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Sample records for cyano-bridged trimers mn2miii-m-iiicn6

  1. Photomagnetism in cyano-bridged bimetal assemblies.

    PubMed

    Ohkoshi, Shin-ichi; Tokoro, Hiroko

    2012-10-16

    The study of photoinduced phase-transition materials has implications for the fields of inorganic chemistry, solid-state chemistry, and materials science. Cyano-bridged bimetal assemblies are promising photomagnetic materials. Because cyano-bridged bimetal assemblies possess various absorption bands in the visible light region, their electronic and spin states can be controlled by visible light irradiation. Moreover, the selection of magnetic metal ions and organic ligands provide a way of controlling spin-spin interactions through a cyano bridge. In this Account, we describe cyano-bridged bimetal assemblies developed in our laboratory. Cu(II)(2)[Mo(IV)(CN)(8)]·8H(2)O (CuMo), Rb(I)Mn(II)[Fe(III)(CN)(6)] (RbMnFe), and Co(II)(3)[W(V)(CN)(8)](2)·(pyrimidine)(4)·6H(2)O (CoW) induce photomagnetism via photoinduced metal-to-metal charge transfers (MM'CT), while Fe(II)(2)[Nb(IV)(CN)(8)]·(4-pyridinealdoxime)(8)·2H(2)O (FeNb) exhibits a photoinduced magnetization via a photoinduced spin crossover. Irradiation with 473 nm light causes the CuMo system to exhibit a spontaneous magnetization with a Curie temperature (T(C)) of 25 K, but irradiation with 532, 785, and 840 nm light reduces the magnetization. In this reversible photomagnetic process, excitation of the MM'CT from Mo(IV) to Cu(II) produces a ferromagnetic mixed-valence isomer of Cu(I)Cu(II)[Mo(V)(CN)(8)]·8H(2)O (CuMo'). CuMo' returns to CuMo upon irradiation in the reverse-M'MCT band. RbMnFe shows a charge transfer (CT)-induced phase transition from the Mn(II)-Fe(III) phase to the Mn(III)-Fe(II) phase. Irradiation with 532 nm light converts the Mn(III)-Fe(II) phase into the Mn(II)-Fe(III) phase, and we observe photodemagnetization. In contrast, irradiation of the Mn(II)-Fe(III) phase with 410 nm light causes the reverse phase transition. A CT-induced Jahn-Teller distortion is responsible for this visible light-induced reversible photomagnetic effect. In the CoW system, a CT-induced spin transition causes the

  2. Cyano-Bridged Trimetallic Coordination Polymer Nanoparticles and Their Thermal Decomposition into Nanoporous Spinel Ferromagnetic Oxides.

    PubMed

    Zakaria, Mohamed B; Hossain, Md Shahriar A; Shiddiky, Muhammad J A; Shahabuddin, Mohammed; Yanmaz, Ekrem; Kim, Jung Ho; Belik, Alexei A; Ide, Yusuke; Hu, Ming; Tominaka, Satoshi; Yamauchi, Yusuke

    2016-10-10

    The synthesis of a novel family of cyano-bridged trimetallic coordination polymers (CPs) with various compositions and shapes has been reported by changing the compositional ratios of Fe, Co, and Ni species in the reaction system. In order to efficiently control the nucleation rate and the crystal growth, trisodium citrate dihydrate plays an important role as a chelating agent. After the obtained cyano-bridged trimetallic CPs undergo thermal treatment in air at three different temperatures (250, 350, and 450 °C), nanoporous spinel metal oxides are successfully obtained. Interestingly, the obtained nanoporous metal oxides are composed of small crstalline grains, and the grains are oriented in the same direction, realizing pseudo-single crystals with nanopores. The resultant nanoporous spinel oxides feature interesting magnetic properties. Cyano-bridged multimetallic CPs with various sizes and shapes can provide a pathway toward functional nanoporous metal oxides that are not attainable from simple cyano-bridged CPs containing single metal ions.

  3. [M(III)(bpym)(CN)(4)](-): a suitable building block to design ferrimagnetic cyano-bridged heterobimetallic chains (M = Fe, Cr; bpym = 2,2'-bypyrimidine).

    PubMed

    Visinescu, Diana; Toma, Luminita Marilena; Lloret, Francesc; Fabelo, Oscar; Ruiz-Pérez, Catalina; Julve, Miguel

    2008-08-21

    Two cyano-bridged M(III)Mn(III) [M = Fe () and Cr ()] ferrimagnetic chains are reported; exhibits metamagnetism with two critical fields of 1250 G and 2.0 T which correspond to the overcoming by the applied dc field of the inter- and intrachain magnetic interactions, respectively.

  4. Tuning the Origin of Magnetic Relaxation by Substituting the 3d or Rare-Earth Ions into Three Isostructural Cyano-Bridged 3d-4f Heterodinuclear Compounds.

    PubMed

    Zhang, Yan; Guo, Zhen; Xie, Shuang; Li, Hui-Li; Zhu, Wen-Hua; Liu, Li; Dong, Xun-Qing; He, Wei-Xun; Ren, Jin-Chao; Liu, Ling-Zhi; Powell, Annie K

    2015-11-02

    Three isostructural cyano-bridged 3d-4f compounds, [YFe(CN)6(hep)2(H2O)4] (1), [DyFe(CN)6(hep)2(H2O)4] (2), and [DyCo(CN)6(hep)2(H2O)4] (3), were successfully assembled by site-targeted substitution of the 3d or rare-earth ions. All compounds have been structurally characterized to display slightly distorted pentagonal-bipyramidal local coordination geometry around the rare-earth ions. Magnetic analyses revealed negligible magnetic coupling in compound 1, antiferromagnetic intradimer interaction in 2, and weak ferromagnetic coupling through dipolar-dipolar interaction in 3. Under an applied direct-current (dc) field, 1 (Hdc = 2.5 kOe, τ0 = 1.3 × 10(-7) s, and Ueff/kB = 23 K) and 3 (Hdc = 2.0 kOe, τ0 = 7.1 × 10(-11) s, and Ueff/kB = 63 K) respectively indicated magnetic relaxation behavior based on a single [Fe(III)]LS ion and a Dy(III) ion; nevertheless, 2 (Hdc = 2.0 kOe, τ0 = 9.7 × 10(-8) s, and Ueff/kB = 23 K) appeared to be a single-molecule magnet based on a cyano-bridged DyFe dimer. Compound 1, which can be regarded as a single-ion magnet of the [Fe(III)]LS ion linked to a diamagnetic Y(III) ion in a cyano-bridged heterodimer, represents one of the rarely investigated examples based on a single Fe(III) ion explored in magnetic relaxation behavior. It demonstrated that the introduction of intradimer magnetic interaction of 2 through a cyano bridge between Dy(III) and [Fe(III)]LS ions negatively affects the energy barrier and χ″(T) peak temperature compared to 3.

  5. Two dimensional cyano-bridged hetero-metallic coordination polymers containing metal⋅⋅⋅π interactions.

    PubMed

    Karaağaç, Dursun; Kürkçüoğlu, Güneş Süheyla; Yeşilel, Okan Zafer; Hökelek, Tuncer

    2014-01-01

    Three cyano bridged hetero-metallic complexes of general formula, [Cu(NH3)2(μ-ampy)M(μ-CN)2(CN)2]n [ampy=4-aminomethylpyridine, M=Ni(II) (1), Pd(II) (2) and Pt(II) (3)] have been synthesized and characterized by vibrational (FT-IR and Raman) spectroscopy, single crystal X-ray diffraction, thermal analyses and elemental analyses. The complexes crystallize in triclinic system with space group P-1. In all complexes, M(II) ions are coordinated by four cyano ligands, and four N atoms in the equatorial plane around the Cu atom form a slightly distorted square-planar arrangement, while the slightly distorted octahedral coordination is completed by the cyanide N atoms in the axial positions. In one-dimensional structures of all the complexes, [Cu(ampy)](2+) cations and [M(CN)4](2-) anions are linked via bridging cyano ligands. The adjacent one-dimensional structures form a 2D network to connect by the μ-ampy bridging ligands. The 2D layers are further linked by metal⋯π and hydrogen bonding interactions to generate a three dimensional network.

  6. Investigation of cyano-bridged coordination nanoparticles Gd3+/[Fe(CN)6]3-/d-mannitol as T1-weighted MRI contrast agents

    NASA Astrophysics Data System (ADS)

    Perrier, M.; Gallud, A.; Ayadi, A.; Kennouche, S.; Porredon, C.; Gary-Bobo, M.; Larionova, J.; Goze-Bac, Ch.; Zanca, M.; Garcia, M.; Basile, I.; Long, J.; de Lapuente, J.; Borras, M.; Guari, Y.

    2015-07-01

    Cyano-bridged Gd3+/[Fe(CN)6]3- coordination polymer nanoparticles of 3-4 nm stabilized with d-mannitol presenting a high r1 relaxivity value of 11.4 mM-1 s-1 were investigated in vivo as contrast agents (CA) for Magnetic Resonance Imaging (MRI). They allow an increase of the MR image contrast and can act as an efficient intravascular T1 CA with a relatively long blood-circulation lifetime (60 min) without specific toxicity.Cyano-bridged Gd3+/[Fe(CN)6]3- coordination polymer nanoparticles of 3-4 nm stabilized with d-mannitol presenting a high r1 relaxivity value of 11.4 mM-1 s-1 were investigated in vivo as contrast agents (CA) for Magnetic Resonance Imaging (MRI). They allow an increase of the MR image contrast and can act as an efficient intravascular T1 CA with a relatively long blood-circulation lifetime (60 min) without specific toxicity. Electronic supplementary information (ESI) available: Experimental details and procedures, toxicological data, physical characterization. See DOI: 10.1039/c5nr01557j

  7. Magnetic coupling in discrete cyano-bridged Mn(III)-Fe(III) motifs: synthesis, crystal structure, magnetic properties and theoretical study.

    PubMed

    Visinescu, Diana; Toma, Luminita Marilena; Cano, Joan; Fabelo, Oscar; Ruiz-Pérez, Catalina; Labrador, Ana; Lloret, Francesc; Julve, Miguel

    2010-05-28

    The preparation, crystal structures and magnetic properties of the heterobimetallic complexes of formula [Mn(III)(n-MeOsalen)(H(2)O)(mu-CN)Fe(III)(bpym)(CN)(3)]·mH(2)O with n = m = 3 (1) and n = 4 and m = 2 (2) [n-MeOsalen(2-) = N,N'-ethylenebis(n-methoxysalicylideneiminate) dianion and bpym = 2,2'-bipyrimidine] are reported. 1 and 2 are dinuclear neutral species where the cyano-bearing low-spin unit [Fe(III)(bpym)(CN)(4)](-) acts as a monodentate ligand towards the [Mn(III)(SB)(solv)(x)](+) entity (SB = tetradentate Schiff-base) through one of its four cyano groups. Adjacent heterobimetallic units are interlinked through hydrogen bonds involving the coordinated water molecule of one dinuclear unit and the phenolate oxygen atoms of the neighbouring one to afford pairs of dimers with values of the interdimer Mn···Mn distance of 4.925(20) (1) and 5.0508(25) Å (2). The analysis of the magnetic data of 1 and 2 in the temperature range 1.9-300 K shows the coexistence of weak ferro- [J = +2.95 (1) and +3.88 cm(-1) (2)] and antiferromagnetic interactions [j = -1.91 (1) and -0.70 cm(-1) (2)] through the single cyano bridge and hydrogen bonds, respectively (the Hamiltonian being of the type Ĥ = J[Ŝ(Fe)·Ŝ(Mn) + Ŝ(Fe')·Ŝ(Mn')] -jŜ(Mn)·Ŝ(Mn')). Theoretical calculations using methods based on density functional theory (DFT) have been used to substantiate the nature and magnitude of the magnetic coupling observed in 1 and 2 and also to analyze the dependence of the magnetic coupling on the structural parameters for the Fe-C-N-Mn skeleton. An extension of the calculations to selected examples of heterobimetallic Fe(III)-C-N-Mn(III) compounds with a different number of cyano groups on the low-spin iron(III) precursor has been carried out allowing us to illustrate the influence of the symmetry of the magnetic orbital of the iron center on the magnetic coupling in this heterobimetallic unit.

  8. Trimerization of aromatic nitriles

    NASA Technical Reports Server (NTRS)

    Hsu, L. C. (Inventor)

    1977-01-01

    Triazine compounds and cross-linked polymer compositions were made by heating aromatic nitriles to a temperature in the range of about 100 C to about 700 C, in the presence of a catalyst or mixture of catalysts. Aromatic nitrile-modified (terminated and/or appended) imide, benzimidazole, imidazopyrrolone, quinoxaline, and other condensation type prepolymers or their precopolymers were made which were trimerized with or without a filler by the aforementioned catalytic trimerization process.

  9. Mechanistic aspects of the chemistry of mononuclear Cr(III) complexes with pendant-arm macrocyclic ligands and formation of discrete Cr(III)/Fe(II) and Cr(III)/Fe(II)/Co(III) cyano-bridged mixed valence compounds.

    PubMed

    Basallote, Manuel G; Bernhardt, Paul V; Calvet, Teresa; Castillo, Carmen E; Font-Bardia, Mercè; Martínez, Manuel; Rodríguez, Carlos

    2009-11-21

    The kinetics and mechanism of the redox reaction between [Fe(II)(CN)(6)](4-) and the macrocyclic ligand complex [CrClL(15)](2+) (L(15) = 6-methyl-1,4,8,12-tetraazacyclopentadecane-6-amine) has been studied at different pH values. In acidic solution, the expected redox process occurs with no formation of any of the possible Cr(III)/Fe(II) mixed valence complexes, as those seen for the Co(III) species of the same family, due to the enhanced lability of the Cr(II) species formed on Fe(II) to Fe(III) oxidation. In alkaline conditions, the formation of the complex [Cr(L(15))(OH)(2)](+) takes place as an initial step that precedes a simple substitution process producing the expected cyano-bridged Cr(III)/Fe(II) complex. In this species the potentially pentadentate ligand, L(15), has a tetradentate coordination mode with a protonated exocyclic primary amine group and the redox potential is shifted to more negative values, thus disfavouring a redox driven reaction; the equivalent complex [CrCl(HL(14))(H(2)O)](3+) (L(14) = 6-methyl-1,4,8,11-tetraazacyclotetradecane-6-amine) has been prepared by the same method and characterized by X-ray crystallography. The final [Fe(II)(CN)(6)](4-) substituted complex, [{(HL(15))(OH)Cr(III)NC}Fe(II)(CN)(5)](-) shows pK(a) values of 3.8 and 7.4, as expected for the aqua and amino ligands, respectively. Its characterization indicated its Class II mixed valence character with a very intense MMCT band at 350 nm showing a much larger extinction coefficient than that observed for the Co(III) complexes of the same family. This fact is in good agreement with the much larger Cr(III)-Fe(II) (t(2g)-t(2g)) coupling through cyanide bridging ligands expected for these complexes. The fully mixed metal/valence/ligand trimetallic complex [{(HL(15))(OH)Cr(III)NC}{L(13)Co(III)NC}Fe(II)(CN)(4)](2+) has been prepared following the same procedures and the results are comparable. The final complex has the same Class II mixed valence character and its electronic

  10. A CNT-like coordination tube with cyano-bridges.

    PubMed

    Xia, Jun; Shi, Wei; Chen, Xiao-Yan; Wang, Hong-Sheng; Cheng, Peng; Liao, Dai-Zheng; Yan, Shi-Ping

    2007-06-21

    Reaction of K2[Ru(bipy)(CN)4] with MnCl2 produces a novel bimetallic compound {Mn(H2O)2[Ru(bipy)(CN)4]} (bipy = 2,2'-bipydine), exhibiting a CNT-like structure bridged by cyanide groups and high thermal stability, which has been first observed in coordination polymers.

  11. A New Approach to Produce HIV-1 Envelope Trimers

    PubMed Central

    AlSalmi, Wadad; Mahalingam, Marthandan; Ananthaswamy, Neeti; Hamlin, Christopher; Flores, Dalia; Gao, Guofen; Rao, Venigalla B.

    2015-01-01

    The trimeric envelope spike of HIV-1 mediates virus entry into human cells. The exposed part of the trimer, gp140, consists of two noncovalently associated subunits, gp120 and gp41 ectodomain. A recombinant vaccine that mimics the native trimer might elicit entry-blocking antibodies and prevent virus infection. However, preparation of authentic HIV-1 trimers has been challenging. Recently, an affinity column containing the broadly neutralizing antibody 2G12 has been used to capture recombinant gp140 and prepare trimers from clade A BG505 that naturally produces stable trimers. However, this antibody-based approach may not be as effective for the diverse HIV-1 strains with different epitope signatures. Here, we report a new and simple approach to produce HIV-1 envelope trimers. The C terminus of gp140 was attached to Strep-tag II with a long linker separating the tag from the massive trimer base and glycan shield. This allowed capture of nearly homogeneous gp140 directly from the culture medium. Cleaved, uncleaved, and fully or partially glycosylated trimers from different clade viruses were produced. Extensive biochemical characterizations showed that cleavage of gp140 was not essential for trimerization, but it triggered a conformational change that channels trimers into correct glycosylation pathways, generating compact three-blade propeller-shaped trimers. Uncleaved trimers entered aberrant pathways, resulting in hyperglycosylation, nonspecific cross-linking, and conformational heterogeneity. Even the cleaved trimers showed microheterogeneity in gp41 glycosylation. These studies established a broadly applicable HIV-1 trimer production system as well as generating new insights into their assembly and maturation that collectively bear on the HIV-1 vaccine design. PMID:26088135

  12. Kinetics of allophycocyanin's trimer-monomer equilibrium.

    PubMed

    Huang, C; Berns, D S; MacColl, R

    1987-01-13

    Kinetic studies of the dissociation of allophycocyanin trimers to monomers have been performed by using stopped-flow techniques. The dissociation was monitored by two techniques: by light scattering to observe the molecular weight changes directly and by 650-nm absorbance to observe the linkage of quaternary structure to spectra. The light-scattering experiments showed a simple exponential decay of trimers to monomers with a dissociation constant of 0.23 s-1. The absorption changes were complex, with two processes occurring. The faster absorption change appeared to be almost simultaneous with the molecular weight change (about 0.27 s-1) and was perhaps totally coordinated with it. The slower absorption change (0.071 s-1) was possibly a result of a conformational change in the chromophore arising during the conversion from newly dissociated monomers to equilibrium monomers.

  13. Radio-frequency association of Efimov trimers.

    PubMed

    Lompe, Thomas; Ottenstein, Timo B; Serwane, Friedhelm; Wenz, Andre N; Zürn, Gerhard; Jochim, Selim

    2010-11-12

    The quantum mechanical three-body problem is one of the fundamental challenges of few-body physics. When the two-body interactions become resonant, an infinite series of universal three-body bound states is predicted to occur, whose properties are determined by the strength of the two-body interactions. We used radio-frequency fields to associate Efimov trimers consisting of three distinguishable fermions. The measurements of their binding energy are consistent with theoretical predictions that include nonuniversal corrections.

  14. Femtosecond excitation transfer processes in biliprotein trimers

    NASA Astrophysics Data System (ADS)

    Sharkov, A. V.; Khoroshilov, E. V.; Kryukov, I. V.; Palsson, Lars-Olof; Kryukov, P. G.; Fischer, R.; Scheer, Hella-Christin; Gillbro, Tomas

    1993-06-01

    Femtosecond processes in allophycocyanin, C-phycocyanin and phycoerythrocyanin trimers and monomers have been examined by means of polarization pump-probe technique. No femtosecond kinetics were observed in monomeric preparations. The isotropic absorption recovery kinetics with (tau) equals 440 +/- 50 fs which is not accompanied by anisotropy decay kinetics was obtained in allophycocyanin trimers at 612 nm. The conclusion about energy transfer between neighboring (alpha) 84 and (beta) 84 chromophores with different absorption spectra was made. The proposed model takes into account a stabilizing role of the linker peptide. Spectral and kinetic measurements were made in the 635 - 690 nm spectral region where the proposed acceptor should absorb. The bleaching of the 650-nm band occurs with a delay relative to the bleaching at 615 nm. Only a rise term was observed at 658 nm in consistence with the proposed model. Anisotropy values calculated around 650 nm at 3 ps after excitation are in the range 0.1 - 0.25 corresponding to an angle of 30 degree(s) - 45 degree(s) between the donor and acceptor transition dipole moments. A 500-fs absorption recovery and anisotropy decay process was obtained for C-phycocyanin trimers and explained by Forster energy transfer over 20.8 angstroms between neighboring (alpha) 84 and (beta) 84 chromophores of different monomeric subunits having similar absorption spectra and with a 65 degree(s) angle between their orientations. Energy transfer between violobilin ((alpha) 84) and phycocyanobilin ((beta) 84) chromophores was examined in donor and acceptor spectral regions of phycoerythrocyanin trimers, and was found to take 400 fs.

  15. Creation of Hybrid Nanorods From Sequences of Natural Trimeric Fibrous Proteins Using the Fibritin Trimerization Motif

    NASA Astrophysics Data System (ADS)

    Papanikolopoulou, Katerina; van Raaij, Mark J.; Mitraki, Anna

    Stable, artificial fibrous proteins that can be functionalized open new avenues in fields such as bionanomaterials design and fiber engineering. An important source of inspiration for the creation of such proteins are natural fibrous proteins such as collagen, elastin, insect silks, and fibers from phages and viruses. The fibrous parts of this last class of proteins usually adopt trimeric, β-stranded structural folds and are appended to globular, receptor-binding domains. It has been recently shown that the globular domains are essential for correct folding and trimerization and can be successfully substituted by a very small (27-amino acid) trimerization motif from phage T4 fibritin. The hybrid proteins are correctly folded nanorods that can withstand extreme conditions. When the fibrous part derives from the adenovirus fiber shaft, different tissue-targeting specificities can be engineered into the hybrid proteins, which therefore can be used as gene therapy vectors. The integration of such stable nanorods in devices is also a big challenge in the field of biomechanical design. The fibritin foldon domain is a versatile trimerization motif and can be combined with a variety of fibrous motifs, such as coiled-coil, collagenous, and triple β-stranded motifs, provided the appropriate linkers are used. The combination of different motifs within the same fibrous molecule to create stable rods with multiple functions can even be envisioned. We provide a comprehensive overview of the experimental procedures used for designing, creating, and characterizing hybrid fibrous nanorods using the fibritin trimerization motif.

  16. Influenza A Virus Hemagglutinin Trimerization Completes Monomer Folding and Antigenicity

    PubMed Central

    Magadán, Javier G.; Khurana, Surender; Das, Suman R.; Frank, Gregory M.; Stevens, James; Golding, Hana; Bennink, Jack R.

    2013-01-01

    Influenza A virus (IAV) remains an important human pathogen largely because of antigenic drift, the rapid emergence of antibody escape mutants that precludes durable vaccination. The most potent neutralizing antibodies interact with cognate epitopes in the globular “head” domain of hemagglutinin (HA), a homotrimeric glycoprotein. The H1 HA possesses five distinct regions defined by a large number of mouse monoclonal antibodies (MAbs), i.e., Ca1, Ca2, Cb, Sa, and Sb. Ca1-Ca2 sites require HA trimerization to attain full antigenicity, consistent with their locations on opposite sides of the trimer interface. Here, we show that full antigenicity of Cb and Sa sites also requires HA trimerization, as revealed by immunofluorescence microscopy of IAV-infected cells and biochemically by pulse-chase radiolabeling experiments. Surprisingly, epitope antigenicity acquired by HA trimerization persists following acid triggering of the globular domains dissociation and even after proteolytic release of monomeric heads from acid-treated HA. Thus, the requirement for HA trimerization by trimer-specific MAbs mapping to the Ca, Cb, and Sa sites is not dependent upon the bridging of adjacent monomers in the native HA trimer. Rather, complete antigenicity of HA (and, by inference, immunogenicity) requires a final folding step that accompanies its trimerization. Once this conformational change occurs, HA trimers themselves would not necessarily be required to induce a highly diverse neutralizing response to epitopes in the globular domain. PMID:23824811

  17. Functional Characterization of Burkholderia pseudomallei Trimeric Autotransporters

    PubMed Central

    Campos, Cristine G.; Byrd, Matthew S.

    2013-01-01

    Burkholderia pseudomallei is a tier 1 select agent and the causative agent of melioidosis, a severe and often fatal disease with symptoms ranging from acute pneumonia and septic shock to a chronic infection characterized by abscess formation in the lungs, liver, and spleen. Autotransporters (ATs) are exoproteins belonging to the type V secretion system family, with many playing roles in pathogenesis. The genome of B. pseudomallei strain 1026b encodes nine putative trimeric AT proteins, of which only four have been described. Using a bioinformatic approach, we annotated putative domains within each trimeric AT protein, excluding the well-studied BimA protein, and found short repeated sequences unique to Burkholderia species, as well as an unexpectedly large proportion of ATs with extended signal peptide regions (ESPRs). To characterize the role of trimeric ATs in pathogenesis, we constructed disruption or deletion mutations in each of eight AT-encoding genes and evaluated the resulting strains for adherence to, invasion of, and plaque formation in A549 cells. The majority of the ATs (and/or the proteins encoded downstream) contributed to adherence to and efficient invasion of A549 cells. Using a BALB/c mouse model of infection, we determined the contributions of each AT to bacterial burdens in the lungs, liver, and spleen. At 48 h postinoculation, only one strain, Bp340::pDbpaC, demonstrated a defect in dissemination and/or survival in the liver, indicating that BpaC is required for wild-type virulence in this model. PMID:23716608

  18. What is the shape of the helium trimer? A comparison with the neon and argon trimers.

    PubMed

    Bressanini, Dario; Morosi, Gabriele

    2011-10-13

    Despite its apparent simplicity and extensive theoretical investigations, the issue of what is the shape of the helium trimer is still debated in the literature. After reviewing previous conflicting interpretations of computational studies, we introduce the angle-angle distribution function as a tool to discuss in a simple way the shape of any trimer. We compute this function along with many different geometrical distributions using variational and diffusion Monte Carlo methods. We compare them with the corresponding ones for the neon and argon trimers. Our analysis shows that while Ne(3) and Ar(3) fluctuate around an equilibrium structure that is an equilateral triangle, (4)He(3) shows an extremely broad angle-angle distribution function, and all kinds of three-atom configurations must be taken into account in its description. Classifying (4)He(3) as either equilateral or linear or any other particular shape, as was done in the past, is not sensible, because in this case the intuitive notion of equilibrium structure is ill defined. Our results could help the interpretation of future experiments aimed at measuring the geometrical properties of the helium trimer.

  19. The Radiation Induced Polymerization of Cyclophosphazene Trimers

    DTIC Science & Technology

    1989-01-04

    conversion-time curves fit a 3/2 power dependance of the rate on the monomer concentration. This is illustrated, for example, in Figure 2. It should be...in Figure 3. These give a scattered dependance of about 1.7 power. A 3/2 order would be expected if the monomer (trimer) also participates, as is...electron acceptor increased from about 0.02 to 0.27% per hour. The temperature dependance is presented as an Arrhenius plot in Figure 4. The activation

  20. Quantum dot display enhances activity of a phosphotriesterase trimer.

    PubMed

    Breger, Joyce C; Walper, Scott A; Oh, Eunkeu; Susumu, Kimihiro; Stewart, Michael H; Deschamps, Jeffrey R; Medintz, Igor L

    2015-04-14

    Phosphotriesterase was engineered into a spontaneously forming trimer by appending it to a synthetic collagen-like triple-helix motif. Enzymatic hydrolysis of the insecticide and organophosphate nerve agent simulant paraoxon was then examined. Assembling the phosphotriesterase trimer onto semiconductor quantum dots increased the enzyme's catalytic rate and efficiency.

  1. Crystallization of a Cyanurate Trimer in Nanopores

    NASA Astrophysics Data System (ADS)

    Koh, Yung P.; Simon, Sindee L.

    2011-03-01

    Nanoconfinement is known to depress the melting temperature through the well-known Gibbs-Thompson equation. Less well studied is the influence of nanoconfinement on crystallization kinetics. In this work we investigate crystallization of a cyanurate trimer using differential scanning calorimetry. The material shows cold crystallization and melting in the bulk state. Under the nanoconfinement of controlled pore glasses (CPG), cold crystallization and melting shift to lower temperatures, following the shift in the glass transition temperature. More importantly, however, the crystallization kinetics slow down and no crystallization occurs in 13 nm-diameter pores. Isothermal crystallization studies indicate that the Avrami exponent is approximately 2.0 for both bulk and nanoconfined samples. The time scale for crystallization is over one order of magnitude longer for samples confined in 50-nm pores in spite of the fact that samples were crystallized the same distance from Tg .

  2. Effective Kondo Model for a Trimer on a Metallic Surface

    NASA Astrophysics Data System (ADS)

    Aligia, A. A.

    2006-03-01

    I consider a Hubbard-Anderson model which describes localized orbitals in three different atoms hybridized both among themselves and with a continuum of extended states. Using a generalized Schrieffer-Wolf transformation, I derive an effective Kondo model for the interaction between the doublet ground state of the isolated trimer and the extended states. For an isoceles trimer with distances a, l, l between the atoms, the Kondo temperature is very small for la when a is small. The results agree with experiments for a Cr trimer on Au(111).

  3. The nature of the bonding in the transition metal trimers

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.; Bauschlicher, Charles W., Jr.

    1986-01-01

    The electronic structure of the transition metal (TM) trimers was studied by comparing the bonding in the Ca3, Sc3, and Cu3 molecules. The complete active space SCF/externally contracted configuration interaction (CI) ratio for the low-lying states of Sc3 and Sc3(+) and the SCF/CI ratio for Ca3 and Cu3 trimers, all for near equilateral triangle geometries, were calculated. In addition, vertical excitation energies for Cu3 were computed, leading to a new assignment of the upper state in the resonant two-photon ionization spectrum. Based on these studies, bonding in other TM trimers was discussed.

  4. Porcine parvovirus removal using trimer and biased hexamer peptides

    PubMed Central

    Heldt, Caryn L.; Gurgel, Patrick V.; Jaykus, Lee-Ann; Carbonell, Ruben G.

    2014-01-01

    Assuring the microbiological safety of biological therapeutics remains an important concern. Our group has recently reported small trimeric peptides that have the ability to bind and remove a model non-enveloped virus, porcine parvovirus (PPV), from complex solutions containing human blood plasma. In an effort to improve the removal efficiency of these small peptides, we created a biased library of hexamer peptides that contain two previously reported trimeric peptides designated WRW and KYY. This library was screened and several hexamer peptides were discovered that also removed PPV from solution, but there was no marked improvement in removal efficiency when compared to the trimeric peptides. Based on simulated docking experiments, it appeared that hexamer peptide binding is dictated more by secondary structure, whereas the binding of trimeric peptides is dominated by charge and hydrophobicity. This study demonstrates that trimeric and hexameric peptides may have different, matrix-specific roles to play in virus removal applications. In general, the hexamer ligand may perform better for binding of specific viruses, whereas the trimer ligand may have more broadly reactive virus-binding properties. PMID:21751387

  5. Role of trimer-trimer interaction of bacteriorhodopsin studied by optical spectroscopy and high-speed atomic force microscopy.

    PubMed

    Yamashita, Hayato; Inoue, Keiichi; Shibata, Mikihiro; Uchihashi, Takayuki; Sasaki, Jun; Kandori, Hideki; Ando, Toshio

    2013-10-01

    Bacteriorhodopsin (bR) trimers form a two-dimensional hexagonal lattice in the purple membrane of Halobacterium salinarum. However, the physiological significance of forming the lattice has long been elusive. Here, we study this issue by comparing properties of assembled and non-assembled bR trimers using directed mutagenesis, high-speed atomic force microscopy (HS-AFM), optical spectroscopy, and a proton pumping assay. First, we show that the bonds formed between W12 and F135 amino acid residues are responsible for trimer-trimer association that leads to lattice assembly; the lattice is completely disrupted in both W12I and F135I mutants. HS-AFM imaging reveals that both crystallized D96N and non-crystallized D96N/W12I mutants undergo a large conformational change (i.e., outward E-F loop displacement) upon light-activation. However, lattice disruption significantly reduces the rate of conformational change under continuous light illumination. Nevertheless, the quantum yield of M-state formation, measured by low-temperature UV-visible spectroscopy, and proton pumping efficiency are unaffected by lattice disruption. From these results, we conclude that trimer-trimer association plays essential roles in providing bound retinal with an appropriate environment to maintain its full photo-reactivity and in maintaining the natural photo-reaction pathway.

  6. The Translocation Domain in Trimeric Autotransporter Adhesins Is Necessary and Sufficient for Trimerization and Autotransportation

    PubMed Central

    Mikula, Kornelia M.; Leo, Jack C.; Łyskowski, Andrzej; Kedracka-Krok, Sylwia; Pirog, Artur

    2012-01-01

    Trimeric autotransporter adhesins (TAAs) comprise one of the secretion pathways of the type V secretion system. The mechanism of their translocation across the outer membrane remains unclear, but it most probably occurs by the formation of a hairpin inside the β-barrel translocation unit, leading to transportation of the passenger domain from the C terminus to the N terminus through the lumen of the β-barrel. We further investigated the phenomenon of autotransportation and the rules that govern it. We showed by coexpressing different Escherichia coli immunoglobulin-binding (Eib) proteins that highly similar TAAs could form stochastically mixed structures (heterotrimers). We further investigated this phenomenon by coexpressing two more distantly related TAAs, EibA and YadA. These, however, did not form heterotrimers; indeed, coexpression was lethal to the cells, leading to elimination of one or another of the genes. However, substituting in either protein the barrel of the other one so that the barrels were identical led to formation of heterotrimers as for Eibs. Our work shows that trimerization of the β-barrel, but not the passenger domain, is necessary and sufficient for TAA secretion while the passenger domain is not. PMID:22155776

  7. Predicted 3D Model of the Rabies Virus Glycoprotein Trimer.

    PubMed

    Fernando, Bastida-González; Yersin, Celaya-Trejo; José, Correa-Basurto; Paola, Zárate-Segura

    2016-01-01

    The RABVG ectodomain is a homotrimer, and trimers are often called spikes. They are responsible for the attachment of the virus through the interaction with nicotinic acetylcholine receptors, neural cell adhesion molecule (NCAM), and the p75 neurotrophin receptor (p75NTR). This makes them relevant in viral pathogenesis. The antigenic structure differs significantly between the trimers and monomers. Surfaces rich in hydrophobic amino acids are important for trimer stabilization in which the C-terminal of the ectodomain plays an important role; to understand these interactions between the G proteins, a mechanistic study of their functions was performed with a molecular model of G protein in its trimeric form. This verified its 3D conformation. The molecular modeling of G protein was performed by a I-TASSER server and was evaluated via a Rachamandran plot and ERRAT program obtained 84.64% and 89.9% of the residues in the favorable regions and overall quality factor, respectively. The molecular dynamics simulations were carried out on RABVG trimer at 310 K. From these theoretical studies, we retrieved the RMSD values from Cα atoms to assess stability. Preliminary model of G protein of rabies virus stable at 12 ns with molecular dynamics was obtained.

  8. Theoretical prediction of the vibrational spectra of group IB trimers

    PubMed Central

    Richtsmeier, Steven C.; Gole, James L.; Dixon, David A.

    1980-01-01

    The molecular structures of the group IB trimers, Cu3, Ag3, and Au3, have been determined by using the semi-empirical diatomics-in-molecules theory. The trimers are found to have C2v symmetry with bond angles between 65° and 80°. The trimers are bound with respect to dissociation to the asymptotic limit of an atom plus a diatom. The binding energies per atom for Cu3, Ag3, and Au3 are 1.08, 0.75, and 1.16 eV, respectively. The vibrational frequencies of the trimers have been determined for comparison with experimental results. The vibrational frequencies are characterized by low values for the bending and asymmetric stretch modes. The frequency of the symmetric stretch of the trimer is higher than the stretching frequency of the corresponding diatomic. A detailed comparison of the theoretical results with the previously measured Raman spectra of matrix isolated Ag3 is presented. PMID:16592885

  9. Predicted 3D Model of the Rabies Virus Glycoprotein Trimer

    PubMed Central

    Fernando, Bastida-González; Yersin, Celaya-Trejo; José, Correa-Basurto; Paola, Zárate-Segura

    2016-01-01

    The RABVG ectodomain is a homotrimer, and trimers are often called spikes. They are responsible for the attachment of the virus through the interaction with nicotinic acetylcholine receptors, neural cell adhesion molecule (NCAM), and the p75 neurotrophin receptor (p75NTR). This makes them relevant in viral pathogenesis. The antigenic structure differs significantly between the trimers and monomers. Surfaces rich in hydrophobic amino acids are important for trimer stabilization in which the C-terminal of the ectodomain plays an important role; to understand these interactions between the G proteins, a mechanistic study of their functions was performed with a molecular model of G protein in its trimeric form. This verified its 3D conformation. The molecular modeling of G protein was performed by a I-TASSER server and was evaluated via a Rachamandran plot and ERRAT program obtained 84.64% and 89.9% of the residues in the favorable regions and overall quality factor, respectively. The molecular dynamics simulations were carried out on RABVG trimer at 310 K. From these theoretical studies, we retrieved the RMSD values from Cα atoms to assess stability. Preliminary model of G protein of rabies virus stable at 12 ns with molecular dynamics was obtained. PMID:27294109

  10. Universal trimer in a three-component Fermi gas

    NASA Astrophysics Data System (ADS)

    Wenz, A. N.; Lompe, T.; Ottenstein, T. B.; Serwane, F.; Zürn, G.; Jochim, S.

    2009-10-01

    We show that the recently measured magnetic field dependence of three-body loss in a three-component mixture of ultracold L6i atoms [T. B. Ottenstein , Phys. Rev. Lett. 101, 203202 (2008); J. H. Huckans , Phys. Rev. Lett. 102, 165302 (2009)] can be explained by the presence of a universal trimer state. Previous work suggested a universal trimer state as a probable explanation, yet it failed to get good agreement between theory and experiment over the whole range of magnetic fields. For our description we adapt the theory of Braaten and Hammer [Phys. Rep. 428, 259 (2006)] for three identical bosons to the case of three distinguishable fermions by combining the three scattering lengths a12 , a23 , and a13 between the three components to an effective interaction parameter am . We show that taking into account a magnetic field variation in the lifetime of the trimer state is essential to obtain a complete understanding of the observed decay rates.

  11. Styrene dimers and trimers affect reproduction of daphnid (Ceriodaphnia dubia).

    PubMed

    Tatarazako, Norihisa; Takao, Yuji; Kishi, Katsuyuki; Onikura, Norio a; Arizono, Koji; Iguchi, Taisen

    2002-08-01

    The endocrine disruptor activity of styrene in humans and other vertebrates appears to be negligible. However, offspring numbers were reduced in Ceriodaphnia dubia bred in polystyrene cups. Styrene dimers and trimers were found to be eluted from the polystyrene cups by hexane and methanol with gas chromatography-mass spectrometry. Styrene dimers and trimers at concentrations of 0.04-1.7 microg/l affected C. dubia fertility (25% reduction after seven days), suggesting that styrenes have the potential to impair crustacean populations in the aquatic environment.

  12. Nonadditive effects in the mixed trimers of HCl and methanethiol

    NASA Astrophysics Data System (ADS)

    Balci, Mine; Boylu, Özgün; Uras-Aytemiz, Nevin

    2007-06-01

    Ab initio and density functional theory calculations with aug-cc-pVDZ and aug-cc-pVTZ basis sets have been performed on the HCl -CH3SH dimer and HCl -(CH3SH)2 and (HCl)2-CH3SH trimers. Structures, energetics, and infrared frequencies are calculated. The results are discussed in terms of the cooperativity effect which is a characteristic of H-bonded systems and compared to oxygen-containing analogs of the same trimers, HCl -(CH3OH)2 and (HCl)2-CH3OH, which have been published recently.

  13. Nonadditive effects in the mixed trimers of HCl and methanethiol.

    PubMed

    Balci, Mine; Boylu, Ozgün; Uras-Aytemiz, Nevin

    2007-06-28

    Ab initio and density functional theory calculations with aug-cc-pVDZ and aug-cc-pVTZ basis sets have been performed on the HCl-CH3SH dimer and HCl-(CH3SH)2 and (HCl)2-CH3SH trimers. Structures, energetics, and infrared frequencies are calculated. The results are discussed in terms of the cooperativity effect which is a characteristic of H-bonded systems and compared to oxygen-containing analogs of the same trimers, HCl-(CH3OH)2 and (HCl)2-CH3OH, which have been published recently.

  14. Uncleaved prefusion-optimized gp140 trimers derived from analysis of HIV-1 envelope metastability

    PubMed Central

    Kong, Leopold; He, Linling; de Val, Natalia; Vora, Nemil; Morris, Charles D.; Azadnia, Parisa; Sok, Devin; Zhou, Bin; Burton, Dennis R.; Ward, Andrew B.; Wilson, Ian A.; Zhu, Jiang

    2016-01-01

    The trimeric HIV-1 envelope glycoprotein (Env) is critical for host immune recognition and neutralization. Despite advances in trimer design, the roots of Env trimer metastability remain elusive. Here we investigate the contribution of two Env regions to metastability. First, we computationally redesign a largely disordered bend in heptad region 1 (HR1) of SOSIP trimers that connects the long, central HR1 helix to the fusion peptide, substantially improving the yield of soluble, well-folded trimers. Structural and antigenic analyses of two distinct HR1 redesigns confirm that redesigned Env closely mimics the native, prefusion trimer with a more stable gp41. Next, we replace the cleavage site between gp120 and gp41 with various linkers in the context of an HR1 redesign. Electron microscopy reveals a potential fusion intermediate state for uncleaved trimers containing short but not long linkers. Together, these results outline a general approach for stabilization of Env trimers from diverse HIV-1 strains. PMID:27349805

  15. Uncleaved prefusion-optimized gp140 trimers derived from analysis of HIV-1 envelope metastability

    NASA Astrophysics Data System (ADS)

    Kong, Leopold; He, Linling; de Val, Natalia; Vora, Nemil; Morris, Charles D.; Azadnia, Parisa; Sok, Devin; Zhou, Bin; Burton, Dennis R.; Ward, Andrew B.; Wilson, Ian A.; Zhu, Jiang

    2016-06-01

    The trimeric HIV-1 envelope glycoprotein (Env) is critical for host immune recognition and neutralization. Despite advances in trimer design, the roots of Env trimer metastability remain elusive. Here we investigate the contribution of two Env regions to metastability. First, we computationally redesign a largely disordered bend in heptad region 1 (HR1) of SOSIP trimers that connects the long, central HR1 helix to the fusion peptide, substantially improving the yield of soluble, well-folded trimers. Structural and antigenic analyses of two distinct HR1 redesigns confirm that redesigned Env closely mimics the native, prefusion trimer with a more stable gp41. Next, we replace the cleavage site between gp120 and gp41 with various linkers in the context of an HR1 redesign. Electron microscopy reveals a potential fusion intermediate state for uncleaved trimers containing short but not long linkers. Together, these results outline a general approach for stabilization of Env trimers from diverse HIV-1 strains.

  16. Designing a Soluble Near Full-Length HIV-1 GP41 Trimer

    DTIC Science & Technology

    2012-11-26

    envelope; gp41 trimer; bacteriophage T4 display; prehairpin fusion intermediate. Background: The envelope glycoprotein gp41 is a key component of...protein into trimers and defined oligomers. These gp41 trimers were displayed on bacteriophage T4 capsid nanoparticles by attaching to the small...gp41 Trimers on the Bacteriophage T4 Nanoparticle—Eight hundred and seventy copies of a small outer capsid protein, Soc (9 kDa), decorate the surface

  17. A Covalently Linked Tetracene Trimer: Synthesis and Singlet Exciton Fission Property.

    PubMed

    Liu, Heyuan; Wang, Rui; Shen, Li; Xu, Yanqing; Xiao, Min; Zhang, Chunfeng; Li, Xiyou

    2017-02-03

    A linear tetracene trimer linked by phenyl groups has been prepared for the first time. The triplet quantum yield formed via intramolecular singlet fission can reach up to 96% in this trimer, which is enhanced significantly compared with that in the dimer. This can be attributed to the stronger electronic coupling between tetracene subunits and more delocalized excitons in the trimer.

  18. DNAzyme-Controlled Cleavage of Dimer and Trimer Origami Tiles.

    PubMed

    Wu, Na; Willner, Itamar

    2016-04-13

    Dimers of origami tiles are bridged by the Pb(2+)-dependent DNAzyme sequence and its substrate or by the histidine-dependent DNAzyme sequence and its substrate to yield the dimers T1-T2 and T3-T4, respectively. The dimers are cleaved to monomer tiles in the presence of Pb(2+)-ions or histidine as triggers. Similarly, trimers of origami tiles are constructed by bridging the tiles with the Pb(2+)-ion-dependent DNAzyme sequence and the histidine-dependent DNAzyme sequence and their substrates yielding the trimer T1-T5-T4. In the presence of Pb(2+)-ions and/or histidine as triggers, the programmed cleavage of trimer proceeds. Using Pb(2+) or histidine as trigger cleaves the trimer to yield T5-T4 and T1 or the dimer T1-T5 and T4, respectively. In the presence of Pb(2+)-ions and histidine as triggers, the cleavage products are the monomer tiles T1, T5, and T4. The different cleavage products are identified by labeling the tiles with 0, 1, or 2 streptavidin labels and AFM imaging.

  19. Immunogenicity of stabilized HIV-1 envelope trimers with reduced exposure of non-neutralizing epitopes

    PubMed Central

    de Taeye, Steven W.; Ozorowski, Gabriel; de la Peña, Alba Torrents; Guttman, Miklos; Julien, Jean-Philippe; van den Kerkhof, Tom L.G.M.; Burger, Judith A.; Pritchard, Laura K.; Pugach, Pavel; Yasmeen, Anila; Crampton, Jordan; Hu, Joyce; Bontjer, Ilja; Torres, Jonathan L.; Arendt, Heather; DeStefano, Joanne; Koff, Wayne C.; Schuitemaker, Hanneke; Eggink, Dirk; Berkhout, Ben; Dean, Hansi; LaBranche, Celia; Crotty, Shane; Crispin, Max; Montefiori, David C.; Klasse, P. J.; Lee, Kelly K.; Moore, John P.; Wilson, Ian A.; Ward, Andrew B.; Sanders, Rogier W.

    2016-01-01

    Summary The envelope glycoprotein trimer mediates HIV-1 entry into cells. The trimer is flexible, fluctuating between closed and more open conformations and sometimes sampling the fully open, CD4-bound form. We hypothesized that conformational flexibility could hinder the induction of broadly neutralizing antibodies (bNAbs). We therefore modified soluble Env trimers to stabilize their closed, ground states. The trimer variants were indeed stabilized in the closed conformation, with a reduced ability to undergo receptor-induced conformational changes and a decreased exposure of non-neutralizing V3-directed antibody epitopes. In rabbits, the stabilized trimers induced similar autologous Tier-1B or Tier-2 NAb titers to those elicited by the corresponding wild-type trimers, but lower levels of V3-directed Tier-1A NAbs. Stabilized, closed trimers might therefore be useful components of vaccines aimed at inducing bNAbs. PMID:26687358

  20. Formation of unique trimer of nitric oxide on Cu(111)

    SciTech Connect

    Shiotari, A.; Hatta, S.; Okuyama, H. Aruga, T.

    2014-10-07

    We report that NO molecules unexpectedly prefer a trimeric configuration on Cu(111). We used scanning tunneling microscopy (STM) at 6 K, and confirmed that the NO molecule is bonded to the face-centered-cubic hollow site in an upright configuration. The individual NO molecule is imaged as a ring protrusion, which is characteristic of the doubly degenerate 2π{sup *} orbital. A triangular trimer is thermodynamically more favorable than the monomer and dimer, and its bonding structure was characterized by STM manipulation. This unique behavior of NO on Cu(111) is ascribed to the threefold symmetry of the surface, facilitating effective mixing of the 2π{sup *} orbitals in a triangular configuration.

  1. Interatomic Coulombic decay widths of helium trimer: Ab initio calculations

    SciTech Connect

    Kolorenč, Přemysl; Sisourat, Nicolas

    2015-12-14

    We report on an extensive study of interatomic Coulombic decay (ICD) widths in helium trimer computed using a fully ab initio method based on the Fano theory of resonances. Algebraic diagrammatic construction for one-particle Green’s function is utilized for the solution of the many-electron problem. An advanced and universal approach to partitioning of the configuration space into discrete states and continuum subspaces is described and employed. Total decay widths are presented for all ICD-active states of the trimer characterized by one-site ionization and additional excitation of an electron into the second shell. Selected partial decay widths are analyzed in detail, showing how three-body effects can qualitatively change the character of certain relaxation transitions. Previously unreported type of three-electron decay processes is identified in one class of the metastable states.

  2. Cerebrosides and tocopherol trimers from the seeds of Euryale ferox.

    PubMed

    Row, Lie-Ching; Ho, Jiau-Ching; Chen, Chiu-Ming

    2007-07-01

    Two new cerebrosides, ferocerebrosides A (1) [(2S,3R,4E,8E,2'R)-1-O-(beta-glucopyranosyl)-N-(2'-hydroxydocosanoyl)-4,8-sphingadienine] and B (2) [(2S,3R,4E,8E,2'R)-1-O-(beta-glucopyranosyl)-N-(2'-hydroxytetracosanoyl)-4,8-sphingadienine], two new tocopherol trimers, ferotocotrimers C (5) and D (6), and two known tocopherol trimers, IVb (3) and IVa (4), were isolated from the seeds of Euryale ferox. Their structures were determined on the basis of spectroscopic data, especially 1D and 2D NMR experiments. Compounds 1 and 2 showed cytotoxicity in the brine shrimp lethality bioassay, with LC50 values of 0.17 and 0.20 mM, respectively.

  3. The Trimeric Model: A New Model of Periodontal Treatment Planning

    PubMed Central

    Tarakji, Bassel

    2014-01-01

    Treatment of periodontal disease is a complex and multidisciplinary procedure, requiring periodontal, surgical, restorative, and orthodontic treatment modalities. Several authors attempted to formulate models for periodontal treatment that orders the treatment steps in a logical and easy to remember manner. In this article, we discuss two models of periodontal treatment planning from two of the most well-known textbook in the specialty of periodontics internationally. Then modify them to arrive at a new model of periodontal treatment planning, The Trimeric Model. Adding restorative and orthodontic interrelationships with periodontal treatment allows us to expand this model into the Extended Trimeric Model of periodontal treatment planning. These models will provide a logical framework and a clear order of the treatment of periodontal disease for general practitioners and periodontists alike. PMID:25177662

  4. OCS Trimer and Tetramer: Calculated Structures and Infrared Spectra

    NASA Astrophysics Data System (ADS)

    Dehghany, Mehdi; Moazzen-Ahmadi, Nasser; McKellar, Bob

    2014-06-01

    An OCS trimer was originally observed in the 1990s by microwave spectroscopy. New broadband chirped-pulse microwave spectra (preceding talk) reveal an OCS tetramer and a second distinct trimer isomer. In the present talk, we discuss OCS cluster structures and infrared spectra. Our structure calculations are based on a recent ab initio potential energy surface and assume pairwise additivity. There are also recent direct ab initio trimer and tetramer calculations, which are (necessarily) at a lower level of theory. We find that the observed OCS trimers indeed correspond to the two lowest energy isomers in both calculations, and that there is fairly good agreement of experimental and theoretical structures. For the tetramer the global minimum is at -2773 wn relative to dissociation, and we calculate (at least) twenty different isomers within 100 wn of this minimum (and seven within 20 wn). Remarkably, the observed microwave tetramer does correspond to our lowest calculated isomer. However this isomer is not included in the published direct ab initio calculation - it may just have been overlooked due to the large number of isomers! In the mid-infrared region of the OCS νb{1} fundamental (˜2060 wn), we observe two bands which are clearly due to the same microwave OCS tetramer. But a third band is assigned to a different tetramer not observed in the microwave spectrum. It appears to correspond to our seventh calculated isomer, located about 20 wn above the most stable one, and it is also missing from the direct ab initio calculation. Neither observed tetramer has any symmetry elements. J.P. Connelly, A. Bauder, A. Chisholm, and B.J. Howard, Mol. Phys. 88, 915 (1996) R.A. Peebles and R.L. Kuczkowski, J. Phys. Chem. A 103, 6344 (1999). N. Sahu, G. Singh, and S.R. Gadre, J. Phys. Chem. A 117, 10964 (2013).

  5. Crystal structures of the TRIC trimeric intracellular cation channel orthologues

    PubMed Central

    Kasuya, Go; Hiraizumi, Masahiro; Maturana, Andrés D; Kumazaki, Kaoru; Fujiwara, Yuichiro; Liu, Keihong; Nakada-Nakura, Yoshiko; Iwata, So; Tsukada, Keisuke; Komori, Tomotaka; Uemura, Sotaro; Goto, Yuhei; Nakane, Takanori; Takemoto, Mizuki; Kato, Hideaki E; Yamashita, Keitaro; Wada, Miki; Ito, Koichi; Ishitani, Ryuichiro; Hattori, Motoyuki; Nureki, Osamu

    2016-01-01

    Ca2+ release from the sarcoplasmic reticulum (SR) and endoplasmic reticulum (ER) is crucial for muscle contraction, cell growth, apoptosis, learning and memory. The trimeric intracellular cation (TRIC) channels were recently identified as cation channels balancing the SR and ER membrane potentials, and are implicated in Ca2+ signaling and homeostasis. Here we present the crystal structures of prokaryotic TRIC channels in the closed state and structure-based functional analyses of prokaryotic and eukaryotic TRIC channels. Each trimer subunit consists of seven transmembrane (TM) helices with two inverted repeated regions. The electrophysiological, biochemical and biophysical analyses revealed that TRIC channels possess an ion-conducting pore within each subunit, and that the trimer formation contributes to the stability of the protein. The symmetrically related TM2 and TM5 helices are kinked at the conserved glycine clusters, and these kinks are important for the channel activity. Furthermore, the kinks of the TM2 and TM5 helices generate lateral fenestrations at each subunit interface. Unexpectedly, these lateral fenestrations are occupied with lipid molecules. This study provides the structural and functional framework for the molecular mechanism of this ion channel superfamily. PMID:27909292

  6. Structural constraints determine the glycosylation of HIV-1 envelope trimers

    PubMed Central

    Pritchard, Laura K.; Vasiljevic, Snezana; Ozorowski, Gabriel; Seabright, Gemma E.; Cupo, Albert; Ringe, Rajesh; Kim, Helen J.; Sanders, Rogier W.; Doores, Katie J.; Burton, Dennis R.; Wilson, Ian A.; Ward, Andrew B.; Moore, John P.; Crispin, Max

    2015-01-01

    A highly glycosylated, trimeric envelope glycoprotein (Env) mediates HIV-1 cell entry. The high density and heterogeneity of the glycans shield Env from recognition by the immune system but, paradoxically, many potent broadly neutralizing antibodies (bNAbs) recognize epitopes involving this glycan shield. To better understand Env glycosylation and its role in bNAb recognition, we characterized a soluble, cleaved recombinant trimer (BG505 SOSIP.664) that is a close structural and antigenic mimic of native Env. Large, unprocessed oligomannose-type structures (Man8-9GlcNAc2) are notably prevalent on the gp120 components of the trimer, irrespective of the mammalian cell expression system or the bNAb used for affinity-purification. In contrast, gp41 subunits carry more highly processed glycans. The glycans on uncleaved, non-native oligomeric gp140 proteins are also highly processed. A homogeneous, oligomannose-dominated glycan profile is therefore a hallmark of a native Env conformation and a potential Achilles’ heel that can be exploited for bNAb recognition and vaccine design. PMID:26051934

  7. Biochemical evidence of a role for matrix trimerization in HIV-1 envelope glycoprotein incorporation

    PubMed Central

    Novikova, Mariia; Ablan, Sherimay D.; Freed, Eric O.

    2016-01-01

    The matrix (MA) domain of HIV Gag has important functions in directing the trafficking of Gag to sites of assembly and mediating the incorporation of the envelope glycoprotein (Env) into assembling particles. HIV-1 MA has been shown to form trimers in vitro; however, neither the presence nor the role of MA trimers has been documented in HIV-1 virions. We developed a cross-linking strategy to reveal MA trimers in virions of replication-competent HIV-1. By mutagenesis of trimer interface residues, we demonstrated a correlation between loss of MA trimerization and loss of Env incorporation. Additionally, we found that truncating the long cytoplasmic tail of Env restores incorporation of Env into MA trimer-defective particles, thus rescuing infectivity. We therefore propose a model whereby MA trimerization is required to form a lattice capable of accommodating the long cytoplasmic tail of HIV-1 Env; in the absence of MA trimerization, Env is sterically excluded from the assembling particle. These findings establish MA trimerization as an obligatory step in the assembly of infectious HIV-1 virions. As such, the MA trimer interface may represent a novel drug target for the development of antiretrovirals. PMID:26711999

  8. LETTER TO THE EDITOR: The dimer-trimer and monomer-trimer models for heterogeneous catalysis: a phase diagram study

    NASA Astrophysics Data System (ADS)

    Khan, K. M.; Basit, A.; Yaldram, K.

    2000-06-01

    The phase diagram of the dimer-trimer model has already been studied for Kagome and hexagonal lattices, the detail of which can be found in the literature. Here, we have studied the same model on a square lattice to look into the effect of lattice type on the phase diagram of the system. The steady reactive window width decreases significantly from 0.12 (for hexagonal lattice) to 0.02 for a square lattice. We have also studied a monomer-trimer model through Monte Carlo simulation. The effect of the lattice type on the phase diagram of the system is studied. The phase diagram qualitatively resembles that of the ZGB model. The lattice type has a significant effect on the steady reactive window width.

  9. Electronic structure of a deformable trimer with a coulomb interaction and a variable number of electrons

    SciTech Connect

    Aplesnin, S. S.; Piskunova, N. I.

    2011-01-15

    The electronic spectrum of a trimer with a variable number of electrons has been calculated in the Hubbard model by exact diagonalization. The dependences of the chemical potential shift, magnetic moment, and energy level splitting near the chemical potential on the magnetic field, Coulomb interaction between the electrons located at the vertices of the triangle, trimer deformation, and three-center interaction have been established. The removal of magnetic degeneracy in the trimer when the intersite Coulomb and three-center interactions are taken into account and the formation of a singlet pair of electrons under trimer deformation have been detected.

  10. Identification of Ata, a Multifunctional Trimeric Autotransporter of Acinetobacter baumannii

    PubMed Central

    Bentancor, Leticia V.; Camacho-Peiro, Ana; Bozkurt-Guzel, Cagla; Pier, Gerald B.

    2012-01-01

    Acinetobacter baumannii has recently emerged as a highly troublesome nosocomial pathogen, especially in patients in intensive care units and in those undergoing mechanical ventilation. We have identified a surface protein adhesin of A. baumannii, designated the Acinetobacter trimeric autotransporter (Ata), that contains all of the typical features of trimeric autotransporters (TA), including a long signal peptide followed by an N-terminal, surface-exposed passenger domain and a C-terminal domain encoding 4 β-strands. To demonstrate that Ata encoded a TA, we created a fusion protein in which we replaced the entire passenger domain of Ata with the epitope tag V5, which can be tracked with specific monoclonal antibodies, and demonstrated that the C-terminal 101 amino acids of Ata were capable of exporting the heterologous V5 tag to the surface of A. baumannii in a trimeric form. We found that Ata played a role in biofilm formation and bound to various extracellular matrix/basal membrane (ECM/BM) components, including collagen types I, III, IV, and V and laminin. Moreover, Ata mediated the adhesion of whole A. baumannii cells to immobilized collagen type IV and played a role in the survival of A. baumannii in a lethal model of systemic infection in immunocompetent mice. Taken together, these results reveal that Ata is a TA of A. baumannii involved in virulence, including biofilm formation, binding to ECM/BM proteins, mediating the adhesion of A. baumannii cells to collagen type IV, and contributing to the survival of A. baumannii in a mouse model of lethal infection. PMID:22609912

  11. Nonlinear optical response of cofacial phthalocyanine dimers and trimers

    SciTech Connect

    Manas, E.S.; Spano, F.C.; Chen, L.X.

    1997-07-01

    The effects of intermacrocycle interactions on the second hyperpolarizabilities {l_angle}{gamma}({minus}{omega};{omega},{minus}{omega},{omega}){r_angle} of cofacial phthalocyanine dimers and trimers are studied. A theoretical analysis is presented based on the Frenkel exciton model for a chain of three level molecules. Using a simplified analysis in the static and near-resonant regimes we identify two mechanisms which lead to enhancements in the dimer or trimer value of {l_angle}{gamma}({minus}{omega};{omega},{minus}{omega},{omega}){r_angle} over that of the monomer. The first mechanism is a disruption of the balance between type I and type II terms in the sum over states expression for the second hyperpolarizability tensor {gamma}{sub kjih}({minus}{omega};{omega},{minus}{omega},{omega}), caused by weak intermacrocycle interactions. The second is a near-resonance enhancement of the type II terms due to an intermacrocycle interaction induced shift in the monomer derived two-photon allowed states towards twice the laser photon energy. This analysis is in good agreement with recent degenerate four wave mixing experiments [SPIE Proc. {bold 2527}, 61 (1995)] which showed a strong enhancement of {l_angle}{gamma}({minus}{omega};{omega},{minus}{omega},{omega}){r_angle} for SiPcO oligomers as a function of the number of macrocycles. Our calculations suggest that the first mechanism is responsible for the 25-fold monomer to dimer enhancement measured in this system, and that the additional 4-fold enhancement found in going from the dimer to the trimer is primarily the result of the second mechanism. {copyright} {ital 1997 American Institute of Physics.}

  12. Photoemission Electron Microscopy of a Plasmonic Silver Nanoparticle Trimer

    SciTech Connect

    Peppernick, Samuel J.; Joly, Alan G.; Beck, Kenneth M.; Hess, Wayne P.; Wang, Jinyong; Wang, Yi-Chung; Wei, Wei

    2013-07-01

    We present a combined experimental and theoretical study to investigate the spatial distribution of photoelectrons emitted from core-shell silver (Ag) nanoparticles. We use two-photon photoemission microscopy (2P-PEEM) to spatially resolve electron emission from a trimeric core-shell aggregate of triangular symmetry. Finite difference time domain (FDTD) simulations are performed to model the intensity distributions of the electromagnetic near-fields resulting from femtosecond (fs) laser excitation of localized surface plasmon oscillations in the triangular core-shell structure. We demonstrate that the predicted FDTD near-field intensity distribution reproduces the 2P-PEEM photoemission pattern.

  13. A monomer-trimer model supports intermittent glucagon fibril growth

    PubMed Central

    Košmrlj, Andrej; Cordsen, Pia; Kyrsting, Anders; Otzen, Daniel E.; Oddershede, Lene B.; Jensen, Mogens H.

    2015-01-01

    We investigate in vitro fibrillation kinetics of the hormone peptide glucagon at various concentrations using confocal microscopy and determine the glucagon fibril persistence length 60μm. At all concentrations we observe that periods of individual fibril growth are interrupted by periods of stasis. The growth probability is large at high and low concentrations and is reduced for intermediate glucagon concentrations. To explain this behavior we propose a simple model, where fibrils come in two forms, one built entirely from glucagon monomers and one entirely from glucagon trimers. The opposite building blocks act as fibril growth blockers, and this generic model reproduces experimental behavior well. PMID:25758791

  14. Hydrolytic polymerization of chromium (III). 2. A trimeric species

    SciTech Connect

    Finholt, J.E.; Thompson, M.E.; Connick, R.E.

    1981-12-01

    With use of an ion-exchange displacement elution, a green species was separated from mixtures of Cr(III) polymers and its absorption spectrum determined. The hydroxides per chromium atom were found to be 4/3, and the charge per chromium atom was shown to be consistent with this value. The degree of polymerization of freezing point depression was close to 3. Measurements are reported for the equilibrium quotient for the formation of the trimer from the monomer. The ESR spectrum and magnetic susceptibility were determined, and the results are discussed in terms of possible structures.

  15. A monomer-trimer model supports intermittent glucagon fibril growth

    NASA Astrophysics Data System (ADS)

    Košmrlj, Andrej; Cordsen, Pia; Kyrsting, Anders; Otzen, Daniel E.; Oddershede, Lene B.; Jensen, Mogens H.

    2015-03-01

    We investigate in vitro fibrillation kinetics of the hormone peptide glucagon at various concentrations using confocal microscopy and determine the glucagon fibril persistence length 60μm. At all concentrations we observe that periods of individual fibril growth are interrupted by periods of stasis. The growth probability is large at high and low concentrations and is reduced for intermediate glucagon concentrations. To explain this behavior we propose a simple model, where fibrils come in two forms, one built entirely from glucagon monomers and one entirely from glucagon trimers. The opposite building blocks act as fibril growth blockers, and this generic model reproduces experimental behavior well.

  16. Reconstitution of active catalytic trimer of aspartate transcarbamoylase from proteolytically cleaved polypeptide chains.

    PubMed Central

    Powers, V. M.; Yang, Y. R.; Fogli, M. J.; Schachman, H. K.

    1993-01-01

    Treatment of the catalytic (C) trimer of Escherichia coli aspartate transcarbamoylase (ATCase) with alpha-chymotrypsin by a procedure similar to that used by Chan and Enns (1978, Can. J. Biochem. 56, 654-658) has been shown to yield an intact, active, proteolytically cleaved trimer containing polypeptide fragments of 26,000 and 8,000 MW. Vmax of the proteolytically cleaved trimer (CPC) is 75% that of the wild-type C trimer, whereas Km for aspartate and Kd for the bisubstrate analog, N-(phosphonacetyl)-L-aspartate, are increased about 7- and 15-fold, respectively. CPC trimer is very stable to heat denaturation as shown by differential scanning microcalorimetry. Amino-terminal sequence analyses as well as results from electrospray ionization mass spectrometry indicate that the limited chymotryptic digestion involves the rupture of only a single peptide bond leading to the production of two fragments corresponding to residues 1-240 and 241-310. This cleavage site involving the bond between Tyr 240 and Ala 241 is in a surface loop known to be involved in intersubunit contacts between the upper and lower C trimers in ATCase when it is in the T conformation. Reconstituted holoenzyme comprising two CPC trimers and three wild-type regulatory (R) dimers was shown by enzyme assays to be devoid of the homotropic and heterotropic allosteric properties characteristic of wild-type ATCase. Moreover, sedimentation velocity experiments demonstrate that the holoenzyme reconstituted from CPC trimers is in the R conformation. These results indicate that the intact flexible loop containing Tyr 240 is essential for stabilizing the T conformation of ATCase. Following denaturation of the CPC trimer in 4.7 M urea and dilution of the solution, the separate proteolytic fragments re-associate to form active trimers in about 60% yield. How this refolding of the fragments, docking, and association to form trimers are achieved is not known. PMID:8318885

  17. The infrared spectrum and structure of the nitrous oxide trimer

    NASA Astrophysics Data System (ADS)

    Miller, R. E.; Pedersen, L.

    1998-01-01

    Reported here are the first spectroscopic observations of the nitrous oxide trimer. Two rotationally resolved vibrational bands have been observed using the optothermal detection method. The ground vibrational state rotational constants obtained from these spectra are A=0.052 606(40), B=0.043 571(15), and C=0.028 736(7) cm-1. Ab initio calculations are also reported here, at the MP2/6-31+G(2d,2p) level, which yield A=0.054 92, B=0.045 17, and C=0.030 52 cm-1. The structure of the nitrous oxide trimer can be thought of as a slightly distorted dimer, which has a slipped parallel geometry [Z. S. Huang and R. E. Miller, J. Chem. Phys. 89, 5408 (1988)], with a third monomer unit lying above this dimer. This structure is similar to the recently observed nonplanar isomer of (CO2)3 [M. J. Weida and D. J. Nesbitt, J. Chem. Phys. 105, 10,210 (1996)].

  18. Structure of a Burkholderia pseudomallei Trimeric Autotransporter Adhesin Head

    PubMed Central

    Edwards, Thomas E.; Phan, Isabelle; Abendroth, Jan; Dieterich, Shellie H.; Masoudi, Amir; Guo, Wenjin; Hewitt, Stephen N.; Kelley, Angela; Leibly, David; Brittnacher, Mitch J.; Staker, Bart L.; Miller, Samuel I.; Van Voorhis, Wesley C.; Myler, Peter J.; Stewart, Lance J.

    2010-01-01

    Background Pathogenic bacteria adhere to the host cell surface using a family of outer membrane proteins called Trimeric Autotransporter Adhesins (TAAs). Although TAAs are highly divergent in sequence and domain structure, they are all conceptually comprised of a C-terminal membrane anchoring domain and an N-terminal passenger domain. Passenger domains consist of a secretion sequence, a head region that facilitates binding to the host cell surface, and a stalk region. Methodology/Principal Findings Pathogenic species of Burkholderia contain an overabundance of TAAs, some of which have been shown to elicit an immune response in the host. To understand the structural basis for host cell adhesion, we solved a 1.35 Å resolution crystal structure of a BpaA TAA head domain from Burkholderia pseudomallei, the pathogen that causes melioidosis. The structure reveals a novel fold of an intricately intertwined trimer. The BpaA head is composed of structural elements that have been observed in other TAA head structures as well as several elements of previously unknown structure predicted from low sequence homology between TAAs. These elements are typically up to 40 amino acids long and are not domains, but rather modular structural elements that may be duplicated or omitted through evolution, creating molecular diversity among TAAs. Conclusions/Significance The modular nature of BpaA, as demonstrated by its head domain crystal structure, and of TAAs in general provides insights into evolution of pathogen-host adhesion and may provide an avenue for diagnostics. PMID:20862217

  19. Accurate calculations of bound rovibrational states for argon trimer

    SciTech Connect

    Brandon, Drew; Poirier, Bill

    2014-07-21

    This work presents a comprehensive quantum dynamics calculation of the bound rovibrational eigenstates of argon trimer (Ar{sub 3}), using the ScalIT suite of parallel codes. The Ar{sub 3} rovibrational energy levels are computed to a very high level of accuracy (10{sup −3} cm{sup −1} or better), and up to the highest rotational and vibrational excitations for which bound states exist. For many of these rovibrational states, wavefunctions are also computed. Rare gas clusters such as Ar{sub 3} are interesting because the interatomic interactions manifest through long-range van der Waals forces, rather than through covalent chemical bonding. As a consequence, they exhibit strong Coriolis coupling between the rotational and vibrational degrees of freedom, as well as highly delocalized states, all of which renders accurate quantum dynamical calculation difficult. Moreover, with its (comparatively) deep potential well and heavy masses, Ar{sub 3} is an especially challenging rare gas trimer case. There are a great many rovibrational eigenstates to compute, and a very high density of states. Consequently, very few previous rovibrational state calculations for Ar{sub 3} may be found in the current literature—and only for the lowest-lying rotational excitations.

  20. Accurate calculations of bound rovibrational states for argon trimer

    NASA Astrophysics Data System (ADS)

    Brandon, Drew; Poirier, Bill

    2014-07-01

    This work presents a comprehensive quantum dynamics calculation of the bound rovibrational eigenstates of argon trimer (Ar3), using the ScalIT suite of parallel codes. The Ar3 rovibrational energy levels are computed to a very high level of accuracy (10-3 cm-1 or better), and up to the highest rotational and vibrational excitations for which bound states exist. For many of these rovibrational states, wavefunctions are also computed. Rare gas clusters such as Ar3 are interesting because the interatomic interactions manifest through long-range van der Waals forces, rather than through covalent chemical bonding. As a consequence, they exhibit strong Coriolis coupling between the rotational and vibrational degrees of freedom, as well as highly delocalized states, all of which renders accurate quantum dynamical calculation difficult. Moreover, with its (comparatively) deep potential well and heavy masses, Ar3 is an especially challenging rare gas trimer case. There are a great many rovibrational eigenstates to compute, and a very high density of states. Consequently, very few previous rovibrational state calculations for Ar3 may be found in the current literature—and only for the lowest-lying rotational excitations.

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

    PubMed

    Wu, Na; Willner, Itamar

    2017-01-26

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

  2. Metal dimer and trimer within spherical carbon cage

    NASA Astrophysics Data System (ADS)

    Kato, Tatsuhisa

    2007-07-01

    C 80 fulleren cage can be used to realize confinement with the highest possible icosahedral ( Ih) symmetry. As examples, La 2@C 80 and Sc 3C 2@C 80 are molecules in which metal dimer and trimer are encapsulated within the C 80 cage. They are recently purified in the substantial amount by using a high performance liquid chromatograph (HPLC), and studied by spectroscopy and X-ray diffraction. The confinement of the metal cluster with the high symmetry ( Ih) cage is reflected in their specific potential of the intra-molecular rotation for the cluster. The result of electron spin resonance (ESR) measurements indicates that the intra-molecular potential is modified by the chemical modification of the C 80 cage as well as by the injection of an excess electron.

  3. Giant local circular dichroism within an asymmetric plasmonic nanoparticle trimer.

    PubMed

    Wang, Hancong; Li, Zhipeng; Zhang, Han; Wang, Peijie; Wen, Shuangchun

    2015-02-03

    We investigated the near-field response in silver nanoparticle aggregates to the excitation of circular polarized light. In a right-angle trimer system, the local field intensity excited by right-hand circularly polarized light is almost one thousand times larger than the left-hand case. By analyzing the polarization and phase of the local field in plasmonic hotspots, we found this local circular dichroism is originated from the near-field interference excited by orthogonal polarized incident lights. The local circular dichroism can be tuned by the rotation of the third particle, the interparticle distance, and the dielectric environment. This phenomenon could also widely exist in more complicated nanoaggregates. These findings would benefit for resolving light handedness, and enhancing circular dichroism and optical activity.

  4. Understanding Magnetic Trimer Interactions in (Cr,Mn)-Substituted Graphene

    NASA Astrophysics Data System (ADS)

    Haraldsen, Jason T.; Crook, Charles B.; Houchins, Gregory; Zhu, Jian-Xin; Constantin, Costel; Balatsky, Alexander V.

    We investigate the magnetic interactions within a graphene superlattice produced by three directly substituted transition-metal atoms (specifically chromium and manganese). Using a first principles approach, we calculate the electronic and magnetic properties for this system assuming an equilateral trimer configuration with varying atomic separations. Through an examination of the electronic band structure, density of states, and Millikan populations (magnetic moment) for each atom, we find that the presence of magnetic impurities establishes a distinct magnetic moment in the graphene lattice, where the interactions are dependent on the spatial and magnetic characteristic between the magnetic atoms and the carbon atoms, which leads to either ferromagnetic or antiferromagnetic behavior. Furthermore, we use magnetization mapping to show that the substituted atoms induce an overall magnetic moment in the graphene lattice, which may help guide the discussion on spintronic graphene. JTH, CBC, GH, and AVB acknowledge support from the Institute for Materials Science via the United States Basic Energy Sciences (E304).

  5. Localization and coherent states in a quantum DNLS trimer

    NASA Astrophysics Data System (ADS)

    Martínez-Galicia, Ricardo; Panayotaros, Panayotis

    2016-11-01

    We compare quantum states obtained from the integration of exact and approximate evolution equations for a quantized discrete nonlinear Schrödinger system (DNLS) with three lattice sites (trimer). The initial conditions are Glauber coherent states, and their projections to subspaces with a definite number of particles, and we are especially interested in coherent states that correspond to classical states that are in the neighborhood of breather solutions of the classical system. The breathers are well defined periodic orbits of the classical DNLS that we heuristically view as examples of spatially localized solutions. The two evolution equations give converging results in the subspaces with an increasing number of particles. This is no longer the case for normalized projections of Glauber states, where we see that the distance between the quantum states obtained by the exact and approximate equations shows recurrence phenomena that depend on the number of quanta and on the dynamical properties of the classical trajectory.

  6. Stoichiometry of Envelope Glycoprotein Trimers in the Entry of Human Immunodeficiency Virus Type 1

    PubMed Central

    Yang, Xinzhen; Kurteva, Svetla; Ren, Xinping; Lee, Sandra; Sodroski, Joseph

    2005-01-01

    The human immunodeficiency virus type 1 (HIV-1) envelope glycoproteins (Envs) function as a trimer, mediating virus entry by promoting the fusion of the viral and target cell membranes. HIV-1 Env trimers induce membrane fusion through a pH-independent pathway driven by the interaction between an Env trimer and its cellular receptors, CD4 and CCR5/CXCR4. We studied viruses with mixed heterotrimers of wild-type and dominant-negative Envs to determine the number (T) of Env trimers required for HIV-1 entry. To our surprise, we found that a single Env trimer is capable of supporting HIV-1 entry; i.e., T = 1. A similar approach was applied to investigate the entry stoichiometry of envelope glycoproteins from amphotropic murine leukemia virus (A-MLV), avian sarcoma/leukosis virus type A (ASLV-A), and influenza A virus. When pseudotyped on HIV-1 virions, the A-MLV and ASLV-A Envs also exhibit a T = 1 entry stoichiometry. In contrast, eight to nine influenza A virus hemagglutinin trimers function cooperatively to achieve membrane fusion and virus entry, using a pH-dependent pathway. The different entry requirements for cooperativity among Env trimers for retroviruses and influenza A virus may influence viral strategies for replication and evasion of the immune system. PMID:16160141

  7. Crystal structure and molecular imaging of the Nav channel β3 subunit indicates a trimeric assembly.

    PubMed

    Namadurai, Sivakumar; Balasuriya, Dilshan; Rajappa, Rajit; Wiemhöfer, Martin; Stott, Katherine; Klingauf, Jurgen; Edwardson, J Michael; Chirgadze, Dimitri Y; Jackson, Antony P

    2014-04-11

    The vertebrate sodium (Nav) channel is composed of an ion-conducting α subunit and associated β subunits. Here, we report the crystal structure of the human β3 subunit immunoglobulin (Ig) domain, a functionally important component of Nav channels in neurons and cardiomyocytes. Surprisingly, we found that the β3 subunit Ig domain assembles as a trimer in the crystal asymmetric unit. Analytical ultracentrifugation confirmed the presence of Ig domain monomers, dimers, and trimers in free solution, and atomic force microscopy imaging also detected full-length β3 subunit monomers, dimers, and trimers. Mutation of a cysteine residue critical for maintaining the trimer interface destabilized both dimers and trimers. Using fluorescence photoactivated localization microscopy, we detected full-length β3 subunit trimers on the plasma membrane of transfected HEK293 cells. We further show that β3 subunits can bind to more than one site on the Nav 1.5 α subunit and induce the formation of α subunit oligomers, including trimers. Our results suggest a new and unexpected role for the β3 subunits in Nav channel cross-linking and provide new structural insights into some pathological Nav channel mutations.

  8. Trimer Enhancement Mutation Effects on HIV-1 Matrix Protein Binding Activities

    PubMed Central

    Alfadhli, Ayna; Mack, Andrew; Ritchie, Christopher; Cylinder, Isabel; Harper, Logan; Tedbury, Philip R.; Freed, Eric O.

    2016-01-01

    ABSTRACT The HIV-1 matrix (MA) protein is the amino-terminal domain of the HIV-1 precursor Gag (Pr55Gag) protein. MA binds to membranes and RNAs, helps transport Pr55Gag proteins to virus assembly sites at the plasma membranes of infected cells, and facilitates the incorporation of HIV-1 envelope (Env) proteins into virions by virtue of an interaction with the Env protein cytoplasmic tails (CTs). MA has been shown to crystallize as a trimer and to organize on membranes in hexamer lattices. MA mutations that localize to residues near the ends of trimer spokes have been observed to impair Env protein assembly into virus particles, and several of these are suppressed by the 62QR mutation at the hubs of trimer interfaces. We have examined the binding activities of wild-type (WT) MA and 62QR MA variants and found that the 62QR mutation stabilized MA trimers but did not alter the way MA proteins organized on membranes. Relative to WT MA, the 62QR protein showed small effects on membrane and RNA binding. However, 62QR proteins bound significantly better to Env CTs than their WT counterparts, and CT binding efficiencies correlated with trimerization efficiencies. Our data suggest a model in which multivalent binding of trimeric HIV-1 Env proteins to MA trimers contributes to the process of Env virion incorporation. IMPORTANCE The HIV-1 Env proteins assemble as trimers, and incorporation of the proteins into virus particles requires an interaction of Env CT domains with the MA domains of the viral precursor Gag proteins. Despite this knowledge, little is known about the mechanisms by which MA facilitates the virion incorporation of Env proteins. To help elucidate this process, we examined the binding activities of an MA mutant that stabilizes MA trimers. We found that the mutant proteins organized similarly to WT proteins on membranes, and that mutant and WT proteins revealed only slight differences in their binding to RNAs or lipids. However, the mutant proteins showed

  9. Gas field ion source current stability for trimer and single atom terminated W(111) tips

    SciTech Connect

    Urban, Radovan; Wolkow, Robert A.; Pitters, Jason L.

    2012-06-25

    Tungsten W(111) oriented trimer-terminated tips as well as single atom tips, fabricated by a gas and field assisted etching and evaporation process, were investigated with a view to scanning ion microscopy and ion beam writing applications. In particular, ion current stability was studied for helium and neon imaging gases. Large ion current fluctuations from individual atomic sites were observed when a trimer-terminated tip was used for the creation of neon ion beam. However, neon ion current was stable when a single atom tip was employed. No such current oscillations were observed for either a trimer or a single atom tip when imaged with helium.

  10. HIV-1 VACCINES. HIV-1 neutralizing antibodies induced by native-like envelope trimers.

    PubMed

    Sanders, Rogier W; van Gils, Marit J; Derking, Ronald; Sok, Devin; Ketas, Thomas J; Burger, Judith A; Ozorowski, Gabriel; Cupo, Albert; Simonich, Cassandra; Goo, Leslie; Arendt, Heather; Kim, Helen J; Lee, Jeong Hyun; Pugach, Pavel; Williams, Melissa; Debnath, Gargi; Moldt, Brian; van Breemen, Mariëlle J; Isik, Gözde; Medina-Ramírez, Max; Back, Jaap Willem; Koff, Wayne C; Julien, Jean-Philippe; Rakasz, Eva G; Seaman, Michael S; Guttman, Miklos; Lee, Kelly K; Klasse, Per Johan; LaBranche, Celia; Schief, William R; Wilson, Ian A; Overbaugh, Julie; Burton, Dennis R; Ward, Andrew B; Montefiori, David C; Dean, Hansi; Moore, John P

    2015-07-10

    A challenge for HIV-1 immunogen design is the difficulty of inducing neutralizing antibodies (NAbs) against neutralization-resistant (tier 2) viruses that dominate human transmissions. We show that a soluble recombinant HIV-1 envelope glycoprotein trimer that adopts a native conformation, BG505 SOSIP.664, induced NAbs potently against the sequence-matched tier 2 virus in rabbits and similar but weaker responses in macaques. The trimer also consistently induced cross-reactive NAbs against more sensitive (tier 1) viruses. Tier 2 NAbs recognized conformational epitopes that differed between animals and in some cases overlapped with those recognized by broadly neutralizing antibodies (bNAbs), whereas tier 1 responses targeted linear V3 epitopes. A second trimer, B41 SOSIP.664, also induced a strong autologous tier 2 NAb response in rabbits. Thus, native-like trimers represent a promising starting point for the development of HIV-1 vaccines aimed at inducing bNAbs.

  11. Monte Carlo and Exact Diagonalization of Copper (II) Trimer Spin Frustrated Systems

    NASA Astrophysics Data System (ADS)

    Egido-Betancourt, Hailey X.; Ter Haar, Leonard W.; Varney, Christopher N.

    We discuss the use and importance of trimer-based systems because of the spin frustration that may arise within extended lattices comprised of trimers. The possible intra- and inter-trimer exchange pathways they posses due to interconnections are evaluated using density functional theory (DFT) to identify the optimal structures that may be used in designing extended lattices. As example, trinuclear Cu36+ cores with each pair of copper atoms bridged by carboxylate ligands have three-fold symmetry. As trimers these structures have the potential to be modeled as a frustrated quantum spin-1/2 system. To analyze the magnetic ground state and topological properties, we utilize exact diagonalization on small clusters and compare with Monte Carlo simulations for a range of system sizes. Research reported in this abstract was supported by UWF NIH MARC U-STAR 1T34GM110517-01.

  12. The Nature of Bonding between Argon and Mixed Gold-Silver Trimers.

    PubMed

    Shayeghi, Armin; Johnston, Roy L; Rayner, David M; Schäfer, Rolf; Fielicke, André

    2015-09-01

    The controversial nature of chemical bonding between noble gases and noble metals is addressed. Experimental evidence of exceptionally strong Au-Ar bonds in Ar complexes of mixed Au-Ag trimers is presented. IR spectra reveal an enormous influence of the attached Ar atoms on vibrational modes, particularly in Au-rich trimers, where Ar atoms are heavily involved owing to a relativistically enhanced covalency. In Ag-rich trimers, vibrational transitions of the metal framework predominate, indicating a pure electrostatic character of the Ag-Ar bonds. The experimental findings are analyzed by means of DFT calculations, which show how the relativistic differences between Au and Ag are manifested in stronger Au-Ar binding energies. Because of the ability to vary composition and charge distribution, the trimers serve as ideal model systems to study the chemical nature of the bonding of noble gases to closed-shell systems containing gold.

  13. Thiamine diphosphate binds to intermediates in the assembly of adenovirus fiber knob trimers in Escherichia coli.

    PubMed

    Schulz, Ryan; Zhang, Yian-Biao; Liu, Chang-Jun; Freimuth, Paul

    2007-12-01

    Assembly of the adenovirus (Ad) homotrimeric fiber protein is nucleated by its C-terminal knob domain, which itself can trimerize when expressed as a recombinant protein fragment. The non-interlocked, globular structure of subunits in the knob trimer implies that trimers assemble from prefolded monomers through a dimer intermediate, but these intermediates have not been observed and the mechanism of assembly therefore remains uncharacterized. Here we report that expression of the Ad serotype 2 (Ad2) knob was toxic for thi- strains of Escherichia coli, which are defective in de novo synthesis of thiamine (vitamin B1). Ad2 knob trimers isolated from a thi+ strain copurified through multiple chromatography steps with a small molecule of mass equivalent to that of thiamine diphosphate (ThDP). Mutant analysis did not implicate any specific site for ThDP binding. Our results suggest that ThDP may associate with assembly intermediates and become trapped in assembled trimers, possibly within one of several large cavities that are partially solvent-accessible or buried completely within the trimer interior.

  14. Presenting native-like trimeric HIV-1 antigens with self-assembling nanoparticles

    PubMed Central

    He, Linling; de Val, Natalia; Morris, Charles D.; Vora, Nemil; Thinnes, Therese C.; Kong, Leopold; Azadnia, Parisa; Sok, Devin; Zhou, Bin; Burton, Dennis R.; Wilson, Ian A; Nemazee, David; Ward, Andrew B.; Zhu, Jiang

    2016-01-01

    Structures of BG505 SOSIP.664 trimer in complex with broadly neutralizing antibodies (bNAbs) have revealed the critical role of trimeric context for immune recognition of HIV-1. Presentation of trimeric HIV-1 antigens on nanoparticles may thus provide promising vaccine candidates. Here we report the rational design, structural analysis and antigenic evaluation of HIV-1 trimer-presenting nanoparticles. We first demonstrate that both V1V2 and gp120 can be presented in native-like trimeric conformations on nanoparticles. We then design nanoparticles presenting various forms of stabilized gp140 trimer based on ferritin and a large, 60-meric E2p that displays 20 spikes mimicking virus-like particles (VLPs). Particle assembly is confirmed by electron microscopy (EM), while antigenic profiles are generated using representative bNAbs and non-NAbs. Lastly, we demonstrate high-yield gp140 nanoparticle production and robust stimulation of B cells carrying cognate VRC01 receptors by gp120 and gp140 nanoparticles. Together, our study provides an arsenal of multivalent immunogens for HIV-1 vaccine development. PMID:27349934

  15. Domain annotation of trimeric autotransporter adhesins—daTAA

    PubMed Central

    Szczesny, Pawel; Lupas, Andrei

    2008-01-01

    Motivation: Trimeric autotransporter adhesins (TAAs), such as Yersinia YadA, Neisseria NadA, Moraxella UspAs, Haemophilus Hia and Bartonella BadA, are important pathogenicity factors of proteobacteria. Their high sequence diversity and distinct mosaic-like structure lead to difficulties in the annotation of their sequences. These stem from the large number of short repeats, the presence of compositionally unusual coiled-coils, fuzzy domain boundaries and regions of seemingly low sequence complexity. Results: We have developed a workflow, named daTAA, for the accurate domain annotation of TAAs. Its core consists of manually curated alignments and of knowledge-based rules that enhance assignments made by sequence similarity. Compared to general domain annotation servers such as PFAM, daTAA captures more domains and provides more sensitive domain detection, as well as integrated and detailed coiled-coil assignments. Availability: The daTAA server is freely accessible at http://toolkit.tuebingen.mpg.de/dataa Contact: andrei.lupas@tuebingen.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:18397894

  16. Optimal efficiency of quantum transport in a disordered trimer.

    PubMed

    Giusteri, Giulio G; Celardo, G Luca; Borgonovi, Fausto

    2016-03-01

    Disordered quantum networks, such as those describing light-harvesting complexes, are often characterized by the presence of peripheral ringlike structures, where the excitation is initialized, and inner structures and reaction centers (RCs), where the excitation is trapped and transferred. The peripheral rings often display distinguished coherent features: Their eigenstates can be separated, with respect to the transfer of excitation, into two classes of superradiant and subradiant states. Both are important to optimize transfer efficiency. In the absence of disorder, superradiant states have an enhanced coupling strength to the RC, while the subradiant ones are basically decoupled from it. Static on-site disorder induces a coupling between subradiant and superradiant states, thus creating an indirect coupling to the RC. The problem of finding the optimal transfer conditions, as a function of both the RC energy and the disorder strength, is very complex even in the simplest network, namely, a three-level system. In this paper we analyze such trimeric structure, choosing as the initial condition an excitation on a subradiant state, rather than the more common choice of an excitation localized on a single site. We show that, while the optimal disorder is of the order of the superradiant coupling, the optimal detuning between the initial state and the RC energy strongly depends on system parameters: When the superradiant coupling is much larger than the energy gap between the superradiant and the subradiant levels, optimal transfer occurs if the RC energy is at resonance with the subradiant initial state, whereas we find an optimal RC energy at resonance with a virtual dressed state when the superradiant coupling is smaller than or comparable to the gap. The presence of dynamical noise, which induces dephasing and decoherence, affects the resonance structure of energy transfer producing an additional incoherent resonance peak, which corresponds to the RC energy being

  17. Optimal efficiency of quantum transport in a disordered trimer

    NASA Astrophysics Data System (ADS)

    Giusteri, Giulio G.; Celardo, G. Luca; Borgonovi, Fausto

    2016-03-01

    Disordered quantum networks, such as those describing light-harvesting complexes, are often characterized by the presence of peripheral ringlike structures, where the excitation is initialized, and inner structures and reaction centers (RCs), where the excitation is trapped and transferred. The peripheral rings often display distinguished coherent features: Their eigenstates can be separated, with respect to the transfer of excitation, into two classes of superradiant and subradiant states. Both are important to optimize transfer efficiency. In the absence of disorder, superradiant states have an enhanced coupling strength to the RC, while the subradiant ones are basically decoupled from it. Static on-site disorder induces a coupling between subradiant and superradiant states, thus creating an indirect coupling to the RC. The problem of finding the optimal transfer conditions, as a function of both the RC energy and the disorder strength, is very complex even in the simplest network, namely, a three-level system. In this paper we analyze such trimeric structure, choosing as the initial condition an excitation on a subradiant state, rather than the more common choice of an excitation localized on a single site. We show that, while the optimal disorder is of the order of the superradiant coupling, the optimal detuning between the initial state and the RC energy strongly depends on system parameters: When the superradiant coupling is much larger than the energy gap between the superradiant and the subradiant levels, optimal transfer occurs if the RC energy is at resonance with the subradiant initial state, whereas we find an optimal RC energy at resonance with a virtual dressed state when the superradiant coupling is smaller than or comparable to the gap. The presence of dynamical noise, which induces dephasing and decoherence, affects the resonance structure of energy transfer producing an additional incoherent resonance peak, which corresponds to the RC energy being

  18. Perinatal toxicity and carcinogenicity studies of styrene-acrylonitrile trimer, a ground water contaminant.

    PubMed

    Behl, Mamta; Elmore, Susan A; Malarkey, David E; Hejtmancik, Milton R; Gerken, Diane K; Chhabra, Rajendra S

    2013-12-06

    Styrene acrylonitrile (SAN) trimer is a by-product in the production of acrylonitrile styrene plastics. Following a report of a childhood cancer cluster in the Toms River section of Dover Township, New Jersey, SAN Trimer was identified as one of the groundwater contaminants at Reich Farm Superfund site in the township. The contaminants from the Reich Farm site's ground water plume impacted two wells at the Parkway well field. The National Toxicology Program (NTP) studied the toxicity and carcinogenicity of SAN Trimer in rats exposed during their perinatal developmental period and adulthood. The chronic toxicity and carcinogenicity studies in F344/N rats were preceded by 7- and 18-week perinatal toxicity studies to determine the exposure concentrations for the 2-year studies. Subsequently, Fisher 344 pregnant dams were exposed to SAN Trimer containing diet at 400, 800, or 1600ppm concentrations during gestation, nursing and weaning periods of offspring followed by two year of adult exposures to both male and female pups. There was no statistically significant evidence of carcinogenic activity following SAN-Trimer exposure; however, rare neoplasms in the brain and spinal cord were observed in males and to lesser extent in female rats. These incidences were considered within the range of historical background in the animal model used in the current studies. Therefore, the presence of a few rarely occurring CNS tumors in the treated groups were not judged to be associated with the SAN Trimer exposure. The major finding was a dose-related peripheral neuropathy associated with the sciatic nerves in females and spinal nerve roots in males and females thereby suggesting that SAN Trimer is potentially a nervous system toxicant.

  19. Perinatal Toxicity and Carcinogenicity Studies of Styrene –Acrylonitrile Trimer, A Ground Water Contaminant

    PubMed Central

    Behl, Mamta; Elmore, Susan A.; Malarkey, David E.; Hejtmancik, Milton R.; Gerken, Diane K.; Chhabra, Rajendra S.

    2015-01-01

    Styrene Acrylonitrile (SAN) Trimer is a by-product in the production of acrylonitrile styrene plastics. Following a report of a childhood cancer cluster in the Toms River section of Dover Township, New Jersey, SAN Trimer was identified as one of the groundwater contaminants at Reich Farm Superfund site in the township. The contaminants from the Reich Farm site’s ground water plume impacted two wells at the Parkway well field. The National Toxicology Program (NTP) studied the toxicity and carcinogenicity of SAN Trimer in rats exposed during their perinatal developmental period and adulthood. The chronic toxicity and carcinogenicity studies in F344/N rats were preceded by 7- and 18-week perinatal toxicity studies to determine the exposure concentrations for the 2-year studies. Subsequently, Fisher 344 pregnant dams were exposed to SAN Trimer containing diet at 400, 800, or 1600 ppm concentrations during gestation, nursing and weaning periods of offspring followed by two year of adult exposures to both male and female pups. There was no statistically significant evidence of carcinogenic activity following SAN-Trimer exposure; however, rare neoplasms in the brain and spinal cord were observed in males and to lesser extent in female rats. These incidences were considered within the range of historical background in the animal model used in the current studies. Therefore, the presence of a few rarely occurring CNS tumors in the treated groups were not judged to be associated with the SAN Trimer exposure. The major finding was a dose-related peripheral neuropathy associated with the sciatic nerves in females and spinal nerve roots in males and females thereby suggesting that SAN trimer is potentially a nervous system toxicant. PMID:24060431

  20. Murine Antibody Responses to Cleaved Soluble HIV-1 Envelope Trimers Are Highly Restricted in Specificity

    PubMed Central

    Hu, Joyce K.; Crampton, Jordan C.; Cupo, Albert; Ketas, Thomas; van Gils, Marit J.; Sliepen, Kwinten; de Taeye, Steven W.; Sok, Devin; Ozorowski, Gabriel; Deresa, Isaiah; Stanfield, Robyn; Ward, Andrew B.; Burton, Dennis R.; Klasse, Per Johan; Sanders, Rogier W.; Moore, John P.

    2015-01-01

    ABSTRACT Generating neutralizing antibodies (nAbs) is a major goal of many current HIV-1 vaccine efforts. To be of practical value, these nAbs must be both potent and cross-reactive in order to be capable of preventing the transmission of the highly diverse and generally neutralization resistant (Tier-2) HIV-1 strains that are in circulation. The HIV-1 envelope glycoprotein (Env) spike is the only target for nAbs. To explore whether Tier-2 nAbs can be induced by Env proteins, we immunized conventional mice with soluble BG505 SOSIP.664 trimers that mimic the native Env spike. Here, we report that it is extremely difficult for murine B cells to recognize the Env epitopes necessary for inducing Tier-2 nAbs. Thus, while trimer-immunized mice raised Env-binding IgG Abs and had high-quality T follicular helper (Tfh) cell and germinal center (GC) responses, they did not make BG505.T332N nAbs. Epitope mapping studies showed that Ab responses in mice were specific to areas near the base of the soluble trimer. These areas are not well shielded by glycans and likely are occluded on virions, which is consistent with the lack of BG505.T332N nAbs. These data inform immunogen design and suggest that it is useful to obscure nonneutralizing epitopes presented on the base of soluble Env trimers and that the glycan shield of well-formed HIV Env trimers is virtually impenetrable for murine B cell receptors (BCRs). IMPORTANCE Human HIV vaccine efficacy trials have not generated meaningful neutralizing antibodies to circulating HIV strains. One possible hindrance has been the lack of immunogens that properly mimic the native conformation of the HIV envelope trimer protein. Here, we tested the first generation of soluble, native-like envelope trimer immunogens in a conventional mouse model. We attempted to generate neutralizing antibodies to neutralization-resistant circulating HIV strains. Various vaccine strategies failed to induce neutralizing antibodies to a neutralization

  1. Tunable trimers: Using temperature and pressure to control luminescent emission in gold(I) pyrazolate-based trimers

    DOE PAGES

    Woodall, Christopher H.; Fuertes, Sara; Beavers, Christine M.; ...

    2014-10-21

    A systematic investigation into the relationship between the solid-state luminescence and the intermolecular Au∙∙∙Au interactions in a series of pyrazolate-based gold(I) trimers; tris(μ2-pyrazolato-N,N')-tri-gold(I) (1), tris(μ2-3,4,5-trimethylpyrazolato-N,N')-tri-gold(I) (2), tris(μ2-3-methyl-5-phenylpyrazolato-N,N')-tri-gold(I) (3) and tris(μ2-3,5-diphenylpyrazolato-N,N')-tri-gold(I) (4) has been carried out using variable temperature and high pressure X-ray crystallography, solid-state emission spectroscopy, Raman spectroscopy and computational techniques. Single-crystal X-ray studies show that there is a significant reduction in the intertrimer Au∙∙∙Au distances both with decreasing temperature and increasing pressure. In the four complexes, the reduction in temperature from 293 to 100 K is accompanied by a reduction in the shortest intermolecular Au∙∙∙Au contacts of between 0.04more » and 0.08 Å. The solid-state luminescent emission spectra of 1 and 2 display a red shift with decreasing temperature or increasing pressure. Compound 3 does not emit under ambient conditions but displays increasingly red-shifted luminescence upon cooling or compression. Compound 4 remains emissionless, consistent with the absence of intermolecular Au∙∙∙Au interactions. The largest pressure induced shift in emission is observed in 2 with a red shift of approximately 630 cm-1 per GPa between ambient and 3.80 GPa. The shifts in all the complexes can be correlated with changes in Au∙∙∙Au distance observed by diffraction.« less

  2. Tunable trimers: Using temperature and pressure to control luminescent emission in gold(I) pyrazolate-based trimers

    SciTech Connect

    Woodall, Christopher H.; Fuertes, Sara; Beavers, Christine M.; Hatcher, Lauren E.; Parlett, Andrew; Shepherd, Helena J.; Christensen, Jeppe; Teat, Simon J.; Intissar, Mourad; Rodrigue-Witchel, Alexandre; Suffren, Yan; Reber, Christian; Hendon, Christopher H.; Tiana, Davide; Walsh, Aron; Raithby, Paul R.

    2014-10-21

    A systematic investigation into the relationship between the solid-state luminescence and the intermolecular Au∙∙∙Au interactions in a series of pyrazolate-based gold(I) trimers; tris(μ2-pyrazolato-N,N')-tri-gold(I) (1), tris(μ2-3,4,5-trimethylpyrazolato-N,N')-tri-gold(I) (2), tris(μ2-3-methyl-5-phenylpyrazolato-N,N')-tri-gold(I) (3) and tris(μ2-3,5-diphenylpyrazolato-N,N')-tri-gold(I) (4) has been carried out using variable temperature and high pressure X-ray crystallography, solid-state emission spectroscopy, Raman spectroscopy and computational techniques. Single-crystal X-ray studies show that there is a significant reduction in the intertrimer Au∙∙∙Au distances both with decreasing temperature and increasing pressure. In the four complexes, the reduction in temperature from 293 to 100 K is accompanied by a reduction in the shortest intermolecular Au∙∙∙Au contacts of between 0.04 and 0.08 Å. The solid-state luminescent emission spectra of 1 and 2 display a red shift with decreasing temperature or increasing pressure. Compound 3 does not emit under ambient conditions but displays increasingly red-shifted luminescence upon cooling or compression. Compound 4 remains emissionless, consistent with the absence of intermolecular Au∙∙∙Au interactions. The largest pressure induced shift in emission is observed in 2 with a red shift of approximately 630 cm-1 per GPa between ambient and 3.80 GPa. The shifts in all the complexes can be correlated with changes in Au∙∙∙Au distance observed by diffraction.

  3. Tunable Trimers: Using Temperature and Pressure to Control Luminescent Emission in Gold(I) Pyrazolate-Based Trimers

    PubMed Central

    Woodall, Christopher H; Fuertes, Sara; Beavers, Christine M; Hatcher, Lauren E; Parlett, Andrew; Shepherd, Helena J; Christensen, Jeppe; Teat, Simon J; Intissar, Mourad; Rodrigue-Witchel, Alexandre; Suffren, Yan; Reber, Christian; Hendon, Christopher H; Tiana, Davide; Walsh, Aron; Raithby, Paul R

    2014-01-01

    A systematic investigation into the relationship between the solid-state luminescence and the intermolecular Au⋅⋅⋅Au interactions in a series of pyrazolate-based gold(I) trimers; tris(μ2-pyrazolato-N,N′)-tri-gold(I) (1), tris(μ2-3,4,5- trimethylpyrazolato-N,N′)-tri-gold(I) (2), tris(μ2-3-methyl-5-phenylpyrazolato-N,N′)-tri-gold(I) (3) and tris(μ2-3,5-diphenylpyrazolato-N,N′)-tri-gold(I) (4) has been carried out using variable temperature and high pressure X-ray crystallography, solid-state emission spectroscopy, Raman spectroscopy and computational techniques. Single-crystal X-ray studies show that there is a significant reduction in the intertrimer Au⋅⋅⋅Au distances both with decreasing temperature and increasing pressure. In the four complexes, the reduction in temperature from 293 to 100 K is accompanied by a reduction in the shortest intermolecular Au⋅⋅⋅Au contacts of between 0.04 and 0.08 Å. The solid-state luminescent emission spectra of 1 and 2 display a red shift with decreasing temperature or increasing pressure. Compound 3 does not emit under ambient conditions but displays increasingly red-shifted luminescence upon cooling or compression. Compound 4 remains emissionless, consistent with the absence of intermolecular Au⋅⋅⋅Au interactions. The largest pressure induced shift in emission is observed in 2 with a red shift of approximately 630 cm−1 per GPa between ambient and 3.80 GPa. The shifts in all the complexes can be correlated with changes in Au⋅⋅⋅Au distance observed by diffraction. PMID:25331304

  4. A liquid crystals modulated optical tunable filter based on Fano resonance of Au nanorod trimer

    NASA Astrophysics Data System (ADS)

    Xin, Huan Peng; Liu, Fei; Ren, Guang Jun; Zhao, Hong Liang; Yao, Jian Quan

    2017-04-01

    We theoretically studied the liquid crystals modulated optical tunable filter based on Fano resonance of Au nanorod trimer. Plasmonic nanorods can support Fano resonances, where the line shape characteristics are controlled by the geometry of nanorods. Here a polarization-dependent Au nanorod trimer was designed, where the three nanorods have the same geometric parameters and form a C-shape. When the plasmon modes of the longitudinal nanorod and the two transverse nanorods couple at resonance wavelength, a Fano resonance occurs. Due to liquid crystals can change the polarization direction of light, the transmission spectra of Au nanorod trimer can be switched on and off with different phases of liquid crystals when incident light passes through liquid crystals before reaching the Au nanorod trimer. Furthermore, filter optical characteristics are highly tunable by changing the thicknesses of Au nanorod trimer and its coating layer. Fano resonances show a large light extinction in periodic array of assembled nanorods, which can be used in optical tunable filter and optical switch.

  5. Structural and Immunogenicity Studies of a Cleaved, Stabilized Envelope Trimer Derived from Subtype A HIV-1

    PubMed Central

    Kang, Yun (Kenneth); Andjelic, Sofija; Binley, James M.; Crooks, Emma T.; Franti, Michael; Iyer, Sai Prasad N.; Donovan, Gerald P.; Dey, Antu K.; Zhu, Ping; Roux, Kenneth H.; Durso, Robert J.; Parsons, Thomas F.; Maddon, Paul J.; Moore, John P.; Olson, William C.

    2015-01-01

    SOSIP gp140 trimers represent a soluble, stabilized, proteolytically cleaved form of the HIV-1 envelope (Env) glycoproteins. SOSIP gp140 derived from a subtype A HIV-1 isolate, KNH1144, forms exceptionally stable trimers that resemble virion-associated Env in antigenicity and topology. Here, we used electron microscopy to demonstrate that KNH1144 SOSIP gp140 trimers bound three soluble CD4 molecules in a symmetrical orientation similar to that seen for native Env. We compared the immunogenicities of KNH1144 SOSIP gp140 trimers and gp120 monomers in rabbits and found that the trimers were superior at eliciting neutralizing antibodies (NAbs) to homologous virus as well as neutralization-sensitive subtype B and C viruses. The NAb specificities for SOSIP antisera mapped in part to the CD4 binding site on gp120. We also observed adjuvant-dependent induction of antibodies to the residual levels of host cell proteins (HCPs) contained in the purified Env preparations. When present, HCP antibodies enhanced pseudovirus infection. Our findings are relevant for the further development of Env-based vaccines for HIV-1. PMID:19567243

  6. Structural and immunogenicity studies of a cleaved, stabilized envelope trimer derived from subtype A HIV-1.

    PubMed

    Kang, Yun Kenneth; Andjelic, Sofija; Binley, James M; Crooks, Emma T; Franti, Michael; Iyer, Sai Prasad N; Donovan, Gerald P; Dey, Antu K; Zhu, Ping; Roux, Kenneth H; Durso, Robert J; Parsons, Thomas F; Maddon, Paul J; Moore, John P; Olson, William C

    2009-08-13

    SOSIP gp140 trimers represent a soluble, stabilized, proteolytically cleaved form of the HIV-1 envelope (Env) glycoproteins. SOSIP gp140 derived from a subtype A HIV-1 isolate, KNH1144, forms exceptionally stable trimers that resemble virion-associated Env in antigenicity and topology. Here, we used electron microscopy to demonstrate that KNH1144 SOSIP gp140 trimers bound three soluble CD4 molecules in a symmetrical orientation similar to that seen for native Env. We compared the immunogenicities of KNH1144 SOSIP gp140 trimers and gp120 monomers in rabbits and found that the trimers were superior at eliciting neutralizing antibodies (NAbs) to homologous virus as well as neutralization-sensitive subtype B and C viruses. The NAb specificities for SOSIP antisera mapped in part to the CD4 binding site on gp120. We also observed adjuvant-dependent induction of antibodies to the residual levels of host cell proteins (HCPs) contained in the purified Env preparations. When present, HCP antibodies enhanced pseudovirus infection. Our findings are relevant for the further development of Env-based vaccines for HIV-1.

  7. Novel Anticancer Agents Based on Targeting the Trimer Interface of the PRL Phosphatase.

    PubMed

    Bai, Yunpeng; Yu, Zhi-Hong; Liu, Sijiu; Zhang, Lujuan; Zhang, Ruo-Yu; Zeng, Li-Fan; Zhang, Sheng; Zhang, Zhong-Yin

    2016-08-15

    Phosphatase of regenerating liver (PRL) oncoproteins are phosphatases overexpressed in numerous types of human cancer. Elevated levels of PRL associate with metastasis and poor clinical outcomes. In principle, PRL phosphatases offer appealing therapeutic targets, but they remain underexplored due to the lack of specific chemical probes. In this study, we address this issue by exploiting a unique property of PRL phosphatases, namely, that they may function as homotrimers. Starting from a sequential structure-based virtual screening and medicinal chemistry strategy, we identified Cmpd-43 and several analogs that disrupt PRL1 trimerization. Biochemical and structural analyses demonstrate that Cmpd-43 and its close analogs directly bind the PRL1 trimer interface and obstruct PRL1 trimerization. Cmpd-43 also specifically blocks the PRL1-induced cell proliferation and migration through attenuation of both ERK1/2 and Akt activity. Importantly, Cmpd-43 exerted potent anticancer activity both in vitro and in vivo in a murine xenograft model of melanoma. Our results validate a trimerization-dependent signaling mechanism for PRL and offer proof of concept for trimerization inhibitors as candidate therapeutics to treat PRL-driven cancers. Cancer Res; 76(16); 4805-15. ©2016 AACR.

  8. Is It Beneficial for the Major Photosynthetic Antenna Complex of Plants To Form Trimers?

    PubMed

    Janik, Ewa; Bednarska, Joanna; Zubik, Monika; Sowinski, Karol; Luchowski, Rafal; Grudzinski, Wojciech; Gruszecki, Wieslaw I

    2015-07-09

    The process of primary electric charge separation in photosynthesis takes place in the reaction centers, but photosynthesis can operate efficiently and fluently due to the activity of several pigment-protein complexes called antenna, which absorb light quanta and transfer electronic excitations toward the reaction centers. LHCII is the major photosynthetic pigment-protein antenna complex of plants and appears in the trimeric form. Several recent reports point to trimeric organization of LHCII as a key factor responsible for the chloroplast architecture via stabilization of granal organization of the thylakoid membranes. In the present work, we address the question of whether such an organization could also directly influence the antenna properties of this pigment-protein complex. Chlorophyll fluorescence analysis reveals that excitation energy transfer in LHCII is substantially more efficient in trimers and dissipative energy losses are higher in monomers. It could be concluded that trimers are exceptionally well suited to perform the antenna function. Possibility of fine regulation of the photosynthetic antenna function via the LHCII trimer-monomer transition is also discussed, based on the fluorescence lifetime analysis in a single chloroplast.

  9. Unexpected Trimerization of Pyrazine in the Coordination Sphere of Low-Valent Titanocene Fragments.

    PubMed

    Jung, Thomas; Beckhaus, Rüdiger; Klüner, Thorsten; Höfener, Sebastian; Klopper, Wim

    2009-08-11

    The titanium mediated trimerization of pyrazine leads to the formation of a tris-chelate complex employing a 4a,4b,8a,8b,12a,12b-hexahydrodiyprazino[2,3-f:2',3'-h]quinoxaline ligand (HATH6, 3). The driving force in the formation of the (Cp*2Ti)3(HATH6) complex 2 is attributed to the formation of six Ti-N bonds. We show that density functional theory (DFT) fails to predict quantitatively correct results. Therefore, post-Hartree-Fock methods, such as second-order Møller-Plesset perturbation theory (MP2), in combination with coupled-cluster (CC) methods must be used. Both MP2 and CCSD(T) levels of theory provide endothermic trimerization energies, showing that the plain pyrazine trimer is not stable with respect to decomposition into its monomers. Complete basis set (CBS) results for the MP2 level of theory were computed using explicitly correlated wave functions. With these, we estimate the CCSD(T) CBS limit of the hypothetical trimerization energy to be +0.78 eV. Thus, the trimerization is facilitated by the formation of six Ti-N bonds with a calculated formation energy of -1.32 eV per bond.

  10. Base of the Measles Virus Fusion Trimer Head Receives the Signal That Triggers Membrane Fusion*

    PubMed Central

    Apte-Sengupta, Swapna; Negi, Surendra; Leonard, Vincent H. J.; Oezguen, Numan; Navaratnarajah, Chanakha K.; Braun, Werner; Cattaneo, Roberto

    2012-01-01

    The measles virus (MV) fusion (F) protein trimer executes membrane fusion after receiving a signal elicited by receptor binding to the hemagglutinin (H) tetramer. Where and how this signal is received is understood neither for MV nor for other paramyxoviruses. Because only the prefusion structure of the parainfluenza virus 5 (PIV5) F-trimer is available, to study signal receipt by the MV F-trimer, we generated and energy-refined a homology model. We used two approaches to predict surface residues of the model interacting with other proteins. Both approaches measured interface propensity values for patches of residues. The second approach identified, in addition, individual residues based on the conservation of physical chemical properties among F-proteins. Altogether, about 50 candidate interactive residues were identified. Through iterative cycles of mutagenesis and functional analysis, we characterized six residues that are required specifically for signal transmission; their mutation interferes with fusion, although still allowing efficient F-protein processing and cell surface transport. One residue is located adjacent to the fusion peptide, four line a cavity in the base of the F-trimer head, while the sixth residue is located near this cavity. Hydrophobic interactions in the cavity sustain the fusion process and contacts with H. The cavity is flanked by two different subunits of the F-trimer. Tetrameric H-stalks may be lodged in apposed cavities of two F-trimers. Because these insights are based on a PIV5 homology model, the signal receipt mechanism may be conserved among paramyxoviruses. PMID:22859308

  11. Designing a soluble near full-length HIV-1 gp41 trimer.

    PubMed

    Gao, Guofen; Wieczorek, Lindsay; Peachman, Kristina K; Polonis, Victoria R; Alving, Carl R; Rao, Mangala; Rao, Venigalla B

    2013-01-04

    The HIV-1 envelope spike is a trimer of heterodimers composed of an external glycoprotein gp120 and a transmembrane glycoprotein gp41. gp120 initiates virus entry by binding to host receptors, whereas gp41 mediates fusion between viral and host membranes. Although the basic pathway of HIV-1 entry has been extensively studied, the detailed mechanism is still poorly understood. Design of gp41 recombinants that mimic key intermediates is essential to elucidate the mechanism as well as to develop potent therapeutics and vaccines. Here, using molecular genetics and biochemical approaches, a series of hypotheses was tested to overcome the extreme hydrophobicity of HIV-1 gp41 and design a soluble near full-length gp41 trimer. The two long heptad repeat helices HR1 and HR2 of gp41 ectodomain were mutated to disrupt intramolecular HR1-HR2 interactions but not intermolecular HR1-HR1 interactions. This resulted in reduced aggregation and improved solubility. Attachment of a 27-amino acid foldon at the C terminus and slow refolding channeled gp41 into trimers. The trimers appear to be stabilized in a prehairpin-like structure, as evident from binding of a HR2 peptide to exposed HR1 grooves, lack of binding to hexa-helical bundle-specific NC-1 mAb, and inhibition of virus neutralization by broadly neutralizing antibodies 2F5 and 4E10. Fusion to T4 small outer capsid protein, Soc, allowed display of gp41 trimers on the phage nanoparticle. These approaches for the first time led to the design of a soluble gp41 trimer containing both the fusion peptide and the cytoplasmic domain, providing insights into the mechanism of entry and development of gp41-based HIV-1 vaccines.

  12. Detection of p75NTR Trimers: Implications for Receptor Stoichiometry and Activation

    PubMed Central

    Barker, Phillip A.; Chao, Moses V.

    2015-01-01

    The p75 neurotrophin receptor (p75NTR) is a multifunctional receptor that participates in many critical processes in the nervous system, ranging from apoptosis to synaptic plasticity and morphological events. It is a member of the tumor necrosis factor receptor (TNFR) superfamily, whose members undergo trimeric oligomerization. Interestingly, p75NTR interacts with dimeric ligands (i.e., proneurotrophins or mature neurotrophins), but several of the intracellular adaptors that mediate p75NTR signaling are trimeric (i.e., TNFR-associated factor 6 or TRAF6). Consequently, the active receptor signaling unit remains uncertain. To identify the functional receptor complex, we evaluated its oligomerization in vitro and in mice brain tissues using a combination of biochemical techniques. We found that the most abundant homotypic arrangement for p75NTR is a trimer and that monomers and trimers coexist at the cell surface. Interestingly, trimers are not required for ligand-independent or ligand-dependent p75NTR activation in a growth cone retraction functional assay. However, monomers are capable of inducing acute morphological effects in neurons. We propose that p75NTR activation is regulated by its oligomerization status and its levels of expression. These results indicate that the oligomeric state of p75NTR confers differential responses and offers an explanation for the diverse and contradictory actions of this receptor in the nervous system. SIGNIFICANCE STATEMENT The p75 neurotrophin receptor (p75NTR) regulates a wide range of cellular functions, including apoptosis, neuronal processes remodeling, and synaptic plasticity. The goal of our work was to inquire whether oligomers of the receptor are required for function. Here we report that p75NTR predominantly assembles as a trimer, similar to other tumor necrosis factor receptors. Interestingly, monomers and trimers coexist at the cell surface, but trimers are not required for p75NTR activation in a functional assay

  13. Glycosylation Benchmark Profile for HIV-1 Envelope Glycoprotein Production Based on Eleven Env Trimers.

    PubMed

    Go, Eden P; Ding, Haitao; Zhang, Shijian; Ringe, Rajesh P; Nicely, Nathan; Hua, David; Steinbock, Robert T; Golabek, Michael; Alin, James; Alam, S Munir; Cupo, Albert; Haynes, Barton F; Kappes, John C; Moore, John P; Sodroski, Joseph G; Desaire, Heather

    2017-05-01

    HIV-1 envelope glycoprotein (Env) glycosylation is important because individual glycans are components of multiple broadly neutralizing antibody epitopes, while shielding other sites that might otherwise be immunogenic. The glycosylation on Env is influenced by a variety of factors, including the genotype of the protein, the cell line used for its expression, and the details of the construct design. Here, we used a mass spectrometry (MS)-based approach to map the complete glycosylation profile at every site in multiple HIV-1 Env trimers, accomplishing two goals. (i) We determined which glycosylation sites contain conserved glycan profiles across many trimeric Envs. (ii) We identified the variables that impact Env's glycosylation profile at sites with divergent glycosylation. Over half of the gp120 glycosylation sites on 11 different trimeric Envs have a conserved glycan profile, indicating that a native consensus glycosylation profile does indeed exist among trimers. We showed that some soluble gp120s and gp140s exhibit highly divergent glycosylation profiles compared to trimeric Env. We also assessed the impact of several variables on Env glycosylation: truncating the full-length Env; producing Env, instead of the more virologically relevant T lymphocytes, in CHO cells; and purifying Env with different chromatographic platforms, including nickel-nitrilotriacetic acid (Ni-NTA), 2G12, and PGT151 affinity. This report provides the first consensus glycosylation profile of Env trimers, which should serve as a useful benchmark for HIV-1 vaccine developers. This report also defines the sites where glycosylation may be impacted when Env trimers are truncated or produced in CHO cells.IMPORTANCE A protective HIV-1 vaccine will likely include a recombinant version of the viral envelope glycoprotein (Env). Env is highly glycosylated, and yet vaccine developers have lacked guidance on how to assess whether their immunogens have optimal glycosylation. The following important

  14. Photoinduced Enhancement of Anisotropic Charge Correlations on Triangular Lattices with Trimers

    NASA Astrophysics Data System (ADS)

    Yonemitsu, Kenji

    2017-02-01

    To explore nontrivial photoinduced modulations of charge correlations, we theoretically study photoinduced dynamics in quarter-filled extended Hubbard models with competing intersite repulsive interactions on triangular lattices with trimers, where the end points are crystallographically equivalent. The exact diagonalization method is used and the time-dependent Schrödinger equation is numerically solved during and after photoexcitation. Time-averaged double occupancy and intersite density-density correlations can be interpreted as due to effective on-site and intersite repulsive interactions, respectively, relative to transfer energies. In the case where the intersite repulsive interactions compete with each other, the anisotropy of their effective interactions can be enhanced with the help of the trimers, irrespective of whether the trimers are linear or bent. In particular, in the case where the arrangement of the trimers is close to that in α-(bis[ethylenedithio]-tetrathiafulvalene)2I3 [α-(BEDT-TTF)2I3] in the metallic phase, the effective on-site repulsion is enhanced relative to the transfer energies. The relevance of this theoretical finding to the experimentally observed optical freezing of charge motion is discussed.

  15. Nonnative SOD1 trimer is toxic to motor neurons in a model of amyotrophic lateral sclerosis

    PubMed Central

    Fee, Lanette; Tao, Yazhong; Redler, Rachel L.; Fay, James M.; Zhang, Yuliang; Lv, Zhengjian; Mercer, Ian P.; Deshmukh, Mohanish; Lyubchenko, Yuri L.; Dokholyan, Nikolay V.

    2016-01-01

    Since the linking of mutations in the Cu,Zn superoxide dismutase gene (sod1) to amyotrophic lateral sclerosis (ALS) in 1993, researchers have sought the connection between SOD1 and motor neuron death. Disease-linked mutations tend to destabilize the native dimeric structure of SOD1, and plaques containing misfolded and aggregated SOD1 have been found in the motor neurons of patients with ALS. Despite advances in understanding of ALS disease progression and SOD1 folding and stability, cytotoxic species and mechanisms remain unknown, greatly impeding the search for and design of therapeutic interventions. Here, we definitively link cytotoxicity associated with SOD1 aggregation in ALS to a nonnative trimeric SOD1 species. We develop methodology for the incorporation of low-resolution experimental data into simulations toward the structural modeling of metastable, multidomain aggregation intermediates. We apply this methodology to derive the structure of a SOD1 trimer, which we validate in vitro and in hybridized motor neurons. We show that SOD1 mutants designed to promote trimerization increase cell death. Further, we demonstrate that the cytotoxicity of the designed mutants correlates with trimer stability, providing a direct link between the presence of misfolded oligomers and neuron death. Identification of cytotoxic species is the first and critical step in elucidating the molecular etiology of ALS, and the ability to manipulate formation of these species will provide an avenue for the development of future therapeutic strategies. PMID:26719414

  16. Replica exchange molecular dynamics study of the truncated amyloid beta (11-40) trimer in solution.

    PubMed

    Ngo, Son Tung; Hung, Huynh Minh; Truong, Duc Toan; Nguyen, Minh Tho

    2017-01-18

    Amyloid beta (Aβ) oligomers are neurotoxic compounds that destroy the brain of Alzheimer's disease patients. Recent studies indicated that the trimer is one of the most cytotoxic forms of low molecular weight Aβ oligomers. As there was limited information about the structure of the Aβ trimer, either by experiment or by computation, we determined in this work the structure of the 3Aβ11-40 oligomer for the first time using the temperature replica exchange molecular dynamics simulations in the presence of an explicit solvent. More than 20.0 μs of MD simulations were performed. The probability of the β-content and random coil structure of the solvated trimer amounts to 42 ± 6 and 49 ± 7% which is in good agreement with experiments. Intermolecular interactions in central hydrophobic cores play a key role in stabilizing the oligomer. Intermolecular polar contacts between D23 and residues 24-29 replace the salt bridge D23-K28 to secure the loop region. The hydrophilic region of the N-terminus is maintained by the intermolecular polar crossing contacts H13A-Q15B and H13B-Q15C. The difference in the free energy of binding between the constituting monomers and the others amounts to -36 ± 8 kcal mol(-1). The collision cross section of the representative structures of the trimer was computed to be 1330 ± 47 Å(2), which is in good agreement with previous experiments.

  17. Polaronic atom-trimer continuity in three-component Fermi gases.

    PubMed

    Nishida, Yusuke

    2015-03-20

    Recently it has been proposed that three-component Fermi gases may exhibit a new type of crossover physics in which an unpaired Fermi sea of atoms smoothly evolves into that of trimers in addition to the ordinary BCS-BEC crossover of condensed pairs. Here we study its corresponding polaron problem in which a single impurity atom of one component interacts with condensed pairs of the other two components with equal populations. By developing a variational approach in the vicinity of a narrow Feshbach resonance, we show that the impurity atom smoothly changes its character from atom to trimer with increasing the attraction and eventually there is a sharp transition to dimer. The emergent polaronic atom-trimer continuity can be probed in ultracold atoms experiments by measuring the impurity spectral function. Our novel crossover wave function properly incorporating the polaronic atom-trimer continuity will provide a useful basis to further investigate the phase diagram of three-component Fermi gases in more general situations.

  18. Unusual H-Bond Topology and Bifurcated H-bonds in the 2-Fluoroethanol Trimer.

    PubMed

    Thomas, Javix; Liu, Xunchen; Jäger, Wolfgang; Xu, Yunjie

    2015-09-28

    By using a combination of rotational spectroscopy and ab initio calculations, an unusual H-bond topology was revealed for the 2-fluoroethanol trimer. The trimer exhibits a strong heterochiral preference and adopts an open OH⋅⋅⋅OH H-bond topology while utilizing two types of bifurcated H-bonds involving organic fluorine. This is in stark contrast to the cyclic OH⋅⋅⋅OH H-bond topology adopted by trimers of water and other simple alcohols. The strengths of different H-bonds in the trimer were analyzed by using the quantum theory of atoms in molecules. The study showcases a remarkable example of a chirality-induced switch in H-bond topology in a simple transient chiral fluoroalcohol. It provides important insight into the H-bond topologies of small fluoroalcohol aggregates, which are proposed to play a key role in protein folding and in enantioselective reactions and separations where fluoroalcohols serve as a (co)solvent.

  19. Theory vs. experiment for molecular clusters: Spectra of OCS trimers and tetramers

    SciTech Connect

    Evangelisti, Luca; Perez, Cristobal; Seifert, Nathan A.; Pate, Brooks H.; Dehghany, M.; Moazzen-Ahmadi, N.; McKellar, A. R. W.

    2015-03-14

    All singly substituted {sup 13}C, {sup 18}O, and {sup 34}S isotopomers of the previously known OCS trimer are observed in natural abundance in a broad-band spectrum measured with a chirped-pulse Fourier transform microwave spectrometer. The complete substitution structure thus obtained critically tests (and confirms) the common assumption that monomers tend to retain their free structure in a weakly bound cluster. A new OCS trimer isomer is also observed, and its structure is determined to be barrel-shaped but with the monomers all approximately aligned, in contrast to the original trimer which is barrel-shaped with two monomers aligned and one anti-aligned. An OCS tetramer spectrum is assigned for the first time, and the tetramer structure resembles an original trimer with an OCS monomer added at the end with two sulfur atoms. Infrared spectra observed in the region of the OCS ν{sub 1} fundamental (≈2060 cm{sup −1}) are assigned to the same OCS tetramer, and another infrared band is tentatively assigned to a different tetramer isomer. The experimental results are compared and contrasted with theoretical predictions from the literature and from new cluster calculations which use an accurate OCS pair potential and assume pairwise additivity.

  20. Pretransitional behavior above the nematic-isotropic phase transition of an auxetic trimer liquid crystal.

    PubMed

    Kang, D; Mahajan, M P; Zhang, S; Petschek, R G; Rosenblatt, C; He, C; Liu, P; Griffin, A C

    1999-10-01

    Static light scattering and electric field-induced Kerr measurements were performed above the nematic-isotropic phase transition of a terminal-lateral-lateral-terminal negative Poisson ratio trimer. For both measurements the inverse susceptibility was observed to be nearly linear with temperature, a result inconsistent with our previously reported Kerr data [Phys. Rev. E 58, 2041 (1998)].

  1. Singlet-singlet annihilation kinetics in aggregates and trimers of LHCII.

    PubMed Central

    Barzda, V; Gulbinas, V; Kananavicius, R; Cervinskas, V; van Amerongen, H; van Grondelle, R; Valkunas, L

    2001-01-01

    Singlet-singlet annihilation experiments have been performed on trimeric and aggregated light-harvesting complex II (LHCII) using picosecond spectroscopy to study spatial equilibration times in LHCII preparations, complementing the large amount of data on spectral equilibration available in literature. The annihilation kinetics for trimers can well be described by a statistical approach, and an annihilation rate of (24 ps)(-1) is obtained. In contrast, the annihilation kinetics for aggregates can well be described by a kinetic approach over many hundreds of picoseconds, and it is shown that there is no clear distinction between inter- and intratrimer transfer of excitation energy. With this approach, an annihilation rate of (16 ps)(-1) is obtained after normalization of the annihilation rate per trimer. It is shown that the spatial equilibration in trimeric LHCII between chlorophyll a molecules occurs on a time scale that is an order of magnitude longer than in Photosystem I-core, after correcting for the different number of chlorophyll a molecules in both systems. The slow transfer in LHCII is possibly an important factor in determining excitation trapping in Photosystem II, because it contributes significantly to the overall trapping time. PMID:11325740

  2. Evaluation of the Initiation/Promotion Potential of CTFE Trimer Acid

    DTIC Science & Technology

    1990-11-01

    Chlorotrifluoroethylene Trimer Acid Hepatocarcinogenesis 43 Initiation Perhalogenated Fatty Acid 16. PRICE CODE Peroxisome Proliferator Promotion 17...peroxisomal proliferation. Several peroxisome proliferators have been shown to inhibit mitochondrial fatty acid oxidation in rat liver (Bone et al., 1982...in the fatty acid oxidase system (Harrison et al., 1988). These findings and the fact that mammals can oxidize n-alkanes to the corresponding fatty

  3. Traveling waves in trimer granular lattice II: Asymptotic prediction of weakly attenuated pulses

    NASA Astrophysics Data System (ADS)

    Shiffer, A.; Jayaprakash, K. R.; Starosvetsky, Y.

    2017-02-01

    In the present study we consider the impulsive response of perfectly aligned, uncompressed, tri-atomic (trimer) granular lattice. In this study, we demonstrate that under particular choice of the system parameters - impulsively loaded, trimer granular lattice can support formation of highly localized, weakly attenuated pulses. These pulses are manifested by the completely non-symmetric wave profiles and can be attributed to the special family of solitary like waves forming in the non-homogenous, periodic trimer granular lattice in the state of acoustic vacuum. Using the recently developed analytical procedure based on the singular, multi-scale perturbation analysis, we derive a simplified reduced order model predicting the special regions in the space of the system parameters corresponding to the formation of the weakly attenuated pulses. Predictions of the asymptotical model are found to be in very good agreement with the results of numerical simulations of the full trimer granular lattice. From a practical point of view, these results can have important implications in complex, structural optimization problems of wave manipulation in the repetitive granular metamaterials.

  4. Thermostability of photosystem I trimers and monomers from the cyanobacterium Thermosynechococcus elongatus

    NASA Astrophysics Data System (ADS)

    Shubin, Vladimir V.; Terekhova, Irina V.; Bolychevtseva, Yulia V.; El-Mohsnawy, Eithar; Rögner, Matthias; Mäntele, Werner; Kopczak, Marta J.; Džafić, Enela

    2017-05-01

    The performance of solar energy conversion into alternative energy sources in artificial systems highly depends on the thermostability of photosystem I (PSI) complexes Terasaki et al. (2007), Iwuchukwu et al. (2010), Kothe et al. (2013) . To assess the thermostability of PSI complexes from the thermophilic cyanobacterium Thermosynechococcus elongatus heating induced perturbations on the level of secondary structure of the proteins were studied. Changes were monitored by Fourier transform infrared (FT-IR) spectra in the mid-IR region upon slow heating (1 °C per minute) of samples in D2O phosphate buffer (pD 7.4) from 20 °C to 100 °C. These spectra showed distinct changes in the Amide I region of PSI complexes as a function of the rising temperature. Absorbance at the Amide I maximum of PSI monomers (centered around 1653 cm- 1), gradually dropped in two temperature intervals, i.e. 60-75 and 80-90 °C. In contrast, absorbance at the Amide I maximum of PSI trimers (around 1656 cm- 1) dropped only in one temperature interval 80-95 °C. The thermal profile of the spectral shift of α-helices bands in the region 1656-1642 cm- 1 confirms the same two temperature intervals for PSI monomers and only one interval for trimers. Apparently, the observed absorbance changes at the Amide I maximum during heating of PSI monomers and trimers are caused by deformation and unfolding of α-helices. The absence of absorbance changes in the interval of 20-65 °C in PSI trimers is probably caused by a greater stability of protein secondary structure as compared to that in monomers. Upon heating above 80 °C a large part of α-helices both in trimers and monomers converts to unordered and aggregated structures. Spectral changes of PSI trimers and monomers heated up to 100 °C are irreversible due to protein denaturation and non-specific aggregation of complexes leading to new absorption bands at 1618-1620 cm- 1. We propose that monomers shield the denaturation sensitive sides at the

  5. Receptor Activation of HIV-1 Env Leads to Asymmetric Exposure of the gp41 Trimer

    PubMed Central

    2016-01-01

    Structural rearrangements of HIV-1 glycoprotein Env promote viral entry through membrane fusion. Env is a symmetric homotrimer with each protomer composed of surface subunit gp120 and transmembrane subunit gp41. Cellular CD4- and chemokine receptor-binding to gp120 coordinate conformational changes in gp41, first to an extended prehairpin intermediate (PHI) and, ultimately, into a fusogenic trimer-of-hairpins (TOH). HIV-1 fusion inhibitors target gp41 in the PHI and block TOH formation. To characterize structural transformations into and through the PHI, we employed asymmetric Env trimers containing both high and low affinity binding sites for individual fusion inhibitors. Asymmetry was achieved using engineered Env heterotrimers composed of protomers deficient in either CD4- or chemokine receptor-binding. Linking receptor engagement to inhibitor affinity allowed us to assess conformational changes of individual Env protomers in the context of a functioning trimer. We found that the transition into the PHI could occur symmetrically or asymmetrically depending on the stoichiometry of CD4 binding. Sequential engagement of multiple CD4s promoted progressive exposure of individual fusion inhibitor binding sites in a CD4-dependent fashion. By contrast, engagement of only a single CD4 molecule led to a delayed, but symmetric, exposure of the gp41 trimer. This complex coupling between Env-CD4 interaction and gp41 exposure explained the multiphasic fusion-inhibitor titration observed for a mutant Env homotrimer with a naturally asymmetric gp41. Our results suggest that the spatial and temporal exposure of gp41 can proceed in a nonconcerted, asymmetric manner depending on the number of CD4s that engage the Env trimer. The findings have important implications for the mechanism of viral membrane fusion and the development of vaccine candidates designed to elicit neutralizing antibodies targeting gp41 in the PHI. PMID:27992602

  6. Targeting Protein-Protein Interactions with Trimeric Ligands: High Affinity Inhibitors of the MAGUK Protein Family

    PubMed Central

    Nissen, Klaus B.; Haugaard-Kedström, Linda M.; Wilbek, Theis S.; Nielsen, Line S.; Åberg, Emma; Kristensen, Anders S.; Bach, Anders; Jemth, Per; Strømgaard, Kristian

    2015-01-01

    PDZ domains in general, and those of PSD-95 in particular, are emerging as promising drug targets for diseases such as ischemic stroke. We have previously shown that dimeric ligands that simultaneously target PDZ1 and PDZ2 of PSD-95 are highly potent inhibitors of PSD-95. However, PSD-95 and the related MAGUK proteins contain three consecutive PDZ domains, hence we envisioned that targeting all three PDZ domains simultaneously would lead to more potent and potentially more specific interactions with the MAGUK proteins. Here we describe the design, synthesis and characterization of a series of trimeric ligands targeting all three PDZ domains of PSD-95 and the related MAGUK proteins, PSD-93, SAP-97 and SAP-102. Using our dimeric ligands targeting the PDZ1-2 tandem as starting point, we designed novel trimeric ligands by introducing a PDZ3-binding peptide moiety via a cysteine-derivatized NPEG linker. The trimeric ligands generally displayed increased affinities compared to the dimeric ligands in fluorescence polarization binding experiments and optimized trimeric ligands showed low nanomolar inhibition towards the four MAGUK proteins, thus being the most potent inhibitors described. Kinetic experiments using stopped-flow spectrometry showed that the increase in affinity is caused by a decrease in the dissociation rate of the trimeric ligand as compared to the dimeric ligands, likely reflecting the lower probability of simultaneous dissociation of all three PDZ ligands. Thus, we have provided novel inhibitors of the MAGUK proteins with exceptionally high affinity, which can be used to further elucidate the therapeutic potential of these proteins. PMID:25658767

  7. Targeting protein-protein interactions with trimeric ligands: high affinity inhibitors of the MAGUK protein family.

    PubMed

    Nissen, Klaus B; Haugaard-Kedström, Linda M; Wilbek, Theis S; Nielsen, Line S; Åberg, Emma; Kristensen, Anders S; Bach, Anders; Jemth, Per; Strømgaard, Kristian

    2015-01-01

    PDZ domains in general, and those of PSD-95 in particular, are emerging as promising drug targets for diseases such as ischemic stroke. We have previously shown that dimeric ligands that simultaneously target PDZ1 and PDZ2 of PSD-95 are highly potent inhibitors of PSD-95. However, PSD-95 and the related MAGUK proteins contain three consecutive PDZ domains, hence we envisioned that targeting all three PDZ domains simultaneously would lead to more potent and potentially more specific interactions with the MAGUK proteins. Here we describe the design, synthesis and characterization of a series of trimeric ligands targeting all three PDZ domains of PSD-95 and the related MAGUK proteins, PSD-93, SAP-97 and SAP-102. Using our dimeric ligands targeting the PDZ1-2 tandem as starting point, we designed novel trimeric ligands by introducing a PDZ3-binding peptide moiety via a cysteine-derivatized NPEG linker. The trimeric ligands generally displayed increased affinities compared to the dimeric ligands in fluorescence polarization binding experiments and optimized trimeric ligands showed low nanomolar inhibition towards the four MAGUK proteins, thus being the most potent inhibitors described. Kinetic experiments using stopped-flow spectrometry showed that the increase in affinity is caused by a decrease in the dissociation rate of the trimeric ligand as compared to the dimeric ligands, likely reflecting the lower probability of simultaneous dissociation of all three PDZ ligands. Thus, we have provided novel inhibitors of the MAGUK proteins with exceptionally high affinity, which can be used to further elucidate the therapeutic potential of these proteins.

  8. Receptor Activation of HIV-1 Env Leads to Asymmetric Exposure of the gp41 Trimer.

    PubMed

    Khasnis, Mukta D; Halkidis, Konstantine; Bhardwaj, Anshul; Root, Michael J

    2016-12-01

    Structural rearrangements of HIV-1 glycoprotein Env promote viral entry through membrane fusion. Env is a symmetric homotrimer with each protomer composed of surface subunit gp120 and transmembrane subunit gp41. Cellular CD4- and chemokine receptor-binding to gp120 coordinate conformational changes in gp41, first to an extended prehairpin intermediate (PHI) and, ultimately, into a fusogenic trimer-of-hairpins (TOH). HIV-1 fusion inhibitors target gp41 in the PHI and block TOH formation. To characterize structural transformations into and through the PHI, we employed asymmetric Env trimers containing both high and low affinity binding sites for individual fusion inhibitors. Asymmetry was achieved using engineered Env heterotrimers composed of protomers deficient in either CD4- or chemokine receptor-binding. Linking receptor engagement to inhibitor affinity allowed us to assess conformational changes of individual Env protomers in the context of a functioning trimer. We found that the transition into the PHI could occur symmetrically or asymmetrically depending on the stoichiometry of CD4 binding. Sequential engagement of multiple CD4s promoted progressive exposure of individual fusion inhibitor binding sites in a CD4-dependent fashion. By contrast, engagement of only a single CD4 molecule led to a delayed, but symmetric, exposure of the gp41 trimer. This complex coupling between Env-CD4 interaction and gp41 exposure explained the multiphasic fusion-inhibitor titration observed for a mutant Env homotrimer with a naturally asymmetric gp41. Our results suggest that the spatial and temporal exposure of gp41 can proceed in a nonconcerted, asymmetric manner depending on the number of CD4s that engage the Env trimer. The findings have important implications for the mechanism of viral membrane fusion and the development of vaccine candidates designed to elicit neutralizing antibodies targeting gp41 in the PHI.

  9. Geometrically frustrated Fe2P-like systems: beyond the Fe-trimer approximation

    NASA Astrophysics Data System (ADS)

    Florez, J. M.; Negrete, O. A.; Vargas, P.; Ross, C. A.

    2015-07-01

    Fe2 P-like structures can be strongly frustrated magnets due to their Kagome/triangular intercalated-layer structure. A complete magnetic solution of the complex spin architecture, and hence the full potential of the magnetic phenomena in Fe2 P-like material prototypes, is yet to be found. A previous magnetic model for a representative FeCrAs-like system used a mean-field effective-spin to describe the 3g-Wyckoff located Fe-triangles. Such an approach demonstrated the outstanding magnetocaloric properties of the material but left the question of whether the intra-trimer interaction could lead to new physical phenomena and therefore more potentially useful properties. In this work Monte Carlo simulations are employed in order to understand both the influence of the additional degrees of freedom introduced by the Fe-trimers and the changes caused by all the possible exchange couplings between them. Complex scenarios arise, in which FM coupling in the trimers gives rise to both in-plane and out-of-plane inter-layer AFM states; whereas AFM exchange in the trimers gives rise to three distinct states, i.e. AFM-canted layers, a non-collinear superposition of ferromagnetic Kagome/triangular orderings, and tilted inter-planar AFM order. These last three configurations generate a double bifurcated magnetic phase diagram while the first one mimics the behavior seen in a model that treats the trimer as an effective-spin under an applied magnetic field.

  10. Geometrically frustrated Fe2P-like systems: beyond the Fe-trimer approximation.

    PubMed

    Florez, J M; Negrete, O A; Vargas, P; Ross, C A

    2015-07-22

    Fe(2)P-like structures can be strongly frustrated magnets due to their Kagome/triangular intercalated-layer structure. A complete magnetic solution of the complex spin architecture, and hence the full potential of the magnetic phenomena in Fe(2)P-like material prototypes, is yet to be found. A previous magnetic model for a representative FeCrAs-like system used a mean-field effective-spin to describe the 3g-Wyckoff located Fe-triangles. Such an approach demonstrated the outstanding magnetocaloric properties of the material but left the question of whether the intra-trimer interaction could lead to new physical phenomena and therefore more potentially useful properties. In this work Monte Carlo simulations are employed in order to understand both the influence of the additional degrees of freedom introduced by the Fe-trimers and the changes caused by all the possible exchange couplings between them. Complex scenarios arise, in which FM coupling in the trimers gives rise to both in-plane and out-of-plane inter-layer AFM states; whereas AFM exchange in the trimers gives rise to three distinct states, i.e. AFM-canted layers, a non-collinear superposition of ferromagnetic Kagome/triangular orderings, and tilted inter-planar AFM order. These last three configurations generate a double bifurcated magnetic phase diagram while the first one mimics the behavior seen in a model that treats the trimer as an effective-spin under an applied magnetic field.

  11. A Structural Study of CESA1 Catalytic Domain of Arabidopsis Cellulose Synthesis Complex: Evidence for CESA Trimers

    SciTech Connect

    Vandavasi, Venu Gopal; Putnam, Daniel K.; Zhang, Qiu; Petridis, Loukas; Heller, William T.; Nixon, B. Tracy; Haigler, Candace H.; Kalluri, Udaya; Coates, Leighton; Langan, Paul; Smith, Jeremy C.; Meiler, Jens; O’Neill, Hugh

    2015-11-10

    In a cellulose synthesis complex a "rosette" shape is responsible for the synthesis of cellulose chains and their assembly into microfibrils within the cell walls of land plants and their charophyte algal progenitors. The number of cellulose synthase proteins in this large multisubunit transmembrane protein complex and the number of cellulose chains in a microfibril have been debated for many years. Our work reports a low resolution structure of the catalytic domain of CESA1 from Arabidopsis (Arabidopsis thaliana; AtCESA1CatD) determined by small-angle scattering techniques and provides the first experimental evidence for the self-assembly of CESA into a stable trimer in solution. The catalytic domain was overexpressed in Escherichia coli, and using a two-step procedure, it was possible to isolate monomeric and trimeric forms of AtCESA1CatD. Moreover, the conformation of monomeric and trimeric AtCESA1CatD proteins were studied using small-angle neutron scattering and small-angle x-ray scattering. A series of AtCESA1CatD trimer computational models were compared with the small-angle x-ray scattering trimer profile to explore the possible arrangement of the monomers in the trimers. Several candidate trimers were identified with monomers oriented such that the newly synthesized cellulose chains project toward the cell membrane. In these models, the class-specific region is found at the periphery of the complex, and the plant-conserved region forms the base of the trimer. Finally, this study strongly supports the "hexamer of trimers" model for the rosette cellulose synthesis complex that synthesizes an 18-chain cellulose microfibril as its fundamental product.

  12. A Structural Study of CESA1 Catalytic Domain of Arabidopsis Cellulose Synthesis Complex: Evidence for CESA Trimers

    DOE PAGES

    Vandavasi, Venu Gopal; Putnam, Daniel K.; Zhang, Qiu; ...

    2015-11-10

    In a cellulose synthesis complex a "rosette" shape is responsible for the synthesis of cellulose chains and their assembly into microfibrils within the cell walls of land plants and their charophyte algal progenitors. The number of cellulose synthase proteins in this large multisubunit transmembrane protein complex and the number of cellulose chains in a microfibril have been debated for many years. Our work reports a low resolution structure of the catalytic domain of CESA1 from Arabidopsis (Arabidopsis thaliana; AtCESA1CatD) determined by small-angle scattering techniques and provides the first experimental evidence for the self-assembly of CESA into a stable trimer inmore » solution. The catalytic domain was overexpressed in Escherichia coli, and using a two-step procedure, it was possible to isolate monomeric and trimeric forms of AtCESA1CatD. Moreover, the conformation of monomeric and trimeric AtCESA1CatD proteins were studied using small-angle neutron scattering and small-angle x-ray scattering. A series of AtCESA1CatD trimer computational models were compared with the small-angle x-ray scattering trimer profile to explore the possible arrangement of the monomers in the trimers. Several candidate trimers were identified with monomers oriented such that the newly synthesized cellulose chains project toward the cell membrane. In these models, the class-specific region is found at the periphery of the complex, and the plant-conserved region forms the base of the trimer. Finally, this study strongly supports the "hexamer of trimers" model for the rosette cellulose synthesis complex that synthesizes an 18-chain cellulose microfibril as its fundamental product.« less

  13. Sedimentation studies reveal a direct role of phosphorylation in Smad3:Smad4 homo- and hetero-trimerization.

    PubMed

    Correia, J J; Chacko, B M; Lam, S S; Lin, K

    2001-02-06

    SMAD proteins are known to oligomerize and hetero-associate during their activation and translocation to the nucleus for transcriptional control. Analytical ultracentrifuge studies on Smad3 and Smad4 protein constructs are presented to clarify the model of homo- and hetero-oligomerization and the role of phosphorylation in the activation process. These constructs all exhibit a tendency to form disulfide cross-linked aggregates, primarily dimers, and a strong reducing agent, TCEP, was found to be required to determine the best estimates for reversible association models and equilibrium constants. A Smad4 construct, S4AF, consisting of the middle linker (L) domain and the C-terminal (C) domain, is shown to be a monomer, while a Smad3 construct, S3LC, consisting of the LC domains, is shown to form a trimer with an affinity K(3) = (1.2-3.1) x 10(9) M(-2). A Smad3 construct that mimics phosphorylation at the C-terminal target sequence, S3LC(3E), has 17--35-fold enhanced ability to form trimer over that of the wild-type construct, S3LC. S4AF associates with either S3LC or S3LC(3E) to form a hetero-trimer. In each case, the hetero-trimer is favored over the formation of the homo-trimer. Despite high sequence homology between Smad3 and Smad4, a chimeric Smad4 construct with an engineered Smad3 C-terminal pseudo-phosphorylation sequence, S4AF(3E), shows no tendency to form trimer. This suggests a Smad4-specific sequence insert inhibits homo-trimer formation, or other domains or sequences in S3LC are required in addition to the target sequence to mediate the formation of trimer. These results represent a direct molecular measure of the importance of hetero-trimerization and phosphorylation in the TGF-beta-activated Smad protein signal transduction process.

  14. Plasmonic Nanolenses: Electrostatic Self-Assembly of Hierarchical Nanoparticle Trimers and Their Response to Optical and Electron Beam Stimuli.

    PubMed

    Lloyd, Julian A; Ng, Soon Hock; Liu, Amelia C Y; Zhu, Ye; Chao, Wei; Coenen, Toon; Etheridge, Joanne; Gómez, Daniel E; Bach, Udo

    2017-02-28

    Asymmetric nanoparticle trimers composed of particles with increasing diameter act as "plasmonic lenses" and have been predicted to exhibit ultrahigh confinement of electromagnetic energy in the space between the two smallest particles. Here we present an electrostatic self-assembly approach for creating gold nanoparticle trimers with an assembly yield of over 60%. We demonstrate that the trimer assembly leads to characteristic red-shifts and show the localization of the relevant plasmon modes by means of cathodoluminescence and electron energy loss spectroscopy. The results are analyzed in terms of surface plasmon hybridization.

  15. Comparative evaluation of trimeric envelope glycoproteins derived from subtype C and B HIV-1 R5 isolates

    SciTech Connect

    Srivastava, Indresh K. Kan, Elaine; Sun Yide; Sharma, Victoria A.; Cisto, Jimna; Burke, Brian; Lian Ying; Hilt, Susan; Biron, Zohar; Hartog, Karin; Stamatatos, Leonidas; Cheng, R. Holland; Ulmer, Jeffrey B.; Barnett, Susan W.

    2008-03-15

    We previously reported that an envelope (Env) glycoprotein immunogen (o-gp140{delta}V2SF162) containing a partial deletion in the second variable loop (V2) derived from the R5-tropic HIV-1 isolate SF162 partially protected vaccinated rhesus macaques against pathogenic SHIV{sub SF162P4} virus. Extending our studies to subtype C isolate TV1, we have purified o-gp140{delta}V2TV1 (subtype C {delta}V2 trimer) to homogeneity, performed glycosylation analysis, and determined its ability to bind CD4, as well as a panel of well-characterized neutralizing monoclonal antibodies (mAb). In general, critical epitopes are preserved on the subtype C {delta}V2 trimer; however, we did not observe significant binding for the b12 mAb. The molecular mass of subtype C {delta}V2 trimer was found to be 450 kDa, and the hydrodynamic radius was found to be 10.87 nm. Our data suggest that subtype C {delta}V2 trimer binds to CD4 with an affinity comparable to o-gp140{delta}V2SF162 (subtype B {delta}V2 trimer). Using isothermal titration calorimetric (ITC) analysis, we demonstrated that all three CD4 binding sites (CD4-BS) in both subtype C and B trimers are exposed and accessible. However, compared to subtype B trimer, the three CD4-BS in subtype C trimer have different affinities for CD4, suggesting a cooperativity of CD4 binding in subtype C trimer but not in subtype B trimer. Negative staining electron microscopy of the subtype C {delta}V2 trimer has demonstrated that it is in fact a trimer. These results highlight the importance of studying subtype C Env, and also of developing appropriate subtype C-specific reagents that may be used for better immunological characterization of subtype C Env for developing an AIDS vaccine.

  16. Binding of inferred germline precursors of broadly neutralizing HIV-1 antibodies to native-like envelope trimers.

    PubMed

    Sliepen, Kwinten; Medina-Ramírez, Max; Yasmeen, Anila; Moore, John P; Klasse, Per Johan; Sanders, Rogier W

    2015-12-01

    HIV-1 envelope glycoproteins (Env) and Env-based immunogens usually do not interact efficiently with the inferred germline precursors of known broadly neutralizing antibodies (bNAbs). This deficiency may be one reason why Env and Env-based immunogens are not efficient at inducing bNAbs. We evaluated the binding of 15 inferred germline precursors of bNAbs directed to different epitope clusters to three soluble native-like SOSIP.664 Env trimers. We found that native-like SOSIP.664 trimers bind to some inferred germline precursors of bNAbs, particularly ones involving the V1/V2 loops at the apex of the trimer. The data imply that native-like SOSIP.664 trimers will be an appropriate platform for structure-guided design improvements intended to create immunogens able to target the germline precursors of bNAbs.

  17. Dynamical coupling of electrons and nuclei for Coulomb explosion of argon trimers in intense laser fields

    NASA Astrophysics Data System (ADS)

    Xie, Xiguo; Wu, Chengyin; Yuan, Zongqiang; Ye, Difa; Wang, Peng; Deng, Yongkai; Fu, Libin; Liu, Jie; Liu, Yunquan; Gong, Qihuang

    2015-08-01

    We have experimentally and theoretically studied the fragmentation dynamics of argon trimer (A r3) in intense laser fields. By coincidently measuring the momentum vectors, we obtained the emission geometry of the three fragmental ions produced in the three-body fragmentation process. In addition to the direct Coulomb explosion channels, we observed the indirect Coulomb explosion channels with Rydberg excitation. We have further developed a classical polyatomic molecular ensemble model, in which all interactions among electrons and nuclei are fully included, to simulate the fragmentation dynamics of argon trimer in intense laser fields. The experimental observations have been reproduced by the model calculation. The simulations show that the Rydberg excitation modifies the kinetic energy release as well as the emission geometry of fragmental ions during the explosion process. The study provides insight into the correlation dynamics of electrons and nuclei of many-body physics driven by intense laser fields.

  18. The four-transmembrane protein IP39 of Euglena forms strands by a trimeric unit repeat.

    PubMed

    Suzuki, Hiroshi; Ito, Yasuyuki; Yamazaki, Yuji; Mineta, Katsuhiko; Uji, Masami; Abe, Kazuhiro; Tani, Kazutoshi; Fujiyoshi, Yoshinori; Tsukita, Sachiko

    2013-01-01

    Euglenoid flagellates have striped surface structures comprising pellicles, which allow the cell shape to vary from rigid to flexible during the characteristic movement of the flagellates. In Euglena gracilis, the pellicular strip membranes are covered with paracrystalline arrays of a major integral membrane protein, IP39, a putative four-membrane-spanning protein with the conserved sequence motif of the PMP-22/EMP/MP20/Claudin superfamily. Here we report the three-dimensional structure of Euglena IP39 determined by electron crystallography. Two-dimensional crystals of IP39 appear to form a striated pattern of antiparallel double-rows in which trimeric IP39 units are longitudinally polymerised, resulting in continuously extending zigzag-shaped lines. Structural analysis revealed an asymmetric molecular arrangement in the trimer, and suggested that at least four different interactions between neighbouring protomers are involved. A combination of such multiple interactions would be important for linear strand formation of membrane proteins in a lipid bilayer.

  19. Hepatitis C Virus Envelope Glycoprotein E1 Forms Trimers at the Surface of the Virion

    PubMed Central

    Falson, Pierre; Bartosch, Birke; Alsaleh, Khaled; Tews, Birke Andrea; Loquet, Antoine; Ciczora, Yann; Riva, Laura; Montigny, Cédric; Montpellier, Claire; Duverlie, Gilles; Pécheur, Eve-Isabelle; le Maire, Marc; Cosset, François-Loïc

    2015-01-01

    ABSTRACT In hepatitis C virus (HCV)-infected cells, the envelope glycoproteins E1 and E2 assemble as a heterodimer. To investigate potential changes in the oligomerization of virion-associated envelope proteins, we performed SDS-PAGE under reducing conditions but without thermal denaturation. This revealed the presence of SDS-resistant trimers of E1 in the context of cell-cultured HCV (HCVcc) as well as in the context of HCV pseudoparticles (HCVpp). The formation of E1 trimers was found to depend on the coexpression of E2. To further understand the origin of E1 trimer formation, we coexpressed in bacteria the transmembrane (TM) domains of E1 (TME1) and E2 (TME2) fused to reporter proteins and analyzed the fusion proteins by SDS-PAGE and Western blotting. As expected for strongly interacting TM domains, TME1–TME2 heterodimers resistant to SDS were observed. These analyses also revealed homodimers and homotrimers of TME1, indicating that such complexes are stable species. The N-terminal segment of TME1 exhibits a highly conserved GxxxG sequence, a motif that is well documented to be involved in intramembrane protein-protein interactions. Single or double mutations of the glycine residues (Gly354 and Gly358) in this motif markedly decreased or abrogated the formation of TME1 homotrimers in bacteria, as well as homotrimers of E1 in both HCVpp and HCVcc systems. A concomitant loss of infectivity was observed, indicating that the trimeric form of E1 is essential for virus infectivity. Taken together, these results indicate that E1E2 heterodimers form trimers on HCV particles, and they support the hypothesis that E1 could be a fusion protein. IMPORTANCE HCV glycoproteins E1 and E2 play an essential role in virus entry into liver cells as well as in virion morphogenesis. In infected cells, these two proteins form a complex in which E2 interacts with cellular receptors, whereas the function of E1 remains poorly understood. However, recent structural data suggest that E1

  20. Computational study of trimer self-assembly and fluid phase behavior

    SciTech Connect

    Hatch, Harold W. Shen, Vincent K.; Mittal, Jeetain

    2015-04-28

    The fluid phase diagram of trimer particles composed of one central attractive bead and two repulsive beads was determined as a function of simple geometric parameters using flat-histogram Monte Carlo methods. A variety of self-assembled structures were obtained including spherical micelle-like clusters, elongated clusters, and densely packed cylinders, depending on both the state conditions and shape of the trimer. Advanced simulation techniques were employed to determine transitions between self-assembled structures and macroscopic phases using thermodynamic and structural definitions. Simple changes in particle geometry yield dramatic changes in phase behavior, ranging from macroscopic fluid phase separation to molecular-scale self-assembly. In special cases, both self-assembled, elongated clusters and bulk fluid phase separation occur simultaneously. Our work suggests that tuning particle shape and interactions can yield superstructures with controlled architecture.

  1. A Structural Study of CESA1 Catalytic Domain of Arabidopsis Cellulose Synthesis Complex: Evidence for CESA Trimers1

    PubMed Central

    Zhang, Qiu; Petridis, Loukas; Nixon, B. Tracy; Haigler, Candace H.; Kalluri, Udaya; Coates, Leighton; Smith, Jeremy C.; Meiler, Jens

    2016-01-01

    A cellulose synthesis complex with a “rosette” shape is responsible for synthesis of cellulose chains and their assembly into microfibrils within the cell walls of land plants and their charophyte algal progenitors. The number of cellulose synthase proteins in this large multisubunit transmembrane protein complex and the number of cellulose chains in a microfibril have been debated for many years. This work reports a low resolution structure of the catalytic domain of CESA1 from Arabidopsis (Arabidopsis thaliana; AtCESA1CatD) determined by small-angle scattering techniques and provides the first experimental evidence for the self-assembly of CESA into a stable trimer in solution. The catalytic domain was overexpressed in Escherichia coli, and using a two-step procedure, it was possible to isolate monomeric and trimeric forms of AtCESA1CatD. The conformation of monomeric and trimeric AtCESA1CatD proteins were studied using small-angle neutron scattering and small-angle x-ray scattering. A series of AtCESA1CatD trimer computational models were compared with the small-angle x-ray scattering trimer profile to explore the possible arrangement of the monomers in the trimers. Several candidate trimers were identified with monomers oriented such that the newly synthesized cellulose chains project toward the cell membrane. In these models, the class-specific region is found at the periphery of the complex, and the plant-conserved region forms the base of the trimer. This study strongly supports the “hexamer of trimers” model for the rosette cellulose synthesis complex that synthesizes an 18-chain cellulose microfibril as its fundamental product. PMID:26556795

  2. Correlated adatom trimer on a metal surface: a continuous-time quantum Monte Carlo study.

    PubMed

    Savkin, V V; Rubtsov, A N; Katsnelson, M I; Lichtenstein, A I

    2005-01-21

    The problem of three interacting Kondo impurities is solved within a numerically exact continuous-time quantum Monte Carlo scheme. A suppression of the Kondo resonance by interatomic exchange interactions for different cluster geometries is investigated. It is shown that a drastic difference between the Heisenberg and Ising cases appears for antiferromagnetically coupled adatoms. The effects of magnetic frustrations in the adatom trimer are investigated, and possible connections with available experimental data are discussed.

  3. Probing of Amyloid Aβ (14–23) Trimers by Single-Molecule Force Spectroscopy

    PubMed Central

    Maity, Sibaprasad; Lyubchenko, Yuri L.

    2016-01-01

    Self-assembly and aggregation of amyloid peptides, such as Aβ(1–40) and Aβ(1–42), lead to the development of Alzheimer disease and similar neurodegenerative disorders associated with protein aggregation. The structures of large aggregates, specifically fibrils, are well characterized. However, our understanding about the structure of oligomeric forms of amyloids is incomplete and needs to be expanded, particularly given the finding that oligomeric rather than fibrillar amyloid morphologies are neurotoxic. This lack of knowledge is primarily due to the existence of transient oligomeric forms that require the use of non-traditional approaches capable of probing transiently existing amyloid forms. We have recently developed the Single-Molecule Force Spectroscopy (SMFS) approach enabling us to probe dimeric forms of amyloids. These studies suggest that the assembly of amyloid proteins into dimers leads to extremely stabilized amyloids in non-native, misfolded states [1]. Herein, we applied the SMFS approach to probe amyloid trimers. We used the Aβ(14–23) segment of Aβ42 protein that is responsible for full-size protein aggregation. The dimerization of this peptide was recently characterized [2]. The dimeric form of Aβ (14–23) was assembled by the use of a tandem Aβ(14–23)-YNGK-Aβ(14–23), in which the YNGK motif between the two Aβ(14–23) monomers makes a β turn to form a hairpin loop with an antiparallel arrangement of Aβ(14–23) monomers[3]. The Aβ(14–23) monomer was tethered to the AFM tip, and trimers were formed by approaching the tip to the mica surface on which the Aβ(14–23)-YNGK-Aβ(14–23) dimer was immobilized via a polyethylene glycol tether. We identified trimers by rupture forces that were considerably larger than those for dimers. Models for the trimer assembly process are discussed.

  4. Synthesis and biological activities of new di- and trimeric quinoline derivatives.

    PubMed

    Broch, Sidonie; Hénon, Hélène; Debaud, Anne-Laure; Fogeron, Marie-Laure; Bonnefoy-Bérard, Nathalie; Anizon, Fabrice; Moreau, Pascale

    2010-10-01

    The synthesis of non-peptidic helix mimetics based on a trimeric quinoline scaffold is described. The ability of these new compounds, as well as their synthetic dimeric intermediates, to bind to various members of the Bcl-2 protein anti-apoptotic group is also evaluated. The most interesting derivative of this new series (compound A) inhibited Bcl-x(L)/Bak, Bcl-x(L)/Bax and Bcl-x(L)/Bid interactions with IC(50) values around 25 μM.

  5. NEMO trimerizes through its coiled-coil C-terminal domain.

    PubMed

    Agou, Fabrice; Ye, Fei; Goffinont, Stéphane; Courtois, Gilles; Yamaoka, Shoji; Israël, Alain; Véron, Michel

    2002-05-17

    NEMO/IkappaB kinase (IKK) gamma is the regulatory component of the IKK complex comprising the two protein kinases, IKKalpha and IKKbeta. To investigate the self-assembly properties of NEMO and to understand further the mechanism of activation of the IKK complex, we purified wild-type and mutant NEMO expressed in Escherichia coli. In the absence of its IKK partners, recombinant NEMO (rNEMO) is a metastable functional monomer correctly folded, according to its fluorescence and far-UV CD spectra, which is binding specifically to the IKK complex. A minor fraction of rNEMO was found tightly associated with DnaK (E. coli Hsp70). We also examined the interaction of NEMO with prokaryotic and eukaryotic Hsp70, and we showed that the Hsp70-NEMO complex forms a supramolecular structure probably corresponding to an assembly intermediate. In vivo cross-linking experiments indicate that native NEMO in association with IKK is in equilibrium between a dimeric and a trimeric form. Similarly to native NEMO, a NEMO mutant deleted from its IKK binding N-terminal domain (residues 242-388) forms a stable trimeric coiled-coil, suggesting that the association of NEMO with IKK or with Hsp70 prevents incorrect interdomain pairing reactions that could lead to aggregation or to an non-native oligomeric state of rNEMO. We propose a model in which the activation of the IKK complex occurs through the trimerization of NEMO upon binding to a not yet identified upstream activator.

  6. Haemophilus influenzae surface fibril (Hsf) is a unique twisted hairpin-like trimeric autotransporter.

    PubMed

    Singh, Birendra; Jubair, Tamim Al; Mörgelin, Matthias; Sundin, Anders; Linse, Sara; Nilsson, Ulf J; Riesbeck, Kristian

    2015-01-01

    The Haemophilus surface fibril (Hsf) is an extraordinary large (2413 amino acids) trimeric autotransporter, present in all encapsulated Haemophilus influenzae. It contributes to virulence by directly functioning as an adhesin. Furthermore, Hsf recruits the host factor vitronectin thereby inhibiting the host innate immune response resulting in enhanced survival in serum. Here we observed by electron microscopy that Hsf appears as an 100 nm long fibril at the bacterial surface albeit the length is approximately 200 nm according to a bioinformatics based model. To unveil this discrepancy, we denaturated Hsf at the surface of Hib by using guanidine hydrochloride (GuHCl). Partial denaturation induced in the presence of GuHCl unfolded the Hsf molecules, and resulted in an increased length of fibres in comparison to the native trimeric form. Importantly, our findings were also verified by E. coli expressing Hsf at its surface. In addition, a set of Hsf-specific peptide antibodies also indicated that the N-terminal of Hsf is located near the C-terminal at the base of the fibril. Taken together, our results demonstrated that Hsf is not a straight molecule but is folded and doubled over. This is the first report that provides the unique structural features of the trimeric autotransporter Hsf.

  7. Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer

    PubMed Central

    Frenz, Brandon; Rottier, Peter J.M.; DiMaio, Frank; Rey, Félix A.; Veesler, David

    2016-01-01

    The tremendous pandemic potential of coronaviruses was demonstrated twice in the last decades by two global outbreaks of deadly pneumonia. Entry of coronaviruses into cells is mediated by the transmembrane spike glycoprotein S, which forms a trimer carrying receptor-binding and membrane fusion functions1. S also contains the principal antigenic determinants and is the target of neutralizing antibodies. Here we present the structure of a murine coronavirus S trimer ectodomain determined at 4.0 Å resolution by single particle cryo-electron microscopy. It reveals the metastable pre-fusion architecture of S and highlights key interactions stabilizing it. The structure shares a common core with paramyxovirus F proteins2,3, implicating mechanistic similarities and an evolutionary connection between these viral fusion proteins. The accessibility of the highly conserved fusion peptide at the periphery of the trimer indicates potential vaccinology strategies to elicit broadly neutralizing antibodies against coronaviruses. Finally, comparison with crystal structures of human coronavirus S domains allows rationalization of the molecular basis for species specificity based on the use of spatially contiguous but distinct domains. PMID:26855426

  8. Charge flipping vortices in the discrete nonlinear Schrödinger trimer and hexamer

    NASA Astrophysics Data System (ADS)

    Jason, Peter; Johansson, Magnus

    2015-02-01

    We examine the existence and properties of charge flipping vortices (CFVs), vortices which periodically flip the topological charge, in three-site (trimer) and six-site (hexamer) discrete nonlinear Schrödinger lattices. We demonstrate numerically that CFVs exist as exact quasiperiodic solutions in continuous families which connect two different stationary solutions without topological charge, and that it is possible to interpret the dynamics of certain CFVs as the result of perturbations of these stationary solutions. The CFVs are calculated with high numerical accuracy and we may therefore accurately determine many of their properties, such as their energy and linear stability, and the CFVs are found to be stable over large parameter regimes. We also show that, like in earlier studies for lattices with a multiple of four sites, trimer and hexamer CFVs can be obtained by perturbing stationary constant amplitude vortices with certain linear eigenmodes. However, in contrast to the former case where the perturbation could be infinitesimal, the magnitude of the perturbations for trimers and hexamers must overcome a quite large threshold value. These CFVs may be interpreted as exact quasiperiodic CFVs, with a small perturbation applied. The concept of a charge flipping energy barrier is introduced and discussed.

  9. Trimers of the fibronectin cell adhesion domain localize to actin filament bundles and undergo rearward translocation.

    PubMed

    Coussen, Françoise; Choquet, Daniel; Sheetz, Michael P; Erickson, Harold P

    2002-06-15

    Previous studies have shown that small beads coated with FN7-10, a four-domain cell adhesion fragment of fibronectin, bind to cell surfaces and translocate rearward. Here we investigate whether soluble constructs containing two to five FN7-10 units might be sufficient for activity. We have produced a monomer, three forms of dimers, a trimer and a pentamer of FN7-10, on the end of spacer arms. These oligomers could bind small clusters of up to five integrins. Fluorescence microscopy showed that the trimer and pentamer bound strongly to the cell surface, and within 5 minutes were prominently localized to actin fiber bundles. Monomers and dimers showed only diffuse localization. Beads coated with a low concentration (probably one complex per bead) of trimer or pentamer showed prolonged binding and rearward translocation, presumably with the translocating actin cytskeleton. Beads containing monomer or dimer showed only brief binding and diffusive movements. We conclude that clusters of three integrin-binding ligands are necessary and sufficient for coupling to and translocating with the actin cytoskeleton.

  10. Electron stimulated desorption of anions from native and brominated single stranded oligonucleotide trimers.

    PubMed

    Polska, Katarzyna; Rak, Janusz; Bass, Andrew D; Cloutier, Pierre; Sanche, Léon

    2012-02-21

    We measured the low energy electron stimulated desorption (ESD) of anions from thin films of native (TXT) and bromine monosubstituted (TBrXT) oligonucleotide trimers deposited on a gold surface (T = thymidine, X = T, deoxycytidine (C), deoxyadenosine (A) or deoxyguanosine (G), Br = bromine). The desorption of H(-), CH(3)(-)/NH(-), O(-)/NH(2)(-), OH(-), CN(-), and Br(-) was induced by 0 to 20 eV electrons. Dissociative electron attachment, below 12 eV, and dipolar dissociation, above 12 eV, are responsible for the formation of these anions. The comparison of the results obtained for the native and brominated trimers suggests that the main pathways of TBrXT degradation correspond to the release of the hydride and bromide anions. Significantly, the presence of bromine in oligonucleotide trimers blocks the electron-induced degradation of nuclobases as evidenced by a dramatic decrease in CN(-) desorption. An increase in the yields of OH(-) is also observed. The debromination yield of particular oligonucleotides diminishes in the following order: BrdU > BrdA > BrdG > BrdC. Based on these results, 5-bromo-2(')-deoxyuridine appears to be the best radiosensitizer among the studied bromonucleosides.

  11. Cycloreversion of the CO2 trimer: a paradigmatic pseudopericyclic [2 + 2 + 2] cycloaddition reaction.

    PubMed

    Villar López, Roberto; Nieto Faza, Olalla; Matito, Eduard; López, Carlos Silva

    2017-01-04

    Very recently, the CO2 trimer has been experimentally synthesized, isolated and characterized. This process opens new ways for the withdrawal and storage of this greenhouse gas. The trimer is reported to be stable up to -40 °C, with a lifetime of about 40 min at this temperature. At these or under harsher thermal conditions it reverts to the three monomers. The mechanism of this reaction has been theoretically studied and the electronic character of the associated transition state has been analyzed from a variety of perspectives (energetic, magnetic, electron localization and delocalization functions) which indicate that it has paradigmatic pseudopericyclic character. To allow for a comparative study, the isoelectronic fragmentations of cyclohexane into three units of ethylene and of benzene into three units of acetylene have been included in this work. The study of a similar series of formally forbidden-four-centered [2 + 2] cycloreversions confirmed the pseudopericyclic nature of these reactions when the CO2 dimer or trimer is involved.

  12. Red antenna states of Photosystem I trimers from Arthrospira platensis revealed by single-molecule spectroscopy.

    PubMed

    Brecht, Marc; Hussels, Martin; Schlodder, Eberhard; Karapetyan, Navassard V

    2012-03-01

    Single-molecule fluorescence spectroscopy at 1.4K was used to investigate the spectral properties of red (long-wavelength) chlorophylls in trimeric Photosystem I (PSI) complexes from the cyanobacterium Arthrospira platensis. Three distinct red antenna states could be identified in the fluorescence spectra of single PSI trimers from A. platensis in the presence of oxidized P700. Two of them are responsible for broad emission bands centered at 726 and 760nm. These bands are similar to those found in bulk fluorescence spectra measured at cryogenic temperatures. The broad fluorescence bands at ≅726 and ≅760nm belong to individual emitters that are broadened by strong electron-phonon coupling giving rise to a large Stokes-shift of about 20nm and rapid spectral diffusion. An almost perpendicular orientation of the transition dipole moments of F726 and F760 has to be assumed because direct excitation energy transfer does not occur between F726 and F760. For the first time a third red state assigned to the pool absorbing around 708nm could be detected by its zero-phonon lines. The center of the zero-phonon line distribution is found at ≅714nm. The spectral properties of the three red antenna states show a high similarity to the red antenna states found in trimeric PSI of Thermosynechoccocus elongatus. Based on these findings a similar organization of the red antenna states in PSI of these two cyanobacteria is discussed.

  13. Wire and extended ladder model predict THz oscillations in DNA monomers, dimers and trimers

    NASA Astrophysics Data System (ADS)

    Lambropoulos, K.; Kaklamanis, K.; Morphis, A.; Tassi, M.; Lopp, R.; Georgiadis, G.; Theodorakou, M.; Chatzieleftheriou, M.; Simserides, C.

    2016-12-01

    We call monomer a B-DNA base pair and study, analytically and numerically, electron or hole oscillations in monomers, dimers and trimers. We employ two tight binding (TB) approaches: (I) at the base-pair level, using the on-site energies of the base pairs and the hopping parameters between successive base pairs i.e. a wire model, and (II) at the single-base level, using the on-site energies of the bases and the hopping parameters between neighbouring bases, specifically between (a) two successive bases in the same strand, (b) complementary bases that define a base pair, and (c) diagonally located bases of successive base pairs, i.e. an extended ladder model since it also includes the diagonal hoppings (c). For monomers, with TB II, we predict periodic carrier oscillations with frequency f≈ 50 -550 THz. For dimers, with TB I, we predict periodic carrier oscillations with f≈ 0.25 -100 THz. For trimers made of identical monomers, with TB I, we predict periodic carrier oscillations with f≈ 0.5 -33 THz. In other cases, either with TB I or TB II, the oscillations may be not strictly periodic, but Fourier analysis shows similar frequency content. For dimers and trimers, TB I and TB II are successfully compared giving complementary aspects of the oscillations.

  14. Electron stimulated desorption of anions from native and brominated single stranded oligonucleotide trimers

    SciTech Connect

    Polska, Katarzyna; Rak, Janusz; Bass, Andrew D.; Cloutier, Pierre; Sanche, Leon

    2012-02-21

    We measured the low energy electron stimulated desorption (ESD) of anions from thin films of native (TXT) and bromine monosubstituted (TBrXT) oligonucleotide trimers deposited on a gold surface (T = thymidine, X = T, deoxycytidine (C), deoxyadenosine (A) or deoxyguanosine (G), Br = bromine). The desorption of H{sup -}, CH{sub 3}{sup -}/NH{sup -}, O{sup -}/NH{sub 2}{sup -}, OH{sup -}, CN{sup -}, and Br{sup -} was induced by 0 to 20 eV electrons. Dissociative electron attachment, below 12 eV, and dipolar dissociation, above 12 eV, are responsible for the formation of these anions. The comparison of the results obtained for the native and brominated trimers suggests that the main pathways of TBrXT degradation correspond to the release of the hydride and bromide anions. Significantly, the presence of bromine in oligonucleotide trimers blocks the electron-induced degradation of nuclobases as evidenced by a dramatic decrease in CN{sup -} desorption. An increase in the yields of OH{sup -} is also observed. The debromination yield of particular oligonucleotides diminishes in the following order: BrdU > BrdA > BrdG > BrdC. Based on these results, 5-bromo-2{sup '}-deoxyuridine appears to be the best radiosensitizer among the studied bromonucleosides.

  15. A trimeric and thermostable lichenase from B. pumilus US570 strain: Biochemical and molecular characterization.

    PubMed

    Elgharbi, Fatma; Ben Hlima, Hajer; Ameri, Rihab; Bejar, Samir; Hmida-Sayari, Aïda

    2017-02-01

    New β-1,3;1,4-glucanase (GluUS570) was purified from a newly isolated Bacillus pumilus US570 strain. The enzyme was active in a wide range of pH and temperature and displayed a great thermostability with a half-life of 30min at 80°C. The enzyme was demonstrated to be a lichenase since it was only active toward glucan containing β-1,3;1,4- linkages. The analysis of the enzyme in native and denaturing conditions suggests that it has a trimeric form (75kDa). This is the first report on the purification and characterization of a bacterial lichenase with a trimeric structure. β-1,3;1,4-glucanase encoding gene was amplified, cloned and sequenced showing an open reading frame of 732bp encoding 243 amino acids. The GluUS570 enzyme showed 97% homology with glucanase from Bacillus lichenoformis. The 3D model of GluUS570 in trimeric form was generated and showed that a region named R2 was involved in the oligomerization of the enzyme.

  16. The trimer interface in the quaternary structure of the bifunctional prokaryotic FAD synthetase from Corynebacterium ammoniagenes.

    PubMed

    Serrano, Ana; Sebastián, María; Arilla-Luna, Sonia; Baquedano, Silvia; Herguedas, Beatriz; Velázquez-Campoy, Adrián; Martínez-Júlvez, Marta; Medina, Milagros

    2017-03-24

    Bifunctional FAD synthetases (FADSs) fold in two independent modules; The C-terminal riboflavin kinase (RFK) catalyzes the RFK activity, while the N-terminal FMN-adenylyltransferase (FMNAT) exhibits the FMNAT activity. The search for macromolecular interfaces in the Corynebacterium ammoniagenes FADS (CaFADS) crystal structure predicts a dimer of trimers organization. Within each trimer, a head-to-tail arrangement causes the RFK and FMNAT catalytic sites of the two neighboring protomers to approach, in agreement with active site residues of one module influencing the activity at the other. We analyze the relevance of the CaFADS head-to-tail macromolecular interfaces to stabilization of assemblies, catalysis and ligand binding. With this aim, we evaluate the effect of point mutations in loop L1c-FlapI, loop L6c, and helix α1c of the RFK module (positions K202, E203, F206, D298, V300, E301 and L304), regions at the macromolecular interface between two protomers within the trimer. Although none of the studied residues is critical in the formation and dissociation of assemblies, residues at L1c-FlapI and helix α1c particularly modulate quaternary architecture, as well as ligand binding and kinetic parameters involved with RFK and FMNAT activities. These data support the influence of transient oligomeric structures on substrate accommodation and catalysis at both CaFADS active sites.

  17. Gram-negative trimeric porins have specific LPS binding sites that are essential for porin biogenesis

    PubMed Central

    Arunmanee, Wanatchaporn; Pathania, Monisha; Solovyova, Alexandra S.; Le Brun, Anton P.; Ridley, Helen; Baslé, Arnaud; van den Berg, Bert; Lakey, Jeremy H.

    2016-01-01

    The outer membrane (OM) of gram-negative bacteria is an unusual asymmetric bilayer with an external monolayer of lipopolysaccharide (LPS) and an inner layer of phospholipids. The LPS layer is rigid and stabilized by divalent cation cross-links between phosphate groups on the core oligosaccharide regions. This means that the OM is robust and highly impermeable to toxins and antibiotics. During their biogenesis, OM proteins (OMPs), which function as transporters and receptors, must integrate into this ordered monolayer while preserving its impermeability. Here we reveal the specific interactions between the trimeric porins of Enterobacteriaceae and LPS. Isolated porins form complexes with variable numbers of LPS molecules, which are stabilized by calcium ions. In earlier studies, two high-affinity sites were predicted to contain groups of positively charged side chains. Mutation of these residues led to the loss of LPS binding and, in one site, also prevented trimerization of the porin, explaining the previously observed effect of LPS mutants on porin folding. The high-resolution X-ray crystal structure of a trimeric porin–LPS complex not only helps to explain the mutagenesis results but also reveals more complex, subtle porin–LPS interactions and a bridging calcium ion. PMID:27493217

  18. Crystal Structure of the Pre-fusion Nipah Virus Fusion Glycoprotein Reveals a Novel Hexamer-of-Trimers Assembly

    PubMed Central

    Dutta, Somnath; Yan, Lianying; Feng, YanRu; Wang, Lin-Fa; Skiniotis, Georgios; Lee, Benhur; Zhou, Z. Hong; Broder, Christopher C.; Aguilar, Hector C.; Nikolov, Dimitar B.

    2015-01-01

    Nipah virus (NiV) is a paramyxovirus that infects host cells through the coordinated efforts of two envelope glycoproteins. The G glycoprotein attaches to cell receptors, triggering the fusion (F) glycoprotein to execute membrane fusion. Here we report the first crystal structure of the pre-fusion form of the NiV-F glycoprotein ectodomain. Interestingly this structure also revealed a hexamer-of-trimers encircling a central axis. Electron tomography of Nipah virus-like particles supported the hexameric pre-fusion model, and biochemical analyses supported the hexamer-of-trimers F assembly in solution. Importantly, structure-assisted site-directed mutagenesis of the interfaces between F trimers highlighted the functional relevance of the hexameric assembly. Shown here, in both cell-cell fusion and virus-cell fusion systems, our results suggested that this hexamer-of-trimers assembly was important during fusion pore formation. We propose that this assembly would stabilize the pre-fusion F conformation prior to cell attachment and facilitate the coordinated transition to a post-fusion conformation of all six F trimers upon triggering of a single trimer. Together, our data reveal a novel and functional pre-fusion architecture of a paramyxoviral fusion glycoprotein. PMID:26646856

  19. Evaluation of ion mobility spectroscopy for determining charge-solvated versus salt-bridge structures of protonated trimers.

    PubMed

    Wong, Richard L; Williams, Evan R; Counterman, Anne E; Clemmer, David E

    2005-07-01

    The cross sections of five different protonated trimers consisting of two base molecules and trifluoroacetic acid were measured by using ion mobility spectrometry. The gas-phase basicities of these five base molecules span an 8-kcal/mol range. These cross sections are compared with those determined from candidate low-energy salt-bridge and charge-solvated structures identified by using molecular mechanics calculations using three different force fields: AMBER*, MMFF, and CHARMm. With AMBER*, the charge-solvated structures are all globular and the salt-bridge structures are all linear, whereas with CHARMm, these two forms of the protonated trimers can adopt either shape. Globular structures have smaller cross sections than linear structures. Conclusions about the structure of these protonated trimers are highly dependent on the force field used to generate low-energy candidate structures. With AMBER*, all of the trimers are consistent with salt-bridge structures, whereas with MMFF the measured cross sections are more consistent with charge-solvated structures, although the assignments are ambiguous for two of the protonated trimers. Conclusions based on structures generated by using CHARMm suggest a change in structure from charge-solvated to salt-bridge structures with increasing gas-phase basicity of the constituent bases, a result that is most consistent with structural conclusions based on blackbody infrared radiative dissociation experiments for these protonated trimers and theoretical calculations on the uncharged base-acid pairs.

  20. Effect of trimerization motifs on quaternary structure, antigenicity, and immunogenicity of a noncleavable HIV-1 gp140 envelope glycoprotein

    SciTech Connect

    Du, Sean X.; Idiart, Rebecca J.; Mariano, Ellaine B.; Chen, Helen; Jiang Peifeng; Xu Li; Ostrow, Kristin M.; Wrin, Terri; Phung, Pham; Binley, James M.; Petropoulos, Christos J.; Ballantyne, John A.; Whalen, Robert G.

    2009-12-05

    The external domains of the HIV-1 envelope glycoprotein (gp120 and the gp41 ectodomain, collectively known as gp140) contain all known viral neutralization epitopes. Various strategies have been used to create soluble trimers of the envelope to mimic the structure of the native viral protein, including mutation of the gp120-gp41 cleavage site, introduction of disulfide bonds, and fusion to heterologous trimerization motifs. We compared the effects on quaternary structure, antigenicity, and immunogenicity of three such motifs: T4 fibritin, a GCN4 variant, and the Escherichia coli aspartate transcarbamoylase catalytic subunit. Fusion of each motif to the C-terminus of a noncleavable JRCSF gp140(-) envelope protein led to enhanced trimerization but had limited effects on the antigenic profile and CD4-binding ability of the trimers. Immunization of rabbits provided no evidence that the trimerized gp140(-) constructs induced significantly improved neutralizing antibodies to several HIV-1 pseudoviruses, compared to gp140 lacking a trimerization motif. However, modest differences in both binding specificity and neutralizing antibody responses were observed among the various immunogens.

  1. Spin and orbital magnetism of coinage metal trimers (Cu{sub 3}, Ag{sub 3}, Au{sub 3}): A relativistic density functional theory study

    SciTech Connect

    Afshar, Mahdi; Sargolzaei, Mohsen

    2013-11-15

    We have demonstrated electronic structure and magnetic properties of Cu{sub 3}, Ag{sub 3} and Au{sub 3} trimers using a full potential local orbital method in the framework of relativistic density functional theory. We have also shown that the non-relativistic generalized gradient approximation for the exchange-correlation energy functional gives reliable magnetic properties in coinage metal trimers compared to experiment. In addition we have indicated that the spin-orbit coupling changes the structure and magnetic properties of gold trimer while the structure and magnetic properties of copper and silver trimers are marginally affected. A significant orbital moment of 0.21μ{sub B} was found for most stable geometry of the gold trimer whereas orbital magnetism is almost quenched in the copper and silver trimers.

  2. Lineage-specific differences between human and simian immunodeficiency virus regulation of gp120 trimer association and CD4 binding.

    PubMed

    Finzi, Andrés; Pacheco, Beatriz; Xiang, Shi-Hua; Pancera, Marie; Herschhorn, Alon; Wang, Liping; Zeng, Xing; Desormeaux, Anik; Kwong, Peter D; Sodroski, Joseph

    2012-09-01

    Metastable conformations of the gp120 and gp41 envelope glycoproteins of human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus (SIV) must be maintained in the unliganded state of the envelope glycoprotein trimer. Binding of gp120 to the primary receptor, CD4, triggers the transition to an open conformation of the trimer, promoting interaction with the CCR5 chemokine receptor and ultimately leading to gp41-mediated virus-cell membrane fusion and entry. Topological layers in the gp120 inner domain contribute to gp120-trimer association in the unliganded state and to CD4 binding. Here we describe similarities and differences between HIV-1 and SIVmac gp120. In both viruses, the gp120 N/C termini and the inner domain β-sandwich and layer 2 support the noncovalent association of gp120 with the envelope glycoprotein trimer. Layer 1 of the SIVmac gp120 inner domain contributes more to trimer association than the corresponding region of HIV-1 gp120. On the other hand, layer 1 plays an important role in stabilizing the CD4-bound conformation of HIV-1 but not SIVmac gp120 and thus contributes to HIV-1 binding to CD4. In SIVmac, CD4 binding is instead enhanced by tryptophan 375, which fills the Phe 43 cavity of gp120. Activation of SIVmac by soluble CD4 is dependent on tryptophan 375 and on layer 1 residues that determine a tight association of gp120 with the trimer. Distinct biological requirements for CD4 usage have resulted in lineage-specific differences in the HIV-1 and SIV gp120 structures that modulate trimer association and CD4 binding.

  3. Genotoxicity of Styrene–Acrylonitrile Trimer in Brain, Liver, and Blood Cells of Weanling F344 Rats

    PubMed Central

    Hobbs, Cheryl A.; Chhabra, Rajendra S.; Recio, Leslie; Streicker, Michael; Witt, Kristine L.

    2012-01-01

    Styrene–acrylonitrile Trimer (SAN Trimer), a by-product in production of acrylonitrile styrene plastics, was identified at a Superfund site in Dover Township, NJ, where childhood cancer incidence rates were elevated for a period of several years. SAN Trimer was therefore tested by the National Toxicology Program in a 2-year perinatal carcinogenicity study in F344/N rats and a bacterial mutagenicity assay; both studies gave negative results. To further characterize its genotoxicity, SAN Trimer was subsequently evaluated in a combined micronucleus (MN)/Comet assay in juvenile male and female F344 rats. SAN Trimer (37.5, 75, 150, or 300 mg/kg/day) was administered by gavage once daily for 4 days. Micronucleated reticulocyte (MN-RET) frequencies in blood were determined by flow cytometry, and DNA damage in blood, liver, and brain cells was assessed using the Comet assay. Highly significant dose-related increases (P < 0.0001) in MN-RET were measured in both male and female rats administered SAN Trimer. The RET population was reduced in high dose male rats, suggesting chemical-related bone marrow toxicity. Results of the Comet assay showed significant, dose-related increases in DNA damage in brain cells of male (P < 0.0074) and female (P < 0.0001) rats; increased levels of DNA damage were also measured in liver cells and leukocytes of treated rats. Chemical-related cytotoxicity was not indicated in any of the tissues examined for DNA damage. The results of this subacute MN/Comet assay indicate induction of significant genetic damage in multiple tissues of weanling F344 male and female rats after oral exposure to SAN Trimer. PMID:22351108

  4. Genotoxicity of styrene-acrylonitrile trimer in brain, liver, and blood cells of weanling F344 rats.

    PubMed

    Hobbs, Cheryl A; Chhabra, Rajendra S; Recio, Leslie; Streicker, Michael; Witt, Kristine L

    2012-04-01

    Styrene-acrylonitrile Trimer (SAN Trimer), a by-product in production of acrylonitrile styrene plastics, was identified at a Superfund site in Dover Township, NJ, where childhood cancer incidence rates were elevated for a period of several years. SAN Trimer was therefore tested by the National Toxicology Program in a 2-year perinatal carcinogenicity study in F344/N rats and a bacterial mutagenicity assay; both studies gave negative results. To further characterize its genotoxicity, SAN Trimer was subsequently evaluated in a combined micronucleus (MN)/Comet assay in juvenile male and female F344 rats. SAN Trimer (37.5, 75, 150, or 300 mg/kg/day) was administered by gavage once daily for 4 days. Micronucleated reticulocyte (MN-RET) frequencies in blood were determined by flow cytometry, and DNA damage in blood, liver, and brain cells was assessed using the Comet assay. Highly significant dose-related increases (P < 0.0001) in MN-RET were measured in both male and female rats administered SAN Trimer. The RET population was reduced in high dose male rats, suggesting chemical-related bone marrow toxicity. Results of the Comet assay showed significant, dose-related increases in DNA damage in brain cells of male (P < 0.0074) and female (P < 0.0001) rats; increased levels of DNA damage were also measured in liver cells and leukocytes of treated rats. Chemical-related cytotoxicity was not indicated in any of the tissues examined for DNA damage. The results of this subacute MN/Comet assay indicate induction of significant genetic damage in multiple tissues of weanling F344 male and female rats after oral exposure to SAN Trimer.

  5. Influences on the Design and Purification of Soluble, Recombinant Native-Like HIV-1 Envelope Glycoprotein Trimers

    PubMed Central

    Ringe, Rajesh P.; Yasmeen, Anila; Ozorowski, Gabriel; Go, Eden P.; Pritchard, Laura K.; Guttman, Miklos; Ketas, Thomas A.; Cottrell, Christopher A.; Wilson, Ian A.; Sanders, Rogier W.; Cupo, Albert; Crispin, Max; Lee, Kelly K.; Desaire, Heather; Ward, Andrew B.; Klasse, P. J.

    2015-01-01

    ABSTRACT We have investigated factors that influence the production of native-like soluble, recombinant trimers based on the env genes of two isolates of human immunodeficiency virus type 1 (HIV-1), specifically 92UG037.8 (clade A) and CZA97.012 (clade C). When the recombinant trimers based on the env genes of isolates 92UG037.8 and CZA97.012 were made according to the SOSIP.664 design and purified by affinity chromatography using broadly neutralizing antibodies (bNAbs) against quaternary epitopes (PGT145 and PGT151, respectively), the resulting trimers are highly stable and they are fully native-like when visualized by negative-stain electron microscopy. They also have a native-like (i.e., abundant) oligomannose glycan composition and display multiple bNAb epitopes while occluding those for nonneutralizing antibodies. In contrast, uncleaved, histidine-tagged Foldon (Fd) domain-containing gp140 proteins (gp140UNC-Fd-His), based on the same env genes, very rarely form native-like trimers, a finding that is consistent with their antigenic and biophysical properties and glycan composition. The addition of a 20-residue flexible linker (FL20) between the gp120 and gp41 ectodomain (gp41ECTO) subunits to make the uncleaved 92UG037.8 gp140-FL20 construct is not sufficient to create a native-like trimer, but a small percentage of native-like trimers were produced when an I559P substitution in gp41ECTO was also present. The further addition of a disulfide bond (SOS) to link the gp120 and gp41 subunits in the uncleaved gp140-FL20-SOSIP protein increases native-like trimer formation to ∼20 to 30%. Analysis of the disulfide bond content shows that misfolded gp120 subunits are abundant in uncleaved CZA97.012 gp140UNC-Fd-His proteins but very rare in native-like trimer populations. The design and stabilization method and the purification strategy are, therefore, all important influences on the quality of trimeric Env proteins and hence their suitability as vaccine components

  6. Accurate structures and binding energies for small water clusters: The water trimer

    SciTech Connect

    Nielsen, I.M.; Seidl, E.T.; Janssen, C.L.

    1999-05-01

    The global minimum on the water trimer potential energy surface has been investigated by means of second-order Mo/ller-Plesset (MP2) perturbation theory employing the series of correlation-consistent basis sets aug-cc-pVXZ (X = D, T, Q, 5, 6), the largest of which contains 1329 basis functions. Definitive predictions are made for the binding energy and equilibrium structure, and improved values are presented for the harmonic vibrational frequencies. A value of 15.82{plus_minus}0.05 kcal mol{sup {minus}1} is advanced for the infinite basis set frozen core MP2 binding energy, obtained by extrapolation of MP2 correlation energies computed at the aug-cc-pVQZ MP2 geometry. Inclusion of core correlation, using the aug-cc-pCV5Z basis set, has been found to increase the binding energy by 0.08 kcal mol{sup {minus}1}, and after consideration of core correlation and higher-order correlation effects, the classical binding energy for the water trimer is estimated to be 15.9{plus_minus}0.2 kcal mol{sup {minus}1}. A zero-point vibrational correction of {minus}5.43 kcal mol{sup {minus}1} has been computed from aug-cc-pVTZ MP2 harmonic vibrational frequencies. The accuracy of different computational schemes for obtaining the binding energies of the water dimer and trimer has been investigated, and computationally feasible methods are suggested for obtaining accurate structures and binding energies for larger water clusters.{copyright} {ital 1999 American Institute of Physics.}

  7. pH-Stimulated Reconfiguration and Structural Isomerization of Origami Dimer and Trimer Systems.

    PubMed

    Wu, Na; Willner, Itamar

    2016-10-12

    Reversible pH-responsive dimer or trimer origami structures are assembled by bridging origami frames with pH-responsive units. The cyclic pH-stimulated separation and reassembly of dimer origami structures is demonstrated using i-motif or Hoogsteen-type (C-G·C(+) or T-A·T) interactions. The duplex-bridged dimer T1-T2 is separated by the pH-induced formation of an i-motif structure (pH = 4.5), and the dimer is reassembled at pH = 7.0. The duplex-bridged dimer, T3-T4, is separated at pH = 4.5 through the formation of C-G·C(+) triplex structures and is reassembled to the dimer at pH = 7.0. Similarly, the T-A·T triplex-bridged dimer, T5-T6, is separated at pH = 9.5 and is reassembled at neutral pH. Finally, a trimer, T3-T7-T6, that includes C-G·C(+) and T-A·T pH-responsive bridges reveals pH-programmed cleavage to selectively yield the dimers T3-T7 or T7-T6, which reassemble to the trimer at pH = 7.0. A linear three-frame origami structure bridged by duplexes including caged i-motif units undergoes pH-stimulated isomerization to a bent structure (pH = 4.5) through the formation of i-motif complex and bridging T-A·T triplex units.

  8. An Improved Chirped Pulse Ftmw Analysis of the Structures of Phenol Dimer and Trimer

    NASA Astrophysics Data System (ADS)

    Seifert, Nathan A.; Perez, Cristobal; Steber, Amanda L.; Zaleski, Daniel P.; Neill, Justin L.; Pate, Brooks H.; Lesarri, Alberto

    2013-06-01

    With the recent improvements for chirped pulse FTMW (CP-FTMW) spectroscopy between 2-18 GHz, substitution structures of molecules and clusters with more than 10 heavy atoms are becoming routine. While previous CP-FTMW results for phenol dimer reported at this conference by Steber et al. necessitated reduced-band measurements in order to achieve the sensitivity to detect the carbon isotopologues, the latest improvements for the 2-8 GHz arrangement have enabled full band detection of all 12 ^{13}C and 2 ^{18}O isotopologues of phenol dimer in natural abundance, with improved fits for all detected species. In addition, the added sensitivity of this new 2-8 GHz configuration has enabled a full carbon substitution structure of phenol trimer. The experimental structure of phenol trimer, in agreement with the M06-2X/6-311++g(d,p) ab initio structure, is a C_{3} oblate symmetric top with 21 heavy atoms; however, all possible isotopic substitutions are off-symmetry axis, so the resulting detected isotopologues have been fit as c-type prolate asymmetric tops. Use of Kraitchman's equations for structural determination of a symmetric top molecule require some assumptions from the ab initio structure for the complete r_{s} structure of the trimer. A detailed summary of these methods, as well as the microwave results for both species, will be presented. A. L. Steber, J. L. Neill, D. P. Zaleski, B. H. Pate, A. Lesarri. 67th OSU Int. Symp. On Mol. Spectrosc., Columbus, OH, 2012, MH13.

  9. Screening-level risk assessment for styrene-acrylonitrile (SAN) trimer detected in soil and groundwater.

    PubMed

    Kirman, C R; Gargas, M L; Collins, J J; Rowlands, J C

    2012-01-01

    A screening-level risk assessment was conducted for styrene-acrylonitrile (SAN) Trimer detected at the Reich Farm Superfund site in Toms River, NJ. Consistent with a screening-level approach, on-site and off-site exposure scenarios were evaluated using assumptions that are expected to overestimate actual exposures and hazards at the site. Environmental sampling data collected for soil and groundwater were used to estimate exposure point concentrations. Several exposure scenarios were evaluated to assess potential on-site and off-site exposures, using parameter values for exposures to soil (oral, inhalation of particulates, and dermal contact) and groundwater (oral, dermal contact) to reflect central tendency exposure (CTE) and reasonable maximum exposure (RME) conditions. Three reference dose (RfD) values were derived for SAN Trimer for short-term, subchronic, and chronic exposures, based upon its effects on the liver in exposed rats. Benchmark (BMD) methods were used to assess the relationship between exposure and response, and to characterize appropriate points of departure (POD) for each RfD. An uncertainty factor of 300 was applied to each POD to yield RfD values of 0.1, 0.04, and 0.03 mg/kg-d for short-term, subchronic, and chronic exposures, respectively. Because a chronic cancer bioassay for SAN Trimer in rats (NTP 2011a) does not provide evidence of carcinogenicity, a cancer risk assessment is not appropriate for this chemical. Potential health hazards to human health were assessed using a hazard index (HI) approach, which considers the ratio of exposure dose (i.e., average daily dose, mg/kg-d) to toxicity dose (RfD, mg/kg-d) for each scenario. All CTE and RME HI values are well below 1 (where the average daily dose is equivalent to the RfD), indicating that there is no concern for potential noncancer effects in exposed populations even under the conservative assumptions of this screening-level assessment.

  10. Techniques and tactics used in determining the structure of the trimeric ebolavirus glycoprotein

    SciTech Connect

    Lee, Jeffrey E.; Fusco, Marnie L.; Abelson, Dafna M.; Hessell, Ann J.; Burton, Dennis R.; Saphire, Erica Ollmann

    2009-11-01

    Here, the techniques, tactics and strategies used to overcome a series of technical roadblocks in crystallization and phasing of the trimeric ebolavirus glycoprotein are described. The trimeric membrane-anchored ebolavirus envelope glycoprotein (GP) is responsible for viral attachment, fusion and entry. Knowledge of its structure is important both for understanding ebolavirus entry and for the development of medical interventions. Crystal structures of viral glycoproteins, especially those in their metastable prefusion oligomeric states, can be difficult to achieve given the challenges in production, purification, crystallization and diffraction that are inherent in the heavily glycosylated flexible nature of these types of proteins. The crystal structure of ebolavirus GP in its trimeric prefusion conformation in complex with a human antibody derived from a survivor of the 1995 Kikwit outbreak has now been determined [Lee et al. (2008 ▶), Nature (London), 454, 177–182]. Here, the techniques, tactics and strategies used to overcome a series of technical roadblocks in crystallization and phasing are described. Glycoproteins were produced in human embryonic kidney 293T cells, which allowed rapid screening of constructs and expression of protein in milligram quantities. Complexes of GP with an antibody fragment (Fab) promoted crystallization and a series of deglycosylation strategies, including sugar mutants, enzymatic deglycosylation, insect-cell expression and glycan anabolic pathway inhibitors, were attempted to improve the weakly diffracting glycoprotein crystals. The signal-to-noise ratio of the search model for molecular replacement was improved by determining the structure of the uncomplexed Fab. Phase combination with Fab model phases and a selenium anomalous signal, followed by NCS-averaged density modification, resulted in a clear interpretable electron-density map. Model building was assisted by the use of B-value-sharpened electron-density maps and the

  11. Saturation Mutagenesis of the HIV-1 Envelope CD4 Binding Loop Reveals Residues Controlling Distinct Trimer Conformations

    PubMed Central

    Bolon, Daniel; Clapham, Paul R.

    2016-01-01

    The conformation of HIV-1 envelope (Env) glycoprotein trimers is key in ensuring protection against waves of neutralizing antibodies generated during infection, while maintaining sufficient exposure of the CD4 binding site (CD4bs) for viral entry. The CD4 binding loop on Env is an early contact site for CD4 while penetration of a proximal cavity by CD4 triggers Env conformational changes for entry. The role of residues in the CD4 binding loop in regulating the conformation of the trimer and trimer association domain (TAD) was investigated using a novel saturation mutagenesis approach. Single mutations identified, resulted in distinct trimer conformations affecting CD4bs exposure, the glycan shield and the TAD across diverse HIV-1 clades. Importantly, mutations that improve access to the CD4bs without exposing the immunodominant V3 loop were identified. The different trimer conformations identified will affect the specificity and breadth of nabs elicited in vivo and are important to consider in design of Env immunogens for vaccines. PMID:27820858

  12. Analysis of the three-dimensional structure of the African horse sickness virus VP7 trimer by homology modelling.

    PubMed

    Bekker, Shani; Burger, Pieter; van Staden, Vida

    2017-02-03

    VP7 is the major core protein of orbiviruses and is essential for virion assembly. African horse sickness virus (AHSV) VP7 self-assembles into highly insoluble crystalline particles - an attribute that may be related to the role of AHSV VP7 in virus assembly but also prevents crystallization. Given that this inherent insolubility is unique to AHSV VP7, we use amino acid sequence conservation analysis between AHSV VP7 and other orbiviruses to identify putative key residues that drive AHSV VP7 self-assembly. A homology model of the AHSV VP7 trimer was generated to analyze surface properties of the trimer and to identify surface residues as candidates for the AHSV VP7 trimer-trimer interactions that drive AHSV VP7 self-assembly. Nine regions were identified as candidate residues for future site-directed mutagenesis experiments that will likely result in a soluble AHSV VP7 protein. Additionally, we identified putative residues that function in the intermolecular interactions within the AHSV VP7 trimer as well as several epitopes. Given the many previous efforts of solubilizing AHSV VP7, we propose a useful strategy that will yield a soluble AHSV VP7 that can be used to study AHSV assembly and increase yield of recombinant vaccine preparations.

  13. Synthesis of Cyclic Porphyrin Trimers through Alkyne Metathesis Cyclooligomerization and Their Host–Guest Binding Study

    SciTech Connect

    Yu, Chao; Long, Hai; Jin, Yinghua; Zhang, Wei

    2016-06-17

    Cyclic porphyrin trimers were synthesized through one-step cyclooligomerization via alkyne metathesis from diyne monomers. These macrocycles show interesting host-guest binding interactions with fullerenes, selectively binding C70 (6 x 103 M-1) over C60 and C84 (no binding observed). The fullerene-encapsulated host-guest complex can undergo guest or host exchange in the presence of another guest (2,4,6-tri(4-pyridyl)-1,3,5-triazine) or host (cage COP5) molecule with higher binding affinity.

  14. Novel metamaterial based on the coupling effect of a dielectric trimer

    NASA Astrophysics Data System (ADS)

    Fu, Jiahui; Chen, Wan; Lv, Bo; Wang, Zhefei

    2017-01-01

    In this paper, a novel periodic 2D all-dielectric metamaterial based on dielectric trimer is proposed. The electromagnetic responses are explained by the corrected equations of motion using coupled mode theory (CMT). An abnormal vanishment mode phenomenon is also discovered and explained using the zero-sum effect of magnetic dipole, by which the relative bandwidth of the metamaterial has been improved significantly compared with other structures. The presented design is easy for fabrication and can be applied in microwave region by scaling the dimensions of the cubes.

  15. Lewis acid promoted titanium alkylidene formation: off-cycle intermediates relevant to olefin trimerization catalysis.

    PubMed

    Sattler, Aaron; VanderVelde, David G; Labinger, Jay A; Bercaw, John E

    2014-07-30

    Two new precatalysts for ethylene and α-olefin trimerization, (FI)Ti(CH2SiMe3)2Me and (FI)Ti(CH2CMe3)2Me (FI = phenoxy-imine), have been synthesized and structurally characterized by X-ray diffraction. (FI)Ti(CH2SiMe3)2Me can be activated with 1 equiv of B(C6F5)3 at room temperature to give the solvent-separated ion pair [(FI)Ti(CH2SiMe3)2][MeB(C6F5)3], which catalytically trimerizes ethylene or 1-pentene to produce 1-hexene or C15 olefins, respectively. The neopentyl analogue (FI)Ti(CH2CMe3)2Me is unstable toward activation with B(C6F5)3 at room temperature, giving no discernible diamagnetic titanium complexes, but at -30 °C the following can be observed by NMR spectroscopy: (i) formation of the bis-neopentyl cation [(FI)Ti(CH2CMe3)2](+), (ii) α-elimination of neopentane to give the neopentylidene complex [(FI)Ti(═CHCMe3)](+), and (iii) subsequent conversion to the imido-olefin complex [(MeOAr2N═)Ti(OArHC═CHCMe3)](+) via an intramolecular metathesis reaction with the imine fragment of the (FI) ligand. If the reaction is carried out at low temperature in the presence of ethylene, catalytic production of 1-hexene is observed, in addition to the titanacyclobutane complex [(FI)Ti(CH(CMe3)CH2CH2)](+), resulting from addition of ethylene to the neopentylidene [(FI)Ti(═CHCMe3)](+). None of the complexes observed spectroscopically subsequent to [(FI)Ti(CH2CMe3)2](+) is an intermediate or precursor for ethylene trimerization, but notwithstanding these off-cycle pathways, [(FI)Ti(CH2CMe3)2](+) is a precatalyst that undergoes rapid initiation to generate a catalyst for trimerizing ethylene or 1-pentene.

  16. Discovery and Evaluation of PRL Trimer Disruptors for Novel Anticancer Agents.

    PubMed

    Bai, Yunpeng; Yu, Zhi-Hong; Zhang, Zhong-Yin

    2016-01-01

    Overexpression of PRL phosphatases (PRL1, PRL2, and PRL3) has been found in a variety of late-stage tumors and their distant metastatic sites. Therefore, the oncogenic PRL phosphatases represent intriguing targets for cancer therapy. There is considerable interest in identifying small molecule inhibitors targeting PRLs as novel anticancer agents. However, it has been difficult to acquire phosphatase activity-based PRL inhibitors due to the unusual wide and shallow catalytic pockets of PRLs revealed by crystal structure studies. Here, we present a novel method to identify PRL1 inhibitors by targeting the PRL1 trimer interface and the procedure to characterize their biochemical and cellular activity.

  17. Synthesis and evaluation of cholecystokinin trimers: a multivalent approach to pancreatic cancer detection and treatment.

    PubMed

    Brabez, Nabila; Nguyen, Kevin L; Saunders, Kara; Lacy, Ryan; Xu, Liping; Gillies, Robert J; Lynch, Ronald M; Chassaing, Gerard; Lavielle, Solange; Hruby, Victor J

    2013-04-15

    In the quest for novel tools for early detection and treatment of cancer, we propose the use of multimers targeting overexpressed receptors at the cancer cell surface. Indeed, multimers are prone to create multivalent interactions, more potent and specific than their corresponding monovalent versions, thus enabling the potential for early detection. There is a lack of tools for early detection of pancreatic cancer, one of the deadliest forms of cancer, but CCK2-R overexpression on pancreatic cancer cells makes CCK based multimers potential markers for these cells. In this Letter, we describe the synthesis and evaluation of CCK trimers targeting overexpressed CCK2-R.

  18. Differential Antibody Responses to Conserved HIV-1 Neutralizing Epitopes in the Context of Multivalent Scaffolds and Native-Like gp140 Trimers

    PubMed Central

    Morris, Charles D.; Azadnia, Parisa; de Val, Natalia; Vora, Nemil; Honda, Andrew; Giang, Erick; Saye-Francisco, Karen; Cheng, Yushao; Lin, Xiaohe; Mann, Colin J.; Tang, Jeffrey; Sok, Devin; Burton, Dennis R.; Law, Mansun; Ward, Andrew B.

    2017-01-01

    ABSTRACT Broadly neutralizing antibodies (bNAbs) have provided valuable insights into the humoral immune response to HIV-1. While rationally designed epitope scaffolds and well-folded gp140 trimers have been proposed as vaccine antigens, a comparative understanding of their antibody responses has not yet been established. In this study, we probed antibody responses to the N332 supersite and the membrane-proximal external region (MPER) in the context of heterologous protein scaffolds and native-like gp140 trimers. Ferritin nanoparticles and fragment crystallizable (Fc) regions were utilized as multivalent carriers to display scaffold antigens with grafted N332 and MPER epitopes, respectively. Trimeric scaffolds were also identified to stabilize the MPER-containing BG505 gp140.681 trimer in a native-like conformation. Following structural and antigenic evaluation, a subset of scaffold and trimer antigens was selected for immunization in BALB/c mice. Serum binding revealed distinct patterns of antibody responses to these two bNAb targets presented in different structural contexts. For example, the N332 nanoparticles elicited glycan epitope-specific antibody responses that could also recognize the native trimer, while a scaffolded BG505 gp140.681 trimer generated a stronger and more rapid antibody response to the trimer apex than its parent gp140.664 trimer. Furthermore, next-generation sequencing (NGS) of mouse splenic B cells revealed expansion of antibody lineages with long heavy-chain complementarity-determining region 3 (HCDR3) loops upon activation by MPER scaffolds, in contrast to the steady repertoires primed by N332 nanoparticles and a soluble gp140.664 trimer. These findings will facilitate the future development of a coherent vaccination strategy that combines both epitope-focused and trimer-based approaches. PMID:28246356

  19. Comparison of calculated and experimentally resolved rate constants for excitation energy transfer in C-phycocyanin. 2. Trimers

    SciTech Connect

    Debreczeny, M.F.; Sauer, K.; Zhou, J.; Bryant, D.A.

    1995-05-18

    Resolution of the absorption spectrum of the {beta}{sub 155} chromophore in C-phycocyanin (PC) trimers is achieved by comparison of the steady state absorption spectra of ({alpha}{sup PC}{beta}{sup PC}){sub 3} and ({alpha}{sup PC}{beta}{sup *}){sub 3}. Comparison of the anisotropy decays of ({alpha}{sup PC}{beta}{sup PC}){sub 3} and ({alpha}{sup PC}{beta}{sup *}){sub 3} also greatly aids in the assignment of the dominant kinetic processes in PC trimers. A comparison is made of calculated Foerster rate constants for energy transfer with those rate constants resolved experimentally in the PC trimers. 35 refs.., 10 figs., 2 tabs.

  20. Solution structure of monomeric and trimeric photosystem I of Thermosynechococcus elongatus investigated by small-angle X-ray scattering.

    PubMed

    Golub, Maksym; Hejazi, Mahdi; Kölsch, Adrian; Lokstein, Heiko; Wieland, D C Florian; Zouni, Athina; Pieper, Jörg

    2017-03-03

    The structure of monomeric and trimeric photosystem I (PS I) of Thermosynechococcus elongatus BP1 (T. elongatus) was investigated by small-angle X-ray scattering (SAXS). The scattering data reveal that the protein-detergent complexes possess radii of gyration of 58 and 78 Å in the cases of monomeric and trimeric PS I, respectively. The results also show that the samples are monodisperse, virtually free of aggregation, and contain empty detergent micelles. The shape of the protein-detergent complexes can be well approximated by elliptical cylinders with a height of 78 Å. Monomeric PS I in buffer solution exhibits minor and major radii of the elliptical cylinder of about 50 and 85 Å, respectively. In the case of trimeric PS I, both radii are equal to about 110 Å. The latter model can be shown to accommodate three elliptical cylinders equal to those describing monomeric PS I. A structure reconstitution also reveals that the protein-detergent complexes are larger than their respective crystal structures. The reconstituted structures are larger by about 20 Å mainly in the region of the hydrophobic surfaces of the monomeric and trimeric PS I complexes. This seeming contradiction can be resolved by the addition of a detergent belt constituted by a monolayer of dodecyl-β-D-maltoside molecules. Assuming a closest possible packing, a number of roughly 1024 and 1472 detergent molecules can be determined for monomeric and trimeric PS I, respectively. Taking the monolayer of detergent molecules into account, the solution structure can be almost perfectly modeled by the crystal structures of monomeric and trimeric PS I.

  1. Genetic engineering of trimers of hypoallergenic fragments of the major birch pollen allergen, Bet v 1, for allergy vaccination.

    PubMed

    Vrtala, Susanne; Fohr, Monika; Campana, Raffaela; Baumgartner, Christian; Valent, Peter; Valenta, Rudolf

    2011-03-03

    An immunotherapy trial performed in allergic patients with hypoallergenic recombinant fragments, comprising aa 1-74 and 75-160 of the major birch pollen allergen, Bet v 1, has indicated that the induction of allergen-specific IgG responses may be an important mechanism of this treatment. To investigate whether the immunogenicity of the rBet v 1 fragments can be increased, recombinant trimers of the fragments were produced. For this purpose, DNA trimers of rBet v 1 aa 1-74 as well as of rBet v 1 aa 75-160 were subcloned into expression plasmid pET 17b, expressed in Escherichia coli and purified. The fragments as well as the fragment trimers showed a reduced IgE-binding capacity and allergenic activity compared to rBet v 1 wildtype when tested in allergic patients. Both rBet v 1 aa 75-160 monomer and trimer induced high titers of allergen-specific IgG1 Abs in mice. Interestingly, rBet v 1 aa 1-74 trimer induced a much higher IgG(1) response to rBet v 1 than rBet v 1 aa 1-74 monomer. Consequently, IgG Abs induced with the rBet v 1 aa 1-74 trimer inhibited birch pollen allergic patients' IgE-binding 10-fold more efficiently than IgG Abs induced with the monomer. Our data show that the immunogenicity of allergy vaccines can be increased by oligomerization.

  2. Stabilized HIV-1 envelope glycoprotein trimers lacking the V1V2 domain, obtained by virus evolution.

    PubMed

    Bontjer, Ilja; Melchers, Mark; Eggink, Dirk; David, Kathryn; Moore, John P; Berkhout, Ben; Sanders, Rogier W

    2010-11-19

    The envelope glycoproteins (Env) are the focus of HIV-1 vaccine development strategies based on the induction of humoral immunity, but the mechanisms the virus has evolved to limit the induction and binding of neutralizing antibodies (NAbs) constitute substantial obstacles. Conserved neutralization epitopes are shielded by variable regions and carbohydrates, so one strategy to increase their exposure and, it is hoped, their immunogenicity is to delete the overlying variable loops. However, deleting the variable regions from Env trimers can be problematic, because hydrophobic patches that are normally solvent-inaccessible now become exposed, causing protein misfolding or aggregation, for example. Here, we describe the construction and characterization of recombinant gp140 trimers lacking variable domains 1 and 2 (ΔV1V2). The design of the trimers was guided by HIV-1 evolution studies that identified compensatory changes in V1V2-deleted but functional Env proteins (Bontjer, I., Land, A., Eggink, D., Verkade, E., Tuin, K., Baldwin, C., Pollakis, G., Paxton, W. A., Braakman, I., Berkhout, B., and Sanders, R. W. (2009) J. Virol. 83, 368-383). We now show that specific compensatory changes improved the function of ΔV1V2 Env proteins and hence HIV-1 replication. The changes acted by reducing the exposure of a hydrophobic surface either by replacing a hydrophobic residue with a hydrophilic one or by covering the surface with a glycan. The compensatory changes allowed the efficient expression of well folded, soluble gp140 trimers derived from various HIV-1 isolates. The evolved ΔV1V2 Env viruses were extremely sensitive to NAbs, indicating that neutralization epitopes are well exposed, which was confirmed by studies of NAb binding to the soluble ΔV1V2 gp140 trimers. These evolved ΔV1V2 trimers could be useful reagents for immunogenicity and structural studies.

  3. Stabilized HIV-1 Envelope Glycoprotein Trimers Lacking the V1V2 Domain, Obtained by Virus Evolution*

    PubMed Central

    Bontjer, Ilja; Melchers, Mark; Eggink, Dirk; David, Kathryn; Moore, John P.; Berkhout, Ben; Sanders, Rogier W.

    2010-01-01

    The envelope glycoproteins (Env) are the focus of HIV-1 vaccine development strategies based on the induction of humoral immunity, but the mechanisms the virus has evolved to limit the induction and binding of neutralizing antibodies (NAbs) constitute substantial obstacles. Conserved neutralization epitopes are shielded by variable regions and carbohydrates, so one strategy to increase their exposure and, it is hoped, their immunogenicity is to delete the overlying variable loops. However, deleting the variable regions from Env trimers can be problematic, because hydrophobic patches that are normally solvent-inaccessible now become exposed, causing protein misfolding or aggregation, for example. Here, we describe the construction and characterization of recombinant gp140 trimers lacking variable domains 1 and 2 (ΔV1V2). The design of the trimers was guided by HIV-1 evolution studies that identified compensatory changes in V1V2-deleted but functional Env proteins (Bontjer, I., Land, A., Eggink, D., Verkade, E., Tuin, K., Baldwin, C., Pollakis, G., Paxton, W. A., Braakman, I., Berkhout, B., and Sanders, R. W. (2009) J. Virol. 83, 368–383). We now show that specific compensatory changes improved the function of ΔV1V2 Env proteins and hence HIV-1 replication. The changes acted by reducing the exposure of a hydrophobic surface either by replacing a hydrophobic residue with a hydrophilic one or by covering the surface with a glycan. The compensatory changes allowed the efficient expression of well folded, soluble gp140 trimers derived from various HIV-1 isolates. The evolved ΔV1V2 Env viruses were extremely sensitive to NAbs, indicating that neutralization epitopes are well exposed, which was confirmed by studies of NAb binding to the soluble ΔV1V2 gp140 trimers. These evolved ΔV1V2 trimers could be useful reagents for immunogenicity and structural studies. PMID:20826824

  4. An N-terminal glycine-rich sequence contributes to retrovirus trimer of hairpins stability

    SciTech Connect

    Wilson, Kirilee A.; Maerz, Anne L.; Baer, Severine; Drummer, Heidi E.; Poumbourios, Pantelis . E-mail: apoumbourios@burnet.edu.au

    2007-08-10

    Retroviral transmembrane proteins (TMs) contain a glycine-rich segment linking the N-terminal fusion peptide and coiled coil core. Previously, we reported that the glycine-rich segment (Met-326-Ser-337) of the human T-cell leukemia virus type 1 (HTLV-1) TM, gp21, is a determinant of membrane fusion function [K.A. Wilson, S. Baer, A.L. Maerz, M. Alizon, P. Poumbourios, The conserved glycine-rich segment linking the N-terminal fusion peptide to the coiled coil of human T-cell leukemia virus type 1 transmembrane glycoprotein gp21 is a determinant of membrane fusion function, J. Virol. 79 (2005) 4533-4539]. Here we show that the reduced fusion activity of an I334A mutant correlated with a decrease in stability of the gp21 trimer of hairpins conformation, in the context of a maltose-binding protein-gp21 chimera. The stabilizing influence of Ile-334 required the C-terminal membrane-proximal sequence Trp-431-Ser-436. Proline substitution of four of five Gly residues altered gp21 trimer of hairpins stability. Our data indicate that flexibility within and hydrophobic interactions mediated by this region are determinants of gp21 stability and membrane fusion function.

  5. Acetylene trimerization on Ag, Pd and Rh atoms deposited on MgO thin films.

    PubMed

    Judai, Ken; Wörz, Anke S; Abbet, Stéphane; Antonietti, Jean-Marie; Heiz, Ueli; Del Vitto, Annalisa; Giordano, Livia; Pacchioni, Gianfranco

    2005-03-07

    The acetylene trimerization on the group VIII transition metal atoms, Rh and Pd, as well as on Ag atoms supported on MgO thin films has been studied experimentally and theoretically. The three metal atoms with the atomic configurations 4d(8)5s1 (Rh), 4d10s0 (Pd) and 4d(10)5s1 (Ag) behave distinctly differently. The coinage metal atom silver is basically inert for this reaction, whereas Pd is active at 220 and 320 K, and Rh produces benzene in a rather broad temperature range from 350 to ca. 430 K. The origins of these differences are not only the different electronic configurations, leading to a weak interaction of acetylene with silver due to strong Pauli repulsion with the 5s electron but also the different stability and dynamics of the three atoms on the MgO surface. In particular, Rh and Pd atoms interact differently with surface defects like the oxygen vacancies (F centers) and the step edges. Pd atoms migrate already at low temperature exclusively to F centers where the cyclotrimerization is efficiently promoted. The Rh atoms on the other hand are not only trapped on F centers but also at step edges up to about 300 K. Interestingly, only Rh atoms on F centers catalyze the trimerization reaction whereas they are turned inert on the step edges due to strong steric effects.

  6. Synthesis of Trimeric Organozinc Compounds and their Subsequent Reaction with Oxygen

    PubMed Central

    Manzi, Joe A.; Knapp, Caroline E.; Parkin, Ivan P.

    2016-01-01

    Abstract A conventional solution‐based route to a cyclic trimeric organozinc compound [{Zn(Et)(β‐diketonate)}3] (β‐diketonate=OC(OMe)CHC(Me)O, 1) is described, with 1 structurally characterized for the first time. The ligand selection of bidentate β‐diketonates is shown to be key to isolating a cyclic trimer. Additional reaction of β‐diketonates with diethyl zinc were spectroscopically characterized as compounds of the type [{Zn(Et)(β‐diketonate)}n] (β‐diketonate=OC(Me)CHC(Me)O, 2, OC(OtBu)CHC(Me)O, 3). Further studies have shown that selective oxidation of these species produces cubanes of the general formula [{Zn(OC(R)CHC(Me)O)2Zn(Et)OEt}2] (R=OMe, 4; Me, 5; OtBu, 6), allowing a high oxygen content whilst remaining structurally suitable for use as precursors. The successful deposition of thin films of zinc oxide through aerosol‐assisted chemical vapor deposition (AACVD), using a novel precursor, is described and fully characterized. PMID:27547637

  7. The extended leader peptide of Haemophilus parasuis trimeric autotransporters conditions their protein expression in Escherichia coli.

    PubMed

    Pina-Pedrero, Sonia; Olvera, Àlex; Bensaid, Albert

    2017-02-28

    Trimeric autotransporters are surface-exposed proteins of Gram-negative bacteria belonging to the type V secretion system. They are involved in virulence and are targets for vaccine and diagnostic tool development, so optimal systems for their expression and purification are required. In the present study, the impact of the extended leader peptide of the Haemophilus parasuis virulence-associated trimeric autotransporters (VtaA) in its production as recombinant proteins in Escherichia coli was evaluated. The 13 genes encoding the VtaA1 to VtaA13 passenger domains of the strain Nagasaki were cloned in the pASK-IBA33plus plasmid and expressed in E. coli. Recombinant protein production was higher for truncated forms in which the entire leader peptide was deleted, and the recombinant protein accumulated in the cytoplasm of the cells. The yield of protein production of the different VtaAs was size dependent, and reached maximal amount at 2-4 h post -induction. The optimization of these conditions allowed to scale-up the production to obtain enough recombinant protein to immunize large animals.

  8. Fundamental mechanisms of DNA radiosensitization: damage induced by low-energy electrons in brominated oligonucleotide trimers.

    PubMed

    Park, Yeunsoo; Polska, Katarzyna; Rak, Janusz; Wagner, J Richard; Sanche, Léon

    2012-08-16

    The replacement of nucleobases with brominated analogs enhances DNA radiosensitivity. We examine the chemistry of low-energy electrons (LEEs) in this sensitization process by experiments with thin films of the oligonucleotide trimers TBrXT, where BrX = 5-BrU (5-bromouracil), 5-BrC (5-bromocytosine), 8-BrA (8-bromoadenine), or 8-BrG (8-bromoguanine). The products induced from irradiation of thin (∼ 2.5 nm) oligonucleotide films, with 10 eV electrons, under ultrahigh vacuum (UHV) are analyzed by HPLC-UV. The number of damaged brominated trimers ranges from about 12 to 15 × 10(-3) molecules per incident electron, whereas under the identical conditions, these numbers drop to 4-7 × 10(-3) for the same, but nonbrominated oligonucleotides. The results of HPLC analysis show that the main degradation pathway of trinucleotides containing brominated bases involve debromination (i.e., loss of the bromine atom and its replacement with a hydrogen atom). The electron-induced sum of products upon bromination increases by factors of 2.1 for the pyrimidines and 3.2 for the purines. Thus, substitution of any native nucleobase with a brominated one in simple models of DNA increases LEE-induced damage to DNA and hence its radiosensitivity. Furthermore, besides the brominated pyrimidines that have already been tested in clinical trials, brominated purines not only appear to be promising sensitizers for radiotherapy, but could provide a higher degree of radiosensitization.

  9. Synthesis of Trimeric Organozinc Compounds and their Subsequent Reaction with Oxygen.

    PubMed

    Manzi, Joe A; Knapp, Caroline E; Parkin, Ivan P; Carmalt, Claire J

    2016-08-01

    A conventional solution-based route to a cyclic trimeric organozinc compound [{Zn(Et)(β-diketonate)}3] (β-diketonate=OC(OMe)CHC(Me)O, 1) is described, with 1 structurally characterized for the first time. The ligand selection of bidentate β-diketonates is shown to be key to isolating a cyclic trimer. Additional reaction of β-diketonates with diethyl zinc were spectroscopically characterized as compounds of the type [{Zn(Et)(β-diketonate)} n ] (β-diketonate=OC(Me)CHC(Me)O, 2, OC(OtBu)CHC(Me)O, 3). Further studies have shown that selective oxidation of these species produces cubanes of the general formula [{Zn(OC(R)CHC(Me)O)2Zn(Et)OEt}2] (R=OMe, 4; Me, 5; OtBu, 6), allowing a high oxygen content whilst remaining structurally suitable for use as precursors. The successful deposition of thin films of zinc oxide through aerosol-assisted chemical vapor deposition (AACVD), using a novel precursor, is described and fully characterized.

  10. Quaternary contact in the initial interaction of CD4 with the HIV-1 envelope trimer.

    PubMed

    Liu, Qingbo; Acharya, Priyamvada; Dolan, Michael A; Zhang, Peng; Guzzo, Christina; Lu, Jacky; Kwon, Alice; Gururani, Deepali; Miao, Huiyi; Bylund, Tatsiana; Chuang, Gwo-Yu; Druz, Aliaksandr; Zhou, Tongqing; Rice, William J; Wigge, Christoph; Carragher, Bridget; Potter, Clinton S; Kwong, Peter D; Lusso, Paolo

    2017-04-01

    Binding of the gp120 envelope (Env) glycoprotein to the CD4 receptor is the first step in the HIV-1 infectious cycle. Although the CD4-binding site has been extensively characterized, the initial receptor interaction has been difficult to study because of major CD4-induced structural rearrangements. Here we used cryogenic electron microscopy (cryo-EM) to visualize the initial contact of CD4 with the HIV-1 Env trimer at 6.8-Å resolution. A single CD4 molecule is embraced by a quaternary HIV-1-Env surface formed by coalescence of the previously defined CD4-contact region with a second CD4-binding site (CD4-BS2) in the inner domain of a neighboring gp120 protomer. Disruption of CD4-BS2 destabilized CD4-trimer interaction and abrogated HIV-1 infectivity by preventing the acquisition of coreceptor-binding competence. A corresponding reduction in HIV-1 infectivity occurred after the mutation of CD4 residues that interact with CD4-BS2. Our results document the critical role of quaternary interactions in the initial HIV-Env-receptor contact, with implications for treatment and vaccine design.

  11. Sequence Analysis of Trimer Isomers Formed by Montmorillonite Catalysis in the Reaction of Binary Monomer Mixtures

    NASA Astrophysics Data System (ADS)

    Ertem, Gözen; Hazen, Robert M.; Dworkin, Jason P.

    2007-10-01

    Oligonucleotides are structurally similar to short RNA strands. Therefore, their formation via non-enzymatic reactions is highly relevant to Gilbert's RNA world scenario (1986) and the origin of life. In laboratory synthesis of oligonucleotides from monomers, it is necessary to remove the water molecules from the reaction medium to shift the equilibrium in favor of oligonucleotide formation, which would have been impossible for reactions that took place in dilute solutions on the early Earth. Model studies designed to address this problem demonstrate that montmorillonite, a phyllosilicate common on Earth and identified on Mars, efficiently catalyzes phosphodiester-bond formation between activated mononucleotides in dilute solutions and produces RNA-like oligomers. The purpose of this study was to examine the sequences and regiospecificity of trimer isomers formed in the reaction of 5'-phosphorimidazolides of adenosine and uridine. Results demonstrated that regiospecificity and sequence specificity observed in the dimer fractions are conserved in their elongation products. With regard to regiospecificity, 61% of the linkages were found to be RNA-like 3',5'-phosphodiester bonds. With regard to sequence specificity, we found that 88% of the linear trimers were hetero-isomers with 61% A-monomer and 39% U-monomer incorporation. These results lend support to Bernal's hypothesis that minerals may have played a significant role in the chemical processes that led to the origin of life by catalyzing the formation of phosphodiester bonds in RNA-like oligomers.

  12. Apa is a trimeric autotransporter adhesin of Actinobacillus pleuropneumoniae responsible for autoagglutination and host cell adherence.

    PubMed

    Xiao, Longwen; Zhou, Liang; Sun, Changjiang; Feng, Xin; Du, ChongTao; Gao, Yu; Ji, Qun; Yang, Shuxin; Wang, Yu; Han, Wenyu; Langford, P R; Lei, Liancheng

    2012-10-01

    Actinobacillus pleuropneumoniae is the causative agent of porcine pleuropneumonia, and adherence to host cells is a key step in the pathogenic process. Although trimeric autotransporter adhesins (TAAs) were identified in many pathogenic bacteria in recent years, none in A. pleuropneumoniae have been characterized. In this study, we identified a TAA from A. pleuropneumoniae, Apa, and characterized the contribution of its amino acid residues to the adhesion process. Sequence analysis of the C-terminal amino acid residues of Apa revealed the presence of a putative translocator domain and six conserved HsfBD1-like or HsfBD2-like binding domains. Western blot analysis revealed that the 126 C-terminal amino acids of Apa could form trimeric molecules. By confocal laser scanning microscopy, one of these six domains (ApaBD3) was determined to mediate adherence to epithelial cells. Adherence assays and adherence inhibition assays using a recombinant E. coli- ApaBD3 strain which expressed ApaBD3 on the surface of E. coli confirmed that this domain was responsible for the adhesion activity. Moreover, cellular enzyme-linked immunosorbent assays demonstrated that ApaBD3 mediated high-level adherence to epithelial cell lines. Intriguingly, autoagglutination was observed with the E. coli- ApaBD3 strain, and this phenomenon was dependent upon the association of the expressed ApaBD3 with the C-terminal translocator domain.

  13. Structure of a trimeric variant of the Epstein-Barr virus glycoprotein B

    SciTech Connect

    Backovic, Marija; Longnecker, Richard; Jardetzky, Theodore S

    2009-03-16

    Epstein-Barr virus (EBV) is a herpesvirus that is associated with development of malignancies of lymphoid tissue. EBV infections are life-long and occur in >90% of the population. Herpesviruses enter host cells in a process that involves fusion of viral and cellular membranes. The fusion apparatus is comprised of envelope glycoprotein B (gB) and a heterodimeric complex made of glycoproteins H and L. Glycoprotein B is the most conserved envelope glycoprotein in human herpesviruses, and the structure of gB from Herpes simplex virus 1 (HSV-1) is available. Here, we report the crystal structure of the secreted EBV gB ectodomain, which forms 16-nm long spike-like trimers, structurally homologous to the postfusion trimers of the fusion protein G of vesicular stomatitis virus (VSV). Comparative structural analyses of EBV gB and VSV G, which has been solved in its pre and postfusion states, shed light on gB residues that may be involved in conformational changes and membrane fusion. Also, the EBV gB structure reveals that, despite the high sequence conservation of gB in herpesviruses, the relative orientations of individual domains, the surface charge distributions, and the structural details of EBV gB differ from the HSV-1 protein, indicating regions and residues that may have important roles in virus-specific entry.

  14. Optical control of trimeric P2X receptors and acid-sensing ion channels.

    PubMed

    Browne, Liam E; Nunes, João P M; Sim, Joan A; Chudasama, Vijay; Bragg, Laricia; Caddick, Stephen; North, R Alan

    2014-01-07

    P2X receptors are trimeric membrane proteins that function as ion channels gated by extracellular ATP. We have engineered a P2X2 receptor that opens within milliseconds by irradiation at 440 nm, and rapidly closes at 360 nm. This requires bridging receptor subunits via covalent attachment of 4,4'-bis(maleimido)azobenzene to a cysteine residue (P329C) introduced into each second transmembrane domain. The cis-trans isomerization of the azobenzene pushes apart the outer ends of the transmembrane helices and opens the channel in a light-dependent manner. Light-activated channels exhibited similar unitary currents, rectification, calcium permeability, and dye uptake as P2X2 receptors activated by ATP. P2X3 receptors with an equivalent mutation (P320C) were also light sensitive after chemical modification. They showed typical rapid desensitization, and they could coassemble with native P2X2 subunits in pheochromocytoma cells to form light-activated heteromeric P2X2/3 receptors. A similar approach was used to open and close human acid-sensing ion channels (ASICs), which are also trimers but are unrelated in sequence to P2X receptors. The experiments indicate that the opening of the permeation pathway requires similar and substantial movements of the transmembrane helices in both P2X receptors and ASICs, and the method will allow precise optical control of P2X receptors or ASICs in intact tissues.

  15. Managing light polarization via plasmon-molecule interactions within an asymmetric metal nanoparticle trimer

    SciTech Connect

    Shegai, Timur; Li, Zhipeng; Zhang, Zhenyu; Xu, Hongxing; Haran, Gilad

    2008-01-01

    The interaction of light with metal nanoparticles leads to novel phenomena mediated by surface plasmon excitations. In this paper we use single molecules to characterize the interaction of surface plasmons with light, and show that such interaction can strongly modulate the polarization of the emitted light. The simplest nanostructures that enable such polarization modulation are asymmetric silver nanocrystal trimers, where individual Raman scattering molecules are located in the gap between two of the nanoparticles. The third particle breaks the dipolar symmetry of the two-particle junction, generating a wavelength-dependent polarization pattern. Indeed, the scattered light becomes elliptically polarized and its intensity pattern is rotated in the presence of the third particle. We use a combination of spectroscopic observations on single molecules, scanning electron microscope imaging, and generalized Mie theory calculations to provide a full picture of the effect of particles on the polarization of the emitted light. Furthermore, our theoretical analysis allows us to show that the observed phenomenon is very sensitive to the size of the trimer particles and their relative position, suggesting future means for precise control of light polarization on the nanoscale.

  16. Molecular architecture of electroactive and biodegradable copolymers composed of polylactide and carboxyl-capped aniline trimer.

    PubMed

    Guo, Baolin; Finne-Wistrand, Anna; Albertsson, Ann-Christine

    2010-04-12

    Two-, four-, and six-armed branched copolymers with electroactive and biodegradable properties were synthesized by coupling reactions between poly(l-lactides) (PLLAs) with different architecture and carboxyl-capped aniline trimer (CCAT). The aniline oligomer CCAT was prepared from amino-capped aniline trimer and succinic anhydride. FT-IR, NMR, and SEC analyses confirmed the structure of the branched copolymers. UV-vis spectra and cyclic voltammetry of CCAT and copolymer solution showed good electroactive properties, similar to those of polyaniline. The water contact angle of the PLLAs was the highest, followed by the undoped copolymer and the doped copolymers. The values of doped four-armed copolymers were 54-63 degrees . Thermal properties of the polymers were studied by DSC and TGA. The copolymers had better thermal stability than the pure PLLAs, and the T(g) between 48-58 degrees C and T(m) between 146-177 degrees C of the copolymers were lower than those of the pure PLLA counterparts. This kind of electroactive and biodegradable copolymer has a great potential for applications in cardiovascular or neuronal tissue engineering.

  17. Purification, refolding and characterization of the trimeric Omp2a outer membrane porin from Brucella melitensis.

    PubMed

    Roussel, G; Matagne, A; De Bolle, X; Perpète, E A; Michaux, C

    2012-06-01

    Brucella melitensis is a gram-negative bacteria known to cause brucellosis and to produce severe infections in humans. Whilst brucella's outer membrane proteins have been extensively studied due to their potential role as antigens or virulence factors, their function is still poorly understood at the structural level, as the 3D structure of Brucella β-barrel membrane proteins are still unknown. In this context, the B. melitensis trimeric Omp2a porin has been overexpressed and refolded in n-dodecyl-β-d-maltopyranoside. We here show that this refolding process is insensitive to urea but is temperature- and ionic strength-dependent. Reassembled species were characterized by fluorescence, size-exclusion chromatography and circular dichroism. A refolding mechanism is proposed, suggesting that Omp2a first refolds under a monomeric form and then self-associates into a trimeric state. This first complete in vitro refolding of a membrane protein from B. melitensis shall eventually lead to functional and 3D structure determination.

  18. Crystal Structure of Trimeric Carbohydrate Recognition and Neck Domains of Surfactant Protein A

    SciTech Connect

    Head,J.; Mealy, T.; McCormack, F.; Seaton, B.

    2003-01-01

    Surfactant protein A (SP-A), one of four proteins associated with pulmonary surfactant, binds with high affinity to alveolar phospholipid membranes, positioning the protein at the first line of defense against inhaled pathogens. SP-A exhibits both calcium-dependent carbohydrate binding, a characteristic of the collectin family, and specific interactions with lipid membrane components. The crystal structure of the trimeric carbohydrate recognition domain and neck domain of SP-A was solved to 2.1-{angstrom} resolution with multiwavelength anomalous dispersion phasing from samarium. Two metalbinding sites were identified, one in the highly conserved lectin site and the other 8.5 {angstrom} away. The interdomain carbohydrate recognition domain-neck angle is significantly less in SP-A than in the homologous collectins, surfactant protein D, and mannose-binding protein. This conformational difference may endow the SP-A trimer with a more extensive hydrophobic surface capable of binding lipophilic membrane components. The appearance of this surface suggests a putative binding region for membrane-derived SP-A ligands such as phosphatidylcholine and lipid A, the endotoxic lipid component of bacterial lipopolysaccharide that mediates the potentially lethal effects of Gram-negative bacterial infection.

  19. On the trimerization of cyanoacetylene: mechanism of formation of tricyanobenzene isomers and laboratory detection of their radio spectra.

    PubMed

    Hopf, Henning; Mlynek, Cornelia; McMahon, Robert J; Menke, Jessica L; Lesarri, Alberto; Rosemeyer, Michael; Grabow, Jens-Uwe

    2010-12-17

    In support of a deeper understanding of the chemistry of cyanoacetylene--a known constituent of planetary atmospheres and interstellar space--theoretical and experimental studies address the chemical mechanism of dimerization and trimerization, and provide high-resolution rotational spectra of two of the trimeric products, 1,2,3- and 1,2,4-tricyanobenzene. Analysis of the rotational spectra is particularly challenging because of quadrupolar coupling from three (14)N nuclei. The laboratory rotational spectra provide the basis for future searches for these polar aromatic compounds in interstellar space by radio astronomy.

  20. A procyanidin type A trimer from cinnamon extract attenuates glial cell swelling and the reduction in glutamate uptake following ischemic injury in vitro

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dietary polyphenols exert neuroprotective effects in ischemic injury. The protective effects of a procyanidin type A trimer (trimer 1) isolated from a water soluble cinnamon extract (CE) were investigated on key features of ischemic injury including cell swelling, increased free radical production, ...

  1. Screening-Level Risk Assessment for Styrene-Acrylonitrile (SAN) Trimer Detected in Soil and Groundwater

    PubMed Central

    Kirman, C. R.; Gargas, M. L.; Collins, J. J.; Rowlands, J. C.

    2012-01-01

    A screening-level risk assessment was conducted for styrene-acrylonitrile (SAN) Trimer detected at the Reich Farm Superfund site in Toms River, NJ. Consistent with a screening-level approach, on-site and off-site exposure scenarios were evaluated using assumptions that are expected to overestimate actual exposures and hazards at the site. Environmental sampling data collected for soil and groundwater were used to estimate exposure point concentrations. Several exposure scenarios were evaluated to assess potential on-site and off-site exposures, using parameter values for exposures to soil (oral, inhalation of particulates, and dermal contact) and groundwater (oral, dermal contact) to reflect central tendency exposure (CTE) and reasonable maximum exposure (RME) conditions. Three reference dose (RfD) values were derived for SAN Trimer for short-term, subchronic, and chronic exposures, based upon its effects on the liver in exposed rats. Benchmark (BMD) methods were used to assess the relationship between exposure and response, and to characterize appropriate points of departure (POD) for each RfD. An uncertainty factor of 300 was applied to each POD to yield RfD values of 0.1, 0.04, and 0.03 mg/kg-d for short-term, subchronic, and chronic exposures, respectively. Because a chronic cancer bioassay for SAN Trimer in rats (NTP 2011a) does not provide evidence of carcinogenicity, a cancer risk assessment is not appropriate for this chemical. Potential health hazards to human health were assessed using a hazard index (HI) approach, which considers the ratio of exposure dose (i.e., average daily dose, mg/kg-d) to toxicity dose (RfD, mg/kg-d) for each scenario. All CTE and RME HI values are well below 1 (where the average daily dose is equivalent to the RfD), indicating that there is no concern for potential noncancer effects in exposed populations even under the conservative assumptions of this screening-level assessment. PMID:23030654

  2. A Carboxy-Terminal Trimerization Domain Stabilizes Conformational Epitopes on the Stalk Domain of Soluble Recombinant Hemagglutinin Substrates

    PubMed Central

    Krammer, Florian; Margine, Irina; Tan, Gene S.; Pica, Natalie; Krause, Jens C.; Palese, Peter

    2012-01-01

    Recently, a new class of broadly neutralizing anti-influenza virus antibodies that target the stalk domain of the viral hemagglutinin was discovered. As such, induction, isolation, characterization, and quantification of these novel antibodies has become an area of intense research and great interest. Since most of these antibodies bind to conformational epitopes, the structural integrity of hemagglutinin substrates for the detection and quantification of these antibodies is of high importance. Here we evaluate the binding of these antibodies to soluble, secreted hemagglutinins with or without a carboxy-terminal trimerization domain based on the natural trimerization domain of T4 phage fibritin. The lack of such a domain completely abolishes binding to group 1 hemagglutinins and also affects binding to group 2 hemagglutinins. Additionally, the presence of a trimerization domain positively influences soluble hemagglutinin stability during expression and purification. Our findings suggest that a carboxy-terminal trimerization domain is a necessary requirement for the structural integrity of stalk epitopes on recombinant soluble influenza virus hemagglutinin. PMID:22928001

  3. Amyloid beta binds trimers as well as monomers of the 75-kDa neurotrophin receptor and activates receptor signaling.

    PubMed

    Yaar, Mina; Zhai, Sen; Fine, Richard E; Eisenhauer, Patricia B; Arble, Bennett L; Stewart, Kenneth B; Gilchrest, Barbara A

    2002-03-08

    p75(NTR), a nerve growth factor co-receptor that has been implicated in apoptosis of neurons, is structurally related to Fas and the receptors for tumor necrosis factor-alpha that display ligand independent assembly into trimers. Using embryonic day 17 fetal rat cortical neurons and p75(NTR)-expressing NIH-3T3 cells, we now show that p75(NTR) exists as a trimer as well as a monomer. Furthermore, we have reported and others have confirmed that amyloid beta binds p75(NTR), and that this binding leads to apoptotic cell death. We now report that amyloid beta binds to trimers of p75(NTR) as well as to p75(NTR) monomers but not to the p140(trkA), the nerve growth factor co-receptor that mediates neuronal survival. Furthermore, amyloid beta activates p75(NTR), strongly inducing the transcription of c-Jun mRNA and stimulating the stress-activated c-Jun NH(2)-terminal kinase, as measured by phosphorylation of its substrate (glutathione S-transferase-c-Jun-(1-79)). Our data suggest that p75(NTR) may be present as a preformed trimer that binds amyloid beta to induce receptor activation, and support the hypothesis that p75(NTR) activation by amyloid beta is causally related to Alzheimer's disease.

  4. Fragmentation dynamics of ionized neon trimer inside helium nanodroplets: a theoretical study.

    PubMed

    Bonhommeau, David; Viel, Alexandra; Halberstadt, Nadine

    2004-06-22

    We report a theoretical study of the fragmentation dynamics of Ne(3) (+) inside helium nanodroplets, following vertical ionization of the neutral neon trimer. The motion of the neon atoms is treated classically, while transitions between the electronic states of the ionic cluster are treated quantum mechanically. A diatomics-in-molecules description of the potential energy surfaces is used, in a minimal basis set consisting of three effective p orbitals on each neon atom for the missing electron. The helium environment is modeled by a friction force acting on the neon atoms when their speed exceeds the Landau velocity. A reasonable range of values for the corresponding friction coefficient is obtained by comparison with existing experimental measurements.

  5. Heteroleptic Tetrapyrrole-Fused Dimeric and Trimeric Skeletons with Unusual Non-Frustrated Fluorescence.

    PubMed

    Zhang, Yuehong; Oh, Juwon; Wang, Kang; Chen, Chao; Cao, Wei; Park, Kyu Hyung; Kim, Dongho; Jiang, Jianzhuang

    2016-03-18

    Phthalocyanine (Pc) and porphyrin (Por) chromophores have been fused through the benzo[α]pyrazine moiety, resulting in unprecedented heteroleptic tetrapyrrole-fused dimers and trimers. The heteroleptic tetrapyrrole nature has been clearly revealed based on single-crystal X-ray diffraction analysis of the zinc dimer. Electrochemical analysis, theoretical calculations, and time-resolved spectroscopic results disclose that the two/three-tetrapyrrole-fused skeletons behave as one totally π-conjugated system as a result of the strong conjugative interaction between/among the tetrapyrrole chromophores. In particular, the effectively extended π-electron system through the fused-bridge induced strong electronic communication between the Pc and Por moieties and large transition dipole moments in the Pc-Por-fused systems, providing high fluorescence quantum yields (>0.13) and relatively long excited state lifetimes (>1.3 ns) in comparison with their homo-tetrapyrrole-fused analogues.

  6. Trimerization of the HIV Transmembrane Domain in Lipid Bilayers Modulates Broadly Neutralizing Antibody Binding.

    PubMed

    Reichart, Timothy M; Baksh, Michael M; Rhee, Jin-Kyu; Fiedler, Jason D; Sligar, Stephen G; Finn, M G; Zwick, Michael B; Dawson, Philip E

    2016-02-18

    The membrane-proximal external region (MPER) of HIV gp41 is an established target of antibodies that neutralize a broad range of HIV isolates. To evaluate the role of the transmembrane (TM) domain, synthetic MPER-derived peptides were incorporated into lipid nanoparticles using natural and designed TM domains, and antibody affinity was measured using immobilized and solution-based techniques. Peptides incorporating the native HIV TM domain exhibit significantly stronger interactions with neutralizing antibodies than peptides with a monomeric TM domain. Furthermore, a peptide with a trimeric, three-helix bundle TM domain recapitulates the binding profile of the native sequence. These studies suggest that neutralizing antibodies can bind the MPER when the TM domain is a three-helix bundle and this presentation could influence the binding of neutralizing antibodies to the virus. Lipid-bilayer presentation of viral antigens in Nanodiscs is a new platform for evaluating neutralizing antibodies.

  7. Postionization fragmentation of rare-gas trimers revisited with new theoretical approaches

    NASA Astrophysics Data System (ADS)

    Janeček, Ivan; Cintavá, Silvie; Hrivňák, Daniel; Kalus, René; Fárník, Michal; Gadea, Florent Xavier

    2009-09-01

    A new theoretical approach is presented for the general treatment of nonadiabatic hybrid dynamics (mixing classical and quantum approach) and applied to the postionization of rare-gas trimers. There was an important disagreement between trajectory surface hopping (TSH) or mean field (MF) approaches and the experimental results; noteworthy, with the new method qualitative and almost quantitative agreement is found for the fragmentation ratios of ionic monomers and dimers. For the first time in the theory as in the experiment, the dimers prevail for argon while monomers strongly dominate for the heavier rare gases, krypton and xenon. A new compromise between MF and TSH approaches is proposed and the new method is found quite robust with results not too sensitive to various possible implementations.

  8. Dynamics of the central-depleted-well regime in the open Bose-Hubbard trimer.

    PubMed

    Penna, Vittorio

    2013-05-01

    We study the quantum dynamics of the central-depleted-well (CDW) regime in a three-mode Bose Hubbard model subject to a confining parabolic potential. By introducing a suitable set of momentum-like modes we identify the microscopic variables involved in the quantization process and the dynamical algebra of the model. We describe the diagonalization procedure showing that the model reduces to a double oscillator. Interestingly, we find that the parameter-space domain where this scheme entails a discrete spectrum well reproduces the two regions where the classical trimer excludes unstable oscillations. Spectral properties are examined in different limiting cases together with various delocalization effects. These are shown to characterize quantum states of the CDW regime in the proximity of the borderline with classically unstable domains.

  9. Theoretical research program to study transition metal trimers and embedded clusters

    NASA Technical Reports Server (NTRS)

    Walch, S. P.

    1984-01-01

    Small transition metal clusters were studied at a high level of approximation, including all the valence electrons in the calculation and extensive electron correlation, in order to understand the electronic structure of these small metal clusters. By comparison of dimers, trimers, and possibly higher clusters, the information obtained was used to provide insights into the electronic structure of bulk transition metals. Small metal clusters are currently of considerable experimental interest and some information is becomming available both from matrix electron spin resonance studies and from gas phase spectroscopy. Collaboration between theorists and experimentalists is thus expected to be especially profitable at this time since there is some experimental information which can serve to guide the theoretical work.

  10. Dimeric and trimeric triazole based molecules as a new class of Hsp90 molecular chaperone inhibitors.

    PubMed

    Terracciano, Stefania; Chini, Maria Giovanna; Piaz, Fabrizio Dal; Vassallo, Antonio; Riccio, Raffaele; Bruno, Ines; Bifulco, Giuseppe

    2013-07-01

    In the last decade Hsp90 inhibitors have emerged as attractive candidates for the development of new potent anticancer therapeutics. In order to identify novel agents able to block the chaperone activity, following a structure-based approach, we used in silico screening to direct the synthesis of potential inhibitors bearing the triazole scaffold, a widespread motif in drug-like molecules. Docking results, performed on a larger collection of dimeric and trimeric triazole derivatives, suggested the synthesis of some molecules showing different calculated binding energies and modes. Surface Plasmon Resonance Binding assay, performed on the synthesized compounds, allow to identify a series of molecules able to potently interact with the target enzyme and to disclose an interesting hit: compound 2b showed to interact with the ATP binding site in the N-terminus domain of Hsp90 and to efficiently inhibit the chaperone activity.

  11. Diverse Regulation of Temperature Sensation by Trimeric G-Protein Signaling in Caenorhabditis elegans

    PubMed Central

    Ujisawa, Tomoyo; Ohta, Akane; Uda-Yagi, Misato

    2016-01-01

    Temperature sensation by the nervous system is essential for life and proliferation of animals. The molecular-physiological mechanisms underlying temperature signaling have not been fully elucidated. We show here that diverse regulatory machinery underlies temperature sensation through trimeric G-protein signaling in the nematode Caenorhabditis elegans. Molecular-genetic studies demonstrated that cold tolerance is regulated by additive functions of three Gα proteins in a temperature-sensing neuron, ASJ, which is also known to be a light-sensing neuron. Optical recording of calcium concentration in ASJ upon temperature-changes demonstrated that three Gα proteins act in different aspects of temperature signaling. Calcium concentration changes in ASJ upon temperature change were unexpectedly decreased in a mutant defective in phosphodiesterase, which is well known as a negative regulator of calcium increase. Together, these data demonstrate commonalities and differences in the molecular components concerned with light and temperature signaling in a single sensory neuron. PMID:27788246

  12. Infrared spectra of the Ne2-N2O, Ar2-N2O trimers

    NASA Astrophysics Data System (ADS)

    Rezaei, M.; Michaelian, K. H.; McKellar, A. R. W.; Moazzen-Ahmadi, N.

    2012-08-01

    Spectra of the van der Waals trimers Ar2-N2O and Ne2-N2O are studied in the region of the N2O ν1 fundamental (≈2220 cm-1) using a tunable quantum cascade laser to probe a pulsed supersonic expansion from a slit jet nozzle. Improved data are obtained for the dimers Ar-N2O and Ne-N2O, and the Q-branch of Ar3-N2O is tentatively assigned. The vibrational shifts for Nen-N2O are almost exactly linear for n = 0-2. However, for Arn-N2O the n = 2 band origin is slightly blue-shifted compared to the linear prediction, and the n = 3 origin (if correct) is more significantly blue-shifted (by 0.09 cm-1).

  13. Theoretical research program to study transition metal trimers and embedded clusters

    NASA Technical Reports Server (NTRS)

    Walch, S. P.

    1985-01-01

    Small transition metal clusters at a high level of approximation i.e. including all the valence electrons in the calculation and also including extensive electron correlation were studied. Perhaps the most useful end result of these studies is the qualitative information about the electronic structure of these small metal clusters, including the nature of the bonding. The electronic structure studies of the small clusters are directly applicable to problems in catalysis. From comparison of dimers, trimers and possibly higher clusters, it is possible to extrapolate the information obtained to provide insights into the electronic structure of bulk transition metals and their interaction with other atoms and molecules at both surface and interior locations.

  14. LINC Complexes Form by Binding of Three KASH Peptides to Domain Interfaces of Trimeric SUN Proteins

    SciTech Connect

    Sosa, Brian A.; Rothballer, Andrea; Kutay, Ulrike; Schwartz, Thomas U.

    2012-08-31

    Linker of nucleoskeleton and cytoskeleton (LINC) complexes span the nuclear envelope and are composed of KASH and SUN proteins residing in the outer and inner nuclear membrane, respectively. LINC formation relies on direct binding of KASH and SUN in the perinuclear space. Thereby, molecular tethers are formed that can transmit forces for chromosome movements, nuclear migration, and anchorage. We present crystal structures of the human SUN2-KASH1/2 complex, the core of the LINC complex. The SUN2 domain is rigidly attached to a trimeric coiled coil that prepositions it to bind three KASH peptides. The peptides bind in three deep and expansive grooves formed between adjacent SUN domains, effectively acting as molecular glue. In addition, a disulfide between conserved cysteines on SUN and KASH covalently links both proteins. The structure provides the basis of LINC complex formation and suggests a model for how LINC complexes might arrange into higher-order clusters to enhance force-coupling.

  15. Characterization of a trimeric MPER containing HIV-1 gp41 antigen

    SciTech Connect

    Hinz, Andreas; Schoehn, Guy; Quendler, Heribert; Hulsik, David Lutje; Stiegler, Gabi; Katinger, Hermann; Seaman, Michael S.; Montefiori, David; Weissenhorn, Winfried

    2009-08-01

    The membrane-proximal external region (MPER) of gp41 is considered as a prime target for the induction of neutralizing antibodies, since it contains the epitopes for three broadly neutralizing antibodies (2F5, 4E10 and Z13). Here we present a novel gp41 construct (HA-gp41) comprising gp41 HR2 and MPER fused to two triple-stranded coiled-coil domains at both ends. HA-gp41 is trimeric, has a high helical content in solution and forms rod-like structures as revealed by negative staining electron microscopy. Immunization of rabbits with HA-gp41 induced antibodies directed against MPER, which failed to exert significant neutralization capacity against envelopes from primary isolates. Thus trimerisation of MPER regions does not suffice to induce a potent neutralizing antibody response specific for conserved regions within gp41.

  16. Theranostic Value of Multimers: Lessons Learned from Trimerization of Neurotensin Receptor Ligands and Other Targeting Vectors

    PubMed Central

    Maschauer, Simone; Einsiedel, Jürgen; Reich, Dominik; Hübner, Harald; Gmeiner, Peter; Wester, Hans-Jürgen; Prante, Olaf; Notni, Johannes

    2017-01-01

    Neurotensin receptor 1 (NTS1) is overexpressed on a variety of cancer entities; for example, prostate cancer, ductal pancreatic adenocarcinoma, and breast cancer. Therefore, it represents an interesting target for the diagnosis of these cancers types by positron emission tomography (PET). The metabolically-stabilized neurotensin (NT) derivative peptide Nlys8-Lys9-Pro10-Tyr11-Tle12-Leu13-OH was elongated at the N-terminus with 6-azido norleucine and coupled with the 1,4,7-triazacyclononane-1,4,7-tris[(2-carboxyethyl)methylenephosphinic acid] (TRAP) chelator TRAP(alkyne)3 in order to synthesize a NT trimer with subnanomolar affinity and high stability. The 68Ga-labeled peptide [68Ga]Ga-TRAP(NT4)3 was characterized in vitro using the NTS1-expressing human colorectal adenocarcinoma cell line HT29. It displayed fast and high internalization rates of >90%, but also fast efflux rates of 50% over 15 min. In vivo, [68Ga]Ga-TRAP(NT4)3 showed moderate HT29 tumor uptake values of 1.7 %ID/g at 60 min post-injection (p.i.), but also high uptake and retention in the kidneys and liver. A comparison of data for trimer/monomer pairs of NT ligands and other targeting vectors (peptides and peptoids targeting integrins αvβ3, α5β1, and αvβ6, the PSMA-ligand DUPA (2-[3-(1,3-dicarboxypropyl)-ureido]pentanedioic acid), and nitroimidazoles targeting hypoxia) revealed that multimers always exhibit higher target affinities and tumor uptake, but not necessarily improved tumor-to-tissue ratios. Thus, although in vitro data are not suitable for prediction of in vivo performance, multimers are potentially superior to monomers, particularly for applications where high tumor accumulation is crucial. PMID:28287433

  17. Biochemical, conformational, and immunogenic analysis of soluble trimeric forms of henipavirus fusion glycoproteins.

    PubMed

    Chan, Yee-Peng; Lu, Min; Dutta, Somnath; Yan, Lianying; Barr, Jennifer; Flora, Michael; Feng, Yan-Ru; Xu, Kai; Nikolov, Dimitar B; Wang, Lin-Fa; Skiniotis, Georgios; Broder, Christopher C

    2012-11-01

    The henipaviruses, Hendra virus (HeV) and Nipah virus (NiV), are paramyxoviruses discovered in the mid- to late 1990s that possess a broad host tropism and are known to cause severe and often fatal disease in both humans and animals. HeV and NiV infect cells by a pH-independent membrane fusion mechanism facilitated by their attachment (G) and fusion (F) glycoproteins. Here, several soluble forms of henipavirus F (sF) were engineered and characterized. Recombinant sF was produced by deleting the transmembrane (TM) and cytoplasmic tail (CT) domains and appending a glycosylphosphatidylinositol (GPI) anchor signal sequence followed by GPI-phospholipase D digestion, appending a trimeric coiled-coil (GCNt) domain (sF(GCNt)), or deleting the TM, CT, and fusion peptide domain. These sF glycoproteins were produced as F(0) precursors, and all were apparent stable trimers recognized by NiV-specific antisera. Surprisingly, however, only the GCNt-appended constructs (sF(GCNt)) could elicit cross-reactive henipavirus-neutralizing antibody in mice. In addition, sF(GCNt) constructs could be triggered in vitro by protease cleavage and heat to transition from an apparent prefusion to postfusion conformation, transitioning through an intermediate that could be captured by a peptide corresponding to the C-terminal heptad repeat domain of F. The pre- and postfusion structures of sF(GCNt) and non-GCNt-appended sF could be revealed by electron microscopy and were distinguishable by F-specific monoclonal antibodies. These data suggest that only certain sF constructs could serve as potential subunit vaccine immunogens against henipaviruses and also establish important tools for further structural, functional, and diagnostic studies on these important emerging viruses.

  18. Trimeric autotransporter DsrA is a major mediator of fibrinogen binding in Haemophilus ducreyi.

    PubMed

    Fusco, William G; Elkins, Christopher; Leduc, Isabelle

    2013-12-01

    Haemophilus ducreyi is the etiologic agent of the sexually transmitted genital ulcer disease chancroid. In both natural and experimental chancroid, H. ducreyi colocalizes with fibrin at the base of the ulcer. Fibrin is obtained by cleavage of the serum glycoprotein fibrinogen (Fg) by thrombin to initiate formation of the blood clot. Fg binding proteins are critical virulence factors in medically important Gram-positive bacteria. H. ducreyi has previously been shown to bind Fg in an agglutination assay, and the H. ducreyi Fg binding protein FgbA was identified in ligand blotting with denatured proteins. To better characterize the interaction of H. ducreyi with Fg, we examined Fg binding to intact, viable H. ducreyi bacteria and identified a novel Fg binding protein. H. ducreyi bound unlabeled Fg in a dose-dependent manner, as measured by two different methods. In ligand blotting with total denatured cellular proteins, digoxigenin (DIG)-Fg bound only two H. ducreyi proteins, the trimeric autotransporter DsrA and the lectin DltA; however, only the isogenic dsrA mutant had significantly less cell-associated Fg than parental strains in Fg binding assays with intact bacteria. Furthermore, expression of DsrA, but not DltA or an empty vector, rendered the non-Fg-binding H. influenzae strain Rd capable of binding Fg. A 13-amino-acid sequence in the C-terminal section of the passenger domain of DsrA appears to be involved in Fg binding by H. ducreyi. Taken together, these data suggest that the trimeric autotransporter DsrA is a major determinant of Fg binding at the surface of H. ducreyi.

  19. HSF1 Protects Neurons through a Novel Trimerization- and HSP-Independent Mechanism

    PubMed Central

    Verma, Pragya; Pfister, Jason A.; Mallick, Sathi

    2014-01-01

    Heat shock factor 1 (HSF1) protects neurons from death caused by the accumulation of misfolded proteins. It is believed that this protective effect is mediated by the transcriptional stimulation of genes encoding heat shock proteins (HSPs), a family of chaperones that refold or degrade misfolded proteins. Whether HSF1 is protective when neuronal death is not caused by protein misfolding has not been studied. Here, we report that HSF1 expression is necessary for the survival of rat neurons and that HSF1 mRNA and protein expression is reduced in neurons primed to die. Knock-down of HSF1 induces death of otherwise healthy neurons, whereas reestablishment of elevated levels of HSF1 protects neurons even when death is not due to accumulation of misfolded proteins. Neuroprotection by HSF1 does not require its trimerization, an event obligatory for the binding of HSF1 to heat shock elements within HSP gene promoters. Moreover, knock-down of HSP70 or blockade of HSP90 signaling does not reduce neuroprotection by HSF1. Although several neuroprotective molecules and signaling pathways, including CaMK, PKA, Casein kinase-II, and the Raf-MEK-ERK and PI-3K-Akt pathways, are not required for HSF1-mediated neuroprotection, protection is abrogated by inhibition of classical histone deacetylases (HDACs). We report that the novel mechanism of neuroprotection by HSF1 involves cooperation with SIRT1, an HDAC with well documented neuroprotective effects. Using a cell culture model of Huntington's disease, we show that HSF1 trimerization is not required for protection against mutant huntingtin-induced neurotoxicity, suggesting that HSF1 can protect neurons against both proteinopathic and nonproteinopathic death through a noncanonical pathway. PMID:24478344

  20. HSF1 protects neurons through a novel trimerization- and HSP-independent mechanism.

    PubMed

    Verma, Pragya; Pfister, Jason A; Mallick, Sathi; D'Mello, Santosh R

    2014-01-29

    Heat shock factor 1 (HSF1) protects neurons from death caused by the accumulation of misfolded proteins. It is believed that this protective effect is mediated by the transcriptional stimulation of genes encoding heat shock proteins (HSPs), a family of chaperones that refold or degrade misfolded proteins. Whether HSF1 is protective when neuronal death is not caused by protein misfolding has not been studied. Here, we report that HSF1 expression is necessary for the survival of rat neurons and that HSF1 mRNA and protein expression is reduced in neurons primed to die. Knock-down of HSF1 induces death of otherwise healthy neurons, whereas reestablishment of elevated levels of HSF1 protects neurons even when death is not due to accumulation of misfolded proteins. Neuroprotection by HSF1 does not require its trimerization, an event obligatory for the binding of HSF1 to heat shock elements within HSP gene promoters. Moreover, knock-down of HSP70 or blockade of HSP90 signaling does not reduce neuroprotection by HSF1. Although several neuroprotective molecules and signaling pathways, including CaMK, PKA, Casein kinase-II, and the Raf-MEK-ERK and PI-3K-Akt pathways, are not required for HSF1-mediated neuroprotection, protection is abrogated by inhibition of classical histone deacetylases (HDACs). We report that the novel mechanism of neuroprotection by HSF1 involves cooperation with SIRT1, an HDAC with well documented neuroprotective effects. Using a cell culture model of Huntington's disease, we show that HSF1 trimerization is not required for protection against mutant huntingtin-induced neurotoxicity, suggesting that HSF1 can protect neurons against both proteinopathic and nonproteinopathic death through a noncanonical pathway.

  1. Ubiquitination of p27 is regulated by Cdk-dependent phosphorylation and trimeric complex formation

    PubMed Central

    Montagnoli, Alessia; Fiore, Francesca; Eytan, Esther; Carrano, Andrea C.; Draetta, Giulio F.; Hershko, Avram; Pagano, Michele

    1999-01-01

    The cellular abundance of the cyclin-dependent kinase (Cdk) inhibitor p27 is regulated by the ubiquitin–proteasome system. Activation of p27 degradation is seen in proliferating cells and in many types of aggressive human carcinomas. p27 can be phosphorylated on threonine 187 by Cdks, and cyclin E/Cdk2 overexpression can stimulate the degradation of wild-type p27, but not of a threonine 187-to-alanine p27 mutant [p27(T187A)]. However, whether threonine 187 phosphorylation stimulates p27 degradation through the ubiquitin–proteasome system or an alternative pathway is still not known. Here, we demonstrate that p27 ubiquitination (as assayed in vivo and in an in vitro reconstituted system) is cell-cycle regulated and that Cdk activity is required for the in vitro ubiquitination of p27. Furthermore, ubiquitination of wild-type p27, but not of p27(T187A), can occur in G1-enriched extracts only upon addition of cyclin E/Cdk2 or cyclin A/Cdk2. Using a phosphothreonine 187 site-specific antibody for p27, we show that threonine 187 phosphorylation of p27 is also cell-cycle dependent, being present in proliferating cells but undetectable in G1 cells. Finally, we show that in addition to threonine 187 phosphorylation, efficient p27 ubiquitination requires formation of a trimeric complex with the cyclin and Cdk subunits. In fact, cyclin B/Cdk1 which can phosphorylate p27 efficiently, but cannot form a stable complex with it, is unable to stimulate p27 ubiquitination by G1 extracts. Furthermore, another p27 mutant [p27(CK−)] that can be phosphorylated by cyclin E/Cdk2 but cannot bind this kinase complex, is refractory to ubiquitination. Thus throughout the cell cycle, both phosphorylation and trimeric complex formation act as signals for the ubiquitination of a Cdk inhibitor. PMID:10323868

  2. Vibronic model for H/D isotopic “self-organization” effects in hydrogen bond cyclic trimeric systems: 4-Bromopyrazole crystal IR spectra

    NASA Astrophysics Data System (ADS)

    Flakus, Henryk T.; Pyzik, Aleksandra

    2006-04-01

    In this paper, a theoretical model has been proposed, aiming to explain a new kind of H/D isotopic effects concerning hydrogen bond systems, i.e. the H/D isotopic "self-organization" effects, recently deduced from the IR spectra of molecular crystals. The problem of existence of these kinds of co-operative effects was considered in the limits of a vibronic model in the Herzberg-Teller approximation, for cyclic trimeric systems of hydrogen bonds. It was shown that non-conventional attraction forces between three identical hydrogen isotope atoms, resulting from the vibronic mechanism, are responsible for excess stabilization energy of cyclic hydrogen bond trimers. The H/D "self-organization" effects were deduced to be negligible in the case of non-symmetric HDD, or HHD-type trimers, containing both, hydrogen and deuterium bonds in one ring trimer. The symmetric trimers of the HHH and of the DDD-type should be more stable, when compared with the HDD, or the HHD-type trimer properties. This thermodynamic effect explains the IR spectral properties of molecular crystals containing cyclic trimers of hydrogen bonds in their lattices, accompanying to isotopic dilution. The results of the theoretical considerations were confronted with the IR spectra of 4-bromopyrazole crystals, which were measured in a wide temperature range (from 298 to 77 K), using polarized light, in the frequency ranges of the proton or deuterium stretching vibrations bands.

  3. pp-GalNAc-T13 induces high metastatic potential of murine Lewis lung cancer by generating trimeric Tn antigen

    SciTech Connect

    Matsumoto, Yasuyuki; Zhang, Qing; Akita, Kaoru; Nakada, Hiroshi; Hamamura, Kazunori; Tokuda, Noriyo; Tsuchida, Akiko; Matsubara, Takeshi; Hori, Tomoko; Okajima, Tetsuya; Furukawa, Keiko; Urano, Takeshi; Furukawa, Koichi

    2012-03-02

    Highlights: Black-Right-Pointing-Pointer ppGalNAc-T13 was up-regulated in high metastatic sublines of Lewis lung cancer. Black-Right-Pointing-Pointer ppGalNAc-T13 expression enhanced cell invasion activity in low metastatic sublines. Black-Right-Pointing-Pointer Trimeric Tn antigen was induced in the transfectant cells of ppGalNAc-T13 cDNA. Black-Right-Pointing-Pointer A major protein carrying trimeric Tn structure was identified as Syndecan-1. Black-Right-Pointing-Pointer Silencing of ppGalNAc-T13 resulted in the reduction of invasion and of metastasis.. -- Abstract: In order to analyze the mechanisms for cancer metastasis, high metastatic sublines (H7-A, H7-Lu, H7-O, C4-sc, and C4-ly) were obtained by repeated injection of mouse Lewis lung cancer sublines H7 and C4 into C57BL/6 mice. These sublines exhibited increased proliferation and invasion activity in vitro. Ganglioside profiles exhibited lower expression of GM1 in high metastatic sublines than the parent lines. Then, we established GM1-Si-1 and GM1-Si-2 by stable silencing of GM1 synthase in H7 cells. These GM1-knockdown clones exhibited increased proliferation and invasion. Then, we explored genes that markedly altered in the expression levels by DNA microarray in the combination of C4 vs. C4-ly or H7 vs. H7 (GM1-Si). Consequently, pp-GalNAc-T13 gene was identified as up-regulated genes in the high metastatic sublines. Stable transfection of pp-GalNAc-T13 cDNA into C4 (T13-TF) resulted in increased invasion and motility. Then, immunoblotting and flow cytometry using various antibodies and lectins were performed. Only anti-trimeric Tn antibody (mAb MLS128), showed increased expression levels of trimeric Tn antigen in T13-TF clones. Moreover, immunoprecipitation/immunoblotting was performed by mAb MLS128, leading to the identification of an 80 kDa band carrying trimeric Tn antigen, i.e. Syndecan-1. Stable silencing of endogenous pp-GalNAc-T13 in C4-sc (T13-KD) revealed that primary tumors generated by

  4. Cyanide-limited complexation of molybdenum(III): synthesis of octahedral [Mo(CN)(6)](3-) and cyano-bridged [Mo(2)(CN)(11)](5-).

    PubMed

    Beauvais, Laurance G; Long, Jeffrey R

    2002-03-13

    Octahedral coordination of molybdenum(III) is achieved by limiting the amount of cyanide available upon complex formation. Reaction of Mo(CF(3)SO(3))(3) with LiCN in DMF affords Li(3)[Mo(CN)(6)] x 6DMF (1), featuring the previously unknown octahedral complex [Mo(CN)(6)](3-). The complex exhibits a room-temperature moment of mu(eff) = 3.80 mu(B), and assignment of its absorption bands leads to the ligand field parameters Delta(o) = 24800 cm(-1) and B = 247 cm(-1). Further restricting the available cyanide in a reaction between Mo(CF(3)SO(3))(3) and (Et(4)N)CN in DMF, followed by recrystallization from DMF/MeOH, yields (Et(4)N)(5)[Mo(2)(CN)(11)] x 2DMF x 2MeOH (2). The dinuclear [Mo(2)(CN)(11)](5-) complex featured therein contains two octahedrally coordinated Mo(III) centers spanned by a bridging cyanide ligand. A fit to the magnetic susceptibility data for 2, gives J = -113 cm(-1) and g = 2.33, representing the strongest antiferromagnetic coupling yet observed through a cyanide bridge. Efforts to incorporate these new complexes in magnetic Prussian blue-type solids are ongoing.

  5. 4,2-Ribbon like ferromagnetic cyano-bridged Fe(III)2Ni(II) chains: a magneto-structural study.

    PubMed

    Toma, Luminita Marilena; Lescouëzec, Rodrigue; Uriel, Santiago; Llusar, Rosa; Ruiz-Pérez, Catalina; Vaissermann, Jacqueline; Lloret, Francesc; Julve, Miguel

    2007-09-07

    The low-spin iron(III) complex AsPh(4)[Fe(III)(bpy)(CN)(4)].CH(3)CN (1) [AsPh(4) = tetraphenylarsonium cation] and the heterobimetallic chains [{Fe(III)(L)(CN)(4)}(2)Ni(II)(H(2)O)(2)].4H(2)O with L = bpy (2) and phen (3) [bpy = 2,2'-bipyridine and phen = 1,10-phenanthroline] have been prepared and their structures determined by X-ray diffraction methods. The structure of 1 consists of mononuclear [Fe(bpy)(CN)(4)](-) anions, tetraphenylarsonium cations and acetonitrile molecules of crystallization. The iron(III) is hexacoordinated with two nitrogen atoms of the bidentate bpy and four carbon atoms of four terminal cyanide groups building a distorted octahedral surrounding around the metal atom. 2 and 3 are isomorphous compounds whose structure is made up of neutral 4,2-ribbon like bimetallic chains of formula [{Fe(III)(L)(CN)(4)}(2)Ni(II)(H(2)O)(2)] where the [Fe(III)(L)(CN)(4)](-) unit acts as a bis-monodentate bridging ligand toward the trans-diaquanickel(II) units through two of its four cyanide groups in cis positions. The chains exhibit two orientations in the unit cell and they interact with each other through hydrogen bonds involving the coordination and crystallization water molecules together with the uncoordinated cyanide nitrogen atoms of the [Fe(L)(CN)(4)](-) units. Compounds 2 and 3 behave as ferromagnetic Fe(III)(2)Ni(II) chains which interact ferromagnetically at very low temperatures in the case of 2, whereas metamagnetic-like behaviour is observed for with a critical field (H(c)) around 200 G. For H > H(c) the ferromagnetic Fe(III)(2)Ni(II) chains of 3 exhibit a frequency dependence of the out-of-phase ac susceptibility signal at T < 3.5 K.

  6. Hydrolyzable tannins of tamaricaceous plants. V. Structures of monomeric-trimeric tannins and cytotoxicity of macrocyclic-type tannins isolated from Tamarix nilotica (1).

    PubMed

    Orabi, Mohamed A A; Taniguchi, Shoko; Sakagami, Hiroshi; Yoshimura, Morio; Yoshida, Takashi; Hatano, Tsutomu

    2013-05-24

    Three new ellagitannin monomers, nilotinins M5-M7 (1-3), a dimer, nilotinin D10 (4), and a trimer, nilotinin T1 (5), together with three known dimers, hirtellin D (7) and tamarixinins B (8) and C (9), and a trimer, hirtellin T2 (6), were isolated from Tamarix nilotica dried leaves. The structures of the tannins were elucidated by intensive spectroscopic methods and chemical conversions into known tannins. The new trimer (5) is a unique macrocyclic type whose monomeric units are linked together by an isodehydrodigalloyl and two dehydrodigalloyl moieties. Additionally, dimeric and trimeric macrocyclic-type tannins isolated from T. nilotica in this study were assessed for possible cytotoxic activity against four human tumor cell lines. Tumor-selective cytotoxicities of the tested compounds were higher than those of synthetic and natural potent cytotoxic compounds, including polyphenols, and comparable with those of 5-fluorouracil and melphalan.

  7. Molecular structure and vibrational analysis of 5-nitro-6-methyluracil molecule based on monomer, dimer and trimer calculations

    NASA Astrophysics Data System (ADS)

    Alam, M. J.; Bhat, S. A.; Ahmad, S.

    2016-05-01

    Molecular structure and vibrational spectra of 5-nitro-6-methyluracil molecule have been studied by the simulation of its monomer, dimer and trimer forms using DFT and MP2 methods with 6-311G(d,p) basis set. Anharmonic force field calculations have been carried out for the isolated monomer, while the calculations on dimer and trimer have been done in the harmonic approximation. An accurate numerical integration grid has been used for geometry optimization as well as frequency calculation. Anharmonic vibrational frequencies have been computed using VPT2 algorithm (Barone's method) as well as VSCF and VSCF-PT2 approaches. These methods yield results that are in remarkable agreement with the experiment. The coupling strengths between pair of modes have been also calculated using coupling integral based on 2MR-QFF approximation. The vibrational assignments have been made with the help of potential energy distribution values and animated modes.

  8. Direct measurement of excitation transfer dynamics between two trimers in C-phycocyanin hexamer from cyanobacterium Anabaena variabilis

    NASA Astrophysics Data System (ADS)

    Zhang, Jingmin; Zhao, Fuli; Zheng, Xiguang; Wang, Hezhou

    1999-05-01

    We provide the first experimental evidence for the excitation transfers between two trimers of an isolated C-phycocyanin hexamer (αβ) 6PCL RC27, at the end of the rod proximal to the core of PBS in cyanobacterium of Anabaena variabilis, with picosecond time-resolved fluorescence spectroscopy. Our results strongly suggest that the observed fluorescence decay constants around 20 and 10 ps time scales, shown in anisotropy decay, not in isotropic decay experiments arose from the excitation transfers between two trimers via two types of transfer pathways such as 1β 155↔6β 155 (2β 155↔5β 155 and 3β 155↔4β 155) and 2α 84↔5α 84 (3α 84↔6α 84 and 1α 84↔4α 84) channels and these could be described by Föster dipole-dipole resonance mechanism.

  9. Honokiol trimers and dimers via biotransformation catalyzed by Momordica charantia peroxidase: novel and potent α-glucosidase inhibitors.

    PubMed

    He, Ye; Wang, Xiao-Bing; Fan, Bo-Yi; Kong, Ling-Yi

    2014-01-15

    Ten honokiol oligomers (1-10), including four novel trimers (1-4) and four novel dimers (5-8), were obtained by means of biotransformation of honokiol catalyzed by Momordica charantia peroxidase (MCP) for the first time. Their structures were established on the basis of spectroscopic methods. The biological results demonstrated that most of the oligomers were capable of inhibiting α-glucosidase with significant abilities, which were one to two orders of magnitude more potent than the substrate, honokiol. In particular, compound 2, the honokiol trimer, displayed the greatest inhibitory activity against α-glucosidase with an IC50 value of 1.38μM. Kinetic and CD studies indicated that 2 inhibited α-glucosidase in a reversible, mixed-type manner and caused conformational changes in the secondary structure of the enzyme protein. These findings suggested that 2 might be exploited as a promising drug candidate for the treatment of diabetes.

  10. Design and structure of two HIV-1 clade C SOSIP.664 trimers that increase the arsenal of native-like Env immunogens.

    PubMed

    Julien, Jean-Philippe; Lee, Jeong Hyun; Ozorowski, Gabriel; Hua, Yuanzi; Torrents de la Peña, Alba; de Taeye, Steven W; Nieusma, Travis; Cupo, Albert; Yasmeen, Anila; Golabek, Michael; Pugach, Pavel; Klasse, P J; Moore, John P; Sanders, Rogier W; Ward, Andrew B; Wilson, Ian A

    2015-09-22

    A key challenge in the quest toward an HIV-1 vaccine is design of immunogens that can generate a broadly neutralizing antibody (bnAb) response against the enormous sequence diversity of the HIV-1 envelope glycoprotein (Env). We previously demonstrated that a recombinant, soluble, fully cleaved SOSIP.664 trimer based on the clade A BG505 sequence is a faithful antigenic and structural mimic of the native trimer in its prefusion conformation. Here, we sought clade C native-like trimers with comparable properties. We identified DU422 and ZM197M SOSIP.664 trimers as being appropriately thermostable (Tm of 63.4 °C and 62.7 °C, respectively) and predominantly native-like, as determined by negative-stain electron microscopy (EM). Size exclusion chromatography, ELISA, and surface plasmon resonance further showed that these trimers properly display epitopes for all of the major bnAb classes, including quaternary-dependent, trimer-apex (e.g., PGT145) and gp120/gp41 interface (e.g., PGT151) epitopes. A cryo-EM reconstruction of the ZM197M SOSIP.664 trimer complexed with VRC01 Fab against the CD4 binding site at subnanometer resolution revealed a striking overall similarity to its BG505 counterpart with expected local conformational differences in the gp120 V1, V2, and V4 loops. These stable clade C trimers contribute additional diversity to the pool of native-like Env immunogens as key components of strategies to induce bnAbs to HIV-1.

  11. Energy transfer dynamics in trimers and aggregates of light-harvesting complex II probed by 2D electronic spectroscopy

    SciTech Connect

    Enriquez, Miriam M.; Zhang, Cheng; Tan, Howe-Siang; Akhtar, Parveen; Garab, Győző; Lambrev, Petar H.

    2015-06-07

    The pathways and dynamics of excitation energy transfer between the chlorophyll (Chl) domains in solubilized trimeric and aggregated light-harvesting complex II (LHCII) are examined using two-dimensional electronic spectroscopy (2DES). The LHCII trimers and aggregates exhibit the unquenched and quenched excitonic states of Chl a, respectively. 2DES allows direct correlation of excitation and emission energies of coupled states over population time delays, hence enabling mapping of the energy flow between Chls. By the excitation of the entire Chl b Q{sub y} band, energy transfer from Chl b to Chl a states is monitored in the LHCII trimers and aggregates. Global analysis of the two-dimensional (2D) spectra reveals that energy transfer from Chl b to Chl a occurs on fast and slow time scales of 240–270 fs and 2.8 ps for both forms of LHCII. 2D decay-associated spectra resulting from the global analysis identify the correlation between Chl states involved in the energy transfer and decay at a given lifetime. The contribution of singlet–singlet annihilation on the kinetics of Chl energy transfer and decay is also modelled and discussed. The results show a marked change in the energy transfer kinetics in the time range of a few picoseconds. Owing to slow energy equilibration processes, long-lived intermediate Chl a states are present in solubilized trimers, while in aggregates, the population decay of these excited states is significantly accelerated, suggesting that, overall, the energy transfer within the LHCII complexes is faster in the aggregated state.

  12. Energy transfer dynamics in trimers and aggregates of light-harvesting complex II probed by 2D electronic spectroscopy.

    PubMed

    Enriquez, Miriam M; Akhtar, Parveen; Zhang, Cheng; Garab, Győző; Lambrev, Petar H; Tan, Howe-Siang

    2015-06-07

    The pathways and dynamics of excitation energy transfer between the chlorophyll (Chl) domains in solubilized trimeric and aggregated light-harvesting complex II (LHCII) are examined using two-dimensional electronic spectroscopy (2DES). The LHCII trimers and aggregates exhibit the unquenched and quenched excitonic states of Chl a, respectively. 2DES allows direct correlation of excitation and emission energies of coupled states over population time delays, hence enabling mapping of the energy flow between Chls. By the excitation of the entire Chl b Qy band, energy transfer from Chl b to Chl a states is monitored in the LHCII trimers and aggregates. Global analysis of the two-dimensional (2D) spectra reveals that energy transfer from Chl b to Chl a occurs on fast and slow time scales of 240-270 fs and 2.8 ps for both forms of LHCII. 2D decay-associated spectra resulting from the global analysis identify the correlation between Chl states involved in the energy transfer and decay at a given lifetime. The contribution of singlet-singlet annihilation on the kinetics of Chl energy transfer and decay is also modelled and discussed. The results show a marked change in the energy transfer kinetics in the time range of a few picoseconds. Owing to slow energy equilibration processes, long-lived intermediate Chl a states are present in solubilized trimers, while in aggregates, the population decay of these excited states is significantly accelerated, suggesting that, overall, the energy transfer within the LHCII complexes is faster in the aggregated state.

  13. HIV-1 Nef responsiveness is determined by Env variable regions involved in trimer association and correlates with neutralization sensitivity.

    PubMed

    Usami, Yoshiko; Göttlinger, Heinrich

    2013-11-14

    HIV-1 Nef and the unrelated murine leukemia virus glycoGag similarly enhance the infectivity of HIV-1 virions. We now show that the effects of Nef and glycoGag are similarly determined by variable regions of HIV-1 gp120 that control Env trimer association and neutralization sensitivity. Whereas neutralization-sensitive X4-tropic Env proteins conferred high responsiveness to Nef and glycoGag, particles bearing neutralization-resistant R5-tropic Envs were considerably less affected. The profoundly different Nef/glycoGag responsiveness of a neutralization-resistant and a neutralization-sensitive R5-tropic Env could be switched by exchanging their gp120 V1/V2 regions, which also switches their neutralization sensitivity. Within V1/V2, the same determinants governed Nef/glycoGag responsiveness and neutralization sensitivity, indicating that these phenotypes are mechanistically linked. The V1/V2 and V3 regions, which form an apical trimer-association domain, together determined the Nef and glycoGag responsiveness of an X4-tropic Env. Our results suggest that Nef and glycoGag counteract the inactivation of Env spikes with relatively unstable apical trimer-association domains.

  14. A “Trimer of Dimers”—Based Model for the Chemotactic Signal Transduction Network in Bacterial Chemotaxis

    PubMed Central

    Xin, Xiangrong

    2013-01-01

    The network that controls chemotaxis in Escherichia coli is one of the most completely characterized signal transduction systems to date. Receptor clustering accounts for characteristics such as high sensitivity, precise adaptation over a wide dynamic range of ligand concentrations, and robustness to variations in the amounts of intracellular proteins. To gain insights into the structure-function relationship of receptor clusters and understand the mechanism behind the high-performance signaling, we develop and analyze a model for a single trimer of dimers. This new model extends an earlier model (Spiro et al. in Proc. Natl. Acad. Sci. 94:7263–7268, 1997) to incorporate the recent experimental findings that the core structure of receptor clusters is the trimer of receptor dimers. We show that the model can reproduce most of the experimentally-observed behaviors, including excitation, adaptation, high sensitivity, and robustness to parameter variations. In addition, the model makes a number of new predictions as to how the adaptation time varies with the expression level of various proteins involved in signal transduction. Our results provide a more mechanistically-based description of the structure-function relationship for the signaling system, and show the key role of the interaction among dimer members of the trimer in the chemotactic response of cells. PMID:22864951

  15. Fractional Mott insulator-to-superfluid transition of Bose-Hubbard model in a trimerized Kagomé optical lattice.

    PubMed

    Chen, Qi-Hui; Li, Peng; Su, Haibin

    2016-06-29

    By generalizing the traditional single-site strong coupling expansion approach to a cluster one, we study the zero-temperature phase diagram of bosonic atoms in a trimerized Kagomé optical lattice. Some new features are present in this system. Due to the strong intra-trimer hopping interaction, there will be a new Mott insulator (MI), which is by definition incompressible but with a fractional filling per trimer. This is different from the traditional MI, which has an integral filling and originates only from the repulsive interaction between particles. We investigate the MI-to-superfluid transition and the nature of the fractional MI by calculating the critical exponents of phase transitions and the low-lying energy excitation spectra of quasiparticles (quasihole). We will show how the low-energy properties of this system can be understood qualitatively as a Bose-Hubbard model in triangular lattice from the point of view of the cluster strong coupling expansion. We also discuss how our results are related to experiment by studying the Bragg spectroscopy.

  16. Fractional Mott insulator-to-superfluid transition of Bose-Hubbard model in a trimerized Kagomé optical lattice

    NASA Astrophysics Data System (ADS)

    Chen, Qi-Hui; Li, Peng; Su, Haibin

    2016-06-01

    By generalizing the traditional single-site strong coupling expansion approach to a cluster one, we study the zero-temperature phase diagram of bosonic atoms in a trimerized Kagomé optical lattice. Some new features are present in this system. Due to the strong intra-trimer hopping interaction, there will be a new Mott insulator (MI), which is by definition incompressible but with a fractional filling per trimer. This is different from the traditional MI, which has an integral filling and originates only from the repulsive interaction between particles. We investigate the MI-to-superfluid transition and the nature of the fractional MI by calculating the critical exponents of phase transitions and the low-lying energy excitation spectra of quasiparticles (quasihole). We will show how the low-energy properties of this system can be understood qualitatively as a Bose-Hubbard model in triangular lattice from the point of view of the cluster strong coupling expansion. We also discuss how our results are related to experiment by studying the Bragg spectroscopy.

  17. Quantifying Dimer and Trimer Formation of Tri-n-butyl Phosphates in Different Alkane Diluents: FTIR Study.

    PubMed

    Vo, Quynh N; Unangst, Jaclynn L; Nguyen, Hung D; Nilsson, Mikael

    2016-07-21

    Tri-n-butyl phosphate (TBP), a representative of neutral organophosphorous metal-ion-extracting reagents, is an important ligand used in solvent extraction processes for the recovery of uranium and plutonium from spent nuclear fuel, as well as other non-nuclear applications. Ligand-ligand and organic solvent-ligand interactions play an important role in these processes. The self-association behavior of TBP in various alkane diluents of different chain lengths (8, 12, and 16 carbons) and a branched alkane (iso-octane) was investigated by Fourier transform infrared spectroscopic measurements. By careful deconvolution of the spectra into multiple peaks, our results indicate that TBP self-associates to form not only dimers, as previous studies showed, but also trimers in the practical concentration range. Using a mathematical fitting procedure, the dimerization and trimerization constants were determined. As expected, these equilibrium constants are dependent on the solvent used. As the alkane chain for linear hydrocarbon solvents becomes longer, dimerization decreases whereas trimerization increases. For the more branched hydrocarbon, we observe a significantly higher dimerization constant. These effects are most likely due to the intermolecular van der Waals interactions between the butyl tails of each TBP molecule and the diluent hydrocarbon chain as all solvents in this study are relatively nonpolar.

  18. Quantifying Dimer and Trimer Formation by Tri-n-butyl Phosphates in n-Dodecane: Molecular Dynamics Simulations.

    PubMed

    Vo, Quynh N; Dang, Liem X; Nilsson, Mikael; Nguyen, Hung D

    2016-07-21

    Tri-n-butyl phosphate (TBP), a representative of neutral organophosphorous ligands, is an important extractant used in the solvent extraction process for the recovery of uranium and plutonium from spent nuclear fuel. Microscopic pictures of TBP isomerism and its behavior in n-dodecane diluent were investigated utilizing MD simulations with previously optimized force field parameters for TBP and n-dodecane. Potential mean force (PMF) calculations on a single TBP molecule show seven probable TBP isomers. Radial distribution functions (RDFs) of TBP suggest the existence of TBP trimers at high TBP concentrations in addition to dimers. 2D PMF calculations were performed to determine the angle and distance criteria for TBP trimers. The dimerization and trimerization constants of TBP in n-dodecane were obtained and match our own experimental values using the FTIR technique. The new insights into the conformational behaviors of the TBP molecule as a monomer and as part of an aggregate could greatly aid in the understanding of the complexation between TBP and metal ions in a solvent extraction system.

  19. High Resolution Infrared Spectroscopy of the CO_2-CO Dimers and (CO_2)_2-CO Trimer

    NASA Astrophysics Data System (ADS)

    Barclay, A. J.; Sheybani-Deloui, S.; Michaelian, K. H.; McKellar, Bob; Moazzen-Ahmadi, Nasser

    2016-06-01

    Infrared spectra in the carbon monoxide CO stretch region (≈2150 cm-1) are assigned to the previously unobserved O-bonded form of the CO_2-CO dimer ("isomer 2"), which has a planar T-shaped structure like that of the previously observed C-bonded form ("isomer 1"). Results will also be reported for both isomers of the 12C18O_2-substituted form of the dimer. In addition, we have observed two combination bands for each isomer yielding the first experimental determinations of intermolecular frequencies for the planar T-shaped structures. Within both of the fundamental bands, weak "satellite bands" are observed. These are tentatively assigned to the trimer He-CO_2-CO. To the higher side of the fundamental for "isomer 1", we have observed a weaker b-type band which we have assigned to (CO_2)_2-CO trimer. This trimer has a "pin wheel" structure with C2 symmetry and the derived experimental structural parameters match well with those obtained from ab initio calculations.

  20. UpaG, a New Member of the Trimeric Autotransporter Family of Adhesins in Uropathogenic Escherichia coli▿ †

    PubMed Central

    Valle, Jaione; Mabbett, Amanda N.; Ulett, Glen C.; Toledo-Arana, Alejandro; Wecker, Karine; Totsika, Makrina; Schembri, Mark A.; Ghigo, Jean-Marc; Beloin, Christophe

    2008-01-01

    The ability of Escherichia coli to colonize both intestinal and extraintestinal sites is driven by the presence of specific virulence factors, among which are the autotransporter (AT) proteins. Members of the trimeric AT adhesin family are important virulence factors for several gram-negative pathogens and mediate adherence to eukaryotic cells and extracellular matrix (ECM) proteins. In this study, we characterized a new trimeric AT adhesin (UpaG) from uropathogenic E. coli (UPEC). Molecular analysis of UpaG revealed that it is translocated to the cell surface and adopts a multimeric conformation. We demonstrated that UpaG is able to promote cell aggregation and biofilm formation on abiotic surfaces in CFT073 and various UPEC strains. In addition, UpaG expression resulted in the adhesion of CFT073 to human bladder epithelial cells, with specific affinity to fibronectin and laminin. Prevalence analysis revealed that upaG is strongly associated with E. coli strains from the B2 and D phylogenetic groups, while deletion of upaG had no significant effect on the ability of CFT073 to colonize the mouse urinary tract. Thus, UpaG is a novel trimeric AT adhesin from E. coli that mediates aggregation, biofilm formation, and adhesion to various ECM proteins. PMID:18424525

  1. Detection of a Trimeric Human Immunodeficiency Virus Type 1 Gag Intermediate Is Dependent on Sequences in the Matrix Protein, p17

    PubMed Central

    Morikawa, Yuko; Zhang, Wei-Hong; Hockley, David J.; Nermut, Milan V.; Jones, Ian M.

    1998-01-01

    Previous studies have shown that single amino acid changes in the amino-terminal matrix (MA) domain, p17, of the human immunodeficiency virus type 1 Gag precursor Pr55, can abrogate virion particle assembly. In the three-dimensional structure of MA such mutations lie in a single helix spanning residues 54 to 68, suggesting a key role for this helix in the assembly process. The fundamental nature of this involvement, however, remains poorly understood. In the present study, the essential features of the MA helix required for virus assembly have been investigated through the analysis of a further 15 site-directed mutants. With previous mutants that failed to assemble, residues mapped as critical for assembly were all located on the hydrophobic face of the helix and had a key role in stabilizing the trimeric interface. This implies a role for the MA trimer in virus assembly. We support this interpretation by showing that purified MA is trimeric in solution and that mutations that prevent virus assembly also prevent trimerization. Trimerization in solution was also a property of a larger MA-capsid (CA) Gag molecule, while under the same conditions CA only was a monomer. These data suggest that Gag trimerization driven by the MA domain is an intermediate stage in normal virion assembly and that it relies, in turn, on an MA conformation dependent on the hydrophobic core of the molecule. PMID:9696871

  2. Bioinformatic Characterization of the Trimeric Intracellular Cation-Specific Channel Protein Family

    PubMed Central

    Silverio, Abe L. F.

    2014-01-01

    Trimeric intracellular cation-specific (TRIC) channels are integral to muscle excitation–contraction coupling. TRIC channels provide counter-ionic flux when calcium is rapidly transported from intracellular stores to the cell cytoplasm. Until recently, knowledge of the presence of these proteins was limited to animals. We analyzed the TRIC family and identified a profusion of prokaryotic family members with topologies and motifs similar to those of their eukaryotic counterparts. Prokaryotic members far outnumber eukaryotic members, and although none has been functionally characterized, the evidence suggests that they function as secondary carriers. The presence of fused N- or C-terminal domains of known biochemical functions as well as genomic context analyses provide clues about the functions of these prokaryotic homologs. They are proposed to function in metabolite (e.g., amino acid/ nucleotide) efflux. Phylogenetic analysis revealed that TRIC channel homologs diverged relatively early during evolutionary history and that horizontal gene transfer was frequent in prokaryotes but not in eukaryotes. Topological analyses of TRIC channels revealed that these proteins possess seven putative transmembrane segments (TMSs), which arose by intragenic duplication of a three-TMS polypeptide-encoding genetic element followed by addition of a seventh TMS at the C terminus to give the precursor of all current TRIC family homologs. We propose that this family arose in prokaryotes. PMID:21519847

  3. Unconventional N-Linked Glycosylation Promotes Trimeric Autotransporter Function in Kingella kingae and Aggregatibacter aphrophilus

    PubMed Central

    Rempe, Katherine A.; Spruce, Lynn A.; Porsch, Eric A.; Seeholzer, Steven H.; Nørskov-Lauritsen, Niels

    2015-01-01

    ABSTRACT Glycosylation is a widespread mechanism employed by both eukaryotes and bacteria to increase the functional diversity of their proteomes. The nontypeable Haemophilus influenzae glycosyltransferase HMW1C mediates unconventional N-linked glycosylation of the adhesive protein HMW1, which is encoded in a two-partner secretion system gene cluster that also encodes HMW1C. In this system, HMW1 is modified in the cytoplasm by sequential transfer of hexose residues. In the present study, we examined Kingella kingae and Aggregatibacter aphrophilus homologues of HMW1C that are not encoded near a gene encoding an obvious acceptor protein. We found both homologues to be functional glycosyltransferases and identified their substrates as the K. kingae Knh and the A. aphrophilus EmaA trimeric autotransporter proteins. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis revealed multiple sites of N-linked glycosylation on Knh and EmaA. Without glycosylation, Knh and EmaA failed to facilitate wild-type levels of bacterial autoaggregation or adherence to human epithelial cells, establishing that glycosylation is essential for proper protein function. PMID:26307167

  4. Spatial subunit distribution and in vitro functions of the novel trimeric PCNA complex from Sulfolobus tokodaii

    SciTech Connect

    Lu Shuhong; Li Zhuo; Wang Zhiyu; Ma Xiaoqing; Sheng Duohong; Ni Jinfeng; Shen Yulong

    2008-11-14

    The relationships among three PCNA (proliferating cell nuclear antigen) subunits in the hyperthermophilic archaeon Sulfolobus tokodaii (StoPCNAs) were analyzed and the effects of two PCNA complexes on the activities of the DNA helicase Hjm, DNA Ligase I, and Holliday junction specific endonuclease Hjc were tested. There was no strong self-interaction of each StoPCNA. StoPCNA1 and StoPCNA3 interacted with each other, so did StoPCNA2 and StoPCNA3, but no interaction between StoPCNA1 and StoPCNA2 was observed. Two trimeric complexes (designed StoPCNA123 and StoPCNA323) were formed in vitro and it was determined that StoPCNA323 was composed of one StoPCNA2 and two StoPCNA3 subunits, with StoPCNA2 bridging the two StoPCNA3 subunits. Both complexes inhibited the unwinding activity of Hjm and the ligation activity of DNA Ligase I. In contrast, both stimulated the Holliday junction cleavage activity of Hjc. Our results provide further evidence that in crenarchaea, the PCNAs exhibit diversity in subunit interaction and complex formation.

  5. Structure-properties relationship of carbazole and fluorene hybrid trimers: experimental and theoretical approaches.

    PubMed

    Tomkeviciene, Ausra; Grazulevicius, Juozas V; Volyniuk, Dmytro; Jankauskas, Vygintas; Sini, Gjergji

    2014-07-21

    Synthesis and properties of fluorene and carbazole derivatives having three electrophores per molecule with different architectures are reported. The synthesized compounds possess high thermal stabilities with 5% weight loss temperatures exceeding 350 °C. They form glasses with glass transition temperatures ranging from 60 to 68 °C. Cyclovoltammetric experiments revealed the high electrochemical stability of the fluorene trimer. In contrast, 2- and 2,7-fluorenyl substituted carbazole derivatives show irreversible oxidation in the CV experiments. The electron photoemission spectra of the films of the synthesized compounds revealed ionization potentials of 5.65-5.89 eV. Hole drift mobilities in the amorphous layers of the synthesized compounds reach 10(-2) cm(2) V(-1) s(-1) at high electric fields, as established by a xerographic time-of-flight technique. DFT calculations show that HOMO and LUMO orbitals of the compounds are very similar in energy and shape. The similar hole mobilities observed for the three compounds are discussed in the frame of the Marcus theory. An important influence of the alkyl groups on the ionization potentials and on the hole mobilities was also observed and its origin is discussed.

  6. The Resveratrol Trimer Miyabenol C Inhibits β-Secretase Activity and β-Amyloid Generation

    PubMed Central

    Hu, Jin; Lin, Ting; Gao, Yuehong; Xu, Junyue; Jiang, Chao; Wang, Guanghui; Bu, Guojun; Xu, Huaxi; Chen, Haifeng; Zhang, Yun-wu

    2015-01-01

    Accumulation and deposition of amyloid-β peptide (Aβ) in the brain is a primary cause of the pathogenesis of Alzheimer’s disease (AD). Aβ is generated from amyloid-β precursor protein (APP) through sequential cleavages first by β-secretase and then by γ-secretase. Inhibiting β-secretase activity is believed to be one of the most promising strategies for AD treatment. In the present study, we found that a resveratrol trimer, miyabenol C, isolated from stems and leaves of the small-leaf grape (Vitisthunbergii var. taiwaniana), can markedly reduce Aβ and sAPPβ levels in both cell cultures and the brain of AD model mice. Mechanistic studies revealed that miyabenol C affects neither protein levels of APP, the two major α-secretases ADAM10 and TACE, and the γ-secretase component Presenilin 1, nor γ-secretase-mediated Notch processing and TACE activity. In contrast, although miyabenol C has no effect on altering protein levels of the β-secretase BACE1, it can inhibit both in vitro and in vivo β-secretase activity. Together, our results indicate that miyabenol C is a prominent β-secretase inhibitor and lead compound for AD drug development. PMID:25629409

  7. Transition states from molecular symmetry groups: Analysis of non-rigid acetylene trimer

    NASA Astrophysics Data System (ADS)

    Bone, Richard G. A.; Rowlands, Timothy W.; Handy, Nicholas C.; Stone, Anthony J.

    We demonstrate that Longuet-Higgins' molecular symmetry (MS) group for describing non-rigid molecules allows deduction of the transition state for an intramolecular rearrangement and that the level of symmetry of the transition state is governed by very simple rules. Key pieces of information are the order of the MS group and the number of distinctly labelled forms represented by it. We also show that the local symmetry at stationary points on the potential energy surface is important and introduce natural definitions of narcissistic reactions and pathways using the laboratory-fixed inversion operation, giving examples of each. Inspection of normal modes is used to depict motion across the potential energy surface between a minimum-energy structure and a transition state. This analysis is applied to acetylene trimer, a recently observed van der Waals cluster. We elucidate the relationships between the stationary points identified by our earlier ab initio work. There are two transition state structures that together allow full interconversion between the 16 distinctly labelled forms of the global minimum.

  8. Time-Periodic Solutions of Driven-Damped Trimer Granular Crystals

    DOE PAGES

    Charalampidis, E. G.; Li, F.; Chong, C.; ...

    2015-01-01

    We consider time-periodic structures of granular crystals consisting of alternate chrome steel (S) and tungsten carbide (W) spherical particles where each unit cell follows the pattern of a 2 : 1 trimer: S-W-S. The configuration at the left boundary is driven by a harmonic in-time actuation with given amplitude and frequency while the right one is a fixed wall. Similar to the case of a dimer chain, the combination of dissipation, driving of the boundary, and intrinsic nonlinearity leads to complex dynamics. For fixed driving frequencies in each of the spectral gaps, we find that the nonlinear surface modes and the statesmore » dictated by the linear drive collide in a saddle-node bifurcation as the driving amplitude is increased, beyond which the dynamics of the system becomes chaotic. While the bifurcation structure is similar for solutions within the first and second gap, those in the first gap appear to be less robust. We also conduct a continuation in driving frequency, where it is apparent that the nonlinearity of the system results in a complex bifurcation diagram, involving an intricate set of loops of branches, especially within the spectral gap. The theoretical findings are qualitatively corroborated by the experimental full-field visualization of the time-periodic structures.« less

  9. Quantum signatures of charge flipping vortices in the Bose-Hubbard trimer

    NASA Astrophysics Data System (ADS)

    Jason, Peter; Johansson, Magnus

    2016-11-01

    In this work we study quantum signatures of charge flipping vortices, found in the classical discrete nonlinear Schrödinger trimer, by use of the Bose-Hubbard model. We are able to identify such signatures in the quantum energy eigenstates, for instance when comparing the site amplitudes of the classical charge flipping vortices with the probability distribution over different particle configurations. It is also discussed how to construct quantum states that correspond to the classical charge flipping vortices and which effects can lead to deviations between the classical and quantum dynamics. We also examine properties of certain coherent states: classical-like quantum states that can be used to derive the classical model. Several quantum signatures are identified when studying the dynamics of these coherent states, for example, when comparing the average number of particles on a site with the classical site amplitude, when comparing the quantum and classical currents and topological charge, and when studying the evolution of the quantum probability amplitudes. The flipping of the quantum currents are found to be an especially robust feature of these states.

  10. A path-integral Monte Carlo study of a small cluster: The Ar trimer

    NASA Astrophysics Data System (ADS)

    Pérez de Tudela, R.; Márquez-Mijares, M.; González-Lezana, T.; Roncero, O.; Miret-Artés, S.; Delgado-Barrio, G.; Villarreal, P.

    2010-06-01

    The Ar3 system has been studied between T =0 K and T =40 K by means of a path-integral Monte Carlo (PIMC) method. The behavior of the average energy in terms of the temperature has been explained by comparison with results obtained with the thermal averaged rovibrational spectra estimated via: (i) a quantum mechanical method based on distributed Gaussian functions for the interparticle distances and (ii) an analytical model which precisely accounts for the participation of the dissociative continua Ar2+Ar and Ar+Ar+Ar. Beyond T ˜20 K, the system explores floppier configurations than the rigid equilateral geometry, as linear and Ar-Ar2-like arrangements, and fragmentates around T ˜40 K. A careful investigation of the specific heat in terms of a confining radius in the PIMC calculation seems to discard a proper phase transition as in larger clusters, in apparent contradiction with previous reports of precise values for a liquid-gas transition. The onset of this noticeable change in the dynamics of the trimer occurs, however, at a remarkably low value of the temperature in comparison with Arn systems formed with more Ar atoms. Quantum mechanical effects are found of relevance at T ≤15 K, with both energies and radial distributions obtained with a quantum PIMC deviating from the corresponding classical results, thus precluding exclusively classical approaches for a precise description of the system at this low temperature range.

  11. Optical limiting properties of trimeric metallo-phthalocyanines/polymer composite films

    NASA Astrophysics Data System (ADS)

    Ali Özdağ, Mehmet; Ceyhan, Tanju; Gul Yaglioglu, H.; Elmali, Ayhan; Bekaroğlu, Özer

    2011-09-01

    The nonlinear absorption and optical limiting properties of two trimeric metallo-phthalocyanines namely, 2,4,6-tris[2-oxa-9,10,16,17,23,24-hexa(hexylthio) phthalocyaninato M(II)]-s-triazine (M=Zn for compound ZnPc and Cu for compound CuPc) doped polyvinyl chloride (PVC) thin film in the nanosecond regime were investigated by using the open-aperture Z-scan technique. The measurements were performed using 4 ns pulses generated from a frequency-doubled Nd:YAG laser at 532 nm wavelength. OL parameters of the ratio of the excited state to ground state absorption cross-sections κ, the effective nonlinear absorption coefficient βeff, the linear absorption coefficient α0 and the saturation density or energy density Fsat values were determined. The results show that MPc/PVC composite displays much larger nonlinear absorption coefficient and lower saturable fluence for optical limiting when compared to the same Pc molecules in solution. The results indicated that both compounds exhibited good OL performances. ZnPc shows slightly better OL parameters than that of CuPc.

  12. Conformational analysis of trimeric maleimide substituted 1,5,9-triazacyclododecane HIV fusion scaffolds.

    PubMed

    Remmert, Sarah; Hollis, Heather; Parish, Carol A

    2009-02-01

    An analysis of the conformational preferences of three trimeric maleimide substituted 1,5,9-triazacyclododecane derivatives, proposed as cross linking reagents for HIV-1 fusion inhibitors, is presented. Exhaustive sampling was performed using the mixed Low Mode Monte Carlo conformational searching technique on the corresponding OPLS2005/GBSA(water) potential energy surface. Geometric structure, molecular length, and hydrogen bonding patterns of the compounds are analyzed. Global minimum energy structures were verified as minima using B3LYP/6-31G * geometry optimization. All structures adopt a crown-like 12-membered ring conformation; however, the system with the shortest maleimide arms (1a) can also adopt alternative ring orientations. Overall, derivatives with longer maleimide arms were more flexible and resulted in ensembles with a larger number of low energy structures. Comparison with biological inhibition data indicates that there is very little relationship between molecular size and the ability of the scaffold to orient CD4M9 miniproteins for optimal inhibition; however hydrophobicity may play a role.

  13. Quantum signatures of charge flipping vortices in the Bose-Hubbard trimer.

    PubMed

    Jason, Peter; Johansson, Magnus

    2016-11-01

    In this work we study quantum signatures of charge flipping vortices, found in the classical discrete nonlinear Schrödinger trimer, by use of the Bose-Hubbard model. We are able to identify such signatures in the quantum energy eigenstates, for instance when comparing the site amplitudes of the classical charge flipping vortices with the probability distribution over different particle configurations. It is also discussed how to construct quantum states that correspond to the classical charge flipping vortices and which effects can lead to deviations between the classical and quantum dynamics. We also examine properties of certain coherent states: classical-like quantum states that can be used to derive the classical model. Several quantum signatures are identified when studying the dynamics of these coherent states, for example, when comparing the average number of particles on a site with the classical site amplitude, when comparing the quantum and classical currents and topological charge, and when studying the evolution of the quantum probability amplitudes. The flipping of the quantum currents are found to be an especially robust feature of these states.

  14. Bacillus cereus Response to a Proanthocyanidin Trimer, a Transcriptional and Functional Analysis.

    PubMed

    Tamura, Tomoko; Ozawa, Megumi; Tanaka, Naoto; Arai, Soichi; Mura, Kiyoshi

    2016-07-01

    Proanthocyanidins are abundant in peanut skin, and in this study, the antibacterial effects of a peanut skin extract (PSE) against food-borne bacteria were investigated to find its minimum inhibitory concentration. Food-borne gram-positive bacteria, and in particular Bacillus cereus, was more sensitive to PSE. In particular, the inhibitory activity of epicatechin-(4β → 6)-epicatechin-(2β → O→7, 4β → 8)-catechin (EEC), a proanthocyanidin trimer from peanut skin, against B. cereus was stronger than that of procyanidin A1, a proanthocyanidin dimer. DNA microarray analysis of B. cereus treated with EEC was carried out, with a finding that 597 genes were significantly up-regulated. Analysis of the up-regulated genes suggested that EEC disrupted the normal condition of the cell membrane and wall of B. cereus and alter its usual nutritional metabolism. Moreover, treatment of B. cereus with EEC inhibited glucose uptake, suggesting that EEC affects the cell-surface adsorption.

  15. Super stretchable electroactive elastomer formation driven by aniline trimer self-assembly

    PubMed Central

    Chen, Jing; Guo, Baolin; Eyster, Thomas W.; Ma, Peter X.

    2015-01-01

    Biomedical electroactive elastomers with a modulus similar to that of soft tissues are highly desirable for muscle, nerve, and other soft tissue replacement or regeneration, but have rarely been reported. In this work, superiorly stretchable electroactive polyurethane-urea elastomers were designed based on poly(lactide), poly(ethylene glycol), and aniline trimer (AT). A strain at break higher than 1600% and a modulus close to soft tissues was achieved from these copolymers. The mechanisms of super stretchability of the copolymer were systematically investigated. Crystallinity, chemical cross-linking, ionic cross-linking and hard domain formation were examined using differential scanning calorimetry (DSC), X-ray photoelectron spectroscopy (XPS), dynamic light scattering (DLS), nuclear magnetic resonance (NMR) measurements and transmission electron microscopy (TEM). The sphere-like hard domains self-assembled from AT segments were found to provide the crucial physical interactions needed for the novel super elastic material formation. These super stretchable copolymers were blended with conductive fillers such as polyaniline nanofibers and nanosized carbon black to achieve a high electric conductivity of 0.1 S/cm while maintaining an excellent stretchability and a modulus similar to that of soft tissues (lower than 10 MPa). PMID:26692638

  16. Infrared Spectra of the NE_2-N_2O, AR_2-N_2O Trimers

    NASA Astrophysics Data System (ADS)

    Rezaei, M.; Moazzen-Ahmadi, N.; Michaelian, K. H.; McKellar, A. R. W.

    2013-06-01

    Spectra of the van der Waals trimers Ar_2-N_2O and Ne_2-N_2O are studied in the region of the N_2O ν_1 fundamental (˜2224 cm^{-1}) using a tunable quantum cascade laser to probe a pulsed supersonic expansion from a slit jet nozzle. Improved data are also obtained for the dimers Ar-N_2O and Ne-N_2O, with the latter representing a significant improvement on the best previous results. As well, a feature in the spectrum is tentatively assigned as the Q-branch of Ar_3-N_2O. The observed vibrational shifts for Ne_n-N_2O are almost exactly linear for n = 0-2. However, for Ar_n-N_2O the n = 2 band origin is slightly blue-shifted compared to the linear prediction, and the n = 3 origin (if correct) is more significantly blue-shifted (by 0.09 cm^{-1}).

  17. A chromium precursor for the Phillips ethylene trimerization catalyst: (2-ethylhexanoate)2CrOH.

    PubMed

    Jeon, Jong Yeob; Park, Dong Sik; Lee, Dong Hwan; Eo, Seong Chan; Park, Seong Yeon; Jeong, Myoung Sun; Kang, Yi Young; Lee, Junseong; Lee, Bun Yeoul

    2015-06-28

    The conventional Phillips ethylene trimerization catalyst prepared by reacting Cr(EH)3 (EH = 2-ethylhexanoate), 2,5-dimethylpyrrole (Me2C4H2NH), Et3Al, and Et2AlCl in an aromatic hydrocarbon solvent was improved to obtain a congener composed of a new chromium precursor (EH)2CrOH, (Me2C4H2N)AlEt2, and Et3Al·ClAlEt2. Reaction of CrCl3 with 3 equiv. Na(EH) in water did not generate Cr(EH)3, but unexpectedly produced (EH)2CrOH. In comparison with the erratic catalytic performance of the original Phillips system, due to the ill-defined nature of the Cr(EH)3 source (16 or 6.8 × 10(6) g per mol-Cr h depending on the source), the improved system exhibited consistently high activity (54 × 10(6) g per mol-Cr h). Reaction of (EH)2CrOH with (Me2C4H2N)AlMe2·OEt2 afforded the dimeric Cr(II)-complex (6) coordinated by (η(5)-Me2C4H2N)AlMe2(NC4H2Me2) and μ2-κ(1):η(2)-Me2C4H2N ligands. 6 provided highly active species when activated with Et3Al·ClAlEt2.

  18. Magnetic properties of linear trimers in fluoride analogs of tetragonal tungsten bronze

    SciTech Connect

    Hong, Yaw-Shun; Boo, William O.J.; Mattern, Daniell L.

    2010-08-15

    The compounds KZnTiF{sub 6}, KZnVF{sub 6}, KVScF{sub 6}, KCrScF{sub 6}, and KMnScF{sub 6} are fluoride analogs of Tetragonal Tungsten Bronze. M{sup 2+}-M{sup 3+} ionic ordering in these fluorides provided systems which contained linear trinuclear complexes of their respective paramagnetic ions. Magnetic coupling within these linear trimers occurred below 100 K in each of the five systems. Derived magnetic susceptibility equations were fitted to observed magnetic susceptibilities for each of the possible spin systems: KZnTiF{sub 6} (S=1/2), J/k=-114 K; KZnVF{sub 6} (S=1), J/k=-39 K; KVScF{sub 6} (S=3/2), J/k=-16 K; KCrScF{sub 6} (S=2), J/k=-4 K; and KMnScF{sub 6} (S=5/2), J/k=-7.5 K. - Graphical abstract: Five fluoride analogs of Tetragonal Tungsten Bronze (KZnTiF{sub 6}, KZnVF{sub 6}, KVScF{sub 6}, KCrScF{sub 6}, and KMnScF{sub 6}) underwent M{sup 2+}-M{sup 3+} ionic ordering below 100 K, providing linear trinuclear complexes of their respective paramagnetic ions.

  19. Ultrafast spectroscopy of trimeric light-harvesting complex II from higher plants

    SciTech Connect

    Connelly, J.P.; Mueller, G.M.; Hucke, M.; Gatzen, G.; Holzwarth, A.R.; Mullineaux, C.W.; Ruban, A.V.; Horton, P.

    1997-03-06

    Time-resolved femtosecond transient absorption measurements have been carried out at room temperature on light-harvesting chlorophyll a/b protein complex of photosystem II (LHC II) trimers prepared from spinach. Exciting in the chlorophyll (Chl) b region at 650 nm with very low intensity, virtually annihilation-free two-color transient absorption measurement of the kinetics over 100 ps, between 645 and 690 nm, yield global lifetimes of 175 fs, 625 fs, and 5 ps and a long component (>=790 ps) where the three fastest lifetimes reflect Chl b to Chl a energy transfer. On the basis of these results and recent electron diffraction structural data, a preliminary three-pool Ch a, three-pool Chl b kinetic model is proposed. The possible influence of variable xanthophyll composition on quenching in LHC II preparations isolated from light- and dark-adapted leaves has been investigated using time-resolved picosecond fluorescence at room temperature. Global lifetimes of 5 ps and 3.6 ns, the lifetimes of the terminal LHC II excited state, were obtained. No discernable quenching effect due to the presence of zeaxanthin was observed. 38 refs., 6 figs., 3 tabs.

  20. Crystal Structure of Escherichia coli-Expressed Haloarcula marismortui Bacteriorhodopsin I in the Trimeric Form

    PubMed Central

    Round, Ekaterina; Borshchevskiy, Valentin; Utrobin, Petr; Popov, Alexander; Balandin, Taras; Büldt, Georg; Gordeliy, Valentin

    2014-01-01

    Bacteriorhodopsins are a large family of seven-helical transmembrane proteins that function as light-driven proton pumps. Here, we present the crystal structure of a new member of the family, Haloarcula marismortui bacteriorhodopsin I (HmBRI) D94N mutant, at the resolution of 2.5 Å. While the HmBRI retinal-binding pocket and proton donor site are similar to those of other archaeal proton pumps, its proton release region is extended and contains additional water molecules. The protein's fold is reinforced by three novel inter-helical hydrogen bonds, two of which result from double substitutions relative to Halobacterium salinarum bacteriorhodopsin and other similar proteins. Despite the expression in Escherichia coli and consequent absence of native lipids, the protein assembles as a trimer in crystals. The unique extended loop between the helices D and E of HmBRI makes contacts with the adjacent protomer and appears to stabilize the interface. Many lipidic hydrophobic tail groups are discernible in the membrane region, and their positions are similar to those of archaeal isoprenoid lipids in the crystals of other proton pumps, isolated from native or native-like sources. All these features might explain the HmBRI properties and establish the protein as a novel model for the microbial rhodopsin proton pumping studies. PMID:25479443

  1. Cross-protection conferred by filovirus virus-like particles containing trimeric hybrid glycoprotein.

    PubMed

    Martins, Karen; Carra, John H; Cooper, Christopher L; Kwilas, Steven A; Robinson, Camenzind G; Shurtleff, Amy C; Schokman, Rowena D; Kuehl, Kathleen A; Wells, Jay B; Steffens, Jesse T; van Tongeren, Sean A; Hooper, Jay W; Bavari, Sina

    2015-02-01

    Filoviruses are causative agents of hemorrhagic fever, and to date no effective vaccine or therapeutic has been approved to combat infection. Filovirus glycoprotein (GP) is the critical immunogenic component of filovirus vaccines, eliciting high levels of antibody after successful vaccination. Previous work has shown that protection against both Ebola virus (EBOV) and Marburg virus (MARV) can be achieved by vaccinating with a mixture of virus-like particles (VLPs) expressing either EBOV GP or MARV GP. In this study, the potential for eliciting effective immune responses against EBOV, Sudan virus, and MARV with a single GP construct was tested. Trimeric hybrid GPs were produced that expressed the sequence of Marburg GP2 in conjunction with a hybrid GP1 composed EBOV and Sudan virus GP sequences. VLPs expressing these constructs, along with EBOV VP40, provided comparable protection against MARV challenge, resulting in 75 or 100% protection. Protection from EBOV challenge differed depending upon the hybrid used, however, with one conferring 75% protection and one conferring no protection. By comparing the overall antibody titers and the neutralizing antibody titers specific for each virus, it is shown that higher antibody responses were elicited by the C terminal region of GP1 than by the N terminal region, and this correlated with protection. These data collectively suggest that GP2 and the C terminal region of GP1 are highly immunogenic, and they advance progress toward the development of a pan-filovirus vaccine.

  2. Antigenic and immunosuppressive properties of a trimeric recombinant transmembrane envelope protein gp41 of HIV-1

    PubMed Central

    Mühle, Michael; Lehmann, Melissa; Hoffmann, Kerstin; Stern, Daniel; Kroniger, Tobias; Luttmann, Werner

    2017-01-01

    The transmembrane envelope (TM) protein gp41 of the human immunodeficiency virus—1 (HIV-1) plays an important role during virus infection inducing the fusion of the viral and cellular membranes. In addition, there are indications that the TM protein plays a role in the immunopathogenesis leading to the acquired immunodeficiency syndrome (AIDS). Inactivated virus particles and recombinant gp41 have been reported to inhibit lymphocyte proliferation, as well as to alter cytokine release and gene expression. The same was shown for a peptide corresponding to a highly conserved domain of all retroviral TM proteins, the immunosuppressive domain. Due to its propensity to aggregate and to be expressed at low levels, studies comprising authentic gp41 produced in eukaryotic cells are extremely rare. Here we describe the production of a secreted, soluble recombinant gp41 in 293 cells. The antigen was purified to homogeneity and characterised thoroughly by various biochemical and immunological methods. It was shown that the protein was glycosylated and assembled into trimers. Binding studies by ELISA and surface plasmon resonance using conformation-specific monoclonal antibodies implied a six-helix bundle conformation. The low binding of broadly neutralising antibodies (bnAb) directed against the membrane proximal external region (MPER) suggested that this gp41 is probably not suited as vaccine to induce such bnAb. Purified gp41 bound to monocytes and to a lesser extent to lymphocytes and triggered the production of specific cytokines when added to normal peripheral blood mononuclear cells. In addition, gp41 expressed on target cells inhibited the antigen-specific response of murine CD8+ T cells by drastically impairing their IFNγ production. To our knowledge, this is the first comprehensive analysis of a gp41 produced in eukaryotic cells including its immunosuppressive properties. Our data provide another line of evidence that gp41 might be directly involved in HIV-1

  3. Thermal behavior of long wavelength absorption transitions in Spirulina platensis photosystem I trimers.

    PubMed Central

    Cometta, A; Zucchelli, G; Karapetyan, N V; Engelmann, E; Garlaschi, F M; Jennings, R C

    2000-01-01

    In photosystem I trimers of Spirulina platensis a major long wavelength transition is irreversibly bleached by illumination with high-intensity white light. The photobleaching hole, identified by both absorption and circular dichroism spectroscopies, is interpreted as the inhomogeneously broadened Q(y) transition of a chlorophyll form that absorbs maximally near 709 nm at room temperature. Analysis of the mean square deviation of the photobleaching hole between 80 and 300 K, in the linear electron-phonon frame, indicates that the optical reorganization energy is 52 cm(-1), four times greater than that for the bulk, short-wavelength-absorbing chlorophylls, and the inhomogenous site distribution bandwidth is close to 150 cm(-1). The room temperature bandwidth, close to 18.5 nm, is dominated by thermal (homogeneous) broadening. Photobleaching induces correlated circular dichroism changes, of opposite sign, at 709 and 670 nm, which suggests that the long wavelength transition may be a low energy excitonic band, in agreement with its high reorganization energy. Clear identification of the 709-nm spectral form was used in developing a Gaussian description of the long wavelength absorption tail by analyzing the changing band shape during photobleaching using a global decomposition procedure. Additional absorption states near 720, 733, and 743 nm were thus identified. The lowest energy state at 743 nm is present in substoichiometric levels at room temperature and its presence was confirmed by fluorescence spectroscopy. This state displays an unusual increase in intensity upon lowering the temperature, which is successfully described by assuming the presence of low-lying, thermally populated states. PMID:11106627

  4. Antigenicity and Immunogenicity of a Trimeric Envelope Protein from an Indian Clade C HIV-1 Isolate*

    PubMed Central

    Sneha Priya, Rangasamy; Veena, Menon; Kalisz, Irene; Whitney, Stephen; Priyanka, Dhopeshwarkar; LaBranche, Celia C.; Sri Teja, Mullapudi; Montefiori, David C.; Pal, Ranajit; Mahalingam, Sundarasamy; Kalyanaraman, Vaniambadi S.

    2015-01-01

    Human immunodeficiency virus type 1 (HIV-1) isolates from India mainly belong to clade C and are quite distinct from clade C isolates from Africa in terms of their phylogenetic makeup, serotype, and sensitivity to known human broadly neutralizing monoclonal antibodies. Because many of these properties are associated with the envelope proteins of HIV-1, it is of interest to study the envelope proteins of Indian clade C isolates as part of the ongoing efforts to develop a vaccine against HIV-1. To this end, we purified trimeric uncleaved gp145 of a CCR5 tropic Indian clade C HIV-1 (93IN101) from the conditioned medium of 293 cells. The purified protein was shown to be properly folded with stable structure by circular dichroism. Conformational integrity was further demonstrated by its high affinity binding to soluble CD4, CD4 binding site antibodies such as b12 and VRC01, quaternary epitope-specific antibody PG9, and CD4-induced epitope-specific antibody 17b. Sera from rabbits immunized with gp145 elicited high titer antibodies to various domains of gp120 and neutralized a broad spectrum of clade B and clade C HIV-1 isolates. Similar to other clade B and clade C envelope immunogens, most of the Tier 1 neutralizing activity could be absorbed with the V3-specific peptide. Subsequent boosting of these rabbits with a clade B HIV-1 Bal gp145 resulted in an expanded breadth of neutralization of HIV-1 isolates. The present study strongly supports the inclusion of envelopes from Indian isolates in a future mixture of HIV-1 vaccines. PMID:25691567

  5. Antigenic and immunosuppressive properties of a trimeric recombinant transmembrane envelope protein gp41 of HIV-1.

    PubMed

    Mühle, Michael; Lehmann, Melissa; Hoffmann, Kerstin; Stern, Daniel; Kroniger, Tobias; Luttmann, Werner; Denner, Joachim

    2017-01-01

    The transmembrane envelope (TM) protein gp41 of the human immunodeficiency virus-1 (HIV-1) plays an important role during virus infection inducing the fusion of the viral and cellular membranes. In addition, there are indications that the TM protein plays a role in the immunopathogenesis leading to the acquired immunodeficiency syndrome (AIDS). Inactivated virus particles and recombinant gp41 have been reported to inhibit lymphocyte proliferation, as well as to alter cytokine release and gene expression. The same was shown for a peptide corresponding to a highly conserved domain of all retroviral TM proteins, the immunosuppressive domain. Due to its propensity to aggregate and to be expressed at low levels, studies comprising authentic gp41 produced in eukaryotic cells are extremely rare. Here we describe the production of a secreted, soluble recombinant gp41 in 293 cells. The antigen was purified to homogeneity and characterised thoroughly by various biochemical and immunological methods. It was shown that the protein was glycosylated and assembled into trimers. Binding studies by ELISA and surface plasmon resonance using conformation-specific monoclonal antibodies implied a six-helix bundle conformation. The low binding of broadly neutralising antibodies (bnAb) directed against the membrane proximal external region (MPER) suggested that this gp41 is probably not suited as vaccine to induce such bnAb. Purified gp41 bound to monocytes and to a lesser extent to lymphocytes and triggered the production of specific cytokines when added to normal peripheral blood mononuclear cells. In addition, gp41 expressed on target cells inhibited the antigen-specific response of murine CD8+ T cells by drastically impairing their IFNγ production. To our knowledge, this is the first comprehensive analysis of a gp41 produced in eukaryotic cells including its immunosuppressive properties. Our data provide another line of evidence that gp41 might be directly involved in HIV-1

  6. Defining Potential Vaccine Targets of Haemophilus ducreyi Trimeric Autotransporter Adhesin DsrA.

    PubMed

    Fusco, William G; Choudhary, Neelima R; Stewart, Shelley M; Alam, S Munir; Sempowski, Gregory D; Elkins, Christopher; Leduc, Isabelle

    2015-04-01

    Haemophilus ducreyi is the causative agent of the sexually transmitted genital ulcer disease chancroid. Strains of H. ducreyi are grouped in two classes (I and II) based on genotypic and phenotypic differences, including those found in DsrA, an outer membrane protein belonging to the family of multifunctional trimeric autotransporter adhesins. DsrA is a key serum resistance factor of H. ducreyi that prevents binding of natural IgM at the bacterial surface and functions as an adhesin to fibronectin, fibrinogen, vitronectin, and human keratinocytes. Monoclonal antibodies (MAbs) were developed to recombinant DsrA (DsrA(I)) from prototypical class I strain 35000HP to define targets for vaccine and/or therapeutics. Two anti-DsrAI MAbs bound monomers and multimers of DsrA from genital and non-genital/cutaneous H. ducreyi strains in a Western blot and reacted to the surface of the genital strains; however, these MAbs did not recognize denatured or native DsrA from class II strains. In a modified extracellular matrix protein binding assay using viable H. ducreyi, one of the MAbs partially inhibited binding of fibronectin, fibrinogen, and vitronectin to class I H. ducreyi strain 35000HP, suggesting a role for anti-DsrA antibodies in preventing binding of H. ducreyi to extracellular matrix proteins. Standard ELISA and surface plasmon resonance using a peptide library representing full-length, mature DsrAI revealed the smallest nominal epitope bound by one of the MAbs to be MEQNTHNINKLS. Taken together, our findings suggest that this epitope is a potential target for an H. ducreyi vaccine.

  7. Evolutionary Conservation of a GPCR-Independent Mechanism of Trimeric G Protein Activation

    PubMed Central

    Coleman, Brantley D.; Marivin, Arthur; Parag-Sharma, Kshitij; DiGiacomo, Vincent; Kim, Seongseop; Pepper, Judy S.; Casler, Jason; Nguyen, Lien T.; Koelle, Michael R.; Garcia-Marcos, Mikel

    2016-01-01

    Trimeric G protein signaling is a fundamental mechanism of cellular communication in eukaryotes. The core of this mechanism consists of activation of G proteins by the guanine-nucleotide exchange factor (GEF) activity of G protein coupled receptors. However, the duration and amplitude of G protein-mediated signaling are controlled by a complex network of accessory proteins that appeared and diversified during evolution. Among them, nonreceptor proteins with GEF activity are the least characterized. We recently found that proteins of the ccdc88 family possess a Gα-binding and activating (GBA) motif that confers GEF activity and regulates mammalian cell behavior. A sequence similarity-based search revealed that ccdc88 genes are highly conserved across metazoa but the GBA motif is absent in most invertebrates. This prompted us to investigate whether the GBA motif is present in other nonreceptor proteins in invertebrates. An unbiased bioinformatics search in Caenorhabditis elegans identified GBAS-1 (GBA and SPK domain containing-1) as a GBA motif-containing protein with homologs only in closely related worm species. We demonstrate that GBAS-1 has GEF activity for the nematode G protein GOA-1 and that the two proteins are coexpressed in many cells of living worms. Furthermore, we show that GBAS-1 can activate mammalian Gα-subunits and provide structural insights into the evolutionarily conserved determinants of the GBA–G protein interface. These results demonstrate that the GBA motif is a functional GEF module conserved among highly divergent proteins across evolution, indicating that the GBA-Gα binding mode is strongly constrained under selective pressure to mediate receptor-independent G protein activation in metazoans. PMID:26659249

  8. Novel Anti-Nicotine Vaccine Using a Trimeric Coiled-Coil Hapten Carrier

    PubMed Central

    Miller, Keith D.; Roque, Richard; Clegg, Christopher H.

    2014-01-01

    Tobacco addiction represents one of the largest public health problems in the world and is the leading cause of cancer and heart disease, resulting in millions of deaths a year. Vaccines for smoking cessation have shown considerable promise in preclinical models, although functional antibody responses induced in humans are only modestly effective in preventing nicotine entry into the brain. The challenge in generating serum antibodies with a large nicotine binding capacity is made difficult by the fact that this drug is non-immunogenic and must be conjugated as a hapten to a protein carrier. To circumvent the limitations of traditional carriers like keyhole limpet hemocyanin (KLH), we have synthesized a short trimeric coiled-coil peptide (TCC) that creates a series of B and T cell epitopes with uniform stoichiometry and high density. Here we compared the relative activities of a TCC-nic vaccine and two control KLH-nic vaccines using Alum as an adjuvant or GLA-SE, which contains a synthetic TLR4 agonist formulated in a stable oil-in-water emulsion. The results showed that the TCC's high hapten density correlated with a better immune response in mice as measured by anti-nicotine Ab titer, affinity, and specificity, and was responsible for a reduction in anti-carrier immunogenicity. The Ab responses achieved with this synthetic vaccine resulted in a nicotine binding capacity in serum that could prevent >90% of a nicotine dose equivalent to three smoked cigarettes (0.05 mg/kg) from reaching the brain. PMID:25494044

  9. Structure of a eukaryotic SWEET transporter in a homo-trimeric complex

    PubMed Central

    Li, Shuo; Eom, Joon-Seob; Chen, Li-Qing; Xu, Yan; Perry, Kay; Frommer, Wolf B.; Feng, Liang

    2016-01-01

    Eukaryotes rely on efficient distribution of energy and carbon skeletons between organs in the form of sugars. Glucose in animals and sucrose in plants serve as dominant distribution forms. Cellular sugar uptake and release require vesicular and/or plasma membrane transport proteins. Humans and plants use related proteins from three superfamilies for sugar translocation: the major facilitator superfamily (MFS), the sodium solute symporter Family (SSF; only animal kingdom), and SWEETs1-5. SWEETs carry mono- and disaccharides6 across vacuolar or plasma membranes. Plant SWEETs play key roles in sugar translocation between compartments, cells, and organs, notably in nectar secretion7, phloem loading for long distance translocation8, pollen nutrition9, and seed filling10. Plant SWEETs cause pathogen susceptibility by sugar leakage from infected cells3,11,12. The vacuolar AtSWEET2 sequesters sugars in root vacuoles; loss-of-function increases susceptibility to Pythium infection13. Here we show that its orthologue, the vacuolar glucose transporter OsSWEET2b from rice, consists of an asymmetrical pair of triple-helix-bundles (THBs), connected by an inversion linker helix (TM4) to create the translocation pathway. Structural and biochemical analyses show OsSWEET2b in an apparent inward (cytosolic) open state forming homomeric trimers. TM4 tightly interacts with the first THB within a protomer and mediates key contacts among protomers. Structure-guided mutagenesis of the close paralogue SWEET1 from Arabidopsis identified key residues in substrate translocation and protomer crosstalk. Insights into the structure-function relationship of SWEETs is valuable for understanding the transport mechanism of eukaryotic SWEETs and may be useful for engineering sugar flux. PMID:26479032

  10. Insights into the Conformation of the Membrane Proximal Regions Critical to the Trimerization of the HIV-1 gp41 Ectodomain Bound to Dodecyl Phosphocholine Micelles

    PubMed Central

    Louis, John M.; Baber, James L.; Ghirlando, Rodolfo; Aniana, Annie; Bax, Ad; Roche, Julien

    2016-01-01

    The transitioning of the ectodomain of gp41 from a pre-hairpin to a six-helix bundle conformation is a crucial aspect of virus-cell fusion. To gain insight into the intermediary steps of the fusion process we have studied the pH and dodecyl phosphocholine (DPC) micelle dependent trimer association of gp41 by systematic deletion analysis of an optimized construct termed 17–172 (residues 528 to 683 of Env) that spans the fusion peptide proximal region (FPPR) to the membrane proximal external region (MPER) of gp41, by sedimentation velocity and double electron-electron resonance (DEER) EPR spectroscopy. Trimerization at pH 7 requires the presence of both the FPPR and MPER regions. However, at pH 4, the protein completely dissociates to monomers. DEER measurements reveal a partial fraying of the C-terminal MPER residues in the 17–172 trimer while the other regions, including the FPPR, remain compact. In accordance, truncating nine C-terminal MPER residues (675–683) in the 17–172 construct does not shift the trimer-monomer equilibrium significantly. Thus, in the context of the gp41 ectodomain spanning residues 17–172, trimerization is clearly dependent on FPPR and MPER regions even when the terminal residues of MPER unravel. The antibody Z13e1, which spans both the 2F5 and 4E10 epitopes in MPER, binds to 17–172 with a Kd of 1 ± 0.12 μM. Accordingly, individual antibodies 2F5 and 4E10 also recognize the 17–172 trimer/DPC complex. We propose that binding of the C-terminal residues of MPER to the surface of the DPC micelles models a correct positioning of the trimeric transmembrane domain anchored in the viral membrane. PMID:27513582

  11. Clarifying and illustrating the electronic energy transfer pathways in trimeric and hexameric aggregation state of cyanobacteria allophycocyanin within the framework of Förster theory.

    PubMed

    Ren, Yanliang; Melhem, Osama; Li, Yongjian; Chi, Bo; Han, Xinya; Zhu, Hao; Feng, Lingling; Wan, Jian; Xu, Xin

    2015-01-30

    Within the framework of the Förster theory, the electronic excitation energy transfer pathways in the cyanobacteria allophycocyanin (APC) trimer and hexamer were studied. The associated physical quantities (i.e., excitation energy, oscillator strength, and transition dipole moments) of the phycocyanobilins (PCBs) located in APC were calculated at time-dependent density functional theory (TDDFT) level of theory. To estimate the influence of protein environment on the preceding calculated physical quantities, the long-range interactions were approximately considered with the polarizable continuum model at the TDDFT level of theory, and the short-range interaction caused by surrounding aspartate residue of PCBs were taken into account as well. The shortest energy transfer time calculated in the framework of the Förster model at TDDFT/B3LYP/6-31+G* level of theory are about 0.10 ps in the APC trimer and about 170 ps in the APC monomer, which are in qualitative agreement with the experimental finding that a very fast lifetime of 0.43-0.44 ps in APC trimers, whereas its monomers lacked any corresponding lifetime. These results suggest that the lifetime of 0.43-0.44 ps in the APC trimers determined by Sharkov et al. was most likely attributed to the energy transfer of α(1) -84 ↔ β(3) -84 (0.23 ps), β(1) -84 ↔ α(2) -84 (0.11 ps) or β(2) -84 ↔ α(3) -84 (0.10 ps). So far, no experimental or theoretical energy transfer rates between two APC trimmers were reported, our calculations predict that the predominate energy transfer pathway between APC trimers is likely to occur from α(3) -84 in one trimer to α(5) -84 in an adjacent trimer with a rate of 32.51 ps.

  12. Structural diversity of the soluble trimers of the human amylin(20-29) peptide revealed by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Mo, Yuxiang; Lu, Yan; Wei, Guanghong; Derreumaux, Philippe

    2009-03-01

    The human islet amyloid polypeptide (hIAPP) or amylin is a 37-residue hormone found as amyloid deposits in pancreatic extracts of nearly all type 2 diabetes patients. The fragment 20-29 of sequence SNNFGAILSS (hIAPP20-29) has been shown to be responsible for the amyloidogenic propensities of the full length protein. Various polymorphic forms of hIAPP20-29 fibrils were described by using Fourier transform infrared (FTIR) and solid-state NMR experiments: unseeded hIAPP20-29 fibril with out-of-register antiparallel β-strands, and two forms of seeded hIAPP20-29 fibril, with in-register antiparallel or in-register parallel β-strands. As a first step toward understanding this polymorphism, we explore the equilibrium structures of the soluble hIAPP20-29 trimer, using multiple molecular dynamics (MD) simulations with the Optimized Potential for Efficient structure Prediction (OPEP) coarse-grained implicit solvent force field for a total length of 3.2 μs. Although, the trimer is found mainly random coil, consistent with the signal measured experimentally during the lag phase of hIAPP20-29 fibril formation, the central FGAIL residues have a relative high propensity to form interpeptide β-sheets and antiparallel β-strands are more probable than parallel β-strands. One MD-predicted out-of-register antiparallel three-stranded β-sheet matches exactly the FTIR-derived unseeded hIAPP20-29 fibril model. Our simulations, however, do not reveal any evidence of in-register parallel or in-register antiparallel β-sheets as reported for seeded hIAPP20-29 fibrils. All these results indicate that fibril polymorphism is partially encoded in a trimer.

  13. Structural diversity of the soluble trimers of the human amylin(20-29) peptide revealed by molecular dynamics simulations.

    PubMed

    Mo, Yuxiang; Lu, Yan; Wei, Guanghong; Derreumaux, Philippe

    2009-03-28

    The human islet amyloid polypeptide (hIAPP) or amylin is a 37-residue hormone found as amyloid deposits in pancreatic extracts of nearly all type 2 diabetes patients. The fragment 20-29 of sequence SNNFGAILSS (hIAPP20-29) has been shown to be responsible for the amyloidogenic propensities of the full length protein. Various polymorphic forms of hIAPP20-29 fibrils were described by using Fourier transform infrared (FTIR) and solid-state NMR experiments: unseeded hIAPP20-29 fibril with out-of-register antiparallel beta-strands, and two forms of seeded hIAPP20-29 fibril, with in-register antiparallel or in-register parallel beta-strands. As a first step toward understanding this polymorphism, we explore the equilibrium structures of the soluble hIAPP20-29 trimer, using multiple molecular dynamics (MD) simulations with the Optimized Potential for Efficient structure Prediction (OPEP) coarse-grained implicit solvent force field for a total length of 3.2 micros. Although, the trimer is found mainly random coil, consistent with the signal measured experimentally during the lag phase of hIAPP20-29 fibril formation, the central FGAIL residues have a relative high propensity to form interpeptide beta-sheets and antiparallel beta-strands are more probable than parallel beta-strands. One MD-predicted out-of-register antiparallel three-stranded beta-sheet matches exactly the FTIR-derived unseeded hIAPP20-29 fibril model. Our simulations, however, do not reveal any evidence of in-register parallel or in-register antiparallel beta-sheets as reported for seeded hIAPP20-29 fibrils. All these results indicate that fibril polymorphism is partially encoded in a trimer.

  14. Insights on the structure and stability of Licanantase: a trimeric acid-stable coiled-coil lipoprotein from Acidithiobacillus thiooxidans.

    PubMed

    Abarca, Fernando; Gutierrez-Maldonado, Sebastian E; Parada, Pilar; Martinez, Patricio; Maass, Alejandro; Perez-Acle, Tomas

    2014-01-01

    Licanantase (Lic) is the major component of the secretome of Acidithiobacillus thiooxidans when grown in elemental sulphur. When used as an additive, Lic improves copper recovery from bioleaching processes. However, this recovery enhancement is not fully understood. In this context, our aim is to predict the 3D structure of Lic, to shed light on its structure-function relationships. Bioinformatics analyses on the amino acid sequence of Lic showed a great similarity with Lpp, an Escherichia coli Lipoprotein that can form stable trimers in solution. Lic and Lpp share the secretion motif, intracellular processing and alpha helix structure, as well as the distribution of hydrophobic residues in heptads forming a hydrophobic core, typical of coiled-coil structures. Cross-linking experiments showed the presence of Lic trimers, supporting our predictions. Taking the in vitro and in silico evidence as a whole, we propose that the most probable structure for Lic is a trimeric coiled-coil. According to this prediction, a suitable model for Lic was produced using the de novo algorithm "Rosetta Fold-and-Dock". To assess the structural stability of our model, Molecular Dynamics (MD) and Replica Exchange MD simulations were performed using the structure of Lpp and a 14-alanine Lpp mutant as controls, at both acidic and neutral pH. Our results suggest that Lic was the most stable structure among the studied proteins in both pH conditions. This increased stability can be explained by a higher number of both intermonomer hydrophobic contacts and hydrogen bonds, key elements for the stability of Lic's secondary and tertiary structure.

  15. Development of a generic adenovirus delivery system based on structure-guided design of bispecific trimeric DARPin adapters.

    PubMed

    Dreier, Birgit; Honegger, Annemarie; Hess, Christian; Nagy-Davidescu, Gabriela; Mittl, Peer R E; Grütter, Markus G; Belousova, Natalya; Mikheeva, Galina; Krasnykh, Victor; Plückthun, Andreas

    2013-03-05

    Adenoviruses (Ads) have shown promise as vectors for gene delivery in clinical trials. Efficient viral targeting to a tissue of choice requires both ablation of the virus' original tropism and engineering of an efficient receptor-mediated uptake by a specific cell population. We have developed a series of adapters binding to the virus with such high affinity that they remain fully bound for >10 d, block its natural receptor binding site and mediate interaction with a surface receptor of choice. The adapter contains two fused modules, both consisting of designed ankyrin repeat proteins (DARPins), one binding to the fiber knob of adenovirus serotype 5 and the other binding to various tumor markers. By solving the crystal structure of the complex of the trimeric knob with three bound DARPins at 1.95-Å resolution, we could use computer modeling to design a link to a trimeric protein of extraordinary kinetic stability, the capsid protein SHP from the lambdoid phage 21. We arrived at a module which binds the knob like a trimeric clamp. When this clamp was fused with DARPins of varying specificities, it enabled adenovirus serotype 5-mediated delivery of a transgene in a human epidermal growth factor receptor 2-, epidermal growth factor receptor-, or epithelial cell adhesion molecule-dependent manner with transduction efficiencies comparable to or even exceeding those of Ad itself. With these adapters, efficiently produced in Escherichia coli, Ad can be converted rapidly to new receptor specificities using any ligand as the receptor-binding moiety. Prefabricated Ads with different payloads thus can be retargeted readily to many cell types of choice.

  16. Conditional trimerization and lytic activity of HIV-1 gp41 variants containing the membrane-associated segments.

    PubMed

    Dai, Zhou; Tao, Yisong; Liu, Nina; Brenowitz, Michael D; Girvin, Mark E; Lai, Jonathan R

    2015-03-03

    Fusion of host and viral membranes is a critical step during infection by membrane-bound viruses. The HIV-1 glycoproteins gp120 (surface subunit) and gp41 (fusion subunit) represent the prototypic system for studying this process; in the prevailing model, the gp41 ectodomain forms a trimeric six-helix bundle that constitutes a critical intermediate and provides the energetic driving force for overcoming barriers associated with membrane fusion. However, most structural studies of gp41 variants have been performed either on ectodomain constructs lacking one or more of the membrane-associated segments (the fusion peptide, FP, the membrane-proximal external region, MPER, and the transmembrane domain, TM) or on variants consisting of these isolated segments alone without the ectodomain. Several recent reports have suggested that the HIV-1 ectodomain, as well as larger construct containing the membrane-bound segments, dissociates from a trimer to a monomer in detergent micelles. Here we compare the properties of a series of gp41 variants to delineate the roles of the ectodomain, FP, and MPER and TM, all in membrane-mimicking environments. We find that these proteins are prone to formation of a monomer in detergent micelles. In one case, we observed exclusive monomer formation at pH 4 but conditional trimerization at pH 7 even at low micromolar (∼5 μM) protein concentrations. Liposome release assays demonstrate that these gp41-related proteins have the capacity to induce content leakage but that this activity is also strongly modulated by pH with much higher activity at pH 4. Circular dichroism, nuclear magnetic resonance, and binding assays with antibodies specific to the MPER provide insight into the structural and functional roles of the FP, MPER, and TM and their effect on structure within the larger context of the fusion subunit.

  17. Novel recombinant engineered gp41 N-terminal heptad repeat trimers and their potential as anti-HIV-1 therapeutics or microbicides.

    PubMed

    Chen, Xi; Lu, Lu; Qi, Zhi; Lu, Hong; Wang, Ji; Yu, Xiaoxia; Chen, Yinghua; Jiang, Shibo

    2010-08-13

    Peptides derived from N-terminal heptad repeat (NHR) of the HIV-1 gp41 are generally poor inhibitors of HIV-1 entry, because they tend to aggregate and do not form a trimeric coiled-coil. In this study, we have fused portions of gp41 NHR, e.g. N36 or N28, to the T4 fibritin trimerization domain, Foldon (Fd), thus constructing novel NHR trimers, designated N36Fd or N28Fd, which could be expressed in Escherichia coli cells. The purified N36Fd and N28Fd exhibited SDS-resistant trimeric coiled-coil conformation with improved alpha-helicity compared with the corresponding N-peptides. They could interact with a C-peptide (e.g. C34) to form stable six-helix bundle and possessed potent anti-HIV-1 activity against a broad spectrum of HIV-1 strains. N28Fd was effective against T20-resistant HIV-1 variants and more resistant to proteinase K compared with T20 (enfuvirtide), a C-peptide-based HIV fusion inhibitor. Therefore, N28Fd trimer has great potentials for further development as an affordable therapeutic or microbicide for treatment and prevention of HIV-1 infection.

  18. Circular trimers of gelatinase B/matrix metalloproteinase-9 constitute a distinct population of functional enzyme molecules differentially regulated by tissue inhibitor of metalloproteinases-1

    PubMed Central

    Vandooren, Jennifer; Born, Benjamin; Solomonov, Inna; Zajac, Ewa; Saldova, Radka; Senske, Michael; Ugarte-Berzal, Estefanía; Martens, Erik; Van den Steen, Philippe E.; Van Damme, Jo; Garcia-Pardo, Angeles; Froeyen, Matheus; Deryugina, Elena I.; Quigley, James P.; Moestrup, Søren K.; Rudd, Pauline M.; Sagi, Irit; Opdenakker, Ghislain

    2015-01-01

    Gelatinase B/matrix metalloproteinase-9 (MMP-9) (EC 3.4.24.35) cleaves many substrates and is produced by most cell types as a zymogen, proMMP-9, in complex with the tissue inhibitor of metalloproteinases-1 (TIMP-1). Natural proMMP-9 occurs as monomers, homomultimers, and heterocomplexes, but our knowledge about the overall structure of proMMP-9 monomers and multimers is limited. We investigated biochemical, biophysical, and functional characteristics of zymogen and activated forms of MMP-9 monomers and multimers. In contrast to a conventional notion of a dimeric nature of MMP-9 homomultimers, we demonstrate that these are reduction-sensitive trimers. Based on the information from electrophoresis, atomic force microscopy (AFM) and transmission electron microscopy (TEM), we generated a 3Dstructure model of the proMMP-9 trimer. Remarkably, the proMMP-9 trimers possessed a 50-fold higher affinity for TIMP-1 than the monomers. In vivo, this finding was reflected in a higher extent of TIMP-1 inhibition of angiogenesis induced by trimers versus monomers. Our results show that proMMP-9 trimers constitute a novel structural and functional entity that is differentially regulated by TIMP-1. PMID:25360794

  19. Spectral studies of a Cr(PNP)-MAO system for selective ethylene trimerization catalysis: searching for the active species

    PubMed Central

    Do, Loi H.; Labinger, Jay A.; Bercaw, John E.

    2013-01-01

    Variable temperature spectroscopic, kinetic, and chemical studies were performed on a soluble CrIIICl3(PNP) (PNP = bis(diarylphosphino)alkylamine) ethylene trimerization precatalyst to map out its methylaluminoxane (MAO) activation sequence. These studies indicate that treatment of CrIIICl3(PNP) with MAO leads to first replacement of chlorides with alkyl groups, followed by alkyl abstraction, and then reduction to lower–valent species. Reactivity studies demonstrate that the majority of the chromium species detected is not catalytically active. PMID:24327931

  20. Novel thermochromism relating to supramolecular cuprophilic interaction: design, synthesis, and luminescence of copper(I) pyrazolate trimer and polymer.

    PubMed

    Zhang, Jing-Xiang; He, Jun; Yin, Ye-Gao; Hu, Mei-Hong; Li, Dan; Huang, Xiao-Chun

    2008-05-05

    Solvothermal reactions of 4-(pyrid-4'-yl)-3,5-dimethylpyrazole (HPpz) with CuBr in two mixed solvents, NH3.H2O/EtOH and NH3.H2O/MeCN, afforded respectively a copper(I) trimer, [Cu(Ppz)]3(1), and a polymer, {[Cu(Ppz)]3[CuCN] 3} (2), both containing the [Cu(Ppz)]3 entity as a building block. The products were found to be photoluminescent and, more interestingly, when cooled from room temperature to 10 K, they showed a blue shift followed by a red shift (hereafter shortened to a red-after-blue shift) of emission.

  1. Subcellular redistribution of trimeric G-proteins--potential mechanism of desensitization of hormone response: internalization, solubilization, down-regulation.

    PubMed

    Drastichová, Z; Bourová, L; Lisý, V; Hejnová, L; Rudajev, V; Stöhr, J; Durchánková, D; Ostasov, P; Teisinger, J; Soukup, T; Novotný, J; Svoboda, P

    2008-01-01

    Agonist-induced subcellular redistribution of G-protein coupled receptors (GPCR) and of trimeric guanine-nucleotide binding regulatory proteins (G-proteins) represent mechanisms of desensitization of hormone response, which have been studied in our laboratory since 1989. This review brings a short summary of these results and also presents information about related literature data covering at least small part of research carried out in this area. We have also mentioned sodium plus potassium dependent adenosine triphosphatase (Na, K-ATPase) and 3H-ouabain binding as useful reference standard of plasma membrane purity in the brain.

  2. Chemical analyses of Ukrain, a semi-synthetic Chelidonium majus alkaloid derivative, fail to confirm its trimeric structure.

    PubMed

    Panzer, A; Joubert, A M; Eloff, J N; Albrecht, C F; Erasmus, E; Seegers, J C

    2000-11-28

    Ukrain has been described as a semi-synthetic Chelidonium majus alkaloid derivative, consisting of three chelidonine alkaloids combined to triaziridide. We found the actions of Ukrain to be similar to the Chelidonium alkaloids it is prepared from, and therefore became concerned about its chemical integrity. Chemical analyses of Ukrain by thin layer chromatography, high-performance liquid chromatography and liquid chromatography-mass spectrometry was inconsistent with the proposed trimeric structure and demonstrated that at least some commercial preparations of Ukrain consist of a mixture of C. majus alkaloids (including chelidonine).

  3. delta-Opioid receptors exhibit high efficiency when activating trimeric G proteins in membrane domains.

    PubMed

    Bourova, Lenka; Kostrnova, Alexandra; Hejnova, Lucie; Moravcova, Zuzana; Moon, Hyo-Eun; Novotny, Jiri; Milligan, Graeme; Svoboda, Petr

    2003-04-01

    Low-density membrane fragments (domains) were separated from the bulk of plasma membranes of human embryonic kidney (HEK)293 cells expressing a delta-opioid (DOP) receptor-Gi1alpha fusion protein by drastic homogenization and flotation on equilibrium sucrose density gradients. The functional activity of trimeric G proteins and capacity of the DOP receptor to stimulate both the fusion protein-linked Gi1alpha and endogenous pertussis-toxin sensitive G proteins was measured as d-Ala2, d-Leu5-enkephalin stimulated high-affinity GTPase or guanosine-5'-[gamma-35S]triphosphate ([35S]GTPgammaS) binding. The maximum d-Ala2-d-Leu5 enkephalin (DADLE)-stimulated GTPase was two times higher in low-density membrane fragments than in bulk of plasma membranes; 58 and 27 pmol/mg/min, respectively. The same difference was obtained for [35S]GTPgammaS binding. Contrarily, the low-density domains contained no more than half the DOP receptor binding sites (Bmax = 6.6 pmol/mg versus 13.6 pmol/mg). Thus, when corrected for expression levels of the receptor, low-density domains exhibited four times higher agonist-stimulated GTPase and [35S]GTPgammaS binding than the bulk plasma membranes. The regulator of G protein signaling RGS1, enhanced further the G protein functional activity but did not remove the difference between domain-bound and plasma membrane pools of G protein. The potency of the agonist in functional studies and the affinity of specific [3H]DADLE binding to the receptor were, however, the same in both types of membranes - EC50 = 4.5 +/- 0.1 x 10(-8) and 3.2 +/- 1.4 x 10(-8) m for GTPase; Kd = 1.2 +/- 0.1 and 1.3 +/- 0.1 nm for [3H]DADLE radioligand binding assay. Similar results were obtained when sodium bicarbonate was used for alkaline isolation of membrane domains. By contrast, detergent-insensitive membrane domains isolated following treatment of cells with Triton X100 exhibited no DADLE-stimulated GTPase or GTPgammaS binding. Functional coupling between the DOP receptor

  4. ADS-J1 inhibits HIV-1 infection and membrane fusion by targeting the highly conserved pocket in the gp41 NHR-trimer.

    PubMed

    Yu, Fei; Lu, Lu; Liu, Qi; Yu, Xiaowen; Wang, Lili; He, Elaine; Zou, Peng; Du, Lanying; Sanders, Rogier W; Liu, Shuwen; Jiang, Shibo

    2014-05-01

    We previously identified a potent small-molecule human immunodeficiency virus type 1 (HIV-1) fusion inhibitor, termed ADS-J1, and hypothesized that it mainly targeted the hydrophobic pocket in the gp41 N-terminal heptad repeat (NHR) trimer. However, this hypothesis has been challenged by the fact that ADS-J1 cannot induce drug-resistance mutation in the gp41 pocket region. Therefore, we show herein that HIV-1 mutants resistant to T2635, a peptide derived from the gp41 C-terminal heptad repeat (CHR) region with pocket-binding domain (PBD), were also resistant to ADS-J1. We also show that pseudoviruses with mutations at positions 64 and 67 in the gp41 pocket region were highly resistant to ADS-J1 and C34, another CHR-peptide with PBD, but relatively sensitive to T20, a CHR-peptide without PBD. ADS-J1 could effectively bind to N36Fd, a mimic of the gp41 NHR-trimer with pocket exposed, and block binding of C34 to N36Fd trimer to form six-helix bundle (6-HB). However, ADS-J1 was less effective in binding to N36Fd trimer with mutations in the gp41 pocket region, such as N36(Q64A)Fd, N36(Q64L)Fd, N36(A67G)Fd, N36(A67S)Fd, and N36(Q66R)Fd, as well as less effective in blocking 6-HB formation between C34 and these mutant N36Fd trimers. These results confirm that ADS-J1 mainly targets the pocket region in the HIV-1 gp41 NHR trimer and suggest that it could be used as a lead for developing small-molecule HIV fusion inhibitors and as a molecule probe for studying the mechanisms of gp41-mediated membrane fusion.

  5. Two Adjacent Trimeric Fas Ligands Are Required for Fas Signaling and Formation of a Death-Inducing Signaling Complex

    PubMed Central

    Holler, Nils; Tardivel, Aubry; Kovacsovics-Bankowski, Magdalena; Hertig, Sylvie; Gaide, Olivier; Martinon, Fabio; Tinel, Antoine; Deperthes, David; Calderara, Silvio; Schulthess, Therese; Engel, Jürgen; Schneider, Pascal; Tschopp, Jürg

    2003-01-01

    The membrane-bound form of Fas ligand (FasL) signals apoptosis in target cells through engagement of the death receptor Fas, whereas the proteolytically processed, soluble form of FasL does not induce cell death. However, soluble FasL can be rendered active upon cross-linking. Since the minimal extent of oligomerization of FasL that exerts cytotoxicity is unknown, we engineered hexameric proteins containing two trimers of FasL within the same molecule. This was achieved by fusing FasL to the Fc portion of immunoglobulin G1 or to the collagen domain of ACRP30/adiponectin. Trimeric FasL and hexameric FasL both bound to Fas, but only the hexameric forms were highly cytotoxic and competent to signal apoptosis via formation of a death-inducing signaling complex. Three sequential early events in Fas-mediated apoptosis could be dissected, namely, receptor binding, receptor activation, and recruitment of intracellular signaling molecules, each of which occurred independently of the subsequent one. These results demonstrate that the limited oligomerization of FasL, and most likely of some other tumor necrosis factor family ligands such as CD40L, is required for triggering of the signaling pathways. PMID:12556501

  6. The New Phases due to Symmetry Protected Piecewise Berry Phases; Enhanced Pumping and Non-reciprocity in Trimer Lattices

    NASA Astrophysics Data System (ADS)

    Liu, Xuele; Agarwal, G. S.

    2017-03-01

    Finding new phase of matter is a fundamental task in physics. Generally, various phases or states of matter (for instance solid/liquid/gas phases) have different symmetries, the phase transitions among them can be explained by Landau’s symmetry breaking theory. The topological phases discovered in recent years show that different phases may have the same symmetry. The different topological phases are characterized by different integer values of the Berry phases. By studying one dimensional (1D) trimer lattices we report new phases beyond topological phases. The new phases that we find are characterized by piecewise continuous Berry phases with the discontinuity occurring at the transition point. With time-dependent changes in trimer lattices, we can generate two dimensional (2D) phases, which are characterized by the Berry phase of half period. This half-period Berry phase changes smoothly within one state of the system while changes discontinuously at the transition point. We further demonstrate the existence of adiabatic pumping for each phase and gain assisted enhanced pumping. The non reciprocity of the pumping process makes the system a good optical diode.

  7. Femtosecond fluorescence depolarization study of photosynthetic antenna proteins: observation of ultrafast energy transfer in trimeric C-phycocyanin and allophycocyanin

    NASA Astrophysics Data System (ADS)

    Xie, Sunney; Du, Mei; Mets, Laurens; Fleming, Graham R.

    1992-04-01

    C-phycocyanin (CPC) and Allophycocyanin (APC) are pigment-protein complexes isolated from antenna systems in cyanobacteria. The crystal structure of CPC has recently been solved and APC has a similar structure. CPC and APC have a trimeric structure, monomeric subunits are composed of an (alpha) and (beta) polypeptide chain, each has a tetrapyrrole chromophore chemically bound to position 84. In CPC and APC trimers, the (alpha) 84 and (beta) 84 chromophores in adjacent monomers are in close proximity, forming relatively strong coupled pairs. Calculation of pairwise energy transfer rates using Foerster theory has suggested an extremely fast transfer (> 1 ps-1) between the (alpha) 84 and (beta) 84 pair in CPC. A femtosecond fluorescence up-conversion apparatus was constructed which achieves subhundred femtosecond time resolution. This allows experimental observation of the fast energy transfer process between the (alpha) 84 and (beta) 84 pair in both CPC and APC. There was also a wavelength dependence of the fluorescence depolarization kinetics which is inconsistent with Foerster inductive resonance energy transfer theory.

  8. The Haemophilus ducreyi trimeric autotransporter adhesin DsrA protects against an experimental infection in the swine model of chancroid.

    PubMed

    Fusco, William G; Choudhary, Neelima R; Routh, Patty A; Ventevogel, Melissa S; Smith, Valerie A; Koch, Gary G; Almond, Glen W; Orndorff, Paul E; Sempowski, Gregory D; Leduc, Isabelle

    2014-06-24

    Adherence of pathogens to cellular targets is required to initiate most infections. Defining strategies that interfere with adhesion is therefore important for the development of preventative measures against infectious diseases. As an adhesin to host extracellular matrix proteins and human keratinocytes, the trimeric autotransporter adhesin DsrA, a proven virulence factor of the Gram-negative bacterium Haemophilus ducreyi, is a potential target for vaccine development. A recombinant form of the N-terminal passenger domain of DsrA from H. ducreyi class I strain 35000HP, termed rNT-DsrAI, was tested as a vaccine immunogen in the experimental swine model of H. ducreyi infection. Viable homologous H. ducreyi was not recovered from any animal receiving four doses of rNT-DsrAI administered with Freund's adjuvant at two-week intervals. Control pigs receiving adjuvant only were all infected. All animals receiving the rNT-DsrAI vaccine developed antibody endpoint titers between 3.5 and 5 logs. All rNT-DsrAI antisera bound the surface of the two H. ducreyi strains used to challenge immunized pigs. Purified anti-rNT-DsrAI IgG partially blocked binding of fibrinogen at the surface of viable H. ducreyi. Overall, immunization with the passenger domain of the trimeric autotransporter adhesin DsrA accelerated clearance of H. ducreyi in experimental lesions, possibly by interfering with fibrinogen binding.

  9. Intramolecular trimerization, a novel strategy for making multispecific antibodies with controlled orientation of the antigen binding domains

    PubMed Central

    Alvarez-Cienfuegos, Ana; Nuñez-Prado, Natalia; Compte, Marta; Cuesta, Angel M.; Blanco-Toribio, Ana; Harwood, Seandean Lykke; Villate, Maider; Merino, Nekane; Bonet, Jaume; Navarro, Rocio; Muñoz-Briones, Clara; Sørensen, Karen Marie Juul; Mølgaard, Kasper; Oliva, Baldo; Sanz, Laura; Blanco, Francisco J.; Alvarez-Vallina, Luis

    2016-01-01

    Here, we describe a new strategy that allows the rapid and efficient engineering of mono and multispecific trivalent antibodies. By fusing single-domain antibodies from camelid heavy-chain-only immunoglobulins (VHHs) to the N-terminus of a human collagen XVIII trimerization domain (TIEXVIII) we produced monospecific trimerbodies that were efficiently secreted as soluble functional proteins by mammalian cells. The purified VHH-TIEXVIII trimerbodies were trimeric in solution and exhibited excellent antigen binding capacity. Furthermore, by connecting with two additional glycine-serine-based linkers three VHH-TIEXVIII modules on a single polypeptide chain, we present an approach for the rational design of multispecific tandem trimerbodies with defined stoichiometry and controlled orientation. Using this technology we report here the construction and characterization of a tandem VHH-based trimerbody capable of simultaneously binding to three different antigens: carcinoembryonic antigen (CEA), epidermal growth factor receptor (EGFR) and green fluorescence protein (GFP). Multispecific tandem VHH-based trimerbodies were well expressed in mammalian cells, had good biophysical properties and were capable of simultaneously binding their targeted antigens. Importantly, these antibodies were very effective in inhibiting the proliferation of human epidermoid carcinoma A431 cells. Multispecific VHH-based trimerbodies are therefore ideal candidates for future applications in various therapeutic areas. PMID:27345490

  10. The New Phases due to Symmetry Protected Piecewise Berry Phases; Enhanced Pumping and Non-reciprocity in Trimer Lattices

    PubMed Central

    Liu, Xuele; Agarwal, G. S.

    2017-01-01

    Finding new phase of matter is a fundamental task in physics. Generally, various phases or states of matter (for instance solid/liquid/gas phases) have different symmetries, the phase transitions among them can be explained by Landau’s symmetry breaking theory. The topological phases discovered in recent years show that different phases may have the same symmetry. The different topological phases are characterized by different integer values of the Berry phases. By studying one dimensional (1D) trimer lattices we report new phases beyond topological phases. The new phases that we find are characterized by piecewise continuous Berry phases with the discontinuity occurring at the transition point. With time-dependent changes in trimer lattices, we can generate two dimensional (2D) phases, which are characterized by the Berry phase of half period. This half-period Berry phase changes smoothly within one state of the system while changes discontinuously at the transition point. We further demonstrate the existence of adiabatic pumping for each phase and gain assisted enhanced pumping. The non reciprocity of the pumping process makes the system a good optical diode. PMID:28337994

  11. Trimeric Structure of (+)-Pinoresinol-forming Dirigent Protein at 1.95 Å Resolution with Three Isolated Active Sites

    SciTech Connect

    Kim, Kye-Won; Smith, Clyde A.; Daily, Michael D.; Cort, John R.; Davin, Laurence B.; Lewis, Norman G.

    2014-11-19

    Control over phenoxy radical-radical coupling reactions in vivo in vascular plants was enigmatic until our discovery of dirigent proteins (DPs, from the Latin dirigere, to guide or align). The first three-dimensional structure of a DP ((+)-pinoresinol-forming DP, 1.95 Å resolution, rhombohedral space group H32)) is reported herein. It has a tightly packed trimeric structure with an eight-stranded β-barrel topology for each DP monomer. Each putative substrate binding and orientation coupling site is located on the trimer surface but too far apart for intermolecular coupling between sites. It is proposed that each site enables stereoselective coupling (using either two coniferyl alcohol radicals or a radical and a monolignol). Interestingly, there are six differentially conserved residues in DPs affording either the (+)- or (₋)-antipodes in the vicinity of the putative binding site and region known to control stereoselectivity. We find DPs are involved in lignan biosynthesis, whereas dirigent domains/sites have been implicated in lignin deposition.

  12. Trimeric Structure of (+)-Pinoresinol-forming Dirigent Protein at 1.95 Å Resolution with Three Isolated Active Sites

    DOE PAGES

    Kim, Kye-Won; Smith, Clyde A.; Daily, Michael D.; ...

    2014-11-19

    Control over phenoxy radical-radical coupling reactions in vivo in vascular plants was enigmatic until our discovery of dirigent proteins (DPs, from the Latin dirigere, to guide or align). The first three-dimensional structure of a DP ((+)-pinoresinol-forming DP, 1.95 Å resolution, rhombohedral space group H32)) is reported herein. It has a tightly packed trimeric structure with an eight-stranded β-barrel topology for each DP monomer. Each putative substrate binding and orientation coupling site is located on the trimer surface but too far apart for intermolecular coupling between sites. It is proposed that each site enables stereoselective coupling (using either two coniferyl alcoholmore » radicals or a radical and a monolignol). Interestingly, there are six differentially conserved residues in DPs affording either the (+)- or (₋)-antipodes in the vicinity of the putative binding site and region known to control stereoselectivity. We find DPs are involved in lignan biosynthesis, whereas dirigent domains/sites have been implicated in lignin deposition.« less

  13. Magnetic Ordering of Antiferromagnetic Trimer System 2b·3CuCl2·2H2O

    NASA Astrophysics Data System (ADS)

    Sanda, M.; Kubo, K.; Asano, T.; Morodomi, H.; Inagaki, Y.; Kawae, T.; Wang, J.; Matsuo, A.; Kindo, K.; Sato, T. J.

    2012-12-01

    In this paper, we present the magnetic properties of 2b·3CuCl2·2H2O (b = betaine, C5H11NO2). 2b·3CuCl2·2H2O is the first model substance for a two-dimensional S = 1/2 orthogonal antiferromagnetic trimer system. We have performed magnetic susceptibility, magnetization curve, and specific heat under extreme conditions: low temperatures and high magnetic fields in this system. The experimental results indicate that this substance is a magnetically S = 1/2 antiferromagnetic trimer system. The magnetization also shows one-third of the saturation value (MS ~ 3.2μB/f.u.) between 5 and 14T The specific heat in a zero field shows a sharp peak at 1.38K corresponding to a long-range magnetic ordering, TN. As the magnetic field increases, the TN shifts remarkably to a lower temperature and is suppressed. Above 5T, the specific heat has no anomaly down to 150mK In the plateau region with an energy gap, the magnetic ordering seems to be disappeared.

  14. Variability of procyanidin type A- and -B trimers content in aerial parts of some Vaccinium species and cultivars.

    PubMed

    Toomik, Peeter; Püssa, Tõnu; Raal, Ain

    2014-06-01

    Based on the ethnopharmacological data showing that either wild bilberry leaves or whole aerial parts of the plants have been used as antidiabetic drugs, it can be hypothesized that the controversial results of various clinical and animal investigations may be caused by different contents of the active principles in different aerial parts of the bilberry/blueberry (Vaccinium spp.) plants, as well as by their geographical and seasonal variability. The aim of this study was to compare the content of procyanidin type A- and -B trimers in different parts of wild bilberry (Vaccinium myrtillus L.) and northern highbush blueberry (V. corymbosum L.) cultivars. Stems (60 samples) and leaves (30 samples) of wild bilberries and northern highbush blueberry cultivars 'Ama' and 'North Blue' were collected at different locations in Estonia around the year, and analyzed for the concentration of the target polyphenols by HPLC-MS/MS. The highest content of type A doubly linked trimer, a known antidiabetic substance, was established in the stems of V. myrtillus. These contained up to 100 times more of the active substance than the leaves of V. myrtillus and at least 1000 times more than the leaves of V. corymbosum, whereas the seasonal/geographical variation was nearly tenfold. We suggest using stems of V. myrtillus for future animal and clinical investigations of bilberry preparations against diabetes.

  15. Changes in Structure and Antigenicity of HIV-1 Env Trimers Resulting from Removal of a Conserved CD4 Binding Site-Proximal Glycan

    PubMed Central

    Liang, Yu; Guttman, Miklos; Williams, James A.; Verkerke, Hans; Alvarado, Daniel

    2016-01-01

    ABSTRACT The envelope glycoprotein (Env) is the major target for HIV-1 broadly neutralizing antibodies (bNAbs). One of the mechanisms that HIV has evolved to escape the host's immune response is to mask conserved epitopes on Env with dense glycosylation. Previous studies have shown that the removal of a particular conserved glycan at N197 increases the neutralization sensitivity of the virus to antibodies targeting the CD4 binding site (CD4bs), making it a site of significant interest from the perspective of vaccine design. At present, the structural consequences that result from the removal of the N197 glycan have not been characterized. Using native-like SOSIP trimers, we examine the effects on antigenicity and local structural dynamics resulting from the removal of this glycan. A large increase in the binding of CD4bs and V3-targeting antibodies is observed for the N197Q mutant in trimeric Env, while no changes are observed with monomeric gp120. While the overall structure and thermostability are not altered, a subtle increase in the flexibility of the variable loops at the trimeric interface of adjacent protomers is evident in the N197Q mutant by hydrogen-deuterium exchange mass spectrometry. Structural modeling of the glycan chains suggests that the spatial occupancy of the N197 glycan leads to steric clashes with CD4bs antibodies in the Env trimer but not monomeric gp120. Our results indicate that the removal of the N197 glycan enhances the exposure of relevant bNAb epitopes on Env with a minimal impact on the overall trimeric structure. These findings present a simple modification for enhancing trimeric Env immunogens in vaccines. IMPORTANCE The HIV-1 Env glycoprotein presents a dense patchwork of host cell-derived N-linked glycans. This so-called glycan shield is considered to be a major protective mechanism against immune recognition. While the positions of many N-linked glycans are isolate specific, some are highly conserved and are believed to play key

  16. Potential Prepore Trimer Formation by the Bacillus thuringiensis Mosquito-specific Toxin: MOLECULAR INSIGHTS INTO A CRITICAL PREREQUISITE OF MEMBRANE-BOUND MONOMERS.

    PubMed

    Sriwimol, Wilaiwan; Aroonkesorn, Aratee; Sakdee, Somsri; Kanchanawarin, Chalermpol; Uchihashi, Takayuki; Ando, Toshio; Angsuthanasombat, Chanan

    2015-08-21

    The insecticidal feature of the three-domain Cry δ-endotoxins from Bacillus thuringiensis is generally attributed to their capability to form oligomeric pores, causing lysis of target larval midgut cells. However, the molecular description of their oligomerization process has not been clearly defined. Here a stable prepore of the 65-kDa trypsin-activated Cry4Ba mosquito-specific toxin was established through membrane-mimetic environments by forming an ∼200-kDa octyl-β-D-glucoside micelle-induced trimer. The SDS-resistant trimer caused cytolysis to Sf9 insect cells expressing Aedes-mALP (a Cry4Ba receptor) and was more effective than a toxin monomer in membrane perturbation of calcein-loaded liposomes. A three-dimensional model of toxin trimer obtained by negative-stain EM in combination with single-particle reconstruction at ∼5 nm resolution showed a propeller-shaped structure with 3-fold symmetry. Fitting the three-dimensional reconstructed EM map with a 100-ns molecular dynamics-simulated Cry4Ba structure interacting with an octyl-β-D-glucoside micelle showed relative positioning of individual domains in the context of the trimeric complex with a major protrusion from the pore-forming domain. Moreover, high-speed atomic force microscopy imaging at nanometer resolution and a subsecond frame rate demonstrated conformational transitions from a propeller-like to a globularly shaped trimer upon lipid membrane interactions, implying prepore-to-pore conversion. Real-time trimeric arrangement of monomers associated with L-α-dimyristoylphosphatidylcholine/3-[(3-cholamidopropyl)dimethylammonio]-2-hydroxy-1-propanesulfonic acid bicelle membranes was also envisaged by successive high-speed atomic force microscopy imaging, depicting interactions among three individual subunits toward trimer formation. Together, our data provide the first pivotal insights into the structural requirement of membrane-induced conformational changes of Cry4Ba toxin monomers for the

  17. A Highly Conserved gp120 Inner Domain Residue Modulates Env Conformation and Trimer Stability

    PubMed Central

    Ding, Shilei; Tolbert, William D.; Prévost, Jérémie; Pacheco, Beatriz; Coutu, Mathieu; Debbeche, Olfa; Xiang, Shi-Hua

    2016-01-01

    double mutant compared to the wild-type protein but identified higher mobility within the interface between layer 1 and layer 2, the bridging sheet region, and the CD4 binding site. IMPORTANCE HIV-1 Env transitions to the CD4-bound conformation are required for viral entry. Previous studies identified a highly conserved residue of the inner domain, W69, as being involved in these conformational transitions (A. Finzi, S. H. Xiang, B. Pacheco, L. Wang, J. Haight, et al., Mol Cell 37:656–667, 2010, http://dx.doi.org/10.1016/j.molcel.2010.02.012). Here, we show that W69, located at the interface between gp120 and gp41 in the PGT151-bound trimer, plays a critical role in the interprotomer signaling induced by CD4 binding. This new information might be useful in immunogen design. PMID:27384653

  18. Dimeric and Trimeric Fusion Proteins Generated with Fimbrial Adhesins of Uropathogenic Escherichia coli.

    PubMed

    Luna-Pineda, Víctor M; Reyes-Grajeda, Juan Pablo; Cruz-Córdova, Ariadnna; Saldaña-Ahuactzi, Zeus; Ochoa, Sara A; Maldonado-Bernal, Carmen; Cázares-Domínguez, Vicenta; Moreno-Fierros, Leticia; Arellano-Galindo, José; Hernández-Castro, Rigoberto; Xicohtencatl-Cortes, Juan

    2016-01-01

    Urinary tract infections (UTIs) are associated with high rates of morbidity and mortality worldwide, and uropathogenic Escherichia coli (UPEC) is the main etiologic agent. Fimbriae assembled on the bacterial surface are essential for adhesion to the urinary tract epithelium. In this study, the FimH, CsgA, and PapG adhesins were fused to generate biomolecules for use as potential target vaccines against UTIs. The fusion protein design was generated using bioinformatics tools, and template fusion gene sequences were synthesized by GenScript in the following order fimH-csgA-papG-fimH-csgA (fcpfc) linked to the nucleotide sequence encoding the [EAAAK]5 peptide. Monomeric (fimH, csgA, and papG), dimeric (fimH-csgA), and trimeric (fimH-csgA-papG) genes were cloned into the pLATE31 expression vector and generated products of 1040, 539, 1139, 1442, and 2444 bp, respectively. Fusion protein expression in BL21 E. coli was induced with 1 mM IPTG, and His-tagged proteins were purified under denaturing conditions and refolded by dialysis using C-buffer. Coomassie blue-stained SDS-PAGE gels and Western blot analysis revealed bands of 29.5, 11.9, 33.9, 44.9, and 82.1 kDa, corresponding to FimH, CsgA, PapG, FC, and FCP proteins, respectively. Mass spectrometry analysis by MALDI-TOF/TOF revealed specific peptides that confirmed the fusion protein structures. Dynamic light scattering analysis revealed the polydispersed state of the fusion proteins. FimH, CsgA, and PapG stimulated the release of 372-398 pg/mL IL-6; interestingly, FC and FCP stimulated the release of 464.79 pg/mL (p ≤ 0.018) and 521.24 pg/mL (p ≤ 0.002) IL-6, respectively. In addition, FC and FCP stimulated the release of 398.52 pg/mL (p ≤ 0.001) and 450.40 pg/mL (p ≤ 0.002) IL-8, respectively. High levels of IgA and IgG antibodies in human sera reacted against the fusion proteins, and under identical conditions, low levels of IgA and IgG antibodies were detected in human urine. Rabbit polyclonal antibodies

  19. Dimeric and Trimeric Fusion Proteins Generated with Fimbrial Adhesins of Uropathogenic Escherichia coli

    PubMed Central

    Luna-Pineda, Víctor M.; Reyes-Grajeda, Juan Pablo; Cruz-Córdova, Ariadnna; Saldaña-Ahuactzi, Zeus; Ochoa, Sara A.; Maldonado-Bernal, Carmen; Cázares-Domínguez, Vicenta; Moreno-Fierros, Leticia; Arellano-Galindo, José; Hernández-Castro, Rigoberto; Xicohtencatl-Cortes, Juan

    2016-01-01

    Urinary tract infections (UTIs) are associated with high rates of morbidity and mortality worldwide, and uropathogenic Escherichia coli (UPEC) is the main etiologic agent. Fimbriae assembled on the bacterial surface are essential for adhesion to the urinary tract epithelium. In this study, the FimH, CsgA, and PapG adhesins were fused to generate biomolecules for use as potential target vaccines against UTIs. The fusion protein design was generated using bioinformatics tools, and template fusion gene sequences were synthesized by GenScript in the following order fimH-csgA-papG-fimH-csgA (fcpfc) linked to the nucleotide sequence encoding the [EAAAK]5 peptide. Monomeric (fimH, csgA, and papG), dimeric (fimH-csgA), and trimeric (fimH-csgA-papG) genes were cloned into the pLATE31 expression vector and generated products of 1040, 539, 1139, 1442, and 2444 bp, respectively. Fusion protein expression in BL21 E. coli was induced with 1 mM IPTG, and His-tagged proteins were purified under denaturing conditions and refolded by dialysis using C-buffer. Coomassie blue-stained SDS-PAGE gels and Western blot analysis revealed bands of 29.5, 11.9, 33.9, 44.9, and 82.1 kDa, corresponding to FimH, CsgA, PapG, FC, and FCP proteins, respectively. Mass spectrometry analysis by MALDI-TOF/TOF revealed specific peptides that confirmed the fusion protein structures. Dynamic light scattering analysis revealed the polydispersed state of the fusion proteins. FimH, CsgA, and PapG stimulated the release of 372–398 pg/mL IL-6; interestingly, FC and FCP stimulated the release of 464.79 pg/mL (p ≤ 0.018) and 521.24 pg/mL (p ≤ 0.002) IL-6, respectively. In addition, FC and FCP stimulated the release of 398.52 pg/mL (p ≤ 0.001) and 450.40 pg/mL (p ≤ 0.002) IL-8, respectively. High levels of IgA and IgG antibodies in human sera reacted against the fusion proteins, and under identical conditions, low levels of IgA and IgG antibodies were detected in human urine. Rabbit polyclonal antibodies

  20. Doubly charged trimeric cluster ions: effective in mutual chiral recognition of tadalafil and three proton pump inhibitors.

    PubMed

    Wang, Lu; Chai, Yunfeng; Zhu, Wenquan; Pan, Yuanjiang; Sun, Cuirong; Zeng, Su

    2017-02-27

    Mutual chiral recognition of four stereoisomers of tadalafil and three pairs of enantiomers of proton pump inhibitors (PPIs) including pantoprazole, lansoprazole, and omeprazole, as well as quantitative analysis of enantiomeric excess is achieved on the basis of the competitive fragmentation of doubly charged trimeric Ni(II) cluster ions. Compared with a singly charged trimeric cluster ion, a doubly charged trimeric cluster ion was proved efficient in the recognition of chiral drugs with one or multiple chiral centers, due to its rich fragmentation ions. Upon collision-induced dissociation (CID), the cluster ion [Ni(II)(PPIs)(tadalafil)2](2+) yielded two diagnostic ions [tadalafil + H](+) and [tadalafil - benzo[d][1,3]dixoloe](+) through electrospray ionization quadrupole time-of-flight mass spectrometry. The abundance ratio of the two fragment ions relied mainly on the configuration of PPIs and tadalafil, and therefore the chiral selectivity (Rchiral) of one enantiomer relative to the others is different. The chiral recognition of all four stereoisomers of tadalafil was achieved by using S configuration PPIs as references, and S-omeprazole showed the best selectivity. The Rchiral values for R,R/S,S, R,S/S,R, R,R/R,S and R,R/S,R-tadalafils were 1.47, 1.17, 2.37, and 2.10, respectively. In a reciprocal process, the Rchiral was 1.36 and 1.31 for R/S-pantoprazole and R/S-lansoprazole, respectively, by using R,R-tadalafil as a reference. Although omeprazole is a racemic drug, it can also be discriminated with S-omeprazole. Calibration curves were constructed with favorable correlation coefficients (r(2) > 0.991) by relating the ln(Rchiral) values to the isomeric composition in a mixture. The sensitivity of the methodology allows mixtures to be analyzed for the enantiomeric excess (ee) by recording the ratios of fragment ion abundances in a mass spectrum. The sensitivity of the methodology allowed the determination of enantiomeric impurities of 5% molar composition in

  1. A method of test for residual isophorone diisocyanate trimer in new polyester-polyurethane coatings on light metal packaging using liquid chromatography with tandem mass spectrometric detection.

    PubMed

    Driffield, Malcolm; Bradley, Emma L; Castle, Laurence

    2007-02-02

    A method of test for residual isophorone diisocyanate (IPDI) trimer in experimental formulation polyester-polyurethane (PEPU) thermoset coatings on metal food packaging is described. The method involves extraction of coated panels using acetonitrile containing dibutylamine for concurrent derivatisation, and then high performance liquid chromatography with electrospray ionisation tandem mass spectrometric detection (LC-MS/MS). Single laboratory validation was carried out using three different experimental PEPU-based coatings. The calibrations were linear, the analytical recovery was good, no interferences were seen, and substance identification criteria were met. The detection limit of the method is around 0.02 micro g/100 cm(2) of coating, which for a typical sized can and assuming complete migration of any residual IPDI trimer, corresponds to about 0.2 micro g/kg food or beverage. Separate studies indicated that, even if migration occurred at such low levels, the IPDI trimer would not be expected to persist in canned aqueous or fatty foodstuffs as it would hydrolyse to the corresponding aliphatic amine or react with food components to destroy the isocyanate moiety. The method of test developed here for residual IPDI trimer in thermoset polyester-polyurethane coatings should prove to be a valuable tool for investigating the cure kinetics of these novel coatings and help to guide the development of enhanced formulations.

  2. Theoretical study on nonlinear optical properties of the Li(+)[calix[4]pyrrole]Li(-)dimer, trimer and its polymer with diffuse excess electrons.

    PubMed

    Yu, Guang Tao; Chen, Wei; Gu, Feng Long; Aoki, Yuriko

    2010-03-01

    The static (hyper)polarizabilities of the dimer and trimer with diffuse excess electrons, [Li(+)[calix[4]pyrrole]Li(-)](n), are firstly investigated by the DFT(B3LYP) method in detail. For the dimer and trimer, a Li atom inside each calix[4]pyrrole unit is ionized to form a diffuse excess electron. The results show that the dimer and trimer containing two and three excess electrons, respectively, have very large first hyperpolarizablities as 2.3 x 10(4) and 4.0 x 10(4) au, which are 30 and 40 times larger than that of the corresponding [calix[4]pyrrole](n) (n = 2, 3) without Li atom. Also, beta values of dimer and trimer are twice and four times as large as that of monomer containing one excess electron. Obviously, not only excess electron but also the number of excess electron plays an important role in increasing the first hyperpolarizability. Moreover, the (hyper)polarizabilities of the [Li(+)[calix[4]pyrrole]Li(-)](n) polymer are investigated at ab initio level by using the elongation finite-field (elongation FF) method. All the oligomers of the [Li(+)[calix[4]pyrrole]Li(-)](n) with many excess electrons exhibit very large first hyperpolarizability and large second hyperpolarizability. The present investigation shows that by introducing several and more excess electrons into the nonlinear optical (NLO) materials will be an important strategy for improving their NLO properties, which will be helpful for design of NLO materials.

  3. Bacillus licheniformis Anti-TRAP can assemble into two types of dodecameric particles with the same symmetry but inverted orientation of trimers

    PubMed Central

    Shevtsov, Mikhail B.; Chen, Yanling; Isupov, Michail N.; Leech, Andrew; Gollnick, Paul; Antson, Alfred A.

    2010-01-01

    Anti-TRAP (AT) protein regulates expression of tryptophan biosynthetic genes by binding to the trp RNA-binding attenuation protein (TRAP) and preventing its interaction with RNA. Bacillus subtilis AT forms trimers that can either interact with TRAP or can further assemble into dodecameric particles. To determine which oligomeric forms are preserved in AT proteins of other Bacilli we studied Bacillus licheniformis AT which shares 66% sequence identity with the B. subtilis protein. We show that in solution B. licheniformis AT forms stable trimers. In crystals, depending on pH, such trimers assemble into two different types of dodecameric particles, both having 23 point group symmetry. The dodecamer formed at pH 6.0 has the same conformation as previously observed for B. subtilis AT. This dodecamer contains a large internal chamber with the volume of ∼700 Å3, which is lined by the side chains of twelve valine residues. The presence of the hydrophobic chamber hints at the possibility that the dodecamer formation could be induced by binding of a ligand. Interestingly, in the dodecamer formed at pH 8.0 all trimers are turned inside out relatively to the form observed at pH 6.0. PMID:20138150

  4. Mimicking Trimeric Interactions in the Aromatic Side Chains of the Proteins: a Gas Phase Study of INDOLE...(PYRROLE)_2 Heterotrimer

    NASA Astrophysics Data System (ADS)

    Das, Aloke; Kumar, Sumit

    2012-06-01

    Aromatic trimeric interactions are extremely important in the stabilization of the specific structures of the proteins as well as protein-protein, and protein-ligand interactions. Here I will present a direct evidence of the observation of a cyclic asymmetric structure of indole...(pyrrole)_2 trimer bound by three N-H...π hydrogen bonding interactions in a supersonic jet. The experiment has been performed by using resonant two-photon ionization (R2PI), IR-UV, and UV-UV double resonance spectroscopic techniques. Density functional theory (DFT) calculations nicely corroborate the experimental results showing one weakly allowed IR-active band due to symmetric stretch of the N-H bonds and two strongly allowed IR-active bands due to two types of asymmetric stretches of the N-H bonds in the trimer. The most significant finding of the present investigation is that there is a direct IR spectral signature for the determination of the geometry of a trimer if it has a cyclic asymmetric structure.

  5. Modeling of the N-terminal Section and the Lumenal Loop of Trimeric Light Harvesting Complex II (LHCII) by Using EPR*

    PubMed Central

    Fehr, Niklas; Dietz, Carsten; Polyhach, Yevhen; von Hagens, Tona; Jeschke, Gunnar; Paulsen, Harald

    2015-01-01

    The major light harvesting complex II (LHCII) of green plants plays a key role in the absorption of sunlight, the regulation of photosynthesis, and in preventing photodamage by excess light. The latter two functions are thought to involve the lumenal loop and the N-terminal domain. Their structure and mobility in an aqueous environment are only partially known. Electron paramagnetic resonance (EPR) has been used to measure the structure of these hydrophilic protein domains in detergent-solubilized LHCII. A new technique is introduced to prepare LHCII trimers in which only one monomer is spin-labeled. These heterogeneous trimers allow to measure intra-molecular distances within one LHCII monomer in the context of a trimer by using double electron-electron resonance (DEER). These data together with data from electron spin echo envelope modulation (ESEEM) allowed to model the N-terminal protein section, which has not been resolved in current crystal structures, and the lumenal loop domain. The N-terminal domain covers only a restricted area above the superhelix in LHCII, which is consistent with the “Velcro” hypothesis to explain thylakoid grana stacking (Standfuss, J., van Terwisscha Scheltinga, A. C., Lamborghini, M., and Kühlbrandt, W. (2005) EMBO J. 24, 919–928). The conformation of the lumenal loop domain is surprisingly different between LHCII monomers and trimers but not between complexes with and without neoxanthin bound. PMID:26316535

  6. Bacterial chemoreceptor arrays are hexagonally packed trimers of receptor dimers networked by rings of kinase and coupling proteins

    PubMed Central

    Briegel, Ariane; Li, Xiaoxiao; Bilwes, Alexandrine M.; Hughes, Kelly T.; Jensen, Grant J.; Crane, Brian R.

    2012-01-01

    Chemoreceptor arrays are supramolecular transmembrane machines of unknown structure that allow bacteria to sense their surroundings and respond by chemotaxis. We have combined X-ray crystallography of purified proteins with electron cryotomography of native arrays inside cells to reveal the arrangement of the component transmembrane receptors, histidine kinases (CheA) and CheW coupling proteins. Trimers of receptor dimers lie at the vertices of a hexagonal lattice in a “two-facing-two” configuration surrounding a ring of alternating CheA regulatory domains (P5) and CheW couplers. Whereas the CheA kinase domains (P4) project downward below the ring, the CheA dimerization domains (P3) link neighboring rings to form an extended, stable array. This highly interconnected protein architecture underlies the remarkable sensitivity and cooperative nature of transmembrane signaling in bacterial chemotaxis. PMID:22355139

  7. The Arabidopsis Cellulose Synthase Complex: A Proposed Hexamer of CESA Trimers in an Equimolar Stoichiometry

    SciTech Connect

    Hill, Joseph L.; Hammudi, Mustafa B.; Tien, Ming

    2014-12-01

    In this study, we show a 1:1:1 stoichiometry between the three Arabidopsis thaliana secondary cell wall isozymes: CESA4, CESA7, and CESA8. This ratio was determined utilizing a simple but elegant method of quantitative immunoblotting using isoform-specific antibodies and 35S-labeled protein standards for each CESA. Additionally, the observed equimolar stoichiometry was found to be fixed along the axis of the stem, which represents a developmental gradient. Our results complement recent spectroscopic analyses pointing toward an 18-chain cellulose microfibril. Taken together, we propose that the CSC is composed of a hexamer of catalytically active CESA trimers, with each CESA in equimolar amounts. This finding is a crucial advance in understanding how CESAs integrate to form higher order complexes, which is a key determinate of cellulose microfibril and cell wall properties.

  8. A non-thermal lattice gas model for a dimer trimer reaction on a catalytic surface: A computer simulation study

    NASA Astrophysics Data System (ADS)

    Ahmad, Waqar; Parvez, M.; Baloach, Musa Kaleem; Qaisrani, A. U.; Khalid, M.

    2006-11-01

    The kinetics of an irreversible dimer-trimer reaction of the type 3A 2 + 2B 3 → 6AB have been studied using a non-thermal (precursor mechanism) model on a square as well as on a hexagonal lattice surface by Monte Carlo simulation. When the range of the precursors (A atoms) is increased, the model gives production rates (reactive window widths) that are quite large as compared with those for thermal (Langmuir-Hanshelwood mechanism) model. The phase diagrams qualitatively resemble with the standard ZGB model except that the continuous transition point is eliminated when the range of the precursors is extended up to the third nearest neighbourhood. The diffusion of A atoms on the surface as well as their desorption from the surface with a certain probability is also considered to see their effects on the reaction mechanism.

  9. HIV Envelope Trimer Specific Immune Response Is Influenced by Different Adjuvant Formulations and Heterologous Prime-Boost

    PubMed Central

    Apostólico, Juliana de Souza; Boscardin, Silvia Beatriz; Yamamoto, Márcio Massao; de Oliveira-Filho, Jethe Nunes; Kalil, Jorge; Cunha-Neto, Edecio; Rosa, Daniela Santoro

    2016-01-01

    The development of a preventive vaccine against human immunodeficiency virus (HIV-1) infection is the most efficient method to control the epidemic. The ultimate goal is to develop a vaccine able to induce specific neutralizing, non-neutralizing antibodies and cellular mediated immunity (CMI). Humoral and CMI responses can be directed to glycoproteins that are normally presented as a trimeric spike on the virus surface (gp140). Despite safer, subunit vaccines are normally less immunogenic/effective and need to be delivered together with an adjuvant. The choice of a suitable adjuvant can induce effective humoral and CMI that utterly lead to full protection against disease. In this report, we established a hierarchy of adjuvant potency on humoral and CMI when admixed with the recombinant HIV gp140 trimer. We show that vaccination with gp140 in the presence of different adjuvants can induce high-affinity antibodies, follicular helper T cells and germinal center B cells. The data show that poly (I:C) is the most potent adjuvant to induce specific CMI responses evidenced by IFN-γ production and CD4+/CD8+ T cell proliferation. Furthermore, we demonstrate that combining some adjuvants like MPL plus Alum and MPL plus MDP exert additive effects that impact on the magnitude and quality of humoral responses while mixing MDP with poly (I:C) or with R848 had no impact on total IgG titers but highly impact IgG subclass. In addition, heterologous DNA prime- protein boost yielded higher IgG titers when compare to DNA alone and improved the quality of humoral response when compare to protein immunization as evidenced by IgG1/IgG2a ratio. The results presented in this paper highlight the importance of selecting the correct adjuvant-antigen combination to potentiate desired cells for optimal stimulation. PMID:26727218

  10. Electronic effect on protonated hydrogen-bonded imidazole trimer and corresponding derivatives cationized by alkali metals (Li+, Na+, and K+)

    NASA Astrophysics Data System (ADS)

    Yan, Shihai; Bu, Yuxiang; Li, Ping

    2005-02-01

    The electronic effects on the protonated hydrogen-bonded imidazole trimer (Im)3H+ and the derivatives cationized by alkali metals (Li+, Na+, and K+) are investigated using B3LYP method in conjunction with the 6-311+G* basis set. The prominent characteristics of (Im)3H+ on reduction are the backflow of the transferred proton to its original fragment and the remoteness of the H atom from the attached side bare N atom. The proton transfer occurs on both reduction and oxidation for the corresponding hydrogen-bonded imidazole trimer. For the derivatives cationized by Li+, (Im)3Li+, the backflow of the transferred proton occurs on reduction. The electron detachment from respective highest occupied molecular orbital of (Im)3Na+ and (Im)3K+ causes the proton transferring from the fragment attached by the alkali metal cation to the middle one. The order of the adiabatic ionization potentials of (Im)3M+ is (Im)3H+>(Im)3Li+>(Im)3Na+>(Im)3K+; the order of (Im)3M indicates that (Im)3H is the easicst complex to be ionized. The polarity of (Im)3M+ (M denotes H, Li, Na, and K) increases on both oxidation and reduction. The (Im)3M+ complexes dissociate into (Im)3 and M+ except (Im)3H+, which dissociates preferably into (Im)3+ and H atom, while the neutral complexes [(Im)3M] dissociate into (Im)3 and M. The stabilization energy of (Im)3Li2+, (Im)3Na2+, and (Im)3K2+ indicate that their energies are higher as compared to those of the monomers.

  11. Structural Basis for Toughness and Flexibility in the C-terminal Passenger Domain of an Acinetobacter Trimeric Autotransporter Adhesin*

    PubMed Central

    Koiwai, Kotaro; Hartmann, Marcus D.; Linke, Dirk; Lupas, Andrei N.; Hori, Katsutoshi

    2016-01-01

    Trimeric autotransporter adhesins (TAAs) on the cell surface of Gram-negative pathogens mediate bacterial adhesion to host cells and extracellular matrix proteins. However, AtaA, a TAA in the nonpathogenic Acinetobacter sp. strain Tol 5, shows nonspecific high adhesiveness to abiotic material surfaces as well as to biotic surfaces. It consists of a passenger domain secreted by the C-terminal transmembrane anchor domain (TM), and the passenger domain contains an N-terminal head, N-terminal stalk, C-terminal head (Chead), and C-terminal stalk (Cstalk). The Chead-Cstalk-TM fragment, which is conserved in many Acinetobacter TAAs, has by itself the head-stalk-anchor architecture of a complete TAA. Here, we show the crystal structure of the Chead-Cstalk fragment, AtaA_C-terminal passenger domain (CPSD), providing the first view of several conserved TAA domains. The YadA-like head (Ylhead) of the fragment is capped by a unique structure (headCap), composed of three β-hairpins and a connector motif; it also contains a head insert motif (HIM1) before its last inner β-strand. The headCap, Ylhead, and HIM1 integrally form a stable Chead structure. Some of the major domains of the CPSD fragment are inherently flexible and provide bending sites for the fiber between segments whose toughness is ensured by topological chain exchange and hydrophobic core formation inside the trimer. Thus, although adherence assays using in-frame deletion mutants revealed that the characteristic adhesive sites of AtaA reside in its N-terminal part, the flexibility and toughness of the CPSD part provide the resilience that enables the adhesive properties of the full-length fiber across a wide range of conditions. PMID:26698633

  12. DFT and experimental study of N, N'-bis(3'-carboxy,4'-aminophenyl)-1,4-quinonediimine, a carboxyl substituted aniline trimer

    NASA Astrophysics Data System (ADS)

    Sein, Lawrence T., Jr.; Lashua, Amanda F.

    2010-08-01

    Density functional calculations were performed on N, N'-bis(3'-carboxy,4'-aminophenyl)-1,4-quinonediimine, a carboxylic acid substituted aniline trimer. Results of the calculations were compared to experimental properties of the herein synthesized trimer, as well as to the properties of the anthranilic acid/aniline co-polymer reported in the literature. The calculated LUMO levels for isomers of the title compound range from -4.45 to -5.05 eV. The calculated electron affinities range from 75.93 kcal mol -1 to 89.04 kcal mol -1 (3.29-3.86 eV). Both the LUMO levels and electron affinities are greatest in magnitude for the anti, syn isomer. The HOMO levels, on the other hand, range from -5.32 eV (for the trans, trans isomer) to -5.36 eV (syn, syn inner). In acetonitrile solvent, the zwitterionic form is calculated to be energetically preferred to the non-zwitterion. Experimental UV-vis and near-IR studies in acetonitrile and ethanol show little evidence for zwitterion formation, but those in water show strong evidence. The predicted electronic transitions for the non-zwitterion in acetonitrile solvent correspond closely to those seen at 533 and 416 nm. The zwitterion present in solvent corresponds to a trimer with the capability to "self-dope", suggesting that the trimer would be effective at corrosion inhibition in the emeraldine base form, unlike other trimers which are only effective in the emeraldine salt form. This effectiveness in the emeraldine base form would enable the material to be utilized in corrosion inhibition applications in alkaline environments where standard oligo- and polyanilines fail.

  13. The Impact of Full-Length, Trimeric and Globular Adiponectin on Lipolysis in Subcutaneous and Visceral Adipocytes of Obese and Non-Obese Women.

    PubMed

    Wedellova, Zuzana; Kovacova, Zuzana; Tencerova, Michaela; Vedral, Tomas; Rossmeislova, Lenka; Siklova-Vitkova, Michaela; Stich, Vladimir; Polak, Jan

    2013-01-01

    Contribution of individual adiponectin isoforms to lipolysis regulation remains unknown. We investigated the impact of full-length, trimeric and globular adiponectin isoforms on spontaneous lipolysis in subcutaneous abdominal (SCAAT) and visceral adipose tissues (VAT) of obese and non-obese subjects. Furthermore, we explored the role of AMPK (5'-AMP-activated protein kinase) in adiponectin-dependent lipolysis regulation and expression of adiponectin receptors type 1 and 2 (AdipoR1 and AdipoR2) in SCAAT and VAT. Primary adipocytes isolated from SCAAT and VAT of obese and non-obese women were incubated with 20 µg/ml of: A) full-length adiponectin (physiological mixture of all adiponectin isoforms), B) trimeric adiponectin isoform or C) globular adiponectin isoform. Glycerol released into media was used as a marker of lipolysis. While full-length adiponectin inhibited lipolysis by 22% in non-obese SCAAT, globular isoform inhibited lipolysis by 27% in obese SCAAT. No effect of either isoform was detected in non-obese VAT, however trimeric isoform inhibited lipolysis by 21% in obese VAT (all p<0.05). Trimeric isoform induced Thr172 p-AMPK in differentiated preadipocytes from a non-obese donor, while globular isoform induced Ser79 p-ACC by 32% (p<0.05) and Ser565 p-HSL by 52% (p = 0.08) in differentiated preadipocytes from an obese donor. AdipoR2 expression was 17% and 37% higher than AdipoR1 in SCAAT of obese and non-obese groups and by 23% higher in VAT of obese subjects (all p<0.05). In conclusion, the anti-lipolytic effect of adiponectin isoforms is modified with obesity: while full-length adiponectin exerts anti-lipolytic action in non-obese SCAAT, globular and trimeric isoforms show anti-lipolytic activity in obese SCAAT and VAT, respectively.

  14. H/D isotopic and temperature effects in the polarized IR spectra of hydrogen-bond cyclic trimers in the crystal lattices of acetone oxime and 3,5-dimethylpyrazole.

    PubMed

    Flakus, Henryk T; Hachuła, Barbara; Garbacz, Aleksandra

    2012-11-29

    Polarized IR spectra of hydrogen-bonded acetone oxime and 3,5-dimethylpyrazole crystals were measured at 293 and 77 K in the ν(X-H) and ν(X-D) band frequency ranges. These crystals contain molecular trimers in their lattices. The individual crystal spectral properties remain in a close relation with the electronic structure of the two different molecular systems. We show that a vibronic coupling mechanism involving the hydrogen-bond protons and the electrons on the π-electronic systems in the molecules determines the way in which the vibrational exciton coupling between the hydrogen bonds in the trimers occurs. A strong coupling in 3,5-dimethylpyrazole trimers prefers a "tail-to-head"-type Davydov coupling widespread via the π-electrons. A weak through-space exciton coupling in acetone oxime trimers involves three adjacent hydrogen bonds in each cycle. The relative contribution of each exciton coupling mechanism in the trimer spectra generation is temperature and the molecular electronic structure-dependent. This explains the observed difference in the temperature-induced evolution of the compared spectra. The mechanism of the H/D isotopic "self-organization" processes in the crystal hydrogen bonds was also analyzed. The two types of the hydrogen-bond trimers exhibit the same way, in which the H/D isotopic recognition mechanism occurs. In acetone oxime and 3,5-dimethylpyrazole trimers, identical hydrogen isotope atoms exist in these entire hydrogen-bond systems.

  15. Understanding microscopic binding of human microsomal prostaglandin E synthase-1 (mPGES-1) trimer with substrate PGH2 and cofactor GSH: insights from computational alanine scanning and site-directed mutagenesis.

    PubMed

    Hamza, Adel; Tong, Min; AbdulHameed, Mohamed Diwan M; Liu, Junjun; Goren, Alan C; Tai, Hsin-Hsiung; Zhan, Chang-Guo

    2010-04-29

    Microsomal prostaglandin E synthase-1 (mPGES-1) is an essential enzyme involved in a variety of diseases and is the most promising target for the design of next-generation anti-inflammatory drugs. In order to establish a solid structural base, we recently developed a model of mPGES-1 trimer structure by using available crystal structures of both microsomal glutathione transferase-1 (MGST1) and ba3-cytochrome c oxidase as templates. The mPGES-1 trimer model has been used in the present study to examine the detailed binding of mPGES-1 trimer with substrate PGH(2) and cofactor GSH. Results obtained from the computational alanine scanning reveal the contribution of each residue at the protein-ligand interaction interface to the binding affinity, and the computational predictions are supported by the data obtained from the corresponding wet experimental tests. We have also compared our mPGES-1 trimer model with other available 3D models, including an alternative homology model and a low-resolution crystal structure, and found that our mPGES-1 trimer model based on the crystal structures of both MGST1 and ba3-cytochrome c oxidase is more reasonable than the other homology model of mPGES-1 trimer constructed by simply using a low-resolution crystal structure of MGST1 trimer alone as a template. The available low-resolution crystal structure of mPGES-1 trimer represents a closed conformation of the enzyme and thus is not suitable for studying mPGES-1 binding with ligands. Our mPGES-1 trimer model represents a reasonable open conformation of the enzyme and is therefore promising for studying mPGES-1 binding with ligands in future structure-based drug design targeting mPGES-1.

  16. Structural and rheological studies on growth of salt-free wormlike micelles formed by star-type trimeric surfactants.

    PubMed

    Kusano, Takumi; Iwase, Hiroki; Yoshimura, Tomokazu; Shibayama, Mitsuhiro

    2012-12-11

    We investigated the growth mechanisms of wormlike micelles formed by star-type trimeric surfactant (3C(12)trisQ) with a hydrocarbon chain length of 12 in an aqueous solution. A 3C(n)trisQ molecule consists of three hydrocarbon chains and three hydrophilic groups connected by spacer chains, where n is the carbon number in the hydrocarbon chain. Our recent studies showed that the aggregates formed by 3C(12)trisQ exhibited sphere-to-rod transition and the growth of wormlike micelles in an aqueous solution in the absence of salt. We performed small-angle neutron scattering (SANS) and rheological measurements and investigated the aggregation behavior of 3C(12)trisQ with various surfactant volume fractions. All SANS profiles for the 3C(12)trisQ indicated peak-profiles in the q range of 0.02 Å(-1) < q < 0.05 Å(-1), where the magnitude of the scattering vector q is defined by q = 4π sin(θ/2)/λ (λ and θ represent the wavelength and scattering angle, respectively). These peaks were attributed to repulsive interparticle interactions between the micelles. The volume fraction dependence of the SANS peak-position was in agreement with the rheological behavior. These results suggest that 3C(12)trisQ shows sphere-to-rod transition and can produce wormlike micelles in the absence of salt. To determine the structural parameters quantitatively, model-fitting analysis was performed using a charged cylindrical or charged ellipsoidal particle scattering function. The radius, length, and number of water molecules per surfactant molecule (n(w)) inside the micelles were evaluated. The length increased and the n(w) value decreased with increasing φ, indicating that the growth of a wormlike micelle accompanies the extrusion of water from the micelle. The end-cap energies of star-type trimeric, gemini, and monomeric surfactants were evaluated from φ dependence of zero-shear viscosity. We found that wormlike micelles formed by 3C(12)trisQ exhibited a higher end-cap energy than gemini

  17. Comparative Analysis of the Glycosylation Profiles of Membrane-Anchored HIV-1 Envelope Glycoprotein Trimers and Soluble gp140

    PubMed Central

    Go, Eden P.; Herschhorn, Alon; Gu, Christopher; Castillo-Menendez, Luis; Zhang, Shijian; Mao, Youdong; Chen, Haiyan; Ding, Haitao; Wakefield, John K.; Hua, David; Liao, Hua-Xin; Kappes, John C.; Sodroski, Joseph

    2015-01-01

    ABSTRACT The human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) trimer, which consists of the gp120 and gp41 subunits, is the focus of multiple strategies for vaccine development. Extensive Env glycosylation provides HIV-1 with protection from the immune system, yet the glycans are also essential components of binding epitopes for numerous broadly neutralizing antibodies. Recent studies have shown that when Env is isolated from virions, its glycosylation profile differs significantly from that of soluble forms of Env (gp120 or gp140) predominantly used in vaccine discovery research. Here we show that exogenous membrane-anchored Envs, which can be produced in large quantities in mammalian cells, also display a virion-like glycan profile, where the glycoprotein is extensively decorated with high-mannose glycans. Additionally, because we characterized the glycosylation with a high-fidelity profiling method, glycopeptide analysis, an unprecedented level of molecular detail regarding membrane Env glycosylation and its heterogeneity is presented. Each glycosylation site was characterized individually, with about 500 glycoforms characterized per Env protein. While many of the sites contain exclusively high-mannose glycans, others retain complex glycans, resulting in a glycan profile that cannot currently be mimicked on soluble gp120 or gp140 preparations. These site-level studies are important for understanding antibody-glycan interactions on native Env trimers. Additionally, we report a newly observed O-linked glycosylation site, T606, and we show that the full O-linked glycosylation profile of membrane-associated Env is similar to that of soluble gp140. These findings provide new insight into Env glycosylation and clarify key molecular-level differences between membrane-anchored Env and soluble gp140. IMPORTANCE A vaccine that protects against human immunodeficiency virus type 1 (HIV-1) infection should elicit antibodies that bind to the surface

  18. On 3d bonding in the transition metal trimers - The electronic structure of equilateral triangle Ca3, Sc3, Sc3(+), and Ti3(+)

    NASA Technical Reports Server (NTRS)

    Walch, S. P.; Bauschlicher, C. W., Jr.

    1985-01-01

    It is pointed out that transition metals and transition metal (TM) compounds are currently of considerable interest because of their relevance to catalysis and to materials science problems such as hydrogen embrittlement and crack propagation in metals. The present paper is concerned with complete active space Self-Consistent Field (SCF) externally contracted configuration interaction (CASSCF/CCI) calculations for the low-lying states of Sc3 and Sc3(+). A comparison is conducted regarding the bonding in the Ca3, Sc3, and Cu3 molecules. This comparison makes it possible to predict general trends for the TM trimers. Attention is given to the qualitative features of the bonding in the TM trimers, the basis sets and other technical details of the calculations, the calculated results for Sc3 and Sc3(+), and conclusions from this work.

  19. The Fusobacterium nucleatum major outer-membrane protein (FomA) forms trimeric, water-filled channels in lipid bilayer membranes.

    PubMed

    Kleivdal, H; Benz, R; Jensen, H B

    1995-10-01

    The pore-forming activity of the major outer-membrane protein FomA of the anaerobic Fusobacterium nucleatum was studied in artificial lipid bilayer membranes. FomA was isolated from F. nucleatum strains Fev1, ATCC 10953, and ATCC 25586 by extraction with lithium dodecyl sulfate and lithium chloride and had an apparent molecular mass of about 40 kDa. When solubilized at low temperatures, the protein ran with an apparent molecular mass of about 62 kDa on SDS/PAGE. Cross-linking experiments and two-dimensional SDS/PAGE gave evidence that the 62-kDa protein band represented the trimeric form of FomA. The protein trimers were susceptible to SDS and temperature. The stability of the porin trimers varied among the strains. The properties of the FomA channels were studied in reconstitution experiments with black lipid bilayer membranes. The F. nucleatum porins formed channels with single-channel conductances in the range 0.66-1.30 nS in M KCl. The single-channel conductance was a function of the mobilities of the ions present in the aqueous solution bathing the bilayer membrane. This means that FomA forms general diffusion channels since (a) the conductance showed a linear dependence on the salt concentration, (b) the ion selectivity was small and varied for the three strains, and (c) the channels did not exhibit any binding site for maltotriose or triglycine. The water-filled channel was voltage dependent, and conductance decrements were observed at transmembrane potentials of +/- 50 mV. The conductance decrement steps were about one-third of the total conductance of a functional unit in its fully 'open' state. This strongly suggests that the trimer is the functional unit of the porin.

  20. Synthesis and Low Temperature Spectroscopic Observation of 1,3,5-Trioxane-2,4,6-Trione: The Cyclic Trimer of Carbon Dioxide

    DTIC Science & Technology

    2016-08-19

    experimentally derived value. (43) Avram, M.; Mateescu, G. H. Infrared Spectroscopy: Applications in Organic Chemistry; Wiley-Interscience: New York, 1972; pp...molecules,6 incorporation into polymers7 and artificial photosynthesis.8 The main products include fuels, solvents, chemical inter- mediates and polymers ...the linear polymer and cyclic oligomers of CO2. 9−14 With respect to thermodynamic stability, the cyclic trimer has been described as “feasible

  1. Structural Basis of HIV-1 Neutralization by Affinity Matured Fabs Directed against the Internal Trimeric Coiled-Coil of gp41

    SciTech Connect

    Gustchina, Elena; Li, Mi; Louis, John M.; Anderson, D.Eric; Lloyd, John; Frisch, Christian; Bewley, Carole A.; Gustchina, Alla; Wlodawer, Alexander; Clore, G.Marius

    2010-12-03

    The conserved internal trimeric coiled-coil of the N-heptad repeat (N-HR) of HIV-1 gp41 is transiently exposed during the fusion process by forming a pre-hairpin intermediate, thus representing an attractive target for the design of fusion inhibitors and neutralizing antibodies. In previous studies we reported a series of broadly neutralizing mini-antibodies derived from a synthetic naive human combinatorial antibody library by panning against a mimetic of the trimeric N-HR coiled coil, followed by affinity maturation using targeted diversification of the CDR-H2 loop. Here we report crystal structures of the N-HR mimetic 5-Helix with two Fabs that represent the extremes of this series: Fab 8066 is broadly neutralizing across a wide panel of B and C type HIV-1 viruses, whereas Fab 8062 is non-neutralizing. The crystal structures reveal important differences in the conformations of the CDR-H2 loops in the complexes that propagate into other regions of the antigen-antibody interface, and suggest that both neutralization properties and affinity for the target can be attributed, at least in part, to the differences in the interactions of the CDR-H2 loops with the antigen. Furthermore, modeling of the complex of an N-HR trimer with three Fabs suggests that the CDR-H2 loop may be involved in close intermolecular contacts between neighboring antibody molecules, and that such contacts may hinder the formation of complexes between the N-HR trimer and more than one antibody molecule depending on the conformation of the bound CDR-H2 loop which is defined by its interactions with antigen. Comparison with the crystal structure of the complex of 5-Helix with another neutralizing monoclonal antibody known as D5, derived using an entirely different antibody library and panning procedure, reveals remarkable convergence in the optimal sequence and conformation of the CDR-H2 loop.

  2. N-terminal substitutions in HIV-1 gp41 reduce the expression of non-trimeric envelope glycoproteins on the virus

    SciTech Connect

    Dey, Antu K.; David, Kathryn B.; Ray, Neelanjana; Ketas, Thomas J.; Klasse, Per J.; Doms, Robert W.; Moore, John P.

    2008-03-01

    The native, functional HIV-1 envelope glycoprotein (Env) complex is a trimer of two non-covalently associated subunits: the gp120 surface glycoprotein and the gp41 transmembrane glycoprotein. However, various non-functional forms of Env are present on virus particles and HIV-1-infected cells, some of which probably arise as the native complex decays. The aberrant forms include gp120-gp41 monomers and oligomers, as well as gp41 subunits from which gp120 has dissociated. The presence of non-functional Env creates binding sites for antibodies that do not recognize native Env complexes and that are, therefore, non-neutralizing. Non-native Env forms (monomers, dimers, tetramers and aggregates) can also arise when soluble gp140 proteins, lacking the cytoplasmic and transmembrane domains of gp41, are expressed for vaccine studies. We recently identified five amino acids in the gp41 N-terminal region (I535, Q543, S553, K567 and R588) that promote gp140 trimerization. We have now studied their influence on the function and antigenic properties of JR-FL Env expressed on the surfaces of pseudoviruses and Env-transfected cells. The 5 substitutions in gp41 reduce the expression of non-trimeric gp160s, without affecting trimer levels. Pseudovirions bearing the mutant Env are fully infectious with similar kinetics of Env-mediated fusion. Various non-neutralizing antibodies bind less strongly to the Env mutant, but neutralizing antibody binding is unaffected. Hence the gp41 substitutions do not adversely affect Env structure, supporting their use for making new Env-based vaccines. The mutant Env might also help in studies intended to correlate antibody binding to virus neutralization. Of note is that the 5 residues are much more frequent, individually or collectively, in viruses from subtypes other than B.

  3. Disulfide-Dependent Self-Assembly of Adiponectin Octadecamers from Trimers and Presence of Stable Octadecameric Adiponectin Lacking Disulfide Bonds In Vitro†

    PubMed Central

    Briggs, David B.; Jones, Christopher M.; Mashalidis, Ellene H.; Nuñez, Martha; Hausrath, Andrew C.; Wysocki, Vicki H.; Tsao, Tsu-Shuen

    2009-01-01

    Adiponectin is a circulating insulin-sensitizing hormone that homo-oligomerizes into trimers, hexamers, and higher molecular weight (HMW) species. Low levels of circulating HMW adiponectin appear to increase the risk for insulin resistance. Currently, assembly of adiponectin oligomers, and consequently mechanisms responsible for decreased HMW adiponectin in insulin resistance, are not well understood. In the work reported here, we analyzed the re-assembly of the most abundant HMW adiponectin species, the octadecamer, following its collapse to smaller oligomers in vitro. Purified bovine serum adiponectin octadecamer was treated with reducing agents at pH 5 to obtain trimers. These reduced trimers partially and spontaneously reassembled into octadecamers upon oxidative formation of disulfide bonds. Disulfide bonds appear to occupy a greater role in the process of oligomerization than in the structural stabilization of mature octadecamer. Stable octadecamers lacking virtually all disulfide bonds could be observed in abundance using native gel electrophoresis, dynamic light scattering, and collision-induced dissociation nano-electrospray ionization mass spectrometry. These findings indicate that while disulfide bonds help to maintain the mature octadecameric adiponectin structure, their more important function is to stabilize intermediates during the assembly of octadecamer. Adiponectin oligomerization must proceed through intermediates that are at least partially reduced. Accordingly, fully oxidized adiponectin hexamers failed to reassemble into octadecamers at a rate comparable to that of reduced trimers. As the findings from the present study are based on in vitro experiments, their in vivo relevance remains unclear. Nevertheless, they describe a redox environment-dependent model of adiponectin oligomerization that can be tested using cell-based approaches. PMID:19943704

  4. Quantifying Dimer and Trimer Formation by Tri- n -butyl Phosphates in n -Dodecane: Molecular Dynamics Simulations

    SciTech Connect

    Vo, Quynh N.; Dang, Liem X.; Nilsson, Mikael; Nguyen, Hung D.

    2016-07-21

    Tri-n-butyl phosphate (TBP), a representative of neutral organophosphorous ligands, is an important extractant used in solvent extraction process for the recovery of uranium and plutonium from spent nuclear fuel. Microscopic pictures of TBP isomerism and its behavior in n-dodecane diluent were investigated utilizing MD simulations with previously optimized force field parameters for TBP and n-dodecane. Potential Mean Force (PMF) calculations on a single TBP molecule show seven probable TBP isomers. Radial Distribution Functions (RDF) of TBP suggests the existence of TBP trimers at high TBP concentrations in addition to dimers. 2D PMF calculations were performed to determine the angle and distance criteria for TBP trimers. The dimerization and trimerization constants of TBP in n-dodecane were obtained and match our own experimental values using FTIR technique. The new insights into the conformational behaviors of TBP molecule as a monomer and as part of an aggregate could greatly aid the understanding of the complexation between TBP and metal ions in solvent extraction system. The U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences funded the work performed by LXD.

  5. Development and characterization of recombinant human Fc:OX40L fusion protein linked via a coiled-coil trimerization domain.

    PubMed

    Morris, Nicholas P; Peters, Carmen; Montler, Ryan; Hu, Hong-Ming; Curti, Brendan D; Urba, Walter J; Weinberg, Andrew D

    2007-05-01

    OX40 (CD134) is a potent costimulatory molecule found on the surface of activated CD4(+) and CD8(+) T cells. Immunotherapy with OX40 agonists administered in vivo has demonstrated efficacy in several murine tumor models. A phase I clinical trial is currently underway in patients with advanced cancer using a mouse anti-CD134 monoclonal antibody. Therapy with this antibody will likely be limited to one cycle because patients develop neutralizing human anti-mouse antibody (HAMA). Therefore, we developed a humanized OX40 agonist that links the extracellular domain of human OX40L to the Fc domain of human IgG(1) via a trimerizing isoleucine zipper domain (ILZ). Physical characterization by velocity sedimentation revealed that this novel construct, hFcILZOX40L, was assembled into hexamers in which the Fc domains formed three disulfide-bonded dimers and the ILZ-OX40L domains formed two trimers. Trimerization of the ILZ domain was necessary to achieve appropriate assembly. In vitro biologic activity of the hFcILZOX40L hexamer was equivalent to the activity of agonist antibodies in plate-bound assays and was superior when the agonists were tested as soluble agents. Our ultimate goal is to use this recombinant molecule in a future clinical trial, and we feel that the OX40L hexamer will have equivalent or superior agonist activity in vivo when compared to an anti-OX40 antibody.

  6. Accidental Conical Intersections in Mixed Trimers of Potassium and Rubidium: a Vibronic Analysis of the 4^4B_2 and 3^4A_1 States

    NASA Astrophysics Data System (ADS)

    Hauser, A. W.; Auböck, G.; Callegari, C.; Ernst, W. E.

    2010-06-01

    We compare the 3^4A_1 and 4^4B_2 states of homonuclear and heteronuclear alkali trimers formed of potassium and rubidium. The Multireference Rayleigh Schrödinger Perturbation Theory of second order is applied to obtain the corresponding adiabatic potential energy surfaces. In the case of homonuclear trimers these pairs of states correspond to the two branches of the E×{}e Jahn-Teller distorted 2^4E^' state. For heteronuclear trimers, the vibrational modes Q_x and Q_y are no longer degenerate, but the two electronic states still show a conical intersection at obtuse (KRb_2) or acute (K_2Rb) isosceles geometries. Spectroscopic consequences of this situation are discussed, vibronic spectra are predicted and compared to LIF spectra obtained in helium droplet isolation spectroscopy experiments of our group. J. Nagl, G. Auböck, A.W. Hauser, O. Allard, C. Callegari and W.E. Ernst, Phys. Rev. Lett. 100, 063001 (2008) J. Nagl, G. Auböck, A.W. Hauser, O. Allard, C. Callegari and W.E. Ernst, J. Chem. Phys. 128, 154320 (2008)

  7. Development and Characterization of Recombinant Human Fc:OX40L fusion protein linked via a coiled-coil trimerization domain

    PubMed Central

    Morris, Nicholas P.; Peters, Carmen; Montler, Ryan; Hu, Hong-Ming; Curti, Brendan D.; Urba, Walter J.; Weinberg, Andrew D.

    2007-01-01

    OX40 (CD134) is a potent costimulatory molecule found on the surface of activated CD4+ and CD8+ T cells. Immunotherapy with OX40 agonists administered in vivo has demonstrated efficacy in several murine tumor models. A phase I clinical trial is currently underway in patients with advanced cancer using a mouse anti-CD134 monoclonal antibody. Therapy with this antibody will likely be limited to one cycle because patients develop neutralizing human anti-mouse antibody (HAMA). Therefore, we developed a humanized OX40 agonist that links the extracellular domain of human OX40L to the Fc domain of human IgG1 via a trimerizing isoleucine zipper domain (ILZ). Physical characterization by velocity sedimentation revealed that this novel construct, hFcILZOX40L, was assembled into hexamers in which the Fc domains formed three disulfide-bonded dimers and the ILZ-OX40L domains formed two trimers. Trimerization of the ILZ domain was necessary to achieve appropriate assembly. In vitro biologic activity of the hFcILZOX40L hexamer was equivalent to the activity of agonist antibodies in plate-bound assays and was superior when the agonists were tested as soluble agents. Our ultimate goal is to use this recombinant molecule in a future clinical trial and we feel that the OX40L hexamer will have equivalent or superior agonist activity in vivo when compared to an anti-OX40 antibody. PMID:17374396

  8. Immunogenic properties of a trimeric gp41-based immunogen containing an exposed membrane-proximal external region

    PubMed Central

    Habte, Habtom H.; Banerjee, Saikat; Shi, Heliang; Qin, Yali; Cho, Michael W

    2015-01-01

    The membrane-proximal external region (MPER) of HIV-1 gp41 is an attractive target for vaccine development. Thus, better understanding of its immunogenic properties in various structural contexts is important. We previously described the crystal structure of a trimeric protein complex named gp41-HR1-54Q, which consists of the heptad repeat regions 1 and 2 and the MPER. The protein was efficiently recognized by broadly neutralizing antibodies. Here, we describe its immunogenic properties in rabbits. The protein was highly immunogenic, especially the C-terminal end of the MPER containing 4E10 and 10E8 epitopes (671NWFDITNWLWYIK683). Although antibodies exhibited strong competition activity against 4E10 and 10E8, neutralizing activity was not detected. Detailed mapping analyses indicated that amino acid residues critical for recognition resided on faces of the alpha helix that are either opposite of or perpendicular to the epitopes recognized by 4E10 and 10E8. These results provide critical information for designing the next generation of MPER-based immunogens. PMID:26454663

  9. Two distinct trimeric conformations of natively membrane-anchored full-length herpes simplex virus 1 glycoprotein B

    PubMed Central

    Zeev-Ben-Mordehai, Tzviya; Vasishtan, Daven; Hernández Durán, Anna; Vollmer, Benjamin; White, Paul; Prasad Pandurangan, Arun; Siebert, C. Alistair; Topf, Maya

    2016-01-01

    Many viruses are enveloped by a lipid bilayer acquired during assembly, which is typically studded with one or two types of glycoproteins. These viral surface proteins act as the primary interface between the virus and the host. Entry of enveloped viruses relies on specialized fusogen proteins to help merge the virus membrane with the host membrane. In the multicomponent herpesvirus fusion machinery, glycoprotein B (gB) acts as this fusogen. Although the structure of the gB ectodomain postfusion conformation has been determined, any other conformations (e.g., prefusion, intermediate conformations) have so far remained elusive, thus restricting efforts to develop antiviral treatments and prophylactic vaccines. Here, we have characterized the full-length herpes simplex virus 1 gB in a native membrane by displaying it on cell-derived vesicles and using electron cryotomography. Alongside the known postfusion conformation, a novel one was identified. Its structure, in the context of the membrane, was determined by subvolume averaging and found to be trimeric like the postfusion conformation, but appeared more condensed. Hierarchical constrained density-fitting of domains unexpectedly revealed the fusion loops in this conformation to be apart and pointing away from the anchoring membrane. This vital observation is a substantial step forward in understanding the complex herpesvirus fusion mechanism, and opens up new opportunities for more targeted intervention of herpesvirus entry. PMID:27035968

  10. LYR71, a derivative of trimeric resveratrol, inhibits tumorigenesis by blocking STAT3-mediated matrix metalloproteinase 9 expression

    PubMed Central

    Kim, Ja Eun; Kim, Hong Sook; Shin, Yong-Jae; Lee, Chang Seok; Won, Cheolhee; Lee, Sin-Ae; Lee, Jung Weon; Kim, Youngsoo; Kang, Jae-Seung; Chung, Myung-Hee

    2008-01-01

    Tumor migration/invasion is the main cause of tumor progression and STAT3 is needed to enhance tumor migration/invasion by up-regulating MMP-9. Thus, agents that inhibit STAT3 activation may be used as an anticancer drug. We present herein that 6-methyl-2-propylimino-6, 7-dihydro-5H-benzo [1, 3]-oxathiol-4-one (LYR71) , a derivative of trimeric resveratrol, has an anticancer activity through inhibition of STAT3 activation. We found that LYR71 suppressed STAT3 activation and inhibited the expression and activity of MMP-9 in RANTES-stimulated breast cancer cells. In addition, LYR71 reduced RANTES-induced MMP-9 transcripts by blocking STAT3 recruitment, dissociating p300 and deacetylating histone H3 and H4 on the MMP-9 promoter. Furthermore, LYR71 inhibited tumor migration/invasion in RANTES-treated breast cancer cells and consequently blocked tumor progression in tumor-bearing mice. Taken together, the results of this study suggest that LYR71 can be therapeutically useful due to the inhibition effect of STAT3-mediated MMP-9 expression in breast cancer cells. PMID:18985009

  11. Modulation of Kingella kingae Adherence to Human Epithelial Cells by Type IV Pili, Capsule, and a Novel Trimeric Autotransporter

    PubMed Central

    Porsch, Eric A.; Kehl-Fie, Thomas E.; Geme, Joseph W. St.

    2012-01-01

    ABSTRACT Kingella kingae is an emerging bacterial pathogen that is being recognized increasingly as an important etiology of septic arthritis, osteomyelitis, and bacteremia, especially in young children. Colonization of the posterior pharynx is a key step in the pathogenesis of K. kingae disease. Previous work established that type IV pili are necessary for K. kingae adherence to the respiratory epithelium. In this study, we set out to identify additional factors that influence K. kingae interactions with human epithelial cells. We found that genetic disruption of the gene encoding a predicted trimeric autotransporter protein called Knh (Kingella NhhA homolog) resulted in reduced adherence to human epithelial cells. In addition, we established that K. kingae elaborates a surface-associated polysaccharide capsule that requires a predicted ABC-type transporter export operon called ctrABCD for surface presentation. Furthermore, we discovered that the presence of a surface capsule interferes with Knh-mediated adherence to human epithelial cells by nonpiliated organisms and that maximal adherence in the presence of a capsule requires the predicted type IV pilus retraction machinery, PilT/PilU. On the basis of the data presented here, we propose a novel adherence mechanism that allows K. kingae to adhere efficiently to human epithelial cells while remaining encapsulated and more resistant to immune clearance. PMID:23093386

  12. Immunogenic properties of a trimeric gp41-based immunogen containing an exposed membrane-proximal external region.

    PubMed

    Habte, Habtom H; Banerjee, Saikat; Shi, Heliang; Qin, Yali; Cho, Michael W

    2015-12-01

    The membrane-proximal external region (MPER) of HIV-1 gp41 is an attractive target for vaccine development. Thus, better understanding of its immunogenic properties in various structural contexts is important. We previously described the crystal structure of a trimeric protein complex named gp41-HR1-54Q, which consists of the heptad repeat regions 1 and 2 and the MPER. The protein was efficiently recognized by broadly neutralizing antibodies. Here, we describe its immunogenic properties in rabbits. The protein was highly immunogenic, especially the C-terminal end of the MPER containing 4E10 and 10E8 epitopes ((671)NWFDITNWLWYIK(683)). Although antibodies exhibited strong competition activity against 4E10 and 10E8, neutralizing activity was not detected. Detailed mapping analyses indicated that amino acid residues critical for recognition resided on faces of the alpha helix that are either opposite of or perpendicular to the epitopes recognized by 4E10 and 10E8. These results provide critical information for designing the next generation of MPER-based immunogens.

  13. Trimeric Autotransporter Adhesins in Members of the Burkholderia Cepacia Complex: A Multifunctional Family of Proteins Implicated in Virulence

    PubMed Central

    Mil-Homens, Dalila; Fialho, Arsénio M.

    2011-01-01

    Trimeric autotransporter adhesins (TAAs) are multimeric surface proteins exclusively found in bacteria. They are involved in various biological traits of pathogenic Gram-negative bacteria including adherence, biofilm formation, invasion, survival within eukaryotic cells, serum resistance, and cytotoxicity. TAAs have a modular architecture composed by a conserved membrane-anchored C-terminal domain and a variable number of stalk and head domains. In this study, a bioinformatic approach has been used to analyze the distribution and architecture of TAAs among Burkholderia cepacia complex (Bcc) genomes. Fifteen genomes were probed revealing a total of 74 encoding sequences. Compared with other bacterial species, the Bcc genomes contain a large number of TAAs (two genes to up to eight genes, such as in B. cenocepacia). Phylogenetic analysis showed that the TAAs grouped into at least eight distinct clusters. TAAs with serine-rich repeats are clearly well separated from others, thereby representing a different evolutionary lineage. Comparative gene mapping across Bcc genomes reveals that TAA genes are inserted within conserved synteny blocks. We further focused our analysis on the epidemic strain B. cenocepacia J2315 in which seven TAAs were annotated. Among these, three TAA-encoding genes (BCAM019, BCAM0223, and BCAM0224) are organized into a cluster and are candidates for multifunctional virulence factors. Here we review the current insights into the functional role of BCAM0224 as a model locus. PMID:22919579

  14. Isolation of dimeric, trimeric, tetrameric and pentameric procyanidins from unroasted cocoa beans (Theobroma cacao L.) using countercurrent chromatography.

    PubMed

    Esatbeyoglu, Tuba; Wray, Victor; Winterhalter, Peter

    2015-07-15

    The main procyanidins, including dimeric B2 and B5, trimeric C1, tetrameric and pentameric procyanidins, were isolated from unroasted cocoa beans (Theobroma cacao L.) using various techniques of countercurrent chromatography, such as high-speed countercurrent chromatography (HSCCC), low-speed rotary countercurrent chromatography (LSRCCC) and spiral-coil LSRCCC. Furthermore, dimeric procyanidins B1 and B7, which are not present naturally in the analysed cocoa beans, were obtained after semisynthesis of cocoa bean polymers with (+)-catechin as nucleophile and separated by countercurrent chromatography. In this way, the isolation of dimeric procyanidin B1 in considerable amounts (500mg, purity>97%) was possible in a single run. This is the first report concerning the isolation and semisynthesis of dimeric to pentameric procyanidins from T. cacao by countercurrent chromatography. Additionally, the chemical structures of tetrameric (cinnamtannin A2) and pentameric procyanidins (cinnamtannin A3) were elucidated on the basis of (1)H NMR spectroscopy. Interflavanoid linkage was determined by NOE-correlations, for the first time.

  15. An Acinetobacter trimeric autotransporter adhesin reaped from cells exhibits its nonspecific stickiness via a highly stable 3D structure

    PubMed Central

    Yoshimoto, Shogo; Nakatani, Hajime; Iwasaki, Keita; Hori, Katsutoshi

    2016-01-01

    Trimeric autotransporter adhesins (TAAs), cell surface proteins of Gram-negative bacteria, mediate bacterial adhesion to host cells and extracellular matrix proteins. However, AtaA, a TAA in the nonpathogenic Acinetobacter sp. strain Tol 5, shows nonspecific, high adhesiveness to abiotic material surfaces as well as to biotic surfaces. AtaA is a homotrimer of polypeptides comprising 3,630 amino acids and forms long nanofibers; therefore, it is too large and structurally complex to be produced as a recombinant protein. In this study, we isolated AtaA’s passenger domain (AtaA PSD), which is translocated to the cell surface through the C-terminal transmembrane domain and exhibits biological functions, using a new method. We introduced a protease recognition site and reaped AtaA nanofibers 225 nm in length from the cell surface through proteolytic cleavage with a specific protease. Biochemical and biophysical analyses of the purified native AtaA PSD revealed that it has a stable structure under alkaline and acidic conditions. Temperatures above 80 °C, which disrupted AtaA’s higher-order structure but maintained the full-length AtaA polypeptide, inactivated AtaA’s nonspecific adhesiveness, suggesting that the stickiness of AtaA requires its 3D structure. This finding refutes the widespread but vague speculation that large unfolded polypeptides readily stick to various surfaces. PMID:27305955

  16. Effects of secreted oligomers of amyloid β-protein on hippocampal synaptic plasticity: a potent role for trimers

    PubMed Central

    Townsend, Matthew; Shankar, Ganesh M; Mehta, Tapan; Walsh, Dominic M; Selkoe, Dennis J

    2006-01-01

    The accumulation of amyloid β-protein (Aβ) in brain regions serving memory and cognition is a central pathogenic feature of Alzheimer's disease (AD). We have shown that small soluble oligomers of human Aβ that are naturally secreted by cultured cells inhibit hippocampal long-term potentiation (LTP) in vitro and in vivo and transiently impair the recall of a complex learned behaviour in rats. These results support the hypothesis that diffusible oligomers of Aβ initiate a synaptic dysfunction that may be an early event in AD. We now report detailed electrophysiological analyses that define conditions under which acute application of soluble Aβ inhibits hippocampal synaptic plasticity in wild-type mice. To ascertain which Aβ assemblies contribute to the impairment of LTP, we fractionated oligomers by size-exclusion chromatography and found that Aβ trimers fully inhibit LTP, whereas dimers and tetramers have an intermediate potency. Natural Aβ oligomers are sensitive to heat denaturation, primarily inhibit the induction phase of LTP, and cause a sustained impairment of LTP even after extensive washout. We observed no effects of Aβ oligomers on presynaptic vesicle release. LTP in juvenile mice is resistant to the effects of Aβ oligomers, as is brain-derived-neurotrophic-factor-induced LTP in adult hippocampus. We conclude that specific assemblies, particularly timers, of naturally secreted Aβ oligomers are potent and selective inhibitors of certain forms of hippocampal LTP. PMID:16469784

  17. Possible Formation of Mitochondrial-RNA Containing Chimeric or Trimeric RNA Implies a Post-Transcriptional and Post-Splicing Mechanism for RNA Fusion

    PubMed Central

    Yang, Wei; Wu, Jian-min; Bi, An-ding; Ou-yang, Yong-chang; Shen, Hai-hong; Chirn, Gung-wei; Zhou, Jian-hua; Weiss, Emily; Holman, Emily Pauline; Liao, D. Joshua

    2013-01-01

    Human cells are known to express many chimeric RNAs, i.e. RNAs containing two genes' sequences. Wondering whether there also is trimeric RNA, i.e. an RNA containing three genes' sequences, we wrote simple computer code to screen human expression sequence tags (ESTs) deposited in different public databases, and obtained hundreds of putative trimeric ESTs. We then used NCBI Blast and UCSC Blat browsers to further analyze their sequences, and identified 61 trimeric and two tetrameric ESTs (one EST containing four different sequences). We also identified 57 chimeric, trimeric or teterameric ESTs that contained both mitochondrial (mt) RNA and nuclear RNA (nRNA), i.e. were mtRNA-nRNA fusions. In some trimeric ESTs, the downstream partner was fused to the poly-A tail of the upstream partner, which, together with the mtRNA-nRNA fusions, suggests a possible new mechanism for RNA fusion that occurs after both transcription and splicing have been terminated, and possibly outside the nucleus, in contrast to the two current hypothetical mechanisms, trans-splicing and transcriptional-slippage, that occur in the nucleus. The mt-sequences in the mtRNA-nRNA fusions had pseudogenes in the nucleus but, surprisingly, localized mainly in chromosomes 1 and 5. In some mtRNA-nRNA fusions, as well as in some ESTs that were derived only from mtRNA, the mt-sequences might be cis- or trans-spliced. Actually, we cloned a new cis-spliced mtRNA, coined as 16SrRNA-s. Hence, mtDNA may not always be intron-less. Fusion of three or more RNAs to one, fusion of nRNA to mtRNA, and cis- or trans-splicing of mtRNA should all enlarge the cellular RNA repertoire, in turn enlarging the cellular functions. Therefore, future experimental verification of the existence of these novel classes of fusion RNAs and spliced mtRNAs in human cells should significantly advance our understanding of biology and medicine. PMID:24204722

  18. Possible formation of mitochondrial-RNA containing chimeric or trimeric RNA implies a post-transcriptional and post-splicing mechanism for RNA fusion.

    PubMed

    Yang, Wei; Wu, Jian-min; Bi, An-ding; Ou-Yang, Yong-chang; Shen, Hai-hong; Chirn, Gung-wei; Zhou, Jian-hua; Weiss, Emily; Holman, Emily Pauline; Liao, D Joshua

    2013-01-01

    Human cells are known to express many chimeric RNAs, i.e. RNAs containing two genes' sequences. Wondering whether there also is trimeric RNA, i.e. an RNA containing three genes' sequences, we wrote simple computer code to screen human expression sequence tags (ESTs) deposited in different public databases, and obtained hundreds of putative trimeric ESTs. We then used NCBI Blast and UCSC Blat browsers to further analyze their sequences, and identified 61 trimeric and two tetrameric ESTs (one EST containing four different sequences). We also identified 57 chimeric, trimeric or teterameric ESTs that contained both mitochondrial (mt) RNA and nuclear RNA (nRNA), i.e. were mtRNA-nRNA fusions. In some trimeric ESTs, the downstream partner was fused to the poly-A tail of the upstream partner, which, together with the mtRNA-nRNA fusions, suggests a possible new mechanism for RNA fusion that occurs after both transcription and splicing have been terminated, and possibly outside the nucleus, in contrast to the two current hypothetical mechanisms, trans-splicing and transcriptional-slippage, that occur in the nucleus. The mt-sequences in the mtRNA-nRNA fusions had pseudogenes in the nucleus but, surprisingly, localized mainly in chromosomes 1 and 5. In some mtRNA-nRNA fusions, as well as in some ESTs that were derived only from mtRNA, the mt-sequences might be cis- or trans-spliced. Actually, we cloned a new cis-spliced mtRNA, coined as 16SrRNA-s. Hence, mtDNA may not always be intron-less. Fusion of three or more RNAs to one, fusion of nRNA to mtRNA, and cis- or trans-splicing of mtRNA should all enlarge the cellular RNA repertoire, in turn enlarging the cellular functions. Therefore, future experimental verification of the existence of these novel classes of fusion RNAs and spliced mtRNAs in human cells should significantly advance our understanding of biology and medicine.

  19. HIV-1 adenoviral vector vaccines expressing multi-trimeric BAFF and 4-1BBL enhance T cell mediated anti-viral immunity.

    PubMed

    Kanagavelu, Saravana; Termini, James M; Gupta, Sachin; Raffa, Francesca N; Fuller, Katherine A; Rivas, Yaelis; Philip, Sakhi; Kornbluth, Richard S; Stone, Geoffrey W

    2014-01-01

    Adenoviral vectored vaccines have shown considerable promise but could be improved by molecular adjuvants. Ligands in the TNF superfamily (TNFSF) are potential adjuvants for adenoviral vector (Ad5) vaccines based on their central role in adaptive immunity. Many TNFSF ligands require aggregation beyond the trimeric state (multi-trimerization) for optimal biological function. Here we describe Ad5 vaccines for HIV-1 Gag antigen (Ad5-Gag) adjuvanted with the TNFSF ligands 4-1BBL, BAFF, GITRL and CD27L constructed as soluble multi-trimeric proteins via fusion to Surfactant Protein D (SP-D) as a multimerization scaffold. Mice were vaccinated with Ad5-Gag combined with Ad5 expressing one of the SP-D-TNFSF constructs or single-chain IL-12p70 as adjuvant. To evaluate vaccine-induced protection, mice were challenged with vaccinia virus expressing Gag (vaccinia-Gag) which is known to target the female genital tract, a major route of sexually acquired HIV-1 infection. In this system, SP-D-4-1BBL or SP-D-BAFF led to significantly reduced vaccinia-Gag replication when compared to Ad5-Gag alone. In contrast, IL-12p70, SP-D-CD27L and SP-D-GITRL were not protective. Histological examination following vaccinia-Gag challenge showed a dramatic lymphocytic infiltration into the uterus and ovaries of SP-D-4-1BBL and SP-D-BAFF-treated animals. By day 5 post challenge, proinflammatory cytokines in the tissue were reduced, consistent with the enhanced control over viral replication. Splenocytes had no specific immune markers that correlated with protection induced by SP-D-4-1BBL and SP-D-BAFF versus other groups. IL-12p70, despite lack of anti-viral efficacy, increased the total numbers of splenic dextramer positive CD8+ T cells, effector memory T cells, and effector Gag-specific CD8+ T cells, suggesting that these markers are poor predictors of anti-viral immunity in this model. In conclusion, soluble multi-trimeric 4-1BBL and BAFF adjuvants led to strong protection from vaccinia

  20. NADP+ binding to the regulatory subunit of methionine adenosyltransferase II increases intersubunit binding affinity in the hetero-trimer.

    PubMed

    González, Beatriz; Garrido, Francisco; Ortega, Rebeca; Martínez-Júlvez, Marta; Revilla-Guarinos, Ainhoa; Pérez-Pertejo, Yolanda; Velázquez-Campoy, Adrián; Sanz-Aparicio, Julia; Pajares, María A

    2012-01-01

    Mammalian methionine adenosyltransferase II (MAT II) is the only hetero-oligomer in this family of enzymes that synthesize S-adenosylmethionine using methionine and ATP as substrates. Binding of regulatory β subunits and catalytic α2 dimers is known to increase the affinity for methionine, although scarce additional information about this interaction is available. This work reports the use of recombinant α2 and β subunits to produce oligomers showing kinetic parameters comparable to MAT II purified from several tissues. According to isothermal titration calorimetry data and densitometric scanning of the stained hetero-oligomer bands on denatured gels, the composition of these oligomers is that of a hetero-trimer with α2 dimers associated to single β subunits. Additionally, the regulatory subunit is able to bind NADP(+) with a 1:1 stoichiometry, the cofactor enhancing β to α2-dimer binding affinity. Mutants lacking residues involved in NADP(+) binding and N-terminal truncations of the β subunit were able to oligomerize with α2-dimers, although the kinetic properties appeared altered. These data together suggest a role for both parts of the sequence in the regulatory role exerted by the β subunit on catalysis. Moreover, preparation of a structural model for the hetero-oligomer, using the available crystal data, allowed prediction of the regions involved in β to α2-dimer interaction. Finally, the implications that the presence of different N-terminals in the β subunit could have on MAT II behavior are discussed in light of the recent identification of several splicing forms of this subunit in hepatoma cells.

  1. A RabGAP Regulates Life-Cycle Duration via Trimeric G-protein Cascades in Dictyostelium discoideum

    PubMed Central

    Kuwayama, Hidekazu; Miyanaga, Yukihiro; Urushihara, Hideko; Ueda, Masahiro

    2013-01-01

    Background The life-cycle of cellular slime molds comprises chronobiologically regulated processes. During the growth phase, the amoeboid cells proliferate at a definite rate. Upon starvation, they synthesize cAMP as both first and second messengers in signalling pathways and form aggregates, migrating slugs, and fruiting bodies, consisting of spores and stalk cells, within 24 h. In Dictyostelium discoideum, because most growth-specific events cease during development, proliferative and heterochronic mutations are not considered to be interrelated and no genetic factor governing the entire life-cycle duration has ever been identified. Methodology/Principal Findings Using yeast 2-hybrid library screening, we isolated a Dictyostelium discoideum RabGAP, Dd Rbg-3, as a candidate molecule by which the Dictyostelium Gα2 subunit directs its effects. Rab GTPase-activating protein, RabGAP, acts as a negative regulator of Rab small GTPases, which orchestrate the intracellular membrane trafficking involved in cell proliferation. Deletion mutants of Dd rbg-3 exhibited an increased growth rate and a shortened developmental period, while an overexpression mutant demonstrated the opposite effects. We also show that Dd Rbg-3 interacts with 2 Gα subunits in an activity-dependent manner in vitro. Furthermore, both human and Caenorhabditis elegans rbg-3 homologs complemented the Dd rbg-3–deletion phenotype in D. discoideum, indicating that similar pathways may be generally conserved in multicellular organisms. Conclusions/Significance Our findings suggest that Dd Rbg-3 acts as a key element regulating the duration of D. discoideum life-span potentially via trimeric G-protein cascades. PMID:24349132

  2. Molecular determinants of transport stimulation of EAAT2 are located at interface between the trimerization and substrate transport domains.

    PubMed

    Mortensen, Ole V; Liberato, José L; Coutinho-Netto, Joaquim; Dos Santos, Wagner F; Fontana, Andréia C K

    2015-04-01

    Excitatory amino acid transporters (EAATs) regulate glutamatergic signal transmission by clearing extracellular glutamate. Dysfunction of these transporters has been implicated in the pathogenesis of various neurological disorders. Previous studies have shown that venom from the spider Parawixia bistriata and a purified compound (Parawixin1) stimulate EAAT2 activity and protect retinal tissue from ischemic damage. In the present study, the EAAT2 subtype specificity of this compound was explored, employing chimeric proteins between EAAT2 and EAAT3 transporter subtypes and mutants to characterize the structural region targeted by the compound. This identified a critical residue (Histidine-71 in EAAT2 and Serine-45 in EAAT3) in transmembrane domain 2 (TM2) to be important for the selectivity between EAAT2 and EAAT3 and for the activity of the venom. Using the identified residue in TM2 as a structural anchor, several neighboring amino acids within TM5 and TM8 were identified to also be important for the activity of the venom. This structural domain of the transporter lies at the interface of the rigid trimerization domain and the central substrate-binding transport domain. Our studies suggest that the mechanism of glutamate transport enhancement involves an interaction with the transporter that facilitates the movement of the transport domain. We identified a domain (purple star) in the glutamate transporter EAAT2 that is important for transport stimulation through a spider venom, and suggest a mechanism for enhanced transporter function through facilitated substrate translocation (arrow). Because the dysfunction of glutamate transporters is implicated in the pathogenesis of neurological disorders, understanding the mechanisms of enhanced transport could have therapeutic implications.

  3. NADP+ Binding to the Regulatory Subunit of Methionine Adenosyltransferase II Increases Intersubunit Binding Affinity in the Hetero-Trimer

    PubMed Central

    Ortega, Rebeca; Martínez-Júlvez, Marta; Revilla-Guarinos, Ainhoa; Pérez-Pertejo, Yolanda; Velázquez-Campoy, Adrián; Sanz-Aparicio, Julia; Pajares, María A.

    2012-01-01

    Mammalian methionine adenosyltransferase II (MAT II) is the only hetero-oligomer in this family of enzymes that synthesize S-adenosylmethionine using methionine and ATP as substrates. Binding of regulatory β subunits and catalytic α2 dimers is known to increase the affinity for methionine, although scarce additional information about this interaction is available. This work reports the use of recombinant α2 and β subunits to produce oligomers showing kinetic parameters comparable to MAT II purified from several tissues. According to isothermal titration calorimetry data and densitometric scanning of the stained hetero-oligomer bands on denatured gels, the composition of these oligomers is that of a hetero-trimer with α2 dimers associated to single β subunits. Additionally, the regulatory subunit is able to bind NADP+ with a 1∶1 stoichiometry, the cofactor enhancing β to α2-dimer binding affinity. Mutants lacking residues involved in NADP+ binding and N-terminal truncations of the β subunit were able to oligomerize with α2-dimers, although the kinetic properties appeared altered. These data together suggest a role for both parts of the sequence in the regulatory role exerted by the β subunit on catalysis. Moreover, preparation of a structural model for the hetero-oligomer, using the available crystal data, allowed prediction of the regions involved in β to α2-dimer interaction. Finally, the implications that the presence of different N-terminals in the β subunit could have on MAT II behavior are discussed in light of the recent identification of several splicing forms of this subunit in hepatoma cells. PMID:23189196

  4. Structures of Aβ17-42 trimers in isolation and with five small-molecule drugs using a hierarchical computational procedure.

    PubMed

    Chebaro, Yassmine; Jiang, Ping; Zang, Tong; Mu, Yuguang; Nguyen, Phuong H; Mousseau, Normand; Derreumaux, Philippe

    2012-07-26

    The amyloid-β protein (Aβ) oligomers are believed to be the main culprits in the cytoxicity of Alzheimer's disease (AD) and p3 peptides (Aβ17-42 fragments) are present in AD amyloid plaques. Many small-molecule or peptide-based inhibitors are known to slow down Aβ aggregation and reduce the toxicity in vitro, but their exact modes of action remain to be determined since there has been no atomic level of Aβ(p3)-drug oligomers. In this study, we have determined the structure of Aβ17-42 trimers both in aqueous solution and in the presence of five small-molecule inhibitors using a multiscale computational study. These inhibitors include 2002-H20, curcumin, EGCG, Nqtrp, and resveratrol. First, we used replica exchange molecular dynamics simulations coupled to the coarse-grained (CG) OPEP force field. These CG simulations reveal that the conformational ensemble of Aβ17-42 trimer can be described by 14 clusters with each peptide essentially adopting turn/random coil configurations, although the most populated cluster is characterized by one peptide with a β-hairpin at Phe19-Leu31. Second, these 14 dominant clusters and the less-frequent fibril-like state with parallel register of the peptides were subjected to atomistic Autodock simulations. Our analysis reveals that the drugs have multiple binding modes with different binding affinities for trimeric Aβ17-42 although they interact preferentially with the CHC region (residues 17-21). The compounds 2002-H20 and Nqtrp are found to be the worst and best binders, respectively, suggesting that the drugs may interfere at different stages of Aβ oligomerization. Finally, explicit solvent molecular dynamics of two predicted Nqtrp-Aβ17-42 conformations describe at atomic level some possible modes of action for Nqtrp.

  5. HIV-1 Receptor Binding Site-Directed Antibodies Using a VH1-2 Gene Segment Orthologue Are Activated by Env Trimer Immunization

    PubMed Central

    Bale, Shridhar; Phad, Ganesh E.; Guenaga, Javier; Wilson, Richard; Soldemo, Martina; McKee, Krisha; Sundling, Christopher; Mascola, John; Li, Yuxing; Wyatt, Richard T.; Karlsson Hedestam, Gunilla B.

    2014-01-01

    Broadly neutralizing antibodies (bNAbs) isolated from chronically HIV-1 infected individuals reveal important information regarding how antibodies target conserved determinants of the envelope glycoprotein (Env) spike such as the primary receptor CD4 binding site (CD4bs). Many CD4bs-directed bNAbs use the same heavy (H) chain variable (V) gene segment, VH1-2*02, suggesting that activation of B cells expressing this allele is linked to the generation of this type of Ab. Here, we identify the rhesus macaque VH1.23 gene segment to be the closest macaque orthologue to the human VH1-2 gene segment, with 92% homology to VH1-2*02. Of the three amino acids in the VH1-2*02 gene segment that define a motif for VRC01-like antibodies (W50, N58, flanking the HCDR2 region, and R71), the two identified macaque VH1.23 alleles described here encode two. We demonstrate that immunization with soluble Env trimers induced CD4bs-specific VH1.23-using Abs with restricted neutralization breadth. Through alanine scanning and structural studies of one such monoclonal Ab (MAb), GE356, we demonstrate that all three HCDRs are involved in neutralization. This contrasts to the highly potent CD4bs-directed VRC01 class of bNAb, which bind Env predominantly through the HCDR2. Also unlike VRC01, GE356 was minimally modified by somatic hypermutation, its light (L) chain CDRs were of average lengths and it displayed a binding footprint proximal to the trimer axis. These results illustrate that the Env trimer immunogen used here activates B cells encoding a VH1-2 gene segment orthologue, but that the resulting Abs interact distinctly differently with the HIV-1 Env spike compared to VRC01. PMID:25166308

  6. The trimerization domain of NEMO is composed of the interacting C-terminal CC2 and LZ coiled-coil subdomains.

    PubMed

    Agou, Fabrice; Traincard, François; Vinolo, Emilie; Courtois, Gilles; Yamaoka, Shoji; Israël, Alain; Véron, Michel

    2004-07-02

    NEMO (NF-kappaB essential modulator) plays a key role in the canonical NF-kappaB pathway as the scaffold/regulatory component of the IkappaB kinase (IKK) complex. The self-association of NEMO involves the C-terminal halves of the polypeptide chains containing two putative coiled-coil motifs (a CC2 and a LZ leucine zipper), a proline-rich region, and a ZF zinc finger motif. Using purified truncation mutants, we showed that the minimal oligomerization domain of NEMO is the CC2-LZ segment and that both CC2 and LZ subdomains are necessary to restore the LPS-dependent activation of the NF-kappaB pathway in a NEMO-deficient cell line. We confirmed the association of the oligomerization domain in a trimer and investigated the specific role of CC2 and LZ subdomains in the building of the oligomer. Whereas a recombinant CC2-LZ polypeptide self-associated into a trimer with an association constant close to that of the wild-type protein, the isolated CC2 and LZ peptides, respectively, formed trimers and dimers with weaker association constants. Upon mixing, isolated CC2 and LZ peptides associated to form a stable hetero-hexamer as shown by gel filtration and fluorescence anisotropy experiments. We propose a structural model for the organization of the oligomerization domain of activated NEMO in which three C-terminal domains associate into a pseudo-hexamer forming a six-helix bundle. This model is discussed in relation to the mechanism of activation of the IKK complex by upstream activators.

  7. The N-terminal domain of DnaT, a primosomal DNA replication protein, is crucial for PriB binding and self-trimerization.

    PubMed

    Huang, Yen-Hua; Huang, Cheng-Yang

    2013-12-13

    DnaT and PriB are replication restart primosomal proteins required for re-initiating chromosomal DNA replication in bacteria. Although the interaction of DnaT with PriB has been proposed, which region of DnaT is involved in PriB binding and self-trimerization remains unknown. In this study, we identified the N-terminal domain in DnaT (aa 1-83) that is important in PriB binding and self-trimerization but not in single-stranded DNA (ssDNA) binding. DnaT and the deletion mutant DnaT42-179 protein can bind to PriB according to native polyacrylamide gel electrophoresis, Western blot analysis, and pull-down assay, whereas DnaT84-179 cannot bind to PriB. In contrast to DnaT, DnaT26-179, and DnaT42-179 proteins, which form distinct complexes with ssDNA of different lengths, DnaT84-179 forms only a single complex with ssDNA. Analysis of DnaT84-179 protein by gel filtration chromatography showed a stable monomer in solution rather than a trimer, such as DnaT, DnaT26-179, and DnaT42-179 proteins. These results constitute a pioneering study of the domain definition of DnaT. Further research can directly focus on determining how DnaT binds to the PriA-PriB-DNA tricomplex in replication restart by the hand-off mechanism.

  8. Bipartite Topology of Treponema pallidum Repeat Proteins C/D and I: OUTER MEMBRANE INSERTION, TRIMERIZATION, AND PORIN FUNCTION REQUIRE A C-TERMINAL β-BARREL DOMAIN.

    PubMed

    Anand, Arvind; LeDoyt, Morgan; Karanian, Carson; Luthra, Amit; Koszelak-Rosenblum, Mary; Malkowski, Michael G; Puthenveetil, Robbins; Vinogradova, Olga; Radolf, Justin D

    2015-05-08

    We previously identified Treponema pallidum repeat proteins TprC/D, TprF, and TprI as candidate outer membrane proteins (OMPs) and subsequently demonstrated that TprC is not only a rare OMP but also forms trimers and has porin activity. We also reported that TprC contains N- and C-terminal domains (TprC(N) and TprC(C)) orthologous to regions in the major outer sheath protein (MOSP(N) and MOSP(C)) of Treponema denticola and that TprC(C) is solely responsible for β-barrel formation, trimerization, and porin function by the full-length protein. Herein, we show that TprI also possesses bipartite architecture, trimeric structure, and porin function and that the MOSP(C)-like domains of native TprC and TprI are surface-exposed in T. pallidum, whereas their MOSP(N)-like domains are tethered within the periplasm. TprF, which does not contain a MOSP(C)-like domain, lacks amphiphilicity and porin activity, adopts an extended inflexible structure, and, in T. pallidum, is tightly bound to the protoplasmic cylinder. By thermal denaturation, the MOSP(N) and MOSP(C)-like domains of TprC and TprI are highly thermostable, endowing the full-length proteins with impressive conformational stability. When expressed in Escherichia coli with PelB signal sequences, TprC and TprI localize to the outer membrane, adopting bipartite topologies, whereas TprF is periplasmic. We propose that the MOSP(N)-like domains enhance the structural integrity of the cell envelope by anchoring the β-barrels within the periplasm. In addition to being bona fide T. pallidum rare outer membrane proteins, TprC/D and TprI represent a new class of dual function, bipartite bacterial OMP.

  9. Comparison of HIV Type 1 ADA gp120 monomers versus gp140 trimers as immunogens for the induction of neutralizing antibodies.

    PubMed

    Kim, Mikyung; Qiao, Zhi-Song; Montefiori, David C; Haynes, Barton F; Reinherz, Ellis L; Liao, Hua-Xin

    2005-01-01

    Designing an immunogen for effective neutralizing antibody induction against diverse primary isolates of human immunodeficiency virus type 1 (HIV-1) is a high priority for HIV-1 vaccine development. Soluble gp120 envelope (Env) glycoprotein subunit vaccines elicit high titers of antibodies that neutralize T cell line-adapted (TCLA) strains but the antibodies possess poor neutralizing activity against many primary isolates. Previously, we generated soluble trimeric recombinant gp140 from the HIV-1 primary isolate ADA. Here we compared monomeric ADAgp120 and trimeric ADAgp140 as immunogens for neutralizing antibody responses in guinea pigs. Both immunogens generated a neutralizing antibody response that was detectable against the vaccine strain and several heterologous strains. The magnitude of this response was significantly greater in ADAgp140-immunized animals when measured against the TCLA strain, MN, and the R5 primary isolate, Bal. Two additional isolates (SS1196 and Bx08) were neutralized equally by sera from both groups of animals whereas other isolates were neutralized weakly or not at all. Despite equal titers of V3 loop specific binding antibodies in sera from both groups of animals, neutralization of ADA by sera from gp140-immunized animals was insensitive to the presence of ADA-V3 peptide, whereas addition of this peptide to sera from gp120- immunized animals blocked all detectable neutralizing activity against ADA. These results support the idea that trimeric gp140 is an improved immunogen compared to monomeric gp120 but that additional improvements are required to afford broad protection against a spectrum of heterologous primary HIV-1 isolates. This ADAgp140 immunogen may be considered a starting point from which to engineer additional improvements for cross-reactive neutralizing antibody induction.

  10. An Evolutionarily Conserved Family of Virion Tail Needles Related to Bacteriophage P22 gp26: Correlation between Structural Stability and Length of the -Helical Trimeric Coiled Coil

    SciTech Connect

    Bhardwaj, A.; Walker-Kopp, N; Casjens, S; Cingolani, G

    2009-01-01

    Bacteriophages of the Podoviridae family use short noncontractile tails to inject their genetic material into Gram-negative bacteria. In phage P22, the tail contains a thin needle, encoded by the phage gene 26, which is essential both for stabilization and for ejection of the packaged viral genome. Bioinformatic analysis of the N-terminal domain of gp26 (residues 1-60) led us to identify a family of genes encoding putative homologues of the tail needle gp26. To validate this idea experimentally and to explore their diversity, we cloned the gp26-like gene from phages HK620, Sf6 and HS1, and characterized these gene products in solution. All gp26-like factors contain an elongated {alpha}-helical coiled-coil core consisting of repeating, adjacent trimerization heptads and form trimeric fibers with length ranging between about 240 to 300 {angstrom}. gp26 tail needles display a high level of structural stability in solution, with Tm (temperature of melting) between 85 and 95 C. To determine how the structural stability of these phage fibers correlates with the length of the {alpha}-helical core, we investigated the effect of insertions and deletions in the helical core. In the P22 tail needle, we identified an 85-residue-long helical domain, termed MiCRU (minimal coiled-coil repeat unit), that can be inserted in-frame inside the gp26 helical core, preserving the straight morphology of the fiber. Likewise, we were able to remove three quarters of the helical core of the HS1 tail needle, minimally decreasing the stability of the fiber. We conclude that in the gp26 family of tail needles, structural stability increases nonlinearly with the length of the {alpha}-helical core. Thus, the overall stability of these bacteriophage fibers is not solely dependent on the number of trimerization repeats in the {alpha}-helical core.

  11. Evaluating the Immunogenicity of a Disulfide-Stabilized, Cleaved, Trimeric Form of the Envelope Glycoprotein Complex of Human Immunodeficiency Virus Type 1

    PubMed Central

    Beddows, Simon; Schülke, Norbert; Kirschner, Marc; Barnes, Kelly; Franti, Michael; Michael, Elizabeth; Ketas, Thomas; Sanders, Rogier W.; Maddon, Paul J.; Olson, William C.; Moore, John P.

    2005-01-01

    The human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) complex comprises three gp120 exterior glycoproteins each noncovalently linked to a gp41 transmembrane glycoprotein. Monomeric gp120 proteins can elicit antibodies capable of neutralizing atypically sensitive test viruses in vitro, but these antibodies are ineffective against representative primary isolates and the gp120 vaccines failed to provide protection against HIV-1 transmission in vivo. Alternative approaches to raising neutralizing antibodies are therefore being pursued. Here we report on the antibody responses generated in rabbits against a soluble, cleaved, trimeric form of HIV-1JR-FL Env. In this construct, the gp120 and gp41 moieties are covalently linked by an intermolecular disulfide bond (SOS gp140), and an I559P substitution has been added to stabilize gp41-gp41 interactions (SOSIP gp140). We investigated the value of DNA priming and compared the use of membrane-bound and soluble priming antigens and of repeat boosting with soluble and particulate protein antigen. Compared to monomeric gp120, SOSIP gp140 trimers elicited approximately threefold lower titers of anti-gp120 antibodies. Priming with DNA encoding a membrane-bound form of the SOS gp140 protein, followed by several immunizations with soluble SOSIP gp140 trimers, resulted in antibodies capable of neutralizing sensitive strains at high titers. A subset of these sera also neutralized, at lower titers, HIV-1JR-FL and some other primary isolates in pseudovirus and/or whole-virus assays. Neutralization of these viruses was immunoglobulin mediated and was predominantly caused by antibodies to gp120 epitopes, but not the V3 region. PMID:15994775

  12. The trimeric serine protease HtrA1 forms a cage-like inhibition complex with an anti-HtrA1 antibody.

    PubMed

    Ciferri, Claudio; Lipari, Michael T; Liang, Wei-Ching; Estevez, Alberto; Hang, Julie; Stawicki, Scott; Wu, Yan; Moran, Paul; Elliott, Mike; Eigenbrot, Charles; Katschke, Kenneth J; van Lookeren Campagne, Menno; Kirchhofer, Daniel

    2015-12-01

    High temperature requirement A1 (HtrA1) is a trypsin-fold serine protease implicated in the progression of age-related macular degeneration (AMD). Our interest in an antibody therapy to neutralize HtrA1 faces the complication that the target adopts a trimeric arrangement, with three active sites in close proximity. In the present study, we describe antibody 94, obtained from a human antibody phage display library, which forms a distinct macromolecular complex with HtrA1 and inhibits the enzymatic activity of recombinant and native HtrA1 forms. Using biochemical methods and negative-staining EM we were able to elucidate the molecular composition of the IgG94 and Fab94 complexes and the associated inhibition mechanism. The 246-kDa complex between the HtrA1 catalytic domain trimer (HtrA1_Cat) and Fab94 had a propeller-like organization with one Fab bound peripherally to each protomer. Low-resolution EM structures and epitope mapping indicated that the antibody binds to the surface-exposed loops B and C of the catalytic domain, suggesting an allosteric inhibition mechanism. The HtrA1_Cat-IgG94 complex (636 kDa) is a cage-like structure with three centrally located IgG94 molecules co-ordinating two HtrA1_Cat trimers and the six active sites pointing into the cavity of the cage. In both complexes, all antigen-recognition regions (paratopes) are found to bind one HtrA1 protomer and all protomers are bound by a paratope, consistent with the complete inhibition of enzyme activity. Therefore, in addition to its potential therapeutic usefulness, antibody 94 establishes a new paradigm of multimeric serine protease inhibition.

  13. Exploring the conformational and binding properties of unphosphorylated/phosphorylated monomeric and trimeric Bcl-2 through docking and molecular dynamics simulations.

    PubMed

    Zacarías-Lara, Oscar J; Correa-Basurto, José; Bello, Martiniano

    2016-07-01

    B-cell lymphoma (Bcl-2) is commonly associated with the progression and preservation of cancer and certain lymphomas; therefore, it is considered as a biological target against cancer. Nevertheless, evidence of all its structural binding sites has been hidden because of the lack of a complete Bcl-2 model, given the presence of a flexible loop domain (FLD), which is responsible for its complex behavior. FLD region has been implicated in phosphorylation, homotrimerization, and heterodimerization associated with Bcl-2 antiapoptotic function. In this contribution, homology modeling, molecular dynamics (MD) simulations in the microsecond (µs) time-scale and docking calculations were combined to explore the conformational complexity of unphosphorylated/phosphorylated monomeric and trimeric Bcl-2 systems. Conformational ensembles generated through MD simulations allowed for identifying the most populated unphosphorylated/phosphorylated monomeric conformations, which were used as starting models to obtain trimeric complexes through protein-protein docking calculations, also submitted to µs MD simulations. Principal component analysis showed that FLD represents the main contributor to total Bcl-2 mobility, and is affected by phosphorylation and oligomerization. Subsequently, based on the most representative unphosphorylated/phosphorylated monomeric and trimeric Bcl-2 conformations, docking studies were initiated to identify the ligand binding site of several known Bcl-2 inhibitors to explain their influence in homo-complex formation and phosphorylation. Docking studies showed that the different conformational states experienced by FLD, such as phosphorylation and oligomerization, play an essential role in the ability to make homo and hetero-complexes. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 393-413, 2016.

  14. (±)-Aspongamide A, an N-acetyldopamine trimer isolated from the insect Aspongopus chinensis, is an inhibitor of p-Smad3.

    PubMed

    Yan, Yong-Ming; Ai, Jun; Shi, Yan-Ni; Zuo, Zhi-Li; Hou, Bo; Luo, Jie; Cheng, Yong-Xian

    2014-01-17

    (±)-Aspongamide A (1), an unusual trimer of N-acetyldopamine (NADA) bearing a novel tetrahydrobenzo[a]dibenzo[b,e][1,4]dioxine structure, and a pair of NADA dimeric enantiomers (2) were isolated from Aspongopus chinensis. The structures of compounds 1 and 2 were assigned using spectroscopic methods. Compound 1 was found to be an inhibitor of Smad3 phosphorylation in transforming growth factor-β1 (TGF-β1) induced rat renal proximal tubular cells and suppressed extracellular matrix expression in mesangial cells under diabetic conditions.

  15. Soluble Envelope Glycoprotein Trimers from a CD4-Independent HIV-1 Elicit Antibody-Dependent Cellular Cytotoxicity-Mediating Antibodies in Guinea Pigs

    PubMed Central

    Murray, Marta K.; Teran, Victor A.; Chapleau, Jean-Philippe; Wang, Baomin; Kim, Su Hyon; LaBranche, Celia C.; Richard, Jonathan; Montefiori, David C.

    2015-01-01

    CD4-independent HIV-1 variants can infect coreceptor-expressing cells lacking CD4. The envelope (Env) glycoproteins on these HIV-1 variants expose a coreceptor binding site that overlaps some CD4-induced (CD4i) epitopes. Reports have demonstrated that CD4i antibodies mediate antibody-dependent cellular cytotoxicity (ADCC). Here we investigated the immunogenicity of soluble Env trimers (sgp140) from a CD4-independent HIV-1 in guinea pigs and found that the sgp140 elicited ADCC-mediating antibodies. Therefore, these sgp140 might be useful in vaccine regimens aimed at eliciting ADCC responses. PMID:26246571

  16. Complexes of neutralizing and non-neutralizing affinity matured Fabs with a mimetic of the internal trimeric coiled-coil of HIV-1 gp41.

    PubMed

    Gustchina, Elena; Li, Mi; Ghirlando, Rodolfo; Schuck, Peter; Louis, John M; Pierson, Jason; Rao, Prashant; Subramaniam, Sriram; Gustchina, Alla; Clore, G Marius; Wlodawer, Alexander

    2013-01-01

    A series of mini-antibodies (monovalent and bivalent Fabs) targeting the conserved internal trimeric coiled-coil of the N-heptad repeat (N-HR) of HIV-1 gp41 has been previously constructed and reported. Crystal structures of two closely related monovalent Fabs, one (Fab 8066) broadly neutralizing across a wide panel of HIV-1 subtype B and C viruses, and the other (Fab 8062) non-neutralizing, representing the extremes of this series, were previously solved as complexes with 5-Helix, a gp41 pre-hairpin intermediate mimetic. Binding of these Fabs to covalently stabilized chimeric trimers of N-peptides of HIV-1 gp41 (named (CCIZN36)3 or 3-H) has now been investigated using X-ray crystallography, cryo-electron microscopy, and a variety of biophysical methods. Crystal structures of the complexes between 3-H and Fab 8066 and Fab 8062 were determined at 2.8 and 3.0 Å resolution, respectively. Although the structures of the complexes with the neutralizing Fab 8066 and its non-neutralizing counterpart Fab 8062 were generally similar, small differences between them could be correlated with the biological properties of these antibodies. The conformations of the corresponding CDRs of each antibody in the complexes with 3-H and 5-Helix are very similar. The adaptation to a different target upon complex formation is predominantly achieved by changes in the structure of the trimer of N-HR helices, as well as by adjustment of the orientation of the Fab molecule relative to the N-HR in the complex, via rigid-body movement. The structural data presented here indicate that binding of three Fabs 8062 with high affinity requires more significant changes in the structure of the N-HR trimer compared to binding of Fab 8066. A comparative analysis of the structures of Fabs complexed to different gp41 intermediate mimetics allows further evaluation of biological relevance for generation of neutralizing antibodies, as well as provides novel structural insights into immunogen design.

  17. Effects of the I559P gp41 change on the conformation and function of the human immunodeficiency virus (HIV-1) membrane envelope glycoprotein trimer.

    PubMed

    Alsahafi, Nirmin; Debbeche, Olfa; Sodroski, Joseph; Finzi, Andrés

    2015-01-01

    The mature human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer is produced by proteolytic cleavage of a precursor and consists of three gp120 exterior and three gp41 transmembrane subunits. The metastable Env complex is induced to undergo conformational changes required for virus entry by the binding of gp120 to the receptors, CD4 and CCR5/CXCR4. An isoleucine-to-proline change (I559P) in the gp41 ectodomain has been used to stabilize soluble forms of HIV-1 Env trimers for structural characterization and for use as immunogens. In the native membrane-anchored HIV-1BG505 Env, the I559P change modestly decreased proteolytic maturation, increased the non-covalent association of gp120 with the Env trimer, and resulted in an Env conformation distinctly different from that of the wild-type HIV-1BG505 Env. Compared with the wild-type Env, the I559P Env was recognized inefficiently by polyclonal sera from HIV-1-infected individuals, by several gp41-directed antibodies, by some antibodies against the CD4-binding site of gp120, and by antibodies that preferentially recognize the CD4-bound Env. Some of the gp120-associated antigenic differences between the wild-type HIV-1BG505 Env and the I559P mutant were compensated by the SOS disulfide bond between gp120 and gp41, which has been used to stabilize cleaved soluble Env trimers. Nonetheless, regardless of the presence of the SOS changes, Envs with proline 559 were recognized less efficiently than Envs with isoleucine 559 by the VRC01 neutralizing antibody, which binds the CD4-binding site of gp120, and the PGT151 neutralizing antibody, which binds a hybrid gp120-gp41 epitope. The I559P change completely eliminated the ability of the HIV-1BG505 Env to mediate cell-cell fusion and virus entry, and abolished the capacity of the SOS Env to support virus infection in the presence of a reducing agent. These results suggest that differences exist between the quaternary structures of functional Env spikes and I559P

  18. Excitation energy transfer in the LHC-II trimer: from carotenoids to chlorophylls in space and time.

    PubMed

    Martiskainen, Jari; Kananavičius, Robertas; Linnanto, Juha; Lehtivuori, Heli; Keränen, Mika; Aumanen, Viivi; Tkachenko, Nikolai; Korppi-Tommola, Jouko

    2011-02-01

    Exciton model for description of experimentally determined excitation energy transfer from carotenoids to chlorophylls in the LHC-II trimer of spinach is presented. Such an approach allows connecting the excitonic states to the spatial structure of the complex and hence descriptions of advancements of the initially created excitations in space and time. Carotenoids were excited at 490 nm and at 500 nm and induced absorbance changes probed in the Chl Q(y) region to provide kinetic data that were interpreted by using the results from exciton calculations. Calculations included the 42 chlorophylls and the 12 carotenoids of the complex, Soret, Q(x) and Q(y) states of the chlorophylls, and the main absorbing S(2) state of the carotenoids. According to the calculations excitation at 500 nm populates mostly a mixed Lut S(2) Chl a Soret state, from where excitation is transferred to the Q(x) and Q(y) states of the Chl a's on the stromal side. Internal conversion of the mixed state to a mixed Lut S(1) and Chl a Q(y) state provides a channel for Lut S(1) to Chl a Q(y) energy transfer. The results from the calculations support a picture where excitation at 490 nm populates primarily a mixed neoxanthin S(2) Chl b Soret state. From this state excitation from neoxanthin is transferred to iso-energetic Chl b Soret states or via internal conversion to S(1) Chl b Q(y) states. From the Soret states excitation proceeds via internal conversion to Q(y) states of Chl b's mostly on the lumenal side. A rapid Chl b to Chl a transfer and subsequent transfer to the stromal side Chl a's and to the final state completes the process after 490 nm excitation. The interpretation is further supported by the fact that excitation energy transfer kinetics after excitation of neoxanthin at 490 nm and the Chl b Q(y) band at 647 nm (Linnanto et al., Photosynth Res 87:267-279, 2006) are very similar.

  19. X-ray Crystallographic Structure of Oligomers Formed by a Toxic β-Hairpin Derived from α-Synuclein: Trimers and Higher-Order Oligomers.

    PubMed

    Salveson, Patrick J; Spencer, Ryan K; Nowick, James S

    2016-04-06

    Oligomeric assemblies of the protein α-synuclein are thought to cause neurodegeneration in Parkinson's disease and related synucleinopathies. Characterization of α-synuclein oligomers at high resolution is an outstanding challenge in the field of structural biology. The absence of high-resolution structures of oligomers formed by α-synuclein impedes understanding the synucleinopathies at the molecular level. This paper reports the X-ray crystallographic structure of oligomers formed by a peptide derived from residues 36-55 of α-synuclein. The peptide 1a adopts a β-hairpin structure, which assembles in a hierarchical fashion. Three β-hairpins assemble to form a triangular trimer. Three copies of the triangular trimer assemble to form a basket-shaped nonamer. Two nonamers pack to form an octadecamer. Molecular modeling suggests that full-length α-synuclein may also be able to assemble in this fashion. Circular dichroism spectroscopy demonstrates that peptide 1a interacts with anionic lipid bilayer membranes, like oligomers of full-length α-synuclein. LDH and MTT assays demonstrate that peptide 1a is toxic toward SH-SY5Y cells. Comparison of peptide 1a to homologues suggests that this toxicity results from nonspecific interactions with the cell membrane. The oligomers formed by peptide 1a are fundamentally different than the proposed models of the fibrils formed by α-synuclein and suggest that α-Syn36-55, rather than the NAC, may nucleate oligomer formation.

  20. Catalytic trimerization of aromatic nitriles and triaryl-s-triazine ring cross-linked high temperature resistant polymers and copolymers made thereby

    NASA Technical Reports Server (NTRS)

    Hsu, L. C. (Inventor)

    1979-01-01

    Triazine compounds and cross-linked polymer compositions are made by heating aromatic nitriles to a temperature in the range of from about 100 C to about 700 C, and preferably in the range of from about 200 C to about 350 C, in the presence of a catalyst or mixture of catalysts selected from one or more of the following groups: (1) organic sulfonic and sulfinic acids, (2) organic phosphonic and phosphinic acids, and (3)metallic acetylacetonates, at a pressure in the range of from about atmospheric pressure to about 10,000 psi and preferably in the range of from about 200 psi to about 750 psi. Aromatic nitrile-modified (terminated and/or appended) imide, benzimidazole, imidazopyrrolone, quinoxaline, and other condensation type prepolymers or their precopolymers are made which are trimerized with or without a filler by the aforementioned catalytic trimerization process into triaryl-s-triazine ring containing or cross-linked polymeric or copolymeric products useful in applications requiring high thermal-oxidative stability and high performance structural properties at elevated temperatures.

  1. X-ray Crystallographic Structures of a Trimer, Dodecamer, and Annular Pore Formed by an Aβ17-36 β-Hairpin.

    PubMed

    Kreutzer, Adam G; Hamza, Imane L; Spencer, Ryan K; Nowick, James S

    2016-04-06

    High-resolution structures of oligomers formed by the β-amyloid peptide Aβ are needed to understand the molecular basis of Alzheimer's disease and develop therapies. This paper presents the X-ray crystallographic structures of oligomers formed by a 20-residue peptide segment derived from Aβ. The development of a peptide in which Aβ17-36 is stabilized as a β-hairpin is described, and the X-ray crystallographic structures of oligomers it forms are reported. Two covalent constraints act in tandem to stabilize the Aβ17-36 peptide in a hairpin conformation: a δ-linked ornithine turn connecting positions 17 and 36 to create a macrocycle and an intramolecular disulfide linkage between positions 24 and 29. An N-methyl group at position 33 blocks uncontrolled aggregation. The peptide readily crystallizes as a folded β-hairpin, which assembles hierarchically in the crystal lattice. Three β-hairpin monomers assemble to form a triangular trimer, four trimers assemble in a tetrahedral arrangement to form a dodecamer, and five dodecamers pack together to form an annular pore. This hierarchical assembly provides a model, in which full-length Aβ transitions from an unfolded monomer to a folded β-hairpin, which assembles to form oligomers that further pack to form an annular pore. This model may provide a better understanding of the molecular basis of Alzheimer's disease at atomic resolution.

  2. Folding studies of Purified LamB Protein, the Maltoporin from the Escherichia coli Outer Membrane: Trimer Dissociation can be separated from Unfolding

    PubMed Central

    Baldwin, Valerie; Bhatia, Mandeep; Luckey, Mary

    2011-01-01

    The folding mechanisms for β-barrel membrane proteins present unique challenges because acquisition of both secondary and tertiary structure is coupled with insertion into the bilayer. For the porins in Escherichia coli outer membrane, the assembly pathway also includes association into homotrimers. We study the folding pathway for purified LamB protein in detergent and observe extreme hysteresis in unfolding and refolding, as indicated by the shift in intrinsic fluorescence. The strong hysteresis is not seen in unfolding and refolding a mutant LamB protein lacking the disulfide bond, as it unfolds at much lower denaturant concentrations than wild type LamB protein. The disulfide bond is proposed to stabilize the structure of LamB protein by clasping together the two sides of Loop 1 as it lines the inner cavity of the barrel. In addition we find that low pH promotes dissociation of the LamB trimer to folded monomers, which run at about one third the size of the native trimer during SDS PAGE and are much more resistant to trypsin than the unfolded protein. We postulate the loss at low pH of two salt bridges between Loop 2 of the neighboring subunit and the inner wall of the monomer barrel destabilizes the quaternary structure. PMID:21640073

  3. A double stranded metal-organic assembly accommodating a pair of water trimers in the host cavity and catalysing Glaser coupling.

    PubMed

    Pradhan, Subhashis; Moon, Dohyun; John, Rohith P

    2016-02-01

    A supramolecular compound, catena-poly{[Cu2(1,3-μ2-(1a))2(μ2-ter)2(H2O)2]n·(6H2O)n} (1) has been synthesized using (1a) [(1a = N(1),N(3),N(5)-trimethyl-N(1),N(3),N(5)-tris((pyridin-4-yl)methyl)-1,3,5-benzene tricarboxamide] and terephthalate (ter) as the pillaring unit by self-assembly. The terephthalate units are connected by copper(II) ions forming a single strand, while a pair of such strands are then linked by (1a) via two pyridyl terminal arms bound to copper(II) nodes on either side forming a one-dimensional double stranded assembly propagating along the c axis. The compound crystallizes in the Fdd2 space group. The cavity created in the interior of this double strand assembly trap six water molecules and are stabilized by hydrogen bonding with the host. The arrangement of the pair of acyclic water trimers in isolated cavities of (1) is such that it resembles a closed-bracket-like formation. The Hirshfeld surface analysis of (1) reveals the presence of strong intermolecular hydrogen-bonding interactions between one-dimensional ladder-like units and with the water trimer in the host cavity. The copper(II)-containing coordination polymer also acts as an efficient catalyst for the Glaser-Hay homo-coupling reaction.

  4. Low-temperature energy transfer in LHC-II trimers from the Chl a/b light-harvesting antenna of photosystem II.

    PubMed Central

    Savikhin, S; van Amerongen, H; Kwa, S L; van Grondelle, R; Struve, W S

    1994-01-01

    Temperature dependence in electronic energy transfer steps within light-harvesting antenna trimers from photosystem II was investigated by studying Chl a pump-probe anisotropy decays at several wavelengths from 675 to 682 nm. The anisotropy lifetime is markedly sensitive to temperature at the longest wavelengths (680-682 nm), increasing by factors of 5 to 6 as the trimers are cooled from room temperature to 13 K. The temperature dependence is muted at 677 and 675 nm. This behavior is modeled using simulations of temperature-broadened Chl a absorption and fluorescence spectra in spectral overlap calculations of Förster energy transfer rates. In this model, the 680 nm anisotropy decays are dominated by uphill energy transfers from 680 nm Chl a pigments at the red edge of the LHC-II spectrum; the 675 nm anisotropy decays reflect a statistical average of uphill and downhill energy transfers from 676-nm pigments. The measured temperature dependence is consistent with essentially uncorrelated inhomogeneous broadening of donor and acceptor Chl a pigments. PMID:8061208

  5. Another look at the mechanism involving trimeric dUTPases in Staphylococcus aureus pathogenicity island induction involves novel players in the party

    PubMed Central

    Maiques, Elisa; Quiles-Puchalt, Nuria; Donderis, Jorge; Ciges-Tomas, J. Rafael; Alite, Christian; Bowring, Janine Z.; Humphrey, Suzanne; Penadés, José R.; Marina, Alberto

    2016-01-01

    We have recently proposed that the trimeric staphylococcal phage encoded dUTPases (Duts) are signaling molecules that act analogously to eukaryotic G-proteins, using dUTP as a second messenger. To perform this regulatory role, the Duts require their characteristic extra motif VI, present in all the staphylococcal phage coded trimeric Duts, as well as the strongly conserved Dut motif V. Recently, however, an alternative model involving Duts in the transfer of the staphylococcal islands (SaPIs) has been suggested, questioning the implication of motifs V and VI. Here, using state-of the-art techniques, we have revisited the proposed models. Our results confirm that the mechanism by which the Duts derepress the SaPI cycle depends on dUTP and involves both motifs V and VI, as we have previously proposed. Surprisingly, the conserved Dut motif IV is also implicated in SaPI derepression. However, and in agreement with the proposed alternative model, the dUTP inhibits rather than inducing the process, as we had initially proposed. In summary, our results clarify, validate and establish the mechanism by which the Duts perform regulatory functions. PMID:27112567

  6. Nanoparticle-nanoparticle vs. nanoparticle-substrate hot spot contributions to the SERS signal: studying Raman labelled monomers, dimers and trimers.

    PubMed

    Sergiienko, Sergii; Moor, Kamila; Gudun, Kristina; Yelemessova, Zarina; Bukasov, Rostislav

    2017-02-08

    We used a combination of Raman microscopy, AFM and TEM to quantify the influence of dimerization on the surface enhanced Raman spectroscopy (SERS) signal for gold and silver nanoparticles (NPs) modified with Raman reporters and situated on gold, silver, and aluminum films and a silicon wafer. The overall increases in the mean SERS enhancement factor (EF) upon dimerization (up by 43% on average) and trimerisation (up by 96% on average) of AuNPs and AgNPs on the studied metal films are within a factor of two, which is moderate when compared to most theoretical models. However, the maximum ratio of EFs for some dimers to the mean EF of monomers can be as high as 5.5 for AgNPs on a gold substrate. In contrast, for dimerization and trimerization of gold and silver NPs on silicon, the mean EF increases by 1-2 orders of magnitude relative to the mean EF of single NPs. Therefore, hot spots in the interparticle gap between gold nanoparticles rather than hot spots between Au nanoparticles and the substrate dominate SERS enhancement for dimers and trimers on a silicon substrate. However, Raman labeled noble metal nanoparticles on plasmonic metal films generate on average SERS enhancement of the same order of magnitude for both types of hot spot zones (e.g. NP/NP and NP/metal film).

  7. Magnetic dimers and trimers in the disordered S =3/2 spin system BaTi1/2Mn1/2O3

    NASA Astrophysics Data System (ADS)

    Garcia, F. A.; Kaneko, U. F.; Granado, E.; Sichelschmidt, J.; Hölzel, M.; Duque, J. G. S.; Nunes, C. A. J.; Amaral, R. P.; Marques-Ferreira, P.; Lora-Serrano, R.

    2015-06-01

    We report a structural-magnetic investigation by x-ray absorption spectroscopy (XAS), neutron diffraction, dc susceptibility (χdc), and electron spin resonance (ESR) of the 12R-type perovskite BaTi1/2Mn1/2O3 . Our structural analysis by neutron diffraction supports the existence of structural trimers with chemically disordered occupancy of Mn4+ and Ti4+ ions, with the valence of the Mn ions confirmed by the XAS measurements. The magnetic properties are explored by combining dc-susceptibility and X -band (9.4 GHz) electron spin resonance, both in the temperature interval of 2 ≤T ≤1000 K. A scenario is presented under which the magnetism is explained by considering magnetic dimers and trimers, with exchange constants Ja/kB=200 (2 ) K and Jb/kB=130 (10 ) K, and orphan spins. Thus, BaTi1/2Mn1/2O3 is proposed as a rare case of an intrinsically disordered S =3/2 spin gap system with a frustrated ground state.

  8. Folding studies of purified LamB protein, the maltoporin from the Escherichia coli outer membrane: trimer dissociation can be separated from unfolding.

    PubMed

    Baldwin, Valerie; Bhatia, Mandeep; Luckey, Mary

    2011-09-01

    The folding mechanisms for β-barrel membrane proteins present unique challenges because acquisition of both secondary and tertiary structure is coupled with insertion into the bilayer. For the porins in Escherichia coli outer membrane, the assembly pathway also includes association into homotrimers. We study the folding pathway for purified LamB protein in detergent and observe extreme hysteresis in unfolding and refolding, as indicated by the shift in intrinsic fluorescence. The strong hysteresis is not seen in unfolding and refolding a mutant LamB protein lacking the disulfide bond, as it unfolds at much lower denaturant concentrations than wild type LamB protein. The disulfide bond is proposed to stabilize the structure of LamB protein by clasping together the two sides of Loop 1 as it lines the inner cavity of the barrel. In addition we find that low pH promotes dissociation of the LamB trimer to folded monomers, which run at about one third the size of the native trimer during SDS PAGE and are much more resistant to trypsin than the unfolded protein. We postulate the loss at low pH of two salt bridges between Loop 2 of the neighboring subunit and the inner wall of the monomer barrel destabilizes the quaternary structure.

  9. A 3-dimensional trimeric β-barrel model for Chlamydia MOMP contains conserved and novel elements of Gram-negative bacterial porins.

    PubMed

    Feher, Victoria A; Randall, Arlo; Baldi, Pierre; Bush, Robin M; de la Maza, Luis M; Amaro, Rommie E

    2013-01-01

    Chlamydia trachomatis is the most prevalent cause of bacterial sexually transmitted diseases and the leading cause of preventable blindness worldwide. Global control of Chlamydia will best be achieved with a vaccine, a primary target for which is the major outer membrane protein, MOMP, which comprises ~60% of the outer membrane protein mass of this bacterium. In the absence of experimental structural information on MOMP, three previously published topology models presumed a16-stranded barrel architecture. Here, we use the latest β-barrel prediction algorithms, previous 2D topology modeling results, and comparative modeling methodology to build a 3D model based on the 16-stranded, trimeric assumption. We find that while a 3D MOMP model captures many structural hallmarks of a trimeric 16-stranded β-barrel porin, and is consistent with most of the experimental evidence for MOMP, MOMP residues 320-334 cannot be modeled as β-strands that span the entire membrane, as is consistently observed in published 16-stranded β-barrel crystal structures. Given the ambiguous results for β-strand delineation found in this study, recent publications of membrane β-barrel structures breaking with the canonical rule for an even number of β-strands, findings of β-barrels with strand-exchanged oligomeric conformations, and alternate folds dependent upon the lifecycle of the bacterium, we suggest that although the MOMP porin structure incorporates canonical 16-stranded conformations, it may have novel oligomeric or dynamic structural changes accounting for the discrepancies observed.

  10. Another look at the mechanism involving trimeric dUTPases in Staphylococcus aureus pathogenicity island induction involves novel players in the party.

    PubMed

    Maiques, Elisa; Quiles-Puchalt, Nuria; Donderis, Jorge; Ciges-Tomas, J Rafael; Alite, Christian; Bowring, Janine Z; Humphrey, Suzanne; Penadés, José R; Marina, Alberto

    2016-06-20

    We have recently proposed that the trimeric staphylococcal phage encoded dUTPases (Duts) are signaling molecules that act analogously to eukaryotic G-proteins, using dUTP as a second messenger. To perform this regulatory role, the Duts require their characteristic extra motif VI, present in all the staphylococcal phage coded trimeric Duts, as well as the strongly conserved Dut motif V. Recently, however, an alternative model involving Duts in the transfer of the staphylococcal islands (SaPIs) has been suggested, questioning the implication of motifs V and VI. Here, using state-of the-art techniques, we have revisited the proposed models. Our results confirm that the mechanism by which the Duts derepress the SaPI cycle depends on dUTP and involves both motifs V and VI, as we have previously proposed. Surprisingly, the conserved Dut motif IV is also implicated in SaPI derepression. However, and in agreement with the proposed alternative model, the dUTP inhibits rather than inducing the process, as we had initially proposed. In summary, our results clarify, validate and establish the mechanism by which the Duts perform regulatory functions.

  11. Trimeric gp120-specific bovine monoclonal antibodies require cysteine and aromatic residues in CDRH3 for high affinity binding to HIV Env.

    PubMed

    Heydarchi, Behnaz; Center, Rob J; Bebbington, Jonathan; Cuthbertson, Jack; Gonelli, Christopher; Khoury, Georges; Mackenzie, Charlene; Lichtfuss, Marit; Rawlin, Grant; Muller, Brian; Purcell, Damian

    2017-04-01

    We isolated HIV-1 Envelope (Env)-specific memory B cells from a cow that had developed high titer polyclonal immunoglobulin G (IgG) with broad neutralizing activity after a long duration vaccination with HIV-1AD8 Env gp140 trimers. We cloned the bovine IgG matched heavy (H) and light (L) chain variable (V) genes from these memory B cells and constructed IgG monoclonal antibodies (mAbs) with either a human constant (C)-region/bovine V-region chimeric or fully bovine C and V regions. Among 42 selected Ig+ memory B cells, two mAbs (6A and 8C) showed high affinity binding to gp140 Env. Characterization of both the fully bovine and human chimeric isoforms of these two mAbs revealed them as highly type-specific and capable of binding only to soluble AD8 uncleaved gp140 trimers and covalently stabilized AD8 SOSIP gp140 cleaved trimers, but not monomeric gp120. Genomic sequence analysis of the V genes showed the third heavy complementarity-determining region (CDRH3) of 6A mAb was 21 amino acids in length while 8C CDRH3 was 14 amino acids long. The entire V heavy (VH) region was 27% and 25% diverged for 6A and 8C, respectively, from the best matched germline V genes available, and the CDRH3 regions of 6A and 8C were 47.62% and 78.57% somatically mutated, respectively, suggesting a high level of somatic hypermutation compared with CDRH3 of other species. Alanine mutagenesis of the VH genes of 6A and 8C, showed that CDRH3 cysteine and tryptophan amino acids were crucial for antigen binding. Therefore, these bovine vaccine-induced anti-HIV antibodies shared some of the notable structural features of elite human broadly neutralizing antibodies, such as CDRH3 size and somatic mutation during affinity-maturation. However, while the 6A and 8C mAbs inhibited soluble CD4 binding to gp140 Env, they did not recapitulate the neutralizing activity of the polyclonal antibodies against HIV infection.

  12. Excited singlet states of covalently bound, cofacial dimers and trimers of perylene-3,4:9,10-bis(dicarboximide)s.

    PubMed

    Giaimo, Jovan M; Lockard, Jenny V; Sinks, Louise E; Scott, Amy M; Wilson, Thea M; Wasielewski, Michael R

    2008-03-20

    Perylene-3,4:9,10-bis(dicarboximide) (PDI) and its derivatives are robust organic dyes that strongly absorb visible light and display a strong tendency to self-assemble into ordered aggregates, having significant interest as photoactive materials in a wide variety of organic electronics. To better understand the nature of the electronics states produced by photoexcitation of such aggregates, the photophysics of a series of covalent, cofacially oriented, pi-stacked dimers and trimers of PDI and 1,7-bis(3',5'-di-t-butylphenoxy)perylene-3,4:9,10-bis(dicarboximide) (PPDI) were characterized using both time-resolved absorption and fluorescence spectroscopy. The covalent linkage between the chromophores was accomplished using 9,9-dimethylxanthene spacers. Placing n-octyl groups on the imide nitrogen atoms at the end of the PDI chromophores not attached to the xanthene spacer results in PDI dimers having near optimal pi-stacking, leading to formation of a low-energy excimer-like state, while substituting the more sterically demanding 12-tricosanyl group on the imides causes deviations from the optimum that result in slower formation of an excimer-like excited state having somewhat higher energy. By comparison, PPDI dimers having terminal n-octyl imide groups have two isomers, whose photophysical properties depend on the ability of the phenoxy groups at the 1,7-positions to modify the pi stacking of the PPDI molecules. In general, disruption of optimal pi-stacking by steric interactions of the phenoxy side groups results in excimer-like states that are higher in energy. The corresponding lowest excited singlet states of the PDI and PPDI trimers are dimer-like in nature and suggest that structural distortions that accompany formation of the trimers are sufficient to confine the electronic interaction on two chromophores within these systems. This further suggests that it may be useful to build into oligomeric PDI and PPDI systems some degree of flexibility that allows the

  13. Trimeric gp120-specific bovine monoclonal antibodies require cysteine and aromatic residues in CDRH3 for high affinity binding to HIV Env

    PubMed Central

    Center, Rob J.; Bebbington, Jonathan; Cuthbertson, Jack; Khoury, Georges; Lichtfuss, Marit; Rawlin, Grant; Purcell, Damian

    2017-01-01

    ABSTRACT We isolated HIV-1 Envelope (Env)-specific memory B cells from a cow that had developed high titer polyclonal immunoglobulin G (IgG) with broad neutralizing activity after a long duration vaccination with HIV-1AD8 Env gp140 trimers. We cloned the bovine IgG matched heavy (H) and light (L) chain variable (V) genes from these memory B cells and constructed IgG monoclonal antibodies (mAbs) with either a human constant (C)-region/bovine V-region chimeric or fully bovine C and V regions. Among 42 selected Ig+ memory B cells, two mAbs (6A and 8C) showed high affinity binding to gp140 Env. Characterization of both the fully bovine and human chimeric isoforms of these two mAbs revealed them as highly type-specific and capable of binding only to soluble AD8 uncleaved gp140 trimers and covalently stabilized AD8 SOSIP gp140 cleaved trimers, but not monomeric gp120. Genomic sequence analysis of the V genes showed the third heavy complementarity-determining region (CDRH3) of 6A mAb was 21 amino acids in length while 8C CDRH3 was 14 amino acids long. The entire V heavy (VH) region was 27% and 25% diverged for 6A and 8C, respectively, from the best matched germline V genes available, and the CDRH3 regions of 6A and 8C were 47.62% and 78.57% somatically mutated, respectively, suggesting a high level of somatic hypermutation compared with CDRH3 of other species. Alanine mutagenesis of the VH genes of 6A and 8C, showed that CDRH3 cysteine and tryptophan amino acids were crucial for antigen binding. Therefore, these bovine vaccine-induced anti-HIV antibodies shared some of the notable structural features of elite human broadly neutralizing antibodies, such as CDRH3 size and somatic mutation during affinity-maturation. However, while the 6A and 8C mAbs inhibited soluble CD4 binding to gp140 Env, they did not recapitulate the neutralizing activity of the polyclonal antibodies against HIV infection. PMID:27996375

  14. Membrane-bound SIV envelope trimers are immunogenic in ferrets after intranasal vaccination with a replication-competent canine distemper virus vector.

    PubMed

    Zhang, Xinsheng; Wallace, Olivia; Wright, Kevin J; Backer, Martin; Coleman, John W; Koehnke, Rebecca; Frenk, Esther; Domi, Arban; Chiuchiolo, Maria J; DeStefano, Joanne; Narpala, Sandeep; Powell, Rebecca; Morrow, Gavin; Boggiano, Cesar; Zamb, Timothy J; Richter King, C; Parks, Christopher L

    2013-11-01

    We are investigating canine distemper virus (CDV) as a vaccine vector for the delivery of HIV envelope (Env) that closely resembles the native trimeric spike. We selected CDV because it will promote vaccine delivery to lymphoid tissues, and because human exposure is infrequent, reducing potential effects of pre-existing immunity. Using SIV Env as a model, we tested a number of vector and gene insert designs. Vectors containing a gene inserted between the CDV H and L genes, which encoded Env lacking most of its cytoplasmic tail, propagated efficiently in Vero cells, expressed the immunogen on the cell surface, and incorporated the SIV glycoprotein into progeny virus particles. When ferrets were vaccinated intranasally, there were no signs of distress, vector replication was observed in the gut-associated lymphoid tissues, and the animals produced anti-SIV Env antibodies. These data show that live CDV-SIV Env vectors can safely induce anti-Env immune responses following intranasal vaccination.

  15. Inhibition of type 1 fimbriae-mediated Escherichia coli adhesion and biofilm formation by trimeric cluster thiomannosides conjugated to diamond nanoparticles

    NASA Astrophysics Data System (ADS)

    Khanal, Manakamana; Larsonneur, Fanny; Raks, Victoriia; Barras, Alexandre; Baumann, Jean-Sébastien; Martin, Fernando Ariel; Boukherroub, Rabah; Ghigo, Jean-Marc; Ortiz Mellet, Carmen; Zaitsev, Vladimir; Garcia Fernandez, Jose M.; Beloin, Christophe; Siriwardena, Aloysius; Szunerits, Sabine

    2015-01-01

    Recent advances in nanotechnology have seen the development of a number of microbiocidal and/or anti-adhesive nanoparticles displaying activity against biofilms. In this work, trimeric thiomannoside clusters conjugated to nanodiamond particles (ND) were targeted for investigation. NDs have attracted attention as a biocompatible nanomaterial and we were curious to see whether the high mannose glycotope density obtained upon grouping monosaccharide units in triads might lead to the corresponding ND-conjugates behaving as effective inhibitors of E. coli type 1 fimbriae-mediated adhesion as well as of biofilm formation. The required trimeric thiosugar clusters were obtained through a convenient thiol-ene ``click'' strategy and were subsequently conjugated to alkynyl-functionalized NDs using a Cu(i)-catalysed ``click'' reaction. We demonstrated that the tri-thiomannoside cluster-conjugated NDs (ND-Man3) show potent inhibition of type 1 fimbriae-mediated E. coli adhesion to yeast and T24 bladder cells as well as of biofilm formation. The biofilm disrupting effects demonstrated here have only rarely been reported in the past for analogues featuring such simple glycosidic motifs. Moreover, the finding that the tri-thiomannoside cluster (Man3N3) is itself a relatively efficient inhibitor, even when not conjugated to any ND edifice, suggests that alternative mono- or multivalent sugar-derived analogues might also be usefully explored for E. coli-mediated biofilm disrupting properties.Recent advances in nanotechnology have seen the development of a number of microbiocidal and/or anti-adhesive nanoparticles displaying activity against biofilms. In this work, trimeric thiomannoside clusters conjugated to nanodiamond particles (ND) were targeted for investigation. NDs have attracted attention as a biocompatible nanomaterial and we were curious to see whether the high mannose glycotope density obtained upon grouping monosaccharide units in triads might lead to the corresponding

  16. The vibrational spectrum of the water trimer: Comparison between anharmonic ab initio calculations and neon matrix infrared data between 11,000 and 90 cm -1

    NASA Astrophysics Data System (ADS)

    Tremblay, B.; Madebène, B.; Alikhani, M. E.; Perchard, J. P.

    2010-12-01

    The infrared spectrum of the water trimer trapped in solid neon has been identified. Eighteen groups of absorptions between 1600 and 11,000 cm -1 were assigned to one-, two- and three-quanta transitions of the intramolecular modes. Because of the near equivalence of the three molecules and their weak interactions most of these modes correspond to quasi degenerate vibrations involving the bending δ, free OH stretching (OH f) and bonded OH stretching (OH b) of the three subunits at 1608, 3725 and 3525-3473 cm -1, respectively. In the last case the 52 cm -1 splitting is due to the coupling between the OH b oscillators. Calculated anharmonic frequencies correctly agree with these observations and allow to propose a new assignment of the intermolecular modes. Finally combinations of intra + intermolecular transitions were identified and assigned on the basis of calculated anharmonicity coefficients.

  17. Trimeric crystal structure of the glycoside hydrolase family 42 beta-galactosidase from Thermus thermophilus A4 and the structure of its complex with galactose.

    PubMed

    Hidaka, Masafumi; Fushinobu, Shinya; Ohtsu, Naomi; Motoshima, Hidemasa; Matsuzawa, Hiroshi; Shoun, Hirofumi; Wakagi, Takayoshi

    2002-09-06

    The beta-galactosidase from an extreme thermophile, Thermus thermophilus A4 (A4-beta-Gal), is thermostable and belongs to the glycoside hydrolase family 42 (GH-42). As the first known structures of a GH-42 enzyme, we determined the crystal structures of free and galactose-bound A4-beta-Gal at 1.6A and 2.2A resolution, respectively. A4-beta-Gal forms a homotrimeric structure resembling a flowerpot. Each monomer has an active site located inside a large central tunnel. The N-terminal domain of A4-beta-Gal has a TIM barrel fold, as predicted from hydrophobic cluster analysis. The putative catalytic residues of A4-beta-Gal (Glu141 and Glu312) superimpose well with the catalytic residues of Escherichia coli beta-galactosidase. The environment around the catalytic nucleophile (Glu312) is similar to that in the case of E.coli beta-galactosidase, but the recognition mechanism for a substrate is different. Trp182 of the next subunit of the trimer constitutes a part of the active-site pocket, indicating that the trimeric structure is essential for the enzyme activity. Structural comparison with other glycoside hydrolases revealed that many features of the 4/7 superfamily are conserved in the A4-beta-Gal structure. On the basis of the results of 1H NMR spectroscopy, A4-beta-Gal was determined to be a "retaining" enzyme. Interestingly, the active site was similar with those of retaining enzymes, but the overall fold of the TIM barrel domain was very similar to that of an inverting enzyme, beta-amylase.

  18. Treatment of severe brain ischemia with di- and tri-Calciphor (dimer and trimer of 16,16'-dimethyl prostaglandin B1).

    PubMed

    Von Lubitz, D K; McKenzie, R J; Kalenak, A; Lin, R C; Devlin, T M

    1992-05-27

    Following 20 min occlusion of both carotid arteries, female gerbils were subjected to treatment with di- or tri-Calciphor (dimer or trimer of 16,16'-dimethyl prostaglandin B1). Dimer was injected i.p. at 5 and 10 mg/kg at 5 min and again at 24 h, 30 min and 24 h, 60 min and 24 h or 180 min and 24 h postischemia (N = 25/group). Trimer was given i.p. at 5, 10 or 15 mg/kg at 5 min and 24 h postischemia (N = 25/group.) The controls (N = 25) were injected with the vehicle. Neurological status and postischemic survival of the animals were monitored for 14 days postischemia. Survival of the treated gerbils was significantly improved following the treatment with either di- or tri-Calciphor administered at 10 mg/kg at 5 min and 24 h postischemia (36 vs. 68% di- and 64% tri-Calciphor, P less than 0.05), and with di-Calciphor at 5 mg/kg at 180 min and 24 h postischemia (64%). All other treatment regimens with either drug resulted in a numerical, statistically insignificant improvement. In addition, treatment with either drug reduced the intensity of postischemic neurological impairment. Treatment with di-Calciphor injected at 10 mg/kg at 5 min and 24 h post 20 min ischemia substantially reduced the period of postischemic locomotor hyperactivity. The drug had no impact on either body temperature or blood pressure. There is evidence that the effects of Calciphor may be mediated via calcium regulatory mechanisms. The results of the present study are discussed in the light of such possibility.

  19. TprC/D (Tp0117/131), a Trimeric, Pore-Forming Rare Outer Membrane Protein of Treponema pallidum, Has a Bipartite Domain Structure

    PubMed Central

    Anand, Arvind; Luthra, Amit; Dunham-Ems, Star; Caimano, Melissa J.; Karanian, Carson; LeDoyt, Morgan; Cruz, Adriana R.; Salazar, Juan C.

    2012-01-01

    Identification of Treponema pallidum rare outer membrane proteins (OMPs) has been a longstanding objective of syphilis researchers. We recently developed a consensus computational framework that employs a battery of cellular localization and topological prediction tools to generate ranked clusters of candidate rare OMPs (D. L. Cox et al., Infect. Immun. 78:5178–5194, 2010). TP0117/TP0131 (TprC/D), a member of the T. pallidum repeat (Tpr) family, was a highly ranked candidate. Circular dichroism, heat modifiability by SDS-PAGE, Triton X-114 phase partitioning, and liposome incorporation confirmed that full-length, recombinant TprC (TprCFl) forms a β-barrel capable of integrating into lipid bilayers. Moreover, TprCFl increased efflux of terbium-dipicolinic acid complex from large unilamellar vesicles and migrated as a trimer by blue-native PAGE. We found that in T. pallidum, TprC is heat modifiable, trimeric, expressed in low abundance, and, based on proteinase K accessibility and opsonophagocytosis assays, surface exposed. From these collective data, we conclude that TprC is a bona fide rare OMP as well as a functional ortholog of Escherichia coli OmpF. We also discovered that TprC has a bipartite architecture consisting of a soluble N-terminal portion (TprCN), presumably periplasmic and bound directly or indirectly to peptidoglycan, and a C-terminal β-barrel (TprCC). Syphilitic rabbits generate antibodies exclusively against TprCC, while secondary syphilis patients fail to mount a detectable antibody response against either domain. The syphilis spirochete appears to have resolved a fundamental dilemma arising from its extracellular lifestyle, namely, how to enhance OM permeability without increasing its vulnerability to the antibody-mediated defenses of its natural human host. PMID:22389487

  20. Complete epitopes for vaccine design derived from a crystal structure of the broadly neutralizing antibodies PGT128 and 8ANC195 in complex with an HIV-1 Env trimer.

    PubMed

    Kong, Leopold; Torrents de la Peña, Alba; Deller, Marc C; Garces, Fernando; Sliepen, Kwinten; Hua, Yuanzi; Stanfield, Robyn L; Sanders, Rogier W; Wilson, Ian A

    2015-10-01

    The HIV-1 envelope gp160 glycoprotein (Env) is a trimer of gp120 and gp41 heterodimers that mediates cell entry and is the primary target of the humoral immune response. Broadly neutralizing antibodies (bNAbs) to HIV-1 have revealed multiple epitopes or sites of vulnerability, but mapping of most of these sites is incomplete owing to a paucity of structural information on the full epitope in the context of the Env trimer. Here, a crystal structure of the soluble BG505 SOSIP gp140 trimer at 4.6 Å resolution with the bNAbs 8ANC195 and PGT128 reveals additional interactions in comparison to previous antibody-gp120 structures. For 8ANC195, in addition to previously documented interactions with gp120, a substantial interface with gp41 is now elucidated that includes extensive interactions with the N637 glycan. Surprisingly, removal of the N637 glycan did not impact 8ANC195 affinity, suggesting that the antibody has evolved to accommodate this glycan without loss of binding energy. PGT128 indirectly affects the N262 glycan by a domino effect, in which PGT128 binds to the N301 glycan, which in turn interacts with and repositions the N262 glycan, thereby illustrating the important role of neighboring glycans on epitope conformation and stability. Comparisons with other Env trimer and gp120 structures support an induced conformation for glycan N262, suggesting that the glycan shield is allosterically modified upon PGT128 binding. These complete epitopes of two broadly neutralizing antibodies on the Env trimer can now be exploited for HIV-1 vaccine design.

  1. Single-Chain Soluble BG505.SOSIP gp140 Trimers as Structural and Antigenic Mimics of Mature Closed HIV-1 Env

    PubMed Central

    Georgiev, Ivelin S.; Joyce, M. Gordon; Yang, Yongping; Sastry, Mallika; Zhang, Baoshan; Baxa, Ulrich; Chen, Rita E.; Druz, Aliaksandr; Lees, Christopher R.; Narpala, Sandeep; Schön, Arne; Van Galen, Joseph; Chuang, Gwo-Yu; Gorman, Jason; Harned, Adam; Pancera, Marie; Stewart-Jones, Guillaume B. E.; Cheng, Cheng; Freire, Ernesto; McDermott, Adrian B.; Mascola, John R.

    2015-01-01

    ABSTRACT Similar to other type I fusion machines, the HIV-1 envelope glycoprotein (Env) requires proteolytic activation; specifically, cleavage of a gp160 precursor into gp120 and gp41 subunits creates an N-terminal gp41 fusion peptide and permits folding from an immature uncleaved state to a mature closed state. While the atomic-level consequences of cleavage for HIV-1 Env are still being determined, the uncleaved state is antigenically distinct from the mature closed state, and cleavage has been reported to be essential for mimicry of the mature viral spike by soluble versions of Env. Here we report the redesign of a current state-of-the-art soluble Env mimic, BG505.SOSIP, to make it cleavage independent. Specifically, we replaced the furin cleavage site between gp120 and gp41 with Gly-Ser linkers of various lengths. The resultant linked gp120-gp41 constructs, termed single-chain gp140 (sc-gp140), exhibited different levels of structural and antigenic mimicry of the parent cleaved BG505.SOSIP. When constructs were subjected to negative selection to remove subspecies recognized by poorly neutralizing antibodies, trimers of high antigenic mimicry of BG505.SOSIP could be obtained; negative-stain electron microscopy indicated these to resemble the mature closed state. Higher proportions of BG505.SOSIP-trimer mimicry were observed in sc-gp140s with linkers of 6 or more residues, with a linker length of 15 residues exhibiting especially promising traits. Overall, flexible linkages between gp120 and gp41 in BG505.SOSIP can thus substitute for cleavage, and sc-gp140s that closely mimicked the vaccine-preferred mature closed state of Env could be obtained. IMPORTANCE The trimeric HIV-1 envelope glycoprotein (Env) is the sole target of virus-directed neutralizing antibody responses and a primary focus of vaccine design. Soluble mimics of Env have proven challenging to obtain and have been thought to require proteolytic cleavage into two-component subunits, gp120 and gp41

  2. Basolateral to apical transcytosis in polarized cells is indirect and involves BFA and trimeric G protein sensitive passage through the apical endosome

    PubMed Central

    1994-01-01

    We have used temperature and nocodazole blocks in an in vivo basolateral to apical transcytosis assay to dissociate the early transcytotic steps occurring during the formation of transcytotic vesicles and their microtubule-dependent translocation into the apical region, from the late steps when transcytotic cargo is delivered into the apical media. We found that polarized MDCK cells transfected with rabbit polymeric IgA receptor (pIgA-R) internalize basolaterally added pIgA-R ligand ([Fab]2 fragment of IgG against the receptor's ectodomain) at 17 degrees C but do not deliver it to the apical PM. Instead, the ligand accumulates in an apically localized transcytotic compartment, distal to the basolateral endosome and the microtubule- requiring translocation step. We have characterized this compartment and show that it is distinct from basolateral transferrin recycling endosomes, basolateral early endosomes or late endosomes or lysosomes. The apical transcytotic compartment colocalizes with the compartment containing apically recycling membrane markers (ricin and apically internalized pIgA-R ligand) but is distinct from the compartment receiving apically internalized fluid phase marker (BSA). This compartment is an intermediate station of the overall pathway since transcytotic ligand can exit the compartment and be released into the apical medium when cells preloaded at 17 degrees C are subsequently incubated at 37 degrees C. We have used this system to examine the effect of Brefeldin A (BFA) and the involvement of trimeric GTPases in the late (post apical transcytotic compartment) steps of the transcytotic pathway. We found that addition of BFA or cholera toxin, a known activator of Gs alpha, to cells preloaded with transcytotic ligand at 17 degrees C significantly inhibits the exit of ligand from the apical transcytotic compartment. General structure and function of the apical endosome are not affected since neither BFA nor cholera toxin inhibit the recycling of

  3. Synthetic trimer and tetramer of 3-beta-D-ribose-(1-1)-D-ribitol-5-phosphate conjugated to protein induce antibody responses to Haemophilus influenzae type b capsular polysaccharide in mice and monkeys.

    PubMed Central

    Peeters, C C; Evenberg, D; Hoogerhout, P; Käyhty, H; Saarinen, L; van Boeckel, C A; van der Marel, G A; van Boom, J H; Poolman, J T

    1992-01-01

    Synthetic oligosaccharides derived from the capsular polysaccharide (PRP) of Haemophilus influenzae type b were conjugated to carrier proteins via a thioether linkage. Conjugates were made of trimeric and tetrameric ribose-ribitol-phosphate and tetanus toxoid or diphtheria toxin. All conjugates elicited anti-PRP antibody responses with an increasing immunoglobulin G/immunoglobulin M ratio in adult mice and monkeys. Trimer conjugates elicited lower anti-PRP antibody responses compared with tetramer conjugates. Adult monkeys responded equally well to the tetrameric oligosaccharide-tetanus toxoid conjugate as to the oligosaccharide-CRM197 conjugate (HbOC), which elicits protective levels of serum antibodies in human infants after two or three injections. PMID:1563770

  4. A CO32--containing, dimanganese-substituted silicotungstate trimer, K9[H14{SiW10MnIIMnIIIO38}3(CO3)]·39H2O.

    PubMed

    Yang, Ling; Liu, Qisen; Ma, Pengtao; Niu, Jingyang; Wang, Jingping

    2015-08-14

    An unprecedented silicotungstate trimer K(9)[H(14){SiW(10)Mn(II)Mn(III)O(38)}(3)(CO(3))]·39H(2)O (1) has been successfully synthesized, in which the CO(3)(2-) resides inside the three Keggin {SiW(10)Mn(II)Mn(III)O(38)} units and the three O atoms serve as μ(2)-O atoms to connect with three Mn(III). Magnetic investigation indicates that 1 exhibits antiferromagnetic coupling.

  5. 2',5'-Oligoadenylates chiral at phosphorus: enzymatic synthesis, properties, and biological activities of 2',5'-phosphorothioate trimer and tetramer analogues synthesized from (SP)-ATP alpha S

    SciTech Connect

    Lee, C.; Suhadolnik, R.J.

    1985-01-29

    The enzymatic synthesis and characterization of (RP)-2',5'-AMPS trimer and tetramer (SP)-5'-O-(1-thiotriphosphates) from chirally substituted (SP)-(alpha-/sup 35/S)ATP alpha S by 2',5'-oligoadenylate synthetase from interferon-treated L cell extracts are described. The (RP)-ATP alpha S isomer is not a substrate for the synthetase. The identification of the trimer and tetramer analogues (molar ratio 70:30) was accomplished by high-performance liquid chromatography and subsequent separation by charge using DEAE-cellulose thin-layer chromatography. The digestion of the analogue by snake venom phosphodiesterase I (SVPD) to (alpha-/sup 35/S)ATP alpha S and (/sup 35/S)AMPS but not by T2 RNase demonstrated the presence of the 2',5' linkage. The assignment of RP configuration of the 2',5'-phosphorothiodiester linkage was based on the highly specific stereoselectivity of SVPD for RP diastereomers. This suggests that the synthesis of the phosphorothioate analogues proceeded via inversion of configuration at the chiral phosphorus of (SP)-ATP alpha S. The putative (RP)-2',5'-AMPS tetramer (SP)-5'-O-(1-thiotriphosphate) displaced the 2',5'-p3A4(/sup 32/P)pCp analogue from 2',5'-oligoadenylate-dependent endonuclease 5 times more efficiently than did equimolar concentrations of authentic 2',5'-adenylate tetramer triphosphate. Furthermore, in studies using the calcium phosphate coprecipitation technique, the 2',5'-phosphorothioate trimer and tetramer analogues inhibited protein synthesis better than did 2',5'-adenylate trimer and tetramer triphosphates.

  6. Metal-free catalyzed oxidative trimerization of indoles by using TEMPO in air: a biomimetic approach to 2-(1H-indol-3-yl)-2,3'-biindolin-3-ones.

    PubMed

    Qin, Wen-Bing; Chang, Qiong; Bao, Yun-Hong; Wang, Ning; Chen, Zheng-Wang; Liu, Liang-Xian

    2012-11-28

    A simple, convenient and efficient metal-free catalyzed oxidative trimeric reaction of indoles toward a variety of 2-(1H-indol-3-yl)-2,3'-biindolin-3-one derivatives in moderate to excellent yields has been developed. This transformation proceeds via a tandem oxidative homocoupling reaction by using TEMPO in air as an environmentally benign oxidant. This methodology provides an alternative approach for the direct generation of all-carbon quaternary centers at the C3 position of indoles.

  7. A multi-trimeric fusion of CD40L and gp100 tumor antigen activates dendritic cells and enhances survival in a B16-F10 melanoma DNA vaccine model.

    PubMed

    Gupta, Sachin; Termini, James M; Rivas, Yaelis; Otero, Miguel; Raffa, Francesca N; Bhat, Vikas; Farooq, Amjad; Stone, Geoffrey W

    2015-09-11

    Vaccination with tumor-associated antigens can induce cancer-specific CD8+ T cells. A recent improvement has been the targeting of antigen to dendritic cells (DC) using antibodies that bind DC surface molecules. This study explored the use of multi-trimers of CD40L to target the gp100 melanoma tumor antigen to DC. The spontaneously-multimerizing gene Surfactant Protein D (SPD) was used to fuse gp100 tumor antigen and CD40L, creating the recombinant protein SPD-gp100-CD40L. This "third generation" DC-targeting vaccine was designed to both target antigen to DC and optimally activate dendritic cells by aggregating CD40 trimers on the DC membrane surface. SPD-gp100-CD40L expressed as a 110kDa protein. Analytical light scattering analysis gave elution data corresponding to 4-trimer and multi-trimer SPD-gp100-CD40L oligomers. The protein was biologically active on dendritic cells and induced CD40-mediated NF-κB signaling. DNA vaccination with SPD-gp100-CD40L plasmid, together with plasmids encoding IL-12p70 and GM-CSF, significantly enhanced survival and inhibited tumor growth in a B16-F10 melanoma model. Expression of gp100 and SPD-CD40L as separate molecules did not enhance survival, highlighting the requirement to encode gp100 within SPD-CD40L for optimal vaccine activity. These data support a model where DNA vaccination with SPD-gp100-CD40L targets gp100 to DC in situ, induces activation of these DC, and generates a protective anti-tumor response when given in combination with IL-12p70 and GM-CSF plasmids.

  8. A 102 kDa subunit of a Golgi-associated particle has homology to beta subunits of trimeric G proteins.

    PubMed Central

    Harrison-Lavoie, K J; Lewis, V A; Hynes, G M; Collison, K S; Nutland, E; Willison, K R

    1993-01-01

    We have identified a 102 kDa protein, p102, which is found on the cytoplasmic face of Golgi membranes, exocytic transport vesicles and in the cytosol. A monoclonal antibody that cross-reacts with p102 is able to immunoprecipitate a 500-600 kDa protein complex containing p102 and additional subunits. The composition of this p102-containing protein complex resembles that of the Golgi coatomer complex, which constitutes the coat of non-clathrin coated vesicles. One of the subunits of the p102 complex reacts with a monoclonal antibody that detects beta-COP, a subunit of the Golgi coatomer complex. Like beta-COP, p102 exists in a brefeldin A-sensitive association with Golgi membranes. The sequence of p102 contains an N-terminal domain composed of six repeats which are similar to those found in the beta subunit of trimeric G proteins and other regulatory proteins. We suggest that p102 may be involved in regulating membrane traffic in the constitutive exocytic pathway. Images PMID:8335000

  9. Major and minor groove conformations of DNA trimers modified on guanine or adenine by 4-aminobiphenyl: Adenine adducts favor the minor groove

    SciTech Connect

    Shapiro, R.; Ellis, S.; Hingerty, B.E.

    1995-01-01

    We have studied the conformational effects of 4-aminobiphenyl modification at C-8 of guanine or adenine on double-stranded DNA trimers. We used sequences with the modified purine at the central base pair and all 16 possible neighboring sequences at the outer pairs. Minimized potential energy calculations were carried out using the molecular mechanics program DUPLEX to survey the conformation space of these adducts, using a total of 1280 starting structures both in the modified guanine series and in the modified adenine series. Conformer families in which the bound 4-aminobiphenyl was located in the DNA major groove, and in the minor groove, were located for both adenine and guanine modification. In the modified guanine series, the major and minor groove families were roughly comparable in energy, and the sequence context determined which was more stable in a particular case. In the modified adenine series, however, the minor groove structure was more that 10 kcal/mol more stable than the major groove for all sequences. As a result, minor groove adducts provided most of the global minima in the adenine-modified series. This result may be relevant to a previous mutagenesis study [Lasko et al. (1988) J. Biol. Chem. 263, 15429-15435] in which the hot spot of most frequent occurrence was located at an adenine, in the sequence GAT. 25 refs., 9 figs., 4 tabs.

  10. Crystal structure of β1→6-galactosidase from Bifidobacterium bifidum S17: trimeric architecture, molecular determinants of the enzymatic activity and its inhibition by α-galactose.

    PubMed

    Godoy, Andre Schutzer; Camilo, Cesar Moises; Kadowaki, Marco Antonio; Muniz, Heloisa Dos S; Espirito Santo, Melissa; Murakami, Mario Tyago; Nascimento, Alessandro S; Polikarpov, Igor

    2016-11-01

    In a search for better comprehension of β-galactosidase function and specificity, we solved the crystal structures of the GH42 β-galactosidase BbgII from Bifidobacterium bifidum S17, a well-adapted probiotic microorganism from the human digestive tract, and its complex with d-α-galactose. BbgII is a three-domain molecule that forms barrel-shaped trimers in solution. BbgII interactions with d-α-galactose, a competitive inhibitor, showed a number of residues that are involved in the coordination of ligands. A combination of site-directed mutagenesis of these amino acid residues with enzymatic activity measurements confirmed that Glu161 and Glu320 are fundamental for catalysis and their substitution by alanines led to catalytically inactive mutants. Mutation Asn160Ala resulted in a two orders of magnitude decrease of the enzyme kcat without significant modification in its Km , whereas mutations Tyr289Phe and His371Phe simultaneously decreased kcat and increased Km values. Enzymatic activity of Glu368Ala mutant was too low to be detected. Our docking and molecular dynamics simulations showed that the enzyme recognizes and tightly binds substrates with β1→6 and β1→3 bonds, while binding of the substrates with β1→4 linkages is less favorable.

  11. A novel trimeric Zn (II) complex based on 8-hydroxyquinoline with trifluoromethylbenzene group: Synthesis, crystal structure, photophysical properties and DNA binding

    NASA Astrophysics Data System (ADS)

    Huo, Yanping; Wang, Chunquan; Lu, Jiguo; Hu, Sheng; Li, Xiaoyang; Zhang, Li

    2015-10-01

    A novel 2-substituted-8-hydroxyquinoline ligand (E)-2-[2-(4-trifluoromethylphenyl)ethenyl]-8-hydroxyquinoline (3, HL) was synthesized and characterized by ESI-MS, NMR spectroscopy and elemental analysis. Using solvothermal method, a trimeric complex [Zn3L6] (4) was fabricated by self-assembly of Zn(II) ions with 3. X-ray structural analysis shows that 4 exhibits a trinuclear core, which was bridged and encapsulated by six 8-hydroxyquinolinate-based ligands. The supramolecular structure of 4 features a lamellar solid constructed by aromatic stacking interactions and nonclassical C-H···F hydrogen bonds derived from 4-trifluoromethylphenyl group of the 3. The coordination behavior of zinc salt and 3 in solution was performed by 1H NMR, UV-vis and Photoluminescence (PL). The experimental results show that the complex 4 emits yellow luminescence in the solid state. To investigate its properties further, we also studied the thermal stability, photophysical properties (fluorescent emission, lifetime) of complex 4, and the interactions between 4 and C60 or EtBr-DNA system.

  12. Heterologous Expression of Bartonella Adhesin A in Escherichia coli by Exchange of Trimeric Autotransporter Adhesin Domains Results in Enhanced Adhesion Properties and a Pathogenic Phenotype

    PubMed Central

    Schmidgen, Thomas; Kaiser, Patrick O.; Ballhorn, Wibke; Franz, Bettina; Göttig, Stephan; Linke, Dirk

    2014-01-01

    Human-pathogenic Bartonella henselae causes cat scratch disease and vasculoproliferative disorders. An important pathogenicity factor of B. henselae is the trimeric autotransporter adhesin (TAA) Bartonella adhesin A (BadA), which is modularly constructed, consisting of a head, a long and repetitive neck-stalk module, and a membrane anchor. BadA is involved in bacterial autoagglutination, binding to extracellular matrix proteins and host cells, and in proangiogenic reprogramming. The slow growth of B. henselae and limited tools for genetic manipulation are obstacles for detailed examination of BadA and its domains. Here, we established a recombinant expression system for BadA mutants in Escherichia coli allowing functional analysis of particular BadA domains. Using a BadA mutant lacking 21 neck-stalk repeats (BadA HN23), the BadA HN23 signal sequence was exchanged with that of E. coli OmpA, and the BadA membrane anchor was additionally replaced with that of Yersinia adhesin A (YadA). Constructs were cloned in E. coli, and hybrid protein expression was detected by immunoblotting, fluorescence microscopy, and flow cytometry. Functional analysis revealed that BadA hybrid proteins mediate autoagglutination and binding to collagen and endothelial cells. In vivo, expression of this BadA construct correlated with higher pathogenicity of E. coli in a Galleria mellonella infection model. PMID:24682330

  13. Localization of the domains of the Haemophilus ducreyi trimeric autotransporter DsrA involved in serum resistance and binding to the extracellular matrix proteins fibronectin and vitronectin.

    PubMed

    Leduc, Isabelle; Olsen, Bonnie; Elkins, Christopher

    2009-02-01

    Resisting the bactericidal activity of naturally occurring antibodies and complement of normal human serum is an important element in the evasion of innate immunity by bacteria. In the gram-negative mucosal pathogen Haemophilus ducreyi, serum resistance is mediated primarily by the trimeric autotransporter DsrA. DsrA also functions as an adhesin for the extracellular matrix proteins fibronectin and vitronectin and mediates attachment of H. ducreyi to keratinocytes. We sought to determine the domain(s) of the 236-residue DsrA protein required for serum resistance and extracellular matrix protein binding. A 140-amino-acid truncated protein containing only the C-terminal portion of the passenger domain and the entire translocator domain of DsrA exhibited binding to fibronectin and vitronectin and conferred serum resistance to an H. ducreyi serum-sensitive strain. A shorter DsrA construct consisting of only 128 amino acids was unable to bind to extracellular matrix proteins but was serum resistant. We concluded that neither fibronectin binding nor vitronectin binding is required for high-level serum resistance in H. ducreyi.

  14. Localization of the Domains of the Haemophilus ducreyi Trimeric Autotransporter DsrA Involved in Serum Resistance and Binding to the Extracellular Matrix Proteins Fibronectin and Vitronectin▿

    PubMed Central

    Leduc, Isabelle; Olsen, Bonnie; Elkins, Christopher

    2009-01-01

    Resisting the bactericidal activity of naturally occurring antibodies and complement of normal human serum is an important element in the evasion of innate immunity by bacteria. In the gram-negative mucosal pathogen Haemophilus ducreyi, serum resistance is mediated primarily by the trimeric autotransporter DsrA. DsrA also functions as an adhesin for the extracellular matrix proteins fibronectin and vitronectin and mediates attachment of H. ducreyi to keratinocytes. We sought to determine the domain(s) of the 236-residue DsrA protein required for serum resistance and extracellular matrix protein binding. A 140-amino-acid truncated protein containing only the C-terminal portion of the passenger domain and the entire translocator domain of DsrA exhibited binding to fibronectin and vitronectin and conferred serum resistance to an H. ducreyi serum-sensitive strain. A shorter DsrA construct consisting of only 128 amino acids was unable to bind to extracellular matrix proteins but was serum resistant. We concluded that neither fibronectin binding nor vitronectin binding is required for high-level serum resistance in H. ducreyi. PMID:19015257

  15. Dissociation of the trimeric gp41 ectodomain at the lipid-water interface suggests an active role in HIV-1 Env-mediated membrane fusion.

    PubMed

    Roche, Julien; Louis, John M; Grishaev, Alexander; Ying, Jinfa; Bax, Adriaan

    2014-03-04

    The envelope glycoprotein gp41 mediates the process of membrane fusion that enables entry of the HIV-1 virus into the host cell. The actual fusion process involves a switch from a homotrimeric prehairpin intermediate conformation, consisting of parallel coiled-coil helices, to a postfusion state where the ectodomains are arranged as a trimer of helical hairpins, adopting a six-helix bundle (6HB) state. Here, we show by solution NMR spectroscopy that a water-soluble 6HB gp41 ectodomain binds to zwitterionic detergents that contain phosphocholine or phosphatidylcholine head groups and phospholipid vesicles that mimic T-cell membrane composition. Binding results in the dissociation of the 6HB and the formation of a monomeric state, where its two α-helices, N-terminal heptad repeat (NHR) and C-terminal heptad repeat (CHR), become embedded in the lipid-water interface of the virus and host cell. The atomic structure of the gp41 ectodomain monomer, based on NOE distance restraints and residual dipolar couplings, shows that the NHR and CHR helices remain mostly intact, but they completely lose interhelical contacts. The high affinity of the ectodomain helices for phospholipid surfaces suggests that unzippering of the prehairpin intermediate leads to a state where the NHR and CHR helices become embedded in the host cell and viral membranes, respectively, thereby providing a physical force for bringing these membranes into close juxtaposition before actual fusion.

  16. A Chimeric HIV-1 Envelope Glycoprotein Trimer with an Embedded Granulocyte-Macrophage Colony-stimulating Factor (GM-CSF) Domain Induces Enhanced Antibody and T Cell Responses*

    PubMed Central

    van Montfort, Thijs; Melchers, Mark; Isik, Gözde; Menis, Sergey; Huang, Po-Ssu; Matthews, Katie; Michael, Elizabeth; Berkhout, Ben; Schief, William R.; Moore, John P.; Sanders, Rogier W.

    2011-01-01

    An effective HIV-1 vaccine should ideally induce strong humoral and cellular immune responses that provide sterilizing immunity over a prolonged period. Current HIV-1 vaccines have failed in inducing such immunity. The viral envelope glycoprotein complex (Env) can be targeted by neutralizing antibodies to block infection, but several Env properties limit the ability to induce an antibody response of sufficient quantity and quality. We hypothesized that Env immunogenicity could be improved by embedding an immunostimulatory protein domain within its sequence. A stabilized Env trimer was therefore engineered with the granulocyte-macrophage colony-stimulating factor (GM-CSF) inserted into the V1V2 domain of gp120. Probing with neutralizing antibodies showed that both the Env and GM-CSF components of the chimeric protein were folded correctly. Furthermore, the embedded GM-CSF domain was functional as a cytokine in vitro. Mouse immunization studies demonstrated that chimeric EnvGM-CSF enhanced Env-specific antibody and T cell responses compared with wild-type Env. Collectively, these results show that targeting and activation of immune cells using engineered cytokine domains within the protein can improve the immunogenicity of Env subunit vaccines. PMID:21515681

  17. Trimeric G protein-CARMA1 axis links smoothened, the hedgehog receptor transducer, to NF-κB activation in diffuse large B-cell lymphoma.

    PubMed

    Qu, Changju; Liu, Yadong; Kunkalla, Kranthi; Singh, Rajesh R; Blonska, Marzenna; Lin, Xin; Agarwal, Nitin Kumar; Vega, Francisco

    2013-06-06

    Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoid malignancy in adults. Aberrant activation of Hedgehog (Hh) and nuclear factor (NF)-κB pathways is ubiquitously observed and known to mediate tumor growth, survival, and chemoresistance in DLBCL. Here, we find that activation of Hh signaling is positively correlated with NF-κB pathway in DLBCL tumors, and that smoothened (SMO), the signal transducer subunit of Hh pathway, contributes to NF-κB activation through recruiting G protein subunits Gαi and Gα12 to activate PKCβ/CARMA1/TRAF6/NEMO signaling axis followed by assembling of the CARMA1/BCL10/MALT1/TRAF6 complex to SMO. Moreover, functional inhibition of SMO enhances the cytotoxic effects of NF-κB inhibitor. Altogether, our study reveals a noncanonical Hh signaling pathway in which SMO activates trimeric G proteins and CARMA1-associated signaling complex, leading to NF-κB activation. This signaling cascade contributes to the survival of DLBCL and may serve as a potential target for combination therapies in DLBCL.

  18. Bulge-out structures in the single-stranded trimer AUA and in the duplex (CUGGUGCGG).(CCGCCCAG). A model-building and NMR study.

    PubMed Central

    van den Hoogen, Y T; van Beuzekom, A A; de Vroom, E; van der Marel, G A; van Boom, J H; Altona, C

    1988-01-01

    Model-building studies were carried out on the trimer AUA. Bulge-out structures which allow incorporation into a continuous RNA helix were generated and energy-minimized. All geometrical features obtained by previous NMR studies on purine-pyrimidine-purine sequences are accounted for in these models. One of the models was used to fit into a double helical fragment. Only minor changes were necessary to construct a central bulge-out in an otherwise intact duplex. NMR and model-building studies were performed on the duplex (CUGGUGCGG).(CCGCCCAG) which contains an unpaired uridine residue. NOE data, chemical-shift profiles and imino-proton resonances provided evidence that the extra U is bulged out of the duplex. The relatively small dispersion in 31P chemical shifts (approximately equal to 0.7 ppm) indicate the absence of t/g or g/t combinations for the phosphodiester angles zeta/alpha. An energy-minimized model of the duplex, which fits the present collection of data, is presented. PMID:3387215

  19. The structure of E. coli IgG-binding protein D suggests a general model for bending and binding in trimeric autotransporter adhesins.

    PubMed

    Leo, Jack C; Lyskowski, Andrzej; Hattula, Katarina; Hartmann, Marcus D; Schwarz, Heinz; Butcher, Sarah J; Linke, Dirk; Lupas, Andrei N; Goldman, Adrian

    2011-07-13

    The Escherichia coli Ig-binding (Eib) proteins are trimeric autotransporter adhesins (TAAs) and receptors for IgG Fc. We present the structure of a large fragment of the passenger domain of EibD, the first TAA structure to have both a YadA-like head domain and the entire coiled-coil stalk. The stalk begins as a right-handed superhelix, but switches handedness halfway down. An unexpected β-minidomain joins the two and inserts a ∼120° rotation such that there is no net twist between the beginning and end of the stalk. This may be important in folding and autotransport. The surprisingly large cavities we found in EibD and other TAAs may explain how TAAs bend to bind their ligands. We identified how IgA and IgG bind and modeled the EibD-IgG Fc complex. We further show that EibD promotes autoagglutination and biofilm formation and forms a fibrillar layer covering the cell surface making zipper-like contacts between cells.

  20. C-terminal truncated cannabinoid receptor 1 coexpressed with G protein trimer in Sf9 cells exists in a precoupled state and shows constitutive activity.

    PubMed

    Chillakuri, Chandramouli Reddy; Reinhart, Christoph; Michel, Hartmut

    2007-12-01

    We have investigated the existence of a precoupled form of the distal C-terminal truncated cannabinoid receptor 1 (CB1-417) and heterotrimeric G proteins in a heterologous insect cell expression system. CB1-417 showed higher production levels than the full-length receptor. The production levels obtained in our expression system were double the values reported in the literature. We also observed that at least the distal C-terminus of the receptor was not involved in receptor dimerization, as was predicted in the literature. Using fluorescence resonance energy transfer, we found that CB1-417 and Galpha(i1)beta(1)gamma(2) proteins were colocalized in the cells. GTPgammaS binding assays with the Sf9 cell membranes containing CB1-417 and the G protein trimer showed that the receptor could constitutively activate the Galpha(i1) protein in the absence of agonists. A CB1-specific antagonist (SR 141716A) inhibited this constitutive activity of the truncated receptor. We found that the CB1-417/Galpha(i1)beta(1)gamma(2) complex could be solubilized from Sf9 cell membranes and coimmunoprecipitated. In this study, we have proven that the receptor and G proteins can be coexpressed in higher yields using Sf9 cells, and that the protein complex is stable in detergent solution. Thus, our system can be used to produce sufficient quantities of the protein complex to start structural studies.

  1. Crystal structure of a trimeric archaeal adenylate kinase from the mesophile Methanococcus maripaludis with an unusually broad functional range and thermal stability.

    PubMed

    Davlieva, Milya; Shamoo, Yousif

    2010-02-01

    The structure of the trimeric adenylate kinase from the Archaebacteria Methanococcus mariplaludis (AK(MAR)) has been solved to 2.5-A resolution and the temperature dependent stability and kinetics of the enzyme measured. The K(M) and V(max) of AK(MAR) exhibit only modest temperature dependence from 30 degrees -60 degrees C. Although M. mariplaludis is a mesophile with a maximum growth temperature of 43 degrees C, AK(MAR) has a very broad functional range and stability (T(m) = 74.0 degrees C) that are more consistent with a thermophilic enzyme with high thermostability and exceptional activity over a wide range of temperatures, suggesting that this microbe may have only recently invaded a mesophilic niche and has yet to fully adapt. A comparison of the Local Structural Entropy (LSE) for AK(MAR) to the related adenylate kinases from the mesophile Methanococcus voltae and thermophile Methanococcus thermolithotrophicus show that changes in LSE are able to fully account for the intermediate stability of AK(MAR) and highlights a general mechanism for protein adaptation in this class of enzymes.

  2. Burkholderia cenocepacia K56-2 trimeric autotransporter adhesin BcaA binds TNFR1 and contributes to induce airway inflammation.

    PubMed

    Mil-Homens, Dalila; Pinto, Sandra N; Matos, Rute G; Arraiano, Cecília; Fialho, Arsenio M

    2017-04-01

    Chronic lung disease caused by persistent bacterial infections is a major cause of morbidity and mortality in patients with cystic fibrosis (CF). CF pathogens acquire antibiotic resistance, overcome host defenses, and impose uncontrolled inflammation that ultimately may cause permanent damage of lungs' airways. Among the multiple CF-associated pathogens, Burkholderia cenocepacia and other Burkholderia cepacia complex bacteria have become prominent contributors of disease progression. Here, we demonstrate that BcaA, a trimeric autotransporter adhesin (TAA) from the epidemic strain B. cenocepacia K56-2, is a tumor necrosis factor receptor 1-interacting protein able to regulate components of the tumor necrosis factor signaling pathway and ultimately leading to a significant production of the proinflammatory cytokine IL-8. Notably, this study is the first to demonstrate that a protein belonging to the TAA family is involved in the induction of the inflammatory response during B. cenocepacia infections, contributing to the success of the pathogen. Moreover, our results reinforce the relevance of the TAA BcaA as a multifunctional protein with a major role in B. cenocepacia virulence.

  3. Dimers or trimers? A characterization of the halogen bonded complexes of CF3X (X = I or Br) with dimethyl ether and acetone in cryosolutions

    NASA Astrophysics Data System (ADS)

    De Beuckeleer, Liene I.; Herrebout, Wouter A.

    2017-01-01

    Acetone molecules dissolved in liquid krypton are inclined to self-associate into dimers. This behavior affects its use as a prototype Lewis base in studies of weak intermolecular interactions. In this study infrared spectra of mixed solutions of dimethyl ether and CF3X and of acetone and CF3X (with X = I or Br) dissolved in liquid argon and liquid krypton are recorded at constant temperature. The dataset for dimethyl ether is used to validate a numerical method based on least-squares fitting of a model including contributions of both monomers and a heterodimer with 1:1 stoichiometry. The resulting monomer and dimer spectra show excellent agreement with previous studies found in literature. The analysis of the dataset for acetone requires an extension of the model with contributions for the acetone homodimer and for (acetone)2·CF3X and acetone·(CF3X)2 trimers. The results show that many signals for acetone·CF3I and (acetone)2·CF3I are observed, while only a few bands due to acetone·(CF3I)2 occur. The use of numerical approaches adjusted to the specificities of a mixture of two compounds allows to reliably resolve overlapping spectra of monomers and heterocomplexes and characterizing heterocomplex features that could not be deduced using earlier methods. To support the assignments made, ab initio calculations predicting geometries, relative stabilities and harmonic vibrational frequencies for the species envisaged are performed.

  4. The BtaF Trimeric Autotransporter of Brucella suis Is Involved in Attachment to Various Surfaces, Resistance to Serum and Virulence

    PubMed Central

    Ruiz-Ranwez, Verónica; Posadas, Diana M.; Estein, Silvia M.; Abdian, Patricia L.; Martin, Fernando A.; Zorreguieta, Angeles

    2013-01-01

    The adhesion of bacterial pathogens to host cells is an event that determines infection, and ultimately invasion and intracellular multiplication. Several evidences have recently shown that this rule is also truth for the intracellular pathogen Brucella. Brucella suis displays the unipolar BmaC and BtaE adhesins, which belong to the monomeric and trimeric autotransporter (TA) families, respectively. It was previously shown that these adhesins are involved in bacterial adhesion to host cells and components of the extracellular matrix (ECM). In this work we describe the role of a new member of the TA family of B. suis (named BtaF) in the adhesive properties of the bacterial surface. BtaF conferred the bacteria that carried it a promiscuous adhesiveness to various ECM components and the ability to attach to an abiotic surface. Furthermore, BtaF was found to participate in bacterial adhesion to epithelial cells and was required for full virulence in mice. Similar to BmaC and BtaE, the BtaF adhesin was expressed in a small subpopulation of bacteria, and in all cases, it was detected at the new pole generated after cell division. Interestingly, BtaF was also implicated in the resistance of B. suis to porcine serum. Our findings emphasize the impact of TAs in the Brucella lifecycle. PMID:24236157

  5. The intrinsic factor-vitamin B12 receptor, cubilin, is assembled into trimers via a coiled-coil alpha-helix.

    PubMed

    Lindblom, A; Quadt, N; Marsh, T; Aeschlimann, D; Mörgelin, M; Mann, K; Maurer, P; Paulsson, M

    1999-03-05

    A large protein was purified from bovine kidney, using selective extraction with EDTA to solubilize proteins anchored by divalent cation-dependent interactions. An antiserum raised against the purified protein labeled the apical cell surface of the epithelial cells in proximal tubules and the luminal surface of small intestine. Ten peptide sequences, derived from the protein, all matched the recently published sequences for rat (Moestrup, S. K., Kozyraki, R., Kristiansen, M., Kaysen, J. H., Holm Rasmussen, H., Brault, D., Pontillon, F., Goda, F. O., Christensen, E. I., Hammond, T. G., and Verroust, P. J. (1998) J. Biol. Chem. 273, 5235-5242) and human cubilin, a receptor for intrinsic factor-vitamin B12 complexes, identifying the protein as bovine cubilin. In electron microscopy, a three-armed structure was seen, indicating an oligomerization of three identical subunits. This model was supported by the Mr values of about 1,500,000 for the intact protein and 440,000 for its subunits obtained by analytical ultracentrifugation. In a search for a potential assembly domain, we identified a region of heptad repeats in the N-terminal part of the cubilin sequence. Computer-assisted analysis supported the presence of a coiled-coil alpha-helix between amino acids 103 and 132 of the human cubilin sequence and predicted the formation of a triple coiled-coil. We therefore conclude that cubilin forms a noncovalent trimer of identical subunits connected by an N-terminal coiled-coil alpha-helix.

  6. Photoionization of cold gas phase coronene and its clusters: Autoionization resonances in monomer, dimer, and trimer and electronic structure of monomer cation

    SciTech Connect

    Bréchignac, Philippe Falvo, Cyril; Parneix, Pascal; Pino, Thomas; Pirali, Olivier; Garcia, Gustavo A.; Nahon, Laurent; Joblin, Christine; Kokkin, Damian; Bonnamy, Anthony; Mulas, Giacomo

    2014-10-28

    Polycyclic aromatic hydrocarbons (PAHs) are key species encountered in a large variety of environments such as the Interstellar Medium (ISM) and in combustion media. Their UV spectroscopy and photodynamics in neutral and cationic forms are important to investigate in order to learn about their structure, formation mechanisms, and reactivity. Here, we report an experimental photoelectron-photoion coincidence study of a prototypical PAH molecule, coronene, and its small clusters, in a molecular beam using the vacuum ultraviolet (VUV) photons provided by the SOLEIL synchrotron facility. Mass-selected high resolution threshold photoelectron (TPES) and total ion yield spectra were obtained and analyzed in detail. Intense series of autoionizing resonances have been characterized as originating from the monomer, dimer, and trimer neutral species, which may be used as spectral fingerprints for their detection in the ISM by VUV absorption spectroscopy. Finally, a full description of the electronic structure of the monomer cation was made and discussed in detail in relation to previous spectroscopic optical absorption data. Tentative vibrational assignments in the near-threshold TPES spectrum of the monomer have been made with the support of a theoretical approach based on density functional theory.

  7. TssK Is a Trimeric Cytoplasmic Protein Interacting with Components of Both Phage-like and Membrane Anchoring Complexes of the Type VI Secretion System*

    PubMed Central

    Zoued, Abdelrahim; Durand, Eric; Bebeacua, Cecilia; Brunet, Yannick R.; Douzi, Badreddine; Cambillau, Christian; Cascales, Eric; Journet, Laure

    2013-01-01

    The Type VI secretion system (T6SS) is a macromolecular machine that mediates bacteria-host or bacteria-bacteria interactions. The T6SS core apparatus assembles from 13 proteins that form two sub-assemblies: a phage-like complex and a trans-envelope complex. The Hcp, VgrG, TssE, and TssB/C subunits are structurally and functionally related to components of the tail of contractile bacteriophages. This phage-like structure is thought to be anchored to the membrane by a trans-envelope complex composed of the TssJ, TssL, and TssM proteins. However, how the two sub-complexes are connected remains unknown. Here we identify TssK, a protein that establishes contacts with the two T6SS sub-complexes through direct interactions with TssL, Hcp, and TssC. TssK is a cytoplasmic protein assembling trimers that display a three-armed shape, as revealed by TEM and SAXS analyses. Fluorescence microscopy experiments further demonstrate the requirement of TssK for sheath assembly. Our results suggest a central role for TssK by linking both complexes during T6SS assembly. PMID:23921384

  8. Intravaginal immunization using the recombinant HIV-1 clade-C trimeric envelope glycoprotein CN54gp140 formulated within lyophilized solid dosage forms

    PubMed Central

    Donnelly, Louise; Curran, Rhonda M.; Tregoning, John S.; McKay, Paul F.; Cole, Tom; Morrow, Ryan J.; Kett, Vicky L.; Andrews, Gavin P.; Woolfson, A. David; Malcolm, R. Karl; Shattock, Robin J.

    2011-01-01

    Vaccine-mediated prevention of primary HIV-1 infection at the heterosexual mucosal portal of entry may be facilitated by highly optimised formulations or drug delivery devices for intravaginal (i.vag) immunization. Previously we described hydroxyethylcellulose (HEC)-based rheologically structured gel vehicles (RSVs) for vaginal immunization of an HIV-1 vaccine candidate, a soluble recombinant trimeric HIV-1 clade-C envelope glycoprotein designated CN54gp140. Here we investigated the efficacy of lyophilized solid dosage formulations (LSDFs) for prolonging antigen stability and as i.vag delivery modalities. LSDFs were designed and developed that upon i.vag administration they would reconstitute with the imbibing of vaginal fluid to mucoadhesive, site-retentive semi-solids. Mice were immunized with lyophilized equivalents of (i) RSVs, (ii) modified versions of the RSVs more suited to lyophilization (sodium carboxymethyl cellulose (NaCMC)-based gels) and (iii) Carbopol® gel, all containing CN54gp140. NaCMC-based LSDFs provided significantly enhanced antigen stability compared to aqueous-based RSVs. Rheological analysis indicated the NaCMC-based LSDFs would offer enhanced vaginal retention in woman compared to more conventional vaginal gel formulations. All LSDFs were well tolerated in the mouse model. Following i.vag administration, all LSDFs boosted systemic CN54gp140-specific antibody responses in sub-cutaneously primed mice. Induction of CN54gp140-specific antibody responses in the female genital tract was evident. Of all the LSDFs the fastest releasing which was lyophilized Carbopol® gel elicited immune responses comparable to buffer instillation of antigen suggesting that rather than slower sustained release, initial high burst release from the LSDFs may suffice. The boosting of specific immune responses upon i.vag administration indicates that LSDFs are viable mucosal vaccine delivery modalities promoting antigen stability and facilitating intimate exposure of

  9. BtaE, an Adhesin That Belongs to the Trimeric Autotransporter Family, Is Required for Full Virulence and Defines a Specific Adhesive Pole of Brucella suis

    PubMed Central

    Ruiz-Ranwez, Verónica; Posadas, Diana M.; Van der Henst, Charles; Estein, Silvia M.; Arocena, Gastón M.; Abdian, Patricia L.; Martín, Fernando A.; Sieira, Rodrigo; De Bolle, Xavier

    2013-01-01

    Brucella is responsible for brucellosis, one of the most common zoonoses worldwide that causes important economic losses in several countries. Increasing evidence indicates that adhesion of Brucella spp. to host cells is an important step to establish infection. We have previously shown that the BmaC unipolar monomeric autotransporter mediates the binding of Brucella suis to host cells through cell-associated fibronectin. Our genome analysis shows that the B. suis genome encodes several additional potential adhesins. In this work, we characterized a predicted trimeric autotransporter that we named BtaE. By expressing btaE in a nonadherent Escherichia coli strain and by phenotypic characterization of a B. suis ΔbtaE mutant, we showed that BtaE is involved in the binding of B. suis to hyaluronic acid. The B. suis ΔbtaE mutant exhibited a reduction in the adhesion to HeLa and A549 epithelial cells compared with the wild-type strain, and it was outcompeted by the wild-type strain in the binding to HeLa cells. The knockout btaE mutant showed an attenuated phenotype in the mouse model, indicating that BtaE is required for full virulence. BtaE was immunodetected on the bacterial surface at one cell pole. Using old and new pole markers, we observed that both the BmaC and BtaE adhesins are consistently associated with the new cell pole, suggesting that, in Brucella, the new pole is functionally differentiated for adhesion. This is consistent with the inherent polarization of this bacterium, and its role in the invasion process. PMID:23319562

  10. The catalytic effect of water, water dimers and water trimers on H2S + (3)O2 formation by the HO2 + HS reaction under tropospheric conditions.

    PubMed

    Zhang, Tianlei; Yang, Chen; Feng, Xukai; Kang, Jiaxin; Song, Liang; Lu, Yousong; Wang, Zhiyin; Xu, Qiong; Wang, Wenliang; Wang, Zhuqing

    2016-06-29

    In this article, the reaction mechanisms of H2S + (3)O2 formation by the HO2 + HS reaction without and with catalyst X (X = H2O, (H2O)2 and (H2O)3) have been investigated theoretically at the CCSD(T)/6-311++G(3df,2pd)//B3LYP/6-311+G(2df,2p) level of theory, coupled with rate constant calculations by using conventional transition state theory. Our results show that in the presence of catalyst X (X = H2O, (H2O)2 and (H2O)3) into the channel of H2S + (3)O2 formation, the reactions between the SH radical and HO2(H2O)n (n = 1-3) complexes are more favorable than the corresponding reactions of the HO2 radical with HS(H2O)n (n = 1-3) complexes due to the lower barrier of the former reactions and the higher concentrations of HO2(H2O)n (n = 1-3) complexes. Meanwhile, the catalytic effect of water, water dimers and water trimers is mainly taken from the contribution of a single water vapor molecule, since the total effective rate constant of HO2H2O + HS and H2OHO2 + HS reactions was, respectively, larger by 7-9 and 9-12 orders of magnitude than that of SH + HO2(H2O)2 and SH + HO2(H2O)3 reactions. Besides, the enhancement factor of water vapor is only 0.37% at 240 K, while at high temperatures, such as 425 K, the positive water vapor effect is enhanced up to 38.00%, indicating that at high temperatures the positive water effect is obvious under atmospheric conditions. Overall, these results show how water and water clusters catalyze the gas phase reactions under atmospheric conditions.

  11. Heteronuclear NMR assignments and secondary structure of the coiled coil trimerization domain from cartilage matrix protein in oxidized and reduced forms.

    PubMed Central

    Wiltscheck, R.; Kammerer, R. A.; Dames, S. A.; Schulthess, T.; Blommers, M. J.; Engel, J.; Alexandrescu, A. T.

    1997-01-01

    The C-terminal oligomerization domain of chicken cartilage matrix protein is a trimeric coiled coil comprised of three identical 43-residue chains. NMR spectra of the protein show equivalent magnetic environments for each monomer, indicating a parallel coiled coil structure with complete threefold symmetry. Sequence-specific assignments for 1H-, 15N-, and 13C-NMR resonances have been obtained from 2D 1H NOESY and TOCSY spectra, and from 3D HNCA, 15N NOESY-HSQC, and HCCH-TOCSY spectra. A stretch of alpha-helix encompassing five heptad repeats (35 residues) has been identified from intra-chain HN-HN and HN-H alpha NOE connectivities. 3JHNH alpha coupling constants, and chemical shift indices. The alpha-helix begins immediately downstream of inter-chain disulfide bonds between residues Cys 5 and Cys 7, and extends to near the C-terminus of the molecule. The threefold symmetry of the molecule is maintained when the inter-chain disulfide bonds that flank the N-terminus of the coiled coil are reduced. Residues Ile 21 through Glu 36 show conserved chemical shifts and NOE connectivities, as well as strong protection from solvent exchange in the oxidized and reduced forms of the protein. By contrast, residues Ile 10 through Val 17 show pronounced chemical shift differences between the oxidized and reduced protein. Strong chemical exchange NOEs between HN resonances and water indicate solvent exchange on time scales faster than 10 s, and suggests a dynamic fraying of the N-terminus of the coiled coil upon reduction of the disulfide bonds. Possible roles for the disulfide crosslinks of the oligomerization domain in the function of cartilage matrix protein are proposed. PMID:9260286

  12. Effects of a Remote Binding Partner on the Electric Field and Electric Field Gradient at AN Atom in a Weakly Bound Trimer: Microwave Spectroscopy and Quantum Mechanical Computations on Kr-SO_{3} and Kr-SO_{3}-CO

    NASA Astrophysics Data System (ADS)

    Mackenzie, Rebecca B.; Timp, Brooke A.; Leopold, Kenneth R.; Mo, Yirong

    2013-06-01

    Microwave spectra have been recorded for the C_{3v} symmetric complexes Kr-SO_{3} and Kr-SO_{3}-CO. The Kr-S distances are 3.438(3) Å in Kr-SO_{3} and 3.488(6) Å in Kr-SO_{3}-CO. Thus, the addition of CO to Kr-SO_{3} increases the Kr-S distance by 0.050(9) Å. In contrast, the C-S distance in the trimer, 2.871(9) Å, is the same as that previously determined for SO_{3}-CO to within the estimated uncertainties. Observed values of the ^{83}Kr nuclear quadrupole coupling constants provide direct probes of the electric field gradient at the Kr nucleus. We find that, although the Kr and CO in the trimer are on opposite sides of the SO_{3} and are thus not in direct contact, the addition of CO to Kr-SO_{3} reduces the electric field gradient at the Kr nucleus by 18%. Calculations using the Block Localized Wavefunction decomposition method are used to understand the physical origins of this change. While the magnitudes of both the electric field and the electric field gradient at the Kr nucleus decrease upon addition of the CO to Kr-SO_{3}, the changes arise from different and rather complex combinations of geometrical distortion, electrostatic, polarization, and electron transfer effects. For the electric field gradient, polarization and structural change in the Kr-SO_{3} make the primary contributions while for the electric field itself, the change in the electrostatic contribution has the largest effect. The calculated binding energies are additive, with that of the trimer very nearly equal to the sum of the binding energies of Kr-SO_{3} and SO_{3}-CO.

  13. Virus-Like Particles Displaying Trimeric Simian Immunodeficiency Virus (SIV) Envelope gp160 Enhance the Breadth of DNA/Modified Vaccinia Virus Ankara SIV Vaccine-Induced Antibody Responses in Rhesus Macaques

    PubMed Central

    Iyer, Smita S.; Gangadhara, Sailaja; Victor, Blandine; Shen, Xiaoying; Chen, Xuemin; Nabi, Rafiq; Kasturi, Sudhir P.; Sabula, Michael J.; Labranche, Celia C.; Reddy, Pradeep B. J.; Tomaras, Georgia D.; Montefiori, David C.; Spearman, Paul; Pulendran, Bali; Kozlowski, Pamela A.

    2016-01-01

    ABSTRACT The encouraging results of the RV144 vaccine trial have spurred interest in poxvirus prime-protein boost human immunodeficiency virus (HIV) vaccine modalities as a strategy to induce protective immunity. Because vaccine-induced protective immunity is critically determined by HIV envelope (Env) conformation, significant efforts are directed toward generating soluble trimeric Env immunogens that assume native structures. Using the simian immunodeficiency virus (SIV)-macaque model, we tested the immunogenicity and efficacy of sequential immunizations with DNA (D), modified vaccinia virus Ankara (MVA) (M), and protein immunogens, all expressing virus-like particles (VLPs) displaying membrane-anchored trimeric Env. A single VLP protein boost displaying trimeric gp160 adjuvanted with nanoparticle-encapsulated Toll-like receptor 4/7/8 (TLR4/7/8) agonists, administered 44 weeks after the second MVA immunization, induced up to a 3-fold increase in Env-specific IgG binding titers in serum and mucosa. Importantly, the VLP protein boost increased binding antibody against scaffolded V1V2, antibody-dependent phagocytic activity against VLP-coated beads, and antibody breadth and neutralizing antibody titers against homologous and heterologous tier 1 SIVs. Following 5 weekly intrarectal SIVmac251 challenges, two of seven DNA/MVA and VLP (DM+VLP)-vaccinated animals were completely protected compared to productive infection in all seven DM-vaccinated animals. Vaccinated animals demonstrated stronger acute viral pulldown than controls, but a trend for higher acute viremia was observed in the DM+VLP group, likely due to a slower recall of Gag-specific CD8 T cells. Our findings support immunization with VLPs containing trimeric Env as a strategy to augment protective antibody but underscore the need for optimal engagement of CD8 T cells to achieve robust early viral control. IMPORTANCE The development of an effective HIV vaccine remains a global necessity for preventing HIV

  14. Bartonella henselae trimeric autotransporter adhesin BadA expression interferes with effector translocation by the VirB/D4 type IV secretion system.

    PubMed

    Lu, Yun-Yueh; Franz, Bettina; Truttmann, Matthias C; Riess, Tanja; Gay-Fraret, Jérémie; Faustmann, Marco; Kempf, Volkhard A J; Dehio, Christoph

    2013-05-01

    The Gram-negative, zoonotic pathogen Bartonella henselae is the aetiological agent of cat scratch disease, bacillary angiomatosis and peliosis hepatis in humans. Two pathogenicity factors of B. henselae - each displaying multiple functions in host cell interaction - have been characterized in greater detail: the trimeric autotransporter Bartonella adhesin A (BadA) and the type IV secretion system VirB/D4 (VirB/D4 T4SS). BadA mediates, e.g. binding to fibronectin (Fn), adherence to endothelial cells (ECs) and secretion of vascular endothelial growth factor (VEGF). VirB/D4 translocates several Bartonella effector proteins (Beps) into the cytoplasm of infected ECs, resulting, e.g. in uptake of bacterial aggregates via the invasome structure, inhibition of apoptosis and activation of a proangiogenic phenotype. Despite this knowledge of the individual activities of BadA or VirB/D4 it is unknown whether these major virulence factors affect each other in their specific activities. In this study, expression and function of BadA and VirB/D4 were analysed in a variety of clinical B. henselae isolates. Data revealed that most isolates have lost expression of either BadA or VirB/D4 during in vitro passages. However, the phenotypic effects of coexpression of both virulence factors was studied in one clinical isolate that was found to stably coexpress BadA and VirB/D4, as well as by ectopic expression of BadA in a strain expressing VirB/D4 but not BadA. BadA, which forms a dense layer on the bacterial surface, negatively affected VirB/D4-dependent Bep translocation and invasome formation by likely preventing close contact between the bacterial cell envelope and the host cell membrane. In contrast, BadA-dependent Fn binding, adhesion to ECs and VEGF secretion were not affected by a functional VirB/D4 T4SS. The obtained data imply that the essential virulence factors BadA and VirB/D4 are likely differentially expressed during different stages of the infection cycle of

  15. A novel prodrug strategy for extremely hydrophobic agents: conjugation to symmetrically branched glycerol trimer improves pharmacological and pharmacokinetic properties of fenofibrate.

    PubMed

    Miyamoto, Licht; Watanabe, Masashi; Taoka, Chiaki; Kono, Mai; Tomida, Yosuke; Matsushita, Tsuyoshi; Kamiya, Masaki; Hattori, Hatsuhiko; Ishizawa, Keisuke; Abe, Shinji; Nemoto, Hisao; Tsuchiya, Koichiro

    2013-07-01

    Management of a lipophilic-hydrophilic balance is a key element in drug design to achieve desirable pharmacokinetic characters. Therefore we have created unique modular molecules, symmetrically branched oligoglycerols (BGL), as an alternative way to endow hydrophobic molecules with sufficient hydrophilicity. We have successfully demonstrated amelioration of the water solubility and thermal stability of several hydrophobic agents by covalent conjugation to BGL so far. However, it has not been clarified whether the molecular modification by BGL also improves the pharmacological and/or pharmacokinetic properties indeed. Recently, we synthesized a novel BGL-prodrug derivative of fenofibrate, which is an antihyperlipidemic agent and one of the most hydrophobic medicinal compounds currently used clinically, by conjugating fenofibric acid to symmetrically branched glycerol trimer (BGL003), the simplest BGL. We have previously demonstrated that the hydrophilicity and water solubility of fenofibrate are improved more than 2000 times just by conjugation to the BGL003. To verify our hypothesis that the prodrug strategy with BGL should improve pharmacological efficacy and pharmacokinetic properties of extremely hydrophobic agents such as fenofibrate by the rise in hydrophilicity, we evaluated the BGL003-prodrug derivative of fenofibrate (FF-BGL) using rodent models. Here we demonstrate that the lipid-lowering effects of fenofibrate are much potentiated by chemical conjugation to BGL003 without exhibiting significant toxicity. Plasma concentration of fenofibric acid, an active metabolite of fenofibrate, after single oral administration of FF-BGL was more than 3 times higher than that of fenofibrate, in accordance. In fasting rats, plasma concentration of fenofibric acid after fenofibrate administration was curtailed into less than half of that in ad libitum-fed rats, while FF-BGL showed about the same plasma level even in the starving rats. This is the first report showing that

  16. F(ab')2 fragment of a gp41 NHR-trimer-induced IgM monoclonal antibody neutralizes HIV-1 infection and blocks viral fusion by targeting the conserved gp41 pocket.

    PubMed

    Lu, Lu; Wei, Meili; Chen, Yanxia; Xiong, Weiliang; Yu, Fei; Qi, Zhi; Jiang, Shibo; Pan, Chungen

    2013-11-01

    Using a recombinant protein N46FdFc that mimics the HIV-1 gp41 N-helix trimer to immunize mice, we identified the first IgM monoclonal antibody 18D3 that specifically bound to the conserved gp41 pocket. Its F(ab')2 fragment potently inhibited HIV-1 Env-mediated cell-cell fusion and neutralized infection by laboratory-adapted and primary HIV-1 isolates with different subtypes and tropism, including the T20-resistant variants. This F(ab')2 fragment can be used to develop a bispecific broad neutralizing monoclonal antibody or HIV-1 inactivator as a novel immunotherapeutic for treatment and prevention of HIV-1 infection.

  17. Theoretical description of hydrogen bonding in oxalic acid dimer and trimer based on the combined extended-transition-state energy decomposition analysis and natural orbitals for chemical valence (ETS-NOCV).

    PubMed

    Mitoraj, Mariusz P; Kurczab, Rafał; Boczar, Marek; Michalak, Artur

    2010-11-01

    In the present study we have analyzed hydrogen bonding in dimer and trimer of oxalic acid, based on a recently proposed charge and energy decomposition scheme (ETS-NOCV). In the case of a dimer, two conformations, α and β, were considered. The deformation density contributions originating from NOCV's revealed that the formation of hydrogen bonding is associated with the electronic charge deformation in both the σ-(Δρ(σ)) and π-networks (Δρ(π)). It was demonstrated that σ-donation is realized by electron transfer from the lone pair of oxygen on one monomer into the empty P*(H-O) orbital of the second oxalic acid fragment. In addition, a covalent contribution is observed by the density transfer from hydrogen of H-O group in one oxalic acid monomer to the oxygen atom of the second fragment. The resonance assisted component (Δρ(π)), is based on the transfer of electron density from the π-orbital localized on the oxygen of OH on one oxalic acid monomer to the oxygen atom of the other fragment. ETS-NOCV allowed to conclude that the σ(O---HO) component is roughly eight times as important as π (RAHB) contribution in terms of energetic estimation. The electrostatic factor (ΔE(elstat)) is equally as important as orbital interaction term (ΔE(orb)). Finally, comparing β-dimer of oxalic acid with trimer we found practically no difference concerning each of the O---HO bonds, neither qualitative nor quantitative.

  18. Virological and Immunological Characterization of Novel NYVAC-Based HIV/AIDS Vaccine Candidates Expressing Clade C Trimeric Soluble gp140(ZM96) and Gag(ZM96)-Pol-Nef(CN54) as Virus-Like Particles

    PubMed Central

    Perdiguero, Beatriz; Gómez, Carmen Elena; Cepeda, Victoria; Sánchez-Sampedro, Lucas; García-Arriaza, Juan; Mejías-Pérez, Ernesto; Jiménez, Victoria; Sánchez, Cristina; Sorzano, Carlos Óscar S.; Oliveros, Juan Carlos; Delaloye, Julie; Roger, Thierry; Calandra, Thierry; Asbach, Benedikt; Wagner, Ralf; Kibler, Karen V.; Jacobs, Bertram L.; Pantaleo, Giuseppe

    2014-01-01

    ABSTRACT The generation of vaccines against HIV/AIDS able to induce long-lasting protective immunity remains a major goal in the HIV field. The modest efficacy (31.2%) against HIV infection observed in the RV144 phase III clinical trial highlighted the need for further improvement of HIV vaccine candidates, formulation, and vaccine regimen. In this study, we have generated two novel NYVAC vectors, expressing HIV-1 clade C gp140(ZM96) (NYVAC-gp140) or Gag(ZM96)-Pol-Nef(CN54) (NYVAC-Gag-Pol-Nef), and defined their virological and immunological characteristics in cultured cells and in mice. The insertion of HIV genes does not affect the replication capacity of NYVAC recombinants in primary chicken embryo fibroblast cells, HIV sequences remain stable after multiple passages, and HIV antigens are correctly expressed and released from cells, with Env as a trimer (NYVAC-gp140), while in NYVAC-Gag-Pol-Nef-infected cells Gag-induced virus-like particles (VLPs) are abundant. Electron microscopy revealed that VLPs accumulated with time at the cell surface, with no interference with NYVAC morphogenesis. Both vectors trigger specific innate responses in human cells and show an attenuation profile in immunocompromised adult BALB/c and newborn CD1 mice after intracranial inoculation. Analysis of the immune responses elicited in mice after homologous NYVAC prime/NYVAC boost immunization shows that recombinant viruses induced polyfunctional Env-specific CD4 or Gag-specific CD8 T cell responses. Antibody responses against gp140 and p17/p24 were elicited. Our findings showed important insights into virus-host cell interactions of NYVAC vectors expressing HIV antigens, with the activation of specific immune parameters which will help to unravel potential correlates of protection against HIV in human clinical trials with these vectors. IMPORTANCE We have generated two novel NYVAC-based HIV vaccine candidates expressing HIV-1 clade C trimeric soluble gp140 (ZM96) and Gag(ZM96)-Pol

  19. Characterization of supramolecular (H2O)18 water morphology and water-methanol (H2O)15(CH3OH)3 clusters in a novel phosphorus functionalized trimeric amino acid host.

    PubMed

    Raghuraman, Kannan; Katti, Kavita K; Barbour, Leonard J; Pillarsetty, Nagavarakishore; Barnes, Charles L; Katti, Kattesh V

    2003-06-11

    Phosphorus functionalized trimeric alanine compounds (l)- and (d)-P(CH(2)NHCH(CH(3))COOH)(3) 2 are prepared in 90% yields by the Mannich reaction of Tris(hydroxymethyl)phosphine 1 with (l)- or (d)- Alanine in aqueous media. The hydration properties of (l)-2 and (d)-2 in water and water-methanol mixtures are described. The crystal structure analysis of (l)-2.4H(2)O, reveals that the alanine molecules pack to form two-dimensional bilayers running parallel to (001). The layered structural motif depicts two closely packed monolayers of 2 each oriented with its phosphorus atoms projected at the center of the bilayer and adjacent monolayers are held together by hydrogen bonds between amine and carboxylate groups. The water bilayers are juxtaposed with the H-bonded alanine trimers leading to 18-membered (H(2)O)(18) water rings. Exposure of aqueous solution of (l)-2 and (d)-2 to methanol vapors resulted in closely packed (l)-2 and (d)-2 solvated with mixed water-methanol (H(2)O)(15)(CH(3)OH)(3) clusters. The O-O distances in the mixed methanol-water clusters of (l)-2.3H(2)O.CH(3)OH and (d)-2.3H(2)O.CH(3)OH (O-O(average) = 2.857 A) are nearly identical to the O-O distance observed in the supramolecular (H(2)O)(18) water structure (O-O(average) = 2.859 A) implying the retention of the hydrogen bonded structure in water despite the accommodation of hydrophobic methanol groups within the supramolecular (H(2)O)(15)(CH(3)OH)(3) framework. The O-O distances in (l)-2.3H(2)O.CH(3)OH and (d)-2.3H(2)O.CH(3)OH and in (H(2)O)(18) are very close to the O-O distance reported for liquid water (2.85 A).

  20. Long-Term Acclimation of the Cyanobacterium Synechocystis sp. PCC 6803 to High Light Is Accompanied by an Enhanced Production of Chlorophyll That Is Preferentially Channeled to Trimeric Photosystem I1[W

    PubMed Central

    Kopečná, Jana; Komenda, Josef; Bučinská, Lenka; Sobotka, Roman

    2012-01-01

    Cyanobacteria acclimate to high-light conditions by adjusting photosystem stoichiometry through a decrease of photosystem I (PSI) abundance in thylakoid membranes. As PSI complexes bind the majority of chlorophyll (Chl) in cyanobacterial cells, it is accepted that the mechanism controlling PSI level/synthesis is tightly associated with the Chl biosynthetic pathway. However, how Chl is distributed to photosystems under different light conditions remains unknown. Using radioactive labeling by 35S and by 14C combined with native/two-dimensional electrophoresis, we assessed the synthesis and accumulation of photosynthetic complexes in parallel with the synthesis of Chl in Synechocystis sp. PCC 6803 cells acclimated to different light intensities. Although cells acclimated to higher irradiances (150 and 300 μE m−2s−1) exhibited markedly reduced PSI content when compared with cells grown at lower irradiances (10 and 40 μE m−2 s−1), they grew much faster and synthesized significantly more Chl, as well as both photosystems. Interestingly, even under high irradiance, almost all labeled de novo Chl was localized in the trimeric PSI, whereas only a weak Chl labeling in photosystem II (PSII) was accompanied by the intensive 35S protein labeling, which was much stronger than in PSI. These results suggest that PSII subunits are mostly synthesized using recycled Chl molecules previously released during PSII repair-driven protein degradation. In contrast, most of the fresh Chl is utilized for synthesis of PSI complexes likely to maintain a constant level of PSI during cell proliferation. PMID:23037506

  1. [68Ga]FSC-(RGD)3 a trimeric RGD peptide for imaging αvβ3 integrin expression based on a novel siderophore derived chelating scaffold—synthesis and evaluation

    PubMed Central

    Knetsch, Peter A.; Zhai, Chuangyan; Rangger, Christine; Blatzer, Michael; Haas, Hubertus; Kaeopookum, Piriya; Haubner, Roland; Decristoforo, Clemens

    2015-01-01

    Over the last years Gallium-68 (68Ga) has received tremendous attention for labeling of radiopharmaceuticals for positron emission tomography (PET). 68Ga labeling of biomolecules is currently based on bifunctional chelators containing aminocarboxylates (mainly DOTA and NOTA). We have recently shown that cyclic peptide siderophores have very good complexing properties for 68Ga resulting in high specific activities and excellent metabolic stabilities, in particular triacetylfusarinine-C (TAFC). We postulated, that, starting from its deacetylated form (Fusarinine-C (FSC)) trimeric bioconjugates are directly accessible to develop novel targeting peptide based 68Ga labeled radiopharmaceuticals. As proof of principle we report on the synthesis and 68Ga-radiolabeling of a trimeric FSC-RGD conjugate, [68Ga]FSC-(RGD)3, targeting αvβ3 integrin, which is highly expressed during tumor-induced angiogenesis. Synthesis of the RGD peptide was carried out applying solid phase peptide synthesis (SPPS), followed by the coupling to the siderophore [Fe]FSC via in situ activation using HATU/HOAt and DIPEA. Subsequent demetalation allowed radiolabeling of FSC-(RGD)3 with 68Ga. The radiolabeling procedure was optimized regarding peptide amount, reaction time, temperature as well buffer systems. For in vitro evaluation partition coefficient, protein binding, serum stability, αvβ3 integrin binding affinity, and tumor cell uptake were determined. For in vitro tests as well as for the biodistribution studies αvβ3 positive human melanoma M21 and αvβ3 negative M21-L cells were used. [68Ga]FSC-(RGD)3 was prepared with high radiochemical yield (> 98%). Distribution coefficient was − 3.6 revealing a hydrophilic character, and an IC50 value of 1.8 ± 0.6 nM was determined indicating a high binding affinity for αvβ3 integrin. [68Ga]FSC-(RGD)3 was stable in PBS (pH 7.4), FeCl3- and DTPA-solution as well as in fresh human serum at 37 °C for 2 hours. Biodistribution assay confirmed

  2. [(68)Ga]FSC-(RGD)3 a trimeric RGD peptide for imaging αvβ3 integrin expression based on a novel siderophore derived chelating scaffold-synthesis and evaluation.

    PubMed

    Knetsch, Peter A; Zhai, Chuangyan; Rangger, Christine; Blatzer, Michael; Haas, Hubertus; Kaeopookum, Piriya; Haubner, Roland; Decristoforo, Clemens

    2015-02-01

    Over the last years Gallium-68 ((68)Ga) has received tremendous attention for labeling of radiopharmaceuticals for positron emission tomography (PET). (68)Ga labeling of biomolecules is currently based on bifunctional chelators containing aminocarboxylates (mainly DOTA and NOTA). We have recently shown that cyclic peptide siderophores have very good complexing properties for (68)Ga resulting in high specific activities and excellent metabolic stabilities, in particular triacetylfusarinine-C (TAFC). We postulated, that, starting from its deacetylated form (Fusarinine-C (FSC)) trimeric bioconjugates are directly accessible to develop novel targeting peptide based (68)Ga labeled radiopharmaceuticals. As proof of principle we report on the synthesis and (68)Ga-radiolabeling of a trimeric FSC-RGD conjugate, [(68)Ga]FSC-(RGD)3, targeting αvβ3 integrin, which is highly expressed during tumor-induced angiogenesis. Synthesis of the RGD peptide was carried out applying solid phase peptide synthesis (SPPS), followed by the coupling to the siderophore [Fe]FSC via in situ activation using HATU/HOAt and DIPEA. Subsequent demetalation allowed radiolabeling of FSC-(RGD)3 with (68)Ga. The radiolabeling procedure was optimized regarding peptide amount, reaction time, temperature as well buffer systems. For in vitro evaluation partition coefficient, protein binding, serum stability, αvβ3 integrin binding affinity, and tumor cell uptake were determined. For in vitro tests as well as for the biodistribution studies αvβ3 positive human melanoma M21 and αvβ3 negative M21-L cells were used. [(68)Ga]FSC-(RGD)3 was prepared with high radiochemical yield (>98%). Distribution coefficient was -3.6 revealing a hydrophilic character, and an IC50 value of 1.8±0.6 nM was determined indicating a high binding affinity for αvβ3 integrin. [(68)Ga]FSC-(RGD)3 was stable in PBS (pH7.4), FeCl3- and DTPA-solution as well as in fresh human serum at 37°C for 2hours. Biodistribution assay

  3. Immunization with the Haemophilus ducreyi trimeric autotransporter adhesin DsrA with alum, CpG or imiquimod generates a persistent humoral immune response that recognizes the bacterial surface.

    PubMed

    Samo, Melissa; Choudhary, Neelima R; Riebe, Kristina J; Shterev, Ivo; Staats, Herman F; Sempowski, Gregory D; Leduc, Isabelle

    2016-02-24

    The Ducreyi serum resistance A (DsrA) protein of Haemophilus ducreyi belongs to a large family of multifunctional outer membrane proteins termed trimeric autotransporter adhesins responsible for resistance to the bactericidal activity of human complement (serum resistance), agglutination and adhesion. The ability of DsrA to confer serum resistance and bind extracellular matrix proteins lies in its N-terminal passenger domain. We have previously reported that immunization with a recombinant form of the passenger domain of DsrA, rNT-DsrA, in complete/incomplete Freund's adjuvant, protects against a homologous challenge in swine. We present herein the results of an immunogenicity study in mice aimed at investigating the persistence, type of immune response, and the effect of immunization route and adjuvants on surrogates of protection. Our results indicate that a 20 μg dose of rNT-DsrA administered with alum elicited antisera with comparable bacterial surface reactivity to that obtained with complete/incomplete Freund's adjuvant. At that dose, high titers and bacterial surface reactivity persisted for 211 days after the first immunization. Administration of rNT-DsrA with CpG or imiquimod as adjuvants elicited a humoral response with similar quantity and quality of antibodies (Abs) as seen with Freund's adjuvant. Furthermore, intramuscular administration of rNT-DsrA elicited high-titer Abs with significantly higher reactivity to the bacterial surface than those obtained with subcutaneous immunization. All rNT-DsrA/adjuvant combinations tested, save CpG, elicited a Th2-type response. Taken together, these findings show that a 20 μg dose of rNT-DsrA administered with the adjuvants alum, CpG or imiquimod elicits high-quality Abs with reactivity to the bacterial surface that could protect against an H. ducreyi infection.

  4. Magnetism of the spin-trimer compound CaNi 3(P 2O 7)2: Microscopic insight from combined 31P NMR and first-principles studies

    NASA Astrophysics Data System (ADS)

    Majumder, M.; Kanungo, S.; Ghoshray, A.; Ghosh, M.; Ghoshray, K.

    2015-03-01

    Magnetization, 31P nuclear magnetic resonance study, and first-principles electronic structure calculations have been performed in the spin-1 trimer chain compound CaNi3(P2O7 )2. Two separate spectra arising from magnetically and crystallographically inequivalent P sites are observed. In the ordered state, the resonance lines for both the P sites (P1 and P2) are found to be split into two, which is clear microscopic evidence of the development of two-sublattice AFM order below TM. A nonnegligible contribution of ferromagnetic hyperfine field and dipolar field have also been seen in the ordered state. The first-principles calculations show that the intratrimer (J1) and intertrimer interactions (J2) are of weak ferromagnetic type with the values 2.85 and 1.49 meV, respectively, whereas the interchain interaction (J3) is of strong antiferromagnetic type with a value of 5.63 meV. The anisotropy of the imaginary part of dynamical spin susceptibility around TM along with the exponential decrement of 1 /T1 below TM indicate the probable participation of the Ni -3 d electron's orbital degrees of freedom in the ferrimagnetic transition. The dominance of orbital fluctuations over the spin fluctuations seems to be responsible for showing low value of the binding energy u of the local spin configuration (estimated from local spin models) and an unusually weak exponent in the power-law behavior of 1 /T1 below 50 K, in the paramagnetic state. Electronic structure calculations also reveal the importance of orbital degrees of freedom of Ni -3 d moments, which is consistent with our NMR data analysis.

  5. Beta-sheet secondary structure of the trimeric globular domain of C1q of complement and collagen types VIII and X by Fourier-transform infrared spectroscopy and averaged structure predictions.

    PubMed Central

    Smith, K F; Haris, P I; Chapman, D; Reid, K B; Perkins, S J

    1994-01-01

    C1q plays a key role in the recognition of immune complexes, thereby initiating the classical pathway of complement activation. Although the triple-helix conformation of its N-terminal segment is well established, the secondary structure of the trimeric globular C-terminal domain is as yet unknown. The secondary structures of human C1q and C1q stalks and pepsin-extracted human collagen types I, III and IV (with no significant non-collagen-like structure) were studied by Fourier-transform i.r. spectroscopy in 2H2O buffers. After second-derivative calculation to resolve the fine structure of the broad amide I band, the Fourier-transform i.r. spectrum of C1q showed two major bands, one at 1637 cm-1, which is a characteristic frequency for beta-sheets, and one at 1661 cm-1. Both major bands were also detected for Clq in H2O buffers. Only the second major band was observed at 1655 cm-1 in pepsin-digested C1q which contains primarily the N-terminal triple-helix region. The Fourier-transform i.r. spectra of collagen in 2H2O also showed a major band at 1659 cm-1 (and minor bands at 1632 cm-1 and 1682 cm-1). It is concluded that the C1q globular heads contain primarily beta-sheet structure. The C-terminal domains of C1q show approximately 25% sequence identity with the non-collagen-like C-terminal regions of the short-chain collagen types VIII and X. To complement the Fourier-transform-i.r. spectroscopic data, averaged Robson and Chou-Fasman structure predictions on 15 similar sequences for the globular domains of C1q and collagen types VIII and X were performed. These showed a clear pattern of ten beta-strands interspersed by beta-turns and /or loops. Residues thought to be important for C1q-immune complex interactions with IgG and IgM were predicted to be at a surface-exposed loop. Sequence insertions and deletions, glycosylation sites, the free cysteine residue and RGD recognition sequences were also predicted to be at surface-exposed positions. Images Figure 4 PMID

  6. FERULATE TRIMERS AND TETRAMERS IN CEREAL GRAINS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant cell walls are a major source of dietary fiber. Hydroxycinnamates that are only minor components within the plant cell wall strongly influence the physico-chemical properties of the cell wall due to their ability to act as cross-links between polysaccharides with each other, to lignin, and to ...

  7. Full-Length Trimeric Influenza Virus Hemagglutinin II Membrane Fusion Protein and Shorter Constructs Lacking the Fusion Peptide or Transmembrane Domain: Hyperthermostability of the Full-Length Protein and the Soluble Ectodomain and Fusion Peptide Make Significant Contributions to Fusion of Membrane Vesicles†

    PubMed Central

    Ratnayake, Punsisi U.; Ekanayaka, E. A. Prabodha; Komanduru, Sweta S.; Weliky, David P.

    2015-01-01

    Influenza virus is a Class I enveloped virus which is initially endocytosed into a host respiratory epithelial cell. Subsequent reduction of the pH to the 5–6 range triggers a structural change of the viral hemagglutinin II (HA2) protein, fusion of the viral and endosomal membranes, and release of the viral nucleocapsid into the cytoplasm. HA2 contains fusion peptide (FP), soluble ectodomain (SE), transmembrane (TM), and intraviral domains with respective lengths of ~25, ~160, ~25, and ~10 residues. The present work provides a straightforward protocol for producing and purifying mg quantities of full-length HA2 from expression in bacteria. Biophysical and structural comparisons are made between full-length HA2 and shorter constructs including SHA2 ≡ SE, FHA2 ≡ FP + SE, and SHA2-TM ≡ SE + TM constructs. The constructs are helical in detergent at pH 7.4 and the dominant trimer species. The proteins are highly thermostable in decylmaltoside detergent with Tm > 90 °C for HA2 with stabilization provided by the SE, FP, and TM domains. The proteins are likely in a trimer-of-hairpins structure, the final protein state during fusion. All constructs induce fusion of negatively-charged vesicles at pH 5.0 with much less fusion at pH 7.4. Attractive protein/vesicle electrostatics play a role in fusion, as the proteins are positively-charged at pH 5.0 and negatively-charged at pH 7.4 and the pH-dependence of fusion is reversed for positively-charged vesicles. Comparison of fusion between constructs supports significant contributions to fusion from the SE and the FP with little effect from the TM. PMID:26297995

  8. Weakly bound states of the He-He-Mg trimer

    SciTech Connect

    Li Yong; Huang Deping; Gou Qingdong; Han Huili; Shi Tingyun

    2011-07-15

    We search for the existence of the weakly bound He-He-Mg molecules. The He-He-Mg molecule is treated as a three-body system. By using hyperspherical coordinates, the Schroedinger equation for the triatomic system is solved in the adiabatic approximation. We obtain that the binding of the three atoms is possible. The binding energies of such molecules are estimated.

  9. Characterization of the weak calcium binding of trimeric globular adiponectin.

    PubMed

    Yu, Dongmei; Zhang, Chao; Wang, Han; Qin, Peiwu

    2013-06-01

    Adiponectin is secreted from adipose tissue and functions as a protein hormone in regulating glucose metabolism and fatty acid catabolism. Adiponectin plays an important role as a novel risk factor and potential diagnostic and prognostic biomarker in cancer. Crystal structures of globular adiponectin have been resolved with three calcium-binding sites on the top of its central tunnel. However, the calcium-binding property of adiponectin remains elusive. Mouse globular adiponectin was cloned into pET11a and expressed in Escherichia coli. The folding of adiponectin was indicated by the spread of resonances in HSQC spectrum. Luminescence resonance energy transfer was used to obtain the binding constant (K(d)) of Tb(3+) and the inhibitor constant (K(i)) of Ca(2+) for globular adiponectin. The obtained calcium-binding affinity to adiponectin is relatively low (~2 mM), which indicates that the high concentration of adiponectin in circulating system may function as calcium storage bank and buffer the free calcium concentration.

  10. Communication: Isotopic effects on tunneling motions in the water trimer

    SciTech Connect

    Videla, Pablo E.; Rossky, Peter J.; Laria, D.

    2016-02-14

    We present results of ring polymer molecular dynamics simulations that shed light on the effects of nuclear quantum fluctuations on tunneling motions in cyclic [H{sub 2}O]{sub 3} and [D{sub 2}O]{sub 3}, at the representative temperature of T = 75 K. In particular, we focus attention on free energies associated with two key isomerization processes: The first one corresponds to flipping transitions of dangling OH bonds, between up and down positions with respect to the O–O–O plane of the cluster; the second involves the interchange between connecting and dangling hydrogen bond character of the H-atoms in a tagged water molecule. Zero point energy and tunneling effects lead to sensible reductions of the free energy barriers. Due to the lighter nature of the H nuclei, these modifications are more marked in [H{sub 2}O]{sub 3} than in [D{sub 2}O]{sub 3}. Estimates of the characteristic time scales describing the flipping transitions are consistent with those predicted based on standard transition-state-approximation arguments.

  11. The ^4He Trimer as an Efimov System: Latest Developments

    NASA Astrophysics Data System (ADS)

    Kolganova, E. A.; Motovilov, A. K.; Sandhas, W.

    2017-03-01

    Kolganova et al. (Few-Body Syst 51:249, 2011) reviewed the results that demonstrate the Efimov nature of the ^4He three-atom system. The present note represents an extension of that survey to the time period which passed since its publication.

  12. Photoabsorption spectrum of helium trimer cation—Theoretical modeling

    SciTech Connect

    Kalus, René; Karlický, František; Lepetit, Bruno; Paidarová, Ivana; Gadea, Florent Xavier

    2013-11-28

    The photoabsorption spectrum of He{sub 3}{sup +} is calculated for two semiempirical models of intracluster interactions and compared with available experimental data reported in the middle UV range [H. Haberland and B. von Issendorff, J. Chem. Phys. 102, 8773 (1995)]. Nuclear delocalization effects are investigated via several approaches comprising quantum samplings using either exact or approximate (harmonic) nuclear wavefunctions, as well as classical samplings based on the Monte Carlo methodology. Good agreement with the experiment is achieved for the model by Knowles et al., [Mol. Phys. 85, 243 (1995); Mol. Phys. 87, 827 (1996)] whereas the model by Calvo et al., [J. Chem. Phys. 135, 124308 (2011)] exhibits non-negligible deviations from the experiment. Predictions of far UV absorption spectrum of He{sub 3}{sup +}, for which no experimental data are presently available, are reported for both models and compared to each other as well as to the photoabsorption spectrum of He{sub 2}{sup +}. A simple semiempirical point-charge approximation for calculating transition probabilities is shown to perform well for He{sub 3}{sup +}.

  13. Trimer and Tetramer Bound States in Heteronuclear Systems

    NASA Astrophysics Data System (ADS)

    Schmickler, Christiane H.; Hammer, Hans-Werner; Hiyama, Emiko

    2017-01-01

    The Efimov effect in heteronuclear cold atomic systems is experimentally more easily accessible than the Efimov effect for identical atoms, because of the potentially smaller scaling factor. We focus on the case of two or three heavy identical bosons and another atom. The former case was recently observed in a mixture of ^{133}Cs and ^{6}Li atoms. We employ the Gaussian Expansion Method as developed by Hiyama, Kino et al. (Prog Part Nucl Phys 51:223-307, 2003). This is a variational method that uses Gaussians that are distributed geometrically over a chosen range. Supplemental calculations are performed using the Skorniakov-Ter- Martirosian equation. Blume et al. (Phys Rev Lett 113:213201, 2014) previously investigated the scaling properties of heteronuclear systems in the unitary limit and at the three-body breakup threshold. We have completed this picture by calculating the behaviour on the positive scattering length side of the Efimov plot, focussing on the dimer threshold.

  14. Structural Characterization of POSS Siloxane Dimer and Trimer (POSTPRINT)

    DTIC Science & Technology

    2006-01-01

    of Chemistry and Biochemistry , UniVersity of California, Santa Barbara, California 93106, Department of Chemistry, Westmont College, Santa Barbara... Devlin , F. J.; Chabalowski, C. F.; Frisch, M. J. J. Phys. Chem. 1994, 98, 11623. tA ) l2 Ko 1 760 273 T ( p V + to) (1) σ ) 3q 16NKo( 2πµkbT) 1/2 (2

  15. Structural Characterization of POSS Siloxane Dimer and Trimer (PREPRINT)

    DTIC Science & Technology

    2005-11-14

    Connie Mitchell, Timothy S. Haddadb, Ashwani Vijc, Joseph J. Schwabd, and Michael T. Bowers* Department of Chemistry & Biochemistry , University of...Rev. B , 1964, 136, 864; (b) Kohn, W.; Sham, L.J., Phys. Rev. 1965, 140, 1133. 61. Stephens, P.J.; Devlin , F.J.; Chabalowski, C.F.; and Frisch

  16. Evaluation of the trimeric autotransporter Ata as a vaccine candidate against Acinetobacter baumannii infections.

    PubMed

    Bentancor, Leticia V; Routray, Abhisek; Bozkurt-Guzel, Cagla; Camacho-Peiro, Ana; Pier, Gerald B; Maira-Litrán, Tomás

    2012-10-01

    Acinetobacter baumannii is a multidrug-resistant (MDR) nosocomial pathogen for which immunotherapeutic alternatives are needed. We previously identified a surface autotransporter of A. baumannii, Ata, that bound to various extracellular matrix/basal membrane proteins and was required for full virulence, biofilm formation, and the adhesion of A. baumannii to collagen type IV. We show here that Ata binding to collagen type IV was inhibited by antibodies to Ata. In addition, in the presence of complement and polymorphonuclear cells (PMNs), antibodies to Ata were highly opsonic against A. baumannii ATCC 17978 and showed low to moderate killing activity against four heterologous A. baumannii strains, whereas in the absence of PMNs, antibody to Ata efficiently promoted complement-dependent bactericidal killing of all of the tested A. baumannii isolates. Using a pneumonia model of infection in both immunocompetent and immunocompromised mice, we found that, compared to normal rabbit sera, antisera to Ata significantly reduced the levels of A. baumannii ATCC 17978 and two MDR strains in the lungs of infected mice. The ability of Ata to engender anti-adhesive, bactericidal, opsonophagocytic, and protective antibodies validates its potential use as an antigenic target against MDR A. baumannii infections.

  17. Evaluation of the Trimeric Autotransporter Ata as a Vaccine Candidate against Acinetobacter baumannii Infections

    PubMed Central

    Bentancor, Leticia V.; Routray, Abhisek; Bozkurt-Guzel, Cagla; Camacho-Peiro, Ana; Pier, Gerald B.

    2012-01-01

    Acinetobacter baumannii is a multidrug-resistant (MDR) nosocomial pathogen for which immunotherapeutic alternatives are needed. We previously identified a surface autotransporter of A. baumannii, Ata, that bound to various extracellular matrix/basal membrane proteins and was required for full virulence, biofilm formation, and the adhesion of A. baumannii to collagen type IV. We show here that Ata binding to collagen type IV was inhibited by antibodies to Ata. In addition, in the presence of complement and polymorphonuclear cells (PMNs), antibodies to Ata were highly opsonic against A. baumannii ATCC 17978 and showed low to moderate killing activity against four heterologous A. baumannii strains, whereas in the absence of PMNs, antibody to Ata efficiently promoted complement-dependent bactericidal killing of all of the tested A. baumannii isolates. Using a pneumonia model of infection in both immunocompetent and immunocompromised mice, we found that, compared to normal rabbit sera, antisera to Ata significantly reduced the levels of A. baumannii ATCC 17978 and two MDR strains in the lungs of infected mice. The ability of Ata to engender anti-adhesive, bactericidal, opsonophagocytic, and protective antibodies validates its potential use as an antigenic target against MDR A. baumannii infections. PMID:22825448

  18. Fluid shear stress sensitizes cancer cells to receptor-mediated apoptosis via trimeric death receptors

    NASA Astrophysics Data System (ADS)

    Mitchell, Michael J.; King, Michael R.

    2013-01-01

    Cancer metastasis, the process of cancer cell migration from a primary to distal location, typically leads to a poor patient prognosis. Hematogenous metastasis is initiated by intravasation of circulating tumor cells (CTCs) into the bloodstream, which are then believed to adhere to the luminal surface of the endothelium and extravasate into distal locations. Apoptotic agents such as tumor necrosis factor apoptosis-inducing ligand (TRAIL), whether in soluble ligand form or expressed on the surface of natural killer cells, have shown promise in treating CTCs to reduce the probability of metastasis. The role of hemodynamic shear forces in altering the cancer cell response to apoptotic agents has not been previously investigated. Here, we report that human colon cancer COLO 205 and prostate cancer PC-3 cells exposed to a uniform fluid shear stress in a cone-and-plate viscometer become sensitized to TRAIL-induced apoptosis. Shear-induced sensitization directly correlates with the application of fluid shear stress, and TRAIL-induced apoptosis increases in a fluid shear stress force- and time-dependent manner. In contrast, TRAIL-induced necrosis is not affected by the application fluid shear stress. Interestingly, fluid shear stress does not sensitize cancer cells to apoptosis when treated with doxorubicin, which also induces apoptosis in cancer cells. Caspase inhibition experiments reveal that shear stress-induced sensitization to TRAIL occurs via caspase-dependent apoptosis. These results suggest that physiological fluid shear forces can modulate receptor-mediated apoptosis of cancer cells in the presence of apoptotic agents.

  19. Helium trimer calculations with a public quantum three-body code

    SciTech Connect

    Kolganova, E. A.; Roudnev, V.; Cavagnero, M.

    2012-10-15

    We present an illustration of using a quantumthree-body code being prepared for public release. The code is based on iterative solving of the three-dimensional Faddeev equations. The code is easy to use and allows users to perform highly-accurate calculations of quantum three-body systems. The previously known results for He{sub 3} ground state are well reproduced by the code.

  20. On The Electronic Structure and Chemical Bonding in the Tantalum Trimer Cluster

    SciTech Connect

    Wang, Xue B.; Zhai, Hua Jin; Huang, Xin; Wang, Lai S.

    2008-10-03

    The electronic structure and chemical bonding in the Ta3- cluster are investigated using photoelectron spectroscopy and density functional theory calculations. Photoelectron spectra are obtained for Ta3- at four photon energies: 532, 355, 266 and 193 nm. While congested spectra are observed at high electron binding energies, several low-lying electronic transitions are well resolved and compared with the theoretical calculations. The electron affinity of Ta3 is determined to be 1.35±0.03 eV. Extensive density functional calculations are performed at the B3LYP/Stuttgart +2f1g level to locate the ground state and low-lying isomers for Ta3 and Ta3-. The ground state for the Ta3- anion is shown to be a quintet (5A1') with D3h symmetry, whereas two nearly isoenergetic states, C2v (4A1) and D3h (6A1'), are found to compete for the ground state for neutral Ta3. A detailed molecular orbital analysis is performed to elucidate the chemical boding in Ta3-, which is found to possess multiple d-orbital aromaticity, commensurate with its highly symmetric D3h structure.

  1. A templating guest sorts out a molecular triangle from a dimer-trimer constitutional dynamic library.

    PubMed

    Rancan, Marzio; Dolmella, Alessandro; Seraglia, Roberta; Orlandi, Simonetta; Quici, Silvio; Armelao, Lidia

    2012-03-25

    Cu(II) and a bis-β-diketone ligand generate a small constitutional dynamic library (CDL). The designed introduction of a well suited guest drives the self-sorting of the system toward a supramolecular triangle. Alternatively, the triangle self-assembly is templated by the same guest in a one-pot synthesis.

  2. Stereoselective trimerization of [(S)R]-[(p-tolylsulfinyl)methyl]-p-quinols and p-quinamines.

    PubMed

    Carreño, M Carmen; Ribagorda, María

    2003-07-10

    [reaction: see text] The asymmetric synthesis of pentacyclic derivatives was achieved in a single step starting from enantiopure [(S)R]-[(p-tolylsulfinyl)methyl]-p-quinols or the nitrogen analogue, through a domino sequence involving four conjugate additions in excellent yields. Eight new stereogenic centers were created in one step and in a highly diastereoselective manner.

  3. Anti-Tat and anti-HIV activities of trimers of n-alkylglycines.

    PubMed

    Márquez, Nieves; Sancho, Rocío; Macho, Antonio; Moure, Alejandra; Masip, Isabel; Messeguer, Angel; Muñoz, Eduardo

    2006-02-28

    Transcription of human immunodeficiency virus (HIV-1) is activated by viral Tat protein which regulates HIV-LTR transcription and elongation. In the present report, the evaluation of the anti-Tat activity of a combinatorial library composed of 5120 N-trialkylglycines is reported. The antiviral activity was studied through luciferase-based assays targeting the HIV-1 promoter activation induced by the HIV-1 Tat protein. We identified five peptoids with specific anti-HIV-1 Tat activity; none of these peptoids affected the binding of HIV-1 Tat protein to the viral TAR RNA. Using a recombinant-virus assay in which luciferase activity correlates with the rate of HIV-1 transcription we have detected that one of the five selected peptoids, NC37-37-15C, is a potent inhibitor of HIV-1-LTR transcription in both primary T lymphocytes and transformed cell lines. The inhibitory effect of NC37-37-15C, which is additive with azidothymidine (AZT), correlates with its ability to inhibit CTD phosphorylation and shows a suitable profile for development of novel anti-HIV-1 drugs. Likewise, the structural simplicity of N-alkylglycine oligomers makes these peptidomimetics amenable to structural manipulation, thus facilitating the optimisation of lead molecules for drug-like properties.

  4. Quantum signatures of an oscillatory instability in the Bose-Hubbard trimer.

    PubMed

    Jason, Peter; Johansson, Magnus; Kirr, Katarina

    2012-07-01

    We study the Bose-Hubbard model for three sites in a symmetric, triangular configuration and search for quantum signatures of the classical regime of oscillatory instabilities, known to appear through Hamiltonian Hopf bifurcations for the "single-depleted-well" family of stationary states in the discrete nonlinear Schrödinger equation. In the regimes of classical stability, single quantum eigenstates with properties analogous to those of the classical stationary states can be identified already for rather small particle numbers. On the other hand, in the instability regime the interaction with other eigenstates through avoided crossings leads to strong mixing, and no single eigenstate with classical-like properties can be seen. We compare the quantum dynamics resulting from initial conditions taken as perturbed quantum eigenstates and SU(3) coherent states, respectively, in a quantum-semiclassical transitional regime of 10-100 particles. While the perturbed quantum eigenstates do not show a classical-like behavior in the instability regime, a coherent state behaves analogously to a perturbed classical stationary state, and exhibits initially resonant oscillations with oscillation frequencies well described by classical internal-mode oscillations.

  5. Synthesis of terpene and steroid dimers and trimers having cyclobutadienyl-Co and aromatic tethers.

    PubMed

    Sierra, Miguel A; Torres, M Rosario; Torre, María C de la; Alvaro, Elsa

    2007-05-25

    The reaction of natural product derived propargylic alcohols with CpCo(CO)2 produces three new types of natural product hybrids having two or three terpene or steroid fragments. The tether joining the natural product subunits is built during the reaction. Type 1 hybrids have two terpene or steroid moieties joined by a CpCo-cyclobutadiene tether, with the two units disposed in a 1,2-arrangement (9, 14, 22). Type 2 hybrids have a Co-cyclopentadienone tether (10). Type 3 has three units of terpene or steroid joined to a benzene ring (11, 12, 15). An unusual Co-mediated beta-carbon elimination pathway of propargylic alcohols leading to ketones (an unknown process in this chemistry) has been observed.

  6. Dimeric and trimeric hydrolyzable tannins from Quercus coccifera and Quercus suber.

    PubMed

    Ito, Hideyuki; Yamaguchi, Koji; Kim, Tae-Hoon; Khennouf, Seddik; Gharzouli, Kamel; Yoshida, Takashi

    2002-03-01

    Three new hydrolyzable tannins, cocciferins D(1) (1), D(2) (2), and T(1) (4), were isolated from the leaves of Quercus coccifera. Cocciferin D(2) (2) and two additional new tannins, cocciferins D(3) (3) and T(2) (5), were also obtained from the leaves of Quercus suber. Their oligomeric structures were elucidated on the basis of spectroscopic methods and chemical evidence. Compounds 2, 3, and 5 were rare oligomers possessing glucose cores with both open-chain and pyranose forms.

  7. Synthesis and conformational analysis of novel trimeric maleimide cross-linking reagents.

    PubMed

    Szczepanska, Agnieszka; Espartero, José Luis; Moreno-Vargas, Antonio J; Carmona, Ana T; Robina, Inmaculada; Remmert, Sarah; Parish, Carol

    2007-08-31

    Nine homotrifunctional cross-linking reagents are presented. Their synthesis and chemical properties as well as their characterization by classical mechanical conformational searching techniques is reported. Mixed Low Mode and Monte Carlo searching techniques were used to exhaustively sample the OPLS2005/GBSA(water) potential energy surface of trisubstituted cyclohexane and benzene derivatives of C3 symmetry. Geometric structure, molecular length, and hydrogen-bonding patterns were analyzed. Nonaromatic compounds exhibited exclusively chair conformations at low energies, with a preference for axial or equatorial arms depending upon the presence of additional ring substituent Me groups. Increasing chain length often resulted in overall shorter molecular length due to additional chain flexibility. These results were consistent with one- and two-dimensional temperature-dependent NMR studies.

  8. Monte Carlo simulation of flexible trimers: from square well chains to amphiphilic primitive models.

    PubMed

    Jiménez-Serratos, Guadalupe; Gil-Villegas, Alejandro; Vega, Carlos; Blas, Felipe J

    2013-09-21

    In this work, we present Monte Carlo computer simulation results of a primitive model of self-assembling system based on a flexible 3-mer chain interacting via square-well interactions. The effect of switching off the attractive interaction in an extreme sphere is analyzed, since the anisotropy in the molecular potential promotes self-organization. Before addressing studies on self-organization it is necessary to know the vapor liquid equilibrium of the system to avoid to confuse self-organization with phase separation. The range of the attractive potential of the model, λ, is kept constant and equal to 1.5σ, where σ is the diameter of a monomer sphere, while the attractive interaction in one of the monomers was gradually turned off until a pure hard body interaction was obtained. We present the vapor-liquid coexistence curves for the different models studied, their critical properties, and the comparison with the SAFT-VR theory prediction [A. Gil-Villegas, A. Galindo, P. J. Whitehead, S. J. Mills, G. Jackson, and A. N. Burgess, J. Chem. Phys. 106, 4168 (1997)]. Evidence of self-assembly for this system is discussed.

  9. Monte Carlo simulation of flexible trimers: From square well chains to amphiphilic primitive models

    NASA Astrophysics Data System (ADS)

    Jiménez-Serratos, Guadalupe; Gil-Villegas, Alejandro; Vega, Carlos; Blas, Felipe J.

    2013-09-01

    In this work, we present Monte Carlo computer simulation results of a primitive model of self-assembling system based on a flexible 3-mer chain interacting via square-well interactions. The effect of switching off the attractive interaction in an extreme sphere is analyzed, since the anisotropy in the molecular potential promotes self-organization. Before addressing studies on self-organization it is necessary to know the vapor liquid equilibrium of the system to avoid to confuse self-organization with phase separation. The range of the attractive potential of the model, λ, is kept constant and equal to 1.5σ, where σ is the diameter of a monomer sphere, while the attractive interaction in one of the monomers was gradually turned off until a pure hard body interaction was obtained. We present the vapor-liquid coexistence curves for the different models studied, their critical properties, and the comparison with the SAFT-VR theory prediction [A. Gil-Villegas, A. Galindo, P. J. Whitehead, S. J. Mills, G. Jackson, and A. N. Burgess, J. Chem. Phys. 106, 4168 (1997)]. Evidence of self-assembly for this system is discussed.

  10. Theoretical research program to study transition metal trimers and embedded clusters

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.

    1986-01-01

    The calculation of potential energy surfaces for chemical reactions was the focus of investigation. Two groups of reactions were considered: the subset of reactions important in H2 combustion, and high temperature air chemistry reactions (O + N yields NO + N and N + O2 yields NO + O).

  11. Synthesis and physical properties of new coco-oleic dimer and trimer plus estolide branched esters

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Estolides are a class of esters based on vegetable oils that are formed when the carboxylic acid functionality of one fatty acid reacts at the site of unsaturation of another fatty acid to form an ester linkage. The objective of this preliminary study was to separate coco-oleic estolide into two com...

  12. Theoretical research program to study transition metal trimers and embedded clusters

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.

    1987-01-01

    The results of ab-initio calculations are reported for (1) small transition metal clusters and (2) potential energy surfaces for chemical reactions important in hydrogen combustion and high temperature air chemistry.

  13. On nd bonding in the transition metal trimers: Comparison of Sc3 and Y3

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.

    1987-01-01

    CASSCF/CCI calculations are presented for the low-lying states of Y3. Comparison of the wave functions for Y3 and Sc3 indicates substantial 4d-5p hybridization in Y3, but little 3d-4p hybridization in Sc3. The increased 4d-5p hybridization leads to stabilization of 4dpi bonding with respect to 4dsigma bonding for equilateral triangle Y3, and also leads to 4d-5p bonding for linear geometries. These effects lead to a different ordering of states for equilateral triangle geometries and a smaller excitation energy to the linear configuration for Y3 as compared to Sc3.

  14. MicroProtein-Mediated Recruitment of CONSTANS into a TOPLESS Trimeric Complex Represses Flowering in Arabidopsis

    PubMed Central

    Graeff, Moritz; Straub, Daniel; Eguen, Tenai; Dolde, Ulla; Rodrigues, Vandasue; Brandt, Ronny; Wenkel, Stephan

    2016-01-01

    MicroProteins are short, single domain proteins that act by sequestering larger, multi-domain proteins into non-functional complexes. MicroProteins have been identified in plants and animals, where they are mostly involved in the regulation of developmental processes. Here we show that two Arabidopsis thaliana microProteins, miP1a and miP1b, physically interact with CONSTANS (CO) a potent regulator of flowering time. The miP1a/b-type microProteins evolved in dicotyledonous plants and have an additional carboxy-terminal PF(V/L)FL motif. This motif enables miP1a/b microProteins to interact with TOPLESS/TOPLESS-RELATED (TPL/TPR) proteins. Interaction of CO with miP1a/b/TPL causes late flowering due to a failure in the induction of FLOWERING LOCUS T (FT) expression under inductive long day conditions. Both miP1a and miP1b are expressed in vascular tissue, where CO and FT are active. Genetically, miP1a/b act upstream of CO thus our findings unravel a novel layer of flowering time regulation via microProtein-inhibition. PMID:27015278

  15. Tau Trimers Are the Minimal Propagation Unit Spontaneously Internalized to Seed Intracellular Aggregation*

    PubMed Central

    Mirbaha, Hilda; Holmes, Brandon B.; Sanders, David W.; Bieschke, Jan; Diamond, Marc I.

    2015-01-01

    Tau amyloid assemblies propagate aggregation from the outside to the inside of a cell, which may mediate progression of the tauopathies. The critical size of Tau assemblies, or “seeds,” responsible for this activity is currently unknown, but this could be important for the design of effective therapies. We studied recombinant Tau repeat domain (RD) and Tau assemblies purified from Alzheimer disease (AD) brain composed largely of full-length Tau. Large RD fibrils were first sonicated to create a range of assembly sizes. We confirmed our ability to resolve stable assemblies ranging from n = 1 to >100 units of Tau using size exclusion chromatography, fluorescence correlation spectroscopy, cross-linking followed by Western blot, and mass spectrometry. All recombinant Tau assemblies bound heparan sulfate proteoglycans on the cell surface, which are required for Tau uptake and seeding, because they were equivalently sensitive to inhibition by heparin and chlorate. However, cells only internalized RD assemblies of n ≥ 3 units. We next analyzed Tau assemblies from AD or control brains. AD brains contained aggregated species, whereas normal brains had predominantly monomer, and no evidence of large assemblies. HEK293 cells and primary neurons spontaneously internalized Tau of n ≥ 3 units from AD brain in a heparin- and chlorate-sensitive manner. Only n ≥ 3-unit assemblies from AD brain spontaneously seeded intracellular Tau aggregation in HEK293 cells. These results indicate that a clear minimum size (n = 3) of Tau seed exists for spontaneous propagation of Tau aggregation from the outside to the inside of a cell, whereas many larger sizes of soluble aggregates trigger uptake and seeding. PMID:25887395

  16. Many low-lying isomers of the cationic and neutral niobium trimer and tetramer

    NASA Astrophysics Data System (ADS)

    Fowler, Joseph E.; García, América; Ugalde, Jesus M.

    1999-10-01

    The experimentally interesting Nb3 and Nb4 clusters and their cations have been studied in great detail using density-functional methodology in conjunction with relativistic effective core potentials. Close attention has been paid to full optimization along the flat potential energy surfaces and numerous minima and several transition states have been characterized. The Nb3 cation is predicted to have a 3A'1 ground state with an equilibrium geometry of D3h symmetry. The ground state of the neutral is predicted to be a 2B1 state of C2v symmetry with two shorter bonds and one longer. The transition state for pseudorotation or ``peak'' atom interchange, however, lies only 0.01 kcal/mol higher in energy, implying a fluxional structure for the neutral species. The global minimum of the Nb4 cationic cluster is a C2v structure, Jahn-Teller distorted from the Td global minimum of the singlet neutral. Numerous other energetically low-lying stationary points are characterized for each species. We discuss the bonding features of these minima and relate our predictions to the existing experimental data.

  17. Doping effects on trimerization and magnetoelectric coupling of single crystal multiferroic (Y,Lu)MnO3

    NASA Astrophysics Data System (ADS)

    Choi, Seongil; Sim, Hasung; Kang, Soonmin; Choi, Ki-Young; Park, Je-Geun

    2017-03-01

    Hexagonal RMnO3 is a multiferroic compound with a giant spin–lattice coupling at an antiferromagnetic transition temperature, Lee et al (2008 Nature 451 805). Despite extensive studies over the past two decades, the origin and underlying microscopic mechanism of strong spin–lattice coupling remain very much elusive. In this study, we have tried to address this problem by measuring the thermal expansion and dielectric constant of doped single crystals Y1‑x Lu x MnO3 where x  =  0, 0.25, 0.5, 0.75, and 1.0. From these measurements, we confirm that there is a progressive change in the physical properties with doping. At the same time, all our samples exhibit clear anomalies at T N, even in the samples where x  =  0.5 and 0.75. This is opposed to some earlier ideas, which suggests an unusual doping dependence of the anomaly. Our work reveals yet another interesting facet of the spin–lattice coupling issue in hexagonal RMnO3.

  18. Utilizing avidity to improve antifreeze protein activity: a type III antifreeze protein trimer exhibits increased thermal hysteresis activity.

    PubMed

    Can, Özge; Holland, Nolan B

    2013-12-03

    Antifreeze proteins (AFPs) are ice growth inhibitors that allow the survival of several species living at temperatures colder than the freezing point of their bodily fluids. AFP activity is commonly defined in terms of thermal hysteresis, which is the difference observed for the solution freezing and melting temperatures. Increasing the thermal hysteresis activity of these proteins, particularly at low concentrations, is of great interest because of their wide range of potential applications. In this study, we have designed and expressed one-, two-, and three-domain antifreeze proteins to improve thermal hysteresis activity through increased binding avidity. The three-domain type III AFP yielded significantly greater activity than the one- and two-domain proteins, reaching a thermal hysteresis of >1.6 °C at a concentration of <1 mM. To elucidate the basis of this increase, the data were fit to a multidomain protein adsorption model based on the classical Langmuir isotherm. Fits of the data to the modified isotherms yield values for the equilibrium binding constants for the adsorption of AFP to ice and indicate that protein surface coverage is proportional to thermal hysteresis activity.

  19. From gas-phase to liquid-water chemical reactions: the fluorine atom plus water trimer system.

    PubMed

    Li, Guoliang; Li, Qian-Shu; Xie, Yaoming; Schaefer, Henry F

    2015-09-14

    The potential energy profile for the F+(H2 O)3 →HF+(H2 O)2 OH reaction has been investigated using the "gold standard" CCSD(T) method with correlation-consistent basis sets up to cc-pVQZ. Four different reaction pathways have been found and these are related, both geometrically and energetically. The entrance complexes F⋅⋅⋅(H2 O)3 for all four reaction pathways are found lying ca. 7 kcal mol(-1) below the separated reactants F+(H2 O)3 . The four reaction barriers on their respective reaction coordinates lie ca. 4 kcal mol(-1) below the reactants. There are also corresponding exit complexes HF⋅⋅⋅(H2 O)2 OH, lying about 13 kcal mol(-1) below the separated products HF+(H2 O)2 OH. Compared with analogous F+(H2 O)2 and F+H2 O reactions, the F+(H2 O)3 reaction is somewhat similar to the former but qualitatively different from the latter. It may be reasonable to predict that the reactions between atomic fluorine and water tetramer (or even larger water clusters) may be similar to the F+(H2 O)3 reaction.

  20. Genotoxicity Assessment of Chlorotrifluoroethylene Trimer Acid Using a Battery of In Vitro and In Vivo/In Vitro Assays

    DTIC Science & Technology

    1990-12-01

    Azarnoff, and M.S. Rao. 1976. Di(2-ethylhexyl)- phthalatet An industrial plasticizer Indices hypolipidemia and enhances hepatic catalase and carnitine ...agar was melted and supplemented with a sterile solution containing 0.5 mM L-histidine and 0.5 mM D-biotin (10% v/v). Minimal Bottom Agart The bottom...agar was Vogel-Bonner minimal medium E (Vogel and Bonner, 1956), supplemented with 0.2% (w/v) glucose. Nutrient Broth: The nutrient broth uted for

  1. Control of the Barrier in Cyanide Based Single Molecule Magnets Mn(III)2Mn(II)3:  Theoretical Analysis.

    PubMed

    Tsukerblat, Boris S; Palii, Andrew V; Ostrovsky, Sergei M; Kunitsky, Sergei V; Klokishner, Sophia I; Dunbar, Kim R

    2005-07-01

    The aim of this communication is to probe the possibility of increasing the barrier for reversal of magnetization in the family of new cyano-bridged pentanuclear Mn(III)2Mn(II)3 clusters in which single molecule magnet behavior has been recently discovered. In this context, we analyze the global magnetic anisotropy arising from the unquenched orbital angular momenta of ground terms (3)T1(t2(4)) of the two apical Mn(III) ions. The model takes into account the trigonal component of the crystal field, spin-orbit interaction in (3)T1(t2(4)), and an isotropic exchange interaction between Mn(III) and Mn(II) ions. The height of the barrier is shown to be sensitive to the change of the trigonal field stabilizing orbital doublet (3)E, which carries the first-order orbital magnetic contribution and enhances with an increase of the trigonal field. This result is expected to be useful for the more rational design of new cyano-bridged SMMs with high blocking temperatures.

  2. CDK-activating kinase (Ee;CDKF;1) of leafy spurge (Euphorbia esula) forms both homo-dimers and homo-trimers in its native state

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Leafy spurge is a deep rooted perennial weed that propagates both by seeds and underground adventitious buds located on the crown and roots (crown and root buds). As buds develop during the normal growing season, they are maintained in a quiescent state through correlative inhibition. To enhance our...

  3. Mimicking zeolite to its core: porous sodalite cages as hangers for pendant trimeric M3(OH) clusters (M = Mg, Mn, Co, Ni, Cd).

    PubMed

    Zheng, Shou-Tian; Wu, Tao; Zuo, Fan; Chou, Chengtsung; Feng, Pingyun; Bu, Xianhui

    2012-02-01

    A new class of zeolite-type porous materials in which 3D frameworks are covalently functionalized with crystallographically ordered pendant metal clusters have been synthesized. This work demonstrates a new paradigm for and the feasibility of functionalizing zeolite-type frameworks through the conversion of extraframework sites in mineral zeolites into part of the framework for occupation by dangling metal clusters in metal-organic frameworks.

  4. Evaluation of a DNA Aβ42 Vaccine in Aged NZW Rabbits: Antibody Kinetics and Immune Profile after Intradermal Immunization with Full-Length DNA Aβ42 Trimer

    PubMed Central

    Lambracht-Washington, Doris; Fu, Min; Wight-Carter, Mary; Riegel, Matthew; Rosenberg, Roger N.

    2017-01-01

    A pathological hallmark of Alzheimer’s disease (AD) are amyloid plaques in the brain consisting of aggregated amyloid-β 42 peptide (Aβ42) derived from cellular amyloid-β protein precursor (AβPP). Based on successful experiments in mouse AD models, active immunization with Aβ42 peptide and passive immunizations with anti-Aβ42 antibodies were started in clinical trials. Active Aβ42 peptide immunization in humans had led to an inflammatory autoimmune response, and the trial was stopped. Passive immunizations had shown some effects in slowing AD pathology. Active DNA Aβ42 immunizations administered with the gene gun into the skin elicits a different immune response and is non-inflammatory. While in rodents, good responses had been found for this type of immunization, positive results in larger mammals are missing. We present here results from sixteen New Zealand White Rabbits, which underwent intradermal DNA Aβ42 immunization via gene gun. The humoral immune response was analyzed from blood throughout the study, and cellular immune responses were determined from spleens at the end of the study. A good anti-Aβ antibody response was found in the rabbit model. The T cell response after re-stimulation in cell culture showed no IFNγ producing cells when ELISPOT assays were analyzed from PBMC, but low numbers of IFNγ and IL-17 producing cells were found in ELISPOTS from spleens (both 5 immunizations). Brains from immunized rabbits showed no signs of encephalitis. Based on these results, DNA Aβ42 immunization is highly likely to be safe and effective to test in a possible clinical AD prevention trial in patients. PMID:28222511

  5. Trimeric l-N-carbamoylase from newly isolated Brevibacillus reuszeri HSN1: a potential biocatalyst for production of l-α-amino acids.

    PubMed

    Nandanwar, Hemraj S; Vohra, Rakesh M; Hoondal, Gurinder S

    2013-01-01

    l-N-carbamoylase was isolated from Brevibacillus reuszeri HSN1 and purified to homogeneity in three steps, which is a reasonably short protocol for native l-N-carbamoylase. The enzyme purification protocol resulted in ≈60-fold purification of l-N-carbamoylase with specific activity of 145 µmol/Min/mg. The subunit and native molecular mass were found to be 44.3 and 132 kDa, respectively. Temperature and pH optima were determined as 50°C and 8.5, respectively. The enzyme had retained ≈86% activity at 50°C when incubated for 60 Min and the half-life was determined as 180 Min at 50°C. N-carbamoyl-l-methionine (l-N-CMet) was found to be a preferred substrate with Km and Vmax values of ≈13.5 mM and ≈103 µmol/Min/mg, respectively. The broad substrate specificity with derivatives of N-carbamoyl amino acids is advantageous to be a better biocatalyst for production of corresponding l-α-amino acids. The enzyme activity was enhanced by 73% in the presence of 0.8 mM Mn(2+) ion during the biotransformation. In the batch experiment, ≈97% conversion of 5.0% l-N-CMet into enantiomerically pure l-methionine was achieved in 10 H when carried out at pH 8.0, 45°C, and 15% wet (w/v) cell loading, under controlled conditions. The overall merits of this enzyme show promise as a potential biocatalyst for l-α-amino acid production.

  6. EPA to Update Community on Toms River, NJ Superfund Site, EPA and National Toxicology Program scientists to Discuss Study of SAN Trimer

    EPA Pesticide Factsheets

    (New York, N.Y. - Jan. 30, 2015) On February 4, 2014, the U.S. Environmental Protection Agency will hold a public meeting to discuss how a new scientific study about a previously unknown contaminant relates to the ongoing cleanup at the Reich Farm Superfun

  7. EPA to Update Community on Toms River, NJ Superfund Site, EPA and National Toxicology Program scientists to Discuss Study of SAN Trimer

    EPA Pesticide Factsheets

    (New York, N.Y. - Jan. 30, 2015) On February 4, 2015, the U.S. Environmental Protection Agency will hold a public meeting to discuss how a new scientific study about a previously unknown contaminant relates to the ongoing cleanup at the Reich Farm Superfun

  8. Pronounced Effects of a Triazine Core on Photovoltaic Performance-Efficient Organic Solar Cells Enabled by a PDI Trimer-Based Small Molecular Acceptor.

    PubMed

    Duan, Yuwei; Xu, Xiaopeng; Yan, He; Wu, Wenlin; Li, Zuojia; Peng, Qiang

    2017-02-01

    A novel-small molecular acceptor with electron-deficient 1,3,5-triazine as the core and perylene diimides as the arms is developed as the acceptor material for efficient bulk heterojunction organic solar cells with an efficiency of 9.15%.

  9. Estimating the probability of polyreactive antibodies 4E10 and 2F5 disabling a gp41 trimer after T cell-HIV adhesion.

    PubMed

    Hu, Bin; Liao, Hua-Xin; Alam, S Munir; Goldstein, Byron

    2014-01-01

    A few broadly neutralizing antibodies, isolated from HIV-1 infected individuals, recognize epitopes in the membrane proximal external region (MPER) of gp41 that are transiently exposed during viral entry. The best characterized, 4E10 and 2F5, are polyreactive, binding to the viral membrane and their epitopes in the MPER. We present a model to calculate, for any antibody concentration, the probability that during the pre-hairpin intermediate, the transient period when the epitopes are first exposed, a bound antibody will disable a trivalent gp41 before fusion is complete. When 4E10 or 2F5 bind to the MPER, a conformational change is induced that results in a stably bound complex. The model predicts that for these antibodies to be effective at neutralization, the time to disable an epitope must be shorter than the time the antibody remains bound in this conformation, about five minutes or less for 4E10 and 2F5. We investigate the role of avidity in neutralization and show that 2F5 IgG, but not 4E10, is much more effective at neutralization than its Fab fragment. We attribute this to 2F5 interacting more stably than 4E10 with the viral membrane. We use the model to elucidate the parameters that determine the ability of these antibodies to disable epitopes and propose an extension of the model to analyze neutralization data. The extended model predicts the dependencies of IC50 for neutralization on the rate constants that characterize antibody binding, the rate of fusion of gp41, and the number of gp41 bridging the virus and target cell at the start of the pre-hairpin intermediate. Analysis of neutralization experiments indicate that only a small number of gp41 bridges must be disabled to prevent fusion. However, the model cannot determine the exact number from neutralization experiments alone.

  10. A Direct Link from the Gas to the Condensed Phase: A Rotational Spectroscopic Study of 2,2,2-Trifluoroethanol Trimers.

    PubMed

    Thomas, Javix; Seifert, Nathan A; Jäger, Wolfgang; Xu, Yunjie

    2017-02-23

    Rotational spectra of the three most stable conformers (I, II, III) of the ternary 2,2,2-trifluoroethanol (TFE) cluster were measured using Fourier transform microwave spectrometers, and unambiguously assigned with the aid of ab initio calculations. The most stable conformer, I, contains one trans-TFE subunit which is unstable in its isolated gas phase form. The study offers new insights into how the trans conformation is stabilized in TFE clusters of increasing size, and eventually becomes a dominant conformation in the liquid phase. A detailed analysis shows that while O-H⋅⋅⋅O-H and O-H⋅⋅⋅F-C hydrogen bonds are the most significant attractive interactions which stabilize all three conformers, the main driving force for the stability of I over III, which has all gauche-TFE subunits, is the attractive interaction of C-F⋅⋅⋅F-C contact pairs. A new type of three-point F⋅⋅⋅F⋅⋅⋅F attractive contact interaction is also identified.

  11. Direct observation of high-spin states in manganese dimer and trimer cations by x-ray magnetic circular dichroism spectroscopy in an ion trap

    SciTech Connect

    Zamudio-Bayer, V.; Hirsch, K.; Langenberg, A.; Kossick, M.; Ławicki, A.; Lau, J. T.; Terasaki, A.; Issendorff, B. von

    2015-06-21

    The electronic structure and magnetic moments of free Mn{sub 2}{sup +} and Mn{sub 3}{sup +} are characterized by 2p x-ray absorption and x-ray magnetic circular dichroism spectroscopy in a cryogenic ion trap that is coupled to a synchrotron radiation beamline. Our results directly show that localized magnetic moments of 5 μ{sub B} are created by 3d{sup 5}({sup 6}S) states at each ionic core, which are coupled ferromagnetically to form molecular high-spin states via indirect exchange that is mediated in both cases by a delocalized valence electron in a singly occupied 4s derived antibonding molecular orbital with an unpaired spin. This leads to total magnetic moments of 11 μ{sub B} for Mn{sub 2}{sup +} and 16 μ{sub B} for Mn{sub 3}{sup +}, with no contribution of orbital angular momentum.

  12. Vaginal delivery of the recombinant HIV-1 clade-C trimeric gp140 envelope protein CN54gp140 within novel rheologically structured vehicles elicits specific immune responses

    PubMed Central

    Curran, Rhonda M.; Donnelly, Louise; Morrow, Ryan J.; Fraser, Carol; Andrews, Gavin; Cranage, Martin; Malcolm, R. Karl; Shattock, Robin J.; Woolfson, A. David

    2009-01-01

    Rheologically structured vehicle (RSV) gels were developed as delivery systems for vaginal mucosal vaccination with an HIV-1 envelope glycoprotein (CN54gp140). RSVs comprised a mucoadhesive matrix-forming and vaginal fluid absorbing polymer. The mucoadhesive and rheological properties of the RSVs were evaluated in vitro, and the distribution, antigenicity and release of CN54gp140 were analysed by ELISA. CN54gp140 was uniformly distributed within the RSVs and continuously released in vitro in an antigenically intact form over 24 h. Vaginal administration to rabbits induced specific serum IgG, and IgG and IgA in genital tract secretions. The RSVs are a viable delivery modality for vaginal immunization. PMID:19747994

  13. Formation of a Trimeric Xpo1-Ran[GTP]-Ded1 Exportin Complex Modulates ATPase and Helicase Activities of Ded1.

    PubMed

    Hauk, Glenn; Bowman, Gregory D

    2015-01-01

    The DEAD-box RNA helicase Ded1, which is essential in yeast and known as DDX3 in humans, shuttles between the nucleus and cytoplasm and takes part in several basic processes including RNA processing and translation. A key interacting partner of Ded1 is the exportin Xpo1, which together with the GTP-bound state of the small GTPase Ran, facilitates unidirectional transport of Ded1 out of the nucleus. Here we demonstrate that Xpo1 and Ran[GTP] together reduce the RNA-stimulated ATPase and helicase activities of Ded1. Binding and inhibition of Ded1 by Xpo1 depend on the affinity of the Ded1 nuclear export sequence (NES) for Xpo1 and the presence of Ran[GTP]. Association with Xpo1/Ran[GTP] reduces RNA-stimulated ATPase activity of Ded1 by increasing the apparent KM for the RNA substrate. Despite the increased KM, the Ded1:Xpo1:Ran[GTP] ternary complex retains the ability to bind single stranded RNA, suggesting that Xpo1/Ran[GTP] may modulate the substrate specificity of Ded1. These results demonstrate that, in addition to transport, exportins such as Xpo1 also have the capability to alter enzymatic activities of their cargo.

  14. Theoretical study of the structures and electron affinities of the dimers and trimers of the group IB metals (Cu, Ag, and Au)

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Partridge, Harry

    1989-01-01

    The molecular structure of both the neutral and negatively charged diatomic and triatomic systems containing the Cu, Ag, and Au metals are determined from ab initio calculations. For the neutral triatomic systems, the lowest energy structure is found to be triangular. The relative stability of the 2A1 and 2B2 structures can be predicted simply by knowing the constituent diatomic bond distances and atomic electron affinities (EAs). The lowest energy structure is linear for all of the negative ions. For anionic clusters containing Au, the Au atom(s) preferentially occupy the terminal position(s). The EAs of the heteronuclear systems can be predicted relatively accurately from a weighted average of the corresponding homonuclear systems. Although the theoretical EAs are systematically too small, accurate predictions for the EAs of the triatomics are obtained by uniformly scaling the ab initio results using the accurate experimental EA values available for the atoms and homonuclear diatomics.

  15. A novel trimeric peptide, Neuropep-1-stimulating brain-derived neurotrophic factor expression in rat brain improves spatial learning and memory as measured by the Y-maze and Morris water maze.

    PubMed

    Shin, Min Kyoo; Kim, Hong Gi; Kim, Kil Lyong

    2011-01-01

    Abundant studies have shown possible links between low levels of brain-derived neurotrophic factor (BDNF) and neurological diseases such as Alzheimer's disease, Parkinson's disease, and depression, as well as stress and anxiety; therefore, BDNF could be a therapeutic target for neurological disorders. In the present study, a positional scanning-synthetic peptide combinatorial library was utilized to identify a peptide modulator of BDNF expression in the hippocampal neuronal cell line, H19-7. A novel tripeptide (Neuropep-1) induced a significant increase of BDNF mRNA and protein levels in H19-7 cells. Pre-treatment of TrkB inhibitor (K252a) did not block Neuropep-1-induced BDNF up-regulation. These results indicate that Neuropep-1 may up-regulate BDNF expression that might be independent of the TrkB receptor pathway. Tail vein injection of Neuropep-1 significantly up-regulated BDNF expression, TrkB phosphorylation, and its downstream signals including activation of Akt, ERK, and cAMP response element binding in the rat hippocampus. To evaluate improvement of spatial learning and memory (SLM) by Neuropep-1-induced BDNF up-regulation, the Y-maze and Morris water maze tests were performed. These results showed Neuropep-1 injection improved SLM performance with increase of BDNF and TrkB expression, activation of TrkB downstream signals in rat hippocampus compared with the control group. However, phosphorylation levels of TrkB were not changed when it was normalized to the level of TrkB expression. The difference on TrkB phosphorylation in Neuropep-1-injected rats may be affected by behavioral tests. These results suggest that Neuropep-1 may improve SLM via activation of the BDNF/TrkB signaling pathway in the rat hippocampus. Therefore, our findings represent that Neuropep-1 might be a potential candidate for treatment of learning and memory disorders as well as neurological diseases involving the abnormal expression of BDNF.

  16. A radiographic, morphologic, biochemical and molecular analysis of a case of achondrogenesis type II resulting from substitution for a glycine residue (Gly691-->Arg) in the type II collagen trimer.

    PubMed

    Mortier, G R; Wilkin, D J; Wilcox, W R; Rimoin, D L; Lachman, R S; Eyre, D R; Cohn, D H

    1995-02-01

    The type II collagenopathies form a continuous spectrum of clinical severity, ranging from lethal achondrogenesis type II and hypochondrogenesis, through spondyloepiphyseal dysplasia, spondyloepimetaphyseal dysplasia and Kniest dysplasia to the Stickler syndrome and familial precocious osteoarthropathy at the mildest end of the spectrum. We have carried out a radiographic, morphologic, biochemical and molecular study in a case of achondrogenesis type II. Electron micrographs showed inclusion bodies of dilated rough endoplasmic reticulum in the chondrocytes and the presence of sparse collagen fibers in the cartilage matrix. Protein analysis of collagen from cartilage indicated posttranslational overmodification of the major cyanogen bromide peptides, and suggested a mutation near the carboxyl terminus of the type II collagen molecule. Analysis at the DNA level demonstrated that the phenotype was produced by a single base change (G-->C) that resulted in the substitution of glycine691 by arginine in the type II collagen triple helical domain. We confirm previous observations in three cases of hypochondrogenesis that glycine substitutions in the alpha 1(II) chain can result in a phenotype at the most severe end of the type II collagenopathy spectrum.

  17. Fixation of carbon dioxide by macrocyclic lanthanide(III) complexes under neutral conditions producing self-assembled trimeric carbonato-bridged compounds with μ3-η2:η2:η2 bonding.

    PubMed

    Bag, Pradip; Dutta, Supriya; Biswas, Papu; Maji, Swarup Kumar; Flörke, Ulrich; Nag, Kamalaksha

    2012-03-28

    A series of mononuclear lanthanide(III) complexes [Ln(LH(2))(H(2)O)(3)Cl](ClO(4))(2) (Ln = La, Nd, Sm, Eu, Gd, Tb, Lu) of the tetraiminodiphenolate macrocyclic ligand (LH(2)) in 95 : 5 (v/v) methanol-water solution fix atmospheric carbon dioxide to produce the carbonato-bridged trinuclear complexes [{Ln(LH(2))(H(2)O)Cl}(3)(μ(3)-CO(3))](ClO(4))(4)·nH(2)O. Under similar conditions, the mononuclear Y(III) complex forms the dimeric compound [{Y(LH(2))(H(2)O)Cl}(μ(2)-CO(3)){Y(LH(2))(H(2)O)(2)}](ClO(4))(3)·4H(2)O. These complexes have been characterized by their IR and NMR ((1)H, (13)C) spectra. The X-ray crystal structures have been determined for the trinuclear carbonato-bridged compounds of Nd(III), Gd(III) and Tb(III) and the dinuclear compound of Y(III). In all cases, each of the metal centers are 8-coordinate involving two imine nitrogens and two phenolate oxygens of the macrocyclic ligand (LH(2)) whose two other imines are protonated and intramolecularly hydrogen-bonded with the phenolate oxygens. The oxygen atoms of the carbonate anion in the trinuclear complexes are bonded to the metal ions in tris-bidentate μ(3)-η(2):η(2):η(2) fashion, while they are in bis-bidentate μ(2)-η(2):η(2) mode in the Y(III) complex. The magnetic properties of the Gd(III) complex have been studied over the temperature range 2 to 300 K and the magnetic susceptibility data indicate a very weak antiferromagnetic exchange interaction (J = -0.042 cm(-1)) between the Gd(III) centers (S = 7/2) in the metal triangle through the carbonate bridge. The luminescence spectral behaviors of the complexes of Sm(III), Eu(III), and Tb(III) have been studied. The ligand LH(2) acts as a sensitizer for the metal ions in an acetonitrile-toluene glassy matrix (at 77 K) and luminescence intensities of the complexes decrease in the order Eu(3+) > Sm(3+) > Tb(3+).

  18. Enhanced ion anisotropy by nonconventional coordination geometry: single-chain magnet behavior for a [{Fe(II)L}2{Nb(IV)(CN)8}] helical chain compound designed with heptacoordinate Fe(II).

    PubMed

    Venkatakrishnan, Thengarai S; Sahoo, Shaon; Bréfuel, Nicolas; Duhayon, Carine; Paulsen, Carley; Barra, Anne-Laure; Ramasesha, S; Sutter, Jean-Pascal

    2010-05-05

    Nonconventional heptacoordination in combination with efficient magnetic exchange coupling is shown to yield a 1-D heteronuclear {Fe(II)Nb(IV)} compound with remarkable magnetic features when compared to other Fe(II)-based single chain magnets (SCM). Cyano-bridged heterometallic {3d-4d} and {3d-5d} chains are formed upon assembling Fe(II) bearing a pentadentate macrocycle as the blocking ligand with octacyano metallates, [M(CN)(8)](4-) (M = Nb(IV), Mo(IV), W(IV)). X-ray diffraction (single-crystal and powder) measurements reveal that the [{(H(2)O)Fe(L(1))}{M(CN)(8)}{Fe(L(1))}](infinity) architectures consist of isomorphous 1-D polymeric structures based on the alternation of {Fe(L(1))}(2+) and {M(CN)(8)}(4-) units (L(1) stands for the pentadentate macrocycle). Analysis of the magnetic susceptibility behavior revealed cyano-bridged {Fe-Nb} exchange interaction to be antiferromagnetic with J = -20 cm(-1) deduced from fitting an Ising model taking into account the noncollinear spin arrangement. For this ferrimagnetic chain a slow relaxation of its magnetization is observed at low temperature revealing a SCM behavior with Delta/k(B) = 74 K and tau(0) = 4.6 x 10(-11) s. The M versus H behavior exhibits a hysteresis loop with a coercive field of 4 kOe at 1 K and reveals at 380 mK magnetic avalanche processes, i.e., abrupt reversals in magnetization as H is varied. The origin of these characteristics is attributed to the combination of efficient {Fe-Nb} exchange interaction and significant anisotropy of the {Fe(L(1))} unit. High field EPR and magnetization experiments have revealed for the parent compound [Fe(L(1))(H(2)O)(2)]Cl(2) a negative zero field splitting parameter of D approximately = -17 cm(-1). The crystal structure, magnetic behavior, and Mossbauer data for [Fe(L(1))(H(2)O)(2)]Cl(2) are also reported.

  19. Single-Chain Magnets Based on Octacyanotungstate with the Highest Energy Barriers for Cyanide Compounds

    PubMed Central

    Wei, Rong-Min; Cao, Fan; Li, Jing; Yang, Li; Han, Yuan; Zhang, Xiu-Ling; Zhang, Zaichao; Wang, Xin-Yi; Song, You

    2016-01-01

    By introducing large counter cations as the spacer, two isolated 3, 3-ladder compounds, (Ph4P)[CoII(3-Mepy)2.7(H2O)0.3WV(CN)8]·0.6H2O (1) and (Ph4As)[CoII(3-Mepy)3WV(CN)8] (2, 3-Mepy = 3-methylpyridine), were synthesized and characterized. Static and dynamic magnetic characterizations reveal that compounds 1 and 2 both behave as the single-chain magnets (SCMs) with very high energy barriers: 252(9) K for 1 and 224(7) K for 2, respectively. These two compounds display the highest relaxation barriers for cyano-bridged SCMs and are preceded only by two cobalt(II)-radical compounds among all SCMs. Meanwhile, a large coercive field of 26.2 kOe (1) and 22.6 kOe (2) were observed at 1.8 K. PMID:27071451

  20. High-temperature molecular magnets based on cyanovanadate building blocks: spontaneous magnetization at 230 k.

    PubMed

    Entley, W R; Girolami, G S

    1995-04-21

    The molecular-based magnetic materials Cs(2)Mn(||)[V(||)(CN)(6)] (1) and (Et(4)N)(0.5)Mn(l.25)- [V(CN)(5)].2H(2)O (2) (where Et is ethyl) were prepared by the addition of manganese(II) triflate to aqueous solutions of the hexacyanovanadate(II) ion at 0 degrees C. Whereas 1 crystallizes in a face-centered cubic lattice, 2 crystallizes in a noncubic space group. The cesium salt (1) has features characteristic of a three-dimensional ferrimagnet with a Néel transition at 125 kelvin. The tetraethylammonium salt (2) also behaves as a three-dimensional ferrimagnet with a Néel temperature of 230 kelvin; only two other molecular magnets have higher magnetic ordering temperatures. Saturation magnetization measurements indicate that in both compounds the V(II) and high-spin Mn(II) centers are antiferromagnetically coupled. Both 1 and 2 exhibit hysteresis loops characteristic of soft magnets below their magnetic phase-transition temperatures. The high magnetic ordering temperatures of these cyano-bridged solids confirm that the incorporation of early transition elements into the lattice promotes stronger magnetic coupling by enhancing the backbonding into the cyanide pi* orbitals.

  1. Thermostability of Well-Ordered HIV Spikes Correlates with the Elicitation of Autologous Tier 2 Neutralizing Antibodies.

    PubMed

    Feng, Yu; Tran, Karen; Bale, Shridhar; Kumar, Shailendra; Guenaga, Javier; Wilson, Richard; de Val, Natalia; Arendt, Heather; DeStefano, Joanne; Ward, Andrew B; Wyatt, Richard T

    2016-08-01

    In the context of HIV vaccine design and development, HIV-1 spike mimetics displaying a range of stabilities were evaluated to determine whether more stable, well-ordered trimers would more efficiently elicit neutralizing antibodies. To begin, in vitro analysis of trimers derived from the cysteine-stabilized SOSIP platform or the uncleaved, covalently linked NFL platform were evaluated. These native-like trimers, derived from HIV subtypes A, B, and C, displayed a range of thermostabilities, and were "stress-tested" at varying temperatures as a prelude to in vivo immunogenicity. Analysis was performed both in the absence and in the presence of two different adjuvants. Since partial trimer degradation was detected at 37°C before or after formulation with adjuvant, we sought to remedy such an undesirable outcome. Cross-linking (fixing) of the well-ordered trimers with glutaraldehyde increased overall thermostability, maintenance of well-ordered trimer integrity without or with adjuvant, and increased resistance to solid phase-associated trimer unfolding. Immunization of unfixed and fixed well-ordered trimers into animals revealed that the elicited tier 2 autologous neutralizing activity correlated with overall trimer thermostability, or melting temperature (Tm). Glutaraldehyde fixation also led to higher tier 2 autologous neutralization titers. These results link retention of trimer quaternary packing with elicitation of tier 2 autologous neutralizing activity, providing important insights for HIV-1 vaccine design.

  2. High energy fuel compositions

    SciTech Connect

    Fisher, D.H.

    1983-07-19

    A high density liquid hydrocarbon fuel composition is disclosed, singularly suited for propelling turbojet limited volume missile systems designed for shipborne deployment. The contemplated fuels are basically composed of the saturated analogues of dimers of methyl cyclopentadiene and of dicyclopentadiene and optionally include the saturated analogues of the co-trimers of said dienes or the trimers of cyclopentadiene. The various dimers and trimers are combined in a relative relationship to provide optimal performing fuels for the indicated purpose.

  3. ELPylated haemagglutinins produced in tobacco plants induce potentially neutralizing antibodies against H5N1 viruses in mice.

    PubMed

    Phan, Hoang T; Pohl, Julia; Floss, Doreen M; Rabenstein, Frank; Veits, Jutta; Le, Binh T; Chu, Ha H; Hause, Gerd; Mettenleiter, Thomas; Conrad, Udo

    2013-06-01

    Reducing the cost of vaccine production is a key priority for veterinary research, and the possibility of heterologously expressing antigen in plants provides a particularly attractive means of achieving this. Here, we report the expression of the avian influenza virus haemagglutinin (AIV HA) in tobacco, both as a monomer and as a trimer in its native and its ELPylated form. We firstly presented evidence to produce stabilized trimers of soluble HA in plants. ELPylation of these trimers does not influence the trimerization. Strong expression enhancement in planta caused by ELPylation was demonstrated for trimerized H5-ELP. ELPylated trimers could be purified by a membrane-based inverse transition cycling procedure with the potential of successful scale-up. The trimeric form of AIV HA was found to enhance the HA-specific immune response compared with the monomeric form. Plant-derived AIV HA trimers elicited potentially neutralizing antibodies interacting with both homologous virus-like particles from plants and heterologous inactivated AIV. ELPylation did not influence the functionality and the antigenicity of the stabilized H5 trimers. These data allow further developments including scale-up of production, purification and virus challenge experiments with the final goal to achieve suitable technologies for efficient avian flu vaccine production.

  4. Assembly of LamB and OmpF in deep rough lipopolysaccharide mutants of Escherichia coli K-12.

    PubMed Central

    Laird, M W; Kloser, A W; Misra, R

    1994-01-01

    Assembly of the OmpF and LamB proteins was kinetically retarded in deep rough lipopolysaccharide mutants of Escherichia coli K-12. OmpF assembly was affected at the step of conversion of metastable trimers to stable trimers, whereas LamB assembly was influenced both at the monomer-to-metastable trimer and metastable-to-stable trimer steps. These assembly defects were reversed in the presence of the sfaA1 and sfaB3 suppressor alleles, which were isolated by using ompF assembly mutants. Images PMID:8157594

  5. Monoclonal Antibodies to Different Components of the Human Cytomegalovirus (HCMV) Pentamer gH/gL/pUL128L and Trimer gH/gL/gO as well as Antibodies Elicited during Primary HCMV Infection Prevent Epithelial Cell Syncytium Formation

    PubMed Central

    Percivalle, Elena; Perez, Laurent; Lanzavecchia, Antonio; Lilleri, Daniele

    2016-01-01

    ABSTRACT Human cytomegalovirus (HCMV) may cause disseminated/end-organ disease in congenitally infected newborns and immunosuppressed transplant recipients. Two glycoprotein complexes, gH/gL/gO and gH/gL/pUL128/pUL130/pUL131 (gH/gL/pUL128L; referred to as the pentamer), are required for HCMV entry into fibroblasts and endothelial/epithelial cells, respectively, in the presence of the viral fusion protein gB. In addition, gH/gL/gO was recently reported to also be required for infection of endothelial/epithelial cells. Virus entry into human fibroblasts involves fusion of the virus envelope with the plasma membrane, whereas entry into endothelial/epithelial cells involves macropinocytosis or endocytosis and low-pH-dependent fusion with endosomes. A large set of neutralizing monoclonal antibodies (MAbs), directed to gH, gB, and multiple components of the pentamer, was developed. In addition, novel anti-gO human monoclonal antibodies were recently isolated. It is known that epithelial cell infection with a wild HCMV strain at a high multiplicity of infection produces a large number of syncytia. Incubation of heavily HCMV VR1814-infected ARPE-19 epithelial cells with neutralizing MAbs to one, two, or three components of the pUL128L portion of the pentamer blocked syncytium formation at an antibody concentration of 10 μg/ml, whereas only a partial inhibitory effect was displayed for MAbs to gO, gH, or gB at the same concentration. A blocking effect was also exhibited by convalescent-phase sera from primary HCMV infections. These findings indicate that the pentamer is required for syncytium formation in epithelial cells. IMPORTANCE Human cytomegalovirus (HCMV) mostly infects epithelial and endothelial cells in vivo. Recently, the pentamer protein complex (gH/gL/pUL128L) was identified as being required for infection of these cells, in association with the other protein complex, gH/gL/gO. In primary infections, HCMV migrates to endothelial cells and then to leukocytes, which disseminate the infection throughout the body. The virus then spreads to organs and tissues, mostly infecting either single cells or multinucleated epithelial giant cells (syncytia), depending on the viral load. Potent neutralizing human MAbs directed to distinct binding sites of the pUL128L portion of the pentamer were shown in the past to block virus dissemination. In the present study, MAbs to pUL128L were shown to block syncytium formation with a higher potency than that of MAbs to gO, gH, or gB, thus suggesting their role in limiting virus dissemination. This finding provides additional information useful for the development of anti-HCMV therapeutic antibodies and subunit vaccines. PMID:27122579

  6. Probing the Electronic and Structural Properties of the Niobium Trimer Cluster and its Mono- and Dioxides. Nb3On- and Nb3On (n=0-2)

    SciTech Connect

    Zhai, Hua Jin; Wang, Bing; Huang, Xin; Wang, Lai S.

    2009-02-06

    We report a photoelectron spectroscopy and density functional theory (DFT) study on the electronic and structural properties of Nb3-, Nb3O-, Nb3O2-, and the corresponding neutrals. Well-resolved photoelectron spectra are obtained for the anion clusters at different photon energies and are compared with DFT calculations to elucidate their structures and chemical bonding. We find that Nb3 - possesses a C2V (3A2) structure, and Nb3 is a scalene Cs (2A'') triangle. Both Nb3O- and Nb3O are found to have C2V structures, in which the O atom bridges two Nb atoms in a Nb3 triangle. The ground-state of Nb3O2 - is found surprisingly to be a low symmetry C1 (1A) structure, which contains a bridging and a terminal O atom. Molecular orbital analyses are carried out to understand the structures and bonding of the three clusters and provide insights into the sequential oxidation from Nb3- to Nb3O2-. The terminal NbdO unit is common in niobia catalysts, and the Nb3O2- cluster with a NbdO unit may be viewed as a molecular model for the catalytic sites or the initial oxidation of a Nb surface.

  7. Reactions of H3Al NMe3 with E(SiMe3)3 (E = P, As). Structural Characterization of the Trimer H2AlP(SiMe3)23 and Base-Stabilized Adduct H2AlAs(SiMe3)2 NMe3, and Their Thermal Decomposition Toward Nanocrystalline AlP and AlAs, Respectively

    DTIC Science & Technology

    1998-05-23

    Watkins, C. L.; Schauer, S. J.; Lake, C. H. Organometallics 1996,15, 3980. (e) Karsch , H. H.; Appelt, A.; Köhler, F. H.; Müller, G Organometallics 1985, 4...231. (f) Haaland, A.; Hougen, J.; Volden, H. V.; Hanika, G H.; Karsch , H. H. J. Organomet. Chem. 1987, 322, C24. (13) Dohmeier, C; Schnöckel, H

  8. Molecular detection using Rydberg, autoionizing, and cluster states. Progress report

    SciTech Connect

    Wessel, J.

    1989-08-17

    Continuing investigations of multiphoton ionization processes in naphthalene have established the geometry and spectroscopy of trimer and tetramer cluster states. A new, highly efficient ionization mechanism has been identified in the trimer. It is closely related to autoionization of 2-electron atoms by resonant 2-photon excitation and to exciton fusion in larger clusters.

  9. General correction to initial rates determined for nonprocessive exo-depolymerases acting on both substrate and product

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We recently reported on the kinetics of the polygalacturonase TtGH28 acting on trimer and dimer substrates. When the starting substrate for hydrolysis is the trimer, the product dimer is also subject to hydrolysis, resulting in discrepancies when either the concentration of dimer or monomer product ...

  10. 75 FR 6314 - Inert Ingredients; Extension of Effective Date of Revocation of Certain Tolerance Exemptions with...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-09

    ..., sodium, and zinc salts of the phosphate esters; the nonyl group is a propylene trimer isomer and the poly... isomer and the poly(oxyethylene) content averages 4 moles. cc. - - - hydroxypoly(oxyethylene) produced by..., potassium, sodium, and zinc salts of the phosphate esters; the nonyl group is a propylene trimer isomer...

  11. Design of a modular tetrameric scaffold for the synthesis of membrane-localized D-peptide inhibitors of HIV-1 entry

    PubMed Central

    Francis, J. Nicholas; Redman, Joseph S.; Eckert, Debra M.; Kay, Michael S.

    2012-01-01

    The highly conserved HIV-1 gp41 “pocket” region is a promising target for inhibiting viral entry. PIE12-trimer is a protease-resistant trimeric D-peptide inhibitor that binds to this pocket and potently blocks HIV entry. PIE12-trimer also possesses a reserve of binding energy that provides it with a strong genetic barrier to resistance (“resistance capacitor”). Here we report the design of a modular scaffold employing PEGs of discrete lengths for the efficient optimization and synthesis of PIE12-trimer. This scaffold also allows us to conjugate PIE12-trimer to several membrane-localizing cargoes, resulting in dramatically improved potency and retention of PIE12-trimer’s ability to absorb the impact of resistance mutations. This scaffold design strategy should be of broad utility for the rapid prototyping of multimeric peptide inhibitors attached to potency- or pharmacokinetic-enhancing groups. PMID:22545664

  12. A novel packing arrangement of AcrB in the lipid bilayer membrane.

    PubMed

    Ly, K; Bartho, J D; Eicher, T; Pos, K M; Mitra, A K

    2014-12-20

    The central component AcrB of the Escherichia coli drug efflux complex AcrA-AcrB-TolC has been extensively investigated by X-ray crystallography of detergent-protein 3-D crystals. In these crystals, AcrB packs as trimers - the functional unit. We visualized the AcrB-AcrB interaction in its native environment by examining E. coli lipid reconstituted 2-D crystals, which were overwhelmingly formed by asymmetric trimers stabilized by strongly-interacting monomers from adjacent trimers. Most interestingly, we observed lattices formed by an arrangement of AcrB monomers distinct from that in traditional trimers. This hitherto unobserved packing, might play a role in the biogenesis of trimeric AcrB.

  13. Design and characterization of ebolavirus GP prehairpin intermediate mimics as drug targets

    PubMed Central

    Clinton, Tracy R; Weinstock, Matthew T; Jacobsen, Michael T; Szabo-Fresnais, Nicolas; Pandya, Maya J; Whitby, Frank G; Herbert, Andrew S; Prugar, Laura I; McKinnon, Rena; Hill, Christopher P; Welch, Brett D; Dye, John M; Eckert, Debra M; Kay, Michael S

    2015-01-01

    Ebolaviruses are highly lethal filoviruses that cause hemorrhagic fever in humans and nonhuman primates. With no approved treatments or preventatives, the development of an anti-ebolavirus therapy to protect against natural infections and potential weaponization is an urgent global health need. Here, we describe the design, biophysical characterization, and validation of peptide mimics of the ebolavirus N-trimer, a highly conserved region of the GP2 fusion protein, to be used as targets to develop broad-spectrum inhibitors of ebolavirus entry. The N-trimer region of GP2 is 90% identical across all ebolavirus species and forms a critical part of the prehairpin intermediate that is exposed during viral entry. Specifically, we fused designed coiled coils to the N-trimer to present it as a soluble trimeric coiled coil as it appears during membrane fusion. Circular dichroism, sedimentation equilibrium, and X-ray crystallography analyses reveal the helical, trimeric structure of the designed N-trimer mimic targets. Surface plasmon resonance studies validate that the N-trimer mimic binds its native ligand, the C-peptide region of GP2. The longest N-trimer mimic also inhibits virus entry, thereby confirming binding of the C-peptide region during viral entry and the presence of a vulnerable prehairpin intermediate. Using phage display as a model system, we validate the suitability of the N-trimer mimics as drug screening targets. Finally, we describe the foundational work to use the N-trimer mimics as targets in mirror-image phage display, which will be used to identify d-peptide inhibitors of ebolavirus entry. PMID:25287718

  14. A Monte Carlo study of the self-assembly of bacteriorhodopsin.

    PubMed Central

    Jagannathan, Kamakshi; Chang, Rakwoo; Yethiraj, Arun

    2002-01-01

    Bacteriorhodopsin (BR) and specific lipid molecules self-assemble into a quasi two-dimensional lattice structure known as the purple membrane (PM). In the PM, BR molecules exist in a trimeric form with lipid molecules present in the space enclosed by each trimeric unit and in the inter-trimer space. These trimeric units, which have a roughly circular cross-section, are arranged in hexagonal patterns with long-ranged crystalline order. In this work, we investigate the self-assembly of BR in the PM via Monte Carlo simulations of a two-dimensional model of the membrane and proteins. The protein molecules are modeled as 120 degrees sectors of a circle and the lipid molecules enter into the model through effective protein-protein interactions. The sectors cannot overlap with each other, and in addition to this excluded volume interaction there are site-site attractive interactions between specific points of the proteins to mimic interactions between helices on the proteins and lipid-induced interactions. At low values of the attractive well depth, the proteins are found in the monomeric form at all concentrations. At moderate and high values of the attractive well depth, trimers are formed as the concentration increases, and with a further increase in concentration the trimers organize into a hexagonal lattice. The interactions between the proteins and those induced by the intra-trimer lipids play an equally important role in the formation of trimers and the lattice. The lipids in the inter-trimer space cause the trimers to orient in a specific direction in the hexagonal crystal lattice. PMID:12324411

  15. A Dual Laser Scanning Confocal and Transmission Electron Microscopy Analysis of the Intracellular Localization, Aggregation and Particle Formation of African Horse Sickness Virus Major Core Protein VP7.

    PubMed

    Wall, Gayle V; Rutkowska, Daria A; Mizrachi, Eshchar; Huismans, Henk; van Staden, Vida

    2017-02-01

    The bulk of the major core protein VP7 in African horse sickness virus (AHSV) self-assembles into flat, hexagonal crystalline particles in a process appearing unrelated to viral replication. Why this unique characteristic of AHSV VP7 is genetically conserved, and whether VP7 aggregation and particle formation have an effect on cellular biology or the viral life cycle, is unknown. Here we investigated how different small peptide and enhanced green fluorescent protein (eGFP) insertions into the VP7 top domain affected VP7 localization, aggregation, and particle formation. This was done using a dual laser scanning confocal and transmission electron microscopy approach in conjunction with analyses of the solubility, aggregation, and fluorescence profiles of the proteins. VP7 top domain modifications did not prevent trimerization, or intracellular trafficking, to one or two discrete sites in the cell. However, modifications that resulted in a misfolded and insoluble VP7-eGFP component blocked trafficking, and precluded protein accumulation at a single cellular site, perhaps by interfering with normal trimer-trimer interactions. Furthermore, the modifications disrupted the stable layering of the trimers into characteristic AHSV VP7 crystalline particles. It was concluded that VP7 trafficking is driven by a balance between VP7 solubility, trimer forming ability, and trimer-trimer interactions.

  16. Characterization of a trinuclear ruthenium species in catalytic water oxidation by Ru(bda)(pic)2 in neutral media.

    PubMed

    Zhang, Biaobiao; Li, Fei; Zhang, Rong; Ma, Chengbing; Chen, Lin; Sun, Licheng

    2016-06-30

    A Ru(III)-O-Ru(IV)-O-Ru(III) type trinuclear species was crystallographically characterized in water oxidation by Ru(bda)(pic)2 (H2bda = 2,2'-bipyridine-6,6'-dicarboxylic acid; pic = 4-picoline) under neutral conditions. The formation of a ruthenium trimer due to the reaction of Ru(IV)[double bond, length as m-dash]O with Ru(II)-OH2 was fully confirmed by chemical, electrochemical and photochemical methods. Since the oxidation of the trimer was proposed to lead to catalyst decomposition, the photocatalytic water oxidation activity was rationally improved by the suppression of the formation of the trimer.

  17. A stamp on the envelope

    PubMed Central

    SANDERS, ROGIER W.; MOORE, JOHN P.

    2015-01-01

    A high-resolution crystal structure of the HIV-1 Env trimer proteins, in their form before they fuse with target cells, will aid the design of vaccines that elicit protective immune responses to this protein complex. PMID:25296251

  18. Homometallic ferrimagnetism in the zig-zag chain compound Na2Cu5Si4O14

    NASA Astrophysics Data System (ADS)

    Reis, M. S.; Dos Santos, A. Moreira; Amaral, V. S.; Brandão, P.; Rocha, J.

    2006-06-01

    The structure of Na2Cu5Si4O14 is comprised of zig-zag chains of alternating Cu edge-sharing dimers and trimers, with different magnetic ground states, allowing the occurrence of homometallic ferrimagnetism. The magnetic susceptibility data are consistent with that of a ferrimagnetic chain compound, and are predicted using a model that considers interactions intra-trimers (related to the exchange integral J1=-224.9K ), intra-dimer (J3=40.22K) , and inter dimer-trimer (J2=-8.01K) . The magnetic interaction between the antiferromagnetic trimer and ferromagnetic dimer is in accordance with the Goodenough rules applied to the Cu-O topology. A three-dimensional antiferromagnetic ordering is observed below TN=8K , corresponding to the magnetic ordering between chains. In addition, since TN˜θp there is not a significant degree of frustration in the chain ordering.

  19. New type of trifunctional alcohol

    NASA Technical Reports Server (NTRS)

    Marsh, H. E., Jr.; Hutchison, J. J.

    1972-01-01

    New type of trifunctional alcohol was synthesized from commercially available trimer acid. Trifunctional alcohol is hydrocarbon with widely separated terminal hydroxyl groups, and was expressly developed as crosslinking agent for preparation of polyurethane propellants, binders and case liners.

  20. 21 CFR 177.2280 - 4,4′-Isopropyl-idenedi-phenol-epichloro-hydrin thermo-setting epoxy resins.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... with mixed dimers and trimers of unsaturated C18 monobasic fatty acids derived from animal and... more than 8 percent of alcohol. 1,2-Epoxy-3-phenoxypropane As curing system additive. Glyoxal Do....

  1. 21 CFR 177.2280 - 4,4′-Isopropyl-idenedi-phenol-epichloro-hydrin thermo-setting epoxy resins.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... with mixed dimers and trimers of unsaturated C18 monobasic fatty acids derived from animal and... more than 8 percent of alcohol. 1,2-Epoxy-3-phenoxypropane As curing system additive. Glyoxal Do....

  2. The organic chemistry of conducting polymers. Annual technical report, February 1, 1993--May 31, 1994

    SciTech Connect

    Tolbert, L.M.

    1994-08-19

    This paper is divided into: solitons in a box (polyacetylene), cyanines as molecular switches/beyond the cyanine limit, low band-gap heteropolymers, ``dimeric`` and ``trimeric monomers,`` and electrically conductive polymeric interconnects.

  3. Synthesis and in vitro antiproliferative activities of quinoline derivatives.

    PubMed

    Broch, Sidonie; Aboab, Bettina; Anizon, Fabrice; Moreau, Pascale

    2010-04-01

    The synthesis of new di- and trimeric quinoline derivatives is described as well as their in vitro antiproliferative activities toward a human fibroblast primary culture and two human solid cancer cell lines (MCF-7 and PA 1).

  4. Two zeolite-type frameworks in one metal-organic framework with Zn24 @Zn104 cube-in-sodalite architecture.

    PubMed

    Bu, Fei; Lin, Qipu; Zhai, Quanguo; Wang, Le; Wu, Tao; Zheng, Shou-Tian; Bu, Xianhui; Feng, Pingyun

    2012-08-20

    Two in one: A metal-organic framework obtained from three different inorganic building blocks (tetrameric Zn(4) O, trimeric Zn(3) OH, and monomeric Zn) posseses a nested cage-in-cage and framework-in-framework architecture. 24 Zn(4) O tetramers and eight Zn monomers form a sodalite cage into which a cubic cage made from eight Zn(3) (OH) trimers is nestled. Eight monomeric Zn(2+) centers interconnect these two cages.

  5. The NC2 domain of type IX collagen determines the chain register of the triple helix.

    PubMed

    Boudko, Sergei P; Bächinger, Hans Peter

    2012-12-28

    Precise mapping and unraveling the mechanism of interaction or degradation of a certain type of collagen triple helix requires the generation of short and stable collagenous fragments. This is a great challenge especially for hetero-trimeric collagens, where chain composition and register (stagger) are important factors. No system has been reported that can be efficiently used to generate a natural collagenous fragment with exact chain composition and desired chain register. The NC2 domain (only 35-50 residues) of FACIT collagens is a potent trimerization domain. In the case of type IX collagen it provides the efficient selection and hetero-trimerization of three distinct chains. The ability of the NC2 domain to determine the chain register of the triple helix is studied. We generated three possible sequence combinations (α1α1α2, α1α2α1, α2α1α1) of a type I collagen fragment (the binding region for the von Willebrand factor A3 domain) attached to the NC2 domain. In addition, two control combinations were produced that constitute homo-trimers of (α1)(3) or (α2)(3). For the hetero-trimeric constructs, α1α1α2 demonstrated a higher melting temperature than the other two. Binding experiments with the von Willebrand factor A3 domain revealed the homo-trimer of (α1)(3) as the strongest binding construct, whereas the homo-trimer of (α2)(3) showed no binding. For hetero-trimers, α1α1α2 was found to be the strongest binding construct. Differences in thermal stability and binding to the A3 domain unambiguously demonstrate that the NC2 domain of type IX collagen determines not only the chain composition but also the chain register of the adjacent triple helix.

  6. Low Solar Absorbing Chemical Agent Resistant Coatings with Nano-Additives

    DTIC Science & Technology

    2009-02-01

    quantify ratio of side products vs. NCO:OH ratio • Adjust additives, reaction conditions, etc. – to make more favorable distribution UNCLASSIFIED...Polyester Resin (functional -OH) HDI Biuret (NCO) 75% resin solids, 25% solvent Siliceous B Army Green Hydroxyl Functional PU Water Dispersible Modified...Nav/Air Grey Conventional Polyester: 100% solid (low MW) Blend of HDI Trimers 100% solid Siliceous w./fluoro additives HDI Biuret HDI Trimer Poly

  7. A novel function of the N-terminal domain of PA in assembly of influenza A virus RNA polymerase.

    PubMed

    Suzuki, Tadaki; Ainai, Akira; Nagata, Noriyo; Sata, Tetsutaro; Sawa, Hirofumi; Hasegawa, Hideki

    2011-11-04

    Transcription and replication of the negative-sense single-stranded influenza A virus genomic viral RNA are catalyzed by the viral RNA polymerase, which is a trimeric complex encoded by the three largest segments of the influenza virus genome: PB1, PB2, and PA. Numerous studies of the trimeric polymerase complex assembly have substantially contributed to current understanding of influenza virus replication. However, the dynamics of spatial and temporal macromolecular interactions involving virus and host proteins during the formation of the trimeric polymerase complex (PA-PB1-PB2) are still not completely understood. In this study, bimolecular fluorescence complementation (BiFC) and Raster image correlation spectroscopy (RICS) were applied to monitor the interactions between PB1, PB2, and PA. The BiFC probes of PA-PB1 and PB1-PB2 could monitor the trimeric polymerase complex as well as the binary complex. Furthermore, the C-terminal domain of PA (PAC) promoted interaction between PB1 and PB2 in the cytoplasm and that the N-terminal domain of PA (PAN) inhibited the aberrant trimeric complex formation and assembly of higher-order oligomers induced by PAC in the cytoplasm. Taken together, these results revealed a novel function of PAN in the formation of the trimeric polymerase complexes of influenza A virus.

  8. Mathematical models: a key to understanding HIV envelope interactions?

    PubMed

    Magnus, Carsten; Brandenberg, Oliver F; Rusert, Peter; Trkola, Alexandra; Regoes, Roland R

    2013-12-15

    The spikes of the human immunodeficiency virus (HIV) mediate viral entry and are the most important targets for neutralizing antibodies. Each spike consists of three identical subunits. The role of the spike's subunits in antibody binding is not fully understood. One experimental approach to analyze trimer function uses assays with mixed envelope trimer expressing cells or viruses. As these experiments do not allow direct observation of subunit functions, mathematical models are required to interpret them. Here we describe a modeling framework to study (i) the interaction of the V1V2 loop with epitopes on the V3 loop and (ii) the composition of quaternary epitopes. In a first step we identify which trimers can form in these assays and how they function under antibody binding. We then derive the behavior of an average trimer. We contrast two experimental reporting systems and list their advantages and disadvantages. In these experiments trimer formation might not be perfectly random and we show how these effects can be tested. As we still lack a potent vaccine against HIV, and this vaccine surely has to stimulate the production of neutralizing antibodies, mixed trimer approaches in combination with mathematical models will help to identify vulnerable sites of the HIV spike.

  9. Sub-one-nanometer gap (SONG) for nanogap-enhanced Raman scattering (NERS)

    NASA Astrophysics Data System (ADS)

    Lee, Haemi; Lee, Jung-Hoon; Nam, Jwa-Min; Suh, Yung Doug

    2016-09-01

    Accurate measurement of Rayleigh scattering is crucially important for fundamental understanding of the plasmonic properties of meltimeric (>= 3) nanoparticles that can be served as efficient SERS sensing platforms and nanophotonic materials. Thus, using the laser-scanning assisted dark-field microscopy that enabled to precisely collect far-field (Rayleigh) scattering from the centers of individual trimeric nanoparticles, we monitored spectral redistributions of oscillating coupled plasmonic modes as a function of trimer symmetry. As a consequence of the precise measurement of the polarization-resolved Rayleigh scattering spectra obtained from triangular trimers to linear trimers via elongated triangular trimers, the in-phase horizontally oscillating plasmonic mode with the largest dipole moment is found to be greatly increased by 20-folds, whereas the axially oscillating plasmonic mode with the second-largest dipole moment is dramatically decreased by 70-folds. Consequently, the overall quantity of the far-field scattering, the total sum of the individual coupled plasmonic modes, was gradually increased by 2-folds. The precise polarization-resolved Rayleigh scat