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Sample records for key structural analogues

  1. Stereocontrolled Synthesis of Key Advanced Intermediates toward Simplified Acetogenin Analogues.

    PubMed

    Le Huérou, Yvan; Doyon, Julien; Grée, René L.

    1999-09-01

    The stereo- and enantiocontrolled synthesis of substituted beta-hydroxy ethers based on glycol and catechol bearing an alkyne group and a series of substituents is reported. These substrates were designed to mimic the bis-THF array of annonaceous acetogenins and to provide an access to simplified and modified analogues. The key steps of the synthesis involve the condensation of the nonracemic mesylate of solketal with ethylene glycol and catechol, followed by an alkylation with a glycidyl derivative. Under appropriate conditions, the reaction is completely stereoselective and allows the synthesis of all the diastereomers. After the epoxide was opened with triethylsilylacetylene, the second epoxide was unmasked and reacted with a series of alkyl, aryl, amine, and alcohol reagents. A series of 28 analogues was prepared having a glycol or a catechol core, a stereodefined configuration of the flanking hydroxyl groups, and an acetylenic appendage suitable for a coupling to a lactone-bearing fragment. PMID:11674687

  2. Dirac structures for higher analogues of Courant algebroids

    NASA Astrophysics Data System (ADS)

    Bi, Yanhui; Sheng, Yunhe

    2015-11-01

    In this paper, we introduce the notion of a (p, k)-Dirac structure in TM ? ?pT*M, where 0 ? k ? p - 1. The (p, 0)-Dirac structures are exactly the higher analogues of Dirac structures of order p introduced by Zambon in [L?-algebras and higher analogues of Dirac structures and Courant algebroids, J. Symplectic Geom.10(4) (2012) 563-599]. The (p, p - 1)-Dirac structures are exactly the Nambu-Dirac structures introduced by Hagiwara in [Nambu-Dirac manifolds, J. Phys. A35(5) (2002) 1263-1281]. In the regular case, such a (p, k)-Dirac structure is characterized by a characteristic pair.

  3. Relationship between antimold activity and molecular structure of cinnamaldehyde analogues.

    PubMed

    Zhang, Yuanyuan; Li, Shujun; Kong, Xianchao

    2013-03-01

    A quantitative structure-activity relationship (QSAR) modeling of the antimold activity of cinnamaldehyde analogues against of Aspergillus niger and Paecilomyces variotii was presented. The molecular descriptors of cinnamaldehyde analogues were calculated by the CODESSA program, and these descriptors were selected by best multi-linear regression method (BMLR). Satisfactory multilinear regression models of Aspergillus niger and Paecilomyces variotii were obtained with R(2)=0.9099 and 0.9444, respectively. The models were also satisfactorily validated using internal validation and leave one out validation. The QSAR models provide the guidance for further synthetic work. PMID:23374870

  4. The International Space Analogue Rock Store (ISAR): A key tool for future planetary exploration.

    NASA Astrophysics Data System (ADS)

    Bost, N.; Westall, F.; Ramboz, C.; Foucher, F.

    2012-04-01

    In order to prepare the next in situ space missions we have created a « lithothèque » of analogue rocks for calibrating and testing future (and existing) space flight instruments. This rock collection is called the International Space Analogue Rockstore (ISAR) and is hosted in the CNRS and the Observatoire des Sciences de l'Univers en Region Centre (OSUC) in Orléans. For maximum science return, all instruments on a single mission should ideally be tested with the same suite of relevant analogue materials. The ISAR lithothéque aims to fulfill this role by providing suitable materials to instrument teams [1]. The lithothèque is accompanied by an online database of all relevant structural, textural, and geochemical data (www.isar.cnrs-orleans.fr).The data base will also be available during missions to aid interpretation of data obtained in situ. Mars is the immediate goal for MSL-2011 and the new international Mars 2018 mission. The lithothèque thus presently contains relevant Mars-analogue rock and mineral samples, a preliminary range of which is now available to the scientific community for instrument testing [2]. The preliminary group of samples covers a range of lithologies to be found on Mars, especially those in Noachain/Hesperian terrains where MSL will land (Gale Crater) and where the 2018 landing site will most likely be located. It includes a variety of basalts (tephrite, primitive basalt, silicified basalt; plus cumulates), komatiites, artificially synthesized martian basalts [3], volcanic sands, a banded iron formation, carbonates associated with volcanic lithologies and hydrothermalism, the clay Nontronite, and hydrothermal cherts. Some of the silicified volcanic sands contain traces of early life that are good analogues for potential martian life [4]. [1] Westall F. et al., LPI contribution 1608, 1346, 42nd LPSC, 2011; [2] Bost N. et al., in review (Icarus); [3] Bost N. et al., in review (Meteoritics); [4] Westall et al., 2011, Planetary and Space Science 59. ISAR Team: N. Bost, F. Westall, C; Ramboz, F. Foucher, D. Pullan, T. Zegers, B. Hoffman, F. Rull, J. Bridges, A; Steele, H. Amundsen, R. Barbieri, A. Hubert, B. Cavalazzi, J. Bridges, M. Viso, J. Vago, S. Petit, A. Meunier, I. Fleischer, G. Klingelhöfer, N. Arndt…

  5. A Structurally Simplified Analogue of Geldanamycin Exhibits Neuroprotective Activity

    PubMed Central

    2013-01-01

    The syntheses of a structurally simplified geldanamycin analogue 2 and two related compounds are described. Compound 2 conferred cytoprotection and quenched ROS and lipid peroxidation in a dose-dependent manner in Friedreich’s ataxia (FRDA) lymphocytes at low micromolar concentrations. It also prevented ROS-induced damage of cellular lipid membranes and maintained the mitochondrial membrane potential of FRDA lymphocytes. In addition, 2 did not inhibit Hsp90 when tested at micromolar concentrations, exhibited no cytotoxicity, and afforded neuroprotection to differentiated SH-SY5Y cells under conditions of A?-induced cell toxicity. PMID:24900591

  6. Structural apelin analogues: mitochondrial ROS inhibition and cardiometabolic protection in myocardial ischaemia reperfusion injury

    PubMed Central

    Pisarenko, Oleg; Shulzhenko, Valentin; Studneva, Irina; Pelogeykina, Yulia; Timoshin, Alexander; Anesia, Rodica; Valet, Philippe; Parini, Angelo; Kunduzova, Oksana

    2015-01-01

    Background and Purpose Mitochondria-derived oxidative stress is believed to be crucially involved in cardiac ischaemia reperfusion (I/R) injury, although currently no therapies exist that specifically target mitochondrial reactive oxygen species (ROS) production. The present study was designed to evaluate the potential effects of the structural analogues of apelin-12, an adipocyte-derived peptide, on mitochondrial ROS generation, cardiomyocyte apoptosis, and metabolic and functional recovery to myocardial I/R injury. Experimental Approach In cultured H9C2 cardiomyoblasts and adult cardiomyocytes, oxidative stress was induced by hypoxia reoxygenation. Isolated rat hearts were subjected to 35?min of global ischaemia and 30?min of reperfusion. Apelin-12, apelin-13 and structural apelin-12 analogues, AI and AII, were infused during 5?min prior to ischaemia. Key Results In cardiac cells, mitochondrial ROS production was inhibited by the structural analogues of apelin, AI and AII, in comparison with the natural peptides, apelin-12 and apelin-13. Treatment of cardiomyocytes with AI and AII decreased cell apoptosis concentration-dependently. In a rat model of I/R injury, pre-ischaemic infusion of AI and AII markedly reduced ROS formation in the myocardial effluent and attenuated cell membrane damage. Prevention of oxidative damage by AI and AII was associated with the improvement of functional and metabolic recovery after I/R in the heart. Conclusions and Implications These data provide the evidence for the potential of the structural apelin analogues in selective reduction of mitochondrial ROS generation and myocardial apoptosis and form the basis for a promising therapeutic strategy in the treatment of oxidative stress-related heart disease. PMID:25521429

  7. Capsaicin and its analogues: structure-activity relationship study.

    PubMed

    Huang, X-F; Xue, J-Y; Jiang, A-Q; Zhu, H-L

    2013-01-01

    Capsaicin, the main ingredient responsible for the hot pungent taste of chilli peppers, is an alkaloid found in the Capsicum family. Capsaicin was traditionally used for muscular pain, headaches, to improve circulation and for its gastrointestinal protective effects. It was also commonly added to herbal formulations because it acts as a catalyst for other herbs and aids in their absorption. In addition, capsaicin and other capsaicinoid compounds showed strong evidence of having promising potential in the fight against many types of cancer. The mechanism of action of capsaicin has been extensively studied over the past decade. It has been established that capsaicin binds to the transient receptor potential vanilloid 1 receptor which was expressed predominantly by sensory neurons. And many analogues of capsaicin have been synthesized and evaluated for diverse bioactivities. In this review, we will attempt to summarize the biology and structure-activity relationship of capsaicinoids. PMID:23627937

  8. Modern freshwater microbialite analogues for ancient dendritic reef structures

    NASA Technical Reports Server (NTRS)

    Laval, B.; Cady, S. L.; Pollack, J. C.; McKay, C. P.; Bird, J. S.; Grotzinger, J. P.; Ford, D. C.; Bohm, H. R.

    2000-01-01

    Microbialites are organosedimentary structures that can be constructed by a variety of metabolically distinct taxa. Consequently, microbialite structures abound in the fossil record, although the exact nature of the biogeochemical processes that produced them is often unknown. One such class of ancient calcareous structures, Epiphyton and Girvanella, appear in great abundance during the Early Cambrian. Together with Archeocyathids, stromatolites and thrombolites, they formed major Cambrian reef belts. To a large extent, Middle to Late Cambrian reefs are similar to Precambrian reefs, with the exception that the latter, including terminal Proterozoic reefs, do not contain Epiphyton or Girvanella. Here we report the discovery in Pavilion Lake, British Columbia, Canada, of a distinctive assemblage of freshwater calcite microbialites, some of which display microstructures similar to the fabrics displayed by Epiphyton and Girvanella. The morphologies of the modern microbialites vary with depth, and dendritic microstructures of the deep water (> 30 m) mounds indicate that they may be modern analogues for the ancient calcareous structures. These microbialites thus provide an opportunity to study the biogeochemical interactions that produce fabrics similar to those of some enigmatic Early Cambrian reef structures.

  9. Isoxazole analogues bind the System xc? Transporter: Structure-activity Relationship and Pharmacophore Model

    PubMed Central

    Patel, Sarjubhai A.; Rajale, Trideep; O’Brien, Erin; Burkhart, David J.; Nelson, Jared K.; Twamley, Brendan; Blumenfeld, Alex; Szabon-Watola, Monika I.; Gerdes, John M.; Bridges, Richard J.; Natale, Nicholas R.

    2009-01-01

    Analogues of amino methylisoxazole propionic acid (AMPA), were prepared from a common intermediate 12, including lipophilic analogues using lateral metalation and electrophilic quenching, and were evaluated at System xc?. Both the 5-naphthylethyl-(16) and 5-naphthylmethoxymethyl-(17) analogues adopt an E-conformation in the solid state, yet while the former has robust binding at System xc?, the latter is virtually devoid of activity. The most potent analogues were amino acid naphthyl-ACPA 7g, and hydrazone carboxylic acid, 11e Y=Y?=3,5-(CF3)2, which both inhibited glutamate up-take by the System xc? transporter with comparable potency to the endogenous substrate cystine, whereas in contrast the closed isoxazolo[3,4-d] pyridazinones 13 have significantly lower activity. A preliminary pharmacophore model has been constructed to provide insight into the analogue structure-activity relationships. PMID:19932968

  10. Preparing to return to the Moon: Lessons from science-driven analogue missions to the Mistastin Lake impact structure, Canada, a unique lunar analogue site

    NASA Astrophysics Data System (ADS)

    Osinski, G. R.; Barfoot, T.; Chanou, A.; Daly, M. G.; Francis, R.; Hodges, K. V.; Jolliff, B. L.; Mader, M. M.; McCullough, E. M.; Moores, J. E.; Pickersgill, A.; Pontefract, A.; Preston, L.; Shankar, B.; Singleton, A.; Sylvester, P.; Tornabene, L. L.; Young, K. E.

    2013-12-01

    Impact cratering is the dominant geological process on the Moon, Near Earth Asteroids (NEAs) and the moons of Mars - the objectives for the new Solar System Exploration Research Virtual Institute (SSERVI). Led by members of the Canadian Lunar Research Network (CLRN), funded by the Canadian Space Agency, and with participants from the U.S., we carried out a series of analogue missions on Earth in order to prepare and train for future potential robotic and human sample return missions. Critically, these analogue missions were driven by the paradigm that operational and technical objectives are conducted while conducting new science and addressing real overarching scientific objectives. An overarching operational goal was to assess the utility of a robotic field reconnaissance mission as a precursor to a human sortie sample return mission. Here, we focus on the results and lessons learned from a robotic precursor mission and follow on human-robotic mission to the Mistastin Lake impact structure in Labrador, northern Canada (55°53'N; 63°18'W). The Mistastin structure was chosen because it represents an exceptional analogue for lunar craters. This site includes both an anorthositic target, a central uplift, well-preserved impact melt rocks - mostly derived from melting anorthosite - and is (or was) relatively unexplored. This crater formed ~36 million years ago and has a diameter of ~28 km. The scientific goals for these analogue missions were to further our understanding of impact chronology, shock processes, impact ejecta and potential resources within impact craters. By combining these goals in an analogue mission campaign key scientific requirements for a robotic precursor were determined. From the outset, these analogue missions were formulated and executed like an actual space mission. Sites of interest were chosen using remote sensing imagery without a priori knowledge of the site through a rigorous site selection process. The first deployment occurred in August and September 2010 and involved simulated robotic surveying of selected 'landing sites' at the Mistastin structure. The second deployment took place at the same location in 2011, which included simulated astronaut surface operations with, and without, the aid of a robotic assistant. A mission control team, based at the University of Western Ontario, London, Ontario, 1,900 km from the field site, oversaw operations. Our study showed the value of precursor reconnaissance missions in providing surface geology visualization at resolutions and from viewpoints not achievable from orbit, including high-resolution surface imagery on the scale of 10s of metres to kilometres. Indeed, data collected during the robotic precursor mission led to the formulation of a hypothesis that a large impact melt outcrop - named Discovery Hill - represents an impact melt pond in the terraced region of the crater, analogous to similar ponds of melt documented around the rim of well-preserved lunar craters such as Tycho. Further discoveries, that will be highlight here, include documentation of ejecta deposits for the first time at Mistastin, quantification of shock in anorthosites, and refined age estimates for the Mistastin impact event.

  11. Structures of the hydrolase domain of human 10-formyltetrahydrofolate dehydrogenase and its complex with a substrate analogue.

    PubMed

    Kursula, Petri; Schüler, Herwig; Flodin, Susanne; Nilsson-Ehle, Petra; Ogg, Derek J; Savitsky, Pavel; Nordlund, Pär; Stenmark, Pål

    2006-11-01

    10-Formyltetrahydrofolate dehydrogenase is a ubiquitously expressed enzyme in the human body. It catalyses the formation of tetrahydrofolate and carbon dioxide from 10-formyltetrahydrofolate, thereby playing an important role in the human metabolism of one-carbon units. It is a two-domain protein in which the N-terminal domain hydrolyses 10-formyltetrahydrofolate into formate and tetrahydrofolate. The high-resolution crystal structure of the hydrolase domain from human 10-formyltetrahydrofolate dehydrogenase has been determined in the presence and absence of a substrate analogue. The structures reveal conformational changes of two loops upon ligand binding, while key active-site residues appear to be pre-organized for catalysis prior to substrate binding. Two water molecules in the structures mark the positions of key oxygen moieties in the catalytic reaction and reaction geometries are proposed based on the structural data. PMID:17057331

  12. Understanding caldera structure and development: An overview of analogue models compared to natural calderas

    NASA Astrophysics Data System (ADS)

    Acocella, Valerio

    2007-12-01

    Understanding the structure and development of calderas is crucial for predicting their behaviour during periods of unrest and to plan geothermal and ore exploitation. Geological data, including that from analysis of deeply eroded examples, allow the overall surface setting of calderas to be defined, whereas deep drillings and geophysical investigations provide insights on their subsurface structure. Collation of this information from calderas worldwide has resulted in the recent literature in five main caldera types (downsag, piston, funnel, piecemeal, trapdoor), being viewed as end-members. Despite its importance, such a classification does not adequately examine: (a) the structure of calderas (particularly the nature of the caldera's bounding faults); and (b) how this is achieved (including the genetic relationships among the five caldera types). Various sets of analogue models, specifically devoted to study caldera architecture and development, have been recently performed, under different conditions (apparatus, materials, scaling parameters, stress conditions). The first part of this study reviews these experiments, which induce collapse as a result of underpressure or overpressure within the chamber analogue. The experiments simulating overpressure display consistent results, but the experimental depressions require an exceptional amount of doming, seldom observed in nature, to form; therefore, these experiments are not appropriate to understand the structure and formation of most natural calderas. The experiments simulating underpressure reveal a consistent scenario for caldera structure and development, regardless of their different boundary conditions. These show that complete collapse proceeds through four main stages, proportional to the amount of subsidence, progressively characterized by: (1) downsag; (2) reverse ring fault; (3) peripheral downsag; (4) peripheral normal ring fault. The second part of this study verifies the possibility that these latter calderas constitute a suitable analogue to nature and consists of a comprehensive comparison of the underpressure experiments to natural calderas. This shows that all the experimental structures, as well as their progressive development, are commonly observed at natural calderas, highlighting a consistency between models and nature. As the shallow structure of experimental calderas corresponds to a precise architecture at depth, it provides a unique key to infer the deeper structure of natural calderas: recognizing diagnostic surface features within a caldera will thus allow it to be categorized within a precise structural and evolutionary context. The general relationship between the evolutionary stage of a caldera and its d/s (diameter/subsidence) ratio allows such a quantification, with stage 1 calderas characterized by d/s > 40, stage 2 by 18 < d/s < 40, stage 3 by 14 < d/s < 18 and stage 4 by d/s < 14. The consistency between experiments and nature suggests that, in principle, the d/s ratio may permit to evaluate the overall structure and evolutionary stage of a caldera even when its surface structure is poorly known. The volume of erupted magma associated with caldera collapse is poorly dependent on the d/s ratio or evolutionary stage; however, the location of sin- and post-collapse volcanism may depend not only upon the amount of collapse, but also on the roof aspect ratio. As the regional tectonic control is concerned, the experiments explain the ellipticity of a part of natural calderas elongated parallel to the regional extension; the control of pre-existing structures may explain the elongation of elliptic calderas oblique or parallel to the regional structures. The four stages adequately explain the architecture and development of the established caldera end-members along a continuum, where one or more end-members (downsag, piston, funnel, piecemeal, trapdoor) may correspond to a specific stage. While such a continuum is controlled by progressive subsidence, specific collapse geometries will result from secondary contributo

  13. Total Synthesis of Viridicatumtoxin B and Analogues Thereof: Strategy Evolution, Structural Revision, and Biological Evaluation

    PubMed Central

    2015-01-01

    The details of the total synthesis of viridicatumtoxin B (1) are described. Initial synthetic strategies toward this intriguing tetracycline antibiotic resulted in the development of key alkylation and Lewis acid-mediated spirocyclization reactions to form the hindered EF spirojunction, as well as Michael–Dieckmann reactions to set the A and C rings. The use of an aromatic A-ring substrate, however, was found to be unsuitable for the introduction of the requisite hydroxyl groups at carbons 4a and 12a. Applying these previous tactics, we developed stepwise approaches to oxidize carbons 12a and 4a based on enol- and enolate-based oxidations, respectively, the latter of which was accomplished after systematic investigations that revealed critical reactivity patterns. The herein described synthetic strategy resulted in the total synthesis of viridicatumtoxin B (1), which, in turn, formed the basis for the revision of its originally assigned structure. The developed chemistry facilitated the synthesis of a series of viridicatumtoxin analogues, which were evaluated against Gram-positive and Gram-negative bacterial strains, including drug-resistant pathogens, revealing the first structure–activity relationships within this structural type. PMID:25317739

  14. The Clar Structure in Inorganic BN Analogues of Polybenzenoid Hydrocarbons: Does it Exist or Not?

    PubMed

    Wu, Jingjing; Zhu, Jun

    2015-12-01

    The Clar structure of polybenzenoid hydrocarbons (PBHs) have attracted considerable interest of both theoretical and experimental chemists since it was proposed in the 1950s. However, it remains unclear whether the Clar structure could exist in inorganic PBHs, the boron nitride (BN) analogues where the alternate boron and nitrogen atoms are used to replace the carbon atoms of PBHs. Here, we carry out thorough density functional theory (DFT) calculations to probe the possibility of Clar structures in BN analogues of PBHs. A strong correlation (r(2) =0.975) between the ring number (n=3-10) of BN analogues of [n]acenes and energy differences between the most and least stable isomers is identified, suggesting the existence of Clar structures in inorganic PBHs. In addition, the slightly weaker correlations in comparison to that (r(2) =0.989) of the organic PBHs is rationalized by the reduced aromaticity, which is revealed by two aromatic indices: ELF? and SCI. PMID:26467786

  15. Lead structures for new antibacterials: stereocontrolled synthesis of a bioactive muraymycin analogue.

    PubMed

    Spork, Anatol P; Büschleb, Martin; Ries, Oliver; Wiegmann, Daniel; Boettcher, Stefan; Mihalyi, Agnes; Bugg, Timothy D H; Ducho, Christian

    2014-11-17

    Naturally occurring muraymycin nucleoside antibiotics represent a promising class of novel antibacterial agents. The structural complexity suggests the investigation of simplified analogues as potential lead structures, which can then be further optimized towards highly potent antimicrobials. Herein we report studies on muraymycin-derived potential lead structures lacking an aminoribose motif found in most naturally occurring muraymycins. We have identified a 5'-defunctionalized motif to be ideal in terms of stability and chemical accessibility and have synthesized a full-length muraymycin analogue based on this structure using a novel fully stereocontrolled route. The obtained 5'-deoxy analogue of the natural product muraymycin C4 showed good inhibitory properties towards the bacterial target protein MraY, sufficient pharmacokinetic stability and no cytotoxicity against human cells, thus making it a promising lead for antibacterial drug development. PMID:25318977

  16. Synthesis of structurally simplified analogues of aplidinone A, a pro-apoptotic marine thiazinoquinone.

    PubMed

    Aiello, Anna; Fattorusso, Ernesto; Luciano, Paolo; Menna, Marialuisa; Calzado, Marco A; Muñoz, Eduardo; Bonadies, Francesco; Guiso, Marcella; Sanasi, Maria Filomena; Cocco, Gianfranco; Nicoletti, Rosario

    2010-01-15

    The synthesis of analogues of aplidinone A (7), a prenylated quinone isolated from the Mediterranean ascidian Aplidium conicum, has been performed. This work not only allowed confirming the structural assignment of aplidinone A, previously made with the support of GIAO shielding calculations, but, above all, made a series of structurally related quinone derivatives (compounds 8-13 and the natural metabolite) available for a screening in vitro for cytotoxic and pro-apoptotic activity and for SAR studies. The study evidenced one of the synthetic analogues (11) as a potent cytotoxic and pro-apoptotic agent against several tumor cell lines which also inhibits the TNFalpha-induced NF-kappaB activation in a human leukemia T cell line. This exemplifies the potential of a natural product to qualify as lead structure for medicinal chemistry campaigns, affording simplified analogues with better bioactivity and easier to synthesize. PMID:20031419

  17. Structural Analysis of Silanediols as Transition-State-Analogue Inhibitors of the Benchmark Metalloprotease Thermolysin,

    E-print Network

    Juers, Doug

    Structural Analysis of Silanediols as Transition-State-Analogue Inhibitors of the Benchmark inhibitors, including aspartic (HIV protease) and metallo (ACE and thermolysin) proteases. The use of silanediols is predicated on its resemblance to the hydrated carbonyl transition-state structure of amide

  18. Unravelling the complex deformation structures at Mt Cameroon: Field evidence and analogue experiments

    NASA Astrophysics Data System (ADS)

    Kervyn, M.; van Wyk de Vries, B.; Walter, T. R.; Mathieu, L.; Ernst, G. G.

    2009-12-01

    Mt. Cameroon is an elongated lava-dominated volcano with a morphology comprising a broad summit plateau, ~30° steep upper flanks, sharp slope breaks and topographic terraces around its base. Despite recent lava eruptions along its rift zone (i.e. 1999, 2000), little geological or geophysical data are available to constrain the structure, and ongoing unrest of this large volcanic system. Here we first report results from a 2008 field campaign dedicated to mapping geological structures in the summit area and at the SE base of Mt. Cameroon. At the edge of the summit plateau, small-scale topographic steps are found to be evidence for subsidence and horizontal extension along inward-dipping faults, being sub-parallel to the volcano edifice elongation at a strike ENE-WSW. The topographic bulge at the SE base of Mt. Cameroon is found to correspond to thrusted and folded weak Miocene sediments of the Douala basin overlain by volcanic products. Combined with the interpretation of large-scale structures delineated on a 30 m Digital Elevation Model, the field observations suggest that Mt Cameroon is affected by gravitational spreading of the edifice over ductile sediments. To better understand the structural configuration and morphology observed, we designed scaled analogue experiments and record fault formation through a digital image correlation procedure. Simple spreading of an elongated edifice favors displacement perpendicular to the long axis, formation of a summit graben and basal thrusts or folds parallel to this axis. This deformation is found to be associated with preservation or minor decrease in flank slopes. Although basal and summit structures are consistent with field observations, these experiments are not able to account for the steep, and locally unstable, slopes observed on Mt. Cameroon upper flanks. A second set of experiments aims to simulate the effect of a ductile layer extending only under the lower flanks and at volcano’s base, as would be expected from syn-volcano growth sedimentation. This assumption is consistent with field observations of lava flows interleaved with Miocene sediments at the volcano base. Lower flank spreading along outward-dipping listric normal faults is found to cause no deformation in the summit zone but to be associated with slope increase and local instabilities on the upper flanks, sharp slope breaks at the base of the steep flanks and irregular basal topography. This second type of experiments more realistically reproduces the key features observed at Mt. Cameroon, the summit graben being accounted for by slower spreading along deeper sediment layers, or more probably, by repetitive dyke intrusion along the rift zone.

  19. The solution structure of a superpotent B-chain-shortened single-replacement insulin analogue.

    PubMed Central

    Kurapkat, G.; Siedentop, M.; Gattner, H. G.; Hagelstein, M.; Brandenburg, D.; Grötzinger, J.; Wollmer, A.

    1999-01-01

    This paper reports on an insulin analogue with 12.5-fold receptor affinity, the highest increase observed for a single replacement, and on its solution structure, determined by NMR spectroscopy. The analogue is [D-AlaB26]des-(B27-B30)-tetrapeptide-insulin-B26-amide. C-terminal truncation of the B-chain by four (or five) residues is known not to affect the functional properties of insulin, provided the new carboxylate charge is neutralized. As opposed to the dramatic increase in receptor affinity caused by the substitution of D-Ala for the wild-type residue TyrB26 in the truncated molecule, this very substitution reduces it to only 18% of that of the wild-type hormone when the B-chain is present in full length. The insulin molecule in solution is visualized as an ensemble of conformers interrelated by a dynamic equilibrium. The question is whether the "active" conformation of the hormone, sought after in innumerable structure/function studies, is or is not included in the accessible conformational space, so that it could be adopted also in the absence of the receptor. If there were any chance for the active conformation, or at least a predisposed state to be populated to a detectable extent, this chance should be best in the case of a superpotent analogue. This was the motivation for the determination of the three-dimensional structure of [D-AlaB26]des-(B27-B30)-tetrapeptide-insulin-B26-amide. However, neither the NMR data nor CD spectroscopic comparison of a number of related analogues provided a clue concerning structural features predisposing insulin to high receptor affinity. After the present study it seems more likely than before that insulin will adopt its active conformation only when exposed to the force field of the receptor surface. PMID:10091652

  20. Analogues of triprolidine: structural influences upon antihistamine activity.

    PubMed

    Casy, A F; Ganellin, C R; Mercer, A D; Upton, C

    1992-10-01

    The synthesis of some geometrical isomers related to triprolidine is reported. Previous configurational assignments, by UV and proton NMR, are validated by high field nuclear Overhauser enhancement methods and the isomeric purity of tested E- and Z-isomers was greater than 99.5% as assessed by an HPLC method developed for these compounds. Affinity constants for triprolidine (E and Z) in guinea-pig ileum showed a potency ratio of approximately 600 whereas at cerebellar sites this ratio was only approximately 100, suggesting that the H1 receptor in these two tissues may not be identical. In-vivo tests using a lethal dose of compound 48/80 (a potent histamine-releasing agent) demonstrated that triprolidine itself was the most active compound to protect the animal among all the isomeric compounds tested: in all isomeric pairs the E-configuration possessed superior activity over Z. The disposition of the aryl groups in these geometrically constrained compounds mimics that seen in the structurally related chiral pheniramines which are sp3 hybridized and whose absolute stereochemistry is known. PMID:1360502

  1. Characterization of electronic structure and physicochemical properties of antiparasitic nifurtimox analogues: A theoretical study

    NASA Astrophysics Data System (ADS)

    Soriano-Correa, Catalina; Raya, A.; Esquivel, Rodolfo O.

    American trypanosomiasis, also known as Chagas' disease, is caused by Trypanosoma cruzi (T. cruzi). It is well known that trypanosomes, and particularly T. cruzi, are highly sensitive towards oxidative stress, i.e., to compounds than are able to produce free radicals. Generally, nifurtimox (NFX) and benznidazol are most effective in the acute phase of the disease; therefore, nitroheterocycles constitute good models to design other nitrocompounds with specific biological characteristics. Thus, we have performed an ab initio study at the Hartree-Fock and Density Functional Theory levels of theory of several NFX analogues recently synthesized, to characterize them by obtaining their electronic, structural, and physicochemical properties, which might be linked to the observed antichagasic activity. The antitrypanosomal activity scale previously reported for the NFX analogues studied in this work is in good agreement with our theoretical results, from which we can conclude that the activity seems to be related to the reactivity along with the acidity observed for the most active molecules.

  2. Synthesis of Silicate Zeolite Analogues Using Organic Sulfonium Compounds as Structure-Directing Agents.

    PubMed

    Jo, Changbum; Lee, Sungjune; Cho, Sung June; Ryoo, Ryong

    2015-10-19

    A microporous crystalline silica zeolite of the MEL structure type and three other zeolite analogues composed of germanosilicate frameworks were synthesized using tributylsulfonium, triphenylsulfonium, or tri(para-tolyl)sulfonium as the structure-directing agent. The germanosilicates thus obtained had ISV, ITT, or a new zeolite structure depending on the synthesis conditions. The structure of the new germanosilicate was solved using X-ray powder diffraction data with the aid of a charge-flipping method. The solution indicated a crystal structure belonging to the P63/mmc space group with cell parameters of a=16.2003?Å and c=21.8579?Å. After calcination, the new germanosilicate material exhibited two types of accessible micropores with diameters of 0.61 and 0.78?nm. PMID:26302889

  3. High resolution structure of an M23 peptidase with a substrate analogue

    PubMed Central

    Grabowska, Maja; Jagielska, Elzbieta; Czapinska, Honorata; Bochtler, Matthias; Sabala, Izabela

    2015-01-01

    LytM is a Staphylococcus aureus autolysin and a homologue of the S. simulans lysostaphin. Both enzymes are members of M23 metallopeptidase family (MEROPS) comprising primarily bacterial peptidoglycan hydrolases. LytM occurs naturally in a latent form, but can be activated by cleavage of an inhibitory N-terminal proregion. Here, we present a 1.45?Å crystal structure of LytM catalytic domain with a transition state analogue, tetraglycine phosphinate, bound in the active site. In the electron density, the active site of the peptidase, the phosphinate and the “diglycine” fragment on the P1? side of the transition state analogue are very well defined. The density is much poorer or even absent for the P1 side of the ligand. The structure is consistent with the involvement of His260 and/or His291 in the activation of the water nucleophile and suggests a possible catalytic role for Tyr204, which we confirmed by mutagenesis. Possible mechanisms of catalysis and the structural basis of substrate specificity are discussed based on the structure analysis. PMID:26437833

  4. Relationship between structure of phenothiazine analogues and their activity on platelet calcium fluxes.

    PubMed Central

    Enouf, J.; Lévy-Toledano, S.

    1984-01-01

    Phenothiazine analogues have been tested for their effect on calcium uptake into platelet membrane vesicles and on ionophore-induced platelet activation, both phenomena being Ca2+-dependent. Both calcium uptake into membrane vesicles and ionophore-induced platelet activation were inhibited by the drugs. Evidence for two inhibitors as potent as chlorpromazine and trifluoperazine was found. These drugs are apparently competitive inhibitors of calcium uptake. A structure-activity relationship has been established. The data suggest that the phenothiazines are able to inhibit calmodulin-insensitive calcium uptake of platelet membrane vesicles and that therefore they cannot be assumed to be selective inhibitors of calmodulin interactions under all circumstances. PMID:6697061

  5. Charge Isomers of Myelin Basic Protein: Structure and Interactions with Membranes, Nucleotide Analogues, and Calmodulin

    PubMed Central

    Wang, Chaozhan; Neugebauer, Ute; Bürck, Jochen; Myllykoski, Matti; Baumgärtel, Peter; Popp, Jürgen; Kursula, Petri

    2011-01-01

    As an essential structural protein required for tight compaction of the central nervous system myelin sheath, myelin basic protein (MBP) is one of the candidate autoantigens of the human inflammatory demyelinating disease multiple sclerosis, which is characterized by the active degradation of the myelin sheath. In this work, recombinant murine analogues of the natural C1 and C8 charge components (rmC1 and rmC8), two isoforms of the classic 18.5-kDa MBP, were used as model proteins to get insights into the structure and function of the charge isomers. Various biochemical and biophysical methods such as size exclusion chromatography, calorimetry, surface plasmon resonance, small angle X-ray and neutron scattering, Raman and fluorescence spectroscopy, and conventional as well as synchrotron radiation circular dichroism were used to investigate differences between these two isoforms, both from the structural point of view, and regarding interactions with ligands, including calmodulin (CaM), various detergents, nucleotide analogues, and lipids. Overall, our results provide further proof that rmC8 is deficient both in structure and especially in function, when compared to rmC1. While the CaM binding properties of the two forms are very similar, their interactions with membrane mimics are different. CaM can be used to remove MBP from immobilized lipid monolayers made of synthetic lipids - a phenomenon, which may be of relevance for MBP function and its regulation. Furthermore, using fluorescently labelled nucleotides, we observed binding of ATP and GTP, but not AMP, by MBP; the binding of nucleoside triphosphates was inhibited by the presence of CaM. Together, our results provide important further data on the interactions between MBP and its ligands, and on the differences in the structure and function between MBP charge isomers. PMID:21647440

  6. Charge isomers of myelin basic protein: structure and interactions with membranes, nucleotide analogues, and calmodulin.

    PubMed

    Wang, Chaozhan; Neugebauer, Ute; Bürck, Jochen; Myllykoski, Matti; Baumgärtel, Peter; Popp, Jürgen; Kursula, Petri

    2011-01-01

    As an essential structural protein required for tight compaction of the central nervous system myelin sheath, myelin basic protein (MBP) is one of the candidate autoantigens of the human inflammatory demyelinating disease multiple sclerosis, which is characterized by the active degradation of the myelin sheath. In this work, recombinant murine analogues of the natural C1 and C8 charge components (rmC1 and rmC8), two isoforms of the classic 18.5-kDa MBP, were used as model proteins to get insights into the structure and function of the charge isomers. Various biochemical and biophysical methods such as size exclusion chromatography, calorimetry, surface plasmon resonance, small angle X-ray and neutron scattering, Raman and fluorescence spectroscopy, and conventional as well as synchrotron radiation circular dichroism were used to investigate differences between these two isoforms, both from the structural point of view, and regarding interactions with ligands, including calmodulin (CaM), various detergents, nucleotide analogues, and lipids. Overall, our results provide further proof that rmC8 is deficient both in structure and especially in function, when compared to rmC1. While the CaM binding properties of the two forms are very similar, their interactions with membrane mimics are different. CaM can be used to remove MBP from immobilized lipid monolayers made of synthetic lipids--a phenomenon, which may be of relevance for MBP function and its regulation. Furthermore, using fluorescently labelled nucleotides, we observed binding of ATP and GTP, but not AMP, by MBP; the binding of nucleoside triphosphates was inhibited by the presence of CaM. Together, our results provide important further data on the interactions between MBP and its ligands, and on the differences in the structure and function between MBP charge isomers. PMID:21647440

  7. Structural Basis for Recognition of Guanosine by a Synthetic Tricyclic Cytosine Analogue: Guanidinium G-Clamp

    SciTech Connect

    Wilds, C.J.; Maier, M.A.; Manoharan, M.; Egli, M.

    2010-03-08

    An oligonucleotide analogue containing a novel heterocyclic analogue, the guanidinium G-clamp, was designed to allow formation of five H-bonds to guanosine. The guanidinium group was introduced postsynthetically by treatment of the deprotected oligonucleotide containing a free amino group with a solution of 1H-pyrazole-1-carboxamidine and purified by a combination of size-exclusion chromatography and reversed-phase HPLC. A single incorporation of this modification into an oligodeoxynucleotide sequence was found to increase duplex stability by 13{sup o} and 16{sup o} per modification to RNA and DNA, respectively. Crystals of a self-complementary decamer sequence containing this modification were grown and diffracted to 1-{angstrom} resolution. The structure was solved by molecular replacement and revealed that the modification forms additional H-bonds to O(6) and N(7) of guanosine through the amino and imino N-atoms, respectively. The origins of enhanced duplex stability are also attributed to increased stacking interactions mediated by the phenoxazine moiety of the G-clamp and formation of H-bond networks between the positively charged guanidinium group, H{sub 2}O molecules, and negatively charged O-atoms from phosphates on the adjacent strand.

  8. Structure-activity relationship of tryptamine analogues on the heart of venus mercenaria

    PubMed Central

    Greenberg, M. J.

    1960-01-01

    A number of tryptamine analogues and other exciter agents have been tested on the heart of Venus mercenaria. The method of estimation of potency, especially for irreversibly acting compounds, is discussed. Specificity of action with respect to the site of action of 5-hydroxytryptamine is defined experimentally. The specific activity of tyramine and phenethylamine and the non-specific excitatory action of indole and skatole indicate that the indole ring is neither necessary nor sufficient for 5-hydroxytryptamine-like activity. Tryptamine analogues differ in mode of action as well as potency. Congeners without a 5-hydroxyl group tend to act more slowly and irreversibly as well as less strongly than 5-hydroxytryptamine. Methyl substitution also increases the time of action and difficulty of reversal. However, the potency of such compounds may be increased or decreased depending upon the position of substitution and the presence of the 5-hydroxyl group. The relations between structure and potency and mode of action are discussed. Suggestions are made concerning the effective conformation of the 5-hydroxytryptamine molecule and the nature of its receptor. ImagesFIG. 7 PMID:13708259

  9. Transition state analogues in structures of ricin and saporin ribosome-inactivating proteins

    SciTech Connect

    Ho, Meng-Chiao; Sturm, Matthew B.; Almo, Steven C.; Schramm, Vern L.

    2010-01-12

    Ricin A-chain (RTA) and saporin-L1 (SAP) catalyze adenosine depurination of 28S rRNA to inhibit protein synthesis and cause cell death. We present the crystal structures of RTA and SAP in complex with transition state analogue inhibitors. These tight-binding inhibitors mimic the sarcin-ricin recognition loop of 28S rRNA and the dissociative ribocation transition state established for RTA catalysis. RTA and SAP share unique purine-binding geometry with quadruple {pi}-stacking interactions between adjacent adenine and guanine bases and 2 conserved tyrosines. An arginine at one end of the {pi}-stack provides cationic polarization and enhanced leaving group ability to the susceptible adenine. Common features of these ribosome-inactivating proteins include adenine leaving group activation, a remarkable lack of ribocation stabilization, and conserved glutamates as general bases for activation of the H{sub 2}O nucleophile. Catalytic forces originate primarily from leaving group activation evident in both RTA and SAP in complex with transition state analogues.

  10. Structural Influences on Preferential Oxazolone versus Diketopiperazine b2+ Ion Formation for Histidine Analogue-containing Peptides

    PubMed Central

    Gucinski, Ashley C.; Chamot-Rooke, Julia; Nicol, Edith; Somogyi, Árpád; Wysocki, Vicki H.

    2012-01-01

    Studies of peptide fragment ion structures are important to aid in the accurate kinetic modeling and prediction of peptide fragmentation pathways for a given sequence. Peptide b2+ ion structures have been of recent interest. While previously studied b2+ ions that contain only aliphatic or simple aromatic residues are oxazolone structures, the HA b2+ ion consists of both oxazolone and diketopiperazine structures. The structures of a series of histidine-analogue-containing Xxx-Ala b2+ ions were studied by using action infrared multiphoton dissociation (IRMPD) spectroscopy, fragment ion hydrogen-deuterium exchange (HDX), and density functional theory (DFT) calculations to systematically probe the influence of different side chain structural elements on the resulting b2+ ion structures formed. The b2+ ions studied include His-Ala (HA), methylated histidine analogues, including pi-methyl-HA and tau-methyl-HA, pyridylalanine (pa) analogues, including 2-(pa)A, 3-(pa)A, and 4-(pa)A, and linear analogues, including diaminobutanoic acid (DabA) and Lys-Ala (KA). The location and accessibility of the histidine pi nitrogen, or an amino nitrogen on an aliphatic side chain, were seen to be essential for diketopiperazine formation in addition to the more typical oxazolone structure formation, while blocking or removal of the tau nitrogen did not change the b2+ ion structures formed. Linear histidine analogues, DabA and KA, formed only diketopiperazine structures, suggesting that a steric interaction in the HisAla case may interfere with the complete trans-cis isomerization of the first amide bond that is necessary for diketopiperazine formation. PMID:22448972

  11. Weed Identification: Using Plant Structures as a Key (Spanish) 

    E-print Network

    Baumann, Paul A.

    1999-08-30

    Weed identification is necessary to the success of any weed control program. Frequently, simple plant keys or "picture book identification guides are used to identify weeds. This handbook, which identifies and labels plant structures, is intended...

  12. Extrapolating surface structures to depth in transpressional systems: the role of rheology and convergence angle deduced from analogue experiments

    NASA Astrophysics Data System (ADS)

    Hsieh, Shang Yu; Neubauer, Franz; Cloetingh, Sierd; Willingshofer, Ernst; Sokoutis, Dimitrios

    2014-05-01

    The internal structure of major strike-slip faults is still poorly understood, particularly how the deep structure could be inferred from its surface expression (Molnar and Dayem, 2011 and references therein). Previous analogue experiments suggest that the convergence angle is the most influential factor (Leever et al., 2011). Further analogue modeling may allow a better understanding how to extrapolate surface structures to the subsurface geometry of strike-slip faults. Various scenarios of analogue experiments were designed to represent strike-slip faults in nature from different geological settings. As such key parameters, which are investigated in this study include: (a) the angle of convergence, (b) the thickness of brittle layer, (c) the influence of a rheological weak layer within the crust, and (d) influence of a thick and rheologically weak layer at the base of the crust. The latter aimed to simulate the effect of a hot metamorphic core complex or an alignment of uprising plutons bordered by a transtensional/transpressional strike-slip fault. The experiments are aimed to explain first order structures along major transcurrent strike-slip faults such as the Altyn, Kunlun, San Andrea and Greendale (Darfield earthquake 2010) faults. The preliminary results show that convergence angle significantly influences the overall geometry of the transpressive system with greater convergence angles resulting in wider fault zones and higher elevation. Different positions, densities and viscosities of weak rheological layers have not only different surface expressions but also affect the fault geometry in the subsurface. For instance, rheological weak material in the bottom layer results in stretching when experiment reaches a certain displacement and a buildup of a less segmented, wide positive flower structure. At the surface, a wide fault valley in the middle of the fault zone is the reflection of stretching along the velocity discontinuity at depth. In models with a thin and rheologically weaker layer in the middle of the brittle layer, deformation is distributed over more faults and the geometry of the fault zone below and above the weak zone shows significant differences, suggesting that the correlation of structures across a weak layer has to be supported by geophysical data, which help constraining the geometry of the deep part. This latter experiment has significantly similar phenomena in reality, such as few pressure ridges along Altyn fault. The experimental results underline the need to understand the role of the convergence angle and the influence of rheology on fault evolution, in order to connect between surface deformation and subsurface geometry. References Leever, K. A., Gabrielsen, R. H., Sokoutis, D., Willingshofer, E., 2011. The effect of convergence angle on the kinematic evolution of strain partitioning in transpressional brittle wedges: Insight from analog modeling and high-resolution digital image analysis. Tectonics, 30(2), TC2013. Molnar, P., Dayem, K.E., 2010. Major intracontinental strike-slip faults and contrasts in lithospheric strength. Geosphere, 6, 444-467.

  13. Effects of structural analogues of apelin-12 in acute myocardial infarction in rats

    PubMed Central

    Pisarenko, Oleg I.; Serebryakova, Larisa I.; Studneva, Irina M.; Pelogeykina, Yulia A.; Tskitishvili, Olga V.; Bespalova, Zhanna D.; Sidorova, Maria V.; Az’muko, Andrei A.; Khatri, Denis N.; Pal’keeva, Maria E.; Molokoedov, Alexander S.

    2013-01-01

    Objective: To examine cardioprotective effects of ?-terminal fragment of adipokine apelin-12 (A12), its novel structural analogue [MeArg1, NLe10]-A12 (I), and [d-Ala12]-A12 (II), a putative antagonist of APJ receptor, employing in vivo model of ischemia/reperfusion (I/R) injury. Materials and Methods: Peptides were synthesized by the automatic solid phase method using Fmoc technology. Anesthetized open-chest male Wistar rats were subjected to left anterior descending (LAD) coronary artery occlusion and coronary reperfusion. Hemodynamic variables and electrocardiogram (ECG) were monitored throughout the experiment. Myocardial injury was assessed by infarct size (IS), activity of necrosis markers in plasma, and metabolic state of the area at risk (AAR). Results: Intravenous injection of A12, I, or II at the onset of reperfusion led to a transient reduction of the mean arterial pressure. A12 or I administration decreased the percent ratio of IS/AAR by 40% and 30%, respectively, compared with control animals which received saline. Both peptides improved preservation of high-energy phosphates, reduced lactate accumulation in the AAR, and lowered CK-MB and LDH activities in plasma at the end of reperfusion compared with these indices in control. Treatment with II did not significantly affect either the IS/AAR, % ratio, or activities of both markers of necrosis compared with control. The overall metabolic protection of the AAR in the treated groups increased in the following rank: II < A12 < I. Conclusions: The structural analogue of apelin-12 [MeArg1, NLe10]-A12 may be a promising basis to create a new drug for the treatment of acute coronary syndrome. PMID:23960425

  14. Verbenone structural analogues isolated from Artemesia aucheri as natural acaricides against Dermatophagoides spp. and Tyrophagus putrescentiae.

    PubMed

    Yang, Ji-Yeon; Lee, Hoi-Seon

    2013-12-18

    The acaricidal activities of Artemisia aucheri oil and (1S)-(-)-verbenone structural analogues were evaluated using a fumigant method against Dermatophagoides farinae , Dermatophagoides pteronyssinus , and Tyrophagus putrescentiae and then compared to those of benzyl benzoate. On the basis of the LD50 values against D. farinae , (1S)-(-)-verbenone (1.38 ?g/cm(2)) was about 7.4 times more active than benzyl benzoate (10.15 ?g/cm(2)), followed by (+)-trans-myrtanol (2.27 ?g/cm(2)), (-)-trans-myrtanol (2.30 ?g/cm(2)), and A. aucheri oil (8.75 ?g/cm(2)). (1S)-(-)-Verbenone (1.25 ?g/cm(2)) was approximately 7.8 times more effective against D. pteronyssinus than benzyl benzoate (9.80 ?g/cm(2)), followed by (+)-trans-myrtanol (2.18 ?g/cm(2)), (-)-trans-myrtanol (2.22 ?g/cm(2)), and A. aucheri oil (8.46 ?g/cm(2)). In the case of T. putrescentiae , (1S)-(-)-verbenone (3.75 ?g/cm(2)) was roughly 3.5 times more toxic than benzyl benzoate (13.25 ?g/cm(2)), followed by (+)-trans-myrtanol (12.57 ?g/cm(2)), (-)-trans-myrtanol (12.95 ?g/cm(2)), and A. aucheri oil (11.55 ?g/cm(2)). These results indicate that A. aucheri oil and (1S)-(-)-verbenone structural analogues may be effective natural agents to control house dust and storage mites. PMID:24295367

  15. Elucidation of the structure of constrained bicyclopeptides in solution by two-dimensional cross-relaxation spectroscopy: amatoxin analogues.

    PubMed

    Isernia, C; Falcigno, L; Macura, S; Paolillo, L; Pastore, A L; Zanotti, G

    1996-01-01

    The evaluation of peptide structures in solution is made feasible by the combined use of two-dimensional NMR in the laboratory (NOESY) and rotating frames (ROESY), and by the use of molecular dynamics calculations. The present paper describes how both the NMR method and molecular dynamics calculations were applied to very rigid synthetic bicycle peptides that are analogues of natural amatoxins. The NMR theory, which allows the estimate of interatomic distances between interacting nuclei, is briefly discussed. The experimental data were compared with those of known solid-state structures. Three amatoxin analogues have been examined. Of these, one is biologically active (S-deoxo gamma[R] OH-Ile3-amaninamide) and its structure in the solid state has recently been worked out. The second and third analogues (S-dexo-Ile3-Ala5-amaninamide and S-deoxo-D-Ile3-amaninamide, respectively) are inactive and their solid-state structures are unknown. The data presented confirm the authors previous hypothesis that lack of biological activity of S-deoxo-Ile3-Ala5-amaninamide is due to the masking of the tryptophan ring by the methyl group of L-Ala and not to massive conformational changes of the analogue. PMID:9225241

  16. Morpho-structural criteria for the identification of volcano deformation processes from analogue modeling

    NASA Astrophysics Data System (ADS)

    Rincon, Marta; Marquez, Alvaro; van Wyk de Vries, Benjamin; Herrera, Raquel; Granja Bruña, Jose Luis; Llanes, Pilar

    2014-05-01

    The morphology of volcanoes provides important information about edifice evolution. Volcanoes can deform by gravitational instability and intrusions. This deformation can compromise volcano structural stability, promoting flank collapse even at dormant edifices. Identification of past/active deformation processes is therefore important not only for the understanding of volcano evolution but also for volcanic hazards. Both deformation due to the flank spreading of a volcano over its weak core and due to the intrusion of a cryptodome in the volcano edifice can produce faulting and changes in the morphology of volcano flanks. These morpho-structural changes in the volcano open the possibility to identify potential deformed and unstable volcanoes using remote sensing techniques and DEMs. We have used analogue models of flank spreading and intrusion processes to make progress in the morpho-structural identification of deformation features which can provide criteria for distinguishing processes. We have geometrically and mechanically scaled two different sets of experiments using a sand-plaster mixture for volcano materials, silicone putty for weak core rocks and Golden Syrup for magma intrusions. For monitoring changes in the volcano morphology we have used a Kinect sensor (Microsoft), which provides us vertical displacements of volcano flanks several times per second with a 1 mm precision. We have synchronized the Kinect sensor with a digital camera for monitoring the spatio-temporal evolution of tectonic structures together with morphology. All experiments produce asymmetrical changes in volcano morphology, developing convex-concave geometries in the deformed flank. However, the spatial relationships of structures with changes in volcano flank curvature are different for the two processes, as noted by previous authors. The morphometric tools developed for analyzing volcano topography allow us to identify intrusion processes due to volcano volume increase. We have compared the results of our experiments with known examples of deformed volcanoes due to intrusions (eg., St Helens) and flank spreading (eg. Casita) and we confirmed that the criteria developed from modeling works well in the natural cases. We consider that further experiments are necessary to fully explore the capacity of application of morphometric tools to analogue modeling of volcano deformation processes, since our first results show a promising research avenue for the remote identification and evaluation of volcano deformation processes in remote volcanoes worldwide.

  17. Structural, Biochemical, and Computational Studies Reveal the Mechanism of Selective Aldehyde Dehydrogenase 1A1 Inhibition by Cytotoxic Duocarmycin Analogues.

    PubMed

    Koch, Maximilian F; Harteis, Sabrina; Blank, Iris D; Pestel, Galina; Tietze, Lutz F; Ochsenfeld, Christian; Schneider, Sabine; Sieber, Stephan A

    2015-11-01

    Analogues of the natural product duocarmycin bearing an indole moiety were shown to bind aldehyde dehydrogenase?1A1 (ALDH1A1) in addition to DNA, while derivatives without the indole solely addressed the ALDH1A1 protein. The molecular mechanism of selective ALDH1A1 inhibition by duocarmycin analogues was unraveled through cocrystallization, mutational studies, and molecular dynamics simulations. The structure of the complex shows the compound embedded in a hydrophobic pocket, where it is stabilized by several crucial ?-stacking and van der Waals interactions. This binding mode positions the cyclopropyl electrophile for nucleophilic attack by the noncatalytic residue Cys302, thereby resulting in covalent attachment, steric occlusion of the active site, and inhibition of catalysis. The selectivity of duocarmycin analogues for ALDH1A1 is unique, since only minor alterations in the sequence of closely related protein isoforms restrict compound accessibility. PMID:26373694

  18. Structure of synthetic peptide analogues of an eggshell protein of Schistosoma mansoni.

    PubMed Central

    Middaugh, C. R.; Thomson, J. A.; Burke, C. J.; Mach, H.; Naylor, A. M.; Bogusky, M. J.; Ryan, J. A.; Pitzenberger, S. M.; Ji, H.; Cordingley, J. S.

    1993-01-01

    The peptide (Gly-L-Tyr-L-Asp-L-Lys-L-Tyr)6, referred to as F4-6, was synthesized as a model for a schistosome eggshell protein in which the Gly-Tyr-Asp-Lys-Tyr consensus sequence is repeated over 40 times. Analysis by CD, Fourier transform infrared spectroscopy, potentiometric and spectrophotomertric titrations, NMR, and molecular modeling suggests that F4-6 forms some type of left-handed structure. A likely possibility appears to be a left-handed alpha-helix stabilized by Lysi-Aspi +4 salt bridges and possibly Aspi-Tyri +4 hydrogen bonding and Tyr-Tyr interactions. Spectroscopic studies of a number of F4-6 analogues support this conclusion. For example, substitution of D-Ala for Gly produces a peptide with enhanced left-handed helical spectral characteristics, whereas an L-Ala substitution results in a peptide with minimal structure. These studies suggest that the F4 protein from Schistosoma mansoni may be the first example of a naturally occurring protein devoid of proline and carbohydrate that forms a left-handed helix composed of L-amino acids, although alternative forms of other left-handed structures have yet to be rigorously excluded. PMID:8318895

  19. Experimental and Theoretical Studies of the Structures and Interactions of Vancomycin Antibiotics with Cell Wall Analogues

    SciTech Connect

    Yang, Zhibo; Vorpagel, Erich R.; Laskin, Julia

    2008-10-01

    Surface-induced dissociation (SID) of the singly protonated complex of vancomycin antibiotic with cell wall peptide analogue (N?,N?-diacetyl-L-Lys-D-Ala-D-Ala) was studied using a 6 T Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (FT-ICR MS) specially configured for SID experiments. The binding energy between the vancomycin and the peptide was obtained from the RRKM modeling of the time- and energy resolved fragmentation efficiency curves (TFECs) of the precursor ion and its fragments. Electronic structure calculations of the geometries, proton affinities and binding energies were performed for several model systems including vancomycin (V), vancomycin aglycon (VA), N?,N?-diacetyl-L-Lys-D-Ala-D-Ala, and non-covalent complexes of VA with N-acetyl-D-Ala-D-Ala and N?,N?-diacetyl-L-Lys-D-Ala-D-Ala at the B3LYP/6-31G(d) level of theory. Comparison between the experimental and computational results suggests that the most probable structure of the complex observed in our experiments corresponds to the neutral peptide bound to the vancomycin protonated at the secondary amino group of the N-methyl-leucine residue. The experimental binding energy of 30.9 ± 1.8 kcal/mol is in good agreement with the binding energy of 29.3 ± 2.5 kcal/mol calculated for the model system representing the preferred structure of the complex.

  20. Structure of a pancreatic alpha-amylase bound to a substrate analogue at 2.03 A resolution.

    PubMed Central

    Qian, M.; Spinelli, S.; Driguez, H.; Payan, F.

    1997-01-01

    The structure of pig pancreatic alpha-amylase in complex with carbohydrate inhibitor and proteinaceous inhibitors is known but the successive events occurring at the catalytic center still remain to be elucidated. The X-ray structure analysis of a crystal of pig pancreatic alpha-amylase (PPA, EC 3.2.1.1.) soaked with an enzyme-resistant substrate analogue, methyl 4,4'-dithio-alpha-maltotrioside, showed electron density corresponding to the binding of substrate analogue molecules at the active site and at the "second binding site." The electron density observed at the active site was interpreted in terms of overlapping networks of oligosaccharides, which show binding of substrate analogue molecules at subsites prior to and subsequent to the cleavage site. A weaker patch of density observed at subsite -1 (using a nomenclature where the site of hydrolysis is taken to be between subsites -1 and +1) was modeled with water molecules. Conformational changes take place upon substrate analogue binding and the "flexible loop" that constitutes the surface edge of the active site is observed in a specific conformation. This confirms that this loop plays an important role in the recognition and binding of the ligand. The crystal structure was refined at 2.03 A resolution, to an R-factor of 16.0 (Rfree, 18.5). PMID:9385631

  1. Phenyl-imidazolo-cytidine analogues: structure-photophysical activity relationship and ability to detect single DNA mismatch.

    PubMed

    Kovaliov, Marina; Weitman, Michal; Major, Dan Thomas; Fischer, Bilha

    2014-08-01

    To expand the arsenal of fluorescent cytidine analogues for the detection of genetic material, we synthesized para-substituted phenyl-imidazolo-cytidine ((Ph)ImC) analogues 5a-g and established a relationship between their structure and fluorescence properties. These analogues were more emissive than cytidine (?em 398-420 nm, ? 0.009-0.687), and excellent correlation was found between ? of 5a-g and ?p(-) of the substituent on the phenyl-imidazolo moiety (R(2) = 0.94). Calculations suggested that the dominant tautomer of (Ph)ImC in methanol solution is identical to that of cytidine. DFT calculations of the stable tautomer of selected (Ph)ImC analogues suggested a relationship between the HOMO-LUMO gap and ? and explained the loss of fluorescence in the nitro analogue. Incorporation of the CF3-(Ph)ImdC analogue into a DNA probe resulted in 6-fold fluorescence quenching of the former. A 17-fold reduction of fluorescence was observed for the G-matched duplex vs ODN(CF3-(Ph)ImdC), while for A-mismatched duplex, only a 2-fold decrease was observed. Furthermore, since the quantum yield of ODN(CF3-(Ph)ImdC):ODN(G) was reduced 17-fold vs that of a single strand, whereas that of ODN(CF3-(Ph)ImdC):ORN(G) was reduced only 3.8-fold, ODN(CF3-(Ph)ImdC) appears to be a DNA-selective probe. We conclude that the ODN(CF3-(Ph)ImdC) probe, exhibiting emission sensitivity upon single nucleotide replacement, may be potentially useful for DNA single nucleotide polymorphism (SNP) typing. PMID:24992467

  2. Lithosphere strength controls oceanic transform zone structure: insights from analogue models

    NASA Astrophysics Data System (ADS)

    Dauteuil, O.; Bourgeois, O.; Mauduit, T.

    2002-09-01

    Oceanic transform zones have often been regarded as plate boundaries. The origin of their structural variability is poorly constrained. A simple observation indicates that the transform zone is narrow and linear when the offset is large; while it is wide with a complex faulting pattern in the case of a small offset. On the other hand, for a given offset, large structural differences exist between transform zones located on the fast-spreading South-East Pacific Rise and on the slow-spreading Mid-Atlantic ridge. In general, the transform zones in slow-spreading environments are linear with a simple fault pattern, while in fast-spreading systems they are wide with a complex pattern of deformation. We perform small-scale analogue modelling to constrain the influence of lithospheric strength on the development of deformation above a transform boundary. The models are made up of sand and silicone putty as analogues of the brittle layer and the viscous layer of the lithosphere, respectively. Two plastic sheets coming from shifted gashes form a set-up of two diverging discontinuities connected by a transform boundary. The rheological layering and strength of the model were modified using different shapes of the viscous layer placed on the transform boundary. Above the divergent discontinuities, the faulting pattern is always formed by parallel normal faults. When no viscous layer is placed on the transform boundary (strong discontinuity), the deformed zone is narrow and has few linear faults. By adding a narrow and thin viscous layer, the deformed zone becomes wider with a complex faulting pattern formed by oblique-slip faults on the limits and by pure strike-slip faults in the inner part. These latter strike-slip faults trend oblique to the transform boundary. When a viscous layer with a wide lateral extent overlays the transform discontinuity (weak strength), the faulting is dominated by obliquely normal faults extending over a wide zone, and the strike-slip is restricted to the inner part of the deformed zone. Therefore, the mechanical strength of the small scale-model controls the shape of the deformed zone and the deformation partitioning. These results were applied to 24 oceanic transforms zones: we point out that the spreading rate and the transform offset are the two dominant parameters controlling the deformation pattern. These two factors directly control the lithospheric strength at the transform boundary. However, the distance to the nearest hotspot, which may generate warmer thermal conditions even in slow-spreading environments, should modify this result.

  3. Carbocyclic nucleoside analogues: classification, target enzymes, mechanisms of action and synthesis

    NASA Astrophysics Data System (ADS)

    Matyugina, E. S.; Khandazhinskaya, A. P.; Kochetkov, Sergei N.

    2012-08-01

    Key biological targets (S-adenosyl-L-homocysteine hydrolase, telomerase, human immunodeficiency virus reverse transcriptase, herpes virus DNA polymerase and hepatitis B virus DNA polymerase) and the mechanisms of action of carbocyclic nucleoside analogues are considered. Structural types of analogues are discussed. Methods of synthesis for the most promising compounds and the spectrum of their biological activities are described. The bibliography includes 126 references.

  4. Spectroscopic, thermal and single crystal structure investigations of 2-bromotrimesic acid and its trimethyl ester analogue

    NASA Astrophysics Data System (ADS)

    Münch, Alexander S.; Katzsch, Felix; Gruber, Tobias; Mertens, Florian O. R. L.

    2014-09-01

    Two analogues of the well investigated trimesic acid viz. the 2-bromobenzene-1,3,5-tricarboxylic acid 1 and their ester trimethyl 2-bromobenzene-1,3,5-tricarboxylate 2, have been synthesised and their X-ray structures were solved. Acid 1 crystallises as 1:1 inclusion compound with water in a layer structure. Like in the solid state structure of trimesic acid, we found strong Osbnd H???O hydrogen bonds between one of the carboxyl groups and a neighbouring molecule to form a hydrogen bonding motif R22(8). Additionally, a water molecule and a second acid function of 1 are involved in further hydrogen bonding featuring the graph set R44(12) forming what might be called a water inserted dimer. As shown by TG-DSC measurements the water molecule in the 1:1 inclusion compound of 1 is engaged in two strong Osbnd H???O hydrogen bonds, it escapes at a rather low temperature of 99 °C. Bromine monosubstitution at the benzene ring forces the third carboxylic acid out of the mean plane of the molecule, which disturbs the coplanar arrangement of the three COOH moieties. Thus, the typical “chicken-wire” network formation is hindered. In the trimethyl 2-bromobenzene-1,3,5-tricarboxylate (2), the formation of strong Osbnd H???O hydrogen bonds is disabled by esterification of the acid functions. Nevertheless, the packing of 2 features solvent free molecular layers formed by Br???O contacts and connected van der Waals interactions. These layers are linked to each other by inverse bifurcated hydrogen bonds in term weak Csbnd H???O contacts. The results of the X-ray analysis could be confirmed by infrared spectroscopy.

  5. Elucidation of structural elements for selectivity across monoamine transporters: novel 2-[(diphenylmethyl)sulfinyl]acetamide (modafinil) analogues.

    PubMed

    Okunola-Bakare, Oluyomi M; Cao, Jianjing; Kopajtic, Theresa; Katz, Jonathan L; Loland, Claus J; Shi, Lei; Newman, Amy Hauck

    2014-02-13

    2-[(Diphenylmethyl)sulfinyl]acetamide (modafinil, (±)-1) is a unique dopamine uptake inhibitor that binds the dopamine transporter (DAT) differently than cocaine and may have potential for the treatment of psychostimulant abuse. To further investigate structural requirements for this divergent binding mode, novel thio- and sulfinylacetamide and ethanamine analogues of (±)-1 were synthesized wherein (1) the diphenyl rings were substituted with methyl, trifluoromethyl, and halogen substituents and (2) substituents were added to the terminal amide/amine nitrogen. Halogen substitution of the diphenyl rings of (±)-1 gave several amide analogues with improved binding affinity for DAT and robust selectivity over the serotonin transporter (SERT), whereas affinity improved at SERT over DAT for the p-halo-substituted amine analogues. Molecular docking studies, using a subset of analogues with DAT and SERT homology models, and functional data obtained with DAT (A480T) and SERT (T497A) mutants defined a role for TM10 in the substrate/inhibitor S1 binding sites of DAT and SERT. PMID:24494745

  6. Elucidation of Structural Elements for Selectivity across Monoamine Transporters: Novel 2-[(Diphenylmethyl)sulfinyl]acetamide (Modafinil) Analogues

    PubMed Central

    2015-01-01

    2-[(Diphenylmethyl)sulfinyl]acetamide (modafinil, (±)-1) is a unique dopamine uptake inhibitor that binds the dopamine transporter (DAT) differently than cocaine and may have potential for the treatment of psychostimulant abuse. To further investigate structural requirements for this divergent binding mode, novel thio- and sulfinylacetamide and ethanamine analogues of (±)-1 were synthesized wherein (1) the diphenyl rings were substituted with methyl, trifluoromethyl, and halogen substituents and (2) substituents were added to the terminal amide/amine nitrogen. Halogen substitution of the diphenyl rings of (±)-1 gave several amide analogues with improved binding affinity for DAT and robust selectivity over the serotonin transporter (SERT), whereas affinity improved at SERT over DAT for the p-halo-substituted amine analogues. Molecular docking studies, using a subset of analogues with DAT and SERT homology models, and functional data obtained with DAT (A480T) and SERT (T497A) mutants defined a role for TM10 in the substrate/inhibitor S1 binding sites of DAT and SERT. PMID:24494745

  7. Structure-activity relationships of eighteen somatostatin analogues on gastric secretion.

    PubMed Central

    Brown, M P; Coy, D H; Gomez-Pan, A; Hirst, B H; Hunter, M; Meyers, C; Reed, J D; Schally, A V; Shaw, B

    1978-01-01

    1. The effect of somatostatin and eighteen somatostatin analogues on pentagastrin-stimulated gastric acid and pepsin secretion was investigated in the conscious vagotomized cat prepared with chronic gastric fistulae. The majority of the analogues are peptides where D-amino acids are incorporated into the molecule instead of the natural L-isomers. 2. The ID50 for cyclic-somatostatin inhibition of near-maximal gastric acid secretion stimulated by pentagastrin 8 microgram kg-1 hr-1 was found to be 1.29 +/- 0.13 n-mole kg-1 hr-1. Pentagastrin-stimulated pepsin secretion had a lower threshold to somatostatin inhibition than did acid secretion. 3. D-Phe6, D-Phe7, D-Thr10, D-Thr12 and D-Phe6-D-Trp8 analogues all show low biological activity against the secretion of gastric acid and pepsin, growth hormone, insulin and glucagon. None of these analogues are antagonists of the cyclic-somatostatin inhibition of gastric secretion, suggesting that they have low affinity for this somatostatin receptor. 4. The analogues under investigation show parallel changes in activity against gastric and growth hormone secretion, suggesting a similarity between the gastric and growth hormone receptors for somatostatin. 5. D-Cys14 analogues are equipotent with or have a greater potency than cyclic-simatostatin in inhibiting the secretion of gastric acid, growth hormone and glucagon but show low insulin inhibiting activity. PMID:349135

  8. Biofunctional constituent isolated from Citrullus colocynthis fruits and structure-activity relationships of its analogues show acaricidal and insecticidal efficacy.

    PubMed

    Jeon, Ju-Hyun; Lee, Hoi-Seon

    2014-08-27

    The acaricidal and insecticidal potential of the active constituent isolated from Citrullus colocynthis fruits and its structurally related analogues was evaluated by performing leaf disk, contact toxicity, and fumigant toxicity bioassays against Tetranychus urticae, Sitophilus oryzae, and Sitophilus zeamais adults. The active constituent of C. colocynthis fruits was isolated by chromatographic techniques and was identified as 4-methylquinoline on the basis of spectroscopic analyses. To investigate the structure-activity relationships, 4-methylquinoline and its structural analogues were tested against mites and two insect pests. On the basis of the LC50 values, 7,8-benzoquinoline was the most effective against T. urticae. Quinoline, 8-hydroxyquinoline, 2-methylquinoline, 4-methylquinoline, 6-methylquinoline, 8-methylquinoline, and 7,8-benzoquinoline showed high insecticidal activities against S. oryzae and S. zeamais regardless of the application method. These results indicate that introduction of a functional group into the quinoline skeleton and changing the position of the group have an important influence on the acaricidal and insecticidal activities. Furthermore, 4-methylquinoline isolated from C. colocynthis fruits, along with its structural analogues, could be effective natural pesticides for managing spider mites and stored grain weevils. PMID:25110971

  9. [Antioxidant properties of apelin-12 and its structural analogue in experimental ischemia and reperfusion].

    PubMed

    Pisarenko, O I; Bespalova, Zh D; Lankin, V Z; Timoshin, A A; Serebriakova, L I; Shul'zhenko, V S; Peloge?kina, Iu A; Studneva, I M; Tskitishvili, O V; Az'muko, A A; Sidorova, M V; Pal'keeva, M E; Konovalova, G G; Chazov, E I

    2013-01-01

    Effects of apelin-12 H-Arg-Pro-Arg-Leu-Ser-His-Lys-Gly-Pro-Met-Pro-Phe-OH (A12) and its modified analogue H-(NMe)Arg-Pro-Arg-Leu-Ser-His-Lys-Gly-Pro-Nle-Pro-Phe-OH (I) on activity of antioxidant enzymes, formation of malonic dialdehyde (MDA) and generation of reactive oxygen species (ROS) were studied in ex vivo and in vivo models of myocardial ischemia and reperfusion (I/R) injury in Wistar rats. Preischemic infusion of peptide A12 or AI enhanced cardiac function recovery of isolated perfused heart and was accompanied by a marked attenuation of ROS generation detected by electron paramagnetic resonance (EPR) technique in myocardial effluent at early reperfusion compared with control. Intravenous administration (i.v.) of peptides in narcotized rats with regional myocardial ischemia limited infarct size and reduced activity of lactate dehydrogenase and MB-fraction of creatine kinase in plasma at the end of reperfusion. Treatment with peptide A12 prevented reduction or augmented activity of myocardial u/Zn superoxide dismutase, catalase and glutathione peroxidase by the end of reperfusion in both I/R models compared with control. Increased MDA content in the area at risk of rat heart in situ at the end of reperfusion was reduced to the initial value under the effect of i.v. A12 administration. Therefore, cardioprotective action of natural apelin-12 and its structural analog AI involve reduction of short-lived ROS generation and improvement of the antioxidant state of ischemic heart during reperfusion. PMID:23952997

  10. Assessment of aquatic experimental versus predicted and extrapolated chronic toxicity data of four structural analogues.

    PubMed

    Dom, Nathalie; Knapen, Dries; Blust, Ronny

    2012-01-01

    The present study was developed to assess the chronic toxicity predictions and extrapolations for a set of chlorinated anilines (aniline (AN), 4-chloroaniline (CA), 3,5-dichloroaniline (DCA) and 2,3,4-trichloroaniline (TCA)). Daphnia magna 21 d chronic experimental data was compared to the chronic toxicity predictions made by the US EPA ECOSAR QSAR tools and to acute-to-chronic extrapolations. Additionally, Species Sensitivity Distributions (SSDs) were constructed to assess the chronic toxicity variability among different species and to investigate the acute versus chronic toxicity in a multi-species context. Since chlorinated anilines are structural analogues with a designated polar narcotic mode of action, similar toxicity responses were assumed. However, rather large interchemical and interspecies differences in toxicity were observed. Compared to the other three test compounds, TCA exposure had a significantly larger impact on growth and reproduction of D. magna. Furthermore, this study illustrated that QSARs or a fixed ACR are not able to account for these interchemical and interspecies differences. Consequently, ECOSAR was found to be inadequate to predict the chronic toxicity of the anilines and the use of a fixed ACR (of 10) led to under of certain species. The experimental ACRs determined in D. magna were substantially different among the four aromatic amines (ACR of 32 for AN, 16.9 for CA, 5.7 for DCA and 60.8 for TCA). Furthermore, the SSDs illustrated that Danio rerio was rather insensitive to AN in comparison to another fish species, Phimphales promelas. It was therefore suggested that available toxicity data should be used in an integrative multi-species way, rather than using individual-based toxicity extrapolations. In this way, a relevant overview of the differences in species sensitivity is given, which in turn can serve as the basis for acute to chronic extrapolations. PMID:21944038

  11. Analogues of deltorphin I containing conformationally restricted amino acids in position 2: structure and opioid activity.

    PubMed

    Lasota, Anika; Fr?czak, Oliwia; Le?niak, Anna; Muchowska, Adriana; Lipkowski, Andrzej W; Nowakowski, Micha?; Ejchart, Andrzej; Olma, Aleksandra

    2015-02-01

    New analogues of deltorphin I (DT I, Tyr-D-Ala-Phe-Asp-Val-Val-Gly-NH2 ), with the D-Ala residue in position 2 replaced by ?-methyl-?-azido(amino, 1-pyrrolidinyl, 1-piperidinyl or 4-morpholinyl)alanine, were synthesized by a combination of solid-phase and solution methods. All ten new analogues were tested for receptor affinity and selectivity to ?- and ?-opioid receptors. The affinity of analogues containing (R) or (S)-?-methyl-?-azidoalanine in position 2 to ?-receptors strongly depended on the chirality of the ?,?-disubstituted residue. Peptide II, containing (S)-?-methyl-?-azidoalanine in position 2, displayed excellent ?-receptor selectivity with its ?-receptor affinity being only three times lower than that of DT I. PMID:25558014

  12. A minimal structural analogue of cyclic ADP-ribose: synthesis and calcium release activity in mammalian cells.

    PubMed

    Guse, Andreas H; Gu, Xianfeng; Zhang, Liangren; Weber, Karin; Krämer, Elisabeth; Yang, Zhenjun; Jin, Hongwei; Li, Qin; Carrier, Lucie; Zhang, Lihe

    2005-04-22

    Cyclic ADP-ribose (cADPR) is an endogenous Ca(2+)-mobilizing second messenger in many cell types and organisms. Although the biological activity of several modified analogues of cADPR has been analyzed, most of these structures were still very similar to the original molecule. Recently, we have introduced simplified analogues in which the northern ribose (N(1)-linked ribose) was replaced by an ether strand. Here we also demonstrate that the southern ribose (N(9)-linked ribose) can be replaced by an ether strand resulting in N(1)-[(phosphoryl-O-ethoxy)-methyl]-N(9)-[(phosphoryl-O-ethoxy)-methyl]-hypoxanthinecyclic pyrophosphate (cIDP-DE). This minimal structural analogue of cyclic ADP-ribose released Ca(2+) from intracellular stores of permeabilized Jurkat T lymphocytes. In intact T lymphocytes initial subcellular Ca(2+) release events, global Ca(2+) release, and subsequent global Ca(2+) entry were observed. Cardiac myocytes freshly prepared from mice responded to cIDP-DE by increased recruitment of localized Ca(2+) signals and by global Ca(2+) waves. PMID:15713671

  13. Design, structure-activity relationship and in vivo efficacy of piperazine analogues of fenarimol as inhibitors of Trypanosoma cruzi.

    PubMed

    Keenan, Martine; Alexander, Paul W; Diao, Hugo; Best, Wayne M; Khong, Andrea; Kerfoot, Maria; Thompson, R C Andrew; White, Karen L; Shackleford, David M; Ryan, Eileen; Gregg, Alison D; Charman, Susan A; von Geldern, Thomas W; Scandale, Ivan; Chatelain, Eric

    2013-04-01

    A scaffold hopping exercise undertaken to expand the structural diversity of the fenarimol series of anti-Trypanosoma cruzi (T. cruzi) compounds led to preparation of simple 1-[phenyl(pyridin-3-yl)methyl]piperazinyl analogues of fenarimol which were investigated for their ability to inhibit T. cruzi in vitro in a whole organism assay. A range of compounds bearing amide, sulfonamide, carbamate/carbonate and aryl moieties exhibited low nM activities and two analogues were further studied for in vivo efficacy in a mouse model of T. cruzi infection. One compound, the citrate salt of 37, was efficacious in a mouse model of acute T. cruzi infection after once daily oral dosing at 20, 50 and 100 mg/kg for 5 days. PMID:23462713

  14. Adenosine Analogues as Selective Inhibitors of Glyceraldehyde-3-phosphate Dehydrogenase of Trypanosomatidae via Structure-Based Drug Design

    PubMed Central

    Bressi, Jerome C.; Verlinde, Christophe L. M. J.; Aronov, Alex M.; Shaw, My Le; Shin, Sam S.; Nguyen, Lisa N.; Suresh, Stephen; Buckner, Frederick S.; Van Voorhis, Wesley C.; Kuntz, Irwin D.; Hol, Wim G. J.; Gelb, Michael H.

    2010-01-01

    In our continuation of the structure-based design of anti-trypanosomatid drugs, parasite-selective adenosine analogues were identified as low micromolar inhibitors of glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Crystal structures of Trypanosoma brucei, Trypanosoma cruzi, Leishmania mexicana, and human GAPDH’s provided details of how the adenosyl moiety of NAD+ interacts with the proteins, and this facilitated the understanding of the relative affinities of a series of adenosine analogues for the various GAPDH’s. From exploration of modifications of the naphthalenemethyl and benzamide substituents of a lead compound, N6-(1-naphthalenemethyl)-2?-deoxy-2?-(3-methoxybenzamido)adenosine (6e), N6-(substituted-naphthalenemethyl)-2?-deoxy-2?-(substituted-benzamido)adenosine analogues were investigated. N6-(1-Naphthalenemethyl)-2?-deoxy-2?-(3,5-dimethoxybenzamido)adenosine (6m), N6-[1-(3-hydroxy-naphthalene)methyl]-2?-deoxy-2?-(3,5-dimethoxybenzamido)adenosine (7m), N6-[1-(3-methoxy-naphthalene)methyl]-2?-deoxy-2?-(3,5-dimethoxybenzamido)adenosine (9m), N6-(2-naphthalene-methyl)-2?-deoxy-2?-(3-methoxybenzamido)adenosine (11e), and N6-(2-naphthalenemethyl)-2?-deoxy-2?-(3,5-dimethoxybenzamido)adenosine (11m) demonstrated a 2- to 3-fold improvement over 6e and a 7100- to 25000-fold improvement over the adenosine template. IC50’s of these compounds were in the range 2–12 ?M for T. brucei, T. cruzi, and L. mexicana GAPDH’s, and these compounds did not inhibit mammalian GAPDH when tested at their solubility limit. To explore more thoroughly the structure–activity relationships of this class of compounds, a library of 240 N6-(substituted)-2?-deoxy-2?-(amido)adenosine analogues was generated using parallel solution-phase synthesis with N6 and C2? substituents chosen on the basis of computational docking scores. This resulted in the identification of 40 additional compounds that inhibit parasite GAPDH’s in the low micromolar range. We also explored adenosine analogues containing 5?-amido substituents and found that 2?,5?-dideoxy-2?-(3,5-dimethoxy-benzamido)-5?-(diphenylacetamido)adenosine (49) displays an IC50 of 60–100 ?M against the three parasite GAPDH’s. PMID:11405646

  15. Structure-activity relationships of a series of analogues of the RFamide-related peptide 26RFa.

    PubMed

    Le Marec, Olivier; Neveu, Cindy; Lefranc, Benjamin; Dubessy, Christophe; Boutin, Jean A; Do-Régo, Jean-Claude; Costentin, Jean; Tonon, Marie-Christine; Tena-Sempere, Manuel; Vaudry, Hubert; Leprince, Jérôme

    2011-07-14

    26RFa is a new member of the RFamide peptide family that has been identified as the endogenous ligand of the orphan GPCR GPR103. As the C-terminal heptapeptide (26RFa((20-26))) mimics the action of the native peptide on food intake and gonadotropin secretion in rodents, we have synthesized a series of analogues of 26RFa((20-26)) and measured their potency to induce [Ca(2+)](i) mobilization in G?(16)-hGPR103-transfected CHO cells. Systematic replacement of each residue by an alanine (Ala scan) and its D-enantiomer (D scan) showed that the last three C-terminal residues were very sensitive to the substitutions while position 23 tolerated rather well both modifications. Most importantly, replacement of Ser(23) by a norvaline led to an analogue, [Nva(23)]26RFa((20-26)), that was 3-fold more potent than the native heptapeptide. These new pharmacological data, by providing the first information regarding the structure-activity relationships of 26RFa analogues, should prove useful for the rational design of potent GPR103 receptor ligands with potential therapeutic application. PMID:21623631

  16. Effect of gambierol and its tetracyclic and heptacyclic analogues in cultured cerebellar neurons: a structure-activity relationships study.

    PubMed

    Pérez, Sheila; Vale, Carmen; Alonso, Eva; Fuwa, Haruhiko; Sasaki, Makoto; Konno, Yu; Goto, Tomomi; Suga, Yuto; Vieytes, Mercedes R; Botana, Luis M

    2012-09-17

    The polycyclic ether class of marine natural products has attracted the attention of researchers due to their complex and large chemical structures and diverse biological activities. Gambierol is a marine polycyclic ether toxin, first isolated along with ciguatoxin congeners from the dinoflagellate Gambierdiscus toxicus. The parent compound gambierol and the analogues evaluated in this work share the main crucial elements for biological activity, previously described to be the C28=C29 double bond within the H ring and the unsaturated side chain [Fuwa, H., Kainuma, N., Tachibana, K., Tsukano, C., Satake, M., and Sasaki, M. (2004) Diverted total synthesis and biological evaluation of gambierol analogues: Elucidation of crucial structural elements for potent toxicity. Chem. Eur. J. 10, 4894-4909]. With the aim to gain a deeper understanding of the cellular mechanisms involved in the biological activity of these compounds, we compared its activity in primary cultured neurons. The three compounds inhibited voltage-gated potassium channels (Kv) in a concentration-dependent manner and with similar potency, caused a small inhibition of voltage-gated sodium channels (Nav), and evoked cytosolic calcium oscillations. Moreover, the three compounds elicited a "loss of function" effect on Kv channels at concentrations of 0.1 nM. Additionally, both the tetracyclic and the heptacyclic derivatives of gambierol elicited synchronous calcium oscillations similar to those previously described for gambierol in cultured cerebellar neurons. Neither gambierol nor its tetracyclic derivative elicited cell toxicity, while the heptacyclic analogue caused a time-dependent decrease in cell viability. Neither the tetracyclic nor the heptacyclic analogues of gambierol exhibited lethality in mice after ip injection of 50 or 80 ?g/kg of each compound. Altogether, the results presented in this work support an identical mechanism of action for gambierol and its tetracyclic and heptacyclic analogues and indicate a "loss of function" effect on potassium channels even after administration of the three compounds at subnanomolar concentrations. In addition, because gambierol is known to stabilize the closed state of Kv3 channels, the results presented in this paper may have implications for understanding of channel functions and for future development of therapies against ciguatera poisoning and potassium channel-related diseases. PMID:22894724

  17. The structure, synthesis, and immunomodulating activity of bacterial lipopeptides and their analogues

    NASA Astrophysics Data System (ADS)

    Ousanova, Mariya P.; Sebyakin, Yurii L.

    1997-10-01

    The current state and prospects for the use of natural lipopeptides and their synthetic analogues in the study of fine mechanisms of functioning of complex biological systems and in the solution of various problems of biochemistry and medicine are considered. The results of investigations related to the synthesis and biological activity of lipopeptides are summarised. The data on the application of lipopeptides as components of synthetic vaccines and antitumour drugs are discussed. The bibliography includes 71 references.

  18. Constrained nucleoside analogues - Crystal and molecular structure of 6,5?-O-anhydrouridines fixed in the anti conformation

    NASA Astrophysics Data System (ADS)

    Gajda, Roman; Bagi?ski, Maciej; Tomczyk, Ewelina; Mieczkowski, Adam; Wo?niak, Krzysztof

    2015-10-01

    A series of analogues of anhydrouridine have been synthesized and their crystal structures established using X-ray diffraction. For all cases, the ribose ring has O(4?)-exo, C(4?)-endo pucker and the pyrimidine base is in the anti conformation. Investigated compounds crystallize in different crystal systems (monoclinic, orthorhombic), have different space group symmetry (P21, P212121) and exhibit different intermolecular interactions (halogen and hydrogen bonds) among molecules in their crystal lattices. Moreover, in the case of the 5-benzyl-6,5?-O-anhydrouridine a significant positional disorder is present with the phenyl rings existing in two orientations.

  19. Three-dimensional quantitative structure-activity relationship study on antioxidant capacity of curcumin analogues

    NASA Astrophysics Data System (ADS)

    Chen, Bohong; Zhu, Zhibo; Chen, Min; Dong, Wenqi; Li, Zhen

    2014-03-01

    A comparative molecular similarity indices analysis (CoMSIA) was performed on a set of 27 curcumin-like diarylpentanoid analogues with the radical scavenging activities. A significant cross-validated correlation coefficient Q2 (0.784), SEP (0.042) for CoMSIA were obtained, indicating the statistical significance of the correlation. Further we adopt a rational approach toward the selection of substituents at various positions in our scaffold,and finally find the favored and disfavoured regions for the enhanced antioxidative activity. The results have been used as a guide to design compounds that, potentially, have better activity against oxidative damage.

  20. Structure–Activity Relationships of Cyclic Lactam Analogues of ?-Melanocyte-Stimulating Hormone (?-MSH) Targeting the Human Melanocortin-3 Receptor

    PubMed Central

    Mayorov, Alexander V.; Cai, Minying; Palmer, Erin S.; Dedek, Matthew M.; Cain, James P.; Van Scoy, April R.; Tan, Bahar; Vagner, Josef; Trivedi, Dev; Hruby, Victor J.

    2008-01-01

    A variety of dicarboxylic acid linkers introduced between the ?-amino group of Pro6 and the ?-amino group of Lys10 of the cyclic lactam ?-melanocyte-stimulating hormone (?-MSH)-derived Pro6-D-Phe7/D-Nal(2?)7-Arg8-Trp9-Lys10-NH2 pentapeptide template lead to nanomolar range and selective hMC3R agonists and antagonists. Replacement of the Pro6 residue and the dicarboxylic acid linker with 2,3-pyrazine-dicarboxylic acid furnished a highly selective nanomolar range hMC3R partial agonist (analogue 12, c[CO-2,3-pyrazine-CO-D-Phe-Arg-Trp-Lys]-NH2, EC50 = 27 nM, 70% max cAMP) and an hMC3R antagonist (analogue 13, c[CO-2,3-pyrazine-CO-D-Nal(2?)-Arg-Trp-Lys]-NH2, IC50 = 23 nM). Modeling experiments suggest that 2,3-pyrazinedicarboxylic acid stabilizes a ?-turn-like structure with the D-Phe/D-Nal(2?) residues, which explains the high potency of the corresponding peptides. Placement of a Nle residue in position 6 produced a hMC3R/hMC5R antagonist (analogue 15, c[CO-(CH2)2-CO-Nle-D-Nal(2?)-Arg-Trp-Lys]-NH2, IC50 = 12 and 17 nM, respectively), similarly to the previously described cyclic ?-melanocyte-stimulating hormone (?-MSH)-derived hMC3R/hMC5R antagonists. These newly developed melanotropins will serve as critical biochemical tools for elucidating the full spectrum of functions performed by the physiologically important melanocortin-3 receptor. PMID:18088090

  1. Parrots as key multilinkers in ecosystem structure and functioning.

    PubMed

    Blanco, Guillermo; Hiraldo, Fernando; Rojas, Abraham; Dénes, Francisco V; Tella, José L

    2015-09-01

    Mutually enhancing organisms can become reciprocal determinants of their distribution, abundance, and demography and thus influence ecosystem structure and dynamics. In addition to the prevailing view of parrots (Psittaciformes) as plant antagonists, we assessed whether they can act as plant mutualists in the dry tropical forest of the Bolivian inter-Andean valleys, an ecosystem particularly poor in vertebrate frugivores other than parrots (nine species). We hypothesised that if interactions between parrots and their food plants evolved as primarily or facultatively mutualistic, selection should have acted to maximize the strength of their interactions by increasing the amount and variety of resources and services involved in particular pairwise and community-wide interaction contexts. Food plants showed different growth habits across a wide phylogenetic spectrum, implying that parrots behave as super-generalists exploiting resources differing in phenology, type, biomass, and rewards from a high diversity of plants (113 species from 38 families). Through their feeding activities, parrots provided multiple services acting as genetic linkers, seed facilitators for secondary dispersers, and plant protectors, and therefore can be considered key mutualists with a pervasive impact on plant assemblages. The number of complementary and redundant mutualistic functions provided by parrots to each plant species was positively related to the number of different kinds of food extracted from them. These mutually enhancing interactions were reflected in species-level properties (e.g., biomass or dominance) of both partners, as a likely consequence of the temporal convergence of eco-(co)evolutionary dynamics shaping the ongoing structure and organization of the ecosystem. A full assessment of the, thus far largely overlooked, parrot-plant mutualisms and other ecological linkages could change the current perception of the role of parrots in the structure, organization, and functioning of ecosystems. PMID:26445664

  2. Information Theoretic Secret Key Generation: Structured Codes and Tree Packing

    ERIC Educational Resources Information Center

    Nitinawarat, Sirin

    2010-01-01

    This dissertation deals with a multiterminal source model for secret key generation by multiple network terminals with prior and privileged access to a set of correlated signals complemented by public discussion among themselves. Emphasis is placed on a characterization of secret key capacity, i.e., the largest rate of an achievable secret key,…

  3. Structural characteristics of chloroquine-bridged ferrocenophane analogues of ferroquine may obviate malaria drug-resistance mechanisms.

    PubMed

    Salas, Paloma F; Herrmann, Christoph; Cawthray, Jacqueline F; Nimphius, Corinna; Kenkel, Alexander; Chen, Jessie; de Kock, Carmen; Smith, Peter J; Patrick, Brian O; Adam, Michael J; Orvig, Chris

    2013-02-28

    Five compounds displaying an unprecedented binding mode of chloroquine to ferrocene through the bridging of the cyclopentadienyl rings were studied alongside their monosubstituted ferrocene analogues and organic fragments. The antiplasmodial activity was evaluated against strains of the malaria parasite (Plasmodium falciparum). While the chloroquine-bridged ferrocenyl derivatives were less active than their five monosubstituted ferrocenyl analogues, they retained activity in the drug-resistant strains. The biological and physical properties were correlated to antiplasmodial activity. Intramolecular hydrogen bonding was associated with increased antiplasmodial action, but it is not the determining factor. Instead, balance between lipophilicity and hydrophilicity had a greater influence. It was found that calculated partition coefficient (log P) values of 4.5-5.0 and topological polar surfaces area (tPSA) values of ?26.0 Å(2) give the best balance. The particular conformation, compact size, and lipophilicity/hydrophilicity balance observed in the bridged compounds provide them with the structural characteristics needed to escape the mechanisms responsible for resistance. PMID:23327489

  4. Characterizing, identifying and mapping structural domains at rifted continental margins: insights from the Bay of Biscay margins and its Pyrenean fossil analogue

    NASA Astrophysics Data System (ADS)

    Tugend, Julie; Manatschal, Gianreto; Kusznir, Nick J.

    2014-05-01

    The occurrence of hyperextended domains at rifted continental margins consisting of extremely thinned crust and/or exhumed mantle has been increasingly recognized over the past decades, both at present-day rifted margins and in deformed remnants preserved in collisional orogens. At present, most studies aiming to characterize rifted continental margin structure and the extreme thinning of the continental crust and lithosphere are either focused offshore using geophysical methods, or onshore on fossil analogues relying on geological field observations. Marine and onland examples provide complementary datasets, but their different scale and resolution of observations prevent straightforward correlations to be done. In this contribution, we use the Bay of Biscay and Western Pyrenees to develop and apply a geological/geophysical approach to characterize and identify distinctive rifted margin domains both in offshore and onshore settings. The Bay of Biscay and Western Pyrenees represent a unique natural laboratory that offer the possibility to have access to seismically imaged, drilled and exposed parts of one and the same hyperextended rift system. Quantitative techniques (gravity inversion and flexural backstripping) are used on offshore examples (Western Approach margin and Parentis basin) to estimate accommodation space, crustal thickness and lithosphere thinning while seismic interpretations enable the recognition of extensional settings (low- and high-? settings). Field observations (Mauléon basin) and drill-hole data (Parentis basin) focused on key outcrops enables the description of the nature of sediment and basement rocks and of the structures forming fossil remnants of rifted margins. This qualitative and quantitative characterisation provides diagnostic elements to identify and map structural domains at magma-poor rifted margins and their fossil analogues. We name these 5 domains proximal, necking, hyperthinned, exhumed mantle and oceanic. This new geological/geophysical approach can be further used as an interface between onshore and offshore observations. Offshore seismic interpretations can take advantage of onshore observations on the nature of sediment, basement and of their interface. The large scale geometry and stratigraphic architecture imaged offshore can be used to restore onshore fossil remnants back into a rifted margin context. The application of this multidisciplinary approach to the Bay of Biscay margins and their onshore Pyrenean fossils remnants enables us to propose a new map of the different rift systems preserved at the transition between the European and Iberian plates. The approach underlying this mapping has general global application to unravelling the spatial and temporal complexity of rifted margin structural domains.

  5. Valles Marineris as a Cryokarstic Structure Formed by a Giant Dyke System: Support From New Analogue Experiments

    NASA Astrophysics Data System (ADS)

    Ozeren, M. S.; Sengor, A. M. C.; Acar, D.; Ülgen, S. C.; Onsel, I. E.

    2014-12-01

    Valles Marineris is the most significant near-linear depression on Mars. It is some 4000 km long, up to about 200 km wide and some 7 km deep. Although its margins look parallel at first sight, the entire structure has a long spindle shape with significant enlargement in its middle (Melas Chasma) caused by cuspate slope retreat mechanisms. Farther to its north is Hebes Chasma which is an entirely closed depression with a more pronounced spindle shape. Tithonium Chasma is a parallel, but much narrower depression to its northeast. All these chasmae have axes parallel with one another and such structures occur nowhere else on Mars. A scabland surface exists to the east of the Valles Marineris and the causative water mass seems to have issued from it. The great resemblance of these chasmae on mars to poljes in the karstic regions on earth have led us to assume that they owed their existence to dissolution of rock layers underlying them. We assumed that the dissolving layer consisted of water ice forming substantial layers, in fact entirely frozen seas of several km depth. We have simulated this geometry by using bentonite and flour layers (in different experiments) overlying layers of ice in which a resistant coil was used to simulate a dyke. We used different thicknesses of bentonite and flour overlying ice layers again of various thicknesses. The flour seems to simulate the Martian crust better because on Mars, g is only about 3/8ths of its value on Earth, so (for equal crustal density) the depth to which the cohesion term C remains important in the Mohr-Coulomb shear failure criterion is about 8/3 times greater. As examples we show two of those experiments in which both the rock analogue and ice layers were of 1.5 cm. thick. Perfect analogues of the Valles Marineris formed above the dyke analogue thermal source complete with the near-linear structure, overall flat spindle shape, cuspate margins, a central ridge, parallel side faults, parallel depressions resembling the Tithonium Chasma. When water was allowed to drain from the beginning, closed depressions formed that have an amazing resemblance to Hebes chasma. We postulate that the entire system of chasmae here discussed formed atop a major dyke swarm some 4000 km length, not dissimilar to the 3500 km long Mesoproterozoic (Ectasian) dyke swarm disrupting the Canadian Shield.

  6. Crystal Structure of Baeyer-Villiger Monooxygenase MtmOIV, the Key Enzyme of the Mithramycin Biosynthetic Pathway†

    PubMed Central

    Beam, Miranda P.; Bosserman, Mary A.; Noinaj, Nicholas; Wehenkel, Marie; Rohr, Jürgen

    2009-01-01

    Baeyer-Villiger monooxygenases (BVMOs), mostly flavoproteins, were shown to be powerful biocatalysts for synthetic organic chemistry applications and were also suggested to play key roles for the biosyntheses of various natural products. Here we present the three-dimensional structure of MtmOIV, a 56 kD homo-dimeric FAD- and NADPH-dependent monooxygenase, which catalyzes the key frame-modifying step of the mithramycin biosynthetic pathway and currently the only BVMO proven to react with its natural substrate via a Baeyer-Villiger reaction. MtmOIV’s structure was determined by X-ray crystallography using molecular replacement to a resolution of 2.9Å. MtmOIV cleaves a C-C bond, essential for the conversion of the biologically inactive precursor, premithramycin B, into the active drug mithramycin. The MtmOIV structure combined with substrate docking calculations and site-directed mutagenesis experiments implicate several residues to participate in co-factor and substrate binding. Future experimentation aimed at broadening the substrate specificity of the enzyme could facilitate the generation of chemically diverse mithramycin analogues through combinatorial biosynthesis. PMID:19364090

  7. Synthesis, structure elucidation, in vitro biological activity, toxicity, and Caco-2 cell permeability of lipophilic analogues of alpha-conotoxin MII.

    PubMed

    Blanchfield, Joanne T; Dutton, Julie L; Hogg, Ronald C; Gallagher, Oliver P; Craik, David J; Jones, Alun; Adams, David J; Lewis, Richard J; Alewood, Paul F; Toth, Istvan

    2003-03-27

    The alpha-conotoxin MII is a two disulfide bridge containing, 16 amino acid long peptide toxin isolated from the marine snail Conus magus. This toxin has been found to be a highly selective and potent inhibitor of neuronal nicotinic acetylcholine receptors (nAChRs) of the subtype alpha3beta2. To improve the bioavailability of this peptide, two lipidic analogues of MII have been synthesized, the first by coupling 2-amino-d,l-dodecanoic acid (Laa) to the N terminus (LaaMII) and the second by replacing Asn5 in the MII sequence with this lipoamino acid (5LaaMII). Both lipidic linear peptides were then oxidized under standard conditions. (1)H NMR shift analysis of these peptides and comparison with the native MII peptide showed that the tertiary structure of the N-conjugated analogue, LaaMII, was consistent with that of the native conotoxin, whereas the 5LaaMII analogue formed the correct disulfide bridges but failed to adopt the native helical tertiary structure. The N terminus conjugate was also found to inhibit nAChRs of the subtype alpha3beta2 with equal potency to the parent peptide, whereas the 5LaaMII analogue showed no inhibitory activity. The active LaaMII analogue was found to exhibit significantly improved permeability across Caco-2 cell monolayers compared to the native MII, and both peptides showed negligible toxicity. PMID:12646037

  8. Synthesis, structure, and properties of SrC(NH)3 , a nitrogen-based carbonate analogue with the trinacria motif.

    PubMed

    Missong, Ronja; George, Janine; Houben, Andreas; Hoelzel, Markus; Dronskowski, Richard

    2015-10-01

    Strontium guanidinate, SrC(NH)3 , the first compound with a doubly deprotonated guanidine unit, was synthesized from strontium and guanidine in liquid ammonia and characterized by X-ray and neutron diffraction, IR spectroscopy, and density-functional theory including harmonic phonon calculations. The compound crystallizes in the hexagonal space group P63 /m, constitutes the nitrogen analogue of strontium carbonate, SrCO3 , and its structure follows a layered motif between Sr(2+) ions and complex anions of the type C(NH)3 (2-) ; the anions adopt the peculiar trinacria shape. A comparison of theoretical phonons with experimental IR bands as well as quantum-chemical bonding analyses yield a first insight into bonding and packing of the formerly unknown anion in the crystal. PMID:26308739

  9. Kinetic, thermodynamic and X-ray structural insights into the interaction of melatonin and analogues with quinone reductase 2

    SciTech Connect

    Calamini, Barbara; Santarsiero, Bernard D.; Boutin, Jean A.; Mesecar, Andrew D.

    2008-09-12

    Melatonin exerts its biological effects through at least two transmembrane G-protein-coupled receptors, MT1 and MT2, and a lower-affinity cytosolic binding site, designated MT3. MT3 has recently been identified as QR2 (quinone reductase 2) (EC 1.10.99.2) which is of significance since it links the antioxidant effects of melatonin to a mechanism of action. Initially, QR2 was believed to function analogously to QR1 in protecting cells from highly reactive quinones. However, recent studies indicate that QR2 may actually transform certain quinone substrates into more highly reactive compounds capable of causing cellular damage. Therefore it is hypothesized that inhibition of QR2 in certain cases may lead to protection of cells against these highly reactive species. Since melatonin is known to inhibit QR2 activity, but its binding site and mode of inhibition are not known, we determined the mechanism of inhibition of QR2 by melatonin and a series of melatonin and 5-hydroxytryptamine (serotonin) analogues, and we determined the X-ray structures of melatonin and 2-iodomelatonin in complex with QR2 to between 1.5 and 1.8 {angstrom} (1 {angstrom} = 0.1 nm) resolution. Finally, the thermodynamic binding constants for melatonin and 2-iodomelatonin were determined by ITC (isothermal titration calorimetry). The kinetic results indicate that melatonin is a competitive inhibitor against N-methyldihydronicotinamide (K{sub i} = 7.2 {mu}M) and uncompetitive against menadione (K{sub i} = 92 {mu}M), and the X-ray structures shows that melatonin binds in multiple orientations within the active sites of the QR2 dimer as opposed to an allosteric site. These results provide new insights into the binding mechanisms of melatonin and analogues to QR2.

  10. Kinetic, thermodynamic and X-ray structural insights into the interaction of melatonin and analogues with quinone reductase 2

    PubMed Central

    CALAMINI, Barbara; SANTARSIERO, Bernard D.; BOUTIN, Jean A.; MESECAR, Andrew D.

    2011-01-01

    Melatonin exerts its biological effects through at least two transmembrane G-protein-coupled receptors, MT1 and MT2, and a lower-affinity cytosolic binding site, designated MT3. MT3 has recently been identified as QR2 (quinone reductase 2) (EC 1.10.99.2) which is of significance since it links the antioxidant effects of melatonin to a mechanism of action. Initially, QR2 was believed to function analogously to QR1 in protecting cells from highly reactive quinones. However, recent studies indicate that QR2 may actually transform certain quinone substrates into more highly reactive compounds capable of causing cellular damage. Therefore it is hypothesized that inhibition of QR2 in certain cases may lead to protection of cells against these highly reactive species. Since melatonin is known to inhibit QR2 activity, but its binding site and mode of inhibition are not known, we determined the mechanism of inhibition of QR2 by melatonin and a series of melatonin and 5-hydroxytryptamine (serotonin) analogues, and we determined the X-ray structures of melatonin and 2-iodomelatonin in complex with QR2 to between 1.5 and 1.8 Å (1 Å =0.1 nm) resolution. Finally, the thermodynamic binding constants for melatonin and 2-iodomelatonin were determined by ITC (isothermal titration calorimetry). The kinetic results indicate that melatonin is a competitive inhibitor against N-methyldihydronicotinamide (Ki = 7.2 ?M) and uncompetitive against menadione (Ki = 92 ?M), and the X-ray structures shows that melatonin binds in multiple orientations within the active sites of the QR2 dimer as opposed to an allosteric site. These results provide new insights into the binding mechanisms of melatonin and analogues to QR2. PMID:18254726

  11. Structure-based design of a streptavidin mutant specific for an artificial biotin analogue.

    PubMed

    Kawato, Tatsuya; Mizohata, Eiichi; Shimizu, Yohei; Meshizuka, Tomohiro; Yamamoto, Tomohiro; Takasu, Noriaki; Matsuoka, Masahiro; Matsumura, Hiroyoshi; Kodama, Tatsuhiko; Kanai, Motomu; Doi, Hirofumi; Inoue, Tsuyoshi; Sugiyama, Akira

    2015-06-01

    For a multistep pre-targeting method using antibodies, a streptavidin mutant with low immunogenicity, termed low immunogenic streptavidin mutant No. 314 (LISA-314), was produced previously as a drug delivery tool. However, endogenous biotins (BTNs) with high affinity (Kd < 10(-10) M) for the binding pocket of LISA-314 prevents access of exogenous BTN-labelled anticancer drugs. In this study, we improve the binding pocket of LISA-314 to abolish its affinity for endogenous BTN species, therefore ensuring that the newly designed LISA-314 binds only artificial BTN analogue. The replacement of three amino acid residues was performed in two steps to develop a mutant termed V212, which selectively binds to 6-(5-((3aS,4S,6aR)-2-iminohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamido)hexanoic acid (iminobiotin long tail, IMNtail). Surface plasmon resonance results showed that V212 has a Kd value of 5.9 × 10(-7) M towards IMNtail, but no binding affinity for endogenous BTN species. This V212/IMNtail system will be useful as a novel delivery tool for anticancer therapy. PMID:25645976

  12. A dinaphtho[8,1,2-cde:2',1',8'-uva]pentacene derivative and analogues: synthesis, structures, photophysical and electrochemical properties.

    PubMed

    Li, Xiao-Jun; Li, Meng; Lu, Hai-Yan; Chen, Chuan-Feng

    2015-07-28

    Dinaphtho[8,1,2-cde:2',1',8'-uva]pentacene and analogues as a new type of acene derivatives with scorpion-shaped structures were conveniently synthesized. Their structures, photophysical and electrochemical properties were experimentally and theoretically investigated. It was found that the pentacene derivative has a twisted configuration, but shows marked intermolecular ?-? interactions, strong electronic delocalization, and a small HOMO-LUMO bandgap, which are different from those of pentacene and pentatwistacene derivatives with similar structures. PMID:26104736

  13. COMPARATIVE ANALYSIS OF THE ELECTROSTATIC POTENTIALS OF SOME STRUCTURAL ANALOGUES OF 2,3,7,8-TETRACHLORODIBENZO-P-DIOXIN AND OF RELATED AROMATIC SYSTEMS

    EPA Science Inventory

    We have carried out an ab initio STO-5G computational analysis of the electrostatic potential of four structural analogues of the highly toxic 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and four related aromatic systems: benzo[a]pyrene, benz[a]anthracene and two isomeric benzofla...

  14. Non-natural acetogenin analogues as potent Trypanosoma brucei inhibitors

    PubMed Central

    Florence, Gordon J.; Fraser, Andrew L.; Gould, Eoin R.; King, Elizabeth F.; Menzies, Stefanie K.; Morris, Joanne C.; Tulloch, Lindsay B.; Smith, Terry K.

    2015-01-01

    A series of novel bis-tetrahydropyran 1,4-triazole analogues based on the acetogenin framework display low micromolar trypanocidal activities towards both bloodstream and insect forms of Trypanosoma brucei, the causative agent of African sleeping sickness. A divergent synthetic strategy was adopted for the synthesis of the key tetrahydropyran intermediates to enable rapid access to diastereochemical variation either side of the 1,4-triazole core. The resulting diastereomeric analogues displayed varying degrees of trypanocidal activity and selectivity in structure activity relationship studies. PMID:25145275

  15. Influence of the Convergence and Stepover Angles in the Structural Style of Strike-Slip Systems: Analogue Models

    NASA Astrophysics Data System (ADS)

    Gonzalez, D.; Pinto, L.

    2008-12-01

    The presented results of analogue models analyze the influence of the relation between the convergence angle and the stepover angle on strike-slip systems. The experiments include 2 stepovers arrays to generate both transpressional and transtensional zones. These experiments were prepared using 5 cm thick sandpack (sand diameter <500 ?m, internal friction angle 30°, density 1,400 kg/m3) to simulate brittle deformation; the base of the model was formed by thin zinc base plates, one of them mobile, cut in such a way so as to produce restraining and releasing strike-slip stepovers; the rate convergence was constant. We carried out 3 series of experiments in which the convergence angles (0°-60°) and stepover angles (30°-60°) were varied systematically. Preliminary results indicate that by increasing the angle between the stepover and the convergence vector: a) the restraining area generated a positive flower structure that is progressively wider; b) progressively more reverse faults which absorb more shortening were generated. Locally, strike-slip faults in the positive flowers were accommodated by the geometry of the stepover base. Areas most complex involved the development of normal faults, which subsequently were inverted. In conclusion, the relation between the convergence and stepover angles is a main factor that determines the structural style of flowers structures on strike-slip systems. This work was done through the ACT-18 PBCT project.

  16. Analysis of Wave Propagation in Stratified Structures Using Circuit Analogues, with Application to Electromagnetic Absorbers

    ERIC Educational Resources Information Center

    Sjoberg, Daniel

    2008-01-01

    This paper presents an overview of how circuit models can be used for analysing wave propagation in stratified structures. Relatively complex structures can be analysed using models which are accessible to undergraduate students. Homogeneous slabs are modelled as transmission lines, and thin sheets between the slabs are modelled as lumped…

  17. Synthesis and biological evaluation of novel myrtucommulones and structural analogues that target mPGES-1 and 5-lipoxygenase.

    PubMed

    Wiechmann, Katja; Müller, Hans; Huch, Volker; Hartmann, David; Werz, Oliver; Jauch, Johann

    2015-08-28

    The natural acylphloroglucinol myrtucommulone A (1) inhibits microsomal prostaglandin E2 synthase (mPGES)-1 and 5-lipoxygenase (5-LO), and induces apoptosis of cancer cells. Starting from 1 as lead, 28 analogues were synthesized following a straightforward modular strategy with high yielding convergent steps. Major structural variations concerned (I) replacement of the syncarpic acid moieties by dimedone or indandione, (II) cyclization of the syncarpic acid with the acylphloroglucinol core, and (III) substitution of the methine bridges and the acyl residue with isopropyl, isobutyl, n-pentyl or phenyl groups, each. The potency for mPGES-1 inhibition was improved by 12.5-fold for 43 (2-(1-(3-hexanoyl-2,4,6-trihydroxy-5-(1-(3-hydroxy-1-oxo-1H-inden-2-yl)-2-methylpropyl)phenyl)-2-methylpropyl)-3-hydroxy-1H-inden-1-one) with IC50 = 0.08 ?M, and 5-LO inhibition was improved 33-fold by 47 (2-((3-hexanoyl-2,4,6-trihydroxy-5-((3-hydroxy-1-oxo-1H-inden-2-yl) (phenyl)methyl)phenyl) (phenyl)methyl)-3-hydroxy-1H-inden-1-one) with IC50 = 0.46 ?M. SAR studies revealed divergent structural determinants for induction of cell death and mPGES-1/5-LO inhibition, revealing 43 and 47 as non-cytotoxic mPGES-1 and 5-LO inhibitors that warrant further preclinical assessment as anti-inflammatory drugs. PMID:26123643

  18. Structural diversity of lamellar zeolite Nu-6(1)--postsynthesis of delaminated analogues.

    PubMed

    Xu, Hao; Jia, Lili; Wu, Haihong; Yang, Boting; Wu, Peng

    2014-07-21

    Nu-6(1) zeolite, the lamellar precursor of NSI topology, was firstly synthesized with 4'4-bipyridine as the structure-directing agent (SDA) and then subjected to HCl-EtOH treatment for the purpose of structural modification. Interlayer deconstruction and reconstruction took place alternately in this acid treatment. An intermediate named ECNU-4 was separated at the initial stage of this continuous treatment process, which exhibited a special X-ray diffraction pattern without obvious reflection peaks at low angles. The zeolitic structure in the intralayer sheets was supposed to be well preserved in ECNU-4, whereas the interlayer structure became extremely disordered. The ECNU-4 intermediate showed structural diversity. It was converted into the reconstructed and interlayer expanded zeolite IEZ-NSI without an external silicon source by prolonging the HCl-EtOH treatment to 24 h. Moreover, with a partially delaminated structure, ECNU-4 was easily interlayer swollen at room temperature with cetyltrimethyl ammonium bromide in the presence of tetrapropyl ammonium hydroxide. The swollen material was further sonicated to yield a more deeply delaminated zeolite, Del-Nu-6. ECNU-4 and Del-Nu-6 differed in delamination degree, structural disordering and textural properties, especially surface area. PMID:24658572

  19. CONSIDERATION OF REACTION INTERMEDIATES IN STRUCTURE-ACTIVITY RELATIONSHIPS: A KEY TO UNDERSTANDING AND PREDICTION

    EPA Science Inventory

    Consideration of Reaction Intermediates in Structure- Activity Relationships: A Key to Understanding and Prediction

    A structure-activity relationship (SAR) represents an empirical means for generalizing chemical information relative to biological activity, and is frequent...

  20. Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch

    E-print Network

    Halazonetis, Thanos

    , commonly referred to as vitamin B1, is composed of a pyrimidine ring, a central thiazole ring shown to exert an antibiotic effect via interaction with TPP-specific riboswitches in bacteria and plants,4 no structural information is available for this complex, either. To better understand

  1. Photomagnetic and structural studies of Prussian blue analogue CoFe@CoCr core@shell heterostructures

    NASA Astrophysics Data System (ADS)

    Quintero, P. A.; Brinzari, T. V.; Meisel, M. W.; Risset, O. N.; Andrus, M. J.; Talham, D. R.; Lufaso, M. W.

    2015-03-01

    The photomagnetic and structural properties of core@shell nanostructures of Prussian blue analogues, Rb0.24Co[Fe(CN)6]0.74@K0.10Co[Cr(CN)6]0.70 . n H2O, with different shell thicknesses have been studied as a function of temperature and under white light irradiation. The nature of the charge transfer induced spin transition (CTIST) of the core was affected by the presence of the shell. Specifically, while a continuous and hysteretic CTIST was observed in the bare cores, a discontinuous and non-hysteretic behavior was observed for the core@shell systems. In addition, the core@shell nanoparticles show light-induced magnetization changes radically different from the bare cores. These changes were modeled as a combination of the expected light-induced magnetism change in the cores and a modification of the magnetism in a region of the shell close to the interface, where the depth of the modified region was found to be about 25 nm for all shell thicknesses investigated. Supported by the NSF via DMR-1202033 (MWM), DMR-1405439 (DRT), and DMR-1157490 (NHMFL).

  2. Structure-toxicity relationship study of para-halogenated styrene analogues in CYP2E1 transgenic cells

    PubMed Central

    Chung, Jou-Ku; Shen, Shuijie; Jiang, Zhiteng; Yuan, Wei; Zheng, Jiang

    2012-01-01

    Styrene is one of the most important industrial intermediates consumed in the world and is mainly used as a monomer for reinforced plastics and rubber. Styrene has been found to be hepatotoxic and pneumotoxic in humans and experimental animals. The toxicity of styrene is suggested to be metabolism-dependent. Styrene-7,8-oxide has been considered as the major metabolite responsible for styrene-induced cytotoxicity. The objective of the study was to investigate the correlation between cytotoxicity of styrene and chemical and biochemical properties of the vinyl group of styrene by development of structure activity relationships (SAR). 4-Fluorostyrene, 4-chlorostyrene and 4-bromostyrene were selected for the SAR study. Cytotoxicity of styrene and the halogenated styrene derivatives with an order of 4-bromostyrene > 4-chlorostyrene > 4-fluorostyrene ? styrene was observed in CYP2E1 transgenic cells. Similar orders in the efficiency of the metabolism of styrene and the halogenated styrene analogues to their oxides and in the electrophilicity of the corresponding oxides were observed. Additionally, the order of the potency of cellular glutathione depletion and the degree of protein adduction induced by styrene and the halogenated styrenes were consistent with that of their cytotoxicities. The wild-type cells were less susceptible to the toxicity of the corresponding model compounds than CYP2E1 cells. The present study provided insight into the roles of the biochemical and chemical properties of styrene in its cytotoxicity. PMID:22366341

  3. Interactions of taurine and structurally related analogues with the GABAergic system and taurine binding sites of rabbit brain

    PubMed Central

    Frosini, Maria; Sesti, Casilde; Dragoni, Stefania; Valoti, Massimo; Palmi, Mitri; Dixon, Henry B F; Machetti, Fabrizio; Sgaragli, Giampietro

    2003-01-01

    The aim of this study was to find taurinergic compounds that do not interact with brain GABA ergic systems. Washed synaptic membranes (SM) from whole rabbit brain were able to bind [3H]muscimol. Saturation experiments of the binding of [3H]GABA to GABAB receptors showed that SM possess two binding components; twice Triton X-100-treated SM contained 0.048 mmol endogenous taurine/kg protein and bound [3H]taurine in a saturable manner (Kd=249.0±6.3 nM and Bmax=3.4±1.0 pmol mg?1 prot). Among the 19 structural analogues of taurine, 6-aminomethyl-3-methyl-4H-1,2,4-benzothiadiazine 1,1-dioxide (TAG), 2-aminoethylarsonic (AEA), 2-hydroxyethanesulfonic (ISE) and (±)cis-2-aminocyclohexane sulfonic acids (CAHS) displaced [3H]taurine binding (Ki=0.13, 0.13, 13.5 and 4.0 ?M, respectively). These analogues did not interact with GABAA and GABAB receptors and did not affect taurine- and GABA-uptake systems and GABA-transaminase activity. 3-Aminopropanesulfonic acid (OMO), ?-alanine, pyridine-3-sulfonic acid, N,N,N-trimethyltaurine (TMT), 2-(guanidino)ethanesulfonic acid (GES), ethanolamine-O-sulphate, N,N-dimethyltaurine (DMT), taurine and (±)piperidine-3-sulfonic acid (PSA) inhibited [3H]muscimol binding to GABAA receptors with different affinities (Ki=0.013, 7.9, 24.6, 47.5, 52.0, 91.0, 47.5, 118.1 and 166.3 ?M, respectively). Taurine, 2-aminoethylphosphonic acid, DMT, TMT and OMO inhibited the binding of [3H]GABA to GABAB receptors with Ki's in the ?M range (0.8, 3.5, 4.4, 11.3 and 5.0, respectively). GES inhibited taurine uptake (IC50=3.72 ?M) and PSA GABA transaminase activity (IC50=103.0 ?M). In conclusion, AEA, TAG, ISE and CAHS fulfill the criteria for taurinergic agents. PMID:12684273

  4. New Mexico structural zone - An analogue of the Colorado mineral belt

    USGS Publications Warehouse

    Sims, P.K.; Stein, H.J.; Finn, C.A.

    2002-01-01

    Updated aeromagnetic maps of New Mexico together with current knowledge of the basement geology in the northern part of the state (Sangre de Cristo and Sandia-Manzano Mountains)-where basement rocks were exposed in Precambrian-cored uplifts-indicate that the northeast-trending Proterozoic shear zones that controlled localization of ore deposits in the Colorado mineral belt extend laterally into New Mexico. The shear zones in New Mexico coincide spatially with known epigenetic precious- and base-metal ore deposits; thus, the mineralized belts in the two states share a common inherited basement tectonic setting. Reactivation of the basement structures in Late Cretaceous-Eocene and Mid-Tertiary times provided zones of weakness for emplacement of magmas and conduits for ore-forming solutions. Ore deposits in the Colorado mineral belt are of both Late Cretaceous-Eocene and Mid-Tertiary age; those in New Mexico are predominantly Mid-Tertiary in age, but include Late Cretaceous porphyry-copper deposits in southwestern New Mexico. The mineralized belt in New Mexico, named the New Mexico structural zone, is 250-km wide. The northwest boundary is the Jemez subzone (or the approximately equivalent Globe belt), and the southeastern boundary was approximately marked by the Santa Rita belt. Three groups (subzones) of mineral deposits characterize the structural zone: (1) Mid-Tertiary porphyry molybdenite and alkaline-precious-metal deposits, in the northeast segment of the Jemez zone; (2) Mid-Tertiary epithermal precious-metal deposits in the Tijeras (intermediate) zone; and (3) Late Cretaceous porphyry-copper deposits in the Santa Rita zone. The structural zone was inferred to extend from New Mexico into adjacent Arizona. The structural zone provides favorable sites for exploration, particularly those parts of the Jemez subzone covered by Neogene volcanic and sedimentary rocks. ?? 2002 Published by Elsevier Science B.V.

  5. Stereoselective facile synthesis of 2'-spiro pyrimidine pyranonucleosides via their key intermediate 2'-C-cyano analogues. Evaluation of their bioactivity.

    PubMed

    Kiritsis, Christos; Manta, Stella; Dimopoulou, Athina; Parmenopoulou, Vanessa; Gkizis, Petros; Balzarini, Jan; Komiotis, Dimitri

    2014-01-13

    A novel series of 2'-spiro pyrimidine pyranonucleosides has been designed and synthesized. Their precursors, 2'-C-cyano nucleosides 5a,b and 6a,b, were obtained by subjecting 1a,b to the sequence of selective protection of the primary hydroxyl group, acetalation, oxidation, and finally treatment with sodium cyanide. Deoxygenation at the 2'-position of cyanohydrins 5a,b or 6a,b led to the 2'-deoxy derivatives 9a,b. Fully deprotection of 5a,b, 6a,b, and 9a,b gave the desired 2'-C-cyano 7a,b, 8a,b, and 2'-C-cyano-2'-deoxy pyranonucleosides 10a,b, respectively. Mesylation of the corresponding cyanohydrins 5a,b and 6a,b afforded compounds 11a,b and 12a,b which after base treatment and subsequent deprotection furnished the spiro nucleosides 15a,b and 16a. The new analogues were evaluated for their potential cytostatic activities in cell culture. PMID:24291356

  6. Synthesis and high-throughput characterization of structural analogues of molecular glassformers: 1,3,5-trisarylbenzenes.

    PubMed

    Liu, Tianyi; Cheng, Kevin; Salami-Ranjbaran, Elmira; Gao, Feng; Glor, Ethan C; Li, Mu; Walsh, Patrick J; Fakhraai, Zahra

    2015-10-14

    We report the synthesis and characterization of an analogous series of small organic molecules derived from a well-known glass former, 1,3-bis(1-naphthyl)-5-(2-naphthyl)benzene (?,?,?-TNB). Synthesized molecules include ?,?,?-TNB, 3,5-di(naphthalen-1-yl)-1-phenylbenzene (?,?-P), 9-(3,5-di(naphthalen-1-yl)phenyl)anthracene (?,?-A), 9,9'-(5-(naphthalen-2-yl)-1,3-phenylene)dianthracene (?-AA) and 3,3',5,5'-tetra(naphthalen-1-yl)-1,1'-biphenyl (?,?,?,?-TNBP). The design of molecules was based on increasing molecular weight with varied ?-? interactions in one or more substituents. The synthesis is based on Suzuki cross-coupling of 1-bromo-3-chloro-5-iodobenzene with arylboronic acids, which allows attachment of various substituents to tailor the chemical structure. The bulk compounds were characterized using NMR spectroscopy and differential scanning calorimetry (DSC). Thin films of these compounds were produced using physical vapor deposition and were subsequently annealed above the glass transition temperatures (Tg). For each molecular glass, cooling rate-dependent glass transition temperature measurements (CR-Tg) were performed using ellipsometry as a high-throughput method to characterize thin film properties. CR-Tg allows rapid characterization of glassy properties, such as Tg, apparent thermal expansion coefficients, apparent activation energy at Tg and fragility. DSC measurements confirmed the general trend that increasing molecular weight leads to increasing melting point (Tm) and Tg. Furthermore, CR-Tg provided evidence that the introduction of stronger ?-interacting substituents in the chosen set of structural analogues increases fragility and decreases the ability to form glasses, such that ?-AA has the largest fragility and highest tendency to crystallize among all the compounds. These strong interactions also significantly elevate Tg and promote more harmonic intermolecular potentials, as observed by decreasing value of the apparent thermal expansion coefficient. PMID:26280737

  7. Formazanate ligands as structurally versatile, redox-active analogues of ?-diketiminates in zinc chemistry.

    PubMed

    Chang, Mu-Chieh; Roewen, Peter; Travieso-Puente, Raquel; Lutz, Martin; Otten, Edwin

    2015-01-01

    A range of tetrahedral bis(formazanate)zinc complexes with different steric and electronic properties of the formazanate ligands were synthesized. The solid-state structures for several of these were determined by X-ray crystallography, which showed that complexes with symmetrical, unhindered ligands prefer coordination to the zinc center via the terminal N atoms of the NNCNN ligand backbone. Steric or electronic modifications can override this preference and give rise to solid-state structures in which the formazanate ligand forms a 5-membered chelate by binding to the metal center via an internal N atom. In solution, these compounds show dynamic equilibria that involve both 5- and 6-membered chelates. All compounds are intensely colored, and the effect of the ligand substitution pattern on the UV-vis absorption spectra was evaluated. In addition, their cyclic voltammetry is reported, which shows that all compounds may be electrochemically reduced to radical anionic (L2Zn(-)) and dianionic (L2Zn(2-)) forms. While unhindered NAr substituents lie in the plane of the ligand backbone (Ar = Ph), the introduction of sterically demanding substituents (Ar = Mes) favors a perpendicular orientation in which the NMes group is no longer in conjugation with the backbone, resulting in hypsochromic shifts in the absorption spectra. The redox potentials in the series of L2Zn compounds may be altered in a straightforward manner over a relatively wide range (?700 mV) via the introduction of electron-donating or -withdrawing substituents on the formazanate framework. PMID:25493709

  8. Inhibition and Structure of Trichomonas vaginalis Purine Nucleoside Phosphorylase with Picomolar Transition State Analogues

    SciTech Connect

    Rinaldo-Matthis,A.; Wing, C.; Ghanem, M.; Deng, H.; Wu, P.; Gupta, A.; Tyler, P.; Evans, G.; Furneaux, R.; et al.

    2007-01-01

    Trichomonas vaginalis is a parasitic protozoan purine auxotroph possessing a unique purine salvage pathway consisting of a bacterial type purine nucleoside phosphorylase (PNP) and a purine nucleoside kinase. Thus, T. vaginalis PNP (TvPNP) functions in the reverse direction relative to the PNPs in other organisms. Immucillin-A (ImmA) and DADMe-Immucillin-A (DADMe-ImmA) are transition stte mimics of adenosine with geometric and electrostatic features that resemble early and late transition states of adenosine at the transition state stabilized by TvPNP. ImmA demonstrates slow-onset tight-binding inhibition with TvPNP, to give an equilibrium dissociation constant of 87 pM, an inhibitor release half-time of 17.2 min, and a K{sub m}/K{sub d} ratio of 70,100. DADMe-ImmA resembles a late ribooxacarbenium ion transition state for TvPNP to give a dissociation constant of 30 pM, an inhibitor release half-time of 64 min, and a K{sub m}/K{sub d} ratio of 203,300. The tight binding of DADMe-ImmA supports a late S{sub N}1 transition state. Despite their tight binding to TvPNP, ImmA and DADMe-ImmA are weak inhibitors of human and P. falciparum PNPs. The crystal structures of the TvPNP-ImmA{center_dot}PO{sub 4} and TvPNP{center_dot}DADMe-ImmA{center_dot}PO{sub 4} ternary complexes differ from previous structures with substrate anologues. The tight binding with DADMe-ImmA is in part due to a 2.7 {angstrom} ionic interaction between a PO{sub 4} oxygen and the N1 cation of the hydroxypyrrolidine and is weaker in the TvPNP{center_dot}ImmA{center_dot}PO{sub 4} structure at 3.5 {angstrom}. However, the TvPNP{center_dot}ImmA{center_dot}PO{sub 4} structure includes hydrogen bonds between the 2'-hydroxyl and the protein that are not present in TvPNP{center_dot}DADMe-ImmA{center_dot}PO{sub 4}. These structures explain why DADMe-ImmA binds tighter than ImmA. Immucillin-H is a 12 nM inhibitor of TvPNP but a 56 pM inhibitor of human PNP. And this difference is explained by isotope-edited difference infrared spectroscopy with [6-{sup 18}O]ImmH to establish that O6 is the keto tautomer in TvPNP{center_dot}ImmH{center_dot}PO{sub 4}, causing an unfavorable leaving-group interaction.

  9. 3-D models and structural analysis of analogue rock avalanche deposits: a kinematic analysis of the propagation mechanism

    NASA Astrophysics Data System (ADS)

    Longchamp, C.; Abellan, A.; Jaboyedoff, M.; Manzella, I.

    2015-11-01

    Rock avalanches are extremely destructive and uncontrollable events that involve a great volume of material (> 106 m3), several complex processes and they are difficult to witness. For this reason the study of these phenomena using analogue modelling and the accurate analysis of deposit structures and features of laboratory data and historic events become of great importance in the understanding of their behavior. The main objective of this research is to analyze rock avalanche dynamics by means of a detailed structural analysis of the deposits coming from data of 3-D measurements of mass movements of different magnitudes, from decimeter level scale laboratory experiments to well-studied rock avalanches of several square kilometers magnitude. Laboratory experiments were performed on a tilting plane on which a certain amount of a well-defined granular material is released, propagates and finally stops on a horizontal surface. The 3-D geometrical model of the deposit is then obtained using either a scan made with a 3-D digitizer (Konica Minolta vivid 9i) either using a photogrammetric method called Structure-from-Motion (SfM) which requires taking several pictures from different point of view of the object to be modeled. In order to emphasize and better detect the fault structures present in the deposits, we applied a median filter with different moving windows sizes (from 3 × 3 to 9 × 9 nearest neighbors) to the 3-D datasets and a gradient operator along the direction of propagation. The application of these filters on the datasets results in: (1) a precise mapping of the longitudinal and transversal displacement features observed at the surface of the deposits; and (2) a more accurate interpretation of the relative movements along the deposit (i.e. normal, strike-slip, inverse faults) by using cross-sections. Results shows how the use of filtering techniques reveal disguised features in the original point cloud and that similar displacement patterns are observable both in the laboratory simulation and in the real scale avalanche, regardless the size of the avalanche. Furthermore, we observed how different structural features including transversal fractures and folding patterns tend to show a constant wavelength proportional to the size of the avalanche event.

  10. NSTX Upgrade Project STRUCTURAL CALCULATION OF THE TF FLAG KEY

    E-print Network

    Princeton Plasma Physics Laboratory

    take the out of plane torque load and safely deliver it to the center stack lid. References (List any source of design information including computer program titles and revision levels.) 1] NSTX-CALC-13] NSTX Structural Design Criteria Document, I. Zatz [3] NSTX Design Point June 2010 http://www.pppl.gov/~neumeyer/NSTX_CSU/Design

  11. Direct Measurement of Time-Frequency Analogues of Sub-Planck Structures

    E-print Network

    Praxmeyer, Ludmila; Yang, Popo; Yang, Shang-Da; Lee, Ray-Kuang

    2015-01-01

    Exploiting the correspondence between Wigner distribution function and a frequency-resolved optical gating (FROG) measurement, we experimentally demonstrate existence of the chessboard-like interference patterns with a time-bandwidth product smaller than that of a transform-limited pulse in the phase space representation of compass states. Using superpositions of four electric pulses as realization of compass states, we have shown via direct measurements that displacements leading to orthogonal states can be smaller than limits set by uncertainty relations. In the experiment we observe an exactly chronocyclic correspondence to the sub-Planck structure in the interference pattern appearing for superposition of two Sch\\"{o}dinger-cat-like states in a position-momentum phase space.

  12. Crystal Structures of HIV-1 gp120 Envelope Glycoprotein in Complex with NBD Analogues That Target the CD4-Binding Site

    PubMed Central

    Kwon, Young Do; LaLonde, Judith M.; Yang, Yongping; Elban, Mark A.; Sugawara, Akihiro; Courter, Joel R.; Jones, David M.; Smith, Amos B.; Debnath, Asim K.; Kwong, Peter D.

    2014-01-01

    Efforts to develop therapeutic agents that inhibit HIV-1 entry have led to the identification of several small molecule leads. One of the most promising is the NBD series, which binds within a conserved gp120 cavity and possesses para-halogen substituted aromatic rings, a central oxalamide linker, and a tetramethylpiperidine moiety. In this study, we characterized structurally the interactions of four NBD analogues containing meta-fluoro substitution on the aromatic ring and various heterocyclic ring replacements of the tetramethylpiperidine group. The addition of a meta-fluorine to the aromatic ring improved surface complementarity and did not alter the position of the analogue relative to gp120. By contrast, heterocyclic ring replacements of the tetramethylpiperidine moiety exhibited diverse positioning and interactions with the vestibule of the gp120 cavity. Overall, the biological profile of NBD-congeners was modulated by ligand interactions with the gp120-cavity vestibule. Herein, six co-crystal structures of NBD-analogues with gp120 provide a structural framework for continued small molecule-entry inhibitor optimization. PMID:24489681

  13. Structure Determination of Cisplatin-Amino Acid Analogues by Infrared Multiple Photon Dissociation Action Spectroscopy

    NASA Astrophysics Data System (ADS)

    He, Chenchen; Bao, Xun; Zhu, Yanlong; Strobehn, Stephen; Kimutai, Bett; Nei, Y.-W.; Chow, C. S.; Rodgers, M. T.; Gao, Juehan; Oomens, J.

    2015-06-01

    To gain a better understanding of the binding mechanism and assist in the optimization of relevant drug and chemical probe design, both experimental and theoretical studies were performed on a series of amino acid-linked cisplatin derivatives, including glycine-, lysine-, and ornithine-linked cisplatin, Gplatin, Kplatin, and Oplatin, respectively. Cisplatin, the first FDA-approved platinum-based anticancer drug, has been widely used in cancer chemotherapy. Its pharmacological mechanism has been identified as its ability to coordinate to genomic DNA, and guanine is its major target. In previous reports, cisplatin was successfully utilized as a chemical probe to detect solvent accessible sites in ribosomal RNA (rRNA). Among the amino-acid-linked cisplatin derivatives, Oplatin exhibits preference for adenine over guanine. The mechanism behind its different selectivity compared to cisplatin may relate to its potential of forming a hydrogen bond between the carboxylate group in Pt (II) complex and the 6-amino moiety of adenosine stabilizes A-Oplatin products. Tandem mass spectrometry analysis also indicates that different coordination sites of Oplatin on adenosine affect glycosidic bond stability. Infrared multiple photon dissociation (IRMPD) action spectroscopy experiments were performed on all three amino acid-linked cisplatin to characterize their structures. An extensive theoretical study has been performed on Gplatin to guide the selection of the most effective theory and basis set based on its geometric information. The results for Gplatin provide the foundation for characterization of the more complex amino acid-linked cisplatin derivatives, Oplatin and Kplatin. Structural and energetic information elucidated for these compounds, particularly Oplatin reveal the reason for its alternative selectivity compared to cisplatin.

  14. Analysis of structure-activity relationships in renin substrate analogue inhibitory peptides.

    PubMed

    Hui, K Y; Carlson, W D; Bernatowicz, M S; Haber, E

    1987-08-01

    On the basis of the minimal octapeptide sequence of the renin substrate, a series of peptides was synthesized containing (3S,4S)-4-amino-3-hydroxy-6-methylheptanoic acid (statine) or (3S,4S)-4-amino-3-hydroxy-5-phenylpentanoic acid (AHPPA) at the P1P1' position. Some of these peptides also contained Nin-formyltryptophan at the P5, P3, or P3' position. Renin-inhibitory potency varied over a wide range (from inactive to IC50 = 3 nM). Potency was reduced by at least 10-fold when the peptide was shortened by two residues at either the amino or carboxy terminus. The AHPPA-containing inhibitors were several-fold less potent than the statine-containing inhibitors. Analysis of models for the three-dimensional structure of inhibitors at the active site of human renin suggests that the diminished potency of the AHPPA peptides in comparison with the statine-containing peptides was caused by a shift in the peptide backbone due to a steric conflict between the phenyl ring of the AHPPA residue and the S1 subsite. The importance of the side chain and the 3(S)-hydroxyl group of the statine residue was demonstrated by substituting 5-aminovaleric acid for a dipeptide unit at the P1P1' position, which resulted in a peptide devoid of renin-inhibitory activity. Substitutions of other basic amino acids for histidine at the P2 position caused a great loss in potency, possibly due to disruption of a hydrogen bond as suggested by molecular modeling. Studies on the plasma renins of four nonhuman species suggest that the isoleucine-histidine segment at the P2'P3' position is important to defining the human specificity of the substrate. This work suggests a number of properties important to the design of potent renin inhibitors, and demonstrates the usefulness of three-dimensional models in the interpretation of structure-activity data. PMID:3302256

  15. Synthesis and molecular structure of a zinc complex of the vitamin K3 analogue phthiocol

    NASA Astrophysics Data System (ADS)

    Kathawate, Laxmi; Sproules, Stephen; Pawar, Omkar; Markad, Ganesh; Haram, Santosh; Puranik, Vedavati; Salunke-Gawali, Sunita

    2013-09-01

    The complex [Zn(phthiocol)2(H2O)2]; 1, where phthiocol is 2-hydroxy-3-methyl-1,4-naphthoquinone, has been synthesized and characterized by elemental analysis, FT-IR, 1H NMR, UV-vis spectroscopy, thermogravimetric (TG) analysis, electrochemical and single crystal X-ray diffraction studies. The ?CO stretch shifts to lower frequencies upon complexation of phthiocol to Zn2+. 1H NMR spectra show an upfield shift of the benzenoid ring protons in 1. There is a bathochromic shift of the LMCT band in the UV-vis spectra of 1. Single crystal X-ray structure of 1 show distorted octahedral geometry around Zn2+. Two phthiocol ligands are in plane with the metal, while water molecules are trans to this plane. Coordination of deprotonated phthiocol ligands is 'trans, trans' to Zn2+. Intra as well as intermolecular interactions are observed in 1. Molecules of 1 show three dimensional network through CH⋯O and OH⋯O interactions. Additional anodic peaks are observed in cyclic voltammogram of phthiocol ligand due to oxidation of reduced species formed during reduction. One-electron reduction of 1 is shown to be reversible and DFT studies define this redox event as ligand-centered.

  16. Structure-activity relationships in the oxidation of benzylamine analogues by bovine liver mitochondrial monoamine oxidase B.

    PubMed

    Walker, M C; Edmondson, D E

    1994-06-14

    The influence of para and meta substitution of benzylamine on its interaction with bovine liver mitochondrial monoamine oxidase B (MAO B) has been investigated by steady-state and reductive half-reaction anaerobic stopped-flow kinetic approaches. Steady-state kinetic properties of each benzylamine analogue suggest that para or meta substitution does not alter the mechanistic pathway of catalysis [Husain, M., et al. (1982) Biochemistry 21, 595-600]. All analogues tested exhibited Dkcat values ranging from 5.5 to 8.9 and D[kcat/Km(amine)] values ranging from 3.3 to 8.1 D[kcat/Km(O2)] values of approximately 1 are observed for all substrate analogues. Values for Kd were calculated from steady-state isotope effect data [Klinman, J.P., & Matthews, R.G. (1985) J. Am. Chem. Soc. 107, 1058-1060] and are in good agreement with Ks values determined from analysis of the rate of MAO B reduction as a function of benzylamine analogue concentration in reductive half-reaction experiments. A linear correlation of benzylamine analogue Kd values with the hydrophobicity parameter (phi) is observed for the para-substituted analogues where the binding affinity increases with increasing hydrophobicity of the substituent. Statistical treatment of the correlation shows a small negative contribution to binding by the van der Waals volume (VW) of the para substituent. meta-Substituted benzylamine analogues show a decreased binding affinity with the VW of the substituent and no correlation with the hydrophobicity value of the substituents tested. No spectral evidence was found for any flavin radical intermediates during the time course of MAO B flavin reduction in anaerobic reductive half-reduction stopped-flow experiments with any of the alpha,alpha-diprotio- or alpha,alpha-dideuteriobenzylamine analogues tested. The limiting rates of enzyme reduction exhibit large Dk values (6.5-14.1) for all of the analogues tested. para-Substituted benzylamine analogues reduce MAO B with limiting rates that correlate with the steric influence (Es value) of the substituent. Statistical analysis shows the rate of MAO B reduction by para-substituted analogues to be retarded by increased values of Es and, with a smaller contribution, by the hydrophobicity value of the substituent. The rate of MAO B reduction by meta-substituted benzylamine analogues is essentially independent of the nature of the substituent. No evidence was found for any electronic contribution to the rate of MAO B flavin reduction by any of the analogues tested. These data demonstrate the steric orientation of the substrate to be important in the rate of amine oxidation by MAO B and that ring meta substituents favor this orientation.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:8003474

  17. The role of pre-existing tectonic structures and magma chamber shape on the geometry of resurgent blocks: Analogue models

    NASA Astrophysics Data System (ADS)

    Marotta, Enrica; de Vita, Sandro

    2014-02-01

    A set of analogue models has been carried out to understand the role of an asymmetric magma chamber on the resurgence-related deformation of a previously deformed crustal sector. The results are then compared with those of similar experiments, previously performed using a symmetric magma chamber. Two lines of experiments were performed to simulate resurgence in an area with a simple graben-like structure and resurgence in a caldera that collapsed within the previously generated graben-like structure. On the basis of commonly accepted scaling laws, we used dry-quartz sand to simulate the brittle behaviour of the crust and Newtonian silicone to simulate the ductile behaviour of the intruding magma. An asymmetric shape of the magma chamber was simulated by moulding the upper surface of the silicone. The resulting empty space was then filled with sand. The results of the asymmetric-resurgence experiments are similar to those obtained with symmetrically shaped silicone. In the sample with a simple graben-like structure, resurgence occurs through the formation of a discrete number of differentially displaced blocks. The most uplifted portion of the deformed depression floor is affected by newly formed, high-angle, inward-dipping reverse ring-faults. The least uplifted portion of the caldera is affected by normal faults with similar orientation, either newly formed or resulting from reactivation of the pre-existing graben faults. This asymmetric block resurgence is also observed in experiments performed with a previous caldera collapse. In this case, the caldera-collapse-related reverse ring-fault is completely erased along the shortened side, and enhances the effect of the extensional faults on the opposite side, so facilitating the intrusion of the silicone. The most uplifted sector, due to an asymmetrically shaped intrusion, is always in correspondence of the thickest overburden. These results suggest that the stress field induced by resurgence is likely dictated by the geometry of the intruding magma body, and the related deformation is partially controlled by pre-existing tectonic and/or volcano-tectonic structures.

  18. Titan's Organic Aerosols : Molecular Composition And Structure Inferred From Systematic Pyrolysis Gas Chromatography Mass Spectrometry Analysis of Analogues

    NASA Astrophysics Data System (ADS)

    Morisson, Marietta; Szopa, Cyril; Buch, Arnaud; Carrasco, Nathalie; Gautier, Thomas

    2015-04-01

    In spite of numerous studies carried out to characterize the chemical composition of laboratory analogues of Titan aerosols (tholins), their molecular composition as well as their structuration are still little known. If Pyrolysis gas chromatography mass spectrometry (Pyr-GCMS) has been used for years to give clues about this composition, the highly disparate results obtained show that they can be attributed to the analytical conditions used, to differences in the nature of the analogues studied, or both. In order to have a better description of Titan's tholins molecular composition, we led a systematic analysis of these materials by pyr-GCMS, exploring the analytical parameters to estimate the biases this technique can induce. With this aim, we used the PAMPRE experiment, a capacitively coupled RF cold plasma reactor (Szopa et al. 2006), to synthetize tholins with 2%, 5% and 10% of CH4 in N2. The three samples were systematically pyrolyzed in the temperature range 200-600°C with a 100°C step. The evolved gases were then injected into a GC-MS device for molecular identification. This systematic pyr-GC-MS analysis had two major objectives: (i) optimizing all the analytical parameters for the detection of a wide range of compounds and thus a characterization of the tholins composition as comprehensive as possible, and (ii) highlighting the role of the CH4 ratio on the tholins molecular structure. About a hundred of molecules have been identified in the pyrolysis products. Although an identical major pattern of nitriles and ethylene appears clearly for the three samples, some discriminant signatures were highlighted. The samples mainly differ by the number of released compounds. The results show especially an increase in the hydrocarbonaceous chains when the CH4 ratio increases. At the opposite, the formation of poly-nitrogenous compounds seems to be easier for lower CH4 ratios. We also performed a semi-quantitative study on the best represented chemical family in our chromatograms - namely nitriles: the existence of a relation between the quantity of a released compound and its molecular mass is consistent with the quantification of nitriles in the PAMPRE gas phase done by Gautier et al., 2011. Moreover, numerous species are present both in tholins and in the gas phase. That allowed us to make out potential precursors of the solid organic particles. From all these results, we conclude that the optimal pyrolysis temperature for a GC-MS analysis of our tholins is 600°C. This temperature choice results from the best compromise between the number of released compounds, the quality of the signal and the appearance of pyrolysis artefacts. Lastly, thanks to a review of pyr-GCMS studies carried out on Titan tholins since the first work of Khare et al. (1981), we compared all the previous analyses between them and with our own results in order to better understand the differences. References B. N. Khare et al., Icarus, vol. 48, no. 2, pp. 290-297, Nov. 1981. C. Szopa et al., Planet. Space Sci., vol. 54, no. 4, pp. 394-404, Apr. 2006. T. Gautier et al., Icarus, vol. 213, no. 2, pp. 625-635, Jun. 2011.

  19. Purine Analogues as Kinase Inhibitors: A Review.

    PubMed

    Sharma, Sahil; Mehndiratta, Samir; Kumar, Sunil; Singh, Jagjeet; Bedi, Preet M S; Nepali, Kunal

    2015-01-01

    Protein kinases constitute one of the largest and most functionally diverse gene families that regulate key cell functions. In past several years, kinase inhibition has emerged as potential anti-cancer drug target. Purine is a priveleged heterocyclic nucleus which exists in the chemical architecture of various bioactive compounds. Numerous reports on the use of purine analogues in the treatment of acute leukemias (thiopurines, pentostatin), as antiviral (acyclovir, penciclovir, ganciclovir), as immunosuppressive (azathioprine), as antitumor (vidarabine), as bronchodilator (theophylline) have been revealed. In the past decade, purine analogues have emerged as significantly potent kinase inhibitors. A fair amount of research has been done and several patents have also been published highlighting the kinase inhibitory action of purines. Caffeine, 2-aminopurine, purvalanol-A, seleciclib, FSBA, adenosine thiol analogue possessing purine as the basic moiety fall under this category. In view of the use of purines for the inhibition of kinases, there is need for compilation of data specifying the prominence of purines in the treatment of cancer through this mechanism. The structure of the potent compounds, their IC50 values, models used and the enzymes/ receptors/ targets involved have been presented in this review. The present compilation covers the patents published entailing the purines as kinase inhibitors and the purine drugs employed in chemotherapy. PMID:26081925

  20. Combined Quantum Chemistry and Photoelectron Spectroscopy Study of the Electronic Structure and Reduction Potentials of Rubredoxin Redox Site Analogues

    SciTech Connect

    Niu, Shuqiang; Wang, Xue B.; Nichols, J. A.; Wang, Lai S.; Ichiye, Toshiko

    2003-04-24

    Iron-sulfur proteins are an important class of electron carriers in a wide variety of biological reactions. Determining the intrinsic contribution of the metal site to the redox potential is crucial in understanding how the protein environment influences the overall redox properties of the Fe-S proteins. Here we combine density functional theory and coupled cluster methods with photodetachment spectroscopy to study the electronic structures and gas-phase redox potentials of the [Fe(SCH3)(4)](2-/-/0) and [Fe(SCH3)(3)](-/0) analogues of the rubredoxin redox site. The calculations show that oxidations of [Fe(SCH3)(4)](2-) and [Fe(SCH3)(4)](-) involve mainly the Fe 3d and S 3p orbitals, respectively. The calculated adiabatic and vertical detachment energies are in good agreement with the experiment for [Fe(SCH3)(3)](-) and [Fe(SCH3)(4)](-). The current results further confirm the "inverted level scheme" for the high-spin [1Fe] systems. The redox couple, [Fe(SCH3)(4)](- /2), which is the one found in rubredoxin, but cannot be accessed experimentally in the gas phase, was investigated using a thermodynamic cycle that relates it to the [Fe(SCH3)(3)](-/0) couple and the ligand association reaction, [Fe(SCH3)(3)](0/-) + SCH3- --> [Fe(SCH3)(4)](-/2-). The calculated reduction energy of [Fe(SCH3)(4)](-) (1.7 eV) compares well with the value (1.6 eV) estimated from the calculated bond energies and the experimental detachment energy of [Fe(SCH3)(3)](-). Thus, this thermodynamic cycle method can be used to estimate metal-ligand bonding energies and determine intrinsic reduction potentials from photodetachment experiments when the reduced forms are not stable in the gas phase.

  1. DATA NORMALIZATION : A KEY FOR STRUCTURAL HEALTH MONITORING

    SciTech Connect

    Farrar, C. R.; Sohn, H.; Worden, K.

    2001-01-01

    Structural health monitoring (SHM) is the implementation of a damage detection strategy for aerospace, civil and mechanical engineering infrastructure. Typical damage experienced by this infrastructure might be the development of fatigue cracks, degradation of structural connections, or bearing wear in rotating machinery. For SHM strategies that rely on vibration response measurements, the ability to normalize the measured data with respect to varying operational and environmental conditions is essential if one is to avoid false-positive indications of damage. Examples of common normalization procedure include normalizing the response measurements by the measured inputs as is commonly done when extracting modal parameters. When environmental cycles influence the measured data, a temporal normalization scheme may be employed. This paper will summarize various strategies for performing this data normalization task. These strategies fall into two general classes: (1) Those employed when measures of the varying environmental and operational parameters are available; (2) Those employed when such measures are not available. Whenever data normalization is performed, one runs the risk that the damage sensitive features to be extracted from the data will be obscured by the data normalization procedure. This paper will summarize several normalization procedures that have been employed by the authors and issues that have arose when trying to implement them on experimental and numerical data.

  2. Structural influence on radical formation and sensitizing capacity of alkylic limonene hydroperoxide analogues in allergic contact dermatitis.

    PubMed

    Johansson, Staffan G H; Emilsson, Katarina; Grøtli, Morten; Börje, Anna

    2010-03-15

    Hydroperoxides are known to be strong contact allergens and a common cause of contact allergy. They are easily formed by the autoxidation of, for example, fragrance terpenes, compounds that are common in perfumes, cosmetics, and household products. A requirement of the immunological mechanisms of contact allergy is the formation of an immunogenic hapten-protein complex. For hydroperoxides, a radical mechanism is postulated for this formation. In our previous investigations of allylic limonene hydroperoxides, we found that the formation of carbon- and oxygen-centered radicals, as well as the sensitizing capacity, is influenced by the structure of the hydroperoxides. The aim of the present work was to further investigate the connection between structure, radical formation, and sensitizing capacity by studying alkylic analogues of the previously investigated allylic limonene hydroperoxides. The radical formation was studied in radical-trapping experiments employing 5,10,15,20-tetraphenyl-21H,23H-porphine iron(III) chloride as an initiator and 1,1,3,3-tetramethylisoindolin-2-yloxyl as a radical trapper. We found that the investigated hydroperoxides initially form carbon- and oxygen-centered radicals that subsequently form alcohols and ketones. Trapped carbon-centered radicals and nonradical products were isolated and identified. Small changes in structure, like the omission of the endocyclic double bond or the addition of a methyl group, resulted in large differences in radical formation. The results indicate that alkoxyl radicals seem to be more important than carbon-centered radicals in the immunogenic complex formation. The sensitizing capacities were studied in the murine local lymph node assay (LLNA), and all hydroperoxides tested were found to be potent sensitizers. For two of the hydroperoxides investigated, the recently suggested thiol-ene reaction is a possible mechanism for the formation of immunogenic complexes. For the third investigated, fully saturated, hydroperoxide, the thiol-ene mechanism is not possible for immunogenic complex formation. This strongly indicates that several radical reaction pathways for immunogenic complex formation of limonene hydroperoxides are active in parallel. PMID:20163165

  3. Structure-Activity Relationships at the Monoamine Transporters for a Novel Series of Modafinil (2-[(diphenylmethyl)sulfinyl]acetamide) Analogues.

    PubMed

    Cao, Jianjing; Prisinzano, Thomas E; Okunola, Oluyomi M; Kopajtic, Theresa; Shook, Matthew; Katz, Jonathan L; Newman, Amy Hauck

    2010-10-10

    A series of modafinil (1) analogues was synthesized wherein 1) para-halo-substitutents were added to the aryl rings, 2) the sulfoxide function was removed, and 3) the primary amide group was replaced with secondary and tertiary amides and amines to investigate the effects of these chemical modifications on DAT, SERT and NET binding. In addition, the locomotor-stimulant effects in mice of (±)-modafinil (1), its R- and S-enantiomers and its para-chloro sulfinylacetamide analogue (5c) were compared to those of cocaine. PMID:21344069

  4. Structures of ceftazidime and its transition-state analogue in complex with AmpC beta-lactamase: Implications for resistance mutations and inhibitor design

    SciTech Connect

    Powers, R.A.; Caselli, E.; Focia, P.J.; Prati, F.; Shoichet, B.K.

    2010-03-08

    Third-generation cephalosporins are widely used {beta}-lactam antibiotics that resist hydrolysis by {beta}-lactamases. Recently, mutant {beta}-lactamases that rapidly inactivate these drugs have emerged. To investigate why third-generation cephalosporins are relatively stable to wild-type class C {beta}-lactamases and how mutant enzymes might overcome this, the structures of the class C {beta}-lactamase AmpC in complex with the third-generation cephalosporin ceftazidime and with a transition-state analogue of ceftazidime were determined by X-ray crystallography to 2.0 and 2.3 {angstrom} resolution, respectively. Comparison of the acyl-enzyme structures of ceftazidime and loracarbef, a {beta}-lactam substrate, reveals that the conformation of ceftazidime in the active site differs from that of substrates. Comparison of the structures of the acyl-enzyme intermediate and the transition-state analogue suggests that ceftazidime blocks formation of the tetrahedral transition state, explaining why it is an inhibitor of AmpC. Ceftazidime cannot adopt a conformation competent for catalysis due to steric clashes that would occur with conserved residues Val211 and Tyr221. The X-ray crystal structure of the mutant {beta}-lactamase GC1, which has improved activity against third-generation cephalosporins, suggests that a tandem tripeptide insertion in the {Omega} loop, which contains Val211, has caused a shift of this residue and also of Tyr221 that would allow ceftazidime and other third-generation cephalosporins to adopt a more catalytically competent conformation. These structural differences may explain the extended spectrum activity of GC1 against this class of cephalosporins. In addition, the complexed structure of the transition-state analogue inhibitor (K{sub i} 20 nM) with AmpC reveals potential opportunities for further inhibitor design.

  5. Effects of Vegetation Structure and Elevation on Lower Keys Marsh Rabbit Density 

    E-print Network

    Dedrickson, Angela

    2012-02-14

    LKMR density on lands managed by the United States Navy, Naval Air Station Key West and evaluate how vegetation structure and patch elevation effect LKMR population density. I conducted fecal pellet counts to determine LKMR density, collected...

  6. Modeling of the binding mode of a non-covalent inhibitor of the 20S proteasome. Application to structure-based analogue design.

    PubMed

    Furet, P; Imbach, P; Fürst, P; Lang, M; Noorani, M; Zimmermann, J; García-Echeverria, C

    2001-05-21

    The 2-aminobenzvlstatine derivative I is a 20S proteasome inhibitor of a novel chemical type identified by high throughput screening. The compound specifically inhibits the chymotrypsin-like catalytic activity of the human proteasome with an IC50 value in the micromolar range. Using the crystal structure of the yeast proteasome, we modeled the structure of the human proteasome in complex with 1. As one of the first applications of the model in our oncology programme targeting the proteasome, we designed an analogue of the inhibitor having enhanced stacking/hydrophobic interactions with the enzyme. One order of magnitude in inhibitory potency was gained. PMID:11392546

  7. Pyrazolate-Bridging Dinucleating Ligands Containing Hydrogen-Bond Donors: Synthesis and Structure of Their Cobalt Analogues

    E-print Network

    Hendrich, Mike

    of Their Cobalt Analogues Paul J. Zinn, Douglas R. Powell, Victor W. Day, Michael P. Hendrich, Thomas N. Sorrell correspondence should be addressed. E-mail: sorrell@unc.edu (T.N.S.), aborovik@ku.edu (A.S.B.). University

  8. Antimicrobial activities of active component isolated from Lawsonia inermis leaves and structure-activity relationships of its analogues against food-borne bacteria.

    PubMed

    Yang, Ji-Yeon; Lee, Hoi-Seon

    2015-04-01

    The antimicrobial activities of Lawsonia inermis leaf extract and 2-hydroxy-1,4-naphthoquinone analogues against food-borne bacteria. The antimicrobial activities of five fractions derived from the methanol extract of Lawsonia inermis leaves were evaluated against 7 food-borne bacteria. 2-Hydroxy-1,4-naphthoquinone was isolated by chromatographic analyses. 2-Hydroxy-1,4-naphthoquinone showed the strong activities against Bacillus cereus, Listeria monocytogenes, Salmonella enterica, Shigella sonnei, Staphylococcus epidermidis, and S. intermedius, but exerted no growth-inhibitory activities against S. typhimurium. The antimicrobial activities of the 2-hydroxy-1,4-naphthoquinone analogues were tested against 7 food-borne bacteria to establish structure-activity relationships. Hydroxyl (2-hydroxy-1,4-naphthoquinone and 5-hydroxy-1,4-naphthoquinone), methoxy (2-methoxy-1,4-naphthoquinone), and methyl (2-methyl-1,4-naphthoquinone, and 5-hydroxy-2-methyl-1,4-naphthoquinone) functional groups on the 1,4-naphthoquinone skeleton possessed potent activities, whereas bromo (2-bromo-1,4-naphthoquinone and 2,3-dibromo-1,4-naphthoquione) and chloro (2,3-dichloro-1,4-naphthoquinone) exhibited no activity against 7 food-borne bacteria. The L. inermis leaf extract and 2-hydroxy-1,4-naphthoquinone analogues should be useful as natural antimicrobial agents against food-borne bacteria. PMID:25829631

  9. Structure-Based Design, Synthesis, Evaluation And Crystal Structures of Transition State Analogue Inhibitors of Inosine Monophosphate Cyclohydrolase

    SciTech Connect

    Xu, L.; Chong, Y.; Hwang, I.; D'Onofrio, A.; Amore, K.; Beardsley, G.P.; Li, C.; Olson, A.J.; Boger, D.L.; Wilson, I.A.; /Skaggs Inst. Chem. Biol. /Scripps Res. Inst. /Yale U.

    2007-07-13

    The inosine monophosphate cyclohydrolase (IMPCH) component (residues 1-199) of the bifunctional enzyme aminoimidazole-4-carboxamide ribonucleotide transformylase (AICAR Tfase, residues 200-593)/IMPCH (ATIC) catalyzes the final step in the de novo purine biosynthesis pathway that produces IMP. As a potential target for antineoplastic intervention, we designed IMPCH inhibitors, 1,5-dihydroimidazo[4,5-c][1,2,6]thiadiazin-4(3H)-one 2,2-dioxide (heterocycle, 1), the corresponding nucleoside (2), and the nucleoside monophosphate (nucleotide) (3), as mimics of the tetrahedral intermediate in the cyclization reaction. All compounds are competitive inhibitors against IMPCH (K(i) values = 0.13-0.23 microm) with the simple heterocycle 1 exhibiting the most potent inhibition (K(i) = 0.13 microm). Crystal structures of bifunctional ATIC in complex with nucleoside 2 and nucleotide 3 revealed IMPCH binding modes similar to that of the IMPCH feedback inhibitor, xanthosine 5'-monophosphate. Surprisingly, the simpler heterocycle 1 had a completely different IMPCH binding mode and was relocated to the phosphate binding pocket that was identified from previous xanthosine 5'-monophosphate structures. The aromatic imidazole ring interacts with a helix dipole, similar to the interaction with the phosphate moiety of 3. The crystal structures not only revealed the mechanism of inhibition of these compounds, but they now serve as a platform for future inhibitor improvements. Importantly, the nucleoside-complexed structure supports the notion that inhibitors lacking a negatively charged phosphate can still inhibit IMPCH activity with comparable potency to phosphate-containing inhibitors. Provocatively, the nucleotide inhibitor 3 also binds to the AICAR Tfase domain of ATIC, which now provides a lead compound for the design of inhibitors that simultaneously target both active sites of this bifunctional enzyme.

  10. Fluorescent nucleic acid base analogues.

    PubMed

    Wilhelmsson, L Marcus

    2010-05-01

    The use of fluorescent nucleic acid base analogues is becoming increasingly important in the fields of biology, biochemistry and biophysical chemistry as well as in the field of DNA nanotechnology. The advantage of being able to incorporate a fluorescent probe molecule close to the site of examination in the nucleic acid-containing system of interest with merely a minimal perturbation to the natural structure makes fluorescent base analogues highly attractive. In recent years, there has been a growing interest in developing novel candidates in this group of fluorophores for utilization in various investigations. This review describes the different classes of fluorophores that can be used for studying nucleic acid-containing systems, with an emphasis on choosing the right kind of probe for the system under investigation. It describes the characteristics of the large group of base analogues that has an emission that is sensitive to the surrounding microenvironment and gives examples of investigations in which this group of molecules has been used so far. Furthermore, the characterization and use of fluorescent base analogues that are virtually insensitive to changes in their microenvironment are described in detail. This group of base analogues can be used in several fluorescence investigations of nucleic acids, especially in fluorescence anisotropy and fluorescence resonance energy transfer (FRET) measurements. Finally, the development and characterization of the first nucleic base analogue FRET pair, tC(O)-tC(nitro), and its possible future uses are discussed. PMID:20478079

  11. OptZyme: Computational Enzyme Redesign Using Transition State Analogues

    PubMed Central

    Grisewood, Matthew J.; Gifford, Nathanael P.; Pantazes, Robert J.; Li, Ye; Cirino, Patrick C.; Janik, Michael J.; Maranas, Costas D.

    2013-01-01

    OptZyme is a new computational procedure for designing improved enzymatic activity (i.e., kcat or kcat/KM) with a novel substrate. The key concept is to use transition state analogue compounds, which are known for many reactions, as proxies for the typically unknown transition state structures. Mutations that minimize the interaction energy of the enzyme with its transition state analogue, rather than with its substrate, are identified that lower the transition state formation energy barrier. Using Escherichia coli ?-glucuronidase as a benchmark system, we confirm that KM correlates (R2?=?0.960) with the computed interaction energy between the enzyme and the para-nitrophenyl- ?, D-glucuronide substrate, kcat/KM correlates (R2?=?0.864) with the interaction energy of the transition state analogue, 1,5-glucarolactone, and kcat correlates (R2?=?0.854) with a weighted combination of interaction energies with the substrate and transition state analogue. OptZyme is subsequently used to identify mutants with improved KM, kcat, and kcat/KM for a new substrate, para-nitrophenyl- ?, D-galactoside. Differences between the three libraries reveal structural differences that underpin improving KM, kcat, or kcat/KM. Mutants predicted to enhance the activity for para-nitrophenyl- ?, D-galactoside directly or indirectly create hydrogen bonds with the altered sugar ring conformation or its substituents, namely H162S, L361G, W549R, and N550S. PMID:24116038

  12. Lactam-stabilized helical analogues of the analgesic ?-conotoxin KIIIA

    PubMed Central

    Khoo, Keith K.; Wilson, Michael J.; Smith, Brian J.; Zhang, Min-Min; Gulyas, Joszef; Yoshikami, Doju; Rivier, Jean E.; Bulaj, Grzegorz; Norton, Raymond S.

    2011-01-01

    ?-Conotoxin KIIIA (?-KIIIA) blocks mammalian voltage-gated sodium channels (VGSCs) and is a potent analgesic following systemic administration in mice. Previous structure-activity studies of ?-KIIIA identified a helical pharmacophore for VGSC blockade. This suggested a route for designing truncated analogues of ?-KIIIA by incorporating the key residues into an ?-helical scaffold. As (i, i+4) lactam bridges constitute a proven approach for stabilizing ?-helices, we designed and synthesized six truncated analogues of ?-KIIIA containing single lactam bridges at various locations. The helicity of these lactam analogues was analysed by NMR spectroscopy, and their activities were tested against mammalian VGSC subtypes NaV1.1 through 1.7. Two of the analogues, Ac-cyclo9/13[Asp9,Lys13]KIIIA7–14 and Ac-cyclo9/13[Lys9,Asp13]KIIIA7–14, displayed µM activity against VGSC subtypes NaV1.2 and NaV1.6; importantly, the subtype selectivity profile for these peptides matched that of ?-KIIIA. Our study highlights structure-activity relationships within these helical mimetics and provides a basis for the design of additional truncated peptides as potential analgesics. PMID:21962108

  13. A lock-and-key mechanism for the controllable fabrication of DNA origami structures.

    PubMed

    Rajendran, Arivazhagan; Endo, Masayuki; Hidaka, Kumi; Shimada, Naohiko; Maruyama, Atsushi; Sugiyama, Hiroshi

    2014-08-14

    Controllable fabrication of DNA origami structures was achieved using cationic comb-type copolymers (CCCs) as locks and polyvinyl sulphonic acid (PVS) as a key. A CCC binds to the phosphate backbone of either M13mp18/staples alone or both together and restricts origami folding, while PVS unlocks the CCC, restoring the formation of origami structures. PMID:24965040

  14. EspR, a key regulator of Mycobacterium tuberculosis virulence, adopts a unique dimeric structure

    E-print Network

    Stroud, Robert

    EspR, a key regulator of Mycobacterium tuberculosis virulence, adopts a unique dimeric structureR is a transcriptional regulator that activates the ESX-1 secretion system during Mycobacterium tuberculosis infection Mycobacterium tuberculosis, an intracellular pathogen that ex- erts an enormous toll on global human health, has

  15. One-step separation of nine structural analogues from Poria cocos (Schw.) Wolf. via tandem high-speed counter-current chromatography.

    PubMed

    Zeng, Hualiang; Liu, Qi; Yu, Jingang; Jiang, Xinyu; Wu, Zhiliang; Wang, Meiling; Chen, Miao; Chen, Xiaoqing

    2015-11-01

    A novel one-step separation strategy-tandem high-speed counter-current chromatography (HSCCC) was developed with a six-port valve serving as the switch interface. Nine structural analogues including three isomers were successfully isolated from Poria cocos (Schw.) Wolf. by one step. Compared with conventional HSCCC, peak resolution of target compounds was effectively improved in tandem one. Purities of isolated compounds were all over 90% as determined by HPLC. Their structures were then identified via UV, MS and (1)H NMR, and eventually assigned as poricoic acid B (1), poricoic acid A (2), 3?,16?-dihydroxylanosta-7, 9(11), 24-trien-21-oic acid (3), dehydrotumulosic acid (4), polyporenic acid C (5), 3-epi-dehydrotumulosic acid (6), 3-o-acetyl-16?-hydroxydehydrotrametenolic acid (7), dehydropachymic acid (8) and dehydrotrametenolic acid (9) respectively. The results indicated that tandem HSCCC can effectively improve peak resolution of target compounds, and can be a good candidate for HSCCC separation of structural analogues. PMID:26435185

  16. Comparative study of the mechanism of action of the antimicrobial peptide gomesin and its linear analogue: The role of the ?-hairpin structure.

    PubMed

    Domingues, Tatiana M; Perez, Katia R; Miranda, Antonio; Riske, Karin A

    2015-10-01

    Gomesin (Gm) is an antimicrobial peptide first isolated from the hemolymph of a Brazilian spider. Its powerful antimicrobial activity is, however, accompanied by hemolysis. As an alternative to this issue, a linear analogue (named GmL) lacking the disulfide bonds was designed. Here, CD spectroscopy, a fluorescence-based leakage assay, isothermal titration calorimetry (ITC) and light scattering are used to study the interaction of both Gm and GmL with large unilamellar vesicles (LUVs) composed of POPC (palmitoyl oleoyl phosphatidylcholine) with 25 and 50 mol% POPG (palmitoyl oleoyl phosphatidylglycerol). The activities of Gm and GmL in respect to their binding affinity/enthalpy, ability to permeabilize membranes and to induce vesicle aggregation are correlated with peptide secondary structure. Whereas Gm displays a quite stable ?-hairpin motif irrespective of the environment, GmL assumes a random conformation in aqueous solution and in the presence of 25 mol% POPG but adopts a ?-like structure in the presence of 50 mol% POPG. Gm exhibited high lytic activity against both surface charge densities. Instead, the activity of GmL was found to be negligible in the presence of 25 mol% POPG LUVs, but comparable to that of the native peptide against 50 mol% POPG as a consequence of peptide structuring. We conclude that the activity of Gm and its linear analogue is intimately related to the formation of a ?-turn motif, in which the hydrophobic residues form a hydrophobic face able to insert into the membrane and disrupt it. PMID:26231588

  17. Comparison of three development approaches for Stationary Phase Optimised Selectivity Liquid Chromatography based screening methods Part II: A group of structural analogues (PDE-5 inhibitors in food supplements).

    PubMed

    Deconinck, E; Ghijs, L; Kamugisha, A; Courselle, P

    2016-02-01

    Three approaches for the development of a screening method to detect adulterated dietary supplements, based on Stationary Phase Optimised Selectivity Liquid Chromatography were compared for their easiness/speed of development and the performance of the optimal method obtained. This comparison was performed for a heterogeneous group of molecules, i.e. slimming agents (Part I) and a group of structural analogues, i.e. PDE-5 inhibitors (Part II). The first approach makes use of primary runs at one isocratic level, the second of primary runs in gradient mode and the third of primary runs at three isocratic levels to calculate the optimal combination of segments of stationary phases. In each approach the selection of the stationary phase was followed by a gradient optimisation. For the PDE-5 inhibitors, the group of structural analogues, only the method obtained with the third approach was able to differentiate between all the molecules in the development set. Although not all molecules are baseline separated, the method allows the identification of the selected adulterants in dietary supplements using only diode array detection. Though, due to the mobile phases used, the method could also be coupled to mass spectrometry. The method was validated for its selectivity following the guidelines as described for the screening of pesticide residues and residues of veterinary medicines in food. PMID:26653459

  18. Effect of inherited structures on strike-slip plate boundaries: insight from analogue modelling of the central Levant Fracture System, Lebanon

    NASA Astrophysics Data System (ADS)

    Ghalayini, Ramadan; Daniel, Jean-Marc; Homberg, Catherine; Nader, Fadi

    2015-04-01

    Analogue sandbox modeling is a tool to simulate deformation style and structural evolution of sedimentary basins. The initial goal is to test what is the effect of inherited and crustal structures on the propagation, evolution, and final geometry of major strike-slip faults at the boundary between two tectonic plates. For this purpose, we have undertaken a series of analogue models to validate and reproduce the structures of the Levant Fracture System, a major NNE-SSW sinistral strike-slip fault forming the boundary between the Arabian and African plates. Onshore observations and recent high quality 3D seismic data in the Levant Basin offshore Lebanon demonstrated that Mesozoic ENE striking normal faults were reactivated into dextral strike-slip faults during the Late Miocene till present day activity of the plate boundary which shows a major restraining bend in Lebanon with a ~ 30°clockwise rotation in its trend. Experimental parameters consisted of a silicone layer at the base simulating the ductile crust, overlain by intercalated quartz sand and glass sand layers. Pre-existing structures were simulated by creating a graben in the silicone below the sand at an oblique (>60°) angle to the main throughgoing strike-slip fault. The latter contains a small stepover at depth to create transpression during sinistral strike-slip movement and consequently result in mountain building similarly to modern day Lebanon. Strike-slip movement and compression were regulated by steady-speed computer-controlled engines and the model was scanned using a CT-scanner continuously while deforming to have a final 4D model of the system. Results showed that existing normal faults were reactivated into dextral strike-slip faults as the sinistral movement between the two plates accumulated. Notably, the resulting restraining bend is asymmetric and segmented into two different compartments with differing geometries. One compartment shows a box fold anticline, while the second shows an asymmetric anticline. Thus, analogue modeling has validated observation in seismic data and onshore geology whereby Mount Lebanon and adjacent folds exhibit similar compartmentalization and geometric dissimilarities along the Levant Fracture System. We suggest that the presence of inherited structures will affect to a certain extent the geometry of restraining bends and control the evolution of large strike-slip faults passing through.

  19. Synthesis and structure--activity relationships of substituted cinnamic acids and amide analogues: a new class of herbicides.

    PubMed

    Vishnoi, Shipra; Agrawal, Vikash; Kasana, Virendra K

    2009-04-22

    In the present investigation, substituted cinnamic acids (3-hydroxy, 4-hydroxy, 2-nitro, 3-nitro, 4-nitro, 3-chloro, and 4-methoxy) and their amide analogues with four different types of substituted anilines have been synthesized. The synthesized compounds have been screened for their germination inhibition activity on radish (Raphanus sativus L. var. Japanese White) seeds at 50, 100, and 200 ppm concentrations, and the activity was compared with standard herbicide, metribuzin formulation (sencor). Significant activity was exhibited by all of the compounds. It was observed that with the increase in concentration of the test solution, the activity also increased. All of the compounds showed more than 70% inhibition at 100 ppm concentration except 4-hydroxy cinnamanilide. The compound, 2-chloro (4'-hydroxy) cinnamanilide was the best among the tested compounds, and it was found to be at par with the standard, metribuzin at all concentrations. Thus, it can be concluded that substituted cinnamic acids and their amide analogues may be developed as potential herbicides. PMID:19368353

  20. One pot synthesis, structural and spectral analysis of some symmetrical curcumin analogues catalyzed by calcium oxide under microwave irradiation

    NASA Astrophysics Data System (ADS)

    Elavarasan, S.; Bhakiaraj, D.; Chellakili, B.; Elavarasan, T.; Gopalakrishnan, M.

    2012-11-01

    A series of sixteen number of curcumin analogues have been synthesized under microwave irradiation using calcium oxide as a catalyst. The synthesized compounds have been characterized using FT-IR, MS, elemental analysis, 1H and 13C NMR spectroscopic techniques. The UV-Vis absorption studies for these compounds have been studied in order to provide the electronic transitions taking place in the molecule. When compared to the curcumin ((1E,4Z,6E)-5-hydroxy-1,7-bis(4-hydroxy-3-methoxyphenyl)hepta-1,4,6-trien-3-one), the absorption maxima, ?max for all the synthesized curcumin analogues with a variety of substituents gets blue shifted i.e., hypsochromic shift was observed. This shift may be assigned to the change of dipole moment within the solvated molecule. Theoretical calculations regarding the optimization of the synthesized molecules, electronic properties like highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and mapped electron density surface diagrams were done. The geometrical energy, dipole moments and heat of formation values have also been calculated using the ArgusLab package by AM1 semi-empirical method.

  1. Structuring institutional analysis for urban ecosystems: A key to sustainable urban forest management

    E-print Network

    Evans, Tom

    and function in the United States jeopardizes the current focus on developing sustainable cities. A numberStructuring institutional analysis for urban ecosystems: A key to sustainable urban forest of social dilemmas--for example, free-rider problems--restrict the sustainable production of ecosystem

  2. Scale-integrated observations of morphological biosignatures and associated relict structures: Addressing the practicalities of in situ astrobiology using martian analogue "field" specimens and space instrumentation

    NASA Astrophysics Data System (ADS)

    Pullan, D.; Cockell, C. S.; Pafs-Net

    We investigate how morphological biosignatures 1 could be identified with an array of viable instruments of choice in the framework of robotic planetary surface operations For purposes of the study a modest number of geological hand specimens from our archive of planetary analogues were selected on the basis of feature morphology scale and analogy Three morphological criteria were considered preserved microbial filaments 2 crypto-chasmoendoliths 3 and relict sedimentatry structures 4 The materials originate from a variety of topical martian analogue localities on Earth including impact craters high latitude deserts ancient epochs i e Early Archaean and hydrothermal deposits Instrumentation and techniques available to us included flight spare assets from the Beagle2 deployable package aka the PAW panoramic camera microscope M o ssbauer spectrometer X-ray spectrometer soil sampling Mole aka Planetary Underground Tool PLUTO and rock corer In addition selected commercial equipment served as emulators of potential future instruments including a multi-spectral imager Nuance system a micro-Raman spectrometer Bruker NIR non-confocal and Renishaw VNIR VIS Raman microscopes and a bespoke in situ X-Ray diffractometer Basic requirements for identifying morphological biosignatures are scale-integrated imaging spatial and spectral characterization of host material by analytical means and accessibility to features sample preparation We introduce a scaling philosophy that defines practical working distances for

  3. New Insights into the Design of Inhibitors of Human S-Adenosylmethionine Decarboxylase: Studies of Adenine C[superscript 8] Substitution in Structural Analogues of S-Adenosylmethionine

    SciTech Connect

    McCloskey, Diane E.; Bale, Shridhar; Secrist, III, John A.; Tiwari, Anita; Moss, III, Thomas H.; Valiyaveettil, Jacob; Brooks, Wesley H.; Guida, Wayne C.; Pegg, Anthony E.; Ealick, Steven E.

    2009-04-02

    S-Adenosylmethionine decarboxylase (AdoMetDC) is a critical enzyme in the polyamine biosynthetic pathway and depends on a pyruvoyl group for the decarboxylation process. The crystal structures of the enzyme with various inhibitors at the active site have shown that the adenine base of the ligands adopts an unusual syn conformation when bound to the enzyme. To determine whether compounds that favor the syn conformation in solution would be more potent AdoMetDC inhibitors, several series of AdoMet substrate analogues with a variety of substituents at the 8-position of adenine were synthesized and analyzed for their ability to inhibit hAdoMetDC. The biochemical analysis indicated that an 8-methyl substituent resulted in more potent inhibitors, yet most other 8-substitutions provided no benefit over the parent compound. To understand these results, we used computational modeling and X-ray crystallography to study C{sup 8}-substituted adenine analogues bound in the active site.

  4. Synthesis and Evaluation of ?-Thymidine Analogues as Novel Antimalarials

    PubMed Central

    2012-01-01

    Plasmodium falciparum thymidylate kinase (PfTMPK) is a key enzyme in pyrimidine nucleotide biosynthesis. 3-Trifluoromethyl-4-chloro-phenyl-urea-?-thymidine has been reported as an inhibitor of Mycobacterium tuberculosis TMPK (MtTMPK). Starting from this point, we designed, synthesized and evaluated a number of thymidine analogues as antimalarials. Both 5?-urea-?- and ?-thymidine derivatives were moderate inhibitors of PfTMPK and furthermore showed moderate inhibition of parasite growth. The structure of several enzyme–inhibitor complexes provides a basis for improved inhibitor design. However, we found that certain 5?-urea-?-thymidine analogues had antimalarial activity where inhibition of PfTMPK is not the major mode of action. Optimization of this series resulted in a compound with potent antimalarial activity (EC50 = 28 nM; CC50 = 29 ?M). PMID:23240776

  5. Initial synthesis and structure of an all-ferrous analogue of the fully reduced [Fe4S4]0 cluster of the nitrogenase iron protein.

    PubMed

    Scott, Thomas A; Berlinguette, Curtis P; Holm, Richard H; Zhou, Hong-Cai

    2005-07-12

    The synthetic cubane-type iron-sulfur clusters [Fe(4)S(4)(SR)(4)](z) form a four-member electron transfer series (z = 3-, 2-, 1-, and 0), all members of which except that with z = 0 have been isolated and characterized. They serve as accurate analogues of protein-bound [Fe(4)S(4)(SCys)(4)](z) redox centers, which, in terms of core oxidation states, exhibit the redox couples [Fe(4)S(4)](3+/2+) and [Fe(4)S(4)](2+/1+). Clusters with the all-ferrous core [Fe(4)S(4)](0) have never been isolated because of their oxidative sensitivity. Recent work on the Fe protein of Azotobacter vinelandii nitrogenase has demonstrated the formation of the all-ferrous state upon reaction with a strong reductant. Treatment of the cyanide cluster [Fe(4)S(4)(CN)(4)](3-) with K[Ph(2)CO] in acetonitrile/tetrahydrofuran affords the all-ferrous cluster [Fe(4)S(4)(CN)(4)](4-), isolated as the Bu(4)N(+) salt. The x-ray structure demonstrates retention of a cubane-type structure with idealized D(2)(d) symmetry. The Mössbauer spectrum unambiguously demonstrates the [Fe(4)S(4)](0) oxidation state. Bond distances, core volumes, (57)Fe isomer shifts, and visible absorption spectra make evident the high degree of structural and electronic similarity with the fully reduced Fe protein. The attribute of cyanide ligation causes positive [Fe(4)S(4)](2+/1+) and [Fe(4)S(4)](1+/0) redox potential shifts, facilitating the initial isolation of an analogue of the [Fe(4)S(4)](0) protein site. PMID:15985547

  6. Comprehensive analysis of three-dimensional activity cliffs formed by kinase inhibitors with different binding modes and cliff mapping of structural analogues.

    PubMed

    Furtmann, Norbert; Hu, Ye; Bajorath, Jürgen

    2015-01-01

    Kinases are among the structurally most extensively characterized therapeutic targets. For many kinases, X-ray structures of inhibitor complexes are publicly available. We have identified all three-dimensional activity cliffs (3D-cliffs) formed by kinase inhibitors. More than 1300 X-ray structures of unique kinase-inhibitor complexes and associated activity data were analyzed. On the basis of binding mode comparison and 3D similarity calculations, 105 3D-cliffs were detected for type I, type II, or type III inhibitors of 13 different kinases. Many of these activity cliffs revealed clear interaction differences between highly and weakly potent inhibitors. More than 200 structural analogues of 3D-cliff compounds were identified whose structure-activity relationships (SARs) can be further explored in three dimensions on the basis of the corresponding 3D-cliffs. In addition to SAR exploration, 3D-cliffs provide useful interaction hypotheses for structure-based design. The kinase inhibitor and activity cliff information is made freely available as a part of our study. PMID:25054653

  7. Analogue to information system based on PLL-based frequency synthesizers with fast locking schemes 

    E-print Network

    Lin, Ming-Lang

    2010-01-01

    Data conversion is the crucial interface between the real world and digital processing systems. Analogue-to-digital converters and digital-to-analogue converters are two key conversion devices and used as the interface. ...

  8. Structural comparison of complexes of methotrexate analogues with Lactobacillus casei dihydrofolate reductase by two-dimensional /sup 1/H NMR at 500 MHz

    SciTech Connect

    Hammond, S.J.; Birdsall, B.; Feeney, J.; Searle, M.S.; Roberts, G.C.K.; Cheung, H.T.A.

    1987-12-29

    The authors have used two-dimensional (2D) NMR methods to examine complexes of Lactobacillus casei dihydrofolate reductase and methotrexate (MTX) analogues having structural modifications of the benzoyl ring and also the glutamic acid moiety. Assignments of the /sup 1/H signals in the spectra of the various complexes were made by comparison of their 2D spectra with those complexes containing methotrexate where we have previously assigned resonances from 32 of the 162 amino acid residues. In the complexes formed with the dihalomethotrexate analogues, the glutamic acid and pteridine ring moieties were shown to bind to the enzyme in a manner similar to that found in the methotrexate-enzyme complex. Perturbations in /sup 1/H chemical shifts of protons in Phe-49, Leu-54, and Leu-27 and the methotrexate H7 and NMe protons were observed in the different complexes and were accounted for by changes in orientation of the benzoyl ring in the various complexes. Binding of oxidized or reduced coenzyme to the binary complexes did not result in different shifts for Leu-27, Leu-54, or Leu-19 protons, and thus, the orientation of the benzoyl ring of the methotrexate analogues is not perturbed greatly by the presence of either oxidized or reduced coenzyme. In the complex with the ..gamma..-monoamide analog, the /sup 1/H signals of assigned residues in the protein had almost identical shifts with the corresponding protons in the methotrexate-enzyme complex for all residues except His-28 and, to a lesser extent, Leu-27. This indicates that while the His-28 interaction with the MTX ..gamma..-CO/sub 2//sup -/ is no longer present in this complex with the ..gamma..-amide, there has not been a major change in the overall structure of the two complexes. This behavior contrasts to that of the ..cap alpha..-amide complex where /sup 1/H signals from protons in several amino acid residues are different compared with their values in the complex formed with methotrexate.

  9. Loratadine and analogues: discovery and preliminary structure-activity relationship of inhibitors of the amino acid transporter B(0)AT2.

    PubMed

    Cuboni, Serena; Devigny, Christian; Hoogeland, Bastiaan; Strasser, Andrea; Pomplun, Sebastian; Hauger, Barbara; Höfner, Georg; Wanner, Klaus T; Eder, Matthias; Buschauer, Armin; Holsboer, Florian; Hausch, Felix

    2014-11-26

    B(0)AT2, encoded by the SLC6A15 gene, is a transporter for neutral amino acids that has recently been implicated in mood and metabolic disorders. It is predominantly expressed in the brain, but little is otherwise known about its function. To identify inhibitors for this transporter, we screened a library of 3133 different bioactive compounds. Loratadine, a clinically used histamine H1 receptor antagonist, was identified as a selective inhibitor of B(0)AT2 with an IC50 of 4 ?M while being less active or inactive against several other members of the SLC6 family. Reversible inhibition of B(0)AT2 was confirmed by electrophysiology. A series of loratadine analogues were synthesized to gain insight into the structure-activity relationships. Our studies provide the first chemical tool for B(0)AT2. PMID:25318072

  10. Structure of Bacillus subtilis ?-glutamyltranspeptidase in complex with acivicin: diversity of the binding mode of a classical and electrophilic active-site-directed glutamate analogue

    SciTech Connect

    Ida, Tomoyo; Suzuki, Hideyuki; Fukuyama, Keiichi; Hiratake, Jun; Wada, Kei

    2014-02-01

    The binding modes of acivicin, a classical and an electrophilic active-site-directed glutamate analogue, to bacterial ?-glutamyltranspeptidases were found to be diverse. ?-Glutamyltranspeptidase (GGT) is an enzyme that plays a central role in glutathione metabolism, and acivicin is a classical inhibitor of GGT. Here, the structure of acivicin bound to Bacillus subtilis GGT determined by X-ray crystallography to 1.8 Å resolution is presented, in which it binds to the active site in a similar manner to that in Helicobacter pylori GGT, but in a different binding mode to that in Escherichia coli GGT. In B. subtilis GGT, acivicin is bound covalently through its C3 atom with sp{sup 2} hybridization to Thr403 O{sup ?}, the catalytic nucleophile of the enzyme. The results show that acivicin-binding sites are common, but the binding manners and orientations of its five-membered dihydroisoxazole ring are diverse in the binding pockets of GGTs.

  11. Phytoplankton community structure defined by key environmental variables in Tagus estuary, Portugal.

    PubMed

    Brogueira, Maria José; Oliveira, Maria do Rosário; Cabeçadas, Graça

    2007-12-01

    In this work, we analyze environmental (physical and chemical) and biological (phytoplankton) data obtained along Tagus estuary during three surveys, carried out in productive period (May/June/July) at ebb tide. The main objective of this study was to identify the key environmental factors affecting phytoplankton structure in the estuary. BIOENV analysis revealed that, in study period, temperature, salinity, silicate and total phosphorus were the variables that best explained the phytoplankton spatial pattern in the estuary (Spearman correlation, rho=0.803). A generalized linear model (GLM) also identified salinity, silicate and phosphate as having a high explanatory power (63%) of phytoplankton abundance. These selected nutrients appear to be consistent with the requirements of the dominant phytoplankton group, Baccilariophyceae. Apparently, phytoplankton community is adapted to fluctuations in light intensity, as suspended particulate matter did not come out as a key factor in shaping phytoplankton structure along Tagus estuary. PMID:17884159

  12. Efficient synthesis and biological activity of Psammaplin A and its analogues as antitumor agents.

    PubMed

    Hong, Suckchang; Shin, Yoonho; Jung, Myunggi; Ha, Min Woo; Park, Yohan; Lee, Yeon-Ju; Shin, Jongheon; Oh, Ki Bong; Lee, Sang Kook; Park, Hyeung-geun

    2015-01-01

    We describe a new concise method for the synthesis of psammaplin A and its analogues, and antitumor activity of psammaplin A analogues. Psammaplin A was obtained with 41% yield in 5 steps from 3-bromo-4-hydroxybenzaldahyde and ethyl acetoacetate via Knoevenagel condensation and ?-nitrosation as key steps. Twenty eight analogues of psammaplin A were prepared employing the new synthetic approach. Structure-activity relationship study against cytotoxicity reveal that the free oxime group and disulfide functional group were responsible for high cytotoxicity. Also the bromotyrosine component was relatively tolerable and hydrophobic aromatic groups preserved the cytotoxicity. The cytotoxicity of aromatic group is dependent on the size and spatial geometry. Among them, five compounds showed comparable cytotoxicity to psammaplin A. Compound 30 exhibited potential HDAC inhibitory activity and in vivo antitumor activity. PMID:25884112

  13. Phosphorylation induces subtle structural changes in SpoIIAA, a key regulator of sporulation.

    PubMed Central

    Clarkson, Joanna; Campbell, Iain D; Yudkin, Michael D

    2003-01-01

    The phosphorylation state of SpoIIAA is a key factor in the regulation of sporulation in Bacillus subtilis. Previous crystallographic studies had led to the conclusion that phosphorylation alters the binding affinity of SpoIIAA for its partner proteins solely through the additional charge and bulk of the phosphoryl group: small structural changes observed elsewhere in the protein were considered to be random fluctuations rather than the result of phosphorylation. The results presented in the present paper show that NMR studies detect the same subtle structural changes in solution as those seen in the crystal, strongly implying that they are the direct result of phosphorylation. These subtle structural changes are similar to those that occur in a non-phosphorylated mutant that is defective in binding to one of its partner proteins. We propose that the structural changes which occur in SpoIIAA on phosphorylation act in concert with the phosphoryl group to alter its binding properties. PMID:12585962

  14. Crystal structure of Streptococcus pneumoniae pneumolysin provides key insights into early steps of pore formation

    PubMed Central

    Lawrence, Sara L.; Feil, Susanne C.; Morton, Craig J.; Farrand, Allison J.; Mulhern, Terrence D.; Gorman, Michael A.; Wade, Kristin R.; Tweten, Rodney K.; Parker, Michael W.

    2015-01-01

    Pore-forming proteins are weapons often used by bacterial pathogens to breach the membrane barrier of target cells. Despite their critical role in infection important structural aspects of the mechanism of how these proteins assemble into pores remain unknown. Streptococcus pneumoniae is the world’s leading cause of pneumonia, meningitis, bacteremia and otitis media. Pneumolysin (PLY) is a major virulence factor of S. pneumoniae and a target for both small molecule drug development and vaccines. PLY is a member of the cholesterol-dependent cytolysins (CDCs), a family of pore-forming toxins that form gigantic pores in cell membranes. Here we present the structure of PLY determined by X-ray crystallography and, in solution, by small-angle X-ray scattering. The crystal structure reveals PLY assembles as a linear oligomer that provides key structural insights into the poorly understood early monomer-monomer interactions of CDCs at the membrane surface. PMID:26403197

  15. Crystal structure of Streptococcus pneumoniae pneumolysin provides key insights into early steps of pore formation.

    PubMed

    Lawrence, Sara L; Feil, Susanne C; Morton, Craig J; Farrand, Allison J; Mulhern, Terrence D; Gorman, Michael A; Wade, Kristin R; Tweten, Rodney K; Parker, Michael W

    2015-01-01

    Pore-forming proteins are weapons often used by bacterial pathogens to breach the membrane barrier of target cells. Despite their critical role in infection important structural aspects of the mechanism of how these proteins assemble into pores remain unknown. Streptococcus pneumoniae is the world's leading cause of pneumonia, meningitis, bacteremia and otitis media. Pneumolysin (PLY) is a major virulence factor of S. pneumoniae and a target for both small molecule drug development and vaccines. PLY is a member of the cholesterol-dependent cytolysins (CDCs), a family of pore-forming toxins that form gigantic pores in cell membranes. Here we present the structure of PLY determined by X-ray crystallography and, in solution, by small-angle X-ray scattering. The crystal structure reveals PLY assembles as a linear oligomer that provides key structural insights into the poorly understood early monomer-monomer interactions of CDCs at the membrane surface. PMID:26403197

  16. Optoelectronic Smart Structure Interface - A key development for practical smart structures

    NASA Astrophysics Data System (ADS)

    Measures, Raymond M.; Alavie, Tino; Liu, Kexing; Melle, Serge

    1993-03-01

    The development of an Optoelectronic Smart Structure Interface (OSSI) will be required for the practical implementation of Smart Structure Technology. Such an interface will permit an extremely user-friendly interconnection to any Smart Structure component permitting the optical signals from an embedded optical fiber sensor array to be transmitted from the structure in a form most acceptable for that specific application. We have developed a simple, passive, fast response wavelength demodulation system for intracore Bragg grating sensors and have demonstrated real time strain measurements. Currently, we are exploring the use of this wavelength demodulation system with Bragg grating tuned fiber laser sensors and intend to show that such a system can form the basis of an OSSI.

  17. Natural analogues of nuclear waste glass corrosion.

    SciTech Connect

    Abrajano, T.A. Jr.; Ebert, W.L.; Luo, J.S.

    1999-01-06

    This report reviews and summarizes studies performed to characterize the products and processes involved in the corrosion of natural glasses. Studies are also reviewed and evaluated on how well the corrosion of natural glasses in natural environments serves as an analogue for the corrosion of high-level radioactive waste glasses in an engineered geologic disposal system. A wide range of natural and experimental corrosion studies has been performed on three major groups of natural glasses: tektite, obsidian, and basalt. Studies of the corrosion of natural glass attempt to characterize both the nature of alteration products and the reaction kinetics. Information available on natural glass was then compared to corresponding information on the corrosion of nuclear waste glasses, specifically to resolve two key questions: (1) whether one or more natural glasses behave similarly to nuclear waste glasses in laboratory tests, and (2) how these similarities can be used to support projections of the long-term corrosion of nuclear waste glasses. The corrosion behavior of basaltic glasses was most similar to that of nuclear waste glasses, but the corrosion of tektite and obsidian glasses involves certain processes that also occur during the corrosion of nuclear waste glasses. The reactions and processes that control basalt glass dissolution are similar to those that are important in nuclear waste glass dissolution. The key reaction of the overall corrosion mechanism is network hydrolysis, which eventually breaks down the glass network structure that remains after the initial ion-exchange and diffusion processes. This review also highlights some unresolved issues related to the application of an analogue approach to predicting long-term behavior of nuclear waste glass corrosion, such as discrepancies between experimental and field-based estimates of kinetic parameters for basaltic glasses.

  18. Emulating exhalative chemistry: synthesis and structural characterization of ilinskite, Na[Cu5O2](SeO3)2Cl3, and its K-analogue

    NASA Astrophysics Data System (ADS)

    Kovrugin, Vadim M.; Siidra, Oleg I.; Colmont, Marie; Mentré, Olivier; Krivovichev, Sergey V.

    2015-08-01

    The K- and Na-synthetic analogues of the fumarolic mineral ilinskite have been synthesized by the chemical vapor transport (CVT) reactions method. The A[Cu5O2](SeO3)2Cl3 ( A + = K+, Na+) compounds crystallize in the orthorhombic space group Pnma: a = 18.1691(6) Å, b = 6.4483(2) Å, c = 10.5684(4) Å, V = 1238.19(7) Å3, R 1 = 0.018 for 1957 unique reflections with F > 4? F for K[Cu5O2](SeO3)2Cl3 ( KI), and a = 17.7489(18) Å, b = 6.4412(6) Å, c = 10.4880(12) Å, V = 1199.0(2) Å3, R 1 = 0.049 for 1300 unique reflections with F > 4? F for Na[Cu5O2](SeO3)2Cl3 ( NaI). The crystal structures of KI and NaI are based upon the [O2Cu5]6+ sheets consisting of corner-sharing (OCu4)6+ tetrahedra. The Na-for-K substitution results in the significant expansion of the interlayer space and changes in local coordination of some of the Cu2+ cations. The A + cation coordination changes from fivefold (for Na+) to ninefold (for K+). The CVT reactions method provides a unique opportunity to model physicochemical conditions existing in fumarolic environments and may be used not only to model exhalative processes, but also to predict possible mineral phases that may form in fumaroles. In particular, the K analogue of ilinskite is not known in nature, whereas it may well form from volcanic gases in a K-rich local geochemical environment.

  19. Strong nonadditivity as a key structure-activity relationship feature: distinguishing structural changes from assay artifacts.

    PubMed

    Kramer, Christian; Fuchs, Julian E; Liedl, Klaus R

    2015-03-23

    Nonadditivity in protein-ligand affinity data represents highly instructive structure-activity relationship (SAR) features that indicate structural changes and have the potential to guide rational drug design. At the same time, nonadditivity is a challenge for both basic SAR analysis as well as many ligand-based data analysis techniques such as Free-Wilson Analysis and Matched Molecular Pair analysis, since linear substituent contribution models inherently assume additivity and thus do not work in such cases. While structural causes for nonadditivity have been analyzed anecdotally, no systematic approaches to interpret and use nonadditivity prospectively have been developed yet. In this contribution, we lay the statistical framework for systematic analysis of nonadditivity in a SAR series. First, we develop a general metric to quantify nonadditivity. Then, we demonstrate the non-negligible impact of experimental uncertainty that creates apparent nonadditivity, and we introduce techniques to handle experimental uncertainty. Finally, we analyze public SAR data sets for strong nonadditivity and use recourse to the original publications and available X-ray structures to find structural explanations for the nonadditivity observed. We find that all cases of strong nonadditivity (??pKi and ??pIC50 > 2.0 log units) with sufficient structural information to generate reasonable hypothesis involve changes in binding mode. With the appropriate statistical basis, nonadditivity analysis offers a variety of new attempts for various areas in computer-aided drug design, including the validation of scoring functions and free energy perturbation approaches, binding pocket classification, and novel features in SAR analysis tools. PMID:25760829

  20. Crystal Structures of Pasteurella multocida Sialyltransferase Complexes with Acceptor and Donor Analogues Reveal Substrate Binding Sites and Catalytic

    E-print Network

    Fisher, Andrew J.

    Crystal Structures of Pasteurella multocida Sialyltransferase Complexes with Acceptor and Donor and pathologically important sialic acid-containing molecules in nature. Binary X-ray crystal structures simultaneously. The four structures presented here reveal that binding of the nucleotide-activated donor sugar

  1. The unsaturated acyclic nucleoside analogues bearing a sterically constrained (Z)-4'-benzamido-2'-butenyl moiety: Synthesis, X-ray crystal structure study, cytostatic and antiviral activity evaluations.

    PubMed

    Benci, Kresimir; Wittine, Karlo; Radan, Malajka; Cetina, Mario; Sedi?, Mirela; Kraljevi? Paveli?, Sandra; Paveli?, Kresimir; Clercq, Erik De; Mintas, Mladen

    2010-09-01

    A series of the novel acyclic unsaturated pyrimidine (1-12) and adenine (13) nucleoside analogues bearing conformationally restricted (Z)-2'-butenyl moiety were synthesized and evaluated for their antiviral and cytostatic activity potency against malignant tumor cell lines and normal human fibroblast (WI38). The N-1 and/or N-3 acyclic side chain substitution in pyrimidine ring in N-3 substituted 5-trifluoromethyluracil derivative (11), N-1, N-3 disubstituted 5-fluorouracil derivative (12) and adenine derivative (13) was deduced from their (1)H and (13)C NMR spectra and confirmed by single crystal X-ray structure analysis. The X-ray crystal structure analysis 11-13 revealed also supramolecular self-assemblies, in which infinite chains or dimers built two- and three-dimensional networks. The results of the in vitro cytostatic activity evaluations of 1-13 indicate that the majority of the compounds tested exhibited a non-specific and moderate antiproliferative effect at the highest concentration (100 microM). Of all evaluated compounds on the cell lines tested only the N-1 4''-fluoro-substituted-benzamide uracil derivative (7) showed rather marked and selective inhibitory activity against the growth of MCF-7 cells at a concentration of 2.7 microM and no cytotoxic effect on normal fibroblasts WI38. This compound can be therefore considered as a potential antitumor lead compound for further synthetic structure modification. PMID:20696582

  2. NMR structure determination of a synthetic analogue of bacillomycin Lc reveals the strategic role of L-Asn1 in the natural iturinic antibiotics

    NASA Astrophysics Data System (ADS)

    Volpon, Laurent; Tsan, Pascale; Majer, Zsuzsa; Vass, Elemer; Hollósi, Miklós; Noguéra, Valérie; Lancelin, Jean-Marc; Besson, Françoise

    2007-08-01

    Iturins are a group of antifungal produced by Bacillus subtilis. All are cyclic lipopeptides with seven ?-amino acids of configuration LDDLLDL and one ?-amino fatty acid. The bacillomycin L is a member of this family and its NMR structure was previously resolved using the sequence Asp-Tyr-Asn-Ser-Gln-Ser-Thr. In this work, we carefully examined the NMR spectra of this compound and detected an error in the sequence. In fact, Asp1 and Gln5 need to be changed into Asn1 and Glu5, which therefore makes it identical to bacillomycin Lc. As a consequence, it now appears that all iturinic peptides with antibiotic activity share the common ?-amino fatty acid 8- L-Asn1- D-Tyr2- D-Asn3 sequence. To better understand the conformational influence of the acidic residue L-Asp1, present, for example in the inactive iturin C, the NMR structure of the synthetic analogue SCP [cyclo ( L-Asp1- D-Tyr2- D-Asn3- L-Ser4- L-Gln5- D-Ser6- L-Thr7-?-Ala8)] was determined and compared with bacillomycin Lc recalculated with the corrected sequence. In both cases, the conformers obtained were separated into two families of similar energy which essentially differ in the number and type of turns. A detailed analysis of both cyclopeptide structures is presented here. In addition, CD and FTIR spectra were performed and confirmed the conformational differences observed by NMR between both cyclopeptides.

  3. Structural Analysis of Peptide-Analogues of Human Zona Pellucida ZP1 Protein with Amyloidogenic Properties: Insights into Mammalian Zona Pellucida Formation

    PubMed Central

    Louros, Nikolaos N.; Iconomidou, Vassiliki A.; Giannelou, Polina; Hamodrakas, Stavros J.

    2013-01-01

    Zona pellucida (ZP) is an extracellular matrix surrounding and protecting mammalian and fish oocytes, which is responsible for sperm binding. Mammalian ZP consists of three to four glycoproteins, called ZP1, ZP2, ZP3, ZP4. These proteins polymerize into long interconnected filaments, through a common structural unit, known as the ZP domain, which consists of two domains, ZP-N and ZP-C. ZP is related in function to silkmoth chorion and in an evolutionary fashion to the teleostean fish chorion, also fibrous structures protecting the oocyte and embryo, that both have been proven to be functional amyloids. Two peptides were predicted as ‘aggregation-prone’ by our prediction tool, AMYLPRED, from the sequence of the human ZP1-N domain. Here, we present results from transmission electron microscopy, X-ray diffraction, Congo red staining and attenuated total reflectance Fourier-transform infrared spectroscopy (ATR FT-IR), of two synthetic peptide-analogues of these predicted ‘aggregation-prone’ parts of the human ZP1-N domain, that we consider crucial for ZP protein polymerization, showing that they both self-assemble into amyloid-like fibrils. Based on our experimental data, we propose that human ZP (hZP) might be considered as a novel, putative, natural protective amyloid, in close analogy to silkmoth and teleostean fish chorions. Experiments are in progress to verify this proposal. We also attempt to provide insights into ZP formation, proposing a possible model for hZP1-N domain polymerization. PMID:24069181

  4. Synthesis, crystal structure, high-temperature behavior and magnetic properties of CoBiO(AsO4), a Co analogue of paganoite

    NASA Astrophysics Data System (ADS)

    Aliev, Almaz; Kozin, Michael S.; Colmont, Marie; Siidra, Oleg I.; Krivovichev, Sergey V.; Mentré, Olivier

    2015-09-01

    Single crystals and powder samples of Co analogue of paganoite CoBiO(AsO4) have been obtained by high-temperature solid-state reactions. Crystal structure [triclinic, , a = 5.2380(3), b = 6.8286(4), c = 7.6150(4) Å, ? = 111.631(2), ? = 108.376(2), ? = 108.388(2)°, V = 209.55(2) Å3] has been refined to R 1 = 0.018 on the basis of 1524 unique observed reflections. CoBiO(AsO4) is isotypic to paganoite, NiBiO(AsO4). The crystal structure can be described as based upon [OCoBi]3+ chains of edge-sharing (OBi2Co2) tetrahedra linked via (AsO4) groups. Differential thermal analysis reveals no phase decomposition till 850 °C, when the compound starts to melt. A small endothermic peak is observed near 330 °C. Thermal expansion has been studied by high-temperature powder X-ray diffraction. Thermal expansion coefficients ( ? a = 10.1 × 10-6, ? b = 12.6 × 10-6, ? c = 10.5 × 10-6 K-1) indicate a relatively isotropic behavior with the less intense expansion direction parallel to the direction of the chains of oxocentered tetrahedra. Magnetic susceptibility of CoBiO(AsO4) reveals the presence of an antiferromagnetic ordering at T N = 15.4 K.

  5. Inhibition of Siderophore Biosynthesis in Mycobacterium tuberculosis with Nucleoside Bisubstrate Analogues: Structure–Activity Relationships of the Nucleobase Domain of 5?-O-[N-(Salicyl)sulfamoyl]adenosine

    PubMed Central

    Neres, João; Labello, Nicholas P.; Somu, Ravindranadh V.; Boshoff, Helena I.; Wilson, Daniel J.; Vannada, Jagadeshwar; Chen, Liqiang; Barry, Clifton E.; Bennett, Eric M.; Aldrich, Courtney C.

    2009-01-01

    5?-O-[N-(salicyl)sulfamoyl]adenosine (Sal-AMS) is a prototype for a new class of antitubercular agents that inhibit the aryl acid adenylating enzyme (AAAE) known as MbtA involved in biosynthesis of the mycobactins. Herein, we report the structure-based design, synthesis, biochemical, and biological evaluation of a comprehensive and systematic series of analogues, exploring the structure–activity relationship of the purine nucleobase domain of Sal-AMS. Significantly, 2-phenyl-Sal-AMS derivative 26 exhibited exceptionally potent antitubercular activity with an MIC99 under iron-deficient conditions of 0.049 µM while the N-6-cyclopropyl-Sal-AMS 16 led to improved potency and to a 64-enhancement in activity under iron-deficient conditions relative to iron-replete conditions, a phenotype concordant with the designed mechanism of action. The most potent MbtA inhibitors disclosed here display in vitro antitubercular activity superior to most current first line TB drugs, and these compounds are also expected to be useful against a wide range of pathogens that require aryl-capped siderphores for virulence. PMID:18690677

  6. Demystifying fluorine chemical shifts: electronic structure calculations address origins of seemingly anomalous (19)F-NMR spectra of fluorohistidine isomers and analogues.

    PubMed

    Kasireddy, Chandana; Bann, James G; Mitchell-Koch, Katie R

    2015-11-11

    Fluorine NMR spectroscopy is a powerful tool for studying biomolecular structure, dynamics, and ligand binding, yet the origins of (19)F chemical shifts are not well understood. Herein, we use electronic structure calculations to describe the changes in (19)F chemical shifts of 2F- and 4F-histidine/(5-methyl)-imidazole upon acid titration. While the protonation of the 2F species results in a deshielded chemical shift, protonation of the 4F isomer results in an opposite, shielded chemical shift. The deshielding of 2F-histidine/(5-methyl)-imidazole upon protonation can be rationalized by concomitant decreases in charge density on fluorine and a reduced dipole moment. These correlations do not hold for 4F-histidine/(5-methyl)-imidazole, however. Molecular orbital calculations reveal that for the 4F species, there are no lone pair electrons on the fluorine until protonation. Analysis of a series of 4F-imidazole analogues, all with delocalized fluorine electron density, indicates that the deshielding of (19)F chemical shifts through substituent effects correlates with increased C-F bond polarity. In summary, the delocalization of fluorine electrons in the neutral 4F species, with gain of a lone pair upon protonation may help explain the difficulty in developing a predictive framework for fluorine chemical shifts. Ideas debated by chemists over 40 years ago, regarding fluorine's complex electronic effects, are shown to have relevance for understanding and predicting fluorine NMR spectra. PMID:26524669

  7. Structural changes accompanying GTP hydrolysis in microtubules: information from a slowly hydrolyzable analogue guanylyl-(alpha,beta)- methylene-diphosphonate

    PubMed Central

    1995-01-01

    We have used cryoelectron microscopy to try to understand the structural basis for the role of GTP hydrolysis in destabilizing the microtubule lattice. We have measured a structural difference introduced into microtubules by replacing GTP with guanylyl- (alpha,beta)-methylene-diphosphonate (GMPCPP). In a stable GMPCPP microtubule lattice, the moire patterns change and the tubulin subunits increase in size by 1.5 A. This information provides a clue to the role of hydrolysis in inducing the structural change at the end of a microtubule during the transition from a growing to a shrinking phase. PMID:7822409

  8. STRUCTURE-ACTIVITY STUDY OF PARACETAMOL ANALOGUES: INHIBITION OF REPLICATIVE DNA SYNTHESIS IN V79 CHINESE HAMSTER CELLS

    EPA Science Inventory

    Experimental and theoretical evidence pertaining to cytotoxic and genotoxic activity of paracetamol in biological systems was used to formulate a simple mechanistic hypothesis to explain the relative inhibition of replicative DNA synthesis by a series of 19 structurally similar p...

  9. Telomere G-strand structure and function analyzed by chemical protection, base analogue substitution, and utilization by telomerase in vitro.

    PubMed

    Henderson, E R; Moore, M; Malcolm, B A

    1990-01-23

    Eukaryotic telomeres have a 12-16 nucleotide long deoxyguanosine (dG) rich single-stranded overhang at their molecular termini. Some of the unique features of telomeres are probably attributable to a specialized structure formed by this overhang. In the ciliated protozoan Tetrahymena thermophila, the dG-rich overhang is comprised of approximately two repeats of the sequence d(TTGGGG). Previous work has shown that the synthetic oligonucleotide d(TTGGGG)4 can form an unusual non-Watson-Crick base-paired structure (the "G-strand structure") containing G-G base pairs and syn-guanines. We have tested the susceptibility of various dGs in this structure to methylation by DMS. At 0-10 degrees C one dG residue is hypersensitive to methylation while others are particularly resistant. By systematically substituting deoxyinosine (dI) for dG in d(TTGGGG)4 we identify N2 groups of guanine essential for formation of the G-strand structure. We show that dI-substituted molecules that cannot form the G-strand structure nonetheless function as substrates for telomere repeat addition in vitro by the telomere lengthening enzyme, telomerase. The implications of these data are discussed. PMID:2337592

  10. Nonstationary analogue black holes

    E-print Network

    Gregory Eskin

    2014-11-26

    We study the existence of analogue nonstationary spherically symmetric black holes. The prime example is the acoustic model (cf. [V], [U]). We consider also a more general class of metrics that could be useful in other physical models of analogue black and white holes. We give examples of the appearance of black holes and of disappearance of white holes. We also discuss the relation between the apparent and the event horizons for the case of analogue black holes. In the end we study the inverse problem of determination of black or white holes by boundary measurements for the spherically symmetric nonstationary metrics.

  11. Crystal structures and hydrogen bonding in the morpholinium salts of four phen­oxy­acetic acid analogues

    PubMed Central

    Smith, Graham; Lynch, Daniel E.

    2015-01-01

    The anhydrous salts morpholinium (tetra­hydro-2-H-1,4-oxazin-4-ium) phen­oxy­acetate, C4H10NO+·C8H7O3 ?, (I), morpholinium (4-fluoro­phen­oxy)acetate, C4H10NO+·C8H6?FO3 ?, (II), and isomeric morpholinium (3,5-di­chloro­phen­oxy)acetate (3,5-D), (III), and morpholinium (2,4-di­chloro­phen­oxy)acetic acid (2,4-D), C4H10NO+·C8H5Cl2O3 ?, (IV), have been determined and their hydrogen-bonded structures are described. In the crystals of (I), (III) and (IV), one of the the aminium H atoms is involved in a three-centre asymmetric cation–anion N—H?O,O? R 1 2(4) hydrogen-bonding inter­action with the two carboxyl O-atom acceptors of the anion. With the structure of (II), the primary N—H?O inter­action is linear. In the structures of (I), (II) and (III), the second N—H?Ocarbox­yl hydrogen bond generates one-dimensional chain structures extending in all cases along [100]. With (IV), the ion pairs are linked though inversion-related N—H?O hydrogen bonds [graph set R 4 2(8)], giving a cyclic hetero­tetra­meric structure. PMID:26594518

  12. Crystal structures and hydrogen bonding in the morpholinium salts of four phen-oxy-acetic acid analogues.

    PubMed

    Smith, Graham; Lynch, Daniel E

    2015-11-01

    The anhydrous salts morpholinium (tetra-hydro-2-H-1,4-oxazin-4-ium) phen-oxy-acetate, C4H10NO(+)·C8H7O3 (-), (I), morpholinium (4-fluoro-phen-oxy)acetate, C4H10NO(+)·C8H6?FO3 (-), (II), and isomeric morpholinium (3,5-di-chloro-phen-oxy)acetate (3,5-D), (III), and morpholinium (2,4-di-chloro-phen-oxy)acetic acid (2,4-D), C4H10NO(+)·C8H5Cl2O3 (-), (IV), have been determined and their hydrogen-bonded structures are described. In the crystals of (I), (III) and (IV), one of the the aminium H atoms is involved in a three-centre asymmetric cation-anion N-H?O,O' R 1 (2)(4) hydrogen-bonding inter-action with the two carboxyl O-atom acceptors of the anion. With the structure of (II), the primary N-H?O inter-action is linear. In the structures of (I), (II) and (III), the second N-H?Ocarbox-yl hydrogen bond generates one-dimensional chain structures extending in all cases along [100]. With (IV), the ion pairs are linked though inversion-related N-H?O hydrogen bonds [graph set R 4 (2)(8)], giving a cyclic hetero-tetra-meric structure. PMID:26594518

  13. A cytotoxic principle of Tamarindus indica, di-n-butyl malate and the structure-activity relationship of its analogues.

    PubMed

    Kobayashi, A; Adenan, M I; Kajiyama, S; Kanzaki, H; Kawazu, K

    1996-01-01

    Bioassay-guided fractionation of the methanolic extract of Tamarindus indica fruits led to the isolation of L-(-)-di-n-butyl malate which exhibited a pronounced cytotoxic activity against sea urchin embryo cells. In order to study structure-activity relationships, close-structure relatives of di-n-butyl malate were synthesized using D-(+)- and L-(-)-malic acid as starting materials, and their cytotoxic activities were examined for the sea urchin embryo assay. L-(-)-Di-n-pentyl malate was the most effective inhibitor to the development of the fertilized eggs. Significant inhibitory activity was not seen in the esters of D-(-)-isomer. PMID:8639230

  14. Adenosine Analogues as Selective Inhibitors of Glyceraldehyde-3-phosphate Dehydrogenase of Trypanosomatidae via Structure-Based Drug Design

    E-print Network

    Gelb, Michael

    dehydrogenase (GAPDH). Crystal structures of Trypanosoma brucei, Trypanosoma cruzi, Leishmania mexicana with respect to available drug treatment, include Chagas' disease (Trypanosoma cruzi)6 and leishmaniasis in the range 2-12 µM for T. brucei, T. cruzi, and L. mexicana GAPDH's, and these compounds did not inhibit

  15. New Kagome metal Sc?Mn?Al?Si? and its gallium-doped analogues: synthesis, crystal structure, and physical properties.

    PubMed

    He, Hua; Miiller, Wojciech; Aronson, Meigan C

    2014-09-01

    We report the synthesis, crystal structure, and basic properties of the new intermetallic compound Sc3Mn3Al7Si5. The structure of the compound was established by single-crystal X-ray diffraction, and it crystallizes with a hexagonal structure (Sc3Ni11Si4 type) with Mn atoms forming the Kagome nets. The dc magnetic susceptibility measurements reveal a Curie-Weiss moment of ~0.51 ?(B)/Mn; however, no magnetic order is found for temperatures as low as 1.8 K. Electrical resistivity and heat capacity measurements show that this compound is definitively metallic, with a relatively large specific heat Sommerfeld coefficient, indicating strong electronic correlations. Intriguingly, these features have revealed Sc3Mn3Al7Si5 as a possible quantum spin liquid. With chemical and lattice disorder introduced by doping, a spin liquid to spin glass transition is observed in the highest Ga-doped compounds. The roles of the geometrically frustrated structure and Mn-ligand hybridization in the magnetism of the title compounds are also discussed. PMID:25144523

  16. Structure of the key species in the enzymatic oxidation of methane to methanol.

    PubMed

    Banerjee, Rahul; Proshlyakov, Yegor; Lipscomb, John D; Proshlyakov, Denis A

    2015-02-19

    Methane monooxygenase (MMO) catalyses the O2-dependent conversion of methane to methanol in methanotrophic bacteria, thereby preventing the atmospheric egress of approximately one billion tons of this potent greenhouse gas annually. The key reaction cycle intermediate of the soluble form of MMO (sMMO) is termed compound Q (Q). Q contains a unique dinuclear Fe(IV) cluster that reacts with methane to break an exceptionally strong 105 kcal mol(-1) C-H bond and insert one oxygen atom. No other biological oxidant, except that found in the particulate form of MMO, is capable of such catalysis. The structure of Q remains controversial despite numerous spectroscopic, computational and synthetic model studies. A definitive structural assignment can be made from resonance Raman vibrational spectroscopy but, despite efforts over the past two decades, no vibrational spectrum of Q has yet been obtained. Here we report the core structures of Q and the following product complex, compound T, using time-resolved resonance Raman spectroscopy (TR(3)). TR(3) permits fingerprinting of intermediates by their unique vibrational signatures through extended signal averaging for short-lived species. We report unambiguous evidence that Q possesses a bis-?-oxo diamond core structure and show that both bridging oxygens originate from O2. This observation strongly supports a homolytic mechanism for O-O bond cleavage. We also show that T retains a single oxygen atom from O2 as a bridging ligand, while the other oxygen atom is incorporated into the product. Capture of the extreme oxidizing potential of Q is of great contemporary interest for bioremediation and the development of synthetic approaches to methane-based alternative fuels and chemical industry feedstocks. Insight into the formation and reactivity of Q from the structure reported here is an important step towards harnessing this potential. PMID:25607364

  17. eIF2B: recent structural and functional insights into a key regulator of translation.

    PubMed

    Wortham, Noel C; Proud, Christopher G

    2015-12-01

    The eukaryotic translation initiation factor (eIF) eIF2B is a key regulator of mRNA translation, being the guanine nt exchange factor (GEF) responsible for the recycling of the heterotrimeric G-protein, eIF2, which is required to allow translation initiation to occur. Unusually for a GEF, eIF2B is a multi-subunit protein, comprising five different subunits termed ? through ? in order of increasing size. eIF2B is subject to tight regulation in the cell and may also serve additional functions. Here we review recent insights into the subunit organization of the mammalian eIF2B complex, gained both from structural studies of the complex and from studies of mutations of eIF2B that result in the neurological disorder leukoencephalopathy with vanishing white matter (VWM). We will also discuss recent data from yeast demonstrating a novel function of the eIF2B complex key for translational regulation. PMID:26614666

  18. Revealing the Mass Loss Structures of Four Key Massive Binaries Using Optical Spectropolarimetry

    NASA Astrophysics Data System (ADS)

    Lomax, Jamie R.

    2015-01-01

    The majority of massive stars are members of binary systems. However, in order to understand their evolutionary pathways, mass and angular momentum loss from these systems needs to be well characterized. Self-consistent explanations for their behavior across many wavelength regimes need to be valid in order to illuminate key evolutionary phases. I present the results of linear spectropolarimetric studies of three key binaries (? Lyrae, V356 Sgr, V444 Cyg, and WR 140) which reveal important geometric information about their circumstellar material. ? Lyrae exhibits a repeatable discrepancy between secondary eclipse in the total and polarized light curves that indicates an accretion hot spot has formed on the edge of the disk in the system. The existence of this hot spot and its relationship to bipolar outflows within the system is important in the understanding of mass transfer dynamics in Roche-lobe overflow binaries. Preliminary work on V356 Sgr suggests the system maybe surrounded by a common envelope. V444 Cyg shows evidence that its shock creates a cone with a large opening angle of missing material around the WN star. This suggests the effects of radiative inhibition or braking, can be significant contributors to the location and shape of the shock within colliding wind binaries. The intrinsic polarization component of WR 140 is likely due to the formation of dust within the system near periastron passages. Continued work on these and additional objects will provide new and important constraints on the mass loss structures within binary systems.

  19. Structures of the hydrolase domain of zebrafish 10-formyltetrahydrofolate dehydrogenase and its complexes reveal a complete set of key residues for hydrolysis and product inhibition

    PubMed Central

    Lin, Chien-Chih; Chuankhayan, Phimonphan; Chang, Wen-Ni; Kao, Tseng-Ting; Guan, Hong-Hsiang; Fun, Hoong-Kun; Nakagawa, Atsushi; Fu, Tzu-Fun; Chen, Chun-Jung

    2015-01-01

    10-Formyltetrahydrofolate dehydrogenase (FDH), which is composed of a small N-terminal domain (Nt-FDH) and a large C-terminal domain, is an abundant folate enzyme in the liver and converts 10-formyltetrahydrofolate (10-FTHF) to tetrahydrofolate (THF) and CO2. Nt-FDH alone possesses a hydrolase activity, which converts 10-FTHF to THF and formate in the presence of ?-mercaptoethanol. To elucidate the catalytic mechanism of Nt-FDH, crystal structures of apo-form zNt-FDH from zebrafish and its complexes with the substrate analogue 10-formyl-5,8-dideazafolate (10-FDDF) and with the products THF and formate have been determined. The structures reveal that the conformations of three loops (residues 86–90, 135–143 and 200–203) are altered upon ligand (10-FDDF or THF) binding in the active site. The orientations and geometries of key residues, including Phe89, His106, Arg114, Asp142 and Tyr200, are adjusted for substrate binding and product release during catalysis. Among them, Tyr200 is especially crucial for product release. An additional potential THF binding site is identified in the cavity between two zNt-FDH molecules, which might contribute to the properties of product inhibition and THF storage reported for FDH. Together with mutagenesis studies and activity assays, the structures of zNt-FDH and its complexes provide a coherent picture of the active site and a potential THF binding site of zNt-FDH along with the substrate and product specificity, lending new insights into the molecular mechanism underlying the enzymatic properties of Nt-FDH. PMID:25849409

  20. Potassium as a key modulator of tropical woody vegetation structure and function

    NASA Astrophysics Data System (ADS)

    Lloyd, Jonathan

    2015-04-01

    Sampling a range of tropical vegetation types across Africa, Australia and South America we find - other things being equal - lower soil and plant potassium concentrations in savanna as opposed to forest species. There is also a trend- similarly observed in cross-continental comparisons, for foliar [K] to increase with declining precipitation. Moreover, when considered in a multivariate context with mean annual precipitation and soil plant available water storage capacity as covariates, soil exchangeable K turns to be an excellent predictor of stand-level canopy areas across vegetation types, providing drastically improved predictions as compared to models considering just precipitation or soil water storage potential alone This underlying basis of an important role for potassium as a modulator of tropical vegetation structure and function will be considered in terms of its role in plant water relations as well as in relation to recent key findings implicating potassium to have an important role in many root-shoot signalling pathways.

  1. An Fe2IVO2 diamond core structure for the key intermediate Q of methane monooxygenase.

    PubMed

    Shu, L; Nesheim, J C; Kauffmann, K; Münck, E; Lipscomb, J D; Que, L

    1997-01-24

    A new paradigm for oxygen activation is required for enzymes such as methane monooxygenase (MMO), for which catalysis depends on a nonheme diiron center instead of the more familiar Fe-porphyrin cofactor. On the basis of precedents from synthetic diiron complexes, a high-valent Fe2(micro-O)2 diamond core has been proposed as the key oxidizing species for MMO and other nonheme diiron enzymes such as ribonucleotide reductase and fatty acid desaturase. The presence of a single short Fe-O bond (1.77 angstroms) per Fe atom and an Fe-Fe distance of 2.46 angstroms in MMO reaction intermediate Q, obtained from extended x-ray absorption fine structure and Mössbauer analysis, provides spectroscopic evidence that the diiron center in Q has an Fe2IVO2 diamond core. PMID:8999792

  2. Planetary habitability: lessons learned from terrestrial analogues

    NASA Astrophysics Data System (ADS)

    Preston, Louisa J.; Dartnell, Lewis R.

    2014-01-01

    Terrestrial analogue studies underpin almost all planetary missions and their use is essential in the exploration of our Solar system and in assessing the habitability of other worlds. Their value relies on the similarity of the analogue to its target, either in terms of their mineralogical or geochemical context, or current physical or chemical environmental conditions. Such analogue sites offer critical ground-truthing for astrobiological studies on the habitability of different environmental parameter sets, the biological mechanisms for survival in extreme environments and the preservation potential and detectability of biosignatures. The 33 analogue sites discussed in this review have been selected on the basis of their congruence to particular extraterrestrial locations. Terrestrial field sites that have been used most often in the literature, as well as some lesser known ones which require greater study, are incorporated to inform on the astrobiological potential of Venus, Mars, Europa, Enceladus and Titan. For example, the possibility of an aerial habitable zone on Venus has been hypothesized based on studies of life at high-altitudes in the terrestrial atmosphere. We also demonstrate why many different terrestrial analogue sites are required to satisfactorily assess the habitability of the changing environmental conditions throughout Martian history, and recommend particular sites for different epochs or potential niches. Finally, habitable zones within the aqueous environments of the icy moons of Europa and Enceladus and potentially in the hydrocarbon lakes of Titan are discussed and suitable analogue sites proposed. It is clear from this review that a number of terrestrial analogue sites can be applied to multiple planetary bodies, thereby increasing their value for astrobiological exploration. For each analogue site considered here, we summarize the pertinent physiochemical environmental features they offer and critically assess the fidelity with which they emulate their intended target locale. We also outline key issues associated with the existing documentation of analogue research and the constraints this has on the efficiency of discoveries in this field. This review thus highlights the need for a global open access database for planetary analogues.

  3. Electronic structure and photoelectron spectra of nickel (II) acetylacetonate and its thio- and amino-substituted analogues

    NASA Astrophysics Data System (ADS)

    Vovna, Vitaliy V.; Korochentsev, Vladimir V.; Komissarov, Aleksandr A.; L'vov, Igor B.; Myshakina, Nataliya S.

    2015-11-01

    Using ultraviolet photoelectron spectroscopy and electron density functional theory (DFT), we investigated the electronic structure of the d8 complex acetylacetonate Ni(a\\scsim a\\scsim)2 and its NH, S and NCH2-substitutes: nickel bis(acetylacetoneiminate) (Ni(acim)2), Ni(Sacac)2 and nickel N,N?-Ethylene-bis(acetylacetoneiminate) (NiEcim), respectively. Based on the spectral regularities and calculated results for these four compounds, we interpreted the PE spectra to approximate the extended Koopmans' theorem IEi = -?i + ?i using the ?i relationship to the molecular orbital type, which differs substantially from earlier published interpretations. We determined the vertical ionization energies for the four pairs of ligand n- and ?-levels and four d-type orbitals for the metal. We further discussed the regularities established both experimentally and theoretically for the influence that substituting S, NH and NCH2- for O exerted on the electronic and spatial structure of the complexes, effective atomic charges and intra-complex coordinate bonds.

  4. Mutational analysis of the Notch2 negative regulatory region identifies key structural elements for mechanical stability

    PubMed Central

    Stephenson, Natalie L.; Avis, Johanna M.

    2015-01-01

    The Notch signalling pathway is fundamental to cell differentiation in developing and self-renewing tissues. Notch is activated upon ligand-induced conformational change of the Notch negative regulatory region (NRR), unmasking a key proteolytic site (S2) and facilitating downstream events. The favoured model requires endocytosis of a tightly bound ligand to transmit force to the NRR region, sufficient to cause a structural change that exposes the S2 site. We have previously shown, using atomic force microscopy and molecular dynamics simulations, that application of force to the N-terminus of the Notch2 NRR facilitates metalloprotease cleavage at an early stage in the unfolding process. Here, mutations are made within the heterodimerization (HD) domain of the NRR that are known to cause constitutive activation of Notch1 whilst having no effect on the chemical stability of Notch2. Comparison of the mechanical stability and simulated forced unfolding of recombinant Notch2 NRR proteins demonstrates a reduced stability following mutation and identifies two critical structural elements of the NRR in its response to force – the linker region between Lin12-Notch repeats LNRA and LNRB and the ?3 helix within the HD domain – both of which mask the S2 cleavage site prior to Notch activation. In two mutated proteins, the LNRC:HD domain interaction is also reduced in stability. The observed changes to mechanical stability following these HD domain mutations highlight key regions of the Notch2 NRR that are important for mechanical, but not chemical, stability. This research could also help determine the fundamental differences in the NRRs of Notch1 and Notch2. PMID:26288744

  5. Crystal Structure of Insulin-Regulated Aminopeptidase with Bound Substrate Analogue Provides Insight on Antigenic Epitope Precursor Recognition and Processing.

    PubMed

    Mpakali, Anastasia; Saridakis, Emmanuel; Harlos, Karl; Zhao, Yuguang; Papakyriakou, Athanasios; Kokkala, Paraskevi; Georgiadis, Dimitris; Stratikos, Efstratios

    2015-09-15

    Aminopeptidases that generate antigenic peptides influence immunodominance and adaptive cytotoxic immune responses. The mechanisms that allow these enzymes to efficiently process a vast number of different long peptide substrates are poorly understood. In this work, we report the structure of insulin-regulated aminopeptidase, an enzyme that prepares antigenic epitopes for cross-presentation in dendritic cells, in complex with an antigenic peptide precursor analog. Insulin-regulated aminopeptidase is found in a semiclosed conformation with an extended internal cavity with limited access to the solvent. The N-terminal moiety of the peptide is located at the active site, positioned optimally for catalysis, whereas the C-terminal moiety of the peptide is stabilized along the extended internal cavity lodged between domains II and IV. Hydrophobic interactions and shape complementarity enhance peptide affinity beyond the catalytic site and support a limited selectivity model for antigenic peptide selection that may underlie the generation of complex immunopeptidomes. PMID:26259583

  6. Water induces a structural conversion and accelerates the oxygenation of carboxylate-bridged non-heme diiron enzyme synthetic analogues.

    PubMed

    Zhao, Min; Song, Datong; Lippard, Stephen J

    2006-08-01

    Recently, we reported the synthesis of a carboxylate-rich non-heme diiron enzyme model compound [Fe2(mu-O2CAr(Tol))4(4-CNPy)2] (1), where (-)O(2)CAr(Tol) is 2,6-di-p-tolylbenzoate and 4-CNPy is 4-cyanopyridine (Yoon, S.; Lippard, S. J. J. Am. Chem. Soc. 2005, 127, 8386-8397). A metal-to-ligand charge-transfer band in the visible region of the optical absorption spectrum involving the nitrogen-donor ligand endowed this complex with a distinctive red color that facilitated analysis of its chemistry. Following this strategy, we prepared and characterized two related isomeric complexes, windmill (3) and paddlewheel (4) species having the formula [Fe2(O2CAr(Tol))4(4-AcPy)2], where 4-AcPy is 4-acetylpyridine. In anhydrous solvents, 1 and 4 adopt paddlewheel structures, but upon the addition of water, they convert to aquated forms, windmill structures having the composition [Fe2(mu-O2CAr(Tol))2(O2CAr(Tol))2(4-RPy)2(H2O)2]. This conversion is favored at low temperature and was studied by NMR spectroscopy. A kinetic analysis of the aquation reaction was undertaken by stopped-flow measurements between 198 and 223 K for both 1 and 4, which revealed a first-order dependence on both the diiron compound and water. The oxygenation rates for the water-containing complexes are much faster than those for the corresponding anhydrous complexes, being 20-fold faster for 4 and 10-fold more rapid for 1. The presence or absence of water had little effect on the activation enthalpies, suggesting that the loss of water may not be necessary prior to dioxygen binding in the transition state. PMID:16878942

  7. Interpretation of Cometary Dust Size, Structure and Composition From Imagery and Analysis of Stardust Foil Craters and Their Laboratory Analogues.

    NASA Astrophysics Data System (ADS)

    Kearsley, A.; Burchell, M.; Graham, G.; Wozniakiewicz, P.; Bridges, J.; Borg, J.; Horz, F.

    2006-12-01

    Passage of the Stardust spacecraft through the coma of comet Wild 2 in 2004 resulted in capture of numerous particles in the low density silica aerogel collection medium, and many impacts onto exposed aluminum foil strips. The abundant craters on the aluminum Al1100 can be interpreted in terms of impacting particle size, density and mass, with some information concerning particle shape, internal structure and chemical composition. The tightly constrained impact velocity (6.1 km s-1 and trajectory (perpendicular to the collection surface) for dust impinging on Stardust provide conditions that can be duplicated in impact simulations by light gas guns using flight-spare aerogel and foil as targets. We can have much greater confidence in the direct comparison of the experiments with Stardust's impact features than is possible for craters formed by hypervelocity impact in low Earth orbit, where individual particle velocities and trajectories are unknown but certainly vary widely, and include much higher speeds. For Stardust foils, we have performed an extensive suite of calibration experiments to determine the crater top-lip diameter dependence on impacting particle dimensions, the role of particle density in creation of recognizable crater shapes, and the modification of particle composition during the impact process for a wide range of minerals that might be found in cometary dust. During the preliminary evaluation phase of Stardust we have used scanning electron microscopy on the aluminum foils to measure the diameters of large numbers of craters for particle size determination, have created three dimensional digital models of crater shapes and depth profiles for density estimation, and have acquired dozens of energy dispersive X-ray maps of crater impact residues, and thousands of analytical spectra to infer particle composition and, in some cases, mineralogy. In this paper we will reveal results for a suite of Stardust craters spanning a size range from sub-micron to sub-millimeter, and will discuss their implications for understanding the size, structure, and composition of Wild 2 dust.

  8. Liquid chromatography coupled to quadrupole-time of flight tandem mass spectrometry based quantitative structure-retention relationships of amino acid analogues derivatized via n-propyl chloroformate mediated reaction.

    PubMed

    Kritikos, Nikolaos; Tsantili-Kakoulidou, Anna; Loukas, Yannis L; Dotsikas, Yannis

    2015-07-17

    In the current study, quantitative structure-retention relationships (QSRR) were constructed based on data obtained by a LC-(ESI)-QTOF-MS/MS method for the determination of amino acid analogues, following their derivatization via chloroformate esters. Molecules were derivatized via n-propyl chloroformate/n-propanol mediated reaction. Derivatives were acquired through a liquid-liquid extraction procedure. Chromatographic separation is based on gradient elution using methanol/water mixtures from a 70/30% composition to an 85/15% final one, maintaining a constant rate of change. The group of examined molecules was diverse, including mainly ?-amino acids, yet also ?- and ?-amino acids, ?-amino acid analogues, decarboxylated and phosphorylated analogues and dipeptides. Projection to latent structures (PLS) method was selected for the formation of QSRRs, resulting in a total of three PLS models with high cross-validated coefficients of determination Q(2)Y. For this reason, molecular structures were previously described through the use of descriptors. Through stratified random sampling procedures, 57 compounds were split to a training set and a test set. Model creation was based on multiple criteria including principal component significance and eigenvalue, variable importance, form of residuals, etc. Validation was based on statistical metrics Rpred(2),QextF2(2),QextF3(2) for the test set and Roy's metrics rm(Av)(2) and rm(?)(2), assessing both predictive stability and internal validity. Based on aforementioned models, simplified equivalent were then created using a multi-linear regression (MLR) method. MLR models were also validated with the same metrics. The suggested models are considered useful for the estimation of retention times of amino acid analogues for a series of applications. PMID:26044385

  9. Stabilization of the potent odorant 2-acetyl-1-pyrroline and structural analogues by complexation with zinc halides.

    PubMed

    Fang, Ming-Chih; Cadwallader, Keith R

    2014-09-01

    2-Acetyl-1-pyrroline (2AP) and the structurally similar compounds 6-acetyl-2,3,4,5-tetrahydropyridine (ATHP, along with its tautomer 6-acetyl-1,2,3,4-tetrahydropyridine), 2-propionyl-1-pyrroline (2PP), and 2-acetyl-2-thiazoline (2A2T) are well-known potent odorants in various food products. However, due to the highly unstable nature of these compounds, especially 2AP and ATHP, they are scarcely used commercially in flavor formulations. A novel and attractive method for the stabilization of these potent odorants in dry powder form is presented. Coordination of 2AP, ATHP, 2PP, and 2A2T to zinc ions (ZnI2, ZnBr2, or ZnCl2) resulted in the formation in high yields of stable crystalline complexes, which upon hydration release the free odorant. Infrared spectroscopy was used to study the coordination complexes. 2AP contains donor atoms, which coordinate (with covalent character) through both the heterocyclic nitrogen and carbonyl oxygen atoms to the zinc ion. This is also the case for ATHP and 2PP, but not for 2A2T, because the sulfur group in 2A2T provides a third possible donor site. Stability studies showed that the 2AP-ZnI2 complex (with 14% loading) maintained >94% retention of 2AP after 3 months of storage at ambient temperature in a dry environment. Meanwhile, the ATHP-ZnI2 complex was similarly stable and retained 89% of the ATHP after 3 months of storage. This stabilization technology may enable the commercial use of this powerful aroma compound as a flavoring agent. PMID:25147956

  10. Effects of Oblique Extension and Inherited Structure Geometry on Transfer Zone Development in Continental Rifts: A 4D Analogue Modeling Approach

    NASA Astrophysics Data System (ADS)

    Zwaan, Frank; Schreurs, Guido

    2015-04-01

    INTRODUCTION Inherited structures in the crust form weak zones along which deformation will focus during rifting. Along-strike connection of rift segments may occur along transfer zones, as observed in East Africa. Previous studies have focused on numerical and analog modeling of transfer zones (e.g. Acocella et al., 1999, Allken et al., 2012). We elaborate upon those by investigating the effects of 1) oblique extension and 2) the geometry of linked and non-linked inherited structures on the development of transfer zones. A further improvement is the use of X-ray Computer Tomography (CT) for detailed internal analysis. METHODS The experimental set-up (see Schreurs & Colleta, 1998) contains two sidewalls with a base of compressed foam and plexiglass bars stacked in between. Decompressing this base results in distributed deformation of the overlying model materials. Deforming the model laterally with a mobile base plate produces the strike-slip components for oblique extension. Divergence velocities are in the order of 5 mm/h, translating to ca. 5 mm/Ma in nature, and 1 cm represents 10 km. A 2 cm thick layer of viscous silicone represents the ductile lower crust and a 2 cm quartz sand layer the brittle upper crust. Inherited structures are created with thin lines of silicon laid down on top of the basal silicone layer. Several models were run in a CT-scanner to reveal the 3D evolution of internal structures with time, hence 4D. RESULTS Localization of deformation along the pre-defined structures works well. The models show that the structural style changes with extension obliquity, from wide rift structures to narrower rifts with internal oblique-slip and finally strike-slip structures. Furthermore, rift offset is an important parameter influencing the occurrence of linkage: increasing rift offset decreases linkage as previously observed by Allken et al. (2012). However, increasing divergence obliquity promotes transfer zone formation, as does the presence of rift-connecting inherited zones, whose strike is at an angle of >15° with respect to the divergence direction. CT-analysis indicates that faulting initiated shortly after the start of the experiments, while structures become only clearly visible at the surface only after 1:30h (4% extension). Rift boundary fault angles tend to decrease from an initial 70° to ca. 55° after 4:00h (10% extension). Further CT-analysis will reveal the 3D evolution of the transform zones in more detail. REFERENCES Acocella, V., Faccenna, C., Funiciello, R., Rossetti, F., 1999. Sand-box modelling of basement-controlled transfer zones in extensional domains. Terra Nova, Vol. 11, No. 4, pp 149-156 Allken, V., Huismans, R. S., Thieulot, C., 2012. Factors controlling the mode of rift interaction in brittle-ductile coupled systems: A 3D numerical study, Geochem. Geophys. Geosyst. Vol. 13, Q05010 Schreurs, G., Colletta, B. (1998) Analogue modelling of faulting in zones of continental transpression and transtension. In: Holdsworth, R. E., Strachan R. A., Dewey, J. F., (eds.) 1998. Continental Transpressional and Transtensional Tectonics. Geological Society, London, Special Publications. No. 135, pp 59-79

  11. Biodegradable analogues of DDT*

    PubMed Central

    Metcalf, Robert L.; Kapoor, Inder P.; Hirwe, Asha S.

    1971-01-01

    Despite the immense utility of DDT for vector control its usefulness is prejudiced by its stability in the environment and by the low rate at which it can be degraded biologically. Metabolic studies in insects, in mice, and in a model ecosystem with several food chains have shown that DDT analogues with substituent groups readily attacked by multifunction oxidases undergo a substantial degree of biological degradation and do not appear to be stored readily in animal tissues or concentrated in food chains. Detailed metabolic pathways have been worked out and it is clear that comparative biochemistry can be used to develop DDT analogues that are adequately persistent yet biodegradable. A number of new DDT analogues have been evaluated for insecticidal activity against flies and mosquitos and for their potential usefulness as safe, persistent, and biodegradable insecticides. PMID:5315354

  12. Discrete analogues of Kakeya problems 

    E-print Network

    Iliopoulou, Marina

    2013-11-28

    This thesis investigates two problems that are discrete analogues of two harmonic analytic problems which lie in the heart of research in the field. More specifically, we consider discrete analogues of the maximal Kakeya ...

  13. Clearance and early hydrolysis of atrial natriuretic factor in vivo. Structural analysis of cleavage sites and design of an analogue that inhibits hormone cleavage.

    PubMed Central

    Condra, C L; Leidy, E A; Bunting, P; Colton, C D; Nutt, R F; Rosenblatt, M; Jacobs, J W

    1988-01-01

    This study examines the clearance and early hydrolysis of atrial natriuretic factor (ANF) in vivo. Radiolabeled ANF was cleared from the circulation of the rat with biphasic kinetics; the majority (90%) of ANF cleared with a t1/2 of 15 s, the remaining peptide was cleared with a t1/2 of 5 min. Microsequence analysis of ANF peptides recovered from the circulation of rats revealed five major degradation products of the intact hormone. The first cleavage occurred between amino acids 12 and 13 of the hormone and would inactivate ANF. Over time, additional fragments of the hormone were generated, including fragments of 6, 7, 21, and 24 amino acids in length. Whole body radioautography of rats injected with [123I]-ANF revealed the kidney as a predominant organ involved in clearance of ANF. Subsequent amino acid sequence analyses of radiolabeled ANF exposed to the kidney in vivo indicated that this organ generated four of the five major hydrolysis products observed in circulation, namely, the 6, 7, 16, and 21 amino acid fragments of the hormone. In an attempt to stabilize ANF in vivo, a synthetic analogue of the hormone was prepared that contained the amino acid analogue, aminoisobutyric acid, substituted at position 13. This analogue completely abolished the in vivo cleavage of ANF at this site. These studies demonstrate the usefulness of a protein chemistry approach in characterizing hormone metabolism in vivo and designing analogues with enhanced in vivo stability to cleavage. Images PMID:2966813

  14. Solanapyrone analogues from a Hawaiian fungicolous fungus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Four new solanayrone analogues (solanapyrones J-M; 1-4) have been isolated from an unidentified fungicolous fungus collected in Hawaii. The structures and relative configurations of these compounds were determined by analysis of ID NMR, 2D NMR, and MS data. Solanapyrone J(1) showed antifungal acti...

  15. Impact melt-bearing breccias of the Mistastin Lake impact structure: A unique planetary analogue for ground-truthing proximal ejecta emplacement

    NASA Astrophysics Data System (ADS)

    Mader, M. M.; Osinski, G. R.

    2013-12-01

    Impact craters are the dominant geological landform on rocky planetary surfaces; however, relationships between specific craters and their ejecta are typically poorly constrained. With limited planetary samples, scientists look to terrestrial craters as analogues. Impact ejecta is defined here as any target material, regardless of its physical state, that is transported beyond the rim of the transient cavity [1]. The original transient cavity reaches its maximum size during the excavation stage of crater formation, before rim collapse begins in the modification stage [2]. In complex craters, during the modification stage, rocks around the periphery of the bowl-shaped transient crater collapse downward and inward to form a series of terraces along the outer margin of the crater structure [3]. Proximal impact ejecta, can therefore be found on the terraces of the modified rim of a complex crater, interior to the final crater rim [1]. Although typically poorly preserved on Earth due to post-impact erosional processes, impact ejecta have been identified in the terraced rim region of the Mistastin Lake impact structure, located in northern Labrador, Canada (55°53'N; 63°18'W) [4]. The Mistastin Lake impact structure is an intermediate-size, complex crater (28 km apparent crater diameter) formed by a meteorite impact ~36 Ma in crystalline target rocks. The original crater has been differentially eroded; however, a terraced rim and distinct central uplift are still observed [5]. The inner portion of the structure is covered by the Mistastin Lake and the surrounding area is locally covered by soil/glacial deposits and vegetation. Locally, allochthonous impactites overlying fractured target rocks are exposed along the lakeshore and along banks of radially cutting streams. They define a consistent stratigraphy, including, from bottom to top: monomict, lithic breccias, allochthonous polymict lithic breccias, and allochthonous impact melt rocks. Mistastin impact breccias range in matrix content, melt-fragment concentration, and contact relationships with adjacent impactites. Initial findings suggest differing origins for impact melt-bearing breccias from a single impact event. Three examples are highlighted: 1) Impact melt-bearing breccias, on an inner terrace, formed in boundary zones where hot impact melt flowed over cooler, ballistically emplaced polymict impact breccias. 2) Locally, a dyke of impact melt-bearing breccia suggests that this unit originated as hot lithic flow that moved laterally along the ground and then intruded as a fracture fill into target rocks. 3) A m-scale lens of melt-bearing breccia within the middle of a thick, 80m impact melt rock unit situated on an inner terrace, suggests that this lens may have originated from the crater floor and been incorporated into the melt pond during emplacement (i.e. movement of the melt from the crater floor to terrace shelf). In summary, the Mistastin Lake impact structure displays a multiple layered ejecta sequence that is consistent with, and requires, a multi-stage ejecta emplacement model as proposed by [1]. References: [1] Osinski et al. (2011) EPSL (310:167-181. [2] Melosh (1989) Oxford Univ. 245 pp. [3] French B. M. (1998) LPI Contribution 954,120pp. [4] Mader et al. (2011) 42nd LPSC, No.1608. [5] Mader et al. (2013) 43rd LPSC, No. 2517.

  16. Lobelane analogues as novel ligands for the vesicular monoamine transporter-2

    PubMed Central

    Zheng, Guangrong; Dwoskin, Linda P.; Deaciuc, Agripina G.; Zhu, Jun; Jones, Marlon D.; Crooks, Peter A.

    2013-01-01

    A series of lobelane analogues has been synthesized and their structure–activity relationships at the vesicular monoamine transporter-2 (VMAT2) have been evaluated. The most potent analogues in this series were the cis-2,6-piperidino analogues, 25b, 27b, 28b, and 30b, with Ki values ranging from 430 to 580 nM. PMID:15911306

  17. The Response of Greek Key Proteins to Changes in Connectivity Depends on the Nature of Their Secondary Structure

    PubMed Central

    Kemplen, Katherine R.; De Sancho, David; Clarke, Jane

    2015-01-01

    What governs the balance between connectivity and topology in regulating the mechanism of protein folding? We use circular permutation to vary the order of the helices in the all-? Greek key protein FADD (Fas-associated death domain) to investigate this question. Unlike all-? Greek key proteins, where changes in the order of secondary structure cause a shift in the folding nucleus, the position of the nucleus in FADD is unchanged, even when permutation reduces the complexity significantly. We suggest that this is because local helical contacts are so dominant that permutation has little effect on the entropic cost of forming the folding nucleus whereas, in all-? Greek key proteins, all interactions in the nucleus are long range. Thus, the type of secondary structure modulates the sensitivity of proteins to changes in connectivity. PMID:25861761

  18. Design and synthesis of novel arctigenin analogues for the amelioration of metabolic disorders.

    PubMed

    Duan, Shudong; Huang, Suling; Gong, Jian; Shen, Yu; Zeng, Limin; Feng, Ying; Ren, Wenming; Leng, Ying; Hu, Youhong

    2015-04-01

    Analogues of the natural product (-)-arctigenin, an activator of adenosine monophosphate activated protein kinase, were prepared in order to evaluate their effects on 2-deoxyglucose uptake in L6 myotubes and possible use in ameliorating metabolic disorders. Racemic arctigenin 2a was found to display a similar uptake enhancement as does (-)-arctigenin. As a result, the SAR study was conducted utilizing racemic compounds. The structure-activity relationship study led to the discovery of key substitution patterns on the lactone motif that govern 2-deoxyglucose uptake activities. The results show that replacement of the para-hydroxyl group of the C-2 benzyl moiety of arctigenin by Cl has a pronounced effect on uptake activity. Specifically, analogue 2p, which contains the p-Cl substituent, stimulates glucose uptake and fatty acid oxidation in L6 myotubes. PMID:25941553

  19. Cells are the small units of living things, and cells have particular structures that underlie their Key concepts

    E-print Network

    Grünbaum, Daniel

    Cells Lab Goal Cells are the small units of living things, and cells have particular structures that underlie their functions. Key concepts 1. All living things are composed of cells 2. Cells are made up of several components that perform different functions 3. Cells can specialize to perform specific tasks

  20. Mobilizing Communities around HIV Prevention for Youth: How Three Coalitions Applied Key Strategies to Bring about Structural Changes

    ERIC Educational Resources Information Center

    Chutuape, Kate S.; Willard, Nancy; Sanchez, Kenia; Straub, Diane M.; Ochoa, Tara N.; Howell, Kourtney; Rivera, Carmen; Ramos, Ibrahim; Ellen, Jonathan M.

    2010-01-01

    Increasingly, HIV prevention efforts must focus on altering features of the social and physical environment to reduce risks associated with HIV acquisition and transmission. Community coalitions provide a vehicle for bringing about sustainable structural changes. This article shares lessons and key strategies regarding how three community…

  1. Quantum Analogue Computing

    E-print Network

    Vivien M. Kendon; Kae Nemoto; William J. Munro

    2010-01-13

    We briefly review what a quantum computer is, what it promises to do for us, and why it is so hard to build one. Among the first applications anticipated to bear fruit is quantum simulation of quantum systems. While most quantum computation is an extension of classical digital computation, quantum simulation differs fundamentally in how the data is encoded in the quantum computer. To perform a quantum simulation, the Hilbert space of the system to be simulated is mapped directly onto the Hilbert space of the (logical) qubits in the quantum computer. This type of direct correspondence is how data is encoded in a classical analogue computer. There is no binary encoding, and increasing precision becomes exponentially costly: an extra bit of precision doubles the size of the computer. This has important consequences for both the precision and error correction requirements of quantum simulation, and significant open questions remain about its practicality. It also means that the quantum version of analogue computers, continuous variable quantum computers (CVQC) becomes an equally efficient architecture for quantum simulation. Lessons from past use of classical analogue computers can help us to build better quantum simulators in future.

  2. Insights into the DNA stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido [2,3-d]pyrimidin-2-one

    PubMed Central

    Magat Juan, Ella Czarina; Shimizu, Satoru; Ma, Xiao; Kurose, Taizo; Haraguchi, Tsuyoshi; Zhang, Fang; Tsunoda, Masaru; Ohkubo, Akihiro; Sekine, Mitsuo; Shibata, Takayuki; Millington, Christopher L.; Williams, David M.; Takénaka, Akio

    2010-01-01

    The incorporation of the bicyclic cytosine analogue 7,8-dihydropyrido[2,3-d]pyrimidin-2-one (X) into DNA duplexes results in a significant enhancement of their stability (3–4?K per modification). To establish the effects of X on the local hydrogen-bonding and base stacking interactions and the overall DNA conformation, and to obtain insights into the correlation between the structure and stability of X-containing DNA duplexes, the crystal structures of [d(CGCGAATT-X-GCG)]2 and [d(CGCGAAT-X-CGCG)]2 have been determined at 1.9–2.9 Å resolutions. In all of the structures, the analogue X base pairs with the purine bases on the opposite strands through Watson–Crick and/or wobble type hydrogen bonds. The additional ring of the X base is stacked on the thymine bases at the 5?-side and overall exhibits greatly enhanced stacking interactions suggesting that this is a major contribution to duplex stabilization. PMID:20554855

  3. Structural biology of the IL-1 superfamily: Key cytokines in the regulation of immune and inflammatory responses

    PubMed Central

    Krumm, Brian; Xiang, Yan; Deng, Junpeng

    2014-01-01

    Interleukin-1 superfamily of cytokines (IL-1, IL-18, IL-33) play key roles in inflammation and regulating immunity. The mechanisms of agonism and antagonism in the IL-1 superfamily have been pursued by structural biologists for nearly 20 years. New insights into these mechanisms were recently provided by the crystal structures of the ternary complexes of IL-1? and its receptors. We will review here the structural biology related to receptor recognition by IL-1 superfamily cytokines and the regulation of its cytokine activities by antagonists. PMID:24677376

  4. On the structure and bonding in the B4O4(+) cluster: a boron oxide analogue of the 3,5-dehydrophenyl cation with ? and ? double aromaticity.

    PubMed

    Ou, Ting; Tian, Wen-Juan; You, Xue-Rui; Wang, Ying-Jin; Wang, Kang; Zhai, Hua-Jin

    2015-11-28

    Boron oxide clusters offer intriguing molecular models for the electron-deficient system, in which the boronyl (BO) group plays a key role and the interplay between the localized BO triple bond and the multicenter electron delocalization dominates the chemical bonding. Here we report the structural, electronic, and bonding properties of the B4O4(+) cationic cluster on the basis of unbiased Coalescence Kick global-minimum searches and first-principles electronic structural calculations at the B3LYP and single-point CCSD(T) levels. The B4O4(+) cluster is shown to possess a Cs (1, (2)A') global minimum. It represents the smallest boron oxide species with a hexagonal boroxol (B3O3) ring as the core, terminated by a boronyl group. Chemical bonding analyses reveal double (? and ?) aromaticity in Cs B4O4(+), which closely mimics that in the 3,5-dehydrophenyl cation C6H3(+) (D3h, (1)A1'), a prototypical molecule with double aromaticity. Alternative D2h (2, (2)B3g) and C2v (3, (2)A1) isomeric structures of B4O4(+) are also analyzed, which are relevant to the global minima of B4O4 neutral and B4O4(-) anion, respectively. These three structural motifs vary drastically in terms of energetics upon changing the charge state, demonstrating an interesting case in which every electron counts. The calculated ionization potentials and electron affinities of the three corresponding neutral isomers are highly uneven, which underlie the conformational changes in the B4O4(+/0/-) series. The current work presents the smallest boron oxide species with a boroxol ring, establishes an analogy between boron oxides and the 3,5-dehydrophenyl cation, and enriches the chemistry of boron oxides and boronyls. PMID:26477331

  5. Laboratory study of cometary analogues

    NASA Astrophysics Data System (ADS)

    Colangeli, L.; Brucato, J.; Mennella, V.; Palumbo, P.

    In situ exploration (e.g., GIOTTO mission) and astronomical observations (e.g., ISO) of comets have provided fundamental information about the structure, chemistry and physical properties of materials present in such primordial bodies of the Solar System. Moreover, it is known that cosmic materials evolve, depending on the efficiency of active processes (e.g., thermal annealing, UV irradiation, ion bombardment, gassolid interactions) in different space environments. Thus, the properties of cometary constituents must be considered in a wider perspective, including cosmic dust formation around cold stars and evolution in the interstellar medium until the formation of proto-planetary nebulae. In this scenario, laboratory experiments provide important hints to clarify the status of cometary compounds. The laboratory work is aimed at both reproducing material properties and at simulating their evolution based on the most effective mechanisms active in space. Several techniques are used to synthesise "analogues" of cometary compounds with controlled chemical and physical characteristics. The study of optical properties, complemented by other analytical techniques, is applied to investigate the products of synthesis in the experiments. The monitoring of the effects produced by processing methods, similar to those active in space, provides information both on the reactivity of materials and on the efficiency of treatments. Such an approach is able to provide quantitative information on chemical and structural modifications produced on organic and refractory materials. The comparison of laboratory results with data coming from space observations and in situ measurements provides a powerful tool to understand the real nature of comets and to place constraints on formation and evolution pathways. The laboratory experiments on analogues gain even more relevance as a sort of training in the future perspective of analysing cometary samples returned to Earth by space missions (e.g., Stardust).

  6. Second-generation fluorescent quadracyclic adenine analogues: environment-responsive probes with enhanced brightness.

    PubMed

    Dumat, Blaise; Bood, Mattias; Wranne, Moa S; Lawson, Christopher P; Larsen, Anders Foller; Preus, Søren; Streling, Jens; Gradén, Henrik; Wellner, Eric; Grøtli, Morten; Wilhelmsson, L Marcus

    2015-03-01

    Fluorescent base analogues comprise a group of increasingly important molecules for the investigation of nucleic acid structure, dynamics, and interactions with other molecules. Herein, we report on the quantum chemical calculation aided design, synthesis, and characterization of four new putative quadracyclic adenine analogues. The compounds were efficiently synthesized from a common intermediate through a two-step pathway with the Suzuki-Miyaura coupling as the key step. Two of the compounds, qAN1 and qAN4, display brightnesses (??F) of 1700 and 2300, respectively, in water and behave as wavelength-ratiometric pH probes under acidic conditions. The other two, qAN2 and qAN3, display lower brightnesses but exhibit polarity-sensitive dual-band emissions that could prove useful to investigate DNA structural changes induced by DNA-protein or -drug interactions. The four qANs are very promising microenvironment-sensitive fluorescent adenine analogues that display considerable brightness for such compounds. PMID:25641628

  7. Protective activity of (1S,2E,4R,6R,7E,11E)-2,7,11-cembratriene-4,6-diol analogues against diisopropylfluorophosphate neurotoxicity: preliminary structure-activity relationship and pharmacophore modeling.

    PubMed

    Eterovi?, Vesna A; Del Valle-Rodriguez, Angelie; Pérez, Dinely; Carrasco, Marimée; Khanfar, Mohammad A; El Sayed, Khalid A; Ferchmin, Pedro A

    2013-08-01

    Diisopropylfluorophosphate (DFP) is an organophosphorous insecticide used as a surrogate for the more toxic chemical warfare nerve agent sarin. DFP produces neurotoxicity in vivo and irreversibly decreases the area of population spikes recorded from the CA1 region of acute hippocampal slices. (1S,2E,4R,6R,7E,11E)-2,7,11-Cembratriene-4,6-diol (1) is a neuroprotective natural cembranoid that reverses DFP-induced damage both in vivo and in the hippocampal slice. Cembranoid 1 acts by noncompetitive inhibition of the ?7 nicotinic acetylcholine receptor. This study aims at establishing a preliminary structure-activity relationship to define the neuroprotective cembranoid pharmacophores using the hippocampal slice assay and pharmacophore modeling. Fourteen natural, semisynthetic, or biocatalytic cembranoid analogues 2-15 related to 1 were tested for their capacity to protect the population spikes from DFP-induced damage and intrinsic toxicity. Twelve cembranoids caused significant reversal of DFP toxicity; only 3 active analogues displayed minor intrinsic toxicity at 10 ?M. The C-4 epimer of 1 (2) and the 4-O-methyl ether analogue of 1 (3), were totally devoid of neuroprotective activity. The results suggested a model for cembranoid binding where the hydrophobic ring surface binds to a hydrophobic (Hbic) patch on the receptor molecule and an electronegative atom (oxygen or sulfur) in proper spatial relationship to the ring surface interacts with an electropositive group in the receptor binding site. A pharmacophore model consisting of 1 hydrogen bond acceptor (HBA), 2 Hbic, and 10 exclusion spheres was established using HipHop-REFINE and supported the above mentioned pharmacophoric hypothesis. PMID:23769165

  8. Protective activity of (1S,2E,4R,6R,7E,11E)-2,7,11-cembratriene-4,6-diol analogues against diisopropylfluorophosphate neurotoxicity: Preliminary structure-activity relationship and pharmacophore modeling

    PubMed Central

    Eterovi?, Vesna A.; Valle-Rodriguez, Angelie Del; Pérez, Dinely; Carrasco, Marimée; Khanfar, Mohammad A.; El Sayed, Khalid A.; Ferchmin, Pedro A.

    2013-01-01

    Diisopropylfluorophosphate (DFP) is an organophosphorous insecticide used as a surrogate for the more toxic chemical warfare nerve agent sarin. DFP produces neurotoxicity in vivo and irreversibly decreases the area of population spikes recorded from the CA1 region of acute hippocampal slices. (1S,2E,4R,6R,7E,11E)-2,7,11-Cembratriene-4,6-diol (1) is a neuroprotective natural cembranoid that reverses DFP-induced damage both in vivo and in the hippocampal slice. Cembranoid 1 acts by noncompetitive inhibition of the ?7 nicotinic acetylcholine receptor. This study aims at establishing a preliminary structure-activity relationship to define the neuroprotective cembranoid pharmacophores using the hippocampal slice assay and pharmacophore modeling. Fourteen natural, semisyntheti or biocatalytic cembranoid analogues 2-15 related to 1 were tested for their capacity to protect the population spikes from DFP-induced damage and intrinsic toxicity. Twelve cembranoids caused significant reversal of DFP toxicity; only 3 active analogues displayed minor intrinsic toxicity at 10 ?M. The C-4 epimer of 1 (2) and the 4-O-methyl ether analogue of 1 (3), were totally devoid of neuroprotective activity. The results suggested a model for cembranoid binding where the hydrophobic ring surface binds to a hydrophobic (Hbic) patch on the receptor molecule and an electronegative atom (oxygen or sulfur) in proper spatial relationship to the ring surface interacts with an electropositive group in the receptor binding site. A pharmacophore model consisting of 1 hydrogen bond acceptor (HBA), 2 Hbic, and 10 exclusion spheres was established using HipHop-REFINE and supported the above mentioned pharmacophoric hypothesis. PMID:23769165

  9. Structure--activity relationship between the in vivo skin sensitizing potency of analogues of phenyl glycidyl ether and the induction of Nrf2-dependent luciferase activity in the KeratinoSens in vitro assay.

    PubMed

    Delaine, Tamara; Niklasson, Ida B; Emter, Roger; Luthman, Kristina; Karlberg, Ann-Therese; Natsch, Andreas

    2011-08-15

    Because of regulatory constraints and ethical considerations, research on alternatives to animal testing to predict the skin sensitization potential of novel chemicals has become a high priority. Ideally, these alternatives should not only predict the hazard of novel chemicals but also rate the potency of skin sensitizers. Currently, no alternative method gives reliable potency estimations for a wide range of chemicals in differing structural classes. Performing potency estimations within specific structural classes has thus been proposed. Detailed structure-activity studies for the in vivo sensitization capacity of a series of analogues of phenyl glycidyl ether (PGE) were recently published. These studies are part of an investigation regarding the allergenic activity of epoxy-resin monomers. Here we report data on the same chemicals in the KeratinoSens in vitro assay, which is based on a stable transgenic keratinocyte cell line with a luciferase gene under the control of an antioxidant response element. A strong correlation between the EC3 values in the local lymph node assay (LLNA) and both the luciferase-inducing concentrations and the cytotoxicity in the cell-based assay was established for six analogues of PGE. This correlation allowed the potency in the LLNA of two novel structurally closely related derivatives to be predicted by read-across with errors of 1.4- and 2.6-fold. However, the LLNA EC3 values of two structurally different bifunctional monomers were overpredicted on the basis of this data set, indicating that accurate potency estimation by read-across based on in vitro data might be restricted to a relatively narrow applicability domain. PMID:21751775

  10. Soil Surface Structure: A key factor for the degree of soil water repellency

    NASA Astrophysics Data System (ADS)

    Ahn, S.; Doerr, S. H.; Douglas, P.; Bryant, R.; Hamlett, C.; McHale, G.; Newton, M.; Shirtcliffe, N.

    2012-04-01

    Despite of considerable efforts, the degree of water repellency has not always been fully explained by chemical property of soil (termed hydrophobicity). That might be because the structure of a soil surface was not considered properly, which is another main factor determining the severity of soil water repellency. Surface structure has only recently been considered in soil science, whilst it has been paid attention for several decades in materials science due to its relevance to industrial applications. In this contribution, comparison of critical contact angles measured on different surface structures (made with glass beads, glass shards and beach sands) is presented and the effect of surface structure on manifestation of soil water repellency is discussed in terms of several different variables such as the individual particles shape, and areal and structural factors of the actual surface.

  11. Analogue models of pull-apart basins

    NASA Astrophysics Data System (ADS)

    McClay, Ken; Dooley, Tim

    1995-08-01

    Sandbox analogue models of pull-apart basins that developed in sedimentary strata above releasing steps in underlying basement faults are characterized by rhombic basins that are flat-bottomed box grabens with a subhorizontal synkinematic basin infill. Steep to nearly vertical, sigmoidal oblique-slip and segmented oblique-extensional faults are the dominant bounding structures of the pull-apart basins. Cross-basin, short-cut faults link the offset principal displacement zones that are characterized by flower structure development. The structural architectures of the physical models compare directly in form and dimensions to natural examples of strike-slip pull-apart basins.

  12. Effects of electrospinning and solution casting protocols on the secondary structure of a genetically engineered dragline spider silk analogue investigated via Fourier transform Raman spectroscopy.

    PubMed

    Stephens, Jean S; Fahnestock, Stephen R; Farmer, Robin S; Kiick, Kristi L; Chase, D Bruce; Rabolt, John F

    2005-01-01

    Micrometer and submicrometer diameter fibers of recombinant dragline spider silk analogues, synthesized via protein engineering strategies, have been electrospun from 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) and compared with cast films via Raman spectroscopy in order to assess changes in protein conformation that may result from the electrospinning process. Although the solvent casting process was shown to result in predominantly beta-sheet conformation similar to that observed in the bulk, the electrospinning process causes a major change in conformation from beta-sheet to alpha-helix. A possible mechanism involving electric field-induced stabilization of alpha-helical segments in HFIP solution during the electrospinning process is discussed. PMID:15877359

  13. Structural Insights into Maize Viviparous14, a Key Enzyme in the Biosynthesis of the Phytohormone Abscisic Acid

    SciTech Connect

    Messing, Simon A.J.; Gabelli, Sandra B.; Echeverria, Ignacia; Vogel, Jonathan T.; Guan, Jiahn Chou; Tan, Bao Cai; Klee, Harry J.; McCarty, Donald R.; Amzel, L. Mario

    2011-09-06

    The key regulatory step in the biosynthesis of abscisic acid (ABA), a hormone central to the regulation of several important processes in plants, is the oxidative cleavage of the 11,12 double bond of a 9-cis-epoxycarotenoid. The enzyme viviparous14 (VP14) performs this cleavage in maize (Zea mays), making it a target for the rational design of novel chemical agents and genetic modifications that improve plant behavior through the modulation of ABA levels. The structure of VP14, determined to 3.2-{angstrom} resolution, provides both insight into the determinants of regio- and stereospecificity of this enzyme and suggests a possible mechanism for oxidative cleavage. Furthermore, mutagenesis of the distantly related CCD1 of maize shows how the VP14 structure represents a template for all plant carotenoid cleavage dioxygenases (CCDs). In addition, the structure suggests how VP14 associates with the membrane as a way of gaining access to its membrane soluble substrate.

  14. Structural Insights into Maize Viviparous14, a Key Enzyme in the Biosynthesis of the Phytohormone Abscisic Acid W

    SciTech Connect

    Messing, S.; Gabelli, S; Echeverria, I; Vogel, J; Guan, J; Tan, B; Klee, H; McCarty, D; Amzela, M

    2010-01-01

    The key regulatory step in the biosynthesis of abscisic acid (ABA), a hormone central to the regulation of several important processes in plants, is the oxidative cleavage of the 11,12 double bond of a 9-cis-epoxycarotenoid. The enzyme viviparous14 (VP14) performs this cleavage in maize (Zea mays), making it a target for the rational design of novel chemical agents and genetic modifications that improve plant behavior through the modulation of ABA levels. The structure of VP14, determined to 3.2-{angstrom} resolution, provides both insight into the determinants of regio- and stereospecificity of this enzyme and suggests a possible mechanism for oxidative cleavage. Furthermore, mutagenesis of the distantly related CCD1 of maize shows how the VP14 structure represents a template for all plant carotenoid cleavage dioxygenases (CCDs). In addition, the structure suggests how VP14 associates with the membrane as a way of gaining access to its membrane soluble substrate.

  15. NASA/ESMD Analogue Mission Plans

    NASA Technical Reports Server (NTRS)

    Hoffman, Stephen J.

    2007-01-01

    A viewgraph presentation exploring Earth and its analogues is shown. The topics include: 1) ESMD Goals for the Use of Earth Analogues; 2) Stakeholders Summary; 3) Issues with Current Analogue Situation; 4) Current state of Analogues; 5) External Implementation Plan (Second Step); 6) Recent Progress in Utilizing Analogues; 7) Website Layout Example-Home Page; 8) Website Layout Example-Analogue Site; 9) Website Layout Example-Analogue Mission; 10) Objectives of ARDIG Analog Initiatives; 11) Future Plans; 12) Example: Cold-Trap Sample Return; 13) Example: Site Characterization Matrix; 14) Integrated Analogue Studies-Prerequisites for Human Exploration; and 15) Rating Scale Definitions.

  16. The Milky Way as a Key to Structural Evolution in Galaxies

    E-print Network

    Martin D. Weinberg

    2001-01-16

    Much of our effort in understanding the long-term evolution and morphology of the Milky Way and other galaxies has focused on the equilibrium of its luminous disk. However, the interplay between all components, seen and unseen, is a major cause of observed features and drives evolution. I will review the key underlying dynamics, and in a number of examples, show how this leads to lopsidedness and offset nuclei, may trigger bars and cause warps. Indeed, the Milky Way like most spiral galaxies show exhibit many of these features. In addition, the mechanisms suggest that observed morphology depends on the properties of the galaxy and only weakly on any particular disturbance. Because of this convergence, understanding a galaxy's history will be subtle and require the level of detail that study of the Milky Way can provide.

  17. Millennial Climatic Fluctuations Are Key to the Structure of Last Glacial Ecosystems

    PubMed Central

    Huntley, Brian; Allen, Judy R. M.; Collingham, Yvonne C.; Hickler, Thomas; Lister, Adrian M.; Singarayer, Joy; Stuart, Anthony J.; Sykes, Martin T.; Valdes, Paul J.

    2013-01-01

    Whereas fossil evidence indicates extensive treeless vegetation and diverse grazing megafauna in Europe and northern Asia during the last glacial, experiments combining vegetation models and climate models have to-date simulated widespread persistence of trees. Resolving this conflict is key to understanding both last glacial ecosystems and extinction of most of the mega-herbivores. Using a dynamic vegetation model (DVM) we explored the implications of the differing climatic conditions generated by a general circulation model (GCM) in “normal” and “hosing” experiments. Whilst the former approximate interstadial conditions, the latter, designed to mimic Heinrich Events, approximate stadial conditions. The “hosing” experiments gave simulated European vegetation much closer in composition to that inferred from fossil evidence than did the “normal” experiments. Given the short duration of interstadials, and the rate at which forest cover expanded during the late-glacial and early Holocene, our results demonstrate the importance of millennial variability in determining the character of last glacial ecosystems. PMID:23613985

  18. Quantum analogues of Schubert varieties in the grassmannian.

    E-print Network

    Lenagan, Tom

    study quantum Schubert varieties from the point of view of regularity conditions. More precisely, weQuantum analogues of Schubert varieties in the grassmannian. T.H. Lenagan and L. Rigal Abstract We which of them are AS-Gorenstein. One key fact that enables us to prove these results is that quantum

  19. Effect of chirality and lipophilicity in the functional activity of evodiamine and its analogues at TRPV1 channels

    PubMed Central

    De Petrocellis, Luciano; Schiano Moriello, Aniello; Fontana, Gabriele; Sacchetti, Alessandro; Passarella, Daniele; Appendino, Giovanni; Di Marzo, Vincenzo

    2014-01-01

    Background and Purpose Evodiamine, a racemic quinazolinocarboline alkaloid isolated from the traditional Chinese medicine Evodiae fructus, has been reported to act as an agonist of the transient receptor potential vanilloid type-1 (TRPV1) cation channel both in vitro and in vivo. Evodiamine is structurally different from all known TRPV1 activators, and has significant clinical potential as a thermogenic agent. Nevertheless, the molecular bases for its actions are still poorly understood. Experimental Approach To investigate the structure-activity relationships of evodiamine, the natural racemate was resolved, and a series of 23 synthetic analogues was prepared, using as the end point the intracellular Ca2+ elevation in HEK-293 cells stably overexpressing either the human or the rat recombinant TRPV1. Key Results S-(+) evodiamine was more efficacious and potent than R-(?) evodiamine, and a new potent lead (Evo30) was identified, more potent than the reference TRPV1 agonist, capsaicin. In general, potency and efficacy correlated with the lipophilicity of the analogues. Like other TRPV1 agonists, several synthetic analogues could efficiently desensitize TRPV1 to activation by capsaicin. Conclusions and Implications Evodiamine qualifies as structurally unique lead structure to develop new potent TRPV1 agonists/desensitizers. Linked Articles This article is part of a themed section on the pharmacology of TRP channels. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2014.171.issue-10 PMID:23902373

  20. Unorganized Cognitive Structures of Illiterate as the Key Factor in Rural E-Learning Design

    ERIC Educational Resources Information Center

    Katre, Dinesh S.

    2006-01-01

    Cognitive Structures and Linguistic Sequential Memory or Memory of Serial Order are not very well developed among illiterate people contrary to educated people. It affects the comprehension of abstract ideas and the usability of the system. Therefore the cognitive limitations of illiterate must be considered for instructional design and user…

  1. Key Sites for P2X Receptor Function and Multimerization: Overview of Mutagenesis Studies on a Structural Basis

    PubMed Central

    Hausmann, Ralf; Kless, Achim; Schmalzing, Günther

    2015-01-01

    P2X receptors constitute a seven-member family (P2X1-7) of extracellular ATP-gated cation channels of widespread expression. Because P2X receptors have been implicated in neurological, inflammatory and cardiovascular diseases, they constitute promising drug targets. Since the first P2X cDNA sequences became available in 1994, numerous site-directed mutagenesis studies have been conducted to disclose key sites of P2X receptor function and oligomerization. The publication of the 3-Å crystal structures of the zebrafish P2X4 (zfP2X4) receptor in the homotrimeric apo-closed and ATP-bound open states in 2009 and 2012, respectively, has ushered a new era by allowing for the interpretation of the wealth of molecular data in terms of specific three-dimensional models and by paving the way for designing more-decisive experiments. Thanks to these structures, the last five years have provided invaluable insight into our understanding of the structure and function of the P2X receptor class of ligandgated ion channels. In this review, we provide an overview of mutagenesis studies of the pre- and post-crystal structure eras that identified amino acid residues of key importance for ligand binding, channel gating, ion flow, formation of the pore and the channel gate, and desensitization. In addition, the sites that are involved in the trimerization of P2X receptors are reviewed based on mutagenesis studies and interface contacts that were predicted by the zfP2X4 crystal structures. PMID:25439586

  2. Defining Key Structural Determinants for the Pro-osteogenic Activity of Flavonoids.

    PubMed

    Swioklo, Stephen; Watson, Kimberly A; Williamson, Elizabeth M; Farrimond, Jonathan A; Putnam, Sophie E; Bicknell, Katrina A

    2015-11-25

    Epidemiological studies suggest that fruits and vegetables may play a role in promoting bone growth and preventing age-related bone loss, attributable, at least in part, to phytochemicals such as flavonoids stimulating osteoblastogenesis. Through systematically screening the effect of flavonoids on the osteogenic differentiation of human mesenchymal stem cells in vitro and correlating activity with chemical structure using comparative molecular field analysis, we have successfully identified important structural features that relate to their activity, as well as reliably predicted the activity of compounds with unknown activity. Contour maps emphasized the importance of electronegativity, steric bulk, and a 2-C-3-C double bond at the flavonoid C-ring, as well as overall electropositivity and reduced steric bulk at the flavonoid B-ring. These results support a role for certain flavonoids in promoting osteogenic differentiation, thus their potential for preventing skeletal deterioration, as well as providing a foundation for the lead optimization of novel bone anabolics. PMID:26517554

  3. Key structure-activity relationships in the vanadium phosphorus oxide catalyst system

    SciTech Connect

    Thompson, M.R. ); Ebner, J.R. )

    1990-04-01

    The crystal structure of vanadyl pyrophosphate has been redetermined using single crystals obtained from a near solidified melt of a microcrystalline catalyst sample. Crystals that index as vanadyl pyrophosphate obtained from this melt are variable in color. Crystallographic refinement of the single crystal x-ray diffraction data indicates that structural differences among these materials can be described in terms of crystal defects associated with linear disorder of the vanadium atoms. The importance of the disorder is outlined in the context of its effect on the proposed surface topology parallel to (1,0,0). Models of the surface topology simply and intuitively account for the non-stoichometric surface atomic P/V ratio exhibited by selective catalysts of this phase. These models also point to the possible role of the excess phosphorus in providing site isolation of reactive centers at the surface. 33 refs., 7 figs.

  4. Smad3 deficiency alters key structural elements of the extracellular matrix and mechanotransduction of wound closure

    PubMed Central

    Arany, Praveen R.; Flanders, Kathleen C.; Kobayashi, Tetsu; Kuo, Catherine K.; Stuelten, Christina; Desai, Kartiki V.; Tuan, Rocky; Rennard, Stephen I.; Roberts, Anita B.

    2006-01-01

    The loss of TGF? or its downstream mediator, Smad3, key players in tissue repair, accelerates closure of incisional wounds in mice. In contrast, we now report that excisional ear wounds in mice lacking Smad3 enlarge compared with wild-type controls resulting from changes in extracellular matrix molecules, which alter the mechanotransduction properties of these wounds. Specifically, levels of elastin and glycosoaminoglycans are increased, collagen fibers are more compactly organized, and matrix modulators like integrins, TGF?1, and matrix metalloproteinases (MMPs) are altered both basally and after wounding in Smad3 knockout mice. Mechanical testing of dorsal skin correlates these changes in matrix composition with functional parameters, specifically an increased elastic modulus, suggesting an imbalance of tissue forces. We propose that the altered mechanical elastic properties translate into a persistent retractile force that is opposed by decreased wound contractile forces contributing to the enlarging ear wound in Smad3 knockout mice. These studies highlight a previously undescribed role for Smad3 in the mechanotransduction of matrix unsupported ear wound closure. PMID:16754864

  5. New materials for analogue experiments: Preliminary tests of magnetorheological fluids

    NASA Astrophysics Data System (ADS)

    Cavozzi, C.; Storti, F.; Nestola, Y.; Salvi, F.; Davoli, G.

    2014-09-01

    New materials and related apparatuses are welcome to advance analogue modelling techniques. In this contribution, we report on a first attempt to use magnetorheological (MR) fluids as analogue materials for simulating the mechanical behavior of mobile décollement layers that change their mechanical properties during deformation. For this purpose, a specific sandbox was designed to include the possibility of quickly applying and removing a magnetic field below a MR fluid layer, in order to induce an instantaneous change from a frictional to a viscous behavior in the basal décollement material. The simulation of gravitational gliding and sediment progradation above a basal mobile shale layer provided results that compare well with analogue models produced with other experimental techniques, and with natural structures like those developed in the Niger delta region. This pilot study thus encourages further research for optimizing the applicability of MR fluids to the analogue simulation of geological processes.

  6. Longevity and thermo-rheological structure of old lithospheres : key constraints form surface and Moho topography.

    NASA Astrophysics Data System (ADS)

    François, Thomas; Burov, Evgueni

    2014-05-01

    Surface topography and Moho are the most robust observables that have been insufficiently exploited for containing the rheological and thermal structure and hence for understanding the longevity and eventual destruction of cratons and "tectons". Craton longevity has been often explained by their buoyancy and analysed by testing gravitational stability of cratonic mantle "keels" as a function of the hypothesized plate thickness and thermo-rheological structure. Destruction of some cratons (e.g. North China) and data indicating little if no buoyancy of some tectons (e.g., Arabian shield) suggest that buoyancy is not the only factor of their stability, and previous studies show that their mechanical strength is as important as buoyancy. The upper bounds on this strength are provided by flexural studies demonstrating that Te values (equivalent elastic thickness) in cratons are highest in the world and may probably reach 150 km. Yet, the sensitivity of common methods is poor for Te values above 80 km while the lower bounds on the strength and the equivalent elastic thickness of cratons are still matter of debate. How this strength is partitioned between crust and mantle, and which set of rheological parameters pertain, remain major unknowns. We show that smooth low topography and "frozen" heterogeneous crustal structure of cratons represent the missing constraints for understanding of craton longevity. The cratonic crust is characterized by isostatically misbalanced density heterogeneities, suggesting that the lithosphere has to be strong enough to keep them "frozen" through the time without producing major gravitational instabilities and topographic undulations. Hence, to constrain thermo-rheological properties of cratons one should first investigate the stability of their topography and internal structure (constrained from seismic and gravity data). Our thermo-mechanical numerical experiments accounting for free surface boundary condition demonstrate that craton stability cannot be warranted by crustal strength only, and that strong dry olivine mantle rheology and cold thick lithosphere are needed for craton survival. We find fairly robust lower-bound limits on their thermo-rheological structure. In particular, the minimal Te needed for long-term stability of continents (cratons or tectons) is approximately 70 km.

  7. Analogue Missions on Earth, a New Approach to Prepare Future Missions on the Moon

    NASA Astrophysics Data System (ADS)

    Lebeuf, Martin

    Human exploration of the Moon is a target by 2020 with an initial lunar outpost planned in polar regions. Current architectures maintain a capability for sorties to other latitudes for science activities. In the early stages of design of lunar outpost infrastructure and science activity planning, it has been recognized that analogue missions could play a major role in Moon mission design. Analogue missions, as high fidelity simulations of human and robotic surface operations, can help field scientists and engineers develop and test strategies as well as user requirements, as they provide opportunities to groundtruth measurements, and for the team to share understanding of key science needs and key engineering trades. These types of missions also provide direct training in planning science operations, and in team building and communication. The Canadian Space Agency's Exploration Core Program targets the development of technology infrastructure elements in key areas of science, technology and robotics in preparation for its role in the future exploration of the Moon and Mars. Within this Program, Analogue Missions specifically target the operations requirements and lessons learned that will reduce costs and lower the risk of planetary surface missions. Analogue missions are simulations of planetary surface operations that take place at analogue sites on Earth. A terrestrial analogue site resembles in some key way: eg. geomorphologically or geochemically, a surface environment of another planet. An analogue mission can, therefore, be defined as an integrated set of activities that represent (or simulate) entire mission designs or narrowly focus on specific aspects of planned or potential future planetary exploration missions. Within the CSA's Exploration Core Program, Analogue Missions facilitate the maturation of science instruments and mission concepts by integrating ongoing space instrument and technology development programs with science and analogue elements. As well as using analogue missions to meet agency programmatic needs, the Canadian Space Agency encourages scientists and engineers to make use of opportunities presented by analogue missions to further their own research objectives. Specific objectives of Analogue Missions are to (1) foster a multidisciplinary approach to planning, data acquisition, processing and interpretation, calibration of instruments, and telemetry during mission operations; (2) integrate new science with emerging technologies; and (3) develop an expertise on exploration architecture design from projects carried out at terrestrial analogue sites. Within Analogue Missions, teams develop planning tools, use mission-specific software and technology, and communicate results as well as lessons learned during tactical operations. The expertise gained through Analogue Missions will contribute to inform on all aspects of exploration architectures, including planetary mobility requirements and astronaut training.

  8. Limitations and Extensions of the Lock-and-Key Principle: Differences between Gas State, Solution and Solid State Structures

    PubMed Central

    Schneider, Hans-Jörg

    2015-01-01

    The lock-and-key concept is discussed with respect to necessary extensions. Formation of supramolecular complexes depends not only, and often not even primarily on an optimal geometric fit between host and guest. Induced fit and allosteric interactions have long been known as important modifications. Different binding mechanisms, the medium used and pH effects can exert a major influence on the affinity. Stereoelectronic effects due to lone pair orientation can lead to variation of binding constants by orders of magnitude. Hydrophobic interactions due to high-energy water inside cavities modify the mechanical lock-and-key picture. That optimal affinities are observed if the cavity is only partially filled by the ligand can be in conflict with the lock-and-key principle. In crystals other forces than those between host and guest often dominate, leading to differences between solid state and solution structures. This is exemplified in particular with calixarene complexes, which by X-ray analysis more often than other hosts show guest molecules outside their cavity. In view of this the particular problems with the identification of weak interactions in crystals is discussed. PMID:25815592

  9. Oligonucleotide analogues as modulators of the expression and function of noncoding RNAs (ncRNAs): emerging therapeutics applications.

    PubMed

    Avitabile, Concetta; Cimmino, Amelia; Romanelli, Alessandra

    2014-12-26

    ncRNAs are emerging as key regulators of physiological and pathological processes and therefore have been identified as pharmacological targets and as markers for some diseases. Oligonucleotide analogues represent so far the most widely employed tool for the modulation of the expression of ncRNAs. In this perspective we briefly describe most of the known classes of ncRNAs and then we discuss the design and the applications of oligonucleotide analogues for their targeting. The effects of modifications of the chemical structure of the oligonucleotides on properties such as the binding affinity toward targets and off targets, and the stability to degradation and their biological effects (when known) are discussed. Examples of molecules currently used in clinical trials are also reported. PMID:25280271

  10. The current structure of key actors involved in research on land and soil degradation

    NASA Astrophysics Data System (ADS)

    Escadafal, Richard; Barbero, Celia; Exbrayat, Williams; Marques, Maria Jose; Ruiz, Manuel; El Haddadi, Anass; Akhtar-Schuster, Mariam

    2013-04-01

    Land and soil conservation topics, the final mandate of the United Convention to Combat desertification in drylands, have been diagnosed as still suffering from a lack of guidance. On the contrary, climate change and biodiversity issues -the other two big subjects of the Rio Conventions- seem to progress and may benefit from the advice of international panels. Arguably the weakness of policy measures and hence the application of scientific knowledge by land users and stakeholders could be the expression of an inadequate research organization and a lack of ability to channel their findings. In order to better understand the size, breadth and depth of the scientific communities involved in providing advice to this convention and to other bodies, this study explores the corpus of international publications dealing with land and/or with soils. A database of several thousands records including a significant part of the literature published so far was performed using the Web of Science and other socio-economic databases such as FRANCIS and CAIRN. We extracted hidden information using bibliometric methods and data mining applied to these scientific publications to map the key actors (laboratories, teams, institutions) involved in research on land and on soils. Several filters were applied to the databases in combination with the word "desertification". The further use of Tetralogie software merges databases, analyses similarities and differences between keywords, disciplines, authors and regions and identifies obvious clusters. Assessing their commonalities and differences, the visualisation of links and gaps between scientists, organisations, policymakers and other stakeholders is possible. The interpretation of the 'clouds' of disciplines, keywords, and techniques will enhance the understanding of interconnections between them; ultimately this will allow diagnosing some of their strengths and weaknesses. This may help explain why land and soil degradation remains a serious global problem that lacks sufficient attention. We hope that this study will contribute to clarify the scientific landscape at stake to remediate possible weaknesses in the future.

  11. Peroxynitrous acid induces structural and functional modifications to basement membranes and its key component, laminin.

    PubMed

    Degendorfer, Georg; Chuang, Christine Y; Hammer, Astrid; Malle, Ernst; Davies, Michael J

    2015-12-01

    Basement membranes (BM) are specialized extracellular matrices underlying endothelial cells in the artery wall. Laminin, the most abundant BM glycoprotein, is a structural and biologically active component. Peroxynitrous acid (ONOOH), a potent oxidizing and nitrating agent, is formed in vivo at sites of inflammation from superoxide and nitric oxide radicals. Considerable data supports ONOOH formation in human atherosclerotic lesions, and an involvement of this oxidant in atherosclerosis development and lesion rupture. These effects may be mediated, at least in part, via extracellular matrix damage. In this study we demonstrate co-localization of 3-nitrotyrosine (a product of tyrosine damage by ONOOH) and laminin in human atherosclerotic lesions. ONOOH-induced damage to BM was characterized for isolated murine BM, and purified murine laminin-111. Exposure of laminin-111 to ONOOH resulted in dose-dependent loss of protein tyrosine and tryptophan residues, and formation of 3-nitrotyrosine, 6-nitrotryptophan and the cross-linked material di-tyrosine, as detected by amino acid analysis and Western blotting. These changes were accompanied by protein aggregation and fragmentation as detected by SDS-PAGE. Endothelial cell adhesion to isolated laminin-111 exposed to 10?M or higher levels of ONOOH was significantly decreased (~25%) compared to untreated controls. These data indicate that laminin is oxidized by equimolar or greater concentrations of ONOOH, with this resulting in structural and functional changes. These modifications, and resulting compromised cell-matrix interactions, may contribute to endothelial cell dysfunction, a weakening of the structure of atherosclerotic lesions, and an increased propensity to rupture. PMID:26453917

  12. Surface topography as key constraint on thermo-rheological structure of cratons

    NASA Astrophysics Data System (ADS)

    Francois, T.; Burov, E.; Meyer, B.; Agard, P.

    2012-04-01

    The question why Archean cratons (i.e., the oldest continental plates such as Canada and Australia) survived for billions of years while the rest of the lithosphere has been reworked for several times is both enigmatic and fundamental for plate tectonics. Craton longetivity has been so far explained by their buoyancy and analysed by testing gravitational stability of hardly detectable cratonic mantle "keels" as a function of a hypothesized plate thickness and thermo-rheological structure. Catastrophic destruction of some cratons suggests that buoyancy is not the only factor of their stability, and previous studies show that their mechanical strength is as important as buoyancy. The upper bounds on their strength are provided by flexural studies demonstrating that Te values (equivalent elastic thickness) in cratons are highest in the world and limited to ~ 150 km. Yet, the lower bounds are still matter of debate, as well as the question how the mechanical strength is partitioned between crust and mantle, and which set of rheological parameters represents this behaviour. We show that primary observed cratonic features - flat topography and "frozen" heterogeneous crustal structure - represent the missing constraints for understanding of craton longevity. The cratonic crust is characterized by huge isostatically misbalanced density heterogeneities, suggesting that the lithosphere has to be strong enough to keep them frozen through the time without producing major gravitational instabilities and topographic undulations. Hence, to constrain thermo-rheological properties of cratons one should first investigate the stability of their topography and internal structure. Our thermo-mechanical numerical experiments accounting for free surface boundary condition notably demonstrate that craton stability cannot be warranted by crustal strength, and that strong dry olivine mantle rheology and cold thick lithosphere (1330°C at ~300 km depth) are needed for craton survival, allowing for discarding weaker, "wetter" or hotter alternatives. Hence, without pretending to explain the whole enigma of cratonic survival, nor to reproduce the evolution of any particular craton, we find fairly robust lower-bound limits on their thermo-rheological structure.

  13. Making Connections in Math: Activating a Prior Knowledge Analogue Matters for Learning

    ERIC Educational Resources Information Center

    Sidney, Pooja G.; Alibali, Martha W.

    2015-01-01

    This study investigated analogical transfer of conceptual structure from a prior-knowledge domain to support learning in a new domain of mathematics: division by fractions. Before a procedural lesson on division by fractions, fifth and sixth graders practiced with a surface analogue (other operations on fractions) or a structural analogue (whole…

  14. Hantavirus Gn and Gc Envelope Glycoproteins: Key Structural Units for Virus Cell Entry and Virus Assembly

    PubMed Central

    Cifuentes-Muñoz, Nicolás; Salazar-Quiroz, Natalia; Tischler, Nicole D.

    2014-01-01

    In recent years, ultrastructural studies of viral surface spikes from three different genera within the Bunyaviridae family have revealed a remarkable diversity in their spike organization. Despite this structural heterogeneity, in every case the spikes seem to be composed of heterodimers formed by Gn and Gc envelope glycoproteins. In this review, current knowledge of the Gn and Gc structures and their functions in virus cell entry and exit is summarized. During virus cell entry, the role of Gn and Gc in receptor binding has not yet been determined. Nevertheless, biochemical studies suggest that the subsequent virus-membrane fusion activity is accomplished by Gc. Further, a class II fusion protein conformation has been predicted for Gc of hantaviruses, and novel crystallographic data confirmed such a fold for the Rift Valley fever virus (RVFV) Gc protein. During virus cell exit, the assembly of different viral components seems to be established by interaction of Gn and Gc cytoplasmic tails (CT) with internal viral ribonucleocapsids. Moreover, recent findings show that hantavirus glycoproteins accomplish important roles during virus budding since they self-assemble into virus-like particles. Collectively, these novel insights provide essential information for gaining a more detailed understanding of Gn and Gc functions in the early and late steps of the hantavirus infection cycle. PMID:24755564

  15. Structural insights into key sites of vulnerability on HIV-1 Env and influenza HA.

    PubMed

    Julien, Jean-Philippe; Lee, Peter S; Wilson, Ian A

    2012-11-01

    Human immunodeficiency virus-1 (HIV-1) envelope protein (Env) and influenza hemagglutinin (HA) are the surface glycoproteins responsible for viral entry into host cells, the first step in the virus life cycle necessary to initiate infection. These glycoproteins exhibit a high degree of sequence variability and glycosylation, which are used as strategies to escape host immune responses. Nonetheless, antibodies with broadly neutralizing activity against these viruses have been isolated that have managed to overcome these barriers. Here, we review recent advances in the structural characterization of these antibodies with their viral antigens that defines a few sites of vulnerability on these viral spikes. These broadly neutralizing antibodies tend to focus their recognition on the sites of similar function between the two viruses: the receptor-binding site and membrane fusion machinery. However, some sites of recognition are unique to the virus neutralized, such as the dense shield of oligomannose carbohydrates on HIV-1 Env. These observations are discussed in the context of structure-based design strategies to aid in vaccine design or development of antivirals. PMID:23046130

  16. Study of Kaempferol Glycoside as an Insulin Mimic Reveals Glycon To Be the Key Active Structure

    PubMed Central

    2010-01-01

    Diabetes mellitus is increasing in prevalence with patient numbers rising throughout the world. Current treatments for diabetes mellitus focus on control of blood glucose levels. Certain kinds of flavonoids or their glycosides stimulate cells to improve glucose uptake and lower blood glucose levels. We synthesized kaempferol 3-O-neohesperidoside (1), a naturally occurring substance present in Cyathea phalerata Mart., reported to mimic the action of insulin. Synthetic 1 promoted glucose uptake in the cultured cell line, L6. Further studies to determine the core structure responsible for this activity using synthetic compounds revealed neohesperidose to be the primary pharmacophore. These findings support the use of certain saccharides as a potential novel treatment for diabetes mellitus by replacing or supporting insulin. PMID:24900249

  17. Key structural and functional differences between early and advanced glycation products.

    PubMed

    Paradela-Dobarro, Beatriz; Rodiño-Janeiro, Bruno K; Alonso, Jana; Raposeiras-Roubín, Sergio; González-Peteiro, Mercedes; González-Juanatey, José R; Álvarez, Ezequiel

    2016-01-01

    Most of the studies on advanced glycation end products (AGE) have been carried out with uncharacterized mixtures of AGE, so the observed effects cannot be linked to defined structures. Therefore, we analysed the structural differences between glycated human serum albumin (gHSA), a low glycated protein, and AGE-human serum albumin (AGE-HSA), a high glycated protein, and we compared their effects on endothelial functionality. Specifically, we characterized glycation and composition on both early and advanced stage glycation products of gHSA and AGE-HSA by using the MALDI-TOF-mass spectrometry assay. Furthermore, we studied the effects of both types of glycation products on reactive oxygen species (ROS) production and in the expression of vascular and intercellular cell adhesion molecules (VCAM-1 and ICAM-1) on human umbilical endothelial cells (HUVEC). We also measured the adhesion of peripheral blood mononuclear cells (PBMC) to HUVEC. Low concentrations of gHSA enhanced long-lasting ROS production in HUVEC, whereas lower concentrations of AGE-HSA caused the anticipation of the induced extracellular ROS production. Both gHSA and AGE-HSA up-regulated the expression of VCAM-1 and ICAM-1 at mRNA levels. Nevertheless, only AGE-HSA increased protein levels and enhanced the adhesion of PBMC to HUVEC monolayers. Functional differences were observed between gHSA and AGE-HSA, causing the latter an anticipation of the pro-oxidant effects in comparison to gHSA. Moreover, although both molecules induced genetic up-regulation of adhesion molecules in HUVEC, only the high glycated protein functionally increased mononuclear cell adhesion to endothelial monolayers. These observations could have important clinical consequences in the development of diabetic vascular complications. PMID:26581238

  18. Tertiary Lymphoid Structure-Associated B Cells are Key Players in Anti-Tumor Immunity

    PubMed Central

    Germain, Claire; Gnjatic, Sacha; Dieu-Nosjean, Marie-Caroline

    2015-01-01

    It is now admitted that the immune system plays a major role in tumor control. Besides the existence of tumor-specific T cells and B cells, many studies have demonstrated that high numbers of tumor-infiltrating lymphocytes are associated with good clinical outcome. In addition, not only the density but also the organization of tumor-infiltrating immune cells has been shown to determine patient survival. Indeed, more and more studies describe the development within the tumor microenvironment of tertiary lymphoid structures (TLS), whose presence has a positive impact on tumor prognosis. TLS are transient ectopic lymphoid aggregates displaying the same organization and functionality as canonical secondary lymphoid organs, with T-cell-rich and B-cell-rich areas that are sites for the differentiation of effector and memory T cells and B cells. However, factors favoring the emergence of such structures within tumors still need to be fully characterized. In this review, we survey the state of the art of what is known about the general organization, induction, and functionality of TLS during chronic inflammation, and more especially in cancer, with a particular focus on the B-cell compartment. We detail the role played by TLS B cells in anti-tumor immunity, both as antigen-presenting cells and tumor antigen-specific antibody-secreting cells, and raise the question of the capacity of chemotherapeutic and immunotherapeutic agents to induce the development of TLS within tumors. Finally, we explore how to take advantage of our knowledge on TLS B cells to develop new therapeutic tools. PMID:25755654

  19. Antimicrobial activity of resveratrol analogues.

    PubMed

    Chalal, Malik; Klinguer, Agnès; Echairi, Abdelwahad; Meunier, Philippe; Vervandier-Fasseur, Dominique; Adrian, Marielle

    2014-01-01

    Stilbenes, especially resveratrol and its derivatives, have become famous for their positive effects on a wide range of medical disorders, as indicated by a huge number of published studies. A less investigated area of research is their antimicrobial properties. A series of 13 trans-resveratrol analogues was synthesized via Wittig or Heck reactions, and their antimicrobial activity assessed on two different grapevine pathogens responsible for severe diseases in the vineyard. The entire series, together with resveratrol, was first evaluated on the zoospore mobility and sporulation level of Plasmopara viticola (the oomycete responsible for downy mildew). Stilbenes displayed a spectrum of activity ranging from low to high. Six of them, including the most active ones, were subsequently tested on the development of Botrytis cinerea (fungus responsible for grey mold). The results obtained allowed us to identify the most active stilbenes against both grapevine pathogens, to compare the antimicrobial activity of the evaluated series of stilbenes, and to discuss the relationship between their chemical structure (number and position of methoxy and hydroxy groups) and antimicrobial activity. PMID:24918540

  20. Crystal Structures of E. coli CcmG and its Mutants Reveal Key Roles of the N-Terminal b-Sheet and the

    E-print Network

    Tian, Weidong

    Crystal Structures of E. coli CcmG and its Mutants Reveal Key Roles of the N-Terminal b deletion mutants were studied by circular dichroism. Structural comparison of E. coli CcmG with its trans-Ala144 and displays redox property changes. Structural comparison of E. coli Ccm

  1. Structural and functional conservation of key domains in InsP[subscript 3] and ryanodine receptors

    SciTech Connect

    Seo, Min-Duk; Velamakanni, Saroj; Ishiyama, Noboru; Stathopulos, Peter B.; Rossi, Ana M.; Khan, Samir A.; Dale, Philippa; Li, Congmin; Ames, James B.; Ikura, Mitsuhiko; Taylor, Colin W.

    2012-07-11

    Inositol-1,4,5-trisphosphate receptors (InsP{sub 3}Rs) and ryanodine receptors (RyRs) are tetrameric intracellular Ca{sup 2+} channels. In each of these receptor families, the pore, which is formed by carboxy-terminal transmembrane domains, is regulated by signals that are detected by large cytosolic structures. InsP{sub 3}R gating is initiated by InsP{sub 3} binding to the InsP{sub 3}-binding core (IBC, residues 224-604 of InsP{sub 3}R1) and it requires the suppressor domain (SD, residues 1-223 of InsP{sub 3}R1). Here we present structures of the amino-terminal region (NT, residues 1-604) of rat InsP{sub 3}R1 with (3.6 {angstrom}) and without (3.0 {angstrom}) InsP{sub 3} bound. The arrangement of the three NT domains, SD, IBC-{beta} and IBC-{alpha}, identifies two discrete interfaces ({alpha} and {beta}) between the IBC and SD. Similar interfaces occur between equivalent domains (A, B and C) in RyR1 (ref. 9). The orientations of the three domains when docked into a tetrameric structure of InsP{sub 3}R and of the ABC domains docked into RyR are remarkably similar. The importance of the {alpha}-interface for activation of InsP{sub 3}R and RyR is confirmed by mutagenesis and, for RyR, by disease-causing mutations. Binding of InsP{sub 3} causes partial closure of the clam-like IBC, disrupting the {beta}-interface and pulling the SD towards the IBC. This reorients an exposed SD loop ('hotspot' (HS) loop) that is essential for InsP{sub 3}R activation. The loop is conserved in RyR and includes mutations that are associated with malignant hyperthermia and central core disease. The HS loop interacts with an adjacent NT, suggesting that activation re-arranges inter-subunit interactions. The A domain of RyR functionally replaced the SD in full-length InsP{sub 3}R, and an InsP{sub 3}R in which its C-terminal transmembrane region was replaced by that from RyR1 was gated by InsP{sub 3} and blocked by ryanodine. Activation mechanisms are conserved between InsP{sub 3}R and RyR. Allosteric modulation of two similar domain interfaces within an N-terminal subunit reorients the first domain (SD or A domain), allowing it, through interactions of the second domain of an adjacent subunit (IBC-{beta} or B domain), to gate the pore.

  2. Thermophysical Fluid Dynamics: the Key to the Structures of Fluid Objects

    NASA Astrophysics Data System (ADS)

    Houben, H.

    2013-12-01

    It has become customary to model the hydrodynamics of fluid planets like Jupiter and Saturn by spinning up general circulation models until they reach a statistical steady state. This approach is physically sound, based on the thermodynamic expectation that the system will eventually achieve a state of maximum entropy, but the models have not been specifically designed for this purpose. Over the course of long integrations, numerical artifacts can drive the system to a state that does not correspond to the physically realistic end state. A different formulation of the governing equations promises better results. The equations of motion are recast as scalar conservation laws in which the diabatic and irreversible terms (both entropy-changing) are clearly identified. The balance between these terms defines the steady state of the system analytically, without the need for any temporal integrations. The conservation of mass in this system is trivial. Conservation of angular momentum replaces the zonal momentum equation and determines the zonal wind from a balance between the tidal torque and frictional dissipation. The principle of wave-mean flow non-interaction is preserved. Bernoulli's Theorem replaces the energy equation. The potential temperature structure is determined by the balance between work done against friction and heat transfer by convection and radiation. An equation of state and the traditional momentum equations in the meridional plane are sufficient to complete the model. Based on the assumption that the final state vertical and meridional winds are small compared to the zonal wind (in any case they are impossible to predict ab initio as they are driven by wave flux convergences), these last equations determine the pressure and density (and hence gravity) fields of the basic state. The thermal wind relation (in its most general form with the axial derivative of the zonal wind balancing the baroclinicity) is preserved. The model is not hydrostatic (in the sense used in planetary modeling) and the zonal wind is not constant on cylinders. Rather, the zonal wind falls off more rapidly with depth --- at least as fast as r3. A similar reformulation of the equations of magnetohydrodynamics is possible. It is found that wave-mean flow non-interaction extends to Alfven waves. Bernoulli's Theorem is augmented by the Poynting Theorem. The components of the traditional dynamo equation can be written as conservation laws. Only a single element of the alpha tensor contributes to the generation of axisymmetric magnetic fields and the mean meridional circulation provides a significant feedback, quenching the omega effect and limiting the amplitudes of non-axisymmetric fields. Thus analytic models are available for all the state variables of Jupiter and Saturn. The unknown independent variables are terms in the equation of state, the eddy viscosity and heat transport coefficients, the magnetic resistivity, and the strength of the tidal torques (which are dependent on the vertical structure of the planet's troposphere). By making new measurements of the atmospheric structure and higher order gravitational moments of Jupiter, JUNO has the potential to constrain these unknowns and contribute greatly to our understanding of the interior of that planet.

  3. ?-Synuclein interactions with phospholipid model membranes: Key roles for electrostatic interactions and lipid-bilayer structure.

    PubMed

    Pirc, Katja; Ulrih, Nataša Poklar

    2015-10-01

    ?-Synuclein is a small presynaptic protein that is critically implicated in the onset of Parkinson's disease and other neurodegenerative disorders. It has been assumed that the pathogenesis of ?-synuclein is associated with its aggregation, while for its physiological function, binding of ?-synuclein to the synaptic vesicle membrane appears to be most important. The present study investigated the mechanism of ?-synuclein binding to the lipid membrane. Upon binding to negatively charged small unilamellar vesicles consisting of 1,2-dipalmitoyl-sn-glycero-3-phosphoglycerol or 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol in the liquid-crystalline state, ?-synuclein undergoes conformational transition from its native unfolded form to an ?-helical structure. The positively charged N-terminal part of ?-synuclein is likely to be involved in interactions with the negatively charged lipid surface. ?-Synuclein did not associate with vesicles consisting of the zwitterionic (neutral) lipids 1,2-dipalmitoyl-sn-glycero-3-phosphocholine or 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine. The data obtained by circular dichroism spectroscopy, fluorescence anisotropy measurements, differential scanning calorimetry, and calcein efflux assays indicate that in addition to electrostatic interactions, hydrophobic interactions are important in the association of ?-synuclein with membranes. The mechanism of ?-synuclein binding to lipid membranes is primarily dependent on the surface charge density of the lipid bilayer and the phase state of the lipids. We propose that ?-synuclein has a lipid ordering effect and thermally stabilises vesicles. PMID:26119565

  4. Condensed matter analogues of cosmology

    NASA Astrophysics Data System (ADS)

    Kibble, Tom; Srivastava, Ajit

    2013-10-01

    It is always exciting when developments in one branch of physics turn out to have relevance in a quite different branch. It would be hard to find two branches farther apart in terms of energy scales than early-universe cosmology and low-temperature condensed matter physics. Nevertheless ideas about the formation of topological defects during rapid phase transitions that originated in the context of the very early universe have proved remarkably fruitful when applied to a variety of condensed matter systems. The mathematical frameworks for describing these systems can be very similar. This interconnection has led to a deeper understanding of the phenomena in condensed matter systems utilizing ideas from cosmology. At the same time, one can view these condensed matter analogues as providing, at least in a limited sense, experimental access to the phenomena of the early universe for which no direct probe is possible. As this special issue well illustrates, this remains a dynamic and exciting field. The basic idea is that when a system goes through a rapid symmetry-breaking phase transition from a symmetric phase into one with spontaneously broken symmetry, the order parameter may make different choices in different regions, creating domains that when they meet can trap defects. The scale of those domains, and hence the density of defects, is constrained by the rate at which the system goes through the transition and the speed with which order parameter information propagates. This is what has come to be known as the Kibble-Zurek mechanism. The resultant scaling laws have now been tested in a considerable variety of different systems. The earliest experiments illustrating the analogy between cosmology and condensed matter were in liquid crystals, in particular on the isotropic-to-nematic transition, primarily because it is very easy to induce the phase transition (typically at room temperature) and to image precisely what is going on. This field remains one of the liveliest. A number of new experiments are reported here studying the dynamical evolution of domains and defects. Another phenomenon that played a key early role was the formation of vortices in the normal-to-superfluid transition in liquid helium-3. The complicated nature of the order parameter energy surface gives rise to a variety of intriguing effects. This too is still a vigorous field. Superconductivity is a special case because the symmetry that is broken is a gauge symmetry. This is also true in fundamental particle physics theories of relevance to cosmology, and for that reason experiments on superconductors are of particular interest to cosmologists. The situation in this case is more complicated because there are competing mechanisms of defect formation. Experiments in the field have not proved easy, either to perform or to interpret, but the papers in this collection show that good progress has been made of late. In recent years a new type of system has proved immensely fruitful, namely atomic Bose-Einstein or Fermi-gas condensates. Experiments on condensates with tunable parameters have in general provided broad support for the theory, and have also revealed a wide range of interesting and novel features, with intriguing possible analogues in cosmology (e.g. causal horizons and particle creation). The basic idea of the Kibble-Zurek mechanism has been shown to be relevant in this whole range of systems. But numerous complexities have also emerged, concerned for example with the role of inhomogeneity or the existence of composite defects. The field is still developing rapidly. Acknowledgments Finally, we would like to thank all the authors who have contributed to this issue, and the staff of Journal of Physics: Condensed Matter who have made it possible. Condensed matter analogues of cosmology contents Condensed matter analogues of cosmologyTom Kibble and Ajit Srivastava Symmetry breaking in nematic liquid crystals: analogy with cosmology and magnetismR Repnik, A Ranjkesh, V Simonka, M Ambrozic, Z Bradac and S Kralj Morphogenesis of defects and tactoids

  5. Synthesis and Biological Evaluation of Carbocyclic Analogues of Pachastrissamine

    PubMed Central

    Kwon, Yongseok; Song, Jayoung; Bae, Hoon; Kim, Woo-Jung; Lee, Joo-Youn; Han, Geun-Hee; Lee, Sang Kook; Kim, Sanghee

    2015-01-01

    A series of carbocyclic analogues of naturally-occurring marine sphingolipid pachastrissamine were prepared and biologically evaluated. The analogues were efficiently synthesized via a tandem enyne/diene-ene metathesis reaction as a key step. We found that the analogue 4b exhibited comparable cytotoxicity and more potent inhibitory activity against sphingosine kinases, compared to pachastrissamine. Molecular modeling studies were conducted to provide more detailed insight into the binding mode of 4b in sphingosine kinase. In our docking model, pachastrissamine and 4b were able to effectively bind to the binding pocket of sphingosine kinase 1 as co-crystalized sphingosine. However, 4b showed a hydrophobic interaction with Phe192, which suggests that it contributes to its increased inhibitory activity against sphingosine kinase 1. PMID:25654428

  6. Influence of the Charge State on the Structures and Interactions of Vancomycin Antibiotics with Cell-Wall Analogue Peptides: Experimental and Theoretical Studies

    SciTech Connect

    Yang, Zhibo; Vorpagel, Erich R.; Laskin, Julia

    2009-02-16

    In this study we examined the effect of the charge state on the energetics and dynamics of dissociation of the non-covalent complex between the vancomycin and the cell wall peptide analogue N?,N?-diacetyl-L-Lys-D-Ala-D-Ala (V-Ac2KDADA). The binding energies between the vancomycin and the peptide were obtained from the RRKM modeling of the time- and energy resolved surface-induced dissociation (SID) experiments. Our results demonstrate that the stability of the complex toward fragmentation increases in the order: [V+Ac2KDADA+H]+2 < [V+Ac2KDADA+H]+ < [V+Ac2KDADA-H]-. Dissociation of the singly protonated and singly deprotonated complex is characterized by very large entropy effects indicating substantial increase in the conformational flexibility of the resulting products. The experimental threshold energies of 1.75 eV and 1.34 eV obtained for the [V+Ac2KDADA-H]- and [V+Ac2KDADA+H]+ , respectively, are in excellent agreement with the results of density functional theory (DFT) calculations. The increased stability of the deprotonated complex observed experimentally is attributed to the presence of three charged sites in the deprotonated complex as compared to only one charged site in the singly protonated complex. The low binding energy of 0.93 eV obtained for the doubly protonated complex suggests that this ion is destabilized by Coulomb repulsion between the singly protonated vancomycin and the singly protonated peptide comprising the complex.

  7. Structural studies of cinnamoyl-CoA reductase and cinnamyl-alcohol dehydrogenase, key enzymes of monolignol biosynthesis.

    PubMed

    Pan, Haiyun; Zhou, Rui; Louie, Gordon V; Mühlemann, Joëlle K; Bomati, Erin K; Bowman, Marianne E; Dudareva, Natalia; Dixon, Richard A; Noel, Joseph P; Wang, Xiaoqiang

    2014-09-01

    The enzymes cinnamoyl-CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD) catalyze the two key reduction reactions in the conversion of cinnamic acid derivatives into monolignol building blocks for lignin polymers in plant cell walls. Here, we describe detailed functional and structural analyses of CCRs from Medicago truncatula and Petunia hybrida and of an atypical CAD (CAD2) from M. truncatula. These enzymes are closely related members of the short-chain dehydrogenase/reductase (SDR) superfamily. Our structural studies support a reaction mechanism involving a canonical SDR catalytic triad in both CCR and CAD2 and an important role for an auxiliary cysteine unique to CCR. Site-directed mutants of CAD2 (Phe226Ala and Tyr136Phe) that enlarge the phenolic binding site result in a 4- to 10-fold increase in activity with sinapaldehyde, which in comparison to the smaller coumaraldehyde and coniferaldehyde substrates is disfavored by wild-type CAD2. This finding demonstrates the potential exploitation of rationally engineered forms of CCR and CAD2 for the targeted modification of monolignol composition in transgenic plants. Thermal denaturation measurements and structural comparisons of various liganded and unliganded forms of CCR and CAD2 highlight substantial conformational flexibility of these SDR enzymes, which plays an important role in the establishment of catalytically productive complexes of the enzymes with their NADPH and phenolic substrates. PMID:25217505

  8. Use of lateral structures to monitor and evaluate degradation of key photovoltaic parameters in an organic bulk heterojunction material

    NASA Astrophysics Data System (ADS)

    Danielson, Eric; Ooi, Zi-En; Dodabalapur, Ananth

    2014-12-01

    Charge transport and recombination mechanisms within organic bulk heterojunction (BHJ) systems have been studied using lateral devices to perform in situ potentiometry. We have developed a simplified measurement technique using two types of lateral structures to elicit key charge transport parameters and study the time and process dependence of the carrier mobilities and their ratio. Small geometry lateral devices are used to evaluate the mobility of the slower carrier within the P3HT:PCBM material system. Larger structures with 5 in situ voltage probes are used to construct a simple potential profile of the device channel and accurately determine the carrier mobility ratio. These two measurements enable the calculation of carrier densities and the recombination coefficient. We monitor the change in these parameters as the P3HT:PCBM film degrades in the presence of oxygen and also examine the effect of the solvent additive 1,8-diiodooctane on this degradation mechanism. By exposing ethanol vapor to the BHJ film, we induce traps in the material and monitor the shift in dominant nongeminate recombination mechanism to a more unimolecular type. We are also able to measure the resulting decrease in carrier mobilities due to the presence of dipole-induced traps. Lateral devices are useful material diagnostic structures for studying degradation in BHJ materials.

  9. Ring closing metathesis reactions of ?-methylene-?-lactams: application to the synthesis of a simplified phyllostictine analogue with herbicidal activity.

    PubMed

    Coe, Samuel; Pereira, Nicole; Geden, Joanna V; Clarkson, Guy J; Fox, David J; Napier, Richard M; Neve, Paul; Shipman, Michael

    2015-07-28

    Ring closing metathesis (RCM) reactions of ?-methylene-?-lactams are used to construct strained 11- and 12-membered macrocycles that mimic key structural elements of phyllostictine A. The highest yield and stereoselectivity was achieved making 12-membered macrocycle Z-19 with use of a p-methoxyphenyl group on the lactam nitrogen. Interestingly, substrate concentration had an important influence on the stereochemical course of the reaction. A simplified analogue produced using this approach displays phytotoxic activity against Chlamydomonas reinhardtii suggesting that the ?-methylene-?-lactam subunit is responsible, at least in part, for the herbicidal activity of phyllostictine A. PMID:26081012

  10. Meassessment of crustal structure beneath thick sedimentary basins in the former soviet union: ray-trace velocity model of 1960s analogue dss data from the Dniepr-Donets basin, Ukraine

    NASA Astrophysics Data System (ADS)

    Stephenson, R. A.; Zeit, C. A.

    2003-04-01

    Reduced crustal thickness and concomitant shallowing of Moho depth is generally observed beneath extensional (rift) basins. Numerous DSS (Deep Seismic Sounding) profiles collected across the Dniepr-Donets intracratonic rift basin (DDB; southern East European Craton, Ukraine) show this also to be the case where basin thickness is least (<~10 km). The DDB thickens substantially to the southeast (to a preserved thickness of up to 20 km) and, in this area, the DSS-based velocity models - and numerous published maps of crustal thickness/Moho depth based on these - indicate a deepening Moho and thickening crust. This feature is related to a high velocity lower crustal layer that thickens as the Moho deepens. Similar velocity structures have also been reported elsewhere beneath very thick sedimentary basins in the former Soviet Union (FSU). Such basins have been sometimes characterised as having a "double Moho", with the top of the high velocity layer being referred to as "Moho 1" and its base as "Moho 2". The recent "DOBRE" wide-angle/refraction seismic profile, however, crossing the thickest part of the DDB, tends to contradict the earlier models. The high velocity lower crustal layer, interpreted as a "rift pillow", is clearly indicated but, in contrast to earlier DSS-based models, depth to Moho does not increase beneath the basin depocentre. The acquisition format of the DOBRE data was typical for recent regional crustal studies (station spacing of 1-2 km, shotpoints every ~30 km, and offsets up to about 330 km) whereas the older (analogue) DSS data (station spacing 100 m, shotpoints every 10-25 km), had maximum offsets generally not greater than 150 km. For deeper structure the main target phase was PmP and direct velocity control beneath mid-crustal depths was weak. Here, we present a new velocity model, using RAYINVR, based on travel-times and phase correlations from analogue DSS data on a profile some 100 km north-west of the DOBRE profile. As with DOBRE, these data can be modelled without, and perhaps does not permit, a substantially deepening Moho beneath the basin centre. We will discuss the reasons for this and implications for understanding crustal structure associated with sedimentary basins in the FSU.

  11. Phonon analogue of topological nodal semimetals

    NASA Astrophysics Data System (ADS)

    Po, Hoi Chun; Bahri, Yasaman; Vishwanath, Ashvin

    2015-03-01

    Recently, Kane and Lubensky proposed a mapping between bosonic phonon problems on isostatic lattices to chiral fermion systems based on factorization of the dynamical matrix [Nat. Phys. 10, 39 (2014)]. The existence of topologically protected zero modes in such mechanical problems is related to their presence in the fermionic system and is dictated by a local index theorem. Here we adopt the proposed mapping to construct a two-dimensional mechanical analogue of a fermionic topological nodal semimetal that hosts a robust bulk node in its linearized phonon spectrum. Such topologically protected soft modes with tunable wavevector may be useful in designing mechanical structures with fault-tolerant properties.

  12. Structure of the Trehalose-6-phosphate Phosphatase from Brugia malayi Reveals Key Design Principles for Anthelmintic Drugs

    PubMed Central

    Farelli, Jeremiah D.; Galvin, Brendan D.; Li, Zhiru; Liu, Chunliang; Aono, Miyuki; Garland, Megan; Hallett, Olivia E.; Causey, Thomas B.; Ali-Reynolds, Alana; Saltzberg, Daniel J.; Carlow, Clotilde K. S.; Dunaway-Mariano, Debra; Allen, Karen N.

    2014-01-01

    Parasitic nematodes are responsible for devastating illnesses that plague many of the world's poorest populations indigenous to the tropical areas of developing nations. Among these diseases is lymphatic filariasis, a major cause of permanent and long-term disability. Proteins essential to nematodes that do not have mammalian counterparts represent targets for therapeutic inhibitor discovery. One promising target is trehalose-6-phosphate phosphatase (T6PP) from Brugia malayi. In the model nematode Caenorhabditis elegans, T6PP is essential for survival due to the toxic effect(s) of the accumulation of trehalose 6-phosphate. T6PP has also been shown to be essential in Mycobacterium tuberculosis. We determined the X-ray crystal structure of T6PP from B. malayi. The protein structure revealed a stabilizing N-terminal MIT-like domain and a catalytic C-terminal C2B-type HAD phosphatase fold. Structure-guided mutagenesis, combined with kinetic analyses using a designed competitive inhibitor, trehalose 6-sulfate, identified five residues important for binding and catalysis. This structure-function analysis along with computational mapping provided the basis for the proposed model of the T6PP-trehalose 6-phosphate complex. The model indicates a substrate-binding mode wherein shape complementarity and van der Waals interactions drive recognition. The mode of binding is in sharp contrast to the homolog sucrose-6-phosphate phosphatase where extensive hydrogen-bond interactions are made to the substrate. Together these results suggest that high-affinity inhibitors will be bi-dentate, taking advantage of substrate-like binding to the phosphoryl-binding pocket while simultaneously utilizing non-native binding to the trehalose pocket. The conservation of the key residues that enforce the shape of the substrate pocket in T6PP enzymes suggest that development of broad-range anthelmintic and antibacterial therapeutics employing this platform may be possible. PMID:24992307

  13. Structure of the trehalose-6-phosphate phosphatase from Brugia malayi reveals key design principles for anthelmintic drugs.

    PubMed

    Farelli, Jeremiah D; Galvin, Brendan D; Li, Zhiru; Liu, Chunliang; Aono, Miyuki; Garland, Megan; Hallett, Olivia E; Causey, Thomas B; Ali-Reynolds, Alana; Saltzberg, Daniel J; Carlow, Clotilde K S; Dunaway-Mariano, Debra; Allen, Karen N

    2014-07-01

    Parasitic nematodes are responsible for devastating illnesses that plague many of the world's poorest populations indigenous to the tropical areas of developing nations. Among these diseases is lymphatic filariasis, a major cause of permanent and long-term disability. Proteins essential to nematodes that do not have mammalian counterparts represent targets for therapeutic inhibitor discovery. One promising target is trehalose-6-phosphate phosphatase (T6PP) from Brugia malayi. In the model nematode Caenorhabditis elegans, T6PP is essential for survival due to the toxic effect(s) of the accumulation of trehalose 6-phosphate. T6PP has also been shown to be essential in Mycobacterium tuberculosis. We determined the X-ray crystal structure of T6PP from B. malayi. The protein structure revealed a stabilizing N-terminal MIT-like domain and a catalytic C-terminal C2B-type HAD phosphatase fold. Structure-guided mutagenesis, combined with kinetic analyses using a designed competitive inhibitor, trehalose 6-sulfate, identified five residues important for binding and catalysis. This structure-function analysis along with computational mapping provided the basis for the proposed model of the T6PP-trehalose 6-phosphate complex. The model indicates a substrate-binding mode wherein shape complementarity and van der Waals interactions drive recognition. The mode of binding is in sharp contrast to the homolog sucrose-6-phosphate phosphatase where extensive hydrogen-bond interactions are made to the substrate. Together these results suggest that high-affinity inhibitors will be bi-dentate, taking advantage of substrate-like binding to the phosphoryl-binding pocket while simultaneously utilizing non-native binding to the trehalose pocket. The conservation of the key residues that enforce the shape of the substrate pocket in T6PP enzymes suggest that development of broad-range anthelmintic and antibacterial therapeutics employing this platform may be possible. PMID:24992307

  14. Dimetallaborane analogues of pentaborane.

    PubMed

    Brânzanic, Adrian M V; Lupan, Alexandru; King, R Bruce

    2015-04-28

    The structures of five-vertex dimetallaboranes Cp2M2B3H7 (Cp = ?(5)-C5H5) of the second and third row transition metals, including the experimentally known Cp*2Rh2B3H7 (Cp* = ?(5)-Me5C5), have been investigated by density functional theory. The predicted low-energy structures for Cp2M2B3H7 (M = Rh, Ir) are tetragonal pyramids similar to Cp*2Rh2B3H7 and pentaborane-9 B5H9 and consistent with their 14 Wadean skeletal electrons. Two Cp*2Rh2B3H7 structures with the same central Rh2B3 tetragonal prism are found with energies within ?1 kcal mol(-1) of each other, consistent with the experimental observation of two isomers in solution. The electron-richer Cp2M2B3H7 (M = Pd, Pt) systems having 16 Wadean skeletal electrons are predicted to exhibit more open structures analogous to the known structure for the valence isoelectronic pentaborane-11 B5H11. Trigonal bipyramids with the metal atoms at equatorial vertices are typically found to be low-energy structures for the hypoelectronic Cp2M2B3H7 systems (M = Ru, Os, Re, Mo, W, Ta). In addition, the low-energy Cp2Re2B3H7 structures of the rhenium derivatives Cp2Re2B3H7 provide examples of structures based on a central Re2B2 tetrahedron with the Re-Re edge bridged by the third boron atom. Such structures can be derived from a trigonal bipyramid by the rupture of one of the axial-equatorial edges. PMID:25797320

  15. Structure of a fusion peptide analogue at the air-water interface, determined from surface activity, infrared spectroscopy and scanning force microscopy.

    PubMed

    Taylor, S E; Desbat, B; Blaudez, D; Jacobi, S; Chi, L F; Fuchs, H; Schwarz, G

    2000-09-15

    We have investigated a point mutant of the HIV-1 fusion peptide in a compressed monolayer at the air-water interface. A variety of surface sensitive techniques were applied to study structural features under conditions mimicking the hydrophobic/hydrophilic environment of a biomembrane. Possible partitioning into the aqueous bulk phase and molecular areas were examined by surface activity based mass conservation plots. This shows that the peptide is practically fully accumulated in the interface. Secondary structure and orientation was analyzed by means of polarized infrared reflectivity. Brewster angle microscopy and scanning force microscopy contributed nanostructural images. At low surface pressures the molecules form anti-parallel beta-sheets lying flat on the interface. Upon a moderate increase of the lateral pressure a flat beta-turn structure appears with inter- and intramolecular H-bonds. We also observed aggregates forming fingerprint-like structures with a diameter of approximately double the hydrophobic length of a beta-turn conformation. Beyond approximately 18 mN m(-1) the beta-turns straighten up. The lowest measured tilt angle was 45 degrees at 36 mN m(-1). PMID:11036970

  16. Crystal structures and catalytic mechanism of the C-methyltransferase Coq5 provide insights into a key step of the yeast coenzyme Q synthesis pathway.

    PubMed

    Dai, Ya-Nan; Zhou, Kang; Cao, Dong-Dong; Jiang, Yong-Liang; Meng, Fei; Chi, Chang-Biao; Ren, Yan-Min; Chen, Yuxing; Zhou, Cong-Zhao

    2014-08-01

    Saccharomyces cerevisiae Coq5 is an S-adenosyl methionine (SAM)-dependent methyltransferase (SAM-MTase) that catalyzes the only C-methylation step in the coenzyme Q (CoQ) biosynthesis pathway, in which 2-methoxy-6-polyprenyl-1,4-benzoquinone (DDMQH2) is converted to 2-methoxy-5-methyl-6-polyprenyl-1,4-benzoquinone (DMQH2). Crystal structures of Coq5 were determined in the apo form (Coq5-apo) at 2.2?Å resolution and in the SAM-bound form (Coq5-SAM) at 2.4?Å resolution, representing the first pair of structures for the yeast CoQ biosynthetic enzymes. Coq5 displays a typical class I SAM-MTase structure with two minor variations beyond the core domain, both of which are considered to participate in dimerization and/or substrate recognition. Slight conformational changes at the active-site pocket were observed upon binding of SAM. Structure-based computational simulation using an analogue of DDMQH2 enabled us to identify the binding pocket and entrance tunnel of the substrate. Multiple-sequence alignment showed that the residues contributing to the dimeric interface and the SAM- and DDMQH2-binding sites are highly conserved in Coq5 and homologues from diverse species. A putative catalytic mechanism of Coq5 was proposed in which Arg201 acts as a general base to initiate catalysis with the help of a water molecule. PMID:25084328

  17. Models and Analogues

    ERIC Educational Resources Information Center

    Maloney, Jane; Curtis, Sheila

    2012-01-01

    How do teachers help children understand the difference between the structure of a flower and that of a root? Depending on the time of year this activity is quite easy. Get a bunch of flowers, germinate some chickpeas and raid the kitchen for carrots and beetroots--the children can experience the "real thing". But what if teachers want the…

  18. Structure and function analysis of Escherichia coli inorganic pyrophosphatase: is a hydroxide ion the key to catalysis?

    PubMed

    Salminen, T; Käpylä, J; Heikinheimo, P; Kankare, J; Goldman, A; Heinonen, J; Baykov, A A; Cooperman, B S; Lahti, R

    1995-01-24

    Using site-directed mutagenesis, we have completed replacing all 17 putative active site residues of Escherichia coli inorganic pyrophosphatase (PPase). We report here the production of 11 new variant proteins and their initial characterization, including thermostability, hydrophobicity, oligomeric structure, and specific activity at pH 8. Studies of the pH-rate profiles of 12 variants containing substitutions for potentially essential residues showed that the effect of the mutation was always to increase the pKa of a basic group essential for both substrate binding and catalysis by 1-3 pH units. The D70E variant had the lowest activity at all pHs; the K29R, R43K, and K142R variants also had low kcat/Km values. The principal effect seen in the other variant proteins was higher and sharper pH optima; their pH-independent kcat and kcat/Km values changed at most by a factor of 8. Our results suggest that the most likely candidate for the essential basic group affected by all mutations in the active site is a hydroxide ion stabilized by coordination to the essential Mg2+ ions. Analyzing our results using the structure recently obtained for E. coli PPase [Kankare et al. (1994) Protein Eng. 7, 823-830] led us to identify a group of residues, centered around Asp70 and including Tyr55, Asp65, Asp67, Asp102, and Lys104, that we believe binds the magnesium ions that are critical for the activity, possibly by stabilizing the essential hydroxide. Others, including Lys29, Arg43, and Lys142, are more spread out and more positively charged. They appear to be involved in binding substrate and product. Tyr55 is also a key part of the hydrophobic core of E. coli PPase; when it or residues that interact with it are conservatively mutated, there are changes in the overall structure of the enzyme as assayed by thermostability, hydrophobicity, or oligomeric structure. PMID:7827037

  19. Nucleic acid analogues and the origins of replication

    NASA Astrophysics Data System (ADS)

    Schwartz, Alan W.

    Recent interest in the properties of ``nucleic acid-like structures'' has been stimulated by difficulties encountered in the synthesis and nonenzymatic oligomerization of nucleotides. However, none of the newly proposed monomers has yet been synthesized in a plausibly prebiotic manner. Arguments are presented that analogues based on 8-hydroxymethyladenine and 5-hydroxymethyluracil are promising candidates for primitive nucleotide precursors.

  20. Naturally occurring crystalline phases: analogues for radioactive waste forms

    SciTech Connect

    Haaker, R.F.; Ewing, R.C.

    1981-01-01

    Naturally occurring mineral analogues to crystalline phases that are constituents of crystalline radioactive waste forms provide a basis for comparison by which the long-term stability of these phases may be estimated. The crystal structures and the crystal chemistry of the following natural analogues are presented: baddeleyite, hematite, nepheline; pollucite, scheelite;sodalite, spinel, apatite, monazite, uraninite, hollandite-priderite, perovskite, and zirconolite. For each phase in geochemistry, occurrence, alteration and radiation effects are described. A selected bibliography for each phase is included.

  1. Synthesis and Cytotoxicity of Semisynthetic Withalongolide A Analogues

    PubMed Central

    2013-01-01

    The natural product withaferin A exhibits potent antitumor activity and other diverse pharmacological activities. The recently discovered withalongolide A, a C-19 hydroxylated congener of withaferin A, was recently reported to possess cytotoxic activity against head and neck squamous cell carcinomas. Semisynthetic acetylated analogues of withalongolide A were shown to be considerably more cytotoxic than the parent compound. To further explore the structure–activity relationships, 20 new semisynthetic analogues of withalongolide A were synthesized and evaluated for cytotoxic activity against four different cancer cell lines. A number of derivatives were found to be more potent than the parent compound and withaferin A. PMID:24273633

  2. Synthesis and bioactivity of analogues of the marine antibiotic tropodithietic acid

    PubMed Central

    Rabe, Patrick; Klapschinski, Tim A; Brock, Nelson L; Citron, Christian A; D’Alvise, Paul; Gram, Lone

    2014-01-01

    Summary Tropodithietic acid (TDA) is a structurally unique sulfur-containing antibiotic from the Roseobacter clade bacterium Phaeobacter inhibens DSM 17395 and a few other related species. We have synthesised several structural analogues of TDA and used them in bioactivity tests against Staphylococcus aureus and Vibrio anguillarum for a structure–activity relationship (SAR) study, revealing that the sulfur-free analogue of TDA, tropone-2-carboxylic acid, has an antibiotic activity that is even stronger than the bioactivity of the natural product. The synthesis of this compound and of several analogues is presented and the bioactivity of the synthetic compounds is discussed. PMID:25161739

  3. STRUCTURES OF A KEY INTERACTION PROTEIN FROM THE TRYPANOSOMA BRUCEI EDITOSOME IN COMPLEX WITH SINGLE DOMAIN ANTIBODIES

    PubMed Central

    Wu, Meiting; Park, Young-jun; Pardon, Els; Turley, Stewart; Hayhurst, Andrew; Deng, Junpeng; Steyaert, Jan; Hol, Wim G. J.

    2010-01-01

    Several major global diseases are caused by single-cell parasites called trypanosomatids. These organisms exhibit many unusual features including a unique and essential U-insertion-deletion RNA editing process in their single mitochondrion. Many key RNA editing steps occur in ~ 20S editosomes, which have a core of 12 proteins. Among these, the “interaction protein” KREPA6 performs a central role in maintaining the integrity of the editosome core and also binds to ssRNA. The use of llama single domain antibodies (VHH domains) accelerated crystal growth of KREPA6 from Trypanosoma brucei dramatically. All three structures obtained are heterotetramers with a KREPA6 dimer in the center, and one VHH domain bound to each KREPA6 subunit. Two of the resultant heterotetramers use complementarity determining region 2 (CDR2) and framework residues to form a parallel pair of beta strands with KREPA6 – a mode of interaction not seen before in VHH domain-antigen complexes. The third type of VHH domain binds in a totally different manner to KREPA6. Intriguingly, while KREPA6 forms tetramers in solution adding either one of the three VHH domains results in the formation of a heterotetramer in solution, in perfect agreement with the crystal structures. Biochemical solution studies indicate that the C-terminal tail of KREPA6 is involved in the dimerization of KREPA6 dimers to form tetramers. The implications of these crystallographic and solution studies for possible modes of interaction of KREPA6 with its many binding partners in the editosome are discussed. PMID:20969962

  4. Transfer RNA structural change is a key element in the reassignment of the CUG codon in Candida albicans.

    PubMed Central

    Santos, M A; Perreau, V M; Tuite, M F

    1996-01-01

    The human pathogenic yeast Candida albicans and a number of other Candida species translate the standard leucine CUG codon as serine. This is the latest addition to an increasing number of alterations to the standard genetic code which invalidate the theory that the code is frozen and universal. The unexpected finding that some organisms evolved alternative genetic codes raises two important questions: how have these alternative codes evolved and what evolutionary advantages could they create to allow for their selection? To address these questions in the context of serine CUG translation in C.albicans, we have searched for unique structural features in seryl-tRNA(CAG), which translates the leucine CUG codon as serine, and attempted to reconstruct the early stages of this genetic code switch in the closely related yeast species Saccharomyces cerevisiae. We show that a purine at position 33 (G33) in the C.albicans Ser-tRNA(CAG) anticodon loop, which replaces a conserved pyrimidine found in all other tRNAs, is a key structural element in the reassignment of the CUG codon from leucine to serine in that it decreases the decoding efficiency of the tRNA, thereby allowing cells to survive low level serine CUG translation. Expression of this tRNA in S.cerevisiae induces the stress response which allows cells to acquire thermotolerance. We argue that acquisition of thermotolerance may represent a positive selection for this genetic code change by allowing yeasts to adapt to sudden changes in environmental conditions and therefore colonize new ecological niches. Images PMID:8890179

  5. Synthesis and analgesic activities of endomorphin-2 and its analogues.

    PubMed

    Shi, Zhi-Hao; Wei, Yun-Yang; Wang, Chuan-Jin; Yu, Li

    2007-03-01

    Endomorphin-2 (1; H-Tyr-Pro-Phe-Phe-NH2; EM2) and its novel cyclic asparagine (cycloAsn) analogues, H-Tyr-cAsn(CHPh)-Phe-Phe-NH2 (2) and H-Tyr-cAsn(CHMe2)-Phe-Phe-NH2 (3), were synthesized via liquid-phase synthesis. The structures of the products and intermediates were characterized by IR, 1H-NMR, MS, and HR-MS analyses. The antinociceptive activity of EM2 and its cyclic asparagine analogues were assessed in AcOH-induced abdominal constriction tests in mice with i.p. injection. The results show that the antinociceptive activities of EM2 and its cyclic asparagine analogue 2 were higher than those of aspirine and meperidine. Analogue 2 was observed to be a stronger analgesic with dose-dependence than EM2. The test mice did not show any tendency to be addicted while administrated of analogue 2 repeatedly and regularly. PMID:17372948

  6. Review of Insulin and its Analogues in Diabetes Mellitus

    PubMed Central

    Mane, Krishnappa; Chaluvaraju, KC; Niranjan, MS; Zaranappa, TR; Manjuthej, TR

    2012-01-01

    Diabetes is a metabolic disorder where in human body does not produce or properly uses insulin, a hormone that is required to convert sugar, starches and other food into energy. Diabetes finally leads to more complications and to prevent these complications insulin and its analogues are used. After more than half a century of treating diabetics with animal insulin’s, recombinant DNA technologies and advanced protein chemistry made human insulin preparations available in the early 1980s. As the next step, over the last decade, insulin analogues were constructed by changing the structure of the native protein with the goal of improving the therapeutic properties of it, because the pharmacokinetic characteristics of rapid, intermediate and long-acting preparations of human insulin make it almost impossible to achieve sustained normoglycemia. The first clinically available insulin analogue, lispro, confirmed the hopes by showing that improved glycaemic control can be achieved without an increase in hypoglycaemic events. Two new insulin analogues, insulin glargine and insulin aspart, have recently been approved for clinical use in the United States and several other analogues are being intensively tested. PMID:24826038

  7. Migrastatin analogues target fascin to block tumour metastasis

    SciTech Connect

    Chen, L.; Jakoncic, J.; Yang, S.; Zhang, J.; Huang, X.Y.

    2010-04-15

    Tumour metastasis is the primary cause of death of cancer patients. Development of new therapeutics preventing tumour metastasis is urgently needed. Migrastatin is a natural product secreted by Streptomyces, and synthesized migrastatin analogues such as macroketone are potent inhibitors of metastatic tumour cell migration, invasion and metastasis. Here we show that these migrastatin analogues target the actin-bundling protein fascin to inhibit its activity. X-ray crystal structural studies reveal that migrastatin analogues bind to one of the actin-binding sites on fascin. Our data demonstrate that actin cytoskeletal proteins such as fascin can be explored as new molecular targets for cancer treatment, in a similar manner to the microtubule protein tubulin.

  8. New rubrolide analogues as inhibitors of photosynthesis light reactions.

    PubMed

    Varejão, Jodieh O S; Barbosa, Luiz C A; Ramos, Gabriela Álvarez; Varejão, Eduardo V V; King-Díaz, Beatriz; Lotina-Hennsen, Blas

    2015-04-01

    Natural products called rubrolides have been investigated as a model for the development of new herbicides that act on the photosynthesis apparatus. This study comprises a comprehensive analysis of the photosynthesis inhibitory ability of 27 new structurally diverse rubrolide analogues. In general, the results revealed that the compounds exhibited efficient inhibition of the photosynthetic process, but in some cases low water solubility may be a limiting factor. To elucidate their mode of action, the effects of the compounds on PSII and PSI, as well as their partial reaction on chloroplasts and the chlorophyll a fluorescence transients were measured. Our results showed that some of the most active rubrolide analogues act as a Hill reaction inhibitors at the QB level by interacting with the D1 protein at the reducing side of PSII. All of the active analogues follow Tice's rule of 5, which indicates that these compounds present physicochemical properties suitable for herbicides. PMID:25748644

  9. Structures of yeast peroxisomal ?(3),?(2)-enoyl-CoA isomerase complexed with acyl-CoA substrate analogues: the importance of hydrogen-bond networks for the reactivity of the catalytic base and the oxyanion hole.

    PubMed

    Onwukwe, Goodluck U; Koski, M Kristian; Pihko, Petri; Schmitz, Werner; Wierenga, Rik K

    2015-11-01

    ?(3),?(2)-Enoyl-CoA isomerases (ECIs) catalyze the shift of a double bond from 3Z- or 3E-enoyl-CoA to 2E-enoyl-CoA. ECIs are members of the crotonase superfamily. The crotonase framework is used by many enzymes to catalyze a wide range of reactions on acyl-CoA thioesters. The thioester O atom is bound in a conserved oxyanion hole. Here, the mode of binding of acyl-CoA substrate analogues to peroxisomal Saccharomyces cerevisiae ECI (ScECI2) is described. The best defined part of the bound acyl-CoA molecules is the 3',5'-diphosphate-adenosine moiety, which interacts with residues of loop 1 and loop 2, whereas the pantetheine part is the least well defined. The catalytic base, Glu158, is hydrogen-bonded to the Asn101 side chain and is further hydrogen-bonded to the side chain of Arg100 in the apo structure. Arg100 is completely buried in the apo structure and a conformational change of the Arg100 side chain appears to be important for substrate binding and catalysis. The oxyanion hole is formed by the NH groups of Ala70 (loop 2) and Leu126 (helix 3). The O atoms of the corresponding peptide units, Gly69?O and Gly125?O, are both part of extensive hydrogen-bond networks. These hydrogen-bond networks are a conserved feature of the crotonase oxyanion hole and their importance for catalysis is discussed. PMID:26527136

  10. An evaluation of indirubin analogues as phosphorylase kinase inhibitors.

    PubMed

    Begum, Jaida; Skamnaki, Vassiliki T; Moffatt, Colin; Bischler, Nicolas; Sarrou, Josephine; Skaltsounis, Alexios-Leandros; Leonidas, Demetres D; Oikonomakos, Nikos G; Hayes, Joseph M

    2015-09-01

    Phosphorylase kinase (PhK) has been linked with a number of conditions such as glycogen storage diseases, psoriasis, type 2 diabetes and more recently, cancer (Camus et al., 2012 [6]). However, with few reported structural studies on PhK inhibitors, this hinders a structure based drug design approach. In this study, the inhibitory potential of 38 indirubin analogues have been investigated. 11 of these ligands had IC50 values in the range 0.170-0.360?M, with indirubin-3'-acetoxime (1c) the most potent. 7-Bromoindirubin-3'-oxime (13b), an antitumor compound which induces caspase-independent cell-death (Ribas et al., 2006 [20]) is revealed as a specific inhibitor of PhK (IC50=1.8?M). Binding assay experiments performed using both PhK-holo and PhK-?trnc confirmed the inhibitory effects to arise from binding at the kinase domain (? subunit). High level computations using QM/MM-PBSA binding free energy calculations were in good agreement with experimental binding data, as determined using statistical analysis, and support binding at the ATP-binding site. The value of a QM description for the binding of halogenated ligands exhibiting ?-hole effects is highlighted. A new statistical metric, the 'sum of the modified logarithm of ranks' (SMLR), has been defined which measures performance of a model for both the "early recognition" (ranking earlier/higher) of active compounds and their relative ordering by potency. Through a detailed structure activity relationship analysis considering other kinases (CDK2, CDK5 and GSK-3?/?), 6'(Z) and 7(L) indirubin substitutions have been identified to achieve selective PhK inhibition. The key PhK binding site residues involved can also be targeted using other ligand scaffolds in future work. PMID:26364215

  11. Methane storage capabilities of diamond analogues

    SciTech Connect

    Haranczyk, M; Lin, LC; Lee, K; Martin, RL; Neaton, JB; Smit, B

    2013-01-01

    Methane can be an alternative fuel for vehicular usage provided that new porous materials are developed for its efficient adsorption-based storage. Herein, we search for materials for this application within the family of diamond analogues. We used density functional theory to investigate structures in which tetrahedral C atoms of diamond are separated by-CC-or-BN-groups, as well as ones involving substitution of tetrahedral C atoms with Si and Ge atoms. The adsorptive and diffusive properties of methane are studied using classical molecular simulations. Our results suggest that the all-carbon structure has the highest volumetric methane uptake of 280 VSTP/V at p = 35 bar and T = 298 K. However, it suffers from limited methane diffusion. Alternatively, the considered Si and Ge-containing analogies have fast diffusive properties but their adsorption is lower, ca. 172-179 VSTP/V, at the same conditions.

  12. Engineering of Insulin Receptor Isoform-Selective Insulin Analogues

    PubMed Central

    Glendorf, Tine; Stidsen, Carsten E.; Norrman, Mathias; Nishimura, Erica; Sørensen, Anders R.; Kjeldsen, Thomas

    2011-01-01

    Background The insulin receptor (IR) exists in two isoforms, A and B, and the isoform expression pattern is tissue-specific. The C-terminus of the insulin B chain is important for receptor binding and has been shown to contact the IR just adjacent to the region where the A and B isoforms differ. The aim of this study was to investigate the importance of the C-terminus of the B chain in IR isoform binding in order to explore the possibility of engineering tissue-specific/liver-specific insulin analogues. Methodology/Principal Findings Insulin analogue libraries were constructed by total amino acid scanning mutagenesis. The relative binding affinities for the A and B isoform of the IR were determined by competition assays using scintillation proximity assay technology. Structural information was obtained by X-ray crystallography. Introduction of B25A or B25N mutations resulted in analogues with a 2-fold preference for the B compared to the A isoform, whereas the opposite was observed with a B25Y substitution. An acidic amino acid residue at position B27 caused an additional 2-fold selective increase in affinity for the receptor B isoform for analogues bearing a B25N mutation. Furthermore, the combination of B25H with either B27D or B27E also resulted in B isoform-preferential analogues (2-fold preference) even though the corresponding single mutation analogues displayed no differences in relative isoform binding affinity. Conclusions/Significance We have discovered a new class of IR isoform-selective insulin analogues with 2–4-fold differences in relative binding affinities for either the A or the B isoform of the IR compared to human insulin. Our results demonstrate that a mutation at position B25 alone or in combination with a mutation at position B27 in the insulin molecule confers IR isoform selectivity. Isoform-preferential analogues may provide new opportunities for developing insulin analogues with improved clinical benefits. PMID:21625452

  13. Synthesis and Temperature-Induced Structural Phase and Spin Transitions in Hexadecylboron-Capped Cobalt(II) Hexachloroclathrochelate and Its Diamagnetic Iron(II)-Encapsulating Analogue.

    PubMed

    Vologzhanina, Anna V; Belov, Alexander S; Novikov, Valentin V; Dolganov, Alexander V; Romanenko, Galina V; Ovcharenko, Victor I; Korlyukov, Alexander A; Buzin, Mikhail I; Voloshin, Yan Z

    2015-06-15

    Template condensation of dichloroglyoxime with n-hexadecylboronic acid on the corresponding metal ion as a matrix under vigorous reaction conditions afforded n-hexadecylboron-capped iron and cobalt(II) hexachloroclathrochelates. The complexes obtained were characterized using elemental analysis, MALDI-TOF mass spectrometry, IR, UV-vis, (1)H and (13)C{(1)H} NMR, (57)Fe Mössbauer spectroscopies, SQUID magnetometry, electron paramagnetic resonance, and cyclic voltammetry (CV) and by X-ray crystallography. The multitemperature single-crystal X-ray diffraction, SQUID magnetometry, and differential scanning calorimetry experiments were performed to study the temperature-induced spin-crossover [for the paramagnetic cobalt(II) complex] and the crystal-to-crystal phase transitions (for both of these clathrochelates) in the solid state. Analysis of their crystal packing using the molecular Voronoi polyhedra and the Hirshfeld surfaces reveals the structural rearrangements of the apical long-chain alkyl substituents resulting from such phase transitions being more pronounced for a macrobicyclic cobalt(II) complex. Its fine-crystalline sample undergoes the gradual and fully reversible spin transition centered at approximately 225 K. The density functional theory calculated parameters for an isolated molecule of this cobalt(II) hexachloroclathrochelate in its low- and high-spin states were found to be in excellent agreement with the experimental data and allowed to localize the spin density within a macrobicyclic framework. CV of the cobalt(II) complex in the cathodic range contains one reversible wave assigned to the Co(2+/+) redox couple with the reduced anionic cobalt(I)-containing species stabilized by the electronic effect of six strong electron-withdrawing chlorine substituents. The quasireversible character of the Fe(2+/+) wave suggests that the anionic iron(I)-containing macrobicyclic species undergo substantial structural changes and side chemical reactions after such metal-centered reduction. PMID:26017024

  14. Crystal Structures of Human MdmX (HdmX) in Complex with p53 Peptide Analogues Reveal Surprising Conformational Changes*

    PubMed Central

    Kallen, Joerg; Goepfert, Arnaud; Blechschmidt, Anke; Izaac, Aude; Geiser, Martin; Tavares, Gisele; Ramage, Paul; Furet, Pascal; Masuya, Keiichi; Lisztwan, Joanna

    2009-01-01

    p53 tumor suppressor activity is negatively regulated through binding to the oncogenic proteins Hdm2 and HdmX. The p53 residues Leu26, Trp23, and Phe19 are crucial to mediate these interactions. Inhibiting p53 binding to both Hdm2 and HdmX should be a promising clinical approach to reactivate p53 in the cancer setting, but previous studies have suggested that the discovery of dual Hdm2/HdmX inhibitors will be difficult. We have determined the crystal structures at 1.3 Å of the N-terminal domain of HdmX bound to two p53 peptidomimetics without and with a 6-chlorine substituent on the indole (which binds in the same subpocket as Trp23 of p53). The latter compound is the most potent peptide-based antagonist of the p53-Hdm2 interaction yet to be described. The x-ray structures revealed surprising conformational changes of the binding cleft of HdmX, including an “open conformation” of Tyr99 and unexpected “cross-talk” between the Trp and Leu pockets. Notably, the 6-chloro p53 peptidomimetic bound with high affinity to both HdmX and Hdm2 (Kd values of 36 and 7 nm, respectively). Our results suggest that the development of potent dual inhibitors for HdmX and Hdm2 should be feasible. They also reveal possible conformational states of HdmX, which should lead to a better prediction of its interactions with potential biological partners. PMID:19153082

  15. Vertical structure and physical processes of the Madden-Julian oscillation: Exploring key model physics in climate simulations

    NASA Astrophysics Data System (ADS)

    Jiang, Xianan; Waliser, Duane E.; Xavier, Prince K.; Petch, Jon; Klingaman, Nicholas P.; Woolnough, Steven J.; Guan, Bin; Bellon, Gilles; Crueger, Traute; DeMott, Charlotte; Hannay, Cecile; Lin, Hai; Hu, Wenting; Kim, Daehyun; Lappen, Cara-Lyn; Lu, Mong-Ming; Ma, Hsi-Yen; Miyakawa, Tomoki; Ridout, James A.; Schubert, Siegfried D.; Scinocca, John; Seo, Kyong-Hwan; Shindo, Eiki; Song, Xiaoliang; Stan, Cristiana; Tseng, Wan-Ling; Wang, Wanqiu; Wu, Tongwen; Wu, Xiaoqing; Wyser, Klaus; Zhang, Guang J.; Zhu, Hongyan

    2015-05-01

    Aimed at reducing deficiencies in representing the Madden-Julian oscillation (MJO) in general circulation models (GCMs), a global model evaluation project on vertical structure and physical processes of the MJO was coordinated. In this paper, results from the climate simulation component of this project are reported. It is shown that the MJO remains a great challenge in these latest generation GCMs. The systematic eastward propagation of the MJO is only well simulated in about one fourth of the total participating models. The observed vertical westward tilt with altitude of the MJO is well simulated in good MJO models but not in the poor ones. Damped Kelvin wave responses to the east of convection in the lower troposphere could be responsible for the missing MJO preconditioning process in these poor MJO models. Several process-oriented diagnostics were conducted to discriminate key processes for realistic MJO simulations. While large-scale rainfall partition and low-level mean zonal winds over the Indo-Pacific in a model are not found to be closely associated with its MJO skill, two metrics, including the low-level relative humidity difference between high- and low-rain events and seasonal mean gross moist stability, exhibit statistically significant correlations with the MJO performance. It is further indicated that increased cloud-radiative feedback tends to be associated with reduced amplitude of intraseasonal variability, which is incompatible with the radiative instability theory previously proposed for the MJO. Results in this study confirm that inclusion of air-sea interaction can lead to significant improvement in simulating the MJO.

  16. Synthesis and characterization of sulfur-voided cubanes. Structural analogues for the MoFe(3)S(3) subunit in the nitrogenase cofactor.

    PubMed

    Coucouvanis, Dimitri; Han, Jaehong; Moon, Namdoo

    2002-01-16

    A new class of Mo/Fe/S clusters with the MoFe(3)S(3) core has been synthesized in attempts to model the FeMo-cofactor in nitrogenase. These clusters are obtained in reactions of the (Cl(4)-cat)(2)Mo(2)Fe(6)S(8)(PR(3))(6) [R = Et (I), (n)Pr (II)] clusters with CO. The new clusters include those preliminarily reported: (Cl(4)-cat)MoFe(3)S(3)(PEt(3))(2)(CO)(6) (III), (Cl(4)-cat)(O)MoFe(3)S(3)(PEt(3))(3)(CO)(5) (IV), (Cl(4)-cat)(Pyr)MoFe(3)S(3)(PEt(3))(2)(CO)(6) (VI), and (Cl(4)-cat)(Pyr)MoFe(3)S(3)(P(n)Pr(3))(3)(CO)(4) (VIII). In addition the new (Cl(4)-cat)(O)MoFe(3)S(3)(P(n)Pr(3))(3)(CO)(5) cluster (IVa), the (Cl(4)-cat)(O)MoFe(3)S(3)(PEt(3))(2)(CO)(6)cluster (V), the (Cl(4)-cat)(O)MoFe(3)S(3)(P(n)Pr(3))(2)(CO)(6) cluster (Va), the (Cl(4)-cat)(Pyr)MoFe(3)S(3)(P(n)Pr(3))(2)(CO)(6) cluster (VIa), and the (Cl(4)-cat)(P(n)Pr(3))MoFe(3)S(3)(P(n)Pr(3))(2)(CO)(6) cluster (VII) also are reported. Clusters III-VIII have been structurally and spectroscopically characterized. EPR, zero-field (57)Fe-Mössbauer spectroscopic characterizations, and magnetic susceptibility measurements have been used for a tentative assignment of the electronic and oxidation states of the MoFe(3)S(3) sulfur-voided cuboidal clusters. A structural comparison of the clusters with the MoFe(3)S(3) subunit of the FeMo-cofactor has led to the suggestion that the storage of reducing equivalents into M-M bonds, and their use in the reduction of substrates, may occur with the FeMo-cofactor, which also appears to have M-M bonding. On the basis of this argument, a possible N(2)-binding and reduction mechanism on the FeMoco-cofactor is proposed. PMID:11782173

  17. Direct Observation of Short-Range Structural Coherence During a Charge Transfer Induced Spin Transition in a CoFe Prussian Blue Analogue by Transmission Electron Microscopy.

    PubMed

    Itoi, Miho; Jike, Toyoharu; Nishio-Hamane, Daisuke; Udagawa, Seiichi; Tsuda, Tetsuya; Kuwabata, Susumu; Boukheddaden, Kamel; Andrus, Matthew J; Talham, Daniel R

    2015-11-25

    The local structure within the Co-Fe atomic array of the photoswitchable coordination polymer magnet, K0.3Co[Fe(CN)6]0.77·nH2O, is directly observed during charge transfer induced spin transition (CTIST), a solid-solid phase change, using high-resolution transmission electron microscopy (HRTEM). Along with the low-spin (LS) or thermally quenched high-spin (HS) states normally observed in CTIST solids at low temperature, slow cooling of K0.3Co[Fe(CN)6]0.77·nH2O results in an intermediate phase containing both HS and LS domains with short coherence length. By mapping individual metal-metal distances, the nanometer-scale HS domains are directly visualized within the LS array. Temperature-dependent analyses allow monitoring of HS domain coarsening along the warming branch of the CTIST, providing direct visualization of the elastic process and insight into the mechanism of phase propagation. Normally sensitive to electron beam damage, the low-temperature TEM measurements of the porous coordination polymer are enabled by using appropriate ionic liquids instead of usual conductive thin-film coatings, an approach that should find general utility in related classes of materials. PMID:26510096

  18. Substrate analogues for isoprenoid enzymes

    SciTech Connect

    Stremler, K.E.

    1987-01-01

    Diphosphonate analogues of geranyl diphosphate, resistant to degradation by phosphatases, were found to be alternate substrates for the reaction with farnesyl diphosphate synthetase isolated from avian liver. The difluoromethane analogue was shown to be the better alternate substrate, in agreement with solvolysis results which indicate that the electronegativity of the difluoromethylene unit more closely approximates that of the normal bridging oxygen. The usefulness of the C/sub 10/ difluoro analogue, for detecting low levels of isoprenoid enzymes in the presence of high levels of phosphatase activity, was demonstrated with a cell-free preparation from lemon peel. A series of C/sub 5/ through C/sub 15/ homoallylic and allylic diphosphonates, as well as two 5'-nucleotide diphosphonates, was prepared in high overall yield using the activation-displacement sequence. Radiolabeled samples of several of the allylic diphosphonates were prepared with tritium located at C1. A series of geraniols, stereospecifically deuterated at C1, was prepared. The enantiomeric purities and absolute configurations were determined by derivatization as the mandelate esters for analysis by /sup 1/H NMR. The stereochemistry of the activation-displacement sequence was examined using C1-deuterated substrates.

  19. Studies towards the total synthesis of Disorazole C1 and its analogues 

    E-print Network

    Ralston, Kevin John

    2014-11-27

    Structure–activity relationships (SARs) in the disorazole family have been revealed through the biological testing of natural disorazoles and their synthetic analogues, but little is known about the contribution of the ...

  20. Tris(2,2'-azobispyridine) complexes of copper(II): X-ray structures, reactivities, and the radical nonradical bis(ligand) analogues.

    PubMed

    Maity, Suvendu; Kundu, Suman; Weyhermüller, Thomas; Ghosh, Prasanta

    2015-02-16

    Tris(abpy) complexes of types mer-[Cu(II)(abpy)3][PF6]2 (mer-1(2+)[PF6(–)]2) and ctc-[Cu(II)(abpy)2(bpy)][PF6]2 (ctc-2(2+)[PF6(–)]2) were successfully isolated and characterized by spectra and single-crystal X-ray structure determinations (abpy = 2,2?-azobispyridine; bpy = 2,2?-bipyridine). Reactions of mer-1(2+) and ctc-2(2+) ions with catechol, o-aminophenol, p-phenylenediamine, and diphenylamine (Ph–NH–Ph) in 2:1 molar ratio afford [CuI(abpy)2](+) (3(+)) and corresponding quinone derivatives. The similar reactions of [Cu(II)(bpy)3](2+) and [Cu(II)(phen)3](2+) with these substrates yielding [Cu(I)(bpy)2](+) and [Cu(I)(phen)2](+) imply that these complexes undergo reduction-induced ligand dissociation reactions (phen = 1,10-phenanthroline). The average ?N?N– lengths in mer-1(2+)[PF6(–)]2 and ctc-2(2+)[PF6(–)]2 are 1.248(4), while that in 3(+)[PF6(–)]·2CH2Cl2 is relatively longer, 1.275(2) Å, due to dCu ? ?azo* back bonding. In cyclic voltammetry, mer-1(2+) exhibits one quasi-reversible wave at ?0.42 V due to Cu(II)/Cu(I) and abpy/abpy(•–) couples and two reversible waves at ?0.90 and ?1.28 V due to abpy/abpy(•–) couple, while those of ctc-2(2+) ion appear at ?0.44, ?0.86, and ?1.10 V versus Fc(+)/Fc couple. The anodic 3(2+)/3(+) and the cathodic 3(+)/3 redox waves at +0.33 and ?0.40 V are reversible. The electron paramagnetic resonance spectra and density functional theory (DFT) calculations authenticated the existence of abpy anion radical (abpy(•–)) in 3, which is defined as a hybrid state of [Cu(I)(abpy(0.5•–))(abpy(0.5•–))] and [Cu(II)(abpy(•–))(abpy(•–))] states. 3(2+) ion is a neutral abpy complex of copper(II) of type [Cu(II)(abpy)2](2+). 3 exhibits a near-IR absorption band at 2400–3000 nm because of the intervalence ligand-to-ligand charge transfer, elucidated by time-dependent DFT calculations in CH2Cl2. PMID:25650719

  1. Analogue Sites for Mars Missions - A report from two workshops

    NASA Astrophysics Data System (ADS)

    Hipkin, V.; Voytek, M. A.; Glamoclija, M.

    2014-12-01

    Fieldwork, at terrestrial sites that are analogous in some way to Mars, has a key role in defining questions addressed by Mars missions. For MSL, the question is whether its landing site was habitable, and for Mars 2020, the question is how do we search for and what are signs of life in ancient habitable environments. Implementing these investigations by means of a rover mission on a distant planetary surface has challenges due to a limited set of tools and period of operations. Using this context of planetary missions is important in shaping how analog research can be used to advance planetary science. Following a successful 2010 AGU fall meeting session entitled "Analogue Sites for Mars Missions", two community workshops were held at The Woodlands, TX March 2011 and the Carnegie Institute of Washington in July 2013. These activities represent an ongoing dialogue with the analogue and mission communities. The AGU session solicited presentations of current analogue research relevant to MSL, at which time the landing site selection process was still considering four final sites. The 2011 Woodlands workshop solicited details on representative science questions and analogue sites by means of an abstract template. The output from The Woodlands workshop was an initial metric to assess the utility of analogue sites against specific science questions, as well as recommendations for future activities. The 2013 Carnegie workshop, followed up on some of the recommendations from 2011. Both on-line interactive dialogue and in person discussions targeted broad topics, including 'the advantages and problems of using a great terrestrial analog for field testing', and 'knowing what we currently do about Mars, what would be the best place on the planet to collect the first suite of samples to be returned to Earth? What would be appropriate analog sites on Earth?'. The results and recommendations from both workshops are summarized to publicize and stimulate this ongoing discussion.

  2. Biological evaluation of a novel sorafenib analogue, t-CUPM.

    PubMed

    Wecksler, Aaron T; Hwang, Sung Hee; Liu, Jun-Yan; Wettersten, Hiromi I; Morisseau, Christophe; Wu, Jian; Weiss, Robert H; Hammock, Bruce D

    2015-01-01

    Sorafenib (Nexavar®) is currently the only FDA-approved small molecule targeted therapy for advanced hepatocellular carcinoma. The use of structural analogues and derivatives of sorafenib has enabled the elucidation of critical targets and mechanism(s) of cell death for human cancer lines. We previously performed a structure-activity relationship study on a series of sorafenib analogues designed to investigate the inhibition overlap between the major targets of sorafenib Raf-1 kinase and VEGFR-2, and an enzyme shown to be a potent off-target of sorafenib, soluble epoxide hydrolase. In the current work, we present the biological data on our lead sorafenib analogue, t-CUPM, demonstrating that this analogue retains cytotoxicity similar to sorafenib in various human cancer cell lines and strongly inhibits growth in the NCI-60 cell line panel. Co-treatment with the pan-caspase inhibitor, Z-VAD-FMK, failed to rescue the cell viability responses of both sorafenib and t-CUPM, and immunofluorescence microscopy shows similar mitochondrial depolarization and apoptosis-inducing factor release for both compounds. These data suggest that both compounds induce a similar mechanism of caspase-independent apoptosis in hepatoma cells. In addition, t-CUPM displays anti-proliferative effects comparable to sorafenib as seen by a halt in G0/G1 in cell cycle progression. The structural difference between sorafenib and t-CUPM significantly reduces inhibitory spectrum of kinases by this analogue, and pharmacokinetic characterization demonstrates a 20-fold better oral bioavailability of t-CUPM than sorafenib in mice. Thus, t-CUPM may have the potential to reduce the adverse events observed from the multikinase inhibitory properties and the large dosing regimens of sorafenib. PMID:25413440

  3. Syntheses and biological activities of renin inhibitors containing statine analogues.

    PubMed

    Nishi, T; Saito, F; Nagahori, H; Kataoka, M; Morisawa, Y; Yabe, Y; Sakurai, M; Higashida, S; Shoji, M; Matsushita, Y

    1990-01-01

    Syntheses and biological activities of dipeptide renin inhibitors that contain statine analogues are described. The key steps of the synthetic approach to dipeptide renin inhibitors are the asymmetric synthesis of 2(R)-substituted-3-aminocarbonylpropionic acids and the diastereoselective syntheses of (3S,4S)-statine analogues. These inhibitors (2,14-40) inhibited human renin in the 3-140 nM range. Inhibitor ES 6864 (2) was found to be a highly potent inhibitor of human renin (IC50: 4.6 x 10(-9) M) and showed high enzyme specificity. Oral administration of ES 6864 at 3 mg/kg to conscious, sodium-depleted marmosets inhibited plasma renin activity (PRA) more than 80% after 1 h. PMID:2110866

  4. POLYCHLORINATED BIPHENYLS AS HORMONALLY ACTIVE STRUCTURAL ANALOGUES

    EPA Science Inventory

    Among the environmental chemicals believed to have the potential to disrupt the endocrine systems of animals including humans, the polychlorinated biphenyls are a chemical class of considerable concern. Possible mechanisms by which these chemicals may interfere with endocrine fun...

  5. Template polymerization of nucleotide analogues

    NASA Technical Reports Server (NTRS)

    Orgel, L. E.

    1991-01-01

    Recent work on the template-directed reactions of the natural D-nucleotides has made it clear that l-nucleotides and nucleotide-like derivatives of other sugars would strongly inhibit the formation of long oligonucleotides. Consequently, attention is focusing on molecules simpler than nucleotides that might have acted as monomers of an information transfer system. We have begun a general exploration of the template directed reactions of diverse peptide analogues. I will present work by Dr. Taifeng Wu on oxidative oligomerization of phosphorothioates and of Dr. Mary Tohidi on the cyclic polymerization of nucleoside and related cyclic pyrophosphates.

  6. Trehalose Analogues: Latest Insights in Properties and Biocatalytic Production.

    PubMed

    Walmagh, Maarten; Zhao, Renfei; Desmet, Tom

    2015-01-01

    Trehalose (?-D-glucopyranosyl ?-D-glucopyranoside) is a non-reducing sugar with unique stabilizing properties due to its symmetrical, low energy structure consisting of two 1,1-anomerically bound glucose moieties. Many applications of this beneficial sugar have been reported in the novel food (nutricals), medical, pharmaceutical and cosmetic industries. Trehalose analogues, like lactotrehalose (?-D-glucopyranosyl ?-D-galactopyranoside) or galactotrehalose (?-D-galactopyranosyl ?-D-galactopyranoside), offer similar benefits as trehalose, but show additional features such as prebiotic or low-calorie sweetener due to their resistance against hydrolysis during digestion. Unfortunately, large-scale chemical production processes for trehalose analogues are not readily available at the moment due to the lack of efficient synthesis methods. Most of the procedures reported in literature suffer from low yields, elevated costs and are far from environmentally friendly. "Greener" alternatives found in the biocatalysis field, including galactosidases, trehalose phosphorylases and TreT-type trehalose synthases are suggested as primary candidates for trehalose analogue production instead. Significant progress has been made in the last decade to turn these into highly efficient biocatalysts and to broaden the variety of useful donor and acceptor sugars. In this review, we aim to provide an overview of the latest insights and future perspectives in trehalose analogue chemistry, applications and production pathways with emphasis on biocatalysis. PMID:26084050

  7. Synthesis and structure-activity relationships of lapacho analogues. 1. Suppression of human keratinocyte hyperproliferation by 2-substituted naphtho[2,3-b]furan-4,9-diones, activation by enzymatic one- and two-electron reduction, and intracellular generation of superoxide.

    PubMed

    Reichstein, Alexandra; Vortherms, Silke; Bannwitz, Sven; Tentrop, Jan; Prinz, Helge; Müller, Klaus

    2012-08-23

    A series of linearly anellated lapacho quinone analogues substituted at the 2-position of the tricyclic naphtho[2,3-b]furan-4,9-dione system were synthesized and evaluated for their ability to suppress keratinocyte hyperproliferation using HaCaT cells as the primary test system. While very good in vitro potency with IC(50) values in the submicromolar range was attained with electron-withdrawing substituents, some compounds were found to induce plasma membrane damage, as evidenced by the release of LDH activity from cytoplasm of the keratinocytes. The most potent analogue against keratinocyte hyperproliferation was the 1,2,4-oxadiazole 18, the potency of which was combined with comparably low cytotoxic membrane damaging effects. Structure-activity relationship studies with either metabolically stable or labile analogues revealed that the quinone moiety was required for activity. Selected compounds were studied in detail for their capability to generate superoxide radicals both in isolated enzymatic one- and two-electron reduction assays as well as in a HaCaT cell-based assay. PMID:22845014

  8. Cryo-EM reveals the conformation of a substrate analogue in the human 20S proteasome core

    NASA Astrophysics Data System (ADS)

    da Fonseca, Paula C. A.; Morris, Edward P.

    2015-07-01

    The proteasome is a highly regulated protease complex fundamental for cell homeostasis and controlled cell cycle progression. It functions by removing a wide range of specifically tagged proteins, including key cellular regulators. Here we present the structure of the human 20S proteasome core bound to a substrate analogue inhibitor molecule, determined by electron cryo-microscopy (cryo-EM) and single-particle analysis at a resolution of around 3.5 Å. Our map allows the building of protein coordinates as well as defining the location and conformation of the inhibitor at the different active sites. These results open new prospects to tackle the proteasome functional mechanisms. Moreover, they also further demonstrate that cryo-EM is emerging as a realistic approach for general structural studies of protein-ligand interactions.

  9. Cryo-EM reveals the conformation of a substrate analogue in the human 20S proteasome core

    PubMed Central

    da Fonseca, Paula C.A.; Morris, Edward P.

    2015-01-01

    The proteasome is a highly regulated protease complex fundamental for cell homeostasis and controlled cell cycle progression. It functions by removing a wide range of specifically tagged proteins, including key cellular regulators. Here we present the structure of the human 20S proteasome core bound to a substrate analogue inhibitor molecule, determined by electron cryo-microscopy (cryo-EM) and single-particle analysis at a resolution of around 3.5?Å. Our map allows the building of protein coordinates as well as defining the location and conformation of the inhibitor at the different active sites. These results open new prospects to tackle the proteasome functional mechanisms. Moreover, they also further demonstrate that cryo-EM is emerging as a realistic approach for general structural studies of protein–ligand interactions. PMID:26133119

  10. Analogue Models of Dike Emplacement

    NASA Astrophysics Data System (ADS)

    Acocella, V.; Cifelli, F.; Funiciello, R.; Minore, L.

    Dike emplacement is a common means for the rise of magmas in the shallow crust and is often responsible for the triggering of an eruption. In order to study the surface and shallow deformations induced by dike emplacement, we performed analogue models. Our models simulate a vertical sheet intrusion, few meters wide, in the shallowest brittle levels. Two experimental set-ups have been used. In the first set-up, a vertical metal sheet, with a variable thickness between 1 and 9 mm, is intruded within dry sand, with a thickness between 2 and 7 cm. In the second set-up, a 2 mm thick sheet of newtonian silicone putty is vertically intruded in dry sand or pre-fractured wet sand. The overall deformation pattern observed in both sets of experiments is characterized by a tensile area above the intruding sheet and two compressive areas at its sides. The analogue results are compared with previous numerical models of dike emplacement and with natural examples observed in volcanic areas.

  11. The Valles natural analogue project

    SciTech Connect

    Stockman, H.; Krumhansl, J.; Ho, C.; McConnell, V.

    1994-12-01

    The contact between an obsidian flow and a steep-walled tuff canyon was examined as an analogue for a highlevel waste repository. The analogue site is located in the Valles Caldera in New Mexico, where a massive obsidian flow filled a paleocanyon in the Battleship Rock tuff. The obsidian flow provided a heat source, analogous to waste panels or an igneous intrusion in a repository, and caused evaporation and migration of water. The tuff and obsidian samples were analyzed for major and trace elements and mineralogy by INAA, XRF, X-ray diffraction; and scanning electron microscopy and electron microprobe. Samples were also analyzed for D/H and {sup 39}Ar/{sup 4O} isotopic composition. Overall,the effects of the heating event seem to have been slight and limited to the tuff nearest the contact. There is some evidence of devitrification and migration of volatiles in the tuff within 10 meters of the contact, but variations in major and trace element chemistry are small and difficult to distinguish from the natural (pre-heating) variability of the rocks.

  12. Anti-angiogenic properties of a sulindac analogue

    PubMed Central

    Pyriochou, A; Tsigkos, S; Vassilakopoulos, T; Cottin, T; Zhou, Z; Gourzoulidou, E; Roussos, C; Waldmann, H; Giannis, A; Papapetropoulos, A

    2007-01-01

    Background and purpose: Angiopoietins (Ang) are crucial for new blood vessel formation and exert their effects by acting on the Tie2 receptor. We have recently described a sulindac analogue 2-((1E,Z)-1-benzylidene-5-bromo-2-methyl-1H-inden-3-yl)acetic acid; termed C-18 from now onwards) that inhibits Tie2 receptor activity in kinase assays in vitro. Here, we have assessed the ability of C-18 to inhibit angiogenesis-related properties of endothelial cells and tested its selectivity for the Tie2 receptor. Experimental approach: For in vitro experiments human umbilical vein endothelial cells (HUVEC) were used. Proliferation was measured using the MTT assay; migration assays were performed in a modified Boyden chamber and tube-like structure formation was determined on matrigel. The effects of C-18 in vivo were evaluated in the chicken chorioallantoic membrane (CAM). Key results: Pre-treatment of HUVEC with C-18 blocked Ang-1-stimulated migration, but also abolished vascular endothelial cell growth factor (VEGF)- and fibroblast growth factor 2-induced responses. Incubation with C-18 inhibited serum-induced proliferation in a concentration-dependent manner; C-18 was, however, without effect on Ang-1-induced survival. In addition, we observed that C-18 did not inhibit ligand-induced receptor phosphorylation of Tie2 or VEGFR2. On the other hand, C-18 blocked activation of members of the mitogen-activated protein kinase family and of the Ser/Thr kinase Akt induced by both VEGF and Ang-1. Furthermore, incubation of CAMs with C-18 led to a dose-dependent inhibition of vascular length. Conclusions and implications: C-18 did not act as a Tie2 inhibitor, as originally thought, but rather inhibited growth factor-stimulated signalling pathways that regulate endothelial cell migration and potently reduces neovascularization in vivo. PMID:17965739

  13. Syntheses and Biological Evaluation of Costunolide, Parthenolide, and Their Fluorinated Analogues.

    PubMed

    Yang, Zhong-Jin; Ge, Wei-Zhi; Li, Qiu-Ying; Lu, Yaxin; Gong, Jian-Miao; Kuang, Bei-Jia; Xi, Xiaonan; Wu, Haiting; Zhang, Quan; Chen, Yue

    2015-09-10

    Inspired by the biosynthesis of sesquiterpene lactones (SLs), herein we report the asymmetric total synthesis of the germacrane ring (24). The synthetic strategy features a selective aldol reaction between ?,?-unsaturated chiral sulfonylamide 15a and aldehyde 13, as well as the intramolecular ?-alkylation of sulfone 21 to construct a 10-membered carbocylic ring. The key intermediate 24 can be used to prepare the natural products costunolide and parthenolide (PTL), which are the key precursors for transformation into other SLs. Furthermore, the described synthetic sequences are amenable to the total synthesis of SL analogues, such as trifluoromethylated analogues 32 and 45. Analogues 32 and 45 maintained high activities against a series of cancer cell lines compared to their parent PTL and costunolide, respectively. In addition, 32 showed enhanced tolerance to acidic media compared with PTL. To our surprise, PTL and 32 showed comparable half-lives in rat plasma and in the presence of human liver microsomes. PMID:26226279

  14. Structure of Rhodococcus equi virulence-associated protein B (VapB) reveals an eight-stranded antiparallel ?-barrel consisting of two Greek-key motifs

    SciTech Connect

    Geerds, Christina; Wohlmann, Jens; Haas, Albert; Niemann, Hartmut H.

    2014-06-18

    The structure of VapB, a member of the Vap protein family that is involved in virulence of the bacterial pathogen R. equi, was determined by SAD phasing and reveals an eight-stranded antiparallel ?-barrel similar to avidin, suggestive of a binding function. Made up of two Greek-key motifs, the topology of VapB is unusual or even unique. Members of the virulence-associated protein (Vap) family from the pathogen Rhodococcus equi regulate virulence in an unknown manner. They do not share recognizable sequence homology with any protein of known structure. VapB and VapA are normally associated with isolates from pigs and horses, respectively. To contribute to a molecular understanding of Vap function, the crystal structure of a protease-resistant VapB fragment was determined at 1.4 Å resolution. The structure was solved by SAD phasing employing the anomalous signal of one endogenous S atom and two bound Co ions with low occupancy. VapB is an eight-stranded antiparallel ?-barrel with a single helix. Structural similarity to avidins suggests a potential binding function. Unlike other eight- or ten-stranded ?-barrels found in avidins, bacterial outer membrane proteins, fatty-acid-binding proteins and lysozyme inhibitors, Vaps do not have a next-neighbour arrangement but consist of two Greek-key motifs with strand order 41238567, suggesting an unusual or even unique topology.

  15. Quadracyclic adenine: a non-perturbing fluorescent adenine analogue.

    PubMed

    Dierckx, Anke; Miannay, Francois-Alexandre; Ben Gaied, Nouha; Preus, Søren; Björck, Markus; Brown, Tom; Wilhelmsson, L Marcus

    2012-05-01

    Fluorescent-base analogues (FBAs) comprise a group of increasingly important molecules for the investigation of nucleic acid structure and dynamics as well as of interactions between nucleic acids and other molecules. Here, we report on the synthesis, detailed spectroscopic characterisation and base-pairing properties of a new environment-sensitive fluorescent adenine analogue, quadracyclic adenine (qA). After developing an efficient route of synthesis for the phosphoramidite of qA it was incorporated into DNA in high yield by using standard solid-phase synthesis procedures. In DNA qA serves as an adenine analogue that preserves the B-form and, in contrast to most currently available FBAs, maintains or even increases the stability of the duplex. We demonstrate that, unlike fluorescent adenine analogues, such as the most commonly used one, 2-aminopurine, and the recently developed triazole adenine, qA shows highly specific base-pairing with thymine. Moreover, qA has an absorption band outside the absorption of the natural nucleobases (>300?nm) and can thus be selectively excited. Upon excitation the qA monomer displays a fluorescence quantum yield of 6.8?% with an emission maximum at 456?nm. More importantly, upon incorporation into DNA the fluorescence of qA is significantly less quenched than most FBAs. This results in quantum yields that in some sequences reach values that are up to fourfold higher than maximum values reported for 2-aminopurine. To facilitate future utilisation of qA in biochemical and biophysical studies we investigated its fluorescence properties in greater detail and resolved its absorption band outside the DNA absorption region into distinct transition dipole moments. In conclusion, the unique combination of properties of qA make it a promising alternative to current fluorescent adenine analogues for future detailed studies of nucleic acid-containing systems. PMID:22437923

  16. CO2 Capture with Enzyme Synthetic Analogue

    SciTech Connect

    Harry Cordatos

    2010-11-08

    Overview of an ongoing, 2 year research project partially funded by APRA-E to create a novel, synthetic analogue of carbonic anhydrase and incorporate it into a membrane for removal of CO2 from flue gas in coal power plants. Mechanism background, preliminary feasibility study results, molecular modeling of analogue-CO2 interaction, and program timeline are provided.

  17. Contact zones and hydrothermal systems as analogues to repository conditions

    SciTech Connect

    Wollenberg, H.A.; Flexser, S.

    1984-10-01

    Radioactive waste isolation efforts in the US are currently focused on examining basalt, tuff, salt, and crystalline rock as candidate rock types to encompass waste repositories. As analogues to near-field conditions, the distributions of radio- and trace-elements have been examined across contacts between these rocks and dikes and stocks that have intruded them. The intensive study of the Stripa quartz monzonite has also offered the opportunity to observe the distribution of uranium and its daughters in groundwater and its relationship to U associated with fracture-filling and alteration minerals. Investigations of intrusive contact zones to date have included (1) a tertiary stock into Precambrian gneiss, (2) a stock into ash flow tuff, (3) a rhyodacite dike into Columbia River basalt, and (4) a kimberlite dike into salt. With respect to temperature and pressure, these contact zones may be considered "worst-case scenario" analogues. Results indicate that there has been no appreciable migration of radioelements from the more radioactive intrusives into the less radioactive country rocks, either in response to the intrusions or in the fracture-controlled hydrological systems that developed following emplacement. In many cases, the radioelements are locked up in accessory minerals, suggesting that artificial analogues to these would make ideal waste forms. Emphasis should now shift to examination of active hydrothermal systems, studying the distribution of key elements in water, fractures, and alteration minerals under pressure and temperature conditions most similar to those expected in the near-field environment of a repository. 14 refs.

  18. Synthesis of Chamaecypanone C Analogues from in situ-Generated Cyclopentadienones and their Biological Evaluation

    PubMed Central

    Dong, Suwei; Qin, Tian; Hamel, Ernest; Beutler, John A.; Porco, John A.

    2012-01-01

    A rhodium-catalyzed dehydrogenation protocol has been developed for conversion of 3,5-diarylcyclopentenones to the corresponding 2,4-diarylcyclopentadienones. Using this protocol, analogues of the cytotoxic agent chamaecypanone C have been synthesized via Diels-Alder cycloaddition between the cyclopentadienones and in situ-generated ortho-quinols. Biological evaluation of these analogues revealed a compound with higher activity as a microtubule inhibitor and cytotoxic agent in comparison with the parent structure. PMID:23110297

  19. Astrobiology Field Research in Moon/Mars Analogue Environments: Preface

    NASA Technical Reports Server (NTRS)

    Foing, B. H.; Stoker, C.; Ehrenfreund, P.

    2011-01-01

    Extreme environments on Earth often provide similar terrain conditions to landing/operation sites on Moon and Mars. Several field campaigns (EuroGeoMars2009 and DOMMEX/ILEWG EuroMoonMars from November 2009 to March 2010) were conducted at the Mars Desert Research Station (MDRS) in Utah. Some of the key astrobiology results are presented in this special issue on Astrobiology field research in Moon/Mars analogue environments relevant to investigate the link between geology, minerals, organics and biota. Preliminary results from a multidisciplinary field campaign at Rio Tinto in Spain are presented.

  20. Towards bottom-up nanopatterning of Prussian blue analogues

    PubMed Central

    Trannoy, Virgile; Faustini, Marco; Grosso, David; Mazerat, Sandra; Brisset, François; Dazzi, Alexandre

    2014-01-01

    Summary Ordered nanoperforated TiO2 monolayers fabricated through sol–gel chemistry were used to grow isolated particles of Prussian blue analogues (PBA). The elaboration of the TiO2/CoFe PBA nanocomposites involves five steps. The samples were characterized by scanning electron microscopy (SEM), atomic force microscopy (AFM), infrared spectroscopy and X-ray photoelectron spectroscopy (XPS) all along the synthesis process. Selected physico-chemical parameters have been varied in order to determine the key steps of the synthesis process and to optimize it. This study is an important step towards the full control of the fabrication process. PMID:25383305

  1. Design, synthesis and biological evaluation of bridged epothilone D analogues

    PubMed Central

    Chen, Qiao-Hong; Ganesh, Thota; Brodie, Peggy; Slebodnick, Carla; Jiang, Yi; Banerjee, Abhijit; Bane, Susan; Snyder, James P.

    2009-01-01

    Six epothilone D analogues with a bridge between the C4-methyl and the C12-methyl carbons were prepared in an attempt to constrain epothilone D to its proposed tubulin-binding conformation. Ring-closing metathesis (RCM) was employed as the key step to build the C4-C26 bridge. In antiproliferative assays in the human ovarian cancer (A2780) and prostate cancer (PC3) cell lines, and also in tubulin assembly assay, all these compounds proved to be less active than epothilone D. PMID:19039362

  2. The future of somatostatin analogue therapy.

    PubMed

    Stewart, P M; James, R A

    1999-10-01

    Since its discovery almost 30 years ago, the mode of action and therapeutic applications of somatostatin have been defined. In particular the cloning and characterization of somatostatin receptor subtypes has facilitated the development of high affinity analogues. In the context of pituitary disease, long-acting somatostatin analogues (octreotide, lanreotide) have been used to treat a variety of pituitary tumours but are most efficacious for the treatment of GH and TSH-secreting adenomas. In patients with acromegaly, depot preparations of these analogues are administered intramuscularly every 10-28 days and provide consistent suppression of GH levels to < 5 mU/l in approximately 50-65% of all cases. Even more specific somatostatin receptor analogues are under development. Finally, radiolabelled somatostatin analogue scintigraphy and, in larger doses, therapy, are now established tools in the evaluation and treatment of neuroendocrine tumours. PMID:10909432

  3. Synthesis, biological activity, and conformational study of N-methylated allatostatin analogues inhibiting juvenile hormone biosynthesis.

    PubMed

    Xie, Yong; Zhang, Li; Zhang, Chuanliang; Wu, Xiaoqing; Deng, Xile; Yang, Xinling; Tobe, Stephen S

    2015-03-25

    An allatostatin (AST) neuropeptide mimic (H17) is a potential insect growth regulator, which inhibits the production of juvenile hormone (JH) by the corpora allata. To determine the effect of conformation of novel AST analogues and their ability to inhibit JH biosynthesis, eight insect AST analogues were synthesized using H17 as the lead compound by N-methylation scanning, which is a common strategy for improving the biological properties of peptides. A bioassay using JH production by corpora allata of the cockroach Diploptera punctata indicated that single N-methylation mimics (analogues 1-4) showed more activity than double N-methylation mimics (analogues 5-8). Especially, analogues 1 and 4 showed roughly equivalent activity to that of H17, with IC50 values of 5.17 × 10(-8) and 6.44 × 10(-8) M, respectively. Molecular modeling based on nuclear magnetic resonance data showed that the conformation of analogues 1 and 4 seems to be flexible, whereas analogues 2 and 3 showed a type IV ?-turn. This flexible linear conformation was hypothesized to be a new important and indispensable structural element beneficial to the activity of AST mimics. PMID:25751662

  4. Florida Keys

    NASA Technical Reports Server (NTRS)

    2002-01-01

    The Florida Keys are a chain of islands, islets and reefs extending from Virginia Key to the Dry Tortugas for about 309 kilometers (192 miles). The keys are chiefly limestone and coral formations. The larger islands of the group are Key West (with its airport), Key Largo, Sugarloaf Key, and Boca Chica Key. A causeway extends from the mainland to Key West.

    This image was acquired on October 28, 2001, by the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) on NASA's Terra satellite. With its 14 spectral bands from the visible to the thermal infrared wavelength region, and its high spatial resolution of 15 to 90 meters (about 50 to 300 feet), ASTER images Earth to map and monitor the changing surface of our planet.

    ASTER is one of five Earth-observing instruments launched December 18, 1999, on NASA's Terra satellite. The instrument was built by Japan's Ministry of Economy, Trade and Industry. A joint U.S./Japan science team is responsible for validation and calibration of the instrument and the data products.

    The broad spectral coverage and high spectral resolution of ASTER will provide scientists in numerous disciplines with critical information for surface mapping, and monitoring of dynamic conditions and temporal change. Example applications are: monitoring glacial advances and retreats; monitoring potentially active volcanoes; identifying crop stress; determining cloud morphology and physical properties; wetlands evaluation; thermal pollution monitoring; coral reef degradation; surface temperature mapping of soils and geology; and measuring surface heat balance.

    Dr. Anne Kahle at NASA's Jet Propulsion Laboratory, Pasadena, Calif., is the U.S. Science team leader; Bjorn Eng of JPL is the project manager. The Terra mission is part of NASA's Earth Science Enterprise, a long- term research effort to understand and protect our home planet. Through the study of Earth, NASA will help to provide sound science to policy and economic decision-makers so as to better life here, while developing the technologies needed to explore the universe and search for life beyond our home planet.

    Size: 51.6 by 29.7 kilometers ( 32.0 by 18.4 miles) Location: 24.7 degrees North latitude, 81.5 degrees West longitude Orientation: North at top Image Data: ASTER bands 1, 2, and 3 Original Data Resolution: 15 meters (49.2 feet) Date Acquired: October 28, 2001

  5. Enantioselective synthesis of pladienolide B and truncated analogues as new anticancer agents.

    PubMed

    Kumar, Vemula Praveen; Chandrasekhar, Srivari

    2013-07-19

    An enantioselective synthesis of natural anticancer macrolide pladienolide B is described. The synthetic highlights include Sharpless asymmetric epoxidation, ring closing metathesis (RCM), Ireland-Claisen rearrangement, Shi epoxidation, and Pd-catalyzed Stille coupling as key steps. The synthetic route also allowed the synthesis of the truncated analogues (41a-d) of pladienolide B. PMID:23822896

  6. Key Nutrients.

    ERIC Educational Resources Information Center

    Federal Extension Service (USDA), Washington, DC.

    Lessons written to help trainer agents prepare aides for work with families in the Food and Nutrition Program are presented in this booklet. The key nutrients discussed in the 10 lessons are protein, carbohydrates, fat, calcium, iron, iodine, and Vitamins A, B, C, and D. the format of each lesson is as follows: Purpose, Presentation, Application…

  7. Natural analogue studies as supplements to biomineralization research

    SciTech Connect

    McNeil, M.B.

    1995-09-01

    Chemical reactions can alter the chemistry and crystal structure of solid objects over archeological or geological times, while preserving external physical shapes. The reactions resulting in these structures offer natural analogues to laboratory experiments in biomineralization and to biologically influenced alteration of nuclear waste packages, and thus, they offer the only available way of validating models that purport waste package behavior over archaeological or geological times. Potential uses of such analogues in the construction and validation of hypothetical mechanisms of microbiological corrosion and biomineralization are reviewed. Evidence from such analogues suggests that biofilms can control materials alteration in ways usually overlooked. The newly hypothesized mechanisms involve control by biofilms of the cation flow near the solid surface and offer plausible mechanisms for the formation of mixed-cation minerals under conditions that would lead to dealloying in abiotic experiments; they also account for the formation of unusual minerals [such as posnjakite, Cu{sub 4}SO{sub 4}(OH){sub 6{center_dot}}H{sub 2}O] and mineral morphologies unusual in corrosion [malachite, Cu{sub 2}CO{sub 3}(OH){sub 2}, rarely forms botryoidally under corrosion conditions and its occasional presence on archaeological objects that appear to have undergone microbiological corrosion may be related to biofilm phenomena].

  8. Structural insights into a key carotenogenesis related enzyme phytoene synthase of P. falciparum: a novel drug target for malaria.

    PubMed

    Agarwal, Shalini; Sharma, Vijeta; Phulera, Swastik; Abdin, M Z; Ayana, R; Singh, Shailja

    2015-12-01

    Carotenoids represent a diverse group of pigments derived from the common isoprenoid precursors and fulfill a variety of critical functions in plants and animals. Phytoene synthase (PSY), a transferase enzyme that catalyzes the first specific step in carotenoid biosynthesis plays a central role in the regulation of a number of essential functions mediated via carotenoids. PSYs have been deeply investigated in plants, bacteria and algae however in apicomplexans it is poorly studied. In an effort to characterize PSY in apicomplexans especially the malaria parasite Plasmodium falciparum (P. falciparum), a detailed bioinformatics analysis is undertaken. We have analysed the Phylogenetic relationship of PSY also referred to as octaprenyl pyrophosphate synthase (OPPS) in P. falciparum with other taxonomic groups. Further, we in silico characterized the secondary and tertiary structures of P. falciparum PSY/OPPS and compared the tertiary structures with crystal structure of Thermotoga maritima (T. maritima) OPPS. Our results evidenced the resemblance of P. falciparum PSY with the active site of T. maritima OPPS. Interestingly, the comparative structural analysis revealed an unconserved unique loop in P. falciparum OPPS/PSY. Such structural insights might contribute novel accessory functions to the protein thus, offering potential drug targets. PMID:26702306

  9. Analogue Transformations in Physics and their Application to Acoustics

    PubMed Central

    García-Meca, C.; Carloni, S.; Barceló, C.; Jannes, G.; Sánchez-Dehesa, J.; Martínez, A.

    2013-01-01

    Transformation optics has shaped up a revolutionary electromagnetic design paradigm, enabling scientists to build astonishing devices such as invisibility cloaks. Unfortunately, the application of transformation techniques to other branches of physics is often constrained by the structure of the field equations. We develop here a complete transformation method using the idea of analogue spacetimes. The method is general and could be considered as a new paradigm for controlling waves in different branches of physics, from acoustics in quantum fluids to graphene electronics. As an application, we derive an “analogue transformation acoustics” formalism that naturally allows the use of transformations mixing space and time or involving moving fluids, both of which were impossible with the standard approach. To demonstrate the power of our method, we give explicit designs of a dynamic compressor, a spacetime cloak for acoustic waves and a carpet cloak for a moving aircraft. PMID:23774575

  10. Analogue transformations in physics and their application to acoustics.

    PubMed

    García-Meca, C; Carloni, S; Barceló, C; Jannes, G; Sánchez-Dehesa, J; Martínez, A

    2013-01-01

    Transformation optics has shaped up a revolutionary electromagnetic design paradigm, enabling scientists to build astonishing devices such as invisibility cloaks. Unfortunately, the application of transformation techniques to other branches of physics is often constrained by the structure of the field equations. We develop here a complete transformation method using the idea of analogue spacetimes. The method is general and could be considered as a new paradigm for controlling waves in different branches of physics, from acoustics in quantum fluids to graphene electronics. As an application, we derive an "analogue transformation acoustics" formalism that naturally allows the use of transformations mixing space and time or involving moving fluids, both of which were impossible with the standard approach. To demonstrate the power of our method, we give explicit designs of a dynamic compressor, a spacetime cloak for acoustic waves and a carpet cloak for a moving aircraft. PMID:23774575

  11. Plant Volatile Analogues Strengthen Attractiveness to Insect

    PubMed Central

    Sun, Yufeng; Yu, Hao; Zhou, Jing-Jiang; Pickett, John A.; Wu, Kongming

    2014-01-01

    Green leaf bug Apolygus lucorum (Meyer-Dür) is one of the major pests in agriculture. Management of A. lucorum was largely achieved by using pesticides. However, the increasing population of A. lucorum since growing Bt cotton widely and the increased awareness of ecoenvironment and agricultural product safety makes their population-control very challenging. Therefore this study was conducted to explore a novel ecological approach, synthetic plant volatile analogues, to manage the pest. Here, plant volatile analogues were first designed and synthesized by combining the bioactive components of ?-ionone and benzaldehyde. The stabilities of ?-ionone, benzaldehyde and analogue 3 g were tested. The electroantennogram (EAG) responses of A. lucorum adult antennae to the analogues were recorded. And the behavior assay and filed experiment were also conducted. In this study, thirteen analogues were acquired. The analogue 3 g was demonstrated to be more stable than ?-ionone and benzaldehyde in the environment. Many of the analogues elicited EAG responses, and the EAG response values to 3 g remained unchanged during seven-day period. 3 g was also demonstrated to be attractive to A. lucorum adults in the laboratory behavior experiment and in the field. Its attractiveness persisted longer than ?-ionone and benzaldehyde. This indicated that 3 g can strengthen attractiveness to insect and has potential as an attractant. Our results suggest that synthetic plant volatile analogues can strengthen attractiveness to insect. This is the first published study about synthetic plant volatile analogues that have the potential to be used in pest control. Our results will support a new ecological approach to pest control and it will be helpful to ecoenvironment and agricultural product safety. PMID:24911460

  12. 20(S)-Protopanaxadiol (PPD) analogues chemosensitize multidrug-resistant cancer cells to clinical anticancer drugs.

    PubMed

    Liu, Junhua; Wang, Xu; Liu, Peng; Deng, Rongxin; Lei, Min; Chen, Wantao; Hu, Lihong

    2013-07-15

    Novel 20(S)-protopanoxadiol (PPD) analogues were designed, synthesized, and evaluated for the chemosensitizing activity against a multidrug resistant (MDR) cell line (KBvcr) overexpressing P-glycoprotein (P-gp). Structure-activity relationship analysis showed that aromatic substituted aliphatic amine at the 24-positions (groups V) effectively and significantly sensitized P-gp overexpressing multidrug resistant (MDR) cells to anticancer drugs, such as docetaxel (DOC), vincristine (VCR), and adriamycin (ADM). PPD derivatives 12 and 18 showed 1.3-2.6 times more effective reversal ability than verapamil (VER) for DOC and VCR. Importantly, no cytotoxicity was observed by the active PPD analogues (5?M) against both non-MDR and MDR cells, suggesting that PPD analogues serve as novel lead compounds toward a potent and safe resistance modulator. Moreover, a preliminary mechanism study demonstrated that the chemosensitizing activity of PPD analogues results from inhibition of P-glycoprotein (P-gp) overexpressed in MDR cancer cells. PMID:23683834

  13. Probing High School Students' Cognitive Structures and Key Areas of Learning Difficulties on Ethanoic Acid Using the Flow Map Method

    ERIC Educational Resources Information Center

    Zhou, Qing; Wang, Tingting; Zheng, Qi

    2015-01-01

    The purpose of this study was primarily to explore high school students' cognitive structures and to identify their learning difficulties on ethanoic acid through the flow map method. The subjects of this study were 30 grade 1 students from Dong Yuan Road Senior High School in Xi'an, China. The interviews were conducted a week after the students…

  14. Hippocampal Structure and Human Cognition: Key Role of Spatial Processing and Evidence Supporting the Efficiency Hypothesis in Females

    ERIC Educational Resources Information Center

    Colom, Roberto; Stein, Jason L.; Rajagopalan, Priya; Martinez, Kenia; Hermel, David; Wang, Yalin; Alvarez-Linera, Juan; Burgaleta, Miguel; Quiroga, Ma. Angeles; Shih, Pei Chun; Thompson, Paul M.

    2013-01-01

    Here we apply a method for automated segmentation of the hippocampus in 3D high-resolution structural brain MRI scans. One hundred and four healthy young adults completed twenty one tasks measuring abstract, verbal, and spatial intelligence, along with working memory, executive control, attention, and processing speed. After permutation tests…

  15. Structure analysis of the flavoredoxin from Desulfovibrio vulgaris Miyazaki F reveals key residues that discriminate the functions and properties of the flavin reductase family.

    PubMed

    Shibata, Naoki; Ueda, Yasufumi; Takeuchi, Daisuke; Haruyama, Yoshihiro; Kojima, Shuichi; Sato, Junichi; Niimura, Youichi; Kitamura, Masaya; Higuchi, Yoshiki

    2009-09-01

    The crystal structure of flavoredoxin from Desulfovibrio vulgaris Miyazaki F was determined at 1.05 A resolution and its ferric reductase activity was examined. The aim was to elucidate whether flavoredoxin has structural similarity to ferric reductase and ferric reductase activity, based on the sequence similarity to ferric reductase from Archaeoglobus fulgidus. As expected, flavoredoxin shared a common overall structure with A. fulgidus ferric reductase and displayed weak ferric reductase and flavin reductase activities; however, flavoredoxin contains two FMN molecules per dimer, unlike A. fulgidus ferric reductase, which has only one FMN molecule per dimer. Compared with A. fulgidus ferric reductase, flavoredoxin forms three additional hydrogen bonds and has a significantly smaller solvent-accessible surface area. These observations explain the higher affinity of flavoredoxin for FMN. Unexpectedly, an electron-density map indicated the presence of a Mes molecule on the re-side of the isoalloxazine ring of FMN, and that two zinc ions are bound to the two cysteine residues, Cys39 and Cys40, adjacent to FMN. These two cysteine residues are close to one of the putative ferric ion binding sites of ferric reductase. Based on their structural similarities, we conclude that the corresponding site of ferric reductase is the most plausible site for ferric ion binding. Comparing the structures with related flavin proteins revealed key structural features regarding the discrimination of function (ferric ion or flavin reduction) and a unique electron transport system. PMID:19708087

  16. Crystal Structure and Identification of Two Key Amino Acids Involved in AI-2 Production and Biofilm Formation in Streptococcus suis LuxS

    PubMed Central

    Wang, Yang; Yi, Li; Wang, Shaohui; Fan, Hongjie; Ding, Chan; Mao, Xiang; Lu, Chengping

    2015-01-01

    Streptococcus suis has emerged as an important zoonotic pathogen that causes meningitis, arthritis, septicemia and even sudden death in pigs and humans. Quorum sensing is the signaling network for cell-to-cell communication that bacterial cells can use to monitor their own population density through production and exchange of signal molecules. S-Ribosylhomocysteinase (LuxS) is the key enzyme involved in the activated methyl cycle. Autoinducer 2 (AI-2) is the adduct of borate and a ribose derivative and is produced from S-adenosylhomocysteine (SAH). AI-2 can mediate interspecies communication and in some species facilitate the bacterial behavior regulation such as biofilm formation and virulence in both Gram-positive and Gram-negative bacteria. Here, we reported the overexpression, purification and crystallographic structure of LuxS from S. suis. Our results showed the catalytically active LuxS exists as a homodimer in solution. Inductively coupled plasma-mass spectrometry (ICP-MS) revealed the presence of Zn2+ in LuxS. Although the core structure shares the similar topology with LuxS proteins from other bacterial species, structural analyses and comparative amino acid sequence alignments identified two key amino acid differences in S. suis LuxS, Phe80 and His87, which are located near the substrate binding site. The results of site-directed mutagenesis and enzymology studies confirmed that these two residues affect the catalytic activity of the enzyme. These in vitro results were corroborated in vivo by expression of the LuxS variants in a S. suis ?luxS strain. The single and two amino acid of LuxS variant decreased AI-2 production and biofilm formation significantly compared to that of the parent strain. Our findings highlight the importance of key LuxS residues that influence the AI-2 production and biofilm formation in S.suis. PMID:26484864

  17. Structural Characterisation of FabG from Yersinia pestis, a Key Component of Bacterial Fatty Acid Synthesis

    PubMed Central

    Nanson, Jeffrey D.; Forwood, Jade K.

    2015-01-01

    Ketoacyl-acyl carrier protein reductases (FabG) are ubiquitously expressed enzymes that catalyse the reduction of acyl carrier protein (ACP) linked thioesters within the bacterial type II fatty acid synthesis (FASII) pathway. The products of these enzymes, saturated and unsaturated fatty acids, are essential components of the bacterial cell envelope. The FASII reductase enoyl-ACP reductase (FabI) has been the focus of numerous drug discovery efforts, some of which have led to clinical trials, yet few studies have focused on FabG. Like FabI, FabG appears to be essential for survival in many bacteria, similarly indicating the potential of this enzyme as a drug target. FabG enzymes are members of the short-chain alcohol dehydrogenase/reductase (SDR) family, and like other SDRs, exhibit highly conserved secondary and tertiary structures, and contain a number of conserved sequence motifs. Here we describe the crystal structures of FabG from Yersinia pestis (YpFabG), the causative agent of bubonic, pneumonic, and septicaemic plague, and three human pandemics. Y. pestis remains endemic in many parts of North America, South America, Southeast Asia, and Africa, and a threat to human health. YpFabG shares a high degree of structural similarity with bacterial homologues, and the ketoreductase domain of the mammalian fatty acid synthase from both Homo sapiens and Sus scrofa. Structural characterisation of YpFabG, and comparison with other bacterial FabGs and the mammalian fatty acid synthase, provides a strong platform for virtual screening of potential inhibitors, rational drug design, and the development of new antimicrobial agents to combat Y. pestis infections. PMID:26539719

  18. ?-Conotoxins synthesized using an acid-cleavable solubility tag approach reveal key structural determinants for NaV subtype selectivity.

    PubMed

    Peigneur, Steve; Paolini-Bertrand, Marianne; Gaertner, Hubert; Biass, Daniel; Violette, Aude; Stöcklin, Reto; Favreau, Philippe; Tytgat, Jan; Hartley, Oliver

    2014-12-19

    Conotoxins are venom peptides from cone snails with multiple disulfide bridges that provide a rigid structural scaffold. Typically acting on ion channels implicated in neurotransmission, conotoxins are of interest both as tools for pharmacological studies and as potential new medicines. ?-Conotoxins act by inhibiting inactivation of voltage-gated sodium channels (Nav). Their pharmacology has not been extensively studied because their highly hydrophobic character makes them difficult targets for chemical synthesis. Here we adopted an acid-cleavable solubility tag strategy that facilitated synthesis, purification, and directed disulfide bridge formation. Using this approach we readily produced three native ?-conotoxins from Conus consors plus two rationally designed hybrid peptides. We observed striking differences in Nav subtype selectivity across this group of compounds, which differ in primary structure at only three positions: 12, 23, and 25. Our results provide new insights into the structure-activity relationships underlying the Nav subtype selectivity of ?-conotoxins. Use of the acid-cleavable solubility tag strategy should facilitate synthesis of other hydrophobic peptides with complex disulfide bridge patterns. PMID:25352593

  19. Structure of Importin13–Ubc9 complex: nuclear import and release of a key regulator of sumoylation

    PubMed Central

    Grünwald, Marlene; Bono, Fulvia

    2011-01-01

    Importin13 (Imp13) is an unusual ?-karyopherin that is able to both import and export cargoes in and out of the nucleus. In the cytoplasm, Imp13 associates with different cargoes such as Mago-Y14 and Ubc9, and facilitates their import into the nucleus where RanGTP binding promotes the release of the cargo. In this study, we present the 2.8 Å resolution crystal structure of Imp13 in complex with the SUMO E2-conjugating enzyme, Ubc9. The structure shows an uncommon mode of cargo–karyopherin recognition with Ubc9 binding at the N-terminal portion of Imp13, occupying the entire RanGTP-binding site. Comparison of the Imp13–Ubc9 complex with Imp13–Mago-Y14 shows the remarkable plasticity of Imp13, whose conformation changes from a closed ring to an open superhelix when bound to the two different cargoes. The structure also shows that the binding mode is compatible with the sumoylated states of Ubc9. Indeed, we find that Imp13 is able to bind sumoylated Ubc9 in vitro and suppresses autosumoylation activity in the complex. PMID:21139563

  20. Synthesis and evaluation of amide side-chain modified Agomelatine analogues as potential antidepressant-like agents.

    PubMed

    Chang, Ying; Pi, Weiyi; Ang, Wei; Liu, Yuanyuan; Li, Chunlong; Zheng, Jiajia; Xiong, Li; Yang, Tao; Luo, Youfu

    2014-04-01

    In this work, nineteen analogues of Agomelatine were readily synthesized through structural modification of the acetamide side-chain starting from the key common intermediate 2-(7-methoxynaphthalen-1-yl) ethanamine (3), which was prepared from commercially available compound 2-(7-methoxynaphthalen-1-yl) acetonitrile (2) in two steps. Corticosterone-induced PC12 pheochromocytoma cells phenotypic in vitro model was utilized to evaluate their potential antidepression activities. Imide compound 4a and acylamino carboxylic acid analogue 5b showed good protective effects on traumatic PC12 cells with protection rates of 34.2% and 23.2%, respectively. Further in vivo assessments in C57 mice FST (forced swim test) model demonstrated that compound 4a significantly reduced the immobility time of the tested subjects, indicating antidepressant-like activity. Preliminary toxicity assays conducted on human normal liver L02 cells and embryonic kidney 293 cells suggested a relatively low safety risk for compound 4a compared with the marketed drugs Agomelatine and Fluoxetine. The promising antidepressant-like efficacy of compound 4a, together with the relatively low toxicity to the normal tested cells and high liability of diffusion through the blood-brain barrier (BBB), presents us insights of exploration of me-better drug candidates of Agomelatine. PMID:24631187

  1. Surface and Moho topography as key constraints for understanding the thermo-rheological structure and longevity of cratons and tectons

    NASA Astrophysics Data System (ADS)

    Burov, E. B.; Francois, T.

    2013-12-01

    Surface topography and Moho are the most robust observables that have been insufficiently exploited for containing the rheological and thermal structure and hence for understanding the longevity and eventual destruction of cratons and 'tectons'. Craton longevity has been often explained by their buoyancy and analysed by testing gravitational stability of cratonic mantle 'keels' as a function of the hypothesized plate thickness and thermo-rheological structure. Destruction of some cratons (e.g. North China) and data indicating little if no buoyancy of some tectons (e.g., Arabian shield) suggest that buoyancy is not the only factor of their stability, and previous studies show that their mechanical strength is as important as buoyancy. The upper bounds on this strength are provided by flexural studies demonstrating that Te values (equivalent elastic thickness) in cratons are highest in the world and may probably reach 150 km. Yet, the sensitivity of common methods is poor for Te values above 80 km while the lower bounds on the strength and the equivalent elastic thickness of cratons are still matter of debate. How this strength is partitioned between crust and mantle, and which set of rheological parameters pertain, remain major unknowns. We show that smooth low topography and 'frozen' heterogeneous crustal structure of cratons represent the missing constraints for understanding of craton longevity. The cratonic crust is characterized by isostatically misbalanced density heterogeneities, suggesting that the lithosphere has to be strong enough to keep them 'frozen' through the time without producing major gravitational instabilities and topographic undulations. Hence, to constrain thermo-rheological properties of cratons one should first investigate the stability of their topography and internal structure (constrained from seismic and gravity data). Our thermo-mechanical numerical experiments accounting for free surface boundary condition demonstrate that craton stability cannot be warranted by crustal strength only, and that strong dry olivine mantle rheology and cold thick lithosphere are needed for craton survival. We find fairly robust lower-bound limits on their thermo-rheological structure. In particular, the minimal Te needed for long-term stability of continents (cratons or tectons) is approximately 70 km.

  2. Space analogue studies in Antarctica

    NASA Technical Reports Server (NTRS)

    Lugg, D.; Shepanek, M.

    1999-01-01

    Medical research has been carried out on the Australian National Antarctic Research Expeditions (ANARE) for 50 years. As an extension of this program collaborative Australian/United States research on immunology, microbiology, psychology and remote medicine has produced important data and insight on how humans adapt to the stress of extreme isolation, confinement and the harsh environment of Antarctica. An outstanding analogue for the isolation and confinement of space missions (especially planetary outposts), ANARE has been used as an international research platform by Australia and the United States since 1993. Collaborative research has demonstrated a lowered responsiveness of the immune system under the isolation and confinement of Antarctic winter-over; a reduction of almost 50% in T cell proliferation to mitogen phytohaemogglutinin, as well as changes in latent herpesvirus states and the expansion of the polyclonal latent Epstein-Barr virus infected B cell populations. Although no clinically significant disease has been found to result from these immune changes, research is currently assessing the effects of psychological factors on the immune system. This and associated research performed to date and its relevance to both organisations is discussed, and comment made on possible extensions to the program in both medical and other fields.

  3. Space analogue studies in Antarctica

    NASA Astrophysics Data System (ADS)

    Lugg, D.; Shepanek, M.

    1999-09-01

    Medical research has been carried out on the Australian National Antarctic Research Expeditions (ANARE) for 50 years. As an extension of this program collaborative Australian/United States research on immunology, microbiology, psychology and remote medicine has produced important data and insight on how humans adapt to the stress of extreme isolation, confinement and the harsh environment of Antarctica. An outstanding analogue for the isolation and confinement of space missions (especially planetary outposts), ANARE has been used as an international research platform by Australia and the United States since 1993. Collaborative research has demonstrated a lowered responsiveness of the immune system under the isolation and confinement of Antarctic winter-over; a reduction of almost 50% in T cell proliferation to mltogen phytohaemogglutinin, as well as changes in latent herpesvirus states and the expansion of the polyclonal latent Epstein-Barr virus infected B cell populations. Although no clinically significant disease has been found to result from these immune changes, research is currently assessing the effects of psychological factors on the immune system. This and associated research performed to date and its relevance to both organisations is discussed, and comment made on possible extensions to the program in both medical and other fields.

  4. Increased food intake with oxyntomodulin analogues

    PubMed Central

    Price, Samantha L.; Minnion, James S.; Bloom, Stephen R.

    2015-01-01

    Oxyntomodulin analogues offer a novel treatment for obesity. However during analogue screening in a rat model increased food intake was consistently observed. To further investigate this finding, a series of representative analogues (OXM14 and OXM15) and their Glu-3 equivalents (OXM14E3 and OXM15E3) were administered to rats for 7 days and food intake and bodyweight measurements taken. To investigate the role of glucagon receptor activation glutamate (Glu/E) was substituted at amino acid position 3. GLP-1 and glucagon receptor efficacy of the oxyntomodulin analogues and their Glu-3 counterparts were measured at the rat receptors in vitro. Doses of 25 n mol/kg of OXM14 and OXM15 increased food intake by up to 20%. Bodyweight was not significantly increased. Food intake was not increased with the Glu-3 peptides, indicating that a glucagon receptor mechanism may be responsible for the increase in food intake. PMID:26431789

  5. Past and present of analogue modelling, and its future trend

    NASA Astrophysics Data System (ADS)

    Koyi, Hemin

    2015-04-01

    Since Hull (1815) published his article on modelling, analogue modelling has expanded to simulate both a wider range of tectonic regimes and target more challenging set-ups, and has become an integrated part of the fields of tectonics and structural geology. Establishment of new laboratories testifies for the increased attention the technique receives. The ties between modellers and field geoscientists have become stronger with the focus being on understanding the parameters that govern the evolution of a tectonic regime and the processes that dominate it. Since the first sand castle was built with damp sand on a beach, sand has proven to be an appropriate material analogue. Even though granular materials is the most widely used analogue material, new materials are also (re)introduced as rock analogues. Emphasis has been on more precise measurements of the mechanical properties of the materials and on minimizing the preparation effects, which have a great impact on scaling, interpretations and benchmarking. The analytical technique used to quantify model results has also seen a great deal of improvement. In addition to X-ray tomography used to visualise internal structures of models, new techniques (e.g. PIV, high-resolution laser scanning, and interferometry) have enabled monitoring kinematics with a higher precision. Benchmarking exercises have given modelling an additional checking tool by outlining, in addition to the rheology of the modelling materials, the impact of different preparation approaches, the effect of boundary conditions, and the human factor on model results. However, despite the different approaches and deformation rigs, results of models of different tectonic laboratories have shown a great deal of similarities. Even with the introduction of more sophisticated numerical codes and usage of more powerful computers which enable the simulation of more challenging material properties and combinations of those, and 3D model set-up, analogue modelling can still play a significant role both as a physical checking tool and a complementary technique. Additional fine-tuning takes enables the technique to take on more challenging tasks. However, the foundation of the technique is in its link to natural prototypes and that model results can only give some hints about a geologic process or structure. Sixty years ago, Ernest Cloos stated that "....Many interpretations would never have been published if the author had only once tried his suggested mechanism of folding or faulting in an experiment". He has also said that "... experimenting is a good deal of fun". Both statements do still hold!

  6. Secondary structure of the rRNA ITS2 region reveals key evolutionary patterns in acroporid corals.

    PubMed

    Coleman, Annette W; van Oppen, Madeleine J H

    2008-10-01

    This study investigates the ribosomal RNA transcript secondary structure in corals as confirmed by compensatory base changes in Isopora/Acropora species. These species are unique versus all other corals in the absence of a eukaryote-wide conserved structural component, the helix III in internal transcriber spacer (ITS) 2, and their variability in the 5.8S-LSU helix basal to ITS2, a helix with pairings identical among all other scleractinian corals. Furthermore, Isopora/Acropora individuals display at least two, and as many as three, ITS sequence isotypes in their genome which appear to be capable of function. From consideration of the conserved elements in ITS2 and flanking regions, it appears that there are three major groups within the IsoporaAcropora lineage: the Isopora + Acropora "longi" group, the large group including Caribbean Acropora + the Acropora "carib" types plus the bulk of the Indo-Pacific Acropora species, and the remaining enigmatic "pseudo" group found in the Pacific. Interbreeding is possible among Caribbean A. palmata and A. cervicornis and among some species of Indo-Pacific Acropora. Recombinant ITS sequences are obvious among these latter, such that morphology (as represented by species name) does not correlate with common ITS sequence. The combination of characters revealed by RNA secondary structure analyses suggests a recent past/current history of interbreeding among the Indo-Pacific Acropora species and a shared ancestry of some of these with the Caribbean Acropora. The unusual absence of helix III of ITS2 of Isopora/Acropora species may have some causative role in the equally unusual instability in the 5.8S-LSU helix basal to ITS2 of this species complex. PMID:18781354

  7. Keys to Lipid Selection in Fatty Acid Amide Hydrolase Catalysis: Structural Flexibility, Gating Residues and Multiple Binding Pockets

    PubMed Central

    Palermo, Giulia; Bauer, Inga; Campomanes, Pablo; Cavalli, Andrea; Armirotti, Andrea; Girotto, Stefania; Rothlisberger, Ursula; De Vivo, Marco

    2015-01-01

    The fatty acid amide hydrolase (FAAH) regulates the endocannabinoid system cleaving primarily the lipid messenger anandamide. FAAH has been well characterized over the years and, importantly, it represents a promising drug target to treat several diseases, including inflammatory-related diseases and cancer. But its enzymatic mechanism for lipid selection to specifically hydrolyze anandamide, rather than similar bioactive lipids, remains elusive. Here, we clarify this mechanism in FAAH, examining the role of the dynamic paddle, which is formed by the gating residues Phe432 and Trp531 at the boundary between two cavities that form the FAAH catalytic site (the “membrane-access” and the “acyl chain-binding” pockets). We integrate microsecond-long MD simulations of wild type and double mutant model systems (Phe432Ala and Trp531Ala) of FAAH, embedded in a realistic membrane/water environment, with mutagenesis and kinetic experiments. We comparatively analyze three fatty acid substrates with different hydrolysis rates (anandamide > oleamide > palmitoylethanolamide). Our findings identify FAAH’s mechanism to selectively accommodate anandamide into a multi-pocket binding site, and to properly orient the substrate in pre-reactive conformations for efficient hydrolysis that is interceded by the dynamic paddle. Our findings therefore endorse a structural framework for a lipid selection mechanism mediated by structural flexibility and gating residues between multiple binding cavities, as found in FAAH. Based on the available structural data, this exquisite catalytic strategy for substrate specificity seems to be shared by other lipid-degrading enzymes with similar enzymatic architecture. The mechanistic insights for lipid selection might assist de-novo enzyme design or drug discovery efforts. PMID:26111155

  8. Crystal Structure and Substrate Recognition of Cellobionic Acid Phosphorylase, Which Plays a Key Role in Oxidative Cellulose Degradation by Microbes.

    PubMed

    Nam, Young-Woo; Nihira, Takanori; Arakawa, Takatoshi; Saito, Yuka; Kitaoka, Motomitsu; Nakai, Hiroyuki; Fushinobu, Shinya

    2015-07-24

    The microbial oxidative cellulose degradation system is attracting significant research attention after the recent discovery of lytic polysaccharide mono-oxygenases. A primary product of the oxidative and hydrolytic cellulose degradation system is cellobionic acid (CbA), the aldonic acid form of cellobiose. We previously demonstrated that the intracellular enzyme belonging to glycoside hydrolase family 94 from cellulolytic fungus and bacterium is cellobionic acid phosphorylase (CBAP), which catalyzes reversible phosphorolysis of CbA into glucose 1-phosphate and gluconic acid (GlcA). In this report, we describe the biochemical characterization and the three-dimensional structure of CBAP from the marine cellulolytic bacterium Saccharophagus degradans. Structures of ligand-free and complex forms with CbA, GlcA, and a synthetic disaccharide product from glucuronic acid were determined at resolutions of up to 1.6 Å. The active site is located near the dimer interface. At subsite +1, the carboxylate group of GlcA and CbA is recognized by Arg-609 and Lys-613. Additionally, one residue from the neighboring protomer (Gln-190) is involved in the carboxylate recognition of GlcA. A mutational analysis indicated that these residues are critical for the binding and catalysis of the aldonic and uronic acid acceptors GlcA and glucuronic acid. Structural and sequence comparisons with other glycoside hydrolase family 94 phosphorylases revealed that CBAPs have a unique subsite +1 with a distinct amino acid residue conservation pattern at this site. This study provides molecular insight into the energetically efficient metabolic pathway of oxidized sugars that links the oxidative cellulolytic pathway to the glycolytic and pentose phosphate pathways in cellulolytic microbes. PMID:26041776

  9. Crystal Structure Analysis of Human Glutamine : Fructose 6-Phosphate Amidotransferase, a Key Regulator in Type 2 Diabetes

    NASA Astrophysics Data System (ADS)

    Nakaishi, Yuichiro; Bando, Masahiko

    Glutamine : fructose 6-phosphate amidotransferase (GFAT) is a rate-limiting enzyme in the hexoamine biosythetic pathway and plays an important role in type 2 diabetes. We now report the first structures of the isomerase domain of the human GFAT in the presence of cyclic glucose 6-phosphate and linear glucosamine 6-phosphate. The C-terminal tail including the active site displays a rigid conformation, similar to the corresponding Escherichia coli enzyme. The diversity of the CF helix near the active site suggests the helix is a major target for drug design. Our study provides insights into the development of therapeutic drugs for type 2 diabetes.

  10. Reactions of ?-Propiolactone with Nucleobase Analogues, Nucleosides, and Peptides

    PubMed Central

    Uittenbogaard, Joost P.; Zomer, Bert; Hoogerhout, Peter; Metz, Bernard

    2011-01-01

    ?-Propiolactone is often applied for inactivation of viruses and preparation of viral vaccines. However, the exact nature of the reactions of ?-propiolactone with viral components is largely unknown. The purpose of the current study was to elucidate the chemical modifications occurring on nucleotides and amino acid residues caused by ?-propiolactone. Therefore, a set of nucleobase analogues was treated with ?-propiolactone, and reaction products were identified and quantified. NMR revealed at least one modification in either deoxyguanosine, deoxyadenosine, or cytidine after treatment with ?-propiolactone. However, no reaction products were found from thymidine and uracil. The most reactive sides of the nucleobase analogues and nucleosides were identified by NMR. Furthermore, a series of synthetic peptides was used to determine the conversion of reactive amino acid residues by liquid chromatography-mass spectrometry. ?-Propiolactone was shown to react with nine different amino acid residues. The most reactive residues are cysteine, methionine, and histidine and, to a lesser degree, aspartic acid, glutamic acid, tyrosine, lysine, serine, and threonine. Remarkably, cystine residues (disulfide groups) do not react with ?-propiolactone. In addition, no reaction was observed for ?-propiolactone with asparagine, glutamine, and tryptophan residues. ?-Propiolactone modifies proteins to a larger extent than expected from current literature. In conclusion, the study determined the reactivity of ?-propiolactone with nucleobase analogues, nucleosides, and amino acid residues and elucidated the chemical structures of the reaction products. The study provides detailed knowledge on the chemistry of ?-propiolactone inactivation of viruses. PMID:21868382

  11. Noble gas encapsulation: clathrate hydrates and their HF doped analogues.

    PubMed

    Mondal, Sukanta; Chattaraj, Pratim Kumar

    2014-09-01

    The significance of clathrate hydrates lies in their ability to encapsulate a vast range of inert gases. Although the natural abundance of a few noble gases (Kr and Xe) is poor their hydrates are generally abundant. It has already been reported that HF doping enhances the stability of hydrogen hydrates and methane hydrates, which prompted us to perform a model study on helium, neon and argon hydrates with their HF doped analogues. For this purpose 5(12), 5(12)6(8) and their HF doped analogues are taken as the model clathrate hydrates, which are among the building blocks of sI, sII and sH types of clathrate hydrate crystals. We use the dispersion corrected and gradient corrected hybrid density functional theory for the calculation of thermodynamic parameters as well as conceptual density functional theory based reactivity descriptors. The method of the ab initio molecular dynamics (AIMD) simulation is used through atom centered density matrix propagation (ADMP) techniques to envisage the structural behaviour of different noble gas hydrates on a 500 fs timescale. Electron density analysis is carried out to understand the nature of Ng-OH2, Ng-FH and Ng-Ng interactions. The current results noticeably demonstrate that the noble gas (He, Ne, and Ar) encapsulation ability of 5(12), 5(12)6(8) and their HF doped analogues is thermodynamically favourable. PMID:25047071

  12. Stereochemical Assignment of Strigolactone Analogues Confirms Their Selective Biological Activity.

    PubMed

    Artuso, Emma; Ghibaudi, Elena; Lace, Beatrice; Marabello, Domenica; Vinciguerra, Daniele; Lombardi, Chiara; Koltai, Hinanit; Kapulnik, Yoram; Novero, Mara; Occhiato, Ernesto G; Scarpi, Dina; Parisotto, Stefano; Deagostino, Annamaria; Venturello, Paolo; Mayzlish-Gati, Einav; Bier, Ariel; Prandi, Cristina

    2015-11-25

    Strigolactones (SLs) are new plant hormones with various developmental functions. They are also soil signaling chemicals that are required for establishing beneficial mycorrhizal plant/fungus symbiosis. In addition, SLs play an essential role in inducing seed germination in root-parasitic weeds, which are one of the seven most serious biological threats to food security. There are around 20 natural SLs that are produced by plants in very low quantities. Therefore, most of the knowledge on SL signal transduction and associated molecular events is based on the application of synthetic analogues. Stereochemistry plays a crucial role in the structure-activity relationship of SLs, as compounds with an unnatural D-ring configuration may induce biological effects that are unrelated to SLs. We have synthesized a series of strigolactone analogues, whose absolute configuration has been elucidated and related with their biological activity, thus confirming the high specificity of the response. Analogues bearing the R-configured butenolide moiety showed enhanced biological activity, which highlights the importance of this stereochemical motif. PMID:26502774

  13. A First Principles Density-Functional Calculation of the Electronic and Vibrational Structure of the Key Melanin Monomers

    E-print Network

    B. J. Powell; T. Baruah; N. Bernstein; K. Brake; Ross H. McKenzie; P. Meredith; M. R. Pederson

    2004-01-23

    We report first principles density functional calculations for hydroquinone (HQ), indolequinone (IQ) and semiquinone (SQ). These molecules are believed to be the basic building blocks of the eumelanins, a class of bio-macromolecules with important biological functions (including photoprotection) and with potential for certain bioengineering applications. We have used the DeltaSCF (difference of self consistent fields) method to study the energy gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), Delta_HL. We show that Delta_HL is similar in IQ and SQ but approximately twice as large in HQ. This may have important implications for our understanding of the observed broad band optical absorption of the eumelanins. The possibility of using this difference in Delta_HL to molecularly engineer the electronic properties of eumelanins is discussed. We calculate the infrared and Raman spectra of the three redox forms from first principles. Each of the molecules have significantly different infrared and Raman signatures, and so these spectra could be used in situ to non-destructively identify the monomeric content of macromolecules. It is hoped that this may be a helpful analytical tool in determining the structure of eumelanin macromolecules and hence in helping to determine the structure-property-function relationships that control the behaviour of the eumelanins.

  14. Key microstructures controlling the mechanical properties of two-phase TiAl alloys with lamellar structures

    SciTech Connect

    Liu, C.T.; Maziasz, P.J.; Wright, J.L.

    1996-12-31

    TiAl alloys with the base composition of Ti-47Al-2Cr-2Nb (at.%) were prepared by arc melting and drop casting, followed by hot extrusion above the {alpha}-transus temperature, T{sub {alpha}}. The hot extruded materials were then heat treated above and below T{sub {alpha}} in order to control microstructural features in these lamellar structures. Mechanical properties of these alloys were determined by tensile testing at temperatures to 1000 C. Tensile elongation at room temperature (RT) is strongly dependent on grain size, showing increased ductility with decreasing grain size. Strength at RT and elevated temperatures is sensitive to interlamellar spacing, showing increased strength with decreasing lamellar spacing. Hall-Petch relations hold well for yield strength at RT and elevated temperatures and for tensile elongation at RT. Tensile elongations of about 5% and yield strengths around 900 MPa are achieved by controlling both colony size and interlamellar spacing. Mechanical properties of the TiAl alloys with controlled lamellar structures produced directly by hot extrusion are much superior to those produced by conventional thermomechanical treatments.

  15. Ring substitution influences oxidative cyclisation and reactive metabolite formation of nordihydroguaiaretic acid analogues.

    PubMed

    Asiamah, Isaac; Hodgson, Heather L; Maloney, Katherine; Allen, Kevin J H; Krol, Ed S

    2015-11-01

    Nordihydroguaiaretic acid (NDGA) is a natural polyphenol with a broad spectrum of pharmacological properties. However, its usefulness is hindered by the lack of understanding of its pharmacological and toxicological pathways. Previously we showed that oxidative cyclisation of NDGA at physiological pH forms a dibenzocyclooctadiene that may have therapeutic benefits whilst oxidation to an ortho-quinone likely mediates toxicological properties. NDGA analogues with higher propensity to cyclise under physiologically relevant conditions might have pharmacological implications, which motivated this study. We synthesized a series of NDGA analogues which were designed to investigate the structural features which influence the intramolecular cyclisation process and help to understand the mechanism of NDGA's autoxidative conversion to a dibenzocyclooctadiene lignan. We determined the ability of the NDGA analogues investigated to form dibenzocyclooctadienes and evaluated the oxidative stability at pH 7.4 of the analogues and the stability of any dibenzocyclooctadienes formed from the NDGA analogues. We found among our group of analogues the catechols were less stable than phenols, a single catechol-substituted ring is insufficient to form a dibenzocyclooctadiene lignan, and only compounds possessing a di-catechol could form dibenzocyclooctadienes. This suggests that quinone formation may not be necessary for cyclisation to occur and the intramolecular cyclisation likely involves a radical-mediated rather than an electrophilic substitution process. We also determined that the catechol dibenzocyclooctadienes autoxidised at comparable rates to the parent catechol. This suggests that assigning in vitro biological activity to the NDGA dibenzocyclooctadiene is premature and requires additional study. PMID:26439661

  16. Strong electron donation induced differential nonradiative decay pathways for para and meta GFP chromophore analogues.

    PubMed

    Chatterjee, Tanmay; Mandal, Mrinal; Gude, Venkatesh; Bag, Partha Pratim; Mandal, Prasun K

    2015-08-28

    Z-E Isomerisation because of rotation around the exocyclic double bond (known as the ?-twist) and not any other internal conversion has been reported to be the major nonradiative decay channel for non-hydroxylic unconstrained para and meta GFP chromophore analogues. The equation ?f + 2?ZE = 1 has been shown to hold well for both para and meta GFP chromophore analogues. If the above equation holds true, then upon reducing the extent of Z-E isomerisation (?ZE), the fluorescence quantum yield (?f) should increase. To probe the above proposition two sets of non-hydroxylic unconstrained para and meta GFP chromophore analogues were synthesized. Quite interestingly by introducing the strongly electron donating -NEt2 group to the benzenic moiety these para and meta GFP chromophore analogues were shown to exhibit differential optical behaviour w.r.t. the extent of the solvatochromic shift, ?f, ?ZE, and ?f. For the first time it has been shown that the well accepted equation ?f + 2?ZE = 1 does not hold at all for these non-hydroxylic unconstrained meta analogues. Although ?ZE has been shown to be <10%, ?f is much lower than the expected near unity value for these meta analogues. After detailed investigation into the nonradiative excited state decay channel, contrary to literature reports, energy gap law governed internal conversion and not Z-E isomerisation was shown to be the major nonradiative decay channel for these meta analogues. Two models are put forward to understand the differential optical behaviour of these para and meta GFP chromophore analogues. Support from X-ray crystal structures, NMR experiments, and computational calculations has also been provided. PMID:26176350

  17. Synthetic chondramide A analogues stabilize filamentous actin and block invasion by Toxoplasma gondii.

    PubMed

    Ma, Christopher I; Diraviyam, Karthikeyan; Maier, Martin E; Sept, David; Sibley, L David

    2013-09-27

    Apicomplexan parasites such as Toxoplasma gondii rely on actin-based motility to cross biological barriers and invade host cells. Key structural and biochemical differences in host and parasite actins make this an attractive target for small-molecule inhibitors. Here we took advantage of recent advances in the synthesis of cyclic depsipeptide compounds that stabilize filamentous actin to test the ability of chondramides to disrupt growth of T. gondii in vitro. Structural modeling of chondramide A (2) binding to an actin filament model revealed variations in the binding site between host and parasite actins. A series of 10 previously synthesized analogues (2b-k) with substitutions in the ?-tyrosine moiety blocked parasite growth on host cell monolayers with EC?? values that ranged from 0.3 to 1.3 ?M. In vitro polymerization assays using highly purified recombinant actin from T. gondii verified that synthetic and natural product chondramides target the actin cytoskeleton. Consistent with this, chondramide treatment blocked parasite invasion into host cells and was more rapidly effective than pyrimethamine, a standard therapeutic agent. Although the current compounds lack specificity for parasite vs host actin, these studies provide a platform for the future design and synthesis of synthetic cyclic peptide inhibitors that selectively disrupt actin dynamics in parasites. PMID:24020843

  18. Model Membrane and Cell Studies of Antimicrobial Activity of Melittin Analogues.

    PubMed

    Jamasbi, Elaheh; Mularski, Anna; Separovic, Frances

    2016-01-01

    Melittin is a 26 residue peptide and the major component of bee (Apis mellifera) venom. Although melittin has both anticancer and antimicrobial properties, utilization has been limited due to its high lytic activity against eukaryotic cells. The mechanism of this lytic activity remains unclear but several mechanisms have been proposed, including pore formation or a detergent like mechanism, which result in lysis of cell membranes. Several analogues of melittin have been synthesized to further understand the role of specific residues in its antimicrobial and lytic activity. Melittin analogues that have a proline residue substituted for an alanine, lysine or cysteine have been studied with both model membrane systems and living cells. These studies have revealed that the proline residue plays a critical role in antimicrobial activity and cytotoxicity. Analogues lacking the proline residue and dimers of these analogues displayed decreased cytotoxicity and minimum inhibition concentrations. Several mutant studies have shown that, when key substitutions are made, the resultant peptides have more activity in terms of pore formation than the native melittin. Designing analogues that retain antimicrobial and anticancer activity while minimizing haemolytic activity will be a promising way to utilize melittin as a potential therapeutic agent. PMID:26139117

  19. Lithospheric flexure: the key to the structural evolution of large volcanic edifices on the terrestrial planets. (Invited)

    NASA Astrophysics Data System (ADS)

    McGovern, P. J.

    2009-12-01

    Large volcanic edifices, such as the majestic Hawaiian islands, the immense Olympus Mons on Mars, and the numerous, broad, but relatively short basaltic shields of Venus, constitute enormous excess masses at the surfaces of their respective planets. The lithosphere, the mechanically strong outer layer of a planet, responds to growing edifice loads on a regional scale by flexing, in a manner similar to a loaded beam in a building. The shape of lithospheric flexure and the resulting stress state exert critical influences on the structure of the evolving edifices, which in turn feed back into the flexural response. Flexural depression of the lithosphere forms topographic moats surrounding volcanoes; these depressions are partially to completely filled by landslide debris, volcaniclastic materials, and sediments (Hawaii, Marquesas, Reunion chains, Olympus Mons), or flat aprons of volcanic flows (Venusian volcanoes, Tharsis Montes on Mars). Flexure produces a "dipole" state of stress in the lithosphere beneath the edifice: extension at the bottom, and compression at the top. The orientation of the most compressive stress,?1, is therefore vertical in the lower lithosphere and horizontal in the upper lithosphere. The effects of this dipole were manifested physically in the Hawaiian earthquake pair of October 15, 2006 (see McGovern, GRL, 2007). By Anderson's criteria for intrusive magma ascent, the lower lithosphere stress state is conducive to magma ascent in vertical dikes, but in the upper lithosphere, ascending magma will get diverted into sub-horizontal sills. Finite element models of pressurization of magma chambers embedded in flexing lithospheres demonstrate this tendency: chambers in the upper (compressional) lithosphere fail near their middles under a stress state that favors sill formation (see Galgana et al., this volume). Thus, chambers are likely to assume oblate forms via lateral expansion, perhaps producing an extensive sill complex. Such complexes may express themselves at the surface by topographic slope breaks and annular zones of faulting (from both tectonic stresses and dikes emanating from the distal ends of the sills), as seen at Alba Patera on Mars and structures termed "coronae" on Venus. The state of compression in the upper lithosphere is generally transmitted into the edifice, unless the edifice is allowed to spread outwards along a basal decollement, as seen at the Hawaiian edifices and Olympus Mons. The absence of flexurally-induced compression at Hawaiian edifices accounts for the prominence of Hawaiian rift zones. Distinct Element models that account for movement-inhibiting effects of flexure show that the concave-up flank shape of Olympus Mons may be related to a flexure-spreading interaction (see McGovern and Morgan, Geology, 2009). Flexural stresses also affect magma ascent by influencing the pressure balance in dikes. Such considerations lead to a second criterion for magma ascent (Rubin, 1995): positive stress gradients in the lithosphere favor ascent. Models of flexure that account for both criteria predict a link between lithospheric thickness Te and edifice shape. Te modulates stress magnitudes and flexural wavelengths such that particular edifice shapes (conical, domical, and annular) correspond to particular ranges of Te (high, moderate, and low, respectively). Annular edifices may correspond to a subset of the coronae on Venus.

  20. Drug-likeness of Phytic Acid and Its Analogues

    PubMed Central

    Joy, Amitha; Balaji, S.

    2015-01-01

    Inositol hexakisphosphate is known to be the phosphorous reserve in plants particularly in the seeds. Though it has been known for its antinutrient properties for many years, recent research shed light to reveal it as a novel anticancer agent. Hence the present study investigates the drug-likeness of phytic acid and its analogues through bioinformatics methods. Two potential cancer drug targets such as mitogen activated kinase and inositol 1,4,5-triphosphate receptor are included in the study. Out of 50 selected analogues of phytic acid, 42 structures interact well with the chosen drug targets. The best interacting structures are 1-diphosinositol pentakisphosphate and 2,3,4,5,6-pentaphosphonooxycyclohexyl dihydrogen phosphate. For both of these structures, the negative binding energy obtained was -49.5 KJ/mol; this affirms the stability of the complex. ADME properties are also predicted to assess the drug-like properties of the compounds. The structure activity relationship model is generated for 12 compounds with experimental IC50 values. PMID:26668666

  1. The Nisi Fault as a key structure for understanding the active deformation of the NW Peloponnese, Greece

    NASA Astrophysics Data System (ADS)

    Zygouri, V.; Koukouvelas, I. K.; Kokkalas, S.; Xypolias, P.; Papadopoulos, G. A.

    2015-05-01

    The previously unknown Nisi Fault in NW Peloponnese was ruptured during the 2008 Movri Mountain earthquake attaining a maximum offset of 25 cm. The fault is interpreted as a branch of a flower structure above a blind strike-slip fault. We investigate the Nisi Fault seismotectonic evolution using morphotectonic analysis in order to determine whether the landscape is affected by tectonic forcing and paleoseismology to determine earthquake recurrence interval and fault slip rates. We applied several geomorphic indices, such as the asymmetry factor (AF), the stream length-gradient index (SL), the valley floor width to valley height ratio (Vf), the mountain-front sinuosity (Smf), the drainage basin shape (Bs) and the hypsometric curve (Hc), in four large drainage basins of the study area. The results show that fault-related vertical motions and the associated tilting influenced the drainage geometry and the landscape development. Values of stream-gradient indices (SL) are relatively high close to the fault trace. Mountain-front sinuosity (Smf) mean values along the fault zones range from 1.12 to 1.23. Valley floor width to valley height ratios (Vf) mean values along the studied fault range between 0.21 and 2.50. Drainage basin shape (BS) mean values along the fault range from 1.04 to 3.72. Lateral fault growth was likely achieved by propagation primarily towards north-northwestward. The paleoseismic history of the fault, investigated by a trench and 14C dating of seven samples, indicates two morphogenic earthquakes in the last 1 kyr. Therefore, we suggest that the Nisi Fault displays a slip rate on the order of 1 mm/yr and a recurrence interval ranging between 300 and 600 years. From a seismotectonic point of view, the fault is classified as high activity rate, with abundant but discontinuous geomorphic evidence of its activity. Other similar faults affecting the western Peloponnese can be envisaged with a similar procedure. Additionally, the seismic history and surface expression of the Nisi Fault, resembles other faults of similar length in Greece and Italy. Particularly, a crucial issue in terms of seismic risk management is that neotectonic analysis has to be envisaged carefully on short in length faults, since these faults can be possibly related to strong earthquakes.

  2. Imperial College London EEE 1L1 Autumn 2009 E2.2 Analogue Electronics E2.2 Analogue Electronics

    E-print Network

    Papavassiliou, Christos

    Imperial College London ­ EEE 1L1 Autumn 2009 E2.2 Analogue Electronics E2.2 Analogue Electronics Autumn 2009 E2.2 Analogue Electronics What analogue electronics is · Engineering, i.e. the analysis ­ EEE 3L1 Autumn 2009 E2.2 Analogue Electronics analogue electronics is not only · CMOS integrated

  3. Structural Studies of Cinnamoyl-CoA Reductase and Cinnamyl-Alcohol Dehydrogenase, Key Enzymes of Monolignol Biosynthesis[C][W

    PubMed Central

    Pan, Haiyun; Zhou, Rui; Louie, Gordon V.; Mühlemann, Joëlle K.; Bomati, Erin K.; Bowman, Marianne E.; Dudareva, Natalia; Dixon, Richard A.; Noel, Joseph P.; Wang, Xiaoqiang

    2014-01-01

    The enzymes cinnamoyl-CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD) catalyze the two key reduction reactions in the conversion of cinnamic acid derivatives into monolignol building blocks for lignin polymers in plant cell walls. Here, we describe detailed functional and structural analyses of CCRs from Medicago truncatula and Petunia hybrida and of an atypical CAD (CAD2) from M. truncatula. These enzymes are closely related members of the short-chain dehydrogenase/reductase (SDR) superfamily. Our structural studies support a reaction mechanism involving a canonical SDR catalytic triad in both CCR and CAD2 and an important role for an auxiliary cysteine unique to CCR. Site-directed mutants of CAD2 (Phe226Ala and Tyr136Phe) that enlarge the phenolic binding site result in a 4- to 10-fold increase in activity with sinapaldehyde, which in comparison to the smaller coumaraldehyde and coniferaldehyde substrates is disfavored by wild-type CAD2. This finding demonstrates the potential exploitation of rationally engineered forms of CCR and CAD2 for the targeted modification of monolignol composition in transgenic plants. Thermal denaturation measurements and structural comparisons of various liganded and unliganded forms of CCR and CAD2 highlight substantial conformational flexibility of these SDR enzymes, which plays an important role in the establishment of catalytically productive complexes of the enzymes with their NADPH and phenolic substrates. PMID:25217505

  4. Synthesis and evaluation of derrubone and select analogues.

    PubMed

    Hastings, Jedidiah M; Hadden, M Kyle; Blagg, Brian S J

    2008-01-18

    Recently, we reported that the natural product derrubone exhibits Hsp90 inhibitory activity. Due to its unique architectural scaffold and proposed rapid assembly, the synthesis of this natural product was pursued with the aim of identifying structure--activity relationships. Synthesis of the natural product was accomplished in eight highly convergent steps, which led to a facile method for the construction of related compounds. Biological evaluation of derrubone and its analogues identified several compounds that exhibit low micromolar inhibitory activity against breast and colon cancer cell lines. PMID:18154304

  5. Synthesis, Preliminary Bioevaluation and Computational Analysis of Caffeic Acid Analogues

    PubMed Central

    Liu, Zhiqian; Fu, Jianjun; Shan, Lei; Sun, Qingyan; Zhang, Weidong

    2014-01-01

    A series of caffeic acid amides were designed, synthesized and evaluated for anti-inflammatory activity. Most of them exhibited promising anti-inflammatory activity against nitric oxide (NO) generation in murine macrophage RAW264.7 cells. A 3D pharmacophore model was created based on the biological results for further structural optimization. Moreover, predication of the potential targets was also carried out by the PharmMapper server. These amide analogues represent a promising class of anti-inflammatory scaffold for further exploration and target identification. PMID:24857914

  6. Excited state properties of a short ?-electron conjugated peridinin analogue

    NASA Astrophysics Data System (ADS)

    Magdaong, Nikki M.; Niedzwiedzki, Dariusz M.; Greco, Jordan A.; Liu, Hongbin; Yano, Koki; Kajikawa, Takayuki; Sakaguchi, Kazuhiko; Katsumura, Shigeo; Birge, Robert R.; Frank, Harry A.

    2014-02-01

    C29-peridinin is a synthetic analogue of the important, naturally-occurring carotenoid, peridinin, found in several marine algal species. C29-peridinin has five conjugated carbon-carbon double bonds compared to eight possessed by peridinin and also lacks the methyl group functionalities typically present along the polyene chain of carotenoids. These structural modifications lead to unique excited state properties and important insights regarding the factors controlling the photophysics of peridinin and other carbonyl-containing carotenoids, which are critical components of the light-harvesting systems of many photosynthetic organisms.

  7. Selective targeting of nuclear receptor FXR by avermectin analogues with therapeutic effects on nonalcoholic fatty liver disease

    PubMed Central

    Jin, Lihua; Wang, Rui; Zhu, Yanlin; Zheng, Weili; Han, Yaping; Guo, Fusheng; Ye, Frank Bin; Li, Yong

    2015-01-01

    Non-alcoholic fatty liver disease (NAFLD) has become a predictive factor of death from many diseases. Farnesoid X receptor (FXR) is an ideal target for NAFLD drug development due to its crucial roles in lipid metabolism. The aim of this work is to examine the molecular mechanisms and functional roles of FXR modulation by avermectin analogues in regulating metabolic syndromes like NAFLD. We found that among avermectin analogues studied, the analogues that can bind and activate FXR are effective in regulating metabolic parameters tested, including reducing hepatic lipid accumulation, lowering serum cholesterol and glucose levels, and improving insulin sensitivity, in a FXR dependent manner. Mechanistically, the avermectin analogues that interact with FXR exhibited features as partial agonists, with distinctive properties in modulating coregulator recruitment. Structural features critical for avermectin analogues to selectively bind to FXR were also revealed. This study indicated that in addition to antiparasitic activity, avermectin analogues are promising drug candidates to treat metabolism syndrome including NAFLD by directly targeting FXR. Additionally, the structural features that discriminate the selective binding of FXR by avermectin analogues may provide a unique safe approach to design drugs targeting FXR signaling. PMID:26620317

  8. Evaluation of novel cyclic analogues of apelin.

    PubMed

    Hamada, Juri; Kimura, Junko; Ishida, Junji; Kohda, Takeo; Morishita, Setsuo; Ichihara, Shigeyasu; Fukamizu, Akiyoshi

    2008-10-01

    Apelin regulates various cell signaling processes through interaction with its specific cell-surface receptor, APJ, which is a member of a seven transmembrane G protein-coupled receptor superfamily. To develop a novel apelin analogue, we synthesized cyclic analogues of minimal apelin fragment RPRLSHKGPMPF (apelin-12), and evaluated their bioactivities in a recombinant human APJ-expressed cell line. Three cyclic analogues were synthesized: cyclo apelin-12 (C1) in combination with amino-terminal to carboxy-terminal, cyclourea apelin-12 (C3) in combination with amino-terminal and amino acid side chain at positions 7, and cyclic apelin-12 (C4) in combination with amino acid side chain at positions 7 to carboxy-terminal. All cyclic analogues exhibited dose-dependent inhibitory effects against forskolin-induced cyclic adenosine monophosphate (cAMP) accumulation, and the maximal effects were almost abolished by pertussis toxin (PTx) treatment. Moreover, they could modulate the intracellular signaling pathways composed of Akt and extracellular signal-regulated kinase 1/2 (ERK1/2) serine/threonine protein kinases in PTx-sensitive manner. This is the first approach to apply cyclization on apelin, and these results provide the basis for the development of drug-like apelin analogues. PMID:18813863

  9. Chalcogen-bonded complexes of some carbon dioxide analogues

    NASA Astrophysics Data System (ADS)

    Ramasami, Ponnadurai; Ford, Thomas A.

    2014-08-01

    Ab initio calculations have been carried out on the sulphur-bonded van der Waals complexes formed between the carbon dioxide analogues carbonyl sulphide, carbon disulphide and thiocarbonyl selenide, and the common electron donors ammonia, water, phosphine and hydrogen sulphide. The structures of these twelve complexes are all similar, and involve an approximately linear XCS⋯Y fragment (X = O, S, Se; Y = N, O, P, S). These structures contrast with those of the oxygen-bound complexes of carbon dioxide, carbonyl sulphide and carbonyl selenide reported earlier which, with the exception of the hydrogen sulphide species, are characterized by four-membered rings with varying orientations involving the C, O, H and Y atoms. The molecular structures, interaction energies and vibrational spectra have been studied, and the variations in these properties have been correlated with the complex structures and with the molecular quadrupole moments of the acid monomers.

  10. Structuralism.

    ERIC Educational Resources Information Center

    Piaget, Jean

    Provided is an overview of the analytical method known as structuralism. The first chapter discusses the three key components of the concept of a structure: the view of a system as a whole instead of so many parts; the study of the transformations in the system; and the fact that these transformations never lead beyond the system but always…

  11. Total synthesis and biological evaluation of amphidinolide V and analogues.

    PubMed

    Fürstner, Alois; Flügge, Susanne; Larionov, Oleg; Takahashi, Yohei; Kubota, Takaaki; Kobayashi, Jun'ichi

    2009-01-01

    The awesome power of metathesis is illustrated by a concise synthesis of the extremely scarce marine natural product amphidinolide V, which hinges on a sequence of ring-closing alkyne metathesis followed by intermolecular enyne metathesis with ethylene (see scheme). As a complete set of conceivable stereoisomers was prepared, the constitution and absolute configuration of this macrolide could be established and first insights into structure-activity relationships governing its cytotoxicity were obtained.A sequence of ring-closing alkyne metathesis followed by an intermolecular enyne metathesis of the resulting cycloalkyne with ethene was used to forge the macrocyclic skeleton and to set the vicinal exo-methylene branches characteristic for the cytotoxic marine natural product amphidinolide V (1). Comparison of the synthetic material with an authentic sample of this extremely scarce metabolite isolated from a dinoflagellate of the Amphidinium sp. eliminated any doubts about its structure and allowed the absolute configuration of amphidinolide V to be determined as 8R,9S,10S,13R. Moreover, the flexibility inherent to the underlying synthesis blueprint also opened access to a comprehensive set of diastereomers of 1 as well as to synthetic analogues differing from the natural lead in the lipophilic chains appended to the macrocyclic core. This set of designed analogues gave first insights into structure-activity relationships, which revealed that the stereostructure of the macrolactone is a highly critical parameter, whereas the examined alterations of the side chain did not diminish the cytotoxicity of the compounds to any notable extent. PMID:19241434

  12. Quantitative comparisons of analogue models of brittle wedge dynamics

    NASA Astrophysics Data System (ADS)

    Schreurs, Guido

    2010-05-01

    Analogue model experiments are widely used to gain insights into the evolution of geological structures. In this study, we present a direct comparison of experimental results of 14 analogue modelling laboratories using prescribed set-ups. A quantitative analysis of the results will document the variability among models and will allow an appraisal of reproducibility and limits of interpretation. This has direct implications for comparisons between structures in analogue models and natural field examples. All laboratories used the same frictional analogue materials (quartz and corundum sand) and prescribed model-building techniques (sieving and levelling). Although each laboratory used its own experimental apparatus, the same type of self-adhesive foil was used to cover the base and all the walls of the experimental apparatus in order to guarantee identical boundary conditions (i.e. identical shear stresses at the base and walls). Three experimental set-ups using only brittle frictional materials were examined. In each of the three set-ups the model was shortened by a vertical wall, which moved with respect to the fixed base and the three remaining sidewalls. The minimum width of the model (dimension parallel to mobile wall) was also prescribed. In the first experimental set-up, a quartz sand wedge with a surface slope of ˜20° was pushed by a mobile wall. All models conformed to the critical taper theory, maintained a stable surface slope and did not show internal deformation. In the next two experimental set-ups, a horizontal sand pack consisting of alternating quartz sand and corundum sand layers was shortened from one side by the mobile wall. In one of the set-ups a thin rigid sheet covered part of the model base and was attached to the mobile wall (i.e. a basal velocity discontinuity distant from the mobile wall). In the other set-up a basal rigid sheet was absent and the basal velocity discontinuity was located at the mobile wall. In both types of experiments, models accommodated initial shortening by a forward- and a backward-verging thrust. Further shortening was taken up by in-sequence formation of forward-verging thrusts. In all experiments, boundary stresses created significant drag of structures along the sidewalls. We therefore compared the surface slope and the location, dip angle and spacing of thrusts in sections through the central part of the model. All models show very similar cross-sectional evolutions demonstrating reproducibility of first-order experimental observations. Nevertheless, there are significant along-strike variations of structures in map view highlighting the limits of interpretations of analogue model results. These variations may be related to the human factor, differences in model width and/or differences in laboratory temperature and especially humidity affecting the mechanical properties of the granular materials. GeoMod2008 Analogue Team: Susanne Buiter, Caroline Burberry, Jean-Paul Callot, Cristian Cavozzi, Mariano Cerca, Ernesto Cristallini, Alexander Cruden, Jian-Hong Chen, Leonardo Cruz, Jean-Marc Daniel, Victor H. Garcia, Caroline Gomes, Céline Grall, Cecilia Guzmán, Triyani Nur Hidayah, George Hilley, Chia-Yu Lu, Matthias Klinkmüller, Hemin Koyi, Jenny Macauley, Bertrand Maillot, Catherine Meriaux, Faramarz Nilfouroushan, Chang-Chih Pan, Daniel Pillot, Rodrigo Portillo, Matthias Rosenau, Wouter P. Schellart, Roy Schlische, Andy Take, Bruno Vendeville, Matteo Vettori, M. Vergnaud, Shih-Hsien Wang, Martha Withjack, Daniel Yagupsky, Yasuhiro Yamada

  13. Dolastatin 11 conformations, analogues and pharmacophore.

    PubMed

    Ali, Md Ahad; Bates, Robert B; Crane, Zackary D; Dicus, Christopher W; Gramme, Michelle R; Hamel, Ernest; Marcischak, Jacob; Martinez, David S; McClure, Kelly J; Nakkiew, Pichaya; Pettit, George R; Stessman, Chad C; Sufi, Bilal A; Yarick, Gayle V

    2005-07-01

    Twenty analogues of the natural antitumor agent dolastatin 11, including majusculamide C, were synthesized and tested for cytotoxicity against human cancer cells and stimulation of actin polymerization. Only analogues containing the 30-membered ring were active. Molecular modeling and NMR evidence showed the low-energy conformations. The amide bonds are all trans except for the one between the Tyr and Val units, which is cis. Since an analogue restricted to negative 2-3-4-5 angles stimulated actin polymerization but was inactive in cells, the binding conformation (most likely the lowest-energy conformation in water) has a negative 2-3-4-5 angle, whereas a conformation with a positive 2-3-4-5 angle (most likely the lowest energy conformation in chloroform) goes through cell walls. The highly active R alcohol from borohydride reduction of dolastatin 11 is a candidate for conversion to prodrugs. PMID:15878670

  14. Dynamics of water in prussian blue analogues: Neutron scattering study

    SciTech Connect

    Sharma, V. K.; Mitra, S.; Thakur, N.; Yusuf, S. M.; Mukhopadhyay, R.; Juranyi, Fanni

    2014-07-21

    Dynamics of crystal water in Prussian blue (PB), Fe(III){sub 4}[Fe(II)(CN){sub 6}]{sub 3}.14H{sub 2}O and its analogue Prussian green (PG), ferriferricynaide, Fe(III){sub 4}[Fe(III)(CN){sub 6}]{sub 4}.16H{sub 2}O have been investigated using Quasielastic Neutron Scattering (QENS) technique. PB and its analogue compounds are important materials for their various interesting multifunctional properties. It is known that crystal water plays a crucial role towards the multifunctional properties of Prussian blue analogue compounds. Three structurally distinguishable water molecules: (i) coordinated water molecules at empty nitrogen sites, (ii) non-coordinated water molecules in the spherical cavities, and (iii) at interstitial sites exist in PB. Here spherical cavities are created due to the vacant sites of Fe(CN){sub 6} units. However, PG does not have any such vacant N or Fe(CN){sub 6} units, and only one kind of water molecules, exists only at interstitial sites. QENS experiments have been carried out on both the compounds in the temperature range of 260–360?K to elucidate the dynamical behavior of different kinds of water molecules. Dynamics is found to be much more pronounced in case of PB, compared to PG. A detailed data analysis showed that localized translational diffusion model could describe the observed data for both PB and PG systems. The average diffusion coefficient is found to be much larger in the PB than PG. The obtained domain of dynamics is found to be consistent with the geometry of the structure of the two systems. Combining the data of the two systems, a quantitative estimate of the dynamics, corresponding to the water molecules at different locations is made.

  15. A microenvironment-sensitive fluorescent pyrimidine ribonucleoside analogue: synthesis, enzymatic incorporation, and fluorescence detection of a DNA abasic site.

    PubMed

    Tanpure, Arun A; Srivatsan, Seergazhi G

    2011-11-01

    Base-modified fluorescent ribonucleoside-analogue probes are valuable tools in monitoring RNA structure and function because they closely resemble the structure of natural nucleobases. Especially, 2-aminopurine, a highly environment-sensitive adenosine analogue, is the most extensively utilized fluorescent nucleoside analogue. However, only a few isosteric pyrimidine ribonucleoside analogues that are suitable for probing the structure and recognition properties of RNA molecules are available. Herein, we describe the synthesis and photophysical characterization of a small series of base-modified pyrimidine ribonucleoside analogues derived from tagging indole, N-methylindole, and benzofuran onto the 5-position of uracil. One of the analogues, based on a 5-(benzofuran-2-yl)pyrimidine core, shows emission in the visible region with a reasonable quantum yield and, importantly, displays excellent solvatochromism. The corresponding triphosphate substrate is effectively incorporated into oligoribonucleotides by T7 RNA polymerase to produce fluorescent oligoribonucleotide constructs. Steady-state and time-resolved spectroscopic studies with fluorescent oligoribonucleotide constructs demonstrate that the fluorescent ribonucleoside photophysically responds to subtle changes in its environment brought about by the interaction of the chromophore with neighboring bases. In particular, the emissive ribonucleoside, if incorporated into an oligoribonucleotide, positively reports the presence of a DNA abasic site with an appreciable enhancement in fluorescence intensity. The straightforward synthesis, amicability to enzymatic incorporation, and sensitivity to changes in the microenvironment highlight the potential of the benzofuran-conjugated pyrimidine ribonucleoside as an efficient fluorescent probe to investigate nucleic acid structure, dynamics, and recognition events. PMID:21956450

  16. A PIM? analogue suppresses allergic airway disease.

    PubMed

    Harper, Jacquie L; Hayman, Colin M; Larsen, David S; Painter, Gavin F; Singh-Gill, Gurmit

    2011-01-15

    Two approaches for the synthesis of a phosphatidylinositol dimannoside (PIM?) analogue 4 that mimics the suppressive activity of natural PIMs and also synthetic PIM? have been developed. This analogue, where the inositol core was replaced by glycerol, was tested for its ability to suppress cellular inflammation in a mouse model of allergic asthma and shown to be effective in suppressing airway eosinophilia. Suppression of all inflammatory cells monitored was observed, indicating a general blockade of cellular activity. These data indicate that the inositol core is not essential for this suppressive activity. PMID:21215641

  17. Key Indistinguishability vs. Strong Key Indistinguishability

    E-print Network

    International Association for Cryptologic Research (IACR)

    1 Key Indistinguishability vs. Strong Key Indistinguishability for Hierarchical Key Assignment Schemes Arcangelo Castiglione, Alfredo De Santis and Barbara Masucci Abstract A hierarchical key assignment scheme is a method to assign some private information and encryption keys to a set of classes

  18. Single molecule experiments emphasize GM1 as a key player of the different cytotoxicity of structurally distinct A?1-42 oligomers.

    PubMed

    Calamai, Martino; Evangelisti, Elisa; Cascella, Roberta; Parenti, Niccoló; Cecchi, Cristina; Stefani, Massimo; Pavone, Francesco

    2016-02-01

    It is well established that cytotoxic A? oligomers are the key factor that triggers the initial tissue and cell modifications eventually culminating in the development of Alzheimer's disease. A?1-42 oligomers display a high degree of polymorphism, and several structurally different oligomers have been described. Amongst them, two types, recently classified as A+ and A-, have been shown to possess similar size but distinct toxic properties, as a consequence of their biophysical and structural differences. Here, we have investigated by means of single molecule tracking the oligomer mobility on the plasma membrane of living neuroblastoma cells and the interaction with the ganglioside GM1, a component of membrane rafts. We have found that A+ and A- oligomers display a similar lateral diffusion on the plasma membrane of living cells. However, only the toxic A+ oligomers appear to interact and alter the mobility of GM1. We have also studied the lateral diffusion of each kind of oligomers in cells depleted or enriched in GM1. We found that the content of GM1 influences the diffusion of both types of oligomer, although the effect of the increased levels of GM1 is higher for the A+ type. Interestingly, the content of GM1 also affects significantly the mobility of GM1 molecules themselves. PMID:26656159

  19. Structural requirements for recognition of the HLA-Dw14 class II epitope: A key HLA determinant associated with rheumatoid arthritis

    SciTech Connect

    Hiraiwa, Akikazu; Yamanaka, Katsuo; Kwok, W.W.; Nepom, G.T. ); Mickelson, E.M.; Masewicz, S.; Hansen, J.A. ); Radka, S.F. )

    1990-10-01

    Although HLA genes have been shown to be associated with certain diseases, the basis for this association is unknown. Recent studies, however, have documented patterns of nucleotide sequence variation among some HLA genes associated with a particular disease. For rheumatoid arthritis, HLA genes in most patients have a shared nucleotide sequence encoding a key structural element of an HLA class II polypeptide; this sequence element is critical for the interaction of the HLA molecule with antigenic peptides and with responding T cells, suggestive of a direct role for this sequence element in disease susceptibility. The authors describe the serological and cellular immunologic characteristics encoded by this rheumatoid arthritis-associated sequence element. Site-directed mutagenesis of the DRB1 gene was used to define amino acids critical for antibody and T-cell recognition of this structural element, focusing on residues that distinguish the rheumatoid arthritis-associated alleles Dw4 and Dw14 from a closely related allele, Dw10, not associated with disease. Both the gain and loss of rheumatoid arthritis-associated epitopes were highly dependent on three residues within a discrete domain of the HLA-DR molecule. Recognition was most strongly influenced by the following amino acids (in order): 70 > 71 > 67. Some alloreactive T-cell clones were also influenced by amino acid variation in portions of the DR molecule lying outside the shared sequence element.

  20. Seven-membered azabridged neonicotinoids: synthesis, crystal structure, insecticidal assay, and molecular docking studies.

    PubMed

    Xu, Renbo; Luo, Ming; Xia, Rui; Meng, Xiaoqing; Xu, Xiaoyong; Xu, Zhiping; Cheng, Jiagao; Shao, Xusheng; Li, Houju; Li, Zhong

    2014-11-19

    To study the influence of the ring sizes, 37 novel seven-membered azabridged neonicotinoid analogues were synthesized by reactions of nitromethylene analogues, succinaldehyde, and aniline hydrochlorides. Most of the title compounds presented higher insecticidal activities than that of imidacloprid (IMI), cycloxaprid (CYC), and eight-membered compounds against cowpea aphid (Aphis craccivora), armyworm (Pseudaletia separata Walker), and brown planthopper (Nilaparvata lugens), which indicated that introducing the structure of a seven-membered azabridge could significantly improve the insecticidal activities of neonicotinoid analogues. Docking study and binding mode analysis also revealed that introducing methyl group into position 2 of phenyl ring could increase the hydrophobic interactions with receptor, which implied that position 2 might be the key site to get high insecticidal compounds. PMID:25347284

  1. The Need for Analogue Missions in Scientific Human and Robotic Planetary Exploration

    NASA Technical Reports Server (NTRS)

    Snook, K. J.; Mendell, W. W.

    2004-01-01

    With the increasing challenges of planetary missions, and especially with the prospect of human exploration of the moon and Mars, the need for earth-based mission simulations has never been greater. The current focus on science as a major driver for planetary exploration introduces new constraints in mission design, planning, operations, and technology development. Analogue missions can be designed to address critical new integration issues arising from the new science-driven exploration paradigm. This next step builds on existing field studies and technology development at analogue sites, providing engineering, programmatic, and scientific lessons-learned in relatively low-cost and low-risk environments. One of the most important outstanding questions in planetary exploration is how to optimize the human and robotic interaction to achieve maximum science return with minimum cost and risk. To answer this question, researchers are faced with the task of defining scientific return and devising ways of measuring the benefit of scientific planetary exploration to humanity. Earth-based and spacebased analogue missions are uniquely suited to answer this question. Moreover, they represent the only means for integrating science operations, mission operations, crew training, technology development, psychology and human factors, and all other mission elements prior to final mission design and launch. Eventually, success in future planetary exploration will depend on our ability to prepare adequately for missions, requiring improved quality and quantity of analogue activities. This effort demands more than simply developing new technologies needed for future missions and increasing our scientific understanding of our destinations. It requires a systematic approach to the identification and evaluation of the categories of analogue activities. This paper presents one possible approach to the classification and design of analogue missions based on their degree of fidelity in ten key areas. Various case studies are discussed to illustrate the approach.

  2. Directional flank spreading at Mount Cameroon volcano: Evidence from analogue modeling

    NASA Astrophysics Data System (ADS)

    Kervyn, M.; Wyk de Vries, B.; Walter, T. R.; Njome, M. S.; Suh, C. E.; Ernst, G. G. J.

    2014-10-01

    Mount Cameroon is characterized by an elongated summit plateau, steep flanks, and topographic terraces around its base. Although some of these features can be accounted for by intrusion-induced deformation, we here focus on the contribution of edifice-scale gravitational spreading in the structure of Mount Cameroon. We review the existing geological and geophysical data and morphostructural features of Mount Cameroon and surrounding sedimentary basins. Volcanic ridge gravitational spreading is then simulated by scaled analogue models on which fault formation is recorded using digital image correlation. Three sets of models are presented (i) models recorded in cross section (Type I), (ii) models recorded from above with a uniform (Type IIa), and (iii) nonuniform ductile layer (Type IIb). Type I models illustrate the formation of faults accommodating summit subsidence and lower flank spreading. Type IIa models favor displacement perpendicular to the long axis, with formation of a summit graben and basal folds, but fail to reproduce the steep flanks. Type IIb models investigate the effect of spatial variations in sediment thickness and/or properties consistent with geological evidence. Directional spreading of the volcano's central part perpendicular to the long axis is accounted for by a sediment layer with restricted lateral extent and increasing thickness away from the volcano axis. The later model closely reproduces key features observed at Mount Cameroon: steep upper flanks are accounted for by enhanced lateral spreading of the lower flanks relative to the summit. The relevance of these findings for understanding flank instabilities at large oceanic volcanoes is finally highlighted.

  3. Synthesis of Ruthenium Boryl Analogues of the Shvo Metal-Ligand Bifunctional Catalyst.

    PubMed

    Koren-Selfridge, Liza; Query, Ian P; Hanson, Joel A; Isley, Nicholas A; Guzei, Ilia A; Clark, Timothy B

    2010-01-01

    Metal boryl complexes have received significant attention in the literature in recent years due to their role as key intermediates in a number of metal-catalyzed borylation reactions. The ligand scaffold is known to have a significant impact on the observed reactivity of these metal boryl complexes. A synthetic strategy to access ruthenium boryl analogues of the Shvo metal-ligand catalysts is described. Heating a precursor to Shvo's catalyst (1) with bis(catecholato)diboron at 50 °C provided ruthenium boryl complex 3 [2,5-Ph(2)-3,4-Tol(2)(?(5)-C(4)COBcat)Ru(CO)(2)Bcat] (Bcat = catecholatoboryl). Addition of bis(catecholato)diboron to complex 1 in the presence of a phenol results in ruthenium boryl complex5 [2,5-Ph(2)-3,4-Tol(2)(?(5)-C(4)COH)Ru(CO)(2)Bcat] at 22 °C in 30% isolated yield. A single crystal X-ray analysis of complex 5 confirmed the assigned structure. An improved synthesis of ruthenium boryl complex 5 was developed by the in situ formation of complex 3 [2,5-Ph(2)-3,4-Tol(2)(?(5)-C(4)COBcat)Ru(CO)(2)Bcat] followed by addition of the phenol, resulting in a 51% yield. PMID:20835402

  4. Synthesis of Ruthenium Boryl Analogues of the Shvo Metal–Ligand Bifunctional Catalyst

    PubMed Central

    Koren-Selfridge, Liza; Query, Ian P.; Hanson, Joel A.; Isley, Nicholas A.; Guzei, Ilia A.; Clark, Timothy B.

    2010-01-01

    Metal boryl complexes have received significant attention in the literature in recent years due to their role as key intermediates in a number of metal-catalyzed borylation reactions. The ligand scaffold is known to have a significant impact on the observed reactivity of these metal boryl complexes. A synthetic strategy to access ruthenium boryl analogues of the Shvo metal–ligand catalysts is described. Heating a precursor to Shvo’s catalyst (1) with bis(catecholato)diboron at 50 °C provided ruthenium boryl complex 3 [2,5-Ph2-3,4-Tol2(?5-C4COBcat)Ru(CO)2Bcat] (Bcat = catecholatoboryl). Addition of bis(catecholato)diboron to complex 1 in the presence of a phenol results in ruthenium boryl complex5 [2,5-Ph2-3,4-Tol2(?5-C4COH)Ru(CO)2Bcat] at 22 °C in 30% isolated yield. A single crystal X-ray analysis of complex 5 confirmed the assigned structure. An improved synthesis of ruthenium boryl complex 5 was developed by the in situ formation of complex 3 [2,5-Ph2-3,4-Tol2(?5-C4COBcat)Ru(CO)2Bcat] followed by addition of the phenol, resulting in a 51% yield. PMID:20835402

  5. Arginine analogues incorporating carboxylate bioisosteric functions are micromolar inhibitors of human recombinant DDAH-1.

    PubMed

    Tommasi, Sara; Zanato, Chiara; Lewis, Benjamin C; Nair, Pramod C; Dall'Angelo, Sergio; Zanda, Matteo; Mangoni, Arduino A

    2015-12-14

    Dimethylarginine dimethylaminohydrolase (DDAH) is a key enzyme involved in the metabolism of asymmetric dimethylarginine (ADMA) and N-monomethyl arginine (NMMA), which are endogenous inhibitors of the nitric oxide synthase (NOS) family of enzymes. Two isoforms of DDAH have been identified in humans, DDAH-1 and DDAH-2. DDAH-1 inhibition represents a promising strategy to limit the overproduction of NO in pathological states without affecting the homeostatic role of this important messenger molecule. Here we describe the design and synthesis of 12 novel DDAH-1 inhibitors and report their derived kinetic parameters, IC50 and Ki. Arginine analogue 10a, characterized by an acylsulfonamide isosteric replacement of the carboxylate, showed a 13-fold greater inhibitory potential relative to the known DDAH-1 inhibitor, L-257. Compound 10a was utilized to study the putative binding interactions of human DDAH-1 inhibition using molecular dynamics simulations. The latter suggests that several stabilizing interactions occur in the DDAH-1 active-site, providing structural insights for the enhanced inhibitory potential demonstrated by in vitro inhibition studies. PMID:26420019

  6. CO2 Capture with Enzyme Synthetic Analogue

    SciTech Connect

    Harry Cordatos

    2010-03-01

    Project overview provides background on carbonic anhydrase transport mechanism for CO2 in the human body and proposed approach for ARPA-E project to create a synthetic enzyme analogue and utilize it in a membrane for CO2 capture from flue gas.

  7. Pyridopyrimidine analogues as novel adenosine kinase inhibitors.

    PubMed

    Zheng, G Z; Lee, C; Pratt, J K; Perner, R J; Jiang, M Q; Gomtsyan, A; Matulenko, M A; Mao, Y; Koenig, J R; Kim, K H; Muchmore, S; Yu, H; Kohlhaas, K; Alexander, K M; McGaraughty, S; Chu, K L; Wismer, C T; Mikusa, J; Jarvis, M F; Marsh, K; Kowaluk, E A; Bhagwat, S S; Stewart, A O

    2001-08-20

    A novel series of pyridopyrimidine analogues 9 was identified as potent adenosine kinase inhibitors based on the SAR and computational studies. Substitution of the C7 position of the pyridopyrimidino core with C2' substituted pyridino moiety increased the in vivo potency and enhanced oral bioavailability of these adenosine kinase inhibitors. PMID:11514141

  8. Differential Client Attractiveness in a Counseling Analogue

    ERIC Educational Resources Information Center

    Davis, Carl S.; And Others

    1977-01-01

    Investigated variations in conceptual complexity level of counselor and client on counselor attraction to the client. Counselor trainees rated attractiveness of clients following two counseling analogue tasks in which the client was depicted as exhibiting high or low conceptual level. More complex clients are more attractive across both levels.…

  9. Lunar Analogue Training at Meteor Crater, Arizona

    E-print Network

    Rathbun, Julie A.

    Lunar Analogue Training at Meteor Crater, Arizona & the San Francisco Volcanic Field, AZ April 28 Shaner Samuel Simmons Matt Weller Oliver White The left panel shows an aerial image of Meteor Crater, - 1 the most Meteor Crater-like of all lunar craters. #12;TABLE OF CONTENTS Reference

  10. UNSTRUCTURED MARINE FOOD WEBS AND "POLLUTANT ANALOGUES"

    E-print Network

    envi- ronments. The concentration factor found in the known and describable food chain of the Salton in the simple linear food chain ex- isting in that isolated marine environment and that the cesium/potassium (CsUNSTRUCTURED MARINE FOOD WEBS AND "POLLUTANT ANALOGUES" JOHN D. ISAACS' ABSTRACT The several

  11. Contemporary Mathematics Analogues of Koshliakov's Formula

    E-print Network

    Berndt, Bruce C.

    details on its proofs, especially that of Ramanujan, see the paper by the first author, Y. Lee, and JContemporary Mathematics Analogues of Koshliakov's Formula Bruce C. Berndt, Sun Kim, and Alexandru supported by NSA grant H98230-11-1-0200. c 0000 (copyright holder) 1 #12;2 BRUCE C. BERNDT, SUN KIM

  12. Edaphic, structural and physiological contrasts across Amazon Basin forest-savanna ecotones suggest a role for potassium as a key modulator of tropical woody vegetation structure and function

    NASA Astrophysics Data System (ADS)

    Lloyd, J.; Domingues, T. F.; Schrodt, F.; Ishida, F. Y.; Feldpausch, T. R.; Saiz, G.; Quesada, C. A.; Schwarz, M.; Torello-Raventos, M.; Gilpin, M.; Marimon, B. S.; Marimon-Junior, B. H.; Ratter, J. A.; Grace, J.; Nardoto, G. B.; Veenendaal, E.; Arroyo, L.; Villarroel, D.; Killeen, T. J.; Steininger, M.; Phillips, O. L.

    2015-11-01

    Sampling along a precipitation gradient in tropical South America extending from ca. 0.8 to 2.0 m a-1, savanna soils had consistently lower exchangeable cation concentrations and higher C / N ratios than nearby forest plots. These soil differences were also reflected in canopy averaged leaf traits with savanna trees typically having higher leaf mass per unit area but lower mass-based nitrogen (Nm) and potassium (Km). Both Nm and Km also increased with declining mean annual precipitation (PA), but most area-based leaf traits such as leaf photosynthetic capacity showed no systematic variation with PA or vegetation type. Despite this invariance, when taken in conjunction with other measures such as mean canopy height, area-based soil exchangeable potassium content, [K]sa , proved to be an excellent predictor of several photosynthetic properties (including 13C isotope discrimination). Moreover, when considered in a multivariate context with PA and soil plant available water storage capacity (?P) as covariates, [K]sa also proved to be an excellent predictor of stand-level canopy area, providing drastically improved fits as compared to models considering just PA and/or ?P. Neither calcium, nor magnesium, nor soil pH could substitute for potassium when tested as alternative model predictors (?AIC > 10). Nor for any model could simple soil texture metrics such as sand or clay content substitute for either [K]sa or ?P. Taken in conjunction with recent work in Africa and the forests of the Amazon Basin, this suggests - in combination with some newly conceptualised interacting effects of PA and ?P also presented here - a critical role for potassium as a modulator of tropical vegetation structure and function.

  13. Synthesis of proline analogues as potent and selective cathepsin S inhibitors.

    PubMed

    Kim, Mira; Jeon, Jiyoung; Song, Jiyeon; Suh, Kwee Hyun; Kim, Young Hoon; Min, Kyung Hoon; Lee, Kwang-Ok

    2013-06-01

    Cathepsin S is a potential target of autoimmune disease. A series of proline derived compounds were synthesized and evaluated as cathepsin S inhibitors. We discovered potent cathepsin S inhibitors through structure-activity relationship studies of proline analogues. In particular, compound 19-(S) showed promising in vitro/vivo pharmacological activities and properties as a selective cathepsin S inhibitor. PMID:23639544

  14. Short and highly efficient synthesis of lipid peroxidation inhibitor pyrrolostatin and some analogues thereof.

    PubMed

    Schmidt, Jens; Adrian, Juliane; Christian B W Stark

    2015-08-14

    A highly efficient and scalable synthesis of potent lipid peroxidation inhibitor pyrrolostatin is reported (4 steps, 48%). In addition to the synthesis of the natural product, strategies for the preparation of analogues differing in the three structural subunits, the polar head group, the N-substituent and the lipophilic tail are described. PMID:26154919

  15. Hymenopsins A and B and a Macrophorin Analogue from a Fungicolous Hymenopsis sp.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Hymenopsin A (1), hymenopsin B (2), and a new macrophorin analogue, 2',3'-epoxy-13-hydroxy-4'-oxomacrophorin A (3), have been isolated from a fungicolous isolate of Hymenopsis sp. (NRRL 37638). The structures and relative configurations of these compounds were assigned on the basis of 2D NMR and MS...

  16. Synthesis of the insecticide prothrin and its analogues from biomass-derived 5-(Chloromethyl) furfural

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Prothrin, a synthetic pyrethroid insecticide, was synthesized from the biomass-derived platform chemical 5 (chloromethyl)furfural in six steps and overall 65% yield. Two structural analogues of prothrin were also prepared following the same synthetic approach. Preliminary testing of these furan-base...

  17. Complementary isonitrile-based multicomponent reactions for the synthesis of diversified cytotoxic hemiasterlin analogues.

    PubMed

    Lesma, Giordano; Bassanini, Ivan; Bortolozzi, Roberta; Colletto, Chiara; Bai, Ruoli; Hamel, Ernest; Meneghetti, Fiorella; Rainoldi, Giulia; Stucchi, Mattia; Sacchetti, Alessandro; Silvani, Alessandra; Viola, Giampietro

    2015-12-28

    A small family of structural analogues of the antimitotic tripeptides, hemiasterlins, have been designed and synthesized as potential inhibitors of tubulin polymerization. The effectiveness of a multicomponent approach was fully demonstrated by applying complementary versions of the isocyanide-based Ugi reaction. Compounds strictly related to the lead natural products, as well as more extensively modified analogues, have been synthesized in a concise and convergent manner. In some cases, biological evaluation provided evidence for strong cytotoxic activity (six human tumor cell lines) and for potent inhibition of tubulin polymerization. PMID:26467486

  18. Elemental step thermodynamics of various analogues of indazolium alkaloids to obtaining hydride in acetonitrile.

    PubMed

    Lei, Nan-Ping; Fu, Yan-Hua; Zhu, Xiao-Qing

    2015-12-21

    A series of analogues of indazolium alkaloids were designed and synthesized. The thermodynamic driving forces of the 6 elemental steps for the analogues of indazolium alkaloids to obtain hydride in acetonitrile were determined using an isothermal titration calorimeter (ITC) and electrochemical methods, respectively. The effects of molecular structure and substituents on the thermodynamic driving forces of the 6 steps were examined. Meanwhile, the oxidation mechanism of NADH coenzyme by indazolium alkaloids was examined using the chemical mimic method. The result shows that the oxidation of NADH coenzyme by indazolium alkaloids in vivo takes place by one-step concerted hydride transfer mechanism. PMID:26451708

  19. Crystallographic analysis of transition-state mimics bound to penicillopepsin: phosphorus-containing peptide analogues.

    PubMed

    Fraser, M E; Strynadka, N C; Bartlett, P A; Hanson, J E; James, M N

    1992-06-01

    The molecular structures of three phosphorus-based peptide inhibitors of aspartyl proteinases complexed with penicillopepsin [1, Iva-L-Val-L-Val-StaPOEt [Iva = isovaleryl, StaP = the phosphinic acid analogue of statine [(S)-4-amino-(S)-3-hydroxy-6-methylheptanoic acid] (IvaVVStaPOEt)]; 2, Iva-L-Val-L-Val-L-LeuP-(O)Phe-OMe [LeuP = the phosphinic acid analogue of L-leucine; (O)Phe = L-3-phenyllactic acid; OMe = methyl ester] [Iva VVLP(O)FOMe]; and 3, Cbz-L-Ala-L-Ala-L-LeuP-(O)-Phe-OMe (Cbz = benzyloxycarbonyl) [CbzAALP(O)FOMe

  20. Synthesis and Evaluation of Novel Triterpene Analogues of Ursolic Acid as Potential Antidiabetic Agent

    PubMed Central

    Wu, Panpan; Zheng, Jie; Huang, Tianming; Li, Dianmeng; Hu, Qingqing; Cheng, Anming; Jiang, Zhengyun; Jiao, Luoying; Zhao, Suqing; Zhang, Kun

    2015-01-01

    Ursolic acid (UA) is a naturally bioactive compound that possesses potential anti-diabetic activity. The relatively safe and effective molecule intrigued us to further explore and to improve its anti-diabetic activity. In the present study, a series of novel UA analogues was synthesized and their structures were characterized. Their bioactivities against the ?-glucosidase from baker's yeast were determined in vitro. The results suggested that most of the analogues exhibited significant inhibitory activity, especially analogues 8b and 9b with the IC50 values of 1.27 ± 0.27 ?M (8b) and 1.28 ± 0.27 ?M (9b), which were lower than the other analogues and the positive control. The molecular docking and 2D-QSAR studies were carried out to prove that the C-3 hydroxyl could interact with the hydrophobic region of the active pocket and form hydrogen bonds to increase the binding affinity of ligand and the homology modelling protein. Thus, these results will be helpful for understanding the relationship between binding mode and bioactivity and for designing better inhibitors from UA analogues. PMID:26406581

  1. A CMOS GENERAL-PURPOSE SAMPLED-DATA ANALOGUE MICROPROCESSOR

    E-print Network

    Dudek, Piotr

    A CMOS GENERAL-PURPOSE SAMPLED-DATA ANALOGUE MICROPROCESSOR Piotr Dudek and Peter J. Hicks.j.hicks@umist.ac.uk Abstract This paper presents a general-purpose sampled-data analogue processing element that essentially functions as an analogue microprocessor (AµP). The AµP executes software programs, in a way akin

  2. Heteroatom Analogues of Hydrocodone: Synthesis and Biological Activity

    PubMed Central

    Giacometti, Robert D.; Duchek, Jan; Werner, Lukas; Husni, Afeef S.; McCurdy, Christopher R.; Cutler, Stephen J.; Cox, D. Phillip; Hudlicky, Tomas

    2013-01-01

    Heteroatom analogues of hydrocodone, in which the N-methyl functionality was replaced with oxygen, sulfur, sulfoxide, and sulfone, were prepared by a short sequence from the ethylene glycol ketal of hydrocodone; a carbocyclic analogue of bisnorhydrocodone was also prepared. The compounds were tested for receptor binding and revealed moderate levels of activity for the sulfone analogue of hydrocodone. PMID:23397939

  3. Synthesis and antiviral activities of new acyclic and “double-headed” nucleoside analogues

    PubMed Central

    Zhang, Xinying; Amer, Adel; Fan, Xuesen; Balzarini, Jan; Neyts, Johan; De Clercq, Erik; Prichard, Mark; Kern, Earl; Torrence, Paul F.

    2014-01-01

    To develop an understanding of the structure-activity relationships for the inhibition of orthopoxviruses by nucleoside analogues, a variety of novel chemical entities were synthesized. These included a series of pyrimidine 5-hypermodified acyclic nucleoside analogues based upon recently discovered new leads, and some previously unknown “double-headed” or “abbreviated” nucleosides. None of the synthetic products possessed significant activity against two representative orthopoxviruses; namely, vaccinia virus and cowpox virus. They were also devoid of significant activity against a battery of other DNA and RNA viruses. So far as the results with the orthopoxviruses and herpes viruses, the results may point to the necessity for nucleoside analogues 5?-phosphorylation for antiviral efficacy. PMID:17270235

  4. Synthesis and Pharmacological Evaluation of DH?E Analogues as Neuronal Nicotinic Acetylcholine Receptor Antagonists

    PubMed Central

    2014-01-01

    Dihydro-?-erythroidine (DH?E) is a member of the Erythrina family of alkaloids and a potent competitive antagonist of the ?4?2-subtype of the nicotinic acetylcholine receptors (nAChRs). Guided by an X-ray structure of DH?E in complex with an ACh binding protein, we detail the design, synthesis, and pharmacological characterization of a series of DH?E analogues in which two of the four rings in the natural product has been excluded. We found that the direct analogue of DH?E maintains affinity for the ?4?2-subtype, but further modifications of the simplified analogues were detrimental to their activities on the nAChRs. PMID:25050162

  5. Total synthesis and cytotoxic activities of longamide B, longamide B methyl ester, hanishin, and their analogues.

    PubMed

    Zhao, Deng-Gao; Ma, Yan-Yan; Peng, Wei; Zhou, Ai-Yu; Zhang, Yu; Ding, Liugang; Du, Zhiyun; Zhang, Kun

    2016-01-01

    The marine alkaloids, longamide B (1), longamide B methyl ester (2), hanishin (3), and a series of non-naturally occurring analogues were synthesized in an efficient manner from inexpensive commercially available dl-aspartic acid dimethyl ester. The cytotoxicities of these natural products (1-3) and their analogues (9-15) were evaluated against human lung adenocarcinoma (A549) and human prostate cancer (PC3) cells. This is the first evaluation of the cytotoxicities of these alkaloids in these cancer cell lines and it revealed that analogue 15 had comparable cytotoxic activity to its natural parent compound, (±)-hanishin (3). This study provides useful information for further structural modification of these alkaloids in order to develop novel antitumor agents. PMID:26615890

  6. Synthesis of cembranoid analogues and evaluation of their potential as quorum sensing inhibitors.

    PubMed

    Tello, Edisson; Castellanos, Leonardo; Duque, Carmenza

    2013-01-01

    Natural cembranoids have shown Quorum Sensing Inhibitory (QSI) activity, but their structure-function interactions are not well understood. Thirty-four cembranoid analogues were synthesized using six natural cembranoids (1-6) previously isolated from the Colombian Caribbean octocorals Eunicea knighti and Pseudoplexaura flagellosa as lead compounds. The analogues (7-40) obtained through the selected chemical transformations were tested in vitro against the QS systems of a Chromobacterium violaceum biosensor. Half of the cembranoid analogues assayed showed superior QSI activity to the lead compounds; three (8, 13, and 18) displayed remarkable potency up to three times higher than the natural compounds. Thereby, we have synthesized a pool of cembranoid QS inhibitors that can be used in concert with natural compounds to develop antipathogenic drugs and antifouling agents. PMID:23177728

  7. Exploiting Enzymatic Promiscuity to Engineer a Focused Library of Highly Selective Antifungal and Antiproliferative Aureothin Analogues

    PubMed Central

    Werneburg, Martina; Busch, Benjamin; He, Jing; Richter, Martin E.A.; Xiang, Longkuan; Moore, Bradley S.; Roth, Martin; Dahse, Hans-Martin

    2010-01-01

    Aureothin is a shikimate-polyketide hybrid metabolite from Streptomyces thioluteus with a rare nitroaryl moiety, a chiral tetrahydrofuran ring and an O-methylated pyrone ring. The antimicrobial and antitumor activities of aureothin have caught our interest in modulating its structure as well as its bioactivity profile. In an integrated approach using mutasynthesis, biotransformation and combinatorial biosynthesis, a defined library of aureothin analogues was generated. The promiscuity of the polyketide synthase assembly line towards different starter units and the plasticity of the pyrone and tetrahydrofuran ring formation were exploited. A selection of fifteen new aureothin analogues with modifications at the aryl residue, the pyrone ring, and the oxygenated backbone was produced on a preparative scale and fully characterized. Remarkably, various new aureothin derivatives are less cytotoxic than aureothin but have improved antiproliferative activities. Furthermore, we found that the THF ring is crucial for the remarkably selective activity of aureothin analogues against certain pathogenic fungi. PMID:20662518

  8. Exploiting enzymatic promiscuity to engineer a focused library of highly selective antifungal and antiproliferative aureothin analogues.

    PubMed

    Werneburg, Martina; Busch, Benjamin; He, Jing; Richter, Martin E A; Xiang, Longkuan; Moore, Bradley S; Roth, Martin; Dahse, Hans-Martin; Hertweck, Christian

    2010-08-01

    Aureothin is a shikimate-polyketide hybrid metabolite from Streptomyces thioluteus with a rare nitroaryl moiety, a chiral tetrahydrofuran ring, and an O-methylated pyrone ring. The antimicrobial and antitumor activities of aureothin have caught our interest in modulating its structure as well as its bioactivity profile. In an integrated approach using mutasynthesis, biotransformation, and combinatorial biosynthesis, a defined library of aureothin analogues was generated. The promiscuity of the polyketide synthase assembly line toward different starter units and the plasticity of the pyrone and tetrahydrofuran ring formation were exploited. A selection of 15 new aureothin analogues with modifications at the aryl residue, the pyrone ring, and the oxygenated backbone was produced on a preparative scale and fully characterized. Remarkably, various new aureothin derivatives are less cytotoxic than aureothin but have improved antiproliferative activities. Furthermore, we found that the THF ring is crucial for the remarkably selective activity of aureothin analogues against certain pathogenic fungi. PMID:20662518

  9. AaeAP1 and AaeAP2: Novel Antimicrobial Peptides from the Venom of the Scorpion, Androctonus aeneas: Structural Characterisation, Molecular Cloning of Biosynthetic Precursor-Encoding cDNAs and Engineering of Analogues with Enhanced Antimicrobial and Anticancer Activities

    PubMed Central

    Du, Qiang; Hou, Xiaojuan; Wang, Lei; Zhang, Yingqi; Xi, Xinping; Wang, Hui; Zhou, Mei; Duan, Jinao; Wei, Minjie; Chen, Tianbao; Shaw, Chris

    2015-01-01

    The main functions of the abundant polypeptide toxins present in scorpion venoms are the debilitation of arthropod prey or defence against predators. These effects are achieved mainly through the blocking of an array of ion channel types within the membranes of excitable cells. However, while these ion channel-blocking toxins are tightly-folded by multiple disulphide bridges between cysteine residues, there are additional groups of peptides in the venoms that are devoid of cysteine residues. These non-disulphide bridged peptides are the subject of much research interest, and among these are peptides that exhibit antimicrobial activity. Here, we describe two novel non-disulphide-bridged antimicrobial peptides that are present in the venom of the North African scorpion, Androctonus aeneas. The cDNAs encoding the biosynthetic precursors of both peptides were cloned from a venom-derived cDNA library using 3'- and 5'-RACE strategies. Both translated precursors contained open-reading frames of 74 amino acid residues, each encoding one copy of a putative novel nonadecapeptide, whose primary structures were FLFSLIPSVIAGLVSAIRN and FLFSLIPSAIAGLVSAIRN, respectively. Both peptides were C-terminally amidated. Synthetic versions of each natural peptide displayed broad-spectrum antimicrobial activities, but were devoid of antiproliferative activity against human cancer cell lines. However, synthetic analogues of each peptide, engineered for enhanced cationicity and amphipathicity, exhibited increases in antimicrobial potency and acquired antiproliferative activity against a range of human cancer cell lines. These data clearly illustrate the potential that natural peptide templates provide towards the design of synthetic analogues for therapeutic exploitation. PMID:25626077

  10. AaeAP1 and AaeAP2: novel antimicrobial peptides from the venom of the scorpion, Androctonus aeneas: structural characterisation, molecular cloning of biosynthetic precursor-encoding cDNAs and engineering of analogues with enhanced antimicrobial and anticancer activities.

    PubMed

    Du, Qiang; Hou, Xiaojuan; Wang, Lei; Zhang, Yingqi; Xi, Xinping; Wang, Hui; Zhou, Mei; Duan, Jinao; Wei, Minjie; Chen, Tianbao; Shaw, Chris

    2015-02-01

    The main functions of the abundant polypeptide toxins present in scorpion venoms are the debilitation of arthropod prey or defence against predators. These effects are achieved mainly through the blocking of an array of ion channel types within the membranes of excitable cells. However, while these ion channel-blocking toxins are tightly-folded by multiple disulphide bridges between cysteine residues, there are additional groups of peptides in the venoms that are devoid of cysteine residues. These non-disulphide bridged peptides are the subject of much research interest, and among these are peptides that exhibit antimicrobial activity. Here, we describe two novel non-disulphide-bridged antimicrobial peptides that are present in the venom of the North African scorpion, Androctonus aeneas. The cDNAs encoding the biosynthetic precursors of both peptides were cloned from a venom-derived cDNA library using 3'- and 5'-RACE strategies. Both translated precursors contained open-reading frames of 74 amino acid residues, each encoding one copy of a putative novel nonadecapeptide, whose primary structures were FLFSLIPSVIAGLVSAIRN and FLFSLIPSAIAGLVSAIRN, respectively. Both peptides were C-terminally amidated. Synthetic versions of each natural peptide displayed broad-spectrum antimicrobial activities, but were devoid of antiproliferative activity against human cancer cell lines. However, synthetic analogues of each peptide, engineered for enhanced cationicity and amphipathicity, exhibited increases in antimicrobial potency and acquired antiproliferative activity against a range of human cancer cell lines. These data clearly illustrate the potential that natural peptide templates provide towards the design of synthetic analogues for therapeutic exploitation. PMID:25626077

  11. E22 Analogue Electronics PS3 Answers p 1/4 E2.2 Analogue electronics

    E-print Network

    Papavassiliou, Christos

    E22 Analogue Electronics PS3 Answers p 1/4 E2.2 Analogue electronics Problem sheet 3 (Week 5) Q1 inZ j j = + + = + - + R2 R1 R1 R2 Vcc Vin Vout #12;E22 Analogue Electronics PS3 Answers p 222 Analogue Electronics PS3 Answers p 3/4 inverting amplifier, the open loop gain of the amplifier

  12. Epoxyeicosatrienoic acid analogue lowers blood pressure through vasodilation and sodium channel inhibition

    PubMed Central

    KHAN, Md. Abdul Hye; PAVLOV, Tengis S.; CHRISTAIN, Sarah V.; NECKÁ?, Jan; STARUSCHENKO, Alexander; GAUTHIER, Kathryn M.; CAPDEVILA, Jorge H.; FALCK, John R.; CAMPBELL, William B.; IMIG, John D.

    2014-01-01

    Epoxyeicosatrienoic acids (EETs) contribute to haemodynamics, electrolyte homoeostasis and blood pressure regulation, leading to the concept that EETs can be therapeutically targeted for hypertension. In the present study, multiple structural EET analogues were synthesized based on the EET pharmacophore and vasodilator structure-activity studies. Four EET analogues with 91–119 % vasodilatory activity in the isolated bovine coronary artery (EC50: 0.18–1.6 ?M) were identified and studied for blood-pressure-lowering in hypertension. Two EET analogues in which the COOH group at carbon 1 of the EET pharmacophore was replaced with either an aspartic acid (EET-A) or a heterocyclic surrogate (EET-X) were administered for 14 days [10 mg/kg per day intraperitoneally (i.p.)]. Both EET-A and EET-X lowered blood pressure in spontaneously hypertensive rats (SHRs) and in angiotensin II (AngII) hypertension. On day 14, the mean arterial pressures in EET analogue-treated AngII-hypertensive and SHRs were 30–50 mmHg (EET-A) and 15–20 mmHg (EET-X) lower than those in vehicle-treated controls. These EET analogues (10 mg/kg per day) were further tested in AngII hypertension by administering orally in drinking water for 14 days and EET-A lowered blood pressure. Additional experiments demonstrated that EET-A inhibits epithelial sodium channel (ENaC) activity in cultured cortical collecting duct cells and reduced renal expression of ENaC subunits in AngII hypertension. In conclusion, we have characterized EET-A as an orally active antihypertensive EET analogue that protects vascular endothelial function and has ENaC inhibitory activity in AngII hypertension. PMID:24707975

  13. Late Pleniglacial vegetation in eastern-central Europe: are there modern analogues in Siberia?

    NASA Astrophysics Data System (ADS)

    Magyari, Enik? Katalin; Kuneš, Petr; Jakab, Gusztáv; Sümegi, Pál; Pelánková, Barbora; Schäbitz, Frank; Braun, Mihály; Chytrý, Milan

    2014-07-01

    To characterize Late Pleniglacial (LPG: 26.5-15 ka cal BP) and particularly Last Glacial Maximum (LGM: 21 ± 2 ka cal BP) vegetation and climate, fossil pollen assemblages are often compared with modern pollen assemblages. Given the non-analogue climate of the LPG, a key question is how glacial pollen assemblages and thereby vegetation compare with modern vegetation. In this paper we present three LPG pollen records from the Carpathian Basin and the adjoining Carpathian Mountains to address this question and provide a concise compositional characterization of the LPG vegetation. Fossil pollen assemblages were compared with surface pollen spectra from the Altai-Sayan Mountains in southern Siberia. This area shows many similarities with the LPG vegetation of eastern-central Europe, and has long been considered as its best modern analogue. Ordination and analogue matching were used to characterize vegetation composition and find the best analogues. Our results show that few LPG pollen assemblages have statistically significant analogues in southern Siberia. When analogue pairings occur they suggest the predominance of wet and mesic grasslands and dry steppe in the studied region. Wooded vegetation types (continental and suboceanic hemiboreal forest, continental taiga) appear as significant analogues only in a few cases during the LGM and more frequently after 16 ka cal BP. These results suggest that the LPG landscape of the Carpathian Basin was dominated by dry steppe that occurred outside the river floodplains, while wet and mesic grasslands occurred in the floodplains and on other sites influenced by ground water. Woody vegetation mainly occurred in river valleys, on wet north-facing hillsides, and scattered trees were likely also present on the loess plateaus. The dominant woody species were Larix, Pinus sylvestris, Pinus mugo, Pinus cembra, Picea abies, Betula pendula/pubescens, Betula nana, Juniperus, Hippophaë rhamnoides, Populus, Salix and Alnus. The pollen records suggest uninterrupted presence of mesophilous temperate trees (Quercus, Ulmus, Corylus, Fagus and Fraxinus excelsior) in the Eastern Carpathian Mountains throughout the LPG. We demonstrate that the LPG vegetation in this area was characterized by increasing grass cover and high frequency of wildfires. We conclude that pollen spectra over represent trees in the forest-steppe landscape of the LPG, furthermore pollen-based quantitative climate reconstructions for the LPG are challenging in this area due to the scarcity of modern analogues.

  14. Review of Current State of the Art and Key Design Issues With Potential Solutions for Liquid Hydrogen Cryogenic Storage Tank Structures for Aircraft Applications

    NASA Technical Reports Server (NTRS)

    Mital, Subodh K.; Gyekenyesi, John Z.; Arnold, Steven M.; Sullivan, Roy M.; Manderscheid, Jane M.; Murthy, Pappu L. N.

    2006-01-01

    Due to its high specific energy content, liquid hydrogen (LH2) is emerging as an alternative fuel for future aircraft. As a result, there is a need for hydrogen tank storage systems, for these aircraft applications, that are expected to provide sufficient capacity for flight durations ranging from a few minutes to several days. It is understood that the development of a large, lightweight, reusable cryogenic liquid storage tank is crucial to meet the goals of and supply power to hydrogen-fueled aircraft, especially for long flight durations. This report provides an annotated review (including the results of an extensive literature review) of the current state of the art of cryogenic tank materials, structural designs, and insulation systems along with the identification of key challenges with the intent of developing a lightweight and long-term storage system for LH2. The broad classes of insulation systems reviewed include foams (including advanced aerogels) and multilayer insulation (MLI) systems with vacuum. The MLI systems show promise for long-term applications. Structural configurations evaluated include single- and double-wall constructions, including sandwich construction. Potential wall material candidates are monolithic metals as well as polymer matrix composites and discontinuously reinforced metal matrix composites. For short-duration flight applications, simple tank designs may suffice. Alternatively, for longer duration flight applications, a double-wall construction with a vacuum-based insulation system appears to be the most optimum design. The current trends in liner material development are reviewed in the case that a liner is required to minimize or eliminate the loss of hydrogen fuel through permeation.

  15. Renin inhibitors. Syntheses of subnanomolar, competitive, transition-state analogue inhibitors containing a novel analogue of statine.

    PubMed

    Boger, J; Payne, L S; Perlow, D S; Lohr, N S; Poe, M; Blaine, E H; Ulm, E H; Schorn, T W; LaMont, B I; Lin, T Y

    1985-12-01

    Analogues of the renin octapeptide substrate were synthesized in which replacement of the scissile dipeptide with (3S,4S)-4-amino-3-hydroxy-6-methylheptanoic acid (statine, Sta) transformed the substrate sequence into potent, transition-state analogue, competitive inhibitors of renin. Synthesis and incorporation of the cyclohexylalanyl analogue of Sta, (3S,4S)-4-amino-5-cyclohexyl-3-hydroxypentanoic acid (ACHPA), gave the most potent inhibitors of renin yet reported, including N-isovaleryl-L-histidyl-L-prolyl-L-phenylalanyl-L-histidyl-ACHPA-L -leucyl-L- phenylalanyl amide [Iva-His-Pro-Phe-His-ACHPA-Leu-Phe-NH2,3], with renin inhibitions of Ki = 1.6 X 10(-10) M (human kidney renin), IC50 = 1.7 X 10(-10)M (human plasma renin), IC50 = 1.9 X 10(-9)M (dog plasma renin), and IC50 = 2.1 X 10(-8) M (rat plasma renin). This inhibitor 3, containing ACHPA, was 55-76 times more potent vs. human renin than the comparable Sta-containing inhibitor 1 and 17 times more potent vs. dog renin than 1. Inhibitor 3 lowered blood pressure in sodium-deficient dogs, with in vivo potency 19 times that shown by 1, in close agreement with the relative in vitro potencies. Structure-activity results are presented that show the minimal N-terminus for these inhibitors. An ACHPA-containing pentapeptide, N-[(ethyloxy)carbonyl]-L-phenylalanyl-L- histidyl-ACHPA-L-leucyl-L-phenylalanyl amide [Etoc-Phe-His-ACHPA-Leu-Phe-NH2,8], retained subnanomolar inhibitory potency. Molecular modelling studies are described that suggested the design of ACHPA. PMID:3906131

  16. Natural analogue synthesis report, TDR-NBS-GS-000027 rev00 icn02

    SciTech Connect

    Simmons, A.; Nieder-Westermann, G.; Stuckless, J.; Dobson, P.; Unger, A.J.A.; Kwicklis, E.; Lichtner, P.; Carey, B.; Wolde, G.; Murrel,M.; Kneafsey, T.J.; Meijer, A.; Faybishenko, B.

    2002-04-01

    The purpose of this report is to present analogue studies and literature reviews designed to provide qualitative and quantitative information to test and provide added confidence in process models abstracted for performance assessment (PA) and model predictions pertinent to PA. This report provides updates to studies presented in the Yucca Mountain Site Description (CRWMS M&O 2000 [151945], Section 13) and new examples gleaned from the literature, along with results of quantitative studies conducted specifically for the Yucca Mountain Site Characterization Project (YMP). The intent of the natural analogue studies was to collect corroborative evidence from analogues to demonstrate additional understanding of processes expected to occur during postclosure at a potential Yucca Mountain repository. The report focuses on key processes by providing observations and analyses of natural and anthropogenic (human-induced) systems to improve understanding and confidence in the operation of these processes under conditions similar to those that could occur in a nuclear waste repository. The process models include those that represent both engineered and natural barrier processes. A second purpose of this report is to document the various applications of natural analogues to geologic repository programs, focusing primarily on the way analogues have been used by the YMP. This report is limited to providing support for PA in a confirmatory manner and to providing corroborative inputs for process modeling activities. Section 1.7 discusses additional limitations of this report. Key topics for this report are analogues to emplacement drift degradation, waste form degradation, waste package degradation, degradation of other materials proposed for the engineered barrier, seepage into drifts, radionuclide flow and transport in the unsaturated zone (UZ), analogues to coupled thermal-hydrologic-mechanical-chemical processes, saturated zone (SZ) transport, impact of radionuclide release on the biosphere, and potentially disruptive events. Results of these studies will be used to corroborate estimates of the magnitude and limitation of operative processes in order to build realism into conceptual and numerical process models used as a foundation for PA in the representative case of postclosure safety.

  17. Revisiting sesquiterpene biosynthetic pathways leading to santalene and its analogues: a comprehensive mechanistic study.

    PubMed

    Jindal, Garima; Sunoj, Raghavan B

    2012-10-21

    Santalene and bergamotene are the major olefinic sesquiterpenes responsible for the fragrance of sandalwood oil. Herein we report the details of density functional theory investigations on the biosynthetic pathway of this important class of terpenes. The mechanistic study has been found to be effective toward gaining significant new insight into different possibilities for the formation of the key intermediates involved in santalene and bergamotene biosynthesis. The stereoelectronic features of the transition states and intermediates for (i) ring closure of the initial bisabolyl cation, and (ii) skeletal rearrangements in the ensuing bicyclic carbocationic intermediates leading to (-)-epi-?-santalene, (-)-?-santalene, (-)-?-santalene, (+)-epi-?-santalene, exo-?-bergamotene, endo-?-bergamotene, exo-?-bergamotene, and endo-?-bergamotene are presented. Interesting structural features pertaining to certain new carbocationic intermediates (such as b) resulting from the ring closure of bisabolyl cation are discussed. Extensive conformational sampling of all key intermediates along the biosynthetic pathway offered new insight into the role of the isoprenyl side chain conformation in the formation of santalene and its analogues. Although the major bicyclic products in Santalum album appear to arise from the right or left handed helical form of farnesyl pyrophosphate (FPP), different alternatives for their formation are found to be energetically feasible. The interconversion of the exo and endo isomers of bisabolyl cation and a likely epimerization, both with interesting mechanistic implications, are presented. The exo to endo conversion is identified to be energetically more favorable than another pathway emanating from the left handed helical FPP. The role of pyrophosphate (OPP(-)) in the penultimate deprotonation step leading to olefinic sesquiterpenes is also examined. PMID:22951817

  18. Investigating biological activity spectrum for novel quinoline analogues.

    PubMed

    Musiol, Robert; Jampilek, Josef; Kralova, Katarina; Richardson, Des R; Kalinowski, Danuta; Podeszwa, Barbara; Finster, Jacek; Niedbala, Halina; Palka, Anna; Polanski, Jaroslaw

    2007-02-01

    The lack of the wide spectrum of biological data is an important obstacle preventing the efficient molecular design. Quinoline derivatives are known to exhibit a variety of biological effects. In the current publication, we tested a series of novel quinoline analogues for their photosynthesis-inhibiting activity (the inhibition of photosynthetic electron transport in spinach chloroplasts (Spinacia oleracea L.) and the reduction of chlorophyll content in Chlorella vulgaris Beij.). Moreover, antiproliferative activity was measured using SK-N-MC neuroepithelioma cell line. We described the structure-activity relationships (SAR) between the chemical structure and biological effects of the synthesized compounds. We also measured the lipophilicity of the novel compounds by means of the RP-HPLC and illustrate the relationships between the RP-HPLC retention parameter logK (the logarithm of capacity factor K) and logP data calculated by available programs. PMID:17142046

  19. The Canadian space agency planetary analogue materials suite

    NASA Astrophysics Data System (ADS)

    Cloutis, Edward A.; Mann, Paul; Izawa, Matthew R. M.; Applin, Daniel M.; Samson, Claire; Kruzelecky, Roman; Glotch, Timothy D.; Mertzman, Stanley A.; Mertzman, Karen R.; Haltigin, Timothy W.; Fry, Christopher

    2015-12-01

    The Canadian Space Agency (CSA) recently commissioned the development of a suite of over fifty well-characterized planetary analogue materials. These materials are terrestrial rocks and minerals that are similar to those known or suspected to occur on the lunar or martian surfaces. These include: Mars analogue sedimentary, hydrothermal, igneous and low-temperature alteration rock suites; lunar analogue basaltic and anorthositic rock suites; and a generic impactite rock suite from a variety of terrestrial impact structures. Representative thin sections of the materials have been characterized by optical microscopy and electron probe microanalysis (EPMA). Reflectance spectra have been collected in the ultraviolet, visible, near-infrared and mid-infrared, covering 0.2-25 ?m. Thermal infrared emission spectra were collected from 5 to 50 ?m. Raman spectra with 532 nm excitation, and laser-induced fluorescence spectra with 405 nm excitation were also measured. Bulk chemical analysis was carried out using X-ray fluorescence, with Fe valence determined by wet chemistry. Chemical and mineralogical data were collected using a field-portable Terra XRD-XRF instrument similar to CheMin on the MSL Curiosity rover. Laser-induced breakdown spectroscopy (LIBS) data similar to those measured by ChemCam on MSL were collected for powdered samples, cut slab surfaces, and as depth profiles into weathered surfaces where present. Three-dimensional laser camera images of rock textures were collected for selected samples. The CSA intends to make available sample powders (<45 ?m and 45-1000 ?m grain sizes), thin sections, and bulk rock samples, and all analytical data collected in the initial characterisation study to the broader planetary science community. Aiming to complement existing planetary analogue rock and mineral libraries, the CSA suite represents a new resource for planetary scientists and engineers. We envision many potential applications for these materials in the definition, development and testing of new analytical instruments for use in planetary missions, as well as possible calibration and ground-truthing of remote sensing data sets. These materials may also be useful as reference materials for cross-calibration between different instruments and laboratories. Comparison of the analytical data for selected samples is useful for highlighting the relative strengths, weaknesses and synergies of different analytical techniques.

  20. Extrapolating subsurface geometry by surface expressions in transpressional strike slip fault, deduced from analogue experiments with settings of rheology and convergence angle

    NASA Astrophysics Data System (ADS)

    Hsieh, Shang Yu; Neubauer, Franz

    2015-04-01

    The internal structure of major strike-slip faults is still poorly understood, particularly how to extrapolate subsurface structures by surface expressions. Series of brittle analogue experiments by Leever et al., 2011 resulted the convergence angle is the most influential factor for surface structures. Further analogue models with different ductile settings allow a better understanding in extrapolating surface structures to the subsurface geometry of strike-slip faults. Fifteen analogue experiments were constructed to represent strike-slip faults in nature in different geological settings. As key parameters investigated in this study include: (a) the angle of convergence, (b) the thickness of brittle layer, (c) the influence of a rheological weak layer within the crust, and (d) influence of a thick and rheologically weak layer at the base of the crust. The experiments are aimed to explain first order structures along major transcurrent strike-slip faults such as the Altyn, Kunlun, San Andrea and Greendale (Darfield earthquake 2010) faults. The preliminary results show that convergence angle significantly influences the overall geometry of the transpressional system with greater convergence angles resulting in wider fault zones and higher elevation. Different positions, densities and viscosities of weak rheological layers have not only different surface expressions but also affect the fault geometry in the subsurface. For instance, rheological weak material in the bottom layer results in stretching when experiment reaches a certain displacement and a buildup of a less segmented, wide positive flower structure. At the surface, a wide fault valley in the middle of the fault zone is the reflection of stretching along the velocity discontinuity at depth. In models with a thin and rheologically weaker layer in the middle of the brittle layer, deformation is distributed over more faults and the geometry of the fault zone below and above the weak zone shows significant differences, suggesting that the correlation of structures across a weak layer has to be supported by geophysical data, which help constraining the geometry of the deep part. This latter experiment has significantly similar phenomena in reality, such as few pressure ridges along Altyn fault. The experimental results underline the need to understand the role of the convergence angle and the influence of rheology on fault evolution, in order to connect between surface deformation and subsurface geometry.

  1. Structures of adenosine kinase from Trypanosoma brucei brucei

    PubMed Central

    Timm, Jennifer; González-Pacanowska, Dolores; Wilson, Keith S.

    2014-01-01

    Trypanosoma brucei is a single-cellular parasite of the genus Kinetoplastida and is the causative agent of African sleeping sickness in humans. Adenosine kinase is a key enzyme in the purine-salvage pathway, phosphorylating adenosine to AMP, and also activates cytotoxic analogues such as cordycepin and Ara-A by their phosphorylation. The structures of T. brucei brucei adenosine kinase (TbAK) in its unliganded open conformation and complexed with adenosine and ADP in the closed conformation are both reported to 2.6?Å resolution. The structures give insight into the binding mode of the substrates and the conformational change induced upon substrate binding. This information can be used to guide the improvement of cytotoxic substrate analogues as potential antitrypanosomal drugs. PMID:24419613

  2. h-analogue of Fibonacci Numbers

    E-print Network

    H. B. Benaoum

    2009-09-30

    In this paper, we introduce the h-analogue of Fibonacci numbers for non-commutative h-plane. For h h'= 1 and h = 0, these are just the usual Fibonacci numbers as it should be. We also derive a collection of identities for these numbers. Furthermore, h-Binet's formula for the h-Fibonacci numbers is found and the generating function that generates these numbers is obtained.

  3. Synthesis of constrained analogues of tryptophan

    PubMed Central

    Negrato, Marco; Abbiati, Giorgio; Dell’Acqua, Monica

    2015-01-01

    Summary A Lewis acid-catalysed diastereoselective [4 + 2] cycloaddition of vinylindoles and methyl 2-acetamidoacrylate, leading to methyl 3-acetamido-1,2,3,4-tetrahydrocarbazole-3-carboxylate derivatives, is described. Treatment of the obtained cycloadducts under hydrolytic conditions results in the preparation of a small library of compounds bearing the free amino acid function at C-3 and pertaining to the class of constrained tryptophan analogues. PMID:26664620

  4. The Brookhaven electron analogue, 1953--1957

    SciTech Connect

    Plotkin, M.

    1991-12-18

    The following topics are discussed on the Brookhaven electron analogue: L.J. Haworth and E.L. VanHorn letters; Original G.K. Green outline for report; General description; Parameter list; Mechanical Assembly; Alignment; Degaussing; Vacuum System; Injection System; The pulsed inflector; RF System; Ferrite Cavity; Pick-up electrodes and preamplifiers; Radio Frequency power amplifier; Lens supply; Controls and Power; and RF acceleration summary.

  5. Biological studies of martian soil analogues

    NASA Astrophysics Data System (ADS)

    Imshenetsky, A. A.; Murzakov, B. G.; Evdokimova, M. D.; Dorofeyeva, I. K.

    Results of the study of the influence of Martian soil analogues, both as described by American scientists and as prepared by us, and of hydrogen peroxide on the viability of microorganisms are presented. The experiments were carried out using mixtures of soil analogues with desert soil and black earth (chernozem) samples, and pure cultures of microorganism. Microorganisms capable of withstanding a concentration of hydrogen peroxide in the medium as high as 1.5-2.0% were isolated. None of the 40 strains of microorganisms studied, all belonging to different systematic and physiological groups, exhibited growth inhibition on solid media in the presence of Martian soil analogues. In view of the fact that Martian soil cannot contain microorganisms in great quantities, we suggest using electroadsorption for their concentration, to make detection reliable. A device was designed for this purpose, using the principle of electroadsorption on a polarisable carrier (sterile cotton wool or cheesecloth). The concentrated suspension of microorganisms thus obtained was then characterized by various physicochemical methods.

  6. Design of Thymidine Analogues Targeting Thymidilate Kinase of Mycobacterium tuberculosis

    PubMed Central

    Owono Owono, Luc Calvin; Keita, Melalie; Megnassan, Eugene; Miertus, Stanislav

    2013-01-01

    We design here new nanomolar antituberculotics, inhibitors of Mycobacterium tuberculosis thymidine monophosphate kinase (TMPKmt), by means of structure-based molecular design. 3D models of TMPKmt-inhibitor complexes have been prepared from the crystal structure of TMPKmt cocrystallized with the natural substrate deoxythymidine monophosphate (dTMP) (1GSI) for a training set of 15 thymidine analogues (TMDs) with known activity to prepare a QSAR model of interaction establishing a correlation between the free energy of complexation and the biological activity. Subsequent validation of the predictability of the model has been performed with a 3D QSAR pharmacophore generation. The structural information derived from the model served to design new subnanomolar thymidine analogues. From molecular modeling investigations, the agreement between free energy of complexation (??Gcom) and Ki values explains 94% of the TMPKmt inhibition (pKi = ?0.2924??Gcom + 3.234; R2 = 0.94) by variation of the computed ??Gcom and 92% for the pharmacophore (PH4) model (pKi = 1.0206 × pKipred ? 0.0832, R2 = 0.92). The analysis of contributions from active site residues suggested substitution at the 5-position of pyrimidine ring and various groups at the 5?-position of the ribose. The best inhibitor reached a predicted Ki of 0.155?nM. The computational approach through the combined use of molecular modeling and PH4 pharmacophore is helpful in targeted drug design, providing valuable information for the synthesis and prediction of activity of novel antituberculotic agents. PMID:23634301

  7. Selenoether oxytocin analogues have analgesic properties in a mouse model of chronic abdominal pain.

    PubMed

    de Araujo, Aline Dantas; Mobli, Mehdi; Castro, Joel; Harrington, Andrea M; Vetter, Irina; Dekan, Zoltan; Muttenthaler, Markus; Wan, JingJing; Lewis, Richard J; King, Glenn F; Brierley, Stuart M; Alewood, Paul F

    2014-01-01

    Poor oral availability and susceptibility to reduction and protease degradation is a major hurdle in peptide drug development. However, drugable receptors in the gut present an attractive niche for peptide therapeutics. Here we demonstrate, in a mouse model of chronic abdominal pain, that oxytocin receptors are significantly upregulated in nociceptors innervating the colon. Correspondingly, we develop chemical strategies to engineer non-reducible and therefore more stable oxytocin analogues. Chemoselective selenide macrocyclization yields stabilized analogues equipotent to native oxytocin. Ultra-high-field nuclear magnetic resonance structural analysis of native oxytocin and the seleno-oxytocin derivatives reveals that oxytocin has a pre-organized structure in solution, in marked contrast to earlier X-ray crystallography studies. Finally, we show that these seleno-oxytocin analogues potently inhibit colonic nociceptors both in vitro and in vivo in mice with chronic visceral hypersensitivity. Our findings have potentially important implications for clinical use of oxytocin analogues and disulphide-rich peptides in general. PMID:24476666

  8. Synthesis of mixed opioid affinity cyclic endomorphin-2 analogues with fluorinated phenylalanines.

    PubMed

    Piekielna, Justyna; Perlikowska, Renata; do-Rego, Jean Claude; do-Rego, Jean-Luc; Cerlesi, Maria Camilla; Calo, Girolamo; Kluczyk, Alicja; ?api?ski, Krzysztof; Tömböly, Csaba; Janecka, Anna

    2015-05-14

    As part of our continuing studies on the structure-activity relationships of cyclic pentapeptides based on the structure of endomorphin-2 (EM-2), we report here the synthesis and biological activities of a new series of analogues of a general sequence Tyr/Dmt-c[d-Lys-Phe-Phe-Asp]NH2 (where Dmt = 2',6'-dimethyltyrosine), incorporating fluorinated amino acids: 4-fluorophenylalanine (4-F-Phe), 2,4-difluorophenylalanine (2,4-F-Phe), or 4-trifluoromethylphenylalanine (4-CF3-Phe) instead of the Phe residue in position 3 or 4. Depending on the fluorinated amino acid residue and its position in the sequence, analogues were mixed, high affinity MOP/KOP receptor agonists, MOP/DOP/KOP agonists, or selective KOP agonists. The in vitro potencies and efficacies of all novel analogues were assessed in calcium mobilization assay. The most potent analogues, Dmt-c[d-Lys-Phe-4-F-Phe-Asp]NH2 and Dmt-c[d-Lys-Phe-2,4-F-Phe-Asp]NH2, were tested in vivo in the mouse hot-plate test. They produced strong antinociceptive effect not only after intracerebroventricular but also after intraperitoneal injection, indicating that they were able to cross the blood-brain barrier. PMID:26005537

  9. The 5' binding MID domain of human Argonaute2 tolerates chemically modified nucleotide analogues.

    PubMed

    Deleavey, Glen F; Frank, Filipp; Hassler, Matthew; Wisnovsky, Simon; Nagar, Bhushan; Damha, Masad J

    2013-02-01

    Small interfering RNAs (siRNAs) can trigger potent gene silencing through the RNA interference (RNAi) pathway. The RNA-induced silencing complex (RISC) is key to this targeted mRNA degradation, and the human Argonaute2 (hAGO2) endonuclease component of RISC is responsible for the actual mRNA cleavage event. During RNAi, hAGO2 becomes loaded with the siRNA guide strand, making several key nucleic acid-enzyme interactions. Chemically modified siRNAs are now widely used in place of natural double-stranded RNAs, and understanding the effects chemical modifications have on guide strand-hAGO2 interactions has become particularly important. Here, interactions between the 5' nucleotide binding domain of hAGO2, MID, and chemically modified nucleotide analogues are investigated. Measured dissociation constants reveal that hAGO2 does not discriminate between nucleotide analogues during binding, regardless of the preferred sugar conformation of the nucleotide analogues. These results correlate well with cell-based gene silencing results employing siRNAs with 5'-modified guide strands. Additionally, chemical modification with 2'-deoxy-2'-fluoroarabino nucleic acid (2'F-ANA) and 2'-deoxy-2'-fluororibonucleic acid (2'F-RNA) at the passenger strand cleavage site of siRNAs has been shown to prevent hAGO2-mediated strand cleavage, an observation that appears to have little impact on overall gene silencing potency. PMID:23289589

  10. The Earliest Phases of Star Formation (EPoS): a Herschel key project. The thermal structure of low-mass molecular cloud cores

    NASA Astrophysics Data System (ADS)

    Launhardt, R.; Stutz, A. M.; Schmiedeke, A.; Henning, Th.; Krause, O.; Balog, Z.; Beuther, H.; Birkmann, S.; Hennemann, M.; Kainulainen, J.; Khanzadyan, T.; Linz, H.; Lippok, N.; Nielbock, M.; Pitann, J.; Ragan, S.; Risacher, C.; Schmalzl, M.; Shirley, Y. L.; Stecklum, B.; Steinacker, J.; Tackenberg, J.

    2013-03-01

    Context. The temperature and density structure of molecular cloud cores are the most important physical quantities that determine the course of the protostellar collapse and the properties of the stars they form. Nevertheless, density profiles often rely either on the simplifying assumption of isothermality or on observationally poorly constrained model temperature profiles. The instruments of the Herschel satellite provide us for the first time with both the spectral coverage and the spatial resolution that is needed to directly measure the dust temperature structure of nearby molecular cloud cores. Aims: With the aim of better constraining the initial physical conditions in molecular cloud cores at the onset of protostellar collapse, in particular of measuring their temperature structure, we initiated the guaranteed time key project (GTKP) "The Earliest Phases of Star Formation" (EPoS) with the Herschel satellite. This paper gives an overview of the low-mass sources in the EPoS project, the Herschel and complementary ground-based observations, our analysis method, and the initial results of the survey. Methods: We study the thermal dust emission of 12 previously well-characterized, isolated, nearby globules using FIR and submm continuum maps at up to eight wavelengths between 100 ?m and 1.2 mm. Our sample contains both globules with starless cores and embedded protostars at different early evolutionary stages. The dust emission maps are used to extract spatially resolved SEDs, which are then fit independently with modified blackbody curves to obtain line-of-sight-averaged dust temperature and column density maps. Results: We find that the thermal structure of all globules (mean mass 7 M?) is dominated by external heating from the interstellar radiation field and moderate shielding by thin extended halos. All globules have warm outer envelopes (14-20 K) and colder dense interiors (8-12 K) with column densities of a few 1022 cm-2. The protostars embedded in some of the globules raise the local temperature of the dense cores only within radii out to about 5000 AU, but do not significantly affect the overall thermal balance of the globules. Five out of the six starless cores in the sample are gravitationally bound and approximately thermally stabilized. The starless core in CB 244 is found to be supercritical and is speculated to be on the verge of collapse. For the first time, we can now also include externally heated starless cores in the Lsmm/Lbol vs. Tbol diagram and find that Tbol < 25 K seems to be a robust criterion to distinguish starless from protostellar cores, including those that only have an embedded very low-luminosity object. Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA.Partially based on observations carried out with the IRAM 30 m Telescope, with the Atacama Pathfinder Experiment (APEX), and with the James Clerk Maxwell Telescope (JCMT). IRAM is supported by INSU/CNRS (France), MPG (Germany) and IGN (Spain). APEX is a collaboration between Max Planck Institut für Radioastronomie (MPIfR), Onsala Space Observatory (OSO), and the European Southern Observatory (ESO). The JCMT is operated by the Joint Astronomy Centre on behalf of the Particle Physics and Astronomy Research Council of the United Kingdom, the Netherlands Association for Scientific Research, and the National Research Council of Canada.Appendices A, B and C are available in electronic form at http://www.aanda.org

  11. Analogue to Digital and Digital to Analogue Converters (ADCs and DACs): A Review Update

    E-print Network

    Pickering, J

    2015-01-01

    This is a review paper updated from that presented for CAS 2004. Essentially, since then, commercial components have continued to extend their performance boundaries but the basic building blocks and the techniques for choosing the best device and implementing it in a design have not changed. Analogue to digital and digital to analogue converters are crucial components in the continued drive to replace analogue circuitry with more controllable and less costly digital processing. This paper discusses the technologies available to perform in the likely measurement and control applications that arise within accelerators. It covers much of the terminology and 'specmanship' together with an application-oriented analysis of the realisable performance of the various types. Finally, some hints and warnings on system integration problems are given.

  12. Differential interaction of 1alpha,25-dihydroxyvitamin D3 analogues and their 20-epi homologues with the vitamin D receptor.

    PubMed

    Liu, Y Y; Collins, E D; Norman, A W; Peleg, S

    1997-02-01

    An important focus of structure-function studies of synthetic ligands for the vitamin D receptor (VDR) concerns the chiral center at carbon 20 of the steroid side chain; 20-epi analogues are 100-10, 000 times more potent transcriptionally than the natural hormone 1alpha,25-dihydroxyvitamin D3 (1alpha,25-(OH)2D3). We have compared the binding properties of three pairs of analogues either with a natural (N) or 20-epi (E) orientation. In intact cells, 45-60% of VDR.N-analogue complexes, but only 5-20% of VDR.E-analogue complexes, dissociated over a 3-h interval. The two groups of ligands induced distinct changes in VDR conformation as revealed by protease clipping assays. Mapping of ligand-VDR binding activity by deletions indicated that amino acids 420-427 were important for high affinity of VDR.N-analogue complexes, but not for VDR.E-analogue complexes. Site-directed mutagenesis revealed that residues 421 and 422 were essential for 1alpha,25-(OH)2D3-induced conformational changes, high affinity of 1alpha,25-(OH)2D3 for VDR, and transcriptional activity, but not for binding of its 20-epi analogue. In contrast, deletion of residues 396-427 abolished binding of 1alpha,25-(OH)2D3, but binding of its 20-epi analogue was still detectable. The results suggest that the ligand-binding domain of VDR has multiple and different contact sites for the two families of side chain-modified ligands, resulting in VDR.ligand complexes with different half-lives and transcriptional activities. PMID:9013574

  13. Isoelectronic analogues of PN: Remarkably stable multiply charged cations

    SciTech Connect

    Wong, Ming Wah; Radom, L. )

    1990-01-25

    The structures and stabilities of PN and its 27 isoelectronic analogues, CS, SiO, BCl, AlF, BeAr, MgNe, Sn{sup +}, PO{sup +}, CCl{sup +}, SiF{sup +}, BAr{sup +}, AlNe{sup +}, SO{sup 2+}, NCl{sup 2+}, PF{sup 2+}, CAr{sup 2+}, SiNe{sup 2+}, OCl{sup 3+}, SF{sup 3+}, NAr{sup 3+}, PNe{sup 3+}, FCl{sup 4+}, OAr{sup 4+}, SNe{sup 4+}, FAr{sup 5+}, ClNe{sup 5+}, and ArNe{sup 6+}, have been examined by ab initio molecular orbital theory. The CASSCF/6-311G(MC)(d) level was used to determine the ground-state potential energy curves and spectroscopic constants for the 28 diatomic systems. Equilibrium structures were also obtained with the 6-311G(MC)(d) basis set at the MP3 and ST4CCD levels, and dissociation energies were determined at the MP4/6-311 + G(MC)(2df) and MP4/6-311 + G(MC)(3d2f) levels. For the neutral and monocation analogues of PN, the calculated equilibrium geometries (at MP3/6-311G(MC)(d)) and dissociation energies (at MP4/6-311 + G(MC)(3d2f)) are in very good agreement with available experimental values. All the dication analogues of PN, namely, SO{sup 2+}, NCl{sup 2+}, PF{sup 2+}, CAr{sup 2+}, and SiNe{sup 2+}, are predicted to be experimentally observable species. Of these, the SO{sup 2+}, NCl{sup 2+}, and CAr{sup 2+} dications are calculated to be kinetically stable species, with large barriers associated with the exothermic charge-separation reactions, while the PF{sup 2+} and SiNe{sup 2+} dications are predicted not only to be kinetically stable but also to be thermodynamically stable species.

  14. Synthesis, characterization and biological studies of diosgenyl analogues.

    PubMed

    Huang, Baozhan; Du, Dan; Zhang, Rui; Wu, Xiaohua; Xing, Zhihua; He, Yang; Huang, Wen

    2012-12-15

    A series of optical amino acid diosgenyl esters and diosgenyl salicylate conjugates were designed and synthesized to develop new anticancer and anti-inflammatory agents. The analogue 9c that contains an 6-aminohexanoic acid residue at C-3 of diosgenin exhibits higher potency against all three tumor cell lines with IC(50) values ranging from 4.7 ?M in C26 cells to 14.6 ?M in Hep G2 cells. In addition, seven of newly synthesized compounds significantly inhibit xylene-induced ear edema and exhibit comparable or better anti-inflammatory activities than those of diosgenin and aspirin. Furthermore, preliminary structure-activity relationship studies demonstrate that diosgenyl salicylate conjugates have stronger anti-inflammatory activities than amino acid diosgenyl esters. PMID:23153797

  15. [A novel trichostatin analogue culture of Streptomyces sp. CPCC 203909].

    PubMed

    Chen, Ming-hua; Wu, Ye-xiang; Xu, Yan-ni; Yu, Li-yan; Hong, Bin; Jiang, Wei; Si, Shu-yi

    2015-05-01

    By using a cell-based high throughput screening model for the CLA-1 up-regulator, Streptomyces 203909 was found to produce up-regulator of CLA-1. A novel trichostatin analogue was isolated from the rice fermentation of Streptomyces sp. CPCC 203909by a combination of various chromatographic techniques including column chromatography (CC) over silica gel, flash C18 CC, and reversed-phase HPLC. Its structure was identified as (-)-(R,2E,4Z)-7-[(4'-dimethylamino) phenyl]-4,6-dimethyl-7-oxohepta-2,4-dienoyl-L-glutamine (1) by the spectroscopic and chemical methods, and combination with the CD spectroscopy and Marfey's method. In the prelimi- nary assays, Compound 1 showed cytotoxicity against human embryonic kidney 293 cell line with IC50 value 35.3 [µmol · L(-1). PMID:26323142

  16. Pushing Up Lithium Storage through Nanostructured Polyazaacene Analogues as Anode.

    PubMed

    Wu, Jiansheng; Rui, Xianhong; Long, Guankui; Chen, Wangqiao; Yan, Qingyu; Zhang, Qichun

    2015-06-15

    According to the evidence from both theoretical calculations and experimental findings, conjugated ladder polymers containing large ?-conjugated structure, a high number of nitrogen heteroatoms, and a multiring aromatic system, could be an ideal organic anode candidate for lithium-ion batteries (LIBs). In this report, we demonstrated that the nanostructured polyazaacene analogue poly(1,6-dihydropyrazino[2,3g]quinoxaline-2,3,8-triyl-7-(2H)-ylidene-7,8-dimethylidene) (PQL) shows high performance as anode materials in LIBs: high capacity (1750?mAh?g(-1), 0.05C), good rate performance (303?mAh?g(-1), 5C), and excellent cycle life (1000 cycles), especially at high temperature of 50?°C. Our results suggest nanostructured conjugated ladder polymers could be alternative electrode materials for the practical application of LIBs. PMID:25960289

  17. Amygdalin analogues inhibit IFN-? signalling and reduce the inflammatory response in human epidermal keratinocytes.

    PubMed

    Paoletti, Iole; De Gregorio, Vincenza; Baroni, Adone; Tufano, Maria Antonietta; Donnarumma, Giovanna; Perez, Juan Jesus

    2013-12-01

    Peptide T (PT), an octapeptide fragment located in the V2 region of the HIV-1 gp120-coating protein, appears to be beneficial in the treatment of psoriasis. Our previous investigations suggest that keratinocytes play a key role in conditioning the therapeutic effects of PT in psoriasis. The aim of this study was to explore the effects of PT and the peptidomimetic natural products, Dhurrin and Prunasin, on the expression of the IL-6, IL-8, IL-23, HSP70 and ICAM-1 on IFN-? and TNF-?-NHEK activated cells. Moreover, we analysed the interference of PT and its analogues through STAT-3 activation. Our results show that the analogues tested exhibit the beneficial biological effects of PT, suggesting the primary role of keratinocytes upon which PT and the peptidomimetics act directly, by reducing proinflammatory responses. Its reduction appears to be important for therapeutic approach in psoriasis pathogenesis. PMID:23933845

  18. Secret Public Key Protocols Revisited

    NASA Astrophysics Data System (ADS)

    Lim, Hoon Wei; Paterson, Kenneth G.

    Password-based protocols are important and popular means of providing human-to-machine authentication. The concept of secret public keys was proposed more than a decade ago as a means of securing password-based authentication protocols against off-line password guessing attacks, but was later found vulnerable to various attacks. In this paper, we revisit the concept and introduce the notion of identity-based secret public keys. Our new identity-based approach allows secret public keys to be constructed in a very natural way using arbitrary random strings, eliminating the structure found in, for example, RSA or ElGamal keys. We examine identity-based secret public key protocols and give informal security analyses, indicating that they are secure against off-line password guessing and other attacks.

  19. Key Reference Agilent Technologies

    E-print Network

    Anlage, Steven

    Key Reference Agilent Technologies E8257D/67D PSG Signal Generators This guide applies Procedures · Safety and Regulatory Information Key Reference · Key function description #12;1 1 Key Reference #12;2 Key Reference Symbols Symbols # of Carriers Supported E8267D with Option 601 or 602 This softkey

  20. The medial periosteal hinge, a key structure in fractures of the proximal humerus: a biomechanical cadaver study of its mechanical properties.

    PubMed

    Kralinger, F; Unger, S; Wambacher, M; Smekal, V; Schmoelz, W

    2009-07-01

    The medial periosteal hinge plays a key role in fractures of the head of the humerus, offering mechanical support during and after reduction and maintaining perfusion of the head by the vessels in the posteromedial periosteum. We have investigated the biomechanical properties of the medial periosteum in fractures of the proximal humerus using a standard model in 20 fresh-frozen cadaver specimens comparable in age, gender and bone mineral density. After creating the fracture, we displaced the humeral head medial or lateral to the shaft with controlled force until complete disruption of the posteromedial periosteum was recorded. As the quality of periosteum might be affected by age and bone quality, the results were correlated with the age and the local bone mineral density of the specimens measured with quantitative CT. Periosteal rupture started at a mean displacement of 2.96 mm (SD 2.92) with a mean load of 100.9 N (SD 47.1). The mean maximum load of 111.4 N (SD 42.5) was reached at a mean displacement of 4.9 mm (SD 4.2). The periosteum was completely ruptured at a mean displacement of 34.4 mm (SD 11.1). There was no significant difference in the mean distance to complete rupture for medial (mean 35.8 mm (SD 13.8)) or lateral (mean 33.0 mm (SD 8.2)) displacement (p = 0.589). The mean bone mineral density was 0.111 g/cm(3) (SD 0.035). A statistically significant but low correlation between bone mineral density and the maximum load uptake (r = 0.475, p = 0.034) was observed. This study showed that the posteromedial hinge is a mechanical structure capable of providing support for percutaneous reduction and stabilisation of a fracture by ligamentotaxis. Periosteal rupture started at a mean of about 3 mm and was completed by a mean displacement of just under 35 mm. The microvascular situation of the rupturing periosteum cannot be investigated with the current model. PMID:19567866

  1. S100A13-C2A binary complex structure-a key component in the acidic fibroblast growth factor for the non-classical pathway

    SciTech Connect

    Mohan, Sepuru K.; Rani, Sandhya G.; Kumar, Sriramoju M.; Yu Chin

    2009-03-13

    Fibroblast growth factors (FGFs) are key regulators of cell proliferation, differentiation, tumor-induced angiogenesis and migration. FGFs are essential for early embryonic development, organ formation and angiogenesis. They play important roles in tumor formation, inflammation, wound healing and restenosis. The biological effects of FGFs are mediated through the activation of the four transmembrane phosphotyrosine kinase receptors (FGFRs) in the presence of heparin sulfate proteoglycans (HSPGs) and therefore require the release of FGFs into the extracellular space. However, FGF-1 lacks the signal peptide required for the releasing of these proteins through the classical endoplasmic reticulum (ER)-Golgi secretary pathway. Maciag et al. demonstrated that FGF-1 is exported through a non-classical release pathway involving the formation of a specific multiprotein complex [M. Landriscina, R. Soldi, C. Bagala, I. Micucci, S. Bellum, F. Tarantini, I. Prudovsky, T. Maciag, S100A13 participates in the release of fibroblast growth factor 1 in response to heat shock in vitro, J. Biol. Chem. 276 (2001) 22544-22552; C.M. Carreira, T.M. LaVallee, F. Tarantini, A. Jackson, J.T. Lathrop, B. Hampton, W.H. Burgess, T. Maciag, S100A13 is involved in the regulation of fibroblast growth factor-1 and p40 synaptotagmin-1 release in vitro, J. Biol. Chem. 273 (1998) 22224-22231; T.M. LaValle, F. Tarantini, S. Gamble, C.M. Carreira, A. Jackson, T. Maciag, Synaptotagmin-1 is required for fibroblast growth factor-1 release, J. Biol. Chem. 273 (1998) 22217-22223; C. Bagala, V. Kolev, A. Mandinova, R. Soldi, C. Mouta, I. Graziani, I, Prudovsky, T. Maciag, The alternative translation of synaptotagmin 1 mediates the non-classical release of FGF1, Biochem. Biophys. Res. Commun. 310 (2003) 1041-1047]. The protein constituents of this complex include FGF-1, S100A13 (a Ca{sup 2+}-binding protein), and the p40 form of synaptotagmin 1 (Syt1). To understand the molecular events in the FGF-1 releasing pathway, we have studied the interactions of S100A13 with C2A by {sup 1}H-{sup 15}N HSQC titration and 3D-filtered NOESY experiments. We characterized the binary complex structure of S100A13-C2A by using a variety of multi-dimensional NMR experiments. This complex acts as a template for FGF-1 dimerization and multiprotein complex formation.

  2. CO2 Removal using a Synthetic Analogue of Carbonic Anhydrase

    SciTech Connect

    Harry Cordatos

    2010-09-14

    Project attempts to develop a synthetic analogue for carbonic anhydrase and incorporate it in a membrane for separation of CO2 from coal power plant flue gas. Conference poster presents result of first 9 months of project progress including concept, basic system architecture and membrane properties target, results of molecular modeling for analogue - CO2 interaction, and next steps of testing analogue resistance to flue gas contaminants.

  3. Four Generations of Transition State Analogues for Human Purine Nucleoside Phosphorylase

    SciTech Connect

    Ho, M.; Shi, W; Rinaldo-Mathis, A; Tyler, P; Evans, G; Almo, S; Schramm, V

    2010-01-01

    Inhibition of human purine nucleoside phosphorylase (PNP) stops growth of activated T-cells and the formation of 6-oxypurine bases, making it a target for leukemia, autoimmune disorders, and gout. Four generations of ribocation transition-state mimics bound to PNP are structurally characterized. Immucillin-H (K*{sub i} = 58 pM, first-generation) contains an iminoribitol cation with four asymmetric carbons. DADMe-Immucillin-H (K*{sub i} = 9 pM, second-generation), uses a methylene-bridged dihydroxypyrrolidine cation with two asymmetric centers. DATMe-Immucillin-H (K*{sub i} = 9 pM, third-generation) contains an open-chain amino alcohol cation with two asymmetric carbons. SerMe-ImmH (K*{sub i} = 5 pM, fourth-generation) uses achiral dihydroxyaminoalcohol seramide as the ribocation mimic. Crystal structures of PNPs establish features of tight binding to be; (1) ion-pair formation between bound phosphate (or its mimic) and inhibitor cation, (2) leaving-group interactions to N1, O6, and N7 of 9-deazahypoxanthine, (3) interaction between phosphate and inhibitor hydroxyl groups, and (4) His257 interacting with the 5{prime}-hydroxyl group. The first generation analogue is an imperfect fit to the catalytic site with a long ion pair distance between the iminoribitol and bound phosphate and weaker interactions to the leaving group. Increasing the ribocation to leaving-group distance in the second- to fourth-generation analogues provides powerful binding interactions and a facile synthetic route to powerful inhibitors. Despite chemical diversity in the four generations of transition-state analogues, the catalytic site geometry is almost the same for all analogues. Multiple solutions in transition-state analogue design are available to convert the energy of catalytic rate enhancement to binding energy in human PNP.

  4. Structure activity-relationship and in vitro and in vivo evaluation of the potent cytotoxic anti-microtubule agent N-(4-methoxyphenyl)-N,2,6-trimethyl-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-aminium chloride and its analogues as antitumor agents

    PubMed Central

    Gangjee, Aleem; Zhao, Ying; Raghavan, Sudhir; Rohena, Cristina; Mooberry, Susan L.; Hamel, Ernest

    2013-01-01

    A series of 21 substituted cyclopenta[d]pyrimidines were synthesized as an extension of our discovery of the parent compound 1·HCl as an antimicrotubule agent. The structure-activity relationship indicates that the N-methyl and a 4?-methoxy groups appear important for potent activity. In addition, the 6-substituent in the parent analogue is not necessary for activity. The most potent compound 30·HCl was a 1–2 digit nanomolar inhibitor of most tumor cell proliferations and was up to 7-fold more potent than the parent compound 1·HCl. In addition, 30·HCl inhibited cancer cell proliferation regardless of Pgp or ?III-tubulin status, both of which are known to cause clinical resistance to several antitubulin agents. In vivo efficacy of 30·HCl was demonstrated against a triple negative breast cancer xenograft mouse model. Compound 30·HCl is water soluble, easily synthesized and serves as a lead compound for further preclinical evaluation as an antitumor agent. PMID:23895532

  5. Structure-activity relationship and in vitro and in vivo evaluation of the potent cytotoxic anti-microtubule agent N-(4-methoxyphenyl)-N,2,6-trimethyl-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-aminium chloride and its analogues as antitumor agents.

    PubMed

    Gangjee, Aleem; Zhao, Ying; Raghavan, Sudhir; Rohena, Cristina C; Mooberry, Susan L; Hamel, Ernest

    2013-09-12

    A series of 21 substituted cyclopenta[d]pyrimidines were synthesized as an extension of our discovery of the parent compound (±)-1·HCl as an anti-microtubule agent. The structure-activity relationship indicates that the N-methyl and a 4N-methoxy groups appear important for potent activity. In addition, the 6-substituent in the parent analogue is not necessary for activity. The most potent compound 30·HCl was a one to two digit nanomolar inhibitor of most tumor cell proliferations and was up to 7-fold more potent than the parent compound (±)-1·HCl. In addition, 30·HCl inhibited cancer cell proliferation regardless of Pgp or ?III-tubulin status, both of which are known to cause clinical resistance to several anti-tubulin agents. In vivo efficacy of 30·HCl was demonstrated against a triple negative breast cancer xenograft mouse model. Compound 30·HCl is water-soluble and easily synthesized and serves as a lead compound for further preclinical evaluation as an antitumor agent. PMID:23895532

  6. Spectroscopic study of solar twins and analogues

    NASA Astrophysics Data System (ADS)

    Datson, Juliet; Flynn, Chris; Portinari, Laura

    2015-02-01

    Context. Many large stellar surveys have been and are still being carried out, providing huge amounts of data, for which stellar physical parameters will be derived. Solar twins and analogues provide a means to test the calibration of these stellar catalogues because the Sun is the best-studied star and provides precise fundamental parameters. Solar twins should be centred on the solar values. Aims: This spectroscopic study of solar analogues selected from the Geneva-Copenhagen Survey (GCS) at a resolution of 48 000 provides effective temperatures and metallicities for these stars. We test whether our spectroscopic parameters, as well as the previous photometric calibrations, are properly centred on the Sun. In addition, we search for more solar twins in our sample. Methods: The methods used in this work are based on literature methods for solar twin searches and on methods we developed in previous work to distinguish the metallicity-temperature degeneracies in the differential comparison of spectra of solar analogues versus a reference solar reflection spectrum. Results: We derive spectroscopic parameters for 148 solar analogues (about 70 are new entries to the literature) and verify with a-posteriori differential tests that our values are well-centred on the solar values. We use our dataset to assess the two alternative calibrations of the GCS parameters; our methods favour the latest revision. We show that the choice of spectral line list or the choice of asteroid or time of observation does not affect the results. We also identify seven solar twins in our sample, three of which are published here for the first time. Conclusions: Our methods provide an independent means to differentially test the calibration of stellar catalogues around the values of a well-known benchmark star, which makes our work interesting for calibration tests of upcoming Galactic surveys. Based on observations made with ESO Telescopes at the La Silla Observatory under programme ID 077.D-0525 and 090.D-0133.Table 1 is also available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/574/A124Full Table 5 is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/574/A124

  7. Phenolic analogues of reversed esters of pethidine.

    PubMed

    Casy, A F; Ogungbamila, F O

    1985-02-01

    The preparation and stereochemical characterization of phenolic analogues of the reversed ester of pethidine, alpha- and beta-prodine and a 1-phenethyl congener are described. All the compounds were weakly active or inactive as agonists in rodent antinociceptive tests and failed to antagonize fentanyl in rats. The results substantiate the view that the morphine and 4-phenylpiperidine groups of analgesics differ in their modes of interaction with opiate receptors, except possibly when the piperidine derivative carries a C-4 carbon substituent. PMID:2858544

  8. Analogues of ethionamide, a drug used for multidrug-resistant tuberculosis, exhibit potent inhibition of tyrosinase.

    PubMed

    Choi, Joonhyeok; Park, Sung-Jean; Jee, Jun-Goo

    2015-12-01

    Tyrosinase catalyzes two distinct sequential reactions in melanin biosynthesis: the hydroxylation of tyrosine to DOPA followed by the oxidation of DOPA to dopaquinone. The central roles of melanin in living species have motivated researchers to maintain constant efforts to discover new agents that modulate tyrosinase activity. In this study, we report on the inhibition of tyrosinase by ethionamide and its analogues. Ethionamide, 2-ethylpyridine-4-carbothioamide, is a second-line antituberculosis drug used for the treatment of multidrug-resistant tuberculosis. The chemical similarity of ethionamide to phenylthiourea, a well-known tyrosinase inhibitor, led us to investigate its inhibitory effects on mushroom tyrosinase and the IC50 was calculated as 4 ?M. Five analogues of ethionamide, including another antituberculosis drug, prothionamide, were also inhibitory, with values for IC50 in the range of 3-43 ?M. Fluorescence quenching experiments supported a mechanism of direct binding. In contrast, isoniazid, a structural analogue and first-line antituberculosis drug, was a poor inhibitor of tyrosinase. We also tested the effects of ethionamide and its analogues on melanin content in B16F10 cells. At a concentration of 50 ?M, the molecules, pyridine-2-carbothioamide and thiobenzamide substantially decreased the melanin content by 44% and 37%, respectively. In addition to identifying other interactions, docking simulations showed that the carbothioamide groups of the molecules make essential contacts with the catalytic di-copper atoms. Our results suggest that carbothioamide can be a central moiety for the development of new and potent tyrosinase inhibitors. PMID:26544630

  9. Solid-Phase Combinatorial Synthesis and Biological Evaluation of Destruxin?E Analogues.

    PubMed

    Yoshida, Masahito; Ishida, Yoshitaka; Adachi, Kenta; Murase, Hayato; Nakagawa, Hiroshi; Doi, Takayuki

    2015-12-01

    The solid-phase combinatorial synthesis of cyclodepsipeptide destruxin?E has been demonstrated. The combinatorial synthesis of cyclization precursors 8 was achieved by using a split and pool method on SynPhase Lanterns. The products were successfully macrolactonized in parallel in the solution phase by using 2-methyl-6-nitrobenzoic anhydride and 4-(dimethylamino)pyridine N-oxide to afford macrolactones 9, and the subsequent formation of an epoxide in the side chain gave 18 member destruxin?E analogues 6. Biological evaluation of analogues 6 indicated that the N-MeAla residue was crucial to the induction of morphological changes in osteoclast-like multinuclear cells (OCLs). Based on structure-activity relationships, azido-containing analogues 15 were then designed for use as a molecular probe. The synthesis and biological evaluation of analogues 15 revealed that 15?b, in which the Ile residue was replaced with a Lys(N3 ) residue, induced morphological changes in OCLs at a sufficient concentration, and modification around the Ile residue would be tolerated for attachment of a chemical tag toward the target identification of destruxin?E (1). PMID:26531322

  10. Andrographolide and analogues in cancer prevention.

    PubMed

    Mishra, Siddhartha Kumar; Tripathi, Swati; Shukla, Archana; Oh, Seung Hyun; Kim, Hwan Mook

    2015-01-01

    Andrographis paniculata is a medicinal plant traditionally used for treatment of cough and cold, fever, laryngitis, and several infectious diseases. Extracts of A. paniculata have shown versatile potency against various diseases including cancer. The active biomolecules of A. paniculata mainly are lactone and diterpene. Andrographolide and analogues have been widely used for prevention of different diseases. Andrographolides have shown potent antiinflammatory and anticancer activities. It showed potentials as chemopreventive agents by suppressing growth of cancer cells by inhibiting NF-kappaB, PI3K/AKT and other kinase pathways and by inducing apoptosis. Andrographolide induced both intrinsic and extrinsic apoptosis pathway in different cancer cells via expression of different anti-apoptotic protein like Bax, p53, and activated caspases. Andrographolide was successfully used as an antineoplastic drug in cancer chemotherapy. Andrographolide inhibited the growth of human breast, prostate, and hepatoma tumors. Andrographolide and analogues need to be subjected to further clinical and biomedical studies in cancer chemoprevention. Andrographolide could be potent anticancer agent when used in combination with other chemotherapeutic agents. PMID:25553378

  11. The Nearby Analogues of Pure Starburst Galaxies

    NASA Astrophysics Data System (ADS)

    Kaiser, Benjamin C.; Crider, Anthony; Richardson, Chris T.

    2016-01-01

    The relationship between active galactic nuclei (AGN) and starburst galaxies is poorly understood, partially due to galaxies exhibiting both AGN and starburst activity. We have a sample of "pure" starburst galaxies at z~0.1 as selected by mean field independent component analysis (MFICA). In order to better understand these starburst galaxies, we attempt to identify nearby analogues. First, we degrade a random sample of nearby galaxies to a redshift of z~0.1 by decreasing brightness and spatial resolution and increasing signal-to-noise. We then compare the magnitude, color, morphology, and concentration of each of these galaxies to our pure starburst galaxies. Finally, we determine if the nearby galaxies most similar to the starbursts when degraded are consistent with the local optimally emitting cloud model (LOC). The LOC model makes predictions for the distribution of HII regions within starburst galaxies which have been previously tested with the spectra of z~0.1 galaxies, and may be further validated by examination of these nearby analogues.

  12. Pepstatin analogues as novel renin inhibitors.

    PubMed

    Guégan, R; Diaz, J; Cazaubon, C; Beaumont, M; Carlet, C; Clément, J; Demarne, H; Mellet, M; Richaud, J P; Segondy, D

    1986-07-01

    Pepstatin analogues corresponding to the general formula A-X-Y-Sta-Ala-Sta-R were synthesized in solution phase. Various changes in the nature of the A, X, and Y groups were made to improve the inhibitory potency against human plasma renin activity. The results were interpreted by use of the active-site model based on the sequence of human angiotensinogen. The tert-butyloxycarbonyl group and the isovaleryl group were found to be the most effective acyl groups (A). The analogues having a Phe residue in place of Val1 (X) and His or amino acid with an aliphatic side chain such as norleucine or norvaline in the Y position showed the highest inhibition of human plasma renin activity with IC50 values of about 10(-8)M. Esterification or amidification of the carboxyl group of the C-terminal statine did not change the inhibitory potency. The selectivity for rat, dog, pig, and monkey plasma renin of the most interesting compounds was studied. PMID:3543358

  13. d-Maurocalcine, a Pharmacologically Inert Efficient Cell-penetrating Peptide Analogue*

    PubMed Central

    Poillot, Cathy; Dridi, Kaouthar; Bichraoui, Hicham; Pêcher, Julien; Alphonse, Sebastien; Douzi, Badreddine; Ronjat, Michel; Darbon, Hervé; De Waard, Michel

    2010-01-01

    Maurocalcine has been the first demonstrated animal toxin acting as a cell-penetrating peptide. Although it possesses competitive advantages, its use as a cell-penetrating peptide (CPP) requires that analogues be developed that lack its characteristic pharmacological activity on ryanodine-sensitive calcium channels without affecting its cell-penetrating and vector efficiencies. Here, we present the synthesis, three-dimensional 1H NMR structure, and activity of d-maurocalcine. We demonstrate that it possesses all of the desired features for an excellent CPP: preserved structure, lack of pharmacological action, conserved vector properties, and absence of cell toxicity. This is the first report of a folded/oxidized animal toxin in its d-diastereomer conformation for use as a CPP. The protease resistance of this new peptide analogue, combined with its efficient cell penetration at concentrations devoid of cell toxicity, suggests that d-maurocalcine should be an excellent vector for in vivo applications. PMID:20610396

  14. Action of Clathrodin and Analogues on Voltage-Gated Sodium Channels

    PubMed Central

    Peigneur, Steve; Žula, Aleš; Zidar, Nace; Chan-Porter, Fiona; Kirby, Robert; Madge, David; Ilaš, Janez; Kikelj, Danijel; Tytgat, Jan

    2014-01-01

    Clathrodin is a marine alkaloid and believed to be a modulator of voltage-gated sodium (NaV ) channels. Since there is an urgent need for small molecule NaV channel ligands as novel therapeutics, clathrodin could represent an interesting lead compound. Therefore, clathrodin was reinvestigated for its potency and NaV channel subtype selectivity. Clathrodin and its synthetic analogues were subjected to screening on a broad range of NaV channel isoforms, both in voltage clamp and patch clamp conditions. Even though clathrodin was not found to exert any activity, some analogues were capable of modulating the NaV channels, hereby validating the pyrrole-2-aminoimidazole alkaloid structure as a core structure for future small molecule-based NaV channel modulators. PMID:24714127

  15. Characterization of structural elements in native autoinducing peptides and non-native analogues that permit the differential modulation of AgrC-type quorum sensing receptors in Staphylococcus aureus.

    PubMed

    Tal-Gan, Yftah; Ivancic, Monika; Cornilescu, Gabriel; Blackwell, Helen E

    2016-01-01

    Staphylococcus aureus uses short macrocyclic peptides (i.e., autoinducing peptides, or AIPs) to assess its local population density in a cell-cell signaling mechanism called quorum sensing (QS). At high cell numbers, this pathogen can initiate many virulent behaviors that allow for the establishment of infection. Binding of the AIP signal to its cognate transmembrane AgrC-type receptor is a critical event in the QS signaling cascade; consequently, interference of AIP:receptor interactions may have the potential to prevent and eradicate certain S. aureus infections. To date, four pairs of AIP:AgrC receptors have been identified in S. aureus, each pair being utilized by a specific S. aureus group (I-IV). Other staphylococcal species also use closely related, but distinct, AIP:AgrC pairs to control QS. We seek to develop non-native ligands capable of intercepting AIP:AgrC binding in each S. aureus group and in related species. As these bacteria may use their respective AIP signal to attenuate the QS systems of other groups/species, such ligands would provide valuable chemical tools to probe possible interference mechanisms in a range of contexts. In the current study, we used solution-phase NMR techniques to characterize the 3-D structures of a set of known native and non-native peptides that have differential modulatory activity in certain AgrC receptors. Analysis of these structures revealed several distinct structural motifs that belay differential activity in selected S. aureus AgrC receptors (i.e., AgrC-I, AgrC-II, and AgrC-III). The results of this study can be leveraged for the design of new synthetic ligands with enhanced selectivities and potencies for these AgrC receptors. PMID:26416476

  16. Key Request (Last) (First)

    E-print Network

    Shlizerman, Eli

    Key Request Form Name: (Last) (First) Contact Info Keys Cardswipe UW Email: Hitchcock Exterior Door Signatures Bring your completed form to the Biology Administrative Office (KIN 106). A deposit of $10 per key/card is required and payable by check or cash (exact change required). By signing the Key Request Form you agree

  17. Synthesis, structure, and magnetism of a family of heterometallic {Cu2Ln7} and {Cu4Ln12} (Ln = Gd, Tb, and Dy) complexes: the Gd analogues exhibiting a large magnetocaloric effect.

    PubMed

    Langley, Stuart K; Moubaraki, Boujemaa; Tomasi, Corrado; Evangelisti, Marco; Brechin, Euan K; Murray, Keith S

    2014-12-15

    The syntheses, structures, and magnetic properties of two heterometallic Cu(II)-Ln(III) (Ln(III) = Gd, Tb, and Dy) families, utilizing triethanolamine and carboxylate ligands, are reported. The first structural motif displays a nonanuclear {Cu(II)2Ln(III)7} metallic core, while the second reveals a hexadecanuclear {Cu(II)4Ln(III)12} core. The differing nuclearities of the two families stem from the choice of carboxylic acid used in the synthesis. Magnetic studies show that the most impressive features are displayed by the {Cu(II)2Gd(III)7} and {Cu(II)4Gd(III)12} complexes, which display a large magnetocaloric effect, with entropy changes -?Sm = 34.6 and 33.0 J kg(-1) K(-1) at T = 2.7 and 2.9 K, respectively, for a 9 T applied field change. It is also found that the {Cu(II)4Dy(III)12} complex displays single-molecule magnet behavior, with an anisotropy barrier to magnetization reversal of 10.1 K. PMID:25494949

  18. Detecting Pyrolysis Products from Bacteria in a Mars Soil Analogue

    NASA Technical Reports Server (NTRS)

    Glavin, D. P.; Cleaves, H. J.; Schubert, M.; Aubrey, A.; Buch, A.; Mahaffy, P. R.; Bada, J. L.

    2004-01-01

    One of the primary objectives of the 1976 Viking missions was to determine whether organic compounds, possibly of biological origin, were present in the Martian surface soils. The Viking gas chromatography mass spectrometry (GCMS) instruments found no evidence for any organic compounds of Martian origin above a few parts per billion in the upper 10 cm of surface soil, suggesting the absence of a widely distributed Martian biota. However, it is now known that key organic compounds important to biology, such as amino acids, carboxylic acids and nucleobases, would likely have been missed by the Viking GCMS instruments. In this study, a Mars soil analogue that was inoculated with approx. 10 billion Escherichia coli cells was heated at 500 C under Martian ambient pressure to release volatile organic compounds from the sample. The pyrolysis products were then analyzed for amino acids and nucleobases using high performance liquid chromatography (HPLC) and GCMS. Our experimental results indicate that at the part per billion level, the degradation products generated from several million bacterial cells per gram of Martian soil would not have been detected by the Viking GCMS instruments. Upcoming strategies for Mars exploration will require in-situ analyses by instruments that can assess whether any organic compounds, especially those that might be associated with life, are present in Martian surface samples.

  19. Synthesis and stereochemical assignment of DNA spore photoproduct analogues.

    PubMed

    Friedel, Marcus G; Pieck, J Carsten; Klages, Jochen; Dauth, Christina; Kessler, Horst; Carell, Thomas

    2006-08-01

    Investigation of the DNA repair process performed by the spore photoproduct (SP) lyase repair enzyme is strongly hampered by the lack of defined substrates needed for detailed enzymatic studies. The problem is particularly severe because the repair enzyme belongs to the class of strongly oxygen-sensitive radical (S)-adenosylmethionine (SAM) enzymes, which are notoriously difficult to handle. We report the synthesis of the spore photoproduct analogues 1 a and 1 b, which have open backbones and are diastereoisomers. In order to solve the problem of stereochemical assignment, two further derivatives 2 a and 2 b with closed backbones were prepared. The key step of the synthesis of 2 a/b is a metathesis-based macrocyclization that strongly increases the conformational rigidity of the synthetic spore photoproduct derivatives. NOESY experiments of the cyclic isomers furnished a clear cross-peak pattern that allowed the unequivocal assignment of the stereochemistry. The results were transferred to the data for isomers 1 a and 1 b, which were subsequently used for enzymatic-repair studies. These studies were performed with the novel spore photoproduct lyase repair enzyme from Geobacillus stearothermophilus. The studies showed an accordance with a recent investigation performed by us with the spore photoproduct lyase from Bacillus subtilis, in that only the S isomer 1 a is recognized and repaired. The ability to prepare a defined functioning substrate now paves the way for detailed enzymatic studies of the SP-lyase lesion recognition and repair process. PMID:16789031

  20. Special polynomials associated with the fourth order analogue to the Painlevé equations

    NASA Astrophysics Data System (ADS)

    Kudryashov, Nikolai A.; Demina, Maria V.

    2007-04-01

    Rational solutions of the fourth order analogue to the Painlevé equations are classified. Special polynomials associated with the rational solutions are introduced. The structure of the polynomials is found. Formulae for their coefficients and degrees are derived. It is shown that special solutions of the Fordy Gibbons, the Caudrey Dodd Gibbon and the Kaup Kupershmidt equations can be expressed through solutions of the equation studied.

  1. VUV irradiation of interstellar ice analogues: an abiotic source for organic matter in planetary systems

    NASA Astrophysics Data System (ADS)

    de Marcellus, P.; Modica, P.; Meinert, C.; Nahon, L.; Meierhenrich, U. J.; Le Sergeant d'Hendecourt, L.

    2014-04-01

    Laboratory organic residues from energetic and thermal evolution of astrophysical ices are sometimes considered as analogues of meteoritic and/or precometary matter, because of similarities in physical structure and chemical composition. In particular, various organic molecules of potential prebiotic interest, such as amino acids, have been detected. Moreover, enantiomeric excesses have been induced in amino acids by the irradiation of the ice samples with asymmetric light (UV-CPL), a scenario that may explain their origin in primitive chondrites.

  2. Aberrant Apoptotic Response of Colorectal Cancer Cells to Novel Nucleoside Analogues

    PubMed Central

    Harmse, Leonie; Dahan-Farkas, Nurit; Panayides, Jenny-Lee; van Otterlo, Willem; Penny, Clement

    2015-01-01

    Despite the increased understanding of colorectal cancer and the introduction of targeted drug therapy, the metastatic phase of the disease remains refractory to treatment. Since the deregulation of normal apoptosis contributes to the pathogenesis of colorectal cancer, novel nucleoside analogues were synthesized here and evaluated for their ability to induce apoptosis and cause cell death in two colorectal adeno-carcinoma cell lines, Caco-2 and HT-29. Three novel nucleoside analogues assessed here showed cytotoxic activity, as measured by the MTT assay against both cell lines: the IC50 values ranged between 3 and 37 ?M, with Caco-2 cells being more sensitive than HT-29 cells. Compared to camptothecin, the positive control, the nucleoside analogues were significantly less toxic to normal unstimulated leukocytes (p>0.05). Moreover, the nucleosides were able to induce apoptosis as measured by an increase in caspase 8 and caspase 3 activity above that of the control. This was additionally supported by data derived from Annexin V-FITC assays. Despite marginal changes to the mitochondrial membrane potential, all three nucleosides caused a significant increase in cytosolic cytochrome c (p>0.05), with a corresponding decrease in mitochondrial cytochrome c. Morphological analysis of both cell lines showed the rapid appearance of vacuoles following exposure to two of the nucleosides, while a third caused cellular detachment, delayed cytoplasmic vacuolisation and nuclear abnormalities. Preliminary investigations, using the autophagic indicator monodansylcadaverine and chloroquine as positive control, showed that two of the nucleosides induced the formation of autophagic vacuoles. In summary, the novel nucleoside analogues showed selective cytotoxicity towards both cancer cell lines and are effective initiators of an unusual apoptotic response, demonstrating their potential to serve as structural scaffolds for more potent analogues. PMID:26390405

  3. Nuclear and magnetic structures and magnetic properties of the layered cobalt hydroxysulfate Co5(OH)6(SO4)2(H2O)4 and its deuterated analogue, Co5(OD)6(SO4)2(D2O)4.

    PubMed

    Salah, Mohsen Ben; Vilminot, Serge; André, Gilles; Richard-Plouet, Mireille; Mhiri, Tahar; Takagi, Seishi; Kurmoo, Mohamedally

    2006-06-21

    The structures (nuclear and magnetic), magnetic properties (2-300 K, 1-10(4) bar), and heat capacity of the layered ferromagnet Co5(OH)6(SO4)2(H2O)4 are reported. The crystal structure consists of brucite-like M(II)-OH layers of edge-sharing octahedra, but having two different Co sites, which are pillared by ...O3SO-Co(H2O)4-OSO3.... The absorption spectrum confirms the presence of divalent Co, and by comparison of the two isotopic materials, the assignment of the vibrational spectra is proposed. The magnetic properties are those of a ferromagnet with a Curie temperature of 14 K. Temperature and field dependence magnetization data taken on an aligned sample suggest an easy-plane magnet. The Curie temperature increases linearly with pressure at a rate of +0.12 K/kbar, suggesting small progressive and uniform modifications of the Co-Co exchange interactions. Rietveld refinement of the neutron powder diffraction data and consideration of a group analysis reveal the direction of the moments of the Co within the layer to be along the b-axis, with a maximum moment of 3.33 micro(B) per cobalt. Those of the pillars remain random. Estimation of the entropy from the heat capacity data accounts for the presence of four ordered moments of Co with spin 1/2 at the long-range ordering temperature, while the moment of the pillaring Co contributes only at lower temperature due to the increase of the internal field as the temperature is lowered. The purely 2D-magnetic ordering in an easy-plane magnet, evidenced by neutron diffraction and heat capacity, challenges the existing theories and is a rare example of a single-layer magnet. PMID:16771512

  4. A Comparison of Two Types of Counseling Analogues

    ERIC Educational Resources Information Center

    Helms, Janet E.

    1976-01-01

    Subjects' attraction to the counselor, self-reported and physiological anxiety, and susceptibility to persuasion were compared using two types of counseling analogues, quasi-counseling and vicarious-participation. Participants in the quasi-counseling analogue were significantly more attracted to the counselor than were vicarious-participation…

  5. Onboard Detection of Active Canadian Sulfur Springs: A Europa Analogue

    E-print Network

    Onboard Detection of Active Canadian Sulfur Springs: A Europa Analogue Rebecca Castano (1) Kiri of in- situ onboard detection in which the Earth Observing-1 spacecraft detects surface sulfur deposits analogue for the Europan surface. In this paper, we describe the process of developing the onboard

  6. PARTIAL-SUM ANALOGUES OF THE ROGERSRAMANUJAN S. OLE WARNAAR

    E-print Network

    Warnaar, Ole

    in the Schur polynomials [11, 7, 13, 8, 22] sparked by the following nice generalization of the RogersPARTIAL-SUM ANALOGUES OF THE ROGERS­RAMANUJAN IDENTITIES S. OLE WARNAAR Abstract. A new polynomial analogue of the Rogers­Ramanujan identities is proven. Here the product-side of the Rogers

  7. The photoinduced transformation of fluorescent DNA base analogue tC triggers DNA melting.

    PubMed

    Preus, Søren; Jønck, Søren; Pittelkow, Michael; Dierckx, Anke; Karpkird, Thitinun; Albinsson, Bo; Wilhelmsson, L Marcus

    2013-08-01

    While fluorescent analogues of the canonical nucleobases have proven to be highly valuable in a large number of applications, up until today, fluorescent DNA base analogues remain virtually inapplicable for single-molecule fluorescence experiments which require extremely bright and photostable dyes. Insight into the photodegradation processes of these fluorophores is thus a key step in the continuous development towards dyes with improved performances. Here, we show that the commercially available fluorescent nucleobase analogue tC under intense long-term illumination and in the presence of O2 is degraded to form a single photoreaction product which we suggest to be the sulfoxide form of tC. The photoproduct is characterized by a blue-shifted absorption and a less intense fluorescence compared to that of tC. Interestingly, when tC is positioned inside double-stranded DNA this photodriven conversion of tC to its photoproduct greatly reduces the duplex stability of the overall double helix in which the probe is positioned. Since tC can be excited selectively at 400 nm, well outside the absorption band of the natural DNA bases, this observation points towards the application of tC as a general light-triggered switch of DNA duplex stability. PMID:23689311

  8. Discovery of the Once-Weekly Glucagon-Like Peptide-1 (GLP-1) Analogue Semaglutide.

    PubMed

    Lau, Jesper; Bloch, Paw; Schäffer, Lauge; Pettersson, Ingrid; Spetzler, Jane; Kofoed, Jacob; Madsen, Kjeld; Knudsen, Lotte Bjerre; McGuire, James; Steensgaard, Dorte Bjerre; Strauss, Holger Martin; Gram, Dorte X; Knudsen, Sanne Møller; Nielsen, Flemming Seier; Thygesen, Peter; Reedtz-Runge, Steffen; Kruse, Thomas

    2015-09-24

    Liraglutide is an acylated glucagon-like peptide-1 (GLP-1) analogue that binds to serum albumin in vivo and is approved for once-daily treatment of diabetes as well as obesity. The aim of the present studies was to design a once weekly GLP-1 analogue by increasing albumin affinity and secure full stability against metabolic degradation. The fatty acid moiety and the linking chemistry to GLP-1 were the key features to secure high albumin affinity and GLP-1 receptor (GLP-1R) potency and in obtaining a prolonged exposure and action of the GLP-1 analogue. Semaglutide was selected as the optimal once weekly candidate. Semaglutide has two amino acid substitutions compared to human GLP-1 (Aib(8), Arg(34)) and is derivatized at lysine 26. The GLP-1R affinity of semaglutide (0.38 ± 0.06 nM) was three-fold decreased compared to liraglutide, whereas the albumin affinity was increased. The plasma half-life was 46.1 h in mini-pigs following i.v. administration, and semaglutide has an MRT of 63.6 h after s.c. dosing to mini-pigs. Semaglutide is currently in phase 3 clinical testing. PMID:26308095

  9. Master Key Secured Quantum Key Distribution

    E-print Network

    Tabish Qureshi; Tabish Shibli; Aditi Sheel

    2013-01-17

    A new scheme of Quantum Key Distribution is proposed using three entangled particles in a GHZ state. Alice holds a 3-particle source and sends two particles to Bob, keeping one with herself. Bob uses one particle to generate a secure key, and the other to generate a master-key. This scheme should prove to be harder to break in non-ideal situations as compared to the standard protocols BB84 and Eckert. The scheme uses the concept of Quantum Disentanglement Eraser. Extension to multi-partite scheme has also been investigated.

  10. Space Analogue Environments: Are the Populations Comparable?

    NASA Astrophysics Data System (ADS)

    Sandal, G. M.

    Background: Much of our present understanding about psychology in space is based on studies of groups operating in so-called analogue environments where personnel are exposed to many of the same stressors as those experienced by astronauts in space. One possible problem with extrapolating results is that personnel operating in various hazardous and confined environments might differ in characteristics influencing coping, interaction, and performance. The object of this study was to compare the psychological similarity of these populations in order to get a better understanding of whether this extrapolation is justifiable. The samples investigated include polar crossings (N= 22), personnel on Antarctic research stations (N= 183), several military occupations (N= 187), and participants in space simulation studies (N=20). Methods: Personnel in each of these environments were assessed using the Personality Characteristic Inventory (PCI) and Utrecht Coping List (UCL). The PCI is a multidimensional trait assessment battery that measures various aspects of achievement orientation and social competence. The UCL is a questionnaire designed to assess habitual coping strategies when encountering stressful or demanding situations. Results: Only minor differences in use of habitual coping strategies were evident across the different samples. In relation to personality scores, the military subjects and participants in space simulation studies indicated higher competitiveness and negative instrumentality compared to both the personnel on Antarctic research stations and participants in polar expedition. Among the personnel on Antarctic research stations, significant gender differences were found with women scoring lower on competitiveness, negative instrumentality and impatience/irritability. Compared to the other samples, the participants in polar expeditions were found to be more homogeneous in personality and no significant gender differences were evident on the traits that were assessed. Most of the polar expeditionners had the combination of high scores on positive expressivity and high achievement motivation- a profile which has sometimes been characterized as "the right stuff" for coping in confined and isolated settings. Conclusion: The findings from this study suggest that populations in various space-analogue environments differ in personality traits which might impact on the comparability of psychological findings obtained in different setting. Gender differences in personality also represent a potential source of variance that need to be addressed when generalizing results across space analogue environments.

  11. Structural factors in the odor of alpha-santalol derivatives.

    PubMed

    Hasegawa, Toshio; Izumi, Hiroaki; Yamada, Hideo

    2013-07-01

    Alpha-Santalol is a sesquiterpene that is a major constituent of sandalwood (Santalum album L.), and is responsible for its distinctive woody odor. We replaced the polycyclic moiety and hydroxyl group of alpha-santalol with other moieties, and we compared the odors of the E/Z-isomers and their saturated analogues. Our previous study of the structure-odor relationships of alpha-santalols bearing hydroxyl, formyl, formyloxy, and acetoxy functional groups showed there was a similarity in odor between the Z-isomer and its saturated analogue. We synthesized alpha-santalols with a benzyl group in place of the hydroxyl group, because many benzyl compounds have strong characteristic odors. We found similar odors for the E-isomer and its saturated analogue. In contrast, the odors of the alpha-santalol derivatives with a hydroxyl, formyl, formyloxy, or acetoxy group were different. We also replaced the bulky polycyclic moiety with a linear alkyl chain. The polycyclic moiety was the most important structural factor in the characteristic sandalwood odor. The synthesis of derivatives and the evaluation of their odor allowed us to identify the key structural factors in the odor of alpha-santalol. PMID:23980413

  12. Photoionization spectroscopy of nucleobases and analogues in the gas phase using synchrotron radiation as excitation light source.

    PubMed

    Schwell, Martin; Hochlaf, Majdi

    2015-01-01

    We review here the photoionization and photoelectron spectroscopy of the gas phase nucleic acid bases adenine, thymine, uracil, cytosine, and guanine, as well as the three base analogues 2-hydroxyisoquinoline, 2-pyridone, and ?-valerolactam in the vacuum ultraviolet (VUV) spectral regime. The chapter focuses on experimental work performed with VUV synchrotron radiation and related ab initio quantum chemical calculations of higher excited states beyond the ionization energy. After a general part, where experimental and theoretical techniques are described in detail, key results are presented by order of growing complexity in the spectra of the molecules. Here we concentrate on (1) the accurate determination of ionization energies of isolated gas phase NABs and investigation of the vibrational structure of involved ionic states, including their mutual vibronic couplings, (2) the treatment of tautomerism after photoionization, in competition with other intramolecular processes, (3) the study of fragmentation of these molecular systems at low and high internal energies, and (4) the study of the evolution of the covalent character of hydrogen bonding upon substitution, i.e., examination of electronic effects (acceptor, donor, etc.). PMID:25238717

  13. Conformational comparisons of oxytocin agonists, partial agonists, and antagonists using laser Raman and circular dichroism spectroscopy. Examination of 1-penicillamine and diastereoisomeric analogues.

    PubMed

    Hruby, V J; Mosberg, H I; Fox, J W; Tu, A T

    1982-05-10

    The biological activity of peptide hormones and analogues depends on the structural and conformational properties of these compounds. A comparative study of the conformational properties of diastereoisomeric analogues of oxytocin with weak agonist activities (fully active but low potency), partial agonist activity (only able to partially induce biological response), and of conformationally restricted 1-penicillamine analogues with potent antagonist activity (no intrinsic activity, but can block the hormone's activity) was made using circular dichroism and laser Raman spectroscopies. Conformational information regarding the peptide amide, disulfide, and tyrosine chromophores was obtained, and indicates differences in the hormone agonists and antagonists. The diastereoisomeric oxytocin analogues [1-hemi-D-cystine]-, [2-D-tyrosine]-, and [5-D-asparagine]-oxytocin, have spectral features consistent with overall backbone conformations similar to oxytocin itself, but with differences in side chain moieties. This suggests that the substantial decrease in potency of the diastereoisomeric oxytocin analogues is due to changes in the relative orientations of the side chains. In contrast, the 1-penicillamine analogues of the present study, [1-penicillamine, 4-threonine]- and [1-penicillamine, 2-phenylalanine, 4-threonine]-oxytocin, like 1-penicillamine oxytocin analogues previously examined, have different backbone and disulfide conformations than oxytocin. All the 1-penicillamine oxytocin derivatives thus far examined appear, from laser Raman and CD data, to have similar topologies. However, those of the present study seem to have more rigid conformations as evidenced by very intense amide n-pi* and tyrosine pi-pi* CD transitions. PMID:7068672

  14. Theoretical and structural analysis of the active site of the transcriptional regulators LasR and TraR, using molecular docking methodology for identifying potential analogues of acyl homoserine lactones (AHLs) with anti-quorum sensing activity.

    PubMed

    Ahumedo, Maicol; Díaz, Antonio; Vivas-Reyes, Ricardo

    2010-02-01

    In the present study the homology of transcriptional receptors LuxR type were evaluated using as point of reference the receptors TraR and LasR of the bacterial types Agrobacterium tumefaciens and Pseudomonas aureginosa respectively. A series of alignments were performed in order to demonstrate that the active site of the protein is conserved in wide range of gram negative bacteria. Moreover, some docking calculations were carried out for analogs of the acyl homoserin lactones (AHLs) and regulatory proteins LasR and TraR, to understand the complex microenvironment in which the ligands are exposed. The molecular alignments show clearly that there are preserved motifs in the residues (Y53, Y61, W57, D70, W85 to TraR, Y56, Y64, W60, D73, W88 to LasR) analyzed, which may serve as site-specific targets for the development of potential antagonists. In this study was found that the anti-quorum sensing activity of the AHLs molecular analogs appears to depend on; the structure of the lactone ring and on appropriate combination of absolute and relative stereochemistry of the carbonyl (C=O) and amide (NH(2)) groups of the side chain of these AHLs molecular analogs, in combination with the interactions with the conserved amino acids (D73, W60, Y56, S129 to LasR and D70, W57, Y53 to TraR) of the LuxR type protein family. PMID:19945196

  15. Efficacy of Antimicrobials on Bacteria Cultured in a Spaceflight Analogue

    NASA Technical Reports Server (NTRS)

    Nickerson, CA; Wotring, Virginia; Barrila, Jennifer; Crabbe, Aurelie; Castro, Sarah; Davis, Richard; Rideout, April; McCarthy, Breanne; Ott, C. Mark

    2014-01-01

    As humans travel in space, they will interact with microbial flora from themselves, other crewmembers, their food, and the environment. While evaluations of microbial ecology aboard the Mir and ISS suggest a predominance of common environmental flora, the presence of (and potential for) infectious agents has been well documented. Likewise, pathogens have been detected during preflight monitoring of spaceflight food, resulting in the disqualification of that production lot from flight. These environmental and food organisms range from the obligate pathogen, Salmonella enterica serovar Typhimurium (S. Typhimurium), which has been responsible for disqualification and removal of food destined for ISS and has previously been reported from Shuttle crew refuse, to the opportunistic pathogen Staphylococcus aureus, isolated numerous times from ISS habitable compartments and the crew. Infectious disease events have affected spaceflight missions, including an upper respiratory infection that delayed the launch of STS-36 and an incapacitating Pseudomonas aeruginosa urinary tract infection of a crewmember during Apollo 13. These observations indicate that the crew has the potential to be exposed to obligate and opportunistic pathogens. This risk of exposure is expected to increase with longer mission durations and increased use of regenerative life support systems. As antibiotics are the primary countermeasure after infection, determining if their efficacy during spaceflight missions is comparable to terrestrial application is of critical importance. The NASA Rotating Wall Vessel (RWV) culture system has been successfully used as a spaceflight culture analogue to identify potential alterations in several key microbial characteristics, such as virulence and gene regulation, in response to spaceflight culture. We hypothesized that bacteria cultured in the low fluid shear RWV environment would demonstrate changes in efficacy of antibiotics compared to higher fluid shear controls. This study investigated the response of three medically significant microorganisms grown in the RWV to antibiotics that could be used on spaceflight missions. Our findings suggest potential alterations in antibiotic efficacy during spaceflight and indicate that future studies on the antibiotic response require additional basic research using the RWV and/or true spaceflight. However, while this analogue has reinforced these potential alterations, the results suggest the best approach for applied forward work is evaluating an in vivo system during spaceflight, including human and rodent studies. The complex nature of the analysis for many antibiotics and organism suggests the best approach to determine in vivo responses during pharmaceutical treatment is evaluating an in vivo system during spaceflight.

  16. Dehydration of planetary ices at high pressure; the role of analogue materials (Invited)

    NASA Astrophysics Data System (ADS)

    Fortes, A. D.

    2013-12-01

    Many planet-forming compounds become unstable with respect to their components under conditions of high pressure. In the Earth, for example, Mg2SiO4 breaks down to MgSiO3 + MgO at ~ 25 GPa, a pressure corresponding to the 670 km seismic discontinuity, with significance for the dynamics of convective flow in the mantle. A similar phenomenon occurs with many hydrate compounds thought to be major ';rock forming minerals' inside outer Solar System bodies, undoubtedly with important consequences for the structure and dynamics of icy worlds. It is well known that clathrates tend to form denser polymorphs with an incrementally greater concentration of the guest molecule, exsolving high-pressure phases of water ice in the process, or else (in the case of CO2), break down to entirely to their component molecular solids. My own recent work using high-pressure neutron powder diffraction has explored not only the behaviour of methane clathrates but also the exsolution of water from ammonia dihydrate and monohydrate, both of which break down eventually to ammonia hemihydrate + ice. In some cases, understanding the sequence of changes in both crystal structure and composition at high pressure is challenging, particularly when the starting materials have a complex crystal structure. Some years ago, I identified a high-pressure phase boundary where MgSO4.11H2O (meridianiite) appeared to break down to another hydrate and high-pressure ice VI. However, the powder diffraction pattern of the hydrate formed under these conditions resembled nothing encountered previously in my high-pressure studies of the next lowest hydrate, MgSO4.7H2O (epsomite). This led me to search for hydration states between 7 and 11 which might have escaped detection over several centuries of study of simple divalent metal sulfates. A wide-ranging systematic study of M2+X6+O4.nH2O compounds at low temperatures uncovered two new hydrates, an 8-hydrate and a 9-hydrate, the former occurring only in NiSO4 solutions, and the latter being found in Ni-, Zn-, Cu-, and Fe-doped MgSO4 solutions. Indeed, I determined that small quantities of pure MgSO4.9H2O can co-crystallise at ambient pressure with meridianiite. However, these all appear to be metastable states, and further work was necessary to try and discover stable forms of these hydrates for further study. In experiments carried out earlier this year, evidence has emerged not only that MgMoO4 can form a (possibly) stable 8-hydrate but also that MgSeO4 can form a 9-hydrate that exists in equilibrium with liquid near the eutectic. These apparently esoteric compounds (from a planetary perspective) may yet hold the key to understanding the high-pressure behaviour of true planetary materials. Just as the search for analogue materials over many decades has substantially advanced our knowledge of Earth materials, similar analogue studies are poised to unlock the mysteries of these planetary ices.

  17. Rationally Designed, Nontoxic, Nonamyloidogenic Analogues of Human Islet Amyloid Polypeptide with Improved Solubility

    PubMed Central

    2015-01-01

    Human islet amyloid polypeptide (hIAPP or amylin) is a polypeptide hormone produced in the pancreatic ?-cells that plays a role in glycemic control. hIAPP is deficient in type 1 and type 2 diabetes and is a promising adjunct to insulin therapy. However, hIAPP rapidly forms amyloid, and its strong tendency to aggregate limits its usefulness. The process of hIAPP amyloid formation is toxic to cultured ?-cells and islets, and islet amyloid formation in vivo has been linked to ?-cell death and islet graft failure. An analogue of hIAPP with a weakened tendency to aggregate, denoted pramlintide (PM), has been approved for clinical applications, but suffers from poor solubility, particularly at physiological pH, and its unfavorable solubility profile prevents coformulation with insulin. We describe a strategy for rationally designing analogues of hIAPP with improved properties; key proline mutations are combined with substitutions that increase the net charge of the molecule. An H18R/G24P/I26P triple mutant and an H18R/A25P/S28P/S29P quadruple mutant are significantly more soluble at neutral pH than hIAPP or PM. They are nonamyloidogenic and are not toxic to rat INS ?-cells. The approach is not limited to these examples; additional analogues can be designed using this strategy. To illustrate this point, we show that an S20R/G24P/I26P triple mutant and an H18R/I26P double mutant are nonamyloidogenic and significantly more soluble than human IAPP or PM. These analogues and second-generation derivatives are potential candidates for the coformulation of IAPP with insulin and other polypeptides. PMID:25140605

  18. Naturalness in an Emergent Analogue Spacetime

    SciTech Connect

    Liberati, Stefano; Visser, Matt; Weinfurtner, Silke

    2006-04-21

    Effective field theories (EFTs) have been widely used as a framework in order to place constraints on the Planck suppressed Lorentz violations predicted by various models of quantum gravity. There are, however, technical problems in the EFT framework when it comes to ensuring that small Lorentz violations remain small - this is the essence of the 'naturalness' problem. Herein we present an 'emergent' spacetime model, based on the 'analogue gravity' program, by investigating a specific condensed-matter system. Specifically, we consider the class of two-component BECs subject to laser-induced transitions between the components, and we show that this model is an example for Lorentz invariance violation due to ultraviolet physics. Furthermore, our model explicitly avoids the naturalness problem, and makes specific suggestions regarding how to construct a physically reasonable quantum gravity phenomenology.

  19. Athermal analogue of sheared dense Brownian suspensions

    E-print Network

    M. Trulsson; M. Bouzid; J. Kurchan; E. Clement; P. Claudin; B. Andreotti

    2015-06-30

    The rheology of dense Brownian suspensions of hard spheres is investigated numerically beyond the low shear rate Newtonian regime. We analyze an athermal analogue of these suspensions, with an effective logarithmic repulsive potential representing the vibrational entropic forces. We show that both systems present the same rheology without adjustable parameters. Moreover, all rheological responses display similar Herschel-Bulkley relations once the shear stress and the shear rate are respectively rescaled by a characteristic stress scale and by a microscopic reorganization time-scale, both related to the normal confining pressure. This pressure-controlled approach, originally developed for granular flows, reveals a striking physical analogy between the colloidal glass transition and granular jamming.

  20. Athermal analogue of sheared dense Brownian suspensions

    NASA Astrophysics Data System (ADS)

    Trulsson, Martin; Bouzid, Mehdi; Kurchan, Jorge; Clément, Eric; Claudin, Philippe; Andreotti, Bruno

    2015-07-01

    The rheology of dense Brownian suspensions of hard spheres is investigated numerically beyond the low-shear-rate Newtonian regime. We analyze an athermal analogue of these suspensions, with an effective logarithmic repulsive potential representing the vibrational entropic forces. We show that both systems present the same rheology without adjustable parameters. Moreover, all rheological responses display similar Herschel-Bulkley relations once the shear stress and the shear rate are respectively rescaled by a characteristic stress scale and by a microscopic reorganization time scale, both related to the normal confining pressure. This pressure-controlled approach, originally developed for granular flows, reveals a striking physical analogy between the colloidal glass transition and granular jamming.

  1. Naturalness in an emergent analogue spacetime.

    PubMed

    Liberati, Stefano; Visser, Matt; Weinfurtner, Silke

    2006-04-21

    Effective field theories (EFTs) have been widely used as a framework in order to place constraints on the Planck suppressed Lorentz violations predicted by various models of quantum gravity. There are, however, technical problems in the EFT framework when it comes to ensuring that small Lorentz violations remain small--this is the essence of the "naturalness" problem. Herein we present an "emergent" spacetime model, based on the "analogue gravity" program, by investigating a specific condensed-matter system. Specifically, we consider the class of two-component BECs subject to laser-induced transitions between the components, and we show that this model is an example for Lorentz invariance violation due to ultraviolet physics. Furthermore, our model explicitly avoids the naturalness problem, and makes specific suggestions regarding how to construct a physically reasonable quantum gravity phenomenology. PMID:16712144

  2. Hexaethylsubporphyrins: ?-alkyl analogues in the subporphyrin family.

    PubMed

    Chandra, Brijesh; Sathish Kumar, B; Mondal, Navendu; Samanta, Anunay; Panda, Pradeepta K

    2015-11-18

    Two new subporphyrins were synthesized for the first time from a ?-substituted pyrrole i.e. 3,4-diethylpyrrole via pyridine-tri-N-(3,4-diethylpyrrolyl)borane as building blocks. These ?-hexaethylsubporphyrins are true contracted congeners of ?-octaethylporphyrin (OEP). While the meso-triphenyl derivative of hexaethylsubporphyrin could be synthesized by following the reported method, the meso-free analogue could only be synthesized by condensation with trioxane, in the presence of catalytic methanesulfonic acid. These contracted macrocycles display interesting absorption, and emission behaviour including substituent dependent S2 fluorescence owing to the presence of flexible electron donating ethyl groups at their ?-positions. The optical response and ultrafast S2 state dynamics of these systems suggest that it may be possible to tune the properties of the subporphyrin to develop efficient systems for solar energy capture and conversion processes. PMID:26524153

  3. Group key management

    SciTech Connect

    Dunigan, T.; Cao, C.

    1997-08-01

    This report describes an architecture and implementation for doing group key management over a data communications network. The architecture describes a protocol for establishing a shared encryption key among an authenticated and authorized collection of network entities. Group access requires one or more authorization certificates. The implementation includes a simple public key and certificate infrastructure. Multicast is used for some of the key management messages. An application programming interface multiplexes key management and user application messages. An implementation using the new IP security protocols is postulated. The architecture is compared with other group key management proposals, and the performance and the limitations of the implementation are described.

  4. MDMA (3,4-Methylenedioxymethamphetamine) Analogues as Tools to Characterize MDMA-Like Effects: An Approach to Understand Entactogen Pharmacology

    PubMed Central

    Sáez-Briones, P.; Hernández, A.

    2013-01-01

    Besides stimulants and hallucinogens, whose psychotropic effects are shared by many structurally related molecules exhibiting different efficacies and potencies in humans, the phenylisopropylamine MDMA (3,4-methylenedioxymethamphetamine, XTC, “Ecstasy”) is the prototypical representative of a separate class of psychotropic substance, able to elicit the so-called entactogenic syndrome in healthy humans. This reversible altered state of consciousness, usually described as an “open mind state”, may have relevant therapeutic applications, both in psychotherapy and as a pharmacological support in many neuropsychiatric disorders with a high rate of treatment failure. Nevertheless, a comprehensive and systematic exploration of the structure-activity relationships associated with entactogenic activity has remained incomplete and controversial, highlighting the possibility that MDMA might represent a pharmacological rarity in the field of psychotropics. As the latter is still an open question, the pharmacological characterization of MDMA analogues remains the logical strategy to attempt the elucidation of the structural requirements needed to elicit typical MDMA-like effects. Intriguingly, almost no experimental evidence supports the existence of actual MDMA analogues that truly resemble the whole pharmacological profile of MDMA, probably due to its complex (and partially not fully understood) mechanism of action that includes a disruption of monoaminergic neurotransmission. The present review presents a brief summary of the pharmacology of MDMA, followed by the evidence accumulated over the years regarding the characterization of classical structurally related MDMA analogues in different models and how this state of the art highlights the need to develop new and better MDMA analogues. PMID:24403876

  5. Diversity-oriented synthesis of analogues of the novel macrocyclic peptide FR-225497 through late stage functionalization

    PubMed Central

    Mukherjee, Jyotiprasad; Sil, Suman

    2015-01-01

    Summary A concise synthetic approach to a class of biologically interesting cyclic tetrapeptides is reported which involves a late-stage functionalization of a macrocyclic scaffold through cross metathesis in an attempt to create diversity. The utility of this protocol is demonstrated through the preparation of three structural analogues of the important naturally occurring histone deacetylase inhibitor FR-225497.

  6. Antibacterial Optimization of 4-Aminothiazolyl Analogues of the Natural Product GE2270 A: Identification of the Cycloalkylcarboxylic Acids

    SciTech Connect

    LaMarche, Matthew J.; Leeds, Jennifer A.; Amaral, Kerri; Brewer, Jason T.; Bushell, Simon M.; Dewhurst, Janetta M.; Dzink-Fox, JoAnne; Gangl, Eric; Goldovitz, Julie; Jain, Akash; Mullin, Steve; Neckermann, Georg; Osborne, Colin; Palestrant, Deborah; Patane, Michael A.; Rann, Elin M.; Sachdeva, Meena; Shao, Jian; Tiamfook, Stacey; Whitehead, Lewis; Yu, Donghui

    2012-11-09

    4-Aminothiazolyl analogues of the antibiotic natural product GE2270 A (1) were designed, synthesized, and optimized for their activity against Gram positive bacterial infections. Optimization efforts focused on improving the physicochemical properties (e.g., aqueous solubility and chemical stability) of the 4-aminothiazolyl natural product template while improving the in vitro and in vivo antibacterial activity. Structure-activity relationships were defined, and the solubility and efficacy profiles were improved over those of previous analogues and 1. These studies identified novel, potent, soluble, and efficacious elongation factor-Tu inhibitors, which bear cycloalkylcarboxylic acid side chains, and culminated in the selection of development candidates amide 48 and urethane 58.

  7. Analogues of uracil nucleosides with intrinsic fluorescence (NIF-analogues): synthesis and photophysical properties.

    PubMed

    Segal, Meirav; Fischer, Bilha

    2012-02-28

    Uridine cannot be utilized as fluorescent probe due to its extremely low quantum yield. For improving the uracil fluorescence characteristics we extended the natural chromophore at the C5 position by coupling substituted aromatic rings directly or via an alkenyl or alkynyl linker to create fluorophores. Extension of the uracil base was achieved by treating 5-I-uridine with the appropriate boronic acid under the Suzuki coupling conditions. Analogues containing an alkynyl linker were obtained from 5-I-uridine and the suitable boronic acid in a Sonogashira coupling reaction. The uracil fluorescent analogues proposed here were designed to satisfy the following requirements: a minimal chemical modification at a position not involved in base-pairing, resulting in relatively long absorption and emission wavelengths and high quantum yield. 5-((4-Methoxy-phenyl)-trans-vinyl)-2'-deoxy-uridine, 6b, was found to be a promising fluorescent probe. Probe 6b exhibits a quantum yield that is 3000-fold larger than that of the natural chromophore (? 0.12), maximum emission (478 nm) which is 170 nm red shifted as compared to uridine, and a Stokes shift of 143 nm. In addition, since probe 6b adopts the anti conformation and S sugar puckering favored by B-DNA, it makes a promising nucleoside analogue to be incorporated in an oligonucleotide probe for detection of genetic material. PMID:22222762

  8. Synthesis and characterization of mixed-valence manganese fluorophosphate and analogues with clathrate-like structures: Mn(III)6F12(PO3(OH))8[Na8(Kx(H3O)4-x(H2O)2)M(IV)(OH)6] (M(IV) = Mn, Ti, Ge).

    PubMed

    Ren, Wei-Jian; Wang, Jing-Quan; Huang, Ya-Xi; Sun, Zhi-Mei; Pan, Yuanming; Mi, Jin-Xiao

    2015-05-01

    A novel, mixed- and high-valence manganese (Mn(3+)/Mn(4+)) fluorophosphate, Mn(III)6F12(PO3(OH))8[Na8(Kx(H3O)4-x(H2O)2)Mn(IV)(OH)6] (denoted as MN), has been prepared via a water-deficient hydrothermal route with phosphoric acid as the sole solvent. This compound features a cubic three-dimensional open-framework structure built from corner-sharing [Mn(III)O4F2] octahedra and [HPO4] groups, which encapsulates a clathrate-like "guest cluster" of Na8(Kx(H3O)4-x(H2O)2)Mn(IV)(OH)6. The guest cluster is architecturally composed of a [Mn(IV)(OH)6] octahedron in a cubic cage of Na(+) cations, which in turn is surrounded by an octahedral arrangement of K(+)/H2O ions, resulting in an unprecedented octahedral @ cubic @ octahedral @ cubic arrangement (OCOC). The +4 oxidation state of Mn in the guest cluster has been confirmed by the synthesis of isotypic Ti- and Ge- analogues (denoted as TI and GE) using TiO2 and GeO2 as the replacement for MnO2 in the starting materials. The compounds MN, TI and GE are not stable in aqueous solution and are peeled off layer-by-layer after the absorption of water. This report provides a new route for the synthesis of mixed- and high-valence manganese phosphates that cannot be produced by conventional hydrothermal methods. PMID:25826670

  9. Two novel amphomycin analogues from Streptomyces canus strain FIM-0916.

    PubMed

    Yang, Huang-Jian; Huang, Xiao-Zhen; Zhang, Zhu-Lan; Wang, Chuan-Xi; Zhou, Jian; Huang, Kai; Zhou, Jing-Ming; Zheng, Wei

    2014-01-01

    Three lipopeptides, the known compound amphomycin, together with two novel compounds named aspartocin D (1) and aspartocin E (2) were obtained from the fermentation broth extraction of Streptomyces canus strain FIM0916 by using various column chromatography techniques. Their structures were elucidated by using spectroscopic methods, mainly by an extensive NMR analysis. It was demonstrated that compounds 1 and 2 are novel analogues of amphomycin, whose structures are similar to aspartocins. Compounds 1 and 2 share the same cyclic decapeptide core of cyclo (Dab2-Pip3-MeAsp4-Asp5-Gly6-Asp7-Gly8-Dab9-Val10-Pro11-), differing only in the side-chain moiety corresponding to Asp1-?3-isohendecenoic acid and Asp1-?3-isododecenoic acid, for aspartocin D and aspartocin E. In bioassays, compounds 1 and 2 exhibited antimicrobial activities against Gram-positive bacteria in the presence of Ca(2+) (1.25 mM); particularly, the activities were enhanced with higher concentrations of calcium. PMID:24568288

  10. Ochracenoids A and B, Guaiazulene-Based Analogues from Gorgonian Anthogorgia ochracea Collected from the South China Sea

    PubMed Central

    Zheng, Juan-Juan; Shao, Chang-Lun; Chen, Min; Gan, Li-She; Fang, Yu-Chun; Wang, Xu-Hui; Wang, Chang-Yun

    2014-01-01

    Two new guaiazulene-based analogues, ochracenoids A (1) and B (2), along with four known analogues (3–6), were isolated from the gorgonian Anthogorgia ochracea collected from the South China Sea. The planar structures of the new compounds were elucidated by comprehensive spectroscopic data. The absolute configuration of 1 was determined as 3R by the comparison of TDDFT calculated electronic circular dichroism with its experimental spectrum. Compound 1 is a rare guaiazulene-based analogue possessing a unique C16 skeleton. The possible generation process of 1 through an intermolecular one-carbon-transfer reaction was also discussed. Compound 2 was previously described as a presumed intermediate involved in the biogenesis of anthogorgienes A and I. Compound 3 exhibited antiproliferative effects on the embryo development of zebrafish Danio rerio. PMID:24637960

  11. Public Key Cryptography.

    ERIC Educational Resources Information Center

    Tapson, Frank

    1996-01-01

    Describes public key cryptography, also known as RSA, which is a system using two keys, one used to put a message into cipher and another used to decipher the message. Presents examples using small prime numbers. (MKR)

  12. The Key to Security.

    ERIC Educational Resources Information Center

    Kennedy, Mike

    2001-01-01

    Provides tips on using low-tech, traditional key and lock systems for effectively securing university and college facilities. Discusses providing keys with utility patents as well as the need to design doors that offer greater deterrence to vandalism. (GR)

  13. The alkynylphosphonate analogue of calcitriol EM1 has potent anti-metastatic effects in breast cancer.

    PubMed

    Ferronato, María J; Obiol, Diego J; Fermento, María E; Gandini, Norberto A; Alonso, Eliana N; Salomón, Débora G; Vitale, Cristian; Mascaró, Evangelina; Fall, Yagamare; Raimondi, Ana R; Curino, Alejandro C; Facchinetti, María M

    2015-11-01

    The active form of vitamin D3, calcitriol, plays a major role in maintaining calcium/phosphate homeostasis. In addition, it is a potent antiproliferative and prodifferentiating agent. However, when effective antitumor doses of calcitriol are employed, hypercalcemic effects are observed, thus precluding its therapeutic application. To overcome this problem, structural analogues have been designed with the aim at retaining or even increasing the antitumor effects while decreasing its calcemic activity. This report shows the biological evaluation of an alkynylphosphonate vitamin D less-calcemic analogue in a murine model of breast cancer. We demonstrate that this compound has potent anti-metastatic effects through its action over cellular migration and invasion likely mediated through the up-regulation of E-cadherin expression. Based on the current in vitro and in vivo results, EM1 is a promising candidate as a therapeutic agent in breast cancer. PMID:26365558

  14. Synthesis and ?-Opioid Receptor Activity of Furan-Substituted Salvinorin A Analogues

    PubMed Central

    2015-01-01

    The neoclerodane diterpene salvinorin A, found in the leaves of Salvia divinorum, is a potent ?-opioid receptor agonist, making it an attractive scaffold for development into a treatment for substance abuse. Although several successful semisynthetic studies have been performed to elucidate structure–activity relationships, the lack of analogues with substitutions to the furan ring of salvinorin A has prevented a thorough understanding of its role in binding to the ?-opioid receptor. Herein we report the synthesis of several salvinorin A derivatives with modified furan rings. Evaluation of these compounds in a functional assay indicated that sterically less demanding substitutions are preferred, suggesting the furan ring is bound in a congested portion of the binding pocket. The most potent of the analogues successfully reduced drug-seeking behavior in an animal model of drug-relapse without producing the sedation observed with other ?-opioid agonists. PMID:25426797

  15. Synthesis of Chondramide A Analogues with Modified ?-Tyrosine and Their Biological Evaluation

    PubMed Central

    Zhdanko, Alexander; Schmauder, Anke; Ma, Christopher I.; Sibley, L. David; Sept, D. David; Sasse, Florenz

    2011-01-01

    Starting from cinnamates 9, obtained by Wittig reaction or Heck coupling, the diols 17 were prepared by asymmetric dihydroxylation. This was followed by a regioselective substitution of the 3-OH group with hydrazoic acid under Mitsunobu conditions. Methylation of the 2-OH group and reduction of the azide group led to the ?-tyrosine derivatives 8. Condensation with the dipeptide acid 6 furnished the tripeptide part of the chondramides. The derived acids 21 were combined with the hydroxy ester 7 to the esters 22. Cleavage of the tert-butyl groups and intramolecular lactam formation gave rise to the chondramide A analogues 2b–k. Growth inhibition assays showed most of the analogues to be biologically active. Some of them even reach the activity of jasplakinolide. It can be concluded that the 4-position of the aryl ring in the ?-tyrosine of chondramide A tolerates structural modifications quite well. PMID:22012705

  16. Isolation and characterization of a tadalafil analogue, N-cyclopentyl nortadalafil in health supplement.

    PubMed

    Xu, Yimin; Kee, Chee-Leong; Ge, Xiaowei; Low, Min-Yong; Koh, Hwee-Ling

    2016-01-25

    A tadalafil analogue was detected for the first time during the screening of a health supplement for undeclared sexual enhancement drugs. The compound had been isolated and purified by preparative high-pressure liquid chromatography (HPLC). Its chemical structure was elucidated using high-resolution mass spectrometry (HRMS), electrospray ionization tandem mass spectrometry (ESI-MS/MS) and nuclear magnetic resonance (NMR) spectroscopy. The compound had a protonated molecular ion at m/z 444 with a chemical formula of C26H25N3O4. The data obtained from the MS analysis of the compound suggested that the N-methyl group on the piperazinedione moiety of tadalafil was substituted with a -C5H9 group. Analysis using NMR was performed and the -C5H9 group was characterized as a cyclopentyl moiety. The analogue was named N-cyclopentyl nortadalafil. PMID:26580820

  17. Keys to Scholarship

    ERIC Educational Resources Information Center

    Hebert, Terri

    2011-01-01

    Up ahead, a foreboding wooden door showing wear from passage of earlier travelers is spotted. As the old porch light emits a pale yellow glow, a key ring emerges from deep inside the coat pocket. Searching for just the right key, the voyager settles on one that also shows age. As the key enters its receptacle and begins to turn, a clicking noise…

  18. Key Reference Agilent Technologies

    E-print Network

    Anlage, Steven

    Key Reference Agilent Technologies PSG Signal Generators This guide applies to the following signal documentation. Please send us an E-mail at sources_manuals@am.exch.agilent.com. #12;1 Key Reference Symbols enables you to define the number of points in a step sweep. When you press this key, the current value

  19. Quantum dense key distribution

    E-print Network

    I. P. Degiovanni; I. Ruo Berchera; S. Castelletto; M. L. Rastello; F. A. Bovino; A. M. Colla; G. Castagnoli

    2003-12-15

    This paper proposes a new protocol for quantum dense key distribution. This protocol embeds the benefits of a quantum dense coding and a quantum key distribution and is able to generate shared secret keys four times more efficiently than BB84 one. We hereinafter prove the security of this scheme against individual eavesdropping attacks, and we present preliminary experimental results, showing its feasibility.

  20. Work Keys USA.

    ERIC Educational Resources Information Center

    Work Keys USA, 1998

    1998-01-01

    "Work Keys" is a comprehensive program for assessing and teaching workplace skills. This serial "special issue" features 18 first-hand reports on Work Keys projects in action in states across North America. They show how the Work Keys is helping businesses and educators solve the challenge of building a world-class work force. The reports are as…

  1. Functionalized Congener Approach to Muscarinic Antagonists: Analogues of Pirenzepine

    PubMed Central

    Karton, Yishai; Bradbury, Barton J.; Baumgold, Jesse; Paek, Robert; Jacobson, Kenneth A.

    2012-01-01

    The M1-selective muscarinic receptor antagonist pirenzepine (5,11-dihydro-11-[(4-methyl-1-piperazinyl)acetyl]-6H-pyrido[2,3-b] [1,4]benzodiazepin-6-one) was derivatized to explore points of attachment of functionalized side chains for the synthesis of receptor probes and ligands for affinity chromatography. The analogues prepared were evaluated in competitive binding assays versus [3H]-N-methylscopolamine at four muscarinic receptor subtypes (m1AChR-m4AChR) in membranes from rat heart tissue and transfected A9L cells. 9-(Hydroxymethyl)pirenzepine, 8-(methylthio)pirenzepine, and a series of 8-aminosulfonyl derivatives were synthesized. Several 5-substituted analogues of pirenzepine also were prepared. An alternate series of analogues substituted on the 4-position of the piperazine ring was prepared by reaction of 4-desmethylpirenzepine with various electrophiles. An N-chloroethyl analogue of pirenzepine was shown to form a reactive aziridine species in aqueous buffer yet failed to affinity label muscarinic receptors. Within a series of aminoalkyl analogues, the affinity increased as the length of the alkyl chain increased. Shorter chain analogues were generally much less potent than pirenzepine, and longer analogues (7–10 carbons) were roughly as potent as pirenzepine at m1 receptors, but were nonselective. Depending on the methylene chain length, acylation or alkyl substitution of the terminal amine also influenced the affinity at muscarinic receptors. PMID:2066986

  2. Analogue Models Of Volcanic Spreading At Mt. Vesuvius

    NASA Astrophysics Data System (ADS)

    De Matteo, Ada; Castaldo, Raffaele; D'Auria, Luca; James, Michael; Lane, Steve; Massa, Bruno; Pepe, Susi; Tizzani, Pietro

    2015-04-01

    Somma-Vesuvius is a quiescent strato-volcano of the Neapolitan district, southern Italy, for which various geophysical and geological evidences (e.g. geodetic measurements, geological and structural data, seismic profiles interpretations and surface deformation analysis with Differential Interferometric Synthetic Aperture Radar (DInSAR)) indicate ongoing spreading deformation. In this research we investigate the spreading deformation and associated surface deformation pattern by performing analogue experiments and comparing the results with actual ground deformation as measured using DInSAR data recorded between 1992 and 2010. Somma-Vesuvius consists of a volcanic cone (Gran Cono) lying within an asymmetric caldera (Somma). The Somma caldera is the result of at least 7 Plinian eruptions, the last of which was the 79 CE. Pompeii eruption. The current cone of Mt. Vesuvius grew within the caldera in the following centuries as the effect of continued explosive and effusive activity of the volcano. The volcano lies on a substratum consisting of a Mesozoic carbonatic basement, overlapped by Holocene clastic sediments and volcanic rocks. Our analogue models were built to simulate the shape of the Somma-Vesuvius top a scale of about 1:100000, emplaced on a sand layer (brittle behaviour) laid on a silicone layer (ductile behaviour). Models are based on the Fluid-dynamics Dimensionless Analysis (FDA), according to the Buckingham-? theorem. In this context, we considered few dimensionless parameters that allowed the setting of a reliable scaled model. To represent the complex Somma-Vesuvius geometry, an asymmetric model was built by setting a truncated cone (mimicking the topography of Somma edifice) topped by another small cone (mimicking the Gran Cono) shifted off the axis of the main cone. Different experiments were carried out in which the thickness of the basal sand layer and of the silicone one were varied. To quantify the vertical and horizontal displacements the models were monitored with three synchronised digital cameras, enabling sequential 3-D models to be derived using a photogrammetric technique. Finally, our models were compared with the 1992 - 2010 SBAS DInSAR measurements of ground deformations obtained using ERS-ENVISAT satellite images. The results show that analogue models are able to reproduce different styles of volcanic spreading and to reproduce the observed surface and deformation pattern. At the end our models show a deformation rather similar to the actual deformation pattern of the Somma-Vesuvius, both in the direction and in the intensity. Further studies will be devoted at find the best combination of parameters (silicone layer thickness and viscosity) to fit observations and to introduce a tridimensional rigid based topography. These studies will be implemented also with new structural and surface deformation (DinSAR) data and will be integrated with a numerical modelling.

  3. Analogue models of subduction megathrust earthquakes: improving rheology and monitoring technique

    NASA Astrophysics Data System (ADS)

    Brizzi, Silvia; Corbi, Fabio; Funiciello, Francesca; Moroni, Monica

    2015-04-01

    Most of the world's great earthquakes (Mw > 8.5, usually known as mega-earthquakes) occur at shallow depths along the subduction thrust fault (STF), i.e., the frictional interface between the subducting and overriding plates. Spatiotemporal occurrences of mega-earthquakes and their governing physics remain ambiguous, as tragically demonstrated by the underestimation of recent megathrust events (i.e., 2011 Tohoku). To help unravel seismic cycle at STF, analogue modelling has become a key-tool. First properly scaled analogue models with realistic geometries (i.e., wedge-shaped) suitable for studying interplate seismicity have been realized using granular elasto-plastic [e.g., Rosenau et al., 2009] and viscoelastic materials [i.e., Corbi et al., 2013]. In particular, viscoelastic laboratory experiments realized with type A gelatin 2.5 wt% simulate, in a simplified yet robust way, the basic physics governing subduction seismic cycle and related rupture process. Despite the strength of this approach, analogue earthquakes are not perfectly comparable to their natural prototype. In this work, we try to improve subduction seismic cycle analogue models by modifying the rheological properties of the analogue material and adopting a new image analysis technique (i.e., PEP - ParticlE and Prediction velocity). We test the influence of lithosphere elasticity by using type A gelatin with greater concentration (i.e., 6 wt%). Results show that gelatin elasticity plays important role in controlling seismogenic behaviour of STF, tuning the mean and the maximum magnitude of analogue earthquakes. In particular, by increasing gelatin elasticity, we observe decreasing mean magnitude, while the maximum magnitude remains the same. Experimental results therefore suggest that lithosphere elasticity could be one of the parameters that tunes seismogenic behaviour of STF. To increase gelatin elasticity also implies improving similarities with their natural prototype in terms of coseismic duration and rupture width. Experimental monitoring has been performed by means of both PEP and PIV (i.e., Particle Image Velocimetry) algorithms. PEP differs from classic cross-correlation techniques (i.e., PIV) in its ability to provide sparse velocity vectors at points coincident with particle barycentre positions, allowing a lagrangian description of the velocity field and a better spatial resolution (i.e., ? 0.03 mm2) with respect to PIV. Results show that PEP algorithm is able to identify a greater number of analogue earthquakes (i.e., ? 20% more than PIV algorithm), decreasing the minimum detectable magnitude from 6.6 to 4.5. Furthermore, earthquake source parameters (e.g., hypocentre position, rupture limits and slip distribution) are more accurately defined. PEP algorithm is then suitable to potentially gain new insights on seismogenic process of STF, by extending the analysable magnitude range of analogue earthquakes and having implications on applicability of scaling relationship, such as Gutenberg - Richter law, to experimental results.

  4. Cis-Trans Isomerizations of Proline Residues Are Key to Bradykinin Conformations

    E-print Network

    Clemmer, David E.

    Cis-Trans Isomerizations of Proline Residues Are Key to Bradykinin Conformations Nicholas A the solution composition [J. Am. Chem. Soc. 2011, 133, 13810]. Here, the role of the three proline residues analogue peptides in which combinations of alanine residues are substituted for prolines. IM

  5. An efficient synthesis of an exo-enone analogue of LL-Z1640-2 and evaluation of its protein kinase inhibitory activities.

    PubMed

    Wang, Stephanie Q; Goh, Shermin S; Chai, Christina L L; Chen, Anqi

    2015-12-23

    An efficient synthesis of an exo-enone analogue () of resorcylic acid lactone (RAL), natural product LL-Z1640-2 (), has been achieved using a Ni-catalysed regioselective reductive coupling macrocyclisation of an alkyne-aldehyde as a key step. The synthetic route is significantly shorter than those for the natural product and avoids the isomerisation problem of the cis-double bond in the molecule. The preliminary biological evaluation showed that the exo-enone analogue is a potent inhibitor of several important kinases relevant to cancer drug development. PMID:26541872

  6. Bisphenol A and its structural analogues in household waste paper.

    PubMed

    Pivnenko, K; Pedersen, G A; Eriksson, E; Astrup, T F

    2015-10-01

    Bisphenol A (BPA) is an industrial chemical produced in large volumes. Its main use is associated with polycarbonate plastic, epoxy resins and thermal paper. In contrast to other applications, thermal paper contains BPA in its un-reacted form as an additive, which is subjected to migration. Receiving a significant amount of attention from the scientific community and beyond, due to its controversial endocrine-disrupting effects, the industry is attempting to substitute BPA in variety of applications. Alternative phenolic compounds have been proposed for use in thermal paper; however, information to what extent BPA alternatives have been used in paper is sparse. The aim of the present work was to quantify BPA and its alternatives (bisphenol S (BPS), bisphenol E (BPE), bisphenol B (BPB), 4-cumylphenol (HPP) and bisphenol F (BPF)) in waste paper and board from Danish households, thermal paper receipts, non-carbon copy paper and conventional printer paper. BPA was found in all waste paper samples analysed, while BPS was identified in 73% of them. Only BPB was not identified in any of the samples. BPA and BPS were found in the majority of the receipts, which contained no measurable concentrations of the remaining alternatives. Although receipts showed the highest concentrations of BPA and BPS, office paper, flyers and corrugated boxes, together with receipts, represented the major flux of the two compounds in waste paper streams. PMID:26194879

  7. Structural Analysis of the Regulatory Domain of ExsA, a Key Transcriptional Regulator of the Type Three Secretion System in Pseudomonas aeruginosa

    PubMed Central

    Shrestha, Manisha; Xiao, Yi; Robinson, Howard; Schubot, Florian D.

    2015-01-01

    Pseudomonas aeruginosa employs a type three secretion system to facilitate infections in mammalian hosts. The operons encoding genes of structural components of the secretion machinery and associated virulence factors are all under the control of the AraC-type transcriptional activator protein, ExsA. ExsA belongs to a unique subfamily of AraC-proteins that is regulated through protein-protein contacts rather than small molecule ligands. Prior to infection, ExsA is inhibited through a direct interaction with the anti-activator ExsD. To activate ExsA upon host cell contact this interaction is disrupted by the anti-antiactivator protein ExsC. Here we report the crystal structure of the regulatory domain of ExsA, which is known to mediate ExsA dimerization as well as ExsD binding. The crystal structure suggests two models for the ExsA dimer. Both models confirmed the previously shown involvement of helix ?-3 in ExsA dimerization but one also suggest a role for helix ?-2. These structural data are supported by the observation that a mutation in ?-2 greatly diminished the ability of ExsA to activate transcription in vitro. Additional in vitro transcription studies revealed that a conserved pocket, used by AraC and the related ToxT protein for the binding of small molecule regulators, although present in ExsA is not involved in binding of ExsD. PMID:26317977

  8. Research Advances: Less Expensive and More Convenient Gaucher's Disease Treatment; Structural Loop Regions: Key to Multidrug-Resistance Transporters?; New Method Identifies Proteins in Old Artwork

    ERIC Educational Resources Information Center

    King, Angela G.

    2006-01-01

    The X-ray structure of EmrD, a multidrug transporter protein from Escherichia coli, common bacteria known to cause several food-borne illnesses was determined by scientists at The Scripps Research Institute. The hydrophobic residues in the EmrD internal cavity are likely to contribute to the general mechanism transporting various compounds through…

  9. Elucidating a Key Anti-HIV-1 and Cancer-Associated Axis: The Structure of CCL5 (Rantes) in Complex with CCR5

    NASA Astrophysics Data System (ADS)

    Tamamis, Phanourios; Floudas, Christodoulos A.

    2014-06-01

    CCL5 (RANTES) is an inflammatory chemokine which binds to chemokine receptor CCR5 and induces signaling. The CCL5:CCR5 associated chemotactic signaling is of critical biological importance and is a potential HIV-1 therapeutic axis. Several studies provided growing evidence for the expression of CCL5 and CCR5 in non-hematological malignancies. Therefore, the delineation of the CCL5:CCR5 complex structure can pave the way for novel CCR5-targeted drugs. We employed a computational protocol which is primarily based on free energy calculations and molecular dynamics simulations, and report, what is to our knowledge, the first computationally derived CCL5:CCR5 complex structure which is in excellent agreement with experimental findings and clarifies the functional role of CCL5 and CCR5 residues which are associated with binding and signaling. A wealth of polar and non-polar interactions contributes to the tight CCL5:CCR5 binding. The structure of an HIV-1 gp120 V3 loop in complex with CCR5 has recently been derived through a similar computational protocol. A comparison between the CCL5 : CCR5 and the HIV-1 gp120 V3 loop : CCR5 complex structures depicts that both the chemokine and the virus primarily interact with the same CCR5 residues. The present work provides insights into the blocking mechanism of HIV-1 by CCL5.

  10. Experimental antitumor activity of new azathioprine analogues.

    PubMed

    H?ado?, B; Gutsche, W; Ba?oniak, S; Sikorska, H

    1989-01-01

    Two newly synthesized azathioprine (AZA) analogues, 6-(1,2-dimethyl-4-nitro-5-imidazolyl)thiopurine (Met-AZA) and 6-(2-methyl-5-nitro-4-imidazolyl)thiopurine (IZO-AZA), were investigated against KB human tumor cells. In 5 transplantable murine tumor models, including sc Sa180, sc Ca755, ip LL and ip leukemias; L1210 and P388 both drugs were found to be antitumor active in all the experiments carried out regardless of dosing regimen or the route of administration. Similar good activity was shown in the KB, ip Sa180, and Ca755 systems and partly against LL as compared to AZA. However, Met-AZA against ip P388 demonstrated therapeutic advantage following qd 1-9 daily dosing, 0.33 log10 tumor cell kill; therapeutic index (TI = ILSmax/ILS 25) = 2, and ILS = 69% in comparison to AZA and IZO-AZA, TI = 1.3, 1.2, and ILS = 31%, 40%, respectively. Met-AZA is comparable to AZA, while seeming to display greater antileukemic activity than AZA. PMID:2719747

  11. A positive Grassmannian analogue of the permutohedron

    E-print Network

    Williams, Lauren K

    2015-01-01

    The classical permutohedron Perm is the convex hull of the points (w(1),...,w(n)) in R^n where w ranges over all permutations in the symmetric group. This polytope has many beautiful properties -- for example it provides a way to visualize the weak Bruhat order: if we orient the permutohedron so that the longest permutation w_0 is at the "top" and the identity e is at the "bottom," then the one-skeleton of Perm is the Hasse diagram of the weak Bruhat order. Equivalently, the paths from e to w_0 along the edges of Perm are in bijection with the reduced decompositions of w_0. Moreover, the two-dimensional faces of the permutohedron correspond to braid and commuting moves, which by the Tits Lemma, connect any two reduced expressions of w_0. In this note we introduce some polytopes Br(k,n) (which we call bridge polytopes) which provide a positive Grassmannian analogue of the permutohedron. In this setting, BCFW bridge decompositions of reduced plabic graphs play the role of reduced decompositions. We define Br(k,...

  12. Irradiation studies of astrophysical ice analogues

    NASA Astrophysics Data System (ADS)

    Holton, Philip D.

    In this thesis the formation of molecular species in cold icy mantles, typical of those in the interstellar medium (ISM) has been studied. The construction of an ultra high vacuum system for the formation and containment of these astrophysical ice analogues is described. The method of preparation of these ices is detailed and analysis methodologies are discussed. VUV spectra of molecular ices (e.g. SO2, CH3NH2, OCS) measured on the UV1 beam line of the Astrid Synchrotron facility at the University of Aarhus in Denmark, are presented. Molecular synthesis (e.g. CO3, CO, H2CO3) induced by ion irradiated CO2/H 2O ices using facilities at Queens University Belfast are also reported. In particular this thesis focuses on the irradiation studies of the binary ice mixture of Methylamine (CH3NH2) and Carbon Dioxide (CO2). The results of irradiation of CH3NH2 and CO2 binary ice mixtures by ultraviolet photons, and electrons are presented. The apparent production of the amino acid - glycine - in our irradiated samples is discussed together with possible production processes.

  13. Impact ionisation spectra of cosmic dust analogues

    NASA Astrophysics Data System (ADS)

    Kempf, S.; Fiege, K.; Hillier, J.; Srama, R.; Mocker, A.; Postberg, F.; Sternovsky, Z.; Horanyi, M.; Munsat, T.; Drake, K. J.

    2011-12-01

    The Cassini dust detector CDA collected a few impact spectra of grains which are most likely of interstellar origin. Such spectra provide unequivocal information about the composition of solid material embedded in the interstellar medium, while the current knowledge of the composition of interstellar dust stemming dominantly from astronomical is limited. Fortunately, interstellar grains can be found even in the vicinity of the Earth orbit because the solar system currently traverses the so-called Local Interstellar Cloud (LIC). The interpretation of impact mass spectra is difficult because (i) the impact ionisation is a non-equilibrium process, (ii) new chemical compounds may form in the impact plasma, and (iii) the likelihood to detect elements or molecules in the resulting spectrum depends on the impact energy. To retrieve reliable information about the composition, the CDA spectra need to be related to spectra obtained from impact experiments with dust analogous in a dust accelerator facility. To this aim we performed impact experiments with cosmic dust analogues in a dust accelerator facility. We recorded spectra of sub-micron pyroxene grains ground from a natural Spinel-Lherzolite sample using a high resolution impact mass spectrometer as well as the CDA flight spare unit. In this talk we will report about calibration experiments using the 2MV Van-der-Graaf dust accelerator in Heidelberg.

  14. Relational Quadrilateralland. Analogues of Isospin and Hypercharge

    E-print Network

    Edward Anderson

    2013-08-07

    I consider the momenta and conserved quantities for CP^2 interpreted as the space of quadrilaterals. This builds on seminar I and II's kinematics via making use of MacFarlane's work considering the SU(3)-like (and thus particle physics-like) conserved quantities that occur for CP^2. I perform the additional step of further interpreting that as the configuration space of all relational quadrilaterals and thus an interesting toy model for whole-universe, relational and geometrodynamical-analogue physics. I also provide the Kuchar observables for the quadrilateral, which is a particular resolution of the Problem of Observables. I study HO-like and highly symmetric potentials. I also provide some exact solutions and qualitative behaviours for dynamics on CP^2. In each case, I reinterpret the results in terms of quadrilaterals. This paves the way for the quantum mechanical study of the relational quadrilateral and for investigations of a number of Problem of Time strategies and of a number of other foundational and qualitative investigations of Quantum Cosmology.

  15. Trustworthiness and Influence: A Reexamination in an Extended Counseling Analogue.

    ERIC Educational Resources Information Center

    Rothmeier, Rosemarie C.; Dixon, David N.

    1980-01-01

    The study demonstrated that: (1) interviewer trustworthiness can be manipulated in an analogue interview setting; and (2) interviewer trustworthiness is related to interpersonal influence in the interview setting. Findings follow a pattern of outcomes predicted by cognitive dissonance theory. (Author)

  16. Sulphur Spring: Busy Intersection and Possible Martian Analogue

    NASA Technical Reports Server (NTRS)

    Nankivell, A.; Andre, N.; Thomas-Keprta, K.; Allen, C.; McKay, D.

    2000-01-01

    Life in extreme environments exhibiting conditions similar to early Earth and Mars, such as Sulphur Spring, may harbor microbiota serving as both relics from the past as well as present day Martian analogues.

  17. Practical enantiospecific syntheses of lysobisphosphatidic acid and its analogues.

    PubMed

    Jiang, Guowei; Xu, Yong; Prestwich, Glenn D

    2006-02-01

    We describe a versatile, efficient, and practical method for the preparation of enantiomerically pure lysobisphosphatidic acid (LBPA), bisether analogues, and phosphorothioate analogues of LBPA from solketal. Phosphorylation of a protected sn-2-O-oleoyl glycerol with 2-cyanoethyl bis(N,N-diisopropylamino)phosphite, followed by oxidation and deprotection, generated the enantiomers of 2,2'-LBPA. The corresponding phosphorothioate analogues were obtained by oxidation with sulfur. The (R,R) and (S,S) enantiomers of both LBPA and phosphorothioate LBPA were synthesized from (S)- and (R)-solketal, respectively. The ether analogue of (S,S)-lysobisphosphatidic acid (LBPA) and its enantiomer were synthesized from the same enantiomer (S)-solketal by simply changing the sequence of deprotection steps. PMID:16438504

  18. Synthesis and antifungal activity of two novel spermidine analogues.

    PubMed

    Mackintosh, C A; Slater, L A; McClintock, C A; Walters, D R; Havis, N D; Robins, D J

    1997-03-01

    Two spermidine analogues were synthesised and examined for antifungal activity. Both compounds used as 1 mM post-inoculation sprays reduced infection of barley seedlings by the powdery mildew fungus, Erysiphe graminis f.sp. hordei, infection of broad bean seedlings by the rust fungus, Uromyces viciae-fabae, and infection of apple seedlings by the powdery mildew fungus, Podosphaera leucotricha. Since these fungal pathogens cannot be cultured axenically, the effects of the two spermidine analogues on mycelial growth in vitro, as well as preliminary investigations on polyamine biosynthesis, were undertaken using the oat stripe pathogen, Pyrenophora avenae. Although neither compound affected radial growth of the fungus on plates, both analogues reduced fungal biomass in liquid culture substantially. The two spermidine analogues, used at a concentration of 1 mM, had no significant effect on the conversion of labelled ornithine into polyamines in P. avenae. PMID:9066105

  19. ORIGINAL ARTICLE Species-specific attraction to pheromonal analogues

    E-print Network

    Eltz, Thomas

    ORIGINAL ARTICLE Species-specific attraction to pheromonal analogues in orchid bees Yvonne 2006 / Published online: 19 July 2006 # Springer-Verlag 2006 Abstract Male orchid bees (Euglossini . Euglossini . Fragrance Introduction Male neotropical orchid bees (Euglossini) have enlarged hind tibiae

  20. Biomimetic cochlea filters : from modelling, design to analogue VLSI implementation 

    E-print Network

    Wang, Shiwei

    2014-11-27

    This thesis presents a novel biomimetic cochlea filter which closely resembles the biological cochlea behaviour. The filter is highly feasible for analogue very-large-scale integration (VLSI) circuits, which leads to a ...

  1. Platonic solids generate their four-dimensional analogues

    E-print Network

    Dechant, Pierre-Philippe

    2013-01-01

    In this paper, we show how regular convex 4-polytopes - the analogues of the Platonic solids in four dimensions - can be constructed from three-dimensional considerations concerning the Platonic solids alone. Via the Cartan-Dieudonne theorem, the reflective symmetries of the Platonic solids generate rotations. In a Clifford algebra framework, the space of spinors generating such three-dimensional rotations has a natural four-dimensional Euclidean structure. The spinors arising from the Platonic Solids can thus in turn be interpreted as vertices in four-dimensional space, giving a simple construction of the 4D polytopes 16-cell, 24-cell, the F_4 root system and the 600-cell. In particular, these polytopes have `mysterious' symmetries, that are almost trivial when seen from the three-dimensional spinorial point of view. In fact, all these induced polytopes are also known to be root systems and thus generate rank-4 Coxeter groups, which can be shown to be a general property of the spinor construction. These cons...

  2. Photoinduced Magnetism in Nanoscale Heterostructures of Prussian Blue Analogues*

    NASA Astrophysics Data System (ADS)

    Knowles, E. S.; Pajerowski, D. M.; Meisel, M. W.; Dumont, M. F.; Guiet, A.; Talham, D. R.; Gomez, A.; Kycia, S. W.

    2011-03-01

    Nanometer-scale cubic heterostructures of two Prussian blue analogues, ferromagnetic Kj Ni k [Cr(CN)6 ]l . nH2 O (A) with Tc ~ 70 ~K and photo-active ferrimagnetic Rb a Co b [Fe(CN)6 ]c . mH2 O (B) with Tc ~ 20 ~K, have been studied., Inorg. Chem., submitted.} These samples exhibit a persistent photoinduced decrease in magnetization at temperatures up to Tc ~ 70 ~K of the A constituent, resembling results from analogous ABA heterostructured films., J. Am. Chem. Soc. 132, 4058 (2010).} This net decrease suggests that the photoinduced structural transition in the B layer generates a strain-induced decrease in the magnetization of the A layer, similar to a pressure-induced decrease previously observed in the pure A material. Core-shell and core-shell-shell configurations AB, BA, ABA, and BAB have been characterized by TEM, FTIR, XRD, and SQUID magnetometry.*Supported, in part, by NSF DMR-0701400 (MWM) and DMR-1005581 (DRT), NSERC, CFI, the NHMFL, and the State of Florida. M. F. Dumont et al., Inorg. Chem., submitted.

  3. Resonance IR: a coherent multidimensional analogue of resonance Raman.

    PubMed

    Boyle, Erin S; Neff-Mallon, Nathan A; Handali, Jonathan D; Wright, John C

    2014-05-01

    This work demonstrates the use of triply resonant sum frequency (TRSF) spectroscopy as a "resonance IR" analogue to resonance Raman spectroscopy. TRSF is a four-wave-mixing process where three lasers with independent frequencies interact coherently with a sample to generate an output at their triple summation frequency. The first two lasers are in the infrared and result in two vibrational excitations, while the third laser is visible and induces a two-quantum anti-Stokes resonance Raman transition. The signal intensity grows when the laser frequencies are all in resonance with coupled vibrational and electronic states. The method therefore provides electronic enhancement of IR-active vibrational modes. These modes may be buried beneath solvent in the IR spectrum and also be Raman-inactive and therefore inaccessible by other techniques. The method is presented on the centrosymmetric complex copper phthalocyanine tetrasulfonate. In this study, the two vibrational frequencies were scanned across ring-breathing modes, while the visible frequency was left in resonance with the copper phthalocyanine tetrasulfonate Q band, resulting in a two-dimensional infrared plot that also reveals coupling between vibrational states. TRSF has the potential to be a very useful probe of structurally similar biological motifs such as hemes, as well as synthetic transition-metal complexes. PMID:24707979

  4. Cetalox and analogues: synthesis via acid-mediated polyene cyclizations.

    PubMed

    Snowden, Roger L

    2008-06-01

    Using a novel, acid-mediated cyclization methodology, a direct access to Cetalox ((+/-)-1; a commercially important ambergris-type odorant) and various structurally related didehydro (i.e., 19, 26, and 30) and tetradehydro (i.e., 28 and 37/38) analogues is described. Treatment of either (E,E)-14 or (E)-15 with an excess of FSO(3)H in 2-nitropropane at -90 degrees stereospecifically afforded (+/-)-1 in 40 and 42% yield, respectively. Under similar conditions, cyclization of (E)-18 or 20 furnished 19 in 60 and 64% yield, respectively. Analogously, using an excess of ClSO(3)H in CH(2)Cl(2) at -80 degrees, 26 is formed with high stereoselectivity by cyclization of either (E)-24 or (Z)-25 (52 and 31% yield, resp.); in the same manner, 28 was prepared from 27 (22% yield). The same principle was applied to the synthesis of racemic Superambrox (30), via cyclization of 35, but only with poor selectivity (22%) and low yield (7%). Another approach via cyclization of (E)-40 under solvolysis conditions (excess TFA in CH(2)Cl(2) at -10 degrees) gave a higher yield (15%) with improved selectivity (43%). Finally, cyclization of 34 (1:1 diastereoisomer mixture) afforded 37/38 (10:1) in 27% yield. The qualitative organoleptic properties of 19, 26, 28, 30, and 37/38 (10:1) are briefly discussed. PMID:18618391

  5. Upheaval Dome, An Analogue Site for Gale Center

    NASA Technical Reports Server (NTRS)

    Conrad, P. G.; Eignebrode, J. L.

    2011-01-01

    We propose Upheaval Dome in southeastern Utah as an impact analogue site on Earth to Mars Science Laboratory candidate landing site Gale Crater. The genesis of Upheaval Dome was a mystery for some time--originally thought to be a salt dome. The 5 km crater was discovered to possess shocked quartz and other shock metamorphic features just a few years ago, compelling evidence that the crater was formed by impact, although the structural geology caused Shoemaker and Herkenhoff to speculate an impact origin some 25 years earlier. The lithology of the crater is sedimentary. The oldest rocks are exposed in the center of the dome, upper Permian sandstones, and progressively younger units are well exposed moving outward from the center. These are Triassic sandstones, siltstones and shales, which are intruded by clastic dikes. There are also other clay-rich strata down section, as is the case with Gale Crater. There is significant deformation in the center of the crater, with folding and steeply tilted beds, unlike the surrounding Canyonlands area, which is relatively undeformed. The rock units are well exposed at Upheaval Dome, and there are shatter cones, impactite fragments, shocked quartz grains and melt rocks present. The mineral shock features suggest that the grains were subjected to dynamic pressures> 10 GPa.

  6. Analogue and digital linear modulation techniques for mobile satellite

    NASA Technical Reports Server (NTRS)

    Whitmarsh, W. J.; Bateman, A.; Mcgeehan, J. P.

    1990-01-01

    The choice of modulation format for a mobile satellite service is complex. The subjective performance is summarized of candidate schemes and voice coder technologies. It is shown that good performance can be achieved with both analogue and digital voice systems, although the analogue system gives superior performance in fading. The results highlight the need for flexibility in the choice of signaling format. Linear transceiver technology capable of using many forms of narrowband modulation is described.

  7. Synthesis and Biological Evaluation of a Teixobactin Analogue.

    PubMed

    Jad, Yahya E; Acosta, Gerardo A; Naicker, Tricia; Ramtahal, Melissa; El-Faham, Ayman; Govender, Thavendran; Kruger, Hendrik G; Torre, Beatriz G de la; Albericio, Fernando

    2015-12-18

    The first synthesis and biological activity of a teixobactin analogue is reported. Substitution of the unusual l-allo-enduracididine residue by the naturally occurring l-arginine was achieved, and the analogue gave an activity trend similar to that of teixobactin (against Gram-postive bacteria) and meropenem, which was approved by the FDA in 1996. The synthetic route used allows for the synthesis of the natural product as well as the development of a program of medicinal chemistry. PMID:26654835

  8. Quantum dense key distribution

    SciTech Connect

    Degiovanni, I.P.; Ruo Berchera, I.; Castelletto, S.; Rastello, M.L.; Bovino, F.A.; Colla, A.M.; Castagnoli, G.

    2004-03-01

    This paper proposes a protocol for quantum dense key distribution. This protocol embeds the benefits of a quantum dense coding and a quantum key distribution and is able to generate shared secret keys four times more efficiently than the Bennet-Brassard 1984 protocol. We hereinafter prove the security of this scheme against individual eavesdropping attacks, and we present preliminary experimental results, showing its feasibility.

  9. Biological activities of curcumin and its analogues (Congeners) made by man and Mother Nature.

    PubMed

    Anand, Preetha; Thomas, Sherin G; Kunnumakkara, Ajaikumar B; Sundaram, Chitra; Harikumar, Kuzhuvelil B; Sung, Bokyung; Tharakan, Sheeja T; Misra, Krishna; Priyadarsini, Indira K; Rajasekharan, Kallikat N; Aggarwal, Bharat B

    2008-12-01

    Curcumin, a yellow pigment present in the Indian spice turmeric (associated with curry powder), has been linked with suppression of inflammation; angiogenesis; tumorigenesis; diabetes; diseases of the cardiovascular, pulmonary, and neurological systems, of skin, and of liver; loss of bone and muscle; depression; chronic fatigue; and neuropathic pain. The utility of curcumin is limited by its color, lack of water solubility, and relatively low in vivo bioavailability. Because of the multiple therapeutic activities attributed to curcumin, however, there is an intense search for a "super curcumin" without these problems. Multiple approaches are being sought to overcome these limitations. These include discovery of natural curcumin analogues from turmeric; discovery of natural curcumin analogues made by Mother Nature; synthesis of "man-made" curcumin analogues; reformulation of curcumin with various oils and with inhibitors of metabolism (e.g., piperine); development of liposomal and nanoparticle formulations of curcumin; conjugation of curcumin prodrugs; and linking curcumin with polyethylene glycol. Curcumin is a homodimer of feruloylmethane containing a methoxy group and a hydroxyl group, a heptadiene with two Michael acceptors, and an alpha,beta-diketone. Structural homologues involving modification of all these groups are being considered. This review focuses on the status of all these approaches in generating a "super curcumin.". PMID:18775680

  10. Liver S9 Fraction-Derived Metabolites of Curcumin Analogue UBS109.

    PubMed

    Moore, Terry W; Zhu, Shijun; Randolph, Ryan; Shoji, Mamoru; Snyder, James P

    2014-04-10

    To address the shortcomings of the natural product curcumin, many groups have created analogues that share similar structural features while displaying superior properties, particularly in anticancer drug discovery. Relatively unexplored have been the mechanisms by which such compounds are metabolized. A comprehensive in vitro study of a curcumin analogue (UBS109) in liver S9 fractions from five different species is presented. Further, we examine the cell-based bioactivity of the major metabolites. In spite of the fact that UBS109 reduces tumor growth in mice, it is quickly metabolized in vitro and 94% protein bound in mouse plasma. The primary monounsaturated metabolite is only modestly bioactive against MDA-MB-231 breast cancer cells. These observations suggest that while the ?,?-unsaturated ketone common to curcumin analogues is important for bioactivity, protein binding and tissue distribution may serve to protect UBS109 from full metabolism in vivo while allowing it to exert a pharmacological effect by means of slow drug release. PMID:24900828

  11. Synthesis and biological activity of new conformationally restricted analogues of pepstatin.

    PubMed

    Szewczuk, Z; Rebholz, K L; Rich, D H

    1992-01-01

    A new statine derivative, 3-hydroxy-4-amino-5-mercaptopentanoic acid; cysteinylstatine (CySta), was synthesized and used to prepare a series of conformationally restricted analogues of pepstatin (Iva-Val-Val-Sta-Ala-Sta) in which the conformational constraint was introduced via a bis-sulfide connecting the appropriately substituted residues in the P1 and the P3 inhibitor side chains. The precursor peptide, Iva-Cys-Val-CySta-Ala-Iaa, was synthesized and alkylated with a series of dibromoalkanes and alkenes to produce the cyclic structures. This strategy permitted the carbon atom spacing between the P1 and the P3 inhibitor side chains to be systematically varied so as to produce inhibitors with 15-, 16-, and 17-membered ring systems. Additional non-cyclic analogues were synthesized as controls by alkylating the bisthiol intermediates with methyl iodide. The inhibitory potency of the analogues were determined against porcine pepsin and penicillopepsin by using standard enzyme kinetic assays. The cyclic inhibitor were found to be potent inhibitors of both aspartic proteases; inhibitor that contained a trans-2-butene link between the two sulfur atoms was found to be the most potent inhibitor with a Ki less than 1 nM against pepsin and 3.94 nM against penicillopepsin. This series of compounds illustrates a new type of conformational restriction that can be used to probe for the bioactive conformation of peptides. PMID:1478780

  12. Membrane-Targeting DCAP Analogues with Broad-Spectrum Antibiotic Activity against Pathogenic Bacteria.

    PubMed

    Hurley, Katherine A; Heinrich, Victoria A; Hershfield, Jeremy R; Demons, Samandra T; Weibel, Douglas B

    2015-04-01

    We performed a structure-activity relationship study of 2-((3-(3,6-dichloro-9H-carbazol-9-yl)-2-hydroxypropyl)amino)-2-(hydroxymethyl)propane-1,3-diol (DCAP), which is an antibacterial agent that disrupts the membrane potential and permeability of bacteria. The stereochemistry of DCAP had no effect on the biological activity of DCAP. The aromaticity and electronegativity of the chlorine-substituted carbazole was required for activity, suggesting that its planar and dipolar characteristics orient DCAP in membranes. Increasing the hydrophobicity of the tail region of DCAP enhanced its antibiotic activity. Two DCAP analogues displayed promising antibacterial activity against the BSL-3 pathogens Bacillus anthracis and Francisella tularensis. Codosing DCAP analogues with ampicillin or kanamycin increased their potency. These studies demonstrate that DCAP and its analogues may be a promising scaffold for developing chemotherapeutic agents that bind to bacterial membranes and kill strains of slow-growing or dormant bacteria that cause persistent infections. PMID:25941556

  13. Type IV kerogens as analogues for organic macromolecular materials in aqueously altered carbonaceous chondrites.

    PubMed

    Matthewman, Richard; Martins, Zita; Sephton, Mark A

    2013-04-01

    Understanding the processes involved in the evolution of organic matter in the early Solar System requires extensive experimental work. The scientifically valuable carbonaceous chondrites are principal targets for organic analyses, but these meteorites are rare. Meteoritic analog materials available in larger quantities, on which experiments can be performed, would be highly beneficial. The bulk of the organic inventory of carbonaceous chondrites is made up of solvent-insoluble macromolecular material. This high-molecular-weight entity provides a record of thermal and aqueous parent-body alteration of precursor organic structures present at the birth of the Solar System. To identify an effective analogue for this macromolecular material, we analyzed a series of terrestrial kerogens by pyrolysis-gas chromatography-mass spectrometry. Type I and II kerogens are unsuitable analogues owing to their highly aliphatic nature. Type III kerogens show some similarities to meteoritic macromolecular materials but display a substantial biological heritage. Type IV kerogens, in this study derived from Mesozoic paleosols and produced by the reworking and oxidation of organic matter, represent an effective analogue. Some isomeric differences exist between meteoritic macromolecular materials and type IV kerogens, and stepped pyrolysis indicates variations in thermal stability. In addition to being a suitable material for novel experimentation, type IV kerogens also have the potential to aid in the optimization of instruments for deployment on Mars. PMID:23551239

  14. Structural, kinetic, and docking studies of artificial imine reductases based on biotin-streptavidin technology: an induced lock-and-key hypothesis.

    PubMed

    Robles, Victor Muñoz; Dürrenberger, Marc; Heinisch, Tillmann; Lledós, Agustí; Schirmer, Tilman; Ward, Thomas R; Maréchal, Jean-Didier

    2014-11-01

    An artificial imine reductase results upon incorporation of a biotinylated Cp*Ir moiety (Cp* = C5Me5(-)) within homotetrameric streptavidin (Sav) (referred to as Cp*Ir(Biot-p-L)Cl] ? Sav). Mutation of S112 reveals a marked effect of the Ir/streptavidin ratio on both the saturation kinetics as well as the enantioselectivity for the production of salsolidine. For [Cp*Ir(Biot-p-L)Cl] ? S112A Sav, both the reaction rate and the selectivity (up to 96% ee (R)-salsolidine, kcat 14-4 min(-1) vs [Ir], KM 65-370 mM) decrease upon fully saturating all biotin binding sites (the ee varying between 96% ee and 45% ee R). In contrast, for [Cp*Ir(Biot-p-L)Cl] ? S112K Sav, both the rate and the selectivity remain nearly constant upon varying the Ir/streptavidin ratio [up to 78% ee (S)-salsolidine, kcat 2.6 min(-1), KM 95 mM]. X-ray analysis complemented with docking studies highlight a marked preference of the S112A and S112K Sav mutants for the SIr and RIr enantiomeric forms of the cofactor, respectively. Combining both docking and saturation kinetic studies led to the formulation of an enantioselection mechanism relying on an "induced lock-and-key" hypothesis: the host protein dictates the configuration of the biotinylated Ir-cofactor which, in turn, by and large determines the enantioselectivity of the imine reductase. PMID:25317660

  15. Structure-based drug design studies of UDP-N-acetylglucosamine pyrophosphosrylase, a key enzyme for the control of witches’ broom disease

    PubMed Central

    2013-01-01

    Background The witches’ broom disease is a plague caused by Moniliophthora perniciosa in the Theobroma cacao, which has been reducing the cocoa production since 1989. This issue motivated a genome project that has showing several new molecular targets, which can be developed inhibitors in order to control the plague. Among the molecular targets obtained, the UDP-N-acetylglucosamine pyrophosphorylase (UNAcP) is a key enzyme to construct the fungal cell wall. The inhibition of this enzyme results in the fungal cell death. Results The results show that the molecular recognition of the enzyme with the substrates occurs mainly by hydrogen bonds between ligands and Arg116, Arg383, Gly381, and Lys408 amino acids; and few hydrophobic interactions with Tyr382 and Lys123 residues. Conclusions Among the compounds analyzed, the NAG5 showed the best binding energy (?95.2 kcal/mol). The next steps for the control of witches’ broom plague involve the synthesis and biological evaluation of these compounds, which are in progress. PMID:23497581

  16. Cladribine Analogues via O?-(Benzotriazolyl) Derivatives of Guanine Nucleosides.

    PubMed

    Satishkumar, Sakilam; Vuram, Prasanna K; Relangi, Siva Subrahmanyam; Gurram, Venkateshwarlu; Zhou, Hong; Kreitman, Robert J; Montemayor, Michelle M Martínez; Yang, Lijia; Kaliyaperumal, Muralidharan; Sharma, Somesh; Pottabathini, Narender; Lakshman, Mahesh K

    2015-01-01

    Cladribine, 2-chloro-2'-deoxyadenosine, is a highly efficacious, clinically used nucleoside for the treatment of hairy cell leukemia. It is also being evaluated against other lymphoid malignancies and has been a molecule of interest for well over half a century. In continuation of our interest in the amide bond-activation in purine nucleosides via the use of (benzotriazol-1yl-oxy)tris(dimethylamino)phosphonium hexafluorophosphate, we have evaluated the use of O?-(benzotriazol-1-yl)-2'-deoxyguanosine as a potential precursor to cladribine and its analogues. These compounds, after appropriate deprotection, were assessed for their biological activities, and the data are presented herein. Against hairy cell leukemia (HCL), T-cell lymphoma (TCL) and chronic lymphocytic leukemia (CLL), cladribine was the most active against all. The bromo analogue of cladribine showed comparable activity to the ribose analogue of cladribine against HCL, but was more active against TCL and CLL. The bromo ribose analogue of cladribine showed activity, but was the least active among the C6-NH?-containing compounds. Substitution with alkyl groups at the exocyclic amino group appears detrimental to activity, and only the C6 piperidinyl cladribine analogue demonstrated any activity. Against adenocarcinoma MDA-MB-231 cells, cladribine and its ribose analogue were most active. PMID:26556315

  17. Cladribine Analogues via O?-(Benzotriazolyl) Derivatives of Guanine Nucleosides.

    PubMed

    Satishkumar, Sakilam; Vuram, Prasanna K; Relangi, Siva Subrahmanyam; Gurram, Venkateshwarlu; Zhou, Hong; Kreitman, Robert J; Martínez Montemayor, Michelle M; Yang, Lijia; Kaliyaperumal, Muralidharan; Sharma, Somesh; Pottabathini, Narender; Lakshman, Mahesh K

    2015-01-01

    Cladribine, 2-chloro-2'-deoxyadenosine, is a highly efficacious, clinically used nucleoside for the treatment of hairy cell leukemia. It is also being evaluated against other lymphoid malignancies and has been a molecule of interest for well over half a century. In continuation of our interest in the amide bond-activation in purine nucleosides via the use of (benzotriazol-1yl-oxy)tris(dimethylamino)phosphonium hexafluorophosphate, we have evaluated the use of O?-(benzotriazol-1-yl)-2'-deoxyguanosine as a potential precursor to cladribine and its analogues. These compounds, after appropriate deprotection, were assessed for their biological activities, and the data are presented herein. Against hairy cell leukemia (HCL), T-cell lymphoma (TCL) and chronic lymphocytic leukemia (CLL), cladribine was the most active against all. The bromo analogue of cladribine showed comparable activity to the ribose analogue of cladribine against HCL, but was more active against TCL and CLL. The bromo ribose analogue of cladribine showed activity, but was the least active among the C6-NH?-containing compounds. Substitution with alkyl groups at the exocyclic amino group appears detrimental to activity, and only the C6 piperidinyl cladribine analogue demonstrated any activity. Against adenocarcinoma MDA-MB-231 cells, cladribine and its ribose analogue were most active. PMID:26473811

  18. Analogue gravitational phenomena in Bose-Einstein condensates

    E-print Network

    Stefano Finazzi

    2012-08-23

    Analogue gravity is based on the simple observation that perturbations propagating in several physical systems can be described by a quantum field theory in a curved spacetime. While phenomena like Hawking radiation are hardly detectable in astrophysical black holes, these effects may be experimentally tested in analogue systems. In this Thesis, focusing on Bose-Einstein condensates, we present our recent results about analogue models of gravity from three main perspectives: as laboratory tests of quantum field theory in curved spacetime, for the techniques that they provide to address various issues in general relativity, and as toy models of quantum gravity. The robustness of Hawking-like particle creation is investigated in flows with a single black hole horizon. Furthermore, we find that condensates with two (white and black) horizons develop a dynamical instability known in general relativity as black hole laser effect. Using techniques borrowed from analogue gravity, we also show that warp drives