present an alternative description for the emergence and behavior of the dimer resonance using a straightforward ``Drude-like'' model and self-assembly experiments creating such structures.

  5. Dimer model for Tau proteins bound in microtubule bundles

    NASA Astrophysics Data System (ADS)

    Hall, Natalie; Kluber, Alexander; Hayre, N. Robert; Singh, Rajiv; Cox, Daniel

    2013-03-01

    The microtubule associated protein tau is important in nucleating and maintaining microtubule spacing and structure in neuronal axons. Modification of tau is implicated as a later stage process in Alzheimer's disease, but little is known about the structure of tau in microtubule bundles. We present preliminary work on a proposed model for tau dimers in microtubule bundles (dimers are the minimal units since there is one microtubule binding domain per tau). First, a model of tau monomer was created and its characteristics explored using implicit solvent molecular dynamics simulation. Multiple simulations yield a partially collapsed form with separate positively/negatively charged clumps, but which are a factor of two smaller than required by observed microtubule spacing. We argue that this will elongate in dimer form to lower electrostatic energy at a cost of entropic ``spring'' energy. We will present preliminary results on steered molecular dynamics runs on tau dimers to estimate the actual force constant. Supported by US NSF Grant DMR 1207624.

  6. Copper-Catalyzed Dimerization/Cyclization of Itaconates.

    PubMed

    Li, Zhiqiang; Li, Ruirui; Jiang, Lan; Li, Zhengning

    2015-01-01

    A copper-catalyzed domino reaction between itaconate esters and diethyl zinc (or silane) is developed, affording itaconate dimerization products, multi-ester-substituted cyclopentanones, in moderate to high yields. PMID:26287154

  7. Superconductivity in the liquid-dimer valence-bond state

    SciTech Connect

    Ioffe, L.B.; Larkin, A.I. )

    1989-10-01

    Introducing an unambiguous prescription which converts singlet dimers into quasidipoles, we describe the low-energy excitations in the liquid-dimer state as fluctuations of the average dipole moment. The exchange of these fluctuations leads to a long-range interaction between holes in this state. This interaction favors the two-particle Bose condensate and destroys the order parameter of the one-particle Bose condensate even at zero temperature.

  8. Synthesis and fluxional behaviour of novel chloroborole dimers.

    PubMed

    Zhang, Zuolun; Wang, Zheng; Haehnel, Martin; Eichhorn, Antonius; Edkins, Robert M; Steffen, Andreas; Krueger, Anke; Lin, Zhenyang; Marder, Todd B

    2016-08-11

    The (B-Cl)-chloroboroles 2-chloro-1,3-di(4-R-phenyl)-2,4,5,6-tetra-hydrocyclopenta[c]borole (R = H, Br) undergo a novel dimerisation process in CH2Cl2 solution. The resulting unsymmetric dimers are highly fluxional in solution via reversible enantiomerisation through an intermediate with mirror symmetry. DFT calculations suggest an unusual dimerisation mechanism and provide insight into the dynamics of the dimers. PMID:27405535

  9. Absorption cross sections of the ClO dimer

    NASA Technical Reports Server (NTRS)

    Huder, K. J.; DeMore, W. B.

    1995-01-01

    The absorption cross sections of the ClO dimer, ClOOCl, are important to the photochemistry of ozone depletion in the Antarctic. In this work, new measurements were made of the dimer cross sections at 195 K. the results yield somewhat lower values in the long wavelength region, compared to those currently recommended in the NASA data evaluation (JPL 94-26). The corresponding solar photodissociation rates in the Antarctic are reduced by about 40%.

  10. Structural Determinants Underlying Constitutive Dimerization of Unoccupied Human Follitropin Receptors

    PubMed Central

    Guan, Rongbin; Wu, Xueqing; Feng, Xiuyan; Zhang, Meilin; Hébert, Terence E.; Segaloff, Deborah L.

    2009-01-01

    The human follitropin receptor (hFSHR) is a G protein-coupled receptor (GPCR) central to reproductive physiology that is composed of an extracellular domain (ECD) fused to a serpentine region. Using bioluminescence resonance energy transfer (BRET) in living cells, we show that hFSHR dimers form constitutively during their biosynthesis. Mutations in TM1 and TM4 had no effect on hFSHR dimerization, alone or when combined with mutation of Tyr110 in the ECD, a residue predicted to mediate dimerization of the soluble hormone-binding portion of the ECD complexed with FSH (Q. Fan and W. Hendrickson, Nature 433:269–277, 2005). Expressed individually, the serpentine region and a membrane-anchored form of the hFSHR ECD each exhibited homodimerization, suggesting that both domains contribute to dimerization of the full-length receptor. However, even in the context of only the membrane-anchored ECD, mutation of Tyr110 to alanine did not inhibit dimerization. The full-length hFSHR and the membrane-anchored ECD were then each engineered to introduce a consensus site for N-linked glycosylation at residue 110. Despite experimental validation of the presence of carbohydrate on residue 110, we failed to observe disruption of dimerization of either the full-length hFSHR or membrane-anchored ECD containing the inserted glycan wedge. Taken altogether, our data suggest that both the serpentine region and the ECD contribute to hFSHR dimerization and that the dimerization interface of the unoccupied hFSHR does not involve Tyr110 of the ECD. PMID:19800402

  11. VUV spectroscopy of rare gas van der Waals dimers

    SciTech Connect

    Dehmer, Patricia M.; Pratt, Stephen T.

    1982-08-01

    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 Ar2, Kr2, Xe2, NeAr, NeKr, NeXe, ArKr, ArXe, and KrXe. Of the remaining dimer species (Ne2 and the Herare gas dimers), only Ne2 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. Human Erythropoietin Dimers with Markedly Enhanced in vivo Activity

    NASA Astrophysics Data System (ADS)

    Sytkowski, Arthur J.; Dotimas Lunn, Elizabeth; Davis, Kerry Lynn; Feldman, Laurie; Siekman, Suvia

    1998-02-01

    Human erythropoietin, a widely used and important therapeutic glycoprotein, has a relatively short plasma half-life due to clearance by glomerular filtration as well as by other mechanisms. We hypothesized that an erythropoietin species with a larger molecular size would exhibit an increased plasma half-life and, potentially, an enhanced biological activity. We now report the production of biologically active erythropoietin dimers and trimers by chemical crosslinking of the conventional monomeric form. We imparted free sulfhydryl residues to a pool of erythropoietin monomer by chemical modification. A second pool was reacted with another modifying reagent to yield monomer with male-imido groups. Upon mixing these two pools, covalently linked dimers and trimers were formed that were biologically active in vitro. The plasma half-life of erythropoietin dimers in rabbits was >24 h compared with 4 h for the monomers. Importantly, erythropoietin dimers were biologically active in vivo as shown by their ability to increase the hematocrits of mice when injected subcutaneously. In addition, the dimers exhibited >26-fold higher activity in vivo than did the monomers and were very effective after only one dose. Dimeric and other oligomeric forms of Epo may have an important role in therapy.

  13. Cholesterol-dependent Conformational Plasticity in GPCR Dimers

    PubMed Central

    Prasanna, Xavier; Sengupta, Durba; Chattopadhyay, Amitabha

    2016-01-01

    The organization and function of the serotonin1A receptor, an important member of the GPCR family, have been shown to be cholesterol-dependent, although the molecular mechanism is not clear. We performed a comprehensive structural and dynamic analysis of dimerization of the serotonin1A receptor by coarse-grain molecular dynamics simulations totaling 3.6 ms to explore the molecular details of its cholesterol-dependent association. A major finding is that the plasticity and flexibility of the receptor dimers increase with increased cholesterol concentration. In particular, a dimer interface formed by transmembrane helices I-I was found to be sensitive to cholesterol. The modulation of dimer interface appears to arise from a combination of direct cholesterol occupancy and indirect membrane effects. Interestingly, the presence of cholesterol at the dimer interface is correlated with increased dimer plasticity and flexibility. These results represent an important step in characterizing the molecular interactions in GPCR organization with potential relevance to therapeutic interventions. PMID:27535203

  14. Dimerization of Bacterial Diaminopimelate Decarboxylase Is Essential for Catalysis.

    PubMed

    Peverelli, Martin G; Soares da Costa, Tatiana P; Kirby, Nigel; Perugini, Matthew A

    2016-04-29

    Diaminopimelate decarboxylase (DAPDC) catalyzes the final step in the diaminopimelate biosynthesis pathway of bacteria. The product of the reaction is the essential amino acid l-lysine, which is an important precursor for the synthesis of the peptidoglycan cell wall, housekeeping proteins, and virulence factors of bacteria. Accordingly, the enzyme is a promising antibacterial target. Previous structural studies demonstrate that DAPDC exists as monomers, dimers, and tetramers in the crystal state. However, the active oligomeric form has not yet been determined. We show using analytical ultracentrifugation, small angle x-ray scattering, and enzyme kinetic analyses in solution that the active form of DAPDC from Bacillus anthracis, Escherichia coli, Mycobacterium tuberculosis, and Vibrio cholerae is a dimer. The importance of dimerization was probed further by generating dimerization interface mutants (N381A and R385A) of V. cholerae DAPDC. Our studies indicate that N381A and R385A are significantly attenuated in catalytic activity, thus confirming that dimerization of DAPDC is essential for function. These findings provide scope for the development of new antibacterial agents that prevent DAPDC dimerization. PMID:26921318

  15. Mechanism of dimerization of the human melanocortin 1 receptor

    SciTech Connect

    Zanna, Paola T.; Sanchez-Laorden, Berta L.; Perez-Oliva, Ana B.; Turpin, Maria C.; Herraiz, Cecilia; Jimenez-Cervantes, Celia; Garcia-Borron, Jose C.

    2008-04-04

    The melanocortin 1 receptor (MC1R) is a dimeric G protein-coupled receptor expressed in melanocytes, where it regulates the amount and type of melanins produced and determines the tanning response to ultraviolet radiation. We have studied the mechanisms of MC1R dimerization. Normal dimerization of a deleted mutant lacking the seventh transmembrane fragment and the C-terminal cytosolic extension excluded coiled-coil interactions as the basis of dimerization. Conversely, the electrophoretic pattern of wild type receptor and several Cys {yields} Ala mutants showed that four disulfide bonds are established between the monomers. Disruption of any of these bonds abolished MC1R function, but only the one involving Cys35 was essential for traffic to the plasma membrane. A quadruple Cys35-267-273-275Ala mutant migrating as a monomer in SDS-PAGE in the absence of reducing agents was able to dimerize with WT, suggesting that in addition to disulfide bond formation, dimerization involves non-covalent interactions, likely of domain swap type.

  16. Conformational stability of dimeric proteins: quantitative studies by equilibrium denaturation.

    PubMed Central

    Neet, K. E.; Timm, D. E.

    1994-01-01

    The conformational stability of dimeric globular proteins can be measured by equilibrium denaturation studies in solvents such as guanidine hydrochloride or urea. Many dimeric proteins denature with a 2-state equilibrium transition, whereas others have stable intermediates in the process. For those proteins showing a single transition of native dimer to denatured monomer, the conformational stabilities, delta Gu (H2O), range from 10 to 27 kcal/mol, which is significantly greater than the conformational stability found for monomeric proteins. The relative contribution of quaternary interactions to the overall stability of the dimer can be estimated by comparing delta Gu (H2O) from equilibrium denaturation studies to the free energy associated with simple dissociation in the absence of denaturant. In many cases the large stabilization energy of dimers is primarily due to the intersubunit interactions and thus gives a rationale for the formation of oligomers. The magnitude of the conformational stability is related to the size of the polypeptide in the subunit and depends upon the type of structure in the subunit interface. The practical use, interpretation, and utility of estimation of conformational stability of dimers by equilibrium denaturation methods are discussed. PMID:7756976

  17. Specific dimerization of the light chains of human immunoglobulin.

    PubMed

    Stevenson, G T; Straus, D

    1968-07-01

    1. The light chains of human immunoglobulin were allowed to dimerize in vitro on removal of the dispersing agents acetic acid or urea. 2. On electrophoresis in polyacrylamide gel at pH8.8 the dimers yielded up to nine regularly spaced bands. This approximates to the number of electrophoretic components known to occur among the monomers. 3. Single electrophoretic components of the dimers were isolated from the gel, dissociated into monomers, and subjected as such to electrophoresis in urea-containing gels. Each gave two adjacent bands. 4. Similarly, after all the light chains as monomers had been subjected to electrophoresis in urea-containing gels, single electrophoretic components were isolated and allowed to dimerize. When examined now as dimers in the absence of urea, each component gave two adjacent bands. 5. These findings are explicable on the following basis. (a) The dimerization of the light chains is specific, at least inasmuch as it occurs between monomers of the same electrophoretic mobilities. (b) With the buffer constant, different light chains undergo different changes in net charge on being transferred from urea-containing to urea-free solution; in this way two different chains of the same initial charge can acquire a charge difference of 1. 6. Experiments with Bence-Jones proteins and other homogeneous light chains gave results substantiating the conclusions (a) and (b). PMID:4174431

  18. Covalently dimerized SecA is functional in protein translocation.

    PubMed

    de Keyzer, Jeanine; van der Sluis, Eli O; Spelbrink, Robin E J; Nijstad, Niels; de Kruijff, Ben; Nouwen, Nico; van der Does, Chris; Driessen, Arnold J M

    2005-10-21

    The ATPase SecA provides the driving force for the transport of secretory proteins across the cytoplasmic membrane of Escherichia coli. SecA exists as a dimer in solution, but the exact oligomeric state of SecA during membrane binding and preprotein translocation is a topic of debate. To study the requirements of oligomeric changes in SecA during protein translocation, a non-dissociable SecA dimer was formed by oxidation of the carboxyl-terminal cysteines. The cross-linked SecA dimer interacts with the SecYEG complex with a similar stoichiometry as non-cross-linked SecA. Cross-linking reversibly disrupts the SecB binding site on SecA. However, in the absence of SecB, the activity of the disulfide-bonded SecA dimer is indistinguishable from wild-type SecA. Moreover, SecYEG binding stabilizes a cold sodium dodecylsulfate-resistant dimeric state of SecA. The results demonstrate that dissociation of the SecA dimer is not an essential feature of the protein translocation reaction. PMID:16115882

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

    SciTech Connect

    Aravind, G.; Klaerke, B.; Rajput, J.; Toker, Y.; Andersen, L. H.; Bochenkova, A. V.; Antoine, R.; Racaud, A.; Dugourd, P.; Lemoine, J.

    2012-01-07

    Photodissociation lifetimes and fragment channels of gas-phase, protonated YA{sub n} (n = 1,2) peptides and their dimers were measured with 266 nm photons. The protonated monomers were found to have a fast dissociation channel with an exponential lifetime of {approx}200 ns while the protonated dimers show an additional slow dissociation component with a lifetime of {approx}2 {mu}s. Laser power dependence measurements enabled us to ascribe the fast channel in the monomer and the slow channel in the dimer to a one-photon process, whereas the fast dimer channel is from a two-photon process. The slow (1 photon) dissociation channel in the dimer was found to result in cleavage of the H-bonds after energy transfer through these H-bonds. In general, the dissociation of these protonated peptides is non-prompt and the decay time was found to increase with the size of the peptides. Quantum RRKM calculations of the microcanonical rate constants also confirmed a statistical nature of the photodissociation processes in the dipeptide monomers and dimers. The classical RRKM expression gives a rate constant as an analytical function of the number of active vibrational modes in the system, estimated separately on the basis of the equipartition theorem. It demonstrates encouraging results in predicting fragmentation lifetimes of protonated peptides. Finally, we present the first experimental evidence for a photo-induced conversion of tyrosine-containing peptides into monocyclic aromatic hydrocarbon along with a formamide molecule both found in space.

  20. Integrability and conformal data of the dimer model

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  1. Designer interface peptide grafts target estrogen receptor alpha dimerization.

    PubMed

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

    2016-09-01

    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. PMID:27462021

  2. D-dimer as a Biomarker for Acute Aortic Dissection

    PubMed Central

    Cui, Jia-sen; Jing, Zai-ping; Zhuang, Shun-jiu; Qi, Shao-hong; Li, Li; Zhou, Jun-wen; Zhang, Wang; Zhao, Yun; Qi, Ning; Yin, Yang-jun

    2015-01-01

    Abstract To perform a meta-analysis and examine the use of D-dimer levels for diagnosing acute aortic dissection (AAD). Medline, Cochrane, EMBASE, and Google Scholar were searched until April 23, 2014, using the following search terms: biomarker, acute aortic dissection, diagnosis, and D-dimer. Inclusion criteria were diagnosis of acute aortic dissection, D-dimer levels obtained, 2-armed study. Outcome measures were the accuracy, sensitivity, specificity, positive predictive value, and negative predictive value of D-dimer level for the diagnosis of AAD. Sensitivity analysis was performed using the leave-one-out approach. Of 34 articles identified, 5 met the inclusion criteria and were included in the analysis. The age of participants was similar between treatments within studies. The number of AAD patients ranged from 16 to 107 (total = 274), and the number of control group patients ranged from 32 to 206 (total = 469). The pooled sensitivity of D-dimer levels in AAD patients was 94.5% (95% confidence interval [CI] 78.1%–98.8%, P < 0.001), and the specificity was 69.1% (95% CI 43.7%–86.5%, P = 0.136). The pooled area under the receiver-operating characteristic curve for D-dimer levels in AAD patients was 0.916 (95% CI 0.863–0.970, P < 0.001). The direction and magnitude of the combined estimates did not change markedly with the exclusion of individual studies, indicating the meta-analysis had good reliability. D-dimer levels are best used for ruling out AAD in patients with low likelihood of the disease. PMID:25634194

  3. Dimerization in Highly Concentrated Solutions of Phosphoimidazolide Activated Mononucleotides

    NASA Technical Reports Server (NTRS)

    Kanavarioti, Anastassia

    1997-01-01

    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-MelmpU and 2-MelmpC produce about 65% of oligomers including 4% of the 3',5'-Iinked 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 intemucleotide linked dimers is enhanced as a function of initial monomer concentration, pyrophosphate dimer yields remain practically unchanged at about 20% for 2-MelmpU, 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.

  4. Theoretical studies on the dimerization of substituted paraphenylenediamine radical cations

    NASA Astrophysics Data System (ADS)

    Punyain, Kraiwan; Kelterer, Anne-Marie; Grampp, Günter

    2011-12-01

    Organic radical cations form dicationic dimers in solution, observed experimentally as diamagnetic species in temperature-dependent EPR and low temperature UV/Vis spectroscopy. Dimerization of paraphenylenediamine, N,N-dimethyl-paraphenylenediamine and 2,3,5,6-tetramethyl-paraphenylenediamine radical cation in ethanol/diethylether mixture was investigated theoretically according to geometry, energetics and UV/Vis spectroscopy. Density Functional Theory including dispersion correction describes stable dimers after geometry optimization with conductor-like screening model of solvation and inclusion of the counter-ion. Energy corrections were done on double-hybrid Density Functional Theory with perturbative second-order correlation (B2PLYP-D) including basis set superposition error (BSSE), and multireference Møller-Plesset second-order perturbation theory method (MRMP2) based on complete active space method (CASSCF(2,2)) single point calculation, respectively. All three dication π-dimers exhibit long multicenter π-bonds around 2.9 ± 0.1 Å with strongly interacting orbitals. Substitution with methyl groups does not influence the dimerization process substantially. Dispersion interaction and electrostatic attraction from counter-ion play an important role to stabilize the dication dimers in solution. Dispersion-corrected double hybrid functional B2PLYP-D and CASSCF(2,2) can describe the interaction energetics properly. Vertical excitations were computed with Tamm-Dancoff approximation for time-dependent Density Functional Theory (TDA-DFT) at the B3LYP level with the cc-pVTZ basis set including ethanol solvent molecules explicitly. A strong interaction of the counter-ion and the solvent ethanol with the monomeric species is observed, whereas in the dimers the strong interaction of both radical cation species is the dominating factor for the additional peak in UV/Vis spectra.

  5. Synthesis of a distinct water dimer inside fullerene C70

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  6. Highly stable tetrathiafulvalene radical dimers in [3]catenanes

    SciTech Connect

    Spruell, Jason M.; Coskun, Ali; Friedman, Douglas C.; Forgan, Ross S.; Sarjeant, Amy A.; Trabolsi, Ali; Fahrenbach, Albert C.; Barin, Gokhan; Paxton, Walter F.; Dey, Sanjeev K.; Olson, Mark A.; Benítez, Diego; Tkatchouk, Ekaterina; Colvin, Michael T.; Carmielli, Raanan; Caldwell, Stuart T.; Rosair, Georgina M.; Hewage, Shanika Gunatilaka; Duclairoir, Florence; Seymour, Jennifer L.; Slawin, Alexandra M.Z.; Goddard, III, William A.; Wasielewski, Michael R.; Cooke, Graeme; Stoddart, J. Fraser

    2010-12-03

    Two [3]catenane 'molecular flasks' have been designed to create stabilized, redox-controlled tetrathiafulvalene (TTF) dimers, enabling their spectrophotometric and structural properties to be probed in detail. The mechanically interlocked framework of the [3]catenanes creates the ideal arrangement and ultrahigh local concentration for the encircled TTF units to form stable dimers associated with their discrete oxidation states. These dimerization events represent an affinity umpolung, wherein the inversion in electronic affinity replaces the traditional TTF-bipyridinium interaction, which is over-ridden by stabilizing mixed-valence (TTF){sub 2}{sup {sm_bullet}+} and radical-cation (TTF{sup {sm_bullet}+}){sub 2} states inside the 'molecular flasks.' The experimental data, collected in the solid state as well as in solution under ambient conditions, together with supporting quantum mechanical calculations, are consistent with the formation of stabilized paramagnetic mixed-valence dimers, and then diamagnetic radical-cation dimers following subsequent one-electron oxidations of the [3]catenanes.

  7. A single ligand is sufficient to activate EGFR dimers

    PubMed Central

    Liu, Ping; Cleveland, Thomas E.; Bouyain, Samuel; Byrne, Patrick O.; Longo, Patti A.; Leahy, Daniel J.

    2012-01-01

    Crystal structures of human epidermal growth factor receptor (EGFR) with bound ligand revealed symmetric, doubly ligated receptor dimers thought to represent physiologically active states. Such complexes fail to rationalize negative cooperativity of epidermal growth factor (EGF) binding to EGFR and the behavior of the ligandless EGFR homolog ErbB2/HER2, however. We report cell-based assays that provide evidence for active, singly ligated dimers of human EGFR and its homolog, ErbB4/HER4. We also report crystal structures of the ErbB4/HER4 extracellular region complexed with its ligand Neuregulin-1β that resolve two types of ErbB dimer when compared to EGFR:Ligand complexes. One type resembles the recently reported asymmetric dimer of Drosophila EGFR with a single high-affinity ligand bound and provides a model for singly ligated human ErbB dimers. These results unify models of vertebrate and invertebrate EGFR/ErbB signaling, imply that the tethered conformation of unliganded ErbBs evolved to prevent crosstalk among ErbBs, and establish a molecular basis for both negative cooperativity of ligand binding to vertebrate ErbBs and the absence of active ErbB2/HER2 homodimers in normal conditions. PMID:22699492

  8. Palladium dimers adsorbed on graphene: A DFT study

    SciTech Connect

    Kaur, Gagandeep; Gupta, Shuchi; Dharamvir, Keya

    2015-05-15

    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{sub 2}) on graphene using SIESTA package, in the generalized gradient approximation (GGA). The adsorption energy, geometry, and charge transfer of Pd{sub 2}-graphene system are calculated. Both horizontal and vertical orientations of Pd{sub 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.

  9. Hydrogenated fullerenes dimer, peanut and capsule: An atomic comparison

    NASA Astrophysics Data System (ADS)

    EL-Barbary, A. A.

    2016-04-01

    Hydrogenated fullerenes are detected in the Universe in space but their identification is still unsolved task. Therefore, this paper provides useful information about hydrogenated fullerenes (dimer, peanut and capsule) using DFT method at the B3LYP/6-31G(d) level of theory. The stability, geometric structures, hydrogen adsorption energies and NMR chemical shifts are calculated. The results show that the energy of most stable isomer of C118 dimer is lower than the energies sum of C60 and C58 cages by 1.77 eV and the energy per carbon atom of C144 capsule is more stable than C60 cage by 126.98 meV. Also, endohedral Ti-doped C118 dimer and C128 peanut are found to be most stable structures than exohedral Ti-doped C118 dimer and C128 peanut by 2.19 eV/Ti and 3.52 eV/Ti, respectively. The hydrogenation process is found to be enhanced (especially at the caps) for endohedral Ti-doped C118 dimer and C128 peanut through electronic surface modifications. The most active hydrogenation sites are selected and it is found that the most stable hydrogenation sites are Houts1 and Houts3 for fullerenes and endohedral Ti-doped fullerenes, respectively.

  10. Altered Dimer Interface Decreases Stability in an Amyloidogenic Protein

    SciTech Connect

    Baden, Elizabeth M.; Owen, Barbara A.L.; Peterson, Francis C.; Volkman, Brian F.; Ramirez-Alvarado, Marina; Thompson, James R.

    2008-07-21

    Amyloidoses are devastating and currently incurable diseases in which the process of amyloid formation causes fatal cellular and organ damage. The molecular mechanisms underlying amyloidoses are not well known. In this study, we address the structural basis of immunoglobulin light chain amyloidosis, which results from deposition of light chains produced by clonal plasma cells. We compare light chain amyloidosis protein AL-09 to its wild-type counterpart, the kl O18/O8 light chain germline. Crystallographic studies indicate that both proteins form dimers. However, AL-09 has an altered dimer interface that is rotated 90 degrees from the kl O18/O8 dimer interface. The three non-conservative mutations in AL-09 are located within the dimer interface, consistent with their role in the decreased stability of this amyloidogenic protein. Moreover, AL-09 forms amyloid fibrils more quickly than kl O18/O8 in vitro. These results support the notion that the increased stability of the monomer and delayed fibril formation, together with a properly formed dimer, may be protective against amyloidogenesis. This could open a new direction into rational drug design for amyloidogenic proteins.

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

    SciTech Connect

    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.

  12. Chemistry of the CO dimer at low temperatures

    NASA Technical Reports Server (NTRS)

    Demore, W. B.; Roux, E. T.

    1988-01-01

    Researchers conducted a series of experiments on the chlorine-catalyzed photodecomposition of O sub 3 both in the gas and in inert solvents such as CF sub 4 and CO sub 2 in the temperature range about 190 to 225 K. The liquid medium was chosen in order to minimize possible surface loss of long-lived ClO dimer, and to aid in the stabilization of transient excited intermediates. The mechanism of dimer formation was as follows: (1) Cl sub 2 + hv yields Cl + Cl; (2) Cl + O sub 3 yields ClO + O sub 2; (3) ClO + ClO yields Cl sub 2 O sub 2. The experiments were done in cooled low temperature cells, with irradiation from an Osram high pressure mercury arc, filtered to remove radiation below 325 nm. Spectral analysis was by means of a Cary Model 2200 UV spectrometer. The principal objectives were: (1) to determine the lifetime of the dimer as a function of temperature; (2) to observe spectral changes in the mixtures which could be attributed to dimer or related products; and (3) to observe chemical or photochemical reactions of the dimer.

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

    PubMed Central

    Kumar, Sunil

    2013-01-01

    A series of neomycin dimers have been synthesized using “click chemistry” with varying linker functionality and length to target the TAR RNA region of HIV virus. TAR (Trans Activation Response) RNA region, a 59 base pair stem loop structure located at 5′-end of all nascent HIV-1 transcripts interacts with a key regulatory protein, Tat, and necessitates the replication of HIV-1 virus. Neomycin, an aminosugar, has been shown to exhibit more than one binding site with HIV TAR RNA. Multiple TAR binding sites of neomycin prompted us to design and synthesize a small library of neomycin dimers using click chemistry. The binding between neomycin dimers and HIV TAR RNA was characterized using spectroscopic techniques including FID (Fluorescent Intercalator Displacement) titration and UV-thermal denaturation. UV thermal denaturation studies demonstrate that neomycin dimer binding increase the melting temperature (Tm) of the HIV TAR RNA up to 10 °C. Ethidium bromide displacement titrations revealed nanomolar IC50 between neomycin dimers and HIV TAR RNA, whereas with neomycin, a much higher IC50 in the micromolar range is observed. PMID:21757341

  14. Structural investigation of protonated azidothymidine and protonated dimer.

    PubMed

    Ziegler, Blake E; Marta, Rick A; Burt, Michael B; Martens, Sabrina M; Martens, Jonathan K; McMahon, Terry B

    2014-02-01

    Infrared multiple photon dissociation (IRMPD) spectroscopy experiments and quantum chemical calculations have been used to explore the possible structures of protonated azidothymidine and the corresponding protonated dimer. Many interesting differences between the protonated and neutral forms of azidothymidine were found, particularly associated with keto-enol tautomerization. Comparison of computational vibrational and the experimental IMRPD spectra show good agreement and give confidence that the dominant protonated species has been identified. The protonated dimer of azidothymidine exhibits three intramolecular hydrogen bonds. The IRMPD spectrum of the protonated dimer is consistent with the spectrum of the most stable computational structure. This work brings to light interesting keto-enol tautomerization and exocyclic hydrogen bonding involving azidothymidine and its protonated dimer. The fact that one dominant protonated species is observed in the gas phase, despite both the keto and enol structures being similar in energy, is proposed to be the direct result of the electrospray ionization process in which the dominant protonated dimer structure dissociates in the most energetically favorable way. PMID:24306778

  15. Mechanism of ubiquitylation by dimeric RING ligase RNF4.

    PubMed

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

    2011-09-01

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

  16. Finite-difference time-domain studies of the optical properties of nanoshell dimers.

    PubMed

    Oubre, C; Nordlander, P

    2005-05-26

    The optical properties of metallic nanoshell dimers are investigated using the finite difference time domain (FDTD) method. We discuss issues of numerical convergence specific for the dimer system. We present results for both homodimers and heterodimers. The results show that retardation effects must be taken into account for an accurate description of realistic size nanoparticle dimers. The optical properties of the nanoshell dimer are found to be strongly polarization dependent. Maximal coupling between the nanoshells in a dimer occurs when the electric field of the incident pulse is aligned parallel to the dimer axis. The wavelengths of the peaks in the extinction cross section of the dimer are shown to vary by more than 100 nm, depending on the incident electric field polarization. The calculations show that electric field enhancements in the dimer junctions depend strongly on dimer separation. The maximum field enhancements occur in the dimer junction and at the expense of a reduced electric field enhancement in other regions of space. We investigate the usefulness of nanoshell dimers substrates for SERS by integrating the fourth power of the electric field enhancements around the surfaces of the nanoparticles as a function of dimer separation and wavelength. The SERS efficiency is shown to depend strongly on dimer separation but much weaker than the fourth power of the maximum electric field enhancement at a particular point. The SERS efficiency is also found to depend strongly on the wavelength of the incident light. Maximum SERS efficiency occurs for resonant excitation of the dimer plasmons. PMID:16852215

  17. Hydrogen bonded and stacked geometries of the temozolomide dimer.

    PubMed

    Kasende, Okuma Emile; Muya, Jules Tshishimbi; de Paul N Nziko, Vincent; Scheiner, Steve

    2016-04-01

    Dispersion-corrected density functional theory (DFT) and MP2 quantum chemical methods are used to examine homodimers of temozolomide (TMZ). Of the 12 dimer configurations found to be minima, the antarafacial stacked dimer is the most favored, it is lower in energy than coplanar dimers which are stabilized by H-bonds. The comparison between B3LYP and B3LYP-D binding energies points to dispersion as a primary factor in stabilizing the stacked geometries. CO(π) → CO(π*) charge transfers between amide groups in the global minimum are identified by NBO, as well as a pair of weak CH∙∙N H-bonds. AIM analysis of the electron density provides an alternative description which includes N∙∙O, N∙∙N, and C∙∙C noncovalent bonds. Graphical Abstract Hydrogen bonded and stacked geometries of the temozolomide dimerᅟ. PMID:26971506

  18. An exploration of the ozone dimer potential energy surface

    SciTech Connect

    Azofra, Luis Miguel; Alkorta, Ibon; Scheiner, Steve

    2014-06-28

    The (O{sub 3}){sub 2} dimer potential energy surface is thoroughly explored at the ab initio CCSD(T) computational level. Five minima are characterized with binding energies between 0.35 and 2.24 kcal/mol. The most stable may be characterized as slipped parallel, with the two O{sub 3} monomers situated in parallel planes. Partitioning of the interaction energy points to dispersion and exchange as the prime contributors to the stability, with varying contributions from electrostatic energy, which is repulsive in one case. Atoms in Molecules analysis of the wavefunction presents specific O⋯O bonding interactions, whose number is related to the overall stability of each dimer. All internal vibrational frequencies are shifted to the red by dimerization, particularly the antisymmetric stretching mode whose shift is as high as 111 cm{sup −1}. In addition to the five minima, 11 higher-order stationary points are identified.

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

    SciTech Connect

    Pin, C.; Renaut, C.; Cluzel, B. Fornel, F. de; Peyrade, D.; Picard, E.; Hadji, E.

    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.

  20. Plasmonic Fano resonances in compositional heterogenous Al- Au nanorod dimers

    NASA Astrophysics Data System (ADS)

    Wu, Botao; Xue, Yingxian; Ma, Qiang; Ding, Chengjie; Rong, Youying; Liu, Yan; Chen, Lingxiao; Wu, E.; Zeng, Heping

    2016-01-01

    We have investigated theoretically the plasmon resonance coupling in compositional heterogenous Al-Au nanorod dimers organized in a close proximity by end-to-end. It has been proved that the destructive interference between the bright dipole mode from Al nanorod and the dark quadrupole mode from Au nanorod nearby results in the appearance of apparent Fano resonance in the extinction spectra. The Fano resonance response on the structural dimension modifications in the proposed nanorod dimers have been estimated and determined. The Al-Au heterogeneous nanorod dimer shows a high sensitivity to the surrounding environment with a local surface plasmon resonance figure of merit of 7.6, which enables its promising applications in plasmonic sensing and detection.

  1. Sequence-Specific DNA Binding by a Short Peptide Dimer

    NASA Astrophysics Data System (ADS)

    Talanian, Robert V.; McKnight, C. James; Kim, Peter S.

    1990-08-01

    A recently described class of DNA binding proteins is characterized by the "bZIP" motif, which consists of a basic region that contacts DNA and an adjacent "leucine zipper" that mediates protein dimerization. A peptide model for the basic region of the yeast transcriptional activator GCN4 has been developed in which the leucine zipper has been replaced by a disulfide bond. The 34-residue peptide dimer, but not the reduced monomer, binds DNA with nanomolar affinity at 4^circC. DNA binding is sequence-specific as judged by deoxyribonuclease I footprinting. Circular dichroism spectroscopy suggests that the peptide adopts a helical structure when bound to DNA. These results demonstrate directly that the GCN4 basic region is sufficient for sequence-specific DNA binding and suggest that a major function of the GCN4 leucine zipper is simply to mediate protein dimerization. Our approach provides a strategy for the design of short sequence-specific DNA binding peptides.

  2. An exploration of the ozone dimer potential energy surface

    NASA Astrophysics Data System (ADS)

    Azofra, Luis Miguel; Alkorta, Ibon; Scheiner, Steve

    2014-06-01

    The (O3)2 dimer potential energy surface is thoroughly explored at the ab initio CCSD(T) computational level. Five minima are characterized with binding energies between 0.35 and 2.24 kcal/mol. The most stable may be characterized as slipped parallel, with the two O3 monomers situated in parallel planes. Partitioning of the interaction energy points to dispersion and exchange as the prime contributors to the stability, with varying contributions from electrostatic energy, which is repulsive in one case. Atoms in Molecules analysis of the wavefunction presents specific O⋯O bonding interactions, whose number is related to the overall stability of each dimer. All internal vibrational frequencies are shifted to the red by dimerization, particularly the antisymmetric stretching mode whose shift is as high as 111 cm-1. In addition to the five minima, 11 higher-order stationary points are identified.

  3. An exploration of the ozone dimer potential energy surface.

    PubMed

    Azofra, Luis Miguel; Alkorta, Ibon; Scheiner, Steve

    2014-06-28

    The (O3)2 dimer potential energy surface is thoroughly explored at the ab initio CCSD(T) computational level. Five minima are characterized with binding energies between 0.35 and 2.24 kcal/mol. The most stable may be characterized as slipped parallel, with the two O3 monomers situated in parallel planes. Partitioning of the interaction energy points to dispersion and exchange as the prime contributors to the stability, with varying contributions from electrostatic energy, which is repulsive in one case. Atoms in Molecules analysis of the wavefunction presents specific O⋯O bonding interactions, whose number is related to the overall stability of each dimer. All internal vibrational frequencies are shifted to the red by dimerization, particularly the antisymmetric stretching mode whose shift is as high as 111 cm(-1). In addition to the five minima, 11 higher-order stationary points are identified. PMID:24985642

  4. ERAP1-ERAP2 dimerization increases peptide-trimming efficiency.

    PubMed

    Evnouchidou, Irini; Weimershaus, Mirjana; Saveanu, Loredana; van Endert, Peter

    2014-07-15

    The endoplasmic reticulum aminopeptidases (ERAP)1 and ERAP2 play a critical role in the production of final epitopes presented by MHC class I molecules. Formation of heterodimers by ERAP1 and ERAP2 has been proposed to facilitate trimming of epitope precursor peptides, but the effects of dimerization on ERAP function remain unknown. In this study, we produced stabilized ERAP1-ERAP2 heterodimers and found that they produced several mature epitopes more efficiently than a mix of the two enzymes unable to dimerize. Physical interaction with ERAP2 changes basic enzymatic parameters of ERAP1 and improves its substrate-binding affinity. Thus, by bringing the two enzymes in proximity and by producing allosteric effects on ERAP1, dimerization of ERAP1/2 creates complexes with superior peptide-trimming efficacy. Such complexes are likely to enhance Ag presentation by cells displaying coordinated expression of the two enzymes. PMID:24928998

  5. Dimer ribbons of ATP synthase shape the inner mitochondrial membrane

    PubMed Central

    Strauss, Mike; Hofhaus, Götz; Schröder, Rasmus R; Kühlbrandt, Werner

    2008-01-01

    ATP synthase converts the electrochemical potential at the inner mitochondrial membrane into chemical energy, producing the ATP that powers the cell. Using electron cryo-tomography we show that the ATP synthase of mammalian mitochondria is arranged in long ∼1-μm rows of dimeric supercomplexes, located at the apex of cristae membranes. The dimer ribbons enforce a strong local curvature on the membrane with a 17-nm outer radius. Calculations of the electrostatic field strength indicate a significant increase in charge density, and thus in the local pH gradient of ∼0.5 units in regions of high membrane curvature. We conclude that the mitochondrial cristae act as proton traps, and that the proton sink of the ATP synthase at the apex of the compartment favours effective ATP synthesis under proton-limited conditions. We propose that the mitochondrial ATP synthase organises itself into dimer ribbons to optimise its own performance. PMID:18323778

  6. Rotational coherence spectroscopy and structure of phenol dimer

    NASA Astrophysics Data System (ADS)

    Connell, L. L.; Ohline, S. M.; Joireman, P. W.; Corcoran, T. C.; Felker, P. M.

    1992-02-01

    Rotational coherence spectroscopy has been used to measure the rotational constants of four isotopomers of phenol dimer and a single isotopomer of p-cresol dimer. From the results of these measurements, together with spectroscopic results reported by others, a geometry for phenol dimer is deduced. The species is found to be bound by an O-HṡṡṡO hydrogen bond. The orientation of the phenyl moieties is such that they make maximal contact consistent with the constraints imposed by the hydrogen bond and by the van der Waals radii of the atoms. This geometric feature is cited as evidence for the significance of aromatic-aromatic attraction in the intermolecular interaction between the phenols.

  7. Epoxidation of propylene dimers and isomerization of mixtures obtained

    SciTech Connect

    Dobrev, D.M.; Kurtev, K.S.

    1988-05-10

    Mixtures of hexenes are obtained in the dimerization of propylene on a Ziegler catalyst. By the epoxidation of this mixture by organic peroxides, followed by isomerization of the oxides, C/sub 6/ ketones, which are used as solvents, can be obtained. The hexenes were obtained by dimerization of propylene in the presence of a Ni(C/sub 5/H/sub 7/O/sub 2/)/sub 2/-P(C/sub 6/H/sub 5/)/sub 3/-(C/sub 3/H/sub 5/)/sub 2/AlCl catalytic system. The epoxidation was carried with technical grade isopropylbenzyl hydroperoxide (IPBHP). MoO/sub 2/(C/sub 5/H/sub 7/O/sub 2/)/sub 2/ was used as the catalyst. The relative rates of epoxidation of different isomers contained in the dimeric fraction, with respect to 2-methyl-1-pentene, was determined by means of competing reactions.

  8. Antiferromagnetic Spin-S Chains with Exactly Dimerized Ground States

    NASA Astrophysics Data System (ADS)

    Michaud, Frédéric; Vernay, François; Manmana, Salvatore R.; Mila, Frédéric

    2012-03-01

    We show that spin S Heisenberg spin chains with an additional three-body interaction of the form (Si-1·Si)(Si·Si+1)+H.c. possess fully dimerized ground states if the ratio of the three-body interaction to the bilinear one is equal to 1/[4S(S+1)-2]. This result generalizes the Majumdar-Ghosh point of the J1-J2 chain, to which the present model reduces for S=1/2. For S=1, we use the density matrix renormalization group method to show that the transition between the Haldane and the dimerized phases is continuous with a central charge c=3/2. Finally, we show that such a three-body interaction appears naturally in a strong-coupling expansion of the Hubbard model, and we discuss the consequences for the dimerization of actual antiferromagnetic chains.

  9. Fluxional σ-Bonds of the 2,5,8-Trimethylphenalenyl Dimer: Direct Observation of the Sixfold σ-Bond Shift via a π-Dimer.

    PubMed

    Uchida, Kazuyuki; Mou, Zhongyu; Kertesz, Miklos; Kubo, Takashi

    2016-04-01

    Direct evidence for σ-bond fluxionality in a phenalenyl σ-dimer was successfully obtained by a detailed investigation of the solution-state dynamics of 2,5,8-trimethylphenalenyl (TMPLY) using both experimental and theoretical approaches. TMPLY formed three diamagnetic dimers, namely, the σ-dimer (RR/SS), σ-dimer (RS), and π-dimer, which were fully characterized by (1)H NMR spectroscopy and electronic absorption measurements. The experimental findings gave the first quantitative insights into the essential preference of these competitive and unusual dimerization modes. The spectroscopic analyses suggested that the σ-dimer (RR/SS) is the most stable in terms of energy, whereas the others are metastable; the energy differences between these three isomers are less than 1 kcal mol(-1). Furthermore, the intriguing dynamics of the TMPLY dimers in the solution state were fully revealed by means of (1)H-(1)H exchange spectroscopy (EXSY) measurements and variable-temperature (1)H NMR studies. Surprisingly, the σ-dimer (RR/SS) demonstrated a sixfold σ-bond shift between the six sets of α-carbon pairs. This unusual σ-bond fluxionality is ascribed to the presence of a direct interconversion pathway between the σ-dimer (RR/SS) and the π-dimer, which was unambiguously corroborated by the EXSY measurements. The proposed mechanism of the sixfold σ-bond shift based on the experimental findings was well-supported by theoretical calculations. PMID:26961216

  10. Structure of the indole-benzene dimer revisited.

    PubMed

    Biswal, Himansu S; Gloaguen, Eric; Mons, Michel; Bhattacharyya, Surjendu; Shirhatti, Pranav R; Wategaonkar, Sanjay

    2011-09-01

    The structure of the indole-benzene dimer has been investigated using experimental techniques, namely, UV spectroscopy and infrared-ultraviolet (IR/UV) double resonance spectroscopy, combined with quantum chemical calculations such as MP2 and dispersion corrected DFT methods. The red shift of the indole N-H stretch frequency in the dimer provides direct evidence that the experimentally observed indole-benzene dimer is an N-H···π bound hydrogen bonded complex. Theoretical investigations suggest that the potential energy surface (PES) of the complex is rather flat along the coordinate describing the tilt angle between the molecular planes of indole and benzene, with several minima of similar energies, namely, parallel displaced (PD), right-angle T-shaped (T), and other intermediate structures which can be categorized as tilted T-shaped (T') and tilted parallel displaced (PD') structures. Three different computational methods, namely, RI-MP2, RI-B97-D, and PBE1-DCP, are used to arrive at a new structural assignment after assessing their performance in predicting the structure of the pyrrole dimer, for which accurate experimental data are available. By comparing the computed IR spectra of PD, T, and T'/PD' structures with the experimental IR spectrum, the tilted T-shaped (T') structure was assigned to the indole-benzene dimer. The empirically dispersion-corrected functionals (RI-B97-D and PBE1-DCP) correctly reproduce the experimental IR spectrum whereas the popular post-Hartree-Fock, MP2 method gives disappointing results. These results are also in agreement with the experimental dissociation energy (D(0)) reported in the literature. The N-H stretch frequency of the indole-benzene dimer has been found to be a more pertinent parameter for the structural assignment than the dissociation energy (D(0)). PMID:21413767

  11. Covalent intermolecular interaction of the nitric oxide dimer (NO)2

    NASA Astrophysics Data System (ADS)

    Zhang, Hui; Zheng, Gui-Li; Lv, Gang; Geng, Yi-Zhao; Ji, Qing

    2015-09-01

    Covalent bonds arise from the overlap of the electronic clouds in the internucleus region, which is a pure quantum effect and cannot be obtained in any classical way. If the intermolecular interaction is of covalent character, the result from direct applications of classical simulation methods to the molecular system would be questionable. Here, we analyze the special intermolecular interaction between two NO molecules based on quantum chemical calculation. This weak intermolecular interaction, which is of covalent character, is responsible for the formation of the NO dimer, (NO)2, in its most stable conformation, a cis conformation. The natural bond orbital (NBO) analysis gives an intuitive illustration of the formation of the dimer bonding and antibonding orbitals concomitant with the breaking of the π bonds with bond order 0.5 of the monomers. The dimer bonding is counteracted by partially filling the antibonding dimer orbital and the repulsion between those fully or nearly fully occupied nonbonding dimer orbitals that make the dimer binding rather weak. The direct molecular mechanics (MM) calculation with the UFF force fields predicts a trans conformation as the most stable state, which contradicts the result of quantum mechanics (QM). The lesson from the investigation of this special system is that for the case where intermolecular interaction is of covalent character, a specific modification of the force fields of the molecular simulation method is necessary. Project supported by the National Natural Science Foundation of China (Grant Nos. 90403007 and 10975044), the Key Subject Construction Project of Hebei Provincial Universities, China, the Research Project of Hebei Education Department, China (Grant Nos. Z2012067 and Z2011133), the National Natural Science Foundation of China (Grant No. 11147103), and the Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China (Grant No. Y5

  12. Geometric Frustration of Colloidal Dimers on a Honeycomb Magnetic Lattice

    NASA Astrophysics Data System (ADS)

    Tierno, Pietro

    2016-01-01

    We study the phase behavior and the collective dynamics of interacting paramagnetic colloids assembled above a honeycomb lattice of triangular shaped magnetic minima. A frustrated colloidal molecular crystal is realized when filling these potential minima with exactly two particles per pinning site. External in-plane rotating fields are used to anneal the system into different phases, including long range ordered stripes, random fully packed loops, labyrinth and disordered states. At a higher amplitude of the annealing field, the dimer lattice displays a two-step melting transition where the initially immobile dimers perform first localized rotations and later break up by exchanging particles across consecutive lattice minima.

  13. Nitric Oxide Inhibitory Dimeric Sesquiterpenoids from Artemisia rupestris.

    PubMed

    Zhang, Chen; Wang, Shu; Zeng, Ke-Wu; Li, Jun; Ferreira, Daneel; Zjawiony, Jordan K; Liu, Bing-Yu; Guo, Xiao-Yu; Jin, Hong-Wei; Jiang, Yong; Tu, Peng-Fei

    2016-01-22

    Twelve new dimeric sesquiterpenoids (1-12) were isolated from the dried whole plants of Artemisia rupestris. Their structures were determined using MS and NMR data, and the absolute configurations were elucidated on the basis of experimental and calculated ECD spectra. Compounds 1-9 are presumably formed via biocatalyzed [2+2] or [4+2] cycloaddition reactions. Stereoselectivity of the [4+2] Diels-Alder reaction dictated the formation of endo-products. The dimeric sesquiterpenoids exhibited moderate inhibition on NO production stimulated by lipopolysaccharide in BV-2 microglial cells, with IC50 values in the range 17.0-71.8 μM. PMID:26696523

  14. A Pfaffian Formula for Monomer-Dimer Partition Functions

    NASA Astrophysics Data System (ADS)

    Giuliani, Alessandro; Jauslin, Ian; Lieb, Elliott H.

    2016-04-01

    We consider the monomer-dimer partition function on arbitrary finite planar graphs and arbitrary monomer and dimer weights, with the restriction that the only non-zero monomer weights are those on the boundary. We prove a Pfaffian formula for the corresponding partition function. As a consequence of this result, multipoint boundary monomer correlation functions at close packing are shown to satisfy fermionic statistics. Our proof is based on the celebrated Kasteleyn theorem, combined with a theorem on Pfaffians proved by one of the authors, and a careful labeling and directing procedure of the vertices and edges of the graph.

  15. Geometric Frustration of Colloidal Dimers on a Honeycomb Magnetic Lattice.

    PubMed

    Tierno, Pietro

    2016-01-22

    We study the phase behavior and the collective dynamics of interacting paramagnetic colloids assembled above a honeycomb lattice of triangular shaped magnetic minima. A frustrated colloidal molecular crystal is realized when filling these potential minima with exactly two particles per pinning site. External in-plane rotating fields are used to anneal the system into different phases, including long range ordered stripes, random fully packed loops, labyrinth and disordered states. At a higher amplitude of the annealing field, the dimer lattice displays a two-step melting transition where the initially immobile dimers perform first localized rotations and later break up by exchanging particles across consecutive lattice minima. PMID:26849619

  16. Increased concentrations of D-dimers in newborn infants.

    PubMed Central

    Hudson, I R; Gibson, B E; Brownlie, J; Holland, B M; Turner, T L; Webber, R G

    1990-01-01

    The concentrations of D-dimers (the D fragments of fibrinogen) were measured in blood from 15 preterm infants, and 45 born at full term, to establish normal ranges. The adult normal range is less than 0.25 mg/l; 31 of the 60 infants (52%) had values less than 0.25 mg/l, in 16 (27%) they were 0.25-0.5, in eight (13%) 0.5-1, in three (5%) 1-2, and in two (3%) 2-4. D-dimer concentrations measured during the neonatal period should be interpreted with caution. PMID:2337364

  17. High-Resolution Rotational Spectroscopy Study of the Smallest Sugar Dimer: Interplay of Hydrogen Bonds in the Glycolaldehyde Dimer.

    PubMed

    Zinn, Sabrina; Medcraft, Chris; Betz, Thomas; Schnell, Melanie

    2016-05-10

    Molecular recognition of carbohydrates plays an important role in nature. The aggregation of the smallest sugar, glycolaldehyde, was studied in a conformer-selective manner using high-resolution rotational spectroscopy. Two different dimer structures were observed. The most stable conformer reveals C2 -symmetry by forming two intermolecular hydrogen bonds, giving up the strong intramolecular hydrogen bonds of the monomers and thus showing high hydrogen bond selectivity. By analyzing the spectra of the (13) C and (18) O isotopologues of the dimer in natural abundance, we could precisely determine the heavy backbone structure of the dimer. Comparison to the monomer structure and the complex with water provides insight into intermolecular interactions. Despite hydrogen bonding being the dominant interaction, precise predictions from quantum-chemical calculations highly rely on the consideration of dispersion. PMID:27060475

  18. Biophysical Characterization of the Dimer and Tetramer Interface Interactions of the Human Cytosolic Malic Enzyme

    PubMed Central

    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. PMID:23284632

  19. Mechanisms of Activation of Receptor Tyrosine Kinases: Monomers or Dimers

    PubMed Central

    Maruyama, Ichiro N.

    2014-01-01

    Receptor tyrosine kinases (RTKs) play essential roles in cellular processes, including metabolism, cell-cycle control, survival, proliferation, motility and differentiation. RTKs are all synthesized as single-pass transmembrane proteins and bind polypeptide ligands, mainly growth factors. It has long been thought that all RTKs, except for the insulin receptor (IR) family, are activated by ligand-induced dimerization of the receptors. An increasing number of diverse studies, however, indicate that RTKs, previously thought to exist as monomers, are present as pre-formed, yet inactive, dimers prior to ligand binding. The non-covalently associated dimeric structures are reminiscent of those of the IR family, which has a disulfide-linked dimeric structure. Furthermore, recent progress in structural studies has provided insight into the underpinnings of conformational changes during the activation of RTKs. In this review, I discuss two mutually exclusive models for the mechanisms of activation of the epidermal growth factor receptor, the neurotrophin receptor and IR families, based on these new insights. PMID:24758840

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

    PubMed Central

    Lippi, Giuseppe; Volpe, Alessandro; Caramaschi, Paola; Salvagno, Gian Luca; Montagnana, Martina; Guidi, Gian Cesare

    2006-01-01

    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. PMID:16420700

  1. The Internal Structure of Nanoparticle Dimers Linked by DNA

    NASA Astrophysics Data System (ADS)

    Vargas Lara, Fernando; Cheng, Ching-Jung; Gang, Oleg; Starr, Francis W.

    2012-02-01

    The self-assembly of inorganic units controlled by the interactions of biological molecules, like DNA, has received attention for the possibility to specify higher-order structure, with potential biological, optical and electronic applications. In biology, self-assembly of complex materials (eg. bone, spider silk) frequently occurs in a stepwise, hierarchical fashion. Here, we consider a first step towards a hierarchical approach for synthetic nanostructures of nanoparticles (NPs) linked by DNA. The most basic unit in this multiscale approach is a dimer of NPs linked by DNA. We use a coarse-grained molecular model to explain experimental measurements of the separation of two DNA-coated NPs connected by linking single-stranded DNA (ssDNA). We show that the dimer separation is primarily controlled by the number of DNA links between NPs. If these links are not constrained to lie along the axis between NPs, the separation is limited by off-axis connections that force the NPs to be closer. We also determine how the number of connections alters the effective persistence length of the ssDNA that connects the dimer. We discuss how these dimers might be used for subsequent assembly at larger scales.

  2. Reversible Adsorption Kinetics of Near Surface Dimer Colloids.

    PubMed

    Salipante, Paul F; Hudson, Steven D

    2016-08-30

    We investigate the effect of shape on reversible adsorption kinetics using colloidal polystyrene dimers near a solid glass surface as a model system. The interaction between colloid and wall is tuned using electrostatic, depletion, and gravity forces to produce a double-well potential. The dwell time in each of the potential wells is measured from long duration particle trajectories. The height of each monomer relative to the glass surface is measured to a resolution of <20 nm by in-line holographic microscopy. The measured transition probability distributions are used in kinetic equations to describe the flux of particles to and from the surface. The dimers are compared to independent isolated monomers to determine the effects of shape on adsorption equilibria and kinetics. To elucidate these differences, we consider both mass and surface coverage and two definitions of surface coverage. The results show that dimers with single coverage produce slower adsorption, lower surface coverage, and higher mass coverage in comparison to those of monomers, while dimers with double coverage adsorb faster and result in higher surface coverage. PMID:27483023

  3. Homogeneous gold-catalyzed efficient oxidative dimerization of propargylic acetates.

    PubMed

    Cui, Li; Zhang, Guozhu; Zhang, Liming

    2009-07-15

    A highly efficient gold-catalyzed oxidative dimerization of propargylic acetates is developed. In this chemistry, Selectfluor oxidation of Au(I) to Au(III) is readily incorporated into Au-catalyzed tandem reactions of propargylic acetates, and transmetallation and reductive elimination on Au(III) intermediates are likely involved. PMID:19362834

  4. Asymptotics of Height Change on Toroidal Temperleyan Dimer Models

    NASA Astrophysics Data System (ADS)

    Dubédat, Julien; Gheissari, Reza

    2015-04-01

    The dimer model is an exactly solvable model of planar statistical mechanics. In its critical phase, various aspects of its scaling limit are known to be described by the Gaussian free field. For periodic graphs, criticality is an algebraic condition on the spectral curve of the model, determined by the edge weights (Kenyon et al. in Ann Math (2) 163(3):1019-1056, 2006); isoradial graphs provide another class of critical dimer models, in which the edge weights are determined by the local geometry. In the present article, we consider another class of graphs: general Temperleyan graphs, i.e. graphs arising in the (generalized) Temperley bijection between spanning trees and dimer models. Building in particular on Forman's formula and representations of Laplacian determinants in terms of Poisson operators, and under a minimal assumption—viz. that the underlying random walk converges to Brownian motion—we show that the natural topological observable on macroscopic tori converges in law to its universal limit, i.e. the law of the periods of the dimer height function converges to that of the periods of a compactified free field.

  5. G domain dimerization controls dynamin's assembly-stimulated GTPase activity

    SciTech Connect

    Chappie, Joshua S.; Acharya, Sharmistha; Leonard, Marilyn; Schmid, Sandra L.; Dyda, Fred

    2010-06-14

    Dynamin is an atypical GTPase that catalyses membrane fission during clathrin-mediated endocytosis. The mechanisms of dynamin's basal and assembly-stimulated GTP hydrolysis are unknown, though both are indirectly influenced by the GTPase effector domain (GED). Here we present the 2.0 {angstrom} resolution crystal structure of a human dynamin 1-derived minimal GTPase-GED fusion protein, which was dimeric in the presence of the transition state mimic GDP.AlF{sub 4}{sup -}. The structure reveals dynamin's catalytic machinery and explains how assembly-stimulated GTP hydrolysis is achieved through G domain dimerization. A sodium ion present in the active site suggests that dynamin uses a cation to compensate for the developing negative charge in the transition state in the absence of an arginine finger. Structural comparison to the rat dynamin G domain reveals key conformational changes that promote G domain dimerization and stimulated hydrolysis. The structure of the GTPase-GED fusion protein dimer provides insight into the mechanisms underlying dynamin-catalysed membrane fission.

  6. Comparative assay of antioxidant packages for dimer of estolide esters

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A series of 26 different antioxidants and commercial antioxidant packages, containing both natural and synthetic-based materials, were evaluated with dimeric coconut-oleic estolide 2-ethylhexyl ester. The different antioxidants were broken down into different classes of materials: phenolic, aminic, ...

  7. Tubulin domains responsible for assembly of dimers and protofilaments.

    PubMed Central

    Kirchner, K; Mandelkow, E M

    1985-01-01

    The protein domains responsible for the dimerization and polymerization of tubulin have been determined using chemical cross-linking and limited proteolysis. The intra-dimer bond is formed by the N-terminal domain of alpha-tubulin and the C-terminal domain of beta-tubulin. Conversely, the inter-dimer bond along protofilaments is formed by the N-terminal domain of beta-tubulin (carrying the exchangeable GTP) and the C-terminal domain of alpha-tubulin. The domains of proteolytically cleaved tubulin remain tightly associated in solution. Apart from the monomer, tubulin shows three levels of assembly: the dimer, oligomer and polymer. Several oligomeric species can be visualized by electron microscopy of rotary shadowed phosphocellulose-tubulin, h.p.l.c. and non-denaturing gel electrophoresis. Tubulin's capacity to form the higher level aggregates is not destroyed by enzymatic nicking. Images Fig. 1. Fig. 2. Fig. 4. Fig. 5. Fig. 6. Fig. 7. PMID:4076170

  8. Electrostatic forces contribute to interactions between trp repressor dimers.

    PubMed Central

    Martin, K S; Royer, C A; Howard, K P; Carey, J; Liu, Y C; Matthews, K; Heyduk, E; Lee, J C

    1994-01-01

    The trp repressor of Escherichia coli (TR), although generally considered to be dimeric, has been shown by fluorescence anisotropy of extrinsically labeled protein to undergo oligomerization in solution at protein concentrations in the micromolar range (Fernando, T., and C. A. Royer 1992. Biochemistry. 31:3429-3441). Providing evidence that oligomerization is an intrinsic property of TR, the present studies using chemical cross-linking, analytical ultracentrifugation, and molecular sieve chromatography demonstrate that unmodified TR dimers form higher order aggregates. Tetramers and higher order species were observed in chemical cross-linking experiments at concentrations between 1 and 40 microM. Results from analytical ultracentrifugation and gel filtration chromatography were consistent with average molecular weight values between tetramer and dimer, although no plateaus in the association were evident over the concentration ranges studied, indicating that higher order species are populated. Analytical ultracentrifugation data in presence of corepressor imply that corepressor binding destabilizes the higher order aggregates, an observation that is consistent with the earlier fluorescence work. Through the investigation of the salt and pH dependence of oligomerization, the present studies have revealed an electrostatic component to the interactions between TR dimers. Images FIGURE 1 PMID:8038388

  9. Cantharimide dimers from the Chinese blister beetle, Mylabris phalerate PALLAS.

    PubMed

    Nakatani, Takafumi; Jinpo, Katsuaki; Noda, Naoki

    2007-01-01

    Five cantharidin-related compounds were isolated from the Chinese blister beetle, Mylabris phalerate PALLAS (Meloidae). Their structures were determined based on spectroscopic and chemical evidence. Three of them were identified as cantharimide dimers, which consist of two units of cantharimide combined with a tri-, tetra-, or penta-methylene group. PMID:17202708

  10. Inhibitors that stabilize a closed RAF kinase domain conformation induce dimerization

    PubMed Central

    Lavoie, Hugo; Thevakumaran, Neroshan; Gavory, Gwenaëlle; Li, John; Padeganeh, Abbas; Guiral, Sébastien; Duchaine, Jean; Mao, Daniel Y. L.; Bouvier, Michel; Sicheri, Frank; Therrien, Marc

    2016-01-01

    RAF kinases play a prominent role in cancer. Their mode of activation is complex, but critically requires dimerization of their kinase domains. Unexpectedly, several ATP-competitive RAF inhibitors were recently found to promote dimerization and transactivation of RAF kinases in a RAS-dependent manner and as a result undesirably stimulate RAS/ERK-mediated cell growth. The mechanism by which these inhibitors induce RAF kinase domain dimerization remains unclear. Here we describe BRET-based biosensors for the extended RAF family enabling the detection of RAF dimerization in living cells. Notably, we demonstrate the utility of these tools for profiling kinase inhibitors that selectively modulate RAF dimerization as well as for probing structural determinants of RAF dimerization in vivo. Our findings, which appear generalizable to other kinase families allosterically regulated by kinase domain dimerization, suggest a model whereby ATP-competitive inhibitors mediate RAF dimerization by stabilizing a rigid closed conformation of the kinase domain. PMID:23685672

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

    NASA Astrophysics Data System (ADS)

    Hayakawa, T.; Song, H.; Ishii, Y.; Kawasaki, S.

    2016-07-01

    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.

  12. Molecular Mechanisms in the Repair of the Cyclobutane Pyrimidine Dimer

    NASA Astrophysics Data System (ADS)

    Hassanali, Ali A.; Zhong, Dongping; Singer, Sherwin J.

    2009-06-01

    Exposure to far UV radiation induces DNA damage in the form of cyclobutane pyrimidine dimers (CPDs). Cyclobutane dimer lesions can be repaired by the enzyme photolyase, in which the absorption of a blue light photon initiates a sequence of photochemical events leading to the injection of an electron at the site of the CPD lesion in DNA. The electron catalyzes the repair of the cyclobutane dimer, splitting the CPD to is original pyrimidine units, and is subsequently recaptured by the photolyase protein. In this work we investigate the molecular mechanism of the repair of the cyclobutane dimer radical anion in aqueous solution using ab initio MD simulations. Umbrella sampling is used to determine a two-dimensional free energy surface as a function of the C5-C5-4 and C6-C6-4 distances. The neutral dimer is unable to surmount a large free energy barrier for repair. Upon addition of an electron, the splitting of the C5-C5-4 coordinate is virtually barrier less. Transition state theory predicts that the splitting of the C6-C6-4 bond is complete on a picosecond timescale. The free energy surface suggests that the splitting of the two bonds is asynchronously concerted. Our work is the first to explicitly include the electronic degrees of freedom for both the cyclobutane dimer and the surrounding water pocket. The ab initio simulations show that at least 30% of the electron density is delocalized onto the surrounding solvent during the splitting process. Simulations on the neutral surface show that back electron transfer from the dimer is critical for the completion of splitting: splitting of the C5-C5' and C6-C6' bonds can be reversed or enhanced depending on when electron return occurs. To maximize splitting yield, the back electron transfer should occur beyond the transition state along the splitting coordinate. Non-equilibrium trajectories are also conducted that begin with the electron added to a neutral unrepaired solvated CPD. Our results indicate that there are two

  13. A continuous mixture of two different dimers in liquid water.

    PubMed

    Pardo, L C; Henao, A; Busch, S; Guàrdia, E; Tamarit, J Ll

    2014-11-28

    It is hitherto thought that liquid water is composed of tetrahedrally coordinated molecules with an asymmetric interaction of the central molecule with neighboring molecules. Kühne et al., Nat. Commun., 2013, 4, 1450 suggested that this asymmetry, energetic rather than geometric, is the cornerstone to reconcile the homogeneous and inhomogeneous viewpoints of liquid water. In order to investigate the geometric origin of that asymmetry, we have scrutinized Molecular Dynamics (MD) simulations of water through a careful analysis of the five-dimensional probability distribution function of Euler angles in which the relative positions and orientations of water molecules are obtained. We demonstrate that, beyond the ubiquitous tetrahedral structure with well-defined molecular dimers, there is a series of possible molecular orientations that define the structure. These orientations are generated by rotating the neighboring molecule around the O-H axis that is involved in the hydrogen bond scheme. Two of the possible orientations have a higher probability, giving rise to two kinds of dimers: one close to the lowest energy of a water dimer in vacuum with an almost perpendicular alignment of the dipole moment, and another one with a parallel orientation of the dipole moment which is less tightly bound. These two different dimers have an effect on the orientation of further water dipole moments up to a distance of ≈6 Å. Liquid water can therefore be described as a continuous mixture of two kinds of dimers where the hydrogen bonds have the same geometry but the interaction energies are different due to a different mutual orientation of the dipoles of the participating water molecules. PMID:25308564

  14. A computational model for the dimerization of allene.

    PubMed

    Skraba, Sarah L; Johnson, Richard P

    2012-12-21

    Computations at the CCSD(T)/6-311+G(d,p)//B3LYP/6-311+G(d,p) level of theory support long-held beliefs that allene dimerization to 1,2-dimethylenecyclobutane proceeds through diradical intermediates rather than a concerted (π)2(s) + (π)2(a) mechanism. Two diastereomeric transition states with orthogonal and skew geometries have been located for C2-C2 dimerization of allene, with predicted barriers of 34.5 and 40.3 kcal/mol, respectively. In dimerization, the outward-facing ligands rotate in a sense opposite to the forming C-C bond. Both transition states lead to nearly orthogonal (D(2)) singlet bisallyl (or tetramethyleneethane) diradical. This diradical has a barrier to planarization of 3.2 kcal/mol through a planar D(2h) geometry and a barrier to methylene rotation of 14.3 kcal/mol. Bisallyl diradical closes through one of four degenerate paths by a conrotatory motion of the methylene groups with a predicted barrier of 15.7 kcal/mol. The low barrier to planarization of bisallyl, and similar barriers for methylene rotation and conrotatory closure are consistent with a stepwise dimerization process which can still maintain stereochemical elements of reactants. These computations support the observation that racemic 1,3-disubstituted allenes, with access to an orthogonal transition state which minimizes steric strain, will dimerize more readily than enantiopure materials and by a mechanism that preferentially bonds M and P enantiomers. PMID:23198916

  15. Dimerization of (+)-Myrmicarin 215B. A Potential Biomimetic Approach to Complex Myrmicarin Alkaloids

    PubMed Central

    Ondrus, Alison E.; Movassaghi, Mohammad

    2009-01-01

    The acid promoted diastereoselective dimerization of myrmicarin 215B is described. The reactivity of these sensitive alkaloids, structural assignment, and a possible mechanism for the observed dimerization are discussed. These finding raise the intriguing possibility of the synthesis of the highly sensitive myrmicarin alkaloids based on a strategy involving the direct dimerization of functional tricyclic myrmicarin derivatives. PMID:20640170

  16. Dimerization of human immunodeficiency virus (type 1) RNA: stimulation by cations and possible mechanism.

    PubMed Central

    Marquet, R; Baudin, F; Gabus, C; Darlix, J L; Mougel, M; Ehresmann, C; Ehresmann, B

    1991-01-01

    The retroviral genome consists of two identical RNA molecules joined close to their 5' ends by the dimer linkage structure. Recent findings indicated that retroviral RNA dimerization and encapsidation are probably related events during virion assembly. We studied the cation-induced dimerization of HIV-1 RNA and results indicate that all in vitro generated HIV-1 RNAs containing a 100 nucleotide domain downstream from the 5' splice site are able to dimerize. RNA dimerization depends on the concentration of RNA, mono- and multivalent cations, the size of the monovalent cation, temperature, and pH. Up to 75% of HIV-1 RNA is dimeric in the presence of spermidine. HIV-1 RNA dimer is fairly resistant to denaturing agents and unaffected by intercalating drugs. Antisense HIV-1 RNA does not dimerize but heterodimers can be formed between HIV-1 RNA and either MoMuLV or RSV RNA. Therefore retroviral RNA dimerization probably does not simply proceed through mechanisms involving Watson-Crick base-pairing. Neither adenine and cytosine protonation, nor quartets containing only guanines appear to determine the stability of the HIV-1 RNA dimer, while quartets involving both adenine(s) and guanine(s) could account for our results. A consensus sequence PuGGAPuA found in the putative dimerization-encapsidation region of all retroviral genomes examined may participate in the dimerization process. Images PMID:1645868

  17. Intermolecular interactions and conformation of antibody dimers present in IgG1 biopharmaceuticals.

    PubMed

    Iwura, Takafumi; Fukuda, Jun; Yamazaki, Katsuyoshi; Kanamaru, Shuji; Arisaka, Fumio

    2014-01-01

    Intermolecular interactions and conformation in dimer species of Palivizumab, a monoclonal antibody (IgG1), were investigated to elucidate the physical and chemical properties of the dimerized antibody. Palivizumab solution contains ∼1% dimer and 99% monomer. The dimer species was isolated by size-exclusion chromatography and analysed by a number of methods including analytical ultracentrifugation-sedimantetion velocity (AUC-SV). AUC-SV in the presence of sodium dodecyl sulphate indicated that approximately half of the dimer fraction was non-covalently associated, whereas the other half was dimerized by covalent bond. Disulphide bond and dityrosine formation were likely to be involved in the covalent dimerization. Limited proteolysis of the isolated dimer by Lys-C and mass spectrometry for the resultant products indicated that the dimer species were formed by Fab-Fc or Fab-Fab interactions, whereas Fc-Fc interactions were not found. It is thus likely that the dimerization occurs mainly via the Fab region. With regard to the conformation of the dimer species, the secondary and tertiary structures were shown to be almost identical to those of the monomer. Furthermore, the thermal stability turned out also to be very similar between the dimer and monomer. PMID:24155259

  18. Dimer-dimer interaction of the bacterial selenocysteine synthase SelA promotes functional active-site formation and catalytic specificity.

    PubMed

    Itoh, Yuzuru; Bröcker, Markus J; Sekine, Shun-ichi; Söll, Dieter; Yokoyama, Shigeyuki

    2014-04-17

    The 21st amino acid, selenocysteine (Sec), is incorporated translationally into proteins and is synthesized on its specific tRNA (tRNA(Sec)). In Bacteria, the selenocysteine synthase SelA converts Ser-tRNA(Sec), formed by seryl-tRNA synthetase, to Sec-tRNA(Sec). SelA, a member of the fold-type-I pyridoxal 5'-phosphate-dependent enzyme superfamily, has an exceptional homodecameric quaternary structure with a molecular mass of about 500kDa. Our previously determined crystal structures of Aquifex aeolicus SelA complexed with tRNA(Sec) revealed that the ring-shaped decamer is composed of pentamerized SelA dimers, with two SelA dimers arranged to collaboratively interact with one Ser-tRNA(Sec). The SelA catalytic site is close to the dimer-dimer interface, but the significance of the dimer pentamerization in the catalytic site formation remained elusive. In the present study, we examined the quaternary interactions and demonstrated their importance for SelA activity by systematic mutagenesis. Furthermore, we determined the crystal structures of "depentamerized" SelA variants with mutations at the dimer-dimer interface that prevent pentamerization. These dimeric SelA variants formed a distorted and inactivated catalytic site and confirmed that the pentamer interactions are essential for productive catalytic site formation. Intriguingly, the conformation of the non-functional active site of dimeric SelA shares structural features with other fold-type-I pyridoxal 5'-phosphate-dependent enzymes with native dimer or tetramer (dimer-of-dimers) quaternary structures. PMID:24456689

  19. Fragmentation dynamics of noble gas dimers in two-color intense laser fields

    NASA Astrophysics Data System (ADS)

    Magrakvelidze, M.; Wu, J.; Doerner, R.; Thumm, U.

    2013-05-01

    We studied the dissociation dynamics of noble gas dimer ions in two-color infrared intense laser fields by analyzing their fragment-kinetic-energy-release spectra as a function of the pump-probe delay. Our calculations predict a striking ``delay gap'' in the kinetic-energy-spectra for all noble gas dimers that was so far only measured for the Ar2 dimer. We identify this phenomenon as a frustrated dissociation mechanism. This mechanism requests different pump- and probe-pulse wavelengths and involves the pump pulse to both, singly ionize the neutral dimers and dipole-couple adiabatic states in the dimer ion. Supported by the US NSF and DOE.

  20. Versatile SPR aptasensor for detection of lysozyme dimer in oligomeric and aggregated mixtures.

    PubMed

    Vasilescu, Alina; Purcarea, Cristina; Popa, Elena; Zamfir, Medana; Mihai, Iuliana; Litescu, Simona; David, Sorin; Gaspar, Szilveszter; Gheorghiu, Mihaela; Jean-Louis Marty

    2016-09-15

    A Surface Plasmon Resonance (SPR) sensor for the quantitation of lysozyme dimer in monomer-dimer mixtures, reaching a detection limit of 1.4nM dimer, has been developed. The sensor is based on an aptamer which, although developed for the monomeric form, binds also the dimeric form but with a strikingly different kinetics. The aptasensor was calibrated using a dimer obtained by cross-linking. Sensorgrams acquired with the aptasensor in monomer-dimer mixtures were analysed using Principal Components Analysis and Multiple Regression to establish correlations with the dimer content in the mixtures. The method allows the detection of 0.1-1% dimer in monomer solutions without any separation. As an application, the aptasensor was used to qualitatively observe the initial stages of aggregation of lysozyme solutions at 60°C and pH 2, through the variations in lysozyme dimer amounts. Several other methods were used to characterize the lysozyme dimer obtained by cross-linking and confirm the SPR results. This work highlights the versatility of the aptasensor, which can be used, by simply tuning the experimental conditions, for the sensitive detection of either the monomer or the dimer and for the observation of the aggregation process of lysozyme. PMID:27135941

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  2. Dimerized phase and entanglement in the one-dimensional spin-1 bilinear biquadratic model

    NASA Astrophysics Data System (ADS)

    Chen, Ai Min; Su, Yao Heng; Wang, Honglei

    2015-10-01

    Dimerized phase and quantum entanglement are investigated in the one-dimensional spin-1 bilinear biquadratic model. Employing the infinite matrix product state representation, groundstate wavefunctions are numerically obtained by using the infinite time evolving block decimation method in the infinite lattice system. From a bipartite entanglement measure of the groundstates, i.e., von Neumann entropy, the phase transition points can be clearly extracted. Moreover, the even-bond and odd-bond von Neumann entropies show two different values in the spontaneous dimerized phase. It implies that the quantum entanglement can distinguish the two degenerate groundstates. Then, we define a dimer entropy in the spontaneous dimerized phase. Comparing to the dimer order parameter, the dimer entropy can play a role of a local order parameter to characterize the spontaneous dimerized phase.

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

    PubMed Central

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

    2016-01-01

    Helix α9 of Bax protein can dimerize in the mitochondrial outer membrane (MOM) and lead to apoptotic pores. However, it remains unclear how different conformations of the dimer contribute to the pore formation on the molecular level. Thus we have investigated various conformational states of the α9 dimer in a MOM model — using computer simulations supplemented with site-specific mutagenesis and crosslinking of the α9 helices. Our data not only confirmed the critical membrane environment for the α9 stability and dimerization, but also revealed the distinct lipid-binding preference of the dimer in different conformational states. In our proposed pathway, a crucial iso-parallel dimer that mediates the conformational transition was discovered computationally and validated experimentally. The corroborating evidence from simulations and experiments suggests that, helix α9 assists Bax activation via the dimer heterogeneity and interactions with specific MOM lipids, which eventually facilitate proteolipidic pore formation in apoptosis regulation. PMID:27381287

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

    PubMed

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

    2016-01-01

    Helix α9 of Bax protein can dimerize in the mitochondrial outer membrane (MOM) and lead to apoptotic pores. However, it remains unclear how different conformations of the dimer contribute to the pore formation on the molecular level. Thus we have investigated various conformational states of the α9 dimer in a MOM model - using computer simulations supplemented with site-specific mutagenesis and crosslinking of the α9 helices. Our data not only confirmed the critical membrane environment for the α9 stability and dimerization, but also revealed the distinct lipid-binding preference of the dimer in different conformational states. In our proposed pathway, a crucial iso-parallel dimer that mediates the conformational transition was discovered computationally and validated experimentally. The corroborating evidence from simulations and experiments suggests that, helix α9 assists Bax activation via the dimer heterogeneity and interactions with specific MOM lipids, which eventually facilitate proteolipidic pore formation in apoptosis regulation. PMID:27381287

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

    PubMed

    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. PMID:25815927

  6. Anisotropy Effects on the Plasmonic Response of Nanoparticle Dimers.

    PubMed

    Varas, Alejandro; García-González, Pablo; García-Vidal, F J; Rubio, Angel

    2015-05-21

    We present an ab initio study of the anisotropy and atomic relaxation effects on the optical properties of nanoparticle dimers. Special emphasis is placed on the hybridization process of localized surface plasmons, plasmon-mediated photoinduced currents, and electric-field enhancement in the dimer junction. We show that there is a critical range of separations between the clusters (0.1-0.5 nm) in which the detailed atomic structure in the junction and the relative orientation of the nanoparticles have to be considered to obtain quantitative predictions for realistic nanoplasmonic devices. It is worth noting that this regime is characterized by the emergence of electron tunneling as a response to the driven electromagnetic field. The orientation of the particles not only modifies the attainable electric field enhancement but can lead to qualitative changes in the optical absorption spectrum of the system. PMID:26263265

  7. Data on dimer formation between importin α subtypes.

    PubMed

    Miyamoto, Yoichi; Oka, Masahiro

    2016-06-01

    This article describes data related to the research article titled "Functional characterization of importin α8 as a classical nuclear localization signal receptor" [1]. A GST pull-down assay showed that both importin α1 and α8, which are classical nuclear localization signal (cNLS) receptors, can form a dimer with importin α6, α7, or α8. Importin α8 has higher dimer-forming ability than importin α1. In addition, our data show that either importin α1 or importin α8 can form a heterodimer with importin α3, which exists in a preformed complex with cNLS substrates such as the conventional SV40TNLS or the p53 protein, resulting in the release of the cNLS substrates from importin α3. PMID:27222842

  8. Electronic signatures of dimerization in IrTe2

    NASA Astrophysics Data System (ADS)

    Dai, Jixia; Wu, Weida; Oh, Yoon Seok; Cheong, S.-W.; Yang, J. J.

    2014-03-01

    Recently, the mysterious phase transition around Tc ~ 260 K in IrTe2 has been intensively studied. A structural supermodulation with q =1/5 was identified below Tc. A variety of microscopic mechanisms have been proposed to account for this transition, including charge-density wave due to Fermi surface nesting, Te p-orbital driven structure instability, anionic depolymerization, ionic dimerization, and so on. However, there has not been an unified picture on the nature of this transition. To address this issue, we have performed low-temperature scanning tunneling microscopy and spectroscopy (STM/STS) experiments on IrTe2 and IrTe2-xSex. Our STM data clearly shows a strong bias dependence in both topography and local density of states (STS) maps. High resolution spectroscopic data further confirms the stripe-like electronic states modulation, which provides insight to the ionic dimerization revealed by X-ray diffraction.

  9. UV resonance Raman analysis of trishomocubane and diamondoid dimers

    SciTech Connect

    Meinke, Reinhard Thomsen, Christian; Maultzsch, Janina; Richter, Robert; Merli, Andrea; Fokin, Andrey A.; Koso, Tetyana V.; Schreiner, Peter R.; Rodionov, Vladimir N.

    2014-01-21

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

  10. High-resolution near-infrared spectroscopy of water dimer

    NASA Technical Reports Server (NTRS)

    Huang, Z. S.; Miller, R. E.

    1989-01-01

    High-resolution near-infrared spectra are reported for all of the O-H stretch vibrational bands of the water dimer. The four O-H vibrations are characterized as essentially independent proton-donor or proton-acceptor motions. In addition to the rotational and vibrational information contained in these spectra, details are obtained concerning the internal tunneling dynamics in both the ground and excited vibrational states. These results show that, for tunneling motions which involve the interchange of the proton donor and acceptor molecules, the associated frequencies decrease substantially due to vibrational excitation. The predissociation lifetimes for the various states of the dimer are determined from linewidth measurements. These results clearly show that the predissociation dynamics is strongly dependent on the tunneling states, as well as the Ka quantum number, indicating that the internal tunneling dynamics plays an important role in determining the dissociation rate in this complex.

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

    PubMed Central

    Macone, Alberto; Fontana, Mario; Barba, Marco; Botta, Bruno; Nardini, Mirella; Ghirga, Francesca; Calcaterra, Andrea; Pecci, Laura; Matarese, Rosa Marina

    2011-01-01

    Aminoethylcysteine ketimine decarboxylated dimer is a natural sulfur-containing compound detected in human plasma and urine, in mammalian brain and in many common edible vegetables. Over the past decade many studies have been undertaken to identify its metabolic role. Attention has been focused on its antioxidant properties and on its reactivity against oxygen and nitrogen reactive species. These properties have been studied in different model systems starting from plasma lipoproteins to specific cellular lines. All these studies report that aminoethylcysteine ketimine decarboxylated dimer is able to interact both with reactive oxygen and nitrogen species (hydrogen peroxide, superoxide anion, hydroxyl radical, peroxynitrite and its derivatives). Its antioxidant activity is similar to that of Vitamin E while higher than other hydrophilic antioxidants, such as trolox and N-acetylcysteine. PMID:21686170

  12. An engineered dimeric protein pore that spans adjacent lipid bilayers

    PubMed Central

    Mantri, Shiksha; Sapra, K. Tanuj; Cheley, Stephen; Sharp, Thomas H.; Bayley, Hagan

    2013-01-01

    The bottom-up construction of artificial tissues is an underexplored area of synthetic biology. An important challenge is communication between constituent compartments of the engineered tissue and between the engineered tissue and additional compartments, including extracellular fluids, further engineered tissue and living cells. Here we present a dimeric transmembrane pore that can span two adjacent lipid bilayers and thereby allow aqueous compartments to communicate. Two heptameric staphylococcal α-hemolysin (αHL) pores were covalently linked in an aligned cap-to-cap orientation. The structure of the dimer, (α7)2, was confirmed by biochemical analysis, transmission electron microscopy (TEM) and single-channel electrical recording. We show that one of two β barrels of (α7)2 can insert into the lipid bilayer of a small unilamellar vesicle, while the other spans a planar lipid bilayer. (α7)2 pores spanning two bilayers were also observed by TEM. PMID:23591892

  13. Bose and Mott glass phases in dimerized quantum antiferromagnets

    NASA Astrophysics Data System (ADS)

    Thomson, S. J.; Krüger, F.

    2015-11-01

    We examine the effects of disorder on dimerized quantum antiferromagnets in a magnetic field, using the mapping to a lattice gas of hard-core bosons with finite-range interactions. Combining a strong-coupling expansion, the replica method, and a one-loop renormalization-group analysis, we investigate the nature of the glass phases formed. We find that away from the tips of the Mott lobes, the transition is from a Mott insulator to a compressible Bose glass, however the compressibility at the tips is strongly suppressed. We identify this finding with the presence of a rare Mott glass phase and demonstrate that the inclusion of replica symmetry breaking is vital to correctly describe the glassy phases. This result suggests that the formation of Bose and Mott glass phases is not simply a weak localization phenomenon but is indicative of much richer physics. We discuss our results in the context of both ultracold atomic gases and spin-dimer materials.

  14. Hydrogen bonding in the benzene-ammonia dimer

    NASA Technical Reports Server (NTRS)

    Rodham, David A.; Suzuki, Sakae; Suenram, Richard D.; Lovas, Frank J.; Dasgupta, Siddharth; Goddard, William A., III; Blake, Geoffrey A.

    1993-01-01

    High-resolution optical and microwave spectra of the gas-phase benzene-ammonia dimer were obtained, showing that the ammonia molecule resides above the benzene plane and undergoes free, or nearly free, internal rotation. To estimate the binding energy (De) and other global properties of the intermolecular potential, theoretical calculations were performed for the benzene-ammonia dimer, using the Gaussian 92 (Fritsch, 1992) program at the MP2/6-31G** level. The predicted De was found to be at the lowest end of the range commonly accepted for hydrogen bonding and considerably below that of C6H6-H2O, consistent with the gas-phase acidities of ammonia and water. The observed geometry greatly resembles the amino-aromatic interaction found naturally in proteins.

  15. Cytotoxic bibenzyl dimers from the stems of Dendrobium fimbriatum Hook.

    PubMed

    Xu, Feng-Qing; Xu, Fang-Cheng; Hou, Bo; Fan, Wei-Wei; Zi, Cheng-Ting; Li, Yan; Dong, Fa-Wu; Liu, Yu-Qing; Sheng, Jun; Zuo, Zhi-Li; Hu, Jiang-Miao

    2014-11-15

    The bioassay-guided chemical investigation of the stems of Dendrobium fimbriatum Hook led to the isolation of seven first reported bibenzyl dimers with a linkage of a methylene moiety, fimbriadimerbibenzyls A-G (1-7), together with a new dihydrophenanthrene derivative (S)-2,4,5,9-tetrahydroxy-9,10-dihydrophenanthrene (8) and thirteen known compounds (9-21). The structure of the new compound was established by spectroscopic analysis. Biological evaluation of bibenzyl derivatives against five human cell lines indicated that seven of those compounds exhibited broad-spectrum and cytotoxic activities with IC50 values ranging from 2.2 to 21.2 μM. Those rare bibenzyl dimers exhibited cytotoxic activities in vitro and the cytotoxicity decreased as the number of oxygen-containing groups in the structure decreases. PMID:25316316

  16. Acylphenols and dimeric acylphenols from Myristica maxima Warb.

    PubMed

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

    2016-06-01

    Giganteone E (1), a new dimeric acylphenol was isolated as a minor constituent from the bark of Myristica maxima Warb. The structure of 1 was established on the basis of 1D and 2D NMR techniques and LCMS-IT-TOF analysis. Malabaricones A-C (2-4), giganteones A and C (5 and 6), maingayones A and B (7 and 8), maingayic acid B (9) and β-sitosteryl oleate (10) were also characterized in this plant for the first time. Compound 10 was identified for the first time in the Myristicaceae. Compounds 2 and 5 were active against human prostate cancer cell-lines, thus making this the first report on the prostate cancer inhibiting potential of acylphenols and dimeric acylphenols. Compounds 1, 4, 5, 7 and 8 exhibited potent DPPH free radical scavenging activity. This is the first report on their free radical scavenging capacity. PMID:27072985

  17. Electron Transport Through Josephson Junction Containing a Dimeric Structure

    NASA Astrophysics Data System (ADS)

    Val'kov, V. V.; Aksenov, S. V.

    2016-02-01

    The dc Josephson effect in a superconductor/dimeric molecule/superconductor junction has been investigated by means of the nonequilibrium Green's function method and the Keldysh diagram technique. The application of the atomic representation has allowed to simplify considerably the computation of the supercurrent and occupation numbers and receive the general expressions which take into account all processes of the Andreev reflection in the loopless approach. It is significant that the expressions for the current and occupation numbers are valid for different multilevel structures in the Josephson junction. The sf-exchange interaction between the electron spin and the spins of the dimer leads to the suppression of the critical current due to a new set of Andreev bound states.

  18. Single nucleotide polymorphism analysis using different colored dye dimer probes

    NASA Astrophysics Data System (ADS)

    Marmé, Nicole; Friedrich, Achim; Denapaite, Dalia; Hakenbeck, Regine; Knemeyer, Jens-Peter

    2006-09-01

    Fluorescence quenching by dye dimer formation has been utilized to develop hairpin-structured DNA probes for the detection of a single nucleotide polymorphism (SNP) in the penicillin target gene pbp2x, which is implicated in the penicillin resistance of Streptococcus pneumoniae. We designed two specific DNA probes for the identification of the pbp2x genes from a penicillin susceptible strain R6 and a resistant strain Streptococcus mitis 661 using green-fluorescent tetramethylrhodamine (TMR) and red-fluorescent DY-636, respectively. Hybridization of each of the probes to its respective target DNA sequence opened the DNA hairpin probes, consequently breaking the nonfluorescent dye dimers into fluorescent species. This hybridization of the target with the hairpin probe achieved single nucleotide specific detection at nanomolar concentrations via increased fluorescence.

  19. Dimer problem for some three dimensional lattice graphs

    NASA Astrophysics Data System (ADS)

    Lin, Fenggen; Chen, Ailian; Lai, Jiangzhou

    2016-02-01

    Dimer problem for three dimensional lattice is an unsolved problem in statistical mechanics and solid-state chemistry. In this paper, we obtain asymptotical expressions of the number of close-packed dimers (perfect matchings) for two types of three dimensional lattice graphs. Let M(G) denote the number of perfect matchings of G. Then log(M(K2 ×C4 ×Pn)) ≈(- 1.171 ṡn-1.1223 + 3.146) n, and log(M(K2 ×P4 ×Pn)) ≈(- 1.164 ṡn-1.196 + 2.804) n, where log() denotes the natural logarithm. Furthermore, we obtain a sufficient condition under which the lattices with multiple cylindrical and multiple toroidal boundary conditions have the same entropy.

  20. Discontinuous phase transition in a dimer lattice gas

    NASA Astrophysics Data System (ADS)

    Dickman, Ronald

    2012-05-01

    I study a dimer model on the square lattice with nearest neighbor exclusion as the only interaction. Detailed simulations using tomographic entropic sampling show that as the chemical potential is varied, there is a strongly discontinuous phase transition, at which the particle density jumps by about 18% of its maximum value, 1/4. The transition is accompanied by the onset of orientational order, to an arrangement corresponding to the {1/2, 0, 1/2} structure identified by Phares et al. [Physica B 409, 1096 (2011)] in a dimer model with finite repulsion at fixed density. Using finite-size scaling and Binder's cumulant, the expected scaling behavior at a discontinuous transition is verified in detail. The discontinuous transition can be understood qualitatively given that the model possesses eight equivalent maximum-density configurations, so that its coarse-grained description corresponds to that of the q = 8 Potts model.

  1. Radiative and rovibrational collisional relaxation of sodium dimer

    NASA Astrophysics Data System (ADS)

    Bayram, Burcin; Horton, Tim; McFarland, Jacob

    2016-05-01

    Radiative and rovibrational collisional relaxation of sodium dimer of the A1Σu+ (8,30) state have been measured by direct observation of the decay fluorescence. Sodium molecular vapor is created in a heatpipe oven at 600 K and excited using a 6-ns pulsed dye laser pumped by a Nd:YAG, operating at 532 nm. The preliminary lifetime measurement was done by directly acquiring lifetime data through boxcar averager from the stored oscilloscope trace of the fluorescence. Analysis of the exponential decay of the fluorescence allows us to obtain the radiative lifetime. By introducing the argon buffer gas and varying the pressure of the heatpipe, a collisional cross section between excited sodium dimer and ground state argon atom collision can be extracted using Stern-Volmer relation.

  2. GLYCOLALDEHYDE FORMATION VIA THE DIMERIZATION OF THE FORMYL RADICAL

    SciTech Connect

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

    2013-11-10

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

  3. Metal Complexes of meso-meso Linked Corrole Dimers.

    PubMed

    Ooi, Shota; Tanaka, Takayuki; Osuka, Atsuhiro

    2016-09-01

    Cobalt, gallium, silver, and copper complexes of 5,5'-linked corrole dimer 1 and 10,10'-linked corrole dimer 2 were synthesized by metalations with Co(OAc)2·4H2O, GaCl3, AgOAc, and Cu(OAc)2·H2O, respectively, in good yields. The structures of cobalt(III), gallium(III), and silver(III) complexes have been unambiguously revealed by X-ray diffraction analysis. Their optical and electrochemical properties have been studied, which revealed different electronic interactions between the two corrole units depending upon the positions of meso-meso linkage and axial-ligand coordination modes. PMID:27533780

  4. Role of the chlorophyll dimer in bacterial photosynthesis

    PubMed Central

    Warshel, Arieh

    1980-01-01

    The role of a special dimer (D) of bacteriochlorophyll molecules in bacterial photosynthesis was examined by calculations of the rates of electron transfer reactions in a system of the dimer and a bacteriopheophytin (BPh) molecule. It was found that the dependence of the potential surfaces of D on the distance between the monomers allows a fast light-induced electron transfer from D to BPh but only a slow back reaction (reduction of D+ by BPh-). The same potential surfaces allow efficient reduction of D+ by cytochrome c. Possible advantages of greatly different values of the electronic matrix elements for the forward and back reactions are pointed out. It is suggested that the electrostatic interaction between D+ and an ionized group of the protein might play an important role in the photosynthetic reaction. PMID:16592832

  5. Data on dimer formation between importin α subtypes

    PubMed Central

    Miyamoto, Yoichi; Oka, Masahiro

    2016-01-01

    This article describes data related to the research article titled “Functional characterization of importin α8 as a classical nuclear localization signal receptor” [1]. A GST pull-down assay showed that both importin α1 and α8, which are classical nuclear localization signal (cNLS) receptors, can form a dimer with importin α6, α7, or α8. Importin α8 has higher dimer-forming ability than importin α1. In addition, our data show that either importin α1 or importin α8 can form a heterodimer with importin α3, which exists in a preformed complex with cNLS substrates such as the conventional SV40TNLS or the p53 protein, resulting in the release of the cNLS substrates from importin α3. PMID:27222842

  6. Ab initio correlated calculations of rare-gas dimer quadrupoles

    NASA Astrophysics Data System (ADS)

    Donchev, Alexander G.

    2007-10-01

    This paper reports ab initio calculations of rare gas ( RG=Kr , Ar, Ne, and He) dimer quadrupoles at the second order of Møller-Plesset perturbation theory (MP2). The study reveals the crucial role of the dispersion contribution to the RG2 quadrupole in the neighborhood of the equilibrium dimer separation. The magnitude of the dispersion quadrupole is found to be much larger than that predicted by the approximate model of Hunt. As a result, the total MP2 quadrupole moment is significantly smaller than was assumed in virtually all previous related studies. An analytical model for the distance dependence of the RG2 quadrupole is proposed. The model is based on the effective-electron approach of Jansen, but replaces the original Gaussian approximation to the electron density in an RG atom by an exponential one. The role of the nonadditive contribution in RG3 quadrupoles is discussed.

  7. Plasmonic dimer antennas for surface enhanced Raman scattering.

    PubMed

    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. PMID:22498764

  8. dimerization and DNA binding alter phosphorylation of Fos and Jun

    SciTech Connect

    Abate, C.; Baker, S.J.; Curran, T. ); Lees-Miller, S.P.; Anderson, C.W. ); Marshak, D.R. )

    1993-07-15

    Fos and Jun form dimeric complexes that bind to activator protein 1 (AP-1) DNA sequences and regulate gene expression. The levels of expression and activities of these proteins are regulated by a variety of extracellular stimuli. They are thought to function in nuclear signal transduction processes in many different cell types. The role of Fos and Jun in gene transcription is complex and may be regulated in several ways including association with different dimerization partners, interactions with other transcription factors, effects on DNA topology, and reduction/oxidation of a conserved cysteine residue in the DNA-binding domain. In addition, phosphorylation has been suggested to control the activity of Fos and Jun. Here the authors show that phosphorylation of Fos and Jun by several protein kinases is affected by dimerization and binding to DNA. Jun homodimers are phosphorylated efficiently by casein kinase II, whereas Fos-Jun heterodimers are not. DNA binding also reduces phosphorylation of Jun by casein kinase II, p34[sup cdc2] (cdc2) kinase, and protein kinase C. Phosphorylation of Fos by cAMP-dependent protein kinase and cdc2 is relatively insensitive to dimerization and DNA binding, whereas phosphorylation of Fos and Jun by DNA-dependent protein kinase is dramatically stimulated by binding to the AP-1 site. These results imply that different protein kinases can distinguish among Fos and Jun proteins in the form of monomers, homodimers, and heterodimers and between DNA-bound and non-DNA-bound proteins. Thus, potentially, these different states of Fos and Jun can be recognized and regulated independently by phosphorylation. 44 refs., 4 figs.

  9. The Tetracyanopyridinide Dimer Dianion, σ-[TCNPy]2 (2.).

    PubMed

    Hao, Jingjun; Rheingold, Arnold L; Kavand, Marzieh; van Schooten, Kipp J; Boehme, Christoph; Capdevila-Cortada, Marçal; Novoa, Juan J; Wöss, Eva; Knör, Günther; Miller, Joel S

    2016-08-22

    The reaction of 2,3,5,6-tetracyanopyridine (TCNPy) and Cr(C6 H6 )2 forms diamagnetic σ-[TCNPy]2 (2-) possessing a 1.572(3) Å intrafragment sp(3) -sp(3) bond. This is in contrast to the structurally related 1,2,4,5-tetracyanobenzene and 1,2,4,5-tetracyanopyrazine that form π-dimer dianions possessing long, multicenter bonds. PMID:27465486

  10. Multiple-charge transfer and trapping in DNA dimers

    NASA Astrophysics Data System (ADS)

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

    2010-11-01

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

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

    PubMed

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

    2016-06-01

    The reaction intermediate in the path leading to UV-induced formation of adenine dimers A═A and AA* is identified for the first time quantum mechanically, using PCM/TD-DFT calculations on (dA)2 (dA: 2'deoxyadenosine). In parallel, its fingerprint is detected in the absorption spectra recorded on the millisecond time-scale for the single strand (dA)20 (dA: 2'deoxyadenosine). PMID:27163876

  12. Monitoring Retroviral RNA Dimerization In Vivo via Hammerhead Ribozyme Cleavage

    PubMed Central

    Pal, Bijay K.; Scherer, Lisa; Zelby, Laurie; Bertrand, Edouard; Rossi, John J.

    1998-01-01

    We have used a strategy for colocalization of Psi (Ψ)-tethered ribozymes and targets to demonstrate that Ψ sequences are capable of specific interaction in the cytoplasm of both packaging and nonpackaging cells. These results indicate that current in vitro dimerization models may have in vivo counterparts. The methodology used may be applied to further genetic analyses on Ψ domain interactions in vivo. PMID:9733882

  13. A xanthanolide diol and a dimeric xanthanolide from Xanthium species.

    PubMed

    Ahmed, A A; Mahmoud, A A; El-Gamal, A A

    1999-06-01

    Extracts of the aerial parts of Xanthium strumarium and fruit of X. pungens afforded a new Xanthanolide diol derivative, 11alpha,13-dihydroxyxanthatin and a new dimeric xanthanolide sesquiterpene lactone, pungiolide C, in addition to some known compounds. The structures of the new compounds were determined by spectroscopic methods particularly high resolution (1)H-, (13)C-NMR and 2D (1)H- (1)H and (1)H- (13)C COSY NMR analysis. PMID:17260271

  14. Bicompartmental phase transfer vehicles based on colloidal dimers.

    PubMed

    Wang, Sijia; Wu, Ning

    2014-11-26

    Colloidal particles have been used extensively for stabilizing oil-water interfaces in petroleum, food, and cosmetics industries. They have also demonstrated promising potential in the encapsulation and delivery of drugs. Our work is motivated by challenging applications that require protecting and transporting active agents across the water-oil interfaces, such as delivering catalysts to underground oil phase through water flooding for in situ cracking of crude oil. In this Research Article, we successfully design, synthesize, and test a unique type of bicompartmental targeting vehicle that encapsulates catalytic molecules, finds and accumulates at oil-water interface, releases the catalysts toward the oil phase, and performs hydrogenation reaction of unsaturated oil. This vehicle is based on colloidal dimers that possess structural anisotropy between two compartments. We encapsulate active species, such as fluorescent dye and catalytic molecules in one lobe which consists of un-cross-linked polymers, while the other polymeric lobe is highly cross-linked. Although dimers are dispersible in water initially, the un-cross-linked lobe swells significantly upon contact with a trace amount of oil in aqueous phase. The dimers then become amphiphilic, migrate toward, and accumulate at the oil-water interface. As the un-cross-linked lobe swells and eventually dissolves in oil, the encapsulated catalysts are fully released. We also show that hydrogenation of unsaturated oil can be performed subsequently with high conversion efficiency. By further creating the interfacial anisotropy on the dimers, we can reduce the catalyst release time from hundred hours to 30 min. Our work demonstrates a new concept in making colloidal emulsifiers and phase-transfer vehicles that are important for encapsulation and sequential release of small molecules across two different phases. PMID:25322697

  15. Dimeric calixarenes: a new family of major-groove binders.

    PubMed

    Hu, Wenbin; Blecking, Caroline; Kralj, Marijeta; Šuman, Lidija; Piantanida, Ivo; Schrader, Thomas

    2012-03-19

    A new class of potent DNA binding agents is presented. Dimeric calix[4]arenes with cationic groups at their upper rims and flexible alkyl bridges can be synthesized from triply acyl-protected calix[4]arene tetramines in relatively short synthetic sequences (3-5 steps). The compounds attach themselves to double-stranded nucleic acids in a noncovalent fashion, with micro- to nanomolar affinities. Guanidinium headgroups with their extended hydrogen-bonding "fingers" are more powerful than ammonium groups, and the benzylamine series is superior to the anilinium series (see below). The new ligands easily distinguish between RNA and various DNA types, and produce characteristic changes in UV/Vis, fluorescence, CD, as well as NMR spectra. Especially extended oligonucleotides of more than 100 base pairs are bound with affinities increasing from RNA (10 μM K(d))dimer per two BP), suggesting a potential aggregation of bound ligands inside the major groove. Most UV/Vis melting curves display an inverted shape, and start from drastically enhanced absorption intensities for the DNA complexes. DAPI displacement studies prove that up to one equivalent of calixarene dimer can be accommodated in the dye-loaded DNA. RNA complexation by calixarene dimers is accompanied by a drastic CD spectral transition from the typical A-form to a perfect B-signature, providing further experimental evidence for major-groove binding. The orientation of the ligands can be deduced from NMR titrations and is reproduced in Monte-Carlo simulations on 1:1 complexes in water. PMID:22336964

  16. Formation of Enhanced Uniform Chiral Fields in Symmetric Dimer Nanostructures.

    PubMed

    Tian, Xiaorui; Fang, Yurui; Sun, Mengtao

    2015-01-01

    Chiral fields with large optical chirality are very important in chiral molecules analysis, sensing and other measurements. Plasmonic nanostructures have been proposed to realize such super chiral fields for enhancing weak chiral signals. However, most of them cannot provide uniform chiral near-fields close to the structures, which makes these nanostructures not so efficient for applications. Plasmonic helical nanostructures and blocked squares have been proved to provide uniform chiral near-fields, but structure fabrication is a challenge. In this paper, we show that very simple plasmonic dimer structures can provide uniform chiral fields in the gaps with large enhancement of both near electric fields and chiral fields under linearly polarized light illumination with polarization off the dimer axis at dipole resonance. An analytical dipole model is utilized to explain this behavior theoretically. 30 times of volume averaged chiral field enhancement is gotten in the whole gap. Chiral fields with opposite handedness can be obtained simply by changing the polarization to the other side of the dimer axis. It is especially useful in Raman optical activity measurement and chiral sensing of small quantity of chiral molecule. PMID:26621558

  17. Hydrogen bond competition in the ethanol-methanol dimer.

    PubMed

    Finneran, Ian A; Carroll, P Brandon; Mead, Griffin J; Blake, Geoffrey A

    2016-08-10

    Previous theoretical work on the ethanol-methanol dimer has been inconclusive in predicting the preferred hydrogen bond donor/acceptor configuration. Here, we report the microwave spectrum of the dimer using a chirped pulse Fourier transform microwave spectrometer from 8-18 GHz. In an argon-backed expansion, 50 transitions have been assigned to a trans-ethanol-acceptor/methanol-donor structure that is likely stabilized by a secondary weak C-HO hydrogen bond. A higher energy conformer was observed in a helium-backed expansion and tentatively assigned to a gauche-ethanol-acceptor/methanol-donor structure. No ethanol-donor/methanol-acceptor dimers have been found, suggesting such interactions are energetically disfavored. A preliminary analysis of the A-E splitting due to the internal rotation of the methanol methyl group in the ground state species is also presented. We find evidence of the Ubbelohde effect in the measured A-E splittings of three deuterated isotopologues and the normal species of this conformer. PMID:27472828

  18. Dimer conformation of soluble PECAM-1, an endothelial marker.

    PubMed

    Jiang, Longguang; Lin, Lin; Li, Rui; Yuan, Cai; Xu, Mingming; Huang, Joy H; Huang, Mingdong

    2016-08-01

    Platelet endothelial cell adhesion molecule 1 (PECAM-1) is a cell surface receptor widely distributed on endothelium and hematopoietic-derived cells, and maintain the integrity of the blood vessels. PECAM-1 is widely recognized as an endothelial cell marker. The homophilic interaction through its extracellular domain of PECAM-1 (soluble PECAM-1, or sPECAM-1) is important to its functions. However, structural details for such dimerization are not fully understood. Here we report the production of recombinant sPECAM-1 in large quantity by Drosophila expression system and the small-angle X-ray diffraction (SAXS) study. The recombinant sPECAM-1 was found to form one population of dimer, but not oligomer, and was able to bind to heparin immobilized on a chip in surface plasmon resonance imaging (SPRi) binding experiments. The results of SAXS demonstrated that sPECAM-1 formed a symmetric homodimer of Ω-shape in solution, and each protomer adopted an extended conformation. The dimer is mediated through the intermolecular interactions through the first N-terminal domain (D1) of sPECAM-1. This model provides new structural information for its homophilic interaction mechanism. PMID:27270333

  19. The dimeric structure of factor XI and zymogen activation

    PubMed Central

    Geng, Yipeng; Verhamme, Ingrid M.; Smith, Stephen B.; Sun, Mao-fu; Matafonov, Anton; Cheng, Qiufang; Smith, Stephanie A.; Morrissey, James H.

    2013-01-01

    Factor XI (fXI) is a homodimeric zymogen that is converted to a protease with 1 (1/2-fXIa) or 2 (fXIa) active subunits by factor XIIa (fXIIa) or thrombin. It has been proposed that the dimeric structure is required for normal fXI activation. Consistent with this premise, fXI monomers do not reconstitute fXI-deficient mice in a fXIIa-dependent thrombosis model. FXI activation by fXIIa or thrombin is a slow reaction that can be accelerated by polyanions. Phosphate polymers released from platelets (poly-P) can enhance fXI activation by thrombin and promote fXI autoactivation. Poly-P increased initial rates of fXI activation 30- and 3000-fold for fXIIa and thrombin, respectively. FXI monomers were activated more slowly than dimers by fXIIa in the presence of poly-P. However, this defect was not observed when thrombin was the activating protease, nor during fXI autoactivation. The data suggest that fXIIa and thrombin activate fXI by different mechanisms. FXIIa may activate fXI through a trans-activation mechanism in which the protease binds to 1 subunit of the dimer, while activating the other subunit. For activation by thrombin, or during autoactivation, the data support a cis-activation mechanism in which the activating protease binds to and activates the same fXI subunit. PMID:23515926

  20. Allosterically controlled threading of polymers through macrocyclic dimers.

    PubMed

    Cantekin, Seda; Markvoort, Albert J; Elemans, Johannes A A W; Rowan, Alan E; Nolte, Roeland J M

    2015-03-25

    As part of an ongoing study to construct a molecular Turing machine in which a polymer chain is encoded via allosteric information transfer between macrocyclic complexes, we describe the thermodynamic and kinetic characterization of a multicomponent self-assembled system based on a zinc porphyrin macrocyclic compound, a bidentate ligand (1,4-diazabicyclo[2.2.2]octane, DABCO), and a viologen-substituted polymer guest. Initial addition of DABCO to the porphyrin macrocycle in chloroform solution leads to the formation of a stable 2:1 (porphyrin:DABCO) dimeric complex, even under dilute conditions, by means of strong cooperative interactions involving hydrogen and metal-ligand bonds. Further titration of the porphyrin-DABCO mixtures with the polymer gives rise to a complex array of species in the solution. The system is analyzed in detail by a combination of spectroscopic measurements and computational modeling. Each association constant in the binding scheme and the fraction of each individual complex that is formed in solution are determined precisely using a mass-balance model. Kinetic studies revealed that the rates of the polymer threading and dethreading in and out of the dimeric system are remarkably slow, indicating that the polymer is locked inside the cavity of the stable 2:1 dimeric complex as a result of strong allosteric interactions. PMID:25734357

  1. Directional Fano resonance in a silicon nanosphere dimer.

    PubMed

    Yan, Jiahao; Liu, Pu; Lin, Zhaoyong; Wang, Hao; Chen, Huanjun; Wang, Chengxin; Yang, Guowei

    2015-03-24

    Fano resonance arising from the interaction between a broad "bright" mode and a narrow "dark" mode has been widely investigated in symmetry-breaking structures made of noble metals such as plasmonic asymmetric oligomers or other well-designed nanostructures. However, Fano resonance in nanoscale all-dielectric dimers has not been experimentally demonstrated so far. We report the first experimental observation of directional Fano resonance in silicon nanosphere dimers (both homodimer and heterodimer) and clarify that the coupling between magnetic and electric dipole modes can easily generate Fano resonance in all-dielectric oligomers, distinctly differing from conventional Fano resonances based on electric responses or artificial optical magnetism. A silicon nanosphere dimer, exhibiting a strong magnetic response inside and an electric enhancement in the gap, is an excellent structure to support magnetic-based Fano scattering. Interactions between magnetic and electric dipoles can suppress backward scattering and enhance forward scattering at Fano wavelengths. This directional scattering is much more prominent than that from a single silicon sphere and shows promising applications in areas such as directional nanoantenna or optical switching, opening up avenues for developing all-dielectric low-loss metamaterials or nanophotonic devices at visible wavelengths. PMID:25683067

  2. Formation of Enhanced Uniform Chiral Fields in Symmetric Dimer Nanostructures

    PubMed Central

    Tian, Xiaorui; Fang, Yurui; Sun, Mengtao

    2015-01-01

    Chiral fields with large optical chirality are very important in chiral molecules analysis, sensing and other measurements. Plasmonic nanostructures have been proposed to realize such super chiral fields for enhancing weak chiral signals. However, most of them cannot provide uniform chiral near-fields close to the structures, which makes these nanostructures not so efficient for applications. Plasmonic helical nanostructures and blocked squares have been proved to provide uniform chiral near-fields, but structure fabrication is a challenge. In this paper, we show that very simple plasmonic dimer structures can provide uniform chiral fields in the gaps with large enhancement of both near electric fields and chiral fields under linearly polarized light illumination with polarization off the dimer axis at dipole resonance. An analytical dipole model is utilized to explain this behavior theoretically. 30 times of volume averaged chiral field enhancement is gotten in the whole gap. Chiral fields with opposite handedness can be obtained simply by changing the polarization to the other side of the dimer axis. It is especially useful in Raman optical activity measurement and chiral sensing of small quantity of chiral molecule. PMID:26621558

  3. On the photophysics and photochemistry of the water dimer

    NASA Astrophysics Data System (ADS)

    Segarra-Martí, Javier; Roca-Sanjuán, Daniel; Merchán, Manuela; Lindh, Roland

    2012-12-01

    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 (WD) and the water acceptor (WA). A red-shift and a blue-shift are predicted for the WD and WA, 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 H2O…HO species plus a hydrogen H atom.

  4. SUMO Chain-Induced Dimerization Activates RNF4

    PubMed Central

    Rojas-Fernandez, Alejandro; Plechanovová, Anna; Hattersley, Neil; Jaffray, Ellis; Tatham, Michael H.; Hay, Ronald T.

    2014-01-01

    Summary Dimeric RING E3 ligases interact with protein substrates and conformationally restrain the ubiquitin-E2-conjugating enzyme thioester complex such that it is primed for catalysis. RNF4 is an E3 ligase containing an N-terminal domain that binds its polySUMO substrates and a C-terminal RING domain responsible for dimerization. To investigate how RNF4 activity is controlled, we increased polySUMO substrate concentration by ablating expression of SUMO protease SENP6. Accumulation of SUMO chains in vivo leads to ubiquitin-mediated proteolysis of RNF4. In vitro we demonstrate that at concentrations equivalent to those found in vivo RNF4 is predominantly monomeric and inactive as an ubiquitin E3 ligase. However, in the presence of SUMO chains, RNF4 is activated by dimerization, leading to both substrate ubiquitylation and autoubiquitylation, responsible for degradation of RNF4. Thus the ubiquitin E3 ligase activity of RNF4 is directly linked to the availability of its polySUMO substrates. PMID:24656128

  5. Ground States of a Disordered Frustrated Quantum Dimer Magnet

    NASA Astrophysics Data System (ADS)

    Hristov, Alexander; Shapiro, Maxwell; Fisher, Ian; Lee, Minseong; Rodenbach, Linsey; Bernheisel, Ashley; Choi, Eun Sang; Park, Ju-Hyun; Civale, Leonardo; Munsie, Tim; Luke, Graeme

    2015-03-01

    We present results of thermodynamic measurements of the site-diluted spin-dimer magnet Ba3 (Mn1-xVx)2 O8, including magnetization, torque magnetometry, and AC susceptibility. The parent compound Ba3Mn2O8 is a frustrated S = 1 quantum dimer-magnet with a singlet ground state, and triplet and quintuplet excitations. A magnetic field can be used to tune the energy spectrum of this system, yielding successive triplet and quintuplet condensates at low temperatures. Site substitution with S = 0 V breaks Mn-dimers, introducing site disorder into the high-field ordered states. This substitution also introduces unpaired S = 1 Mn ions, and it has been an open question whether such spins order at low temperatures. Here, we present evidence of the spin-freezing of unpaired Mn ions below 240mK for all compositions measured, from x=0.05 to 0.85. We also present the evolution of the high field ordered state with increasing disorder. NSF DMR-Award 1205165.

  6. On the photophysics and photochemistry of the water dimer

    SciTech Connect

    Segarra-Marti, Javier; Merchan, Manuela; Roca-Sanjuan, Daniel; Lindh, Roland

    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.

  7. Theory and simulations of adhesion receptor dimerization on membrane surfaces.

    PubMed

    Wu, Yinghao; Honig, Barry; Ben-Shaul, Avinoam

    2013-03-19

    The equilibrium constants of trans and cis dimerization of membrane bound (2D) and freely moving (3D) adhesion receptors are expressed and compared using elementary statistical-thermodynamics. Both processes are mediated by the binding of extracellular subdomains whose range of motion in the 2D environment is reduced upon dimerization, defining a thin reaction shell where dimer formation and dissociation take place. We show that the ratio between the 2D and 3D equilibrium constants can be expressed as a product of individual factors describing, respectively, the spatial ranges of motions of the adhesive domains, and their rotational freedom within the reaction shell. The results predicted by the theory are compared to those obtained from a novel, to our knowledge, dynamical simulations methodology, whereby pairs of receptors perform realistic translational, internal, and rotational motions in 2D and 3D. We use cadherins as our model system. The theory and simulations explain how the strength of cis and trans interactions of adhesive receptors are affected both by their presence in the constrained intermembrane space and by the 2D environment of membrane surfaces. Our work provides fundamental insights as to the mechanism of lateral clustering of adhesion receptors after cell-cell contact and, more generally, to the formation of lateral microclusters of proteins on cell surfaces. PMID:23528081

  8. SUMO chain-induced dimerization activates RNF4.

    PubMed

    Rojas-Fernandez, Alejandro; Plechanovová, Anna; Hattersley, Neil; Jaffray, Ellis; Tatham, Michael H; Hay, Ronald T

    2014-03-20

    Dimeric RING E3 ligases interact with protein substrates and conformationally restrain the ubiquitin-E2-conjugating enzyme thioester complex such that it is primed for catalysis. RNF4 is an E3 ligase containing an N-terminal domain that binds its polySUMO substrates and a C-terminal RING domain responsible for dimerization. To investigate how RNF4 activity is controlled, we increased polySUMO substrate concentration by ablating expression of SUMO protease SENP6. Accumulation of SUMO chains in vivo leads to ubiquitin-mediated proteolysis of RNF4. In vitro we demonstrate that at concentrations equivalent to those found in vivo RNF4 is predominantly monomeric and inactive as an ubiquitin E3 ligase. However, in the presence of SUMO chains, RNF4 is activated by dimerization, leading to both substrate ubiquitylation and autoubiquitylation, responsible for degradation of RNF4. Thus the ubiquitin E3 ligase activity of RNF4 is directly linked to the availability of its polySUMO substrates. PMID:24656128

  9. Multipole analysis of unidirectional light scattering from plasmonic dimers

    NASA Astrophysics Data System (ADS)

    Poutrina, E.; Urbas, A.

    2014-11-01

    We analyze unidirectional scattering produced by sub-wavelength plasmonic dimers formed by two silver strips separated by a thin dielectric spacer and embedded in a uniform dielectric medium. Achieving the Kerker condition, which requires matching the strengths of the electric and magnetic-type contributions of the same multipolar order, is possible with such structures for both forward and backward unidirectional scattering by matching the geometric shape-leveraged resonant magnetic dipolar response with the off-resonant electric dipolar contribution. However, unidirectionality is strongly affected by coupling between the two elements in the dimer structure, leading to the manifestation of the electric quadrupole response in the far field. We develop an approach allowing for an easy inverse scattering retrieval of various multipole contributions to the far-field pattern produced by this type of geometry. The retrieval shows unambiguously that the electric quadrupole response contributes up to 30% of the scattered far-field intensity, in addition to strong manifestation of both electric and magnetic dipolar modes. A modified condition for unidirectionality can be developed based on the principle that suppression of radiation in either the forward or backward direction can be achieved whenever the combined strength of multipolar modes of a certain parity, radiating along the propagation direction, matches that of an opposite parity, and noting that parities of electric and magnetic modes interchange with increasing multipole order. With this condition satisfied, unidirectionality of 26 dB/17 dB for forward/backward scattering, respectively, can be achieved with dimer geometries. We also perform a detailed quantitative analysis of scattering cross sections of dimer structures compared to those of Si and gold spheres, accounting for the actual material losses. We show that dimer structures allow for improving backscattering unidirectionality by 10 dB compared to what

  10. Density functional theory study of Fe, Co, and Ni adatoms and dimers adsorbed on graphene

    NASA Astrophysics Data System (ADS)

    Johll, Harman; Kang, Hway Chuan; Tok, Eng Soon

    2009-06-01

    Metal clusters have been investigated rather intensely for both fundamental and technological reasons. In this work we report the results of plane-wave density functional theory calculations of Fe, Co, and Ni adatoms and dimers adsorbed on graphene. We study both homonuclear and heteronuclear dimers, and the latter includes mixed dimers of Fe, Co, and Ni along with dimers of these elements with Pt. Our work is motivated by the fundamental interest in their configurational and magnetic properties. We calculated the adsorption site, the structure and relative stabilities of various adsorption configurations, the band structures, the atomic projected electronic density of states, and the magnetic moments of the adatoms and dimers. Contrary to previous work, our results show that adatoms bind weakly to graphene with binding energies ranging from 0.2 to 1.4 eV depending on the adsorption site and species. For both homonuclear and heteronuclear dimers the binding energies per atom are lower than the respective adatom cases, ranging from 0.1 to 0.5 eV per metal atom. The most strongly bound configurations for all the dimers studied are those with the dimer axis (nearly) perpendicular to the graphene plane and bound at the hole site. These configurations, which, to our knowledge, have not been considered in previous work, also turn out to have the largest enhancement of the magnetic moment at least for the atom farther from the graphene. The binding energies of these most strongly bound dimers are dependent on three factors, namely, the interconfigurational energy change in the dimer atom farther from graphene upon desorption, the charge transfer from the dimer to the graphene, and the adsorption site favored by the atom closer to the graphene sheet. The first factor is dominant for all the dimers studied here except for CoPt and NiPt. The relatively high electronegativity of Pt affects the character of the charge transfer from the dimer to graphene. In most of the dimers

  11. Kinetic mechanism for formation of the active, dimeric UvrD helicase-DNA complex.

    PubMed

    Maluf, Nasib K; Ali, Janid A; Lohman, Timothy M

    2003-08-22

    Escherichia coli UvrD protein is a 3' to 5' SF1 helicase required for DNA repair as well as DNA replication of certain plasmids. We have shown previously that UvrD can self-associate to form dimers and tetramers in the absence of DNA, but that a UvrD dimer is required to form an active helicase-DNA complex in vitro. Here we have used pre-steady state, chemical quenched flow methods to examine the kinetic mechanism for formation of the active, dimeric helicase-DNA complex. Experiments were designed to examine the steps leading to formation of the active complex, separate from the subsequent DNA unwinding steps. The results show that the active dimeric complex can form via two pathways. The first, faster path involves direct binding to the DNA substrate of a pre-assembled UvrD dimer (dimer path), whereas the second, slower path proceeds via sequential binding to the DNA substrate of two UvrD monomers (monomer path), which then assemble on the DNA to form the dimeric helicase. The rate-limiting step within the monomer pathway involves dimer assembly on the DNA. These results show that UvrD dimers that pre-assemble in the absence of DNA are intermediates along the pathway to formation of the functional dimeric UvrD helicase. PMID:12788954

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  13. Kit receptor dimerization is driven by bivalent binding of stem cell factor.

    PubMed

    Lemmon, M A; Pinchasi, D; Zhou, M; Lax, I; Schlessinger, J

    1997-03-01

    Most growth factors and cytokines activate their receptors by inducing dimerization upon binding. We have studied binding of the dimeric cytokine stem cell factor (SCF) to the extracellular domain of its receptor Kit, which is a receptor tyrosine kinase similar to the receptors for platelet-derived growth factor and colony-stimulating factor-1. Calorimetric studies show that one SCF dimer binds simultaneously to two molecules of the Kit extracellular domain. Gel filtration and other methods show that this results in Kit dimerization. It has been proposed that SCF-induced Kit dimerization proceeds via a conformational change that exposes a key receptor dimerization site in the fourth of the five immunoglobulin (Ig)-like domains in Kit. We show that a form of Kit containing just the first three Ig domains (Kit-123) binds to SCF with precisely the same thermodynamic parameters as does Kit-12345. Analytical ultracentrifugation, light scattering, and gel filtration show that Kit-123 dimerizes upon SCF binding in a manner indistinguishable from that seen with Kit-12345. These data argue that the fourth Ig-like domain of Kit is not required for SCF-induced receptor dimerization and provide additional support for a model in which bivalent binding of the SCF dimer provides the driving force for Kit dimerization. PMID:9045650

  14. Different channel properties of Torpedo acetylcholine receptor monomers and dimers reconstituted in planar membranes.

    PubMed Central

    Schindler, H; Spillecke, F; Neumann, E

    1984-01-01

    It is demonstrated that the monomeric and dimeric structures of the nicotinic acetylcholine receptor of Torpedo californica electric tissue, reconstituted in planar lipid bilayers, are functionally different. The native dimer D of Mr 500,000 (heavy-form) exhibits a "single" channel conductance about twice as large as that of the monomer M of Mr 250,000 (light form). Under conditions where monomers aggregate, the conductance changes from the level of the monomer M to that of dimers M2. The dimer conductances (D and M2) seem to result from synchronous opening and closing of the two channels in the dimer, giving the impression of "single channel" activity. This channel cooperativity is apparently mediated by noncovalent interactions between the two monomers, since it requires no disulfide linkage between monomers. Both the monomers M and the dimers D and M2 show at least one substate of lower conductivity. The relative population of the two conductance levels depends on the ion type (Na+ and K+), indicating ion-specific channel states. Since the channel conductance of isolated dimers resembles those obtained from unextracted microsacs, the dimer with two synchronized channels appears to be the in vivo predominant gating unit. In the linear association of dimers, observed in the native membrane, channel synchronization may extend to more than two channels as suggested by oligomeric channel cooperativity in associations of monomers and dimers. PMID:6091143

  15. HIV-1 RNA genome dimerizes on the plasma membrane in the presence of Gag protein.

    PubMed

    Chen, Jianbo; Rahman, Sheikh Abdul; Nikolaitchik, Olga A; Grunwald, David; Sardo, Luca; Burdick, Ryan C; Plisov, Sergey; Liang, Edward; Tai, Sheldon; Pathak, Vinay K; Hu, Wei-Shau

    2016-01-12

    Retroviruses package a dimeric genome comprising two copies of the viral RNA. Each RNA contains all of the genetic information for viral replication. Packaging a dimeric genome allows the recovery of genetic information from damaged RNA genomes during DNA synthesis and promotes frequent recombination to increase diversity in the viral population. Therefore, the strategy of packaging dimeric RNA affects viral replication and viral evolution. Although its biological importance is appreciated, very little is known about the genome dimerization process. HIV-1 RNA genomes dimerize before packaging into virions, and RNA interacts with the viral structural protein Gag in the cytoplasm. Thus, it is often hypothesized that RNAs dimerize in the cytoplasm and the RNA-Gag complex is transported to the plasma membrane for virus assembly. In this report, we tagged HIV-1 RNAs with fluorescent proteins, via interactions of RNA-binding proteins and motifs in the RNA genomes, and studied their behavior at the plasma membrane by using total internal reflection fluorescence microscopy. We showed that HIV-1 RNAs dimerize not in the cytoplasm but on the plasma membrane. Dynamic interactions occur among HIV-1 RNAs, and stabilization of the RNA dimer requires Gag protein. Dimerization often occurs at an early stage of the virus assembly process. Furthermore, the dimerization process is probably mediated by the interactions of two RNA-Gag complexes, rather than two RNAs. These findings advance the current understanding of HIV-1 assembly and reveal important insights into viral replication mechanisms. PMID:26712001

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

    PubMed

    Khan, Imran; Hong, Jisang

    2016-09-23

    We studied the geometries, electronic structure and magnetic properties of substitutional doping and adsorption of transition metal (Mn, Fe and Co) dimers on phosphorene monolayer in the framework of the generalized gradient approximation (GGA) and GGA + U. Electronic band structures and magnetic properties were dependent on the doping type and dopant materials. For Mn and Fe substitutional and adsorption dimers, we obtained semiconducting band structures with spin polarization. However, we found a half-metallic feature in Co substitutional dimer while the Co adsorption dimer showed a semiconducting behavior without any spin polarization. With GGA + U, all the systems showed spin polarized semiconducting band structures except Co adsorption dimer which remained unaffected. The hybridization between transition metal (TM) and phosphorene sheet contributed to suppressing the magnetic moment of TM dimers. For instance, the total magnetic moments of -2.0, 4.24 and 1.28 μ B/cell for Mn, Fe and Co substitutional dimers were obtained while the Mn and Fe adsorption dimers showed magnetic moments of -1.69 and 0.46 μ B/cell. These magnetic moments were enhanced with GGA + U. The same magnetic ground states were obtained both from GGA and GGA + U approaches except for the Mn dimers. We observed that the Mn and Fe substitutional dimers showed an out-of-plane magnetization while an in-plane magnetization was observed in Co substitutional dimer. The Mn adsorption dimer still displayed a perpendicular magnetization whereas the Fe adsorption dimer had an in-plane magnetization. We found that the both GGA and GGA + U showed the same magnetization direction in all the systems. PMID:27512907

  17. Direct Detection of α-Synuclein Dimerization Dynamics: Single-Molecule Fluorescence Analysis

    PubMed Central

    Lv, Zhengjian; Krasnoslobodtsev, Alexey V.; Zhang, Yuliang; Ysselstein, Daniel; Rochet, Jean-Christophe; Blanchard, Scott C.; Lyubchenko, Yuri L.

    2015-01-01

    The aggregation of α-synuclein (α-Syn) is linked to Parkinson’s disease. The mechanism of early aggregation steps and the effect of pathogenic single-point mutations remain elusive. We report here a single-molecule fluorescence study of α-Syn dimerization and the effect of mutations. Specific interactions between tethered fluorophore-free α-Syn monomers on a substrate and fluorophore-labeled monomers diffusing freely in solution were observed using total internal reflection fluorescence microscopy. The results showed that wild-type (WT) α-Syn dimers adopt two types of dimers. The lifetimes of type 1 and type 2 dimers were determined to be 197 ± 3 ms and 3334 ± 145 ms, respectively. All three of the mutations used, A30P, E46K, and A53T, increased the lifetime of type 1 dimer and enhanced the relative population of type 2 dimer, with type 1 dimer constituting the major fraction. The kinetic stability of type 1 dimers (expressed in terms of lifetime) followed the order A30P (693 ± 14 ms) > E46K (292 ± 5 ms) > A53T (226 ± 6 ms) > WT (197 ± 3 ms). Type 2 dimers, which are more stable, had lifetimes in the range of several seconds. The strongest effect, observed for the A30P mutant, resulted in a lifetime 3.5 times higher than observed for the WT type 1 dimer. This mutation also doubled the relative fraction of type 2 dimer. These data show that single-point mutations promote dimerization, and they suggest that the structural heterogeneity of α-Syn dimers could lead to different aggregation pathways. PMID:25902443

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

    NASA Astrophysics Data System (ADS)

    Khan, Imran; Hong, Jisang

    2016-09-01

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

  19. Dimerization of SLX4 contributes to functioning of the SLX4-nuclease complex

    PubMed Central

    Yin, Jinhu; Wan, Bingbing; Sarkar, Jaya; Horvath, Kent; Wu, Jian; Chen, Yong; Cheng, Guangjuan; Wan, Ke; Chin, Peiju; Lei, Ming; Liu, Yie

    2016-01-01

    The Fanconi anemia protein SLX4 assembles a genome and telomere maintenance toolkit, consisting of the nucleases SLX1, MUS81 and XPF. Although it is known that SLX4 acts as a scaffold for building this complex, the molecular basis underlying this function of SLX4 remains unclear. Here, we report that functioning of SLX4 is dependent on its dimerization via an oligomerization motif called the BTB domain. We solved the crystal structure of the SLX4BTB dimer, identifying key contacts (F681 and F708) that mediate dimerization. Disruption of BTB dimerization abrogates nuclear foci formation and telomeric localization of not only SLX4 but also of its associated nucleases. Furthermore, dimerization-deficient SLX4 mutants cause defective cellular response to DNA interstrand crosslinking agent and telomere maintenance, underscoring the contribution of BTB domain-mediated dimerization of SLX4 in genome and telomere maintenance. PMID:27131364

  20. Diffusion of Cu adatoms and dimers on Cu(111) and Ag(111) surfaces

    NASA Astrophysics Data System (ADS)

    Mińkowski, Marcin; Załuska-Kotur, Magdalena A.

    2015-12-01

    Diffusion of Cu adatoms and dimers on Cu(111) and Ag(111) surfaces is analyzed based on ab initio surface potentials. Single adatom diffusion is compared with dimer diffusion on both surfaces. Surface geometry makes the adatoms jump alternately between two states in the same way in both systems, whereas dimers undergo more complex diffusion process that combines translational and rotational motion. Small difference in the surface lattice constant between Cu and Ag crystals results in a completely different energy landscape for dimer jumps. As an effect the character of diffusion process changes. Homogeneous Cu dimer diffusion is more difficult and dimers rather rotate within single surface cell, whereas diffusion over Ag surface is faster and happens more smoothly. The temperature dependence of diffusion coefficient and its parameters: energy barrier and prefactor is calculated and compared for both surfaces.

  1. ROLE OF ANTIBODIES IN DEVELOPING DRUGS THAT TARGET G PROTEIN-COUPLED RECEPTOR DIMERS

    PubMed Central

    Hipser, Chris; Bushlin, Ittai; Gupta, Achla; Gomes, Ivone; Devi, Lakshmi A.

    2010-01-01

    G protein-coupled receptors (GPCRs) are important molecular targets in drug discovery. These receptors play a pivotal role in physiological signaling pathways and are targeted by nearly 50% of currently available drugs. Mounting evidence suggests that GPCRs form dimers and various studies have shown that dimerization is necessary for receptor maturation, signaling and trafficking. However, the physiological implications of dimerization in vivo have not been well explored since detection of GPCR dimers in endogenous systems has been a challenging task. One exciting new approach to this challenge is the generation of antibodies against specific GPCR dimers. Such antibodies could be used as tools for characterization of heteromer-specific function, as reagents for their purification, tissue localization and regulation in vivo and as probes for mapping their functional domains. In addition, such antibodies could serve as alternative ligands for GPCR heteromers. Thus, heteromer-specific antibodies represent novel tools for the exploration and manipulation of GPCR dimer pharmacology. PMID:20687183

  2. Thiazole Orange Dimers in DNA: Fluorescent Base Substitutions with Hybridization Readout.

    PubMed

    Berndl, Sina; Dimitrov, Stoichko D; Menacher, Florian; Fiebig, Torsten; Wagenknecht, Hans-Achim

    2016-02-12

    By using (S)-2-amino-1,3-propanediol as a linker, thiazole orange (TO) was incorporated in a dimeric form into DNA. The green fluorescence (λ=530 nm) of the intrastrand TO dimer is quenched, whereas the interstrand TO dimer shows a characteristic redshifted orange emission (λ=585 nm). Steady-state optical spectroscopic methods reveal that the TO dimer fluorescence is independent of the sequential base contexts. Time-resolved pump-probe measurements and excitation spectra reveal the coexistence of conformations, including mainly stacked TO dimers and partially unstacked ones, which yield exciton and excimer contributions to the fluorescence, respectively. The helicity of the DNA framework distorts the excitonic coupling. In particular, the interstrand TO dimer could be regarded as an excitonically interacting base pair with fluorescence readout for DNA hybridization. Finally, the use of this fluorescent readout was representatively demonstrated in molecular beacons. PMID:26773846

  3. Excision repair of UV-induced pyrimidine dimers in human skin in vivo

    SciTech Connect

    D'Ambrosio, S.M.; Slazinski, L.; Whetstone, J.W.; Lowney, E.

    1981-09-01

    The induction and loss of pyrimidine dimers in human skin in vivo was determined using UV endonuclease, alkaline sucrose sedimentations, and the fluorescent detection of nonradiolabeled DNA. The number of dimers induced following exposure of the skin to radiation emitted from a Burdick UV-800 sunlamp was quantitated by reacting the extracted DNA with Micrococcus luteus endonuclease specific for pyrimidine dimers. Exposure to 15 and 30 seconds of radiation emitted from this lamp produced the formation of 12.8 and 23.6 dimers per 10(8) daltons DNA, respectively. Approximately 50% of the dimers induced were lost 58 min after irradiation. Only a small percentage (less than 10) remained 24 hr postirradiation. These data partially characterize the process by which pyrimidine dimers are excised from human skin DNA in vivo.

  4. UV laser multiphoton ionization--dissociation of phenylsilane and its homogeneous dimers

    NASA Astrophysics Data System (ADS)

    Kosmidis, Constantine; Philis, John G.

    1998-01-01

    Homogeneous dimers of phenylsilane, formed in a rare-gas seeded supersonic expansion have been studied by laser resonant two-photon ionization combined with a time-of-flight mass spectrometer. The resonant intermediate states are the S1 (270 nm) and S2 (210 nm) ones. The ionization of phenylsilane monomer is inefficient at 210 nm whereas phenylsilane homo-dimers are resonantly ionized with high efficiency at this wavelength region. The wavelength dependence of the dimer at S1<-- S0 origin region implies the existence of at least two, almost isoenergetic, dimer conformers in the molecular beam. Photoionization of phenylsilane dimer induces chemical reactions within the dimer. The detected dissociation channels have to do with -SiH3 and -C6H6 loss and proton-transfer. Van der Waals fragmentation (evaporation of a neutral phenylsilane) is also taking place.

  5. Dimerization of SLX4 contributes to functioning of the SLX4-nuclease complex.

    PubMed

    Yin, Jinhu; Wan, Bingbing; Sarkar, Jaya; Horvath, Kent; Wu, Jian; Chen, Yong; Cheng, Guangjuan; Wan, Ke; Chin, Peiju; Lei, Ming; Liu, Yie

    2016-06-01

    The Fanconi anemia protein SLX4 assembles a genome and telomere maintenance toolkit, consisting of the nucleases SLX1, MUS81 and XPF. Although it is known that SLX4 acts as a scaffold for building this complex, the molecular basis underlying this function of SLX4 remains unclear. Here, we report that functioning of SLX4 is dependent on its dimerization via an oligomerization motif called the BTB domain. We solved the crystal structure of the SLX4BTB dimer, identifying key contacts (F681 and F708) that mediate dimerization. Disruption of BTB dimerization abrogates nuclear foci formation and telomeric localization of not only SLX4 but also of its associated nucleases. Furthermore, dimerization-deficient SLX4 mutants cause defective cellular response to DNA interstrand crosslinking agent and telomere maintenance, underscoring the contribution of BTB domain-mediated dimerization of SLX4 in genome and telomere maintenance. PMID:27131364

  6. The native cyclobutane pyrimidine dimer photolyase of rice is phosphorylated.

    PubMed

    Teranishi, Mika; Nakamura, Kentaro; Morioka, Hiroshi; Yamamoto, Kazuo; Hidema, Jun

    2008-04-01

    The cyclobutane pyrimidine dimer (CPD) is a major type of DNA damage induced by ultraviolet B (UVB) radiation. CPD photolyase, which absorbs blue/UVA light as an energy source to monomerize dimers, is a crucial factor for determining the sensitivity of rice (Oryza sativa) to UVB radiation. Here, we purified native class II CPD photolyase from rice leaves. As the final purification step, CPD photolyase was bound to CPD-containing DNA conjugated to magnetic beads and then released by blue-light irradiation. The final purified fraction contained 54- and 56-kD proteins, whereas rice CPD photolyase expressed from Escherichia coli was a single 55-kD protein. Western-blot analysis using anti-rice CPD photolyase antiserum suggested that both the 54- and 56-kD proteins were the CPD photolyase. Treatment with protein phosphatase revealed that the 56-kD native rice CPD photolyase was phosphorylated, whereas the E. coli-expressed rice CPD photolyase was not. The purified native rice CPD photolyase also had significantly higher CPD photorepair activity than the E. coli-expressed CPD photolyase. According to the absorption, emission, and excitation spectra, the purified native rice CPD photolyase possesses both a pterin-like chromophore and an FAD chromophore. The binding activity of the native rice CPD photolyase to thymine dimers was higher than that of the E. coli-expressed CPD photolyase. These results suggest that the structure of the native rice CPD photolyase differs significantly from that of the E. coli-expressed rice CPD photolyase, and the structural modification of the native CPD photolyase leads to higher activity in rice. PMID:18235036

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

    PubMed

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

    2016-03-01

    The antineoplastic and antibiotic natural product mithramycin (MTM) is used against cancer-related hypercalcemia and, experimentally, against Ewing sarcoma and lung cancers. MTM exerts its cytotoxic effect by binding DNA as a divalent metal ion (Me(2+))-coordinated dimer and disrupting the function of transcription factors. A precise molecular mechanism of action of MTM, needed to develop MTM analogues selective against desired transcription factors, is lacking. Although it is known that MTM binds G/C-rich DNA, the exact DNA recognition rules that would allow one to map MTM binding sites remain incompletely understood. Towards this goal, we quantitatively investigated dimerization of MTM and several of its analogues, MTM SDK (for Short side chain, DiKeto), MTM SA-Trp (for Short side chain and Acid), MTM SA-Ala, and a biosynthetic precursor premithramycin B (PreMTM B), and measured the binding affinities of these molecules to DNA oligomers of different sequences and structural forms at physiological salt concentrations. We show that MTM and its analogues form stable dimers even in the absence of DNA. All molecules, except for PreMTM B, can bind DNA with the following rank order of affinities (strong to weak): MTM=MTM SDK>MTM SA-Trp>MTM SA-Ala. An X(G/C)(G/C)X motif, where X is any base, is necessary and sufficient for MTM binding to DNA, without a strong dependence on DNA conformation. These recognition rules will aid in mapping MTM sites across different promoters towards development of MTM analogues as useful anticancer agents. PMID:26760230

  8. Comparability of D-dimer assays in clinical samples.

    PubMed

    Freyburger, Geneviève; Labrouche, Sylvie

    2005-11-01

    D-dimers (DD) have shown sufficient proof of their efficiency in the last 10 years to play an important role in hemostasis laboratories for excluding thromboembolic events. Numerous reagents are available on the market but their performances differ. This overview takes stock of the methods used to evaluate the performances of DD assays, the results published in the literature, the technical parameters influencing assay performance, the difficulties caused by the lack of harmonization of DD units, and the attempts to tackle this problem. It raises the issue of the potential optimization of their use with regard to better adaptation to multidisciplinary diagnostic strategies and to target patient populations. PMID:16302154

  9. Unexpected methyl migrations of ethanol dimer under synchrotron VUV radiation

    SciTech Connect

    Xiao, Weizhan; Hu, Yongjun E-mail: lssheng@ustc.edu.cn; Li, Weixing; Guan, Jiwen; Liu, Fuyi; Shan, Xiaobin; Sheng, Liusi E-mail: lssheng@ustc.edu.cn

    2015-01-14

    While methyl transfer is well known to occur in the enzyme- and metal-catalyzed reactions, the methyl transfer in the metal-free organic molecules induced by the photon ionization has been less concerned. Herein, vacuum ultraviolet single photon ionization and dissociation of ethanol dimer are investigated with synchrotron radiation photoionization mass spectroscopy and theoretical methods. Besides the protonated clusters cation (C{sub 2}H{sub 5}OH) ⋅ H{sup +} (m/z = 47) and the β-carbon-carbon bond cleavage fragment CH{sub 2}O ⋅ (C{sub 2}H{sub 5}OH)H{sup +} (m/z = 77), the measured mass spectra revealed that a new fragment (C{sub 2}H{sub 5}OH) ⋅ (CH{sub 3}){sup +} (m/z = 61) appeared at the photon energy of 12.1 and 15.0 eV, where the neutral dimer could be vertically ionized to higher ionic state. Thereafter, the generated carbonium ions are followed by a Wagner-Meerwein rearrangement and then dissociate to produce this new fragment, which is considered to generate after surmounting a few barriers including intra- and inter-molecular methyl migrations by the aid of theoretical calculations. The appearance energy of this new fragment is measured as 11.55 ± 0.05 eV by scanning photoionization efficiency curve. While the signal intensity of fragment m/z = 61 starts to increase, the fragments m/z = 47 and 77 tend to slowly incline around 11.55 eV photon energy. This suggests that the additional fragment channels other than (C{sub 2}H{sub 5}OH) ⋅ H{sup +} and CH{sub 2}O ⋅ (C{sub 2}H{sub 5}OH)H{sup +} have also been opened, which consume some dimer cations. The present report provides a clear description of the photoionization and dissociation processes of the ethanol dimer in the range of the photon energy 12-15 eV.

  10. A new dimeric anthraquinone from endophytic Talaromyces sp. YE3016.

    PubMed

    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. PMID:26815015

  11. Conducting dimerized cobalt complexes with tetrathiafulvalene dithiolate ligands.

    PubMed

    Fujiwara, Emiko; Hosoya, Kazumasa; Kobayashi, Akiko; Tanaka, Hisashi; Tokumoto, Madoka; Okano, Yoshinori; Fujiwara, Hideki; Kobayashi, Hayao; Fujishiro, Yuichi; Nishibori, Eiji; Takata, Masaki; Sakata, Makoto

    2008-02-01

    To obtain novel single-component molecular metals, we attempted to synthesize several cobalt complexes coordinated by TTF (tetrathiafulvalene)-type dithiolate ligands. We succeeded in the syntheses and structure determinations of ((n)Bu(4)N)(2)[Co(chdt)(2)](2) (1), ((n)Bu(4)N)(2)[Co(dmdt)(2)](2) (2), [Co(dmdt)(2)](2) (3), and [Co(dt)(2)](2) (4) (chdt = cyclohexeno-TTF-dithiolate, dmdt = dimethyl-TTF-dithiolate, and dt = TTF-dithiolate). Structure analyses of complexes 1-4 revealed that two monomeric [Co(ligand)2]- or [Co(ligand)(2)](0) units are connected by two Co-S bonds resulting in dimeric [Co(ligand)(2)](2)(2-) or [Co(ligand)(2)](2) molecules. Complex 1 has a cation-anion-intermingled structure and exhibited Curie-Weiss magnetic behavior with a large Curie constant (C = 2.02 K x emu x mol(-1)) and weak antiferromagnetic interactions (theta = -8.3 K). Complex 2 also has a cation-anion-intermingled structure. However, the dimeric molecules are completely isolated by cations. Complexes 3 and 4 are single-component molecular crystals. The molecules of complex 3 form two-dimensional molecular stacking layers and exhibit a room-temperature conductivity of sigmart = 1.2 x 10(-2) S.cm(-1) and an activation energy of E(a) = 85 meV. The magnetic behavior is almost consistent with Curie-Weiss law, where the Curie constant and Weiss temperature are 8.7 x 10(-2) K x emu x mol(-1) and -0.85 K, respectively. Complex 4 has a rare chair form of the dimeric structure. The electrical conductivity was fairly large (sigmart = 19 S.cm(-1)), and its temperature dependence was very small (sigma(0.55K)/sigma(rt) = ca. 1:10), although the measurements were performed on the compressed pellet sample. Complex 4 showed an almost constant paramagnetic susceptibility (chi(300) (K) = 3.5 x 10(-4) emu x mol(-1)) from 300 to 50 K. The band structure calculation of complex 4 suggested the metallic nature of the system. Complex 4 is a novel single-component molecular conductor with a dimeric

  12. Molecular orbital analysis of the hydrogen bonded water dimer

    NASA Astrophysics Data System (ADS)

    Wang, Bo; Jiang, Wanrun; Dai, Xin; Gao, Yang; Wang, Zhigang; Zhang, Rui-Qin

    2016-02-01

    As an essential interaction in nature, hydrogen bonding plays a crucial role in many material formations and biological processes, requiring deeper understanding. Here, using density functional theory and post-Hartree-Fock methods, we reveal two hydrogen bonding molecular orbitals crossing the hydrogen-bond’s O and H atoms in the water dimer. Energy decomposition analysis also shows a non-negligible contribution of the induction term. Our finding sheds light on the essential understanding of hydrogen bonding in ice, liquid water, functional materials and biological systems.

  13. Theoretical study of electron correlation effects in transition metal dimers

    NASA Astrophysics Data System (ADS)

    Das, Guru P.; Jaffe, Richard L.

    1984-08-01

    Introduction of partially localized orbitals (PLOs) is shown to reduce the number of configurations needed to describe the bonding in transition metal clusters. Using this formalism, estimates are made of the molecular electron correlation energy that arises from including such terms as 3d → 3d', 3p → 3p' and 4s 2 → 4p 2 in the wavefunction. When this estimate of the additional correlation is added to the CAS SCF results of Walch, Bauschlicher, Roos and Nelin improved interaction potentials are obtained for the dimers V 2 and Cr 2.

  14. Molecular orbital analysis of the hydrogen bonded water dimer

    PubMed Central

    Wang, Bo; Jiang, Wanrun; Dai, Xin; Gao, Yang; Wang, Zhigang; Zhang, Rui-Qin

    2016-01-01

    As an essential interaction in nature, hydrogen bonding plays a crucial role in many material formations and biological processes, requiring deeper understanding. Here, using density functional theory and post-Hartree-Fock methods, we reveal two hydrogen bonding molecular orbitals crossing the hydrogen-bond’s O and H atoms in the water dimer. Energy decomposition analysis also shows a non-negligible contribution of the induction term. Our finding sheds light on the essential understanding of hydrogen bonding in ice, liquid water, functional materials and biological systems. PMID:26905305

  15. Negative ion photoelectron spectroscopy of bare transition metal dimers

    NASA Astrophysics Data System (ADS)

    Barker, Beau J.

    This thesis contains gas phase negative ion photoelectron spectra of Mo2, MoV, CrCu, MoCu and Cu2. Spectra were taken with 488 nm and 514 nm light at a resolution of 4-5 meV. Information such as electron affinities, vibrational frequencies, anharmonicities and bond dissociation energies are reported for the ground and excited electronic states of both the anion and neutral species. Theoretical calculations at the density functional level are also reported for these species. Experiment and theory are used to analyze the bonding in these bare transition metal dimers.

  16. Laser synthesis of ultracold alkali metal dimers: optimization and control

    NASA Astrophysics Data System (ADS)

    Pazyuk, E. A.; Zaitsevskii, A. V.; Stolyarov, A. V.; Tamanis, M.; Ferber, R.

    2015-10-01

    The review concerns the potential of modern high-resolution laser spectroscopy and state-of-the-art ab initio electronic structure calculations used to obtain comprehensive information on the energy and radiative properties of strongly coupled rovibronic diatomic states. The possibility of deperturbation treatment of the intermediate electronically excited states at the experimental (spectroscopic) level of accuracy is demonstrated taking alkali metal dimers as examples. The deperturbation analysis is of crucial importance to optimize multistep laser synthesis and stabilization of ultracold molecular ensembles in their absolute ground level. The bibliography includes 227 references.

  17. Factors Associated with D-Dimer Levels in HIV-Infected Individuals

    PubMed Central

    Borges, Álvaro H.; O’Connor, Jemma L.; Phillips, Andrew N.; Baker, Jason V.; Vjecha, Michael J.; Losso, Marcelo H.; Klinker, Hartwig; Lopardo, Gustavo; Williams, Ian; Lundgren, Jens D.

    2014-01-01

    Background Higher plasma D-dimer levels are strong predictors of mortality in HIV+ individuals. The factors associated with D-dimer levels during HIV infection, however, remain poorly understood. Methods In this cross-sectional study, participants in three randomized controlled trials with measured D-dimer levels were included (N = 9,848). Factors associated with D-dimer were identified by linear regression. Covariates investigated were: age, gender, race, body mass index, nadir and baseline CD4+ count, plasma HIV RNA levels, markers of inflammation (C-reactive protein [CRP], interleukin-6 [IL-6]), antiretroviral therapy (ART) use, ART regimens, co-morbidities (hepatitis B/C, diabetes mellitus, prior cardiovascular disease), smoking, renal function (estimated glomerular filtration rate [eGFR] and cystatin C) and cholesterol. Results Women from all age groups had higher D-dimer levels than men, though a steeper increase of D-dimer with age occurred in men. Hepatitis B/C co-infection was the only co-morbidity associated with higher D-dimer levels. In this subgroup, the degree of hepatic fibrosis, as demonstrated by higher hyaluronic acid levels, but not viral load of hepatitis viruses, was positively correlated with D-dimer. Other factors independently associated with higher D-dimer levels were black race, higher plasma HIV RNA levels, being off ART at baseline, and increased levels of CRP, IL-6 and cystatin C. In contrast, higher baseline CD4+ counts and higher high-density lipoprotein cholesterol were negatively correlated with D-dimer levels. Conclusions D-dimer levels increase with age in HIV+ men, but are already elevated in women at an early age due to reasons other than a higher burden of concomitant diseases. In hepatitis B/C co-infected individuals, hepatic fibrosis, but not hepatitis viral load, was associated with higher D-dimer levels. PMID:24626096

  18. Dimerization of the 3'UTR of bicoid mRNA involves a two-step mechanism.

    PubMed

    Wagner, C; Palacios, I; Jaeger, L; St Johnston, D; Ehresmann, B; Ehresmann, C; Brunel, C

    2001-10-26

    The proper localization of bicoid (bcd) mRNA requires cis-acting signals within its 3' untranslated region (UTR) and trans-acting factors such as Staufen. Dimerization of bcd mRNA through intermolecular base-pairing between two complementary loops of domain III of the 3'UTR was proposed to be important for particle formation in the embryo. The participation in the dimerization process of each domain building the 3'UTR was evaluated by thermodynamic and kinetic analysis of various mutated and truncated RNAs. Although sequence complementarity between the two loops of domain III is required for initiating mRNA dimerization, the initial reversible loop-loop complex is converted rapidly into an almost irreversible complex. This conversion involves parts of RNA outside of domain III that promote initial recognition, and dimerization can be inhibited by sense or antisense oligonucleotides only before conversion has proceeded. Injection of the different bcd RNA variants into living Drosophila embryos shows that all elements that inhibit RNA dimerization in vitro prevent formation of localized particles containing Staufen. Particle formation appeared to be dependent on both mRNA dimerization and other element(s) in domains IV and V. Domain III of bcd mRNA could be substituted by heterologous dimerization motifs of different geometry. The resulting dimers were converted into stable forms, independently of the dimerization module used. Moreover, these chimeric RNAs were competent in forming localized particles and recruiting Staufen. The finding that the dimerization domain of bcd mRNA is interchangeable suggests that dimerization by itself, and not the precise geometry of the intermolecular interactions, is essential for the localization process. This suggests that the stabilizing interactions that are formed during the second step of the dimerization process might represent crucial elements for Staufen recognition and localization. PMID:11676536

  19. Photochemical dimerization and functionalization of alkanes, ethers, primary alcohols and silanes

    DOEpatents

    Crabtree, Robert H.; Brown, Stephen H.

    1988-01-01

    The space-time yield and/or the selectivity of the photochemical dimerization of alkanes, ethers, primary alcohols and tertiary silanes with Hg and U.V. light is enhanced by refluxing the substrate in the irradiated reaction zone at a temperature at which the dimer product condenses and remains condensed promptly upon its formation. Cross-dimerization of the alkanes, ethers and silanes with primary alcohols is disclosed, as is the functionalization to aldehydes of the alkanes with carbon monoxide.

  20. Photochemical dimerization and functionalization of alkanes, ethers, primary alcohols and silanes

    DOEpatents

    Crabtree, R.H.; Brown, S.H.

    1988-02-16

    The space-time yield and/or the selectivity of the photochemical dimerization of alkanes, ethers, primary alcohols and tertiary silanes with Hg and U.V. light is enhanced by refluxing the substrate in the irradiated reaction zone at a temperature at which the dimer product condenses and remains condensed promptly upon its formation. Cross-dimerization of the alkanes, ethers and silanes with primary alcohols is disclosed, as is the functionalization to aldehydes of the alkanes with carbon monoxide.

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

    PubMed

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

    2016-09-01

    Several DNA binding proteins exist in dimeric form when bound with DNA to be able to exhibit various biological processes such as DNA repair, DNA replication and gene expression. Various dimeric forms of Ribonuclease A (RNase A) and other members of the ribonuclease A superfamily are endowed with a multitude of biological activities such as antitumor and antiviral activity. In the present study, we have compared the DNA binding properties between the RNase A monomer and the dityrosine (DT) cross-linked RNase A dimer, and checked the inhibitory effect of DNA on the ribonucleolytic activity of the dimeric protein. An agarose gel based assay shows that like the monomer, the dimer also binds with DNA. The number of nucleotides bound per monomer unit of the dimer is higher than the number of nucleotides that bind with the each monomer. From fluorescence measurements, the association constant (Ka) values for complexation of the monomer and the dimer with ct-DNA are (4.95±0.45)×10(4)M(-1) and (1.29±0.05)×10(6)M(-1) respectively. Binding constant (Kb) values for the binding of the monomer and the dimer with ct-DNA were determined using UV-vis spectroscopy and were found to be (4.96±1.67)×10(4)M(-1) and (4.32±0.31)×10(5)M(-1) respectively. Circular dichroism studies shows that the dimer possesses significant effect on DNA conformation. The melting profile for the ct-DNA-dimer indicated that the melting temperature (Tm) for the ct-DNA-dimer complex is lower compared to the ct-DNA-monomer complex. The ribonucleolytic activity of the dimer, like the monomer, diminishes upon binding with DNA. PMID:27475778

  2. Involucratusins A–H: Unusual Cadinane Dimers from Stahlianthus involucratus with Multidrug Resistance Reversal Activity

    PubMed Central

    Li, Qiang-Ming; Luo, Jian-Guang; Wang, Rui-Zhi; Wang, Xiao-Bing; Yang, Ming-Hua; Luo, Jun; Kong, Ling-Yi

    2016-01-01

    Three novel cadinane dimers, involucratusins A–C (1–3), five unique nor-cadinane-dimers, involucratusins D–H (4–8), together with a known compound (9) were isolated from the rhizomes of Stahlianthus involucratus. Their challenging structures and absolute configurations were determined by spectroscopic data, CD experimentation, chemical conversions and single-crystal X-ray diffraction. Compounds 1–3 are unusual cadinane dimers with new connection and novel cores. Compound 4 is a unique nor-cadinane-dimer, and 5 and 6 are two pairs of hemiketal racemates with novel dinor-cadinane-dimer backbone. Compounds 7 and 8 represent unusual dodecanor-cadinane-dimer and tetradecanor-cadinane-dimer carbon skeletons, respectively. The possible biogenetic pathways of 1–8 were proposed, involving nucleophilic addition, SN2 nucleophilic displacement, [3 + 3] benzannulation, oxidative cleavage, decarboxylation, and oxidative phenol coupling reactions. Multidrug resistance (MDR) reversal activity assay of the isolates were evaluated in doxorubicin-resistant human breast cancer cells (MCF-7/DOX). The combined use of these novel cadinane dimers at a concentration of 10 μM increased the cytotoxicity of doxorubicin by 2.2–5.8-fold. It is the first report about the MDR reversal activity of cadinane dimers. PMID:27406627

  3. The missing linker: a dimerization motif located within polyketide synthase modules

    PubMed Central

    Zheng, Jianting; Fage, Christopher D.; Demeler, Borries; Hoffman, David W.; Keatinge-Clay, Adrian T.

    2015-01-01

    The dimerization of multimodular polyketide synthases is essential for their function. Motifs that supplement the contacts made by dimeric polyketide synthase enzymes have previously been characterized outside the boundaries of modules, at the N- and C-terminal ends of polyketide synthase subunits. Here we describe a heretofore-uncharacterized dimerization motif located within modules. The dimeric state of this dimerization element was elucidated through the 2.6 Å-resolution crystal structure of a fragment containing a dimerization element and a ketoreductase. The solution structure of a standalone dimerization element was revealed by nuclear magnetic resonance spectroscopy to be consistent with that of the crystal structure, and its dimerization constant was measured through analytical ultracentrifugation to be ~20 μM. The dimer buries ~990 Å2 at its interface, and its C-terminal helices rigidly connect to ketoreductase domains to constrain their locations within a module. These structural restraints permitted the construction of a common type of polyketide synthase module. PMID:23489133

  4. High D-dimer levels increase the likelihood of pulmonary embolism.

    PubMed

    Tick, L W; Nijkeuter, M; Kramer, M H H; Hovens, M M C; Büller, H R; Leebeek, F W G; Huisman, M V

    2008-08-01

    Objective. To determine the utility of high quantitative D-dimer levels in the diagnosis of pulmonary embolism. Methods. D-dimer testing was performed in consecutive patients with suspected pulmonary embolism. We included patients with suspected pulmonary embolism with a high risk for venous thromboembolism, i.e. hospitalized patients, patients older than 80 years, with malignancy or previous surgery. Presence of pulmonary embolism was based on a diagnostic management strategy using a clinical decision rule (CDR), D-dimer testing and computed tomography. Results. A total of 1515 patients were included with an overall pulmonary embolism prevalence of 21%. The pulmonary embolism prevalence was strongly associated with the height of the D-dimer level, and increased fourfold with D-dimer levels greater than 4000 ng mL(-1) compared to levels between 500 and 1000 ng mL(-1). Patients with D-dimer levels higher than 2000 ng mL(-1) and an unlikely CDR had a pulmonary embolism prevalence of 36%. This prevalence is comparable to the pulmonary embolism likely CDR group. When D-dimer levels were above 4000 ng mL(-1), the observed pulmonary embolism prevalence was very high, independent of CDR score. Conclusion. Strongly elevated D-dimer levels substantially increase the likelihood of pulmonary embolism. Whether this should translate into more intensive diagnostic and therapeutic measures in patients with high D-dimer levels irrespective of CDR remains to be studied. PMID:18452520

  5. Involucratusins A-H: Unusual Cadinane Dimers from Stahlianthus involucratus with Multidrug Resistance Reversal Activity.

    PubMed

    Li, Qiang-Ming; Luo, Jian-Guang; Wang, Rui-Zhi; Wang, Xiao-Bing; Yang, Ming-Hua; Luo, Jun; Kong, Ling-Yi

    2016-01-01

    Three novel cadinane dimers, involucratusins A-C (1-3), five unique nor-cadinane-dimers, involucratusins D-H (4-8), together with a known compound (9) were isolated from the rhizomes of Stahlianthus involucratus. Their challenging structures and absolute configurations were determined by spectroscopic data, CD experimentation, chemical conversions and single-crystal X-ray diffraction. Compounds 1-3 are unusual cadinane dimers with new connection and novel cores. Compound 4 is a unique nor-cadinane-dimer, and 5 and 6 are two pairs of hemiketal racemates with novel dinor-cadinane-dimer backbone. Compounds 7 and 8 represent unusual dodecanor-cadinane-dimer and tetradecanor-cadinane-dimer carbon skeletons, respectively. The possible biogenetic pathways of 1-8 were proposed, involving nucleophilic addition, SN2 nucleophilic displacement, [3 + 3] benzannulation, oxidative cleavage, decarboxylation, and oxidative phenol coupling reactions. Multidrug resistance (MDR) reversal activity assay of the isolates were evaluated in doxorubicin-resistant human breast cancer cells (MCF-7/DOX). The combined use of these novel cadinane dimers at a concentration of 10 μM increased the cytotoxicity of doxorubicin by 2.2-5.8-fold. It is the first report about the MDR reversal activity of cadinane dimers. PMID:27406627

  6. Neither Two-State nor Three-State: Dimerization of Lambda Cro Repressor.

    PubMed

    Yao, John; Wang, Jin

    2015-06-01

    Lambda Cro repressor is one of the best studied dimeric transcription factors. However, there has still been an unsettled debate for decades about whether it is a two-state dimer or three-state dimer. We provide a new mechanism model that can reconcile these seemingly conflicting (mutually exclusive) experimental results. From simulations with all-atom structure-based model, we observe that the dimerization process of Lambda Cro repressor starts from one folded monomer with one unfolded monomer. Intrasubunit folding and intersubunit binding are partially coupled, in a fly casting manner. PMID:26266496

  7. Headgroup dimerization in methanethiol monolayers on the Au(111) surface: A density functional theory study

    NASA Astrophysics Data System (ADS)

    Zhou, Jian-Ge; Williams, Quinton L.; Hagelberg, Frank

    2007-08-01

    A long-standing controversy related to the dimer pattern formed by S atoms in methanethiol (CH3SH) on the Au(111) surface has been resolved using density functional theory. Here, dimerization of methanethiol adsorbates on the Au(111) surface is established by computational modeling. For methylthiolate (CH3S) , it is shown that the S atoms do not dimerize at high coverage but reveal a dimer pattern at intermediate coverage. Molecular dynamics simulation at high coverage demonstrates that the observed dialkyl disulfide species are formed during the desorption process, and thus are not attached to the surface.

  8. Induction of pyrimidine dimers in epidermal DNA of hairless mice by UVB: an action spectrum

    SciTech Connect

    Ley, R.D.; Peak, M.J.; Lyon, L.L.

    1983-03-01

    An action spectrum for the induction of pyrimidine dimers in the epidermis of hairless mice was determined between 288 and 307 nm. The presence of pyrimidine dimers in tritium-labeled DNA extracted from exposed SKH:hairless-1 mouse skin was determined using dimer-specific nucleases from Micrococcus luteus in conjunction with sedimentation of the irradiated DNA in alkaline sucrose gradients. The rate of induction of pyrimidine dimers was maximal at 293 nm. These values were used to propose a UVB transmission curve for mouse epidermis.

  9. Quantitation of pyrimidine dimer contents of nonradioactive deoxyribonucleic acid by electrophoresis in alkaline agarose gels

    SciTech Connect

    Sutherland, B.M.; Shih, A.G.

    1983-02-15

    We have developed a method of quantitating the pyrimidine dimer content of nonradioactive DNAs. DNA samples are treated with the UV-endonuclease from Micrococcus luteus and then separated according to molecular weight by electrophoresis on alkaline agarose gels. From their migration relative to known molecular weight standards, their median molecular weight and thus the number of dimers per DNA molecule in each sample can be calculated. Results of action spectra for dimer formation in T7 bacteriophage measured by this method agree well with action spectra for T7 killing. In addition, the method gives dimer yields in good agreement with those obtained by others using alkaline sucrose gradient sedimentation.

  10. Water dimer rotationally resolved millimeter-wave spectrum observation at room temperature.

    PubMed

    Tretyakov, M Yu; Serov, E A; Koshelev, M A; Parshin, V V; Krupnov, A F

    2013-03-01

    Water dimers (H(2)O)(2) are believed to affect Earth's radiation balance and climate, homogeneous condensation, and atmospheric chemistry. Moreover, the pairwise interaction which binds the dimer appears to be of paramount importance for expounding a complete molecular description of the liquid and solid phases of water. However, there have been no secure, direct observations of water dimers at environmentally relevant temperatures despite decades of studies. We report the first unambiguous observation of the dimer spectrum recorded in equilibrium water vapor at room temperature. PMID:23496706

  11. Dicarabrol, a new dimeric sesquiterpene from Carpesium abrotanoides L.

    PubMed

    Wang, Jun-Feng; He, Wei-Jun; Zhang, Xiao-Xiao; Zhao, Bi-Qing; Liu, Yong-Hong; Zhou, Xiao-Jiang

    2015-10-01

    A new dimeric sesquiterpene, dicarabrol (1), together with three known sesquiterpenes, carabrol (2), 11(13)-dehydroivaxillin (3), and 2-desoxy-4-epi-pulchellin (4), were isolated from the whole plant of Carpesium abrotanoides L. Their structures were elucidated on the basis of spectroscopic analysis, and single crystal X-ray diffraction analysis. Compound 1 possessed a dimeric sesquiterpene core featured with a cyclopentane ring connecting two sesquiterpene lactone units rarely discovered in nature. Dicarabrol (1), as well as three known sesquiterpenes (2-4), had potent in vitro cytotoxicities against the K562, MCF-7, Hela, DU145, U937, H1975, SGC-7901, A549, MOLT-4, and HL60 cell lines with IC50 values ranging from 0.10 to 46.7 μM, while they showed significant antiviral (H1N1 and H3N2) activities. Furthermore, compounds 1, 3 and 4 displayed significant antimycobacterial activity (IC50 3.7, 6.0, and 7.6 μM, respectively). PMID:26316467

  12. Density functional theory and chromium: Insights from the dimers

    SciTech Connect

    Würdemann, Rolf; Kristoffersen, Henrik H.; Moseler, Michael; Walter, Michael

    2015-03-28

    The binding in small Cr clusters is re-investigated, where the correct description of the dimer in three charge states is used as criterion to assign the most suitable density functional theory approximation. The difficulty in chromium arises from the subtle interplay between energy gain from hybridization and energetic cost due to exchange between s and d based molecular orbitals. Variations in published bond lengths and binding energies are shown to arise from insufficient numerical representation of electron density and Kohn-Sham wave-functions. The best functional performance is found for gradient corrected (GGA) functionals and meta-GGAs, where we find severe differences between functionals from the same family due to the importance of exchange. Only the “best fit” from Bayesian error estimation is able to predict the correct energetics for all three charge states unambiguously. With this knowledge, we predict small bond-lengths to be exclusively present in Cr{sub 2} and Cr{sub 2}{sup −}. Already for the dimer cation, solely long bond-lengths appear, similar to what is found in the trimer and in chromium bulk.

  13. Ionization satellites of the ArHe dimer

    SciTech Connect

    Miteva, Tsveta; Klaiman, Shachar; Gokhberg, Kirill; Gromov, Evgeniy V.

    2014-05-28

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

  14. Laser Stimulated Desorption from Compound Semiconductors, Dimerization Enhanced Phase Transition

    NASA Astrophysics Data System (ADS)

    Namiki, Akira; Cho, Seiji; Ichige, Kenji

    1987-01-01

    Laser stimulated desorption (LSD) of neutral particles has been investigated in compound semiconductors MX of GaN, GaP, GaAs and CdS. No effects of crystallographic orientations on the characteristics of LSD, desorption yields, mean kinetic energies, and speed ratios have been recognized among (111) and (100) orientations in GaP and GaAs. This fact suggests that LSD does not follow the unimolecular dissociation of locally excited surface bonds, but occurs via a bulky event involving a phase transtion. The threshold laser powers for LSD were correlated to the crystal bond ionicities fi, which are good measures for the structural stability of tetrahedral covalent solids. It was found that with increasing fi of the solids, threshold laser powers tend to decrease. The dominant species ejected from MX were found to be in the forms of monomer M and X as well as dimer X2. The ratio of the yields of X2 to those of X increases as the single-bond energy of X2 increases. Considering these experimental results, we propose a model of a non-local electronic excitation mechanism for LSD; namely, LSD occurs via the dimerization enhanced phase transition in a high-density electron-hole plasma.

  15. Resonating valence bond wave functions and classical interacting dimer models.

    PubMed

    Damle, Kedar; Dhar, Deepak; Ramola, Kabir

    2012-06-15

    We relate properties of nearest-neighbor resonating valence-bond (NNRVB) wave functions for SU(g) spin systems on two-dimensional bipartite lattices to those of fully packed interacting classical dimer models on the same lattice. The interaction energy can be expressed as a sum of n-body potentials V(n), which are recursively determined from the NNRVB wave function on finite subgraphs of the original lattice. The magnitude of the n-body interaction V(n) (n>1) is of order O(g(-(n-1))) for small g(-1). The leading term is a two-body nearest-neighbor interaction V2(g) favoring two parallel dimers on elementary plaquettes. For SU(2) spins, using our calculated value of V2(g=2), we find that the long-distance behavior of the bond-energy correlation function is dominated by an oscillatory term that decays as 1/|r|α with α≈1.22. This result is in remarkable quantitative agreement with earlier direct numerical studies of the corresponding wave function, which give α≈1.20. PMID:23004328

  16. Monomer-dimer problem on random planar honeycomb lattice

    SciTech Connect

    Ren, Haizhen; Zhang, Fuji; Qian, Jianguo

    2014-02-15

    We consider the monomer-dimer (MD) problem on a random planar honeycomb lattice model, namely, the random multiple chain. This is a lattice system with non-periodic boundary condition, whose generating process is inspired by the growth of single walled zigzag carbon nanotubes. By applying algebraic and combinatorial techniques we establish a calculating expression of the MD partition function for bipartite graphs, which corresponds to the permanent of a matrix. Further, by using the transfer matrix argument we show that the computing problem of the permanent of high order matrix can be converted into some lower order matrices for this family of lattices, based on which we derive an explicit recurrence formula for evaluating the MD partition function of multiple chains and random multiple chains. Finally, we analyze the expectation of the number of monomer-dimer arrangements on a random multiple chain and the asymptotic behavior of the annealed MD entropy when the multiple chain becomes infinite in width and length, respectively.

  17. Dimerization of a Viral SET Protein Endows its Function

    SciTech Connect

    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.

  18. Tunneling splittings in ( XY3) 2-type dimers

    NASA Astrophysics Data System (ADS)

    Coudert, L. H.; Hougen, J. T.

    1991-09-01

    Tunneling-rotational energy level expressions are derived for ( XY3) 2-type dimers using an internal-axis-method-like formalism previously developed for high-barrier tunneling problems involving several large-amplitude motions. The tunneling-rotational Hamiltonian matrix is set up and block diagonalized using symmetry considerations from G36, the permutation-inversion group known to be appropriate when ammonia-like inversion within either XY3 subunit and exchange of Y atoms between subunits are both absent. It is shown that only 10 different tunneling matrix elements arise, corresponding to one nontunneling motion, five twofold or sixfold "interconversion" motions, which exchange the roles of the two inequivalent XY3 subunits, and four threefold noninterconverting motions, which just rotate one or both XY3 subunits about the appropriate threefold symmetry axis. More than 10 tunneling paths can contribute to these 10 matrix elements, and a number of these paths are described, assuming a non-hydrogen-bonded equilibrium configuration similar to that found experimentally for (NH 3) 2. The rotational dependence of all 10 tunneling matrix elements is determined, and three tunneling motions are selected, on the basis of chemical intuition, as probably the most feasible for (NH 3) 2 and (ND 3) 2. The resultant formalism is then applied to obtain qualitative tunneling-rotational energy level patterns for the fully protonated and fully deuterated ammonia dimer species.

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

    PubMed Central

    2011-01-01

    Background During the replication process of bacteria with circular chromosomes, an odd number of homologous recombination events results in concatenated dimer chromosomes that cannot be partitioned into daughter cells. However, many bacteria harbor a conserved dimer resolution machinery consisting of one or two tyrosine recombinases, XerC and XerD, and their 28-bp target site, dif. Results To study the evolution of the dif/XerCD system and its relationship with replication termination, we report the comprehensive prediction of dif sequences in silico using a phylogenetic prediction approach based on iterated hidden Markov modeling. Using this method, dif sites were identified in 641 organisms among 16 phyla, with a 97.64% identification rate for single-chromosome strains. The dif sequence positions were shown to be strongly correlated with the GC skew shift-point that is induced by replicational mutation/selection pressures, but the difference in the positions of the predicted dif sites and the GC skew shift-points did not correlate with the degree of replicational mutation/selection pressures. Conclusions The sequence of dif sites is widely conserved among many bacterial phyla, and they can be computationally identified using our method. The lack of correlation between dif position and the degree of GC skew suggests that replication termination does not occur strictly at dif sites. PMID:21223577

  20. Dissection of the Dimerization Modes in the DJ-1 Superfamily

    PubMed Central

    Jung, Hoi Jong; Kim, Sangok; Kim, Yun Jae; Kim, Min-Kyu; Kang, Sung Gyun; Lee, Jung-Hyun; Kim, Wankyu; Cha, Sun-Shin

    2012-01-01

    The DJ-1 superfamily (DJ-1/ThiJ/PfpI superfamily) is distributed across all three kingdoms of life. These proteins are involved in a highly diverse range of cellular functions, including chaperone and protease activity. DJ-1 proteins usually form dimers or hexamers in vivo and show at least four different binding orientations via distinct interface patches. Abnormal oligomerization of human DJ-1 is related to neurodegenerative disorders including Parkinson’s disease, suggesting important functional roles of quaternary structures. However, the quaternary structures of the DJ-1 superfamily have not been extensively studied. Here, we focus on the diverse oligomerization modes among the DJ-1 superfamily proteins and investigate the functional roles of quaternary structures both computationally and experimentally. The oligomerization modes are classified into 4 types (DJ-1, YhbO, Hsp, and YDR types) depending on the distinct interface patches (I–IV) upon dimerization. A unique, rotated interface via patch I is reported, which may potentially be related to higher order oligomerization. In general, the groups based on sequence similarity are consistent with the quaternary structural classes, but their biochemical functions cannot be directly inferred using sequence information alone. The observed phyletic pattern suggests the dynamic nature of quaternary structures in the course of evolution. The amino acid residues at the interfaces tend to show lower mutation rates than those of non-interfacial surfaces. PMID:22228183

  1. Dimerization of truncated melittin analogues results in cytolytic peptides.

    PubMed Central

    Rivett, D E; Kirkpatrick, A; Hewish, D R; Reilly, W; Werkmeister, J A

    1996-01-01

    A synthetic peptide with the sequence of the first 20 residues of melittin and terminating with an additional cysteine amide was found to have cytolytic activity similar to that of melittin. It was apparent from MS data that the cysteine-terminating peptides had formed disulphide dimers. A peptide in which the thiol was blocked by iodoacetate showed no activity, whereas the same peptide blocked by acetamidomethyl showed activity marginally less haemolytic than that of melittin. Cytolytic activity of melittin analogues comprising the full 26 residues could be obtained with wide sequence permutations providing that a general amphipathic helical structure was preserved. In contrast, the activity of the dimers was dependent not only on retention of an amphipathic helix but also on certain individual residues and a free positive charge. A free N-terminus was essential for haemolytic activity. In addition, a lysine or arginine residue at position 7 and a proline at position 14 were found to be necessary for activity, although it was apparent that additional residues are important for retention of the full lytic potential. PMID:8687396

  2. A dimeric form of lipocortin-1 in human placenta.

    PubMed Central

    Pepinsky, R B; Sinclair, L K; Chow, E P; O'Brine-Greco, B

    1989-01-01

    We have characterized a 68 kDa lipocortin from human placenta that was identified as a covalently linked homodimer of lipocortin-1 by peptide mapping and sequence analysis. The site of cross-linking was localized within the 3 kDa N-terminal tail region, an exposed domain that contains the phosphorylation sites for protein tyrosine kinase and protein kinase C and is sensitive to proteolysis. Sequence analysis of the corresponding peptide revealed that glutamine-18 was modified, suggesting that the cross-link may be generated by a transglutaminase. By incubating lipocortin-1 with placental membranes and with labelled glycine ethyl ester we observed a Ca2+-dependent labelling of lipocortin-1 within the tail region, supporting this notion. Like lipocortin-1, the dimer inhibits phospholipase Ad2 activity, is a substrate for the epidermal-growth-factor (EGF) receptor/kinase, and display Ca2+-dependent binding to phosphatidylserine-containing vesicles. In preparations from human placenta the dimer is particularly abundant, accounting for approx. 20% of the lipocortin-1. Images Fig. 1. Fig. 2. Fig. 3. Fig. 5. Fig. 7. PMID:2532504

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

    PubMed

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

    2016-07-01

    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. PMID:26990589

  4. Monomer-dimer problem on random planar honeycomb lattice

    NASA Astrophysics Data System (ADS)

    Ren, Haizhen; Zhang, Fuji; Qian, Jianguo

    2014-02-01

    We consider the monomer-dimer (MD) problem on a random planar honeycomb lattice model, namely, the random multiple chain. This is a lattice system with non-periodic boundary condition, whose generating process is inspired by the growth of single walled zigzag carbon nanotubes. By applying algebraic and combinatorial techniques we establish a calculating expression of the MD partition function for bipartite graphs, which corresponds to the permanent of a matrix. Further, by using the transfer matrix argument we show that the computing problem of the permanent of high order matrix can be converted into some lower order matrices for this family of lattices, based on which we derive an explicit recurrence formula for evaluating the MD partition function of multiple chains and random multiple chains. Finally, we analyze the expectation of the number of monomer-dimer arrangements on a random multiple chain and the asymptotic behavior of the annealed MD entropy when the multiple chain becomes infinite in width and length, respectively.

  5. Ankyrin-G Inhibits Endocytosis of Cadherin Dimers.

    PubMed

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

    2016-01-01

    Dynamic regulation of endothelial cell adhesion is central to vascular development and maintenance. Furthermore, altered endothelial adhesion is implicated in numerous diseases. Therefore, normal vascular patterning and maintenance require tight regulation of endothelial cell adhesion dynamics. However, the mechanisms that control junctional plasticity are not fully understood. Vascular endothelial cadherin (VE-cadherin) is an adhesive protein found in adherens junctions of endothelial cells. VE-cadherin mediates adhesion through trans interactions formed by its extracellular domain. Trans binding is followed by cis interactions that laterally cluster the cadherin in junctions. VE-cadherin is linked to the actin cytoskeleton through cytoplasmic interactions with β- and α-catenin, which serve to increase adhesive strength. Furthermore, p120-catenin binds to the cytoplasmic tail of cadherin and stabilizes it at the plasma membrane. Here we report that induced cis dimerization of VE-cadherin inhibits endocytosis independent of both p120 binding and trans interactions. However, we find that ankyrin-G, a protein that links membrane proteins to the spectrin-actin cytoskeleton, associates with VE-cadherin and inhibits its endocytosis. Ankyrin-G inhibits VE-cadherin endocytosis independent of p120 binding. We propose a model in which ankyrin-G associates with and inhibits the endocytosis of VE-cadherin cis dimers. Our findings support a novel mechanism for regulation of VE-cadherin endocytosis through ankyrin association with cadherin engaged in lateral interactions. PMID:26574545

  6. Dimeric Structure of the Bacterial Extracellular Foldase PrsA*

    PubMed Central

    Jakob, Roman P.; Koch, Johanna R.; Burmann, Björn M.; Schmidpeter, Philipp A. M.; Hunkeler, Moritz; Hiller, Sebastian; Schmid, Franz X.; Maier, Timm

    2015-01-01

    Secretion of proteins into the membrane-cell wall space is essential for cell wall biosynthesis and pathogenicity in Gram-positive bacteria. Folding and maturation of many secreted proteins depend on a single extracellular foldase, the PrsA protein. PrsA is a 30-kDa protein, lipid anchored to the outer leaflet of the cell membrane. The crystal structure of Bacillus subtilis PrsA reveals a central catalytic parvulin-type prolyl isomerase domain, which is inserted into a larger composite NC domain formed by the N- and C-terminal regions. This domain architecture resembles, despite a lack of sequence conservation, both trigger factor, a ribosome-binding bacterial chaperone, and SurA, a periplasmic chaperone in Gram-negative bacteria. Two main structural differences are observed in that the N-terminal arm of PrsA is substantially shortened relative to the trigger factor and SurA and in that PrsA is found to dimerize in a unique fashion via its NC domain. Dimerization leads to a large, bowl-shaped crevice, which might be involved in vivo in protecting substrate proteins from aggregation. NMR experiments reveal a direct, dynamic interaction of both the parvulin and the NC domain with secretion propeptides, which have been implicated in substrate targeting to PrsA. PMID:25525259

  7. Examination of Glycosaminoglycan Binding Sites on the XCL1 Dimer.

    PubMed

    Fox, Jamie C; Tyler, Robert C; Peterson, Francis C; Dyer, Douglas P; Zhang, Fuming; Linhardt, Robert J; Handel, Tracy M; Volkman, Brian F

    2016-03-01

    Known for its distinct metamorphic behavior, XCL1 interconverts between a canonical chemokine folded monomer (XCL1mon) that interacts with the receptor, XCR1, and a unique dimer (XCL1dim) that interacts with glycosaminoglycans and inhibits HIV-1 activity. This study presents the first detailed analysis of the GAG binding properties of XCL1dim. Basic residues within a conformationally selective dimeric variant of XCL1 (W55D) were mutated and analyzed for their effects on heparin binding. Mutation of Arg23 and Arg43 greatly diminished the level of heparin binding in both heparin Sepharose chromatography and surface plasmon resonance assays. To assess the contributions of different GAG structures to XCL1 binding, we developed a solution fluorescence polarization assay and correlated affinity with the length and level of sulfation of heparan sulfate oligosaccharides. It was recently demonstrated that the XCL1 GAG binding form, XCL1dim, is responsible for preventing HIV-1 infection through interactions with gp120. This study defines a GAG binding surface on XCL1dim that includes residues that are important for HIV-1 inhibition. PMID:26836755

  8. Role of dimerization in dopamine D(4) receptor biogenesis.

    PubMed

    Van Craenenbroeck, Kathleen; Borroto-Escuela, Dasiel O; Skieterska, Kamila; Duchou, Jolien; Romero-Fernandez, Wilber; Fuxe, Kjell

    2014-01-01

    Dopamine receptors are G protein-coupled receptors critically involved in locomotion, reward, and cognitive processes. Export of dopamine receptors to the plasma membrane is thought to follow the default secretory pathway, whereby proteins travel from the endoplasmatic reticulum (ER), through the Golgi apparatus, to arrive at the cell surface. Several observations indicate that trafficking from the ER to the plasma membrane is tightly regulated, and that correct folding in the ER acts as a bottle neck to the maturation of the dopamine D4 receptors. The dopamine D(4) receptor is an interesting receptor since it has a polymorphic region in its third intracellular loop, resulting in receptor isoforms of varying length and amino acid composition. Correct folding is enhanced by: (1) interaction with specific proteins, such as ER resident chaperones, (2) interaction with pharmacological chaperones, for example, ligands that are membrane permeable and can bind to the receptor in the ER, and (3) receptor dimerization; the assembly of multisubunit proteins into a quaternary structure is started in the ER before cell surface delivery, which helps in correct folding and subsequent expression. These interactions help the process of GPCR folding, but more importantly they ensure that only properly folded proteins proceed from the ER to the trans-Golgi network. In this review we will mainly focus on the role of receptor dimerization in dopamine D(4) receptor maturation. PMID:25175456

  9. EDEM1 targets misfolded HLA-B27 dimers for endoplasmic reticulum associated degradation

    PubMed Central

    Guiliano, David B.; Fussell, Helen; Lenart, Izabela; Tsao, Edward; Nesbeth, Darren; Fletcher, Adam J.; Campbell, Elaine C.; Yousaf, Nasim; Williams, Sarah; Santos, Susana; Cameron, Amy; Towers, Greg J.; Kellam, Paul; Hebert, Daniel N.; Gould, Keith; Powis, Simon J.; Antoniou, Antony N.

    2015-01-01

    Objective HLA-B27 forms misfolded heavy chain dimers, which may predispose individuals to inflammatory arthritis by inducing endoplasmic reticulum (ER) stress and the unfolded protein response (UPR). We wanted to define the role of the UPR induced ER associated degradation (ERAD) pathway in the disposal of HLA-B27 dimeric conformers. Methods HeLa cell lines expressing only two copies of a carboxy terminally Sv5 tagged HLA-B27 were generated. The ER stress induced EDEM1 protein was over expressed by transfection and dimer levels monitored by immunoblotting. EDEM1, the UPR associated transcription factor XBP-1, the E3 ubiquitin ligase HRD1, the degradation associated derlin 1 and 2 proteins were inhibited by either short hairpin RNA or dominant negative mutants. The UPR associated ERAD of HLA-B27 was confirmed using ER stress inducing pharamacological agents in kinetic and pulse chase assays. Results We demonstrate that UPR induced machinery can target HLA-B27 dimers, and that dimer formation can be controlled by alterations to expression levels of components of the UPR induced ERAD pathway. HLA-B27 dimers and misfolded MHC class I monomeric molecules were detected bound to EDEM1, with overexpression of EDEM1 inhibiting HLA-B27 dimer formation. EDEM1 inhibition resulted in upregulation of HLA-B27 dimers, whilst UPR induced ERAD of dimers was prevented in the absence of EDEM1. HLA-B27 dimer formation was also enhanced in the absence of XBP-1, HRD1 and derlin1/2. Conclusion The UPR ERAD pathway as described here can dispose of HLA-B27 dimers and presents a potential novel therapeutic target for the modulation of HLA-B27 associated inflammatory disease. PMID:25132672

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

    PubMed

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

    2015-03-01

    The enzyme 5-phosphoribosyl-1-α-diphosphate (PRPP) synthase (EC 2.7.6.1) catalyses the Mg(2+)-dependent transfer of a diphosphoryl group from ATP to the C1 hydroxyl group of ribose 5-phosphate resulting in the production of PRPP and AMP. A nucleotide sequence specifying Sulfolobus solfataricus PRPP synthase was synthesised in vitro with optimised codon usage for expression in Escherichia coli. Following expression of the gene in E. coli PRPP synthase was purified by heat treatment and ammonium sulphate precipitation and the structure of S. solfataricus PRPP synthase was determined at 2.8 Å resolution. A bent dimer oligomerisation was revealed, which seems to be an abundant feature among PRPP synthases for defining the adenine specificity of the substrate ATP. Molecular replacement was used to determine the S. solfataricus PRPP synthase structure with a monomer subunit of Methanocaldococcus jannaschii PRPP synthase as a search model. The two amino acid sequences share 35 % identity. The resulting asymmetric unit consists of three separated dimers. The protein was co-crystallised in the presence of AMP and ribose 5-phosphate, but in the electron density map of the active site only AMP and a sulphate ion were observed. Sulphate ion, reminiscent of the ammonium sulphate precipitation step of the purification, seems to bind tightly and, therefore, presumably occupies and blocks the ribose 5-phosphate binding site. The activity of S. solfataricus PRPP synthase is independent of phosphate ion. PMID:25605536

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

    NASA Astrophysics Data System (ADS)

    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.

  12. dimers differ from monomers in structural propensity, aggregation paths and population of synaptotoxic assemblies.

    PubMed

    O'Malley, Tiernan T; Oktaviani, Nur Alia; Zhang, Dainan; Lomakin, Aleksey; O'Nuallain, Brian; Linse, Sara; Benedek, George B; Rowan, Michael J; Mulder, Frans A A; Walsh, Dominic M

    2014-08-01

    Dimers of Aβ (amyloid β-protein) are believed to play an important role in Alzheimer's disease. In the absence of sufficient brain-derived dimers, we studied one of the only possible dimers that could be produced in vivo, [Aβ](DiY) (dityrosine cross-linked Aβ). For comparison, we used the Aβ monomer and a design dimer cross-linked by replacement of Ser²⁶ with cystine [AβS26C]₂. We showed that similar to monomers, unaggregated dimers lack appreciable structure and fail to alter long-term potentiation. Importantly, dimers exhibit subtly different structural propensities from monomers and each other, and can self-associate to form larger assemblies. Although [Aβ](DiY) and [AβS26C]₂ have distinct aggregation pathways, they both populate bioactive soluble assemblies for longer durations than Aβ monomers. Our results indicate that the link between Aβ dimers and Alzheimer's disease results from the ability of dimers to further assemble and form synaptotoxic assemblies that persist for long periods of time. PMID:24785004

  13. Dimerization of the bacterial RsrI N6-adenine DNA methyltransferase

    PubMed Central

    2006-01-01

    Dimeric restriction endonucleases and monomeric modification methyltransferases were long accepted as the structural paradigm for Type II restriction systems. Recent studies, however, have revealed an increasing number of apparently dimeric DNA methyltransferases. Our initial characterization of RsrI methyltransferase (M.RsrI) was consistent with the enzyme functioning as a monomer, but, subsequently, the enzyme crystallized as a dimer with 1500 Å2 of buried surface area. This result led us to re-examine the biochemical properties of M.RsrI. Gel-shift studies of M.RsrI binding to DNA suggested that binding cooperativity targets hemimethylated DNA preferentially over unmethylated DNA. Size-exclusion chromatography indicated that the M.RsrI–DNA complex had a size and stoichiometry consistent with a dimeric enzyme binding to the DNA. Kinetic measurements revealed a quadratic relationship between enzyme velocity and concentration. Site-directed mutagenesis at the dimer interface affected the kinetics and DNA-binding of the enzyme, providing support for a model proposing an active enzyme dimer. We also identified a conserved motif in the dimer interfaces of the β-class methyltransferases M.RsrI, M.MboIIA and M2.DpnII. Taken together, these data suggest that M.RsrI may be part of a sub-class of MTases that function as dimers. PMID:16464821

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

    PubMed Central

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

    2016-01-01

    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. PMID:27532129

  15. Insights into the Interferon Regulatory Factor Activation from the Crystal Structure of Dimeric IRF5

    SciTech Connect

    Chen, W.; Lam, S; Srinath, H; Jiang, Z; Correia, J; Schiffer, C; Fitzgerald, K; Lin, K; Royer, Jr., W

    2008-01-01

    The interferon regulatory factors (IRFs) are involved in the innate immune response and are activated by phosphorylation. The structure of a pseudophosphorylated IRF5 activation domain now reveals structural changes in the activated form that would turn an autoinhibitory region into a dimerization interface. In vivo analysis supports the relevance of such a dimer to transcriptional activation.

  16. Live cell imaging shows hepatocyte growth factor-induced Met dimerization.

    PubMed

    Koschut, David; Richert, Ludovic; Pace, Giuseppina; Niemann, Hartmut H; Mély, Yves; Orian-Rousseau, Véronique

    2016-07-01

    The canonical model of receptor tyrosine kinase (RTK) activation assumes that ligand-induced dimerization of inactive receptor monomers is a prerequisite for autophosphorylation. For several RTK families, recent results of fluorescence microscopy provided evidence for preformed receptor dimers that may or may not require ligand binding for kinase activity. Here we report, for the first time, the application of advanced quantitative fluorescence microscopy techniques to study changes in the oligomerization state of the RTK Met in response to stimulation by its endogenous ligand hepatocyte growth factor (HGF). We used inducible C-terminal fusions between Met and enhanced green fluorescent protein (EGFP) or red fluorescent protein (RFP) in combination with fluorescence resonance energy transfer (FRET)-based fluorescence-lifetime imaging microscopy (FLIM) and fluorescence correlation spectroscopy (FCS). A small fraction of HGF-independent Met dimers appeared to be present in cells even at low receptor density. At high receptor density, both the fraction of Met dimers and the level of Met autophosphorylation increased in the absence of HGF. Stimulation with HGF at low receptor density significantly increased the fraction of Met dimers on live cells. We found no indications of Met oligomers larger than dimers. Our findings thus confirm a model of Met activation through HGF-induced dimerization and at the same time they support previous reports of Met dimers in unstimulated cells. The tools established in this work will be useful to further characterize the mechanism of Met activation and to define the contribution of co-receptors. PMID:27094128

  17. Cold-active alkaline phosphatase is irreversibly transformed into an inactive dimer by low urea concentrations.

    PubMed

    Hjörleifsson, Jens Guðmundur; Ásgeirsson, Bjarni

    2016-07-01

    Alkaline phosphatase is a homodimeric metallo-hydrolase where both Zn(2+) and Mg(2+) are important for catalysis and stability. Cold-adapted alkaline phosphatase variants have high activity at low temperatures and lower thermal stability compared with variants from mesophilic hosts. The instability, and thus inactivation, could be due to loose association of the dimers and/or loosely bound Mg(2)(+) in the active site, but this has not been studied in detail for the cold-adapted variants. Here, we focus on using the intrinsic fluorescence of Trp in alkaline phosphatase from the marine bacterium Vibrio splendidus (VAP) to probe for dimerization. Trp→Phe substitutions showed that two out of the five native Trp residues contributed mostly to the fluorescence emission. One residue, 15Å away from the active site (W460) and highly solvent excluded, was phosphorescent and had a distant role in substrate binding. An additional Trp residue was introduced to the dimer interface to act as a possible probe for dimerization. Urea denaturation curves indicated that an inactive dimer intermediate, structurally equivalent to the native state, was formed before dimer dissociation took place. This is the first example of the transition of a native dimer to an inactive dimer intermediate for alkaline phosphatase without using mutagenesis, ligands, or competitive inhibition. PMID:27043172

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

    PubMed Central

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

    2006-01-01

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

  19. Helical arrays of U-shaped ATP synthase dimers form tubular cristae in ciliate mitochondria

    PubMed Central

    Mühleip, Alexander W.; Joos, Friederike; Wigge, Christoph; Frangakis, Achilleas S.; Kühlbrandt, Werner; Davies, Karen M.

    2016-01-01

    F1Fo-ATP synthases are universal energy-converting membrane protein complexes that synthesize ATP from ADP and inorganic phosphate. In mitochondria of yeast and mammals, the ATP synthase forms V-shaped dimers, which assemble into rows along the highly curved ridges of lamellar cristae. Using electron cryotomography and subtomogram averaging, we have determined the in situ structure and organization of the mitochondrial ATP synthase dimer of the ciliate Paramecium tetraurelia. The ATP synthase forms U-shaped dimers with parallel monomers. Each complex has a prominent intracrista domain, which links the c-ring of one monomer to the peripheral stalk of the other. Close interaction of intracrista domains in adjacent dimers results in the formation of helical ATP synthase dimer arrays, which differ from the loose dimer rows in all other organisms observed so far. The parameters of the helical arrays match those of the cristae tubes, suggesting the unique features of the P. tetraurelia ATP synthase are directly responsible for generating the helical tubular cristae. We conclude that despite major structural differences between ATP synthase dimers of ciliates and other eukaryotes, the formation of ATP synthase dimer rows is a universal feature of mitochondria and a fundamental determinant of cristae morphology. PMID:27402755

  20. Helical arrays of U-shaped ATP synthase dimers form tubular cristae in ciliate mitochondria.

    PubMed

    Mühleip, Alexander W; Joos, Friederike; Wigge, Christoph; Frangakis, Achilleas S; Kühlbrandt, Werner; Davies, Karen M

    2016-07-26

    F1Fo-ATP synthases are universal energy-converting membrane protein complexes that synthesize ATP from ADP and inorganic phosphate. In mitochondria of yeast and mammals, the ATP synthase forms V-shaped dimers, which assemble into rows along the highly curved ridges of lamellar cristae. Using electron cryotomography and subtomogram averaging, we have determined the in situ structure and organization of the mitochondrial ATP synthase dimer of the ciliate Paramecium tetraurelia. The ATP synthase forms U-shaped dimers with parallel monomers. Each complex has a prominent intracrista domain, which links the c-ring of one monomer to the peripheral stalk of the other. Close interaction of intracrista domains in adjacent dimers results in the formation of helical ATP synthase dimer arrays, which differ from the loose dimer rows in all other organisms observed so far. The parameters of the helical arrays match those of the cristae tubes, suggesting the unique features of the P. tetraurelia ATP synthase are directly responsible for generating the helical tubular cristae. We conclude that despite major structural differences between ATP synthase dimers of ciliates and other eukaryotes, the formation of ATP synthase dimer rows is a universal feature of mitochondria and a fundamental determinant of cristae morphology. PMID:27402755

  1. Dimerization of functional pyrroloindolizines for the synthesis of complex myrmicarin alkaloids

    PubMed Central

    Ondrus, Alison E.; Kaniskan, H. Ümit; Movassaghi, Mohammad

    2010-01-01

    The union of functionalized pyrroloindolizines for the synthesis of heterodimeric products relevant to myrmicarin alkaloids is described. Design and synthesis of tricyclic substrates and new methods for their union enable the investigation of late-stage cyclopentannulation strategies. The rapid assembly of dimeric structures using unique modes of pyrroloindolizine reactivity presents a concise approach to the dimeric myrmicarins and relevant derivatives. PMID:20798891

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

    PubMed

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

    2016-07-19

    Bovine cytochrome c oxidase is an integral membrane protein complex comprising 13 protein subunits and associated lipids. Dimerization of the complex has been proposed; however, definitive evidence for the dimer is lacking. We used advanced mass spectrometry methods to investigate the oligomeric state of cytochrome c oxidase and the potential role of lipids and posttranslational modifications in its subunit interfaces. Mass spectrometry of the intact protein complex revealed that both the monomer and the dimer are stabilized by large lipid entities. We identified these lipid species from the purified protein complex, thus implying that they interact specifically with the enzyme. We further identified phosphorylation and acetylation sites of cytochrome c oxidase, located in the peripheral subunits and in the dimer interface, respectively. Comparing our phosphorylation and acetylation sites with those found in previous studies of bovine, mouse, rat, and human cytochrome c oxidase, we found that whereas some acetylation sites within the dimer interface are conserved, suggesting a role for regulation and stabilization of the dimer, phosphorylation sites were less conserved and more transient. Our results therefore provide insights into the locations and interactions of lipids with acetylated residues within the dimer interface of this enzyme, and thereby contribute to a better understanding of its structure in the natural membrane. Moreover dimeric cytochrome c oxidase, comprising 20 transmembrane, six extramembrane subunits, and associated lipids, represents the largest integral membrane protein complex that has been transferred via electrospray intact into the gas phase of a mass spectrometer, representing a significant technological advance. PMID:27364008

  3. Zinc inhibition of monomeric and dimeric proton channels suggests cooperative gating

    PubMed Central

    Musset, Boris; Smith, Susan M E; Rajan, Sindhu; Cherny, Vladimir V; Sujai, Sukrutha; Morgan, Deri; DeCoursey, Thomas E

    2010-01-01

    Voltage-gated proton channels are strongly inhibited by Zn2+, which binds to His residues. However, in a molecular model, the two externally accessible His are too far apart to coordinate Zn2+. We hypothesize that high-affinity Zn2+ binding occurs at the dimer interface between pairs of His residues from both monomers. Consistent with this idea, Zn2+ effects were weaker in monomeric channels. Mutation of His193 and His140 in various combinations and in tandem dimers revealed that channel opening was slowed by Zn2+ only when at least one His was present in each monomer, suggesting that in wild-type (WT) HV1, Zn2+ binding between His of both monomers inhibits channel opening. In addition, monomeric channels opened exponentially, and dimeric channels opened sigmoidally. Monomeric channel gating had weaker temperature dependence than dimeric channels. Finally, monomeric channels opened 6.6 times faster than dimeric channels. Together, these observations suggest that in the proton channel dimer, the two monomers are closely apposed and interact during a cooperative gating process. Zn2+ appears to slow opening by preventing movement of the monomers relative to each other that is prerequisite to opening. These data also suggest that the association of the monomers is tenuous and allows substantial freedom of movement. The data support the idea that native proton channels are dimeric. Finally, the idea that monomer–dimer interconversion occurs during activation of phagocytes appears to be ruled out. PMID:20231140

  4. 40 CFR 721.9484 - Dimer acid/rosin amidoamine reaction product (generic).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... (CONTINUED) TOXIC SUBSTANCES CONTROL ACT SIGNIFICANT NEW USES OF CHEMICAL SUBSTANCES Significant New Uses for Specific Chemical Substances § 721.9484 Dimer acid/rosin amidoamine reaction product (generic). (a... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Dimer acid/rosin amidoamine...

  5. 40 CFR 721.9484 - Dimer acid/rosin amidoamine reaction product (generic).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... (CONTINUED) TOXIC SUBSTANCES CONTROL ACT SIGNIFICANT NEW USES OF CHEMICAL SUBSTANCES Significant New Uses for Specific Chemical Substances § 721.9484 Dimer acid/rosin amidoamine reaction product (generic). (a... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Dimer acid/rosin amidoamine...

  6. 40 CFR 721.9484 - Dimer acid/rosin amidoamine reaction product (generic).

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... (CONTINUED) TOXIC SUBSTANCES CONTROL ACT SIGNIFICANT NEW USES OF CHEMICAL SUBSTANCES Significant New Uses for Specific Chemical Substances § 721.9484 Dimer acid/rosin amidoamine reaction product (generic). (a... 40 Protection of Environment 32 2012-07-01 2012-07-01 false Dimer acid/rosin amidoamine...

  7. 40 CFR 721.9484 - Dimer acid/rosin amidoamine reaction product (generic).

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... (CONTINUED) TOXIC SUBSTANCES CONTROL ACT SIGNIFICANT NEW USES OF CHEMICAL SUBSTANCES Significant New Uses for Specific Chemical Substances § 721.9484 Dimer acid/rosin amidoamine reaction product (generic). (a... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Dimer acid/rosin amidoamine...

  8. 40 CFR 721.9484 - Dimer acid/rosin amidoamine reaction product (generic).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... (CONTINUED) TOXIC SUBSTANCES CONTROL ACT SIGNIFICANT NEW USES OF CHEMICAL SUBSTANCES Significant New Uses for Specific Chemical Substances § 721.9484 Dimer acid/rosin amidoamine reaction product (generic). (a... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Dimer acid/rosin amidoamine...

  9. Synthesis and electronic properties of nitrogen-bridged dimers of boron subphthalocyanines.

    PubMed

    Guilleme, J; González-Rodríguez, D; Torres, T

    2016-07-28

    The synthesis of new symmetric and unsymmetric axial nitrogen-bridged dimers of subphthalocyanines (μ-azo dimers) has been carried out via activated triflate intermediates. Their spectroscopic and electrochemical properties have been studied and compared to their μ-oxo analogues. PMID:27416999

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

    PubMed Central

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

    2016-01-01

    Bovine cytochrome c oxidase is an integral membrane protein complex comprising 13 protein subunits and associated lipids. Dimerization of the complex has been proposed; however, definitive evidence for the dimer is lacking. We used advanced mass spectrometry methods to investigate the oligomeric state of cytochrome c oxidase and the potential role of lipids and posttranslational modifications in its subunit interfaces. Mass spectrometry of the intact protein complex revealed that both the monomer and the dimer are stabilized by large lipid entities. We identified these lipid species from the purified protein complex, thus implying that they interact specifically with the enzyme. We further identified phosphorylation and acetylation sites of cytochrome c oxidase, located in the peripheral subunits and in the dimer interface, respectively. Comparing our phosphorylation and acetylation sites with those found in previous studies of bovine, mouse, rat, and human cytochrome c oxidase, we found that whereas some acetylation sites within the dimer interface are conserved, suggesting a role for regulation and stabilization of the dimer, phosphorylation sites were less conserved and more transient. Our results therefore provide insights into the locations and interactions of lipids with acetylated residues within the dimer interface of this enzyme, and thereby contribute to a better understanding of its structure in the natural membrane. Moreover dimeric cytochrome c oxidase, comprising 20 transmembrane, six extramembrane subunits, and associated lipids, represents the largest integral membrane protein complex that has been transferred via electrospray intact into the gas phase of a mass spectrometer, representing a significant technological advance. PMID:27364008

  11. Formation and properties of dimeric recombinant horseradish peroxidase in a system of reversed micelles.

    PubMed Central

    Gazaryan, I G; Klyachko, N L; Dulkis, Y K; Ouporov, I V; Levashov, A V

    1997-01-01

    Wild-type recombinant horseradish peroxidase purified and refolded from Escherichia coli inclusion bodies has been studied in the system of bis(2-ethylhexyl)sulphosuccinate sodium salt (Aerosol OT)-reversed micelles in octane. In contrast with native horseradish peroxidase the wild-type recombinant enzyme forms dimeric structures as judged by sedimentation analysis. Peroxidase substrates affect the equilibrium between monomeric and dimeric enzyme forms. The dependence of the catalytic activity of recombinant peroxidase on the degree of hydration of the surfactant exhibits two maxima with pyrogallol, o-phenylene- diamine, guaiacol and o-dianisidine, with different ratios of activities for the first and second maxima. The differences in activities of monomeric and dimeric forms of the recombinant horseradish peroxidase provide evidence for active-site screening in dimeric forms. This has been used to model a dimeric structure of recombinant horseradish peroxidase with the screened entrance to the active site. In the model structure obtained, three of eight glycosylation sites were screened. This might explain the absence of dimeric structures in native enzyme peroxidase. The system of reversed micelles provides, for the first time, evidence for the formation of dimeric structures by recombinant plant peroxidase with an altered substrate specificity compared with the native enzyme. Thus one can assume that haem-containing peroxidases in general are able to form dimeric structures. PMID:9371726

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    SciTech Connect

    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.

  14. RNA Binding-independent Dimerization of Adenosine Deaminases Acting on RNA and Dominant Negative Effects of Nonfunctional Subunits on Dimer Functions*

    PubMed Central

    Valente, Louis; Nishikura, Kazuko

    2010-01-01

    RNA editing that converts adenosine to inosine in double-stranded RNA (dsRNA) is mediated by adenosine deaminases acting on RNA (ADAR). ADAR1 and ADAR2 form respective homodimers, and this association is essential for their enzymatic activities. In this investigation, we set out experiments aiming to determine whether formation of the homodimer complex is mediated by an amino acid interface made through protein-protein interactions of two monomers or via binding of the two subunits to a dsRNA substrate. Point mutations were created in the dsRNA binding domains (dsRBDs) that abolished all RNA binding, as tested for two classes of ADAR ligands, long and short dsRNA. The mutant ADAR dimer complexes were intact, as demonstrated by their ability to co-purify in a sequential affinity-tagged purification and also by their elution at the dimeric fraction position on a size fractionation column. Our results demonstrated ADAR dimerization independent of their binding to dsRNA, establishing the importance of protein-protein interactions for dimer formation. As expected, these mutant ADARs could no longer perform their catalytic function due to the loss in substrate binding. Surprisingly, a chimeric dimer consisting of one RNA binding mutant monomer and a wild type partner still abolished its ability to bind and edit its substrate, indicating that ADAR dimers require two subunits with functional dsRBDs for binding to a dsRNA substrate and then for editing activity to occur. PMID:17428802

  15. Measuring acetic acid dimer modes by ultrafast time-domain Raman spectroscopy.

    PubMed

    Heisler, Ismael A; Mazur, Kamila; Yamaguchi, Sayuri; Tominaga, Keisuke; Meech, Stephen R

    2011-09-14

    Acetic acid is capable of forming strong multiple hydrogen bonds and therefore different dimeric H-bonded structures in neat liquid phase and in solutions. The low frequency Raman spectra of acetic acid (neat, in aqueous solution and as a function of temperature) were obtained by ultrafast time and polarization resolved optical Kerr effect (OKE) measurements. Isotropic OKE measurements clearly reveal a specific totally symmetric mode related to the dimeric structure H-bond stretching mode. The effects of isotope substitution, water dilution and temperature on this mode were investigated. These results together with anisotropic OKE measurements and density functional theory calculations for a number of possible dimers provide strong evidence for the cyclic dimer structure being the main structure in liquid phase persisting down to acetic acid concentrations of 10 M. Some information about the dimer structure and concentration dependence was inferred. PMID:21625711

  16. Localized surface plasmons in face to face dimer silver triangular prism nanoparticles

    NASA Astrophysics Data System (ADS)

    Azarian, Abas; Babaei, Ferydon

    2016-05-01

    Using the discrete dipole approximation method, all plasmonic bands in 80 nm silver face to face dimer triangular prism nanoparticles were reported. The characteristics of plasmonics peaks were investigated with variations of dimer gap and refractive index of the surrounding medium of dimer. We found that there are three and four plasmonic bands, respectively, for dimer separation 2 and 4 nm. The extinction spectra and electric field distribution showed that the dipole-dipole interaction creates strong plasmonic band, but the quadrupole-quadrupole interaction relates to weak plasmonic band. The results revealed that the strong plasmonic bands have high sensitivity factors with respect to weak plasmonic bands. This study may be used in the synthesis of asymmetric dimers made of metal nanoparticles with new plasmonics properties.

  17. Anion Photoelectron Spectroscopy of the Homogenous 2-Hydroxypyridine Dimer Electron Induced Proton Transfer System

    NASA Astrophysics Data System (ADS)

    Vlk, Alexandra; Stokes, Sarah; Wang, Yi; Hicks, Zachary; Zhang, Xinxing; Blando, Nicolas; Frock, Andrew; Marquez, Sara; Bowen, Kit; Bowen Lab JHU Team

    Anion photoelectron spectroscopic (PES) and density functional theory (DFT) studies on the dimer anion of (2-hydroxypyridine)2-are reported. The experimentally measured vertical detachment energy (VDE) of 1.21eV compares well with the theoretically predicted values. The 2-hydroxypyridine anionic dimer system was investigated because of its resemblance to the nitrogenous heterocyclic pyrimidine nucleobases. Experimental and theoretical results show electron induced proton transfer (EIPT) in both the lactim and lactam homogeneous dimers. Upon electron attachment, the anion can serve as the intermediate between the two neutral dimers. A possible double proton transfer process can occur from the neutral (2-hydroxypyridine)2 to (2-pyridone)2 through the dimer anion. This potentially suggests an electron catalyzed double proton transfer mechanism of tautomerization. Research supported by the NSF Grant No. CHE-1360692.

  18. The Rate of Vitamin A Dimerization in Lipofuscinogenesis, Fundus Autofluorescence, Retinal Senescence and Degeneration.

    PubMed

    Washington, Ilyas; Saad, Leonide

    2016-01-01

    One of the earliest events preceding several forms of retinal degeneration is the formation and accumulation of vitamin A dimers in the retinal pigment epithelium (RPE) and underlying Bruch's membrane (BM). Such degenerations include Stargardt disease, Best disease, forms of retinitis pigmentosa, and age-related macular degeneration (AMD). Since their discovery in the 1990's, dimers of vitamin A, have been postulated as chemical triggers driving retinal senescence and degeneration. There is evidence to suggest that the rate at which vitamin A dimerizes and the eye's response to the dimerization products may dictate the retina's lifespan. Here, we present outstanding questions, finding the answers to which may help to elucidate the role of vitamin A dimerization in retinal degeneration. PMID:26427431

  19. Dissociation dynamics of noble-gas dimers in intense two-color IR laser fields

    NASA Astrophysics Data System (ADS)

    Magrakvelidze, M.; Thumm, U.

    2013-07-01

    We numerically model the dissociation dynamics of the noble-gas dimer ions He2+, Ne2+, Ar2+, Kr2+, and Xe2+ in ultrashort pump and probe laser pulses of different wavelengths. Our calculations reveal a distinguished “gap” in the kinetic energy spectra, observed experimentally for the Ar2 dimer [J. Wu , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.110.033005 110, 033005 (2013)], for all noble-gas dimers for appropriate wavelength combinations. This striking phenomenon can be explained by the dissociation of dimer ions on dipole-coupled Born-Oppenheimer adiabatic potential curves. Comparing pump-probe-pulse-delay-dependent kinetic-energy-release spectra for different noble-gas dimer cations of increasing mass, we discuss increasingly prominent (i) fine-structure effects in and (ii) classical aspects of the nuclear vibrational motion.

  20. Is HIV-1 RNA dimerization a prerequisite for packaging? Yes, no, probably?

    PubMed Central

    Russell, Rodney S; Liang, Chen; Wainberg, Mark A

    2004-01-01

    During virus assembly, all retroviruses specifically encapsidate two copies of full-length viral genomic RNA in the form of a non-covalently linked RNA dimer. The absolute conservation of this unique genome structure within the Retroviridae family is strong evidence that a dimerized genome is of critical importance to the viral life cycle. An obvious hypothesis is that retroviruses have evolved to preferentially package two copies of genomic RNA, and that dimerization ensures the proper packaging specificity for such a genome. However, this implies that dimerization must be a prerequisite for genome encapsidation, a notion that has been debated for many years. In this article, we review retroviral RNA dimerization and packaging, highlighting the research that has attempted to dissect the intricate relationship between these two processes in the context of HIV-1, and discuss the therapeutic potential of these putative antiretroviral targets. PMID:15345057

  1. Assembly Pathway of Hepatitis B Core Virus-like Particles from Genetically Fused Dimers*

    PubMed Central

    Holmes, Kris; Shepherd, Dale A.; Ashcroft, Alison E.; Whelan, Mike; Rowlands, David J.; Stonehouse, Nicola J.

    2015-01-01

    Macromolecular complexes are responsible for many key biological processes. However, in most cases details of the assembly/disassembly of such complexes are unknown at the molecular level, as the low abundance and transient nature of assembly intermediates make analysis challenging. The assembly of virus capsids is an example of such a process. The hepatitis B virus capsid (core) can be composed of either 90 or 120 dimers of coat protein. Previous studies have proposed a trimer of dimers as an important intermediate species in assembly, acting to nucleate further assembly by dimer addition. Using novel genetically-fused coat protein dimers, we have been able to trap higher-order assembly intermediates and to demonstrate for the first time that both dimeric and trimeric complexes are on pathway to virus-like particle (capsid) formation. PMID:25953902

  2. [Cooperative mechanism of phosphorylation of the monomeric and dimeric forms of inorganic pyrophosphatase from baker's yeast].

    PubMed

    Bakulevá, N P; Kasho, V N; Baĭkov, A A; Nazarova, T I; Avaeva, S M

    1982-07-01

    A comparative study of phosphorylation of native dimeric and artificial monomeric forms of inorganic pyrophosphatase and its fluoride-stabilized complex with PPi has been carried out. The maximal incorporation of Pi for the dimeric and monomeric proteins is 0.5 and 1 mole per mole of subunit, respectively. The saturation kinetic curves are suggestive of strong positive cooperative interactions. The value of the Hill coefficient (5.5) for the free dimeric enzyme drastically changes upon the active center blockage and/or transition to the monomeric enzyme. Acceleration of dephosphorylation induced by Pi in the presence of Mg2+ is observed only in the case of the dimeric protein. The data obtained indicate that phosphorylation of native dimeric pyrophosphatase occurs according to a "flip-flop" mechanism; the Pi binding in the active center exerts a strong influence on individual steps of the reaction. PMID:6126224

  3. The L3MBTL3 Methyl-Lysine Reader Domain Functions As a Dimer.

    PubMed

    Baughman, Brandi M; Pattenden, Samantha G; Norris, Jacqueline L; James, Lindsey I; Frye, Stephen V

    2016-03-18

    L3MBTL3 recognizes mono- and dimethylated lysine residues on histone tails. The recently reported X-ray cocrystal structures of the chemical probe UNC1215 and inhibitor UNC2533 bound to the methyl-lysine reading MBT domains of L3MBTL3 demonstrate a unique and flexible 2:2 dimer mode of recognition. In this study, we describe our in vitro analysis of L3MBTL3 dimerization via its MBT domains and additionally show that this dimerization occurs within a cellular context in the absence of small molecule ligands. Furthermore, mutations to the first and second MBT domains abrogated L3MBTL3 dimerization both in vitro and in cells. These observations are consistent with the hypothesis that L3MBTL3 engages methylated histone tails as a dimer while carrying out its normal function and provides an explanation for the presence of repeated MBT domains within L3MBTL3. PMID:26317848

  4. Effect of thanatophoric dysplasia type I mutations on FGFR3 dimerization.

    PubMed

    Del Piccolo, Nuala; Placone, Jesse; Hristova, Kalina

    2015-01-20

    Thanatophoric dysplasia type I (TDI) is a lethal human skeletal growth disorder with a prevalence of 1 in 20,000 to 1 in 50,000 births. TDI is known to arise because of five different mutations, all involving the substitution of an amino acid with a cysteine in fibroblast growth factor receptor 3 (FGFR3). Cysteine mutations in receptor tyrosine kinases (RTKs) have been previously proposed to induce constitutive dimerization in the absence of ligand, leading to receptor overactivation. However, their effect on RTK dimer stability has never been measured experimentally. In this study, we characterize the effect of three TDI mutations, Arg248Cys, Ser249Cys, and Tyr373Cys, on FGFR3 dimerization in mammalian membranes, in the absence of ligand. We demonstrate that the mutations lead to surprisingly modest dimer stabilization and to structural perturbations of the dimers, challenging the current understanding of the molecular interactions that underlie TDI. PMID:25606676

  5. Rigid Conjugated Twisted Truxene Dimers and Trimers as Electron Acceptors.

    PubMed

    Zhang, Gang; Lami, Vincent; Rominger, Frank; Vaynzof, Yana; Mastalerz, Michael

    2016-03-14

    A new class of rigid twisted truxenone oligomers with an enlarged π backbone has been established by oxidative dimerization reactions. The resulting extended conjugated systems have large extinction coefficients and low-lying LUMO levels and show good solubility in common organic solvents, thus making them attractive compounds as new electron acceptors in organic electronics. Their suitability as electron acceptors has been demonstrated in bulk-heterojunction organic solar cells with poly({4,8-bis[(2-ethylhexyl)oxy]benzo[1,2-b:4,5-b']dithiophene-2,6-diyl}{3-fluoro-2-[(2-ethylhexyl)carbonyl]thieno[3,4-b]thiophenediyl}) (PTB7) as the donor material. PMID:26891096

  6. PT-symmetric dimer of coupled nonlinear oscillators

    NASA Astrophysics Data System (ADS)

    Cuevas, Jesús; Kevrekidis, Panayotis G.; Saxena, Avadh; Khare, Avinash

    2013-09-01

    We provide a systematic analysis of a prototypical nonlinear oscillator system respecting PT symmetry i.e., one of them has gain and the other an equal and opposite amount of loss. Starting from the linear limit of the system, we extend considerations to the nonlinear case for both soft and hard cubic nonlinearities identifying symmetric and antisymmetric breather solutions, as well as symmetry-breaking variants thereof. We propose a reduction of the system to a Schrödinger-type PT-symmetric dimer, whose detailed earlier understanding can explain many of the phenomena observed herein, including the PT phase transition. Nevertheless, there are also significant parametric as well as phenomenological potential differences between the two models and we discuss where these arise and where they are most pronounced. Finally, we also provide examples of the evolution dynamics of the different states in their regimes of instability.

  7. Group 14 Dithienometallole-Linked Ethynylene-Conjugated Porphyrin Dimers.

    PubMed

    Morisue, Mitsuhiko; Hoshino, Yuki; Nakamura, Masashi; Yumura, Takashi; Machida, Shinjiro; Ooyama, Yousuke; Shimizu, Masaki; Ohshita, Joji

    2016-08-01

    The considerably conjugated π systems of the group 14 dithienometallole-linked ethynylene-conjugated porphyrin dimers (1Ms) were described based on comprehensive experimental and theoretical studies. The electronic absorption spectra of 1M displayed a large splitting in the Soret band and a red-shifted Q-band, indicating that the dithienometallole spacer was effective in facilitating the porphyrin-porphyrin electronic coupling. Torsional planarization behaviors of 1M were observed in the time-resolved fluorescence spectra. Density functional theory (DFT) calculations revealed that the dithienometallole spacer is an ideal partner for the ethynylene-conjugated porphyrin to produce fully delocalized highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) levels due to their similar HOMO and LUMO levels. Finally, 1M exhibited a strong propensity for the quinoidal-cummulenic conjugation in the dithienometallole spacer when in a photoexcited state. PMID:27410779

  8. Calculation of vibrational spectra for dioxouranium monochloride monomer and dimers

    NASA Astrophysics Data System (ADS)

    Umreiko, D. S.; Shundalau, M. B.; Zazhogin, A. P.; Komyak, A. I.

    2010-09-01

    Structural models were built and spectral characteristics were calculated based on ab initio calculations for the monomer and dimers of dioxouranium monochoride UO2Cl. The calculations were carried out in the effective core potential LANL2DZ approximation for the uranium atom and all-electron basis sets using DFT methods for oxygen and chlorine atoms (B3LYP/cc-pVDZ). The monomer UO2Cl was found to possess an equilibrium planar (close to T-shaped) configuration with C2v symmetry. The obtained spectral characteristics were analyzed and compared with experimental data. The adequacy of the proposed models and the qualitative agreement between calculation and experiment were demonstrated.

  9. Dimer excision in Escherichia coli in the presence of caffeine

    SciTech Connect

    Rothman, R.H.

    1980-07-01

    The observation that polA1 and recL152 mutations result in both slow pyrimidine dimer excision and large repair patch size leads to the hypothesis that patch size is directly related to the rate of excision. In this study caffeine, a known inhibitor of excision repair, was used to examine the extent of correlation between excision rate and patch size by measuring patch size in the presence of several concentrations of caffeine. Both the rate of excision and the resistance to ultraviolet radiation were reduced with increasing concentrations of caffeine after irradiation. Caffeine also inhibited the rate at which incisions were made and prolonged the time required to rejoin the discontinuities. Patch size, however, was unaffected by caffeine treatment.

  10. Emergence of cooperative dynamics in fully packed classical dimers

    NASA Astrophysics Data System (ADS)

    Oakes, Tom; Garrahan, Juan P.; Powell, Stephen

    2016-03-01

    The classical dimer model on the square lattice is a paradigmatic example of a system subject to strong local constraints. We study its behavior under local stochastic dynamics, by means of Monte Carlo simulations and theoretical arguments. We observe clear signatures of correlated dynamics in both global and local observables and over a broad range of time scales, indicating a breakdown of the simple continuum description that approximates well the statics. We show that this collective dynamics can be understood in terms of one-dimensional "strings" of high mobility, which govern both local and long-wavelength dynamical properties. We introduce a coarse-grained description of the strings, based on the Edwards-Wilkinson model, which leads to exact results in the limit of low string density and provides a detailed qualitative understanding of the dynamics in all flux sectors. We discuss the implications of our results for the dynamics of constrained systems more generally.

  11. Magnetic hysteresis in a lanthanide molecular magnet dimer system

    NASA Astrophysics Data System (ADS)

    Atkinson, James; Cebulka, Rebecca; Del Barco, Enrique; Roubeau, Olivier; Velasco, Veronica; Barrios, Leo; Aromi, Guillem

    Molecular magnets present a wonderful means for studying the dynamics of spin. Often synthesized as a crystal lattice of identical systems, ensemble measurements enable thorough detailing of the internal degrees of freedom. Here we present the results of characterization performed on a dimer system, CeTm(HL)2(H2L)NO3pyH2O (L = ligand, C45H31O15N3), consisting of two lanthanide spins (Cerium and Thulium) with expected local axial anisotropies tilted with respect to each other. Microwave EPR spectroscopy at low temperature reveals hysteresis in observed absorption features, with angle dependence studies indicating the presence of several ``easy axis'' orientations. We attempt to understand this system through modelling via a spin Hamiltonian, and to determine the strength and nature of the coupling between the lanthanide centers. This research was funded through NSF Grant # 24086159.

  12. Excitation spectra of disordered dimer magnets near quantum criticality.

    PubMed

    Vojta, Matthias

    2013-08-30

    For coupled-dimer magnets with quenched disorder, we introduce a generalization of the bond-operator method, appropriate to describe both singlet and magnetically ordered phases. This allows for a numerical calculation of the magnetic excitations at all energies across the phase diagram, including the strongly inhomogeneous Griffiths regime near quantum criticality. We apply the method to the bilayer Heisenberg model with bond randomness and characterize both the broadening of excitations and the transfer of spectral weight induced by disorder. Inside the antiferromagnetic phase this model features the remarkable combination of sharp magnetic Bragg peaks and broad magnons, the latter arising from the tendency to localization of low-energy excitations. PMID:24033066

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

    SciTech Connect

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

    2010-08-20

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

  14. Blocking cyclobutane pyrimidine dimer formation by steric hindrance.

    PubMed

    Vendrell-Criado, Victoria; Lhiaubet-Vallet, Virginie; Yamaji, Minoru; Cuquerella, M Consuelo; Miranda, Miguel A

    2016-04-26

    The efficiency of thymine (Thy) and uracil (Ura) to form cyclobutane pyrimidine dimers (CPDs) in solution, upon UV irradiation differs by one order of magnitude. This could to be partially related to the steric hindrance induced by the methyl at C5 in thymine. The aim of the present work is to establish the influence of a bulky moiety at this position on the photoreactivity of pyrimidines. With this purpose, photosensitization with benzophenone and acetone of a 5-tert-butyl uracil derivative () and the equivalent Thy () has been compared. Introduction of the tert-butyl group completely blocks CPD formation. Moreover, the mechanistic insight obtained by laser flash photolysis is in accordance with the observed photoreactivity. PMID:27112630

  15. Hydrogen bonding in the ethanol-water dimer.

    PubMed

    Finneran, Ian A; Carroll, P Brandon; Allodi, Marco A; Blake, Geoffrey A

    2015-10-01

    We report the first rotational spectrum of the ground state of the isolated ethanol-water dimer using chirped-pulse Fourier transform microwave spectroscopy between 8-18 GHz. With the aid of isotopic substitutions, and ab initio calculations, we identify the measured conformer as a water-donor/ethanol-acceptor structure. Ethanol is found to be in the gauche conformation, while the monomer distances and orientations likely reflect a cooperation between the strong (O-HO) and weak (C-HO) hydrogen bonds that stabilizes the measured conformer. No other conformers were assigned in an argon expansion, confirming that this is the ground-state structure. This result is consistent with previous vibrationally-resolved Raman and infrared work, but sheds additional light on the structure, due to the specificity of rotational spectroscopy. PMID:26325657

  16. Mapping Thymine Dimer Splitting in Damaged DNA by Photolyase

    NASA Astrophysics Data System (ADS)

    Liu, Zheyun; Tan, Chuang; Li, Jiang; Guo, Xunmin; Wang, Lijuan; Zhong, Dongping

    2010-06-01

    Photolyases uses light energy to convert UV-damaged cyclobutane pyrimidine dimer (CPD) to normal bases. We observed the formation and decay of semiquinone flavin and CPD anion intermediate, the recovery of hydroquinone flavin in ground state, and the formation of normal thymine bases in real time with femtosecond time resolution. By monitoring the decay and formation of all reactants, intermediates and products, the functional dynamics of the elementary steps during CPD repair have been mapped out. All elementary reaction steps, namely forward electron transfer, back electron transfer, bond breakage and electron return occur in sub-nanosecond scale. These dynamics are synergistically correlated for maximum of repair efficiency through a redox photocycle with no net change of electrons.

  17. Fano fingerprints of Majoranas in Kitaev dimers of superconducting adatoms

    NASA Astrophysics Data System (ADS)

    Dessotti, F. A.; Ricco, L. S.; Marques, Y.; Machado, R. S.; Guessi, L. H.; Figueira, M. S.; de Souza, M.; Seridonio, A. C.

    2016-09-01

    We investigate theoretically a Fano interferometer composed by STM and AFM tips close to a Kitaev dimer of superconducting adatoms, in which the adatom placed under the AFM tip, encloses a pair of Majorana fermions (MFs). For the binding energy Δ of the Cooper pair delocalized into the adatoms under the tips coincident with the tunneling amplitude t between them, namely Δ=t, we find that only one MF beneath the AFM tip hybridizes with the adatom coupled to the STM tips. As a result, a gate invariance feature emerges: the Fano profile of the transmittance rises as an invariant quantity depending upon the STM tips Fermi energy, due to the symmetric swap in the gate potential of the AFM tip.

  18. Dimeric structure of single chloride channels from Torpedo electroplax.

    PubMed Central

    Miller, C; White, M M

    1984-01-01

    The inhibition by 4,4'-diisothiocyano-2,2'-stilbenedisulfonate (DIDS) of Cl- channels from Torpedo electroplax incorporated in planar phospholipid bilayer membranes is studied. DIDS irreversibly and rapidly inhibits the macroscopic conductance of membranes containing many channels. At the single-channel level, the effect of DIDS is more complicated. The uninhibited single channel displays three "substates" of conductances 20, 10, and 0 pS. Short exposure (5-30 s) to 10 microM DIDS converts this three-level active channel into a "conventional" channel of 10-pS conductance. Longer exposure eliminates all channel fluctuations. The results are taken as strong evidence that the Cl- channel is constructed as a functional dimer of identical protein subunits. PMID:6326143

  19. Multiple functions of the histone chaperone Jun dimerization protein 2.

    PubMed

    Tsai, Ming-Ho; Wuputra, Kenly; Lin, Yin-Chu; Lin, Chang-Shen; Yokoyama, Kazunari K

    2016-09-30

    The Jun dimerization protein 2 (JDP2) is part of the family of stress-responsible transcription factors such as the activation protein-1, and binds the 12-O-tetradecanoylphorbol-13-acetateresponse element and the cAMP response element. It also plays a role as a histone chaperone and participates in diverse processes, such as cell-cycle arrest, cell differentiation, apoptosis, senescence, and metastatic spread, and functions as an oncogene and anti-oncogene, and as a cellular reprogramming factor. However, the molecular mechanisms underlying these multiple functions of JDP2 have not been clarified. This review summarizes the structure and function of JDP2, highlighting the specific role of JDP2 in cellular-stress regulation and prevention. PMID:27041241

  20. Dispersion Energy Enforced Dimerization of a Cyclic Disilylated Plumbylene

    PubMed Central

    2012-01-01

    By reaction of 1,4-dipotassio-1,1,4,4-tetrakis(trimethylsilyl)tetramethyltetrasilane with PbBr2 in the presence of triethylphosphine a base adduct of a cyclic disilylated plumbylene could be obtained. Phosphine abstraction with B(C6F5)3 led to formation of a base-free plumbylene dimer, which features an unexpected single donor–acceptor PbPb bond. The results of density functional computations at the M06-2X and B3LYP level of theory indicate that the dominating interactions which hold the plumbylene subunits together and which define its actual molecular structure are attracting van der Waals forces between the two large and polarizable plumbylene subunits. PMID:22455750

  1. Reduced density-matrix functionals applied to the Hubbard dimer

    NASA Astrophysics Data System (ADS)

    Kamil, Ebad; Schade, Robert; Pruschke, Thomas; Blöchl, Peter E.

    2016-02-01

    Common density-matrix functionals, the Müller and the power functional, have been benchmarked for the half-filled Hubbard dimer, which allows us to model the bond dissociation problem and the transition from the weakly to the strongly correlated limit. Unbiased numerical calculations are combined with analytical results. Despite the well known successes of the Müller functional, the ground state is degenerate with a one-dimensional manifold of ferromagnetic solutions. The resulting infinite magnetic susceptibility indicates another qualitative flaw of the Müller functional. The derivative discontinuity with respect to particle number is not present indicating an incorrect metal-like behavior. The power functional actually favors the ferromagnetic state for weak interaction. Analogous to the Hartree-Fock approximation, the power functional undergoes a transition beyond a critical interaction strength, in this case, however, to a noncollinear antiferromagnetic state.

  2. Dimeric peroxiredoxins are druggable targets in human Burkitt lymphoma

    PubMed Central

    Trzeciecka, Anna; Klossowski, Szymon; Bajor, Malgorzata; Zagozdzon, Radoslaw; Gaj, Pawel; Muchowicz, Angelika; Malinowska, Agata; Czerwoniec, Anna; Barankiewicz, Joanna; Domagala, Antoni; Chlebowska, Justyna; Prochorec-Sobieszek, Monika; Winiarska, Magdalena; Ostaszewski, Ryszard; Gwizdalska, Iwonna; Golab, Jakub; Nowis, Dominika; Firczuk, Malgorzata

    2016-01-01

    Burkitt lymphoma is a fast-growing tumor derived from germinal center B cells. It is mainly treated with aggressive chemotherapy, therefore novel therapeutic approaches are needed due to treatment toxicity and developing resistance. Disturbance of red-ox homeostasis has recently emerged as an efficient antitumor strategy. Peroxiredoxins (PRDXs) are thioredoxin-family antioxidant enzymes that scavenge cellular peroxides and contribute to red-ox homeostasis. PRDXs are robustly expressed in various malignancies and critically involved in cell proliferation, differentiation and apoptosis. To elucidate potential role of PRDXs in lymphoma, we studied their expression level in B cell-derived primary lymphoma cells as well as in cell lines. We found that PRDX1 and PRDX2 are upregulated in tumor B cells as compared with normal counterparts. Concomitant knockdown of PRDX1 and PRDX2 significantly attenuated the growth rate of lymphoma cells. Furthermore, in human Burkitt lymphoma cell lines, we isolated dimeric 2-cysteine peroxiredoxins as targets for SK053, a novel thiol-specific small-molecule peptidomimetic with antitumor activity. We observed that treatment of lymphoma cells with SK053 triggers formation of covalent PRDX dimers, accumulation of intracellular reactive oxygen species, phosphorylation of ERK1/2 and AKT and leads to cell cycle arrest and apoptosis. Based on site-directed mutagenesis and modeling studies, we propose a mechanism of SK053-mediated PRDX crosslinking, involving double thioalkylation of active site cysteine residues. Altogether, our results suggest that peroxiredoxins are novel therapeutic targets in Burkitt lymphoma and provide the basis for new approaches to the treatment of this disease. PMID:26636537

  3. Dimeric peroxiredoxins are druggable targets in human Burkitt lymphoma.

    PubMed

    Trzeciecka, Anna; Klossowski, Szymon; Bajor, Malgorzata; Zagozdzon, Radoslaw; Gaj, Pawel; Muchowicz, Angelika; Malinowska, Agata; Czerwoniec, Anna; Barankiewicz, Joanna; Domagala, Antoni; Chlebowska, Justyna; Prochorec-Sobieszek, Monika; Winiarska, Magdalena; Ostaszewski, Ryszard; Gwizdalska, Iwonna; Golab, Jakub; Nowis, Dominika; Firczuk, Malgorzata

    2016-01-12

    Burkitt lymphoma is a fast-growing tumor derived from germinal center B cells. It is mainly treated with aggressive chemotherapy, therefore novel therapeutic approaches are needed due to treatment toxicity and developing resistance. Disturbance of red-ox homeostasis has recently emerged as an efficient antitumor strategy. Peroxiredoxins (PRDXs) are thioredoxin-family antioxidant enzymes that scavenge cellular peroxides and contribute to red-ox homeostasis. PRDXs are robustly expressed in various malignancies and critically involved in cell proliferation, differentiation and apoptosis. To elucidate potential role of PRDXs in lymphoma, we studied their expression level in B cell-derived primary lymphoma cells as well as in cell lines. We found that PRDX1 and PRDX2 are upregulated in tumor B cells as compared with normal counterparts. Concomitant knockdown of PRDX1 and PRDX2 significantly attenuated the growth rate of lymphoma cells. Furthermore, in human Burkitt lymphoma cell lines, we isolated dimeric 2-cysteine peroxiredoxins as targets for SK053, a novel thiol-specific small-molecule peptidomimetic with antitumor activity. We observed that treatment of lymphoma cells with SK053 triggers formation of covalent PRDX dimers, accumulation of intracellular reactive oxygen species, phosphorylation of ERK1/2 and AKT and leads to cell cycle arrest and apoptosis. Based on site-directed mutagenesis and modeling studies, we propose a mechanism of SK053-mediated PRDX crosslinking, involving double thioalkylation of active site cysteine residues. Altogether, our results suggest that peroxiredoxins are novel therapeutic targets in Burkitt lymphoma and provide the basis for new approaches to the treatment of this disease. PMID:26636537

  4. Dimerize RACK1 upon transformation with oncogenic ras

    SciTech Connect

    Chu, L.-Y.; Chen, Y.-H.; Chuang, N.-N. . E-mail: zonnc@sinica.edu.tw

    2005-05-06

    From our previous studies, we learned that syndecan-2/p120-GAP complex provided docking site for Src to prosecute tyrosine kinase activity upon transformation with oncogenic ras. And, RACK1 protein was reactive with syndecan-2 to keep Src inactivated, but not when Ras was overexpressed. In the present study, we characterized the reaction between RACK1 protein and Ras. RACK1 was isolated from BALB/3T3 cells transfected with plasmids pcDNA3.1-[S-ras(Q{sub 61}K)] of shrimp Penaeus japonicus and RACK1 was revealed to react with GTP-K{sub B}-Ras(Q{sub 61}K), not GDP-K{sub B}-Ras(Q{sub 61}K). This selective interaction between RACK1 and GTP-K{sub B}-Ras(Q{sub 61}K) was further confirmed with RACK1 of human placenta and mouse RACK1-encoded fusion protein. We found that RACK1 was dimerized upon reaction with GTP-K{sub B}-Ras(Q{sub 61}K), as well as with 14-3-3{beta} and geranylgeranyl pyrophosphate, as revealed by phosphorylation with Src tyrosine kinase. We reported the complex of RACK1/GTP-K{sub B}-Ras(Q{sub 61}K) reacted selectively with p120-GAP. This interaction was sufficient to dissemble RACK1 into monomers, a preferred form to compete for the binding of syndecan-2. These data indicate that the reaction of GTP-K{sub B}-Ras(Q{sub 61}K) with RACK1 in dimers may operate a mechanism to deplete RACK1 from reaction with syndecan-2 upon transformation by oncogenic ras and the RACK1/GTP-Ras complex may provide a route to react with p120-GAP and recycle monomeric RACK1 to syndecan-2.

  5. Ionization dynamics of water dimer on ice surface

    NASA Astrophysics Data System (ADS)

    Tachikawa, Hiroto

    2016-05-01

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

  6. Plasmonic interactions and optical forces between Au bypyramidal nanoparticle dimers.

    SciTech Connect

    Nome, R. A.; Guffey, M. J.; Scherer, N. F.; Gray, S. K.; Univ. of Chicago

    2009-04-23

    Interparticle forces that can be driven by applied (optical) fields could lead to the formation of new particle arrangements when assembled in arrays. Furthermore, the potentially large interactions and large local fields associated with plasmon excitations in anisotropic nanoparticles can lead to enhanced nonlinear responses and applications for sensing. These and other applications would benefit from simulations of spectra and forces arising from plasmonic interactions. We present the results of rigorous three-dimensional, finite-difference, time-domain calculations of near- and far-field properties of pairs of Au bipyramidal nanoparticles in three different configurations: side-by-side, head-to-tail, and face-on. The absorption and scattering spectra depend strongly on the geometry as well as on the interparticle separation, as intuitively expected from a dipole coupling picture. Bipyramidal dimers in head-to-tail and face-on geometries exhibit an increasingly red-shifted (longitudinal) plasmon resonance with decreasing separation, whereas side-by-side dimers exhibit a blue shift. Large resonant field enhancements at the gap between particles in a head-to-tail configuration indicate the strong coupling of plasmonic modes. The Maxwell stress tensor formalism is employed to calculate the optical force one particle exerts on the other. Both significant attraction and weak repulsion can be obtained, depending on the relative arrangement of the particles. The force between bipyramids in the head-to-tail configuration can be greater than 10 times the force between pairs of Au nanospheres with the same volume. Experimental linear scattering spectra of particles trapped using the plasmon-resonance-based optical trapping method are found to be consistent with two particles trapped in the side-by-side configuration.

  7. Cooperative, Heparan Sulfate-Dependent Cellular Uptake of Dimeric Guanidinoglycosides

    PubMed Central

    Dix, Andrew V.; Fischer, Lucile; Sarrazin, Stéphane; Redgate, Christopher P. H.

    2010-01-01

    Oligoarginine and guanidinium-rich molecular transporters have been shown to facilitate the intracellular delivery of a diverse range of biologically relevant cargos. Several such transporters have been suggested to interact with cell surface heparan sulfate proteoglycans as part of their cell entry pathway. Unlike other guanidinium-rich transporters, the cellular uptake of guanidinoglycosides at nanomolar concentrations is exclusively heparan sulfate dependent. As distinct cells differ in their expression levels and/or composition of cell-surface heparan sulfate proteoglycans, one may be able to exploit such differences to selectively target certain cell types. To systematically investigate the nature of their cell surface interactions, monomeric and dimeric guanidinoglycosides were synthesized using neomycin, paromomycin, and tobramycin as scaffolds. These transporters differ in the number and 3-dimensional arrangement of guanidinium groups. Their cellular uptake was measured by flow cytometry in wild type and mutant Chinese hamster ovary cells after generating the corresponding fluorescent streptavidin-phycoerythrinCy5 conjugates. All derivatives showed negligible uptake in mutant cells lacking heparan sulfate. Decreasing the number of guanidinium groups diminished uptake, but the three dimensional arrangement of these groups was less important for cellular delivery. Whereas conjugates prepared with the monomeric carriers showed significantly reduced uptake in mutant cells expressing heparan sulfate chains with altered patterns of sulfation, conjugates prepared with the dimeric guanidinoglycosides could overcome this deficiency and maintain high levels of uptake in such deficient cells. This finding suggests that cellular uptake depends on the valency of the transporter and both the content and arrangement of the sulfate groups on the cell surface receptors. Competition studies with chemically desulfated or carboxy-reduced heparin derivatives corroborated these

  8. Functional Roles of the Dimer-Interface Residues in Human Ornithine Decarboxylase

    PubMed Central

    Lee, Chien-Yun; Liu, Yi-Liang; Lin, Chih-Li; Liu, Guang-Yaw; Hung, Hui-Chih

    2014-01-01

    Ornithine decarboxylase (ODC) catalyzes the decarboxylation of ornithine to putrescine and is the rate-limiting enzyme in the polyamine biosynthesis pathway. ODC is a dimeric enzyme, and the active sites of this enzyme reside at the dimer interface. Once the enzyme dissociates, the enzyme activity is lost. In this paper, we investigated the roles of amino acid residues at the dimer interface regarding the dimerization, protein stability and/or enzyme activity of ODC. A multiple sequence alignment of ODC and its homologous protein antizyme inhibitor revealed that 5 of 9 residues (residues 165, 277, 331, 332 and 389) are divergent, whereas 4 (134, 169, 294 and 322) are conserved. Analytical ultracentrifugation analysis suggested that some dimer-interface amino acid residues contribute to formation of the dimer of ODC and that this dimerization results from the cooperativity of these interface residues. The quaternary structure of the sextuple mutant Y331S/Y389D/R277S/D332E/V322D/D134A was changed to a monomer rather than a dimer, and the Kd value of the mutant was 52.8 µM, which is over 500-fold greater than that of the wild-type ODC (ODC_WT). In addition, most interface mutants showed low but detectable or negligible enzyme activity. Therefore, the protein stability of these interface mutants was measured by differential scanning calorimetry. These results indicate that these dimer-interface residues are important for dimer formation and, as a consequence, are critical for enzyme catalysis. PMID:25140796

  9. Role of extracellular domain dimerization in agonist-induced activation of natriuretic peptide receptor A.

    PubMed

    Parat, Marie; McNicoll, Normand; Wilkes, Brian; Fournier, Alain; De Léan, André

    2008-02-01

    Natriuretic peptide receptor (NPR) A is composed of an extracellular domain (ECD) with a ligand binding site, a single transmembrane region, a kinase homology domain, and a guanylyl cyclase domain. The natural agonists atrial and brain natriuretic peptides (ANP, BNP) bind and activate NPRA, leading to cyclic GMP production, which is responsible for their role in cardiovascular homeostasis. Previous studies suggested that stabilization of a dimeric form of NPRA by agonist is essential for receptor activation. However, ligand specificity and sequential steps of this dimerization process have not been investigated. We used radioligand binding, fluorescence resonance energy transfer homoquenching, and molecular modeling to characterize the interaction of human NPRA-ECD with ANP, BNP, the superagonist (Arg(10),Leu(12),Ser(17),Leu(18))-rANP-(1-28), the minimized analog mini-ANP and the antagonist (Arg(6),beta-cyclohexyl-Ala(8),d-Tic(16),Arg(17),Cys(18))-rANP-(6-18)-amide (A71915). ANP binds to preformed ECD dimers and spontaneous dimerization is the rate-limiting step of the ligand binding process. All the studied peptides, including A71915 antagonist, induce a dose-dependent fluorescence homoquenching, specific to dimerization, with potencies highly correlated with their binding affinities. A71915 induced more quenching than other peptides, suggesting stabilization by the antagonist of ECD dimer in a distinct inactive conformation. In summary, these results indicate that the ligand-induced dimerization process of NPRA is different from that for cytokine receptor model. Agonists or antagonists bind to preformed dimeric ECD, leading to dimer stabilization in an active or inactive conformation, respectively. Furthermore, the highly sensitive fluorescence assay designed to assess dimerization could serve as a powerful tool for further detailing the kinetic steps involved in natriuretic peptide receptor binding and activation. PMID:17965196

  10. Plant Kinesin-Like Calmodulin Binding Protein Employs Its Regulatory Domain for Dimerization

    PubMed Central

    Vinogradova, Maia V.; Malanina, Galina G.; Waitzman, Joshua S.; Rice, Sarah E.; Fletterick, Robert J.

    2013-01-01

    Kinesin-like calmodulin binding protein (KCBP), a Kinesin-14 family motor protein, is involved in the structural organization of microtubules during mitosis and trichome morphogenesis in plants. The molecular mechanism of microtubule bundling by KCBP remains unknown. KCBP binding to microtubules is regulated by Ca2+-binding proteins that recognize its C-terminal regulatory domain. In this work, we have discovered a new function of the regulatory domain. We present a crystal structure of an Arabidopsis KCBP fragment showing that the C-terminal regulatory domain forms a dimerization interface for KCBP. This dimerization site is distinct from the dimerization interface within the N-terminal domain. Side chains of hydrophobic residues of the calmodulin binding helix of the regulatory domain form the C-terminal dimerization interface. Biochemical experiments show that another segment of the regulatory domain located beyond the dimerization interface, its negatively charged coil, is unexpectedly and absolutely required to stabilize the dimers. The strong microtubule bundling properties of KCBP are unaffected by deletion of the C-terminal regulatory domain. The slow minus-end directed motility of KCBP is also unchanged in vitro. Although the C-terminal domain is not essential for microtubule bundling, we suggest that KCBP may use its two independent dimerization interfaces to support different types of bundled microtubule structures in cells. Two distinct dimerization sites may provide a mechanism for microtubule rearrangement in response to Ca2+ signaling since Ca2+- binding proteins can disengage KCBP dimers dependent on its C-terminal dimerization interface. PMID:23805258

  11. Plant Kinesin-Like Calmodulin Binding Protein Employs Its Regulatory Domain for Dimerization.

    PubMed

    Vinogradova, Maia V; Malanina, Galina G; Waitzman, Joshua S; Rice, Sarah E; Fletterick, Robert J

    2013-01-01

    Kinesin-like calmodulin binding protein (KCBP), a Kinesin-14 family motor protein, is involved in the structural organization of microtubules during mitosis and trichome morphogenesis in plants. The molecular mechanism of microtubule bundling by KCBP remains unknown. KCBP binding to microtubules is regulated by Ca(2+)-binding proteins that recognize its C-terminal regulatory domain. In this work, we have discovered a new function of the regulatory domain. We present a crystal structure of an Arabidopsis KCBP fragment showing that the C-terminal regulatory domain forms a dimerization interface for KCBP. This dimerization site is distinct from the dimerization interface within the N-terminal domain. Side chains of hydrophobic residues of the calmodulin binding helix of the regulatory domain form the C-terminal dimerization interface. Biochemical experiments show that another segment of the regulatory domain located beyond the dimerization interface, its negatively charged coil, is unexpectedly and absolutely required to stabilize the dimers. The strong microtubule bundling properties of KCBP are unaffected by deletion of the C-terminal regulatory domain. The slow minus-end directed motility of KCBP is also unchanged in vitro. Although the C-terminal domain is not essential for microtubule bundling, we suggest that KCBP may use its two independent dimerization interfaces to support different types of bundled microtubule structures in cells. Two distinct dimerization sites may provide a mechanism for microtubule rearrangement in response to Ca(2+) signaling since Ca(2+)- binding proteins can disengage KCBP dimers dependent on its C-terminal dimerization interface. PMID:23805258

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

    SciTech Connect

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

    2013-04-01

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

  13. Role of bulk and of interface contacts in the behavior of lattice model dimeric proteins.

    PubMed

    Tiana, G; Provasi, D; Broglia, R A

    2003-05-01

    Some dimeric proteins first fold and then dimerize (three-state dimers) while others first dimerize and then fold (two-state dimers). Within the framework of a minimal lattice model, we can distinguish between sequences following one or the other mechanism on the basis of the distribution of the ground state energy between bulk and interface contacts. The topology of contacts is very different for the bulk than for the interface: while the bulk displays a rich network of interactions, the dimer interface is built up of a set of essentially independent contacts. Consequently, the two sets of interactions play very different roles both, in the folding and in the evolutionary history of the protein. Three-state dimers, where a large fraction of energy is concentrated in few contacts buried in the bulk, and where the relative contact energy of interface contacts is considerably smaller than that associated with bulk contacts, fold according to a hierarchical pathway controlled by local elementary structures, as also happens in the folding of single-domain monomeric proteins. On the other hand, two-state dimers display a relative contact energy of interface contacts, which is larger than the corresponding quantity associated with the bulk. In this case, the assembly of the interface stabilizes the system and leads the two chains to fold. The specific properties of three-state dimers acquired through evolution are expected to be more robust than those of two-state dimers; a fact that has consequences on proteins connected with viral diseases. PMID:12786180

  14. Dimerization of the thyrotropin-releasing hormone receptor potentiates hormone-dependent receptor phosphorylation.

    PubMed

    Song, Gyun Jee; Jones, Brian W; Hinkle, Patricia M

    2007-11-13

    The G protein-coupled thyrotropin (TSH)-releasing hormone (TRH) receptor forms homodimers. Regulated receptor dimerization increases TRH-induced receptor endocytosis. These studies test whether dimerization increases receptor phosphorylation, which could potentiate internalization. Phosphorylation at residues 355-365, which is critical for internalization, was measured with a highly selective phospho-site-specific antibody. Two strategies were used to drive receptor dimerization. Dimerization of a TRH receptor-FK506-binding protein (FKBP) fusion protein was stimulated by a dimeric FKBP ligand. The chemical dimerizer caused a large increase in TRH-dependent phosphorylation within 1 min, whereas a monomeric FKBP ligand had no effect. The dimerizer did not alter phoshorylation of receptors lacking the FKBP domain. Dimerization of receptors containing an N-terminal HA epitope also was induced with anti-HA antibody. Anti-HA IgG strongly increased TRH-induced phosphorylation, whereas monomeric Fab fragments had no effect. Anti-HA antibody did not alter phosphorylation in receptors lacking an HA tag. Furthermore, two phosphorylation-defective TRH receptors functionally complemented one another and permitted phosphorylation. Receptors with a D71A mutation in the second transmembrane domain do not signal, whereas receptors with four Ala mutations in the 355-365 region signal normally but lack phosphorylation sites. When D71A- and 4Ala-TRH receptors were expressed alone, neither underwent TRH-dependent phosphorylation. When they were expressed together, D71A receptor was phosphorylated by G protein-coupled receptor kinases in response to TRH. These results suggest that the TRH receptor is phosphorylated preferentially when it is in dimers or when preexisting receptor dimers are driven into microaggregates. Increased receptor phosphorylation may amplify desensitization. PMID:17989235

  15. Dimerization of Matrix Protein Is Required for Budding of Respiratory Syncytial Virus

    PubMed Central

    Förster, Andreas; Maertens, Goedele N.; Farrell, Paul J.

    2015-01-01

    ABSTRACT Respiratory syncytial virus (RSV) infects epithelial cells of the respiratory tract and is a major cause of bronchiolitis and pneumonia in children and the elderly. The virus assembles and buds through the plasma membrane, forming elongated membrane filaments, but details of how this happens remain obscure. Oligomerization of the matrix protein (M) is a key step in the process of assembly and infectious virus production. In addition, it was suggested to affect the conformation of the fusion protein, the major current target for RSV antivirals, in the mature virus. The structure and assembly of M are thus key parameters in the RSV antiviral development strategy. The structure of RSV M was previously published as a monomer. Other paramyxovirus M proteins have been shown to dimerize, and biochemical data suggest that RSV M also dimerizes. Here, using size exclusion chromatography-multiangle laser light scattering, we show that the protein is dimeric in solution. We also crystallized M in two crystal forms and show that it assembles into equivalent dimers in both lattices. Dimerization interface mutations destabilize the M dimer in vitro. To assess the biological relevance of dimerization, we used confocal imaging to show that dimerization interface mutants of M fail to assemble into viral filaments on the plasma membrane. Additionally, budding and release of virus-like particles are prevented in M mutants that fail to form filaments. Importantly, we show that M is biologically active as a dimer and that the switch from M dimers to higher-order oligomers triggers viral filament assembly and virus production. IMPORTANCE Human respiratory syncytial virus (RSV) is the most frequent cause of infantile bronchiolitis and pneumonia. The enormous burden of RSV makes it a major unmet target for a vaccine and antiviral drug therapy. Oligomerization of the matrix protein is a key step in the process of assembly and production of infectious virus, but the molecular

  16. New developments in porphyrin-like macrocyclic chemistry: a novel family of dibenzotetraaza[14]annulene-based cofacial dimers.

    PubMed

    Zwoliński, K M; Eilmes, J

    2016-03-01

    The first known homoleptic cofacial dimers, based on covalently linked dibenzotetraaza[14]annulenes, were synthesized in reasonable 35-40% yields, without recourse to high-dilution techniques. Dinuclear zinc(ii) dimer showed strong binding affinity toward DABCO. Site-selective monometallation of the dimer, triggered by the linkers' structure, was observed, allowing access to heterobimetallic co-receptors. PMID:26899791

  17. Assessment of naturally occurring covalent and total dimer levels in human IgG1 and IgG2.

    PubMed

    Yang, Jane; Goetze, Andrew M; Flynn, Gregory C

    2014-03-01

    Antibody dimers, two self-associated monomers, have been detected on both recombinantly expressed and endogenous human IgG proteins. Nearly 10 years ago, Yoo et al. (2003) described low levels of IgG2 covalent dimer, in human serum, but did not quantify the levels. Here we quantify the total and covalent dimer levels of IgG2 and IgG1 in human blood, and study the origin of covalent dimer formation. Low levels (<1%) of total IgG1 and IgG2 dimers were measured in freshly prepared human plasma. Both IgG1 and IgG2 covalent dimers were also found in plasma. Whereas IgG1 covalent dimer levels were significantly reduced by steps intended to eliminate artifacts during sample preparation, IgG2 covalent dimer levels remain stable in such conditions. About 0.4% of IgG2 in plasma was in a covalent dimer form, yet very little (<0.03%) of IgG1 covalent dimer could be considered naturally occurring. IgG2 dimer also formed in vitro under conditions designed to mimic those in blood, suggesting that formation occurs in vivo during circulation. Thus, small amounts of covalent IgG2 dimer do appear to form naturally. PMID:24321397

  18. 40 CFR 721.6980 - Dimer acids, polymer with polyalkylene glycol, bisphenol A-diglycidyl ether, and alky-lenepolyols...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Dimer acids, polymer with polyalkylene... Substances § 721.6980 Dimer acids, polymer with polyalkylene glycol, bisphenol A-diglycidyl ether, and alky... reporting. (1) The chemical substance dimer acids, polymer with polyalkylene glycol, bisphenol...

  19. 40 CFR 721.6980 - Dimer acids, polymer with polyalkylene glycol, bisphenol A-diglycidyl ether, and alky-lenepolyols...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Dimer acids, polymer with polyalkylene... Substances § 721.6980 Dimer acids, polymer with polyalkylene glycol, bisphenol A-diglycidyl ether, and alky... reporting. (1) The chemical substance dimer acids, polymer with polyalkylene glycol, bisphenol...

  20. Pair density wave superconducting states and statistical mechanics of dimers

    NASA Astrophysics Data System (ADS)

    Soto Garrido, Rodrigo Andres

    The following thesis is divided in two main parts. Chapters 2, 3 and 4 are devoted to the study of the so called pair-density-wave (PDW) superconducting state and some of its connections to electronic liquid crystal (ELC) phases, its topological aspects in a one dimensional model and its appearance in a quasi-one dimensional system. On the other hand, chapter 5 is focused on the investigation of the classical statistical mechanics properties of dimers, in particular, the dimer model on the Aztec diamond graph and its relation with the octahedron equation. In chapter 2 we present a theory of superconducting states where the Cooper pairs have a nonzero center-of-mass momentum, inhomogeneous superconducting states known as a pair-density-waves (PDWs) states. We show that in a system of spin-1/2 fermions in two dimensions in an electronic nematic spin-triplet phase where rotational symmetry is broken in both real and spin space PDW phases arise naturally in a theory that can be analysed using controlled approximations. We show that several superfluid phases that may arise in this phase can be treated within a controlled BCS mean field theory, with the strength of the spin-triplet nematic order parameter playing the role of the small parameter of this theory. We find that in a spin-triplet nematic phase, in addition to a triplet p-wave and spin-singlet d-wave (or s depending on the nematic phase) uniform superconducting states, it is also possible to have a d-wave (or s) PDW superconductor. The PDW phases found here can be either unidirectional, bidirectional, or tridirectional depending on the spin-triplet nematic phase and which superconducting channel is dominant. In addition, a triple-helix state is found in a particular channel. We show that these PDW phases are present in the weak-coupling limit, in contrast to the usual Fulde-Ferrell-Larkin-Ovchinnikov phases, which require strong coupling physics in addition to a large magnetic field (and often both). In chapter

  1. Structural Basis for a Reciprocating Mechanism of Negative Cooperativity in Dimeric Phosphagen Kinase Activity

    SciTech Connect

    Wu, X.; Ye, S; Guo, S; Yan, W; Bartlam, M; Rao, Z

    2010-01-01

    Phosphagen kinase (PK) family members catalyze the reversible phosphoryl transfer between phosphagen and ADP to reserve or release energy in cell energy metabolism. The structures of classic quaternary complexes of dimeric creatine kinase (CK) revealed asymmetric ligand binding states of two protomers, but the significance and mechanism remain unclear. To understand this negative cooperativity further, we determined the first structure of dimeric arginine kinase (dAK), another PK family member, at 1.75 {angstrom}, as well as the structure of its ternary complex with AMPPNP and arginine. Further structural analysis shows that the ligand-free protomer in a ligand-bound dimer opens more widely than the protomers in a ligand-free dimer, which leads to three different states of a dAK protomer. The unexpected allostery of the ligand-free protomer in a ligand-bound dimer should be relayed from the ligand-binding-induced allostery of its adjacent protomer. Mutations that weaken the interprotomer connections dramatically reduced the catalytic activities of dAK, indicating the importance of the allosteric propagation mediated by the homodimer interface. These results suggest a reciprocating mechanism of dimeric PK, which is shared by other ATP related oligomeric enzymes, e.g., ATP synthase. - Wu, X., Ye, S., Guo, S., Yan, W., Bartlam, M., Rao, Z. Structural basis for a reciprocating mechanism of negative cooperativity in dimeric phosphagen kinase activity.

  2. Ultraviolet radiation-induced lethality and repair of pyrimidine dimers in fish embryos.

    PubMed

    Applegate, L A; Ley, R D

    1988-03-01

    Pimephales promelas (fathead minnow) embryos were used to show a correlation between induction of pyrimidine dimers in DNA and embryo death. Embryo killing was measured by a lack of heart-beat and blood circulation at 48 h post-ultraviolet radiation (UVR). When the embryos were exposed to various doses of UVR from a FS-40 sunlamp followed by exposure to photoreactivating light (PRL) (320-400 nm), the number of pyrimidine dimers decreased significantly. The photorepair of dimers was accompanied by a substantial increase in embryo survival. When embryo killing was examined as a function of the number of dimers present, dimers were identified as a major lesion involved in UVR-induced killing in these fish embryos. This in vivo study on photoreactivation treatment of fish embryos shows a direct association between UVR-induced pyrimidine dimers and embryo killing. In addition, when embryos were held in the dark for 9 h after UVR, 50% of the dimers were removed by excision repair. PMID:3352631

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

    SciTech Connect

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

    2011-12-31

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

  4. Programmed pH-Driven Reversible Association and Dissociation of Interconnected Circular DNA Dimer Nanostructures.

    PubMed

    Hu, Yuwei; Ren, Jiangtao; Lu, Chun-Hua; Willner, Itamar

    2016-07-13

    The switchable pH-driven reversible assembly and dissociation of interlocked circular DNA dimers is presented. The circular DNA dimers are interconnected by pH-responsive nucleic acid bridges. In one configuration, the two-ring nanostructure is separated at pH = 5.0 to individual rings by reconfiguring the interlocking bridges into C-G·C(+) triplex units, and the two-ring assembly is reformed at pH = 7.0. In the second configuration, the dimer of circular DNAs is bridged at pH = 7.0 by the T-A·T triplex bridging units that are separated at pH = 10.0, leading to the dissociation of the dimer to single circular DNA nanostructures. The two circular DNA units are also interconnected by two pH-responsive locks. The pH-programmed opening of the locks at pH = 5.0 or pH = 10.0 yields two isomeric dimer structures composed of two circular DNAs. The switchable reconfigured states of the circular DNA nanostructures are followed by time-dependent fluorescence changes of fluorophore/quencher labeled systems and by complementary gel electrophoresis experiments. The dimer circular DNA structures are further implemented as scaffolds for the assembly of Au nanoparticle dimers exhibiting controlled spatial separation. PMID:27225955

  5. Direct visualization of a cycloaddition reaction on frozen asymmetric Si dimers at room temperature

    NASA Astrophysics Data System (ADS)

    Baik, Jaeyoon; Ihm, Kyuwook; Ha, Taekyun; An, Ki-Seok; Ahn, Joung Real; Park, Chong-Yun

    2016-07-01

    We firstly report an experimental visualization of a cycloaddition reaction on RT frozen asymmetric Si dimers. The frozen Si dimers with a local c(4 × 2) order were prepared by pinning flip-flopping Si dimers by using molecules. This RT pristine c(4 × 2) structure was used to determine what Si atom of an asymmetric Si dimer bonds to a molecule at the initial stage of the RT cycloaddition reaction, which has been a long-standing puzzling issue. This made it possible to compare directly experimental cycloaddition reactions with theoretical ones. As a prototype for the experiment, a 1,3-butadiene molecule adsorbed between Si dimer rows was used. The 1,3-butadiene molecule was found to prefer a symmetric Si pair on the frozen Si dimers, i.e., two electrophilic lower atoms of asymmetric Si dimers. This result is consistent with the theoretical prediction that a 1,3-diene molecule prefers a symmetric Si pair on the Si(001)c(4 × 2) surface. This experimental approach can also be applied to other studies for the adsorption of a molecule on a Si(001) surface at room temperature.

  6. STIM1 dimers undergo unimolecular coupling to activate Orai1 channels

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

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

    PubMed Central

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

    2011-01-01

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

  8. Identification of the Serratia endonuclease dimer: structural basis and implications for catalysis.

    PubMed Central

    Miller, M. D.; Krause, K. L.

    1996-01-01

    The Serratia endonuclease is an extracellularly secreted enzyme capable of cleaving both single- and double-stranded forms of DNA and RNA. It is the first member of a large class of related and usually dimeric endonucleases for which a structure is known. Using X-ray crystallography, the structure of monomer of this enzyme was reported by us previously (Miller MD et al., 1994, Nature Struct Biol 1:461-468). We now confirm the dimeric nature of this enzyme through light-scattering experiments and identify the physiologic dimer interface through crystal packing analysis. This dimerization occurs through an isologous twofold interaction localized to the carboxy-terminal subdomain of the enzyme. The dimer is a prolate ellipsoid with dimensions 30 A x 35 A x 90 A. The dimer interface is flat and contains four salt links, several hydrogen bonds, and nonpolar interactions. Buried water is prominent in this interface and it includes an unusual "cubic" water cluster. The position of the two active sites in the dimer suggests that they can act independently in their cleavage of DNA, but have a geometrical advantage in attacking substrate relative to the monomer. PMID:8771193

  9. The regulatory domain of human tryptophan hydroxylase 1 forms a stable dimer.

    PubMed

    Zhang, Shengnan; Hinck, Cynthia S; Fitzpatrick, Paul F

    2016-08-01

    The three eukaryotic aromatic amino acid hydroxylases phenylalanine hydroxylase, tyrosine hydroxylase, and tryptophan hydroxylase have essentially identical catalytic domains and discrete regulatory domains. The regulatory domains of phenylalanine hydroxylase form ACT domain dimers when phenylalanine is bound to an allosteric site. In contrast the regulatory domains of tyrosine hydroxylase form a stable ACT dimer that does not bind the amino acid substrate. The regulatory domain of isoform 1 of human tryptophan hydroxylase was expressed and purified; mutagenesis of Cys64 was required to prevent formation of disulfide-linked dimers. The resulting protein behaved as a dimer upon gel filtration and in analytical ultracentrifugation. The sw value of the protein was unchanged from 2.7 to 35 μM, a concentration range over which the regulatory domain of phenylalanine hydroxylase forms both monomers and dimers, consistent with the regulatory domain of tryptophan hydroxylase 1 forming a stable dimer stable that does not undergo a monomer-dimer equilibrium. Addition of phenylalanine, a good substrate for the enzyme, had no effect on the sw value, consistent with there being no allosteric site for the amino acid substrate. PMID:27255998

  10. Neuroprotective Secreted Amyloid Precursor Protein Acts by Disrupting Amyloid Precursor Protein Dimers*S⃞

    PubMed Central

    Gralle, Matthias; Botelho, Michelle Gralle; Wouters, Fred S.

    2009-01-01

    The amyloid precursor protein (APP) is implied both in cell growth and differentiation and in neurodegenerative processes in Alzheimer disease. Regulated proteolysis of APP generates biologically active fragments such as the neuroprotective secreted ectodomain sAPPα and the neurotoxic β-amyloid peptide. Furthermore, it has been suggested that the intact transmembrane APP plays a signaling role, which might be important for both normal synaptic plasticity and neuronal dysfunction in dementia. To understand APP signaling, we tracked single molecules of APP using quantum dots and quantitated APP homodimerization using fluorescence lifetime imaging microscopy for the detection of Förster resonance energy transfer in living neuroblastoma cells. Using selective labeling with synthetic fluorophores, we show that the dimerization of APP is considerably higher at the plasma membrane than in intracellular membranes. Heparan sulfate significantly contributes to the almost complete dimerization of APP at the plasma membrane. Importantly, this technique for the first time structurally defines the initiation of APP signaling by binding of a relevant physiological extracellular ligand; our results indicate APP as receptor for neuroprotective sAPPα, as sAPPα binding disrupts APP dimers, and this disruption of APP dimers by sAPPα is necessary for the protection of neuroblastoma cells against starvation-induced cell death. Only cells expressing reversibly dimerized wild-type, but not covalently dimerized mutant APP are protected by sAPPα. These findings suggest a potentially beneficial effect of increasing sAPPα production or disrupting APP dimers for neuronal survival. PMID:19336403

  11. Dimerization of core complexes as an efficient strategy for energy trapping in Rhodobacter sphaeroides.

    PubMed

    Chenchiliyan, Manoop; Timpmann, Kõu; Jalviste, Erko; Adams, Peter G; Hunter, C Neil; Freiberg, Arvi

    2016-06-01

    In the purple phototrophic bacterium Rhodobacter sphaeroides, light harvesting LH2 complexes transfer absorbed solar energy to RC-LH1-PufX core complexes, which are mainly found in the dimeric state. Many other purple phototrophs have monomeric core complexes and the basis for requiring dimeric cores is not fully established, so we analysed strains of Rba. sphaeroides that contain either native dimeric core complexes or altered monomeric cores harbouring a deletion of the first 12 residues from the N-terminus of PufX, which retains the PufX polypeptide but removes the major determinant of core complex dimerization. Membranes were purified from strains with dimeric or monomeric cores, and with either high or low levels of the LH2 complex. Samples were interrogated with absorption, steady-state fluorescence, and picosecond time-resolved fluorescence kinetic spectroscopies to reveal their light-harvesting and energy trapping properties. We find that under saturating excitation light intensity the photosynthetic membranes containing LH2 and monomeric core complexes have fluorescence lifetimes nearly twice that of membranes with LH2 plus dimeric core complexes. This trend of increased lifetime is maintained with RCs in the open state as well, and for two different levels of LH2 content. Thus, energy trapping is more efficient when photosynthetic membranes of Rba. sphaeroides consist of RC-LH1-PufX dimers and LH2 complexes. PMID:27013332

  12. H-type Dimer Formation of Fluorophores: A Mechanism for Activatable, in vivo Optical Molecular Imaging

    PubMed Central

    Ogawa, Mikako; Kosaka, Nobuyuki; Choyke, Peter L; Kobayashi, Hisataka

    2009-01-01

    In vivo molecular imaging with target-specific activatable “smart” probes, which only yield fluorescence at the intended target, enables sensitive and specific cancer detection because of high target to background ratios (TBR). Dimerization and fluorescence quenching has been shown to occur in concentrated aqueous solutions of various fluorophores. Here, we hypothesized that fluorophore dimerization and quenching after conjugation to targeting proteins can occur at low concentration, which is reasonable for in vivo imaging probes, because protein molecules can stabilize the fluorophore dimers based on physico-chemical interactions. This dimerization can be exploited as a mechanism for fluorescence activation. Rhodamine derivatives were conjugated to the cancer targeting molecules, avidin and trastuzumab, which target D-galactose receptor and HER2/neu antigen, respectively. After conjugation, a large proportion of R6G and TAMRA formed H-type dimers, even at low concentrations, but could be fully dequenched upon dissociation of the dimers to monomers. Lipophilicity was a potential factor in promoting H-dimer formation. To demonstrate the fluorescence activation effect during in vivo fluorescence endoscopic molecular imaging, a highly quenched probe, avidin-TAMRA or a minimally quenched probe, avidin-Alexa488 was administered into mice with ovarian metastases to the peritoneum. The tumors were clearly visualized with avidin-TAMRA, with low background fluorescence; in contrast, the background fluorescence was high for avidin-Alexa488. Thus, H-dimer formation as a mechanism of fluorescence quenching could be used to develop fluorescence activatable probes for in vivo molecular imaging. Effective activatable optical probes can be designed by focusing on the H-dimer formation of fluorophores. PMID:19480464

  13. Base Pair Opening in a Deoxynucleotide Duplex Containing a cis-syn Thymine Cyclobutane Dimer Lesion

    PubMed Central

    Wenke, Belinda B.; Huiting, Leah N.; Frankel, Elisa B.; Lane, Benjamin F.; Núñez, Megan E.

    2014-01-01

    The cis-syn thymine cyclobutane dimer is a DNA photoproduct implicated in skin cancer. We compared the stability of individual base pairs in thymine dimer-containing duplexes to undamaged parent 10-mer duplexes. UV melting thermodynamic measurements, CD spectroscopy, and 2D NOESY NMR spectroscopy confirm that the thymine dimer lesion is locally and moderately destabilizing within an overall B-form duplex conformation. We measured the rates of exchange of individual imino protons by NMR using magnetization transfer from water and determined the equilibrium constant for the opening of each base pair Kop. In the normal duplex Kop decreases from the frayed ends of the duplex toward the center, such that the central TA pair is the most stable with a Kop of 8×10−7. In contrast, base pair opening at the 5’T of the thymine dimer is facile. The 5’T of the dimer has the largest equilibrium constant (Kop =3×10−4) in its duplex, considerably larger than even the frayed penultimate base pairs. Notably, base pairing by the 3’T of the dimer is much more stable than by the 5’T, indicating that the predominant opening mechanism for the thymine dimer lesion is not likely to be flipping out into solution as a single unit. The dimer asymmetrically affects the stability of the duplex in its vicinity, destabilizing base pairing on its 5’ side more than on the 3’ side. The striking differences in base pair opening between parent and dimer duplexes occur independently of the duplex-single strand melting transitions. PMID:24328089

  14. Dimeric human sulfotransferase 1B1 displays cofactor-dependent subunit communication

    PubMed Central

    Tibbs, Zachary E; Falany, Charles N

    2015-01-01

    The cytosolic sulfotransferases (SULTs) are dimeric enzymes that catalyze the transformation of hydrophobic drugs and hormones into hydrophilic sulfate esters thereby providing the body with an important pathway for regulating small molecule activity and excretion. While SULT dimerization is highly conserved, the necessity for the interaction has not been established. To perform its function, a SULT must efficiently bind the universal sulfate donor, 3′-phosphoadenosine-5′-phosphosulfate (PAPS), and release the byproduct, 3′, 5′-diphosphoadenosine (PAP), following catalysis. We hypothesize this efficient binding and release of PAPS/PAP may be connected to SULT dimerization. To allow for the visualization of dynamic protein interactions critical for addressing this hypothesis and to generate kinetically testable hypotheses, molecular dynamic simulations (MDS) of hSULT1B1 were performed with PAPS and PAP bound to each dimer subunit in various combinations. The results suggest the dimer subunits may possess the capability of communicating with one another in a manner dependent on the presence of the cofactor. PAP or PAPS binding to a single side of the dimer results in decreased backbone flexibility of both the bound and unbound subunits, implying the dimer subunits may not act independently. Further, binding of PAP to one subunit of the dimer and PAPS to the other caused increased flexibility in the subunit bound to the inactive cofactor (PAP). These results suggest SULT dimerization may be important in maintaining cofactor binding/release properties of SULTs and provide hypothetical explanations for SULT half-site reactivity and substrate inhibition, which can be analyzed in vitro. PMID:26236487

  15. Structural requirements for nucleocapsid protein-mediated dimerization of avian leukosis virus RNA.

    PubMed

    Ali, Moez Ben; Chaminade, Françoise; Kanevsky, Igor; Ennifar, Eric; Josset, Laurence; Ficheux, Damien; Darlix, Jean-Luc; Fossé, Philippe

    2007-09-28

    The avian leukosis virus (ALV) belongs to the alpha group of retroviruses that are widespread in nature. The 5'-untranslated region of ALV genome contains the L3 element that is important for virus infectivity and the formation of an unstable RNA dimer in vitro. The L3 sequence is predicted to fold into a long stem-loop structure with two internal loops and an apical one. Phylogenetic analysis predicts that the L3 stem-loop is conserved in alpharetroviruses. Furthermore, a significant selection mechanism maintains a palindrome in the apical loop. The nucleocapsid protein of the alpharetroviruses (NCp12) is required for RNA dimer formation and replication in vivo. It is not known whether L3 can be an NCp12-mediated RNA dimerization site able to bind NCp12 with high affinity. Here, we report that NCp12 chaperones formation of a stable ALV RNA dimer through L3. To investigate the NCp12-mediated L3 dimerization reaction, we performed site-directed mutagenesis, gel retardation and heterodimerization assays and analysis of thermostability of dimeric RNAs. We show that the affinity of NCp12 for L3 is lower than its affinity for the microPsi RNA packaging signal. Results show that conservation of a long stem-loop structure and a loop-loop interaction are not required for NCp12-mediated L3 dimerization. We show that the L3 apical stem-loop is sufficient to form an extended duplex and the whole stem-loop L3 cannot be converted by NCp12 into a duplex extending throughout L3. Three-dimensional modelling of the stable L3 dimer supports the notion that the extended duplex may represent the minimal dimer linkage structure found in the genomic RNA. PMID:17706668

  16. Interaction between dimer interface residues of native and mutated SOD1 protein: a theoretical study.

    PubMed

    Keerthana, S P; Kolandaivel, P

    2015-04-01

    Cu-Zn superoxide dismutase 1 (SOD1) is a highly conserved bimetallic protein enzyme, used for the scavenging the superoxide radicals (O2 (-)) produced due to aerobic metabolism in the mitochondrial respiratory chain. Over 100 mutations have been identified and found to be in the homodimeric structure of SOD1. The enzyme has to be maintained in its dimeric state for the structural stability and enzymatic activity. From our investigation, we found that the mutations apart from the dimer interface residues are found to affect the dimer stability of protein and hence enhancing the aggregation and misfolding tendency of mutated protein. The homodimeric state of SOD1 is found to be held together by the non-covalent interactions. The molecular dynamics simulation has been used to study the hydrogen bond interactions between the dimer interface residues of the monomers in native and mutated forms of SOD1 in apo- and holo-states. The results obtained by this analysis reveal the fact that the loss of hydrogen bond interactions between the monomers of the dimer is responsible for the reduced stability of the apo- and holo-mutant forms of SOD1. The conformers with dimer interface residues in native and mutated protein obtained by the molecular dynamics simulation is subjected to quantum mechanical study using M052X/6-31G(d) level of theory. The charge transfer between N-H···O interactions in the dimer interface residues were studied. The weak interaction between the monomers of the dimer accounts for the reduced dimerization and enhanced deformation energy in the mutated SOD1 protein. PMID:25578810

  17. Ribosome dimerization is essential for the efficient regrowth of Bacillus subtilis.

    PubMed

    Akanuma, Genki; Kazo, Yuka; Tagami, Kazumi; Hiraoka, Hirona; Yano, Koichi; Suzuki, Shota; Hanai, Ryo; Nanamiya, Hideaki; Kato-Yamada, Yasuyuki; Kawamura, Fujio

    2016-03-01

    Ribosome dimers are a translationally inactive form of ribosomes found in Escherichia coli and many other bacterial cells. In this study, we found that the 70S ribosomes of Bacillus subtilis dimerized during the early stationary phase and these dimers remained in the cytoplasm until regrowth was initiated. Ribosome dimerization during the stationary phase required the hpf gene, which encodes a homologue of the E. coli hibernation-promoting factor (Hpf). The expression of hpf was induced at an early stationary phase and its expression was observed throughout the rest of the experimental period, including the entire 6 h of the stationary phase. Ribosome dimerization followed the induction of hpf in WT cells, but the dimerization was impaired in cells harbouring a deletion in the hpf gene. Although the absence of ribosome dimerization in these Hpf-deficient cells did not affect their viability in the stationary phase, their ability to regrow from the stationary phase decreased. Thus, following the transfer of stationary-phase cells to fresh LB medium, Δhpf mutant cells grew slower than WT cells. This observed lag in growth of Δhpf cells was probably due to a delay in restoring their translational activity. During regrowth, the abundance of ribosome dimers in WT cells decreased with a concomitant increase in the abundance of 70S ribosomes and growth rate. These results suggest that the ribosome dimers, by providing 70S ribosomes to the cells, play an important role in facilitating rapid and efficient regrowth of cells under nutrient-rich conditions. PMID:26743942

  18. Structural and energetic requirements for a second binding site at the dimeric β-lactoglobulin interface.

    PubMed

    Bello, Martiniano

    2016-09-01

    Through experimental and theoretical approaches, it has been shown that bovine β-lactoglobulin (βlg) uses its hydrophobic cavity or calyx as the primary binding site for hydrophobic molecules, whereas the existence of a second ligand binding site at the dimeric interface has only been structurally identified for vitamin D3 (VD3). This binding exists even in the thermally denatured state, suggesting the prevalence of this secondary site. Although crystallographic experiments have suggested that VD3 can bind to both monomeric and dimeric states without significant structural differences, theoretical and experimental reports have proposed some structural requirements. Thus, in this study, based on known experimental data, the dynamic interaction of VD3 with the monomeric or dimeric forms of βlg was investigated through a protocol combining blind docking and 2 microsecond molecular dynamics simulations coupled with binding free energy and per-residue binding free energy decomposition analyses using the Molecular Mechanics Generalized Born Surface Area approach. Binding free energy calculations allowed us to estimate the energetic differences of coupling VD3 at the calyx and the dimeric interface for the monomeric or dimeric state, revealing that the dimeric structure is required to form a stable complex with VD3 at the dimeric interface. This also has an important impact on the dimerization process, whereas although the monomeric state also forms a stable complex with VD3 at the dimeric interface, the incorporation of the entropy component contributed to producing a marginally favorable binding free energy. Finally, the per-residue decomposition analysis provided energetic information about the most relevant residues in stabilizing the different systems. PMID:26375627

  19. Monoclonal antibodies with equal specificity to D-dimer and high-molecular-weight fibrin degradation products

    PubMed Central

    Kogan, Alexander E.; Mukharyamova, Kadriya S.; Bereznikova, Anastasia V.; Filatov, Vladimir L.; Koshkina, Ekaterina V.; Bloshchitsyna, Marina N.; Katrukha, Alexey G.

    2016-01-01

    Fibrin degradation results in the formation of fibrin degradation products (FDPs) of different molecular weights, which include D-dimer. Commercial D-dimer assays recognize multiple forms of FDP with different specificity. As a result, the absence of an international D-dimer standard and the marked discrepancy in the D-dimer values in the same samples measured by assays from different manufacturers have become the primary problems that clinicians face in the D-dimer determination. We consider that an assay with equal specificity to all FDP forms regardless of their molecular weights could help to solve these problems. We aimed to produce mAbs that could equally recognize high-molecular-weight FDP (HMW FDP) and D-dimer. mAbs against D-dimer were produced. The HMW FDP/D-dimer ratios in plasma samples were analyzed following protein separation by gel filtration using the developed fluoroimmunoassay. A sandwich immunoassay with equal specificity to HMW FDP and D-dimer was developed and applied to determine HMW FDP/D-dimer ratios in patients with different diseases. Although the HMW FDP levels prevailed in thrombotic patients, the FDP and D-dimer levels were comparable in septic patients. Meanwhile, the D-dimer levels often exceeded the HMW FDP levels in patients who had undergone surgery. The ‘D-dimer’ levels that were detected by different assays also varied greatly depending on the assay specificities to FDP and D-dimer. Our findings show that the introduction of assays with equal specificities to FDP and D-dimer in clinical practice is a possible way of standardizing D-dimer measurements. PMID:26656897

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

    PubMed Central

    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

  1. Photoelectron spectroscopy of the nitrogen dimer (N2)2 and clusters (N2)n: N2 dimer revealed as the chromophore in photoionization of condensed nitrogen

    NASA Astrophysics Data System (ADS)

    Carnovale, Frank; Peel, J. Barrie; Rothwell, Richard G.

    1988-01-01

    The He i photoelectron spectra of gas-phase nitrogen dimer and nitrogen clusters have been measured in a pulsed cluster beam. The dimer (N2)2 is characterized by broad bands with vertical ionization energies which are 0.3±0.1 eV lower than for N2 monomer. The bands observed for a mixture of small clusters, estimated to be of average size N¯=10, are identical to the dimer bands except for further shifts of 0.3 eV to lower ionization energies. The clusters bandwidths and band shapes are virtually the same as measured for thin films of condensed N2, indicating that the nitrogen dimer (N2)2 is the ionization chromophore in each case. This offers support for Haberland's hypothesis that ionization of any Mn cluster produces the ion M+2Mn-2 provided M is a closed-shell atom or molecule. The theory of electronic relaxation polarization of the dielectric medium, which explains the gas-to-solid ionization energy shifts, is modified for the case of finite clusters and to account for dimer ion formation.

  2. Dimer motion on a periodic substrate: Spontaneous symmetry breaking and absolute negative mobility

    NASA Astrophysics Data System (ADS)

    Speer, David; Eichhorn, Ralf; Evstigneev, Mykhaylo; Reimann, Peter

    2012-06-01

    We consider two coupled particles moving along a periodic substrate potential with negligible inertia effects (overdamped limit). Even when the particles are identical and the substrate spatially symmetric, a sinusoidal external driving of appropriate amplitude and frequency may lead to spontaneous symmetry breaking in the form of a permanent directed motion of the dimer. Thermal noise restores ergodicity and thus zero net velocity, but entails arbitrarily fast diffusion of the dimer for sufficiently weak noise. Moreover, upon application of a static bias force, the dimer exhibits a motion opposite to that force (absolute negative mobility). The key requirement for all these effects is a nonconvex interaction potential of the two particles.

  3. Dynamic dimer formation between superionic fluorines in PbF2

    NASA Astrophysics Data System (ADS)

    Nakamura, Nobutaka; Tsumuraya, Kazuo

    2013-03-01

    Recently Tsumuraya et al .(J. Phys. Soc. Jpn. 81,055603(2012).) have elucidated the formation of the dynamic dimers in the superionic conductor α-CuI with the first principles molecular dynamics (MD) method. They, for the first time in research, confirmed the dimer formation through the analyses the origin of the correlation peaks of the partial pair distribution functions and the partial angle distribution functions. The present study elucidates the dynamic structure of the superionc fluorines in PbF2 crystal with the MD method through identifying the origins of the correlation peaks. The fluorines form the dynamic 32 f-8 c and 4 b-8 c dimers.

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

    PubMed

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

    2016-05-26

    Two isomers of both the lowest excited singlet (S1) and triplet (T1) states of the directly para, para'-connected covalent dimer of the singlet-fission chromophore 1,3-diphenylisobenzofuran have been observed. In one isomer, excitation is delocalized over both halves of the dimer, and in the other, it is localized on one or the other half. For a covalent dimer in solution, such "excitation isomerism" is extremely rare. The vibrationally relaxed isomers do not interconvert, and their photophysical properties, including singlet fission, differ significantly. PMID:27158903

  5. Photochemical dimerization and functionalization of alkanes, ethers, primary and secondary alcohols, phosphine oxides and silanes

    DOEpatents

    Crabtree, Robert H.; Brown, Stephen H.

    1989-01-01

    The space-time yield and/or the selectivity of the photochemical dimerization of alkanes, ethers, primary and secondary alcohols, phosphine oxides and primary, secondary and tertiary silanes with Hg and U.V. light is enhanced by refluxing the substrate in the irradiated reaction zone at a temperature at which the dimer product condenses and remains condensed promptly upon its formation. Cross-dimerization of the alkanes, ethers and silanes with primary alcohols is disclosed, as is the functionalization to aldehydes of the alkanes with carbon monoxide.

  6. The role of dimeric molecules of metalloporphyrins in phototransfer of an electron through liposome membranes

    SciTech Connect

    Yusupov, R.G.; Asanov, A.N.; Khairutdinov, R.F.

    1985-08-10

    The possibility of the participation of dimers of Mg and Zn porphyrins in phototransfer of an electron through the liposome membrane is demonstrated. The authors discovered and investigated two-quantum photoionization of the dimers of some metalloporphyrins (MP) with electron transfer to great distances in glassy concentrated solutions of MP in alcohol matrices in the absence of photoionization of the monomeric molecules. Charge separation in solutions of liposomes sensitized by MP at low temperatures and apparently also at ca 20 degrees C takes place according to a mechanism of two-quantum photoionization of dimeric molecules of the metalloporphyrins.

  7. The role of the partner atom and resonant excitation energy in ICD in rare gas dimers

    NASA Astrophysics Data System (ADS)

    O'Keeffe, Patrick; Ripani, Enrico; Bolognesi, Paola; Coreno, Marcello; Avaldi, Lorenzo; Devetta, Michele; Callegari, Carlo; Di Praia, Michele; Prince, Kevin; Richter, Robert; Alagial, Michele; Kivimäkil, Antti

    2014-04-01

    We show experimental evidence for Interatomic Coulombic Decay (ICD) in mixed rare gas dimers following resonant Auger decay. A velocity map imaging apparatus together with a cooled supersonic beam containing Ar2, ArNe and ArKr dimers was used to record electron VMI images in coincidence with two mass selected ions following excitation on five resonances converging to the Ar+ 2p-11/2 and 2p-13/2 thresholds using the synchrotron radiation. The results show that the kinetic energy distribution of the ICD electrons observed in coincidence with the ions from Coulomb explosion of the dimers depends on the partner ion and resonant photon energy.

  8. β-Alaninium tetrafluoroborate: a new salt with di-β-alaninium dimeric cation.

    PubMed

    Ghazaryan, V V; Fleck, M; Petrosyan, A M

    2015-07-01

    β-Alaninium tetrafluoroborate crystallizes in the monoclinic system (space group P21/n, Z=4). The asymmetric unit contains one β-alaninium cation and one tetrafluoroborate anion, in which the fluorine atoms are disordered. All β-alaninium cations are connected with the symmetry related cations via an inversion center, thus forming dimeric centrosymmetric β-Ala(+)···β-Ala(+) cations. The O···O distance (2.698(2)Å) in the dimeric cation is relatively long compared to known distances of previously reported salts with A(+)···A(+) type dimeric cations. The infrared and Raman spectra are studied. PMID:25813178

  9. Photochemical dimerization and functionalization of alkanes, ethers, primary and secondary alcohols, phosphine oxides and silanes

    DOEpatents

    Crabtree, R.H.; Brown, S.H.

    1989-10-17

    The space-time yield and/or the selectivity of the photochemical dimerization of alkanes, ethers, primary and secondary alcohols, phosphine oxides and primary, secondary and tertiary silanes with Hg and U.V. light is enhanced by refluxing the substrate in the irradiated reaction zone at a temperature at which the dimer product condenses and remains condensed promptly upon its formation. Cross-dimerization of the alkanes, ethers and silanes with primary alcohols is disclosed, as is the functionalization to aldehydes of the alkanes with carbon monoxide.

  10. Phenylalanine Binding Is Linked to Dimerization of the Regulatory Domain of Phenylalanine Hydroxylase

    PubMed Central

    2015-01-01

    Analytical ultracentrifugation has been used to analyze the oligomeric structure of the isolated regulatory domain of phenylalanine hydroxylase. The protein exhibits a monomer–dimer equilibrium with a dissociation constant of ∼46 μM; this value is unaffected by the removal of the 24 N-terminal residues or by phosphorylation of Ser16. In contrast, phenylalanine binding (Kd = 8 μM) stabilizes the dimer. These results suggest that dimerization of the regulatory domain of phenylalanine hydroxylase is linked to allosteric activation of the enzyme. PMID:25299136

  11. Passage time statistics in the formation of ultracold dimers from fermionic atoms

    NASA Astrophysics Data System (ADS)

    Uys, Hermann

    2005-05-01

    We investigate the temporal fluctuations characteristic of the formation of molecular dimers from ultracold fermionic atoms via either photoassociation or a Feshbach resonance. The quantum fluctuations inherent to the initial atomic state result in large fluctuations in the passage time from atoms to molecules. A heuristic classical stochastic model yields an excellent agreement with the full quantum treatment in the initial stages of the dynamics. We also show that in contrast to the association of atoms into dimers, the reverse process of dissociation from a condensate of bosonic dimers exhibits little passage time fluctuations.

  12. Nonadiabatic alignment of van der Waals--force-bound argon dimers by femtosecond laser pulses

    SciTech Connect

    Wu, J.; Vredenborg, A.; Ulrich, B.; Schmidt, L. Ph. H.; Meckel, M.; Voss, S.; Sann, H.; Kim, H.; Jahnke, T.; Doerner, R.

    2011-06-15

    We demonstrated that the weak van der Waals-force-bound argon dimer can be nonadiabatically aligned by nonresonant femtosecond laser pulses, showing periodic alignment and anti-alignment revivals after the extinction of the laser pulse. Based on the measured nonadiabatic alignment trace, the rotational constant of the argon dimer ground state is determined to be B{sub 0}= 0.05756 {+-} 0.00004 cm{sup -1}. Noticeable alignment dependence of frustrated tunneling ionization and bond-softening induced dissociation of the argon dimer are observed.

  13. Matching Measure, Benjamini-Schramm Convergence and the Monomer-Dimer Free Energy

    NASA Astrophysics Data System (ADS)

    Abért, Miklós; Csikvári, Péter; Hubai, Tamás

    2015-10-01

    We define the matching measure of a lattice L as the spectral measure of the tree of self-avoiding walks in L. We connect this invariant to the monomer-dimer partition function of a sequence of finite graphs converging to L. This allows us to express the monomer-dimer free energy of L in terms of the matching measure. Exploiting an analytic advantage of the matching measure over the Mayer series then leads to new, rigorous bounds on the monomer-dimer free energies of various Euclidean lattices. While our estimates use only the computational data given in previous papers, they improve the known bounds significantly.

  14. Laser Spectroscopy and Density Functional Study on Niobium Dimer Cation

    NASA Astrophysics Data System (ADS)

    Aydin, Metin; Lombardi, John R.

    2009-06-01

    Resonant multiphoton fragmentation spectra of niobium dimer cation (Nb2+) have been obtained by utilizing laser vaporization of a Nb metal target. Ions are mass-selected with a time-of-flight mass spectrometer followed by a mass gate, then fragmented with a pulsed dye laser, and the resulting fragment ions are detected with a second time-of-flight reflectron mass spectrometer and multichannel plate. Photon resonances are detected by monitoring ion current as a function of fragmentation laser wavelength. A rich, but complex spectrum of the cation is obtained. The bands display a characteristic multiplet structure that may be interpreted as due to transitions from the ground state X^{4}{Σ}^{-}({Ω}g) to several excited states, X^{4}{Π}({Ω}u) and X^{4}{Σ}(^{-}{Ω}u). The ground state X^{4}{Σ}^{-}({Ω}g) is derived from the electron configuration ({π}{_u})^{4} (1{σ}{_g})^{2}(2{σ}{_g})^{1} ({δ}{_g})^{2}. The two spin-orbit components are split by 145 cm^{-1} due to a strong second-order isoconfigurational spin-orbit interaction with the low-lying ^{2}{Σ}^{+}({Ω}g) state. The vibrational frequencies of the ground sate and the excited state of Nb2+ are identified as well as molecular spin-orbit constants (A{_S}{_O}) in the excited state. The electronic structure of niobium dimer cation was investigated using density functional theory. For the electronic ground state, the predicted spectroscopic properties were in good agreement with experiment. Calculations on excited states reveal congested manifolds of quartet and doublet electronic states in the range 0-30,000 cm^{-1}, reflecting the multitude of possible electronic promotions among the 4d- and 5s-based molecular orbitals. Comparisons are drawn between Nb^{+}{_2} and the prevalent isoelectronic molecules V^{+}{_2}/NbV^{+}/Nb{_2}/V{_2}/NbV. M. Aydin and John R. Lombardi J. Phys. Chem. A. xx XXXX 2009.

  15. Effect of disorder on the dimer transition of the honeycomb-lattice compound Li2RuO3

    NASA Astrophysics Data System (ADS)

    Jimenez-Segura, Marco-Polo; Ikeda, Atsutoshi; Yonezawa, Shingo; Maeno, Yoshiteru

    2016-02-01

    We report the dependence of magnetic properties on the crystalline disorder in Li2RuO3 with Ru honeycomb lattice. This oxide exhibits unconventional Ru-dimer transition below Td˜540 K. We demonstrate that the cell parameters, related to the coherence of the dimer formation, are strongly dependent on the synthesis procedure. We show that the magnetic behavior at the dimer transition is closely related to the lattice parameters. In particular, we revealed that samples with well-ordered dimers exhibit a first-order magnetic transition with the onset exceeding 550 K, higher than that reported previously. We discuss possible dimer configurations leading to this magnetolattice coupling.

  16. Identification of Phe187 as a crucial dimerization determinant facilitates crystallization of a monomeric retroviral integrase core domain.

    PubMed

    Galilee, Meytal; Alian, Akram

    2014-10-01

    Retroviral DNA integration into the host genome is mediated by nucleoprotein assemblies containing tetramers of viral integrase (IN). Whereas the fully active form of IN comprises a dimer of dimers, the molecular basis of IN multimerization has not been fully characterized. IN has consistently been crystallized in an analogous dimeric form in all crystallographic structures and experimental evidence as to the level of similarity between IN monomeric and dimeric conformations is missing because of the lack of IN monomeric structures. Here we identify Phe187 as a critical dimerization determinant of IN from feline immunodeficiency virus (FIV), a nonprimate lentivirus that causes AIDS in the natural host, and report, in addition to a canonical dimeric structure of the FIV IN core-domain, a monomeric structure revealing the preservation of the backbone structure between the two multimeric forms and suggest a role for Phe187 in "hinging" the flexible IN dimer. PMID:25199694

  17. Decreasing D-dimer after recent negative computed tomographic pulmonary angiogram does not rule out pulmonary embolism.

    PubMed

    Lo, Bruce M

    2013-06-01

    An algorithmic approach to testing utilizing risk stratification and quantitative D-dimer has been considered an acceptable approach to ruling out pulmonary embolism (PE). When D-dimer is elevated, further testing for PE is indicated. However, no evidence exists to guide practitioners when patients return after a recent negative workup for PE who previously had an elevated D-dimer. This case describes a patient who initially had an elevated D-dimer with negative workup for PE who, on repeat visit, had a decreasing D-dimer but was diagnosed with a PE. When evaluating patients after a negative workup for PE after an elevated D-dimer, a decrease in D-dimer cannot be used to rule out PE. PMID:23465871

  18. Wetting dynamics of alkyl ketene dimer on cellulosic model surfaces

    SciTech Connect

    Garnier, G.; Bertin, M.; Smrckova, M.

    1999-10-26

    The dynamic wetting of a commercial alkyl ketene dimer (AKD) wax was measured on model cellulosic surfaces. The variables investigated were temperature and the surface composition. The model surfaces consisted of cellulose and cellulose acetate films as well as glass. These surfaces are smooth by industrial standards but not on a molecular level. The objective of the study was to predict the extent of AKD wetting during the time frame of papermaking. For smooth surfaces, AKD particles wet but do not spread on the hydrophilic surfaces investigated. AKD wetting proceeds from the balance of the interfacial forces with the viscous dissipation. The effect of gravity can be neglected for papermaking conditions. The Hoffman-Tanner equation modified for partial wetting provided a very good fit of the dynamic wetting. The slope of the graph is a function of temperature but not of the solid surface composition. Maslyiah's model also fits the experimental results well, but with a physically unrealistic value of the fitting parameter. For partial wetting, the complex but rigorous Cox equation is recommended to estimate the slip length over macroscopic wetting dimensions.

  19. New measurements of microwave transitions in the water dimer

    NASA Astrophysics Data System (ADS)

    Coudert, L. H.; Lovas, F. J.; Suenram, R. D.; Hougen, J. T.

    1987-12-01

    New measurements of ten K=1 lines, including six Q type and four R type, were made on the completely protonated species of the water dimer. For some of these lines, as well as for some K=0 transitions known from the literature, Stark coefficients were determined, and these Stark coefficients provide a confirmation of the assignments. The new K=1 measurements show that the splitting associated with the (HF)2-like tunneling motion decreases from about 19.5 GHz for K=0 to about 16.2 GHz for K=1. To understand the fact that K=1 lines are populated in our 1 K beam, we must assume, in accordance with the results of beam studies on other molecules, that levels of different nuclear spin modification relax separately. In an attempt to gain information on tunneling splittings other than that caused by the (HF)2-like motion, we have made new measurements on 1-0 and 2-1 transitions with K=0 for several partially deuterated species, in which the (HF)2-like motion cannot occur. Small splittings ranging from 4 to 145 MHz were observed. Because of the nature of the tunneling motions involved, these new data yield only the difference of the tunneling splitting in the upper and lower states of the transition.

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

    PubMed

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

    2016-01-26

    Plasmonic antennas are able to concentrate and re-emit light in a controllable manner through strong coupling between metallic nanostructures. Only recently has it found that quantum mechanical effects can drastically change the coupling strength as the feature size approaches atomic scales. Here, we present a comprehensive experimental and theoretical study of the evolution of the resonance peak and its polarization state as the dimer-antenna gap narrows to subnanometer scale. We clearly can identify the classical plasmonic regime, a crossover regime where nonlocal screening plays an important role, and the quantum regime where a charge transfer plasmon appears due to interparticle electron tunneling. Moreover, as the gap decreases from tens of to a few nanometers, the bonding dipole mode tends to emit photons with increasing polarizability. When the gap narrows to quantum regime, a significant depolarization of the mode emission is observed due to the reduction of the charge density of coupled quantum plasmons. These results would be beneficial for the understanding of quantum effects on emitting-polarization of nanoantennas and the development of quantum-based photonic nanodevices. PMID:26700823

  1. Electrooptics of chiral nematics formed by molecular dimers

    NASA Astrophysics Data System (ADS)

    Xiang, Jie; Shiyanovskii, Sergij V.; Li, Yannian; Imrie, Corrie T.; Li, Quan; Lavrentovich, Oleg D.

    2014-10-01

    Electrically induced reorientation of liquid crystal (LC) director caused by dielectric anisotropy is a fundamental phenomenon widely used in modern technologies. We demonstrate an electrooptic effect in a chiral nematic LC with a distinct oblique-helicoidal director deformation. The effect, predicted theoretically in late 1960-ies, is observed in a chiral nematic (cholesteric) in which the ground field-free state of the director is a right-angle helicoid. In the electric field, the director forms an oblique helicoid with the pitch and cone angle controlled by the field. The effect is observed in a dimer nematic material in which the bend elastic constant is much smaller than its twist counterpart. The heliconical structure can be used in two different geometries of a sandwich-type cell, with the axis of the oblique helicoid being either parallel or perpendicular to the bounding plates. In the first case, the structure can be used as tunable diffraction grating controlled by the in-plane electric field. In the second case, the structure represents an optical Bragg reflector in which the wavelength of reflected light is controlled in a broad spectral range (from ultraviolet to infrared and beyond, depending on the composition) by a top-down electric field; it can find applications in reflective displays, tunable color filters and lasers.

  2. The nature of monomer inversion in the ammonia dimer

    NASA Astrophysics Data System (ADS)

    Olthof, E. H. T.; van der Avoird, A.; Wormer, P. E. S.; Loeser, J. G.; Saykally, R. J.

    1994-11-01

    A model is presented for calculating the splittings due to umbrella inversion of the monomers in (NH3)2. Input to the model are the six-dimensional dimer bound state wave functions for rigid monomers, calculated previously [E. H. T. Olthof, A. van der Avoird, and P. E. S. Wormer, J. Chem. Phys. 101, 8430 (1994)]. This model is based on first-order (quasi) degenerate perturbation theory and adaptation of the wave functions to the group chain G36⊆G72⊆G144. The umbrella inversion splittings depend sensitively on the intermolecular potential from which the bound state wave functions are obtained. A complete interpretation of the observed splitting pattern [J. G. Loeser, C. A. Schmuttenmaer, R. C. Cohen, M. J. Elrod, D. W. Steyert, R. J. Saykally, R. E. Bumgarner, and G. A. Blake, J. Chem. Phys. 97, 4727 (1992)] and quantitative agreement with the measured splittings, which range over three orders of magnitude, are obtained from the potential that reproduces the far-infrared spectrum of (NH3)2 and the dipole moment and nuclear quadrupole splittings of (NH3)2 and (ND3)2. The umbrella inversion splittings of (ND3)2 are predicted.

  3. Ising tricriticality in the extended Hubbard model with bond dimerization

    NASA Astrophysics Data System (ADS)

    Ejima, Satoshi; Essler, Fabian H. L.; Lange, Florian; Fehske, Holger

    2016-06-01

    We explore the quantum phase transition between Peierls and charge-density-wave insulating states in the one-dimensional, half-filled, extended Hubbard model with explicit bond dimerization. We show that the critical line of the continuous Ising transition terminates at a tricritical point, belonging to the universality class of the tricritical Ising model with central charge c =7 /10 . Above this point, the quantum phase transition becomes first order. Employing a numerical matrix-product-state based (infinite) density-matrix renormalization group method we determine the ground-state phase diagram, the spin and two-particle charge excitations gaps, and the entanglement properties of the model with high precision. Performing a bosonization analysis we can derive a field description of the transition region in terms of a triple sine-Gordon model. This allows us to derive field theory predictions for the power-law (exponential) decay of the density-density (spin-spin) and bond-order-wave correlation functions, which are found to be in excellent agreement with our numerical results.

  4. Surface hopping simulation of vibrational predissociation of methanol dimer

    NASA Astrophysics Data System (ADS)

    Jiang, Ruomu; Sibert, Edwin L.

    2012-06-01

    The mixed quantum-classical surface hopping method is applied to the vibrational predissociation of methanol dimer, and the results are compared to more exact quantum calculations. Utilizing the vibrational SCF basis, the predissociation problem is cast into a curve crossing problem between dissociative and quasibound surfaces with different vibrational character. The varied features of the dissociative surfaces, arising from the large amplitude OH torsion, generate rich predissociation dynamics. The fewest switches surface hopping algorithm of Tully [J. Chem. Phys. 93, 1061 (1990), 10.1063/1.459170] is applied to both diabatic and adiabatic representations. The comparison affords new insight into the criterion for selecting the suitable representation. The adiabatic method's difficulty with low energy trajectories is highlighted. In the normal crossing case, the diabatic calculations yield good results, albeit showing its limitation in situations where tunneling is important. The quadratic scaling of the rates on coupling strength is confirmed. An interesting resonance behavior is identified and is dealt with using a simple decoherence scheme. For low lying dissociative surfaces that do not cross the quasibound surface, the diabatic method tends to overestimate the predissociation rate whereas the adiabatic method is qualitatively correct. Analysis reveals the major culprits involve Rabi-like oscillation, treatment of classically forbidden hops, and overcoherence. Improvements of the surface hopping results are achieved by adopting a few changes to the original surface hopping algorithms.

  5. Mercury dimer spectroscopy and an Einstein-Podolsky-Rosen experiment

    NASA Astrophysics Data System (ADS)

    Qu, Xinmei

    The dissociation of a 199Hg2 dimer prepares an entangled state of two spatially separated 199Hg atoms, each with nuclear spin 1/2, and with zero total electron and nuclear spin angular momenta. This is identical to the entangled state of the two spin 1/2 particles in Bohm's classic version of the EPR gedankenexperiment . An analysis of the rotational structure of the upsilon'=57←upsilon''=0 band of the D3S+u 1u ← X1S+g 0+g transition in Hg2 (natural abundance) is presented. The analysis of the fluorescence excitation spectrum using a dye laser gives the values of the constants Bupsilon'=57 and Bupsilon''=0 for the excited and ground electronic energy states involved in the transition, respectively. To increase the accuracy of the rotational constants and resolve the fine spectrum of the Hg2, a continuously tunable single longitudinal mode laser with ultra-narrow line-width is needed. Measurements using a narrow line-width alexandrite laser had been attempted and the values of Bupsilon'=57 and Bupsilon''=0 were determined. To improve the quality of the laser beam and hence the precision of the rotational constants, modifications have been made to the cavity of the alexandrite laser. This provides a possibility for further investigation.

  6. Photoexcited energy transfer in a weakly coupled dimer

    DOE PAGESBeta

    Hernandez, Laura Alfonso; Nelson, Tammie; Tretiak, Sergei; Fernandez-Alberti, Sebastian

    2015-01-08

    Nonadiabatic excited-state molecular dynamics (NA-ESMD) simulations have been performed in order to study the time-dependent exciton localization during energy transfer between two chromophore units of the weakly coupled anthracene dimer dithia-anthracenophane (DTA). Simulations are done at both low temperature (10 K) and room temperature (300 K). The initial photoexcitation creates an exciton which is primarily localized on a single monomer unit. Subsequently, the exciton experiences an ultrafast energy transfer becoming localized on either one monomer unit or the other, whereas delocalization between both monomers never occurs. In half of the trajectories, the electronic transition density becomes completely localized on themore » same monomer as the initial excitation, while in the other half, it becomes completely localized on the opposite monomer. In this article, we present an analysis of the energy transfer dynamics and the effect of thermally induced geometry distortions on the exciton localization. Finally, simulated fluorescence anisotropy decay curves for both DTA and the monomer unit dimethyl anthracene (DMA) are compared. As a result, our analysis reveals that changes in the transition density localization caused by energy transfer between two monomers in DTA is not the only source of depolarization and exciton relaxation within a single DTA monomer unit can also cause reorientation of the transition dipole.« less

  7. Photoexcited energy transfer in a weakly coupled dimer

    SciTech Connect

    Hernandez, Laura Alfonso; Nelson, Tammie; Tretiak, Sergei; Fernandez-Alberti, Sebastian

    2015-01-08

    Nonadiabatic excited-state molecular dynamics (NA-ESMD) simulations have been performed in order to study the time-dependent exciton localization during energy transfer between two chromophore units of the weakly coupled anthracene dimer dithia-anthracenophane (DTA). Simulations are done at both low temperature (10 K) and room temperature (300 K). The initial photoexcitation creates an exciton which is primarily localized on a single monomer unit. Subsequently, the exciton experiences an ultrafast energy transfer becoming localized on either one monomer unit or the other, whereas delocalization between both monomers never occurs. In half of the trajectories, the electronic transition density becomes completely localized on the same monomer as the initial excitation, while in the other half, it becomes completely localized on the opposite monomer. In this article, we present an analysis of the energy transfer dynamics and the effect of thermally induced geometry distortions on the exciton localization. Finally, simulated fluorescence anisotropy decay curves for both DTA and the monomer unit dimethyl anthracene (DMA) are compared. As a result, our analysis reveals that changes in the transition density localization caused by energy transfer between two monomers in DTA is not the only source of depolarization and exciton relaxation within a single DTA monomer unit can also cause reorientation of the transition dipole.

  8. Extracting Structure Parameters of Dimers for Molecular Tunneling Ionization Model

    NASA Astrophysics Data System (ADS)

    Song-Feng, Zhao; Fang, Huang; Guo-Li, Wang; Xiao-Xin, Zhou

    2016-03-01

    We determine structure parameters of the highest occupied molecular orbital (HOMO) of 27 dimers for the molecular tunneling ionization (so called MO-ADK) model of Tong et al. [Phys. Rev. A 66 (2002) 033402]. The molecular wave functions with correct asymptotic behavior are obtained by solving the time-independent Schrödinger equation with B-spline functions and molecular potentials which are numerically created using the density functional theory. We examine the alignment-dependent tunneling ionization probabilities from MO-ADK model for several molecules by comparing with the molecular strong-field approximation (MO-SFA) calculations. We show the molecular Perelomov–Popov–Terent'ev (MO-PPT) can successfully give the laser wavelength dependence of ionization rates (or probabilities). Based on the MO-PPT model, two diatomic molecules having valence orbital with antibonding systems (i.e., Cl2, Ne2) show strong ionization suppression when compared with their corresponding closest companion atoms. Supported by National Natural Science Foundation of China under Grant Nos. 11164025, 11264036, 11465016, 11364038, the Specialized Research Fund for the Doctoral Program of Higher Education of China under Grant No. 20116203120001, and the Basic Scientific Research Foundation for Institution of Higher Learning of Gansu Province

  9. Extracting Structure Parameters of Dimers for Molecular Tunneling Ionization Model

    NASA Astrophysics Data System (ADS)

    Zhao, Song-Feng; Huang, Fang; Wang, Guo-Li; Zhou, Xiao-Xin

    2016-03-01

    We determine structure parameters of the highest occupied molecular orbital (HOMO) of 27 dimers for the molecular tunneling ionization (so called MO-ADK) model of Tong et al. [Phys. Rev. A 66 (2002) 033402]. The molecular wave functions with correct asymptotic behavior are obtained by solving the time-independent Schrödinger equation with B-spline functions and molecular potentials which are numerically created using the density functional theory. We examine the alignment-dependent tunneling ionization probabilities from MO-ADK model for several molecules by comparing with the molecular strong-field approximation (MO-SFA) calculations. We show the molecular Perelomov-Popov-Terent'ev (MO-PPT) can successfully give the laser wavelength dependence of ionization rates (or probabilities). Based on the MO-PPT model, two diatomic molecules having valence orbital with antibonding systems (i.e., Cl2, Ne2) show strong ionization suppression when compared with their corresponding closest companion atoms. Supported by National Natural Science Foundation of China under Grant Nos. 11164025, 11264036, 11465016, 11364038, the Specialized Research Fund for the Doctoral Program of Higher Education of China under Grant No. 20116203120001, and the Basic Scientific Research Foundation for Institution of Higher Learning of Gansu Province

  10. Ligand-induced ErbB receptor dimerization

    PubMed Central

    Lemmon, Mark A.

    2009-01-01

    Structural studies have provided important new insights into how ligand binding promotes homodimerization and activation of the EGF receptor and the other members of the ErbB family or receptor tyrosine kinases. These structures have also suggested possible explanations for the unique properties of ErbB2, which has no known ligand and can cause cell transformation (and tumorigenesis) by simple overexpression. In parallel with these advances, studies of the EGF receptor at the cell surface increasingly argue that the structural studies are missing key mechanistic components. This is particularly evident in the structural prediction that EGF binding linked to receptor dimerization should be positively cooperative, whereas cell-surface EGF-binding studies suggest negative cooperativity. In this review, I summarize studies of ErbB receptor extracellular regions in solution and of intact receptors at the cell surface, and attempt to reconcile the differences suggested by the two approaches. By combining results obtained with receptor ‘parts’, it is qualitatively possible to explain some models for the properties of the whole receptor. These considerations underline the need to consider the intact ErbB receptors as intact allosterically regulated enzymes, and to combine cellular and structural studies into a complete picture. PMID:19038249

  11. Sr(2+) induces unusually stable d(GGGTGGGTGGGTGGG) quadruplex dimers.

    PubMed

    Lomidze, Levan; Kelley, Sean; Gogichaishvili, Shota; Metreveli, Nunu; Musier-Forsyth, Karin; Kankia, Besik

    2016-11-01

    Guanine-rich sequences are able to form quadruplexes consisting of G-quartet structural units. Quadruplexes play an important role in the regulation of gene expression and have therapeutic and biotechnological potential. The HIV-1 integrase inhibitor, (GGGT)4 , and its variants demonstrate unusually high thermal stability. This property has been exploited in the use of quadruplex formation to drive various endergonic reactions of nucleic acids such as isothermal DNA amplification. Quadruplex stability is mainly determined by cations, which specifically bind into the inner core of the structure. In the present work, we report a systematic study of a variant of the HIV-1 integrase inhibitor, GGGTGGGTGGGTGGG (G3T), in the presence of alkali and alkaline-earth cations. We show that Sr(2+) -G3T is characterized by the highest thermal stability and that quadruplex formation requires only one Sr(2+) ion that binds with low micromolar affinity. These concentrations are sufficient to drive robust isothermal quadruplex priming DNA amplification reaction. The Sr(2+) -quadruplexes are also able to form unusually stable dimers through end-to-end stacking. The multimerization can be induced by a combination of quadruplex forming cations (i.e., K(+) or Sr(2+) ) and non-specific Mg(2+) . PMID:27416320

  12. Fragmentation dynamics of Ar2^+ dimers in intense laser fields

    NASA Astrophysics Data System (ADS)

    Magrakvelidze, M.; Wu, J.; Dörner, R.; Thumm, U.

    2012-06-01

    We studied the fragmentation dynamics of the Ar2 dimers in 790 nm pump and 1400 nm probe pulses with intensities of 10^14 W/cm^2 by analyzing kinetic energy release (KER) spectra as a function of the pump probe delay. The KER spectra are measured by detecting Ar-ion fragments in a COLTRIMS [1] setup and are compared with model calculations based on the numerical propagations of the time-dependent Schr"odinger equation [2]. The measured spectra are best reproduced by two-state calculations that include the adiabatic electronic states I(1/2)u and II(1/2)g of Ar2^+, dipole coupled in the pump- and probe-laser electric fields. [4pt] [1] J. Wu, A. Vredenborg, B. Ulrich, L. Ph. H. Schmidt, M. Meckel, S. Voss, H. Sann, H. Kim, T. Jahnke, and R. D"orner, PRA 83, 061403(R) (2011) [0pt] [2] M. Magrakvelidze, F. He, Th. Niederhausen, I. V. Litvinyuk, and U. Thumm, PRA 79, 033410 (2009).

  13. High-Resolution Infrared Spectroscopy of the Formic Acid Dimer

    NASA Astrophysics Data System (ADS)

    Birer, Özgür; Havenith, Martina

    2009-05-01

    The formic acid dimer (HCOOH)2 (FAD), an eight-membered ring with double hydrogen bonds, has been a model complex for physical chemists. The acidic protons of the complex interchange between the oxygens of different units in a concerted tunneling motion. This proton tunneling can be described by a symmetric double-well potential. The double well results in a splitting of each rovibrational level. The magnitude of the splitting depends sensitively on the shape of the potential and the reduced mass along the tunneling path. Experimentally, one can determine the proton transfer tunneling splittings in the ground and vibrationally excited states separately. It is possible to work out the splitting of the energy levels, assign the correct symmetry, and obtain the sum and the difference of the tunneling splitting in the ground and vibrationally excited states independently using isotopically labeled molecules. Conversely, an accurate prediction of tunneling splitting even for this small prototype system still remains a challenge for theoretical chemistry because of the splitting's great sensitivity to the shape and barrier height of the potential surface. The FAD therefore has evolved into a prototype system to study theoretical methods for a description of proton transfer.

  14. Proton association constants of His 37 in the Influenza-A M218-60 dimer-of-dimers.

    PubMed

    Colvin, Michael T; Andreas, Loren B; Chou, James J; Griffin, Robert G

    2014-09-30

    The membrane protein M2 from influenza-A forms a single-pass transmembrane helix that assembles in lipid membrane as homotetramers whose primary function is to act as a proton transporter for viral acidification. A single residue, histidine 37 (His 37), is known to be responsible for selectivity and plays an integral role in the protein's function. We report pH-dependent (15)N MAS NMR spectra of His 37 within the influenza-A proton conduction domain of M2, M218-60, which has been previously shown to be a fully functional construct and was recently determined to adopt a dimer-of-dimers structure in lipids. By extracting the ratio of [His]/[HisH(+)] as a function of pH, we obtained two doubly degenerate proton disassociation constants, 7.63 ± 0.15 and 4.52 ± 0.15, despite a possible maximum of four. We also report the (1)HNε chemical shifts at pH 6.5 recorded at 60 kHz MAS in a CP-based (1)H-(15)N spectrum. We were unable to detect resonances indicative of direct proton sharing among His 37 side chains when the tetramer is in the +2 state. In the neutral state, His 37 is exclusively in the τ tautomer, indicating that the δ nitrogen is protonated solely as a function of pH. We also found that the plot of [HisH(+)]/[His] as a function of pH is qualitatively similar to previously reported proton conduction rates, indicating that proton conduction rate is proportional to the level of histidine protonation within the channel. Two-dimensional (13)C-(13)C and (13)C-(15)N correlations suggest that at low pH multiple conformations are populated as the spectra broaden and eventually disappear as the acidity is increased. A second highly resolved state at low pH was not observed. PMID:25184631

  15. Simulations of potentials of mean force for separating a leucine zipper dimer and the basic region of a basic region leucine zipper dimer.

    PubMed

    Cukier, Robert I

    2014-09-01

    Basic region leucine zipper (bZIP) transcription factors involved in DNA recognition are dimeric proteins. The monomers consist of two subdomains, a leucine zipper sequence responsible for dimerization and a highly basic DNA recognition sequence. Leucine zippers are strongly dimerized, and in a bZIP, the basic region can, in the absence of DNA, undergo extensive relative monomer-to-monomer fluctuations. In this work, LZ and bZIP potentials of mean force (PMFs), which provide free energies along reaction coordinates, are simulated with a distance replica exchange method. The method uses restraint potentials to provide sampling along a reaction coordinate and enhances configuration space exploration by exchanging information between neighboring restraint potential configurations. Restraint potentials that are constructed from sums over a number of atom distances are employed. Their use requires a modification of the Weighted Histogram Analysis Method (WHAM) procedure to combine and unbias the data from the different restraint-potential-biased window densities to provide a PMF. These methods are first used to obtain a PMF for separating a leucine zipper (GCN4-p1) of the yeast transcriptional activator GCN4. The PMF indicates a very strong binding free energy that only weakens when the monomers are separated by about 12 Å, which is about 6 Å beyond their bound, dimer equilibrium distance. PMFs are also obtained for separating the basic subdomain monomer parts of the GCN4 bZIP transcriptional factor, in the absence of DNA. In a monomer separation range spanning the open, crystal-based structure to closer configurations, the basic subdomain PMF is quite flat, implying essentially thermal sampling in this distance range. A PMF generated starting from a "collapsed" state, taken from a previous simulation ( J. Phys. Chem. B 2012 , 116 , 6071 ), where collapsed refers to the feature that the basic subdomain monomers are also effectively dimerized, shows that this state is

  16. Analytical and clinical performance of a new point of care LABGEOIB D-dimer test for diagnosis of venous thromboembolism.

    PubMed

    Song, Jaewoo; Kweon, Tae Dong; Song, Yeajin; Lee, Eun Young; Kim, Sue Jung; Park, Rojin

    2014-01-01

    LABGEO(IB) D-dimer Test is a newly developed POC D-dimer assay and the first commercially available POC immunoassay instrument that exploits the disk rotation method for extraction of plasma. Citrate plasma was obtained from 201 apparently healthy subjects and 91 patients suspected for VTE, and their D-dimer level was measured by the LABGEO(IB) D-Dimer Test (LABGEO D-dimer) and HemosIL D-dimer test as a comparative method. To examine the effect of blood cells and anticoagulant, paired blood samples anticoagulated by heparin and citrate were obtained from various postoperative patients. The overall diagnostic performance of LABGEO(IB) D-dimer and HemosIL was comparable with similar area under ROC curve (p=0.79). The cut-off levels recommended by manufacturers (LABGEO D-dimer: 0.45 μg/ml fibrinogen equivalent unit (FEU), HemosIL: 0.23 μg/ml D-dimer unit (DDU)) and those yielding highest diagnostic efficiency (LABGEO D-dimer: 1.41 μg/ml FEU; HemosIL: 0.85 μg/ml DDU), were chosen for the evaluation. For LABGEO D-dimer negative predictive value (NPV), positive predictive value (PPV), sensitivity, specificity, and negative likelihood ratio (LR-neg) were 93-100%, 67-89%, 93-100%, 53-89% and 0.00-0.08. For HemosIL D-dimer, NPV, PPV, sensitivity, specificity and LR-neg were 90 - 100%, 76-95%, 89-100%, 70-96% and 0.00-0.12, all comparable to results for LABGEO D-dimer. LABGEO D-dimer test demonstrated acceptable performance when used for the VTE diagnostic work-up. PMID:25117092

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

    SciTech Connect

    Chen, L.X.Q.

    1992-12-31

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

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

    PubMed

    Goffinont, S; Davidkova, M; Spotheim-Maurizot, M

    2009-08-21

    The wild type lactose repressor of Escherichia coli is a tetrameric protein formed by two identical dimers. They are associated via a C-terminal 4-helix bundle (called tetramerization domain) whose stability is ensured by the interaction of leucine zipper motifs. Upon in vitro gamma-irradiation the repressor losses its ability to bind the operator DNA sequence due to damage of its DNA-binding domains. Using an engineered dimeric repressor for comparison, we show here that irradiation induces also the change of repressor oligomerisation state from tetramer to dimer. The splitting of the tetramer into dimers can result from the oxidation of the leucine residues of the tetramerization domain. PMID:19520056

  19. Transition between locked and running states for dimer motion induced by periodic external driving.

    PubMed

    Hennig, D; Martens, S; Fugmann, S

    2008-07-01

    We study the motion of a dimer in a one-dimensional spatially periodic washboard potential. The tilt of the latter is time-periodically modulated by an ac field. We focus interest on the detrapping of the (static) ground state solution of the dimer caused by the ac field. Moreover, we demonstrate that slow tilt modulations not only induce a trapping-detrapping transition but drive the dimer dynamics into a regime of transient long-range running states. Most strikingly, the motion proceeds then unidirectionally, so that the dimer covers huge distances regardless of the fact that the bias force in the driven system vanishes on the average. We elucidate the underlying dynamics in phase space and associate long-lasting running states with the motion in ballistic channels occurring due to stickiness to invariant tori. PMID:18763916

  20. Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate Transactivation.

    PubMed

    Jambrina, Pablo G; Rauch, Nora; Pilkington, Ruth; Rybakova, Katja; Nguyen, Lan K; Kholodenko, Boris N; Buchete, Nicolae-Viorel; Kolch, Walter; Rosta, Edina

    2016-01-18

    RAF kinases are key players in the MAPK signaling pathway and are important targets for personalized cancer therapy. RAF dimerization is part of the physiological activation mechanism, together with phosphorylation, and is known to convey resistance to RAF inhibitors. Herein, molecular dynamics simulations are used to show that phosphorylation of a key N-terminal acidic (NtA) motif facilitates RAF dimerization by introducing several interprotomer salt bridges between the αC-helix and charged residues upstream of the NtA motif. Additionally, we show that the R-spine of RAF interacts with a conserved Trp residue in the vicinity of the NtA motif, connecting the active sites of two protomers and thereby modulating the cooperative interactions in the RAF dimer. Our findings provide a first structure-based mechanism for the auto-transactivation of RAF and could be generally applicable to other kinases, opening new pathways for overcoming dimerization-related drug resistance. PMID:26644280

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

    SciTech Connect

    Chen, L.X.Q.

    1992-01-01

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

  2. New Insight into Secreted Ribonuclease Structure: Binase Is a Natural Dimer

    PubMed Central

    Dudkina, Elena; Kayumov, Airat; Ulyanova, Vera; Ilinskaya, Olga

    2014-01-01

    The biological effects of ribonucleases (RNases), such as the control of the blood vessels growth, the toxicity towards tumour cells and antiviral activity, require a detailed explanation. One of the most intriguing properties of RNases which can contribute to their biological effects is the ability to form dimers, which facilitates efficient RNA hydrolysis and the evasion of ribonuclease inhibitor. Dimeric forms of microbial RNase binase secreted by Bacillus pumilus (former B. intermedius) have only been found in crystals to date. Our study is the first report directly confirming the existence of binase dimers in solution and under natural conditions of enzyme biosynthesis and secretion by bacilli. Using different variants of gel electrophoresis, immunoblotting, size-exclusion chromatography and mass-spectrometry, we revealed that binase is a stable natural dimer with high catalytic activity. PMID:25551440

  3. A Strategy for Complex Dimer Formation When Biomimicry Fails: Total Synthesis of Ten Coccinellid Alkaloids

    PubMed Central

    2015-01-01

    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. PMID:24959981

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

    PubMed

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

    2014-07-01

    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. PMID:24959981

  5. Evidence for zinc ion sharing in metallothionein dimers provided by collision-induced dissociation

    NASA Astrophysics Data System (ADS)

    Afonso, Carlos; Hathout, Yetrib; Fenselau, Catherine

    2004-02-01

    Nanospray and collisionally-induced dissociation are used to evaluate the presence and absence of interstrand co-chelation of zinc ions in dimers of metallothionein. As was reported in a previous publication from this laboratory, co-chelation stabilizes the dimer to collisional activation, and facilitates asymmetrical zinc ion transfers during fragmentation. In the case of metallothionein, dimers of the holoprotein are found to share zinc ions, while dimers of metallothionein, in which one domain has been denatured, do not. Zinc ions are silent to most physicochemical probes, e.g., NMR and Mossbauer spectroscopies, and the capability of mass spectrometry to provide information on zinc complexes has widespread potential application in biochemistry.

  6. Infrared spectroscopy of pyrrole-2-carboxaldehyde and its dimer: A planar β-sheet peptide model?

    NASA Astrophysics Data System (ADS)

    Rice, Corey A.; Dauster, Ingo; Suhm, Martin A.

    2007-04-01

    Intermolecular interactions relevant for antiparallel β-sheet formation between peptide strands are studied by Fourier transform infrared spectroscopy of the low temperature, vacuum-isolated model compound pyrrole-2-carboxaldehyde and its dimer in the N-H and C O stretching range. Comparison to quantum chemical predictions shows that even for some triple-zeta quality basis sets, hybrid density functionals and Møller-Plesset perturbation calculations fail to provide a consistent and fully satisfactory description of hydrogen bond induced frequency shifts and intensity ratios in the double-harmonic approximation. The latter approach even shows problems in reproducing the planar structure of the dimer and the correct sign of the C O stretching shift for standard basis sets. The effect of matrix isolation is modeled by condensing layers of Ar atoms on the isolated monomer and dimer. The dimer structure is discussed in the context of the peptide β-sheet motif.

  7. Infrared spectroscopy of pyrrole-2-carboxaldehyde and its dimer: a planar beta-sheet peptide model?

    PubMed

    Rice, Corey A; Dauster, Ingo; Suhm, Martin A

    2007-04-01

    Intermolecular interactions relevant for antiparallel beta-sheet formation between peptide strands are studied by Fourier transform infrared spectroscopy of the low temperature, vacuum-isolated model compound pyrrole-2-carboxaldehyde and its dimer in the N-H and C=O stretching range. Comparison to quantum chemical predictions shows that even for some triple-zeta quality basis sets, hybrid density functionals and Møller-Plesset perturbation calculations fail to provide a consistent and fully satisfactory description of hydrogen bond induced frequency shifts and intensity ratios in the double-harmonic approximation. The latter approach even shows problems in reproducing the planar structure of the dimer and the correct sign of the C=O stretching shift for standard basis sets. The effect of matrix isolation is modeled by condensing layers of Ar atoms on the isolated monomer and dimer. The dimer structure is discussed in the context of the peptide beta-sheet motif. PMID:17430038

  8. Dimeric subunit stoichiometry of the human voltage-dependent proton channel Hv1

    PubMed Central

    Lee, Seok-Yong; Letts, James A.; MacKinnon, Roderick

    2008-01-01

    In voltage-gated Na+, K+, and Ca2+ channels, four voltage-sensor domains operate on a central pore domain in response to membrane voltage. In contrast, the voltage-gated proton channel (Hv) contains only a voltage-sensor domain, lacking a separate pore domain. The subunit stoichiometry and organization of Hv has been unknown. Here, we show that human Hv1 forms a dimer in the membrane and define regions that are close to the dimer interface by using cysteine cross-linking. Two dimeric interfaces appear to exist in Hv1, one mediated by S1 and the adjacent extracellular loop, and the other mediated by a putative intracellular coiled-coil domain. It may be significant that Hv1 uses for its dimer interface a surface that corresponds to the interface between the voltage sensor and pore in Kv channels. PMID:18509058

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

    NASA Astrophysics Data System (ADS)

    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.

  10. Raman study of the temperature-induced decomposition of the fullerene dimers C120

    NASA Astrophysics Data System (ADS)

    Meletov, K. P.; Arvanitidis, J.; Christofilos, D.; Kourouklis, G. A.; Davydov, V. A.

    2016-06-01

    Raman spectra of the C120 crystalline fullerene dimers, synthesized by high-pressure/high-temperature (HPHT) treatment of the C60 fullerite, were measured at ambient and elevated temperatures (T > 130 °C) in order to study the kinetics of their thermal decomposition. Measurements exhibit an intensity decrease of the dimer-related pentagon pinch (PP) mode and an increase of the monomer's one. The relative intensity of the dimer's PP mode decreases exponentially with the thermal treatment time and becomes faster at elevated temperatures. The activation energy EA of the dimer decomposition, obtained from the Arrhenius dependence of the exponential decay time constant on temperature, is (1.71 ± 0.06) eV.

  11. Stabilization of EphA2 dimers as a novel anti-cancer strategy

    NASA Astrophysics Data System (ADS)

    Singh, Deo; Ahmed, Fozia; Salloto, Matt; Hristova, Kalina

    We have recently shown that EphA2 receptors exist in a monomer-dimer equilibrium in the absence of ligand. The monomers promote tumorigenic activity and thus a therapeutic strategy that minimizes the monomer population may be beneficial in the clinic. The YSA peptide is an EphA2-targeting peptide that effectively delivers anticancer agents to cancer tumors. The quantitative measurements of the dimerization of EphA2 receptors in the presence of these peptides using quantitative spectral Forster resonance transfer (QS-FRET) methodology in conjunction with two-photon microscopy that has been developed recently in our lab suggests that this peptide stabilizes the EphA2 dimers. Thus, such peptides that stabilize the EphA2 dimers may be used for the treatment of some cancers that overexpress EphA2.

  12. Mechanothermally induced conformational switch of a porphyrin dimer in a polymer film.

    PubMed

    Doan, Hung; Raut, Sangram L; Yale, David; Balaz, Milan; Dzyuba, Sergei V; Gryczynski, Zygmunt

    2016-07-21

    Stretching a polymer film induces a conformational change (from the twisted to planar state) in the embedded porphyrin dimer, as evidenced by steady-state and time-resolved emission spectra. PMID:27294828

  13. Electron transfer beyond the static picture: A TDDFT/TD-ZINDO study of a pentacene dimer

    SciTech Connect

    Reslan, Randa; Lopata, Kenneth A.; Arntsen, Christopher D.; Govind, Niranjan; Neuhauser, Daniel

    2012-12-14

    We use time-dependent density functional theory and time-dependent ZINDO (a semi-empirical method) to study transfer of an extra electron between a pair of pentacene dimers. A measure of the electronic transfer integral is computed in a dynamic picture via the vertical excitation energy from a delocalized anionic ground state. With increasing dimer separation, this dynamical measurement of charge transfer is shown to be significantly larger than the commonly used static approximation (i.e., LUMO+1 - LUMO of the neutral dimer, or HOMO - LUMO of the charged dimer), up to an order of magnitude higher at 6 Å. These results offer a word of caution for calculations involving large separations, as in organic photovoltaics, where care must be taken when using a static picture to model charge transfer.

  14. Dimeric peptides of the C-terminal region of CXCL14 function as CXCL12 inhibitors.

    PubMed

    Tanegashima, Kosuke; Tsuji, Kohei; Suzuki, Kenji; Shigenaga, Akira; Otaka, Akira; Hara, Takahiko

    2013-11-29

    We recently reported that CXCL14 binds to CXCR4 with high affinity and inhibits CXCL12-mediated chemotaxis. Here we found that the C-terminal 51-77 amino acid residues of CXCL14 are responsible for CXCR4 binding. A disulfide dimer peptide of CXCL14(51-77) bound to CXCR4 with comparable affinity to full length CXCL14, and exhibited CXCL12 inhibitor activity. CXCR4 was efficiently internalized upon binding of dimeric CXCL14(51-77), thereby being reduced on the cell surface. Substitution of 5 amino acid residues in combination with the use of an oxime linker for dimerization increased the solubility and chemical stability of the dimeric CXCL14(51-77). PMID:24161674

  15. Ratchet rotation of a 3D dimer on a vibrating plate.

    PubMed

    Wang, Jiao; Liu, Caishan; Jia, Yan-Bin; Ma, Daolin

    2014-01-01

    This work studies the dynamics of a 3D dimer bouncing upon a horizontal plate undergoing a vertical harmonic vibration. Despite complex interactions within the system due to impacts and friction, numerical simulation shows that, under certain conditions prescribed for the dynamics, the center of mass of the dimer, when projected onto a horizontal plane, will follow a circular orbit. The phenomenon is like a particle under Coulomb friction performing a ratchet motion that rotates around. Investigations further reveal that the dimer dynamics bear some typical characteristics of a nonlinear system, including sensitivity to the initial conditions and bifurcation behaviors related to the physical parameters of the dynamics. Our results indicate that the coefficient of restitution and the plate's vibration intensity play critical roles in exciting the circular orbit, while the dimer's geometry and the vibration frequency mainly influence the trajectory characteristics. These findings may help understand transport mechanisms underlying systems of granular matter with anisotropic particles. PMID:24458553

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

    PubMed

    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. PMID:27627230

  17. Functional Role of Dimerization of Human Peptidylarginine Deiminase 4 (PAD4)

    PubMed Central

    Liu, Yi-Liang; Chiang, Yu-Hsiu; Liu, Guang-Yaw; Hung, Hui-Chih

    2011-01-01

    Peptidylarginine deiminase 4 (PAD4) is a homodimeric enzyme that catalyzes Ca2+-dependent protein citrullination, which results in the conversion of arginine to citrulline. This paper demonstrates the functional role of dimerization in the regulation of PAD4 activity. To address this question, we created a series of dimer interface mutants of PAD4. The residues Arg8, Tyr237, Asp273, Glu281, Tyr435, Arg544 and Asp547, which are located at the dimer interface, were mutated to disturb the dimer organization of PAD4. Sedimentation velocity experiments were performed to investigate the changes in the quaternary structures and the dissociation constants (Kd) between wild-type and mutant PAD4 monomers and dimers. The kinetic data indicated that disrupting the dimer interface of the enzyme decreases its enzymatic activity and calcium-binding cooperativity. The Kd values of some PAD4 mutants were much higher than that of the wild-type (WT) protein (0.45 µM) and were concomitant with lower kcat values than that of WT (13.4 s−1). The Kd values of the monomeric PAD4 mutants ranged from 16.8 to 45.6 µM, and the kcat values of the monomeric mutants ranged from 3.3 to 7.3 s−1. The kcat values of these interface mutants decreased as the Kd values increased, which suggests that the dissociation of dimers to monomers considerably influences the activity of the enzyme. Although dissociation of the enzyme reduces the activity of the enzyme, monomeric PAD4 is still active but does not display cooperative calcium binding. The ionic interaction between Arg8 and Asp547 and the Tyr435-mediated hydrophobic interaction are determinants of PAD4 dimer formation. PMID:21731701

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

    PubMed Central

    Lara-Gonzalez, Samuel; Estrella, Priscilla; Portillo, Carmen; Cruces, María E.; Jimenez-Sandoval, Pedro; Fattori, Juliana; Migliorini-Figueira, Ana C.; Lopez-Hidalgo, Marisol; Diaz-Quezada, Corina; Lopez-Castillo, Margarita; Trasviña-Arenas, Carlos H.; Sanchez-Sandoval, Eugenia; Gómez-Puyou, Armando; Ortega-Lopez, Jaime; Arroyo, Rossana; Benítez-Cardoza, Claudia G.; Brieba, Luis G.

    2015-01-01

    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. PMID:26618356

  19. Replica Exchange Molecular Dynamics Study of Dimerization in Prion Protein: Multiple Modes of Interaction and Stabilization.

    PubMed

    Chamachi, Neharika G; Chakrabarty, Suman

    2016-08-01

    The pathological forms of prions are known to be a result of misfolding, oligomerization, and aggregation of the cellular prion. While the mechanism of misfolding and aggregation in prions has been widely studied using both experimental and computational tools, the structural and energetic characterization of the dimer form have not garnered as much attention. On one hand dimerization can be the first step toward a nucleation-like pathway to aggregation, whereas on the other hand it may also increase the conformational stability preventing self-aggregation. In this work, we have used extensive all-atom replica exchange molecular dynamics simulations of both monomer and dimer forms of a mouse prion protein to understand the structural, dynamic, and thermodynamic stability of dimeric prion as compared to the monomeric form. We show that prion proteins can dimerize spontaneously being stabilized by hydrophobic interactions as well as intermolecular hydrogen bonding and salt bridge formation. We have computed the conformational free energy landscapes for both monomer and dimer forms to compare the thermodynamic stability and misfolding pathways. We observe large conformational heterogeneity among the various modes of interactions between the monomers and the strong intermolecular interactions may lead to as high as 20% β-content. The hydrophobic regions in helix-2, surrounding coil regions, terminal regions along with the natively present β-sheet region appear to actively participate in prion-prion intermolecular interactions. Dimerization seems to considerably suppress the inherent dynamic instability observed in monomeric prions, particularly because the regions of structural frustration constitute the dimer interface. Further, we demonstrate an interesting reversible coupling between the Q160-G131 interaction (which leads to inhibition of β-sheet extension) and the G131-V161 H-bond formation. PMID:27390876

  20. High D-dimer levels after stopping anticoagulants in pulmonary embolism with sleep apnoea.

    PubMed

    García Suquia, Angela; Alonso-Fernández, Alberto; de la Peña, Mónica; Romero, David; Piérola, Javier; Carrera, Miguel; Barceló, Antonia; Soriano, Joan B; Arque, Meritxell; Fernández-Capitán, Carmen; Lorenzo, Alicia; García-Río, Francisco

    2015-12-01

    Obstructive sleep apnoea is a risk factor for pulmonary embolism. Elevated D-dimer levels and other biomarkers are associated with recurrent pulmonary embolism. The objectives were to compare the frequency of elevated D-dimer levels (>500 ng·mL(-1)) and further coagulation biomarkers after oral anticoagulation withdrawal in pulmonary embolism patients, with and without obstructive sleep apnoea, including two control groups without pulmonary embolism.We performed home respiratory polygraphy. We also measured basic biochemical profile and haemogram, and coagulation biomarkers (D-dimer, prothrombin fragment 1+2, thrombin-antithrombin complex, plasminogen activator inhibitor 1, and soluble P-selectin).64 (74.4%) of the pulmonary embolism cases and 41 (46.11%) of the controls without pulmonary embolism had obstructive sleep apnoea. Plasmatic D-dimer was higher in PE patients with OSA than in those without obstructive sleep apnoea. D-dimer levels were significantly correlated with apnoea-hypopnoea index, and nocturnal hypoxia. There were more patients with high D-dimer after stopping anticoagulants in those with pulmonary embolism and obstructive sleep apnoea compared with PE without obstructive sleep apnoea (35.4% versus 19.0%, p=0.003). Apnoea-hypopnoea index was independently associated with high D-dimer.Pulmonary embolism patients with obstructive sleep apnoea had higher rates of elevated D-dimer levels after anticoagulation discontinuation for pulmonary embolism than in patients without obstructive sleep apnoea and, therefore, higher procoagulant state that might increase the risk of pulmonary embolism recurrence. PMID:26206870

  1. Experimental separation of virtual photon exchange and electron transfer in interatomic coulombic decay of neon dimers.

    PubMed

    Jahnke, T; Czasch, A; Schöffler, M; Schössler, S; Käsz, M; Titze, J; Kreidi, K; Grisenti, R E; Staudte, A; Jagutzki, O; Schmidt, L Ph H; Weber, Th; Schmidt-Böcking, H; Ueda, K; Dörner, R

    2007-10-12

    We investigate the interatomic Coulombic decay (ICD) of neon dimers following photoionization with simultaneous excitation of the ionized atom (shakeup) in a multiparticle coincidence experiment. We find that, depending on the parity of the excited state, which determines whether ICD takes place via virtual dipole photon emission or overlap of the wave functions, the decay happens at different internuclear distances, illustrating that nuclear dynamics heavily influence the electronic decay in the neon dimer. PMID:17995162

  2. Effectiveness of D-Dimer as a Screening Test for Venous Thromboembolism: An Update

    PubMed Central

    Pulivarthi, Swaroopa; Gurram, Murali Krishna

    2014-01-01

    Venous thromboembolism (VTE) is the leading cause of morbidity and mortality among hospitalized patients. We searched the PubMed database and reviewed the articles published until June 2011. Articles related to the D-dimer and VTE were considered to write this paper. Many factors play a key role in changing the sensitivity and specificity of D-dimer testing, including the extent of thrombosis and fibrinolytic activity, duration of symptoms, anticoagulant therapy, comorbidity due to surgical or medical illnesses, inflammatory diseases, cancer, elderly age, pregnancy and the postpartum period, and previous VTE. Many previous studies have shown that the D-dimer test is highly sensitive (>95%) in acute deep venous thrombosis or pulmonary embolism, usually with a cut-off value of 500 μg FEU/l, which reasonably rules out acute VTE, particularly in patients with low clinical probability (LCP) or intermediate clinical probability. Patients with high D-dimer levels upon presentation may prompt a more intense diagnostic approach, irrespective of pretest probability. Studies performed after a negative D-dimer for 3 months proved the high negative predictive value (NPV) of D-dimer testing together with LCP in patients with suspected VTE. Among oncology patients, D-dimer testing has the highest sensitivity and NPV in excluding VTE. The new cutoff values of D-dimer testing were analyzed in a recent prospective study of pregnant women; they are 286 ng DDU/ml, 457 ng DDU/ml, and 644 ng DDU/ml for the first, second, and third trimesters, respectively. PMID:25489560

  3. Effectiveness of d-dimer as a screening test for venous thromboembolism: an update.

    PubMed

    Pulivarthi, Swaroopa; Gurram, Murali Krishna

    2014-10-01

    Venous thromboembolism (VTE) is the leading cause of morbidity and mortality among hospitalized patients. We searched the PubMed database and reviewed the articles published until June 2011. Articles related to the D-dimer and VTE were considered to write this paper. Many factors play a key role in changing the sensitivity and specificity of D-dimer testing, including the extent of thrombosis and fibrinolytic activity, duration of symptoms, anticoagulant therapy, comorbidity due to surgical or medical illnesses, inflammatory diseases, cancer, elderly age, pregnancy and the postpartum period, and previous VTE. Many previous studies have shown that the D-dimer test is highly sensitive (>95%) in acute deep venous thrombosis or pulmonary embolism, usually with a cut-off value of 500 μg FEU/l, which reasonably rules out acute VTE, particularly in patients with low clinical probability (LCP) or intermediate clinical probability. Patients with high D-dimer levels upon presentation may prompt a more intense diagnostic approach, irrespective of pretest probability. Studies performed after a negative D-dimer for 3 months proved the high negative predictive value (NPV) of D-dimer testing together with LCP in patients with suspected VTE. Among oncology patients, D-dimer testing has the highest sensitivity and NPV in excluding VTE. The new cutoff values of D-dimer testing were analyzed in a recent prospective study of pregnant women; they are 286 ng DDU/ml, 457 ng DDU/ml, and 644 ng DDU/ml for the first, second, and third trimesters, respectively. PMID:25489560

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

    PubMed

    Lara-Gonzalez, Samuel; Estrella, Priscilla; Portillo, Carmen; Cruces, María E; Jimenez-Sandoval, Pedro; Fattori, Juliana; Migliorini-Figueira, Ana C; Lopez-Hidalgo, Marisol; Diaz-Quezada, Corina; Lopez-Castillo, Margarita; Trasviña-Arenas, Carlos H; Sanchez-Sandoval, Eugenia; Gómez-Puyou, Armando; Ortega-Lopez, Jaime; Arroyo, Rossana; Benítez-Cardoza, Claudia G; Brieba, Luis G

    2015-01-01

    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. PMID:26618356

  5. C...H...N Hydrogen Bond Formation in Trimethylamine Dimer upon One-Photon Ionization

    NASA Astrophysics Data System (ADS)

    Nakayama, Yuichiro; Matsuda, Yoshiyuki; Fujii, Asuka

    2011-06-01

    Structures of trimethylamine dimer cluster cations which are generated by the vacuum-ultraviolet photoionization are investigated by a combination of infrared spectroscopic methods and theoretical reaction-pass calculations. In the trimethylamine dimer cluster cation, a proton of a methyl group is shared with the N atom of the other trimethylamine moiety. This is evidence that the methyl group acts as a proton donor in the cation state.

  6. New 3,4-seco-ent-kaurene dimers from Croton micans.

    PubMed

    Mateu, Elsa; Chavez, Katiuska; Riina, Ricarda; Compagnone, Reinaldo S; Delle Monache, Franco; Suárez, Alírica I

    2012-01-01

    From the stems of Croton micans Sw., five new 3,4-seco-ent-kaurene dimers: micansinoic acid (1), isomicansinoic acid (2), and the dimethyl (3), monomethyl (4) and monoethyl ester (5) of micansinoic acid were isolated. The structures of the new compounds were elucidated by spectroscopic data interpretation, mainly 1D and 2D NMR experiments and MS. These compounds are the first 3,4-seco-ent-kaurene dimers from a Croton species. PMID:22428229

  7. Molecular Basis of Glycosaminoglycan Heparin Binding to the Chemokine CXCL1 Dimer*

    PubMed Central

    Poluri, Krishna Mohan; Joseph, Prem Raj B.; Sawant, Kirti V.; Rajarathnam, Krishna

    2013-01-01

    Glycosaminoglycan (GAG)-bound and soluble chemokine gradients in the vasculature and extracellular matrix mediate neutrophil recruitment to the site of microbial infection and sterile injury in the host tissue. However, the molecular principles by which chemokine-GAG interactions orchestrate these gradients are poorly understood. This, in part, can be directly attributed to the complex interrelationship between the chemokine monomer-dimer equilibrium and binding geometry and affinities that are also intimately linked to GAG length. To address some of this missing knowledge, we have characterized the structural basis of heparin binding to the murine CXCL1 dimer. CXCL1 is a neutrophil-activating chemokine and exists as both monomers and dimers (Kd = 36 μm). To avoid interference from monomer-GAG interactions, we designed a trapped dimer (dCXCL1) by introducing a disulfide bridge across the dimer interface. We characterized the binding of GAG heparin octasaccharide to dCXCL1 using solution NMR spectroscopy. Our studies show that octasaccharide binds orthogonally to the interhelical axis and spans the dimer interface and that heparin binding enhances the structural integrity of the C-terminal helical residues and stability of the dimer. We generated a quadruple mutant (H20A/K22A/K62A/K66A) on the basis of the binding data and observed that this mutant failed to bind heparin octasaccharide, validating our structural model. We propose that the stability enhancement of dimers upon GAG binding regulates in vivo neutrophil trafficking by increasing the lifetime of “active” chemokines, and that this structural knowledge could be exploited for designing inhibitors that disrupt chemokine-GAG interactions and neutrophil homing to the target tissue. PMID:23864653

  8. Synthesis of Chiral Piperazinones Using Amphoteric Aziridine Aldehyde Dimers and Functionalized Isocyanides.

    PubMed

    Heine, Niklas B; Kaldas, Sherif J; Belding, Lee; Shmatova, Olga; Dudding, Travis; Nenajdenko, Valentine G; Studer, Armido; Yudin, Andrei K

    2016-06-17

    We have evaluated a range of functionalized isocyanides in the aziridine aldehyde-driven multicomponent synthesis of piperazinones. High diasteroselectivity for each isocyanide was observed. A theoretical evaluation of the reaction course corroborates the experimental data. Moreover, the reactivity of cis- and trans-configured aziridine aldehyde dimers has been compared. This study further probes the dimer-driven mechanism of cyclization and enables an efficient access to a wide range of chiral piperazinones bearing functionalized side chains. PMID:27156711

  9. The dimerization equilibrium of a ClC Cl−/H+ antiporter in lipid bilayers

    PubMed Central

    Chadda, Rahul; Krishnamani, Venkatramanan; Mersch, Kacey; Wong, Jason; Brimberry, Marley; Chadda, Ankita; Kolmakova-Partensky, Ludmila; Friedman, Larry J; Gelles, Jeff; Robertson, Janice L

    2016-01-01

    Interactions between membrane protein interfaces in lipid bilayers play an important role in membrane protein folding but quantification of the strength of these interactions has been challenging. Studying dimerization of ClC-type transporters offers a new approach to the problem, as individual subunits adopt a stable and functionally verifiable fold that constrains the system to two states – monomer or dimer. Here, we use single-molecule photobleaching analysis to measure the probability of ClC-ec1 subunit capture into liposomes during extrusion of large, multilamellar membranes. The capture statistics describe a monomer to dimer transition that is dependent on the subunit/lipid mole fraction density and follows an equilibrium dimerization isotherm. This allows for the measurement of the free energy of ClC-ec1 dimerization in lipid bilayers, revealing that it is one of the strongest membrane protein complexes measured so far, and introduces it as new type of dimerization model to investigate the physical forces that drive membrane protein association in membranes. DOI: http://dx.doi.org/10.7554/eLife.17438.001 PMID:27484630

  10. Photorepair of ultraviolet radiation-induced pyrimidine dimers in corneal DNA.

    PubMed

    Ley, R D; Applegate, L A; Freeman, S E

    1988-07-01

    The induction and photorepair of pyrimidine dimers in DNA have been measured in the ultraviolet-irradiated, corneal epithelium of the marsupial, Monodelphis domestica, using damage-specific nucleases from Micrococcus luteus in conjunction with agarose gel electrophoresis. We observed that FS-40 sunlamps (280-400 nm) induced 7.2 +/- 1.0 X 10(-5) pyrimidine dimers per kilobase (kb) of DNA per J/m2. Following 100 J/m2, 50% and greater than 90% of the dimers were photorepaired during a 10- and 30-min exposure to photoreactivating light (320-400 nm), respectively. In addition, approximately 70% and approximately 60% of the dimers induced by 300 and 500 J/m2, respectively, were repaired by a 60-min exposure to photoreactivating light. The capacity of the corneal epithelium of M. domestica to photorepair pyrimidine dimers identifies this animal as a potentially useful model with which to determine whether pyrimidine dimers are involved in pathological changes of the irradiated eye. PMID:3386657

  11. Calmodulin regulates dimerization, motility, and lipid binding of Leishmania myosin XXI

    PubMed Central

    Batters, Christopher; Ellrich, Heike; Helbig, Constanze; Woodall, Katy Anna; Hundschell, Christian; Brack, Dario; Veigel, Claudia

    2014-01-01

    Myosin XXI is the only myosin expressed in Leishmania parasites. Although it is assumed that it performs a variety of motile functions, the motor’s oligomerization states, cargo-binding, and motility are unknown. Here we show that binding of a single calmodulin causes the motor to adopt a monomeric state and to move actin filaments. In the absence of calmodulin, nonmotile dimers that cross-linked actin filaments were formed. Unexpectedly, structural analysis revealed that the dimerization domains include the calmodulin-binding neck region, essential for the generation of force and movement in myosins. Furthermore, monomeric myosin XXI bound to mixed liposomes, whereas the dimers did not. Lipid-binding sections overlapped with the dimerization domains, but also included a phox-homology domain in the converter region. We propose a mechanism of myosin regulation where dimerization, motility, and lipid binding are regulated by calmodulin. Although myosin-XXI dimers might act as nonmotile actin cross-linkers, the calmodulin-binding monomers might transport lipid cargo in the parasite. PMID:24379364

  12. Ras-GTP dimers activate the Mitogen-Activated Protein Kinase (MAPK) pathway

    PubMed Central

    Nan, Xiaolin; Tamgüney, Tanja M.; Collisson, Eric A.; Lin, Li-Jung; Pitt, Cameron; Galeas, Jacqueline; Lewis, Sophia; Gray, Joe W.; McCormick, Frank; Chu, Steven

    2015-01-01

    Rat sarcoma (Ras) GTPases regulate cell proliferation and survival through effector pathways including Raf-MAPK, and are the most frequently mutated genes in human cancer. Although it is well established that Ras activity requires binding to both GTP and the membrane, details of how Ras operates on the cell membrane to activate its effectors remain elusive. Efforts to target mutant Ras in human cancers to therapeutic benefit have also been largely unsuccessful. Here we show that Ras-GTP forms dimers to activate MAPK. We used quantitative photoactivated localization microscopy (PALM) to analyze the nanoscale spatial organization of PAmCherry1-tagged KRas 4B (hereafter referred to KRas) on the cell membrane under various signaling conditions. We found that at endogenous expression levels KRas forms dimers, and KRasG12D, a mutant that constitutively binds GTP, activates MAPK. Overexpression of KRas leads to formation of higher order Ras nanoclusters. Conversely, at lower expression levels, KRasG12D is monomeric and activates MAPK only when artificially dimerized. Moreover, dimerization and signaling of KRas are both dependent on an intact CAAX (C, cysteine; A, aliphatic; X, any amino acid) motif that is also known to mediate membrane localization. These results reveal a new, dimerization-dependent signaling mechanism of Ras, and suggest Ras dimers as a potential therapeutic target in mutant Ras-driven tumors. PMID:26080442

  13. Nonadiabatic dynamics of floppy hydrogen bonded complexes: the case of the ionized ammonia dimer.

    PubMed

    Chalabala, Jan; Slavíček, Petr

    2016-07-27

    In the case of the ammonia dimer, we address the following questions: how ultrafast ionization dynamics is controlled by hydrogen bonding and whether we can control the products via selective ionization of a specific electron. We use quantum chemical calculations and ab initio non-adiabatic molecular dynamics simulations to model the femtosecond dynamics of the ammonia dimer upon ionization. The role of nuclear quantum effects and thermal fluctuations in predicting the structure of the dimer is emphasized; it is shown that the minimum energy and vibrationally averaged structures are rather different. The ground state structure subsequently controls the ionization dynamics. We describe reaction pathways, electronic population transfers and reaction yields with respect to ionization from different molecular orbitals. The simulations showed that the ionized ammonia dimer is highly unstable and its decay rate is primarily driven by the position of the electron hole. In the case of ground state ionization (i.e. the HOMO electron is ionized), the decay is likely to be preceded by a proton transfer (PT) channel yielding NH4(+) and NH2˙ fragments. The PT is less intense and slower compared with the ionized water dimer. After ionizing deeper lying electrons, mainly NH3(+)˙ and NH3 fragments are formed. Overall, our results show that the ionization dynamics of the ammonia and water dimers differ due to the nature of the hydrogen bond in these systems. PMID:27402376

  14. Rotationally-Resolved Spectroscopy of the Bending Modes of Deuterated Water Dimer

    NASA Astrophysics Data System (ADS)

    Stewart, Jacob T.; McCall, Benjamin J.

    2013-06-01

    High-resolution spectroscopy of small gas-phase water clusters has provided a wealth of information regarding the intermolecular interactions between water molecules. Water dimer is of particular interest because high-resolution spectroscopy can yield detailed information about the water pair potential. While there have been extensive studies of water dimer throughout the microwave and infrared regions of the spectrum, to date there has been no reported high-resolution spectrum of the intramolecular bending modes of water dimer. We have obtained rotationally-resolved spectra of the bending modes of deuterated water dimer (D_2O)_2, which are, to our knowledge, the first reported spectra of the bending modes of water dimer with rotational resolution. Dimers were produced in a supersonic expansion by bubbling Ar or He through D_2O and expanding the mixture through a 150 μm × 12 mm slit. The expansion was then probed using continuous wave cavity ringdown spectroscopy with light generated by a quantum cascade laser (QCL) operating near 8.5 μm. We have assigned the K_a = 1 ← 0 and K_a = 2 ← 1 sub-bands of the bending mode belonging to the hydrogen bond donor and have observed additional transitions which we attribute to the bending mode associated with the hydrogen bond acceptor.

  15. Dimerization of Plasmodium vivax DBP is induced upon receptor binding and drives recognition of DARC

    PubMed Central

    Batchelor, Joseph D.; Zahm, Jacob A.; Tolia, Niraj H.

    2011-01-01

    Plasmodium vivax and Plasmodium knowlesi depend on the Duffy-Binding Protein DBL domain (RII-PvDBP or RII-PkDBP) engaging Duffy Antigen/Receptor for Chemokines on red blood cells during invasion. Inhibition of this key interaction provides an excellent opportunity for parasite control. There are competing models for whether Plasmodium ligands engage receptors as monomers or dimers, resolution of which has profound implications for parasite biology and control. We report crystallographic, solution and functional studies of RII-PvDBP, showing dimerization is required for and driven by receptor engagement. This work provides a unifying framework for prior studies and accounts for the action of naturally-acquired blocking-antibodies and the mechanism of immune evasion. We show dimerization is conserved in DBL-domain receptor-engagement, and propose receptor-mediated ligand-dimerization drives receptor affinity and specificity. Since dimerization is prevalent in signaling, our studies raise the possibility that induced dimerization activates pathways for invasion. PMID:21743458

  16. Investigation of the hydrated 7-hydroxy-4-methylcoumarin dimer by combined IR/UV spectroscopy

    SciTech Connect

    Stamm, A.; Schwing, K.; Gerhards, M.

    2014-11-21

    The first molecular beam investigations on a coumarin dimer and clusters of a coumarin dimer with water both in the neutral (S{sub 0}) and cationic (D{sub 0}) electronic ground state are performed. The structure and structural changes due to ionization of the isolated 7-hydroxy-4-methylcoumarin dimer (7H4MC){sub 2} as well as its mono- and dihydrate (7H4MC){sub 2}(H{sub 2}O){sub 1-2} are analyzed by applying combined IR/UV spectroscopy compared with density functional theory calculations. In case of the neutral dimer of 7H4MC a doubly hydrogen-bonded structure is formed. This doubly hydrogen-bonded arrangement opens to a singly hydrogen-bonded structure in the ion presenting a rearrangement reaction within an isolated dimer. By attaching one or two water molecules to the neutral 7H4MC dimer water is inserted into the hydrogen bonds. In contrast to the non-hydrated species this general binding motif with water in a bridging function does not change via ionization but especially for the dihydrate the spatial arrangement of the two 7H4MC units changes strengthening the interaction between the aromatic chromophores. The presented analyses illustrate the strong dependence of binding motifs as a function of successive hydration and charge including a rearrangement reaction.

  17. Coulomb bound states and resonances due to groups of Ca dimers adsorbed on suspended graphene

    NASA Astrophysics Data System (ADS)

    Saffarzadeh, Alireza; Kirczenow, George

    2014-10-01

    The electronic bound states and resonances in the vicinity of the Dirac point energy due to the adsorption of calcium dimers on a suspended graphene monolayer are explored theoretically using density functional theory (DFT) and an improved extended Hückel model that includes electrostatic potentials. The Mulliken atomic charges and the electrostatic potentials are obtained from DFT calculations and reveal charge transfer from the Ca dimers to the graphene which is responsible for the emergence of resonant states in the electronic spectrum. The number of resonant states increases as the number of adsorbed dimers is increased. We find a bound "atomic-collapse" state in the graphene local density of states, as has been observed experimentally [Wang et al., Science 340, 734 (2013), 10.1126/science.1234320]. We find the formation of the atomic-collapse state and its population with electrons to require fewer adsorbed Ca dimers than in the experiment, possibly due to the different spacing between dimers and the dielectric screening by a boron nitride substrate in the experiment. We also predict the onset of filling of a second atomic-collapse state with electrons when six Ca dimers are adsorbed on the suspended graphene monolayer. Experiments testing these predictions would be of interest.

  18. Distance within colloidal dimers probed by rotation-induced oscillations of scattered light.

    PubMed

    van Vliembergen, Roland W L; van IJzendoorn, Leo J; Prins, Menno W J

    2016-01-25

    Aggregation processes of colloidal particles are of broad scientific and technological relevance. The earliest stage of aggregation, when dimers appear in an ensemble of single particles, is very important to characterize because it opens routes for further aggregation processes. Furthermore, it represents the most sensitive phase of diagnostic aggregation assays. Here, we characterize dimers by rotating them in a magnetic field and by recording the angle dependence of light scattering. At small scattering angles, the scattering cross section can be approximated by the total cross-sectional area of the dimer. In contrast, at scattering angles around 90 degrees, we reveal that the dependence of the scattering cross section on the dimer angle shows a series of peaks per single 2π rotation of the dimers. These characteristics originate from optical interactions between the two particles, as we have verified with two-particle Mie scattering simulations. We have studied in detail the angular positions of the peaks. It appears from simulations that the influence of particle size polydispersity, Brownian rotation and refractive index on the angular positions of the peaks is relatively small. However, the angular positions of the peaks strongly depend on the distance between the particles. We find a good correspondence between measured data and calculations for a gap of 180 nm between particles having a diameter of 1 micrometer. The experiment and simulations pave the way for extracting distance-specific data from ensembles of dimerizing colloidal particles, with application for sensitive diagnostic aggregation assays. PMID:26832566

  19. Can cofactor-binding sites in proteins be flexible? Desulfovibrio desulfuricans flavodoxin binds FMN dimer.

    PubMed

    Muralidhara, B K; Wittung-Stafshede, Pernilla

    2003-11-11

    Flavodoxins catalyze redox reactions using the isoalloxazine moiety of the flavin mononucleotide (FMN) cofactor stacked between two aromatic residues located in two peptide loops. At high FMN concentrations that favor stacked FMN dimers in solution, isothermal titration calorimetric studies show that these dimers bind strongly to apo-flavodoxin from Desulfovibrio desulfuricans (30 degrees C, 20 mM Hepes, pH 7, K(D) = 5.8 microM). Upon increasing the temperature so the FMN dimers dissociate (as shown by (1)H NMR), only one-to-one (FMN-to-protein) binding is observed. Calorimetric titrations result in one-to-one binding also in the presence of phosphate or sulfate (30 degrees C, 13 mM anion, pH 7, K(D) = 0.4 microM). FMN remains dimeric in the presence of phosphate and sulfate, suggesting that specific binding of a divalent anion to the phosphate-binding site triggers ordering of the peptide loops so only one isoalloxazine can fit. Although the physiological relevance of FMN and other nucleotides as dimers has not been explored, our study shows that high-affinity binding to proteins of such dimers can occur in vitro. This emphasizes that the cofactor-binding site in flavodoxin is more flexible than previously expected. PMID:14596623

  20. Complete Structure of an Epithelial Keratin Dimer: Implications for Intermediate Filament Assembly

    PubMed Central

    Bray, David J.; Walsh, Tiffany R.; Noro, Massimo G.; Notman, Rebecca

    2015-01-01

    Keratins are cytoskeletal proteins that hierarchically arrange into filaments, starting with the dimer sub-unit. They are integral to the structural support of cells, in skin, hair and nails. In skin, keratin is thought to play a critical role in conferring the barrier properties and elasticity of skin. In general, the keratin dimer is broadly described by a tri-domain structure: a head, a central rod and a tail. As yet, no atomistic-scale picture of the entire dimer structure exists; this information is pivotal for establishing molecular-level connections between structure and function in intermediate filament proteins. The roles of the head and tail domains in facilitating keratin filament assembly and function remain as open questions. To address these, we report results of molecular dynamics simulations of the entire epithelial human K1/K10 keratin dimer. Our findings comprise: (1) the first three-dimensional structural models of the complete dimer unit, comprising of the head, rod and tail domains; (2) new insights into the chirality of the rod-domain twist gained from analysis of the full domain structure; (3) evidence for tri-subdomain partitioning in the head and tail domains; and, (4) identification of the residue characteristics that mediate non-covalent contact between the chains in the dimer. Our findings are immediately applicable to other epithelial keratins, such as K8/K18 and K5/K14, and to intermediate filament proteins in general. PMID:26181054

  1. Ras-GTP dimers activate the mitogen-activated protein kinase (MAPK) pathway

    DOE PAGESBeta

    Nan, Xiaolin; Tamgüney, Tanja M.; Collisson, Eric A.; Lin, Li -Jung; Pitt, Cameron; Galeas, Jacqueline; Lewis, Sophia; Gray, Joe W.; McCormick, Frank; Chu, Steven

    2015-06-16

    Rat sarcoma (Ras) GTPases regulate cell proliferation and survival through effector pathways including Raf-MAPK, and are the most frequently mutated genes in human cancer. Although it is well established that Ras activity requires binding to both GTP and the membrane, details of how Ras operates on the cell membrane to activate its effectors remain elusive. Efforts to target mutant Ras in human cancers to therapeutic benefit have also been largely unsuccessful. Here we show that Ras-GTP forms dimers to activate MAPK. We used quantitative photoactivated localization microscopy (PALM) to analyze the nanoscale spatial organization of PAmCherry1-tagged KRas 4B (hereafter referredmore » to KRas) on the cell membrane under various signaling conditions. We found that at endogenous expression levels KRas forms dimers, and KRasG12D, a mutant that constitutively binds GTP, activates MAPK. Overexpression of KRas leads to formation of higher order Ras nanoclusters. Conversely, at lower expression levels, KRasG12D is monomeric and activates MAPK only when artificially dimerized. Moreover, dimerization and signaling of KRas are both dependent on an intact CAAX (C, cysteine; A, aliphatic; X, any amino acid) motif that is also known to mediate membrane localization. These results reveal a new, dimerization-dependent signaling mechanism of Ras, and suggest Ras dimers as a potential therapeutic target in mutant Ras-driven tumors.« less

  2. Origin of Symmetric Dimer Images of Si(001) Observed by Low-Temperature Scanning Tunneling Microscopy

    NASA Astrophysics Data System (ADS)

    Ren, Xiao-Yan; Kim, Hyun-Jung; Niu, Chun-Yao; Jia, Yu; Cho, Jun-Hyung

    2016-06-01

    It has been a long-standing puzzle why buckled dimers of the Si(001) surface appeared symmetric below ~20 K in scanning tunneling microscopy (STM) experiments. Although such symmetric dimer images were concluded to be due to an artifact induced by STM measurements, its underlying mechanism is still veiled. Here, we demonstrate, based on a first-principles density-functional theory calculation, that the symmetric dimer images are originated from the flip-flop motion of buckled dimers, driven by quantum tunneling (QT). It is revealed that at low temperature the tunneling-induced surface charging with holes reduces the energy barrier for the flipping of buckled dimers, thereby giving rise to a sizable QT-driven frequency of the flip-flop motion. However, such a QT phenomenon becomes marginal in the tunneling-induced surface charging with electrons. Our findings provide an explanation for low-temperature STM data that exhibits apparent symmetric (buckled) dimer structure in the filled-state (empty-state) images.

  3. Symmetry-directed control of electronic coupling for singlet fission in covalent bis-acene dimers.

    PubMed

    Damrauer, Niels H; Snyder, Jamie L

    2015-11-19

    While singlet fission (SF) has developed in recent years within material settings, much less is known about its control in covalent dimers. Such platforms are of fundamental importance and may also find practical use in next-generation dye-sensitized solar cell applications or for seeding SF at interfaces following exciton transport. Here, facile theoretical tools based on Boys localization methods are used to predict diabatic coupling for SF via determination of one-electron orbital coupling matrix elements. The results expose important design rules that are rooted in point group symmetry. For Cs-symmetric dimers, pathways for SF that are mediated by virtual charge transfer excited states destructively interfere with negative impact on the magnitude of diabatic coupling for SF. When dimers have C2 symmetry, constructive interference is enabled for certain readily achievable interchromophore orientations. Three sets of dimers exploiting these ideas are explored: a bis-tetracene pair and two sets of aza-substituted tetracene dimers. Remarkable control is shown. In one aza-substituted set, symmetry has no impact on SF reaction thermodynamics but leads to a 16-fold manipulation in SF diabatic coupling. This translates to a difference of nearly 300 in kSF with the faster of the two dimers (C2) being predicted to undergo the process on a nearly ultrafast 1.5 ps time scale. PMID:26505732

  4. Ras-GTP dimers activate the mitogen-activated protein kinase (MAPK) pathway

    SciTech Connect

    Nan, Xiaolin; Tamgüney, Tanja M.; Collisson, Eric A.; Lin, Li -Jung; Pitt, Cameron; Galeas, Jacqueline; Lewis, Sophia; Gray, Joe W.; McCormick, Frank; Chu, Steven

    2015-06-16

    Rat sarcoma (Ras) GTPases regulate cell proliferation and survival through effector pathways including Raf-MAPK, and are the most frequently mutated genes in human cancer. Although it is well established that Ras activity requires binding to both GTP and the membrane, details of how Ras operates on the cell membrane to activate its effectors remain elusive. Efforts to target mutant Ras in human cancers to therapeutic benefit have also been largely unsuccessful. Here we show that Ras-GTP forms dimers to activate MAPK. We used quantitative photoactivated localization microscopy (PALM) to analyze the nanoscale spatial organization of PAmCherry1-tagged KRas 4B (hereafter referred to KRas) on the cell membrane under various signaling conditions. We found that at endogenous expression levels KRas forms dimers, and KRasG12D, a mutant that constitutively binds GTP, activates MAPK. Overexpression of KRas leads to formation of higher order Ras nanoclusters. Conversely, at lower expression levels, KRasG12D is monomeric and activates MAPK only when artificially dimerized. Moreover, dimerization and signaling of KRas are both dependent on an intact CAAX (C, cysteine; A, aliphatic; X, any amino acid) motif that is also known to mediate membrane localization. These results reveal a new, dimerization-dependent signaling mechanism of Ras, and suggest Ras dimers as a potential therapeutic target in mutant Ras-driven tumors.

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

    SciTech Connect

    Danielsen, E.M. )

    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.

  6. Major ligand-induced rearrangement of the heptahelical domain interface in a GPCR dimer.

    PubMed

    Xue, Li; Rovira, Xavier; Scholler, Pauline; Zhao, Han; Liu, Jianfeng; Pin, Jean-Philippe; Rondard, Philippe

    2015-02-01

    G protein-coupled receptors (GPCRs) are major players in cell communication. Although they form functional monomers, increasing evidence indicates that GPCR dimerization has a critical role in cooperative phenomena that are important for cell signal integration. However, the structural bases of these phenomena remain elusive. Here, using well-characterized receptor dimers, the metabotropic glutamate receptors (mGluRs), we show that structural changes at the dimer interface are linked to receptor activation. We demonstrate that the main dimer interface is formed by transmembrane α helix 4 (TM4) and TM5 in the inactive state and by TM6 in the active state. This major change in the dimer interface is required for receptor activity because locking the TM4-TM5 interface prevents activation by agonist, whereas locking the TM6 interface leads to a constitutively active receptor. These data provide important information on the activation mechanism of mGluRs and improve our understanding of the structural basis of the negative cooperativity observed in these GPCR dimers. PMID:25503927

  7. Structural relaxation of acridine orange dimer in bulk water and inside a single live lung cell

    NASA Astrophysics Data System (ADS)

    Chowdhury, Rajdeep; Nandi, Somen; Halder, Ritaban; Jana, Biman; Bhattacharyya, Kankan

    2016-02-01

    Structural relaxation of the acridine orange (AO) dimer in bulk water and inside a single live lung cell is studied using time resolved confocal microscopy and molecular dynamics (MD) simulations. The emission maxima ( λem max ˜ 630 nm) of AO in a lung cancer cell (A549) and a non-cancer lung fibroblast cell (WI38) suggest that AO exists as a dimer inside the cell. Time-dependent red shift in emission maximum indicates dynamic relaxation of the AO dimer (in the excited state) with a time constant of 500-600 ps, both in bulk water and inside the cell. We have calculated the equilibrium relaxation dynamics of the AO dimer in the ground state using MD simulations and found a slow component of time scale ˜350 ps. The intra- and inter-molecular components of the total relaxation dynamics of the AO dimer reveal the presence of a slow component of the order of a few hundred picoseconds. Upon restricting intra-molecular dye dynamics by harmonic constraint between AO monomers, the slow component vanishes. Combining the experimental observations and MD simulation results, we ascribe the slow component of the dynamic relaxation of the AO dimer to the structural relaxation, namely, fluctuations in the distance between the two monomers and associated fluctuation in the number of water molecules.

  8. Potential energy of H2 inside the C116 fullerene dimerization: An atomic analysis

    NASA Astrophysics Data System (ADS)

    EL-Barbary, A. A.

    2016-05-01

    DFT method has proved useful for its ability to provide an atomic analysis of the dimerization of fullerene molecules. Such atomic analysis may provide information that is not available by experimental methods. Here, the structures of possible three isomers of C116 fullerene dimerization obtained from two C58 fullerene cages have been optimized using DFT method at the B3LYP/6-31G(d,p) level of theory. The orientation of C58 fullerene and bond reorganization during the dimerization process have been studied. The transition structures and energy barriers between the three isomers are obtained. The potential energies of the H2 molecule motion along and perpendicular to the axial dimer with possible rotational angles are calculated. Also, the 13C NMR chemical shifts and electron density distribution have been applied to distinguish between the C58 fullerene cages and the three isomers of C116 fullerene dimerization. Our results show that the C116 fullerene dimerization could be considered to be good candidate for hydrogen storage.

  9. Serum D-Dimer Concentrations are Increased after Pediatric Traumatic Brain Injury

    PubMed Central

    Berger, Rachel P.; Fromkin, Janet; Rubin, Pam; Snyder, John; Richichi, Rudolph; Kochanek, Patrick

    2015-01-01

    Objective To determine whether d-dimer would be increased in children with traumatic brain injury (TBI), specifically mild abusive head trauma (AHT). Study design D-dimer was measured using multiplex bead technology in 195 children <4 years old (n=93 controls without TBI, n=102 cases with TBI) using previously collected serum. D-dimer was then measured prospectively in a clinical setting in 44 children (n=24 controls, n=20 cases). Receiver operator curves (ROC) were generated for prospective data. Results In both the retrospective and prospective cohorts, median (25th–75th percentile) d-dimer was significantly higher in cases vs. controls. An ROC demonstrated an area under the curve (AUC) of 0.91 (95% CI: 0.83 – 0.99) in the prospective cohort. At a cut-off of 0.59μg/L, the sensitivity and specificity for identification of a case was 90% and 75%, respectively. Conclusions Our data suggest that serum d-dimer may be able to be used to identify which young children at risk for AHT might benefit from a head computer tomography or other additional evaluation. Additional data are needed in order to better identify the clinical scenarios which may result in false positive or false negative d-dimer concentrations. PMID:25454315

  10. Quantitation of pyrimidine dimers in DNA from UVB-irradiated alfalfa (@ L. ) seedlings

    SciTech Connect

    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{sup 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.

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

    PubMed Central

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

    2010-01-01

    Objective Prostacyclin and thromboxane mediate opposing cardiovascular effects through their receptors, the IP and TP, respectively. Individuals heterozygous for an IP variant, IPR212C, displayed exaggerated loss of platelet IP responsiveness and accelerated cardiovascular disease. We examined association of IPR212C into homo- and hetero- dimeric receptor complexes and the impact on prostacyclin and thromboxane biology. Methods and Results Dimerization of the IP, IPR212C and TPα and was examined by Bioluminescent Resonance Energy Transfer in transfected HEK293 cells. We observed an equal propensity for formation of IPIP homo- and IPTPα hetero- dimers. Compared to the IP alone, IPR212C displayed reduced cAMP generation and increased ER localization, but underwent normal homo- and hetero- dimerization. When the IPR212C and IP were co-expressed a dominant negative action of variant was evident with enhanced wild type IP localization to the ER and reduced agonist-dependent signaling. Further, the TPα activation response, which was shifted from inositol phosphate to cAMP generation following IPTPα heterodimerization, was normalized when the TPα instead dimerized with IPR212C. Conclusions IPR212C exerts a dominant action on the wild type IP and TPα through dimerization. This likely contributes to accelerated cardiovascular disease in individuals carrying one copy of the variant allele. PMID:20522800

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

    SciTech Connect

    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.

  13. Origin of Symmetric Dimer Images of Si(001) Observed by Low-Temperature Scanning Tunneling Microscopy.

    PubMed

    Ren, Xiao-Yan; Kim, Hyun-Jung; Niu, Chun-Yao; Jia, Yu; Cho, Jun-Hyung

    2016-01-01

    It has been a long-standing puzzle why buckled dimers of the Si(001) surface appeared symmetric below ~20 K in scanning tunneling microscopy (STM) experiments. Although such symmetric dimer images were concluded to be due to an artifact induced by STM measurements, its underlying mechanism is still veiled. Here, we demonstrate, based on a first-principles density-functional theory calculation, that the symmetric dimer images are originated from the flip-flop motion of buckled dimers, driven by quantum tunneling (QT). It is revealed that at low temperature the tunneling-induced surface charging with holes reduces the energy barrier for the flipping of buckled dimers, thereby giving rise to a sizable QT-driven frequency of the flip-flop motion. However, such a QT phenomenon becomes marginal in the tunneling-induced surface charging with electrons. Our findings provide an explanation for low-temperature STM data that exhibits apparent symmetric (buckled) dimer structure in the filled-state (empty-state) images. PMID:27292000

  14. Investigation of the hydrated 7-hydroxy-4-methylcoumarin dimer by combined IR/UV spectroscopy.

    PubMed

    Stamm, A; Schwing, K; Gerhards, M

    2014-11-21

    The first molecular beam investigations on a coumarin dimer and clusters of a coumarin dimer with water both in the neutral (S0) and cationic (D0) electronic ground state are performed. The structure and structural changes due to ionization of the isolated 7-hydroxy-4-methylcoumarin dimer (7H4MC)2 as well as its mono- and dihydrate (7H4MC)2(H2O)1-2 are analyzed by applying combined IR/UV spectroscopy compared with density functional theory calculations. In case of the neutral dimer of 7H4MC a doubly hydrogen-bonded structure is formed. This doubly hydrogen-bonded arrangement opens to a singly hydrogen-bonded structure in the ion presenting a rearrangement reaction within an isolated dimer. By attaching one or two water molecules to the neutral 7H4MC dimer water is inserted into the hydrogen bonds. In contrast to the non-hydrated species this general binding motif with water in a bridging function does not change via ionization but especially for the dihydrate the spatial arrangement of the two 7H4MC units changes strengthening the interaction between the aromatic chromophores. The presented analyses illustrate the strong dependence of binding motifs as a function of successive hydration and charge including a rearrangement reaction. PMID:25416888

  15. Kinetics of Endophilin N-BAR Domain Dimerization and Membrane Interactions*

    PubMed Central

    Capraro, Benjamin R.; Shi, Zheng; Wu, Tingting; Chen, Zhiming; Dunn, Joanna M.; Rhoades, Elizabeth; Baumgart, Tobias

    2013-01-01

    The recruitment to plasma membrane invaginations of the protein endophilin is a temporally regulated step in clathrin-mediated endocytosis. Endophilin is believed to sense or stabilize membrane curvature, which in turn likely depends on the dimeric structure of the protein. The dynamic nature of the membrane association and dimerization of endophilin is thus functionally important and is illuminated herein. Using subunit exchange Förster resonance energy transfer (FRET), we determine dimer dissociation kinetics and find a dimerization equilibrium constant orders of magnitude lower than previously published values. We characterize N-BAR domain membrane association kinetics under conditions where the dimeric species predominates, by stopped flow, observing prominent electrostatic sensitivity of membrane interaction kinetics. Relative to membrane binding, we find that protein monomer/dimer species equilibrate with far slower kinetics. Complementary optical microscopy studies reveal strikingly slow membrane dissociation and an increase of dissociation rate constant for a construct lacking the amphipathic segment helix 0 (H0). We attribute the slow dissociation kinetics to higher-order protein oligomerization on the membrane. We incorporate our findings into a kinetic scheme for endophilin N-BAR membrane binding and find a significant separation of time scales for endophilin membrane binding and subsequent oligomerization. This separation may facilitate the regulation of membrane trafficking phenomena. PMID:23482561

  16. Calmodulin regulates dimerization, motility, and lipid binding of Leishmania myosin XXI.

    PubMed

    Batters, Christopher; Ellrich, Heike; Helbig, Constanze; Woodall, Katy Anna; Hundschell, Christian; Brack, Dario; Veigel, Claudia

    2014-01-14

    Myosin XXI is the only myosin expressed in Leishmania parasites. Although it is assumed that it performs a variety of motile functions, the motor's oligomerization states, cargo-binding, and motility are unknown. Here we show that binding of a single calmodulin causes the motor to adopt a monomeric state and to move actin filaments. In the absence of calmodulin, nonmotile dimers that cross-linked actin filaments were formed. Unexpectedly, structural analysis revealed that the dimerization domains include the calmodulin-binding neck region, essential for the generation of force and movement in myosins. Furthermore, monomeric myosin XXI bound to mixed liposomes, whereas the dimers did not. Lipid-binding sections overlapped with the dimerization domains, but also included a phox-homology domain in the converter region. We propose a mechanism of myosin regulation where dimerization, motility, and lipid binding are regulated by calmodulin. Although myosin-XXI dimers might act as nonmotile actin cross-linkers, the calmodulin-binding monomers might transport lipid cargo in the parasite. PMID:24379364

  17. Controlling optical field enhancement of a nanoring dimer for plasmon-based applications

    NASA Astrophysics Data System (ADS)

    Nana Koya, Alemayehu; Ji, Boyu; Hao, Zuoqiang; Lin, Jingquan

    2016-05-01

    Control of resonance dynamics and gap plasmons of coupled nanostructures beyond commonly used parameters such as the dimer gap has a paramount importance in practical applications where a fixed feed-gap is needed. In this report, we show control of resonance peak shift and gap plasmon intensity of a closely spaced nanoring dimer through polarization and illumination angle of incident light, geometry of the constituent nanorings and refractive index of the substrate underneath. For fixed outer radii and constant dimer gap, the resonance peak of the nanodimer shows universal redshift as the inner radii of nanorings increase and polarization of the incident light approaches the dimer axis. Furthermore, we show that increasing inner dimer radii and introducing a small split gap to the nanodimer results in highly enhanced gap plasmon intensity. Finally, at optimized dimer geometry and illumination of the incident light, 682 nm RIU‑1 refractive index sensitivity of the nanodimer was obtained and its implication for surface-based sensing is discussed in detail.

  18. The in vitro loose dimer structure and rearrangements of the HIV-2 leader RNA

    PubMed Central

    Purzycka, Katarzyna J.; Pachulska-Wieczorek, Katarzyna; Adamiak, Ryszard W.

    2011-01-01

    RNA dimerization is an essential step in the retroviral life cycle. Dimerization and encapsidation signals, closely linked in HIV-2, are located in the leader RNA region. The SL1 motif and nucleocapsid protein are considered important for both processes. In this study, we show the structure of the HIV-2 leader RNA (+1–560) captured as a loose dimer. Potential structural rearrangements within the leader RNA were studied. In the loose dimer form, the HIV-2 leader RNA strand exists in vitro as a single global fold. Two kissing loop interfaces within the loose dimer were identified: SL1/SL1 and TAR/TAR. Evidence for these findings is provided by RNA probing using SHAPE, chemical reagents, enzymes, non-denaturing PAGE mobility assays, antisense oligonucleotides hybridization and analysis of an RNA mutant. Both TAR and SL1 as isolated domains are bound by recombinant NCp8 protein with high affinity, contrary to the hairpins downstream of SL1. Foot-printing of the SL1/NCp8 complex indicates that the major binding site maps to the SL1 upper stem. Taken together, these data suggest a model in which TAR hairpin III, the segment of SL1 proximal to the loop and the PAL palindromic sequence play specific roles in the initiation of dimerization. PMID:21622659

  19. Cholesterol Modulates the Dimer Interface of the β2-Adrenergic Receptor via Cholesterol Occupancy Sites

    PubMed Central

    Prasanna, Xavier; Chattopadhyay, Amitabha; Sengupta, Durba

    2014-01-01

    The β2-adrenergic receptor is an important member of the G-protein-coupled receptor (GPCR) superfamily, whose stability and function are modulated by membrane cholesterol. The recent high-resolution crystal structure of the β2-adrenergic receptor revealed the presence of possible cholesterol-binding sites in the receptor. However, the functional relevance of cholesterol binding to the receptor remains unexplored. We used MARTINI coarse-grained molecular-dynamics simulations to explore dimerization of the β2-adrenergic receptor in lipid bilayers containing cholesterol. A novel (to our knowledge) aspect of our results is that receptor dimerization is modulated by membrane cholesterol. We show that cholesterol binds to transmembrane helix IV, and cholesterol occupancy at this site restricts its involvement at the dimer interface. With increasing cholesterol concentration, an increased presence of transmembrane helices I and II, but a reduced presence of transmembrane helix IV, is observed at the dimer interface. To our knowledge, this study is one of the first to explore the correlation between cholesterol occupancy and GPCR organization. Our results indicate that dimer plasticity is relevant not just as an organizational principle but also as a subtle regulatory principle for GPCR function. We believe these results constitute an important step toward designing better drugs for GPCR dimer targets. PMID:24655504

  20. Origin of Symmetric Dimer Images of Si(001) Observed by Low-Temperature Scanning Tunneling Microscopy

    PubMed Central

    Ren, Xiao-Yan; Kim, Hyun-Jung; Niu, Chun-Yao; Jia, Yu; Cho, Jun-Hyung

    2016-01-01

    It has been a long-standing puzzle why buckled dimers of the Si(001) surface appeared symmetric below ~20 K in scanning tunneling microscopy (STM) experiments. Although such symmetric dimer images were concluded to be due to an artifact induced by STM measurements, its underlying mechanism is still veiled. Here, we demonstrate, based on a first-principles density-functional theory calculation, that the symmetric dimer images are originated from the flip-flop motion of buckled dimers, driven by quantum tunneling (QT). It is revealed that at low temperature the tunneling-induced surface charging with holes reduces the energy barrier for the flipping of buckled dimers, thereby giving rise to a sizable QT-driven frequency of the flip-flop motion. However, such a QT phenomenon becomes marginal in the tunneling-induced surface charging with electrons. Our findings provide an explanation for low-temperature STM data that exhibits apparent symmetric (buckled) dimer structure in the filled-state (empty-state) images. PMID:27292000