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Sample records for binding pocket nmr-based

  1. Protein Binding Pocket Dynamics.

    Science.gov (United States)

    Stank, Antonia; Kokh, Daria B; Fuller, Jonathan C; Wade, Rebecca C

    2016-05-17

    The dynamics of protein binding pockets are crucial for their interaction specificity. Structural flexibility allows proteins to adapt to their individual molecular binding partners and facilitates the binding process. This implies the necessity to consider protein internal motion in determining and predicting binding properties and in designing new binders. Although accounting for protein dynamics presents a challenge for computational approaches, it expands the structural and physicochemical space for compound design and thus offers the prospect of improved binding specificity and selectivity. A cavity on the surface or in the interior of a protein that possesses suitable properties for binding a ligand is usually referred to as a binding pocket. The set of amino acid residues around a binding pocket determines its physicochemical characteristics and, together with its shape and location in a protein, defines its functionality. Residues outside the binding site can also have a long-range effect on the properties of the binding pocket. Cavities with similar functionalities are often conserved across protein families. For example, enzyme active sites are usually concave surfaces that present amino acid residues in a suitable configuration for binding low molecular weight compounds. Macromolecular binding pockets, on the other hand, are located on the protein surface and are often shallower. The mobility of proteins allows the opening, closing, and adaptation of binding pockets to regulate binding processes and specific protein functionalities. For example, channels and tunnels can exist permanently or transiently to transport compounds to and from a binding site. The influence of protein flexibility on binding pockets can vary from small changes to an already existent pocket to the formation of a completely new pocket. Here, we review recent developments in computational methods to detect and define binding pockets and to study pocket dynamics. We introduce five

  2. Free enthalpies of replacing water molecules in protein binding pockets

    Science.gov (United States)

    Riniker, Sereina; Barandun, Luzi J.; Diederich, François; Krämer, Oliver; Steffen, Andreas; van Gunsteren, Wilfred F.

    2012-12-01

    Water molecules in the binding pocket of a protein and their role in ligand binding have increasingly raised interest in recent years. Displacement of such water molecules by ligand atoms can be either favourable or unfavourable for ligand binding depending on the change in free enthalpy. In this study, we investigate the displacement of water molecules by an apolar probe in the binding pocket of two proteins, cyclin-dependent kinase 2 and tRNA-guanine transglycosylase, using the method of enveloping distribution sampling (EDS) to obtain free enthalpy differences. In both cases, a ligand core is placed inside the respective pocket and the remaining water molecules are converted to apolar probes, both individually and in pairs. The free enthalpy difference between a water molecule and a CH3 group at the same location in the pocket in comparison to their presence in bulk solution calculated from EDS molecular dynamics simulations corresponds to the binding free enthalpy of CH3 at this location. From the free enthalpy difference and the enthalpy difference, the entropic contribution of the displacement can be obtained too. The overlay of the resulting occupancy volumes of the water molecules with crystal structures of analogous ligands shows qualitative correlation between experimentally measured inhibition constants and the calculated free enthalpy differences. Thus, such an EDS analysis of the water molecules in the binding pocket may give valuable insight for potency optimization in drug design.

  3. Binding Hydrated Anions with Hydrophobic Pockets.

    Science.gov (United States)

    Sokkalingam, Punidha; Shraberg, Joshua; Rick, Steven W; Gibb, Bruce C

    2016-01-13

    Using a combination of isothermal titration calorimetry and quantum and molecular dynamics calculations, we demonstrate that relatively soft anions have an affinity for hydrophobic concavity. The results are consistent with the anions remaining partially hydrated upon binding, and suggest a novel strategy for anion recognition.

  4. The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding

    DEFF Research Database (Denmark)

    Zhang, H.; Lund, Ole; Nielsen, M.

    2009-01-01

    of the specificities of MHC molecules in this library weighted by the similarity of their pocket-residues to the query. This PickPocket method is demonstrated to accurately predict MHC-peptide binding for a broad range of MHC alleles, including human and non-human species. In contrast to neural network-based pan......-specific methods, PickPocket was shown to be robust both when data is scarce and when the similarity to MHC molecules with characterized binding specificity is low. A consensus method combining the PickPocket and NetMHCpan methods was shown to achieve superior predictive performance. This study demonstrates how...

  5. Exploring the inhibitor binding pocket of respiratory complex I.

    Science.gov (United States)

    Fendel, Uta; Tocilescu, Maja A; Kerscher, Stefan; Brandt, Ulrich

    2008-01-01

    Numerous hydrophobic and amphipathic compounds including several detergents are known to inhibit the ubiquinone reductase reaction of respiratory chain complex I (proton pumping NADH:ubiquinone oxidoreductase). Guided by the X-ray structure of the peripheral arm of complex I from Thermus thermophilus we have generated a large collection of site-directed mutants in the yeast Yarrowia lipolytica targeting the proposed ubiquinone and inhibitor binding pocket of this huge multiprotein complex at the interface of the 49-kDa and PSST subunits. We could identify a number of residues where mutations changed I(50) values for representatives from all three groups of hydrophobic inhibitors. Many mutations around the domain of the 49-kDa subunit that is homologous to the [NiFe] centre binding region of hydrogenase conferred resistance to DQA (class I/type A) and rotenone (class II/type B) indicating a wider overlap of the binding sites for these two types of inhibitors. In contrast, a region near iron-sulfur cluster N2, where the binding of the n-alkyl-polyoxyethylene-ether detergent C(12)E(8) (type C) was exclusively affected, appeared comparably well separated. Taken together, our data provide structure-based support for the presence of distinct but overlapping binding sites for hydrophobic inhibitors possibly extending into the ubiquinone reduction site of mitochondrial complex I.

  6. Auto-FACE: an NMR based binding site mapping program for fast chemical exchange protein-ligand systems.

    Directory of Open Access Journals (Sweden)

    Janarthanan Krishnamoorthy

    than the former one. Further NMR based model fitting for individual residues suggest single site model for residues present at these binding sites and two site model for residues present between these sites. This implies that chemical shift perturbation can represent the local binding event much more accurately than the global binding event. CONCLUSION/SIGNIFICANCE: Detail NMR chemical shift perturbation analysis enabled binding site residues to be distinguished from non-binding site residues for accurate mapping of interaction site in complex fast exchange system between small molecule and protein. The methodology is automated and implemented in a program called "Auto-FACE", which also allowed quantitative information of each interaction site and elucidation of binding mechanism.

  7. The minor binding pocket: a major player in 7TM receptor activation

    DEFF Research Database (Denmark)

    Rosenkilde, Mette Marie; Benned-Jensen, Tau; Frimurer, Thomas M.;

    2010-01-01

    From the deep part of the main ligand-binding crevice, a minor, often shallower pocket extends between the extracellular ends of transmembrane domains (TM)-I, II, III and VII of 7TM receptors. This minor binding pocket is defined by a highly conserved kink in TM-II that is induced by a proline...... residue located in one of two adjacent positions. Here we argue that this minor binding pocket is important for receptor activation. Functional coupling of the receptors seems to be mediated through the hydrogen bond network located between the intracellular segments of these TMs, with the allosteric...... interface between TM-II and TM-VII being of particular significance. Importantly, the minor binding pocket, especially the proline-kink in TM-II, is involved in G protein versus arrestin pathway-biased signaling, for example in the angiotensin AT1 system. Consequently, this pocket could be specifically...

  8. Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets

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    Ashford Paul

    2012-03-01

    Full Text Available Abstract Background Protein structures provide a valuable resource for rational drug design. For a protein with no known ligand, computational tools can predict surface pockets that are of suitable size and shape to accommodate a complementary small-molecule drug. However, pocket prediction against single static structures may miss features of pockets that arise from proteins' dynamic behaviour. In particular, ligand-binding conformations can be observed as transiently populated states of the apo protein, so it is possible to gain insight into ligand-bound forms by considering conformational variation in apo proteins. This variation can be explored by considering sets of related structures: computationally generated conformers, solution NMR ensembles, multiple crystal structures, homologues or homology models. It is non-trivial to compare pockets, either from different programs or across sets of structures. For a single structure, difficulties arise in defining particular pocket's boundaries. For a set of conformationally distinct structures the challenge is how to make reasonable comparisons between them given that a perfect structural alignment is not possible. Results We have developed a computational method, Provar, that provides a consistent representation of predicted binding pockets across sets of related protein structures. The outputs are probabilities that each atom or residue of the protein borders a predicted pocket. These probabilities can be readily visualised on a protein using existing molecular graphics software. We show how Provar simplifies comparison of the outputs of different pocket prediction algorithms, of pockets across multiple simulated conformations and between homologous structures. We demonstrate the benefits of use of multiple structures for protein-ligand and protein-protein interface analysis on a set of complexes and consider three case studies in detail: i analysis of a kinase superfamily highlights the

  9. Solvent fluctuations induce non-Markovian kinetics in hydrophobic pocket-ligand binding

    CERN Document Server

    Weiß, R Gregor; Dzubiella, Joachim

    2016-01-01

    We investigate the impact of water fluctuations on the key-lock association kinetics of a hydrophobic ligand (key) binding to a hydrophobic pocket (lock) by means of a minimalistic stochastic model system. It describes the collective hydration behavior of the pocket by bimodal fluctuations of a water-pocket interface that dynamically couples to the diffusive motion of the approaching ligand via the hydrophobic interaction. This leads to a set of overdamped Langevin equations in 2D-coordinate-space, that is Markovian in each dimension. Numerical simulations demonstrate locally increased friction of the ligand, decelerated binding kinetics, and local non-Markovian (memory) effects in the ligand's reaction coordinate as found previously in explicit-water molecular dynamics studies of model hydrophobic pocket-ligand binding [1,2]. Our minimalistic model elucidates the origin of effectively enhanced friction in the process that can be traced back to long-time decays in the force-autocorrelation function induced by...

  10. Competitive binding of a benzimidazole to the histone-binding pocket of the Pygo PHD finger.

    Science.gov (United States)

    Miller, Thomas C R; Rutherford, Trevor J; Birchall, Kristian; Chugh, Jasveen; Fiedler, Marc; Bienz, Mariann

    2014-12-19

    The Pygo-BCL9 complex is a chromatin reader, facilitating β-catenin-mediated oncogenesis, and is thus emerging as a potential therapeutic target for cancer. Its function relies on two ligand-binding surfaces of Pygo's PHD finger that anchor the histone H3 tail methylated at lysine 4 (H3K4me) with assistance from the BCL9 HD1 domain. Here, we report the first use of fragment-based screening by NMR to identify small molecules that block protein-protein interactions by a PHD finger. This led to the discovery of a set of benzothiazoles that bind to a cleft emanating from the PHD-HD1 interface, as defined by X-ray crystallography. Furthermore, we discovered a benzimidazole that docks into the H3K4me specificity pocket and displaces the native H3K4me peptide from the PHD finger. Our study demonstrates the ligandability of the Pygo-BCL9 complex and uncovers a privileged scaffold as a template for future development of lead inhibitors of oncogenesis.

  11. The human olfactory receptor 17-40: requisites for fitting into the binding pocket.

    Science.gov (United States)

    Anselmi, Cecilia; Buonocore, Anna; Centini, Marisanna; Facino, Roberto Maffei; Hatt, Hanns

    2011-06-01

    To gain structural insight on the interactions between odorants and the human olfactory receptor, we did homology modelling of the receptor structure, followed by molecular docking simulation with ligands. Molecular dynamics simulation on the structures resulting from docking served to estimate the binding free energy of the various odorant families. A correlation with the odorous properties of the ligands is proposed. We also investigated which residues were involved in the binding of a set of properly synthesised ligands and which were required for fitting inside the binding pocket. Olfactive stimulation of the olfactory receptor with odorous molecules was also investigated, using calcium imaging or electrophysiological recordings.

  12. Spontaneous activation of visual pigments in relation to openness/closedness of chromophore-binding pocket

    Science.gov (United States)

    Yue, Wendy Wing Sze; Frederiksen, Rikard; Ren, Xiaozhi; Luo, Dong-Gen; Yamashita, Takahiro; Shichida, Yoshinori; Cornwall, M Carter; Yau, King-Wai

    2017-01-01

    Visual pigments can be spontaneously activated by internal thermal energy, generating noise that interferes with real-light detection. Recently, we developed a physicochemical theory that successfully predicts the rate of spontaneous activity of representative rod and cone pigments from their peak-absorption wavelength (λmax), with pigments having longer λmax being noisier. Interestingly, cone pigments may generally be ~25 fold noisier than rod pigments of the same λmax, possibly ascribed to an ‘open’ chromophore-binding pocket in cone pigments defined by the capability of chromophore-exchange in darkness. Here, we show in mice that the λmax-dependence of pigment noise could be extended even to a mutant pigment, E122Q-rhodopsin. Moreover, although E122Q-rhodopsin shows some cone-pigment-like characteristics, its noise remained quantitatively predictable by the ‘non-open’ nature of its chromophore-binding pocket as in wild-type rhodopsin. The openness/closedness of the chromophore-binding pocket is potentially a useful indicator of whether a pigment is intended for detecting dim or bright light. DOI: http://dx.doi.org/10.7554/eLife.18492.001 PMID:28186874

  13. Identification of potential small molecule binding pockets on Rho family GTPases.

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    Juan Manuel Ortiz-Sanchez

    Full Text Available Rho GTPases are conformational switches that control a wide variety of signaling pathways critical for eukaryotic cell development and proliferation. They represent attractive targets for drug design as their aberrant function and deregulated activity is associated with many human diseases including cancer. Extensive high-resolution structures (>100 and recent mutagenesis studies have laid the foundation for the design of new structure-based chemotherapeutic strategies. Although the inhibition of Rho signaling with drug-like compounds is an active area of current research, very little attention has been devoted to directly inhibiting Rho by targeting potential allosteric non-nucleotide binding sites. By avoiding the nucleotide binding site, compounds may minimize the potential for undesirable off-target interactions with other ubiquitous GTP and ATP binding proteins. Here we describe the application of molecular dynamics simulations, principal component analysis, sequence conservation analysis, and ensemble small-molecule fragment mapping to provide an extensive mapping of potential small-molecule binding pockets on Rho family members. Characterized sites include novel pockets in the vicinity of the conformationaly responsive switch regions as well as distal sites that appear to be related to the conformations of the nucleotide binding region. Furthermore the use of accelerated molecular dynamics simulation, an advanced sampling method that extends the accessible time-scale of conventional simulations, is found to enhance the characterization of novel binding sites when conformational changes are important for the protein mechanism.

  14. Interactions between Hofmeister anions and the binding pocket of a protein.

    Science.gov (United States)

    Fox, Jerome M; Kang, Kyungtae; Sherman, Woody; Héroux, Annie; Sastry, G Madhavi; Baghbanzadeh, Mostafa; Lockett, Matthew R; Whitesides, George M

    2015-03-25

    This paper uses the binding pocket of human carbonic anhydrase II (HCAII, EC 4.2.1.1) as a tool to examine the properties of Hofmeister anions that determine (i) where, and how strongly, they associate with concavities on the surfaces of proteins and (ii) how, upon binding, they alter the structure of water within those concavities. Results from X-ray crystallography and isothermal titration calorimetry show that most anions associate with the binding pocket of HCAII by forming inner-sphere ion pairs with the Zn(2+) cofactor. In these ion pairs, the free energy of anion-Zn(2+) association is inversely proportional to the free energetic cost of anion dehydration; this relationship is consistent with the mechanism of ion pair formation suggested by the "law of matching water affinities". Iodide and bromide anions also associate with a hydrophobic declivity in the wall of the binding pocket. Molecular dynamics simulations suggest that anions, upon associating with Zn(2+), trigger rearrangements of water that extend up to 8 Å away from their surfaces. These findings expand the range of interactions previously thought to occur between ions and proteins by suggesting that (i) weakly hydrated anions can bind complementarily shaped hydrophobic declivities, and that (ii) ion-induced rearrangements of water within protein concavities can (in contrast with similar rearrangements in bulk water) extend well beyond the first hydration shells of the ions that trigger them. This study paints a picture of Hofmeister anions as a set of structurally varied ligands that differ in size, shape, and affinity for water and, thus, in their ability to bind to—and to alter the charge and hydration structure of—polar, nonpolar, and topographically complex concavities on the surfaces of proteins.

  15. Computational approaches for identification of conserved/unique binding pockets in the A chain of ricin

    Energy Technology Data Exchange (ETDEWEB)

    Ecale Zhou, C L; Zemla, A T; Roe, D; Young, M; Lam, M; Schoeniger, J; Balhorn, R

    2005-01-29

    Specific and sensitive ligand-based protein detection assays that employ antibodies or small molecules such as peptides, aptamers, or other small molecules require that the corresponding surface region of the protein be accessible and that there be minimal cross-reactivity with non-target proteins. To reduce the time and cost of laboratory screening efforts for diagnostic reagents, we developed new methods for evaluating and selecting protein surface regions for ligand targeting. We devised combined structure- and sequence-based methods for identifying 3D epitopes and binding pockets on the surface of the A chain of ricin that are conserved with respect to a set of ricin A chains and unique with respect to other proteins. We (1) used structure alignment software to detect structural deviations and extracted from this analysis the residue-residue correspondence, (2) devised a method to compare corresponding residues across sets of ricin structures and structures of closely related proteins, (3) devised a sequence-based approach to determine residue infrequency in local sequence context, and (4) modified a pocket-finding algorithm to identify surface crevices in close proximity to residues determined to be conserved/unique based on our structure- and sequence-based methods. In applying this combined informatics approach to ricin A we identified a conserved/unique pocket in close proximity (but not overlapping) the active site that is suitable for bi-dentate ligand development. These methods are generally applicable to identification of surface epitopes and binding pockets for development of diagnostic reagents, therapeutics, and vaccines.

  16. Glutamate Water Gates in the Ion Binding Pocket of Na+ Bound Na+, K+-ATPase

    Science.gov (United States)

    Han, Minwoo; Kopec, Wojciech; Solov’yov, Ilia A.; Khandelia, Himanshu

    2017-01-01

    The dynamically changing protonation states of the six acidic amino acid residues in the ion binding pocket of the Na+, K+ -ATPase (NKA) during the ion transport cycle are proposed to drive ion binding, release and possibly determine Na+ or K+ selectivity. We use molecular dynamics (MD) and density functional theory (DFT) simulations to determine the protonation scheme of the Na+ bound conformation of NKA. MD simulations of all possible protonation schemes show that the bound Na+ ions are most stably bound when three or four protons reside in the binding sites, and that Glu954 in site III is always protonated. Glutamic acid residues in the three binding sites act as water gates, and their deprotonation triggers water entry to the binding sites. From DFT calculations of Na+ binding energies, we conclude that three protons in the binding site are needed to effectively bind Na+ from water and four are needed to release them in the next step. Protonation of Asp926 in site III will induce Na+ release, and Glu327, Glu954 and Glu779 are all likely to be protonated in the Na+ bound occluded conformation. Our data provides key insights into the role of protons in the Na+ binding and release mechanism of NKA. PMID:28084301

  17. A substrate-induced biotin binding pocket in the carboxyltransferase domain of pyruvate carboxylase.

    Science.gov (United States)

    Lietzan, Adam D; St Maurice, Martin

    2013-07-05

    Biotin-dependent enzymes catalyze carboxyl transfer reactions by efficiently coordinating multiple reactions between spatially distinct active sites. Pyruvate carboxylase (PC), a multifunctional biotin-dependent enzyme, catalyzes the bicarbonate- and MgATP-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in mammalian tissues. To complete the overall reaction, the tethered biotin prosthetic group must first gain access to the biotin carboxylase domain and become carboxylated and then translocate to the carboxyltransferase domain, where the carboxyl group is transferred from biotin to pyruvate. Here, we report structural and kinetic evidence for the formation of a substrate-induced biotin binding pocket in the carboxyltransferase domain of PC from Rhizobium etli. Structures of the carboxyltransferase domain reveal that R. etli PC occupies a symmetrical conformation in the absence of the biotin carboxylase domain and that the carboxyltransferase domain active site is conformationally rearranged upon pyruvate binding. This conformational change is stabilized by the interaction of the conserved residues Asp(590) and Tyr(628) and results in the formation of the biotin binding pocket. Site-directed mutations at these residues reduce the rate of biotin-dependent reactions but have no effect on the rate of biotin-independent oxaloacetate decarboxylation. Given the conservation with carboxyltransferase domains in oxaloacetate decarboxylase and transcarboxylase, the structure-based mechanism described for PC may be applicable to the larger family of biotin-dependent enzymes.

  18. Distinct pose of discodermolide in taxol binding pocket drives a complementary mode of microtubule stabilization.

    Science.gov (United States)

    Khrapunovich-Baine, Marina; Menon, Vilas; Verdier-Pinard, Pascal; Smith, Amos B; Angeletti, Ruth Hogue; Fiser, Andras; Horwitz, Susan Band; Xiao, Hui

    2009-12-15

    The microtubule cytoskeleton has proven to be an effective target for cancer therapeutics. One class of drugs, known as microtubule stabilizing agents (MSAs), binds to microtubule polymers and stabilizes them against depolymerization. The prototype of this group of drugs, Taxol, is an effective chemotherapeutic agent used extensively in the treatment of human ovarian, breast, and lung carcinomas. Although electron crystallography and photoaffinity labeling experiments determined that the binding site for Taxol is in a hydrophobic pocket in beta-tubulin, little was known about the effects of this drug on the conformation of the entire microtubule. A recent study from our laboratory utilizing hydrogen-deuterium exchange (HDX) in concert with various mass spectrometry (MS) techniques has provided new information on the structure of microtubules upon Taxol binding. In the current study we apply this technique to determine the binding mode and the conformational effects on chicken erythrocyte tubulin (CET) of another MSA, discodermolide, whose synthetic analogues may have potential use in the clinic. We confirmed that, like Taxol, discodermolide binds to the taxane binding pocket in beta-tubulin. However, as opposed to Taxol, which has major interactions with the M-loop, discodermolide orients itself away from this loop and toward the N-terminal H1-S2 loop. Additionally, discodermolide stabilizes microtubules mainly via its effects on interdimer contacts, specifically on the alpha-tubulin side, and to a lesser extent on interprotofilament contacts between adjacent beta-tubulin subunits. Also, our results indicate complementary stabilizing effects of Taxol and discodermolide on the microtubules, which may explain the synergy observed between the two drugs in vivo.

  19. Progress in antiandrogen design targeting hormone binding pocket to circumvent mutation based resistance

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    Xiaohong eTian

    2015-03-01

    Full Text Available Androgen receptor (AR plays a critical role in the development and progression of prostate cancer (PCa. Current clinically used antiandrogens such as flutamide, bicalutamide, and newly approved enzalutamide mainly target the hormone binding pocket (HBP of AR. However, over time, drug resistance invariably develops and switches these antiandrogens from antagonist to agonist of the AR. Accumulated evidence indicates that AR mutation is an important cause for the drug resistance. This review will give an overview of the mutation based resistance of the current clinically used antiandrogens and the rational drug design to overcome the resistance, provides a promising strategy for the development of the new generation of antiandrogens targeting HBP.

  20. Gates and binding pockets for nitric oxide with cytochrome c', according to molecular dynamics.

    Science.gov (United States)

    Pietra, Francesco

    2013-09-01

    Random-acceleration molecular-dynamics (RAMD) simulations with models of homodimeric 6-ligated distal-NO and 5-ligated proximal-NO cytochrome c' complexes, in TIP3 H2 O, showed two distinct, non-intercommunicating worlds. In the framework of a long cavity formed by four protein helices with heme at one extremity, NO was observed to follow different pathways with the two complexes to reach the solvent. With the 6-ligated complex, NO was observed to progress by exploiting protein internal channels created by thermal fluctuations, and be temporarily trapped into binding pockets before reaching the preferred gate at the heme end of the cavity. In contrast, with the 5-ligated complex, NO was observed to surface the solvent-exposed helix 7, up to a gate at the other extremity of the protein, only occasionally finding an earlier, direct way out toward the solvent. That only bulk NO gets involved in forming the 5-ligated proximal-NO complex is in agreement with previous experimental observations, while the occurrence of binding pockets suggests that also reservoir NO might play a role with the distal-NO complex.

  1. The same pocket in menin binds both MLL and JUND but has opposite effects on transcription

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Jing; Gurung, Buddha; Wan, Bingbing; Matkar, Smita; Veniaminova, Natalia A.; Wan, Ke; Merchant, Juanita L.; Hua, Xianxin; Lei, Ming (Michigan); (Michigan-Med); (UPENN-MED)

    2013-04-08

    Menin is a tumour suppressor protein whose loss or inactivation causes multiple endocrine neoplasia 1 (MEN1), a hereditary autosomal dominant tumour syndrome that is characterized by tumorigenesis in multiple endocrine organs. Menin interacts with many proteins and is involved in a variety of cellular processes. Menin binds the JUN family transcription factor JUND and inhibits its transcriptional activity. Several MEN1 missense mutations disrupt the menin-JUND interaction, suggesting a correlation between the tumour-suppressor function of menin and its suppression of JUND-activated transcription. Menin also interacts with mixed lineage leukaemia protein 1 (MLL1), a histone H3 lysine 4 methyltransferase, and functions as an oncogenic cofactor to upregulate gene transcription and promote MLL1-fusion-protein-induced leukaemogenesis. A recent report on the tethering of MLL1 to chromatin binding factor lens epithelium-derived growth factor (LEDGF) by menin indicates that menin is a molecular adaptor coordinating the functions of multiple proteins. Despite its importance, how menin interacts with many distinct partners and regulates their functions remains poorly understood. Here we present the crystal structures of human menin in its free form and in complexes with MLL1 or with JUND, or with an MLL1-LEDGF heterodimer. These structures show that menin contains a deep pocket that binds short peptides of MLL1 or JUND in the same manner, but that it can have opposite effects on transcription. The menin-JUND interaction blocks JUN N-terminal kinase (JNK)-mediated JUND phosphorylation and suppresses JUND-induced transcription. In contrast, menin promotes gene transcription by binding the transcription activator MLL1 through the peptide pocket while still interacting with the chromatin-anchoring protein LEDGF at a distinct surface formed by both menin and MLL1.

  2. Specificity of anion-binding in the substrate-pocket ofbacteriorhodopsin

    Energy Technology Data Exchange (ETDEWEB)

    Facciotti, Marc T.; Cheung, Vincent S.; Lunde, Christopher S.; Rouhani, Shahab; Baliga, Nitin S.; Glaeser, Robert M.

    2003-08-30

    The structure of the D85S mutant of bacteriorhodopsin with a nitrate anion bound in the Schiff-base binding site, and the structure of the anion-free protein have been obtained in the same crystal form. Together with the previously solved structures of this anion pump, in both the anion-free state and bromide-bound state, these new structures provide insight into how this mutant of bacteriorhodopsin is able to bind a variety of different anions in the same binding pocket. The structural analysis reveals that the main structural change that accommodates different anions is the repositioning of the polar side-chain of S85. On the basis of these x-ray crystal structures, the prediction is then made that the D85S/D212N double mutant might bind similar anions and do so over a broader pH range than does the single mutant. Experimental comparison of the dissociation constants, K{sub d}, for a variety of anions confirms this prediction and demonstrates, in addition, that the binding affinity is dramatically improved by the D212N substitution.

  3. Broadly neutralizing human antibody that recognizes the receptor-binding pocket of influenza virus hemagglutinin

    Energy Technology Data Exchange (ETDEWEB)

    Whittle, James R.R.; Zhang, Ruijun; Khurana, Surender; King, Lisa R.; Manischewitz, Jody; Golding, Hana; Dormitzer, Philip R.; Haynes, Barton F.; Walter, Emmanuel B.; Moody, M. Anthony; Kepler, Thomas B.; Liao, Hua-Xin; Harrison, Stephen C. (Harvard-Med); (Novartis); (US-FDA); (Duke)

    2011-09-20

    Seasonal antigenic drift of circulating influenza virus leads to a requirement for frequent changes in vaccine composition, because exposure or vaccination elicits human antibodies with limited cross-neutralization of drifted strains. We describe a human monoclonal antibody, CH65, obtained by isolating rearranged heavy- and light-chain genes from sorted single plasma cells, coming from a subject immunized with the 2007 trivalent influenza vaccine. The crystal structure of a complex of the hemagglutinin (HA) from H1N1 strain A/Solomon Islands/3/2006 with the Fab of CH65 shows that the tip of the CH65 heavy-chain complementarity determining region 3 (CDR3) inserts into the receptor binding pocket on HA1, mimicking in many respects the interaction of the physiological receptor, sialic acid. CH65 neutralizes infectivity of 30 out of 36 H1N1 strains tested. The resistant strains have a single-residue insertion near the rim of the sialic-acid pocket. We conclude that broad neutralization of influenza virus can be achieved by antibodies with contacts that mimic those of the receptor.

  4. Structural and functional insights into the HIV-1 maturation inhibitor binding pocket.

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    Kayoko Waki

    Full Text Available Processing of the Gag precursor protein by the viral protease during particle release triggers virion maturation, an essential step in the virus replication cycle. The first-in-class HIV-1 maturation inhibitor dimethylsuccinyl betulinic acid [PA-457 or bevirimat (BVM] blocks HIV-1 maturation by inhibiting the cleavage of the capsid-spacer peptide 1 (CA-SP1 intermediate to mature CA. A structurally distinct molecule, PF-46396, was recently reported to have a similar mode of action to that of BVM. Because of the structural dissimilarity between BVM and PF-46396, we hypothesized that the two compounds might interact differentially with the putative maturation inhibitor-binding pocket in Gag. To test this hypothesis, PF-46396 resistance was selected for in vitro. Resistance mutations were identified in three regions of Gag: around the CA-SP1 cleavage site where BVM resistance maps, at CA amino acid 201, and in the CA major homology region (MHR. The MHR mutants are profoundly PF-46396-dependent in Gag assembly and release and virus replication. The severe defect exhibited by the inhibitor-dependent MHR mutants in the absence of the compound is also corrected by a second-site compensatory change far downstream in SP1, suggesting structural and functional cross-talk between the HIV-1 CA MHR and SP1. When PF-46396 and BVM were both present in infected cells they exhibited mutually antagonistic behavior. Together, these results identify Gag residues that line the maturation inhibitor-binding pocket and suggest that BVM and PF-46396 interact differentially with this putative pocket. These findings provide novel insights into the structure-function relationship between the CA MHR and SP1, two domains of Gag that are critical to both assembly and maturation. The highly conserved nature of the MHR across all orthoretroviridae suggests that these findings will be broadly relevant to retroviral assembly. Finally, the results presented here provide a framework

  5. Divergence of Pumilio/fem-3 mRNA binding factor (PUF) protein specificity through variations in an RNA-binding pocket.

    Science.gov (United States)

    Qiu, Chen; Kershner, Aaron; Wang, Yeming; Holley, Cynthia P; Wilinski, Daniel; Keles, Sunduz; Kimble, Judith; Wickens, Marvin; Hall, Traci M Tanaka

    2012-02-24

    mRNA control networks depend on recognition of specific RNA sequences. Pumilio-fem-3 mRNA binding factor (PUF) RNA-binding proteins achieve that specificity through variations on a conserved scaffold. Saccharomyces cerevisiae Puf3p achieves specificity through an additional binding pocket for a cytosine base upstream of the core RNA recognition site. Here we demonstrate that this chemically simple adaptation is prevalent and contributes to the diversity of RNA specificities among PUF proteins. Bioinformatics analysis shows that mRNAs associated with Caenorhabditis elegans fem-3 mRNA binding factor (FBF)-2 in vivo contain an upstream cytosine required for biological regulation. Crystal structures of FBF-2 and C. elegans PUF-6 reveal binding pockets structurally similar to that of Puf3p, whereas sequence alignments predict a pocket in PUF-11. For Puf3p, FBF-2, PUF-6, and PUF-11, the upstream pockets and a cytosine are required for maximal binding to RNA, but the quantitative impact on binding affinity varies. Furthermore, the position of the upstream cytosine relative to the core PUF recognition site can differ, which in the case of FBF-2 originally masked the identification of this consensus sequence feature. Importantly, other PUF proteins lack the pocket and so do not discriminate upstream bases. A structure-based alignment reveals that these proteins lack key residues that would contact the cytosine, and in some instances, they also present amino acid side chains that interfere with binding. Loss of the pocket requires only substitution of one serine, as appears to have occurred during the evolution of certain fungal species.

  6. A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction

    Directory of Open Access Journals (Sweden)

    Zaslavskiy Mikhail

    2010-02-01

    Full Text Available Abstract Background Predicting which molecules can bind to a given binding site of a protein with known 3D structure is important to decipher the protein function, and useful in drug design. A classical assumption in structural biology is that proteins with similar 3D structures have related molecular functions, and therefore may bind similar ligands. However, proteins that do not display any overall sequence or structure similarity may also bind similar ligands if they contain similar binding sites. Quantitatively assessing the similarity between binding sites may therefore be useful to propose new ligands for a given pocket, based on those known for similar pockets. Results We propose a new method to quantify the similarity between binding pockets, and explore its relevance for ligand prediction. We represent each pocket by a cloud of atoms, and assess the similarity between two pockets by aligning their atoms in the 3D space and comparing the resulting configurations with a convolution kernel. Pocket alignment and comparison is possible even when the corresponding proteins share no sequence or overall structure similarities. In order to predict ligands for a given target pocket, we compare it to an ensemble of pockets with known ligands to identify the most similar pockets. We discuss two criteria to evaluate the performance of a binding pocket similarity measure in the context of ligand prediction, namely, area under ROC curve (AUC scores and classification based scores. We show that the latter is better suited to evaluate the methods with respect to ligand prediction, and demonstrate the relevance of our new binding site similarity compared to existing similarity measures. Conclusions This study demonstrates the relevance of the proposed method to identify ligands binding to known binding pockets. We also provide a new benchmark for future work in this field. The new method and the benchmark are available at http://cbio.ensmp.fr/paris/.

  7. Cytochrome c Can Form a Well-Defined Binding Pocket for Hydrocarbons.

    Science.gov (United States)

    McClelland, Levi J; Steele, Harmen B B; Whitby, Frank G; Mou, Tung-Chung; Holley, David; Ross, J B Alexander; Sprang, Stephen R; Bowler, Bruce E

    2016-12-28

    Cytochrome c can acquire peroxidase activity when it binds to cardiolipin in mitochondrial membranes. The resulting oxygenation of cardiolipin by cytochrome c provides an early signal for the onset of apoptosis. The structure of this enzyme-substrate complex is a matter of considerable debate. We present three structures at 1.7-2.0 Å resolution of a domain-swapped dimer of yeast iso-1-cytochrome c with the detergents, CYMAL-5, CYMAL-6, and ω-undecylenyl-β-d-maltopyranoside, bound in a channel that places the hydrocarbon moieties of these detergents next to the heme. The heme is poised for peroxidase activity with water bound in place of Met80, which serves as the axial heme ligand when cytochrome c functions as an electron carrier. The hydroxyl group of Tyr67 sits 3.6-4.0 Å from the nearest carbon of the detergents, positioned to act as a relay in radical abstraction during peroxidase activity. Docking studies with linoleic acid, the most common fatty acid component of cardiolipin, show that C11 of linoleic acid can sit adjacent to Tyr67 and the heme, consistent with the oxygenation pattern observed in lipidomics studies. The well-defined hydrocarbon binding pocket provides atomic resolution evidence for the extended lipid anchorage model for cytochrome c/cardiolipin binding. Dimer dissociation/association kinetics for yeast versus equine cytochrome c indicate that formation of mammalian cytochrome c dimers in vivo would require catalysis. However, the dimer structure shows that only a modest deformation of monomeric cytochrome c would suffice to form the hydrocarbon binding site occupied by these detergents.

  8. Evolutionary diversification of retinoic acid receptor ligand-binding pocket structure by molecular tinkering

    Science.gov (United States)

    Gutierrez-Mazariegos, Juliana; Nadendla, Eswar Kumar; Studer, Romain A.; Alvarez, Susana; de Lera, Angel R.; Kuraku, Shigehiro; Bourguet, William; Laudet, Vincent

    2016-01-01

    Whole genome duplications (WGDs) have been classically associated with the origin of evolutionary novelties and the so-called duplication–degeneration–complementation model describes the possible fates of genes after duplication. However, how sequence divergence effectively allows functional changes between gene duplicates is still unclear. In the vertebrate lineage, two rounds of WGDs took place, giving rise to paralogous gene copies observed for many gene families. For the retinoic acid receptors (RARs), for example, which are members of the nuclear hormone receptor (NR) superfamily, a unique ancestral gene has been duplicated resulting in three vertebrate paralogues: RARα, RARβ and RARγ. It has previously been shown that this single ancestral RAR was neofunctionalized to give rise to a larger substrate specificity range in the RARs of extant jawed vertebrates (also called gnathostomes). To understand RAR diversification, the members of the cyclostomes (lamprey and hagfish), jawless vertebrates representing the extant sister group of gnathostomes, provide an intermediate situation and thus allow the characterization of the evolutionary steps that shaped RAR ligand-binding properties following the WGDs. In this study, we assessed the ligand-binding specificity of cyclostome RARs and found that their ligand-binding pockets resemble those of gnathostome RARα and RARβ. In contrast, none of the cyclostome receptors studied showed any RARγ-like specificity. Together, our results suggest that cyclostome RARs cover only a portion of the specificity repertoire of the ancestral gnathostome RARs and indicate that the establishment of ligand-binding specificity was a stepwise event. This iterative process thus provides a rare example for the diversification of receptor–ligand interactions of NRs following WGDs. PMID:27069642

  9. Definition of the G protein-coupled receptor transmembrane bundle binding pocket and calculation of receptor similarities for drug design

    DEFF Research Database (Denmark)

    Gloriam, David Erik Immanuel; Foord, Steven M; Blaney, Frank E;

    2009-01-01

    Recent advances in structural biology for G-protein-coupled receptors (GPCRs) have provided new opportunities to improve the definition of the transmembrane binding pocket. Here a reference set of 44 residue positions accessible for ligand binding was defined through detailed analysis of all curr...... the pharmacology/selectivity profile of ligands at Family A GPCRs. This has wide applicability to GPCR drug design problems across many disease areas....

  10. Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles.

    Science.gov (United States)

    Grones, Peter; Chen, Xu; Simon, Sibu; Kaufmann, Walter A; De Rycke, Riet; Nodzyński, Tomasz; Zažímalová, Eva; Friml, Jiří

    2015-08-01

    The plant hormone auxin is a key regulator of plant growth and development. Auxin levels are sensed and interpreted by distinct receptor systems that activate a broad range of cellular responses. The Auxin-Binding Protein1 (ABP1) that has been identified based on its ability to bind auxin with high affinity is a prime candidate for the extracellular receptor responsible for mediating a range of auxin effects, in particular, the fast non-transcriptional ones. Contradictory genetic studies suggested prominent or no importance of ABP1 in many developmental processes. However, how crucial the role of auxin binding to ABP1 is for its functions has not been addressed. Here, we show that the auxin-binding pocket of ABP1 is essential for its gain-of-function cellular and developmental roles. In total, 16 different abp1 mutants were prepared that possessed substitutions in the metal core or in the hydrophobic amino acids of the auxin-binding pocket as well as neutral mutations. Their analysis revealed that an intact auxin-binding pocket is a prerequisite for ABP1 to activate downstream components of the ABP1 signalling pathway, such as Rho of Plants (ROPs) and to mediate the clathrin association with membranes for endocytosis regulation. In planta analyses demonstrated the importance of the auxin binding pocket for all known ABP1-mediated postembryonic developmental processes, including morphology of leaf epidermal cells, root growth and root meristem activity, and vascular tissue differentiation. Taken together, these findings suggest that auxin binding to ABP1 is central to its function, supporting the role of ABP1 as auxin receptor.

  11. Variations in the binding pocket of an inhibitor of the bacterial division protein FtsZ across genotypes and species.

    Directory of Open Access Journals (Sweden)

    Amanda Miguel

    2015-03-01

    Full Text Available The recent increase in antibiotic resistance in pathogenic bacteria calls for new approaches to drug-target selection and drug development. Targeting the mechanisms of action of proteins involved in bacterial cell division bypasses problems associated with increasingly ineffective variants of older antibiotics; to this end, the essential bacterial cytoskeletal protein FtsZ is a promising target. Recent work on its allosteric inhibitor, PC190723, revealed in vitro activity on Staphylococcus aureus FtsZ and in vivo antimicrobial activities. However, the mechanism of drug action and its effect on FtsZ in other bacterial species are unclear. Here, we examine the structural environment of the PC190723 binding pocket using PocketFEATURE, a statistical method that scores the similarity between pairs of small-molecule binding sites based on 3D structure information about the local microenvironment, and molecular dynamics (MD simulations. We observed that species and nucleotide-binding state have significant impacts on the structural properties of the binding site, with substantially disparate microenvironments for bacterial species not from the Staphylococcus genus. Based on PocketFEATURE analysis of MD simulations of S. aureus FtsZ bound to GTP or with mutations that are known to confer PC190723 resistance, we predict that PC190723 strongly prefers to bind Staphylococcus FtsZ in the nucleotide-bound state. Furthermore, MD simulations of an FtsZ dimer indicated that polymerization may enhance PC190723 binding. Taken together, our results demonstrate that a drug-binding pocket can vary significantly across species, genetic perturbations, and in different polymerization states, yielding important information for the further development of FtsZ inhibitors.

  12. Structures of BmrR-Drug Complexes Reveal a Rigid Multidrug Binding Pocket And Transcription Activation Through Tyrosine Expulsion

    Energy Technology Data Exchange (ETDEWEB)

    Newberry, K.J.; Huffman, J.L.; Miller, M.C.; Vazquez-Laslop, N.; Neyfakh, A.A.; Brennan, R.G.

    2009-05-22

    BmrR is a member of the MerR family and a multidrug binding transcription factor that up-regulates the expression of the bmr multidrug efflux transporter gene in response to myriad lipophilic cationic compounds. The structural mechanism by which BmrR binds these chemically and structurally different drugs and subsequently activates transcription is poorly understood. Here, we describe the crystal structures of BmrR bound to rhodamine 6G (R6G) or berberine (Ber) and cognate DNA. These structures reveal each drug stacks against multiple aromatic residues with their positive charges most proximal to the carboxylate group of Glu-253 and that, unlike other multidrug binding pockets, that of BmrR is rigid. Substitution of Glu-253 with either alanine (E253A) or glutamine (E253Q) results in unpredictable binding affinities for R6G, Ber, and tetraphenylphosphonium. Moreover, these drug binding studies reveal that the negative charge of Glu-253 is not important for high affinity binding to Ber and tetraphenylphosphonium but plays a more significant, but unpredictable, role in R6G binding. In vitro transcription data show that E253A and E253Q are constitutively active, and structures of the drug-free E253A-DNA and E253Q-DNA complexes support a transcription activation mechanism requiring the expulsion of Tyr-152 from the multidrug binding pocket. In sum, these data delineate the mechanism by which BmrR binds lipophilic, monovalent cationic compounds and suggest the importance of the redundant negative electrostatic nature of this rigid drug binding pocket that can be used to discriminate against molecules that are not substrates of the Bmr multidrug efflux pump.

  13. An induced pocket for the binding of potent fusion inhibitor CL-385319 with H5N1 influenza virus hemagglutinin.

    Directory of Open Access Journals (Sweden)

    Runming Li

    Full Text Available The influenza glycoprotein hemagglutinin (HA plays crucial roles in the early stage of virus infection, including receptor binding and membrane fusion. Therefore, HA is a potential target for developing anti-influenza drugs. Recently, we characterized a novel inhibitor of highly pathogenic H5N1 influenza virus, CL-385319, which specifically inhibits HA-mediated viral entry. Studies presented here identified the critical binding residues for CL-385319, which clustered in the stem region of the HA trimer by site-directed mutagenesis. Extensive computational simulations, including molecular docking, molecular dynamics simulations, molecular mechanics generalized Born surface area (MM_GBSA calculations, charge density and Laplacian calculations, have been carried out to uncover the detailed molecular mechanism that underlies the binding of CL-385319 to H5N1 influenza virus HA. It was found that the recognition and binding of CL-385319 to HA proceeds by a process of "induced fit" whereby the binding pocket is formed during their interaction. Occupation of this pocket by CL-385319 stabilizes the neutral pH structure of hemagglutinin, thus inhibiting the conformational rearrangements required for membrane fusion. This "induced fit" pocket may be a target for structure-based design of more potent influenza fusion inhibitors.

  14. Dynamics of the substrate binding pocket in the presence of an inhibitor covalently attached to a fungal lipase.

    Science.gov (United States)

    Peters, G H; Jensen, M O; Bywater, R P

    2001-08-01

    To gain insight into the mobility of the occupied ligand-binding pocket of the Rhizomucor miehei lipase we have conducted a rigorous molecular dynamics analysis. The covalently attached inhibitor, ethylhexylphosphonate, was employed as a mimic of the putative tetrahedral intermediate in the esterolytic reaction. Our results show that in this lipase, ligand recognition is influenced by the flexibility of the binding pocket, a feature that is common to many other enzymes. Several regions around the active site were found to move significantly to adapt to the inhibitor. These motions are correlated to the flexibility of the inhibitor. In particular, the hexyl chain of the inhibitor shows considerable mobility, and adjacent residues in the binding cleft accommodate to this flexibility. Pronounced fluctuations in the binding pocket induced by the flexibility of the inhibitor are observed in the hinge region F79-S82, the active site loop region W88-V95 and the protein regions P209-F215/H257-Y260. The flexibility in the regions F79-S82 and H257-Y260, where the shorter ethyl chain is located, indicates that additional space in this binding cleft region is available for accommodating a larger moiety. Fluctuations in the region W88-V95 and P209-F215 are due to the relatively short flexible hexyl carbon chain. This part of the binding pocket could be stiffened by the presence of a longer carbon chain. Though the inhibitor is covalently attached through the phosphonate moiety, interaction of the remainder of the molecule and the enzyme are determined by hydrophobic interactions, where the Van der Waals energies are approximately 25% lower than the electrostatic contributions.

  15. Flanking p10 contribution and sequence bias in matrix based epitope prediction: revisiting the assumption of independent binding pockets

    Directory of Open Access Journals (Sweden)

    Parry Christian S

    2008-10-01

    Full Text Available Abstract Background Eluted natural peptides from major histocompatibility molecules show patterns of conserved residues. Crystallographic structures show that the bound peptide in class II major histocompatibility complex adopts a near uniform polyproline II-like conformation. This way allele-specific favoured residues are able to anchor into pockets in the binding groove leaving other peptide side chains exposed for recognition by T cells. The anchor residues form a motif. This sequence pattern can be used to screen large sequences for potential epitopes. Quantitative matrices extend the motif idea to include the contribution of non-anchor peptide residues. This report examines two new matrices that extend the binding register to incorporate the polymorphic p10 pocket of human leukocyte antigen DR1. Their performance is quantified against experimental binding measurements and against the canonical nine-residue register matrix. Results One new matrix shows significant improvement over the base matrix; the other does not. The new matrices differ in the sequence of the peptide library. Conclusion One of the extended quantitative matrices showed significant improvement in prediction over the original nine residue matrix and over the other extended matrix. Proline in the sequence of the peptide library of the better performing matrix presumably stabilizes the peptide conformation through neighbour interactions. Such interactions may influence epitope prediction in this test of quantitative matrices. This calls into question the assumption of the independent contribution of individual binding pockets.

  16. Conformational Plasticity of the NNRTI-Binding Pocket in HIV-1 Reverse Transcriptase: A Fluorine Nuclear Magnetic Resonance Study.

    Science.gov (United States)

    Sharaf, Naima G; Ishima, Rieko; Gronenborn, Angela M

    2016-07-19

    HIV-1 reverse transcriptase (RT) is a major drug target in the treatment of HIV-1 infection. RT inhibitors currently in use include non-nucleoside, allosteric RT inhibitors (NNRTIs), which bind to a hydrophobic pocket, distinct from the enzyme's active site. We investigated RT-NNRTI interactions by solution (19)F nuclear magnetic resonance (NMR), using singly (19)F-labeled RT proteins. Comparison of (19)F chemical shifts of fluorinated RT and drug-resistant variants revealed that the fluorine resonance is a sensitive probe for identifying mutation-induced changes in the enzyme. Our data show that in the unliganded enzyme, the NNRTI-binding pocket is highly plastic and not locked into a single conformation. Upon inhibitor binding, the binding pocket becomes rigidified. In the inhibitor-bound state, the (19)F signal of RT is similar to that of drug-resistant mutant enzymes, distinct from what is observed for the free state. Our results demonstrate the power of (19)F NMR spectroscopy to characterize conformational properties using selectively (19)F-labeled protein.

  17. A phosphoserine/threonine-binding pocket in AGC kinases and PDK1 mediates activation by hydrophobic motif phosphorylation

    DEFF Research Database (Denmark)

    Frödin, Morten; Antal, Torben L; Dümmler, Bettina A;

    2002-01-01

    The growth factor-activated AGC protein kinases RSK, S6K, PKB, MSK and SGK are activated by serine/threonine phosphorylation in the activation loop and in the hydrophobic motif, C-terminal to the kinase domain. In some of these kinases, phosphorylation of the hydrophobic motif creates a specific...... docking site that recruits and activates PDK1, which then phosphorylates the activation loop. Here, we discover a pocket in the kinase domain of PDK1 that recognizes the phosphoserine/phosphothreonine in the hydrophobic motif by identifying two oppositely positioned arginine and lysine residues that bind...... the phosphate. Moreover, we demonstrate that RSK2, S6K1, PKBalpha, MSK1 and SGK1 contain a similar phosphate-binding pocket, which they use for intramolecular interaction with their own phosphorylated hydrophobic motif. Molecular modelling and experimental data provide evidence for a common activation mechanism...

  18. Tertiary structure of human alpha1-acid glycoprotein (orosomucoid). Straightforward fluorescence experiments revealing the presence of a binding pocket.

    Science.gov (United States)

    Albani, Jihad R

    2004-02-25

    Binding of hemin to alpha1-acid glycoprotein has been investigated. Hemin binds to the hydrophobic pocket of hemoproteins. The fluorescent probe 2-(p-toluidino)-6-naphthalenesulfonate (TNS) binds to a hydrophobic domain in alpha1-acid glycoprotein with a dissociation constant equal to 60 microM. Addition of hemin to an alpha1-acid glycoprotein-TNS complex induces the displacement of TNS from its binding site. At saturation (1 hemin for 1 protein) all the TNS has been displaced from its binding site. The dissociation constant of hemin-alpha1-acid glycoprotein was found equal to 2 microM. Thus, TNS and hemin bind to the same hydrophobic site: the pocket of alpha1-acid glycoprotein. Energy-transfer studies performed between the Trp residues of alpha1-acid glycoprotein and hemin indicated that efficiency (E) of Trp fluorescence quenching was equal to 80% and the Förster distance, R0 at which the efficiency of energy transfer is 50% was calculated to be 26 A, revealing a very high energy transfer.

  19. Phosphate-binding pocket in Dicer-2 PAZ domain for high-fidelity siRNA production.

    Science.gov (United States)

    Kandasamy, Suresh K; Fukunaga, Ryuya

    2016-12-06

    The enzyme Dicer produces small silencing RNAs such as micro-RNAs (miRNAs) and small interfering RNAs (siRNAs). In Drosophila, Dicer-1 produces ∼22-24-nt miRNAs from pre-miRNAs, whereas Dicer-2 makes 21-nt siRNAs from long double-stranded RNAs (dsRNAs). How Dicer-2 precisely makes 21-nt siRNAs with a remarkably high fidelity is unknown. Here we report that recognition of the 5'-monophosphate of a long dsRNA substrate by a phosphate-binding pocket in the Dicer-2 PAZ (Piwi, Argonaute, and Zwille/Pinhead) domain is crucial for the length fidelity, but not the efficiency, in 21-nt siRNA production. Loss of the length fidelity, meaning increased length heterogeneity of siRNAs, caused by point mutations in the phosphate-binding pocket of the Dicer-2 PAZ domain decreased RNA silencing activity in vivo, showing the importance of the high fidelity to make 21-nt siRNAs. We propose that the 5'-monophosphate of a long dsRNA substrate is anchored by the phosphate-binding pocket in the Dicer-2 PAZ domain and the distance between the pocket and the RNA cleavage active site in the RNaseIII domain corresponds to the 21-nt pitch in the A-form duplex of a long dsRNA substrate, resulting in high-fidelity 21-nt siRNA production. This study sheds light on the molecular mechanism by which Dicer-2 produces 21-nt siRNAs with a remarkably high fidelity for efficient RNA silencing.

  20. Mutations in FMN Binding Pocket Diminish Chromate Reduction Rates for Gh-ChrR Isolated from Gluconacetobacter hansenii

    Energy Technology Data Exchange (ETDEWEB)

    Khaleel, Janin A.; Gong, Chunhong; Zhang, Yanfeng; Tan, Ruimin; Squier, Thomas C.; Jin, Hongjun

    2013-06-01

    A putative chromate ion binding site was identified proximal to a rigidly bound FMN from electron densities in the crystal structure of the quinone reductase from Gluconacetobacter hansenii (Gh-ChrR) (3s2y.pdb). To clarify the location of the chromate binding site, and to understand the role of FMN in the NADPH-dependent reduction of chromate, we have expressed and purified four mutant enzymes involving the site-specific substitution of individual side chains within the FMN binding pocket that form non-covalent bonds with the ribityl phosphate (i.e., S15A and R17A in loop 1 between β1 sheet and α1 helix) or the isoalloxanzine ring (E83A or Y84A in loop 4 between the β3 sheet and α4 helix). Mutations that selectively disrupt hydrogen bonds between either the N3 nitrogen on the isoalloxanzine ring (i.e., E83) or the ribitylphos- phoate (i.e., S15) respectively result in 50% or 70% reductions in catalytic rates of chromate reduction. In comparison, mutations that disrupt π-π ring stacking interactions with the isoal-loxanzine ring (i.e., Y84) or a salt bridge with the ribityl phosphate result in 87% and 97% inhibittion. In all cases there are minimal alterations in chromate binding affinities. Collectively, these results support the hypothesis that chromate binds proximal to FMN, and implicate a structural role for FMN positioning for optimal chromate reduction rates. As side chains proximal to the β3/α4 FMN binding loop 4 contribute to both NADH and metal ion binding, we propose a model in which structural changes around the FMN binding pocket couples to both chromate and NADH binding sites.

  1. Structure and function of Plasmodium falciparum malate dehydrogenase: role of critical amino acids in co-substrate binding pocket.

    Science.gov (United States)

    Pradhan, Anupam; Tripathi, Abhai K; Desai, Prashant V; Mukherjee, Prasenjit K; Avery, Mitchell A; Walker, Larry A; Tekwani, Babu L

    2009-01-01

    The malaria parasite thrives on anaerobic fermentation of glucose for energy. Earlier studies from our laboratory have demonstrated that a cytosolic malate dehydrogenase (PfMDH) with striking similarity to lactate dehydrogenase (PfLDH) might complement PfLDH function in Plasmodium falciparum. The N-terminal glycine motif, which forms a characteristic Rossman dinucleotide-binding fold in the co-substrate binding pocket, differentiates PfMDH (GlyXGlyXXGly) from other eukaryotic and prokaryotic malate dehydrogenases (GlyXXGlyXXGly). The amino acids lining the co-substrate binding pocket are completely conserved in MDHs from different species of human, primate and rodent malaria parasites. Based on this knowledge and conserved domains among prokaryotic and eukaryotic MDH, the role of critical amino acids lining the co-substrate binding pocket was analyzed in catalytic functions of PfMDH using site-directed mutagenesis. Insertion of Ala at the 9th or 10th position, which converts the N-terminal GlyXGlyXXGly motif (characteristic of malarial MDH and LDH) to GlyXXGlyXXGly (as in bacterial and eukaryotic MDH), uncoupled regulation of the enzyme through substrate inhibition. The dinucleotide fold GlyXGlyXXGly motif seems not to be responsible for the distinct affinity of PfMDH to 3-acetylpyridine-adenine dinucleotide (APAD, a synthetic analog of NAD), since Ala9 and Ala10 insertion mutants still utilized APADH. The Gln11Met mutation, which converts the signature glycine motif in PfMDH to that of PfLDH, did not change the enzyme function. However, the Gln11Gly mutant showed approximately a 5-fold increase in catalytic activity, and higher susceptibility to inhibition with gossypol. Asn119 and His174 participate in binding of both co-substrate and substrate. The Asn119Gly mutant exhibited approximately a 3-fold decrease in catalytic efficiency, while mutation of His174 to Asn or Ala resulted in an inactive enzyme. These studies provide critical insights into the co

  2. The structure of the SBP-Tag–streptavidin complex reveals a novel helical scaffold bridging binding pockets on separate subunits

    Energy Technology Data Exchange (ETDEWEB)

    Barrette-Ng, Isabelle H.; Wu, Sau-Ching; Tjia, Wai-Mui; Wong, Sui-Lam; Ng, Kenneth K. S., E-mail: ngk@ucalgary.ca [University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4 (Canada)

    2013-05-01

    The structure of the SBP-Tag–streptavidin complex reveals a novel mode of peptide recognition in which a single peptide binds simultaneously to biotin-binding pockets from adjacent subunits of streptavidin. The molecular details of peptide recognition suggest how the SBP-Tag can be further modified to become an even more useful tag for a wider range of biotechnological applications. The 38-residue SBP-Tag binds to streptavidin more tightly (K{sub d} ≃ 2.5–4.9 nM) than most if not all other known peptide sequences. Crystallographic analysis at 1.75 Å resolution shows that the SBP-Tag binds to streptavidin in an unprecedented manner by simultaneously interacting with biotin-binding pockets from two separate subunits. An N-terminal HVV peptide sequence (residues 12–14) and a C-terminal HPQ sequence (residues 31–33) form the bulk of the direct interactions between the SBP-Tag and the two biotin-binding pockets. Surprisingly, most of the peptide spanning these two sites (residues 17–28) adopts a regular α-helical structure that projects three leucine side chains into a groove formed at the interface between two streptavidin protomers. The crystal structure shows that residues 1–10 and 35–38 of the original SBP-Tag identified through in vitro selection and deletion analysis do not appear to contact streptavidin and thus may not be important for binding. A 25-residue peptide comprising residues 11–34 (SBP-Tag2) was synthesized and shown using surface plasmon resonance to bind streptavidin with very similar affinity and kinetics when compared with the SBP-Tag. The SBP-Tag2 was also added to the C-terminus of β-lactamase and was shown to be just as effective as the full-length SBP-Tag in affinity purification. These results validate the molecular structure of the SBP-Tag–streptavidin complex and establish a minimal bivalent streptavidin-binding tag from which further rational design and optimization can proceed.

  3. Allosteric Regulation of Serine Protease HtrA2 through Novel Non-Canonical Substrate Binding Pocket

    Science.gov (United States)

    Singh, Nitu; Gadewal, Nikhil; Chaganti, Lalith K.; Sastry, G. Madhavi; Bose, Kakoli

    2013-01-01

    HtrA2, a trimeric proapoptotic serine protease is involved in several diseases including cancer and neurodegenerative disorders. Its unique ability to mediate apoptosis via multiple pathways makes it an important therapeutic target. In HtrA2, C-terminal PDZ domain upon substrate binding regulates its functions through coordinated conformational changes the mechanism of which is yet to be elucidated. Although allostery has been found in some of its homologs, it has not been characterized in HtrA2 so far. Here, with an in silico and biochemical approach we have shown that allostery does regulate HtrA2 activity. Our studies identified a novel non-canonical selective binding pocket in HtrA2 which initiates signal propagation to the distal active site through a complex allosteric mechanism. This non-classical binding pocket is unique among HtrA family proteins and thus unfolds a novel mechanism of regulation of HtrA2 activity and hence apoptosis. PMID:23457469

  4. Allosteric regulation of serine protease HtrA2 through novel non-canonical substrate binding pocket.

    Directory of Open Access Journals (Sweden)

    Pruthvi Raj Bejugam

    Full Text Available HtrA2, a trimeric proapoptotic serine protease is involved in several diseases including cancer and neurodegenerative disorders. Its unique ability to mediate apoptosis via multiple pathways makes it an important therapeutic target. In HtrA2, C-terminal PDZ domain upon substrate binding regulates its functions through coordinated conformational changes the mechanism of which is yet to be elucidated. Although allostery has been found in some of its homologs, it has not been characterized in HtrA2 so far. Here, with an in silico and biochemical approach we have shown that allostery does regulate HtrA2 activity. Our studies identified a novel non-canonical selective binding pocket in HtrA2 which initiates signal propagation to the distal active site through a complex allosteric mechanism. This non-classical binding pocket is unique among HtrA family proteins and thus unfolds a novel mechanism of regulation of HtrA2 activity and hence apoptosis.

  5. Computational fragment-based drug design to explore the hydrophobic sub-pocket of the mitotic kinesin Eg5 allosteric binding site

    Science.gov (United States)

    Oguievetskaia, Ksenia; Martin-Chanas, Laetitia; Vorotyntsev, Artem; Doppelt-Azeroual, Olivia; Brotel, Xavier; Adcock, Stewart A.; de Brevern, Alexandre G.; Delfaud, Francois; Moriaud, Fabrice

    2009-08-01

    Eg5, a mitotic kinesin exclusively involved in the formation and function of the mitotic spindle has attracted interest as an anticancer drug target. Eg5 is co-crystallized with several inhibitors bound to its allosteric binding pocket. Each of these occupies a pocket formed by loop 5/helix α2 (L5/α2). Recently designed inhibitors additionally occupy a hydrophobic pocket of this site. The goal of the present study was to explore this hydrophobic pocket with our MED-SuMo fragment-based protocol, and thus discover novel chemical structures that might bind as inhibitors. The MED-SuMo software is able to compare and superimpose similar interaction surfaces upon the whole protein data bank (PDB). In a fragment-based protocol, MED-SuMo retrieves MED-Portions that encode protein-fragment binding sites and are derived from cross-mining protein-ligand structures with libraries of small molecules. Furthermore we have excluded intra-family MED-Portions derived from Eg5 ligands that occupy the hydrophobic pocket and predicted new potential ligands by hybridization that would fill simultaneously both pockets. Some of the latter having original scaffolds and substituents in the hydrophobic pocket are identified in libraries of synthetically accessible molecules by the MED-Search software.

  6. c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets.

    Science.gov (United States)

    Ren, Aiming; Patel, Dinshaw J

    2014-09-01

    The ydaO riboswitch, involved in sporulation, osmotic stress responses and cell wall metabolism, targets the second messenger cyclic-di-AMP with subnanomolar affinity. We have solved the structure of c-di-AMP bound to the Thermoanaerobacter tengcongensis ydaO riboswitch, thereby identifying a five-helical scaffold containing a zippered-up bubble, a pseudoknot and long-range tertiary base pairs. Highlights include the identification of two c-di-AMP binding pockets on the same face of the riboswitch, related by pseudo-two-fold symmetry, with potential for cross-talk between sites mediated by adjacently positioned base-stacking alignments connecting pockets. The adenine rings of bound c-di-AMP molecules are wedged between bases and stabilized by stacking, base-sugar and sugar-sugar intermolecular hydrogen bonding interactions. The structural studies are complemented by isothermal titration calorimetry-based binding studies of mutants mediating key tertiary intermolecular contacts. The T. tengcongensis ydaO riboswitch, like its Bacillus subtilis counterpart, most likely functions through a transcription termination mechanism, with the c-di-AMP bound state representing an 'off' switch.

  7. Titration kinetics of Asp-85 in bacteriorhodopsin: exclusion of the retinal pocket as the color-controlling cation binding site.

    Science.gov (United States)

    Fu, X; Bressler, S; Ottolenghi, M; Eliash, T; Friedman, N; Sheves, M

    1997-10-20

    The spectrum (the purple blue transition) and function of the light-driven proton pump bacteriorhodopsin are determined by the state of protonation of the Asp-85 residue located in the vicinity of the retinal chromophore. The titration of Asp-85 is controlled by the binding/unbinding of one or two divalent metal cations (Ca2+ or Mg2+). The location of such metal binding site(s) is approached by studying the kinetics of the cation-induced titration of Asp-85 using metal ions and large molecular cations, such as quaternary ammonium ions, R4N+ (R = Et, Pr, a divalent 'bolaform ion' [Et3N+-(CH2)4-N+Et3] and the 1:3 molecular complex formed between Fe2+ and 1,10-phenanthroline (OP). The basic multi-component kinetic features of the titration, extending from 10(-2) to 10(4) s, are unaffected by the charge and size of the cation. This indicates that cation binding to bR triggers the blue --> purple titration in a fast step, which is not rate-determining. In view of the size of the cations involved, these observations indicate that the cation binding site is in an exposed location on, or close to, the membrane surface. This excludes previous models, which placed the color-controlling Ca2+ ion in the retinal binding pocket.

  8. Probing the ATP-Binding Pocket of Protein Kinase DYRK1A with Benzothiazole Fragment Molecules.

    Science.gov (United States)

    Rothweiler, Ulli; Stensen, Wenche; Brandsdal, Bjørn Olav; Isaksson, Johan; Leeson, Frederick Alan; Engh, Richard Alan; Svendsen, John S Mjøen

    2016-11-10

    DYRK1A has emerged as a potential target for therapies of Alzheimer's disease using small molecules. On the basis of the observation of selective DYRK1A inhibition by firefly d-luciferin, we have explored static and dynamic structural properties of fragment sized variants of the benzothiazole scaffold with respect to DYRK1A using X-ray crystallography and NMR techniques. The compounds have excellent ligand efficiencies and show a remarkable diversity of binding modes in dynamic equilibrium. Binding geometries are determined in part by interactions often considered "weak", including "orthogonal multipolar" types represented by, for example, F-CO, sulfur-aromatic, and halogen-aromatic interactions, together with hydrogen bonds that are modulated by variation of electron withdrawing groups. These studies show how the benzothiazole scaffold is highly promising for the development of therapeutic DYRK1A inhibitors. In addition, the subtleties of the binding interactions, including dynamics, show how full structural studies are required to fully interpret the essential physical determinants of binding.

  9. Ancestral reconstruction of the ligand-binding pocket of Family C G protein-coupled receptors

    OpenAIRE

    Kuang, Donghui; Yao, Yi; MacLean, David; Wang, Minghua; Hampson, David R.; Chang, Belinda S. W.

    2006-01-01

    The metabotropic glutamate receptors (mGluRs) within the Family C subclass of G protein-coupled receptors are crucial modulators of synaptic transmission. However, their closest relatives include a diverse group of sensory receptors whose biological functions are not associated with neurotransmission, raising the question of the evolutionary origin of amino acid-binding Family C receptors. A common feature of most, if not all, functional Family C receptors is the presence of an amino acid-bin...

  10. N,C-Capped dipeptides with selectivity for mycobacterial proteasome over human proteasomes: role of S3 and S1 binding pockets.

    Science.gov (United States)

    Lin, Gang; Chidawanyika, Tamutenda; Tsu, Christopher; Warrier, Thulasi; Vaubourgeix, Julien; Blackburn, Christopher; Gigstad, Kenneth; Sintchak, Michael; Dick, Lawrence; Nathan, Carl

    2013-07-10

    We identified N,C-capped dipeptides that are selective for the Mycobacterium tuberculosis proteasome over human constitutive and immunoproteasomes. Differences in the S3 and S1 binding pockets appeared to account for the species selectivity. The inhibitors can penetrate mycobacteria and kill nonreplicating M. tuberculosis under nitrosative stress.

  11. Structure-Based Design of a Novel SMYD3 Inhibitor that Bridges the SAM-and MEKK2-Binding Pockets.

    Science.gov (United States)

    Van Aller, Glenn S; Graves, Alan P; Elkins, Patricia A; Bonnette, William G; McDevitt, Patrick J; Zappacosta, Francesca; Annan, Roland S; Dean, Tony W; Su, Dai-Shi; Carpenter, Christopher L; Mohammad, Helai P; Kruger, Ryan G

    2016-05-03

    SMYD3 is a lysine methyltransferase overexpressed in colorectal, breast, prostate, and hepatocellular tumors, and has been implicated as an oncogene in human malignancies. Methylation of MEKK2 by SMYD3 is important for regulation of the MEK/ERK pathway, suggesting the possibility of selectively targeting SMYD3 in RAS-driven cancers. Structural and kinetic characterization of SMYD3 was undertaken leading to a co-crystal structure of SMYD3 with a MEKK2-peptide substrate bound, and the observation that SMYD3 follows a partially processive mechanism. These insights allowed for the design of GSK2807, a potent and selective, SAM-competitive inhibitor of SMYD3 (Ki = 14 nM). A high-resolution crystal structure reveals that GSK2807 bridges the gap between the SAM-binding pocket and the substrate lysine tunnel of SMYD3. Taken together, our data demonstrate that small-molecule inhibitors of SMYD3 can be designed to prevent methylation of MEKK2 and these could have potential use as anticancer therapeutics.

  12. Study on the Gas Phase Stability of Heme-binding Pocket in Cytochrome Tb5 and Its Mutants by Electrospray Mass Spectrometry

    Institute of Scientific and Technical Information of China (English)

    YU,Chong-Tian(余翀天); GUO,Yin-Long(郭寅龙); L(U),Long(吕龙); WANG,Yun-Hua(王韵华); YAO,Ping(姚萍); HUANG,Zhong-Xian(黄仲贤)

    2002-01-01

    To ehucidate the effect of various amino acid residues on the heme-binding pocket in cytochrome Tbs, several residues were chosen for replacement by means of site-directed mutagenesis.Comparison of the mass spectrmn between the F35Y mutant and the wild type shows that the relative abundance of holoprotein ion of F35Y is lower than that of the wild type in gas phase. It is concluded that mutation from Phe35 residue to tyrosine decreases the hydrophobic character of cytochrome Tbs heme pocket, which decreases the stability of heme-binding pocket. ESI-MS spectra of the mutants V61E, V61K, V61H and V61Y show various contribution of amino acid to the stability of heme-binding pocket. The small and non-polar residue Vat61 was replaced with large or polar residues, resulting in enhancing the trend of heme leaving from the pocket. In addition, comparison of the mass relative abundance of bolo-proteins among all the Va161-mutants, shows that their stability in gas phase appropriately submit the following order: wild type > V61H > V61E > V61K ≈ V61Y. The extra great stability of quadruple sites mutant E44/48/56A/D60A shows that reduction of electrostatic or hydrogen bond interactions among the residues locating in the outside region of the heme edge remarkably affect the stability of heme. The results of analyzing the oxidation states of heme iron in Tbs and its mutants by insource-CAD experiment suggest that the charge states of heme iron maintain inflexible in mutation process.

  13. NMR-Based Milk Metabolomics

    Directory of Open Access Journals (Sweden)

    Hanne C. Bertram

    2013-04-01

    Full Text Available Milk is a key component in infant nutrition worldwide and, in the Western parts of the world, also in adult nutrition. Milk of bovine origin is both consumed fresh and processed into a variety of dairy products including cheese, fermented milk products, and infant formula. The nutritional quality and processing capabilities of bovine milk is closely associated to milk composition. Metabolomics is ideal in the study of the low-molecular-weight compounds in milk, and this review focuses on the recent nuclear magnetic resonance (NMR-based metabolomics trends in milk research, including applications linking the milk metabolite profiling with nutritional aspects, and applications which aim to link the milk metabolite profile to various technological qualities of milk. The metabolite profiling studies encompass the identification of novel metabolites, which potentially can be used as biomarkers or as bioactive compounds. Furthermore, metabolomics applications elucidating how the differential regulated genes affects milk composition are also reported. This review will highlight the recent advances in NMR-based metabolomics on milk, as well as give a brief summary of when NMR spectroscopy can be useful for gaining a better understanding of how milk composition is linked to nutritional or quality traits.

  14. Pocket Money

    Institute of Scientific and Technical Information of China (English)

    刘杰莹; 赵惠; 李世芹; 袁琳

    2007-01-01

    Do you get any poch’et money from your parents? What do you do with it?刘杰莹Pocket Money (1st Floor) I get some pocket money from Mom every day.But I never spend it casually.Except the money for breakfast,

  15. NMR-based milk metabolomics

    DEFF Research Database (Denmark)

    Sundekilde, Ulrik; Larsen, Lotte Bach; Bertram, Hanne Christine S.

    2013-01-01

    Milk is a key component in infant nutrition worldwide and, in the Western parts of the world, also in adult nutrition. Milk of bovine origin is both consumed fresh and processed into a variety of dairy products including cheese, fermented milk products, and infant formula. The nutritional quality...... and processing capabilities of bovine milk is closely associated to milk composition. Metabolomics is ideal in the study of the low-molecular-weight compounds in milk, and this review focuses on the recent nuclear magnetic resonance (NMR)-based metabolomics trends in milk research, including applications linking...... the milk metabolite profiling with nutritional aspects, and applications which aim to link the milk metabolite profile to various technological qualities of milk. The metabolite profiling studies encompass the identification of novel metabolites, which potentially can be used as biomarkers or as bioactive...

  16. CORCEMA refinement of the bound ligand conformation within the protein binding pocket in reversibly forming weak complexes using STD-NMR intensities

    Science.gov (United States)

    Jayalakshmi, V.; Rama Krishna, N.

    2004-05-01

    We describe an intensity-restrained optimization procedure for refining approximate structures of ligands within the protein binding pockets using STD-NMR intensity data on reversibly forming weak complexes. In this approach, the global minimum for the bound-ligand conformation is obtained by a hybrid structure refinement method involving CORCEMA calculation of intensities and simulated annealing optimization of torsion angles of the bound ligand using STD-NMR intensities as experimental constraints and the NOE R-factor as the pseudo-energy function to be minimized. This method is illustrated using simulated STD data sets for typical carbohydrate and peptide ligands. Our procedure also allows for the optimization of side chain torsion angles of protein residues within the binding pocket. This procedure is useful in refining and improving initial models based on crystallography or computer docking or other algorithms to generate models for the bound ligand (e.g., a lead compound) within the protein binding pocket compatible with solution STD-NMR data. This method may facilitate structure-based drug design efforts.

  17. Switch control pocket inhibitors of p38-MAP kinase. Durable type II inhibitors that do not require binding into the canonical ATP hinge region

    Energy Technology Data Exchange (ETDEWEB)

    Ahn, Yu Mi; Clare, Michael; Ensinger, Carol L.; Hood, Molly M.; Lord, John W.; Lu, Wei-Ping; Miller, David F.; Patt, William C.; Smith, Bryan D.; Vogeti, Lakshminarayana; Kaufman, Michael D.; Petillo, Peter A.; Wise, Scott C.; Abendroth, Jan; Chun, Lawrence; Clark, Robin; Feese, Michael; Kim, Hidong; Stewart, Lance; Flynn, Daniel L. (Deciphera); (Emerald); (Cocrystal)

    2012-01-20

    Switch control pocket inhibitors of p38-alpha kinase are described. Durable type II inhibitors were designed which bind to arginines (Arg67 or Arg70) that function as key residues for mediating phospho-threonine 180 dependant conformational fluxing of p38-alpha from an inactive type II state to an active type I state. Binding to Arg70 in particular led to potent inhibitors, exemplified by DP-802, which also exhibited high kinase selectivity. Binding to Arg70 obviated the requirement for binding into the ATP Hinge region. X-ray crystallography revealed that DP-802 and analogs induce an enhanced type II conformation upon binding to either the unphosphorylated or the doubly phosphorylated form of p38-alpha kinase.

  18. Switch control pocket inhibitors of p38-MAP kinase. Durable type II inhibitors that do not require binding into the canonical ATP hinge region.

    Science.gov (United States)

    Ahn, Yu Mi; Clare, Michael; Ensinger, Carol L; Hood, Molly M; Lord, John W; Lu, Wei-Ping; Miller, David F; Patt, William C; Smith, Bryan D; Vogeti, Lakshminarayana; Kaufman, Michael D; Petillo, Peter A; Wise, Scott C; Abendroth, Jan; Chun, Lawrence; Clark, Robin; Feese, Michael; Kim, Hidong; Stewart, Lance; Flynn, Daniel L

    2010-10-01

    Switch control pocket inhibitors of p38-alpha kinase are described. Durable type II inhibitors were designed which bind to arginines (Arg67 or Arg70) that function as key residues for mediating phospho-threonine 180 dependant conformational fluxing of p38-alpha from an inactive type II state to an active type I state. Binding to Arg70 in particular led to potent inhibitors, exemplified by DP-802, which also exhibited high kinase selectivity. Binding to Arg70 obviated the requirement for binding into the ATP Hinge region. X-ray crystallography revealed that DP-802 and analogs induce an enhanced type II conformation upon binding to either the unphosphorylated or the doubly phosphorylated form of p38-alpha kinase.

  19. Comparative study of the binding pockets of mammalian proprotein convertases and its implications for the design of specific small molecule inhibitors

    Directory of Open Access Journals (Sweden)

    Sun Tian, Wu Jianhua

    2010-01-01

    Full Text Available Proprotein convertases are enzymes that proteolytically cleave protein precursors in the secretory pathway to yield functional proteins. Seven mammalian subtilisin/Kex2p-like proprotein convertases have been identified: furin, PC1, PC2, PC4, PACE4, PC5 and PC7. The binding pockets of all seven proprotein convertases are evolutionarily conserved and highly similar. Among the seven proprotein convertases, the furin cleavage site motif has recently been characterized as a 20-residue motif that includes one core region P6-P2´ inside the furin binding pocket. This study extended this information by examining the 3D structural environment of the furin binding pocket surrounding the core region P6-P2´ of furin substrates. The physical properties of mutations in the binding pockets of the other six mammalian proprotein convertases were compared. The results suggest that: 1 mutations at two positions, Glu230 and Glu257, change the overall density of the negative charge of the binding pockets, and govern the substrate specificities of mammalian proprotein convertases; 2 two proprotein convertases (PC1 and PC2 may have reduced sensitivity for positively charged residues at substrate position P5 or P6, whereas the substrate specificities of three proprotein convertases (furin, PACE4, and PC5 are similar to each other. This finding led to a novel design of a short peptide pattern for small molecule inhibitors: [K/R]-X-V-X-K-R. Compared with the widely used small molecule dec-RVKR-cmk that inhibits all seven proprotein convertases, a finely-tuned derivative of the short peptide pattern [K/R]-X-V-X-K-R may have the potential to more effectively inhibit five of the proprotein convertases (furin, PC4, PACE4, PC5 and PC7 compared to the remaining two (PC1 and PC2. The results not only provide insights into the molecular evolution of enzyme function in the proprotein convertase family, but will also aid the study of the functional redundancy of proprotein

  20. Modulation of ligand-heme reactivity by binding pocket residues demonstrated in cytochrome c' over the femtosecond-second temporal range.

    Science.gov (United States)

    Russell, Henry J; Hardman, Samantha J O; Heyes, Derren J; Hough, Michael A; Greetham, Gregory M; Towrie, Michael; Hay, Sam; Scrutton, Nigel S

    2013-12-01

    The ability of hemoproteins to discriminate between diatomic molecules, and the subsequent affinity for their chosen ligand, is fundamental to the existence of life. These processes are often controlled by precise structural arrangements in proteins, with heme pocket residues driving reactivity and specificity. One such protein is cytochrome c', which has the ability to bind nitric oxide (NO) and carbon monoxide (CO) on opposite faces of the heme, a property that is shared with soluble guanylate cycle. Like soluble guanylate cyclase, cytochrome c' also excludes O2 completely from the binding pocket. Previous studies have shown that the NO binding mechanism is regulated by a proximal arginine residue (R124) and a distal leucine residue (L16). Here, we have investigated the roles of these residues in maintaining the affinity for NO in the heme binding environment by using various time-resolved spectroscopy techniques that span the entire femtosecond-second temporal range in the UV-vis spectrum, and the femtosecond-nanosecond range by IR spectroscopy. Our findings indicate that the tightly regulated NO rebinding events following excitation in wild-type cytochrome c' are affected in the R124A variant. In the R124A variant, vibrational and electronic changes extend continuously across all time scales (from fs-s), in contrast to wild-type cytochrome c' and the L16A variant. Based on these findings, we propose a NO (re)binding mechanism for the R124A variant of cytochrome c' that is distinct from that in wild-type cytochrome c'. In the wider context, these findings emphasize the importance of heme pocket architecture in maintaining the reactivity of hemoproteins towards their chosen ligand, and demonstrate the power of spectroscopic probes spanning a wide temporal range.

  1. Pocket Bikes

    Institute of Scientific and Technical Information of China (English)

    Terry Mccarthy; 陈青

    2004-01-01

    @@ The next big thing out of California is 18 in. High, weighs about 50 lbs. And is capable of traveling up to 70 m. P. H. Meet the pocket bike, a scaled-down①motorcycle that is selling faster than low-carb hot cakes across the Golden State②-and causing nightmares③ for traffic police.

  2. A covalent adduct of MbtN, an acyl-ACP dehydrogenase from Mycobacterium tuberculosis, reveals an unusual acyl-binding pocket.

    Science.gov (United States)

    Chai, Ai-Fen; Bulloch, Esther M M; Evans, Genevieve L; Lott, J Shaun; Baker, Edward N; Johnston, Jodie M

    2015-04-01

    Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis. Access to iron in host macrophages depends on iron-chelating siderophores called mycobactins and is strongly correlated with Mtb virulence. Here, the crystal structure of an Mtb enzyme involved in mycobactin biosynthesis, MbtN, in complex with its FAD cofactor is presented at 2.30 Å resolution. The polypeptide fold of MbtN conforms to that of the acyl-CoA dehydrogenase (ACAD) family, consistent with its predicted role of introducing a double bond into the acyl chain of mycobactin. Structural comparisons and the presence of an acyl carrier protein, MbtL, in the same gene locus suggest that MbtN acts on an acyl-(acyl carrier protein) rather than an acyl-CoA. A notable feature of the crystal structure is the tubular density projecting from N(5) of FAD. This was interpreted as a covalently bound polyethylene glycol (PEG) fragment and resides in a hydrophobic pocket where the substrate acyl group is likely to bind. The pocket could accommodate an acyl chain of 14-21 C atoms, consistent with the expected length of the mycobactin acyl chain. Supporting this, steady-state kinetics show that MbtN has ACAD activity, preferring acyl chains of at least 16 C atoms. The acyl-binding pocket adopts a different orientation (relative to the FAD) to other structurally characterized ACADs. This difference may be correlated with the apparent ability of MbtN to catalyse the formation of an unusual cis double bond in the mycobactin acyl chain.

  3. Pathogenicity of the BRCA1 Missense Variant M1775K is Determined by the Disruption of the BRCT Phosphopeptide-Binding Pocket: a Multi-Modal Approach

    Energy Technology Data Exchange (ETDEWEB)

    Tischkowitz,M.; Hamel, N.; Carvalho, M.; Birrane, G.; Soni, A.; van Beers, E.; Joosse, S.; Wong, N.; Novak, D.; et al

    2008-01-01

    A number of germ-line mutations in the BRCA1 gene confer susceptibility to breast and ovarian cancer. However, it remains difficult to determine whether many single amino-acid (missense) changes in the BRCA1 protein that are frequently detected in the clinical setting are pathologic or not. Here, we used a combination of functional, crystallographic, biophysical, molecular and evolutionary techniques, and classical genetic segregation analysis to demonstrate that the BRCA1 missense variant M1775K is pathogenic. Functional assays in yeast and mammalian cells showed that the BRCA1 BRCT domains carrying the amino-acid change M1775K displayed markedly reduced transcriptional activity, indicating that this variant represents a deleterious mutation. Importantly, the M1775K mutation disrupted the phosphopeptide-binding pocket of the BRCA1 BRCT domains, thereby inhibiting the BRCA1 interaction with the proteins BRIP1 and CtIP, which are involved in DNA damage-induced checkpoint control. These results indicate that the integrity of the BRCT phosphopeptide-binding pocket is critical for the tumor suppression function of BRCA1. Moreover, this study demonstrates that multiple lines of evidence obtained from a combination of functional, structural, molecular and evolutionary techniques, and classical genetic segregation analysis are required to confirm the pathogenicity of rare variants of disease-susceptibility genes and obtain important insights into the underlying pathogenetic mechanisms.

  4. The distal pocket histidine residue in horse heart myoglobin directs the O-binding mode of nitrite to the heme iron.

    Science.gov (United States)

    Yi, Jun; Heinecke, Julie; Tan, Hui; Ford, Peter C; Richter-Addo, George B

    2009-12-23

    It is now well-established that mammalian heme proteins are reactive with various nitrogen oxide species and that these reactions may play significant roles in mammalian physiology. For example, the ferrous heme protein myoglobin (Mb) has been shown to reduce nitrite (NO(2)(-)) to nitric oxide (NO) under hypoxic conditions. We demonstrate here that the distal pocket histidine residue (His64) of horse heart metMb(III) (i.e., ferric Mb(III)) has marked effects on the mode of nitrite ion coordination to the iron center. X-ray crystal structures were determined for the mutant proteins metMb(III) H64V (2.0 A resolution) and its nitrite ion adduct metMb(III) H64V-nitrite (1.95 A resolution), and metMb(III) H64V/V67R (1.9 A resolution) and its nitrite ion adduct metMb(III) H64V/V67R-nitrite (2.0 A resolution). These are compared to the known structures of wild-type (wt) hh metMb(III) and its nitrite ion adduct hh metMb(III)-nitrite, which binds NO(2)(-) via an O-atom in a trans-FeONO configuration. Unlike wt metMb(III), no axial H(2)O is evident in either of the metMb(III) mutant structures. In the ferric H64V-nitrite structure, replacement of the distal His residue with Val alters the binding mode of nitrite from the nitrito (O-binding) form in the wild-type protein to a weakly bound nitro (N-binding) form. Reintroducing a H-bonding residue in the H64V/V67R double mutant restores the O-binding mode of nitrite. We have also examined the effects of these mutations on reactivities of the metMb(III)s with cysteine as a reducing agent and of the (ferrous) Mb(II)s with nitrite ion under anaerobic conditions. The Mb(II)s were generated by reduction of the Mb(III) precursors in a second-order reaction with cysteine, the rate constants for this step following the order H64V/V67R > H64V > wt. The rate constants for the oxidation of the Mb(II)s by nitrite (giving NO as the other product) follow the order wt > H64V/V67R > H64V and suggest a significant role of the distal pocket H

  5. Two types of antibodies are induced by vaccination with A/California/2009 pdm virus: binding near the sialic acid-binding pocket and neutralizing both H1N1 and H5N1 viruses.

    Directory of Open Access Journals (Sweden)

    Nobuko Ohshima

    Full Text Available Many people have a history of catching the flu several times during childhood but no additional flu in adulthood, even without vaccination. We analyzed the total repertoire of antibodies (Abs against influenza A group 1 viruses induced in such a flu-resistant person after vaccination with 2009 H1N1 pandemic influenza virus. They were classified into two types, with no exceptions. The first type, the products of B cells newly induced through vaccination, binds near the sialic acid-binding pocket. The second type, the products of long-lived memory B cells established before vaccination, utilizes the 1-69 VH gene, binds to the stem of HA, and neutralizes both H1N1 and H5N1 viruses with few exceptions. These observations indicate that the sialic acid-binding pocket and its surrounding region are immunogenically very potent and majority of the B cells whose growth is newly induced by vaccination produce Abs that recognize these regions. However, they play a role in protection against influenza virus infection for a short period since variant viruses that have acquired resistance to these Abs become dominant. On the other hand, although the stem of HA is immunogenically not potent, the second type of B cells eventually becomes dominant. Thus, a selection system should function in forming the repertoire of long-lived memory B cells and the stability of the epitope would greatly affect the fate of the memory cells. Acquisition of the ability to produce Abs that bind to the stable epitope could be a major factor of flu resistance.

  6. Fine-tuning of the binding and dissociation of CO by the amino acids of the heme pocket of Coprinus cinereus peroxidase.

    Science.gov (United States)

    Feis, Alessandro; Santoni, Elisa; Neri, Francesca; Ciaccio, Chiara; De Sanctis, Giampiero; Coletta, Massimo; Welinder, Karen G; Smulevich, Giulietta

    2002-11-01

    Resonance Raman and infrared spectra and the CO dissociation rates (k(off)) were measured in Coprinus cinereus peroxidase (CIP) and several mutants in the heme binding pocket. These mutants included the Asp245Asn, Arg51Leu, Arg51Gln, Arg51Asn, Arg51Lys, Phe54Trp, and Phe54Val mutants. Binding of CO to CIP produced different CO adducts at pH 6 and 10. At pH 6, the bound CO is H-bonded to the protonated distal His55 residue, whereas at alkaline pH, the vibrational signatures and the rate of CO dissociation indicate a distal side which is more open or flexible than in other plant peroxidases. The distal Arg51 residue is important in determining the rate of dissociation in the acid form, increasing by 8-17-fold in the Arg51 mutants compared to that for the wild-type protein. Replacement of the distal Phe with Trp created a new acid form characterized by vibrational frequencies and k(off) values very similar to those of cytochrome c peroxidase.

  7. Host-Primed Ebola Virus GP Exposes a Hydrophobic NPC1 Receptor-Binding Pocket, Revealing a Target for Broadly Neutralizing Antibodies

    Directory of Open Access Journals (Sweden)

    Zachary A. Bornholdt

    2016-02-01

    Full Text Available The filovirus surface glycoprotein (GP mediates viral entry into host cells. Following viral internalization into endosomes, GP is cleaved by host cysteine proteases to expose a receptor-binding site (RBS that is otherwise hidden from immune surveillance. Here, we present the crystal structure of proteolytically cleaved Ebola virus GP to a resolution of 3.3 Å. We use this structure in conjunction with functional analysis of a large panel of pseudotyped viruses bearing mutant GP proteins to map the Ebola virus GP endosomal RBS at molecular resolution. Our studies indicate that binding of GP to its endosomal receptor Niemann-Pick C1 occurs in two distinct stages: the initial electrostatic interactions are followed by specific interactions with a hydrophobic trough that is exposed on the endosomally cleaved GP1 subunit. Finally, we demonstrate that monoclonal antibodies targeting the filovirus RBS neutralize all known filovirus GPs, making this conserved pocket a promising target for the development of panfilovirus therapeutics.

  8. Tetranectin-binding site on plasminogen kringle 4 involves the lysine-binding pocket and at least one additional amino acid residue

    DEFF Research Database (Denmark)

    Graversen, Jonas Heilskov; Sigurskjold, B W; Thøgersen, H C;

    2000-01-01

    , we analyze the interaction of wild-type and six single-residue mutants of recombinant plasminogen kringle 4 expressed in Escherichia coli with the recombinant C-type lectin domain of tetranectin and trans-aminomethyl-cyclohexanoic acid (t-AMCHA) using isothermal titration calorimetry. We find...... that all amino acid residues of plasminogen kringle 4 found to be involved in t-AMCHA binding are also involved in binding tetranectin. Notably, one amino acid residue of plasminogen kringle 4, Arg 32, not involved in binding t-AMCHA, is critical for binding tetranectin. We also find that Asp 57 and Asp 55...

  9. Probing the effect of MODY mutations near the co-activator-binding pocket of HNF4α.

    Science.gov (United States)

    Rha, Geun Bae; Wu, Guangteng; Chi, Young-In

    2011-10-01

    HNF4α (hepatocyte nuclear factor 4α) is a culprit gene product for a monogenic and dominantly inherited form of diabetes, referred to as MODY (maturity onset diabetes of the young). As a member of the NR (nuclear receptor) superfamily, HNF4α recruits transcriptional co-activators such as SRC-1α (steroid receptor co-activator-1α) and PGC-1α (peroxisome-proliferator-activated receptor γ co-activator-1α) through the LXXLL-binding motifs for its transactivation, and our recent crystal structures of the complex provided the molecular details and the mechanistic insights into these co-activator recruitments. Several mutations have been identified from the MODY patients and, among these, point mutations can be very instructive site-specific measures of protein function and structure. Thus, in the present study, we probed the functional effects of the two MODY point mutations (D206Y and M364R) found directly near the LXXLL motif-binding site by conducting a series of experiments on their structural integrity and specific functional roles such as overall transcription, ligand selectivity, target gene recognition and co-activator recruitment. While the D206Y mutation has a subtle effect, the M364R mutation significantly impaired the overall transactivation by HNF4α. These functional disruptions are mainly due to their reduced ability to recruit co-activators and lowered protein stability (only with M364R mutation), while their DNA-binding activities and ligand selectivities are preserved. These results confirmed our structural predictions and proved that MODY mutations are loss-of-function mutations leading to impaired β-cell function. These findings should help target selective residues for correcting mutational defects or modulating the overall activity of HNF4α as a means of therapeutic intervention.

  10. Nucleotides adjacent to the ligand-binding pocket are linked to activity tuning in the purine riboswitch.

    Science.gov (United States)

    Stoddard, Colby D; Widmann, Jeremy; Trausch, Jeremiah J; Marcano-Velázquez, Joan G; Knight, Rob; Batey, Robert T

    2013-05-27

    Direct sensing of intracellular metabolite concentrations by riboswitch RNAs provides an economical and rapid means to maintain metabolic homeostasis. Since many organisms employ the same class of riboswitch to control different genes or transcription units, it is likely that functional variation exists in riboswitches such that activity is tuned to meet cellular needs. Using a bioinformatic approach, we have identified a region of the purine riboswitch aptamer domain that displays conservation patterns linked to riboswitch activity. Aptamer domain compositions within this region can be divided into nine classes that display a spectrum of activities. Naturally occurring compositions in this region favor rapid association rate constants and slow dissociation rate constants for ligand binding. Using X-ray crystallography and chemical probing, we demonstrate that both the free and bound states are influenced by the composition of this region and that modest sequence alterations have a dramatic impact on activity. The introduction of non-natural compositions result in the inability to regulate gene expression in vivo, suggesting that aptamer domain activity is highly plastic and thus readily tunable to meet cellular needs.

  11. CNDOL: A fast and reliable method for the calculation of electronic properties of very large systems. Applications to retinal binding pocket in rhodopsin and gas phase porphine.

    Science.gov (United States)

    Montero-Cabrera, Luis Alberto; Röhrig, Ute; Padrón-Garcia, Juan A; Crespo-Otero, Rachel; Montero-Alejo, Ana L; Garcia de la Vega, José M; Chergui, Majed; Rothlisberger, Ursula

    2007-10-14

    Very large molecular systems can be calculated with the so called CNDOL approximate Hamiltonians that have been developed by avoiding oversimplifications and only using a priori parameters and formulas from the simpler NDO methods. A new diagonal monoelectronic term named CNDOL/21 shows great consistency and easier SCF convergence when used together with an appropriate function for charge repulsion energies that is derived from traditional formulas. It is possible to obtain a priori molecular orbitals and electron excitation properties after the configuration interaction of single excited determinants with reliability, maintaining interpretative possibilities even being a simplified Hamiltonian. Tests with some unequivocal gas phase maxima of simple molecules (benzene, furfural, acetaldehyde, hexyl alcohol, methyl amine, 2,5 dimethyl 2,4 hexadiene, and ethyl sulfide) ratify the general quality of this approach in comparison with other methods. The calculation of large systems as porphine in gas phase and a model of the complete retinal binding pocket in rhodopsin with 622 basis functions on 280 atoms at the quantum mechanical level show reliability leading to a resulting first allowed transition in 483 nm, very similar to the known experimental value of 500 nm of "dark state." In this very important case, our model gives a central role in this excitation to a charge transfer from the neighboring Glu(-) counterion to the retinaldehyde polyene chain. Tests with gas phase maxima of some important molecules corroborate the reliability of CNDOL/2 Hamiltonians.

  12. Strength of hydrogen bond network takes crucial roles in the dissociation process of inhibitors from the HIV-1 protease binding pocket.

    Directory of Open Access Journals (Sweden)

    Dechang Li

    Full Text Available To understand the underlying mechanisms of significant differences in dissociation rate constant among different inhibitors for HIV-1 protease, we performed steered molecular dynamics (SMD simulations to analyze the entire dissociation processes of inhibitors from the binding pocket of protease at atomistic details. We found that the strength of hydrogen bond network between inhibitor and the protease takes crucial roles in the dissociation process. We showed that the hydrogen bond network in the cyclic urea inhibitors AHA001/XK263 is less stable than that of the approved inhibitor ABT538 because of their large differences in the structures of the networks. In the cyclic urea inhibitor bound complex, the hydrogen bonds often distribute at the flap tips and the active site. In contrast, there are additional accessorial hydrogen bonds formed at the lateral sides of the flaps and the active site in the ABT538 bound complex, which take crucial roles in stabilizing the hydrogen bond network. In addition, the water molecule W301 also plays important roles in stabilizing the hydrogen bond network through its flexible movement by acting as a collision buffer and helping the rebinding of hydrogen bonds at the flap tips. Because of its high stability, the hydrogen bond network of ABT538 complex can work together with the hydrophobic clusters to resist the dissociation, resulting in much lower dissociation rate constant than those of cyclic urea inhibitor complexes. This study may provide useful guidelines for design of novel potent inhibitors with optimized interactions.

  13. Strength of hydrogen bond network takes crucial roles in the dissociation process of inhibitors from the HIV-1 protease binding pocket.

    Science.gov (United States)

    Li, Dechang; Ji, Baohua; Hwang, Keh-Chih; Huang, Yonggang

    2011-01-01

    To understand the underlying mechanisms of significant differences in dissociation rate constant among different inhibitors for HIV-1 protease, we performed steered molecular dynamics (SMD) simulations to analyze the entire dissociation processes of inhibitors from the binding pocket of protease at atomistic details. We found that the strength of hydrogen bond network between inhibitor and the protease takes crucial roles in the dissociation process. We showed that the hydrogen bond network in the cyclic urea inhibitors AHA001/XK263 is less stable than that of the approved inhibitor ABT538 because of their large differences in the structures of the networks. In the cyclic urea inhibitor bound complex, the hydrogen bonds often distribute at the flap tips and the active site. In contrast, there are additional accessorial hydrogen bonds formed at the lateral sides of the flaps and the active site in the ABT538 bound complex, which take crucial roles in stabilizing the hydrogen bond network. In addition, the water molecule W301 also plays important roles in stabilizing the hydrogen bond network through its flexible movement by acting as a collision buffer and helping the rebinding of hydrogen bonds at the flap tips. Because of its high stability, the hydrogen bond network of ABT538 complex can work together with the hydrophobic clusters to resist the dissociation, resulting in much lower dissociation rate constant than those of cyclic urea inhibitor complexes. This study may provide useful guidelines for design of novel potent inhibitors with optimized interactions.

  14. Structure of an odorant-binding protein from the mosquito Aedes aegypti suggests a binding pocket covered by a pH-sensitive "Lid".

    Directory of Open Access Journals (Sweden)

    Ney Ribeiro Leite

    Full Text Available BACKGROUND: The yellow fever mosquito, Aedes aegypti, is the primary vector for the viruses that cause yellow fever, mostly in tropical regions of Africa and in parts of South America, and human dengue, which infects 100 million people yearly in the tropics and subtropics. A better understanding of the structural biology of olfactory proteins may pave the way for the development of environmentally-friendly mosquito attractants and repellents, which may ultimately contribute to reduction of mosquito biting and disease transmission. METHODOLOGY: Previously, we isolated and cloned a major, female-enriched odorant-binding protein (OBP from the yellow fever mosquito, AaegOBP1, which was later inadvertently renamed AaegOBP39. We prepared recombinant samples of AaegOBP1 by using an expression system that allows proper formation of disulfide bridges and generates functional OBPs, which are indistinguishable from native OBPs. We crystallized AaegOBP1 and determined its three-dimensional structure at 1.85 A resolution by molecular replacement based on the structure of the malaria mosquito OBP, AgamOBP1, the only mosquito OBP structure known to date. CONCLUSION: The structure of AaegOBP1 ( = AaegOBP39 shares the common fold of insect OBPs with six alpha-helices knitted by three disulfide bonds. A long molecule of polyethylene glycol (PEG was built into the electron-density maps identified in a long tunnel formed by a crystallographic dimer of AaegOBP1. Circular dichroism analysis indicated that delipidated AaegOBP1 undergoes a pH-dependent conformational change, which may lead to release of odorant at low pH (as in the environment in the vicinity of odorant receptors. A C-terminal loop covers the binding cavity and this "lid" may be opened by disruption of an array of acid-labile hydrogen bonds thus explaining reduced or no binding affinity at low pH.

  15. Detection of multiscale pockets on protein surfaces using mathematical morphology.

    Science.gov (United States)

    Kawabata, Takeshi

    2010-04-01

    Detection of pockets on protein surfaces is an important step toward finding the binding sites of small molecules. In a previous study, we defined a pocket as a space into which a small spherical probe can enter, but a large probe cannot. The radius of the large probes corresponds to the shallowness of pockets. We showed that each type of binding molecule has a characteristic shallowness distribution. In this study, we introduced fundamental changes to our previous algorithm by using a 3D grid representation of proteins and probes, and the theory of mathematical morphology. We invented an efficient algorithm for calculating deep and shallow pockets (multiscale pockets) simultaneously, using several different sizes of spherical probes (multiscale probes). We implemented our algorithm as a new program, ghecom (grid-based HECOMi finder). The statistics of calculated pockets for the structural dataset showed that our program had a higher performance of detecting binding pockets, than four other popular pocket-finding programs proposed previously. The ghecom also calculates the shallowness of binding ligands, R(inaccess) (minimum radius of inaccessible spherical probes) that can be obtained from the multiscale molecular volume. We showed that each part of the binding molecule had a bias toward a specific range of shallowness. These findings will be useful for predicting the types of molecules that will be most likely to bind putative binding pockets, as well as the configurations of binding molecules. The program ghecom is available through the Web server (http://biunit.naist.jp/ghecom).

  16. Molecular topology applied to the discovery of 1-benzyl-2-(3-fluorophenyl)-4-hydroxy-3-(3-phenylpropanoyl)-2H-pyrrole-5-one as a non-ligand-binding-pocket antiandrogen.

    Science.gov (United States)

    Caboni, Laura; Gálvez-Llompart, Maria; Gálvez, Jorge; Blanco, Fernando; Rubio-Martinez, Jaime; Fayne, Darren; Lloyd, David G

    2014-10-27

    We report the discovery of 1-benzyl-2-(3-fluorophenyl)-4-hydroxy-3-(3-phenylpropanoyl)-2H-pyrrole-5-one as a novel non-ligand binding pocket (non-LBP) antagonist of the androgen receptor (AR) through the application of molecular topology techniques. This compound, validated through time-resolved fluorescence resonance energy transfer and fluorescence polarization biological assays, provides the basis for lead optimization and structure-activity relationship analysis of a new series of non-LBP AR antagonists. Induced-fit docking and molecular dynamics studies have been performed to establish a consistent hypothesis for the interaction of the new active molecule on the AR surface.

  17. Pocket pumped image analysis

    Energy Technology Data Exchange (ETDEWEB)

    Kotov, I.V., E-mail: kotov@bnl.gov [Brookhaven National Laboratory, Upton, NY 11973 (United States); O' Connor, P. [Brookhaven National Laboratory, Upton, NY 11973 (United States); Murray, N. [Centre for Electronic Imaging, Open University, Milton Keynes, MK7 6AA (United Kingdom)

    2015-07-01

    The pocket pumping technique is used to detect small electron trap sites. These traps, if present, degrade CCD charge transfer efficiency. To reveal traps in the active area, a CCD is illuminated with a flat field and, before image is read out, accumulated charges are moved back and forth number of times in parallel direction. As charges are moved over a trap, an electron is removed from the original pocket and re-emitted in the following pocket. As process repeats one pocket gets depleted and the neighboring pocket gets excess of charges. As a result a “dipole” signal appears on the otherwise flat background level. The amplitude of the dipole signal depends on the trap pumping efficiency. This paper is focused on trap identification technique and particularly on new methods developed for this purpose. The sensor with bad segments was deliberately chosen for algorithms development and to demonstrate sensitivity and power of new methods in uncovering sensor defects.

  18. Verification of a novel NADH-binding motif: combinatorial mutagenesis of three amino acids in the cofactor-binding pocket of Corynebacterium 2,5-diketo-D-gluconic acid reductase.

    Science.gov (United States)

    Banta, Scott; Anderson, Stephen

    2002-12-01

    A screening method has been developed to support randomized mutagenesis of amino acids in the cofactor-binding pocket of the NADPH-dependent 2,5-diketo-D-gluconic acid (2,5-DKG) reductase. Such an approach could enable the isolation of an enzyme that can better catalyze the reduction of 2,5-DKG to 2-keto-L-gulonic acid (2-KLG) using NADH as a cofactor. 2-KLG is a valuable precursor to ascorbic acid, or vitamin C, and an enzyme with increased activity with NADH may be able to improve two potential vitamin C production processes. Previously we have identified three amino acid residues that can be mutated to improve activity with NADH as a cofactor. As a pilot study to show feasibility, a library was made with these three amino acids randomized, and 300 random colonies were screened for increased NADH activity. The activities of seven mutants with apparent improvements were verified using activity-stained native gels, and sequencing showed that the amino acids obtained were similar to some of those already discovered using rational design. The four most active mutants were purified and kinetically characterized. All of the new mutations resulted in apparent kcat values that were equal to or higher than that of the best mutant obtained through rational design. At saturating levels of cofactor, the best mutant obtained was almost twice as active with NADH as a cofactor as the wild-type enzyme is with NADPH. This screen is a valuable tool for improving 2,5-DKG reductase, and it could easily be modified for improving other aspects of this protein or similar enzymes.

  19. Structure of the HIV-1 reverse transcriptase Q151M mutant: insights into the inhibitor resistance of HIV-1 reverse transcriptase and the structure of the nucleotide-binding pocket of Hepatitis B virus polymerase

    Energy Technology Data Exchange (ETDEWEB)

    Nakamura, Akiyoshi; Tamura, Noriko; Yasutake, Yoshiaki, E-mail: y-yasutake@aist.go.jp [National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo, Hokkaido 062-8517 (Japan)

    2015-10-23

    The structure of the HIV-1 reverse transcriptase Q151M mutant was determined at a resolution of 2.6 Å in space group P321. Hepatitis B virus polymerase (HBV Pol) is an important target for anti-HBV drug development; however, its low solubility and stability in vitro has hindered detailed structural studies. Certain nucleotide reverse transcriptase (RT) inhibitors (NRTIs) such as tenofovir and lamivudine can inhibit both HBV Pol and Human immunodeficiency virus 1 (HIV-1) RT, leading to speculation on structural and mechanistic analogies between the deoxynucleotide triphosphate (dNTP)-binding sites of these enzymes. The Q151M mutation in HIV-1 RT, located at the dNTP-binding site, confers resistance to various NRTIs, while maintaining sensitivity to tenofovir and lamivudine. The residue corresponding to Gln151 is strictly conserved as a methionine in HBV Pol. Therefore, the structure of the dNTP-binding pocket of the HIV-1 RT Q151M mutant may reflect that of HBV Pol. Here, the crystal structure of HIV-1 RT Q151M, determined at 2.6 Å resolution, in a new crystal form with space group P321 is presented. Although the structure of HIV-1 RT Q151M superimposes well onto that of HIV-1 RT in a closed conformation, a slight movement of the β-strands (β2–β3) that partially create the dNTP-binding pocket was observed. This movement might be caused by the introduction of the bulky thioether group of Met151. The structure also highlighted the possibility that the hydrogen-bonding network among amino acids and NRTIs is rearranged by the Q151M mutation, leading to a difference in the affinity of NRTIs for HIV-1 RT and HBV Pol.

  20. The CK2 alpha/CK2 beta interface of human protein kinase CK2 harbors a binding pocket for small molecules

    DEFF Research Database (Denmark)

    Raaf, Jennifer; Brunstein, Elena; Issinger, Olaf-Georg;

    2008-01-01

    , selective CK2 inhibitors are required. An often-used CK2 inhibitor is 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB). In a complex structure with human CK2 alpha, DRB binds to the canonical ATP cleft, but additionally it occupies an allosteric site that can be alternatively filled by glycerol....... Inhibition kinetic studies corroborate the dual binding mode of the inhibitor. Structural comparisons reveal a surprising conformational plasticity of human CK2 alpha around both DRB binding sites. After local rearrangement, the allosteric site serves as a CK2 beta interface. This opens the potential...

  1. Google Pocket Guide

    CERN Document Server

    Calishain, Tara; Adams, DJ

    2003-01-01

    Beneath its deceptively simple search form, Google is a remarkably powerful and flexible search engine that indexes billions of web pages, handling more than 150 million searches a day. You know that what you're looking for must be in there somewhere, but how do you make Google work for you? Crafted from our best-selling Google Hacks title, the Google Pocket Guide provides exactly the information you need to make your searches faster and more effective, right from the start. The Google Pocket Guide unleashes the power behind that blinking cursor by delivering: A thorough but concise tour o

  2. HTML & XHTML Pocket Reference

    CERN Document Server

    Robbins, Jennifer

    2010-01-01

    After years of using spacer GIFs, layers of nested tables, and other improvised solutions for building your web sites, getting used to the more stringent standards-compliant design can be intimidating. HTML and XHTML Pocket Reference is the perfect little book when you need answers immediately. Jennifer Niederst-Robbins, author Web Design in a Nutshell, has revised and updated the fourth edition of this pocket guide by taking the top 20% of vital reference information from her Nutshell book, augmenting it judiciously, cross-referencing everything, and organizing it according to the most com

  3. Newnes electrical pocket book

    CERN Document Server

    Reeves, E A

    2013-01-01

    Newnes Electrical Pocket Book, Twenty-first Edition, provides engineers with convenient access to various facts, tables, and formulae relating to the particular branch of engineering being dealt with. In the case of electrical engineering, it is essential that the engineer have a clear understanding of the methods by which the various formulae are derived to ensure that any particular formulae is applicable to the conditions being considered. The first section of the Pocket Book is devoted to the theoretical groundwork upon which all the practical applications are based. This covers symbols,

  4. VBScript pocket reference

    CERN Document Server

    Lomax, Paul; Petrusha, Ron

    2008-01-01

    Microsoft's Visual Basic Scripting Edition (VBScript), a subset of Visual Basic for Applications, is a powerful language for Internet application development, where it can serve as a scripting language for server-side, client-side, and system scripting. Whether you're developing code for Active Server Pages, client-side scripts for Internet Explorer, code for Outlook forms, or scripts for Windows Script Host, VBScript Pocket Reference will be your constant companion. Don't let the pocket-friendly format fool you. Based on the bestsellingVBScript in a Nutshell, this small book details every V

  5. Molecular recognition of CYP26A1 binding pockets and structure-activity relationship studies for design of potent and selective retinoic acid metabolism blocking agents.

    Science.gov (United States)

    Sun, Bin; Song, Shuai; Hao, Chen-Zhou; Huang, Wan-Xu; Liu, Chun-Chi; Xie, Hong-Lei; Lin, Bin; Cheng, Mao-Sheng; Zhao, Dong-Mei

    2015-03-01

    All-trans-retinoic acid (ATRA), the biologically most active metabolite of vitamin A, plays a major role in the regulation of cellular differentiation and proliferation, and it is also an important pharmacological agent particularly used in the treatment of cancer, skin, neurodegenerative and autoimmune diseases. However, ATRA is very easy to be metabolized into 4-hydroxyl-RA in vivo by CYP26A1, an inducible cytochrome P450 enzyme, eventually into more polar metabolites. Therefore, it is vital to develop specific retinoic acid metabolism blocking agents (RAMBAs) to inhibit the metabolic enzyme CYP26A1 in the treatment of relevant diseases aforementioned. In this study, CYP26A1 and its interactions with retinoic acid-competitive metabolism blocking agents were investigated by a combined ligand- and structure-based approach. First, since the crystal structure of CYP26A1 protein has not been determined, we constructed the 3D structure of CYP26A1 using homology modeling. In order to achieve a deeper insight into the mode of action of RAMBAs in the active site, the molecular superimposition model and the common feature pharmacophore model were constructed, and molecular docking was performed. The molecular superimposition model is composed of three features: the main chain groups, side chain groups, and azole groups. The common feature pharmacophore model consists of five chemical features: four hydrophobic groups and one hydrogen acceptor (HHHHA). The results of molecular docking show that the characteristic groups of RAMBAs were mapped into three different active pockets, respectively. A structure-activity relationship (SAR) was obtained by a combination of the molecular superimposition and docking results with the pharmacophore model. This study gives more insight into the interaction model inside the CYP26A1 active site and provides guidance for the design of more potent and possibly more selective RAMBAs.

  6. Data communications pocket book

    CERN Document Server

    Tooley, Michael

    2014-01-01

    Data Communications Pocket Book, Second Edition presents information relevant to data communication. The book provides tabulated reference materials with a brief description and diagrams. The coverage of the text includes abbreviations, terminal control codes, and conversion tables. The text will be of great use to individuals involved in the interconnection of computer systems.

  7. NMR-based screening of membrane protein ligands

    NARCIS (Netherlands)

    Yanamala, Naveena; Dutta, Arpana; Beck, Barbara; Van Fleet, Bart; Hay, Kelly; Yazbak, Ahmad; Ishima, Rieko; Doemling, Alexander; Klein-Seetharaman, Judith

    2010-01-01

    Membrane proteins pose problems for the application of NMR-based ligand-screening methods because of the need to maintain the proteins in a membrane mimetic environment such as detergent micelles: they add to the molecular weight of the protein, increase the viscosity of the solution, interact with

  8. Influence of the conserved disulphide bond, exposed to the putative binding pocket, on the structure and function of the immunoglobulin-like molecular chaperone Caf1M of Yersinia pestis.

    Science.gov (United States)

    Zav'yalov, V P; Chernovskaya, T V; Chapman, D A; Karlyshev, A V; MacIntyre, S; Zavialov, A V; Vasiliev, A M; Denesyuk, A I; Zav'yalova, G A; Dudich, I V; Korpela, T; Abramov, V M

    1997-06-01

    The Yersinia pestis protein Caf1M is a typical representative of a subfamily of periplasmic molecular chaperones with characteristic structural and functional features, one of which is the location of two conserved cysteine residues close to the putative binding pocket. We show that these residues form a disulphide bond, the reduction and alkylation of which significantly increases the dissociation constant of the Caf1M-Caf1 (where Caf 1 is a polypeptide subunit of the capsule) complex [from a Kd of (4.77+/-0.50)x10(-9) M for the intact protein to one of (3.68+/-0.68)x10(-8) M for the modified protein]. The importance of the disulphide bond for the formation of functional Caf1M in vivo was demonstrated using an Escherichia coli dsbA mutant carrying the Y. pestis f1 operon. In accordance with the CD and fluorescence measurements, the disulphide bond is not important for maintenance of the overall structure of the Caf1M molecule, but would appear to affect the fine structural properties of the subunit binding site. A three-dimensional model of the Caf1M-Caf1 complex was designed based on the published crystal structure of PapD (a chaperone required for Pap pili assembly) complexed with a peptide corresponding to the C-terminus of the papG subunit. In the model the disulphide bond is in close proximity to the invariant Caf1M Arg-23 and Lys-142 residues that are assumed to anchor the C-terminal group of the subunit. The importance of this characteristic disulphide bond for the orchestration of the binding site and subunit binding, as well as for the folding of the protein in vivo, is likely to be a common feature of this subfamily of Caf1M-like chaperones. A possible model for the role of the disulphide bond in Caf1 assembly is discussed.

  9. Structure of an Odorant-Vinding Protein form the Mosquito Aedes aegypti Suggests a Binding Pocket Covered by a pH-Sensitive

    Energy Technology Data Exchange (ETDEWEB)

    N Leite; R Krogh; W Xu; Y Ishida; J Iulek; W Leal; G Oliva

    2011-12-31

    The yellow fever mosquito, Aedes aegypti, is the primary vector for the viruses that cause yellow fever, mostly in tropical regions of Africa and in parts of South America, and human dengue, which infects 100 million people yearly in the tropics and subtropics. A better understanding of the structural biology of olfactory proteins may pave the way for the development of environmentally-friendly mosquito attractants and repellents, which may ultimately contribute to reduction of mosquito biting and disease transmission. Previously, we isolated and cloned a major, female-enriched odorant-binding protein (OBP) from the yellow fever mosquito, AaegOBP1, which was later inadvertently renamed AaegOBP39. We prepared recombinant samples of AaegOBP1 by using an expression system that allows proper formation of disulfide bridges and generates functional OBPs, which are indistinguishable from native OBPs. We crystallized AaegOBP1 and determined its three-dimensional structure at 1.85 {angstrom} resolution by molecular replacement based on the structure of the malaria mosquito OBP, AgamOBP1, the only mosquito OBP structure known to date. The structure of AaegOBP1 (= AaegOBP39) shares the common fold of insect OBPs with six {alpha}-helices knitted by three disulfide bonds. A long molecule of polyethylene glycol (PEG) was built into the electron-density maps identified in a long tunnel formed by a crystallographic dimer of AaegOBP1. Circular dichroism analysis indicated that delipidated AaegOBP1 undergoes a pH-dependent conformational change, which may lead to release of odorant at low pH (as in the environment in the vicinity of odorant receptors). A C-terminal loop covers the binding cavity and this 'lid' may be opened by disruption of an array of acid-labile hydrogen bonds thus explaining reduced or no binding affinity at low pH.

  10. Functions of key residues in the ligand-binding pocket of vitamin D receptor: Fragment molecular orbital interfragment interaction energy analysis

    Science.gov (United States)

    Yamagishi, Kenji; Yamamoto, Keiko; Yamada, Sachiko; Tokiwa, Hiroaki

    2006-03-01

    Fragment molecular orbital-interfragment interaction energy calculations of the vitamin D receptor (VDR)/1α,25-dihydroxyvitamin D 3 complex were utilized to assign functions of key residues of the VDR. Only one residue forms a significant interaction with the corresponding hydroxy group of the ligand, although two residues are located around each hydroxy group. The degradation of binding affinity for derivatives upon removal of a hydroxy group is closely related to the trend in the strength of the hydrogen bonds. Type II hereditary rickets due to an Arg274 point mutation is caused by the lack of the strongest hydrogen bond.

  11. GDB Pocket Reference

    CERN Document Server

    Robbins, Arnold

    2009-01-01

    The GNU debugger is valuable for testing, fixing, and retesting software because it allows you to see exactly what's going on inside of a program as it's executing. This new pocket reference shows you how to specify a target for debugging, perform a careful examination to find the cause of program failure, and make quick changes for further testing. The guide covers several popular programming languages.

  12. Software engineer's pocket book

    CERN Document Server

    Tooley, Michael

    2013-01-01

    Software Engineer's Pocket Book provides a concise discussion on various aspects of software engineering. The book is comprised of six chapters that tackle various areas of concerns in software engineering. Chapter 1 discusses software development, and Chapter 2 covers programming languages. Chapter 3 deals with operating systems. The book also tackles discrete mathematics and numerical computation. Data structures and algorithms are also explained. The text will be of great use to individuals involved in the specification, design, development, implementation, testing, maintenance, and qualit

  13. Identifying Instability Pockets

    Science.gov (United States)

    2014-12-04

    TYPE SAMS Monograph 3. DATES COVERED (From - To) FEB 2014 – DEC 2014 4. TITLE AND SUBTITLE IDENTIFYING INSTABILITY POCKETS 5a. CONTRACT...century, and if the first few years of the new century are indicative of the future, Central Asia is surely destined to be a focus of the world...reasons. First, there is a possibility of the collapse and instability of Afghanistan once all the U.S troops vacate .107 This stability will most

  14. Interaction pattern of Arg 62 in the A-pocket of differentially disease-associated HLA-B27 subtypes suggests distinct TCR binding modes.

    Directory of Open Access Journals (Sweden)

    Elisa Nurzia

    Full Text Available The single amino acid replacement Asp116His distinguishes the two subtypes HLA-B*2705 and HLA-B*2709 which are, respectively, associated and non-associated with Ankylosing Spondylitis, an autoimmune chronic inflammatory disease. The reason for this differential association is so far poorly understood and might be related to subtype-specific HLA:peptide conformations as well as to subtype/peptide-dependent dynamical properties on the nanoscale. Here, we combine functional experiments with extensive molecular dynamics simulations to investigate the molecular dynamics and function of the conserved Arg62 of the α1-helix for both B27 subtypes in complex with the self-peptides pVIPR (RRKWRRWHL and TIS (RRLPIFSRL, and the viral peptides pLMP2 (RRRWRRLTV and NPflu (SRYWAIRTR. Simulations of HLA:peptide systems suggest that peptide-stabilizing interactions of the Arg62 residue observed in crystal structures are metastable for both B27 subtypes under physiological conditions, rendering this arginine solvent-exposed and, probably, a key residue for TCR interaction more than peptide-binding. This view is supported by functional experiments with conservative (R62K and non-conservative (R62A B*2705 and B*2709 mutants that showed an overall reduction in their capability to present peptides to CD8+ T cells. Moreover, major subtype-dependent differences in the peptide recognition suggest distinct TCR binding modes for the B*2705 versus the B*2709 subtype.

  15. A KAS2 cDNA complements the phenotypes of the Arabidopsis fab1 mutant that differs in a single residue bordering the substrate binding pocket

    DEFF Research Database (Denmark)

    Carlsson, A.S.; LaBrie, S.T.; Kinney, A.J.;

    2002-01-01

    The fab1 mutant of Arabidopsis is partially deficient in activity of ß-ketoacyl-[acyl carrier protein] synthase II (KAS II). This defect results in increased levels of 16 : 0 fatty acid and is associated with damage and death of the mutants at low temperature. Transformation of fab1 plants with a c...... chain to bend. For functional analysis the equivalent Leu207Phe mutation was introduced into the fabB gene encoding the E. coli KAS I enzyme. Compared to wild-type, the Leu207Phe protein showed a 10-fold decrease in binding affinity for the fatty acid substrate, exhibited a modified behavior during size...

  16. CSS Pocket Reference

    CERN Document Server

    Meyer, Eric

    2011-01-01

    When you're working with CSS and need a quick answer, CSS Pocket Reference delivers. This handy, concise book provides all of the essential information you need to implement CSS on the fly. Ideal for intermediate to advanced web designers and developers, the 4th edition is revised and updated for CSS3, the latest version of the Cascading Style Sheet specification. Along with a complete alphabetical reference to CSS3 selectors and properties, you'll also find a short introduction to the key concepts of CSS. Based on Cascading Style Sheets: The Definitive Guide, this reference is an easy-to-us

  17. Regular Expression Pocket Reference

    CERN Document Server

    Stubblebine, Tony

    2007-01-01

    This handy little book offers programmers a complete overview of the syntax and semantics of regular expressions that are at the heart of every text-processing application. Ideal as a quick reference, Regular Expression Pocket Reference covers the regular expression APIs for Perl 5.8, Ruby (including some upcoming 1.9 features), Java, PHP, .NET and C#, Python, vi, JavaScript, and the PCRE regular expression libraries. This concise and easy-to-use reference puts a very powerful tool for manipulating text and data right at your fingertips. Composed of a mixture of symbols and text, regular exp

  18. XSLT 10 Pocket Reference

    CERN Document Server

    Lenz, Evan

    2008-01-01

    XSLT is an essential tool for converting XML into other kinds of documents: HTML, PDF file, and many others. It's a critical technology for XML-based platforms such as Microsoft .NET, Sun Microsystems' Sun One, as well as for most web browsers and authoring tools. As useful as XSLT is, however, most people have a difficult time getting used to its peculiar characteristics. The ability to use advanced techniques depends on a clear and exact understanding of how XSLT templates work and interact. The XSLT 1.0 Pocket Reference from O'Reilly wants to make sure you achieve that level of understan

  19. Newnes microprocessor pocket book

    CERN Document Server

    Money, Steve

    2014-01-01

    Newnes Microprocessor Pocket Book explains the basic hardware operation of a microprocessor and describes the actions of the various types of instruction that can be executed. A summary of the characteristics of many of the popular microprocessors is presented. Apart from the popular 8- and 16-bit microprocessors, some details are also given of the popular single chip microcomputers and of the reduced instruction set computer (RISC) type processors such as the Transputer, Novix FORTH processor, and Acorn ARM processor.Comprised of 15 chapters, this book discusses the principles involved in bot

  20. Perl Pocket Reference

    CERN Document Server

    Vromans, Johan

    2011-01-01

    If you have a Perl programming question, you'll find the answer quickly in this handy, easy-to-use quick reference. The Perl Pocket Reference condenses and organizes stacks of documentation down to the most essential facts, so you can find what you need in a heartbeat. Updated for Perl 5.14, the 5th edition provides a summary of Perl syntax rules and a complete list of operators, built-in functions, and other features. It's the perfect companion to O'Reilly's authoritative and in-depth Perl programming books, including Learning Perl, Programming Perl, and the Perl Cookbook..

  1. Linux Desktop Pocket Guide

    CERN Document Server

    Brickner, David

    2005-01-01

    While Mac OS X garners all the praise from pundits, and Windows XP attracts all the viruses, Linux is quietly being installed on millions of desktops every year. For programmers and system administrators, business users, and educators, desktop Linux is a breath of fresh air and a needed alternative to other operating systems. The Linux Desktop Pocket Guide is your introduction to using Linux on five of the most popular distributions: Fedora, Gentoo, Mandriva, SUSE, and Ubuntu. Despite what you may have heard, using Linux is not all that hard. Firefox and Konqueror can handle all your web bro

  2. Python pocket reference

    CERN Document Server

    Lutz, Mark

    2010-01-01

    This is the book to reach for when you're coding on the fly and need an answer now. It's an easy-to-use reference to the core language, with descriptions of commonly used modules and toolkits, and a guide to recent changes, new features, and upgraded built-ins -- all updated to cover Python 3.X as well as version 2.6. You'll also quickly find exactly what you need with the handy index. Written by Mark Lutz -- widely recognized as the world's leading Python trainer -- Python Pocket Reference, Fourth Edition, is the perfect companion to O'Reilly's classic Python tutorials, also written by Mark

  3. STL pocket reference

    CERN Document Server

    Lischner, Ray

    2003-01-01

    The STL Pocket Reference describes the functions, classes, and templates in that part of the C++ standard library often referred to as the Standard Template Library (STL). The STL encompasses containers, iterators, algorithms, and function objects, which collectively represent one of the most important and widely used subsets of standard library functionality. The C++ standard library, even the subset known as the STL, is vast. It's next to impossible to work with the STL without some sort of reference at your side to remind you of template parameters, function invocations, return types--ind

  4. Electronics pocket book

    CERN Document Server

    Parr, E A

    1981-01-01

    Electronics Pocket Book, Fourth Edition is a nonmathematical presentation of the many varied topics covered by electronics. The book tackles electron physics, electronic components (i.e. resistors, capacitors, and conductors), integrated circuits, and the principles of a.c. and d.c. amplifiers. The text also discusses oscillators, digital circuits, digital computers, and optoelectronics (i.e., sensors, emitters, and devices that utilize light). Communications (such as line and radio communications, transmitters, receivers, and digital techniques); the principles and examples of servosystems; a

  5. CSS Pocket Reference

    CERN Document Server

    Meyer, Eric A

    2007-01-01

    They say that good things come in small packages, and it's certainly true for this edition of CSS Pocket Reference. Completely revised and updated to reflect the latest Cascading Style Sheet specifications in CSS 2.1, this indispensable little book covers the most essential information that web designers and developers need to implement CSS effectively across all browsers. Inside, you'll find: A short introduction to the key concepts of CSS A complete alphabetical reference to all CSS 2.1 selectors and properties A chart displaying detailed information about CSS support for every style ele

  6. JDBC Pocket Reference

    CERN Document Server

    Bales, Donald

    2003-01-01

    JDBC--the Java Database Connectivity specification--is a complex set of application programming interfaces (APIs) that developers need to understand if they want their Java applications to work with databases. JDBC is so complex that even the most experienced developers need to refresh their memories from time to time on specific methods and details. But, practically speaking, who wants to stop and thumb through a weighty tutorial volume each time a question arises? The answer is the JDBC Pocket Reference, a data-packed quick reference that is both a time-saver and a lifesaver. The JDBC P

  7. Rails Pocket Reference

    CERN Document Server

    Berry, Eric

    2008-01-01

    Rails 2.1 brings a new level of stability and power to this acclaimed web development framework, but keeping track of its numerous moving parts is still a chore. Rails Pocket Reference offers you a painless alternative to hunting for resources online, with brief yet thorough explanations of the most frequently used methods and structures supported by Rails 2.1, along with key concepts you need to work through the framework's most tangled corners. Organized to help you quickly find what you need, this book will not only get you up to speed on how Rails works, it also provides a handy referenc

  8. RTF Pocket Guide

    CERN Document Server

    Burke, Sean

    2008-01-01

    Rich Text Format, or RTF, is the internal markup language used by Microsoft Word and understood by dozens of other word processors. RTF is a universal file format that pervades practically every desktop. Because RTF is text, it's much easier to generate and process than binary .doc files. Any programmer working with word processing documents needs to learn enough RTF to get around, whether it's to format text for Word (or almost any other word processor), to make global changes to an existing document, or to convert Word files to (or from) another format. RTF Pocket Guide is a concise and e

  9. LINQ Pocket Reference

    CERN Document Server

    Albahari, Joseph

    2008-01-01

    Ready to take advantage of LINQ with C# 3.0? This guide has the detail you need to grasp Microsoft's new querying technology, and concise explanations to help you learn it quickly. And once you begin to apply LINQ, the book serves as an on-the-job reference when you need immediate reminders. All the examples in the LINQ Pocket Reference are preloaded into LINQPad, the highly praised utility that lets you work with LINQ interactively. Created by the authors and free to download, LINQPad will not only help you learn LINQ, it will have you thinking in LINQ. This reference explains: LINQ's ke

  10. Pocket ECG electrode

    Science.gov (United States)

    Lund, Gordon F. (Inventor)

    1982-01-01

    A low-noise electrode suited for sensing electrocardiograms when chronically and subcutaneously implanted in a free-ranging subject. The electrode comprises a pocket-shaped electrically conductive member with a single entrance adapted to receive body fluids. The exterior of the member and the entrance region is coated with electrical insulation so that the only electrolyte/electrode interface is within the member remote from artifact-generating tissue. Cloth straps are bonded to the member to permit the electrode to be sutured to tissue and to provide electrical lead flexure relief.

  11. Computer-aided design of fragment mixtures for NMR-based screening.

    Directory of Open Access Journals (Sweden)

    Xavier Arroyo

    Full Text Available Fragment-based drug discovery is widely applied both in industrial and in academic screening programs. Several screening techniques rely on NMR to detect binding of a fragment to a target. NMR-based methods are among the most sensitive techniques and have the further advantage of yielding a low rate of false positives and negatives. However, NMR is intrinsically slower than other screening techniques; thus, to increase throughput in NMR-based screening, researchers often assay mixtures of fragments, rather than single fragments. Herein we present a fast and straightforward computer-aided method to design mixtures of fragments taken from a library that have minimized NMR signal overlap. This approach enables direct identification of one or several active fragments without the need for deconvolution. Our approach entails encoding of NMR spectra into a computer-readable format that we call a fingerprint, and minimizing the global signal overlap through a Monte Carlo algorithm. The scoring function used favors a homogenous distribution of the global signal overlap. The method does not require additional experimental work: the only data required are NMR spectra, which are generally recorded for each compound as a quality control measure before its insertion into the library.

  12. The corneal pocket assay.

    Science.gov (United States)

    Ziche, Marina; Morbidelli, Lucia

    2015-01-01

    The cornea in most species is physiologically avascular, and thus this assay allows the measurement of newly formed vessels. The continuous monitoring of neovascular growth in the same animal allows the evaluation of drugs acting as suppressors or stimulators of angiogenesis. Under anesthesia a micropocket is produced in the cornea thickness and the angiogenesis stimulus (tumor tissue, cell suspension, growth factor) is placed into the pocket in order to induce vascular outgrowth from the limbal capillaries. Neovascular development and progression can be modified by the presence of locally released or applied inhibitory factors or by systemic treatments. In this chapter the experimental details of the avascular cornea assay, the technical challenges, and advantages and disadvantages in different species are discussed. Protocols for local drug treatment and tissue sampling for histology and pharmacokinetic profile are reported.

  13. Exploring human breast milk composition by NMR-based metabolomics.

    Science.gov (United States)

    Praticò, Giulia; Capuani, Giorgio; Tomassini, Alberta; Baldassarre, Maria Elisabetta; Delfini, Maurizio; Miccheli, Alfredo

    2014-01-01

    Breast milk is a complex fluid evolutionarily adapted to satisfy the nutritional requirements of growing infants. In addition, milk biochemical and immunological components protect newborns against infective agents in the new environment. Human milk oligosaccharides, the third most abundant component of breast milk, are believed to modulate the microbiota composition, thus influencing a wide range of physiological processes of the infant. Human milk also contains a number of other bioactive compounds, the functional role of which has not yet been clearly elucidated. In this scenario, NMR-based metabolic profiling can provide a rapid characterisation of breast milk composition, thus allowing a better understanding of its nutritional properties.

  14. A serpin-induced extensive proteolytic susceptibility of urokinase-type plasminogen activator implicates distortion of the proteinase substrate-binding pocket and oxyanion hole in the serpin inhibitory mechanism.

    Science.gov (United States)

    Egelund, R; Petersen, T E; Andreasen, P A

    2001-02-01

    The formation of stable complexes between serpins and their target serine proteinases indicates formation of an ester bond between the proteinase active-site serine and the serpin P1 residue [Egelund, R., Rodenburg, K.W., Andreasen, P.A., Rasmussen, M.S., Guldberg, R.E. & Petersen, T.E. (1998) Biochemistry 37, 6375-6379]. An important question concerning serpin inhibition is the contrast between the stability of the ester bond in the complex and the rapid hydrolysis of the acyl-enzyme intermediate in general serine proteinase-catalysed peptide bond hydrolysis. To answer this question, we used limited proteolysis to detect conformational differences between free urokinase-type plasminogen activator (uPA) and uPA in complex with plasminogen activator inhibitor-1 (PAI-1). Whereas the catalytic domain of free uPA, pro-uPA, uPA in complex with non-serpin inhibitors and anhydro-uPA in a non-covalent complex with PAI-1 was resistant to proteolysis, the catalytic domain of PAI-1-complexed uPA was susceptible to proteolysis. The cleavage sites for four different proteinases were localized in specific areas of the C-terminal beta-barrel of the catalytic domain of uPA, providing evidence that the serpin inhibitory mechanism involves a serpin-induced massive rearrangement of the proteinase active site, including the specificity pocket, the oxyanion hole, and main-chain binding area, rendering the proteinase unable to complete the normal hydrolysis of the acyl-enzyme intermediate. The distorted region includes the so-called activation domain, also known to change conformation on zymogen activation.

  15. Importance of Residues Outside the Cation Binding Pocket for Na+ and K+ Binding to the Na+/K+-ATPase

    DEFF Research Database (Denmark)

    Christiansen, Line; Toustrup-Jensen, Mads Schak; Einholm, Anja P.;

    Mutagenesis studies have identified several oxygen-containing residues in the transmembrane region which are important for the coordination of Na+ and/or K+. These were later confirmed by the high-resolution crystal structures of the Na+/K+-ATPase with bound Na+ or K+. However, more information......-established that K+ antagonizes ouabain binding, and vice versa. Furthermore, recent crystal structures have shown that ouabain binds in an extracellular cavity created by residues of transmembrane helices 4, 5, and 6 (3). This cavity, which is lined by Phe785 and Phe788, as well as Phe318, Arg882, and Asp886, may...... aromatic ring, while Arg882 and Asp886 were mutated to leucine and alanine, respectively, to investigate the importance of charge and size of the residues. All three mutants could sustain growth and proliferation under ouabain pressure. However, the mutants exhibited a reduced turnover number. All three...

  16. Towards Coleoptera-specific high-throughput screening systems for compounds with ecdysone activity: development of EcR reporter assays using weevil (Anthonomus grandis)-derived cell lines and in silico analysis of ligand binding to A. grandis EcR ligand-binding pocket.

    Science.gov (United States)

    Soin, Thomas; Iga, Masatoshi; Swevers, Luc; Rougé, Pierre; Janssen, Colin R; Smagghe, Guy

    2009-08-01

    Molting in insects is regulated by ecdysteroids and juvenile hormones. Several synthetic non-steroidal ecdysone agonists are on the market as insecticides. These ecdysone agonists are dibenzoylhydrazine (DBH) analogue compounds that manifest their toxicity via interaction with the ecdysone receptor (EcR). Of the four commercial available ecdysone agonists, three (tebufenozide, methoxyfenozide and chromafenozide) are highly lepidopteran specific, one (halofenozide) is used to control coleopteran and lepidopteran insects in turf and ornamentals. However, compared to the very high binding affinity of these DBH analogues to lepidopteran EcRs, halofenozide has a low binding affinity for coleopteran EcRs. For the discovery of ecdysone agonists that target non-lepidopteran insect groups, efficient screening systems that are based on the activation of the EcR are needed. We report here the development and evaluation of two coleopteran-specific reporter-based screening systems to discover and evaluate ecdysone agonists. The screening systems are based on the cell lines BRL-AG-3A and BRL-AG-3C that are derived from the weevil Anthonomus grandis, which can be efficiently transduced with an EcR reporter cassette for evaluation of induction of reporter activity by ecdysone agonists. We also cloned the almost full length coding sequence of EcR expressed in the cell line BRL-AG-3C and used it to make an initial in silico 3D-model of its ligand-binding pocket docked with ponasterone A and tebufenozide.

  17. Computer forensics a pocket guide

    CERN Document Server

    Clarke, Nathan

    2010-01-01

    This pocket guide illustrates the technical complexities involved in computer forensics, and shows managers what makes the discipline relevant to their organisation. For technical staff, the book offers an invaluable insight into the key processes and procedures that are required

  18. Progress in NMR-based metabolomics of Catharanthus roseus

    Directory of Open Access Journals (Sweden)

    Qifang PAN,Jingya ZHAO,Yuliang WANG,Kexuan TANG

    2015-09-01

    Full Text Available Metabolomics has been rapidly developed as an important field in plant sciences and natural products chemistry. As the only natural source for a diversity of monoterpenoid indole alkaloids (MIAs, especially the low-abundance antitumor agents vinblastine and vincristine, Catharanthus roseus is highly valued and has been studied extensively as a model for medicinal plants improvement. Due to multistep enzymatic biosynthesis and complex regulation, genetic modification in the MIA pathway has resulted in complicated changes of both secondary and primary metabolism in C. roseus, affecting not only the MIA pathway but also other pathways. Research at the metabolic level is necessary to increase knowledge on the genetic regulation of the whole metabolic network connected to MIA biosynthesis. Nuclear magnetic resonance (NMR is a very suitable and powerful complementary technique for the identification and quantification of metabolites in the plant matrix. NMR-based metabolomics has been used in studies of C. roseus for pathway elucidation, understanding stress responses, classification among different cultivars, safety and quality controls of transgenic plants, cross talk between pathways, and diversion of carbon fluxes, with the aim of fully unravelling MIA biosynthesis, its regulation and the function of the alkaloids in the plant from a systems biology point of view.

  19. Newnes electronics assembly pocket book

    CERN Document Server

    Brindley, Keith

    2013-01-01

    Produced in association with the Engineering Training Authority with contributions from dozens of people in the electronics industry. The material covers common skills in electrical and electronic engineering and concentrates mainly on wiring and assembly. 'Newnes Electronics Assembly Pocket Book' is for electronics technicians, students and apprentices.

  20. IT governance a pocket guide

    CERN Document Server

    Calder, Alan

    2007-01-01

    This new downloadable pocket guide in the Practical IT Governance series, is designed to provide the reader with a basic understanding of how an organization's Information Technology supports and enables the achievement of its strategies and objectives.

  1. TclTk Pocket Reference

    CERN Document Server

    Raines, Paul

    1998-01-01

    The Tcl/Tk combination is increasingly popular because it lets you produce sophisticated graphical interfaces with a few easy commands, develop and change scripts quickly, and conveniently tie together existing utilities or programming libraries. The Tcl/Tk Pocket Reference,a handy reference guide to the basic Tcl language elements, Tcl and Tk commands, and Tk widgets, is a companion volume to Tcl/Tk in a Nutshell.

  2. Prince2 2009 edition a pocket guide

    CERN Document Server

    Hedeman, Bert

    2010-01-01

    This Pocket Guide supplies a summary of the PRINCE2 method, to provide a quick introduction as well as a structured overview of the method;Main target Group for this pocket guide is anyone who wants to get to know the method PRINCE2 or a methodical approach for project management. The book is also very useful for members of a project management team on a project using the PRINCE2 method. Furthermore this pocket guide can be used as literature for the preparation of the PRINCE2 2009 Edition Foundation exam;This pocket guide is based on PRINCE2 2009 Edition;This pocket book deals with processes,

  3. GPCR crystal structures: Medicinal chemistry in the pocket.

    Science.gov (United States)

    Shonberg, Jeremy; Kling, Ralf C; Gmeiner, Peter; Löber, Stefan

    2015-07-15

    Recent breakthroughs in GPCR structural biology have significantly increased our understanding of drug action at these therapeutically relevant receptors, and this will undoubtedly lead to the design of better therapeutics. In recent years, crystal structures of GPCRs from classes A, B, C and F have been solved, unveiling a precise snapshot of ligand-receptor interactions. Furthermore, some receptors have been crystallized in different functional states in complex with antagonists, partial agonists, full agonists, biased agonists and allosteric modulators, providing further insight into the mechanisms of ligand-induced GPCR activation. It is now obvious that there is enormous diversity in the size, shape and position of the ligand binding pockets in GPCRs. In this review, we summarise the current state of solved GPCR structures, with a particular focus on ligand-receptor interactions in the binding pocket, and how this can contribute to the design of GPCR ligands with better affinity, subtype selectivity or efficacy.

  4. Electrical engineering a pocket reference

    CERN Document Server

    Schmidt-Walter, Heinz

    2007-01-01

    This essential reference offers you a well-organized resource for accessing the basic electrical engineering knowledge you need for your work. Whether you're an experienced engineer who appreciates an occasional refresher in key areas, or a student preparing to enter the field, Electrical Engineering: A Pocket Reference provides quick and easy access to fundamental principles and their applications. You also find an extensive collection of time-saving equations that help simplify your daily projects.Supported with more than 500 diagrams and figures, 60 tables, and an extensive index, this uniq

  5. Windows Vista Administrator's Pocket Guide

    CERN Document Server

    Stanek, William R

    2007-01-01

    Portable and precise, this pocket-sized guide delivers immediate answers for the day-to-day administration of Windows Vista. Zero in on core support and maintenance tasks using quick-reference tables, instructions, and lists. You'll get the precise information you need to solve problems and get the job done-whether you're at your desk or in the field! Get fast facts to: Install and configure Windows Vista-and optimize the user workspaceMaintain operating system components, hardware devices, and driversCreate user and group accounts-and control rights and permissionsAdminister group policy se

  6. Pocket atlas of dental radiology

    Energy Technology Data Exchange (ETDEWEB)

    Pasler, F.A. [Geneva Univ. (Switzerland). Dept. of Radiology, Dental Institute; Visser, H. [Goettingen Univ. (Germany). Dental School

    2007-07-01

    In this age of highly specialized medical imaging, an examination of the teeth and alveolar bone is almost unthinkable without the use of radiographs. This highly informative and easy-to-read book with a collection of 798 radiographs, tables, and photos provides a myriad of problem-solving tips concerning the fundamentals of radiographic techniques, quality assurance, image processing, radiographic anatomy, and radiographic diagnosis. Information is easy to find, enabling the reader to literally get a grasp of essential new knowledge in next to no time. The dental practice team now has a pocket 'consultant' at its fingertips, providing practical ways to incorporate new technique into daily practice. (orig.)

  7. Oracle Data Dictionary Pocket Reference

    CERN Document Server

    Kreines, David

    2003-01-01

    If you work with Oracle, then you don't need to be told that the data dictionary is large and complex, and grows larger with each new Oracle release. It's one of the basic elements of the Oracle database you interact with regularly, but the sheer number of tables and views makes it difficult to remember which view you need, much less the name of the specific column. Want to make it simpler? The Oracle Data Dictionary Pocket Reference puts all the information you need right at your fingertips. Its handy and compact format lets you locate the table and view you need effortlessly without stoppin

  8. Newnes electronics engineers pocket book

    CERN Document Server

    Brindley, Keith

    2013-01-01

    This book is packed with information and material which everyone involved in electronics will find indispensable. Now when you need to know a transistor's characteristics, or an integrated circuit's pinout details, simply look it up! The book is full of tables, symbols, formulae, conversions and illustrations.Promotion via the new Newnes Pocket Book catalogue to the electronics trade will drive sales into the book trade Covers component data; encapsulations; pin-outs; symbols & codings Extensive material on conversion factors, formulae; units and relationships

  9. Raf kinase inhibitory protein function is regulated via a flexible pocket and novel phosphorylation-dependent mechanism.

    Science.gov (United States)

    Granovsky, Alexey E; Clark, Matthew C; McElheny, Dan; Heil, Gary; Hong, Jia; Liu, Xuedong; Kim, Youngchang; Joachimiak, Grazyna; Joachimiak, Andrzej; Koide, Shohei; Rosner, Marsha Rich

    2009-03-01

    Raf kinase inhibitory protein (RKIP/PEBP1), a member of the phosphatidylethanolamine binding protein family that possesses a conserved ligand-binding pocket, negatively regulates the mammalian mitogen-activated protein kinase (MAPK) signaling cascade. Mutation of a conserved site (P74L) within the pocket leads to a loss or switch in the function of yeast or plant RKIP homologues. However, the mechanism by which the pocket influences RKIP function is unknown. Here we show that the pocket integrates two regulatory signals, phosphorylation and ligand binding, to control RKIP inhibition of Raf-1. RKIP association with Raf-1 is prevented by RKIP phosphorylation at S153. The P74L mutation increases kinase interaction and RKIP phosphorylation, enhancing Raf-1/MAPK signaling. Conversely, ligand binding to the RKIP pocket inhibits kinase interaction and RKIP phosphorylation by a noncompetitive mechanism. Additionally, ligand binding blocks RKIP association with Raf-1. Nuclear magnetic resonance studies reveal that the pocket is highly dynamic, rationalizing its capacity to interact with distinct partners and be involved in allosteric regulation. Our results show that RKIP uses a flexible pocket to integrate ligand binding- and phosphorylation-dependent interactions and to modulate the MAPK signaling pathway. This mechanism is an example of an emerging theme involving the regulation of signaling proteins and their interaction with effectors at the level of protein dynamics.

  10. Identification of active pocket and protein druggability within envelope glycoprotein GP2 from Ebola virus

    Institute of Scientific and Technical Information of China (English)

    Beuy Joob; Viroj Wiwanitkit

    2014-01-01

    The drug searching for combating the present outbreak of Ebola virus infection is the urgent activity at present. Finding the new effective drug at present must base on the molecular analysis of the pathogenic virus. The in-depth analysis of the viral protein to find the binding site, active pocket is needed. Here, the authors analyzed the envelope glycoprotein GP2 from Ebola virus. Identification of active pocket and protein druggability within envelope glycoprotein GP2 from Ebola virus was done. According to this assessment, 7 active pockets with varied druggability could be identified.

  11. Identification of active pocket and protein druggability within envelope glycoprotein GP2 from Ebola virus

    Institute of Scientific and Technical Information of China (English)

    Beuy; Joob; Viroj; Wiwanitkit

    2014-01-01

    The drug searching for combating the present outbreak of Ebola virus infection is the urgent activity at present.Finding the new effective drug at present must base on the molecular analysis of the pathogenic virus.The in-depth analysis of the viral protein to find the binding site,active pocket is needed.Here,the authors analyzed the envelope glycoprotein GP2 from Ebola virus.Identification of active pocket and protein draggability within envelope glycoprotein GP2 from Ebola virus was done.According to this assessment,7 active pockets with varied draggability could be identified.

  12. Single-chain antibody-fragment M6P-1 possesses a mannose 6-phosphate monosaccharide-specific binding pocket that distinguishes N-glycan phosphorylation in a branch-specific manner†

    Science.gov (United States)

    Blackler, Ryan J; Evans, Dylan W; Smith, David F; Cummings, Richard D; Brooks, Cory L; Braulke, Thomas; Liu, Xinyu; Evans, Stephen V; Müller-Loennies, Sven

    2016-01-01

    The acquisition of mannose 6-phosphate (Man6P) on N-linked glycans of lysosomal enzymes is a structural requirement for their transport from the Golgi apparatus to lysosomes mediated by the mannose 6-phosphate receptors, 300 kDa cation-independent mannose 6-phosphate receptor (MPR300) and 46 kDa cation-dependent mannose 6-phosphate receptor (MPR46). Here we report that the single-chain variable domain (scFv) M6P-1 is a unique antibody fragment with specificity for Man6P monosaccharide that, through an array-screening approach against a number of phosphorylated N-glycans, is shown to bind mono- and diphosphorylated Man6 and Man7 glycans that contain terminal αMan6P(1 → 2)αMan(1 → 3)αMan. In contrast to MPR300, scFv M6P-1 does not bind phosphodiesters, monophosphorylated Man8 or mono- or diphosphorylated Man9 structures. Single crystal X-ray diffraction analysis to 2.7 Å resolution of Fv M6P-1 in complex with Man6P reveals that specificity and affinity is achieved via multiple hydrogen bonds to the mannose ring and two salt bridges to the phosphate moiety. In common with both MPRs, loss of binding was observed for scFv M6P-1 at pH values below the second pKa of Man6P (pKa = 6.1). The structures of Fv M6P-1 and the MPRs suggest that the change of the ionization state of Man6P is the main driving force for the loss of binding at acidic lysosomal pH (e.g. lysosome pH ∼ 4.6), which provides justification for the evolution of a lysosomal enzyme transport pathway based on Man6P recognition. PMID:26503547

  13. Air pocket removal from downward sloping pipes

    NARCIS (Netherlands)

    Pothof, I.W.M.; Clemens, F.H.L.R.

    2012-01-01

    Air-water flow is an undesired condition in water pipelines and hydropower tunnels. Water pipelines and wastewater pressure mains in particular are subject to air pocket accumulation in downward sloping reaches, such as inverted siphons or terrain slopes. Air pockets cause energy losses and an assoc

  14. The system architecture of the Pocket Companion

    NARCIS (Netherlands)

    Havinga, Paul J.M.; Smit, Gerard J.M.

    1997-01-01

    In the Moby Dick project we design the architecture of a so-called Pocket Companion. It is a small personal portable computer with wireless communication facilities for every day use. The typical use of the Pocket Companion induces a number of requirements concerning security, performance, energy co

  15. NMR-based Structural Analysis of Threonylcarbamoyl-AMP Synthase and Its Substrate Interactions.

    Science.gov (United States)

    Harris, Kimberly A; Bobay, Benjamin G; Sarachan, Kathryn L; Sims, Alexis F; Bilbille, Yann; Deutsch, Christopher; Iwata-Reuyl, Dirk; Agris, Paul F

    2015-08-14

    The hypermodified nucleoside N(6)-threonylcarbamoyladenosine (t(6)A37) is present in many distinct tRNA species and has been found in organisms in all domains of life. This post-transcriptional modification enhances translation fidelity by stabilizing the anticodon/codon interaction in the ribosomal decoding site. The biosynthetic pathway of t(6)A37 is complex and not well understood. In bacteria, the following four proteins have been discovered to be both required and sufficient for t(6)A37 modification: TsaC, TsaD, TsaB, and TsaE. Of these, TsaC and TsaD are members of universally conserved protein families. Although TsaC has been shown to catalyze the formation of L-threonylcarbamoyl-AMP, a key intermediate in the biosynthesis of t(6)A37, the details of the enzymatic mechanism remain unsolved. Therefore, the solution structure of Escherichia coli TsaC was characterized by NMR to further study the interactions with ATP and L-threonine, both substrates of TsaC in the biosynthesis of L-threonylcarbamoyl-AMP. Several conserved amino acids were identified that create a hydrophobic binding pocket for the adenine of ATP. Additionally, two residues were found to interact with L-threonine. Both binding sites are located in a deep cavity at the center of the protein. Models derived from the NMR data and molecular modeling reveal several sites with considerable conformational flexibility in TsaC that may be important for L-threonine recognition, ATP activation, and/or protein/protein interactions. These observations further the understanding of the enzymatic reaction catalyzed by TsaC, a threonylcarbamoyl-AMP synthase, and provide structure-based insight into the mechanism of t(6)A37 biosynthesis.

  16. Pocket companion to PMI's PMBOK guide

    CERN Document Server

    Snijders, Paul; Zandhuis, Anton

    2010-01-01

    This pocket guide is based on the PMBOK Guide® Fourth Edition.This pocket guide supplies a summary of the PMBOK Guide® , to provide a quick introduction as well as a structured overview of this method for project management.This pocket guide deals with the key issues and themes within project management and PMBOK:A short overview of the activities of PMI Inc., The organization and its standards: PMBOK Guide®, Standard for Project Portfolio Management, Standard for Program Management, OPM3.The essentials of the Project Lifecycle and Organization.What are the key project management knowledge ar

  17. Parameter selection of pocket extraction algorithm using interaction interface

    Institute of Scientific and Technical Information of China (English)

    KIM Chong-Min; WON Chung-In; RYU Joonghyun; CHO Cheol-Hyung; BHAK Jonghwa; KIM Deok-Soo

    2006-01-01

    Pockets in proteins have been known to be very important for the life process. There have been several studies in the past to automatically extract the pockets from the structure information of known proteins. However, it is difficult to find a study comparing the precision of the extracted pockets from known pockets on the protein. In this paper, we propose an algorithm for extracting pockets from structure data of proteins and analyze the quality of the algorithm by comparing the extracted pockets with some known pockets. These results in this paper can be used to set the parameter values of the pocket extraction algorithm for getting better results.

  18. Macintosh Troubleshooting Pocket Guide for Mac OS

    CERN Document Server

    Lerner, David; Corporation, Tekserve

    2009-01-01

    The Macintosh Troubleshooting Pocket Guide covers the most common user hardware and software trouble. It's not just a book for Mac OS X (although it includes tips for OS X and Jaguar), it's for anyone who owns a Mac of any type-- there are software tips going back as far as OS 6. This slim guide distills the answers to the urgent questions that Tekserve's employee's answer every week into a handy guide that fits in your back pocket or alongside your keyboard.

  19. Optimization problems related to zigzag pocket machining

    Energy Technology Data Exchange (ETDEWEB)

    Arkin, E.M.; Held, M.; Smith, C.L. [State Univ. of New York, Stony Brook, NY (United States)

    1996-12-31

    A fundamental problem of manufacturing is to produce mechanical parts from billets by clearing areas within specified boundaries from the material. Based on a graph-theoretical formulation, the algorithmic handling of one particular machining problem {open_quote}zigzag pocket machining{close_quote} is investigated. We present a linear-time algorithm that ensures that no region of the pocket is machined repeatedly, thereby attempting to minimize the number of tool retractions required. This problem is shown to be NP-hard for pockets with holes. Our algorithm is a provable good in the sense that the machining path generated for a pocket with h holes requires at most 5. OPT+ 6 - h retractions, where OPT is the (unknown) minimum number of retractions required by any algorithm. The algorithm has been implemented, and practical tests for pockets without holes clearly showed that one can expect an approximation factor of about 1.5 for practical examples, rather than the factor 5 as proved by our analysis.

  20. Evidence for designing health promoting pocket parks

    DEFF Research Database (Denmark)

    Peschardt, Karin Kragsig; Stigsdotter, Ulrika K.

    2014-01-01

    The use of urban green environments has repeatedly been associated with improved health and well-being for people living in cities. This study focuses on the health promoting potential of pocket parks in the dense city area of Copenhagen. A natural experiment was conducted, which evaluated one...... pocket park, Dantes Plads, before and after a redesign. Six people were interviewed about their perception of the change. First of all, the results show that Dantes Plads is primarily used for ‘rest and restitution’. Furthermore, the interviewees prefer to have the presence of sun, shade and planting....... The findings add to existing knowledge on the design of health promoting pocket parks for ‘rest and restitution’ in dense city areas....

  1. Chemical Composition and Seasonality of Aromatic Mediterranean Plant Species by NMR-Based Metabolomics

    Directory of Open Access Journals (Sweden)

    Monica Scognamiglio

    2015-01-01

    Full Text Available An NMR-based metabolomic approach has been applied to analyse seven aromatic Mediterranean plant species used in traditional cuisine. Based on the ethnobotanical use of these plants, the approach has been employed in order to study the metabolic changes during different seasons. Primary and secondary metabolites have been detected and quantified. Flavonoids (apigenin, quercetin, and kaempferol derivatives and phenylpropanoid derivatives (e.g., chlorogenic and rosmarinic acid are the main identified polyphenols. The richness in these metabolites could explain the biological properties ascribed to these plant species.

  2. NMR-based metabolomics of prostate cancer: a protagonist in clinical diagnostics.

    Science.gov (United States)

    Kumar, Deepak; Gupta, Ashish; Nath, Kavindra

    2016-06-01

    Advances in the application of NMR spectroscopy-based metabolomic profiling of prostate cancer comprises a potential tactic for understanding the impaired biochemical pathways arising due to a disease evolvement and progression. This technique involves qualitative and quantitative estimation of plethora of small molecular weight metabolites of body fluids or tissues using state-of-the-art chemometric methods delivering an important platform for translational research from basic to clinical, to reveal the pathophysiological snapshot in a single step. This review summarizes the present arrays and recent advancements in NMR-based metabolomics and a glimpse of currently used medical imaging tactics, with their role in clinical diagnosis of prostate cancer.

  3. Comparison of Fruits of Forsythia suspensa at Two Different Maturation Stages by NMR-Based Metabolomics.

    Science.gov (United States)

    Jia, Jinping; Zhang, Fusheng; Li, Zhenyu; Qin, Xuemei; Zhang, Liwei

    2015-05-29

    Forsythiae Fructus (FF), the dried fruit of Forsythia suspensa, has been widely used as a heat-clearing and detoxifying herbal medicine in China. Green FF (GF) and ripe FF (RF) are fruits of Forsythia suspensa at different maturity stages collected about a month apart. FF undergoes a complex series of physical and biochemical changes during fruit ripening. However, the clinical uses of GF and RF have not been distinguished to date. In order to comprehensively compare the chemical compositions of GF and RF, NMR-based metabolomics coupled with HPLC and UV spectrophotometry methods were adopted in this study. Furthermore, the in vitro antioxidant and antibacterial activities of 50% methanol extracts of GF and RF were also evaluated. A total of 27 metabolites were identified based on NMR data, and eight of them were found to be different between the GF and RF groups. The GF group contained higher levels of forsythoside A, forsythoside C, cornoside, rutin, phillyrin and gallic acid and lower levels of rengyol and β-glucose compared with the RF group. The antioxidant activity of GF was higher than that of RF, but no significant difference was observed between the antibacterial activities of GF and RF. Given our results showing their distinct chemical compositions, we propose that NMR-based metabolic profiling can be used to discriminate between GF and RF. Differences in the chemical and biological activities of GF and RF, as well as their clinical efficacies in traditional Chinese medicine should be systematically investigated in future studies.

  4. Frameworks for IT management a pocket guide

    CERN Document Server

    Rozemeijer, Eric

    2008-01-01

    This Pocket Guide is a concise summary of the Frameworks for IT Management. A quick, portable reference tool to the standards used within the Service Management community.English version available: September 2007, Dutch, French, Japanese, Spanish, German available February 2008.

  5. Pocket Checklists of Indonesian timber trees

    NARCIS (Netherlands)

    Prawira, Soewanda A.; Tantra, I.G.M.; Whitmore, T.C.

    1984-01-01

    Indonesia as yet does not have a comprehensive account of the forest trees which reach timber size (35 cm dbh = 14 inch or 105 cm gbh = 42 inch). A project has been started in August 1983 by the Botany Section of the Forest Research Institute in Bogor, Indonesia, to prepare pocket checklists of the

  6. Evidence for designing health promoting pocket parks

    DEFF Research Database (Denmark)

    Peschardt, Karin Kragsig; Stigsdotter, Ulrika K.

    2014-01-01

    pocket park, Dantes Plads, before and after a redesign. Six people were interviewed about their perception of the change. First of all, the results show that Dantes Plads is primarily used for ‘rest and restitution’. Furthermore, the interviewees prefer to have the presence of sun, shade and planting......The use of urban green environments has repeatedly been associated with improved health and well-being for people living in cities. This study focuses on the health promoting potential of pocket parks in the dense city area of Copenhagen. A natural experiment was conducted, which evaluated one...... in relation to rest and restitution, while varied ‘terrain’ may create fascination thereby providing the opportunity for restoration. ‘Noise level’ is perceived differently from subject to subject, while ‘benches’ as well as ‘visual angels’ should not be oriented directly towards disturbing surroundings...

  7. NMR-based metabolic profiling of rice wines by F(2)-selective total correlation spectra.

    Science.gov (United States)

    Koda, Masanori; Furihata, Kazuo; Wei, Feifei; Miyakawa, Takuya; Tanokura, Masaru

    2012-05-16

    In this study, we performed NMR-based metabolic profiling of major rice wines (Japanese sake, Chinese Shaoxing wine, and Korean makgeolli). In the (1)H NMR spectra, the rice wines showed broad resonances in the region of about 7.9-9.0 ppm. These resonances showed many and complex correlations with approximately 0.5-4.5 ppm in the F(2)-selective TOCSY (total correlation spectroscopy) spectra, and these correlations were attributed mainly to peptides. These spectral patterns were characteristic of individual rice wines, and the combination of F(2)-selective TOCSY spectra and principal component analysis enabled us to classify the rice wine species. Furthermore, it also provided information about raw materials, namely, what type of koji (rice koji or wheat koji) was used. These spectra may be useful as a new "fingerprint" for quality control or food authentication.

  8. NMR-Based Multi Parametric Quality Control of Fruit Juices: SGF Profiling

    Directory of Open Access Journals (Sweden)

    Fang Fang

    2009-11-01

    Full Text Available With SGF Profiling™ we introduce an NMR-based screening method for the quality control of fruit juices. This method has been developed in a joint effort by Bruker BioSpin GmbH and SGF International e.V. The system is fully automated with respect to sample transfer, measurement, data analysis and reporting and is set up on an Avance 400 MHz flow-injection NMR spectrometer. For each fruit juice a multitude of parameters related to quality and authenticity are evaluated simultaneously from a single data set acquired within a few minutes. This multimarker/multi-aspect NMR screening approach features low cost-per-sample and is highly competitive with conventional and targeted fruit juice quality control methods.

  9. Windows® 7 Administrator's Pocket Consultant

    CERN Document Server

    Stanek, William

    2009-01-01

    Portable and precise, this pocket-sized guide delivers immediate answers for the day-to-day administration of Windows 7-from desktop configuration and management to networking and security issues. Zero in on core support and maintenance tasks by using quick-reference tables, instructions, and lists. You'll get the precise information you need to solve problems and get the job done-whether at your desk or in the field!

  10. Newnes radio and electronics engineer's pocket book

    CERN Document Server

    Moorshead, H W; Perry, J

    1978-01-01

    Newnes Radio and Electronics Engineer's Pocket Book, Fifteenth Edition provides reference of the information relevant in radio and electronics engineering. The book presents tables, illustrations, and diagrams of various data used in radio and electronics engineering. The coverage of the text includes abbreviations and symbols, electrical equations, and code conversions. The text will be useful to engineers, technicians, and other professionals who require a reference about the different aspects of radio and electronics.

  11. ISO27001 / ISO27002 a pocket guide

    CERN Document Server

    Calder, Alan

    2013-01-01

    Information is one of your organisation's most important resources. Keeping it secure is therefore vital to your business. This handy pocket guide is an essential overview of two key information security standards that cover the formal requirements (ISO27001:2013) for creating an Information Security Management System (ISMS), and the best-practice recommendations (ISO27002:2013) for those responsible for initiating, implementing or maintaining it.

  12. Comparison of Fruits of Forsythia suspensa at Two Different Maturation Stages by NMR-Based Metabolomics

    Directory of Open Access Journals (Sweden)

    Jinping Jia

    2015-05-01

    Full Text Available Forsythiae Fructus (FF, the dried fruit of Forsythia suspensa, has been widely used as a heat-clearing and detoxifying herbal medicine in China. Green FF (GF and ripe FF (RF are fruits of Forsythia suspensa at different maturity stages collected about a month apart. FF undergoes a complex series of physical and biochemical changes during fruit ripening. However, the clinical uses of GF and RF have not been distinguished to date. In order to comprehensively compare the chemical compositions of GF and RF, NMR-based metabolomics coupled with HPLC and UV spectrophotometry methods were adopted in this study. Furthermore, the in vitro antioxidant and antibacterial activities of 50% methanol extracts of GF and RF were also evaluated. A total of 27 metabolites were identified based on NMR data, and eight of them were found to be different between the GF and RF groups. The GF group contained higher levels of forsythoside A, forsythoside C, cornoside, rutin, phillyrin and gallic acid and lower levels of rengyol and β-glucose compared with the RF group. The antioxidant activity of GF was higher than that of RF, but no significant difference was observed between the antibacterial activities of GF and RF. Given our results showing their distinct chemical compositions, we propose that NMR-based metabolic profiling can be used to discriminate between GF and RF. Differences in the chemical and biological activities of GF and RF, as well as their clinical efficacies in traditional Chinese medicine should be systematically investigated in future studies.

  13. NMR-based metabolomics in human disease diagnosis: Applications, limitations, and recommendations

    KAUST Repository

    Emwas, Abdul-Hamid M.

    2013-04-03

    Metabolomics is a dynamic and emerging research field, similar to proteomics, transcriptomics and genomics in affording global understanding of biological systems. It is particularly useful in functional genomic studies in which metabolism is thought to be perturbed. Metabolomics provides a snapshot of the metabolic dynamics that reflect the response of living systems to both pathophysiological stimuli and/or genetic modification. Because this approach makes possible the examination of interactions between an organism and its diet or environment, it is particularly useful for identifying biomarkers of disease processes that involve the environment. For example, the interaction of a high fat diet with cardiovascular disease can be studied via such a metabolomics approach by modeling the interaction between genes and diet. The high reproducibility of NMR-based techniques gives this method a number of advantages over other analytical techniques in large-scale and long-term metabolomic studies, such as epidemiological studies. This approach has been used to study a wide range of diseases, through the examination of biofluids, including blood plasma/serum, urine, blister fluid, saliva and semen, as well as tissue extracts and intact tissue biopsies. However, complicating the use of NMR spectroscopy in biomarker discovery is the fact that numerous variables can effect metabolic composition including, fasting, stress, drug administration, diet, gender, age, physical activity, life style and the subject\\'s health condition. To minimize the influence of these variations in the datasets, all experimental conditions including sample collection, storage, preparation as well as NMR spectroscopic parameters and data analysis should be optimized carefully and conducted in an identical manner as described by the local standard operating protocol. This review highlights the potential applications of NMR-based metabolomics studies and gives some recommendations to improve sample

  14. Mac OS X Snow Leopard pocket guide

    CERN Document Server

    Seiblod, Chris

    2009-01-01

    Whether you're new to the Mac or a longtime user, this handy book is the quickest way to get up to speed on Snow Leopard. Packed with concise information in an easy-to-read format, Mac OS X Snow Leopard Pocket Guide covers what you need to know and is an ideal resource for problem-solving on the fly. This book goes right to the heart of Snow Leopard, with details on system preferences, built-in applications, and utilities. You'll also find configuration tips, keyboard shortcuts, guides for troubleshooting, lots of step-by-step instructions, and more. Learn about new features and changes s

  15. Newnes passive and discrete circuits pocket book

    CERN Document Server

    MARSTON, R M

    2000-01-01

    Newnes Passive and Discrete Circuits Pocket Book is aimed at all engineers, technicians, students and experimenters who can build a design directly from a circuit diagram. In a highly concise form Ray Marston presents a huge compendium of circuits that can be built as they appear, adapted or used as building blocks. The devices used have been carefully chosen for their ease of availability and reasonable price. The selection of devices has been thoroughly updated for the second edition, which has also been expanded to cover the latest ICs.The three sections of the book cover: Moder

  16. Python pocket reference, version 2.4

    CERN Document Server

    Lutz, Mark

    2005-01-01

    Python is optimized for quality, productivity, portability, and integration. Hundreds of thousands of Python developers around the world rely on Python for general-purpose tasks, Internet scripting, systems programming, user interfaces, and product customization. Available on all major computing platforms, including commercial versions of Unix, Linux, Windows, and Mac OS X, Python is portable, powerful and remarkable easy to use. With its convenient, quick-reference format, Python Pocket Reference, 3rd Edition is the perfect on-the-job reference. More importantly, it's now been refreshed

  17. AIR for Javascript Developers Pocket Guide

    CERN Document Server

    Chambers, Mike; Hoyt, Kevin; Georgita, Dragos

    2009-01-01

    This book is the official guide to Adobe ® AIR[TM], written by members of the AIR team. With Adobe AIR, web developers can use technologies like HTML and JavaScript to build and deploy web applications to the desktop. Packed with examples, this book explains how AIR works and features recipes for performing common runtime tasks. Part of the Adobe Developer Library, this concise pocket guide explains: What Adobe AIR is, and the problems this runtime aims to solveHow to set up your development environmentThe HTML and JavaScript environments within AIRHow to create your first AIR application

  18. Pardon my French pocket French slang dictionary

    CERN Document Server

    Nicholson, Kate

    2009-01-01

    A runaway bestseller since its launch, Pardon My French! is a pocket-sized dictionary of French and English slang as it is spoken today. This edition includes even more non-standard language from the colloquial to the vulgar, with over 2,500 terms added. Ideal for both Francophobes and Francophiles alike. Over 14,000 referencesDozens of helpful usage notes to explain interesting meanings and originsThematic panels on the slang of sex, alcohol, violence etcFully updated and revised panels on varieties of slang (eg verlan, javanais, Black American slang)

  19. Evidence of vintage effects on grape wines using 1H NMR-based metabolomic study.

    Science.gov (United States)

    Lee, Jang-Eun; Hwang, Geum-Sook; Van Den Berg, Frans; Lee, Cherl-Ho; Hong, Young-Shick

    2009-08-19

    The chemical composition of grape wines varies with grape variety, environmental factors of climate and soil, and bacterial strains, which can each affect the wine quality. Using (1)H NMR analysis coupled with multivariate statistical data sets, we investigated the effects of grape vintage on metabolic profiles of wine and the relationship between wine metabolites and meteorological data. Principal component analysis (PCA) showed a clear differentiation between Meoru wines that were vinified with the same yeast strain and Meoru grapes harvested from the same vineyard but with a different vintage. The metabolites contributing to the differentiation were identified as 2,3-butandiol, lactic acid, alanine, proline, gamma-aminobutyric acid (GABA), choline, and polyphenols, by complementary PCA loading plot. Markedly higher levels of proline, lactic acid and polyphenols were observed in the 2006 vintage wines compared to those of 2007 vintage, showing excellent agreement with the meteorological data that the sun-exposed time and rainfall in 2006 were approximately two times more and four times less, respectively, than those in 2007. These results revealed the important role of climate during ripening period in the chemical compositions of the grape. This study highlights the reliability of NMR-based metabolomic data by integration with meteorological data in characterizing wine or grape.

  20. 1H NMR-based serum metabolic profiling in compensated and decompensated cirrhosis

    Institute of Scientific and Technical Information of China (English)

    Su-Wen Qi; Zhi-Guang Tu; Wu-Jian Peng; Lin-Xian Wang; Xin Ou-Yang; An-Ji Cai; Yong Dai

    2012-01-01

    AIM: To study the metabolic profiling of serum samples from compensated and decompensated cirrhosis patients.METHODS: A pilot metabolic profiling study was conducted using three groups: compensated cirrhosis patients (n = 30), decompensated cirrhosis patients (n = 30) and healthy controls (n = 30). A 1H nuclear magnetic resonance (NMR)-based metabonomics approach was used to obtain the serum metabolic profiles of the samples. The acquired data were processed by multivariate principal component analysis and orthogonal partial least-squares discriminant analysis (OPLS-DA). RESULTS: The OPLS-DA model was capable of distinguishing between decompensated and compensated cirrhosis patients, with an R2Y of 0.784 and a Q2Y of 0.598. Twelve metabolites, such as pyruvate, phenylalanine and succinate, were identified as the most influential factors for the difference between the two groups. The validation of the diagnosis prediction showed that the accuracy of the OPLSDA model was 85% (17/20). CONCLUSION: 1H NMR spectra combined with pattern recognition analysis techniques offer a new way to diagnose compensated and decompensated cirrhosis in the future.

  1. Quantification of organic acids in beer by nuclear magnetic resonance (NMR)-based methods

    Energy Technology Data Exchange (ETDEWEB)

    Rodrigues, J.E.A. [CICECO-Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro (Portugal); Erny, G.L. [CESAM - Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro (Portugal); Barros, A.S. [QOPNAA-Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro (Portugal); Esteves, V.I. [CESAM - Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro (Portugal); Brandao, T.; Ferreira, A.A. [UNICER, Bebidas de Portugal, Leca do Balio, 4466-955 S. Mamede de Infesta (Portugal); Cabrita, E. [Department of Chemistry, New University of Lisbon, 2825-114 Caparica (Portugal); Gil, A.M., E-mail: agil@ua.pt [CICECO-Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro (Portugal)

    2010-08-03

    The organic acids present in beer provide important information on the product's quality and history, determining organoleptic properties and being useful indicators of fermentation performance. NMR spectroscopy may be used for rapid quantification of organic acids in beer and different NMR-based methodologies are hereby compared for the six main acids found in beer (acetic, citric, lactic, malic, pyruvic and succinic). The use of partial least squares (PLS) regression enables faster quantification, compared to traditional integration methods, and the performance of PLS models built using different reference methods (capillary electrophoresis (CE), both with direct and indirect UV detection, and enzymatic essays) was investigated. The best multivariate models were obtained using CE/indirect detection and enzymatic essays as reference and their response was compared with NMR integration, either using an internal reference or an electrical reference signal (Electronic REference To access In vivo Concentrations, ERETIC). NMR integration results generally agree with those obtained by PLS, with some overestimation for malic and pyruvic acids, probably due to peak overlap and subsequent integral errors, and an apparent relative underestimation for citric acid. Overall, these results make the PLS-NMR method an interesting choice for organic acid quantification in beer.

  2. NMR based serum metabolomics reveals a distinctive signature in patients with Lupus Nephritis

    Science.gov (United States)

    Guleria, Anupam; Pratap, Avadhesh; Dubey, Durgesh; Rawat, Atul; Chaurasia, Smriti; Sukesh, Edavalath; Phatak, Sanat; Ajmani, Sajal; Kumar, Umesh; Khetrapal, Chunni Lal; Bacon, Paul; Misra, Ramnath; Kumar, Dinesh

    2016-01-01

    Management of patient with Lupus Nephritis (LN) continues to remain a challenge for the treating physicians because of considerable morbidity and even mortality. The search of biomarkers in serum and urine is a focus of researchers to unravel new targets for therapy. In the present study, the utility of NMR-based serum metabolomics has been evaluated for the first time in discriminating LN patients from non-nephritis lupus patients (SLE) and further to get new insights into the underlying disease processes for better clinical management. Metabolic profiling of sera obtained from 22 SLE patients, 40 LN patients and 30 healthy controls (HC) were performed using high resolution 1D 1H-CPMG and diffusion edited NMR spectra to identify the potential molecular biomarkers. Using multivariate analysis, we could distinguish SLE and LN patients from HC and LN from SLE patients. Compared to SLE patients, the LN patients had increased serum levels of lipid metabolites (including LDL/VLDL lipoproteins), creatinine and decreased levels of acetate. Our results revealed that metabolic markers especially lipids and acetate derived from NMR spectroscopy has high sensitivity and specificity to distinguish LN among SLE patients and has the potential to be a useful adjunctive tool in diagnosis and clinical management of LN. PMID:27739464

  3. Spectroscopic correlation analysis of NMR-based metabonomics in exercise science.

    Science.gov (United States)

    Kirwan, Gemma M; Coffey, Vernon G; Niere, Julie O; Hawley, John A; Adams, Michael J

    2009-10-12

    Spectroscopic studies of complex clinical fluids have led to the application of a more holistic approach to their chemical analysis becoming more popular and widely employed. The efficient and effective interpretation of multidimensional spectroscopic data relies on many chemometric techniques and one such group of tools is represented by so-called correlation analysis methods. Typical of these techniques are two-dimensional correlation analysis and statistical total correlation spectroscopy (STOCSY). Whilst the former has largely been applied to optical spectroscopic analysis, STOCSY was developed and has been applied almost exclusively to NMR metabonomic studies. Using a (1)H NMR study of human blood plasma, from subjects recovering from exhaustive exercise trials, the basic concepts and applications of these techniques are examined. Typical information from their application to NMR-based metabonomics is presented and their value in aiding interpretation of NMR data obtained from biological systems is illustrated. Major energy metabolites are identified in the NMR spectra and the dynamics of their appearance and removal from plasma during exercise recovery are illustrated and discussed. The complementary nature of two-dimensional correlation analysis and statistical total correlation spectroscopy are highlighted.

  4. (1)H NMR-based metabolomic approach for understanding the fermentation behaviors of wine yeast strains.

    Science.gov (United States)

    Son, Hong-Seok; Hwang, Geum-Sook; Kim, Ki Myong; Kim, Eun-Young; van den Berg, Frans; Park, Won-Mok; Lee, Cherl-Ho; Hong, Young-Shick

    2009-02-01

    (1)H NMR spectroscopy coupled with multivariate statistical analysis was used for the first time to investigate metabolic changes in musts during alcoholic fermentation and wines during aging. Three Saccharomyces cerevisiae yeast strains (RC-212, KIV-1116, and KUBY-501) were also evaluated for their impacts on the metabolic changes in must and wine. Pattern recognition (PR) methods, including PCA, PLS-DA, and OPLS-DA scores plots, showed clear differences for metabolites among musts or wines for each fermentation stage up to 6 months. Metabolites responsible for the differentiation were identified as valine, 2,3-butanediol (2,3-BD), pyruvate, succinate, proline, citrate, glycerol, malate, tartarate, glucose, N-methylnicotinic acid (NMNA), and polyphenol compounds. PCA scores plots showed continuous movements away from days 1 to 8 in all musts for all yeast strains, indicating continuous and active fermentation. During alcoholic fermentation, the highest levels of 2,3-BD, succinate, and glycerol were found in musts with the KIV-1116 strain, which showed the fastest fermentation or highest fermentative activity of the three strains, whereas the KUBY-501 strain showed the slowest fermentative activity. This study highlights the applicability of NMR-based metabolomics for monitoring wine fermentation and evaluating the fermentative characteristics of yeast strains.

  5. NMR-based screening method for transglutaminases: rapid analysis of their substrate specificities and reaction rates.

    Science.gov (United States)

    Shimba, Nobuhisa; Yokoyama, Kei-ichi; Suzuki, Ei-ichiro

    2002-03-13

    Incorporation of inter- or intramolecular covalent cross-links into food proteins with microbial transglutaminase (MTG) improves the physical and textural properties of many food proteins such as tofu, boiled fish paste, and sausage. Other transglutaminases (TGases) are expected to be used in the same way, and also to extend the scope of industrial applications to materials, drugs, and so on. The TGases have great diversity, not only in amino acid sequence and size, but also in their substrate specificities and catalytic activities, and therefore, it is quite difficult to estimate their reactivity. We have developed an NMR-based method using the enzymatic labeling technique (ELT) for simultaneous analysis of the substrate specificities and reaction rates of TGases. It is quite useful for comparing the existing TGases and for screening new TGases or TGases variants. This method has shown that MTG is superior for industrial use because of its lower substrate specificity compared with those of guinea pig liver transglutaminase (GTG) and red sea bream liver transglutaminase (FTG). We have also found that an MTG variant lacking an N-terminal aspartic acid residue has higher activity than that of the native enzyme.

  6. Approaches for Identification of HIV-1 Entry Inhibitors Targeting gp41 Pocket

    Directory of Open Access Journals (Sweden)

    Asim K. Debnath

    2013-01-01

    Full Text Available The hydrophobic pocket in the HIV-1 gp41 N-terminal heptad repeat (NHR domain plays an important role in viral fusion and entry into the host cell, and serves as an attractive target for development of HIV-1 fusion/entry inhibitors. The peptide anti-HIV drug targeting gp41 NHR, T-20 (generic name: enfuvirtide; brand name: Fuzeon, was approved by the U.S. FDA in 2003 as the first HIV fusion/entry inhibitor for treatment of HIV/AIDS patients who fail to respond to the current antiretroviral drugs. However, because T20 lacks the pocket-binding domain (PBD, it exhibits low anti-HIV-1 activity and short half-life. Therefore, several next-generation HIV fusion inhibitory peptides with PBD have been developed. They possess longer half-life and more potent antiviral activity against a broad spectrum of HIV-1 strains, including the T-20-resistant variants. Nonetheless, the clinical application of these peptides is still limited by the lack of oral availability and the high cost of production. Thus, development of small molecule compounds targeting the gp41 pocket with oral availability has been promoted. This review describes the main approaches for identification of HIV fusion/entry inhibitors targeting the gp41 pocket and summarizes the latest progress in developing these inhibitors as a new class of anti-HIV drugs.

  7. PoLi: A Virtual Screening Pipeline Based on Template Pocket and Ligand Similarity.

    Science.gov (United States)

    Roy, Ambrish; Srinivasan, Bharath; Skolnick, Jeffrey

    2015-08-24

    Often in pharmaceutical research the goal is to identify small molecules that can interact with and appropriately modify the biological behavior of a new protein target. Unfortunately, most proteins lack both known structures and small molecule binders, prerequisites of many virtual screening, VS, approaches. For such proteins, ligand homology modeling, LHM, that copies ligands from homologous and perhaps evolutionarily distant template proteins, has been shown to be a powerful VS approach to identify possible binding ligands. However, if we want to target a specific pocket for which there is no homologous holo template protein structure, then LHM will not work. To address this issue, in a new pocket-based approach, PoLi, we generalize LHM by exploiting the fact that the number of distinct small molecule ligand-binding pockets in proteins is small. PoLi identifies similar ligand-binding pockets in a holo template protein library, selectively copies relevant parts of template ligands, and uses them for VS. In practice, PoLi is a hybrid structure and ligand-based VS algorithm that integrates 2D fingerprint-based and 3D shape-based similarity metrics for improved virtual screening performance. On standard DUD and DUD-E benchmark databases, using modeled receptor structures, PoLi achieves an average enrichment factor of 13.4 and 9.6, respectively, in the top 1% of the screened library. In contrast, traditional docking-based VS using AutoDock Vina and homology-based VS using FINDSITE(filt) have an average enrichment of 1.6 (3.0) and 9.0 (7.9) on the DUD (DUD-E) sets, respectively. Experimental validation of PoLi predictions on dihydrofolate reductase, DHFR, using differential scanning fluorimetry, DSF, identifies multiple ligands with diverse molecular scaffolds, thus demonstrating the advantage of PoLi over current state-of-the-art VS methods.

  8. Oracle PL/SQL Language Pocket Reference

    CERN Document Server

    Feuerstein, Steven; Dawes, Chip

    2004-01-01

    While it's good to have a book with all the answers--like your trusty copy of Oracle PL/SQL Programming-- how often do you need all the answers? More likely, you just need a reminder, a quick answer to a problem you're up against. For these times, nothing's handier than the new edition of the Oracle PL/SQL Language Pocket Reference by PL/SQL experts Stephen Feuerstein, Bill Pribyl, and Chip Dawes. Newly updated for Oracle10g, this little book is always at the ready for the quick problem solving you need. The 3rd edition of this popular mini-reference boils down the most vital information fr

  9. 1H NMR- based metabolomics approaches as non- invasive tools for diagnosis of endometriosis

    Directory of Open Access Journals (Sweden)

    Negar Ghazi

    2016-01-01

    Full Text Available Background: So far, non-invasive diagnostic approaches such as ultrasound, magnetic resonance imaging, or blood tests do not have sufficient diagnostic power for endometriosis disease. Lack of a non-invasive diagnostic test contributes to the long delay between onset of symptoms and diagnosis of endometriosis. Objective: The present study focuses on the identification of predictive biomarkers in serum by pattern recognition techniques and uses partial least square discriminant analysis, multi-layer feed forward artificial neural networks (ANNs and quadratic discriminant analysis (QDA modeling tools for the early diagnosis of endometriosis in a minimally invasive manner by 1H- NMR based metabolomics. Materials and Methods: This prospective cohort study was done in Pasteur Institute, Iran in June 2013. Serum samples of 31 infertile women with endometriosis (stage II and III who confirmed by diagnostic laparoscopy and 15 normal women were collected and analyzed by nuclear magnetic resonance spectroscopy. The model was built by using partial least square discriminant analysis, QDA, and ANNs to determine classifier metabolites for early prediction risk of disease. Results: The levels of 2- methoxyestron, 2-methoxy estradiol, dehydroepiandrostion androstendione, aldosterone, and deoxy corticosterone were enhanced significantly in infertile group. While cholesterol and primary bile acids levels were decreased. QDA model showed significant difference between two study groups. Positive and negative predict value levels obtained about 71% and 78%, respectively. ANNs provided also criteria for detection of endometriosis. Conclusion: The QDA and ANNs modeling can be used as computational tools in noninvasive diagnose of endometriosis. However, the model designed by QDA methods is more efficient compared to ANNs in diagnosis of endometriosis patients.

  10. Automatic NMR-based identification of chemical reaction types in mixtures of co-occurring reactions.

    Science.gov (United States)

    Latino, Diogo A R S; Aires-de-Sousa, João

    2014-01-01

    The combination of chemoinformatics approaches with NMR techniques and the increasing availability of data allow the resolution of problems far beyond the original application of NMR in structure elucidation/verification. The diversity of applications can range from process monitoring, metabolic profiling, authentication of products, to quality control. An application related to the automatic analysis of complex mixtures concerns mixtures of chemical reactions. We encoded mixtures of chemical reactions with the difference between the (1)H NMR spectra of the products and the reactants. All the signals arising from all the reactants of the co-occurring reactions were taken together (a simulated spectrum of the mixture of reactants) and the same was done for products. The difference spectrum is taken as the representation of the mixture of chemical reactions. A data set of 181 chemical reactions was used, each reaction manually assigned to one of 6 types. From this dataset, we simulated mixtures where two reactions of different types would occur simultaneously. Automatic learning methods were trained to classify the reactions occurring in a mixture from the (1)H NMR-based descriptor of the mixture. Unsupervised learning methods (self-organizing maps) produced a reasonable clustering of the mixtures by reaction type, and allowed the correct classification of 80% and 63% of the mixtures in two independent test sets of different similarity to the training set. With random forests (RF), the percentage of correct classifications was increased to 99% and 80% for the same test sets. The RF probability associated to the predictions yielded a robust indication of their reliability. This study demonstrates the possibility of applying machine learning methods to automatically identify types of co-occurring chemical reactions from NMR data. Using no explicit structural information about the reactions participants, reaction elucidation is performed without structure elucidation of

  11. Ehrlich and sarcoma 180 tumour characterisation and early detection by {sup 1}H NMR-based metabonomics of mice serum

    Energy Technology Data Exchange (ETDEWEB)

    Grandizoli, Caroline W.P. da S.; Simonelli, Fabio; Nagata, Noemi; Barison, Andersson, E-mail: andernmr@ufpr.br [Universidade Federal do Parana (UFPR), Curitiba, PR (Brazil). Dept. de Quimica; Carrenho, Luise Z.B.; Francisco, Thais M.G. de; Campos, Francinete R. [Universidade Federal do Parana (UFPR), Curitiba, PR (Brazil). Dept. de Farmacia; Santana Filho, Arquimedes P. de; Sassaki, Guilherme L. [Universidade Federal do Parana (UFPR), Curitiba, PR (Brazil). Dept. de Bioquimica; Kreuger, Maria R.O. [Universidade do Vale do Itajai (UNIVALI), (Brazil). Centro de Ciencias da Saude

    2014-05-15

    The success of cancer treatment is directly related to early detection before symptoms emerge, although nowadays few cancers can be detected early. In this sense, {sup 1}H nuclear magnetic resonance ({sup 1}H NMR)-based metabonomics was used to identify metabolic changes in biofluid as a consequence of tumours growing in mice. Through partial least squares discriminant analysis (PLS-DA) analysis of {sup 1}H NMR spectra from serum samples it was possible to diagnose Ehrlich ascites and Sarcoma 180 tumours five and ten days after cell inoculation, respectively. Lipids, lipoproteins and lactate were the main biomarkers at onset as well as in the progress of carcinogenic process. Thus, NMR-based metabonomics can be a valuable tool to study the effects of tumour establishment on the chemical composition of biofluids. (author)

  12. 2D NMR-based metabolomics uncovers interactions between conserved biochemical pathways in the model organism Caenorhabditis elegans

    OpenAIRE

    Izrayelit, Yevgeniy; Robinette, Steven L; Bose, Neelanjan; von Reuss, Stephan H.; Schroeder, Frank C.

    2012-01-01

    Ascarosides are small-molecule signals that play a central role in C. elegans biology, including dauer formation, aging, and social behaviors, but many aspects of their biosynthesis remain unknown. Using automated 2D NMR-based comparative metabolomics, we identified ascaroside ethanolamides as shunt metabolites in C. elegans mutants of daf-22, a gene with homology to mammalian 3-ketoacyl-CoA thiolases predicted to function in conserved peroxisomal lipid β-oxidation. Two groups of ethanolamide...

  13. Fpocket: An open source platform for ligand pocket detection

    Directory of Open Access Journals (Sweden)

    Le Guilloux Vincent

    2009-06-01

    Full Text Available Abstract Background Virtual screening methods start to be well established as effective approaches to identify hits, candidates and leads for drug discovery research. Among those, structure based virtual screening (SBVS approaches aim at docking collections of small compounds in the target structure to identify potent compounds. For SBVS, the identification of candidate pockets in protein structures is a key feature, and the recent years have seen increasing interest in developing methods for pocket and cavity detection on protein surfaces. Results Fpocket is an open source pocket detection package based on Voronoi tessellation and alpha spheres built on top of the publicly available package Qhull. The modular source code is organised around a central library of functions, a basis for three main programs: (i Fpocket, to perform pocket identification, (ii Tpocket, to organise pocket detection benchmarking on a set of known protein-ligand complexes, and (iii Dpocket, to collect pocket descriptor values on a set of proteins. Fpocket is written in the C programming language, which makes it a platform well suited for the scientific community willing to develop new scoring functions and extract various pocket descriptors on a large scale level. Fpocket 1.0, relying on a simple scoring function, is able to detect 94% and 92% of the pockets within the best three ranked pockets from the holo and apo proteins respectively, outperforming the standards of the field, while being faster. Conclusion Fpocket provides a rapid, open source and stable basis for further developments related to protein pocket detection, efficient pocket descriptor extraction, or drugablity prediction purposes. Fpocket is freely available under the GNU GPL license at http://fpocket.sourceforge.net.

  14. {sup 1}H NMR-based spectroscopy detects metabolic alterations in serum of patients with early-stage ulcerative colitis

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Ying; Lin, Lianjie [Second Department of Gastroenterology, Shengjing Hospital, China Medical University, Shenyang 110004 (China); Xu, Yanbin [Wanlei Life Sciences (Shenyang) Co., Ltd., Shenyang 110179 (China); Lin, Yan; Jin, Yu [Second Department of Gastroenterology, Shengjing Hospital, China Medical University, Shenyang 110004 (China); Zheng, Changqing, E-mail: changqing_zheng@126.com [Second Department of Gastroenterology, Shengjing Hospital, China Medical University, Shenyang 110004 (China)

    2013-04-19

    Highlights: •Twenty ulcerative colitis patients and nineteen healthy controls were enrolled. •Increased 3-hydroxybutyrate, glucose, phenylalanine, and decreased lipid were found. •We report early stage diagnosis of ulcerative colitis using NMR-based metabolomics. -- Abstract: Ulcerative colitis (UC) has seriously impaired the health of citizens. Accurate diagnosis of UC at an early stage is crucial to improve the efficiency of treatment and prognosis. In this study, proton nuclear magnetic resonance ({sup 1}H NMR)-based metabolomic analysis was performed on serum samples collected from active UC patients (n = 20) and healthy controls (n = 19), respectively. The obtained spectral profiles were subjected to multivariate data analysis. Our results showed that consistent metabolic alterations were present between the two groups. Compared to healthy controls, UC patients displayed increased 3-hydroxybutyrate, β-glucose, α-glucose, and phenylalanine, but decreased lipid in serum. These findings highlight the possibilities of NMR-based metabolomics as a non-invasive diagnostic tool for UC.

  15. 30 CFR 56.19103 - Dumping facilities and loading pockets.

    Science.gov (United States)

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Dumping facilities and loading pockets. 56.19103 Section 56.19103 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR... Personnel Hoisting Shafts § 56.19103 Dumping facilities and loading pockets. Dumping facilities and...

  16. 30 CFR 57.19103 - Dumping facilities and loading pockets.

    Science.gov (United States)

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Dumping facilities and loading pockets. 57.19103 Section 57.19103 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR... MINES Personnel Hoisting Shafts § 57.19103 Dumping facilities and loading pockets. Dumping...

  17. Algorithm for Pocket Milling using Zig-zag Tool Path

    Directory of Open Access Journals (Sweden)

    P. Selvaraj

    2006-04-01

    Full Text Available Pocket-milling operations are widely used for scooping out materials during the machiningof aircraft components. This paper presents a tool-path planning algorithm for pocket-millingusing zig-zag method. The algorithm consists of basically three modules, viz., generating toolpathelements using pocket geometry entities as input, finding out intersection points (edgepoints, and rearranging points in a zig-zag fashion. OPTPATH algorithm1,2 is used for generatingtool-path elements. These elements thus generated are used to find out the intersection pointswith all entities. The valid points are arranged in a zig-zag way, which are used for machiningany pocket considered. This algorithm works satisfactorily for all the pocket boundaries havingline-line, line-arc, and arc-arc geometry entities.

  18. Role of pocket flexibility in the modulation of estrogen receptor alpha by key residue arginine 394.

    Science.gov (United States)

    Mu, Yunsong; Peng, Sufen; Zhang, Aiqian; Wang, Liansheng

    2011-02-01

    Estradiol derivatives, with similar structures as estradiol (E2) or estradiol metabolites, have been recognized to have detrimental health effects on wildlife and humans. However, data at the molecular level about interactions of these compounds with biological targets are still lacking. Herein, a flexible docking approach was used to characterize the molecular interaction of nine estradiol derivatives with estrogen receptor alpha (ERα) in the ligand-binding domain. All ligands were docked in the buried hydrophobic cavity of the steroid hormone pocket. In addition, the plasticity of an active site was also identified by reversing amino acid arginine 394 for better ligand-receptor binding affinity. Finally, bioassays based on genetically modified yeast strains were used to validate the quality of molecular simulation because of their rapidity and high sensitivity. The experimental findings about logarithm values of the median effective concentration (EC50) value had a linear correlation with computational binding affinity from molecular docking, which described a pattern of interaction between estradiol derivatives and ER. The estrogenic activity of all compounds, although more or less lower than E2, was proved to possess high severe environmental risks. Considering the sidechain flexibility in the ligand binding pocket, 17α-ethylestradiol-3-cyclopentylether was reported to correlate highly significantly with known induced fit conformational changes based upon proof-of-principle calculations on human ERα with the preservation of a strong salt bridge between glutamic acid 353 and arginine 394.

  19. A Swiss Pocket Knife for Computability

    Directory of Open Access Journals (Sweden)

    Neil D. Jones

    2013-09-01

    Full Text Available This research is about operational- and complexity-oriented aspects of classical foundations of computability theory. The approach is to re-examine some classical theorems and constructions, but with new criteria for success that are natural from a programming language perspective. Three cornerstones of computability theory are the S-m-ntheorem; Turing's "universal machine''; and Kleene's second recursion theorem. In today's programming language parlance these are respectively partial evaluation, self-interpretation, and reflection. In retrospect it is fascinating that Kleene's 1938 proof is constructive; and in essence builds a self-reproducing program. Computability theory originated in the 1930s, long before the invention of computers and programs. Its emphasis was on delimiting the boundaries of computability. Some milestones include 1936 (Turing, 1938 (Kleene, 1967 (isomorphism of programming languages, 1985 (partial evaluation, 1989 (theory implementation, 1993 (efficient self-interpretation and 2006 (term register machines. The "Swiss pocket knife'' of the title is a programming language that allows efficient computer implementation of all three computability cornerstones, emphasising the third: Kleene's second recursion theorem. We describe experiments with a tree-based computational model aiming for both fast program generation and fast execution of the generated programs.

  20. Pocket book of integrals and mathematical formulas

    CERN Document Server

    Tallarida, Ronald J

    2008-01-01

    Convenient Organization of Essential Material so You Can Look up Formulas Fast Containing a careful selection of standard and timely topics, the Pocket Book of Integrals and Mathematical Formulas, Fourth Edition presents many numerical and statistical tables, scores of worked examples, and the most useful mathematical formulas for engineering and scientific applications. This fourth edition of a bestseller provides even more comprehensive coverage with the inclusion of several additional topics, all while maintaining its accessible, clear style and handy size. New to the Fourth Edition           An expanded chapter on series that covers many fascinating properties of the natural numbers that follow from number theory           New applications such as geostationary satellite orbits and drug kinetics           An expanded statistics section that discusses nonlinear regression as well as the normal approximation of the binomial distribution           Revised f...

  1. Characteristics of cellular composition of periodontal pockets

    Science.gov (United States)

    Hasiuk, Petro; Hasiuk, Nataliya; Kindiy, Dmytro; Ivanchyshyn, Victoriya; Kalashnikov, Dmytro; Zubchenko, Sergiy

    2016-01-01

    Purpose The development of inflammatory periodontal disease in young people is an urgent problem of today's periodontology, and requires a development of new methods that would give an opportunity not only to diagnose but also for prognosis of periodontitis course in a given patients contingent. Results Cellular structure of periodontal pockets is presented by hematogenous and epithelial cells. Our results are confirmed by previous studies, and show that the penetration of periodontal pathogens leads to formation in periodontal tissue of a highly active complex compounds—cytokines that are able to modify the activity of neutrophils and reduce their specific antibacterial properties. Cytokines not only adversely affect the periodontal tissues, but also cause further activation of cells that synthesized them, and inhibit tissue repair and process of resynthesis of connective tissue by fibroblasts. Conclusion Neutrophilic granulocytes present in each of the types of smear types, but their functional status and quantitative composition is different. The results of our cytological study confirmed the results of immunohistochemical studies, and show that in generalized periodontitis, an inflammatory cellular elements with disorganized epithelial cells and connective tissue of the gums and periodontium, and bacteria form specific types of infiltration in periodontal tissues. PMID:28180007

  2. Assessing the structural conservation of protein pockets to study functional and allosteric sites: implications for drug discovery

    Directory of Open Access Journals (Sweden)

    Daura Xavier

    2010-03-01

    Full Text Available Abstract Background With the classical, active-site oriented drug-development approach reaching its limits, protein ligand-binding sites in general and allosteric sites in particular are increasingly attracting the interest of medicinal chemists in the search for new types of targets and strategies to drug development. Given that allostery represents one of the most common and powerful means to regulate protein function, the traditional drug discovery approach of targeting active sites can be extended by targeting allosteric or regulatory protein pockets that may allow the discovery of not only novel drug-like inhibitors, but activators as well. The wealth of available protein structural data can be exploited to further increase our understanding of allosterism, which in turn may have therapeutic applications. A first step in this direction is to identify and characterize putative effector sites that may be present in already available structural data. Results We performed a large-scale study of protein cavities as potential allosteric and functional sites, by integrating publicly available information on protein sequences, structures and active sites for more than a thousand protein families. By identifying common pockets across different structures of the same protein family we developed a method to measure the pocket's structural conservation. The method was first parameterized using known active sites. We characterized the predicted pockets in terms of sequence and structural conservation, backbone flexibility and electrostatic potential. Although these different measures do not tend to correlate, their combination is useful in selecting functional and regulatory sites, as a detailed analysis of a handful of protein families shows. We finally estimated the numbers of potential allosteric or regulatory pockets that may be present in the data set, finding that pockets with putative functional and effector characteristics are widespread across

  3. CIED infection with either pocket or systemic infection presentation

    DEFF Research Database (Denmark)

    Ihlemann, Nikolaj; Møller-Hansen, Michael; Salado-Rasmussen, Kirsten;

    2016-01-01

    OBJECTIVE: Cardiovascular implantable electronic device (CIED) infections are increasing in numbers. The objective was to review the clinical presentation and outcome in patients affected with CIED infections with either local pocket or systemic presentation. DESIGN: All device removals due to CIED...... infection during the period from 2005 to 2012 were retrospectively reviewed. CIED infections were categorized as systemic or pocket infections. Treatment included complete removal of the device, followed by antibiotic treatment of six weeks. RESULTS: Seventy-one device removals due to infection (32 systemic...... and 39 pocket infections) were recorded during the study period. Median follow-up time was 26 (IQR 9-41) months, 30 day and 12 month mortality were 4% and 14%, respectively. There was no long-term difference in mortality between patients with pocket vs. systemic infection (p = 0.48). During follow...

  4. Pocket epithelium in the pathological setting for HMGB1 release.

    Science.gov (United States)

    Ebe, N; Hara-Yokoyama, M; Iwasaki, K; Iseki, S; Okuhara, S; Podyma-Inoue, K A; Terasawa, K; Watanabe, A; Akizuki, T; Watanabe, H; Yanagishita, M; Izumi, Y

    2011-02-01

    High-mobility group box-1 (HMGB1) protein acts as a transcription factor in the nucleus and also as a pro-inflammatory cytokine when released into extracellular fluids. The presence of higher levels of HMGB1 is reported in the gingival crevicular fluid from periodontal patients. Since the proliferation of bacteria within the periodontal pocket is closely involved in the exacerbation of periodontal disease, it is hypothesized that the periodontal pocket causes the release of HMGB1. Immunohistochemical staining of inflamed gingiva revealed that HMGB1 is exclusively dislocated from the nucleus to the cytoplasm in the pocket epithelium, whereas it is mainly present in the nucleus in the gingival epithelium. Butyric acid, an extracellular metabolite from periodontopathic bacteria populating the periodontal pocket, induced the passive release of HMGB1 as a result of eliciting necrosis in the human gingival epithelial cell line. Thus, the periodontal epithelium may provide a unique pathological setting for HMGB1 release by bacterial insult.

  5. Investigation on the gas pockets in a rotodynamic multiphase pump

    Science.gov (United States)

    Zhang, J. Y.; Li, Y. J.; Cai, S. J.; Zhu, H. W.; Zhang, Y. X.

    2016-05-01

    The appearance of gas pockets has an obvious impact on the performance of the rotodynamic multiphase pump. In order to study the formation of gas pockets in the pump and its effects on pump's performance, the unsteady numerical simulation and the visualization experiments were done to investigate gas pockets in a three-stage rotodynamic multiphase pump developed by authors. Meanwhile, the mixture of water and air was selected as the medium. According to the distributions of pressure, gas volume fraction and velocity vector in three compression cells in unsteady flow process, the process of the formation of gas pockets in the pump were analysed generally. The visualization experiments were used to verify the validity of the numerical simulation. The results will be benefit for the hydraulic design of the compression cell of rotodynamic multiphase pump.

  6. Health Promoting Pocket Parks in a Landscape Architectural Perspective

    DEFF Research Database (Denmark)

    Peschardt, Karin Kragsig

    This thesis presents how the health potential of pocket parks can be improved through design from a landscape architectural perspective. In developed countries, the densification of cities is a wide-spread tendency which often results in a compact city planning structure. People who live in dense...... shown to have a positive influence on preventing lifestyle related diseases, although only limited research suggests how the various green spaces in the urban green infrastructure (UGI) can benefit health. Especially knowledge about the role of pocket parks is lacking. The study evaluates the health...... promoting potential of nine pocket parks in Copenhagen. From a landscape architectural perspective the health potential is investigated based on both qualitative and quantitative methods. The study elucidates use, the restorative potential as well as how physical content within the pocket parks can...

  7. Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison.

    Science.gov (United States)

    Sael, Lee; Kihara, Daisuke

    2012-04-01

    Functional elucidation of proteins is one of the essential tasks in biology. Function of a protein, specifically, small ligand molecules that bind to a protein, can be predicted by finding similar local surface regions in binding sites of known proteins. Here, we developed an alignment free local surface comparison method for predicting a ligand molecule which binds to a query protein. The algorithm, named Patch-Surfer, represents a binding pocket as a combination of segmented surface patches, each of which is characterized by its geometrical shape, the electrostatic potential, the hydrophobicity, and the concaveness. Representing a pocket by a set of patches is effective to absorb difference of global pocket shape while capturing local similarity of pockets. The shape and the physicochemical properties of surface patches are represented using the 3D Zernike descriptor, which is a series expansion of mathematical 3D function. Two pockets are compared using a modified weighted bipartite matching algorithm, which matches similar patches from the two pockets. Patch-Surfer was benchmarked on three datasets, which consist in total of 390 proteins that bind to one of 21 ligands. Patch-Surfer showed superior performance to existing methods including a global pocket comparison method, Pocket-Surfer, which we have previously introduced. Particularly, as intended, the accuracy showed large improvement for flexible ligand molecules, which bind to pockets in different conformations.

  8. Recommendations and Standardization of Biomarker Quantification Using NMR-based Metabolomics with Particular Focus on Urinary Analysis

    KAUST Repository

    Emwas, Abdul-Hamid M.

    2016-01-08

    NMR-based metabolomics has shown considerable promise in disease diagnosis and biomarker discovery because it allows one to non-destructively identify and quantify large numbers of novel metabolite biomarkers in both biofluids and tissues. Indeed, precise metabolite quantification is a necessary prerequisite to move any chemical biomarker or biomarker panel from the lab into the clinic. Among the many biofluids (urine, serum, plasma, cerebrospinal fluid and saliva) commonly used for disease diagnosis and prognosis, urine has several advantages. It is abundant, sterile, easily obtained, needs little sample preparation and does not require any invasive medical procedures for collection. Furthermore, urine captures and concentrates many “unwanted” or “undesirable” compounds throughout the body, thereby providing a rich source of potentially useful disease biomarkers. However, the incredible variation in urine chemical concentrations due to effects such as gender, age, diet, life style, health conditions, and physical activity make the analysis of urine and the identification of useful urinary biomarkers by NMR quite challenging. In this review, we discuss a number of the most significant issues regarding NMR-based urinary metabolomics with a specific emphasis on metabolite quantification for disease biomarker applications. We also propose a number of data collection and instrumental recommendations regarding NMR pulse sequences, acceptable acquisition parameter ranges, relaxation effects on quantitation, proper handling of instrumental differences, as well as recommendations regarding sample preparation and biomarker assessment.

  9. Evaluation of Pacific white shrimp (Litopenaeus vannamei health during a superintensive aquaculture growout using NMR-based metabolomics.

    Directory of Open Access Journals (Sweden)

    Tracey B Schock

    Full Text Available Success of the shrimp aquaculture industry requires technological advances that increase production and environmental sustainability. Indoor, superintensive, aquaculture systems are being developed that permit year-round production of farmed shrimp at high densities. These systems are intended to overcome problems of disease susceptibility and of water quality issues from waste products, by operating as essentially closed systems that promote beneficial microbial communities (biofloc. The resulting biofloc can assimilate and detoxify wastes, may provide nutrition for the farmed organisms resulting in improved growth, and may aid in reducing disease initiated from external sources. Nuclear magnetic resonance (NMR-based metabolomic techniques were used to assess shrimp health during a full growout cycle from the nursery phase through harvest in a minimal-exchange, superintensive, biofloc system. Aberrant shrimp metabolomes were detected from a spike in total ammonia nitrogen in the nursery, from a reduced feeding period that was a consequence of surface scum build-up in the raceway, and from the stocking transition from the nursery to the growout raceway. The biochemical changes in the shrimp that were induced by the stressors were essential for survival and included nitrogen detoxification and energy conservation mechanisms. Inosine and trehalose may be general biomarkers of stress in Litopenaeus vannamei. This study demonstrates one aspect of the practicality of using NMR-based metabolomics to enhance the aquaculture industry by providing physiological insight into common environmental stresses that may limit growth or better explain reduced survival and production.

  10. Evaluation of Pacific white shrimp (Litopenaeus vannamei) health during a superintensive aquaculture growout using NMR-based metabolomics.

    Science.gov (United States)

    Schock, Tracey B; Duke, Jessica; Goodson, Abby; Weldon, Daryl; Brunson, Jeff; Leffler, John W; Bearden, Daniel W

    2013-01-01

    Success of the shrimp aquaculture industry requires technological advances that increase production and environmental sustainability. Indoor, superintensive, aquaculture systems are being developed that permit year-round production of farmed shrimp at high densities. These systems are intended to overcome problems of disease susceptibility and of water quality issues from waste products, by operating as essentially closed systems that promote beneficial microbial communities (biofloc). The resulting biofloc can assimilate and detoxify wastes, may provide nutrition for the farmed organisms resulting in improved growth, and may aid in reducing disease initiated from external sources. Nuclear magnetic resonance (NMR)-based metabolomic techniques were used to assess shrimp health during a full growout cycle from the nursery phase through harvest in a minimal-exchange, superintensive, biofloc system. Aberrant shrimp metabolomes were detected from a spike in total ammonia nitrogen in the nursery, from a reduced feeding period that was a consequence of surface scum build-up in the raceway, and from the stocking transition from the nursery to the growout raceway. The biochemical changes in the shrimp that were induced by the stressors were essential for survival and included nitrogen detoxification and energy conservation mechanisms. Inosine and trehalose may be general biomarkers of stress in Litopenaeus vannamei. This study demonstrates one aspect of the practicality of using NMR-based metabolomics to enhance the aquaculture industry by providing physiological insight into common environmental stresses that may limit growth or better explain reduced survival and production.

  11. The P9 pocket of HLA-DQ2 (non-Aspbeta57) has no particular preference for negatively charged anchor residues found in other type 1 diabetes-predisposing non-Aspbeta57 MHC class II molecules

    DEFF Research Database (Denmark)

    Quarsten, H; Paulsen, G; Johansen, B H;

    1998-01-01

    residues at P9 and that there is no particular preference for binding peptides with negatively charged residues at this position. The specificity of the P9 pocket in the mutated DQ molecule is altered, indicating that the beta57 residue contributes to determining the specificity of the P9 pocket. Our data...... anchor residues. We have investigated the specificity of the P9 pocket of the type 1 diabetes-associated DQ2 molecule and in particular examined for charge effects at this anchor position. Different approaches were undertaken. We analyzed binding of a high-affinity binding ligand and P9-substituted...... variants of this peptide, and we analyzed the binding of a set of synthetic random peptide libraries. The binding analyses were performed with wild-type DQ2 and a mutated DQ2 with Ala at beta57 substituted with Asp. Our results indicate that the wild-type DQ2 (non-Aspbeta57) prefers large hydrophobic...

  12. Dissociation of an antiviral compound from the internal pocket of human rhinovirus 14 capsid.

    Science.gov (United States)

    Li, Yumin; Zhou, Zhigang; Post, Carol Beth

    2005-05-24

    WIN antiviral compounds bind human rhinovirus, as well as enterovirus and parechovirus, in an internal cavity located within the viral protein capsid. Access to the buried pocket necessitates deviation from the average viral protein structure identified by crystallography. We investigated the dissociation of WIN 52084 from the pocket in human rhinovirus 14 by using an adiabatic, biased molecular dynamics simulation method. Multiple dissociation trajectories are used to characterize the pathway. WIN 52084 exits between the polypeptide chain near the ends of betaC and betaH in a series of steps. Small, transient packing defects in the protein are sufficient for dissociation. A number of torsion-angle transitions of the antiviral compound are involved, which suggests that flexibility in antiviral compounds is important for binding. It is interesting to note that dissociation is associated with an increase in the conformational fluctuations of residues never in direct contact with WIN 52084 over the course of dissociation. These residues are N-terminal residues in the viral proteins VP3 and VP4 and are located in the interior of the capsid near the icosahedral 5-fold axis. The observed changes in dynamics may be relevant to structural changes associated with virion uncoating and its inhibition by antiviral compounds.

  13. NMR-based metabolomics for the environmental assessment of Kaohsiung Harbor sediments exemplified by a marine amphipod (Hyalella azteca).

    Science.gov (United States)

    Chiu, K H; Dong, C D; Chen, C F; Tsai, M L; Ju, Y R; Chen, T M; Chen, C W

    2017-03-03

    Inflow of wastewater from upstream causes a large flux of pollutants to enter Kaohsiung Harbor in Taiwan daily. To reveal the ecological risk posed by Kaohsiung Harbor sediments, an ecological metabolomic approach was employed to investigate environmental factors pertinent to the physiological regulation of the marine amphipod Hyalella azteca. The amphipods were exposed to sediments collected from different stream inlets of the Love River (LR), Canon River (CR), Jen-Gen River (JR), and Salt River (SR). Harbor entrance 1 (E1) was selected as a reference site. After 10-day exposure, metabolomic analysis of the Hyalella azteca revealed differences between two groups: {E1, LR, CR} and {JR, SR}. The metabolic pathways identified in the two groups of amphipods were significantly different. The results demonstrated that NMR-based metabolomics can be effectively used to characterize metabolic response related to sediment from polluted areas.

  14. NMR-based metabolomic investigation of bioactivity of chemical constituents in black raspberry (Rubus occidentalis L.) fruit extracts.

    Science.gov (United States)

    Paudel, Liladhar; Wyzgoski, Faith J; Giusti, M Monica; Johnson, Jodee L; Rinaldi, Peter L; Scheerens, Joseph C; Chanon, Ann M; Bomser, Joshua A; Miller, A Raymond; Hardy, James K; Reese, R Neil

    2014-02-26

    Black raspberry (Rubus occidentalis L.) (BR) fruit extracts with differing compound profiles have shown variable antiproliferative activities against HT-29 colon cancer cell lines. This study used partial least-squares (PLS) regression analysis to develop a high-resolution (1)H NMR-based multivariate statistical model for discerning the biological activity of BR constituents. This model identified specific bioactive compounds and ascertained their relative contribution against cancer cell proliferation. Cyanidin 3-rutinoside and cyanidin 3-xylosylrutinoside were the predominant contributors to the extract bioactivity, but salicylic acid derivatives (e.g., salicylic acid glucosyl ester), quercetin 3-glucoside, quercetin 3-rutinoside, p-coumaric acid, epicatechin, methyl ellagic acid derivatives (e.g., methyl ellagic acetyl pentose), and citric acid derivatives also contributed significantly to the antiproliferative activity of the berry extracts. This approach enabled the identification of new bioactive components in BR fruits and demonstrates the utility of the method for assessing chemopreventive compounds in foods and food products.

  15. NMR-based metabolomics of urine for the atherosclerotic mouse model using apolipoprotein-E deficient mice.

    Science.gov (United States)

    Leo, Gregory C; Darrow, Andrew L

    2009-12-01

    NMR-based metabolomics of mouse urine was used in conjunction with the traditional staining and imaging of aortas for the characterization of disease advancement, that is, plaque formation in untreated and drug-treated apolipoprotein-E (apoE) knockout mice. The metabolomics approach with multivariate analysis was able to differentiate the captopril-treated from the untreated mice in general agreement with the staining results. Principal component analysis showed a pattern shift in both the drug-treated and untreated samples as a function of time that could possibly be explained as the effect of aging. Allantoin, a marker attributed to captopril treatment was elevated in the drug-treated mice. From partial least squares-discriminant analysis, xanthine and ascorbate were elevated in the untreated mice and were possible markers of plaque formation in the apoE knockout mice. Several additional peaks in the spectra characterizing the study endpoint were found but their respective metabolite identities were unknown.

  16. NMR-Based Metabonomic Investigation of Heat Stress in Myotubes Reveals a Time-Dependent Change in the Metabolites

    DEFF Research Database (Denmark)

    Straadt, Ida K; Young, Jette F; Bross, Peter;

    2010-01-01

    NMR-based metabonomics was applied to elucidate the time-dependent stress responses in mouse myotubes after heat exposure of either 42 or 45 degrees C for 1 h. Principal component analysis (PCA) revealed that the gradual time-dependent changes in metabolites contributing to the clustering...... and separation of the control samples from the different time points after heat stress primarily are in the metabolites glucose, leucine, lysine, phenylalanine, creatine, glutamine, and acetate. In addition, PC scores revealed a maximum change in metabolite composition 4 h after the stress exposure; thereafter......, samples returned toward control samples, however, without reaching the control samples even 10 h after stress. The results also indicate that the myotubes efficiently regulate the pH level by release of lactate to the culture medium at a heat stress level of 42 degrees C, which is a temperature level...

  17. Study of the cardiotoxicity of Venenum Bufonis in rats using an 1H NMR-based metabolomics approach.

    Directory of Open Access Journals (Sweden)

    Ge Dong

    Full Text Available Venenum Bufonis, a well-known traditional Chinese medicine, has been widely used in Asia and has gained popularity in Western countries over the last decade. Venenum Bufonis has obvious side effects that have been observed in clinical settings, but few studies have reported on its cardiotoxicity. In this work, the cardiotoxicity of Venenum Bufonis was investigated using a 11H NMR-based metabolomics approach. The 1H NMR profiles of the serum, myocardial extracts and liver extracts of specific-pathogen-free rats showed that Venenum Bufonis produced significant metabolic perturbations dose-dependently with a distinct time effect, peaking at 2 hr after dosing and attenuating gradually. Clinical chemistry, electrocardiographic recordings, and histopathological evaluation provided additional evidence of Venenum Bufonis-induced cardiac damage that complemented and supported the metabolomics findings. The combined results demonstrated that oxidative stress, mitochondrial dysfunction, and energy metabolism perturbations were associated with the cardiac damage that results from Venenum Bufonis.

  18. NMR-based metabolomics approach to study the toxicity of lambda-cyhalothrin to goldfish (Carassius auratus)

    Energy Technology Data Exchange (ETDEWEB)

    Li, Minghui [State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009 (China); Wang, Junsong, E-mail: wang.junsong@gmail.com [Center for Molecular Metabolism, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiao Ling Wei Street, Nanjing 210094 (China); Lu, Zhaoguang; Wei, Dandan; Yang, Minghua [State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009 (China); Kong, Lingyi, E-mail: cpu_lykong@126.com [State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009 (China)

    2014-01-15

    Highlights: •A goldfish model was established to investigate the toxicity of lambda-cyhalothrin (LCT) exposure on multiple organs. •NMR based metabolomics approach were firstly used to provide a global view of the toxicity of LCT. •LCT induced neurotransmitters and osmoregulatory imbalances, oxidative stress, energy and amino acid metabolic disorders. •Glutamate–glutamine–GABA axis as a potential target for LCT toxicity was first found. -- Abstract: In this study, a {sup 1}H nuclear magnetic resonance (NMR) based metabolomics approach was applied to investigate the toxicity of lambda-cyhalothrin (LCT) in goldfish (Carassius auratus). LCT showed tissue-specific damage to gill, heart, liver and kidney tissues of goldfish. NMR profiling combined with statistical methods such as orthogonal partial least squares discriminant analysis (OPLS-DA) and two-dimensional statistical total correlation spectroscopy (2D-STOCSY) was developed to discern metabolite changes occurring after one week LCT exposure in brain, heart and kidney tissues of goldfish. LCT exposure influenced levels of many metabolites (e.g., leucine, isoleucine and valine in brain and kidney; lactate in brain, heart and kidney; alanine in brain and kidney; choline in brain, heart and kidney; taurine in brain, heart and kidney; N-acetylaspartate in brain; myo-inositol in brain; phosphocreatine in brain and heart; 2-oxoglutarate in brain; cis-aconitate in brain, and etc.), and broke the balance of neurotransmitters and osmoregulators, evoked oxidative stress, disturbed metabolisms of energy and amino acids. The implication of glutamate–glutamine–gamma-aminobutyric axis in LCT induced toxicity was demonstrated for the first time. Our findings demonstrated the applicability and potential of metabolomics approach for the elucidation of toxicological effects of pesticides and the underlying mechanisms, and the discovery of biomarkers for pesticide pollution in aquatic environment.

  19. Ethics pocket cards: an educational tool for busy clinicians.

    Science.gov (United States)

    Volpe, Rebecca L; Levi, Benjamin H; Blackhall, George F; Green, Michael J

    2014-01-01

    The adage "an ounce of prevention is worth a pound of cure" is widely used in healthcare settings and can be applied to the work of institutional clinical ethics committees. The model of clinical ethics consultation, however, is inherently reactive: a crisis or question emerges, and ethics experts are called to help. In an effort to employ a proactive component to the model of clinical ethics consultation (as well as to standardize our educational interventions), we developed ethics pocket cards. The purpose of this article is to: (1) describe the rationale for using ethics pocket cards, (2) provide examples of our cards, and (3) begin a dialogue about the potential uses of ethics pocket cards. In doing so, we hope to explore how such portable, economical devices can advance the goals of ethics consultation as well as the educational aims of ethics committees.

  20. Exploration of pH-dependent behavior of the anion receptor pocket of subdomain IIA of HSA: determination of effective pocket charge using the Debye-Hückel limiting law.

    Science.gov (United States)

    Bolel, Priyanka; Datta, Shubhashis; Mahapatra, Niharendu; Halder, Mintu

    2014-01-09

    Protein-ligand electrostatic interaction can be looked upon as ion receptor-ligand interaction, and the binding cavity of protein can be either an anion or cation receptor depending on the charge of the guest. Here we focus on the exploration of pH-modulated binding of a number of anionic ligands, specific to the subdomain IIA cavity of HSA, such as carmoisine, tartrazine, cochineal red, and warfarin. The logarithm of the binding constant is found to vary linearly with the square-root of ionic strength, indicating applicability of the Debye-Hückel limiting law to protein-ligand electrostatic binding equilibrium, and concludes that the subdomain IIA cavity is an anion receptor. The present approach is very unique that one can calculate the effective charge of the protein-based anion receptor pocket, and the calculated charge has been found to vary between +1 and +3 depending on the pH and ligand itself. The study also indicates that in such cases of specific ligand binding the pocket charge rather than the overall or surface charge of the macromolecule seems to have a paramount role in determining the strength of interaction. For the first time, it is demonstrated that the Debye-Hückel interionic interaction model can be successfully applied to understand the protein-based receptor-ligand electrostatic interaction in general.

  1. UML 2.0 Pocket Reference UML Syntax and Usage

    CERN Document Server

    Pilone, Dan

    2006-01-01

    Globe-trotting travelers have long resorted to handy, pocket-size dictionaries as an aid to communicating across the language barrier. Dan Pilone's UML 2.0 Pocket Reference is just such an aid for on-the-go developers who need to converse in the Unified Modeling Language (UML). Use this book to decipher the many UML diagrams you'll encounter on the path to delivering a modern software system. Updated to cover the very latest in UML, you'll find coverage of the following UML 2.0 diagram types: Class diagramsComponent diagrams*Sequence diagrams*Communication diagrams*Timing diagrams*Interactio

  2. Canvas Pocket Reference Scripted Graphics for HTML5

    CERN Document Server

    Flanagan, David

    2010-01-01

    The Canvas element is a revolutionary feature of HTML5 that enables powerful graphics for rich Internet applications, and this pocket reference provides the essentials you need to put this element to work. If you have working knowledge of JavaScript, this book will help you create detailed, interactive, and animated graphics -- from charts to animations to video games -- whether you're a web designer or a programmer interested in graphics. Canvas Pocket Reference provides both a tutorial that covers all of the element's features with plenty of examples and a definitive reference to each of t

  3. Apache 2 Pocket Reference For Apache Programmers & Administrators

    CERN Document Server

    Ford, Andrew

    2008-01-01

    Even if you know the Apache web server inside and out, you still need an occasional on-the-job reminder -- especially if you're moving to the newer Apache 2.x. Apache 2 Pocket Reference gives you exactly what you need to get the job done without forcing you to plow through a cumbersome, doorstop-sized reference. This Book provides essential information to help you configure and maintain the server quickly, with brief explanations that get directly to the point. It covers Apache 2.x, giving web masters, web administrators, and programmers a quick and easy reference solution. This pocket r

  4. Pocket radar guide key facts, equations, and data

    CERN Document Server

    Curry, G Richard

    2010-01-01

    ThePocket Radar Guideis a concise collection of key radar facts and important radar data that provides you with necessary radar information when you are away from your office or references. It includes statements and comments on radar design, operation, and performance; equations describing the characteristics and performance of radar systems and their components; and tables with data on radar characteristics and key performance issues.It is intended to supplement other radar information sources by providing a pocket companion to refresh memory and provide details whenever you need them such a

  5. Vibration Characteristics of Hydrodynamic Fluid Film Pocket Journal Bearings

    Directory of Open Access Journals (Sweden)

    N. S. Feng

    2010-01-01

    Full Text Available Theoretical analyses of hydrodynamic fluid film bearings with different bearing profiles rely on solutions of the Reynolds equation. This paper presents an approach used for analysing the so-called pocket bearings formed from a combination of offset circular bearing profiles. The results show that the variation of the dynamic bearing characteristics with different load inclinations for the pocket bearings is less than that for the elliptic bearing counterpart. It is shown that the natural frequencies as well as the critical speeds, and hence the vibrational behaviour, can also be significantly different for an industrial rotor supported by the different bearings.

  6. NMR-assisted computational studies of peptidomimetic inhibitors bound in the hydrophobic pocket of HIV-1 glycoprotein 41

    Science.gov (United States)

    Gochin, Miriam; Whitby, Landon R.; Phillips, Aaron H.; Boger, Dale L.

    2013-07-01

    Due to the inherently flexible nature of a protein-protein interaction surface, it is difficult both to inhibit the association with a small molecule, and to predict how it might bind to the surface. In this study, we have examined small molecules that mediate the interaction between a WWI motif on the C-helix of HIV-1 glycoprotein-41 (gp41) and a deep hydrophobic pocket contained in the interior N-helical trimer. Association between these two components of gp41 leads to virus-cell and cell-cell fusion, which could be abrogated in the presence of an inhibitor that binds tightly in the pocket. We have studied a comprehensive combinatorial library of α-helical peptidomimetics, and found that compounds with strongly hydrophobic side chains had the highest affinity. Computational docking studies produced multiple possible binding modes due to the flexibility of both the binding site and the peptidomimetic compounds. We applied a transferred paramagnetic relaxation enhancement experiment to two selected members of the library, and showed that addition of a few experimental constraints enabled definitive identification of unique binding poses. Computational docking results were extremely sensitive to side chain conformations, and slight variations could preclude observation of the experimentally validated poses. Different receptor structures were required for docking simulations to sample the correct pose for the two compounds. The study demonstrated the sensitivity of predicted poses to receptor structure and indicated the importance of experimental verification when docking to a malleable protein-protein interaction surface.

  7. Binding of disodium cromoglycate to human serum albumin

    Science.gov (United States)

    Ochoa de Aspuru, Eduardo; Zatón, Ana M. L.

    1998-07-01

    The binding of several benzopiranone derivatives to human serum albumin was determined. The antiallergic drug disodium cromoglycate binds weakly to serum albumin. However, its precursors, chromones of smaller size, were able to bind in a hydrophobic pocket in the protein, and are carried by serum albumin in blood.

  8. Structure and localisation of drug binding sites on neurotransmitter transporters.

    Science.gov (United States)

    Ravna, Aina W; Sylte, Ingebrigt; Dahl, Svein G

    2009-10-01

    The dopamine (DAT), serotontin (SERT) and noradrenalin (NET) transporters are molecular targets for different classes of psychotropic drugs. The crystal structure of Aquifex aeolicus LeuT(Aa) was used as a template for molecular modeling of DAT, SERT and NET, and two putative drug binding sites (pocket 1 and 2) in each transporter were identified. Cocaine was docked into binding pocket 1 of DAT, corresponding to the leucine binding site in LeuT(Aa), which involved transmembrane helices (TMHs) 1, 3, 6 and 8. Clomipramine was docked into binding pocket 2 of DAT, involving TMHs 1, 3, 6, 10 and 11, and extracellular loops 4 and 6, corresponding to the clomipramine binding site in a crystal structure of a LeuT(Aa)-clomipramine complex. The structures of the proposed cocaine- and tricyclic antidepressant-binding sites may be of particular interest for the design of novel DAT interacting ligands.

  9. 5-Aza-2'-deoxycytidine reactivates gene expression via degradation of pRb pocket proteins.

    Science.gov (United States)

    Zheng, Zhixing; Li, Lian; Liu, Xiangyu; Wang, Donglai; Tu, Bo; Wang, Lina; Wang, Haiying; Zhu, Wei-Guo

    2012-01-01

    Not only does 5-aza-2'-deoxycytidine (5-aza-CdR) induce the reexpression of silenced genes through the demethylation of CpG islands, but it increases the expression of unmethylated genes. However, the mechanism by which 5-aza-CdR activates the expression of genes is not completely understood. Here, we report that the pRb pocket proteins pRb, p107, and p130 were degraded in various cancer cell lines in response to 5-aza-CdR treatment, and this effect was dependent on the proteasome pathway. Mouse double minute 2 (MDM2) played a critical role in this 5-aza-CdR-induced degradation of pRb. Furthermore, PP2A phosphatase-induced MDM2 dephosphorylation at S260 was found to be essential for MDM2 binding to pRb in the presence of 5-aza-CdR. pRb degradation resulted in the significant reexpression of several genes, including methylated CDKN2A, RASFF1A, and unmethylated CDKN2D. Finally, knockdown of pRb pocket proteins by either RNAi or 5-aza-CdR treatment induced a significant decrease in the recruitment of SUV39H1 and an increase in the enrichment of KDM3B and KDM4A to histones around the promoter of RASFF1A and thus reduced H3K9 di- and trimethylation, by which RASFF1A expression is activated. Our data reveal a novel mechanism by which 5-aza-CdR induces the expression of both methylated and unmethylated genes by degrading pRb pocket proteins.

  10. The pocket epithelium: a light- and electronmicroscopic study.

    Science.gov (United States)

    Müller-Glauser, W; Schroeder, H E

    1982-03-01

    The POCKET epithelium is important for the pathogenesis of gingivitis and periodontitis. However, this epithelial variant has never been adequately described. The bioptic material with supraalveolar pockets originated from previous studies in which cotton floss ligatures were placed around the crowns of premolars in eight dogs. After periods of 4 to 21 days or up to 5 months, block biopsies comprising dental and gingival tissues were taken on the buccal side. The tissues were processed for light- and electron microscopic examination. The observations revealed that the pocket epithelium (1) does not attach to the tooth, (2) forms irregular ridges and, over connective tissue papillae, thin coverings which occasionally ulcerate, (3) consists of cells only some of which show a tendency to differentiate, (4) presents a basal lamina complex with discontinuities and multiplications, and (5) is infiltrated mainly by lymphocytes, T- and B-blasts and plasma cells, and is transmigrated by neutrophilic granulocytes. It is concluded that the mosaic-like structure of the pocket epithelium reflects the heterogeneity of the adjacent plaque, that this structure together with the absence of membrane coating granules is the basis for an extremely high permeability, and that epithelial ridges may conduct and collect foreign substances which thereby become more easily recognizable for leukocytes.

  11. Slicing Recognition of Aircraft Integral Panel Generalized Pocket

    Institute of Scientific and Technical Information of China (English)

    Yu Fangfang; Du Baorui; Ren Wenjie; Zheng Guolei; Chu Hongzhen

    2008-01-01

    To automatically obtain a machining area in numerical control (NC) programming, a data model of generalized pocket is estab-lished by analyzing aireraft integral panel characteristics, and a feature recognition approach is proposed. First, by reference to the prao- tieal slice-machining process of an aircraft integral panel, both the part and the blank are sliced in the Z-axis direction; hence a feature profile is created acceding to the slicing planes and the contours are formed by the intersection of the slicing planes with the part and its blanK. Second, the auxiliary features of the generalized pocket are also determined based on the face type and the position, to correct the profile of the pocket. Finally, the generalized pocket feature relationship tree is constructed by matching the vertical relationships among the features. Machining feature information produced by using this method can be directly used to calculate the cutter path. The validity and practicability of the method is verified by NC programming for aircraft panels.

  12. Adhesion of Porphyromonas gingivalis serotypes to pocket epithelium

    NARCIS (Netherlands)

    Dierickx, K; Pauwels, M; Laine, ML; Van Eldere, J; Cassiman, JJ; van Winkelhoff, AJ; van Steenberghe, D; Quirynen, M

    2003-01-01

    Background: Porphyromonas gingivalis, a key pathogen in periodontitis, is able to adhere to and invade the pocket epithelium. Different capsular antigens of P gingivalis have been identified (K-serotyping). These P gingivalis capsular types show differences in adhesion capacity to human cell lines o

  13. A pocket aide-memoire on drug interactions.

    Science.gov (United States)

    Stockley, I H

    1975-04-01

    A pocket size "slide-rule" type device designed to be used by physicians, pharmacists and nurses as a memory aid on potential drug-drug interactions is described. Color-coded symbols on the device indicate both the type and clinical significance of the potential interactions involving 56 drugs or groups of drugs.

  14. Effect of magnetic field strength on NMR-based metabonomic human urine data. Comparative study of 250, 400, 500, and 800 MHz

    DEFF Research Database (Denmark)

    Bertram, Hanne Christine; Malmendal, Anders; Petersen, Bent O.;

    2007-01-01

    Metabonomic analysis of urine utilizing high-resolution NMR spectroscopy and chemometric techniques has proven valuable in characterizing the biochemical response to an intervention. To assess the effect of magnetic field strength on information contained in NMR-based metabonomic data sets, 1H NM...

  15. (1)H-NMR-based metabolomic analysis of the effect of moderate wine consumption on subjects with cardiovascular risk factors.

    Science.gov (United States)

    Vázquez-Fresno, Rosa; Llorach, Rafael; Alcaro, Francesca; Rodríguez, Miguel Ángel; Vinaixa, Maria; Chiva-Blanch, Gemma; Estruch, Ramon; Correig, Xavier; Andrés-Lacueva, Cristina

    2012-08-01

    Moderate wine consumption is associated with health-promoting activities. An H-NMR-based metabolomic approach was used to identify urinary metabolomic differences of moderate wine intake in the setting of a prospective, randomized, crossover, and controlled trial. Sixty-one male volunteers with high cardiovascular risk factors followed three dietary interventions (28 days): dealcoholized red wine (RWD) (272mL/day, polyphenol control), alcoholized red wine (RWA) (272mL/day) and gin (GIN) (100mL/day, alcohol control). After each period, 24-h urine samples were collected and analyzed by (1) H-NMR. According to the results of a one-way ANOVA, significant markers were grouped in four categories: alcohol-related markers (ethanol); gin-related markers; wine-related markers; and gut microbiota markers (hippurate and 4-hydroxphenylacetic acid). Wine metabolites were classified into two groups; first, metabolites of food metabolome: tartrate (RWA and RWD), ethanol, and mannitol (RWA); and second, biomarkers that relates to endogenous modifications after wine consumption, comprising branched-chain amino acid (BCAA) metabolite (3-methyl-oxovalerate). Additionally, a possible interaction between alcohol and gut-related biomarkers has been identified. To our knowledge, this is the first time that this approach has been applied in a nutritional intervention with red wine. The results show the capacity of this approach to obtain a comprehensive metabolome picture including food metabolome and endogenous biomarkers of moderate wine intake.

  16. NMR-based metabonomic analyses of the effects of ultrasmall superparamagnetic particles of iron oxide (USPIO) on macrophage metabolism

    Science.gov (United States)

    Feng, Jianghua; Zhao, Jing; Hao, Fuhua; Chen, Chang; Bhakoo, Kishore; Tang, Huiru

    2011-05-01

    The metabonomic changes in murine RAW264.7 macrophage-like cell line induced by ultrasmall superparamagnetic particles of iron oxides (USPIO) have been investigated, by analyzing both the cells and culture media, using high-resolution NMR in conjunction with multivariate statistical methods. Upon treatment with USPIO, macrophage cells showed a significant decrease in the levels of triglycerides, essential amino acids such as valine, isoleucine, and choline metabolites together with an increase of glycerophospholipids, tyrosine, phenylalanine, lysine, glycine, and glutamate. Such cellular responses to USPIO were also detectable in compositional changes of cell media, showing an obvious depletion of the primary nutrition molecules, such as glucose and amino acids and the production of end-products of glycolysis, such as pyruvate, acetate, and lactate and intermediates of TCA cycle such as succinate and citrate. At 48 h treatment, there was a differential response to incubation with USPIO in both cell metabonome and medium components, indicating that USPIO are phagocytosed and released by macrophages. Furthermore, information on cell membrane modification can be derived from the changes in choline-like metabolites. These results not only suggest that NMR-based metabonomic methods have sufficient sensitivity to identify the metabolic consequences of murine RAW264.7 macrophage-like cell line response to USPIO in vitro, but also provide useful information on the effects of USPIO on cellular metabolism.

  17. NMR-based metabonomic analyses of the effects of ultrasmall superparamagnetic particles of iron oxide (USPIO) on macrophage metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Feng Jianghua [Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics (China); Zhao Jing [China Institute of Atomic Energy (China); Hao Fuhua [Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics (China); Chen Chang [Institute of Biophysics, The Chinese Academy of Sciences, National Laboratory of Biomacromolecules (China); Bhakoo, Kishore [Singapore Bioimaging Consortium Agency for Science, Technology and Research (A-STAR) (Singapore); Tang, Huiru, E-mail: huiru.tang@wipm.ac.cn [Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics (China)

    2011-05-15

    The metabonomic changes in murine RAW264.7 macrophage-like cell line induced by ultrasmall superparamagnetic particles of iron oxides (USPIO) have been investigated, by analyzing both the cells and culture media, using high-resolution NMR in conjunction with multivariate statistical methods. Upon treatment with USPIO, macrophage cells showed a significant decrease in the levels of triglycerides, essential amino acids such as valine, isoleucine, and choline metabolites together with an increase of glycerophospholipids, tyrosine, phenylalanine, lysine, glycine, and glutamate. Such cellular responses to USPIO were also detectable in compositional changes of cell media, showing an obvious depletion of the primary nutrition molecules, such as glucose and amino acids and the production of end-products of glycolysis, such as pyruvate, acetate, and lactate and intermediates of TCA cycle such as succinate and citrate. At 48 h treatment, there was a differential response to incubation with USPIO in both cell metabonome and medium components, indicating that USPIO are phagocytosed and released by macrophages. Furthermore, information on cell membrane modification can be derived from the changes in choline-like metabolites. These results not only suggest that NMR-based metabonomic methods have sufficient sensitivity to identify the metabolic consequences of murine RAW264.7 macrophage-like cell line response to USPIO in vitro, but also provide useful information on the effects of USPIO on cellular metabolism.

  18. Toxicological effects induced by cadmium in gills of Manila clam ruditapes philippinarum using NMR-based metabolomics

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Linbao; Liu, Xiaoli; You, Liping; Zhou, Di [Key Laboratory of Coastal Zone Environment Processes, CAS, Shandong Provincial Key Laboratory of Coastal Zone Environment Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai (China); The Graduate School of Chinese Academy of Sciences, Beijing (China); Yu, Junbao; Zhao, Jianmin; Wu, Huifeng [Key Laboratory of Coastal Zone Environment Processes, CAS, Shandong Provincial Key Laboratory of Coastal Zone Environment Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai (China); Feng, Jianghua [Department of Electronic Science, Fujian Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen (China)

    2011-11-15

    Cadmium (Cd) has become an important heavy metal contaminant in the sediment and seawater along the Bohai Sea and been of great ecological risk due to its toxic effects to marine organisms. In this work, the toxicological effects caused by environmentally relevant concentrations (10 and 40 {mu}g L{sup -1}) of Cd were studied in the gill tissues of Manila clam Ruditapes philippinarum after exposure for 24, 48, and 96 h. Both low (10 {mu}g L{sup -1}) and high (40 {mu}g L{sup -1}) doses of Cd caused the disturbances in energy metabolism and osmotic regulation and neurotoxicity based on the metabolic biomarkers such as succinate, alanine, branched chain amino acids, betaine, hypotaurine, and glutamate in clam gills after 24 h of exposure. However, the recovery of toxicological effects of Cd after exposure for 96 h was obviously observed in clam to Cd exposures. Overall, these results indicated that NMR-based metabolomics was applicable to elucidate the toxicological effects of heavy metal contaminants in the marine bioindicator. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  19. 1H-NMR-based metabolic signatures of clinical outcomes in trauma patients--beyond lactate and base deficit.

    Science.gov (United States)

    Cohen, Mitchell J; Serkova, Natalie J; Wiener-Kronish, Jeanine; Pittet, Jean-Francois; Niemann, Claus U

    2010-07-01

    The determination of reliable biomarkers capable to predict clinical outcome of a trauma patient remains essential toward better therapeutic management of the patient in the intensive care unit. Assessment of global metabolic profiling using quantitative nuclear magnetic resonance (NMR)-based metabolomics offers an attractive modern methodology for fast and comprehensive determination of multiple circulating metabolites and for establishing metabolic phenotype of survivors versus nonsurvivors. Multivariate data analysis on 43 quantitative metabolic parameters identified three lipid metabolites, triacylglycerol, glycerol heads of phospholipids, and monounsaturated fatty acids, as being the most discriminative markers to separate survivors versus nonsurvivors at the time of admission. Glucose and glutamate were intermediate predictors, followed by lactate and hydroxybutyrate as two low-weight predictors. Ultimately, cellular and subcellular failure in nonsurviving trauma patients results in multiple systemic biochemical effects and in changes in circulating metabolites in the blood that are characteristic for decreased lipid synthesis and urea cycle activity in the liver, and for increased hyperglycemia, lactic, and ketoacidosis.

  20. ¹H NMR-based metabolomics studies on the effect of sesamin in Atlantic salmon (Salmo salar).

    Science.gov (United States)

    Wagner, Liane; Trattner, Sofia; Pickova, Jana; Gómez-Requeni, Pedro; Moazzami, Ali A

    2014-03-15

    A (1)H NMR-based metabolomics approach was used to explore the impact of dietary sesamin on the liver and white muscle metabolic profile of Atlantic salmon (Salmo salar). Fish were fed diets containing different n-6/n-3 fatty acid ratios (V0.5 or V1) and sesamin contents [without (S0), low (SL) 1.16 g/kg feed, and high (SH) 5.8 g/kg feed] for 4 months. Liver and white muscle extracts of aqueous polar and chloroform lipid phases were collected. Multivariate data analyses (PCA and OPLS-DA) of liver chloroform phase showed that high levels of sesamin affected the metabolic profile impartially of the n-6/n-3 ratio. In the aqueous phase, the metabolome of liver and white muscle were affected in fish fed an n-6/n-3 ratio of 1.0 and 0.5, respectively. With high inclusion of sesamin, the levels of several metabolites (e.g. glucose, glycogen, leucine, valine, creatine, carnitine, lactate, nucleosides) were increased. These metabolites are mainly associated with energy metabolism, suggesting that high sesamin inclusion affects liver and white muscle metabolism in fish. This is consistent with lower body weights found in fish fed high sesamin content.

  1. NMR-based metabolomic studies on the toxicological effects of cadmium and copper on green mussels Perna viridis

    Energy Technology Data Exchange (ETDEWEB)

    Wu Huifeng [Section of Marine Ecology and Biotechnology, Division of Life Science, Hong Kong University of Science and Technology (HKUST), Clear Water Bay, Kowloon (Hong Kong); Wang Wenxiong, E-mail: wwang@ust.hk [Section of Marine Ecology and Biotechnology, Division of Life Science, Hong Kong University of Science and Technology (HKUST), Clear Water Bay, Kowloon (Hong Kong)

    2010-11-15

    Traditional toxicology studies have focused on selected biomarkers to characterize the biological stress induced by metals in marine organisms. In this study, a system biology tool, metabolomics, was applied to the marine mussel Perna viridis to investigate changes in the metabolic profiles of soft tissue as a response to copper (Cu) and cadmium (Cd), both as single metal and as a mixture. The major metabolite changes corresponding to metal exposure are related to amino acids, osmolytes, and energy metabolites. Following metal exposure for 1 week, there was a significant increase in the levels of branched chain amino acids, histidine, glutamate, glutamine, hypotaurine, dimethylglycine, arginine and ATP/ADP. For the Cu + Cd co-exposed mussels, the levels of lactate, branched chain amino acid, succinate, and NAD increased, whereas the levels of glucose, glycogen, and ATP/ADP decreased, indicating a different metabolic profile for the single metal exposure groups. After 2 weeks of exposure, the mussels showed acclimatization to Cd exposure based on the recovery of some metabolites. However, the metabolic profile induced by the metal mixture was very similar to that from Cu exposure, suggesting that Cu dominantly induced the metabolic disturbances. Both Cu and Cd may lead to neurotoxicity, disturbances in energy metabolism, and osmoregulation changes. These results demonstrate the high applicability and reliability of NMR-based metabolomics in interpreting the toxicological mechanisms of metals using global metabolic biomarkers.

  2. 1H NMR-based metabolite profiling of plasma in a rat model of chronic kidney disease.

    Directory of Open Access Journals (Sweden)

    Ju-Ae Kim

    Full Text Available Chronic kidney disease (CKD is characterized by the gradual loss of the kidney function to excrete wastes and fluids from the blood. (1H NMR-based metabolomics was exploited to investigate the altered metabolic pattern in rats with CKD induced by surgical reduction of the renal mass (i.e., 5/6 nephrectomy (5/6 Nx, particularly for identifying specific metabolic biomarkers associated with early of CKD. Plasma metabolite profiling was performed in CKD rats (at 4- or 8-weeks after 5/6 Nx compared to sham-operated rats. Principle components analysis (PCA, partial least squares-discriminant analysis (PLS-DA and orthogonal partial least squares-discriminant analysis (OPLS-DA score plots showed a significant separation between the groups. The resulting metabolic profiles demonstrated significantly increased plasma levels of organic anions, including citrate, β-hydroxybutyrate, lactate, acetate, acetoacetate, and formate in CKD. Moreover, levels of alanine, glutamine, and glutamate were significantly higher. These changes were likely to be associated with complicated metabolic acidosis in CKD for counteracting systemic metabolic acidosis or increased protein catabolism from muscle. In contrast, levels of VLDL/LDL (CH2n and N-acetylglycoproteins were decreased. Taken together, the observed changes of plasma metabolite profiles in CKD rats provide insights into the disturbed metabolism in early phase of CKD, in particular for the altered metabolism of acid-base and/or amino acids.

  3. (1)H NMR based metabolomics approach to study the toxic effects of herbicide butachlor on goldfish (Carassius auratus).

    Science.gov (United States)

    Xu, Hua-Dong; Wang, Jun-Song; Li, Ming-Hui; Liu, Yan; Chen, Ting; Jia, Ai-Qun

    2015-02-01

    Butachlor, one of the most widely used herbicides in agriculture, has been reported with high ecotoxicity to aquatic plants and animals. In this study, a (1)H NMR based metabolomics approach combined with histopathological examination and biochemical assays was applied to comprehensively investigate the toxic effects of butachlor on four important organs (gill, brain, liver and kidney) of goldfish (Carassius auratus) for the first time. After 10 days' butachlor exposure at two dosages of 3.2 and 0.64 μmol/L, fish tissues (gill, brain, liver and kidney) and serum were collected. Histopathological inspection revealed severe impairment of gill filaments and obvious cellular edema in livers and kidneys. The increase of glutathione peroxidase (GSH-Px) activity in gill and methane dicarboxylic aldehyde (MDA) level in four tissues reflected the disturbance of antioxidative system in the intoxicated goldfish. Serum lactate dehydrogenase (LDH) activity and creatinine (CRE) level were increased in butachlor exposure groups, suggesting liver and kidney injuries induced by butachlor. Orthogonal signal correction partial least-squares discriminant analysis (OSC-PLS-DA) of NMR profiles disclosed metabolic changes that were related to the toxic effects of butachlor including oxidative stress, disorder of energy metabolism and amino acids metabolism, and disturbance of neurotransmitter balance in butachlor exposed goldfish. This integrated metabolomics approach provided a molecular basis underlying the toxicity of butachlor and demonstrated that metabolomics was a powerful and highly effective approach to elucidate the toxicity and underlying mechanisms of herbicides and pesticides, applicable for their risk assessment.

  4. {sup 1}H NMR-based metabolic profiling reveals inherent biological variation in yeast and nematode model systems

    Energy Technology Data Exchange (ETDEWEB)

    Szeto, Samuel S. W.; Reinke, Stacey N.; Lemire, Bernard D., E-mail: bernard.lemire@ualberta.ca [University of Alberta, Department of Biochemistry, School of Molecular and Systems Medicine (Canada)

    2011-04-15

    The application of metabolomics to human and animal model systems is poised to provide great insight into our understanding of disease etiology and the metabolic changes that are associated with these conditions. However, metabolomic studies have also revealed that there is significant, inherent biological variation in human samples and even in samples from animal model systems where the animals are housed under carefully controlled conditions. This inherent biological variability is an important consideration for all metabolomics analyses. In this study, we examined the biological variation in {sup 1}H NMR-based metabolic profiling of two model systems, the yeast Saccharomyces cerevisiae and the nematode Caenorhabditis elegans. Using relative standard deviations (RSD) as a measure of variability, our results reveal that both model systems have significant amounts of biological variation. The C. elegans metabolome possesses greater metabolic variance with average RSD values of 29 and 39%, depending on the food source that was used. The S. cerevisiae exometabolome RSD values ranged from 8% to 12% for the four strains examined. We also determined whether biological variation occurs between pairs of phenotypically identical yeast strains. Multivariate statistical analysis allowed us to discriminate between pair members based on their metabolic phenotypes. Our results highlight the variability of the metabolome that exists even for less complex model systems cultured under defined conditions. We also highlight the efficacy of metabolic profiling for defining these subtle metabolic alterations.

  5. 2D NMR-based metabolomics uncovers interactions between conserved biochemical pathways in the model organism Caenorhabditis elegans.

    Science.gov (United States)

    Izrayelit, Yevgeniy; Robinette, Steven L; Bose, Neelanjan; von Reuss, Stephan H; Schroeder, Frank C

    2013-02-15

    Ascarosides are small-molecule signals that play a central role in C. elegans biology, including dauer formation, aging, and social behaviors, but many aspects of their biosynthesis remain unknown. Using automated 2D NMR-based comparative metabolomics, we identified ascaroside ethanolamides as shunt metabolites in C. elegans mutants of daf-22, a gene with homology to mammalian 3-ketoacyl-CoA thiolases predicted to function in conserved peroxisomal lipid β-oxidation. Two groups of ethanolamides feature β-keto functionalization confirming the predicted role of daf-22 in ascaroside biosynthesis, whereas α-methyl substitution points to unexpected inclusion of methylmalonate at a late stage in the biosynthesis of long-chain fatty acids in C. elegans. We show that ascaroside ethanolamide formation in response to defects in daf-22 and other peroxisomal genes is associated with severe depletion of endocannabinoid pools. These results indicate unexpected interaction between peroxisomal lipid β-oxidation and the biosynthesis of endocannabinoids, which are major regulators of lifespan in C. elegans. Our study demonstrates the utility of unbiased comparative metabolomics for investigating biochemical networks in metazoans.

  6. Pocket PC-based portable gamma-ray spectrometer

    Directory of Open Access Journals (Sweden)

    Kamontip Ploykrachang

    2011-04-01

    Full Text Available A portable gamma-ray spectrometer based on a Pocket PC has been developed. A 12-bit pipeline analog-to-digitalconverter (ADC associated with an implemented pulse height histogram function on field programmable gate array (FPGAoperating at 15 MHz is employed for pulse height analysis from built-in pulse amplifier. The system, which interfaces withthe Pocket PC via an enhanced RS-232 serial port under the microcontroller facilitation, is utilized for spectrum acquisition,display and analysis. The pulse height analysis capability of the system was tested and it was found that the ADC integralnonlinearity of ±0.45% was obtained with the throughput rate at 160 kcps. The overall system performance was tested usinga PIN photodiode-CsI(Tl crystal coupled scintillation detector and gamma standard radioactive sources of Cs-137 andCo-60. Low cost and the compact system size as a result of the implemented logical function are also discussed.

  7. Pocket-book for the fuel trade 1982/83

    Energy Technology Data Exchange (ETDEWEB)

    Temming, D.

    1982-01-01

    The 'Pocket-book for the fuel trade 82/83' has been planned as a compendium of the fuel trade and as a buyer's guide for the fuel tradesman. It contains beside technical and economical informations about solid and liquid fuels indications to legal questions (competition, price and cartel laws, labor and social laws, responsability questions) and taxes and duties. A comprehensive list of the trade organizations of the fuel trade is also included.

  8. Newnes circuit calculations pocket book with computer programs

    CERN Document Server

    Davies, Thomas J

    2013-01-01

    Newnes Circuit Calculations Pocket Book: With Computer Programs presents equations, examples, and problems in circuit calculations. The text includes 300 computer programs that help solve the problems presented. The book is comprised of 20 chapters that tackle different aspects of circuit calculation. The coverage of the text includes dc voltage, dc circuits, and network theorems. The book also covers oscillators, phasors, and transformers. The text will be useful to electrical engineers and other professionals whose work involves electronic circuitry.

  9. Performance of vintage direct reading pocket ionization chambers.

    Science.gov (United States)

    Bergen, Robert J; Harvey, John A; Kearfott, Kimberlee J

    2010-05-01

    The linearity, accuracy, and precision of each of two groups of vintage 51.6 microC-kg-1 maximum scale passive direct reading pocket ionization chambers, each from a different manufacturer and all aged at least 50 years since manufacture, were tested. The pocket ionization chambers were suspended on a phantom and exposed using a 137Cs source. Variations from trial to trial were smaller than variations from chamber to chamber. The average percent standard deviations ranged from 5.7% to 14% across all exposures. The accuracy of the dosimeter readings increased as the exposure level increased. Percent error from known exposure values decreased as exposure increased. An independent samples t test indicated there was a statistically significant difference between the two groups only at a delivered exposure of 6.45 microC-kg-1. Testing was performed in a 222Rn drum to determine the effect of Rn on the pocket ionization chambers. Exposure of five chambers to an average Rn level of 4.70 kBq m-3 and thirty chambers to 3.86 kBq m-3 over a 7-d period produced abnormally high readings at least three times background in eight of the 35 chambers tested.

  10. Relationship between acid pocket and acid reflux in gastroesophageal reflux disease

    Institute of Scientific and Technical Information of China (English)

    姚东英

    2014-01-01

    Objective To explore the relationship between acid pocket and acid reflux in gastroesophageal reflux disease(GERD).Methods From March 2011 to January 2012,29 patients with GERD were enrolled and nine healthy individuals were set as control.All objects of this study accepted esophageal manometry test,acid pocket test,test of the occurrence time of acid pocket and ambulatory

  11. 24 CFR 570.466 - Additional application submission requirements for Pockets of Poverty-employment opportunities.

    Science.gov (United States)

    2010-04-01

    ... requirements for Pockets of Poverty-employment opportunities. 570.466 Section 570.466 Housing and Urban... application submission requirements for Pockets of Poverty—employment opportunities. Applicants for Action Grants under the Pockets of Poverty provision must describe the number and, to the extent possible,...

  12. Biomarker-based diagnosis of pacemaker and implantable cardioverter defibrillator pocket infections: A prospective, multicentre, case-control evaluation

    Science.gov (United States)

    Vrazic, Hrvoje; Haller, Bernhard; Braun, Siegmund; Petzold, Tobias; Ott, Ilka; Lennerz, Agnes; Michel, Jonathan; Blažek, Patrick; Deisenhofer, Isabel; Whittaker, Peter; Kolb, Christof

    2017-01-01

    Background The use of cardiac implantable electronic devices (CIED) has risen steadily, yet the rate of cardiac device infections (CDI) has disproportionately increased. Amongst all cardiac device infections, the pocket infection is the most challenging diagnosis. Therefore, we aimed to improve diagnosis of such pocket infection by identifying relevant biomarkers. Methods We enrolled 25 consecutive patients with invasively and microbiologically confirmed pocket infection. None of the patients had any confounding conditions. Pre-operative levels of 14 biomarkers were compared in infected and control (n = 50) patients. Our selected biomarkers included white blood cell count (WBC), C-reactive protein (CRP), procalcitonin (PCT), lipopolysaccharide binding protein, high-sensitivity C-reactive protein (HS-CRP), polymorphonuclear-elastase, presepsin, various interleukins, tumor necrosis factor α (TNF-α), and granulocyte macrophage colony-stimulating factor (GM-CSF). Results Of the 25 patients with isolated pocket infection (70±13years, 76% male, 40% ICDs), none presented with leukocytosis. In contrast, they had higher serum levels of HS-CRP (p = 0.019) and PCT (p = 0.010) than control patients. Median PCT-level was 0.06 ng/mL (IQR 0.03–0.07 ng/mL) in the study group versus 0.03 ng/mL (IQR 0.02–0.04 ng/mL) in controls. An optimized PCT cut-off value of 0.05 ng/mL suggests pocket infection with a sensitivity of 60% and specificity of 82%. In addition TNF-α- and GM-CSF-levels were lower in the study group. Other biomarkers did not differ between groups. Conclusion Diagnosis of isolated pocket infections requires clinical awareness, physical examination, evaluation of blood cultures and echocardiography assessment. Nevertheless, measurement of PCT- and HS-CRP-levels can aid diagnosis. However, no conclusion can be drawn from normal WBC-values. Clinical trial registration clinicaltrials.gov identifier: NCT01619267 PMID:28264059

  13. Biphenyl/diphenyl ether renin inhibitors: filling the S1 pocket of renin via the S3 pocket.

    Science.gov (United States)

    Yuan, Jing; Simpson, Robert D; Zhao, Wei; Tice, Colin M; Xu, Zhenrong; Cacatian, Salvacion; Jia, Lanqi; Flaherty, Patrick T; Guo, Joan; Ishchenko, Alexey; Wu, Zhongren; McKeever, Brian M; Scott, Boyd B; Bukhtiyarov, Yuri; Berbaum, Jennifer; Panemangalore, Reshma; Bentley, Ross; Doe, Christopher P; Harrison, Richard K; McGeehan, Gerard M; Singh, Suresh B; Dillard, Lawrence W; Baldwin, John J; Claremon, David A

    2011-08-15

    Structure-based design led to the discovery of a novel class of renin inhibitors in which an unprecedented phenyl ring filling the S1 site is attached to the phenyl ring filling the S3 pocket. Optimization for several parameters including potency in the presence of human plasma, selectivity against CYP3A4 inhibition and improved rat oral bioavailability led to the identification of 8d which demonstrated antihypertensive efficacy in a transgenic rat model of human hypertension.

  14. An NMR-based metabolomic approach to investigate the effects of supplementation with glutamic acid in piglets challenged with deoxynivalenol.

    Science.gov (United States)

    Wu, Miaomiao; Xiao, Hao; Ren, Wenkai; Yin, Jie; Hu, Jiayu; Duan, Jielin; Liu, Gang; Tan, Bie; Xiong, Xia; Oso, Abimbola Oladele; Adeola, Olayiwola; Yao, Kang; Yin, Yulong; Li, Tiejun

    2014-01-01

    Deoxynivalenol (DON) has various toxicological effects in humans and pigs that result from the ingestion of contaminated cereal products. This study was conducted to investigate the protective effects of dietary supplementation with glutamic acid on piglets challenged with DON. A total of 20 piglets weaned at 28 d of age were randomly assigned to receive 1 of 4 treatments (5 piglets/treatment): 1) basal diet, negative control (NC); 2) basal diet +4 mg/kg DON (DON); 3) basal diet +2% (g/g) glutamic acid (GLU); 4) basal diet +4 mg/kg DON +2% glutamic acid (DG). A 7-d adaptation period was followed by 30 days of treatment. A metabolite analysis using nuclear magnetic resonance spectroscopy (1H-NMR)-based metabolomic technology and the determination of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) activities for plasma, as well as the activity of Caspase-3 and the proliferation of epithelial cells were conducted. The results showed that contents of low-density lipoprotein, alanine, arginine, acetate, glycoprotein, trimethylamine-N-oxide (TMAO), glycine, lactate, and urea, as well as the glutamate/creatinine ratio were higher but high-density lipoprotein, proline, citrate, choline, unsaturated lipids and fumarate were lower in piglets of DON treatment than that of NC treatment (Pglutamic acid increased the plasma concentrations of proline, citrate, creatinine, unsaturated lipids, and fumarate, and decreased the concentrations of alanine, glycoprotein, TMAO, glycine, and lactate, as well as the glutamate/creatinine ratio (Pglutamic acid to DON treatment increased the plasma activities of SOD and GSH-Px and the proliferating cell nuclear antigen (PCNA) labeling indexes for the jejunum and ileum (Pglutamic acid has the potential to repair the injuries associated with oxidative stress as well as the disturbances of energy and amino acid metabolism induced by DON.

  15. NMR-based metabonomic study of the sub-acute toxicity of titanium dioxide nanoparticles in rats after oral administration

    Energy Technology Data Exchange (ETDEWEB)

    Bu Qian; Lin Hongjun; Xu Youzhi; Cao Zhixing; Zhou Tian; Zhao Yinglan [State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041 (China); Yan Guangyan; Cen Xiaobo [National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041 (China); Deng Pengchi [Analytical and Testing Center, Sichuan University, Chengdu 610041 (China); Peng Feng [Department of Thoracic Oncology of Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041 (China); Xue Aiqin [Institute of Bioengineering, Zhejiang Sci-Tech University Road 2, Xiasha, Hangzhou 310018 (China); Wang Yanli, E-mail: alancenxb@sina.com [Tianjin Children' s Hospital, Tianjin 300074 (China)

    2010-03-26

    As titanium dioxide nanoparticles (TiO{sub 2} NPs) are widely used commercially, their potential toxicity on human health has attracted particular attention. In the present study, the oral toxicological effects of TiO{sub 2} NPs (dosed at 0.16, 0.4 and 1 g kg{sup -1}, respectively) were investigated using conventional approaches and metabonomic analysis in Wistar rats. Serum chemistry, hematology and histopathology examinations were performed. The urine and serum were investigated by {sup 1}H nuclear magnetic resonance (NMR) using principal components and partial least squares discriminant analysis. The metabolic signature of urinalysis in TiO{sub 2} NP-treated rats showed increases in the levels of taurine, citrate, hippurate, histidine, trimethylamine-N-oxide (TMAO), citrulline, {alpha}-ketoglutarate, phenylacetylglycine (PAG) and acetate; moreover, decreases in the levels of lactate, betaine, methionine, threonine, pyruvate, 3-D-hydroxybutyrate (3-D-HB), choline and leucine were observed. The metabonomics analysis of serum showed increases in TMAO, choline, creatine, phosphocholine and 3-D-HB as well as decreases in glutamine, pyruvate, glutamate, acetoacetate, glutathione and methionine after TiO{sub 2} NP treatment. Aspartate aminotransferase (AST), creatine kinase (CK) and lactate dehydrogenase (LDH) were elevated and mitochondrial swelling in heart tissue was observed in TiO{sub 2} NP-treated rats. These findings indicate that disturbances in energy and amino acid metabolism and the gut microflora environment may be attributable to the slight injury to the liver and heart caused by TiO{sub 2} NPs. Moreover, the NMR-based metabolomic approach is a reliable and sensitive method to study the biochemical effects of nanomaterials.

  16. 1H NMR-based metabolomics investigation of copper-laden rat: a model of Wilson's disease.

    Directory of Open Access Journals (Sweden)

    Jingjing Xu

    Full Text Available Wilson's disease (WD, also known as hepatoleticular degeneration (HLD, is a rare autosomal recessive genetic disorder of copper metabolism, which causes copper to accumulate in body tissues. In this study, rats fed with copper-laden diet are used to render the clinical manifestations of WD, and their copper toxicity-induced organ lesions are studied. To investigate metabolic behaviors of 'decoppering' process, penicillamine (PA was used for treating copper-laden rats as this chelating agent could eliminate excess copper through the urine. To date, there has been limited metabolomics study on WD, while metabolic impacts of copper accumulation and PA administration have yet to be established.A combination of 1HNMR spectroscopy and multivariate statistical analysis was applied to examine the metabolic profiles of the urine and blood serum samples collected from the copper-laden rat model of WD with PA treatment.Copper accumulation in the copper-laden rats is associated with increased lactate, creatinine, valine and leucine, as well as decreased levels of glucose and taurine in the blood serum. There were also significant changes in p-hydroxyphenylacetate (p-HPA, creatinine, alpha-ketoglutarate (α-KG, dimethylamine, N-acetylglutamate (NAG, N-acetylglycoprotein (NAC in the urine of these rats. Notably, the changes in p-HPA, glucose, lactate, taurine, valine, leucine, and NAG were found reversed following PA treatment. Nevertheless, there were no changes for dimethylamine, α-KG, and NAC as a result of the treatment. Compared with the controls, the concentrations of hippurate, formate, alanine, and lactate were changed when PA was applied and this is probably due to its side effect. A tool named SMPDB (Small Molecule Pathway Database is introduced to identify the metabolic pathway influenced by the copper-laden diet.The study has shown the potential application of NMR-based metabolomic analysis in providing further insights into the molecular

  17. NMR-based metabonomic study of the sub-acute toxicity of titanium dioxide nanoparticles in rats after oral administration

    Science.gov (United States)

    Bu, Qian; Yan, Guangyan; Deng, Pengchi; Peng, Feng; Lin, Hongjun; Xu, Youzhi; Cao, Zhixing; Zhou, Tian; Xue, Aiqin; Wang, Yanli; Cen, Xiaobo; Zhao, Ying-Lan

    2010-03-01

    As titanium dioxide nanoparticles (TiO2 NPs) are widely used commercially, their potential toxicity on human health has attracted particular attention. In the present study, the oral toxicological effects of TiO2 NPs (dosed at 0.16, 0.4 and 1 g kg - 1, respectively) were investigated using conventional approaches and metabonomic analysis in Wistar rats. Serum chemistry, hematology and histopathology examinations were performed. The urine and serum were investigated by 1H nuclear magnetic resonance (NMR) using principal components and partial least squares discriminant analysis. The metabolic signature of urinalysis in TiO2 NP-treated rats showed increases in the levels of taurine, citrate, hippurate, histidine, trimethylamine-N-oxide (TMAO), citrulline, α-ketoglutarate, phenylacetylglycine (PAG) and acetate; moreover, decreases in the levels of lactate, betaine, methionine, threonine, pyruvate, 3-D-hydroxybutyrate (3-D-HB), choline and leucine were observed. The metabonomics analysis of serum showed increases in TMAO, choline, creatine, phosphocholine and 3-D-HB as well as decreases in glutamine, pyruvate, glutamate, acetoacetate, glutathione and methionine after TiO2 NP treatment. Aspartate aminotransferase (AST), creatine kinase (CK) and lactate dehydrogenase (LDH) were elevated and mitochondrial swelling in heart tissue was observed in TiO2 NP-treated rats. These findings indicate that disturbances in energy and amino acid metabolism and the gut microflora environment may be attributable to the slight injury to the liver and heart caused by TiO2 NPs. Moreover, the NMR-based metabolomic approach is a reliable and sensitive method to study the biochemical effects of nanomaterials.

  18. Ligand binding-dependent functions of the lipocalin NLaz: an in vivo study in Drosophila.

    Science.gov (United States)

    Ruiz, Mario; Ganfornina, Maria D; Correnti, Colin; Strong, Roland K; Sanchez, Diego

    2014-04-01

    Lipocalins are small extracellular proteins mostly described as lipid carriers. The Drosophila lipocalin NLaz (neural Lazarillo) modulates the IIS pathway and regulates longevity, stress resistance, and behavior. Here, we test whether a native hydrophobic pocket structure is required for NLaz to perform its functions. We use a point mutation altering the binding pocket (NLaz(L130R)) and control mutations outside NLaz binding pocket. Tryptophan fluorescence titration reveals that NLaz(L130R) loses its ability to bind ergosterol and the pheromone 7(z)-tricosene but retains retinoic acid binding. Using site-directed transgenesis in Drosophila, we test the functionality of the ligand binding-altered lipocalin at the organism level. NLaz-dependent life span reduction, oxidative stress and starvation sensitivity, aging markers accumulation, and deficient courtship are rescued by overexpression of NLaz(WT), but not of NLaz(L130R). Transcriptional responses to aging and oxidative stress show a large set of age-responsive genes dependent on the integrity of NLaz binding pocket. Inhibition of IIS activity and modulation of oxidative stress and infection-responsive genes are binding pocket-dependent processes. Control of energy metabolites on starvation appears to be, however, insensitive to the modification of the NLaz binding pocket.

  19. Relationship between the metabolite profile and technological properties of bovine milk from two dairy breeds elucidated by NMR-based metabolomics.

    Science.gov (United States)

    Sundekilde, Ulrik Kræmer; Frederiksen, Pernille Dorthea; Clausen, Morten Rahr; Larsen, Lotte Bach; Bertram, Hanne Christine

    2011-07-13

    The aim of the present study was to investigate the relationship between the metabolite profile of milk and important technological properties by using nuclear magnetic resonance (NMR)-based metabolomics. The metabolomics approach was introduced for the metabolic profiling of a set of milk samples from two dairy breeds representing a wide span in coagulation properties. The milk metabolite profiles obtained by proton and carbon NMR spectroscopy could be correlated to breed and, more interestingly, also with the coagulation profile, as established by traditional methods by using principal component analysis (PCA). The metabolites responsible for the separation into breed could mainly be ascribed to carnitine and lactose, whereas the metabolites varying in the samples with respect to coagulation properties included citrate, choline, carnitine, and lactose. The results found in the present study demonstrated a promising potential of NMR-based metabolomics for a rapid analysis and classification of milk samples, both of which are useful for the dairy industry.

  20. {sup 1}H NMR-based metabolomics of time-dependent responses of Eisenia fetida to sub-lethal phenanthrene exposure

    Energy Technology Data Exchange (ETDEWEB)

    Lankadurai, Brian P.; Wolfe, David M.; Simpson, Andre J. [Department of Chemistry, University of Toronto, 1265 Military Trail, Toronto, Ontario M1C 1A4 Canada (Canada); Simpson, Myrna J., E-mail: myrna.simpson@utoronto.ca [Department of Chemistry, University of Toronto, 1265 Military Trail, Toronto, Ontario M1C 1A4 Canada (Canada)

    2011-10-15

    {sup 1}H NMR-based metabolomics was used to examine the response of the earthworm Eisenia fetida after exposure to sub-lethal concentrations of phenanthrene over time. Earthworms were exposed to 0.025 mg/cm{sup 2} of phenanthrene (1/64th of the LC{sub 50}) via contact tests over four days. Earthworm tissues were extracted using a mixture of chloroform, methanol and water, resulting in polar and non-polar fractions that were analyzed by {sup 1}H NMR after one, two, three and four days. NMR-based metabolomic analyses revealed heightened E. fetida responses with longer phenanthrene exposure times. Amino acids alanine and glutamate, the sugar maltose, the lipids cholesterol and phosphatidylcholine emerged as potential indicators of phenanthrene exposure. The conversion of succinate to fumarate in the Krebs cycle was also interrupted by phenanthrene. Therefore, this study shows that NMR-based metabolomics is a powerful tool for elucidating time-dependent relationships in addition to the mode of toxicity of phenanthrene in earthworm exposure studies. - Highlights: > NMR-based earthworm metabolomic analysis of the mode of action of phenanthrene is presented. > The earthworm species E. fetida were exposed to sub-lethal phenanthrene concentrations. > Both polar and non-polar metabolites of E. fetida tissue extracts were analyzed by {sup 1}H NMR. > Longer phenanthrene exposure times resulted in heightened earthworm responses. > An interruption of the Krebs cycle was also observed due to phenanthrene exposure. - {sup 1}H NMR metabolomics is used to determine the relationship between phenanthrene exposure and the metabolic response of the earthworm E. fetida over time and also to elucidate the phenanthrene mode of toxicity.

  1. Ameliorating effects of Mango (Mangifera indica L.) fruit on plasma ethanol level in a mouse model assessed with 1H-NMR based metabolic profiling

    OpenAIRE

    Kim, So-Hyun; K. Cho, Somi; Min, Tae-Sun; Kim, Yujin; Yang, Seung-Ok; Kim, Hee-Su; Hyun, Sun-Hee; Kim, Hana; Kim, Young-Suk; Choi, Hyung-Kyoon

    2011-01-01

    The ameliorating effects of Mango (Mangifera indica L.) flesh and peel samples on plasma ethanol level were investigated using a mouse model. Mango fruit samples remarkably decreased mouse plasma ethanol levels and increased the activities of alcohol dehydrogenase and acetaldehyde dehydrogenase. The 1H-NMR-based metabolomic technique was employed to investigate the differences in metabolic profiles of mango fruits, and mouse plasma samples fed with mango fruit samples. The partial least squar...

  2. 1H NMR-Based Metabolomic Analysis of Sub-Lethal Perfluorooctane Sulfonate Exposure to the Earthworm, Eisenia fetida, in Soil

    Directory of Open Access Journals (Sweden)

    Myrna J. Simpson

    2013-08-01

    Full Text Available 1H NMR-based metabolomics was used to measure the response of Eisenia fetida earthworms after exposure to sub-lethal concentrations of perfluorooctane sulfonate (PFOS in soil. Earthworms were exposed to a range of PFOS concentrations (five, 10, 25, 50, 100 or 150 mg/kg for two, seven and fourteen days. Earthworm tissues were extracted and analyzed by 1H NMR. Multivariate statistical analysis of the metabolic response of E. fetida to PFOS exposure identified time-dependent responses that were comprised of two separate modes of action: a non-polar narcosis type mechanism after two days of exposure and increased fatty acid oxidation after seven and fourteen days of exposure. Univariate statistical analysis revealed that 2-hexyl-5-ethyl-3-furansulfonate (HEFS, betaine, leucine, arginine, glutamate, maltose and ATP are potential indicators of PFOS exposure, as the concentrations of these metabolites fluctuated significantly. Overall, NMR-based metabolomic analysis suggests elevated fatty acid oxidation, disruption in energy metabolism and biological membrane structure and a possible interruption of ATP synthesis. These conclusions obtained from analysis of the metabolic profile in response to sub-lethal PFOS exposure indicates that NMR-based metabolomics is an excellent discovery tool when the mode of action (MOA of contaminants is not clearly defined.

  3. 1H NMR-Based Metabolomic Analysis of Sub-Lethal Perfluorooctane Sulfonate Exposure to the Earthworm, Eisenia fetida, in Soil.

    Science.gov (United States)

    Lankadurai, Brian P; Furdui, Vasile I; Reiner, Eric J; Simpson, André J; Simpson, Myrna J

    2013-08-27

    1H NMR-based metabolomics was used to measure the response of Eisenia fetida earthworms after exposure to sub-lethal concentrations of perfluorooctane sulfonate (PFOS) in soil. Earthworms were exposed to a range of PFOS concentrations (five, 10, 25, 50, 100 or 150 mg/kg) for two, seven and fourteen days. Earthworm tissues were extracted and analyzed by 1H NMR. Multivariate statistical analysis of the metabolic response of E. fetida to PFOS exposure identified time-dependent responses that were comprised of two separate modes of action: a non-polar narcosis type mechanism after two days of exposure and increased fatty acid oxidation after seven and fourteen days of exposure. Univariate statistical analysis revealed that 2-hexyl-5-ethyl-3-furansulfonate (HEFS), betaine, leucine, arginine, glutamate, maltose and ATP are potential indicators of PFOS exposure, as the concentrations of these metabolites fluctuated significantly. Overall, NMR-based metabolomic analysis suggests elevated fatty acid oxidation, disruption in energy metabolism and biological membrane structure and a possible interruption of ATP synthesis. These conclusions obtained from analysis of the metabolic profile in response to sub-lethal PFOS exposure indicates that NMR-based metabolomics is an excellent discovery tool when the mode of action (MOA) of contaminants is not clearly defined.

  4. Analysis of Pocket Double Gate Tunnel FET for Low Stand by Power Logic Circuits

    Directory of Open Access Journals (Sweden)

    Kamal K. Jha

    2013-12-01

    Full Text Available For low power circuits downscaling of MOSFET has a major issue of scaling of voltage which has ceased after 1V. This paper highlights comparative study and analysis of pocket double gate tunnel FET (DGTFET with MOSFET for low standby power logic circuits. The leakage current of pocket DGTFET and MOSFET have been studied and the analysis results shows that the pocket DGTFET gives the lower leakage current than the MOSFET. Further a pocket DGTFET inverter circuit is design in 32 nm technology node at VDD =0.6 V. The pocket DGTFET inverter shows the significant improvement on the leakage power than multi-threshold CMOS (MTCMOS inverter. The leakage power of pocket DGFET and MTCMOS inverter are 0.116 pW and 1.83 pW respectively. It is found that, the pocket DGTFET can replace the MOSFET for low standby power circuits.

  5. Thermodynamics of fragment binding.

    Science.gov (United States)

    Ferenczy, György G; Keserű, György M

    2012-04-23

    The ligand binding pockets of proteins have preponderance of hydrophobic amino acids and are typically within the apolar interior of the protein; nevertheless, they are able to bind low complexity, polar, water-soluble fragments. In order to understand this phenomenon, we analyzed high resolution X-ray data of protein-ligand complexes from the Protein Data Bank and found that fragments bind to proteins with two near optimal geometry H-bonds on average. The linear extent of the fragment binding site was found not to be larger than 10 Å, and the H-bonding region was found to be restricted to about 5 Å on average. The number of conserved H-bonds in proteins cocrystallized with multiple different fragments is also near to 2. These fragment binding sites that are able to form limited number of strong H-bonds in a hydrophobic environment are identified as hot spots. An estimate of the free-energy gain of H-bond formation versus apolar desolvation supports that fragment sized compounds need H-bonds to achieve detectable binding. This suggests that fragment binding is mostly enthalpic that is in line with their observed binding thermodynamics documented in Isothermal Titration Calorimetry (ITC) data sets and gives a thermodynamic rationale for fragment based approaches. The binding of larger compounds tends to more rely on apolar desolvation with a corresponding increase of the entropy content of their binding free-energy. These findings explain the reported size-dependence of maximal available affinity and ligand efficiency both behaving differently in the small molecule region featured by strong H-bond formation and in the larger molecule region featured by apolar desolvation.

  6. Practical Pocket PC Application w/Biometric Security

    Science.gov (United States)

    Logan, Julian

    2004-01-01

    I work in the Flight Software Engineering Branch, where we provide design and development of embedded real-time software applications for flight and supporting ground systems to support the NASA Aeronautics and Space Programs. In addition, this branch evaluates, develops and implements new technologies for embedded real-time systems, and maintains a laboratory for applications of embedded technology. The majority of microchips that are used in modern society have been programmed using embedded technology. These small chips can be found in microwaves, calculators, home security systems, cell phones and more. My assignment this summer entails working with an iPAQ HP 5500 Pocket PC. This top-of-the-line hand-held device is one of the first mobile PC's to introduce biometric security capabilities. Biometric security, in this case a fingerprint authentication system, is on the edge of technology as far as securing information. The benefits of fingerprint authentication are enormous. The most significant of them are that it is extremely difficult to reproduce someone else's fingerprint, and it is equally difficult to lose or forget your own fingerprint as opposed to a password or pin number. One of my goals for this summer is to integrate this technology with another Pocket PC application. The second task for the summer is to develop a simple application that provides an Astronaut EVA (Extravehicular Activity) Log Book capability. The Astronaut EVA Log Book is what an astronaut would use to report the status of field missions, crew physical health, successes, future plans, etc. My goal is to develop a user interface into which these data fields can be entered and stored. The applications that I am developing are created using eMbedded Visual C++ 4.0 with the Pocket PC 2003 Software Development Kit provided by Microsoft.

  7. Windows® Group Policy Administrators Pocket Consultant

    CERN Document Server

    Stanek, William

    2009-01-01

    Portable and precise, this pocket-sized guide delivers ready answers for the day-to-day administration of Group Policy. Zero in on core support and maintenance tasks using quick-reference tables, instructions, and lists. You'll get the focused information you need to solve problems and get the job done-whether at your desk or in the field! Get fast facts to: Configure Local GPOs and Active Directory®-based GPOsManage policy preferences and settingsModel policy changes through the consoleMigrate and maintain the SYSVOLDiagnose and troubleshoot replication issuesKnow when to enforce, block,

  8. Newnes audio and Hi-Fi engineer's pocket book

    CERN Document Server

    Capel, Vivian

    2013-01-01

    Newnes Audio and Hi-Fi Engineer's Pocket Book, Second Edition provides concise discussion of several audio topics. The book is comprised of 10 chapters that cover different audio equipment. The coverage of the text includes microphones, gramophones, compact discs, and tape recorders. The book also covers high-quality radio, amplifiers, and loudspeakers. The book then reviews the concepts of sound and acoustics, and presents some facts and formulas relevant to audio. The text will be useful to sound engineers and other professionals whose work involves sound systems.

  9. Windows® Small Business Server 2008 Administrator's Pocket Consultant

    CERN Document Server

    Zacker, Craig

    2009-01-01

    Portable and precise, this pocket-sized guide delivers ready answers for administering Windows Small Business Server 2008. Zero in on core support tasks and tools using quick-reference tables, instructions, and lists. You'll get the focused information you need to solve problems and get the job done-whether at your desk or in the field. Get fast facts to: Plan, install, and configure a small business network Navigate the Windows SBS Console toolCreate and administer user and group accounts Manage automatic updates, disk storage, and shared printersConfigure mail settings and customize inte

  10. Pharmacophore fingerprint-based approach to binding site subpocket similarity and its application to bioisostere replacement

    NARCIS (Netherlands)

    Wood, D.J.; Vlieg, J. de; Wagener, M.; Ritschel, T.

    2012-01-01

    Bioisosteres have been defined as structurally different molecules or substructures that can form comparable intermolecular interactions, and therefore, fragments that bind to similar protein structures exhibit a degree of bioisosterism. We present KRIPO (Key Representation of Interaction in POckets

  11. Leukocyte integrin αLβ2 headpiece structures: The αI domain, the pocket for the internal ligand, and concerted movements of its loops.

    Science.gov (United States)

    Sen, Mehmet; Springer, Timothy A

    2016-03-15

    High-resolution crystal structures of the headpiece of lymphocyte function-associated antigen-1 (integrin αLβ2) reveal how the αI domain interacts with its platform formed by the α-subunit β-propeller and β-subunit βI domains. The αLβ2 structures compared with αXβ2 structures show that the αI domain, tethered through its N-linker and a disulfide to a stable β-ribbon pillar near the center of the platform, can undergo remarkable pivoting and tilting motions that appear buffered by N-glycan decorations that differ between αL and αX subunits. Rerefined β2 integrin structures reveal details including pyroglutamic acid at the β2 N terminus and bending within the EGF1 domain. Allostery is relayed to the αI domain by an internal ligand that binds to a pocket at the interface between the β-propeller and βI domains. Marked differences between the αL and αX subunit β-propeller domains concentrate near the binding pocket and αI domain interfaces. Remarkably, movement in allostery in the βI domain of specificity determining loop 1 (SDL1) causes concerted movement of SDL2 and thereby tightens the binding pocket for the internal ligand.

  12. Response of ionization chamber based pocket dosimeter to beta radiation.

    Science.gov (United States)

    Kumar, Munish; Gupta, Anil; Pradhan, S M; Bakshi, A K; Chougaonkar, M P; Babu, D A R

    2013-12-01

    Quantitative estimate of the response of ionization chamber based pocket dosimeters (DRDs) to various beta sources was performed. It has been established that the ionization chamber based pocket dosimeters do not respond to beta particles having energy (Emax)1 MeV, the DRDs exhibit measureable response and the values are ~8%, ~14% and ~27% per mSv for natural uranium, (90)Sr/(90)Y and (106)Ru/(106)Rh beta sources respectively. As the energy of the beta particles increases, the response also increases. The response of DRDs to beta particles having energy>1 MeV arises due to the fact that the thickness of the chamber walls is less than the maximum range of beta particles. This may also be one of the reasons for disparity between doses measured with passive/legal dosimeters (TLDs) and DRDs in those situations in which radiation workers are exposed to mixed field of gamma photons and beta particles especially at uranium processing plants, nuclear (power and research) reactors, waste management facilities and fuel reprocessing plants etc. The paper provides the reason (technical) for disparity between the doses recorded by TLDs and DRDs in mixed field of photons and beta particles.

  13. Detection of the amoeba Entamoeba gingivalis in periodontal pockets.

    Science.gov (United States)

    Bonner, Mark; Amard, Véronique; Bar-Pinatel, Charlotte; Charpentier, Frédéric; Chatard, Jean-Michel; Desmuyck, Yvan; Ihler, Serge; Rochet, Jean-Pierre; Roux de La Tribouille, Véronique; Saladin, Luc; Verdy, Marion; Gironès, Núria; Fresno, Manuel; Santi-Rocca, Julien

    2014-01-01

    Periodontitis is a public health issue, being one of the most prevalent diseases worldwide. However, the aetiology of the disease is still unclear: genetics of patients cannot explain the dispersed or isolated localisation of gingival pockets, while bacteria-based models are insufficient to distinguish gingivitis and periodontitis. The possible role of parasites in the establishment of periodontitis has been poorly studied until now. The aim of this project was to study a potential link between colonisation of gingival crevices by the amoeba Entamoeba gingivalis and periodontitis. In eight different dental clinics in France, samples were taken in periodontal pockets (72) or healthy sites (33), and submitted to microscopic observation and molecular identification by PCR with a new set of primers designed to specifically detect E. gingivalis. This blind sample analysis showed the strong sensitivity of PCR compared with clinical diagnosis (58/72 = 81%), and microscopy (51/65 = 78%). The results of this work show that the parasites detected by microscopy mainly - if not exclusively - belong to the species E. gingivalis and that the presence of the parasite is correlated with periodontitis.

  14. Detection of the amoeba Entamoeba gingivalis in periodontal pockets

    Directory of Open Access Journals (Sweden)

    Bonner Mark

    2014-01-01

    Full Text Available Periodontitis is a public health issue, being one of the most prevalent diseases worldwide. However, the aetiology of the disease is still unclear: genetics of patients cannot explain the dispersed or isolated localisation of gingival pockets, while bacteria-based models are insufficient to distinguish gingivitis and periodontitis. The possible role of parasites in the establishment of periodontitis has been poorly studied until now. The aim of this project was to study a potential link between colonisation of gingival crevices by the amoeba Entamoeba gingivalis and periodontitis. In eight different dental clinics in France, samples were taken in periodontal pockets (72 or healthy sites (33, and submitted to microscopic observation and molecular identification by PCR with a new set of primers designed to specifically detect E. gingivalis. This blind sample analysis showed the strong sensitivity of PCR compared with clinical diagnosis (58/72 = 81%, and microscopy (51/65 = 78%. The results of this work show that the parasites detected by microscopy mainly – if not exclusively – belong to the species E. gingivalis and that the presence of the parasite is correlated with periodontitis.

  15. Uranium pyrrolylamine complexes featuring a trigonal binding pocket and interligand noncovalent interactions.

    Science.gov (United States)

    Lewis, Andrew J; Williams, Ursula J; Kikkawa, James M; Carroll, Patrick J; Schelter, Eric J

    2012-01-02

    The syntheses of tri- and tetravalent uranium complexes of the Ar(F)(3)TPA(3-) ligand [Ar(F) = 3,5-bis(trifluoromethyl)phenyl; TPA = tris(pyrrolyl-α-methylamine)] are described. Interligand noncovalent interactions between arene groups within the complexes are detected both in the solid state and in solution.

  16. Rasp21 sequences opposite the nucleotide binding pocket are required for GRF-mediated nucleotide release

    DEFF Research Database (Denmark)

    Leonardsen, L; DeClue, J E; Lybaek, H;

    1996-01-01

    , the sensitivity of H-Ras to GRF was abolished when residues 130-139 were replaced by proline-aspartic acid-glutamine, whereas substitution of the entire loop 8 (residues 123-130 replaced by leucine-isoleucine-arginine) had no effect on the stimulation of guanine nucleotide release by GRF. Substrate activity...

  17. Repurposing metformin: an old drug with new tricks in its binding pockets.

    Science.gov (United States)

    Pryor, Rosina; Cabreiro, Filipe

    2015-11-01

    Improvements in healthcare and nutrition have generated remarkable increases in life expectancy worldwide. This is one of the greatest achievements of the modern world yet it also presents a grave challenge: as more people survive into later life, more also experience the diseases of old age, including type 2 diabetes (T2D), cardiovascular disease (CVD) and cancer. Developing new ways to improve health in the elderly is therefore a top priority for biomedical research. Although our understanding of the molecular basis of these morbidities has advanced rapidly, effective novel treatments are still lacking. Alternative drug development strategies are now being explored, such as the repurposing of existing drugs used to treat other diseases. This can save a considerable amount of time and money since the pharmacokinetics, pharmacodynamics and safety profiles of these drugs are already established, effectively enabling preclinical studies to be bypassed. Metformin is one such drug currently being investigated for novel applications. The present review provides a thorough and detailed account of our current understanding of the molecular pharmacology and signalling mechanisms underlying biguanide-protein interactions. It also focuses on the key role of the microbiota in regulating age-associated morbidities and a potential role for metformin to modulate its function. Research in this area holds the key to solving many of the mysteries of our current understanding of drug action and concerted effects to provide sustained and long-life health.

  18. Does widowhood explain gender differences in out-of-pocket medical spending among the elderly?

    Science.gov (United States)

    Goda, Gopi Shah; Shoven, John B; Slavov, Sita Nataraj

    2013-05-01

    Despite the presence of Medicare, out-of-pocket medical spending is a large expenditure risk facing the elderly. While women live longer than men, elderly women incur higher out-of-pocket medical spending than men at each age. In this paper, we examine whether differences in marital status and living arrangements can explain this difference. We find that out-of-pocket medical spending is approximately 24 percent higher when an individual becomes widowed, a large portion of which is spending on nursing homes. Our results suggest a substantial role of living arrangements in out-of-pocket medical spending. Our estimates combined with differences in rates of widowhood across gender suggest that marital status can explain about one third of the gender difference in total out-of-pocket medical spending, leaving a large portion unexplained. On the other hand, gender differences in widowhood more than explain the observed gender difference in out-of-pocket spending on nursing homes.

  19. STUDY OF RELATIONSHIP BETWEEN DEPTH OF PERIODONTAL POCKETS, ANAEROBIC BACTERIA AND INFLAMMATORY CELLS IN PERIODONTITIS

    OpenAIRE

    Owlia, P.; Salari MH.; Saderi, H; Z. Kadkhoda

    2000-01-01

    In this study 100 cases of advanced periodontitis were compared with a control group of 100 persons. The parameters were the depth of the periodontal pockets, radiographic images, presence of inflammatory cells and different types of anaerobic bacteria in the pockets. The depth of pocket was measured by a sterile probe and the presence of inflammatory cells was determined through sterile curettage. The smears were stained by Gimsa and Gram methods. For the purpose of microbiological studies, ...

  20. The structure of haemoglobin bound to the haemoglobin receptor IsdH from Staphylococcus aureus shows disruption of the native α-globin haem pocket.

    Science.gov (United States)

    Dickson, Claire F; Jacques, David A; Clubb, Robert T; Guss, J Mitchell; Gell, David A

    2015-06-01

    Staphylococcus aureus is a common and serious cause of infection in humans. The bacterium expresses a cell-surface receptor that binds to, and strips haem from, human haemoglobin (Hb). The binding interface has previously been identified; however, the structural changes that promote haem release from haemoglobin were unknown. Here, the structure of the receptor-Hb complex is reported at 2.6 Å resolution, which reveals a conformational change in the α-globin F helix that disrupts the haem-pocket structure and alters the Hb quaternary interactions. These features suggest potential mechanisms by which the S. aureus Hb receptor induces haem release from Hb.

  1. 1H NMR-based metabonomics for the classification of Greek wines according to variety, region, and vintage. Comparison with HPLC data.

    Science.gov (United States)

    Anastasiadi, Maria; Zira, Athina; Magiatis, Prokopios; Haroutounian, Serkos A; Skaltsounis, Alexios Leandros; Mikros, Emmanuel

    2009-12-01

    A sensitive and simple method was developed for the classification of wines according to variety, geographical origin, and vintage using NMR-based metabonomics. Polyphenol-rich extracts were prepared from 67 varietal wines from the principal wine-producing regions of Greece, using adsorption resin XAD-4. 1D (1)H NMR spectra obtained from the corresponding extracts were segmented, integrated, and normalized, and the data were subjected to principal component analysis. The chemometric classification of wines according to their phenolic profile allows discrimination between wines from different wineries of the same wine-producing zone and between different vintages for wines of the same variety.

  2. 1H NMR-Based Metabolomic Analysis of Sub-Lethal Perfluorooctane Sulfonate Exposure to the Earthworm, Eisenia fetida, in Soil

    OpenAIRE

    SIMPSON, Myrna J.; André J. Simpson; Reiner, Eric J.; Brian P. Lankadurai; Furdui, Vasile I.

    2013-01-01

    1H NMR-based metabolomics was used to measure the response of Eisenia fetida earthworms after exposure to sub-lethal concentrations of perfluorooctane sulfonate (PFOS) in soil. Earthworms were exposed to a range of PFOS concentrations (five, 10, 25, 50, 100 or 150 mg/kg) for two, seven and fourteen days. Earthworm tissues were extracted and analyzed by 1H NMR. Multivariate statistical analysis of the metabolic response of E. fetida to PFOS exposure identified time-dependent responses that wer...

  3. Exploitation of pocket gophers and their food caches by grizzly bears

    Science.gov (United States)

    Mattson, D.J.

    2004-01-01

    I investigated the exploitation of pocket gophers (Thomomys talpoides) by grizzly bears (Ursus arctos horribilis) in the Yellowstone region of the United States with the use of data collected during a study of radiomarked bears in 1977-1992. My analysis focused on the importance of pocket gophers as a source of energy and nutrients, effects of weather and site features, and importance of pocket gophers to grizzly bears in the western contiguous United States prior to historical extirpations. Pocket gophers and their food caches were infrequent in grizzly bear feces, although foraging for pocket gophers accounted for about 20-25% of all grizzly bear feeding activity during April and May. Compared with roots individually excavated by bears, pocket gopher food caches were less digestible but more easily dug out. Exploitation of gopher food caches by grizzly bears was highly sensitive to site and weather conditions and peaked during and shortly after snowmelt. This peak coincided with maximum success by bears in finding pocket gopher food caches. Exploitation was most frequent and extensive on gently sloping nonforested sites with abundant spring beauty (Claytonia lanceolata) and yampah (Perdieridia gairdneri). Pocket gophers are rare in forests, and spring beauty and yampah roots are known to be important foods of both grizzly bears and burrowing rodents. Although grizzly bears commonly exploit pocket gophers only in the Yellowstone region, this behavior was probably widespread in mountainous areas of the western contiguous United States prior to extirpations of grizzly bears within the last 150 years.

  4. Pocket data mining big data on small devices

    CERN Document Server

    Gaber, Mohamed Medhat; Gomes, Joao Bartolo

    2014-01-01

    Owing to continuous advances in the computational power of handheld devices like smartphones and tablet computers, it has become possible to perform Big Data operations including modern data mining processes onboard these small devices. A decade of research has proved the feasibility of what has been termed as Mobile Data Mining, with a focus on one mobile device running data mining processes. However, it is not before 2010 until the authors of this book initiated the Pocket Data Mining (PDM) project exploiting the seamless communication among handheld devices performing data analysis tasks that were infeasible until recently. PDM is the process of collaboratively extracting knowledge from distributed data streams in a mobile computing environment. This book provides the reader with an in-depth treatment on this emerging area of research. Details of techniques used and thorough experimental studies are given. More importantly and exclusive to this book, the authors provide detailed practical guide on the depl...

  5. MARTINDALE'S DRUGS RESTRICTED IN SPORT POCKET COMPANION 2009

    Directory of Open Access Journals (Sweden)

    Sean C. Sweetman

    2009-06-01

    Full Text Available Over 500 drugs restricted in sport presented in alphabetical order. To inform and alert the athlete about the potential problem of drug taking for any kind of reasons on and off during training and competition.A comprehensive index of drug names, synonyms, medical usage, single and multi-ingredient preparations and trade (on occasion street names of drugs from 40 countries worldwide (Martindale data. The classification of World Anti-Doping Agency (WADA is added to the explanation of drugs limitation in sport in and out of competition. A glossary of common medical terms is also included.This pocket publication is a must-have list of restricted drugs for athletes, trainers, sports medicine professionals, in short for anyone in exercise physiology and human performance fields.

  6. Pocket book of environmental engineering; Taschenbuch der Umwelttechnik

    Energy Technology Data Exchange (ETDEWEB)

    Schwister, K. (ed.) [Fachhochschule Duesseldorf (Germany)

    2003-07-01

    The pocket book of environmental engineering presents compact, practical, and easy-to-understand information on the complex mechanisms of environmental protection and environmental engineering. The interdependences between soil, water and air are outlined, and measures in the fields of soil and water protection, air pollution abatement, waste volume reduction, noise protection, energy conservation and renewable energy sources are listed. The fundamentals of environmental management are gone into, and current problems like ozone depletion, forest die-back and global climate change are discussed. [German] Das Taschenbuch der Umwelttechnik enthaelt eine kompakte, verstaendliche und an den Beduerfnissen der Praxis ausgerichtete Gesamtdarstellung des Umweltschutzes sowie der Umwelttechnik. Es zeigt die vernetzten stofflichen Zusammenhaenge zwischen den Umweltmedien Boden - Wasser - Luft und stellt die notwendigen Massnahmen in den Bereichen Boden- und Wasserschutz, Luftreinhaltung, Abfallreduzierung, Laermschutz, Energieeinsparung sowie Umstellung auf regenerative Energietraeger uebersichtlich zusammen. Neben den Grundlagen des Umweltmanagements werden konkrete Umweltfragen, z.B. Ozonloch, Waldsterben und Klimawandel, beispielhaft besprochen. (orig.)

  7. The Six-Inch Lunar Atlas A Pocket Field Guide

    CERN Document Server

    Spain, Don

    2009-01-01

    The Six-Inch Lunar Atlas has been designed specifically for use in the field by lunar observers so it’s perfect for fitting into an observer’s pocket! The author’s own lunar photographs were taken with a 6-inch (150mm) telescope and CCD camera, and closely match the visual appearance of the Moon when viewed through 3-inch to 8-inch telescopes. Each picture is shown oriented "as the Moon really is" when viewed from the northern hemisphere, and is supplemented by exquisite computer sketches that list the main features. Two separate computer sketches are provided to go with each photograph, one oriented to appear as seen through an SCT telescope (e.g. the Meade and Celestron ranges), the other oriented for Newtonian and refracting telescopes. Observers using the various types telescopes will find it extremely helpful to identify lunar features as the human brain is very poor at making "mirror-image" visual translations.

  8. Study of Application Software Based on Pocket PC Database%基POCKET PC数据库应用程序的研究

    Institute of Scientific and Technical Information of China (English)

    詹捷; 陆玲; 程志梅; 张爱华

    2005-01-01

    本文主要是对在Windows CE 3.0平台下,利用EVC软件开发Pocket PC数据库应用程序的基本方法进行研究,其中重点探讨了在POCKET PC中如何利用EVC对数据库进行各种操作.

  9. Metabolic discrimination of Swertia mussotii and Swertia chirayita known as "Zangyinchen" in traditional Tibetan medicine by (1)H NMR-based metabolomics.

    Science.gov (United States)

    Fan, Gang; Luo, Wei-Zao; Luo, Shang-Hua; Li, Yan; Meng, Xian-Li; Zhou, Xiang-Dong; Zhang, Yi

    2014-09-01

    Swertia mussotii Franch. and Swertia chirayita Buch.-Ham. have been commonly used under the same name "Zangyinchen" for the treatment of liver and gallbladder diseases in traditional Tibetan medicine. Detailed characterization and comparison of the complete set of metabolites of these two species are critical for their objective identification and quality control. In this study, a rapid, simple and comprehensive (1)H NMR-based metabolomics method was first developed to differentiate the two species. A broad range of metabolites, including iridoid glycosides, xanthones, triterpenoids, flavonoids, carbohydrates, and amino acids, were identified. Statistical analysis showed evident differences between the two species, and the major markers responsible for the differences were screened. In addition, quantitative (1)H NMR method (qHNMR) was used for the target analysis of the discriminating metabolites. The results showed that S. mussotii had significantly higher contents of gentiopicrin, isoorientin, glucose, loganic acid, and choline, whereas S. chirayita exhibited higher levels of swertiamarin, oleanolic acid, valine, and fatty acids. These findings indicate that (1)H NMR-based metabolomics is a reliable and effective method for the metabolic profiling and discrimination of the two Swertia species, and can be used to verify the genuine origin of Zangyinchen.

  10. Standardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a review

    KAUST Repository

    Emwas, Abdul-Hamid M.

    2014-11-21

    The metabolic composition of human biofluids can provide important diagnostic and prognostic information. Among the biofluids most commonly analyzed in metabolomic studies, urine appears to be particularly useful. It is abundant, readily available, easily stored and can be collected by simple, noninvasive techniques. Moreover, given its chemical complexity, urine is particularly rich in potential disease biomarkers. This makes it an ideal biofluid for detecting or monitoring disease processes. Among the metabolomic tools available for urine analysis, NMR spectroscopy has proven to be particularly well-suited, because the technique is highly reproducible and requires minimal sample handling. As it permits the identification and quantification of a wide range of compounds, independent of their chemical properties, NMR spectroscopy has been frequently used to detect or discover disease fingerprints and biomarkers in urine. Although protocols for NMR data acquisition and processing have been standardized, no consensus on protocols for urine sample selection, collection, storage and preparation in NMR-based metabolomic studies have been developed. This lack of consensus may be leading to spurious biomarkers being reported and may account for a general lack of reproducibility between laboratories. Here, we review a large number of published studies on NMR-based urine metabolic profiling with the aim of identifying key variables that may affect the results of metabolomics studies. From this survey, we identify a number of issues that require either standardization or careful accounting in experimental design and provide some recommendations for urine collection, sample preparation and data acquisition.

  11. Relating the shape of protein binding sites to binding affinity profiles: is there an association?

    Directory of Open Access Journals (Sweden)

    Bitter István

    2010-10-01

    Full Text Available Abstract Background Various pattern-based methods exist that use in vitro or in silico affinity profiles for classification and functional examination of proteins. Nevertheless, the connection between the protein affinity profiles and the structural characteristics of the binding sites is still unclear. Our aim was to investigate the association between virtual drug screening results (calculated binding free energy values and the geometry of protein binding sites. Molecular Affinity Fingerprints (MAFs were determined for 154 proteins based on their molecular docking energy results for 1,255 FDA-approved drugs. Protein binding site geometries were characterized by 420 PocketPicker descriptors. The basic underlying component structure of MAFs and binding site geometries, respectively, were examined by principal component analysis; association between principal components extracted from these two sets of variables was then investigated by canonical correlation and redundancy analyses. Results PCA analysis of the MAF variables provided 30 factors which explained 71.4% of the total variance of the energy values while 13 factors were obtained from the PocketPicker descriptors which cumulatively explained 94.1% of the total variance. Canonical correlation analysis resulted in 3 statistically significant canonical factor pairs with correlation values of 0.87, 0.84 and 0.77, respectively. Redundancy analysis indicated that PocketPicker descriptor factors explain 6.9% of the variance of the MAF factor set while MAF factors explain 15.9% of the total variance of PocketPicker descriptor factors. Based on the salient structures of the factor pairs, we identified a clear-cut association between the shape and bulkiness of the drug molecules and the protein binding site descriptors. Conclusions This is the first study to investigate complex multivariate associations between affinity profiles and the geometric properties of protein binding sites. We found that

  12. Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation.

    Science.gov (United States)

    Jain, Ajay N

    2009-06-01

    Computational methods for docking ligands have been shown to be remarkably dependent on precise protein conformation, where acceptable results in pose prediction have been generally possible only in the artificial case of re-docking a ligand into a protein binding site whose conformation was determined in the presence of the same ligand (the "cognate" docking problem). In such cases, on well curated protein/ligand complexes, accurate dockings can be returned as top-scoring over 75% of the time using tools such as Surflex-Dock. A critical application of docking in modeling for lead optimization requires accurate pose prediction for novel ligands, ranging from simple synthetic analogs to very different molecular scaffolds. Typical results for widely used programs in the "cross-docking case" (making use of a single fixed protein conformation) have rates closer to 20% success. By making use of protein conformations from multiple complexes, Surflex-Dock yields an average success rate of 61% across eight pharmaceutically relevant targets. Following docking, protein pocket adaptation and rescoring identifies single pose families that are correct an average of 67% of the time. Consideration of the best of two pose families (from alternate scoring regimes) yields a 75% mean success rate.

  13. Modeling the met form of human tyrosinase: a refined and hydrated pocket for antagonist design.

    Science.gov (United States)

    Favre, Elisabeth; Daina, Antoine; Carrupt, Pierre-Alain; Nurisso, Alessandra

    2014-08-01

    Tyrosinases are type 3 copper proteins involved in melanin biosynthesis, responsible for skin and hair color in mammals. To steer tyrosinase inhibitor discovery for therapeutic and cosmetic purposes, structural information about human tyrosinase is necessary. As this protein has never been crystallized so far, we derived a robust homology model built using structural information from Streptomyces castaneoglobisporus and Ipomea batata catecholoxidase enzymes. The active site containing two copper atoms in co-ordination with six histidine residues was refined through an optimization protocol based on molecular mechanics parameters for copper co-ordination and charges calculated by quantum mechanics methods. Five structural water molecules and a hydroxyl ion were found to be essential for optimization. The superimposition of the human homology model on crystallographic structures of tyrosinases from other species revealed similar overall backbone topologies, active site conformations, and conserved water molecules. Phenylthiourea (PTU), the tyrosinase inhibitor of reference, was then docked into the solvated human active pocket. A binding mode consistent with crystallographic information was obtained. Taken together, these findings demonstrated that the human tyrosinase model, deposited in the Protein Model Database, is a reliable structure for future rational inhibitor design projects.

  14. Transcriptional regulation of Sox2 by the retinoblastoma family of pocket proteins.

    Science.gov (United States)

    Vilas, Jéssica M; Ferreirós, Alba; Carneiro, Carmen; Morey, Lluis; Da Silva-Álvarez, Sabela; Fernandes, Tânia; Abad, María; Di Croce, Luciano; García-Caballero, Tomás; Serrano, Manuel; Rivas, Carmen; Vidal, Anxo; Collado, Manuel

    2015-02-20

    Cellular reprogramming to iPSCs has uncovered unsuspected links between tumor suppressors and pluripotency factors. Using this system, it was possible to identify tumor suppressor p27 as a repressor of Sox2 during differentiation. This led to the demonstration that defects in the repression of Sox2 can contribute to tumor development. The members of the retinoblastoma family of pocket proteins, pRb, p107 and p130, are negative regulators of the cell cycle with tumor suppressor activity and with roles in differentiation. In this work we studied the relative contribution of the retinoblastoma family members to the regulation of Sox2 expression. We found that deletion of Rb or p130 leads to impaired repression of Sox2, a deffect amplified by inactivation of p53. We also identified binding of pRb and p130 to an enhancer with crucial regulatory activity on Sox2 expression. Using cellular reprogramming we tested the impact of the defective repression of Sox2 and confirmed that Rb deficiency allows the generation of iPSCs in the absence of exogenous Sox2. Finally, partial depletion of Sox2 positive cells reduced the pituitary tumor development initiated by Rb loss in vivo. In summary, our results show that Sox2 repression by pRb is a relevant mechanism of tumor suppression.

  15. Transcriptional regulation of Sox2 by the retinoblastoma family of pocket proteins

    Science.gov (United States)

    Carneiro, Carmen; Morey, Lluis; Silva-Álvarez, Sabela Da; Fernandes, Tânia; Abad, María; Croce, Luciano Di; García-Caballero, Tomás; Serrano, Manuel; Rivas, Carmen; Vidal, Anxo; Collado, Manuel

    2015-01-01

    Cellular reprogramming to iPSCs has uncovered unsuspected links between tumor suppressors and pluripotency factors. Using this system, it was possible to identify tumor suppressor p27 as a repressor of Sox2 during differentiation. This led to the demonstration that defects in the repression of Sox2 can contribute to tumor development. The members of the retinoblastoma family of pocket proteins, pRb, p107 and p130, are negative regulators of the cell cycle with tumor suppressor activity and with roles in differentiation. In this work we studied the relative contribution of the retinoblastoma family members to the regulation of Sox2 expression. We found that deletion of Rb or p130 leads to impaired repression of Sox2, a deffect amplified by inactivation of p53. We also identified binding of pRb and p130 to an enhancer with crucial regulatory activity on Sox2 expression. Using cellular reprogramming we tested the impact of the defective repression of Sox2 and confirmed that Rb deficiency allows the generation of iPSCs in the absence of exogenous Sox2. Finally, partial depletion of Sox2 positive cells reduced the pituitary tumor development initiated by Rb loss in vivo. In summary, our results show that Sox2 repression by pRb is a relevant mechanism of tumor suppression. PMID:25576924

  16. The Role of Electronic Pocket Dictionaries as an English Learning Tool among Chinese Students

    Science.gov (United States)

    Jian, Hua-Li; Sandnes, Frode Eika; Law, Kris M. Y.; Huang, Yo-Ping; Huang, Yueh-Min

    2009-01-01

    This study addressed the role of electronic pocket dictionaries as a language learning tool among university students in Hong Kong and Taiwan. The target groups included engineering and humanities students at both undergraduate and graduate level. Speed of reference was found to be the main motivator for using an electronic pocket dictionary.…

  17. Denaturing gradient gel electrophoresis analysis to study bacterial community structure in pockets of periodontitis patients

    NARCIS (Netherlands)

    Zijnge, V.; Harmsen, H.J.M.; Kleinfelder, J.W.; Rest, M.E. van der; Degener, J.E.; Welling, G.W.

    2003-01-01

    Bacteria are involved in the onset and progression of periodontitis. A promising molecular technique, denaturing gradient gel electrophoresis (DGGE), to study microbial population dynamics in the subgingival pocket is presented. Twenty-three samples were taken from the subgingival pockets of nine pa

  18. The Harpoon Security System for Helper Programs on a Pocket Companion

    NARCIS (Netherlands)

    Smit, Gerard J.M.; Havinga, Paul J.M.; Os, van Daniel

    1997-01-01

    We present a security framework for executing foreign programs, called helpers, on a Pocket Companion: a wireless hand-held computer. A helper program as proposed in this paper is a service program that can migrate once from a server to a Pocket Companion or vice-versa. A helper program is convenien

  19. Influence of Lubricant Pocket Geometry upon Lubrication Mechanisms on Tool-Workpiece Interfaces in Metal Forming

    DEFF Research Database (Denmark)

    Shimizu, I; Martins, P.A.F.; Bay, Niels

    2004-01-01

    Micro lubricant pockets located on the surface of plastically deforming workpieces are recognized to improve the performance of fluid lubrication in a metal forming processes. This work investigates the joint influence of pocket geometry and process working conditions on micro lubrication mechani...

  20. Micro-Pocket Fission Detectors (MPFD) For Fuel Assembly Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Troy Unruh; Michael Reichenberger; Phillip Ugorowski

    2013-09-01

    Neutron sensors capable of real-time measurement of thermal flux, fast flux, and temperature in a single miniaturized probe are needed in irradiation tests required to demonstrate the performance of candidate new fuels, and cladding materials. In-core ceramic-based miniature neutron detectors or “Micro-Pocket Fission Detectors” (MPFDs) have been studied at Kansas State University (KSU). The first MPFD prototypes were tested in various neutron fields at the KSU TRIGA research reactor with successful results. Currently, a United States Department of Energy-sponsored joint KSU/Idaho National Laboratory (INL) effort is underway to develop a high-temperature, high-pressure version of the MPFD using radiation-resistant, high temperature materials, which would be capable of withstanding irradiation test conditions in high performance material and test reactors (MTRs). Ultimately, this more compact, more accurate, and longer lifetime flux sensor for critical mock-ups, existing and advanced reactor designs, high performance MTRs, and transient test reactors has the potential to lead to higher accuracy and resolution data from irradiation testing, more detailed core flux measurements and enhanced fuel assembly processing. Prior evaluations by KSU indicate that these sensors could also be used to monitor burn-up of nuclear fuel. If integrated into nuclear fuel assemblies, MPFDs offer several advantages to current spent fuel management systems.

  1. NMR-Based Metabonomic Analysis for Sulprostone-Induced Mice%硫前列酮影响小鼠代谢的NMR研究

    Institute of Scientific and Technical Information of China (English)

    严星; 张利民; 安艳捧; 李洪德; 唐惠儒

    2013-01-01

    前列腺素E2 (PGE2)作为一种体内广泛分布的活性物质,通过与其特异性受体EP1,EP2,EP3和EP4结合实现信号跨膜转导,参与许多重要的生理病理过程.硫前列酮作为PGE2的类似物,通过激活EP1和EP3受体发挥其生理作用,但相关的代谢基础还不甚清楚.该研究运用基于核磁共振(NMR)技术的代谢组学方法研究了EP1和EP3受体激活剂硫前列酮对小鼠血清和肝脏代谢组的影响.结果表明,中高剂量硫前列酮处理32天会导致小鼠肝脏代谢组中的烟酰胺腺嘌呤二核苷酸磷酸、烟酰胺腺嘌呤二核苷酸、二磷酸尿苷、磷酸腺苷和胆汁酸的明显增加,同时肝糖原、葡萄糖、苯丙氨酸、酪氨酸、尿苷、肌苷、烟碱酸和氧化型谷胱甘肽明显减少.恢复3周后,高剂量硫前列酮处理小鼠会导致肝脏代谢组中的胆碱水平比对照组高.这些结果表明EP1和EP3受体激活剂硫前列酮会对小鼠肝脏的糖、核酸和氨基酸等代谢产生影响.同时,未发现硫前列酮对血清代谢组产生明显影响,这可能与血液循环系统维持机体内环境相对稳定有关.以上研究结果为认识PGE2 EP1/3信号通路在代谢中的作用提供了基础数据.%Prostaglandin E2 (PGE2) is a widely distributed substance in body, and involved in many physiological and pathological processes. It regulates signal transduction pathways through binding to EP1, EP2, EP3 and EP4 receptors. PGE2 is also. Sulpr-ostone is an analogue of PGE2, playing its physiological functions through activation of EP1 and EP3. The metabolic foundation of PGE2 is still poorly understood. This work studied the metabonome of serum and liver in sulprostone-induced mice using nuclear magnetic resonance (NMR)-based analysis. The results showed that following 32 days of sulprostone treatment (i. e. , 0. 1 mg/kg, medium dose; 1 mg/kg, high dose), the animals showed significantly increased NADP+ , NAD+ , UDP, AMP and bile acids

  2. Identification of an Allosteric Pocket on Human Hsp70 Reveals a Mode of Inhibition of This Therapeutically Important Protein

    Science.gov (United States)

    Rodina, Anna; Patel, Pallav D.; Kang, Yanlong; Patel, Yogita; Baaklini, Imad; Wong, Michael J.H.; Taldone, Tony; Yan, Pengrong; Yang, Chenghua; Maharaj, Ronnie; Gozman, Alexander; Patel, Maulik R.; Patel, Hardik J.; Chirico, William; Erdjument-Bromage, Hediye; Talele, Tanaji T.; Young, Jason C.; Chiosis, Gabriela

    2014-01-01

    SUMMARY Hsp70s are important cancer chaperones that act upstream of Hsp90 and exhibit independent anti-apoptotic activities. To develop chemical tools for the study of human Hsp70, we developed a homology model that unveils a previously unknown allosteric site located in the nucleotide binding domain of Hsp70. Combining structure-based design and phenotypic testing, we discovered a previously unknown inhibitor of this site, YK5. In cancer cells, this compound is a potent and selective binder of the cytosolic but not the organellar human Hsp70s and has biological activity partly by interfering with the formation of active oncogenic Hsp70/Hsp90/client protein complexes. YK5 is a small molecule inhibitor rationally designed to interact with an allosteric pocket of Hsp70 and represents a previously unknown chemical tool to investigate cellular mechanisms associated with Hsp70. PMID:24239008

  3. Sonographic assessment of predictors of depth of the corner pocket for ultrasound-guided supraclavicular brachial plexus block

    Directory of Open Access Journals (Sweden)

    Naveen Yadav

    2016-01-01

    Conclusion: Prescanning of supraclavicular region for estimating depth of corner pocket should be done before choosing an appropriate size needle. Furthermore, the needle should not be advanced more than the predicted corner pocket depth.

  4. Binding-site assessment by virtual fragment screening.

    Directory of Open Access Journals (Sweden)

    Niu Huang

    Full Text Available The accurate prediction of protein druggability (propensity to bind high-affinity drug-like small molecules would greatly benefit the fields of chemical genomics and drug discovery. We have developed a novel approach to quantitatively assess protein druggability by computationally screening a fragment-like compound library. In analogy to NMR-based fragment screening, we dock approximately 11,000 fragments against a given binding site and compute a computational hit rate based on the fraction of molecules that exceed an empirically chosen score cutoff. We perform a large-scale evaluation of the approach on four datasets, totaling 152 binding sites. We demonstrate that computed hit rates correlate with hit rates measured experimentally in a previously published NMR-based screening method. Secondly, we show that the in silico fragment screening method can be used to distinguish known druggable and non-druggable targets, including both enzymes and protein-protein interaction sites. Finally, we explore the sensitivity of the results to different receptor conformations, including flexible protein-protein interaction sites. Besides its original aim to assess druggability of different protein targets, this method could be used to identifying druggable conformations of flexible binding site for lead discovery, and suggesting strategies for growing or joining initial fragment hits to obtain more potent inhibitors.

  5. Dynamic water behaviour due to one trapped air pocket in a laboratory pipeline apparatus

    Science.gov (United States)

    Bergant, A.; Karadžić, U.; Tijsseling, A.

    2016-11-01

    Trapped air pockets may cause severe operational problems in hydropower and water supply systems. A locally isolated air pocket creates distinct amplitude, shape and timing of pressure pulses. This paper investigates dynamic behaviour of a single trapped air pocket. The air pocket is incorporated as a boundary condition into the discrete gas cavity model (DGCM). DGCM allows small gas cavities to form at computational sections in the method of characteristics (MOC). The growth of the pocket and gas cavities is described by the water hammer compatibility equation(s), the continuity equation for the cavity volume, and the equation of state of an ideal gas. Isentropic behaviour is assumed for the trapped gas pocket and an isothermal bath for small gas cavities. Experimental investigations have been performed in a laboratory pipeline apparatus. The apparatus consists of an upstream end high-pressure tank, a horizontal steel pipeline (total length 55.37 m, inner diameter 18 mm), four valve units positioned along the pipeline including the end points, and a downstream end tank. A trapped air pocket is captured between two ball valves at the downstream end of the pipeline. The transient event is initiated by rapid opening of the upstream end valve; the downstream end valve stays closed during the event. Predicted and measured results for a few typical cases are compared and discussed.

  6. Robustness of NMR-based metabolomics to generate comparable data sets for olive oil cultivar classification. An inter-laboratory study on Apulian olive oils.

    Science.gov (United States)

    Piccinonna, Sara; Ragone, Rosa; Stocchero, Matteo; Del Coco, Laura; De Pascali, Sandra Angelica; Schena, Francesco Paolo; Fanizzi, Francesco Paolo

    2016-05-15

    Nuclear Magnetic Resonance (NMR) spectroscopy is emerging as a powerful technique in olive oil fingerprinting, but its analytical robustness has to be proved. Here, we report a comparative study between two laboratories on olive oil (1)H NMR fingerprinting, aiming to demonstrate the robustness of NMR-based metabolomics in generating comparable data sets for cultivar classification. Sample preparation and data acquisition were performed independently in two laboratories, equipped with different resolution spectrometers (400 and 500 MHz), using two identical sets of mono-varietal olive oils. Partial Least Squares (PLS)-based techniques were applied to compare the data sets produced by the two laboratories. Despite differences in spectrum baseline, and in intensity and shape of peaks, the amount of shared information was significant (almost 70%) and related to cultivar (same metabolites discriminated between cultivars). In conclusion, regardless of the variability due to operator and machine, the data sets from the two participating units were comparable for the purpose of classification.

  7. Ameliorating effects of Mango (Mangifera indica L.) fruit on plasma ethanol level in a mouse model assessed with H-NMR based metabolic profiling.

    Science.gov (United States)

    Kim, So-Hyun; K Cho, Somi; Min, Tae-Sun; Kim, Yujin; Yang, Seung-Ok; Kim, Hee-Su; Hyun, Sun-Hee; Kim, Hana; Kim, Young-Suk; Choi, Hyung-Kyoon

    2011-05-01

    The ameliorating effects of Mango (Mangifera indica L.) flesh and peel samples on plasma ethanol level were investigated using a mouse model. Mango fruit samples remarkably decreased mouse plasma ethanol levels and increased the activities of alcohol dehydrogenase and acetaldehyde dehydrogenase. The (1)H-NMR-based metabolomic technique was employed to investigate the differences in metabolic profiles of mango fruits, and mouse plasma samples fed with mango fruit samples. The partial least squares-discriminate analysis of (1)H-NMR spectral data of mouse plasma demonstrated that there were clear separations among plasma samples from mice fed with buffer, mango flesh and peel. A loading plot demonstrated that metabolites from mango fruit, such as fructose and aspartate, might stimulate alcohol degradation enzymes. This study suggests that mango flesh and peel could be used as resources for functional foods intended to decrease plasma ethanol level after ethanol uptake.

  8. Detailed scrutiny of the anion receptor pocket in subdomain IIA of serum proteins toward individual response to specific ligands: HSA-pocket resembles flexible biological slide-wrench unlike BSA.

    Science.gov (United States)

    Datta, Shubhashis; Halder, Mintu

    2014-06-12

    Present study reveals that the subdomain IIA cavity of two homologous serum albumins (HSA, BSA) has inherent mutual structural and functional deviations which render noticeable difference in behavior toward specific ligands. The major drug binding site (subdomain IIA) of HSA is found to be largely hydrophobic while that of BSA is partially exposed to water. Larger shift in REE spectra and greater change in solvent reorganization energy of coumarin 343 (C343)-anion in HSA clearly reveals that binding pocket is relatively large and water molecules penetrate deeper into it unlike BSA. The individual response of proteins to perturbation by ligands is found to be way different. Although the subdomain IIA is primarily anion receptive (prefers anionic ligands), the present study suggests that HSA may also like to bind neutral guests due to its remarkable conformational features. Actually, HSA is capable of adopting favorable conformation like mechanical slide-wrench, when required, to accommodate neutral ligands [e.g., coumarin 314 (C314)], as well. But due to less flexible solution structure, BSA behaves like fixed mechanical spanners and hence is not very responsive to C314. Therefore, the generally speaking functional-structural similarities of homologous proteins can be apparent and needs to be analyzed exhaustively.

  9. α-Hemoglobin-stabilizing Protein (AHSP) Perturbs the Proximal Heme Pocket of Oxy-α-hemoglobin and Weakens the Iron-Oxygen Bond*

    Science.gov (United States)

    Dickson, Claire F.; Rich, Anne M.; D'Avigdor, William M. H.; Collins, Daniel A. T.; Lowry, Jason A.; Mollan, Todd L.; Khandros, Eugene; Olson, John S.; Weiss, Mitchell J.; Mackay, Joel P.; Lay, Peter A.; Gell, David A.

    2013-01-01

    α-Hemoglobin (αHb)-stabilizing protein (AHSP) is a molecular chaperone that assists hemoglobin assembly. AHSP induces changes in αHb heme coordination, but how these changes are facilitated by interactions at the αHb·AHSP interface is not well understood. To address this question we have used NMR, x-ray absorption spectroscopy, and ligand binding measurements to probe αHb conformational changes induced by AHSP binding. NMR chemical shift analyses of free CO-αHb and CO-αHb·AHSP indicated that the seven helical elements of the native αHb structure are retained and that the heme Fe(II) remains coordinated to the proximal His-87 side chain. However, chemical shift differences revealed alterations of the F, G, and H helices and the heme pocket of CO-αHb bound to AHSP. Comparisons of iron-ligand geometry using extended x-ray absorption fine structure spectroscopy showed that AHSP binding induces a small 0.03 Å lengthening of the Fe-O2 bond, explaining previous reports that AHSP decreases αHb O2 affinity roughly 4-fold and promotes autooxidation due primarily to a 3–4-fold increase in the rate of O2 dissociation. Pro-30 mutations diminished NMR chemical shift changes in the proximal heme pocket, restored normal O2 dissociation rate and equilibrium constants, and reduced O2-αHb autooxidation rates. Thus, the contacts mediated by Pro-30 in wild-type AHSP promote αHb autooxidation by introducing strain into the proximal heme pocket. As a chaperone, AHSP facilitates rapid assembly of αHb into Hb when βHb is abundant but diverts αHb to a redox resistant holding state when βHb is limiting. PMID:23696640

  10. α-Hemoglobin-stabilizing protein (AHSP) perturbs the proximal heme pocket of oxy-α-hemoglobin and weakens the iron-oxygen bond.

    Science.gov (United States)

    Dickson, Claire F; Rich, Anne M; D'Avigdor, William M H; Collins, Daniel A T; Lowry, Jason A; Mollan, Todd L; Khandros, Eugene; Olson, John S; Weiss, Mitchell J; Mackay, Joel P; Lay, Peter A; Gell, David A

    2013-07-01

    α-Hemoglobin (αHb)-stabilizing protein (AHSP) is a molecular chaperone that assists hemoglobin assembly. AHSP induces changes in αHb heme coordination, but how these changes are facilitated by interactions at the αHb·AHSP interface is not well understood. To address this question we have used NMR, x-ray absorption spectroscopy, and ligand binding measurements to probe αHb conformational changes induced by AHSP binding. NMR chemical shift analyses of free CO-αHb and CO-αHb·AHSP indicated that the seven helical elements of the native αHb structure are retained and that the heme Fe(II) remains coordinated to the proximal His-87 side chain. However, chemical shift differences revealed alterations of the F, G, and H helices and the heme pocket of CO-αHb bound to AHSP. Comparisons of iron-ligand geometry using extended x-ray absorption fine structure spectroscopy showed that AHSP binding induces a small 0.03 Å lengthening of the Fe-O2 bond, explaining previous reports that AHSP decreases αHb O2 affinity roughly 4-fold and promotes autooxidation due primarily to a 3-4-fold increase in the rate of O2 dissociation. Pro-30 mutations diminished NMR chemical shift changes in the proximal heme pocket, restored normal O2 dissociation rate and equilibrium constants, and reduced O2-αHb autooxidation rates. Thus, the contacts mediated by Pro-30 in wild-type AHSP promote αHb autooxidation by introducing strain into the proximal heme pocket. As a chaperone, AHSP facilitates rapid assembly of αHb into Hb when βHb is abundant but diverts αHb to a redox resistant holding state when βHb is limiting.

  11. Focused surveys for the Pacific Pocket Mouse in Orange County, California

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The purpose of this report is to document the results of confirmation trapping surveys for the Pacific Pocket Mouse performed by the San Diego Natural History...

  12. Yeasts associated with the infrabuccal pocket and colonies of the carpenter ant Camponotus vicinus.

    Science.gov (United States)

    Mankowski, M E; Morrell, J J

    2004-01-01

    After scanning electron microscopy indicated that the infrabuccal pockets of carpenter ants (Camponotus vicinus) contained numerous yeast-like cells, yeast associations were examined in six colonies of carpenter ants from two locations in Benton County in western Oregon. Samples from the infrabuccal-pocket contents and worker ant exoskeletons, interior galleries of each colony, and detritus and soil around the colonies were plated on yeast-extract/ malt-extract agar augmented with 1 M hydrochloric acid and incubated at 25 C. Yeasts were identified on the basis of morphological characteristics and physiological attributes with the BIOLOG(®) microbial identification system. Yeast populations from carpenter ant nest material and material surrounding the nest differed from those obtained from the infrabuccal pocket. Debaryomyces polymorphus was isolated more often from the infrabuccal pocket than from other material. This species has also been isolated from other ant species, but its role in colony nutrition is unknown.

  13. Identifying features of pocket parks that may be related to health promoting use

    DEFF Research Database (Denmark)

    Peschardt, Karin Kragsig; Stigsdotter, Ulrika K.; Schipperijn, Jasper

    2016-01-01

    Urban green spaces have been shown to promote health and well-being and recent research indicates that the two primary potentially health promoting uses of pocket parks are ‘rest and restitution’ and ‘socialising’. The aim of this study is to identify features in pocket parks that may support...... these uses. The relationship between the two types of use and the shape, size, noise level, greenness, as well as ‘elements’ (paved and unpaved trails, café, historical feature, table, other seating than benches, flowerbeds, view outside park, playground) in nine pocket parks in Copenhagen were analysed...... features’ (playground, view outside park) should be avoided. The results add knowledge about the features which support the health promoting use of pocket parks to the existing body of research....

  14. NEET Micro-Pocket Fission Detector -- FY 2012 Status Report

    Energy Technology Data Exchange (ETDEWEB)

    Troy Unruh; Joy Rempe; Douglas McGregor; Philip Ugorowski; Michael Reichenberger

    2012-09-01

    A research program has been initiated by the NEET program for developing and testing compact miniature fission chambers capable of simultaneously measuring thermal neutron flux, fast neutron flux and temperature within a single package. When implemented, these sensors will significantly advance flux detection capabilities for irradiation tests in US Materials Test Reactors (MTRs).Ultimately, evaluations may lead to a more compact, more accurate, and longer lifetime flux sensor for critical mock-ups, high performance reactors and commercial nuclear power plants. Deployment of Micro-Pocket Fission Detectors (MPFDs) in US DOE-NE program irradiation tests will address several challenges: Current fission chamber technologies do not offer the ability to measure fast flux, thermal flux and temperature within a single compact probe, MPFDs offer this option. MPFD construction is very different then current fission chamber construction; the use of high temperature materials allow MPFDs to be specifically tailored to survive harsh conditions in typical high performance MTR irradiation tests. New high-fidelity reactor physics codes will need a small, accurate, multipurpose in-core sensor to validate the codes without perturbing the validation experiment; MPFDs fill this requirement. MPFDs can be built with variable sensitivities to survive the lifetime of an experiment or fuel assembly in some MTRs; allowing for more efficient and cost effective power monitoring. The small size of the MPFDs allows multiple sensors to be simultaneously deployed; obtaining data required to visualize the reactor flux and temperature profiles. This report summarizes the research progress for year 1 of this 3 year project. An updated design of the MPFD has been developed, materials and tools to support the new design have been procured, construction methods to support the new design have been initiated at INL’s HTTL and KSU’s SMART Laboratory, plating methods are being updated at KSU, new

  15. NEET Micro-Pocket Fission Detector. Final Project report

    Energy Technology Data Exchange (ETDEWEB)

    Unruh, T. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Rempe, Joy [Idaho National Lab. (INL), Idaho Falls, ID (United States); McGregor, Douglas [Idaho National Lab. (INL), Idaho Falls, ID (United States); Ugorowski, Philip [Idaho National Lab. (INL), Idaho Falls, ID (United States); Reichenberger, Michael [Idaho National Lab. (INL), Idaho Falls, ID (United States); Ito, Takashi [Idaho National Lab. (INL), Idaho Falls, ID (United States); Villard, J. -F. [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2014-09-01

    A collaboration between the Idaho National Laboratory (INL), the Kansas State University (KSU), and the French Alternative Energies and Atomic Energy Commission, Commissariat à l'Énergie Atomique et aux Energies Alternatives, (CEA), is funded by the Nuclear Energy Enabling Technologies (NEET) program to develop and test Micro-Pocket Fission Detectors (MPFDs), which are compact fission chambers capable of simultaneously measuring thermal neutron flux, fast neutron flux and temperature within a single package. When deployed, these sensors will significantly advance flux detection capabilities for irradiation tests in US Material Test Reactors (MTRs). Ultimately, evaluations may lead to a more compact, more accurate, and longer lifetime flux sensor for critical mock-ups, and high performance reactors, allowing several Department of Energy Office of Nuclear Energy (DOE-NE) programs to obtain higher accuracy/higher resolution data from irradiation tests of candidate new fuels and materials. Specifically, deployment of MPFDs will address several challenges faced in irradiations performed at MTRs: Current fission chamber technologies do not offer the ability to measure fast flux, thermal flux and temperature within a single compact probe; MPFDs offer this option. MPFD construction is very different than current fission chamber construction; the use of high temperature materials allow MPFDs to be specifically tailored to survive harsh conditions encountered in-core of high performance MTRs. The higher accuracy, high fidelity data available from the compact MPFD will significantly enhance efforts to validate new high-fidelity reactor physics codes and new multi-scale, multi-physics codes. MPFDs can be built with variable sensitivities to survive the lifetime of an experiment or fuel assembly in some MTRs, allowing for more efficient and cost effective power monitoring. The small size of the MPFDs allows multiple sensors to be deployed, offering the potential to

  16. Role of a Hydrophobic Pocket in Polyamine Interactions with the Polyspecific Organic Cation Transporter OCT3.

    Science.gov (United States)

    Li, Dan C; Nichols, Colin G; Sala-Rabanal, Monica

    2015-11-13

    Organic cation transporter 3 (OCT3, SLC22A3) is a polyspecific, facilitative transporter expressed in astrocytes and in placental, intestinal, and blood-brain barrier epithelia, and thus elucidating the molecular mechanisms underlying OCT3 substrate recognition is critical for the rational design of drugs targeting these tissues. The pharmacology of OCT3 is distinct from that of other OCTs, and here we investigated the role of a hydrophobic cavity tucked within the translocation pathway in OCT3 transport properties. Replacement of an absolutely conserved Asp by charge reversal (D478E), neutralization (D478N), or even exchange (D478E) abolished MPP(+) uptake, demonstrating this residue to be obligatory for OCT3-mediated transport. Mutations at non-conserved residues lining the putative binding pocket of OCT3 to the corresponding residue in OCT1 (L166F, F450L, and E451Q) reduced the rate of MPP(+) transport, but recapitulated the higher sensitivity pharmacological profile of OCT1. Thus, interactions of natural polyamines (putrescine, spermidine, spermine) and polyamine-like potent OCT1 blockers (1,10-diaminodecane, decamethonium, bistriethylaminodecane, and 1,10-bisquinuclidinedecane) with wild-type OCT3 were weak, but were significantly potentiated in the mutant OCT3s. Conversely, a reciprocal mutation in OCT1 (F161L) shifted the polyamine-sensitivity phenotype toward that of OCT3. Further analysis indicated that OCT1 and OCT3 can recognize essentially the same substrates, but the strength of substrate-transporter interactions is weaker in OCT3, as informed by the distinct makeup of the hydrophobic cleft. The residues identified here are key contributors to both the observed differences between OCT3 and OCT1 and to the mechanisms of substrate recognition by OCTs in general.

  17. Refrigeration, heating and air conditioning pocket book 2012; Kaelte, Waerme, Klima. Taschenbuch 2012

    Energy Technology Data Exchange (ETDEWEB)

    Schaedlich, Sylvia (ed.)

    2011-07-01

    The refrigeration, heating and air conditioning pocket book 2012 contains a calendar of important events and technical fairs. A publication of this type requires constant updating, and this is what was done in this pocket book. The technical documentation contains the following aspects: General working basis; special working basis of refrigeration; coolants; refrigeration; air-conditioning technology; heating technology; measurement and control technology; general information.

  18. Hypoxia and hypercapnia during respiration into an artificial air pocket in snow: implications for avalanche survival.

    Science.gov (United States)

    Brugger, Hermann; Sumann, Günther; Meister, Roland; Adler-Kastner, Liselotte; Mair, Peter; Gunga, Hanns Christian; Schobersberger, Wolfgang; Falk, Markus

    2003-07-01

    Snow avalanche case reports have documented the survival of skiers apparently without permanent hypoxic sequelae, after prolonged complete burial despite there being only a small air pocket on extrication. We investigated the underlying pathophysiological changes in a prospective, randomised 2 x 2 crossover study in 12 volunteers (28 tests) breathing into an artificial air pocket (1- or 2-l volume) in snow. Peripheral SpO(2), ETCO(2), arterialised capillary blood variables, air pocket O(2) and CO(2), snow density, and snow conditions at the inner surface of the air pocket were determined. SpO(2) decreased from a median of 99% (93-100%) to 88% (71-94%; Psnow density (r=0.50, P=0.021, partial correlation coefficient). ETCO(2) rose simultaneously from median 5.07 kPa (3.47-6.93 kPa) to 6.8 kPa (5.87-8.27 kPa; Pavalanche burial is dependent on air pocket volume, snow density and unknown individual personal characteristics, yet long-term survival is possible with only a small air pocket. Hence, the definition of an air pocket, "any space surrounding mouth and nose with the proviso of free air passages" is validated as the main criterion for triage and management of avalanche victims. Our experimental model will facilitate evaluating the interrelation between volume and inner surface area of an air pocket for survival of avalanche victims, whilst the present findings have laid the basis for future investigation of possible interactions between hypoxia, hypercapnia, and hypothermia (triple H syndrome) in snow burial.

  19. Pocket PC基于XML的异构数据库同步

    Institute of Scientific and Technical Information of China (English)

    王璐

    2012-01-01

    介绍Pocket PC在微软的Windows mobile操作系统下,通过XML方式进行的一种跨平台的数据库同步方法.并介绍了Pocket PC以XML方式分别对PC服务器中的Microsoft SQLServer数据库和Microsoft Access数据库的同步过程,对比了RDA,提出了优势和局限所在.

  20. High resolution crystal structures of unliganded and liganded human liver ACBP reveal a new mode of binding for the acyl-CoA ligand

    DEFF Research Database (Denmark)

    Taskinen, Jukka P; van Aalten, Daan M; Knudsen, Jens;

    2007-01-01

    The acyl-CoA binding protein (ACBP) is essential for the fatty acid metabolism, membrane structure, membrane fusion, and ceramide synthesis. Here high resolution crystal structures of human cytosolic liver ACBP, unliganded and liganded with a physiological ligand, myristoyl-CoA are described....... The binding of the acyl-CoA molecule induces only few structural differences near the binding pocket. The crystal form of the liganded ACBP, which has two ACBP molecules in the asymmetric unit, shows that in human ACBP the same acyl-CoA binding pocket is present as previously described for the bovine...... and Plasmodium falciparum ACBP and the mode of binding of the 3'-phosphate-AMP moiety is conserved. Unexpectedly, in one of the acyl-CoA binding pockets the acyl moiety is bound in a reversed mode as compared with the bovine and P. falciparum structures. In this binding mode, the myristoyl-CoA molecule is fully...

  1. Interplay between Magnetism, Superconductivity, and Orbital Order in 5-Pocket Model for Iron-Based Superconductors: Parquet Renormalization Group Study.

    Science.gov (United States)

    Classen, Laura; Xing, Rui-Qi; Khodas, Maxim; Chubukov, Andrey V

    2017-01-20

    We report the results of the parquet renormalization group (RG) analysis of the phase diagram of the most general 5-pocket model for Fe-based superconductors. We use as an input the orbital structure of excitations near the five pockets made out of d_{xz}, d_{yz}, and d_{xy} orbitals and argue that there are 40 different interactions between low-energy fermions in the orbital basis. All interactions flow under the RG, as one progressively integrates out fermions with higher energies. We find that the low-energy behavior is amazingly simple, despite the large number of interactions. Namely, at low energies the full 5-pocket model effectively reduces either to a 3-pocket model made of one d_{xy} hole pocket and two electron pockets or a 4-pocket model made of two d_{xz}/d_{yz} hole pockets and two electron pockets. The leading instability in the effective 4-pocket model is a spontaneous orbital (nematic) order, followed by s^{+-} superconductivity. In the effective 3-pocket model, orbital fluctuations are weaker, and the system develops either s^{+-} superconductivity or a stripe spin-density wave. In the latter case, nematicity is induced by composite spin fluctuations.

  2. Periodontal pocket as a potential reservoir of high risk human papilloma virus: A pilot study

    Directory of Open Access Journals (Sweden)

    Manjunath Mundoor Dayakar

    2016-01-01

    Full Text Available Aim: Human papilloma viruses (HPVs are small DNA viruses that have been identified in periodontal pocket as well as gingival sulcus. High risk HPVs are also associated with a subset of head and neck carcinomas. HPV detection in periodontium has previously involved DNA detection. This study attempts to: (a Detect the presence or absence of high risk HPV in marginal periodontiun by identifying E6/E7 messenger RNA (mRNA in cells from samples obtained by periodontal pocket scraping. (b Detect the percentage of HPV E6/E7 mRNA in cells of pocket scrapings, which is responsible for producing oncoproteins E6 and E7. Materials and Methods: Pocket scrapings from the periodontal pockets of eight subjects with generalized chronic periodontitis were taken the detection of presence or absence of E6, E7 mRNA was performed using in situ hybridization and flow cytometry. Results: HPV E6/E7 mRNA was detected in four of the eight samples. Conclusion: Presence of high risk human papillomaviruses in periodontal pockets patients of diagnosed with chronic periodontitis, not suffering from head and neck squamous cell carcinoma in the present day could link periodontitis to HPV related squamous cell carcinoma. Prevalence studies are needed detecting the presence of HPV in marginal periodontium as well as prospective studies of HPV positive periodontitis patients are required to explore this possible link.

  3. Retiree out-of-pocket healthcare spending: a study of consumer expectations and policy implications.

    Science.gov (United States)

    Hoffman, Allison K; Jackson, Howell E

    2013-01-01

    Even though most American retirees benefit from Medicare coverage, a mounting body of research predicts that many will face large and increasing out-of-pocket expenditures for healthcare costs in retirement and that many already struggle to finance these costs. It is unclear, however, whether the general population understands the likely magnitude of these out-of-pocket expenditures well enough to plan for them effectively. This study is the first comprehensive examination of Americans' expectations regarding their out-of-pocket spending on healthcare in retirement. We surveyed over 1700 near retirees and retirees to assess their expectations regarding their own spending and then compared their responses to experts' estimates. Our main findings are twofold. First, overall expectations of out-of-pocket spending are mixed. While a significant proportion of respondents estimated out-of-pocket costs in retirement at or above expert estimates of what the typical retiree will spend, a disproportionate number estimated their future spending substantially below what experts view as likely. Estimates by members of some demographic subgroups, including women and younger respondents, deviated relatively further from the experts' estimates. Second, respondents consistently misjudged spending uncertainty. In particular, respondents significantly underestimated how much individual health experience and changes in government policy can affect individual out-of-pocket spending. We discuss possible policy responses, including efforts to improve financial planning and ways to reduce unanticipated financial risk through reform of health insurance regulation.

  4. Coexistence of Fermi arcs and Fermi pockets in a high-T(c) copper oxide superconductor.

    Science.gov (United States)

    Meng, Jianqiao; Liu, Guodong; Zhang, Wentao; Zhao, Lin; Liu, Haiyun; Jia, Xiaowen; Mu, Daixiang; Liu, Shanyu; Dong, Xiaoli; Zhang, Jun; Lu, Wei; Wang, Guiling; Zhou, Yong; Zhu, Yong; Wang, Xiaoyang; Xu, Zuyan; Chen, Chuangtian; Zhou, X J

    2009-11-19

    In the pseudogap state of the high-transition-temperature (high-T(c)) copper oxide superconductors, angle-resolved photoemission (ARPES) measurements have seen Fermi arcs-that is, open-ended gapless sections in the large Fermi surface-rather than a closed loop expected of an ordinary metal. This is all the more puzzling because Fermi pockets (small closed Fermi surface features) have been suggested by recent quantum oscillation measurements. The Fermi arcs cannot be understood in terms of existing theories, although there is a solution in the form of conventional Fermi surface pockets associated with competing order, but with a back side that is for detailed reasons invisible to photoemission probes. Here we report ARPES measurements of Bi(2)Sr(2-x)La(x)CuO(6+delta) (La-Bi2201) that reveal Fermi pockets. The charge carriers in the pockets are holes, and the pockets show an unusual dependence on doping: they exist in underdoped but not overdoped samples. A surprise is that these Fermi pockets appear to coexist with the Fermi arcs. This coexistence has not been expected theoretically.

  5. Directed evolution of the Escherichia coli cAMP receptor protein at the cAMP pocket.

    Science.gov (United States)

    Gunasekara, Sanjiva M; Hicks, Matt N; Park, Jin; Brooks, Cory L; Serate, Jose; Saunders, Cameron V; Grover, Simranjeet K; Goto, Joy J; Lee, Jin-Won; Youn, Hwan

    2015-10-30

    The Escherichia coli cAMP receptor protein (CRP) requires cAMP binding to undergo a conformational change for DNA binding and transcriptional regulation. Two CRP residues, Thr(127) and Ser(128), are known to play important roles in cAMP binding through hydrogen bonding and in the cAMP-induced conformational change, but the connection between the two is not completely clear. Here, we simultaneously randomized the codons for these two residues and selected CRP mutants displaying high CRP activity in a cAMP-producing E. coli. Many different CRP mutants satisfied the screening condition for high CRP activity, including those that cannot form any hydrogen bonds with the incoming cAMP at the two positions. In vitro DNA-binding analysis confirmed that these selected CRP mutants indeed display high CRP activity in response to cAMP. These results indicate that the hydrogen bonding ability of the Thr(127) and Ser(128) residues is not critical for the cAMP-induced CRP activation. However, the hydrogen bonding ability of Thr(127) and Ser(128) was found to be important in attaining high cAMP affinity. Computational analysis revealed that most natural cAMP-sensing CRP homologs have Thr/Ser, Thr/Thr, or Thr/Asn at positions 127 and 128. All of these pairs are excellent hydrogen bonding partners and they do not elevate CRP activity in the absence of cAMP. Taken together, our analyses suggest that CRP evolved to have hydrogen bonding residues at the cAMP pocket residues 127 and 128 for performing dual functions: preserving high cAMP affinity and keeping CRP inactive in the absence of cAMP.

  6. Characterization of molecular determinants of the conformational stability of macrophage migration inhibitory factor: leucine 46 hydrophobic pocket.

    Directory of Open Access Journals (Sweden)

    Farah El-Turk

    Full Text Available Macrophage Migration Inhibitory Factor (MIF is a key mediator of inflammatory responses and innate immunity and has been implicated in the pathogenesis of several inflammatory and autoimmune diseases. The oligomerization of MIF, more specifically trimer formation, is essential for its keto-enol tautomerase activity and probably mediates several of its interactions and biological activities, including its binding to its receptor CD74 and activation of certain signaling pathways. Therefore, understanding the molecular factors governing the oligomerization of MIF and the role of quaternary structure in modulating its structural stability and multifunctional properties is crucial for understanding the function of MIF in health and disease. Herein, we describe highly conserved intersubunit interactions involving the hydrophobic packing of the side chain of Leu46 onto the β-strand β3 of one monomer within a hydrophobic pocket from the adjacent monomer constituted by residues Arg11, Val14, Phe18, Leu19, Val39, His40, Val41, Val42, and Pro43. To elucidate the structural significance of these intersubunit interactions and their relative contribution to MIF's trimerization, structural stability and catalytic activity, we generated three point mutations where Leu46 was replaced by glycine (L46G, alanine (L46A and phenylalanine (L46F, and their structural properties, stability, oligomerization state, and catalytic activity were characterized using a battery of biophysical methods and X-ray crystallography. Our findings provide new insights into the role of the Leu46 hydrophobic pocket in stabilizing the conformational state of MIF in solution. Disrupting the Leu46 hydrophobic interaction perturbs the secondary and tertiary structure of the protein but has no effect on its oligomerization state.

  7. Effect of baclofen on the acid pocket at the gastroesophageal junction.

    Science.gov (United States)

    Scarpellini, E; Boecxstaens, V; Farré, R; Bisschops, R; Dewulf, D; Gasbarrini, A; Pauwels, A; Blondeau, K; Tack, J

    2015-07-01

    Previous studies established that a pocket of highly acidic gastric juice is present postprandially at the gastroesophageal junction in man. The GABA-B agonist baclofen inhibits postprandial reflux events through its effects on the lower esophageal sphincter (LES). The aim of the current study was to investigate whether baclofen would affect the location and the extent of the postprandial acid pocket in healthy volunteers. Twelve healthy volunteers underwent acid pocket studies on two different occasions, at least 1 week apart. LES position was determined preprandially with pull-through manometry. Dual pH electrode and manometry probe stepwise pull-through (1 cm/minute, LES-10 to +5 cm) was performed at 30-minute intervals for 150 minutes, with administration of placebo or baclofen 40 mg after the first and ingestion of a liquid meal after the second pull-through. After placebo, a significant drop in intragastric gastric pH was present at the gastroesophageal junction after the meal, reflecting the acid pocket, and this was associated with a drop in LES pressure. Baclofen did not affect the presence of the acid pocket, but prevented the postprandial drop in LES pressure, and the extent of the acid pocket above the upper margin of the manometrically located LES was significantly decreased by baclofen (1.6 ± 0.7 vs. 0.3 ± 0.4 cm at 60 minutes, 2.2 ± 0.6 vs. 0.2 ± 0.6 at 90 minutes, and 1.5 ± 0.5 vs. 0.7 ± 0.7 cm at 120 minutes, all P Baclofen does not alter the intragastric acid pocket, but limits its extension into the distal esophagus, probably through an increase in postprandial LES pressure.

  8. Pea fiber and wheat bran fiber show distinct metabolic profiles in rats as investigated by a 1H NMR-based metabolomic approach.

    Directory of Open Access Journals (Sweden)

    Guangmang Liu

    Full Text Available This study aimed to examine the effect of pea fiber (PF and wheat bran fiber (WF supplementation in rat metabolism. Rats were assigned randomly to one of three dietary groups and were given a basal diet containing 15% PF, 15% WF, or no supplemental fiber. Urine and plasma samples were analyzed by NMR-based metabolomics. PF significantly increased the plasma levels of 3-hydroxybutyrate, and myo-inositol as well as the urine levels of alanine, hydroxyphenylacetate, phenylacetyglycine, and α-ketoglutarate. However, PF significantly decreased the plasma levels of isoleucine, leucine, lactate, and pyruvate as well as the urine levels of allantoin, bile acids, and trigonelline. WF significantly increased the plasma levels of acetone, isobutyrate, lactate, myo-inositol, and lipids as well as the urine levels of alanine, lactate, dimethylglycine, N-methylniconamide, and α-ketoglutarate. However, WF significantly decreased the plasma levels of amino acids, and glucose as well as the urine levels of acetate, allantoin, citrate, creatine, hippurate, hydroxyphenylacetate, and trigonelline. Results suggest that PF and WF exposure can promote antioxidant activity and can exhibit common systemic metabolic changes, including lipid metabolism, energy metabolism, glycogenolysis and glycolysis metabolism, protein biosynthesis, and gut microbiota metabolism. PF can also decrease bile acid metabolism. These findings indicate that different fiber diet may cause differences in the biofluid profile in rats.

  9. Effect of magnetic field strength on NMR-based metabonomic human urine data. Comparative study of 250, 400, 500, and 800 MHz.

    Science.gov (United States)

    Bertram, Hanne Christine; Malmendal, Anders; Petersen, Bent O; Madsen, Jens Chr; Pedersen, Henrik; Nielsen, Niels Chr; Hoppe, Camilla; Mølgaard, Christian; Michaelsen, Kim F; Duus, Jens Ø

    2007-09-15

    Metabonomic analysis of urine utilizing high-resolution NMR spectroscopy and chemometric techniques has proven valuable in characterizing the biochemical response to an intervention. To assess the effect of magnetic field strength on information contained in NMR-based metabonomic data sets, 1H NMR spectra were acquired on 250-, 400-, 500-, and 800-MHz instruments, respectively, on the same set of human urine samples collected before and after dietary interventions with milk and with meat proteins. Partial least-squares regression discriminant analyses (PLS-DA) were performed in order to elucidate the ability of the 1H spectra acquired at various field strengths to identify possible spectral differences and discriminate between pre- and postintervention samples. The loadings from PLS-DA contained the same spectral regions, implying that the same metabolites were involved in the discrimination independent of magnetic field strength. The investigation revealed a strong increase in prediction performance and thereby spectral information content when increasing the magnetic field strength from 250 to 500 MHz, while from 500 to 800 MHz the increase was less pronounced.

  10. NMR-Based Metabolomic Investigations on the Differential Responses in Adductor Muscles from Two Pedigrees of Manila Clam Ruditapes philippinarum to Cadmium and Zinc

    Directory of Open Access Journals (Sweden)

    Junbao Yu

    2011-09-01

    Full Text Available Manila clam Ruditapes philippinarum is one of the most important economic species in shellfishery in China due to its wide geographic distribution and high tolerance to environmental changes (e.g., salinity, temperature. In addition, Manila clam is a good biomonitor/bioindicator in “Mussel Watch Programs” and marine environmental toxicology. However, there are several pedigrees of R. philippinarum distributed in the marine environment in China. No attention has been paid to the biological differences between various pedigrees of Manila clams, which may introduce undesirable biological variation in toxicology studies. In this study, we applied NMR-based metabolomics to detect the biological differences in two main pedigrees (White and Zebra of R. philippinarum and their differential responses to heavy metal exposures (Cadmium and Zinc using adductor muscle as a target tissue to define one sensitive pedigree of R. philippinarum as biomonitor for heavy metals. Our results indicated that there were significant metabolic differences in adductor muscle tissues between White and Zebra clams, including higher levels of alanine, glutamine, hypotaurine, phosphocholine and homarine in White clam muscles and higher levels of branched chain amino acids (valine, leucine and isoleucine, succinate and 4-aminobutyrate in Zebra clam muscles, respectively. Differential metabolic responses to heavy metals between White and Zebra clams were also found. Overall, we concluded that White pedigree of clam could be a preferable bioindicator/biomonitor in marine toxicology studies and for marine heavy metals based on the relatively high sensitivity to heavy metals.

  11. Prospective evaluation of potential toxicity of repeated doses of Thymus vulgaris L. extracts in rats by means of clinical chemistry, histopathology and NMR-based metabonomic approach.

    Science.gov (United States)

    Benourad, Fouzia; Kahvecioglu, Zehra; Youcef-Benkada, Mokhtar; Colet, Jean-Marie

    2014-10-01

    In the field of natural extracts, research generally focuses on the study of their biological activities for food, cosmetic, or pharmacological purposes. The evaluation of their adverse effects is often overlooked. In this study, the extracts of Thymus vulgaris L. were obtained by two different extraction methods. Intraperitoneal injections of both extracts were given daily for four days to male Wistar Han rats, at two different doses for each extract. The evaluation of the potential toxic effects included histopathological examination of liver, kidney, and lung tissues, as well as serum biochemistry of liver and kidney parameters, and (1)H-NMR-based metabonomic profiles of urine. The results showed that no histopathological changes were observed in the liver and kidney in rats treated with both extracts of thyme. Serum biochemical investigations revealed significant increases in blood urea nitrogen, creatinine, and uric acid in animals treated with polyphenolic extract at both doses. In these latter groups, metabonomic analysis revealed alterations in a number of urine metabolites involved in the energy metabolism in liver mitochondria. Indeed, the results showed alterations of glycolysis, Krebs cycle, and β-oxidative pathways as evidenced by increases in lactate and ketone bodies, and decreases in citrate, α-ketoglutarate, creatinine, hippurate, dimethylglycine, and dimethyalanine. In conclusion, this work showed that i.p. injection of repeated doses of thyme extracts causes some disturbances of intermediary metabolism in rats. The metabonomic study revealed interesting data which could be further used to determine the cellular pathways affected by such treatments.

  12. Pea fiber and wheat bran fiber show distinct metabolic profiles in rats as investigated by a 1H NMR-based metabolomic approach.

    Science.gov (United States)

    Liu, Guangmang; Xiao, Liang; Fang, Tingting; Cai, Yimin; Jia, Gang; Zhao, Hua; Wang, Jing; Chen, Xiaoling; Wu, Caimei

    2014-01-01

    This study aimed to examine the effect of pea fiber (PF) and wheat bran fiber (WF) supplementation in rat metabolism. Rats were assigned randomly to one of three dietary groups and were given a basal diet containing 15% PF, 15% WF, or no supplemental fiber. Urine and plasma samples were analyzed by NMR-based metabolomics. PF significantly increased the plasma levels of 3-hydroxybutyrate, and myo-inositol as well as the urine levels of alanine, hydroxyphenylacetate, phenylacetyglycine, and α-ketoglutarate. However, PF significantly decreased the plasma levels of isoleucine, leucine, lactate, and pyruvate as well as the urine levels of allantoin, bile acids, and trigonelline. WF significantly increased the plasma levels of acetone, isobutyrate, lactate, myo-inositol, and lipids as well as the urine levels of alanine, lactate, dimethylglycine, N-methylniconamide, and α-ketoglutarate. However, WF significantly decreased the plasma levels of amino acids, and glucose as well as the urine levels of acetate, allantoin, citrate, creatine, hippurate, hydroxyphenylacetate, and trigonelline. Results suggest that PF and WF exposure can promote antioxidant activity and can exhibit common systemic metabolic changes, including lipid metabolism, energy metabolism, glycogenolysis and glycolysis metabolism, protein biosynthesis, and gut microbiota metabolism. PF can also decrease bile acid metabolism. These findings indicate that different fiber diet may cause differences in the biofluid profile in rats.

  13. Medicare Advantage Members' Expected Out-Of-Pocket Spending For Inpatient And Skilled Nursing Facility Services.

    Science.gov (United States)

    Keohane, Laura M; Grebla, Regina C; Mor, Vincent; Trivedi, Amal N

    2015-06-01

    Inpatient and skilled nursing facility (SNF) cost sharing in Medicare Advantage (MA) plans may reduce unnecessary use of these services. However, large out-of-pocket expenses potentially limit access to care and encourage beneficiaries at high risk of needing inpatient and postacute care to avoid or leave MA plans. In 2011 new federal regulations restricted inpatient and skilled nursing facility cost sharing and mandated limits on out-of-pocket spending in MA plans. After these regulations, MA members in plans with low premiums averaged $1,758 in expected out-of-pocket spending for an episode of seven hospital days and twenty skilled nursing facility days. Among members with the same low-premium plan in 2010 and 2011, 36 percent of members belonged to plans that added an out-of-pocket spending limit in 2011. However, these members also had a $293 increase in average cost sharing for an inpatient and skilled nursing facility episode, possibly to offset plans' expenses in financing out-of-pocket limits. Some MA beneficiaries may still have difficulty affording acute and postacute care despite greater regulation of cost sharing.

  14. Pocket proteins critically regulate cell cycle exit of the trabecular myocardium and the ventricular conduction system

    Directory of Open Access Journals (Sweden)

    David S. Park

    2013-07-01

    During development, the ventricular conduction system (VCS arises from the trabecular or spongy myocardium. VCS and trabecular myocytes proliferate at a significantly slower rate than compact zone myocardial cells, establishing a transmural cell cycle gradient. The molecular determinants of VCS/trabecular myocyte cell cycle arrest are not known. Given the importance of pocket proteins (Rb, p107 and p130 in mediating G0/G1 arrest in many cell types, we examined the role of this gene family in regulating cell cycle exit of the trabecular myocardium and ventricular conduction system. Using a combinatorial knockout strategy, we found that graded loss of pocket proteins results in a spectrum of heart and lung defects. p107/p130 double knockout (dKO hearts manifest dysregulated proliferation within the compact myocardium and trabecular bases, while the remaining trabecular region cell cycle exits normally. Consequently, dKO hearts exhibit defective cardiac compaction, septal hyperplasia and biventricular outflow tract obstruction, while the VCS appears relatively normal. Loss of all three pocket proteins (3KO is necessary to completely disrupt the transmural cell cycle gradient. 3KO hearts exhibit massive overgrowth of the trabecular myocardium and ventricular conduction system, which leads to fetal heart failure and death. Hearts carrying a single pocket protein allele are able to maintain the transmural cell cycle gradient. These results demonstrate the exquisite sensitivity of trabecular and conduction myocytes to pocket protein function during ventricular chamber development.

  15. Medicare Advantage Members’ Expected Out-Of-Pocket Spending For Inpatient And Skilled Nursing Facility Services

    Science.gov (United States)

    Keohane, Laura M.; Grebla, Regina C.; Mor, Vincent; Trivedi, Amal N.

    2015-01-01

    Inpatient and skilled nursing facility (SNF) cost sharing in Medicare Advantage (MA) plans may reduce unnecessary use of these services. However, large out-of-pocket expenses potentially limit access to care and encourage beneficiaries at high risk of needing inpatient and postacute care to avoid or leave MA plans. In 2011 new federal regulations restricted inpatient and skilled nursing facility cost sharing and mandated limits on out-of-pocket spending in MA plans. After these regulations, MA members in plans with low premiums averaged $1,758 in expected out-of-pocket spending for an episode of seven hospital days and twenty skilled nursing facility days. Among members with the same low-premium plan in 2010 and 2011, 36 percent of members belonged to plans that added an out-of-pocket spending limit in 2011. However, these members also had a $293 increase in average cost sharing for an inpatient and skilled nursing facility episode, possibly to offset plans’ expenses in financing out-of-pocket limits. Some MA beneficiaries may still have difficulty affording acute and postacute care despite greater regulation of cost sharing. PMID:26056208

  16. Treatment of Fingertip Amputation in Adults by Palmar Pocketing of the Amputated Part

    Directory of Open Access Journals (Sweden)

    Mi Sun Jung

    2012-07-01

    Full Text Available Background First suggested by Brent in 1979, the pocket principle is an alternative methodfor patients for whom a microsurgical replantation is not feasible. We report the successfulresults of a modified palmar pocket method in adults.Methods Between 2004 and 2008, we treated 10 patients by nonmicrosurgical replantationusing palmar pocketing. All patients were adults who sustained a complete fingertip amputationfrom the tip to lunula in a digits. In all of these patients, the amputation occurred due to a crushor avulsion-type injury, and a microsurgical replantation was not feasible. We used the palmarpocketing method following a composite graft in these patients and prepared the pocket in thesubcutaneous layer of the ipsilateral palm.Results Of a total of 10 cases, nine had complete survival of the replantation and one had20% partial necrosis. All of the cases were managed to conserve the fingernails, which led toacceptable cosmetic results.Conclusions A composite graft and palmar pocketing in adult cases of fingertip injuryconstitute a simple, reliable operation for digital amputation extending from the tip to thelunula. These methods had satisfactory results.

  17. STUDY OF RELATIONSHIP BETWEEN DEPTH OF PERIODONTAL POCKETS, ANAEROBIC BACTERIA AND INFLAMMATORY CELLS IN PERIODONTITIS

    Directory of Open Access Journals (Sweden)

    P. Owlia

    2000-08-01

    Full Text Available In this study 100 cases of advanced periodontitis were compared with a control group of 100 persons. The parameters were the depth of the periodontal pockets, radiographic images, presence of inflammatory cells and different types of anaerobic bacteria in the pockets. The depth of pocket was measured by a sterile probe and the presence of inflammatory cells was determined through sterile curettage. The smears were stained by Gimsa and Gram methods. For the purpose of microbiological studies, subgingival plaque samples were taken on paper points and were plated on brucella agar medium supplemented with rabbit blood, haemin and vitamin K1. The results indicated that with increasing depth of the pocket, the number of mixed anaerobic infections increases, and the presence of inflammatory cells especially polymorphonuclears is more prominent in comparison to the control group. As the pocket depth increases the conditions become more favourable for anaerobic bacteria and in consequence the incidence of isolation of these bacteria increases. On the other hand as the number of anaerobic bacteria and inflammatory cells and the secretion of destructive enzymes increases, the resultant injury to periodontal tissue increases.

  18. Efficacy of a physicians' pocket guide about prenatal substance use: a randomized trial.

    Science.gov (United States)

    Midmer, Deana; Kahan, Meldon; Kim, Theresa; Ordean, Alice; Graves, Lisa

    2011-10-01

    A pocket guide on management of substance use during pregnancy was developed by a group of Canadian care providers. One hundred and fifteen family medicine residents in 6 Canadian teaching sites were randomized to receive either the pocket guide or a paper summary on similar clinical topics, based on UpToDate, a comprehensive Web-based resource. At baseline, both groups completed a survey containing questions on beliefs, attitudes, experience, and training on pregnancy and substance use. Participants then answered 28 multiple choice questions about substance use in pregnancy, using either the pocket guide or UpToDate. Finally participants were asked to rate ease of use for the 2 resources. The results showed that the pocket guide group had higher knowledge scores than the UpToDate group overall and at each study site (61.27% vs. 42.86%, P UpToDate (mean = 2.73 vs. 4.36, P UpToDate, P = .005). It is concluded that the pocket guide is a practical source of clinical information at point of care, particularly for "orphan" subjects such as substance use in pregnancy.

  19. Iranian Households’ Payments on Food and Health Out-of-Pocket Expenditures: Evidence of Inequality

    Directory of Open Access Journals (Sweden)

    Hesam GHIASVAND

    2015-10-01

    Full Text Available Background: Inequality in households’ payments on food and health expenditures presents the accessibility and utili-zation patterns between them. This study investigated the Iranian rural and urban households’ inequality in payments on food and Out-of-Pocket health expenditures from 1998 to 2012.Methods: This descriptive study was conducted through the analysis of Iranian Statistics Centre data on Iranian households’ income and expenditures. The Gini Coefficients, Concentration and Kakwani indices have been calculat-ed for Iranian rural and urban households’ Out-of-Pocket health and food expenditures.Results: The means of Iranian rural and urban total consumption expenditures inequality were 0.48 and 0.48, respec-tively. The means of concentration index of food expenditures for rural and urban regions were 0.35 and 0.34, respec-tively. The means of Out-of-Pocket payments for health services for rural and urban regions were 0.51 and 0.5, re-spectively. Finally the means of Kakwani index of Out-of-Pocket health payments in rural and urban households were -0.005 and -0.018, respectively.Conclusion: There are relative high levels of inequality in Iranian households’ payments on food and Out-of-Pocket health expenditures.

  20. The human fatty acid-binding protein family: Evolutionary divergences and functions

    Directory of Open Access Journals (Sweden)

    Smathers Rebecca L

    2011-03-01

    Full Text Available Abstract Fatty acid-binding proteins (FABPs are members of the intracellular lipid-binding protein (iLBP family and are involved in reversibly binding intracellular hydrophobic ligands and trafficking them throughout cellular compartments, including the peroxisomes, mitochondria, endoplasmic reticulum and nucleus. FABPs are small, structurally conserved cytosolic proteins consisting of a water-filled, interior-binding pocket surrounded by ten anti-parallel beta sheets, forming a beta barrel. At the superior surface, two alpha-helices cap the pocket and are thought to regulate binding. FABPs have broad specificity, including the ability to bind long-chain (C16-C20 fatty acids, eicosanoids, bile salts and peroxisome proliferators. FABPs demonstrate strong evolutionary conservation and are present in a spectrum of species including Drosophila melanogaster, Caenorhabditis elegans, mouse and human. The human genome consists of nine putatively functional protein-coding FABP genes. The most recently identified family member, FABP12, has been less studied.

  1. Discover binding pathways using the sliding binding-box docking approach: application to binding pathways of oseltamivir to avian influenza H5N1 neuraminidase

    Science.gov (United States)

    Tran, Diem-Trang T.; Le, Ly T.; Truong, Thanh N.

    2013-08-01

    Drug binding and unbinding are transient processes which are hardly observed by experiment and difficult to analyze by computational techniques. In this paper, we employed a cost-effective method called "pathway docking" in which molecular docking was used to screen ligand-receptor binding free energy surface to reveal possible paths of ligand approaching protein binding pocket. A case study was applied on oseltamivir, the key drug against influenza a virus. The equilibrium pathways identified by this method are found to be similar to those identified in prior studies using highly expensive computational approaches.

  2. Bacterial periplasmic sialic acid-binding proteins exhibit a conserved binding site

    Energy Technology Data Exchange (ETDEWEB)

    Gangi Setty, Thanuja [Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065 (India); Cho, Christine [Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109 (United States); Govindappa, Sowmya [Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065 (India); Apicella, Michael A. [Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109 (United States); Ramaswamy, S., E-mail: ramas@instem.res.in [Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065 (India)

    2014-07-01

    Structure–function studies of sialic acid-binding proteins from F. nucleatum, P. multocida, V. cholerae and H. influenzae reveal a conserved network of hydrogen bonds involved in conformational change on ligand binding. Sialic acids are a family of related nine-carbon sugar acids that play important roles in both eukaryotes and prokaryotes. These sialic acids are incorporated/decorated onto lipooligosaccharides as terminal sugars in multiple bacteria to evade the host immune system. Many pathogenic bacteria scavenge sialic acids from their host and use them for molecular mimicry. The first step of this process is the transport of sialic acid to the cytoplasm, which often takes place using a tripartite ATP-independent transport system consisting of a periplasmic binding protein and a membrane transporter. In this paper, the structural characterization of periplasmic binding proteins from the pathogenic bacteria Fusobacterium nucleatum, Pasteurella multocida and Vibrio cholerae and their thermodynamic characterization are reported. The binding affinities of several mutations in the Neu5Ac binding site of the Haemophilus influenzae protein are also reported. The structure and the thermodynamics of the binding of sugars suggest that all of these proteins have a very well conserved binding pocket and similar binding affinities. A significant conformational change occurs when these proteins bind the sugar. While the C1 carboxylate has been identified as the primary binding site, a second conserved hydrogen-bonding network is involved in the initiation and stabilization of the conformational states.

  3. Half-bow sliding knot: modified suture technique for scleral fixation using the corneoscleral pocket.

    Science.gov (United States)

    Chee, Soon-Phaik

    2011-09-01

    A modified suture technique for precise knot placement in the Hoffman corneoscleral pocket technique of scleral fixation is described. Both loops of the polypropylene suture passing from the intraocular device through the sclera and conjunctiva are retrieved from the pocket. A loop of suture is pulled through 3 suture throws made using the second suture loop, forming a half bow. Centration of the intraocular lens (IOL)-capsular bag is checked. If the suture tension is too tight, the surgeon can easily undo the knot of the half-bow knot by pulling it free and can then retie the sliding knot. When the IOL-capsular bag is centered, the suture loop is cut and the free end removed. The second suture end is retrieved from the pocket, and knot tying is completed without further adjustment to the tension. Posterior pressure on the intraocular device centers it and settles the knot within the sclera at the fixation point.

  4. Neurology diagnostics security and terminal adaptation for PocketNeuro project.

    Science.gov (United States)

    Chemak, C; Bouhlel, M-S; Lapayre, J-C

    2008-09-01

    This paper presents new approaches of medical information security and terminal mobile phone adaptation for the PocketNeuro project. The latter term refers to a project created for the management of neurological diseases. It consists of transmitting information about patients ("desk of patients") to a doctor's mobile phone during a visit and examination of a patient. These new approaches for the PocketNeuro project were analyzed in terms of medical information security and adaptation of the diagnostic images to the doctor's mobile phone. Images were extracted from a DICOM library. Matlab and its library were used as software to test our approaches and to validate our results. Experiments performed on a database of 30 256 x 256 pixel-sized neuronal medical images indicated that our new approaches for PocketNeuro project are valid and support plans for large-scale studies between French and Swiss hospitals using secured connections.

  5. Modeling of ultrasound transmission through a solid-liquid interface comprising a network of gas pockets

    Science.gov (United States)

    Paumel, K.; Moysan, J.; Chatain, D.; Corneloup, G.; Baqué, F.

    2011-08-01

    Ultrasonic inspection of sodium-cooled fast reactor requires a good acoustic coupling between the transducer and the liquid sodium. Ultrasonic transmission through a solid surface in contact with liquid sodium can be complex due to the presence of microscopic gas pockets entrapped by the surface roughness. Experiments are run using substrates with controlled roughness consisting of a network of holes and a modeling approach is then developed. In this model, a gas pocket stiffness at a partially solid-liquid interface is defined. This stiffness is then used to calculate the transmission coefficient of ultrasound at the entire interface. The gas pocket stiffness has a static, as well as an inertial component, which depends on the ultrasonic frequency and the radiative mass.

  6. The $^{13}C$-pockets in AGB Stars and Their Fingerprints in Mainstream SiC Grains

    CERN Document Server

    Liu, Nan; Gallino, Roberto; Savina, Michael R; Bisterzo, Sara; Gyngard, Frank; Pellin, Michael J; Dauphas, Nicolas

    2015-01-01

    We identify three isotopic tracers that can be used to constrain the $^{13}C$-pocket and show the correlated isotopic ratios of Sr and Ba in single mainstream presolar SiC grains. These newly measured data can be explained by postprocess AGB model calculations with large $^{13}C$-pockets with a range of relatively low $^{13}C$ concentrations, which may suggest that multiple mixing processes contributed to the $^{13}C$-pocket formation in parent AGB stars.

  7. PROSTAGLANDIN E2 LEVEL IN GINGIVAL CREVICULAR FLUID AND ITS RELATION TO THE PERIODONTAL POCKET DEPTH IN PATIENTS WITH PERIODONTITIS

    Institute of Scientific and Technical Information of China (English)

    周坚; 邹石莹; 赵戚; 赵玉霞

    1994-01-01

    Prostaglandin E2(PGE2)levels in gingival crevicular fluid (GCF)of 46 normal controls and 90 patients suf-fering from periodontitis with different periodontal pocket depths were measured by radioimmunoassay (RIA).The results demonstrated that PGE2 levels in the periodontal pockets are higher in patients with peri-odontitis.The PGE2 level rises as the periodontal pocket deepens,especially in casses where the periodontal pocket depth exceeds 6 mm.This study shows that PGE2 level is significantly related to the severity of bone destruc-tion in periodontitis.

  8. How the Proximal Pocket May Influence the Enantiospecificities of Chloroperoxidase-Catalyzed Epoxidations of Olefins

    Science.gov (United States)

    Morozov, Alexander N.; Chatfield, David C.

    2016-01-01

    Chloroperoxidase-catalyzed enantiospecific epoxidations of olefins are of significant biotechnological interest. Typical enantiomeric excesses are in the range of 66%–97% and translate into free energy differences on the order of 1 kcal/mol. These differences are generally attributed to the effect of the distal pocket. In this paper, we show that the influence of the proximal pocket on the electron transfer mechanism in the rate-limiting event may be just as significant for a quantitatively accurate account of the experimentally-measured enantiospecificities. PMID:27517911

  9. Compact DC-DC Converter for Pocket Micro-Controller Systems

    Institute of Scientific and Technical Information of China (English)

    1996-01-01

    Novel compact DC-C converters for pocket micro-controller systems are discussed in the paper,which are based on switched capcotprs and inductorless,consequently are more suitable for being hybridized.The new converters enable the pocket microcontroller system to be powered by only one+12V source,while+5V and -12V are converted from the +12V source.The basic principle,voltage ratio,efficiency and ripples are analysed.Experiment and SPICE simulation are also given,which show positive results.

  10. LIBSA--a method for the determination of ligand-binding preference to allosteric sites on receptor ensembles.

    Science.gov (United States)

    Hocker, Harrison J; Rambahal, Nandini; Gorfe, Alemayehu A

    2014-02-24

    Incorporation of receptor flexibility into computational drug discovery through the relaxed complex scheme is well suited for screening against a single binding site. In the absence of a known pocket or if there are multiple potential binding sites, it may be necessary to do docking against the entire surface of the target (global docking). However no suitable and easy-to-use tool is currently available to rank global docking results based on the preference of a ligand for a given binding site. We have developed a protocol, termed LIBSA for LIgand Binding Specificity Analysis, that analyzes multiple docked poses against a single or ensemble of receptor conformations and returns a metric for the relative binding to a specific region of interest. By using novel filtering algorithms and the signal-to-noise ratio (SNR), the relative ligand-binding frequency at different pockets can be calculated and compared quantitatively. Ligands can then be triaged by their tendency to bind to a site instead of ranking by affinity alone. The method thus facilitates screening libraries of ligand cores against a large library of receptor conformations without prior knowledge of specific pockets, which is especially useful to search for hits that selectively target a particular site. We demonstrate the utility of LIBSA by showing that it correctly identifies known ligand binding sites and predicts the relative preference of a set of related ligands for different pockets on the same receptor.

  11. Fast Identification of Radical Scavengers from Securigera varia by Combining 13C-NMR-Based Dereplication to Bioactivity-Guided Fractionation.

    Science.gov (United States)

    Sientzoff, Pacôme; Hubert, Jane; Janin, Coralie; Voutquenne-Nazabadioko, Laurence; Renault, Jean-Hugues; Nuzillard, Jean-Marc; Harakat, Dominique; Magid, Abdulmagid Alabdul

    2015-08-14

    Securigera varia (Fabaceae) is a common herbaceous perennial plant widely growing in Europe and Asia and purposely established for erosion control, roadside planting, and soil rehabilitation. The aim of this study was to determine the radical scavenging activity of a crude methanol extract of S. varia aerial parts by using the free radical DPPH (1,1-diphenyl-2-picrylhydrazyl) and to rapidly identify the compounds involved in this activity. The crude extract was initially separated in five fractions on Diaion HP20 resin and the most active part was fractionated by Centrifugal Partition Extraction (CPE). Known compounds were directly identified by a (13)C-NMR-based dereplication method. Semi-preparative high performance liquid chromatography purification experiments were further performed to identify unknown or minor active compounds. As a result, one new (13) and twelve known flavonoid glycosides together with three nitropropanoylglucopyranoses were isolated, including astragalin (1), kaempferol-3-O-(6-O-acetyl)-β-D-glucopyranoside (2), kaempferol-3,4'-di-O-β-D-glucopyranoside (3), trifolin (4), isoquercitrin (5), hyperoside (6), isovitexin (7), isoorientin (8), isovitexin 4'-O-β-D-glucopyranoside (9), apigenin 7-O-β-D-glucuronopyranoside (10), luteolin 7-O-β-D-glucuronopyranoside (11), apigenin 7-O-α-L-rhamnopyranosyl-(1→2)-β-D-glucuronopyranoside (12), apigenin 7-O-β-D-glucopyranosyl-(1 → 2)-β-D-glucuronopyranoside (13), 6-O-(3-nitropropanoyl)-β-D-glucopyranoside (14), coronillin (16) and coronarian (15). 120 mg of the most active compound isoorientin against the free radical DPPH was recovered by CPE with an HPLC purity of 99%.

  12. NMR-Based Metabolic Profiling of Field-Grown Leaves from Sugar Beet Plants Harbouring Different Levels of Resistance to Cercospora Leaf Spot Disease

    Directory of Open Access Journals (Sweden)

    Yasuyo Sekiyama

    2017-01-01

    Full Text Available Cercospora leaf spot (CLS is one of the most serious leaf diseases for sugar beet (Beta vulgaris L. worldwide. The breeding of sugar beet cultivars with both high CLS resistance and high yield is a major challenge for breeders. In this study, we report the nuclear magnetic resonance (NMR-based metabolic profiling of field-grown leaves for a subset of sugar beet genotypes harbouring different levels of CLS resistance. Leaves were collected from 12 sugar beet genotypes at four time points: seedling, early growth, root enlargement, and disease development stages. 1H-NMR spectra of foliar metabolites soluble in a deuterium-oxide (D2O-based buffer were acquired and subjected to multivariate analyses. A principal component analysis (PCA of the NMR data from the sugar beet leaves shows clear differences among the growth stages. At the later time points, the sugar and glycine betaine contents were increased, whereas the choline content was decreased. The relationship between the foliar metabolite profiles and resistance level to CLS was examined by combining partial least squares projection to latent structure (PLS or orthogonal PLS (OPLS analysis and univariate analyses. It was difficult to build a robust model for predicting precisely the disease severity indices (DSIs of each genotype; however, GABA and Gln differentiated susceptible genotypes (genotypes with weak resistance from resistant genotypes (genotypes with resistance greater than a moderate level before inoculation tests. The results suggested that breeders might exclude susceptible genotypes from breeding programs based on foliar metabolites profiled without inoculation tests, which require an enormous amount of time and effort.

  13. 1H-NMR-based metabolic analysis of human serum reveals novel markers of myocardial energy expenditure in heart failure patients.

    Directory of Open Access Journals (Sweden)

    Zhiyong Du

    Full Text Available OBJECTIVE: Elevated myocardial energy expenditure (MEE is related with reduced left ventricular ejection fraction, and has also been documented as an independent predictor of cardiovascular mortality. However, the serum small-molecule metabolite profiles and pathophysiological mechanisms of elevated MEE in heart failure (HF are still lacking. Herein, we used 1H-NMR-based metabolomics analysis to screen for potential biomarkers of MEE in HF. METHODS: A total of 61 subjects were enrolled, including 46 patients with heart failure and 15 age-matched controls. Venous serum samples were collected from subjects after an 8-hour fast. An INOVA 600 MHz nuclear magnetic resonance spectrometer with Carr-Purcell-Melboom-Gill (CPMG pulse sequence was employed for the metabolomics analysis and MEE was calculated using colored Doppler echocardiography. Metabolomics data were processed using orthogonal signal correction and regression analysis was performed using the partial least squares method. RESULTS: The mean MEE levels of HF patients and controls were 139.61±58.18 cal/min and 61.09±23.54 cal/min, respectively. Serum metabolomics varied with MEE changed, and 3-hydroxybutyrate, acetone and succinate were significantly elevated with the increasing MEE. Importantly, these three metabolites were independent of administration of angiotensin converting enzyme inhibitor, β-receptor blockers, diuretics and statins (P>0.05. CONCLUSIONS: These results suggested that in patients with heart failure, MEE elevation was associated with significant changes in serum metabolomics profiles, especially the concentration of 3-hydroxybutyrate, acetone and succinate. These compounds could be used as potential serum biomarkers to study myocardial energy mechanism in HF patients.

  14. Metallomics and NMR-based metabolomics of Chlorella sp. reveal the synergistic role of copper and cadmium in multi-metal toxicity and oxidative stress.

    Science.gov (United States)

    Zhang, Wenlin; Tan, Nicole G J; Fu, Baohui; Li, Sam F Y

    2015-03-01

    Industrial wastewaters often contain high levels of metal mixtures, in which metal mixtures may have synergistic or antagonistic effects on aquatic organisms. A combination of metallomics and nuclear magnetic resonance spectroscopy (NMR)-based metabolomics was employed to understand the consequences of multi-metal systems (Cu, Cd, Pb) on freshwater microalgae. Morphological characterization, cell viability and chlorophyll a determination of metal-spiked Chlorella sp. suggested synergistic effects of Cu and Cd on growth inhibition and toxicity. While Pb has no apparent effect on Chlorella sp. metabolome, a substantial decrease of sucrose, amino acid content and glycerophospholipid precursors in Cu-spiked microalgae revealed Cu-induced oxidative stress. Addition of Cd to Cu-spiked cultures induced more drastic metabolic perturbations, hence we confirmed that Cu and Cd synergistically influenced photosynthesis inhibition, oxidative stress and membrane degradation. Total elemental analysis revealed a significant decrease in K, and an increase in Na, Mg, Zn and Mn concentrations in Cu-spiked cultures. This indicated that Cu is more toxic to Chlorella sp. as compared to Cd or Pb, and the combination of Cu and Cd has a strong synergistic effect on Chlorella sp. oxidative stress induction. Oxidative stress is confirmed by liquid chromatography tandem mass spectrometry analysis, which demonstrated a drastic decrease in the GSH/GSSG ratio solely in Cu-spiked cultures. Interestingly, we observed Cu-facilitated Cd and Pb bioconcentration in Chlorella sp. The absence of phytochelatins and an increment of extracellular polymeric substances (EPS) yields in Cu-spiked cultures suggested that the mode of bioconcentration of Cd and Pb is through adsorption of free metals onto the algal EPS rather than intracellular chelation to phytochelatins.

  15. NMR-based metabolomics and LC-MS/MS quantification reveal metal-specific tolerance and redox homeostasis in Chlorella vulgaris.

    Science.gov (United States)

    Zhang, Wenlin; Tan, Nicole G J; Li, Sam F Y

    2014-01-01

    Live green algae are promising candidates for phytoremediation, but a suitable algal species which bio-accumulates high concentrations of heavy metals, and survives well in industrial water is yet to be identified. Potential metabolic engineering may be applied to improve algal phytoremediation performance, but the metal tolerance and bioaccumulation mechanisms in green algae have to be first fully understood. In this study, NMR-based metabolomics was used to study the effect of different metal species (copper, cadmium and lead) and metal concentrations in green microalgae, Chlorella vulgaris. High Cu concentrations influenced substantial decrease in organic osmolytes (betaine and glycerophosphocholine), which indicated Cu-induced redox imbalance. Accompanying redox imbalance, growth inhibition and photosynthesis impairments in Cu-spiked C. vulgaris revealed a clear relationship between Cu toxicity and redox homeostasis. As these metabolic changes were less prominent in Cd and Pb-spiked cultures, we inferred metal-specific toxicity in C. vulgaris, where redox active Cu(2+) is more potent than non-redox active Cd(2+) and Pb(2+) in causing redox imbalance. Subsequently, ICP-MS and LC-MS/MS quantification shed light on the metal-specific bioaccumulation and detoxification mechanisms. The metal bioconcentration factor (BCF) correlated well with the phytochelatin (PC) content in Cu and Cd-spiked C. vulgaris biomass. High BCF and PC levels with increasing Cu and Cd exposure concentrations indicated that PCs played a significant role in Cu and Cd bioaccumulation and detoxification. In contrast, the undetectable PC levels in Pb-spiked cultures despite high Pb BCF suggest an alternative detoxification mechanism for Pb: either by passive absorption to the algal cell wall or interaction with glutathione (GSH).

  16. Nutri-metabolomics: subtle serum metabolic differences in healthy subjects by NMR-based metabolomics after a short-term nutritional intervention with two tomato sauces.

    Science.gov (United States)

    Bondia-Pons, Isabel; Cañellas, Nicolau; Abete, Itziar; Rodríguez, Miguel Ángel; Perez-Cornago, Aurora; Navas-Carretero, Santiago; Zulet, M Ángeles; Correig, Xavier; Martínez, J Alfredo

    2013-12-01

    Postgenomics research and development is witnessing novel intersections of omics data intensive technology and applications in health and personalized nutrition. Chief among these is the nascent field of nutri-metabolomics that harnesses metabolomics platforms to discern person-to-person variations in nutritional responses. To this end, differences in the origin and ripening stage of fruits might have a strong impact on their phytochemical composition, and consequently, on their potential nutri-metabolomics effects on health. The objective of the present study was to evaluate the effects of a 4-week cross-over nutritional intervention on the metabolic status of 24 young healthy subjects. The intervention was carried out with two tomato sauces differing in their natural lycopene content, which was achieved by using tomatoes harvested at different times. Blood samples were drawn from each subject before and after each intervention period. Aqueous and lipid extracts from serum samples were analyzed by 1H-NMR metabolic profiling combined with analysis of variance simultaneous component analysis (ASCA) and multilevel simultaneous component analysis (MSCA). These methods allowed the interpretation of the variation induced by the main factors of the study design (sauce treatment and time). The levels of creatine, creatinine, leucine, choline, methionine, and acetate in aqueous extracts were increased after the intervention with the high-lycopene content sauce, while those of ascorbic acid, lactate, pyruvate, isoleucine, alanine were increased after the normal-lycopene content sauce. In conclusion, NMR-based metabolomics of aqueous and lipid extracts allowed the detection of different metabolic changes after the nutritional intervention. This outcome might partly be due to the different ripening state of the fruits used in production of the tomato sauces. The findings presented herein collectively attest to the emergence of the field of nutri-metabolomics as a novel

  17. Fast Identification of Radical Scavengers from Securigera varia by Combining 13C-NMR-Based Dereplication to Bioactivity-Guided Fractionation

    Directory of Open Access Journals (Sweden)

    Pacôme Sientzoff

    2015-08-01

    Full Text Available Securigera varia (Fabaceae is a common herbaceous perennial plant widely growing in Europe and Asia and purposely established for erosion control, roadside planting, and soil rehabilitation. The aim of this study was to determine the radical scavenging activity of a crude methanol extract of S. varia aerial parts by using the free radical DPPH (1,1-diphenyl-2-picrylhydrazyl and to rapidly identify the compounds involved in this activity. The crude extract was initially separated in five fractions on Diaion HP20 resin and the most active part was fractionated by Centrifugal Partition Extraction (CPE. Known compounds were directly identified by a 13C-NMR-based dereplication method. Semi-preparative high performance liquid chromatography purification experiments were further performed to identify unknown or minor active compounds. As a result, one new (13 and twelve known flavonoid glycosides together with three nitropropanoylglucopyranoses were isolated, including astragalin (1, kaempferol-3-O-(6-O-acetyl-β-D-glucopyranoside (2, kaempferol-3,4′-di-O-β-D-glucopyranoside (3, trifolin (4, isoquercitrin (5, hyperoside (6, isovitexin (7, isoorientin (8, isovitexin 4′-O-β-D-glucopyranoside (9, apigenin 7-O-β-D-glucuronopyranoside (10, luteolin 7-O-β-D-glucuronopyranoside (11, apigenin 7-O-α-L-rhamnopyranosyl-(1→2-β-D-glucuronopyranoside (12, apigenin 7-O-β-D-glucopyranosyl-(1→2-β-D-glucuronopyranoside (13, 6-O-(3-nitropropanoyl-β-D-glucopyranoside (14, coronillin (16 and coronarian (15. 120 mg of the most active compound isoorientin against the free radical DPPH was recovered by CPE with an HPLC purity of 99%.

  18. Pharmacophore screening of the protein data bank for specific binding site chemistry.

    Science.gov (United States)

    Campagna-Slater, Valérie; Arrowsmith, Andrew G; Zhao, Yong; Schapira, Matthieu

    2010-03-22

    A simple computational approach was developed to screen the Protein Data Bank (PDB) for putative pockets possessing a specific binding site chemistry and geometry. The method employs two commonly used 3D screening technologies, namely identification of cavities in protein structures and pharmacophore screening of chemical libraries. For each protein structure, a pocket finding algorithm is used to extract potential binding sites containing the correct types of residues, which are then stored in a large SDF-formatted virtual library; pharmacophore filters describing the desired binding site chemistry and geometry are then applied to screen this virtual library and identify pockets matching the specified structural chemistry. As an example, this approach was used to screen all human protein structures in the PDB and identify sites having chemistry similar to that of known methyl-lysine binding domains that recognize chromatin methylation marks. The selected genes include known readers of the histone code as well as novel binding pockets that may be involved in epigenetic signaling. Putative allosteric sites were identified on the structures of TP53BP1, L3MBTL3, CHEK1, KDM4A, and CREBBP.

  19. Kinetically inert lanthanide complexes as reporter groups for binding of potassium by 18-crown-6

    DEFF Research Database (Denmark)

    Junker, Anne Kathrine Ravnsborg; Tropiano, Manuel; Faulkner, Stephen

    2016-01-01

    The barcode-like spectrum of lanthanide-centered emission has been used in imaging and to make responsive luminescent reporters. The intensities and the shapes of each line in the luminescence spectrum can also report on the coordination environment of the lanthanide ion. Here, we used lanthanide......-centered emission to report on the binding of potassium in an 18-crown-6 binding pocket. The responsive systems were made by linking a crown ether to a kinetically inert lanthanide binding pocket using a molecular building block approach. Specifically, an alkyne-appended Ln.DO3A was used as a building block...... of the lanthanide emission spectra was shown to be unperturbed by the binding of potassium, while the binding was reported by an overall increased intensity of the lanthanide-centered emission. This observation was contrasted to the change in spectral shape between propargyl-Ln.DO3A and the triazolyl-Ln.DO3A...

  20. Kinetic properties and heme pocket structure of two domains of the polymeric hemoglobin of Artemia in comparison with the native molecule.

    Science.gov (United States)

    Borhani, Heshmat Akbari; Berghmans, Herald; Trashin, Stanislav; De Wael, Karolien; Fago, Angela; Moens, Luc; Habibi-Rezaei, Mehran; Dewilde, Sylvia

    2015-10-01

    In this project, we studied some physicochemical properties of two different globin domains of the polymeric hemoglobin of the brine shrimp Artemia salina and compared them with those of the native molecule. Two domains (AsHbC1D1 and AsHbC1D5) were cloned and expressed in BL21(DE3)pLysS strain of Escherichia coli. The recombinant proteins as well as the native hemoglobin (AfHb) were purified from bacteria and frozen Artemia, respectively by standard chromatographic methods and assessed by SDS-PAGE. The heme environment of these proteins was studied by optical spectroscopy and ligand-binding kinetics (e.g. CO association and O2 binding affinity) were measured for the two recombinant proteins and the native hemoglobin. This indicates that the CO association rate for AsHbC1D1 is higher than that of AsHbC1D5 and AfHb, while the calculated P50 value for AsHbC1D1 is lower than that of AsHbC1D5 and AfHb. The geminate and bimolecular rebinding parameters indicate a significant difference between both domains. Moreover, EPR results showed that the heme pocket in AfHb is in a more closed conformation than the heme pocket in myoglobin. Finally, the reduction potential of -0.13V versus the standard hydrogen electrode was determined for AfHb by direct electrochemical measurements. It is about 0.06V higher than the potential of the single domain AsHbC1D5. This work shows that each domain in the hemoglobin of Artemia has different characteristics of ligand binding.

  1. Optimal design of Tilting-Pad Thrust Bearings with High Pressure Injection Pockets

    DEFF Research Database (Denmark)

    Heinrichson, Niels; Santos, Ilmar

    2006-01-01

    A thermo-elasto-hydrodynamic(TEHD) model based on the Reynolds equation has been used to study the effect of oil injection pockets on the performance of tilting pad thrust bearings. The optimal position of the pivot both with respect to load carrying capacity and minimal power consumption is seen...

  2. TGF-β Signaling Is Associated with Endocytosis at the Pocket Region of the Primary Cilium

    DEFF Research Database (Denmark)

    Clement, Christian Alexandro; Ajbro, Katrine Dalsgaard; Koefoed, Karen;

    2013-01-01

    Transforming growth factor β (TGF-β) signaling is regulated by clathrin-dependent endocytosis (CDE) for the control of cellular processes during development and in tissue homeostasis. The primary cilium coordinates several signaling pathways, and the pocket surrounding the base and proximal part...

  3. Estimating Leaf Area Index (LAI) in Vineyards Using the PocketLAI Smart-App.

    Science.gov (United States)

    Orlando, Francesca; Movedi, Ermes; Coduto, Davide; Parisi, Simone; Brancadoro, Lucio; Pagani, Valentina; Guarneri, Tommaso; Confalonieri, Roberto

    2016-11-26

    Estimating leaf area index (LAI) of Vitis vinifera using indirect methods involves some critical issues, related to its discontinuous and non-homogeneous canopy. This study evaluates the smart app PocketLAI and hemispherical photography in vineyards against destructive LAI measurements. Data were collected during six surveys in an experimental site characterized by a high level of heterogeneity among plants, allowing us to explore a wide range of LAI values. During the last survey, the possibility to combine remote sensing data and in-situ PocketLAI estimates (smart scouting) was evaluated. Results showed a good agreement between PocketLAI data and direct measurements, especially for LAI ranging from 0.13 to 1.41 (R² = 0.94, RRMSE = 17.27%), whereas the accuracy decreased when an outlying value (vineyard LAI = 2.84) was included (R² = 0.77, RRMSE = 43.00%), due to the saturation effect in case of very dense canopies arising from lack of green pruning. The hemispherical photography showed very high values of R², even in presence of the outlying value (R² = 0.94), although it showed a marked and quite constant overestimation error (RRMSE = 99.46%), suggesting the need to introduce a correction factor specific for vineyards. During the smart scouting, PocketLAI showed its reliability to monitor the spatial-temporal variability of vine vigor in cordon-trained systems, and showed a potential for a wide range of applications, also in combination with remote sensing.

  4. Adaptation of a Pocket PC for Use as a Wearable Voice Dosimeter

    Science.gov (United States)

    Popolo, Peter S.; Svec, Jan G.; Titze, Ingo R.

    2005-01-01

    This article deals with the adaptation of a commercially available Pocket PC for use as a voice dosimeter, a wearable device that measures the vocal dose of teachers or other individuals on the job, at home, and elsewhere during the course of an entire day. An engineering approach for designing a voice dosimeter is described, and design data are…

  5. 78 FR 54214 - Endangered and Threatened Wildlife and Plants; Removing Five Subspecies of Mazama Pocket Gopher...

    Science.gov (United States)

    2013-09-03

    ... statement that it is not possible to conclusively determine that Brush Prairie pocket gopher is not T.... mazama using standard, scientifically accepted morphological characteristics to separate the species. Our... that the summary statement for Factor E in our threats analysis for all nine subspecies was not...

  6. Out-of-Pocket Net Price for College. Data Point. NCES 2014-902

    Science.gov (United States)

    Horn, Laura; Paslov, Jonathan

    2014-01-01

    This Data Point uses data from four administrations of the National Postsecondary Student Aid Study (NPSAS:2000, NPSAS:04, NPSAS:08, and NPSAS:12) to briefly present trends in out-of-pocket net price for college, the amount that students and their families must pay to attend college after subtracting grants, loans, work-study, and all other…

  7. Pseudogap-generated a coexistence of Fermi arcs and Fermi pockets in cuprate superconductors

    Science.gov (United States)

    Zhao, Huaisong; Gao, Deheng; Feng, Shiping

    2017-03-01

    One of the most intriguing puzzle is why there is a coexistence of Fermi arcs and Fermi pockets in the pseudogap phase of cuprate superconductors? This puzzle is calling for an explanation. Based on the t - J model in the fermion-spin representation, the coexistence of the Fermi arcs and Fermi pockets in cuprate superconductors is studied by taking into account the pseudogap effect. It is shown that the pseudogap induces an energy band splitting, and then the poles of the electron Green's function at zero energy form two contours in momentum space, however, the electron spectral weight on these two contours around the antinodal region is gapped out by the pseudogap, leaving behind the low-energy electron spectral weight only located at the disconnected segments around the nodal region. In particular, the tips of these disconnected segments converge on the hot spots to form the closed Fermi pockets, generating a coexistence of the Fermi arcs and Fermi pockets. Moreover, the single-particle coherent weight is directly related to the pseudogap, and grows linearly with doping. The calculated result of the overall dispersion of the electron excitations is in qualitative agreement with the experimental data. The theory also predicts that the pseudogap-induced peak-dip-hump structure in the electron spectrum is absent from the hot-spot directions.

  8. Pocket proteins pRb and p107 are required for cortical lamination independent of apoptosis.

    Science.gov (United States)

    Svoboda, D S; Paquin, A; Park, D S; Slack, R S

    2013-12-01

    Pocket proteins (pRb, p107 and p130) are well studied in their role of regulating cell cycle progression. Increasing evidence suggests that these proteins also control early differentiation and even later stages of cell maturation, such as migration. However, pocket proteins also regulate apoptosis, and many of the developmental defects in knock out models have been attributed to increased cell death. Here, we eliminate ectopic apoptosis in the developing brain through the deletion of Bax, and show that pocket proteins are required for radial migration independent of their role in cell death regulation. Following loss of pRb and p107, a population of cortical neurons fails to pass through the intermediate zone into the cortical plate. Importantly, these neurons are born at the appropriate time and this migration defect cannot be rescued by eliminating ectopic cell death. In addition, we show that pRb and p107 regulate radial migration through a cell autonomous mechanism since pRb/p107 deficient neurons fail to migrate to the correct cortical layer within a wild type brain. These results define a novel role of pocket proteins in regulating cortical lamination through a cell autonomous mechanism independent of their role in apoptosis.

  9. An experimental study of geyser-like flows induced by a pressurized air pocket

    Science.gov (United States)

    Elayeb, I. S.; Leon, A.; Choi, Y.; Alnahit, A. O.

    2015-12-01

    Previous studies argues that the entrapment of pressurized air pockets within combined sewer systems can produce geyser flows, which is an oscillating jetting of a mixture of gas-liquid flows. To verify that pressurized air pockets can effectively produce geysers, laboratory experiments were conducted. However, past experiments were conducted in relatively small-scale apparatus (i.e. maximum φ2" vertical shaft). This study conducted a set of experiments in a larger apparatus. The experimental setup consists of an upstream head tank, a downstream head tank, a horizontal pipe (46.5ft long, φ6") and a vertical pipe (10ft long, φ6"). The initial condition for the experiments is constant flow discharge through the horizontal pipe. The experiments are initiated by injecting an air pocket with pre-determined volume and pressure at the upstream end of the horizontal pipe. The air pocket propagates through the horizontal pipe until it arrives to the vertical shaft, where it is released producing a geyser-like flow. Three flow rates in the horizontal pipe and three injected air pressures were tested. The variables measured were pressure at two locations in the horizontal pipe and two locations in the vertical pipe. High resolution videos at two regions in the vertical shaft were also recorded. To gain further insights in the physics of air-water interaction, the laboratory experiments were complemented with numerical simulations conducted using a commercial 3D CFD model, previously validated with experiments.

  10. Creating a portable data-collection system with Microsoft Embedded Visual Tools for the Pocket PC.

    Science.gov (United States)

    Dixon, Mark R

    2003-01-01

    This paper describes an overview and illustrative example for creating a portable data-collection system using Microsoft Embedded Visual Tools for the Pocket PC. A description of the Visual Basic programming language is given, along with examples of computer code procedures for developing data-collection software. Program specifications, strategies for customizing the collection system, and troubleshooting tips are also provided.

  11. 利用EVC实现Pocket PC和工控机串行通信%Implementation of serial communication software between pocket PC and industry control computer based on EVC

    Institute of Scientific and Technical Information of China (English)

    张军; 蒋铁登

    2006-01-01

    串口通信广泛应用于工业控制领域,PocketPC利用自身串口通信功能和使用方便的特点,使得它具有广泛的应用范围和良好的应用前景.为了实现PocketPC对工业控制系统的现场控制,通过对eMbedded visual C++(EVC)3.0在PocketPC2002操作系统平台和LabWindows/CVI在Windows操作系统平台上的串口通信软件的关键技术进行了研究,实现了PocketPC和工控机之间的串口通信,从而利用Pocket PC实现对工业设备的现场控制.

  12. The migration of fragments of glass from the pockets to the surfaces of clothing.

    Science.gov (United States)

    O'Sullivan, S; Geddes, T; Lovelock, T J

    2011-05-20

    During the last decade or so there has been some discussion in the forensic community in the United Kingdom concerning whether it is necessary to search the pockets for glass particles in garments attributed to suspects arrested for glass breaking crimes. The removal of this practice would help expedite the searching and recovery process since examining only the surfaces of clothing would reduce the cost of recovering glass evidence. However, it is believed by many scientists that some glass fragments originally acquired in pockets can migrate to the surfaces of clothing prior to examination by the forensic scientist. As glass fragments have been encountered in the pockets of garments during examinations of casework items in the LGC Laboratories, the implications of this change in practice needs to be assessed. Hence, the aim of this study was to investigate this possibility that fragments of glass migrate from a pocket of a garment to its surfaces during police and laboratory handling after a person is suspected of breaking glass during an offence. If this occurs to a significant extent then it could affect the evaluation of the glass evidence when using a Bayesian approach. Sixty fragments of glass were seeded into a pocket of a fleece jacket and a pair of denim jeans. Three experiments were performed; one examined a searching, recovery and blanking procedure, another examined the pre-laboratory 'handling' process of an item in an evidence bag, and the third experiment looked at the removal of an object from a pocket laden with glass and subsequent removal and packaging of the garment. Up to two (3.3%) fragments were recovered from the surfaces of the fleece jacket and the denim jeans via the searching, recovery and blanking procedure. Similar numbers were also recovered from the insides of the evidence bags. Up to four (6.7%) fragments were recovered from the surface of the fleece jacket and up to five (8.3%) fragments were recovered from the surface of the

  13. Early wound healing and refractive response of different pocket configurations following presbyopic inlay implantation

    Science.gov (United States)

    Konstantopoulos, Aris; Liu, Yu-Chi; Teo, Ericia Pei Wen; Lwin, Nyein Chan; Yam, Gary Hin Fai; Mehta, Jodhbir S.

    2017-01-01

    Background Presbyopic inlays have mostly been implanted under a corneal flap. Implantation in a pocket has advantages including less postoperative dry eye and neurotrophic effect, and better biomechanical corneal stability. This study investigated the effect of different pocket and flocket dimensions on corneal stability and refractive power after Raindrop™ implantation, and the associated wound healing response. Methodology Ten New Zealand White rabbits had bilateral pocket Raindrop™ implantation. Eyes were allocated to 4 groups: pockets with 4mm, 6mm, and 8mm diameters, and 8mm flocket. They were examined pre-operatively, at day 1, weeks 1, 2, 3 and 4 post-surgery with anterior segment optical coherence tomography, corneal topography and in-vivo confocal microscopy. After euthanasia (week 4), CD11b, heat shock protein (HSP) 47 and fibronectin corneal immunohistochemistry was performed. Results Corneal thickness (mean±SD) increased from 360.0±16.2μm pre-operatively to 383.9±32.5, 409.4±79.3, 393.6±35.2, 396.4±50.7 and 405±20.3μm on day 1, weeks 1,2,3 and 4 respectively (pCorneal refractive power increased by 11.1±5.5, 7.5±2.5, 7.5±3.1, 7.0±3.6 and 6.3±2.9D (pCorneal astigmatism increased from 1.1±0.3D to 2.3±1.6, 1.7±0.7, 1.8±1.0, 1.6±0.9 and 1.6±0.9D respectively (p = 0.033). CT, refractive power change and astigmatism were not different between groups. The 8mm pocket and 8mm flocket groups had the least stromal keratocyte reflectivity. CD11b, fibronectin or HSP47 weren’t detected. Conclusions Anatomical and refractive stability was achieved by 1 week; the outcomes were not affected by pocket or flocket configuration. No scarring or inflammation was identified. The 8mm pocket and flocket showed the least keratocyte activation, suggesting they might be the preferred configuration. PMID:28235010

  14. Pairwise structure alignment specifically tuned for surface pockets and interaction interfaces

    KAUST Repository

    Cui, Xuefeng

    2015-09-09

    To detect and evaluate the similarities between the three-dimensional (3D) structures of two molecules, various kinds of methods have been proposed for the pairwise structure alignment problem [6, 9, 7, 11]. The problem plays important roles when studying the function and the evolution of biological molecules. Recently, pairwise structure alignment methods have been extended and applied on surface pocket structures [10, 3, 5] and interaction interface structures [8, 4]. The results show that, even when there are no global similarities discovered between the global sequences and the global structures, biological molecules or complexes could share similar functions because of well conserved pockets and interfaces. Thus, pairwise pocket and interface structure alignments are promising to unveil such shared functions that cannot be discovered by the well-studied global sequence and global structure alignments. State-of-the-art methods for pairwise pocket and interface structure alignments [4, 5] are direct extensions of the classic pairwise protein structure alignment methods, and thus such methods share a few limitations. First, the goal of the classic protein structure alignment methods is to align single-chain protein structures (i.e., a single fragment of residues connected by peptide bonds). However, we observed that pockets and interfaces tend to consist of tens of extremely short backbone fragments (i.e., three or fewer residues connected by peptide bonds). Thus, existing pocket and interface alignment methods based on the protein structure alignment methods still rely on the existence of long-enough backbone fragments, and the fragmentation issue of pockets and interfaces rises the risk of missing the optimal alignments. Moreover, existing interface structure alignment methods focus on protein-protein interfaces, and require a "blackbox preprocessing" before aligning protein-DNA and protein-RNA interfaces. Therefore, we introduce the PROtein STucture Alignment

  15. Influence of length and flexibility of spacers on the binding affinity of divalent ligands

    Directory of Open Access Journals (Sweden)

    Susanne Liese

    2015-05-01

    Full Text Available We present a quantitative model for the binding of divalent ligand–receptor systems. We study the influence of length and flexibility of the spacers on the overall binding affinity and derive general rules for the optimal ligand design. To this end, we first compare different polymeric models and determine the probability to simultaneously bind to two neighboring receptor binding pockets. In a second step the binding affinity of divalent ligands in terms of the IC50 value is derived. We find that a divalent ligand has the potential to bind more efficiently than its monovalent counterpart only, if the monovalent dissociation constant is lower than a critical value. This critical monovalent dissociation constant depends on the ligand-spacer length and flexibility as well as on the size of the receptor. Regarding the optimal ligand-spacer length and flexibility, we find that the average spacer length should be equal or slightly smaller than the distance between the receptor binding pockets and that the end-to-end spacer length fluctuations should be in the same range as the size of a receptor binding pocket.

  16. Influence of length and flexibility of spacers on the binding affinity of divalent ligands.

    Science.gov (United States)

    Liese, Susanne; Netz, Roland R

    2015-01-01

    We present a quantitative model for the binding of divalent ligand-receptor systems. We study the influence of length and flexibility of the spacers on the overall binding affinity and derive general rules for the optimal ligand design. To this end, we first compare different polymeric models and determine the probability to simultaneously bind to two neighboring receptor binding pockets. In a second step the binding affinity of divalent ligands in terms of the IC50 value is derived. We find that a divalent ligand has the potential to bind more efficiently than its monovalent counterpart only, if the monovalent dissociation constant is lower than a critical value. This critical monovalent dissociation constant depends on the ligand-spacer length and flexibility as well as on the size of the receptor. Regarding the optimal ligand-spacer length and flexibility, we find that the average spacer length should be equal or slightly smaller than the distance between the receptor binding pockets and that the end-to-end spacer length fluctuations should be in the same range as the size of a receptor binding pocket.

  17. Coarse-grained molecular dynamics simulations of protein-ligand binding.

    Science.gov (United States)

    Negami, Tatsuki; Shimizu, Kentaro; Terada, Tohru

    2014-09-30

    Coarse-grained molecular dynamics (CGMD) simulations with the MARTINI force field were performed to reproduce the protein-ligand binding processes. We chose two protein-ligand systems, the levansucrase-sugar (glucose or sucrose), and LinB-1,2-dichloroethane systems, as target systems that differ in terms of the size and shape of the ligand-binding pocket and the physicochemical properties of the pocket and the ligand. Spatial distributions of the Coarse-grained (CG) ligand molecules revealed potential ligand-binding sites on the protein surfaces other than the real ligand-binding sites. The ligands bound most strongly to the real ligand-binding sites. The binding and unbinding rate constants obtained from the CGMD simulation of the levansucrase-sucrose system were approximately 10 times greater than the experimental values; this is mainly due to faster diffusion of the CG ligand in the CG water model. We could obtain dissociation constants close to the experimental values for both systems. Analysis of the ligand fluxes demonstrated that the CG ligand molecules entered the ligand-binding pockets through specific pathways. The ligands tended to move through grooves on the protein surface. Thus, the CGMD simulations produced reasonable results for the two different systems overall and are useful for studying the protein-ligand binding processes.

  18. Binding Procurement

    Science.gov (United States)

    Rao, Gopalakrishna M.; Vaidyanathan, Hari

    2007-01-01

    This viewgraph presentation reviews the use of the binding procurement process in purchasing Aerospace Flight Battery Systems. NASA Engineering and Safety Center (NESC) requested NASA Aerospace Flight Battery Systems Working Group to develop a set of guideline requirements document for Binding Procurement Contracts.

  19. 数英雄还看今朝——Pocket PC 2002新品横向评测

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    写在测试前从惠普(HP)首推Pocket PC 2002机型Jornada 565以来,Pocket PC之风越发强劲,更闻索尼(SONY)公司会在今年6.7月间推出最后一款采用Palm OS的掌上电脑,随后索尼公司的掌上电脑产品将全面采用Pocket PC 2002操作系统。我们现在姑且不谈论这个消息的确切性,但从目前Palm系统的某些功能逐渐向Pocket PC靠拢来看,Pocket PC也不再是华而不实的鸡肋产品了。

  20. Enhanced performance of GeSn source-pocket tunnel field-effect transistors for low-power applications

    Science.gov (United States)

    Liu, Lei; Liang, Renrong; Wang, Jing; Xu, Jun

    2016-07-01

    Germanium-tin (GeSn) source-pocket tunnel field-effect transistors (TFETs) are comprehensively investigated by numerical device simulations at low supply voltages. Device configurations with homo- and hetero-tunneling junctions (TJ) are analyzed and compared. It is shown that direct-gap GeSn alloys are favorable for increasing the source-pocket tunneling rate. Increasing the source Sn composition of the device may aid the on-state current increase, but the subthreshold swing (SS) is degraded because of the reduced band gap. At ultrascaled supply voltages, the GeSn hetero-TJ TFET with higher pocket Sn composition exhibits the best performance and SS, and the device performance can be further improved by increasing the Sn composition in the pocket region. These simulation results could be used to understand and optimize the performance of GeSn source-pocket TFETs, which are very promising electronic devices for low-power applications.

  1. Molecular mechanism of AMD3100 antagonism in the CXCR4 receptor: transfer of binding site to the CXCR3 receptor

    DEFF Research Database (Denmark)

    Rosenkilde, Mette M; Gerlach, Lars-Ole; Jakobsen, Janus S

    2004-01-01

    AMD3100 is a symmetric bicyclam, prototype non-peptide antagonist of the CXCR4 chemokine receptor. Mutational substitutions at 16 positions located in TM-III, -IV, -V, -VI, and -VII lining the main ligand-binding pocket of the CXCR4 receptor identified three acid residues: Asp(171) (AspIV:20), Asp......, respectively. Metal ion binding in the cyclam rings of AMD3100 increased its dependence on Asp(262) and provided a tighter molecular map of the binding site, where borderline mutational hits became clear hits for the Zn(II)-loaded analog. The proposed binding site for AMD3100 was confirmed by a gradual build...... that AMD3100 binds through interactions with essentially only three acidic anchor-point residues, two of which are located at one end and the third at the opposite end of the main ligand-binding pocket of the CXCR4 receptor. We suggest that non-peptide antagonists with, for example, improved oral...

  2. The Impact of Health Insurance Programs on Out-of-Pocket Expenditures in Indonesia: An Increase or a Decrease?

    Directory of Open Access Journals (Sweden)

    Aurelia Souares

    2013-07-01

    Full Text Available We used panel data from the Indonesian Family Life Survey to investigate the impact of health insurance programs on reducing out-of-pocket expenditures. We employed three linear panel data models, two of which accounted for endogeneity: pooled ordinary least squares (OLS, pooled two-stage least squares (2SLS for instrumental variable (IV, and fixed effects (FE. The study revealed that two health insurance programs had a significantly negative impact on out-of-pocket expenditures by using IV estimates. In the IV model, Askeskin decreased out-of-pocket expenditures by 34% and Askes by 55% compared with non-Askeskin and non-Askes, respectively, while Jamsostek was found to bear a nonsignificant effect on out-of-pocket expenditures. In the FE model, only Askeskin had a significant negative effect with an 11% reduction on out-of-pocket expenditures. This study showed that two large existing health insurance programs in Indonesia, Askeskin and Askes, effectively reduced household out-of-pocket expenditures. The ability of programs to offer financial protection by reducing out-of-pocket expenditures is likely to be a direct function of their benefits package and co-payment policies.

  3. Pocket PC基于XML的异构数据库同步

    Institute of Scientific and Technical Information of China (English)

    王璐

    2011-01-01

    在嵌入式数据库领域,世界各大数据库厂商都有各自的移动解决方案,但每种数据同步方案都针对自己的数据库,不能兼容其他的数据库产品。该文介绍的是Pocket PC在微软的Windows mobile操作系统平台下,通过XML方式进行的一种跨平台的数据库同步方法。文中介绍了Pocket PC以XML方式分别对PC服务器中的Microsoft SQL Server数据库和Microsoft Access数据库的同步过程,并对比RDA,提出了优势和局限所在。

  4. Micro-pocket fission detectors (MPFD) for in-core neutron flux monitoring

    Energy Technology Data Exchange (ETDEWEB)

    McGregor, Douglas S. [S.M.A.R.T. Laboratory, Department of Mechanical and Nuclear Engineering, Kansas State University, Manhattan, KS 66506 (United States)]. E-mail: mcgregor@ksu.edu; Ohmes, Martin F. [S.M.A.R.T. Laboratory, Department of Mechanical and Nuclear Engineering, Kansas State University, Manhattan, KS 66506 (United States); Ortiz, Rylan E. [S.M.A.R.T. Laboratory, Department of Mechanical and Nuclear Engineering, Kansas State University, Manhattan, KS 66506 (United States); Sabbir Ahmed, A.S.M. [S.M.A.R.T. Laboratory, Department of Mechanical and Nuclear Engineering, Kansas State University, Manhattan, KS 66506 (United States); Kenneth Shultis, J. [S.M.A.R.T. Laboratory, Department of Mechanical and Nuclear Engineering, Kansas State University, Manhattan, KS 66506 (United States)

    2005-12-01

    Micro-pocket fission detectors (MPFD) have been fabricated and tested as in-core flux monitors in the 250 kW TRIGA nuclear reactor at Kansas State University. The prototype devices have been coated with a natural uranyl-nitrate to provide a neutron reactive coating. The devices are composed of alumina substrates sealed together to form a miniature gas pocket 3 mm in diameter and 1 mm wide. The devices are radiation hard and can operate in pulse mode in a neutron flux exceeding 10{sup 12} cm{sup -2} s{sup -1}. Placed in the central thimble of the reactor core, the MPFDs have shown count rate linearity from low to high power. Dead time losses become apparent at power levels exceeding 100 kW, yet are still low enough to allow for pulse mode operation.

  5. Experimental study of combustion characteristics of isolated pockets of hydrogen-air mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Manoubi, M.; LaFleche, M. [Univ. of Ottawa, Dept. of Mechanical Engineering, Ottawa, Ontario (Canada); Liang, Z., E-mail: zhe.liang@cnl.ca [Canadian Nuclear Laboratories, Chalk River, Ontario (Canada); Radulescu, M. [Univ. of Ottawa, Dept. of Mechanical Engineering, Ottawa, Ontario (Canada)

    2016-06-15

    This paper examines the dynamics of unconfined hydrogen-air flames and the criterion for flame propagation between neighbouring pockets of reactive gas separated by air using the soap bubble technique. The combustion events were visualized using high-speed schlieren or large-scale shadowgraph systems. It was revealed that for sufficiently lean hydrogen-air mixtures characterized by low flame speeds, buoyancy effects become important at small scales. The critical radius of hemispherical flame that will rise due to buoyancy is highly sensitive to the hydrogen concentration. The test results demonstrate that for transition of a flame between neighbouring pockets, the separation distance between the bubbles is mainly determined by the expansion ratio for near stoichiometric mixture, but it becomes much smaller for leaner mixtures because the flame kernel rises due to buoyant effects before the flame can reach the second bubble, thus the separation distance is no longer governed by the expansion ratio. (author)

  6. Characterization of vertical strain silicon MOSFET incorporating dielectric pocket (SDP-VMOSFET)

    Energy Technology Data Exchange (ETDEWEB)

    Napiah, Z. A. F. M., E-mail: zulatfyi@utem.edu.my, E-mail: nazirah6969@gmail.com, E-mail: azlishah@utem.edu.my, E-mail: idzdihar@utem.edu.my, E-mail: faiz.arith@utem.edu.my, E-mail: yashidar@yahoo.com, E-mail: sitinabilahtaib@gmail.com; Makhtar, N., E-mail: zulatfyi@utem.edu.my, E-mail: nazirah6969@gmail.com, E-mail: azlishah@utem.edu.my, E-mail: idzdihar@utem.edu.my, E-mail: faiz.arith@utem.edu.my, E-mail: yashidar@yahoo.com, E-mail: sitinabilahtaib@gmail.com; Othman, M. A., E-mail: zulatfyi@utem.edu.my, E-mail: nazirah6969@gmail.com, E-mail: azlishah@utem.edu.my, E-mail: idzdihar@utem.edu.my, E-mail: faiz.arith@utem.edu.my, E-mail: yashidar@yahoo.com, E-mail: sitinabilahtaib@gmail.com; Idris, M. I., E-mail: zulatfyi@utem.edu.my, E-mail: nazirah6969@gmail.com, E-mail: azlishah@utem.edu.my, E-mail: idzdihar@utem.edu.my, E-mail: faiz.arith@utem.edu.my, E-mail: yashidar@yahoo.com, E-mail: sitinabilahtaib@gmail.com; Arith, F., E-mail: zulatfyi@utem.edu.my, E-mail: nazirah6969@gmail.com, E-mail: azlishah@utem.edu.my, E-mail: idzdihar@utem.edu.my, E-mail: faiz.arith@utem.edu.my, E-mail: yashidar@yahoo.com, E-mail: sitinabilahtaib@gmail.com; Yasin, N. Y. M., E-mail: zulatfyi@utem.edu.my, E-mail: nazirah6969@gmail.com, E-mail: azlishah@utem.edu.my, E-mail: idzdihar@utem.edu.my, E-mail: faiz.arith@utem.edu.my, E-mail: yashidar@yahoo.com, E-mail: sitinabilahtaib@gmail.com; Taib, S. N., E-mail: zulatfyi@utem.edu.my, E-mail: nazirah6969@gmail.com, E-mail: azlishah@utem.edu.my, E-mail: idzdihar@utem.edu.my, E-mail: faiz.arith@utem.edu.my, E-mail: yashidar@yahoo.com, E-mail: sitinabilahtaib@gmail.com [Centre for Telecommunication Research and Innovation (CeTRI), Faculty of Electronic and Computer Engineering, Universiti Teknikal Malaysia Melaka, Hang Tuah Jaya, 76100 Durian Tunggal, Melaka (Malaysia)

    2014-02-24

    The vertical Metal-Oxide-Semiconductor Field-Effect-Transistor (MOSFET) leads to a double channel width that can increase the packaging density. The strained silicon MOSFET was introduced to modify the carrier transport properties of silicon in order to enhance transport of both electrons and holes within strained layer. Dielectric pocket was act to control encroachment of the drain doping into the channel and reduce short channel effects (SCE). SDP-VMOSFET which was a combination of those advantages was proposed to overcome the SCE in term of leakage current, threshold voltage roll-off also Drain Induce Barrier Lowering (DIBL). As a result, SDP-VMOSFET produces a better threshold voltage and DIBL compared to related structures. Meanwhile, it gives slightly increased for leakage current compared to Vertical MOSFET Incorporating Dielectric Pocket. The characteristics of the SDP-VMOSFET are analyzed in order to optimize the performance of the device and leading to the next generation of IC technology.

  7. Assessment of left ventricular function by GPs using pocket-sized ultrasound

    OpenAIRE

    Mjølstad, Ole Christian; Snare, Sten Roar; Folkvord, Lasse; Helland, Frode; Grimsmo, Anders; Torp, Hans; Haraldseth, Olav; Haugen, Bjørn Olav

    2012-01-01

    Background Assessment of left ventricular (LV) function with echocardiography is mandatory in patients with suspected heart failure (HF). Objectives To investigate if GPs were able to evaluate the LV function in patients at risk of developing or with established HF by using pocket-sized ultrasound (pUS). Methods Feasibility study in general practice, seven GPs in three different Norwegian primary care centres participated. Ninety-two patients with reduced or at risk of developing reduced LV f...

  8. Efficiency of cellular growth when creating small pockets of electric current along the walls of cells.

    Science.gov (United States)

    Kletetschka, Gunther; Zila, Vojtech; Klimova, Lucie

    2014-04-01

    Pulses up to 11 Tesla magnetic fields may generate pockets of currents along the walls of cellular material and may interfere with the overall ability of cell division. We used prokaryotic cells (Escherichia coli) and eukaryotic cells (murine fibroblasts) and exposed them to magnetic pulses of intensities ranging from 1 millitesla (mT) to 11,000 mT. We found prokaryotic cells to be more sensitive to magnetic field pulses than eukaryotic cells.

  9. Average Out-of-Pocket Expenses Across Different Drug Categories and Commercial Third-Party Payers

    OpenAIRE

    Lenderts, Susan; Kalali, Amir H.

    2010-01-01

    In this Trend Watch, we look at retail pharmacy prescriptions for branded and generic attention deficit hyperactivity disorder treatments, atypical antipsychotics, selective serotonin reuptake inhibitors, and serotonin and norepinephrine reuptake inhibitors and analyze the average out-of-pocket costs incurred by patients who are covered by commercial third-party prescription plans (i.e., as opposed to patients covered by Medicaid or patients with no prescription coverage). Overall, patient ou...

  10. Morphological adaptations for digging and climate-impacted soil properties define pocket gopher (Thomomys spp. distributions.

    Directory of Open Access Journals (Sweden)

    Ariel E Marcy

    Full Text Available Species ranges are mediated by physiology, environmental factors, and competition with other organisms. The allopatric distribution of five species of northern Californian pocket gophers (Thomomys spp. is hypothesized to result from competitive exclusion. The five species in this environmentally heterogeneous region separate into two subgenera, Thomomys or Megascapheus, which have divergent digging styles. While all pocket gophers dig with their claws, the tooth-digging adaptations of subgenus Megascapheus allow access to harder soils and climate-protected depths. In a Northern Californian locality, replacement of subgenus Thomomys with subgenus Megascapheus occurred gradually during the Pleistocene-Holocene transition. Concurrent climate change over this transition suggests that environmental factors--in addition to soil--define pocket gopher distributional limits. Here we show 1 that all pocket gophers occupy the subset of less energetically costly soils and 2 that subgenera sort by percent soil clay, bulk density, and shrink-swell capacity (a mineralogical attribute. While clay and bulk density (without major perturbations stay constant over decades to millennia, low precipitation and high temperatures can cause shrink-swell clays to crack and harden within days. The strong yet underappreciated interaction between soil and moisture on the distribution of vertebrates is rarely considered when projecting species responses to climatic change. Furthermore, increased precipitation alters the weathering processes that create shrink-swell minerals. Two projected outcomes of ongoing climate change--higher temperatures and precipitation--will dramatically impact hardness of soil with shrink-swell minerals. Current climate models do not include factors controlling soil hardness, despite its impact on all organisms that depend on a stable soil structure.

  11. Efficiency of Cellular Growth When Creating Small Pockets of Electric Current Along the Walls of Cells

    OpenAIRE

    Kletetschka, Gunther; Zila, Vojtech; Klimova, Lucie

    2014-01-01

    Pulses up to 11 Tesla magnetic fields may generate pockets of currents along the walls of cellular material and may interfere with the overall ability of cell division. We used prokaryotic cells (Escherichia coli) and eukaryotic cells (murine fibroblasts) and exposed them to magnetic pulses of intensities ranging from 1 millitesla (mT) to 11,000 mT. We found prokaryotic cells to be more sensitive to magnetic field pulses than eukaryotic cells.

  12. Estimating Leaf Area Index (LAI in Vineyards Using the PocketLAI Smart-App

    Directory of Open Access Journals (Sweden)

    Francesca Orlando

    2016-11-01

    Full Text Available Estimating leaf area index (LAI of Vitis vinifera using indirect methods involves some critical issues, related to its discontinuous and non-homogeneous canopy. This study evaluates the smart app PocketLAI and hemispherical photography in vineyards against destructive LAI measurements. Data were collected during six surveys in an experimental site characterized by a high level of heterogeneity among plants, allowing us to explore a wide range of LAI values. During the last survey, the possibility to combine remote sensing data and in-situ PocketLAI estimates (smart scouting was evaluated. Results showed a good agreement between PocketLAI data and direct measurements, especially for LAI ranging from 0.13 to 1.41 (R2 = 0.94, RRMSE = 17.27%, whereas the accuracy decreased when an outlying value (vineyard LAI = 2.84 was included (R2 = 0.77, RRMSE = 43.00%, due to the saturation effect in case of very dense canopies arising from lack of green pruning. The hemispherical photography showed very high values of R2, even in presence of the outlying value (R2 = 0.94, although it showed a marked and quite constant overestimation error (RRMSE = 99.46%, suggesting the need to introduce a correction factor specific for vineyards. During the smart scouting, PocketLAI showed its reliability to monitor the spatial-temporal variability of vine vigor in cordon-trained systems, and showed a potential for a wide range of applications, also in combination with remote sensing.

  13. Influence of entrapped air pockets on hydraulic transients in water pipelines

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Ling [Hohai University, China; Liu, Prof. Deyou [Hohai University, China; Karney, Professor Byran W. [University of Toronto; Zhang, Qin Fen [ORNL

    2011-01-01

    The pressure variations associated with a filling undulating pipeline containing an entrapped air pocket are investigated both experimentally and numerically. The influence of entrapped air on abnormal transient pressures is often ambiguous since the compressibility of the air pocket permits the liquid flow to accelerate but also partly cushions the system, with the balance of these tendencies being associated with the initial void fraction of the air pocket. Earlier experimental research involved systems with an initial void fraction greater than 5.8%; this paper focuses on initial void fractions ranging from 0% to 10%, in order to more completely characterize the transient response. Experimental results show that the maximum pressure increases and then decreases as the initial void fraction decreases. A simplified model is developed by neglecting the liquid inertia and energy loss of a short water column near the air-water interface. Comparisons of the calculated and observed results show the model is able to accurately predict peak pressures as a function of void fraction and filling conditions. Rigid water column models, however, perform poorly with small void fractions.

  14. EFFECTIVNESS OF TARGET ANTIMICROBIAL THERAPY OF SEVERE CHRONIC PERIODONTITIS PART II: PREVALENCE OF RESIDUAL POCKETS

    Directory of Open Access Journals (Sweden)

    Kamen Kotsilkov

    2010-10-01

    Full Text Available Comprehensive treatment of periodontitis is very different from the treatment of most bacterial infections. While periodontitis is traditionally considered a bacterial infection, many variables influence treatment outcomes. The reduction of the probing depth of the periodontal pockets is one of the main criteria for the success of the periodontal treatment. The prevalence of the residual pockets with probing depth greater than 4 mm determines the risk of disease progression. The reduction of the periodontal sites with PD above 7mm with non-surgical periodontal treatment could limit the necessity of periodontal surgery. Aim: Evaluation of the effectiveness of treatment of severe chronic periodontitis with additional target antibiotic administration in comparison with the therapy with adjunctive antimicrobial combination amoxicillin+metronidazole and conventional mechanical periodontal treatment regarding the prevalence and the achieved mean reduction of PD of periodontal pockets with initial PPD below 3mm, from 3 to 5mm, from 5-7mm and above 7mm.Results: In all study groups a reduction of the mean PD has been achieved. The prevalence of periodontal sites with PD above 7mm after therapy is the lowest in the group with target antibiotic administration. These results advocate the effectiveness of the target adjunctive antimicrobial treatment in order to limit the extent of the surgical procedures in the therapy of the periodontal disease.

  15. Effect of Intraoperative Corneal Stromal Pocket Irrigation in Small Incision Lenticule Extraction

    Directory of Open Access Journals (Sweden)

    Yu-Chi Liu

    2015-01-01

    Full Text Available This study aimed at evaluating the effect of intraoperative corneal pocket irrigation in small incision lenticule extraction (SMILE and compares it to that in femtosecond laser-assisted in situ keratomileusis (FS-LASIK. Sixteen rabbit eyes underwent a SMILE procedure, with 8 eyes having corneal pocket irrigation, while the other 8 eyes were without irrigation. Another 16 eyes underwent a FS-LASIK procedure for comparison, with 8 eyes having flap irrigation, while the other 8 eyes were without irrigation. The results showed that the changes in the total corneal thickness, anterior and posterior lamellar thickness, measured by the anterior segment optical coherence tomography, were comparable between the SMILE with and without irrigation groups, suggesting that the irrigation did not lead to significant changes in the corneal thickness. However, at postoperative 8 hours, in vivo confocal microscopy showed that the interface reflectivity in the SMILE with irrigation group was significantly higher than that in other three groups. The presence of interface fluid was further confirmed by the identification of fluid pockets with undulated collagen shown on histological section in the post-SMILE with irrigation eyes. Our findings might contribute to the occurrence of post-SMILE delayed immediate visual quality recovery and further clinical study is required.

  16. Mutations in the CRE pocket of bacterial RNA polymerase affect multiple steps of transcription.

    Science.gov (United States)

    Petushkov, Ivan; Pupov, Danil; Bass, Irina; Kulbachinskiy, Andrey

    2015-07-13

    During transcription, the catalytic core of RNA polymerase (RNAP) must interact with the DNA template with low-sequence specificity to ensure efficient enzyme translocation and RNA extension. Unexpectedly, recent structural studies of bacterial promoter complexes revealed specific interactions between the nontemplate DNA strand at the downstream edge of the transcription bubble (CRE, core recognition element) and a protein pocket formed by core RNAP (CRE pocket). We investigated the roles of these interactions in transcription by analyzing point amino acid substitutions and deletions in Escherichia coli RNAP. The mutations affected multiple steps of transcription, including promoter recognition, RNA elongation and termination. In particular, we showed that interactions of the CRE pocket with a nontemplate guanine immediately downstream of the active center stimulate RNA-hairpin-dependent transcription pausing but not other types of pausing. Thus, conformational changes of the elongation complex induced by nascent RNA can modulate CRE effects on transcription. The results highlight the roles of specific core RNAP-DNA interactions at different steps of RNA synthesis and suggest their importance for transcription regulation in various organisms.

  17. Influences of lubricant pocket geometry and working conditions upon micro lubrication mechanisms in upsetting and strip drawing

    DEFF Research Database (Denmark)

    Shimizu, Ichiro; Martins, P. A. F.; Bay, Niels

    2010-01-01

    Micro-lubricant pockets located in the surface of plastically deforming workpieces are recognised to improve the performance of fluid lubrication in a metal-forming process. This work investigates the joint influence of pocket geometry and process working conditions on micro-lubrication mechanisms......, during upsetting and strip drawing, by means of a rigid-viscoplastic finite-element formulation. Special emphasis is placed on the effect of pocket geometry on the build-up of hydrostatic pressure, which is responsible for the onset of micro-lubrication mechanisms. A good agreement is found between...

  18. Pocket PC 2002国内首见惠普Jornada 565详细报道

    Institute of Scientific and Technical Information of China (English)

    洪汉妮; 黄士庭

    2002-01-01

    @@ 微软在催生Windows XP的同时,也不忘对于PDA市场趁胜追出,于2001年10月4日,正式发表新版本Pocket PC操作系统--Pocket PC2002.随着新系统的问世,多家硬件大厂也纷纷表示将支持该操作系统,并且会陆续推出Pocket PC2002机种,其中包括有惠普、康柏、卡西欧以及NEC等等.

  19. Holo- And Apo- Structures of Bacterial Periplasmic Heme Binding Proteins

    Energy Technology Data Exchange (ETDEWEB)

    Ho, W.W.; Li, H.; Eakanunkul, S.; Tong, Y.; Wilks, A.; Guo, M.; Poulos, T.L.

    2009-06-01

    An essential component of heme transport in Gram-negative bacterial pathogens is the periplasmic protein that shuttles heme between outer and inner membranes. We have solved the first crystal structures of two such proteins, ShuT from Shigella dysenteriae and PhuT from Pseudomonas aeruginosa. Both share a common architecture typical of Class III periplasmic binding proteins. The heme binds in a narrow cleft between the N- and C-terminal binding domains and is coordinated by a Tyr residue. A comparison of the heme-free (apo) and -bound (holo) structures indicates little change in structure other than minor alterations in the heme pocket and movement of the Tyr heme ligand from an 'in' position where it can coordinate the heme iron to an 'out' orientation where it points away from the heme pocket. The detailed architecture of the heme pocket is quite different in ShuT and PhuT. Although Arg{sup 228} in PhuT H-bonds with a heme propionate, in ShuT a peptide loop partially takes up the space occupied by Arg{sup 228}, and there is no Lys or Arg H-bonding with the heme propionates. A comparison of PhuT/ShuT with the vitamin B{sub 12}-binding protein BtuF and the hydroxamic-type siderophore-binding protein FhuD, the only two other structurally characterized Class III periplasmic binding proteins, demonstrates that PhuT/ShuT more closely resembles BtuF, which reflects the closer similarity in ligands, heme and B{sub 12}, compared with ligands for FhuD, a peptide siderophore.

  20. NMR-based identification of the phenolic profile of fruits of Lycium barbarum (goji berries). Isolation and structural determination of a novel N-feruloyl tyramine dimer as the most abundant antioxidant polyphenol of goji berries.

    Science.gov (United States)

    Forino, Martino; Tartaglione, Luciana; Dell'Aversano, Carmela; Ciminiello, Patrizia

    2016-03-01

    Biological properties of fruits of Lycium barbarum (goji berries) have been ascribed to their high content of nutrients and phenolics. Comprehensive studies aimed at unambiguously identifying the phenolic components in goji berries are still lacking. In this paper, we report on the isolation and NMR-based identification of the major phenolics in commercially available goji berries. Together with already known phenolics, including caffeic acid, p-coumaric acid, rutin, scopoletin, N-trans-feruloyl tyramine, and N-cis-feruloyl tyramine, an unreported N-feruloyl tyramine dimer was characterized as the most abundant polyphenol isolated from the berries. Usually divalent molecules show enhanced biological activities than their corresponding monomers.

  1. Response of SCP-2L domain of human MFE-2 to ligand removal: binding site closure and burial of peroxisomal targeting signal.

    Science.gov (United States)

    Lensink, M F; Haapalainen, A M; Hiltunen, J K; Glumoff, T; Juffer, A H

    2002-10-11

    In the study of the structure and function relationship of human MFE-2, we have investigated the dynamics of human MFE-2SCP-2L (hSCP-2L) and its response to ligand removal. A comparison was made with homologous rabbit SCP-2. Breathing and a closing motion are found, identifiable with an adjustment in size and a closing off of the binding pocket. Crucial residues for structural integrity have been identified. Particularly mobile areas of the protein are loop 1 that is connecting helices A and C in space, and helix D, next to the entrance of the pocket. In hSCP-2L, the binding pocket gets occupied by Phe93, which is making a tight hydrophobic contact with Trp36. In addition, it is found that the C-terminal peroxisomal targeting signal (PTS1) that is solvent exposed in the complexed structure becomes buried when no ligand is present. Moreover, an anti-correlation exists between burial of PTS1 and the size of the binding pocket. The results are in accordance with plant nsLTPs, where a similar accommodation of binding pocket size was found after ligand binding/removal. Furthermore, the calculations support the suggestion of a ligand-assisted targeting mechanism.

  2. Apolipoprotein M binds oxidized phospholipids and increases the antioxidant effect of HDL

    DEFF Research Database (Denmark)

    Elsøe, Sara; Ahnström, Josefin; Christoffersen, Christina;

    2012-01-01

    Oxidation of LDL plays a key role in the development of atherosclerosis. HDL may, in part, protect against atherosclerosis by inhibiting LDL oxidation. Overexpression of HDL-associated apolipoprotein M (apoM) protects mice against atherosclerosis through a not yet clarified mechanism. Being...... a lipocalin, apoM contains a binding pocket for small lipophilic molecules. Here, we report that apoM likely serves as an antioxidant in HDL by binding oxidized phospholipids, thus enhancing the antioxidant potential of HDL....

  3. Out-Of-Pocket Expenditure on Institutional Delivery in Rural Lucknow

    Directory of Open Access Journals (Sweden)

    Mukesh Shukla

    2015-06-01

    Full Text Available AbstractIntroduction: Promotion of reproductive health through institutional delivery has been adopted by government as a strategy for reducing maternal mortality rate but still about half of the deliveries have been conducted at home. Cost barrier is one of the major cause for preferring home delivery instead of institutional delivery. Not only the direct costs responsible for low institutional delivery but also indirect costs too accountable for less number of institutional births in the country. Aims & Objectives: To estimate the out of pocket expenditure incurred by households during delivery and its determinants. Materials and methods: A community based cross sectional study was conducted during which a total 272 households having women who had recently delivered in government institutions were interviewed. Result: The mean out of pocket expenditure was found to be Rs. 1406.04 ± 103.27 including spending’s on drugs, travel, pathological tests and unofficial payments. Low socioeconomic class, residence outside the catchment area of delivery point, tertiary and secondary health care facilities as place of delivery and low literacy status of head of the family below high school  were found to be significantly associated with out of pocket expenditure bivariate analysis (p<0.05. On multivariate analysis low socioeconomic (OR 22.40; 95% CI 9.44-53.15; p = 0.01   and residence (OR 13.07; 95% CI (1.58-116.55; p = 0.03  outside the catchment area of delivery point were found to be independent predictors of catastrophic out of pocket expenditure during delivery. Conclusions: Although government has been running lot of schemes for availing free of cost health services but still one has to pay from their pocket as medical expenses. In order to bear these expenses, they have to borrow money, sell their assets and securities due to which households suffer a lot. In the present study, unofficial payment was found prevalent in public institutions

  4. New Insights into Cooperative Binding of Homeodomain Transcription Factors PREP1 and PBX1 to DNA

    Science.gov (United States)

    Zucchelli, Chiara; Ferrari, Elena; Blasi, Francesco; Musco, Giovanna; Bruckmann, Chiara

    2017-01-01

    PREP1 and PBX1 are homeodomain (HD) transcription factors that play crucial roles in embryonic development. Here, we present the first biophysical characterization of a PREP1 HD, and the NMR spectroscopic study of its DNA binding pocket. The data show that residues flanking the HD participate in DNA binding. The kinetic parameters for DNA binding of individual PREP1 and PBX1 HDs, and of their combination, show that isolated PREP1 and PBX1 HDs bind to DNA in a cooperative manner. A novel PREP1 motif, flanking the HD at the C-terminus, is required for cooperativity. PMID:28094776

  5. An in silico analysis of the binding modes and binding affinities of small molecule modulators of PDZ-peptide interactions.

    Directory of Open Access Journals (Sweden)

    Garima Tiwari

    Full Text Available Inhibitors of PDZ-peptide interactions have important implications in a variety of biological processes including treatment of cancer and Parkinson's disease. Even though experimental studies have reported characterization of peptidomimetic inhibitors of PDZ-peptide interactions, the binding modes for most of them have not been characterized by structural studies. In this study we have attempted to understand the structural basis of the small molecule-PDZ interactions by in silico analysis of the binding modes and binding affinities of a set of 38 small molecules with known K(i or K(d values for PDZ2 and PDZ3 domains of PSD-95 protein. These two PDZ domains show differential selectivity for these compounds despite having a high degree of sequence similarity and almost identical peptide binding pockets. Optimum binding modes for these ligands for PDZ2 and PDZ3 domains were identified by using a novel combination of semi-flexible docking and explicit solvent molecular dynamics (MD simulations. Analysis of the binding modes revealed most of the peptidomimectic ligands which had high K(i or K(d moved away from the peptide binding pocket, while ligands with high binding affinities remained in the peptide binding pocket. The differential specificities of the PDZ2 and PDZ3 domains primarily arise from differences in the conformation of the loop connecting βB and βC strands, because this loop interacts with the N-terminal chemical moieties of the ligands. We have also computed the MM/PBSA binding free energy values for these 38 compounds with both the PDZ domains from multiple 5 ns MD trajectories on each complex i.e. a total of 228 MD trajectories of 5 ns length each. Interestingly, computational binding free energies show good agreement with experimental binding free energies with a correlation coefficient of approximately 0.6. Thus our study demonstrates that combined use of docking and MD simulations can help in identification of potent inhibitors

  6. Use of an active fixation lead and a subpectoral pacemaker pocket may not avoid Twiddler′s syndrome

    Directory of Open Access Journals (Sweden)

    Floris E A Udink ten Cate

    2012-01-01

    Full Text Available Manipulation of a pacemaker with consequent malfunction of the device has been called Twiddler′s syndrome. Use of active-fixation leads and subpectoral pacemaker pockets has been considered to help in avoiding this problem. We describe a child in whom twiddling was not prevented despite implantation of a lumenless atrial lead and insertion of the pacemaker generator in a subpectoral pocket.

  7. The sweet quartet: Binding of fucose to the norovirus capsid.

    Science.gov (United States)

    Koromyslova, Anna D; Leuthold, Mila M; Bowler, Matthew W; Hansman, Grant S

    2015-09-01

    Human noroviruses bind histo-blood group antigens (HBGAs) and this interaction is thought to be important for an infection. We identified two additional fucose-binding pockets (termed fucose-3/4 sites) on a genogroup II human (GII.10) norovirus-protruding (P) dimer using X-ray crystallography. Fucose-3/4 sites were located between two previously determined HBGA binding pockets (termed fucose-1/2 sites). We found that four fucose molecules were capable of binding altogether at fucose-1/2/3/4 sites on the P dimer, though the fucose molecules bound in a dose-dependent and step-wise manner. We also showed that HBGA B-trisaccharide molecules bound in a similar way at the fucose-1/2 sites. Interestingly, we discovered that the monomers of the P dimer were asymmetrical in an unliganded state and when a single B-trisaccharide molecule bound, but were symmetrical when two B-trisaccharide molecules bound. We postulate that the symmetrical dimers might favor HBGA binding interactions at fucose-1/2 sites.

  8. Formyl peptide receptor chimeras define domains involved in ligand binding.

    Science.gov (United States)

    Perez, H D; Holmes, R; Vilander, L R; Adams, R R; Manzana, W; Jolley, D; Andrews, W H

    1993-02-05

    We have begun to study the structural requirements for the binding of formyl peptides to their specific receptors. As an initial approach, we constructed C5a-formyl peptide receptor chimeras. Unique (and identical) restriction sites were introduced within the transmembrane domains of these receptors that allowed for the exchange of specific areas. Four types of chimeric receptors were generated. 1) The C5a receptor was progressively substituted by the formyl peptide receptor. 2) The formyl peptide receptor was progressively substituted by the C5a receptor. 3) Specific domains of the C5a receptor were substituted by the corresponding domain of the formyl peptide receptor. 4) Specific domains of the formyl peptide receptor were replaced by the same corresponding domain of the C5a receptor. Wild type and chimeric receptors were transfected into COS 7 cells and their ability to bind formyl peptide determined, taking into account efficiency of transfection and expression of chimeric protein. Based on these results, a ligand binding model is presented in which the second, third, and fourth extracellular (and/or their transmembrane) domains together with the first transmembrane domain form a ligand binding pocket for formyl peptides. It is proposed that the amino-terminal domain plays a role by presumably providing a "lid" to the pocket. The carboxyl-terminal cytoplasmic tail appears to modulate ligand binding by regulating receptor affinity.

  9. Molecular Mechanisms of Pharmaceutical Drug Binding into Calsequestrin

    Directory of Open Access Journals (Sweden)

    ChulHee Kang

    2012-11-01

    Full Text Available Calsequestrin (CASQ is a major Ca2+-storage/buffer protein present in the sarcoplasmic reticulum of both skeletal (CASQ1 and cardiac (CASQ2 muscles. CASQ has significant affinity for a number of pharmaceutical drugs with known muscular toxicities. Our approach, with in silico molecular docking, single crystal X-ray diffraction, and isothermal titration calorimetry (ITC, identified three distinct binding pockets on the surface of CASQ2, which overlap with 2-methyl-2,4-pentanediol (MPD binding sites observed in the crystal structure. Those three receptor sites based on canine CASQ1 crystal structure gave a high correlation (R2 = 0.80 to our ITC data. Daunomycin, doxorubicin, thioridazine, and trifluoperazine showed strong affinity to the S1 site, which is a central cavity formed between three domains of CASQ2. Some of the moderate-affinity drugs and some high-affinity drugs like amlodipine and verapamil displayed their binding into S2 sites, which are the thioredoxin-like fold present in each CASQ domain. Docking predictions combined with dissociation constants imply that presence of large aromatic cores and less flexible functional groups determines the strength of binding affinity to CASQ. In addition, the predicted binding pockets for both caffeine and epigallocatechin overlapped with the S1 and S2 sites, suggesting competitive inhibition by these natural compounds as a plausible explanation for their antagonistic effects on cardiotoxic side effects.

  10. LAMP using a disposable pocket warmer for anthrax detection, a highly mobile and reliable method for anti-bioterrorism.

    Science.gov (United States)

    Hatano, Ben; Maki, Takayuki; Obara, Takeyuki; Fukumoto, Hitomi; Hagisawa, Kohsuke; Matsushita, Yoshitaro; Okutani, Akiko; Bazartseren, Boldbaastar; Inoue, Satoshi; Sata, Tetsutaro; Katano, Harutaka

    2010-01-01

    A quick, reliable detection system is necessary to deal with bioterrorism. Loop-mediated isothermal amplification (LAMP) is a DNA amplification method that can amplify specific DNA fragments in isothermal conditions. We developed a new highly mobile and practical LAMP anthrax detection system that uses a disposable pocket warmer without the need for electricity (pocket-warmer LAMP). In our tests, the detection limit of the pocket-warmer LAMP was 1,000 copies of Bacillus anthracis pag and capB gene fragments per tube. The pocket-warmer LAMP also detected B. anthracis genes from DNA extracted from 0.1 volume of a B. anthracis colony. The lower detection limit of the pocket-warmer LAMP was not significantly different from that of a conventional LAMP using a heat block, and was not changed under cold (4 degrees C) or warm (37 degrees C) conditions in a Styrofoam box. The pocket-warmer LAMP could be useful against bioterrorism, and as a sensitive, reliable detection tool in areas with undependable electricity infrastructures.

  11. Incidence of pocket hematoma after electrophysiological device placement:dual antiplatelet therapy versus low-molecular-weight heparin regimen

    Institute of Scientific and Technical Information of China (English)

    Yan CHEN; Xin-Cun YANG; Kang MENG; Yun-Tao LI; Ming-Dong GAO; Ze-Chun ZENG; Jin-Rong ZHANG; Hong-Liang CONG; Yin LIU; Ru ZHAO; Le-Feng WANG

    2014-01-01

    Background Given the increasing number of patients who require dual antiplatelet (DAP) therapy and electrophysiological device (EPD) placement, perioperative antiplatelet management is a current challenge. In this study, we investigated the incidence of pocket hema-toma formation after EPD placement in patients undergoing DAP therapy or an alternative low-molecular-weight heparin (LMWH) regimen. Methods This clinical observational study was performed from July 2010 to July 2012. In total, 171 patients were enrolled in the analysis after meeting the inclusion criteria. These patients were divided into two groups: 86 patients were treated with DAP therapy at the time of device implantation, and the DAP therapy was discontinued for 5 to 7 days and replaced with enoxaparin before device implantation in the other 85 patients. Adenosine phosphate (ADP)-mediated platelet aggregation and arachidonic acid-induced platelet aggregation were tested preoperatively. We compared the incidence of pocket hematoma between the two groups and the association of pocket hematoma develop-ment with ADP-mediated platelet aggregation and arachidonic acid-induced platelet aggregation.Results The incidence of pocket hema-toma in the patients who continued DAP was lower than that in the patients who replaced the dual antiplatelet regimen with LMWH (3.49%vs. 16.47%, respectively;X2 = 6.66,P < 0.01). Among the patients who continued DAP therapies, the rate of ADP-mediated platelet aggre-gation inhibition in patients with pocket hematomas was higher than that in patients without pocket hematomas. None of the patients under-going DAP or enoxaparin therapy developed pocket infection, thromboembolic events, or other serious complications. Multiple logistic re-gression analysis revealed that LMWH therapy was an independent risk factor for the development of pocket hematoma (RR = 0.054, 95%CI = 0.012-0.251). Furthermore, patients undergoing LMWH therapy were 5.1-fold more likely to develop pocket

  12. [Species composition of anaerobic microflora in parodontal pocket depending upon disease stage].

    Science.gov (United States)

    Zyrianova, N V; Grigor'ian, A S; Grudianov, A I; Frolova, O A; Shil'nikova, I I; Kobozev, M I

    2009-01-01

    With the help of polymerase chain reaction (PCR) the dynamic of species composition of anaerobic microflora in cases of generalized parodontitis was established. It was detected that disease severity increase was followed by the increase of the number of anaerobic microflora species in parodontal pocket; at that it was impossible to connect the presence of some determined type of microorganism with the inflammatory parodontal process intensity. It was shown that proteins fimbrilin and gingipain were not the only parodontitis pathogenic factors although the first one (fimbrilin) could be connected with aggressive disease flow. The suggested PCR scheme could be useful for early disease stage diagnostic and substantiation of antimicrobial therapy method selection.

  13. Evaluation of centrifugation parameters for density gradient experiments by means of a programmable pocket calculator.

    Science.gov (United States)

    Kreutzfeldt, C

    1980-10-01

    A calculation program is proposed suitable for programmable pocket calculators (e.g. HP series) to estimate s20,w f omega2 dt values from density gradient centrifugation data. The program can be applied to linear or exponential density gradients prepared from sucrose or glycerol solutions spun in zonal rotors or swinging bucket rotors. A wide solute concentration range and temperature range is accounted for. Constants for empirical density calculation of glycerol and sucrose solutions concentrated in % (w/v) are estimated. Experimental verification of the program was carried out.

  14. Improved quality control of silicon wafers using novel off-line air pocket image analysis

    Science.gov (United States)

    Valley, John F.; Sanna, M. Cristina

    2014-08-01

    Air pockets (APK) occur randomly in Czochralski (Cz) grown silicon (Si) crystals and may become included in wafers after slicing and polishing. Previously the only APK of interest were those that intersected the front surface of the wafer and therefore directly impacted device yield. However mobile and other electronics have placed new demands on wafers to be internally APK-free for reasons of thermal management and packaging yield. We present a novel, recently patented, APK image processing technique and demonstrate the use of that technique, off-line, to improve quality control during wafer manufacturing.

  15. vi and Vim Editors Pocket Reference Support for every text editing task

    CERN Document Server

    Robbins, Arnold

    2011-01-01

    Many Unix, Linux, and Mac OS X geeks enjoy using the powerful, platform-agnostic text editors vi and Vim, but there are far too many commands for anyone to remember. Author Arnold Robbins has chosen the most valuable commands for vi, Vim, and vi's main clones-vile, elvis, and nvi-and packed them into this easy-to-browse pocket reference. You'll find commands for all kinds of editing tasks, such as programming, modifying system files, and writing and marking up articles. This second edition includes: Command-line optionsvi commands and set optionsInput mode shortcutsSubstitution and regular e

  16. Structural Dynamics of the Cereblon Ligand Binding Domain

    Science.gov (United States)

    Hartmann, Marcus D.; Boichenko, Iuliia; Coles, Murray; Lupas, Andrei N.; Hernandez Alvarez, Birte

    2015-01-01

    Cereblon, a primary target of thalidomide and its derivatives, has been characterized structurally from both bacteria and animals. Especially well studied is the thalidomide binding domain, CULT, which shows an invariable structure across different organisms and in complex with different ligands. Here, based on a series of crystal structures of a bacterial representative, we reveal the conformational flexibility and structural dynamics of this domain. In particular, we follow the unfolding of large fractions of the domain upon release of thalidomide in the crystalline state. Our results imply that a third of the domain, including the thalidomide binding pocket, only folds upon ligand binding. We further characterize the structural effect of the C-terminal truncation resulting from the mental-retardation linked R419X nonsense mutation in vitro and offer a mechanistic hypothesis for its irresponsiveness to thalidomide. At 1.2Å resolution, our data provide a view of thalidomide binding at atomic resolution. PMID:26024445

  17. Structural dynamics of the cereblon ligand binding domain.

    Directory of Open Access Journals (Sweden)

    Marcus D Hartmann

    Full Text Available Cereblon, a primary target of thalidomide and its derivatives, has been characterized structurally from both bacteria and animals. Especially well studied is the thalidomide binding domain, CULT, which shows an invariable structure across different organisms and in complex with different ligands. Here, based on a series of crystal structures of a bacterial representative, we reveal the conformational flexibility and structural dynamics of this domain. In particular, we follow the unfolding of large fractions of the domain upon release of thalidomide in the crystalline state. Our results imply that a third of the domain, including the thalidomide binding pocket, only folds upon ligand binding. We further characterize the structural effect of the C-terminal truncation resulting from the mental-retardation linked R419X nonsense mutation in vitro and offer a mechanistic hypothesis for its irresponsiveness to thalidomide. At 1.2Å resolution, our data provide a view of thalidomide binding at atomic resolution.

  18. Crystal structure of the adenosine A 2A receptor bound to an antagonist reveals a potential allosteric pocket

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Bingfa; Bachhawat, Priti; Chu, Matthew Ling-Hon; Wood, Martyn; Ceska, Tom; Sands, Zara A.; Mercier, Joel; Lebon, Florence; Kobilka, Tong Sun; Kobilka, Brian K.

    2017-02-06

    The adenosine A2A receptor (A2AR) has long been implicated in cardiovascular disorders. As more selective A2AR ligands are being identified, its roles in other disorders, such as Parkinson’s disease, are starting to emerge, and A2AR antagonists are important drug candidates for nondopaminergic anti-Parkinson treatment. Here we report the crystal structure of A2A receptor bound to compound 1 (Cmpd-1), a novel A2AR/N-methyl D-aspartate receptor subtype 2B (NR2B) dual antagonist and potential anti-Parkinson candidate compound, at 3.5 Å resolution. The A2A receptor with a cytochrome b562-RIL (BRIL) fusion (A2AR–BRIL) in the intracellular loop 3 (ICL3) was crystallized in detergent micelles using vapor-phase diffusion. Whereas A2AR–BRIL bound to the antagonist ZM241385 has previously been crystallized in lipidic cubic phase (LCP), structural differences in the Cmpd-1–bound A2AR–BRIL prevented formation of the lattice observed with the ZM241385–bound receptor. The crystals grew with a type II crystal lattice in contrast to the typical type I packing seen from membrane protein structures crystallized in LCP. Cmpd-1 binds in a position that overlaps with the native ligand adenosine, but its methoxyphenyl group extends to an exosite not previously observed in other A2AR structures. Structural analysis revealed that Cmpd-1 binding results in the unique conformations of two tyrosine residues, Tyr91.35 and Tyr2717.36, which are critical for the formation of the exosite. The structure reveals insights into antagonist binding that are not observed in other A2AR structures, highlighting flexibility in the binding pocket that may facilitate the development of A2AR-selective compounds for the treatment of Parkinson’s disease.

  19. Classification of a Haemophilus influenzae ABC transporter HI1470/71 through its cognate molybdate periplasmic binding protein, MolA

    OpenAIRE

    Tirado-Lee, Leidamarie; Lee, Allen; Rees, Douglas C.; Pinkett, Heather W

    2011-01-01

    molA(HI1472) from H. influenzae encodes a periplasmic binding protein (PBP) that delivers substrate to the ABC transporter MolB2C2 (formerly HI1470/71). The structures of MolA with molybdate and tungstate in the binding pocket were solved to 1.6 and 1.7-Å resolution, respectively. The MolA binding protein binds molybdate and tungstate but not other oxyanions such as sulfate and phosphate, making it the first class III molybdate binding protein structurally solved. The ~100 μM binding affinity...

  20. Single reconstructed Fermi surface pocket in an underdoped single-layer cuprate superconductor.

    Science.gov (United States)

    Chan, M K; Harrison, N; McDonald, R D; Ramshaw, B J; Modic, K A; Barišić, N; Greven, M

    2016-01-01

    The observation of a reconstructed Fermi surface via quantum oscillations in hole-doped cuprates opened a path towards identifying broken symmetry states in the pseudogap regime. However, such an identification has remained inconclusive due to the multi-frequency quantum oscillation spectra and complications accounting for bilayer effects in most studies. We overcome these impediments with high-resolution measurements on the structurally simpler cuprate HgBa2CuO4+δ (Hg1201), which features one CuO2 plane per primitive unit cell. We find only a single oscillatory component with no signatures of magnetic breakdown tunnelling to additional orbits. Therefore, the Fermi surface comprises a single quasi-two-dimensional pocket. Quantitative modelling of these results indicates that a biaxial charge density wave within each CuO2 plane is responsible for the reconstruction and rules out criss-crossed charge stripes between layers as a viable alternative in Hg1201. Lastly, we determine that the characteristic gap between reconstructed pockets is a significant fraction of the pseudogap energy.

  1. Focused Cardiac Ultrasound Using a Pocket-Size Device in the Emergency Room

    Energy Technology Data Exchange (ETDEWEB)

    Mancuso, Frederico José Neves, E-mail: frederico.mancuso@grupofleury.com.br [Disciplina de Cardiologia - Escola Paulista de Medicina - Universidade Federal de São Paulo (Unifesp), São Paulo, SP (Brazil); Disciplina de Medicina de Urgência - Escola Paulista de Medicina - Universidade Federal de São Paulo (Unifesp), São Paulo, SP (Brazil); Siqueira, Vicente Nicoliello; Moisés, Valdir Ambrósio [Disciplina de Cardiologia - Escola Paulista de Medicina - Universidade Federal de São Paulo (Unifesp), São Paulo, SP (Brazil); Gois, Aécio Flavio Teixeira [Disciplina de Medicina de Urgência - Escola Paulista de Medicina - Universidade Federal de São Paulo (Unifesp), São Paulo, SP (Brazil); Paola, Angelo Amato Vincenzo de; Carvalho, Antonio Carlos Camargo; Campos, Orlando [Disciplina de Cardiologia - Escola Paulista de Medicina - Universidade Federal de São Paulo (Unifesp), São Paulo, SP (Brazil)

    2014-12-15

    Cardiovascular urgencies are frequent reasons for seeking medical care. Prompt and accurate medical diagnosis is critical to reduce the morbidity and mortality of these conditions. To evaluate the use of a pocket-size echocardiography in addition to clinical history and physical exam in a tertiary medical emergency care. One hundred adult patients without known cardiac or lung diseases who sought emergency care with cardiac complaints were included. Patients with ischemic changes in the electrocardiography or fever were excluded. A focused echocardiography with GE Vscan equipment was performed after the initial evaluation in the emergency room. Cardiac chambers dimensions, left and right ventricular systolic function, intracardiac flows with color, pericardium, and aorta were evaluated. The mean age was 61 ± 17 years old. The patient complaint was chest pain in 51 patients, dyspnea in 32 patients, arrhythmia to evaluate the left ventricular function in ten patients, hypotension/dizziness in five patients and edema in one patient. In 28 patients, the focused echocardiography allowed to confirm the initial diagnosis: 19 patients with heart failure, five with acute coronary syndrome, two with pulmonary embolism and two patients with cardiac tamponade. In 17 patients, the echocardiography changed the diagnosis: ten with suspicious of heart failure, two with pulmonary embolism suspicious, two with hypotension without cause, one suspicious of acute coronary syndrome, one of cardiac tamponade and one of aortic dissection. The focused echocardiography with pocket-size equipment in the emergency care may allow a prompt diagnosis and, consequently, an earlier initiation of the therapy.

  2. Multitemporal Monitoring of Plant Area Index in the Valencia Rice District with PocketLAI

    Directory of Open Access Journals (Sweden)

    Manuel Campos-Taberner

    2016-03-01

    Full Text Available Leaf area index (LAI is a key biophysical parameter used to determine foliage cover and crop growth in environmental studies in order to assess crop yield. Frequently, plant canopy analyzers (LAI-2000 and digital cameras for hemispherical photography (DHP are used for indirect effective plant area index (PAIeff estimates. Nevertheless, these instruments are expensive and have the disadvantages of low portability and maintenance. Recently, a smartphone app called PocketLAI was presented and tested for acquiring PAIeff measurements. It was used during an entire rice season for indirect PAIeff estimations and for deriving reference high-resolution PAIeff maps. Ground PAIeff values acquired with PocketLAI, LAI-2000, and DHP were well correlated (R2 = 0.95, RMSE = 0.21 m2/m2 for Licor-2000, and R2 = 0.94, RMSE = 0.6 m2/m2 for DHP. Complementary data such as phenology and leaf chlorophyll content were acquired to complement seasonal rice plant information provided by PAIeff. High-resolution PAIeff maps, which can be used for the validation of remote sensing products, have been derived using a global transfer function (TF made of several measuring dates and their associated satellite radiances.

  3. Compare local pocket and global protein structure models by small structure patterns

    KAUST Repository

    Cui, Xuefeng

    2015-09-09

    Researchers proposed several criteria to assess the quality of predicted protein structures because it is one of the essential tasks in the Critical Assessment of Techniques for Protein Structure Prediction (CASP) competitions. Popular criteria include root mean squared deviation (RMSD), MaxSub score, TM-score, GDT-TS and GDT-HA scores. All these criteria require calculation of rigid transformations to superimpose the the predicted protein structure to the native protein structure. Yet, how to obtain the rigid transformations is unknown or with high time complexity, and, hence, heuristic algorithms were proposed. In this work, we carefully design various small structure patterns, including the ones specifically tuned for local pockets. Such structure patterns are biologically meaningful, and address the issue of relying on a sufficient number of backbone residue fragments for existing methods. We sample the rigid transformations from these small structure patterns; and the optimal superpositions yield by these small structures are refined and reported. As a result, among 11; 669 pairs of predicted and native local protein pocket models from the CASP10 dataset, the GDT-TS scores calculated by our method are significantly higher than those calculated by LGA. Moreover, our program is computationally much more efficient. Source codes and executables are publicly available at http://www.cbrc.kaust.edu.sa/prosta/

  4. Utilizing Wireless PocketPC's in Earth System Science Lectures to Expand Discourse

    Science.gov (United States)

    Samson, P. J.; van der Pluijm, B.

    2004-12-01

    Introductory science teaching, including otherwise engaging topics such as climate change and natural hazards, traditionally relies on static textbooks and/or course packs, and presentation is often delivered as a monologue in front of a passive audience. Add to this the advent of extensive lecture notes on the Internet and the students are left with little incentive to attend class, much less participate. Clearly this model does not provide much opportunity for students to critically think through the arguments being developed. In order to address this issue, we are experimenting with the use of interactive spatial concept challenges utilizing wireless PocketPC computers in Earth Systems classes at the University of Michigan. The tools being developed have the goal of involving students in their own learning during lecture and focusing their attention on underlying concepts. Following Mazur (1997) students respond to spatial questions offered through the PocketPC and formulate their own answers; followed by an in-class discussion in small groups, attempting to reach consensus on the best answer. Successful implementation of this approach in climate change offers new opportunities to engage students in discourse and improved learning through peer and interactive instruction. Eric Mazur, 1997: Peer Instruction: A User's Manual, Prentice-Hall, Upper Saddle River, NJ.

  5. Pocket wheel engine as an internal combustion engine. Taschenscheibenmotor als Verbrennungsmotor

    Energy Technology Data Exchange (ETDEWEB)

    Hellmuth, H.J.

    1990-09-27

    All spark ignition and diesel engines have large oscillating masses, a high frictional resistance and do not run vibration-free. Wankel engines effect only a partial combustion due to the unfavourable shape of the combustion chamber: the expansive force is converted into rotating movement via mechanical deflection. The new internal combustion engine is to have a low weight, require little space and run vibration-free with a high efficiency. The expansive force is to be converted directly into rotating movement. A screw compressor (3) suctions and compresses an air-fuel mixture. The combustion chamber is charged periodically with the compressed mixture via a slit side shaft (6). The slit side shaft (6) closes the combustion chamber (7) at the rear. The mixture is ignited. The flap (8) opens the combustion chamber (7) at the front and the exanding gas sets the pocket wheel connected to the main shaft (15) rotating. The compressor (3) and the slit side shaft (6) are driven directly by the main shaft (15). The pocket wheel engine can be employed in all fields where internal combustion engines have been used until now.

  6. TGF-β Signaling Is Associated with Endocytosis at the Pocket Region of the Primary Cilium

    Directory of Open Access Journals (Sweden)

    Christian Alexandro Clement

    2013-06-01

    Full Text Available Transforming growth factor β (TGF-β signaling is regulated by clathrin-dependent endocytosis (CDE for the control of cellular processes during development and in tissue homeostasis. The primary cilium coordinates several signaling pathways, and the pocket surrounding the base and proximal part of the cilium is a site for CDE. We report here that TGF-β receptors localize to the ciliary tip and endocytic vesicles at the ciliary base in fibroblasts and that TGF-β stimulation increases receptor localization and activation of SMAD2/3 and ERK1/2 at the ciliary base. Inhibition of CDE reduced TGF-β-mediated signaling at the cilium, and TGF-β signaling and CDE activity are reduced at stunted primary cilia in Tg737orpk fibroblasts. Similarly, TGF-β signaling during cardiomyogenesis correlated with accumulation of TGF-β receptors and activation of SMAD2/3 at the ciliary base. Our results indicate that the primary cilium regulates TGF-β signaling and that the ciliary pocket is a compartment for CDE-dependent regulation of signal transduction.

  7. Double gate graphene nanoribbon field effect transistor with single halo pocket in channel region

    Science.gov (United States)

    Naderi, Ali

    2016-01-01

    A new structure for graphene nanoribbon field-effect transistors (GNRFETs) is proposed and investigated using quantum simulation with a nonequilibrium Green's function (NEGF) method. Tunneling leakage current and ambipolar conduction are known effects for MOSFET-like GNRFETs. To minimize these issues a novel structure with a simple change of the GNRFETs by using single halo pocket in the intrinsic channel region, "Single Halo GNRFET (SH-GNRFET)", is proposed. An appropriate halo pocket at source side of channel is used to modify potential distribution of the gate region and weaken band to band tunneling (BTBT). In devices with materials like Si in channel region, doping type of halo and source/drain regions are different. But, here, due to the smaller bandgap of graphene, the mentioned doping types should be the same to reduce BTBT. Simulations have shown that in comparison with conventional GNRFET (C-GNRFET), an SH-GNRFET with appropriately halo doping results in a larger ON current (Ion), smaller OFF current (Ioff), a larger ON-OFF current ratio (Ion/Ioff), superior ambipolar characteristics, a reduced power-delay product and lower delay time.

  8. Studies on development of controlled delivery of combination drug(s to periodontal pocket

    Directory of Open Access Journals (Sweden)

    Tiwari Gaurav

    2010-01-01

    Full Text Available Aim: The aim of this study to develop the controlled delivery of combination drug(s to periodontal pocket. Materials and Methods: In the present investigation mucoadhesive gel formulations were prepared using carboxy methylcellulose (CMC, methylcellulose (MC, hydroxyethylcellulose (HEC, polyvinylpirrolidone (PVP, polycarbophil (PC, and poloxamer. Each formulation was characterized in terms of polarizing light microscopy, gelation, gel melting, hardness, compressibility, adhesiveness, cohesiveness, syringeability, adhesion to a mucin disk, rheological studies, drug release, and antibacterial activities. Addition of CMC and PVP to the gel favored hexagonal phase formation. The gelation temperature was decreased linearly with an increasing concentration of drug(s, whereas, the melting temperature increased with the concentration of drug(s. Increasing the concentrations of each polymeric component significantly increased formulation hardness, compressibility, adhesiveness, mucoadhesion, and syringeability, yet a decreased cohesiveness. Increased time of contact between the formulation and mucin significantly increased the required force of detachment. Drug release from all formulations was non-diffusion controlled and significantly decreased as the concentration of the polymer was increased, due to the concomitant increased viscosity of the formulations and the swelling kinetics of PC, following contact with the dissolution fluid. Result: Antibacterial studies revealed that a gel with 30% HEC had a growth inhibition zone on agar with all three strains. Conclusion: Formulations containing HEC exhibited superior physical characteristics for improved drug delivery to the periodontal pocket and are now the subject of long-term clinical investigations.

  9. Radial-firing optical fiber tip containing conical-shaped air-pocket for biomedical applications.

    Science.gov (United States)

    Lee, Seung Ho; Ryu, Yong-Tak; Son, Dong Hoon; Jeong, Seongmook; Kim, Youngwoong; Ju, Seongmin; Kim, Bok Hyeon; Han, Won-Taek

    2015-08-10

    We report a novel radial-firing optical fiber tip containing a conical-shaped air-pocket fabricated by deforming a hollow optical fiber using electric arc-discharge process. The hollow optical fiber was fusion spliced with a conventional optical fiber, simultaneously deforming into the intagliated conical-shaped region along the longitudinal fiber-axis of the fiber due to the gradual collapse of the cavity of the hollow optical fiber. Then the distal-end of the hollow optical fiber was sealed by the additional arc-discharge in order to obstruct the inflow of an external bio-substance or liquid to the inner air surface during the surgical operations, resulting in the formation of encased air-pocket in the silica glass fiber. Due to the total internal reflection of the laser beam at the conical-shaped air surface, the laser beam (λ = 632.8 nm) was deflected to the circumferential direction up to 87 degree with respect to the fiber-axis.

  10. Sequence similarity between the erythrocyte binding domain 1 of the Plasmodium vivax Duffy binding protein and the V3 loop of HIV-1 strain MN reveals binding residues for the Duffy Antigen Receptor for Chemokines

    Directory of Open Access Journals (Sweden)

    Garry Robert F

    2011-01-01

    Full Text Available Abstract Background The surface glycoprotein (SU, gp120 of the human immunodeficiency virus (HIV must bind to a chemokine receptor, CCR5 or CXCR4, to invade CD4+ cells. Plasmodium vivax uses the Duffy Binding Protein (DBP to bind the Duffy Antigen Receptor for Chemokines (DARC and invade reticulocytes. Results Variable loop 3 (V3 of HIV-1 SU and domain 1 of the Plasmodium vivax DBP share a sequence similarity. The site of amino acid sequence similarity was necessary, but not sufficient, for DARC binding and contained a consensus heparin binding site essential for DARC binding. Both HIV-1 and P. vivax can be blocked from binding to their chemokine receptors by the chemokine, RANTES and its analog AOP-RANTES. Site directed mutagenesis of the heparin binding motif in members of the DBP family, the P. knowlesi alpha, beta and gamma proteins abrogated their binding to erythrocytes. Positively charged residues within domain 1 are required for binding of P. vivax and P. knowlesi erythrocyte binding proteins. Conclusion A heparin binding site motif in members of the DBP family may form part of a conserved erythrocyte receptor binding pocket.

  11. 5-(Piperidin-4-yl)-3-Hydroxypyrazole: A Novel Scaffold for Probing the Orthosteric γ-Aminobutyric Acid Type A Receptor Binding Site

    DEFF Research Database (Denmark)

    Krall, Jacob; Kongstad, Kenneth Thermann; Nielsen, Birgitte

    2014-01-01

    indicate that the N1-substituted analogues of 4-PIOL and 4-PHP, 2 a–k, and previously reported 3-substituted 4-PHP analogues share a common binding mode to the orthosteric binding site in the receptor. Interestingly, the core scaffold of the N2-substituted analogues of 4-PIOL and 4-PHP, 3 b......–k, are suggested to flip 180° thereby adapting to the binding pocket and addressing a cavity situated above the core scaffold....

  12. Comparative binding energy COMBINE analysis for understanding the binding determinants of type II dehydroquinase inhibitors.

    Science.gov (United States)

    Peón, Antonio; Coderch, Claire; Gago, Federico; González-Bello, Concepción

    2013-05-01

    Herein we report comparative binding energy (COMBINE) analyses to derive quantitative structure-activity relationship (QSAR) models that help rationalize the determinants of binding affinity for inhibitors of type II dehydroquinase (DHQ2), the third enzyme of the shikimic acid pathway. Independent COMBINE models were derived for Helicobacter pylori and Mycobacterium tuberculosis DHQ2, which is an essential enzyme in both these pathogenic bacteria that has no counterpart in human cells. These studies quantify the importance of the hydrogen bonding interactions between the ligands and the water molecule involved in the DHQ2 reaction mechanism. They also highlight important differences in the ligand interactions with the interface pocket close to the active site that could provide guides for future inhibitor design.

  13. How the ACA's Health Insurance Expansions Have Affected Out-of-Pocket Cost-Sharing and Spending on Premiums.

    Science.gov (United States)

    Glied, Sherry; Solís-Román, Claudia; Parikh, Shivani

    2016-09-01

    One important benefit gained by the millions of Americans with health insurance through the Affordable Care Act (ACA) is protection from high out-of-pocket health spending. While Medicaid unambiguously reduces out-of-pocket premium and medical costs for low-income people, it is less certain that marketplace coverage and other types of insurance purchased to comply with the law's individual mandate also protect from high health spending. Goal: To compare out-of-pocket spending in 2014 to spending in 2013; assess how this spending changed in states where many people enrolled in the marketplaces relative to states where few people enrolled; and project the decline in the percentage of people paying high amounts out-of-pocket. Methods: Linear regression models were used to estimate whether people under age 65 spent above certain thresholds. Key findings and conclusions: The probability of incurring high out-of-pocket costs and premium expenses declined as marketplace enrollment increased. The percentage reductions were greatest among those with incomes between 250 percent and 399 percent of poverty, those who were eligible for premium subsidies, and those who previously were uninsured or had very limited nongroup coverage. These effects appear largely attributable to marketplace enrollment rather than to other ACA provisions or to economic trends.

  14. Study Of Physician And Patient Communication Identifies Missed Opportunities To Help Reduce Patients' Out-Of-Pocket Spending.

    Science.gov (United States)

    Ubel, Peter A; Zhang, Cecilia J; Hesson, Ashley; Davis, J Kelly; Kirby, Christine; Barnett, Jamison; Hunter, Wynn G

    2016-04-01

    Some experts contend that requiring patients to pay out of pocket for a portion of their care will bring consumer discipline to health care markets. But are physicians prepared to help patients factor out-of-pocket expenses into medical decisions? In this qualitative study of audiorecorded clinical encounters, we identified physician behaviors that stand in the way of helping patients navigate out-of-pocket spending. Some behaviors reflected a failure to fully engage with patients' financial concerns, from never acknowledging such concerns to dismissing them too quickly. Other behaviors reflected a failure to resolve uncertainty about out-of-pocket expenses or reliance on temporary solutions without making long-term plans to reduce spending. Many of these failures resulted from systemic barriers to health care spending conversations, such as a lack of price transparency. For consumer health care markets to work as intended, physicians need to be prepared to help patients navigate out-of-pocket expenses when financial concerns arise during clinical encounters.

  15. Impact of body mass index on the development of pocket hematoma:A retrospective study in Chinese people

    Institute of Scientific and Technical Information of China (English)

    Jian-Ping GUO; Zhao-Liang SHAN; Hong-Yang GUO; Hong-Tao YUAN; Kun LIN; Yue-Xiang ZHAO; Yu-Tang WANG

    2014-01-01

    BackgroundPocket hematoma is one of the major complications associated with cardiovascular implantable electronic devices (CIEDs) implantation. The aim of this study is to evaluate the impact of body mass index (BMI) on the occurrence of pocket hematoma after CIEDs implantation.MethodsThe study is a retrospective review of 972 patients receiving CIEDs implantation between 2008 and 2012 in a tertiary hospital.ResultsTwenty two patients (2.2%) developed severe pocket hematoma requiring re-intervention. The hematoma rate (4.6%,n = 15) of patients with a BMI of < 23 kg/m2 was significantly higher compared with that of patients with a BMI of≥23 kg/m2 (1.1%, n = 7,P< 0.001). In multivariate regression analysis, a BMI < 23.0 kg/m2 may be associated with the development of severe pocket hema-toma. An increase of 1.0 kg/m2 in BMI was associated with lower incidence of hematoma formation (OR: 0.84; 95% CI: 0.74-0.95;P = 0.006).ConclusionBMI < 23 kg/m2 was associated with a higher incidence of pocket hematoma, requiring re-intervention. The data sup-port that great care must be taken when patients were with a lower BMI received CIEDs implantation.

  16. GeoPad and GeoPocket: GIS-Enabled Field Science Education

    Science.gov (United States)

    Knoop, P. A.; van der Pluijm, B.

    2005-12-01

    Over the past three years we have successfully incorporated and evaluated the use of field-based information technology in introductory through senior-level field courses offered at the University of Michigan's Camp Davis Geology Field Station, near Jackson, WY. The use of GeoPads (field-durable Tablet PCs) and GeoPockets (field-durable Pocket PCs) -- both equipped with GIS, GPS, wireless networking, electronic notebook and other pertinent software -- have significantly enhanced our field exercises and excursions, for both students and instructors. In addition to describing our on-going work, the results of an external, independent review of GeoPad-curriculum integration are presented. For example, using GeoPads to teach field mapping not only supports the traditional approaches and advantages of field instruction, but also offers important benefits in the development of students' spatial reasoning skills. Students are able to record observations and directly create geologic maps in the field, using a combination of an electronic field notebook (Microsoft OneNote) tightly integrated with intuitive, pen-enabled GIS software (ArcGIS-ArcMap). Specifically, this arrangement permits students to analyze and manipulate their data in multiple contexts and representations -- while still in the field -- using both traditional 2-D map views, as well as richer 3-D contexts. Such enhancements provide students with powerful exploratory tools that aid the development of spatial reasoning skills, allowing more intuitive interactions with 2-D representations of our 3-D world. Additionally, field-based GIS mapping enables better error-detection, through immediate interaction with current observations in the context of both supporting data (e.g., topographic maps, aerial photos, magnetic surveys) and students' ongoing observations. GeoPockets provide instructional staff with a more portable, though less feature-rich device, which is highly suitable to the role of "electronic

  17. Health service use, out-of-pocket payments and catastrophic health expenditure among older people in India

    DEFF Research Database (Denmark)

    Brinda, Ethel Mary; Kowal, Paul; Attermann, Jørn;

    2015-01-01

    BACKGROUND: Healthcare financing through out-of-pocket payments and inequities in healthcare utilisation are common in low and middle income countries (LMICs). Given the dearth of pertinent studies on these issues among older people in LMICs, we investigated the determinants of health service use......, out-of-pocket and catastrophic health expenditures among older people in one LMIC, India. METHODS: We accessed data from a nationally representative, multistage sample of 2414 people aged 65 years and older from the WHO's Study on global Ageing and adult health in India. Sociodemographic...... the number of health visits and out-of-pocket health expenditures. The prevalence of catastrophic health expenditure among older people in India was 7% (95% CI 6% to 8%). Older men and individuals with chronic diseases were at higher risk of catastrophic health expenditure, while access to health insurance...

  18. Method for establishing a combustion zone in an in situ oil shale retort having a pocket at the top

    Science.gov (United States)

    Cha, Chang Y.

    1980-01-01

    An in situ oil shale retort having a top boundary of unfragmented formation and containing a fragmented permeable mass has a pocket at the top, that is, an open space between a portion of the top of the fragmented mass and the top boundary of unfragmented formation. To establish a combustion zone across the fragmented mass, a combustion zone is established in a portion of the fragmented mass which is proximate to the top boundary. A retort inlet mixture comprising oxygen is introduced to the fragmented mass to propagate the combustion zone across an upper portion of the fragmented mass. Simultaneously, cool fluid is introduced to the pocket to prevent overheating and thermal sloughing of formation from the top boundary into the pocket.

  19. Steered molecular dynamics study of inhibitor binding in the internal binding site in dehaloperoxidase-hemoglobin.

    Science.gov (United States)

    Zhang, Zhisen; Santos, Andrew P; Zhou, Qing; Liang, Lijun; Wang, Qi; Wu, Tao; Franzen, Stefan

    2016-04-01

    The binding free energy of 4-bromophenol (4-BP), an inhibitor that binds in the internal binding site in dehaloperoxidase-hemoglobin (DHP) was calculated using Molecular Dynamics (MD) methods combined with pulling or umbrella sampling. The effects of systematic changes in the pulling speed, pulling force constant and restraint force constant on the calculated potential of mean force (PMF) are presented in this study. The PMFs calculated using steered molecular dynamics (SMD) were validated by umbrella sampling (US) in the strongly restrained regime. A series of restraint force constants ranging from 1000 down to 5 kJ/(mol nm(2)) were used in SMD simulations. This range was validated using US, however noting that weaker restraints give rise to a broader sampling of configurations. This comparison was further tested by a pulling simulation conducted without any restraints, which was observed to have a value closest to the experimentally measured free energy for binding of 4-BP to DHP based on ultraviolet-visible (UV-vis) and resonance Raman spectroscopies. The protein-inhibitor system is well suited for fundamental study of free energy calculations because the DHP protein is relatively small and the inhibitor is quite rigid. Simulation configuration structures are compared to the X-ray crystallography structures of the binding site of 4-BP in the distal pocket above the heme.

  20. Prevalence of Staphylococcus spp and Candida spp in the oral cavity and periodontal pockets of periodontal disease patients.

    Science.gov (United States)

    Cuesta, Alicia I; Jewtuchowicz, Virginia; Brusca, María I; Nastri, María L; Rosa, Alcira C

    2010-01-01

    The oral cavity can act as a reservoir of certain pathogens that can cause systemic infections. The periodontal pocket is an ecological niche appropriate for hosting microorganisms that could act as opportunistic pathogens. The ability of Staphylococcus spp and Candida spp to form a biofilm and live within certain niches allows them to develop mechanisms that increase persistence, such as the evasion of host defenses and antibiotic efficacy. These microorganisms can easily be or become resistant to antibiotics and lead to superinfection. The aims of this study were to assess the presence of Staphylococcus aureus and Staphylococcus spp in biofilm in subgingival plaque and oral cavity of individuals with gingival-periodontal disease, to identify isolates and the relationship with Candida spp. The study included eighty-two patients, aged 18-70 years with periodontal disease and at least two sites with probing depth > or = 3 mm. Participants' data were evaluated individually. Subgingival biofilm samples were obtained using Gracey curettes 7/8, after supragingival biofilm removal, and a sample from the oral cavity (buccal mucosa, tongue and cheek mucosa) by sterile swab. Of all the patients studied, 42.7% exhibited Staphylococcus spp in the periodontal pocket and 69.5% in the oral cavity while 25.6% exhibited Candida spp in the periodontal pocket and 42.7% in the oral cavity. However, 13.4% had both microorganisms in the periodontal pocket and 36.6% in the oral cavity. The prevalence of Staphylococcus aureus was 13.4% in the periodontal pocket and 15.8% in the oral cavity. Candida albicans was the most prevalent yeast in the periodontal pocket (76.2%) and in the oral cavity (63.0%).

  1. Spectroscopic characterization of mutations at the Phe41 position in the distal haem pocket of horseradish peroxidase C: structural and functional consequences.

    Science.gov (United States)

    Heering, Hendrik A; Smith, Andrew T; Smulevich, Giulietta

    2002-05-01

    Three mutants of horseradish peroxidase isoenzyme C (HRPC) have been constructed in which the conserved distal aromatic residue Phe(41) has been substituted by Trp, Val or Ala and the properties of the mutant proteins have been compared with that of the wild-type. The ferric and ferrous states have been studied by resonance Raman, electronic absorption and Fourier-transform infrared spectroscopies, together with their respective fluoride and CO complexes as probes for the integrity of the distal haem-pocket hydrogen-bonding network. The catalytic properties of the mutants, most notably the HRPC-mutant Phe(41)-->Trp (F41W) variant, were also affected. Structural modelling suggests that the bulky indole group of the F41W mutant blocks the distal cavity, inhibiting the binding of fluoride and CO to the haem iron, severely impairing the reaction of the enzyme with H(2)O(2) to form Compound I. Substitution with the smaller side-chain residues Val or Ala resulted in a 2-fold increase in the affinity of the mutants for the aromatic donor benzhydroxamic acid (BHA) compared with the wild-type, whereas the sterically hindered F41W mutant was not able to bind BHA at all. All the mutations studied increased the amount of a ferric six-coordinate aquo-high-spin species. On the other hand, the similarity in the Fe-Im stretching frequencies of the mutants and wild-type protein suggests that the distal haem-pocket mutations do not cause any substantive changes on the proximal side of the haem. Spectra of the HRPC mutant Phe(41)-->Ala-CO and the HRPC mutant Phe(41)-->Val-CO complexes strongly suggested a weakening of the interaction between CO and Arg(38) due to a secondary rearrangement of the haem relative to helix B. The effects observed for these HRP mutants were somewhat different from those noted recently for the analogous Coprinus cinereus peroxidase (CIP) mutants, particularly the Trp mutant. These differences can be reconciled in part as being due to the smaller size of the

  2. Proline 107 Is a Major Determinant in Maintaining the Structure of the Distal Pocket and Reactivity of the High-Spin Heme of MauG

    Energy Technology Data Exchange (ETDEWEB)

    Feng, Manliang; Jensen, Lyndal M.R.; Yukl, Erik T.; Wei, Xiaoxi; Liu, Aimin; Wilmot, Carrie M.; Davidson, Victor L. (Central Florida); (GSU); (Tougaloo); (UMM)

    2012-05-09

    The diheme enzyme MauG catalyzes a six-electron oxidation required for posttranslational modification of a precursor of methylamine dehydrogenase (preMADH) to complete the biosynthesis of its protein-derived tryptophan tryptophylquinone (TTQ) cofactor. Crystallographic studies had shown that Pro107, which resides in the distal pocket of the high-spin heme of MauG, changes conformation upon binding of CO or NO to the heme iron. In this study, Pro107 was converted to Cys, Val, and Ser by site-directed mutagenesis. The structures of each of these MauG mutant proteins in complex with preMADH were determined, as were their physical and catalytic properties. P107C MauG was inactive, and the crystal structure revealed that Cys107 had been oxidatively modified to a sulfinic acid. Mass spectrometry revealed that this modification was present prior to crystallization. P107V MauG exhibited spectroscopic and catalytic properties that were similar to those of wild-type MauG, but P107V MauG was more susceptible to oxidative damage. The P107S mutation caused a structural change that resulted in the five-coordinate high-spin heme being converted to a six-coordinate heme with a distal axial ligand provided by Glu113. EPR and resonance Raman spectroscopy revealed this heme remained high-spin but with greatly increased rhombicity as compared to that of the axial signal of wild-type MauG. P107S MauG was resistant to reduction by dithionite and reaction with H{sub 2}O{sub 2} and unable to catalyze TTQ biosynthesis. These results show that the presence of Pro107 is critical in maintaining the proper structure of the distal heme pocket of the high-spin heme of MauG, allowing exogenous ligands to bind and directing the reactivity of the heme-activated oxygen during catalysis, thus minimizing the oxidation of other residues of MauG.

  3. Fluorescence quenching studies of γ-butyrolactone binding protein (CprB) from Streptomyces coelicolor A3(2).

    Science.gov (United States)

    Biswas, Anwesha; Swarnkar, Ravi K; Hussain, Bhukya; Sahoo, Suraj K; Pradeepkumar, P I; Patwari, G Naresh; Anand, Ruchi

    2014-08-28

    Quorum sensing is a cell density dependent phenomenon that utilizes small molecule inducers like γ-butyrolactones (GBLs) and their receptor proteins for adaptation to the environment. The cognate GBLs that bind to several of this GBL receptor family of proteins remain elusive. Here, using CprB protein from Streptomyces coelicolor A3(2) as a model system, we devise a method suited for ligand screening that would be applicable to the entire family of GBL receptors. Docking studies were performed to confirm the identity of the ligand binding pocket, and it was ascertained that the common γ-butyrolactone moiety interacts with the conserved tryptophan residue (W127) residing in the ligand binding pocket. The presence of W127 in the cavity was exploited to monitor its fluorescence quenching on the addition of two chemically synthesized GBLs. Analysis of the data with both the native and W185L mutant versions of the protein confirmed that the compounds used as quenchers reside in the ligand binding pocket. Furthermore, fluorescence lifetime and potassium iodide (KI) quenching studies established that the quenching is static in nature and that the tryptophan residue is buried and inaccessible to surface quenchers. Additionally, a combination of concentration dependent fluorescence quenching and dynamic light scattering experiments revealed that the binding properties of the protein are concentration dependent and it was concluded that the most efficient binding of the ligand is evoked by working at the lowest concentration of protein, providing a sufficient signal, where the aggregation effects are negligible.

  4. Financial burden of medical out-of-pocket spending by state and the implications of the 2014 Medicaid expansions.

    Science.gov (United States)

    Caswell, Kyle J; Waidmann, Timothy; Blumberg, Linda J

    2013-08-01

    This study is the first to offer a detailed look at the burden of medical out-of-pocket spending, defined as total family medical out-of-pocket spending as a proportion of income, for each state. It further investigates which states have greater shares of individuals with high burden levels and no Medicaid coverage but would be Medicaid eligible under the 2014 rules of the Affordable Care Act should their state choose to participate in the expansion. This work suggests which states have the largest populations likely to benefit, in terms of lowering medical spending burden, from participating in the 2014 adult Medicaid expansions.

  5. Structural and Functional Studies Indicate That the EPEC Effector, EspG, Directly Binds p21-Activated Kinase

    Energy Technology Data Exchange (ETDEWEB)

    Germane, Katherine L.; Spiller, Benjamin W. (Vanderbilt)

    2011-09-20

    Bacterial pathogens secrete effectors into their hosts that subvert host defenses and redirect host processes. EspG is a type three secretion effector with a disputed function that is found in enteropathogenic Escherichia coli. Here we show that EspG is structurally similar to VirA, a Shigella virulence factor; EspG has a large, conserved pocket on its surface; EspG binds directly to the amino-terminal inhibitory domain of human p21-activated kinase (PAK); and mutations to conserved residues in the surface pocket disrupt the interaction with PAK.

  6. TGF-β Signaling Is Associated with Endocytosis at the Pocket Region of the Primary Cilium

    DEFF Research Database (Denmark)

    Clement, Christian Alexandro; Ajbro, Katrine Dalsgaard; Koefoed, Karen;

    2013-01-01

    Transforming growth factor β (TGF-β) signaling is regulated by clathrin-dependent endocytosis (CDE) for the control of cellular processes during development and in tissue homeostasis. The primary cilium coordinates several signaling pathways, and the pocket surrounding the base and proximal part...... of the cilium is a site for CDE. We report here that TGF-β receptors localize to the ciliary tip and endocytic vesicles at the ciliary base in fibroblasts and that TGF-β stimulation increases receptor localization and activation of SMAD2/3 and ERK1/2 at the ciliary base. Inhibition of CDE reduced TGF......-β-mediated signaling at the cilium, and TGF-β signaling and CDE activity are reduced at stunted primary cilia in Tg737(orpk) fibroblasts. Similarly, TGF-β signaling during cardiomyogenesis correlated with accumulation of TGF-β receptors and activation of SMAD2/3 at the ciliary base. Our results indicate...

  7. SambVca 2. A Web Tool for Analyzing Catalytic Pockets with Topographic Steric Maps

    KAUST Repository

    Falivene, Laura

    2016-06-27

    Developing more efficient catalysts remains one of the primary targets of organometallic chemists. To accelerate reaching this goal, effective molecular descriptors and visualization tools can represent a remarkable aid. Here, we present a Web application for analyzing the catalytic pocket of metal complexes using topographic steric maps as a general and unbiased descriptor that is suitable for every class of catalysts. To show the broad applicability of our approach, we first compared the steric map of a series of transition metal complexes presenting popular mono-, di-, and tetracoordinated ligands and three classic zirconocenes. This comparative analysis highlighted similarities and differences between totally unrelated ligands. Then, we focused on a recently developed Fe(II) catalyst that is active in the asymmetric transfer hydrogenation of ketones and imines. Finally, we expand the scope of these tools to rationalize the inversion of enantioselectivity in enzymatic catalysis, achieved by point mutation of three amino acids of mononuclear p-hydroxymandelate synthase.

  8. Results of examination of the calvarium, brain, and meninges. [in Apollo 17 BIOCORE pocket mice

    Science.gov (United States)

    Haymaker, W.; Zeman, W.; Turnbill, C. E.; Clayton, R. K.; Bailey, O. T.; Samorajski, T.; Vogel, F. S.; Lloyd, B.; Cruty, M. R.; Benton, E. V.

    1975-01-01

    Tissue reactions were found around the monitor (dosimeter) assemblies that had been implanted beneath the scalp of the five pocket mice that flew on Apollo XVII. Mitosis in the dentate gyrus of the hippocampal formation was considerably reduced in comparison with that in control animals. Otherwise the brain tissue as well as the meninges in the flight animals appeared unaltered. Since the animals were exposed primarily to high Z-high energy (HZE) cosmic-ray particles at the lower end of the high LET spectrum, the lack of changes in the brain cannot be taken as evidence that the brain will suffer no damage from the heavier HZE particles on prolonged manned missions.

  9. Highly sensitive resistive type single-axis tactile sensor with liquid pocket

    Science.gov (United States)

    Kim, Seonggi; Kim, Baek-chul; Jung, Jiyeon; Koo, Ja Choon; Choi, Hyouk Ryeol; Moon, Hyungpil

    2014-03-01

    In this paper, we propose the resistive type tactile sensor with a liquid pocket. The tactile sensor with polymer substrate has two components which are the sensing element and the structural part. The sensing part is surrounded by PDMS (Sylgard 184) which is relatively solid. To make the sensor more sensitive, we design the upper part of the sensing element in a shape of half-sphere filled with a liquid (silicone oil). When the force is applied to the sensor, the liquid pressure increases and evenly presses down the sensing element to deform. The size of sensor is 7 x 3 x 1 mm including the wiring part. The good sensitivity (0.012 S/kPa-1) of the fabricated sensor is experimentally verified.

  10. Approaching an organic semimetal: Electron pockets at the Fermi level for a p-benzoquinonemonoimine zwitterion

    Energy Technology Data Exchange (ETDEWEB)

    Rosa, Luis G.; Velev, Julian [Department of Physics and Electronics, University of Puerto Rico, Humacao (United States); Institute for Functional Nanomaterials, University of Puerto Rico, San Juan (United States); Department of Physics and Astronomy, Nebraska Center for Materials and Nanoscience, University of Nebraska-Lincoln, NE (United States); Zhang, Zhengzheng [Department of Physics, University of Puerto Rico, Rio Piedras, San Juan (United States); Alvira, Jose; Vega, Omar; Diaz, Gerson [Department of Physics and Electronics, University of Puerto Rico, Humacao (United States); Routaboul, Lucie; Braunstein, Pierre [Laboratoire de Chimie de Coordination, Institut de Chimie (UMR 7177 CNRS), Universite de Strasbourg (France); Doudin, Bernard [Institut de Physique, Applique de Physique et Chimie des Materiaux de Strasbourg, Universite Louis Pasteur Strasbourg (France); Losovyj, Yaroslav B. [Institute for Functional Nanomaterials, University of Puerto Rico, San Juan (United States); J. Bennett Johnston Sr. Center for Advanced Microstructures and Devices, Louisiana State Univ., Baton Rouge, LA (United States); Dowben, Peter A. [Institute for Functional Nanomaterials, University of Puerto Rico, San Juan (United States)

    2012-08-15

    There is compelling evidence of electron pockets, at the Fermi level, in the band structure for an organic zwitterion molecule of the p-benzoquinonemonoimine type. The electronic structure of the zwitterion molecular film has a definite, although small, density of states evident at the Fermi level as well as a nonzero inner potential and thus is very different from a true insulator. In spite of a small Brillouin zone, significant band width is observed in the intermolecular band dispersion. The results demonstrate that Bloch's theorem applies to the wave vector dependence of the electronic band structure formed from the molecular orbitals of adjacent molecules in a molecular thin film of a p-benzoquinonemonoimine type zwitterion. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  11. Low-Level Laser Therapy (LLLT) for periodontal pockets: a review

    Science.gov (United States)

    Pribac, Valentin; Todea, Carmen; Duma, Virgil-Florin

    2016-03-01

    The applications of lasers in medicine, both in the field of diagnosis and treatment are gaining momentum. In dentistry in particular, numerous types of lasers with a wide range of characteristics are being utilized in all fields. In consequence, a lot of experience and knowledge has been gained in the last two decades in this domain; this resulted in the development of novel technologies and devices. A brief overview is made in the first part of this article on these topics. The treatment of periodontal disease with laser therapy is pointed out, as well as the photodynamic therapy which is using LLLT for the activation of the sensitizing gel that is introduced in the periodontal pockets. This paper reviews also the application of photodynamic therapy in clinical trials which have different results; a standardization of the protocol utilized for this procedure is concluded to be necessary.

  12. Using wireless (Pocket)PCs in Large Introductory Courses to Expand Discourse and Interactivity

    Science.gov (United States)

    van der Pluijm, B. A.; Knoop, P. A.; Samson, P. J.; Teasley, S. D.

    2005-12-01

    Teaching methods in introductory, undergraduate courses traditionally rely on static textbooks and/or course packs, with presentation delivered as a monologue in front of a mostly passive, large audience. The concepts presented in class are often best illustrated using visualizations and/or demonstrations, but even the most stunning of images or spectacular exhibits, while motivating, offer students only passive participation in the learning process. Add to this the advent of course websites with lecture notes and PowerPoint presentations and the students are left with little incentive to attend, much less participate. Clearly this model does not provide much opportunity or motivation for today's students to learn and think more critically about the arguments being developed. What is needed is a coupling of the rich imagery of many fields with advances in technology and in learning, toward revitalizing pedagogical approaches in survey-level courses and student-instructor interaction. Our IT-enhanced classroom project couples the use of peer instruction techniques in large classes (as originally described by Mazur, 1997) with the use of interactive spatial concept challenges, utilizing wireless PocketPCs (handhelds) or student-owned wireless-enabled laptops. The technologies employed (web, PocketPC/laptop, WiFi) are off-the-shelf technologies and the Peer Instruction technique is increasingly documented in undergraduate science classes. However, the combination is not employed due to its initial cost, wrongly perceived level of effort to implement, availability of engaging activities and modest volume of data on student learning. We'll show our development, implementation and preliminary cognitive assessment efforts of this IT-enhanced classroom experience, involving interactive image quizzes and data manipulation in large introductory classes at the University of Michigan.

  13. Pocket pathologist: A mobile application for rapid diagnostic surgical pathology consultation

    Directory of Open Access Journals (Sweden)

    Douglas J Hartman

    2014-01-01

    Full Text Available Introduction: Telepathology allows the digital transmission of images for rapid access to pathology experts. Recent technologic advances in smartphones have allowed them to be used to acquire and transmit digital images of the glass slide, representing cost savings and efficiency gains over traditional forms of telepathology. We report our experience with developing an iPhone application (App - Pocket Pathologist to facilitate rapid diagnostic pathology teleconsultation utilizing a smartphone. Materials and Methods: A secure, web-based portal (http://pathconsult.upmc.com/ was created to facilitate remote transmission of digital images for teleconsultation. The App augments functionality of the web-based portal and allows the user to quickly and easily upload digital images for teleconsultation. Image quality of smartphone cameras was evaluated by capturing images using different adapters that directly attach phones to a microscope ocular lens. Results: The App was launched in August 2013. The App facilitated easy submission of cases for teleconsultation by limiting the number of data entry fields for users and enabling uploading of images from their smartphone′s gallery wirelessly. Smartphone cameras properly attached to a microscope create static digital images of similar quality to a commercial digital microscope camera. Conclusion: Smartphones have great potential to support telepathology because they are portable, provide ubiquitous internet connectivity, contain excellent digital cameras, and can be easily attached to a microscope. The Pocket Pathologist App represents a significant reduction in the cost of creating digital images and submitting them for teleconsultation. The iPhone App provides an easy solution for global users to submit digital pathology images to pathology experts for consultation.

  14. Development of Pocket Vision Screener and its effectiveness at screening visual acuity deficits

    Directory of Open Access Journals (Sweden)

    Monica Raja

    2014-01-01

    Full Text Available Aim: The aim was to construct a visual acuity chart and find its effectiveness at screening visual acuity deficits. Materials and Methods: Two phases were involved in this study.Construction of the screener: Ten Sloan letters (C, D, H, K, N, O, R, S, V, and Z were selected and the letters were constructed and reduced to 0.2 logMAR acuity size (6.92 mm for viewing at 3 m. The screener contains three lines with seven letters in each. Few combinations of the seven letter sequences were chosen based on the row legibility scores. Three seven letter combinations close to the median of all combinations were selected, such that maximum difficulty score difference between the lines are <1%. Finding the effectiveness of the screener: 100 literate subjects with unaided visual acuity better than or equal to 6/60 were recruited for the study. Unaided visual acuity was tested using both the newly constructed Pocket Vision Screener and a logMAR visual acuity chart and the time taken to measure the visual acuity using both the charts was noted. Results: The mean age of the subjects was 43 ± 17 years. Subjects were classified as normal or deficient based on the logMAR visual acuity measurement. The screener was found to have 81% sensitivity, 94% specificity. The positive and negative predictive values were found to be 91% and 87%, respectively. A significant difference (P < 0.001 was found in the time taken to record visual acuity using both the charts. Conclusion: The Pocket Vision Screener can be used as a quick and accurate tool to screen subjects for visual acuity deficits, being highly sensitive, specific, and cost-effective.

  15. GeoPad and GeoPocket: Information Technology for Field Science Education

    Science.gov (United States)

    Knoop, P. A.; van der Pluijm, B.

    2006-12-01

    Over the past four years we have successfully incorporated and evaluated the use of field-based Information Technology (IT) in introductory through senior-level field courses offered at the University of Michigan's Camp Davis Geology Field Station, near Jackson, WY. The use of GeoPads (field-durable Tablet PCs) and GeoPockets (field-durable Pocket PCs) -- both equipped with GIS, GPS, wireless networking, electronic notebook and other pertinent software -- have significantly enhanced our field exercises and excursions, for both students and instructors. We have focused on three main applications: (1) Mapping facilitating the development of spatial reasoning skills via powerful, intuitive capabilities for in-the-field data entry, visualization, analysis, and interpretation in both 2-D and 3-D representations; (2) Field-Trips enriching the overall experience by providing in-the-field access to a broad, relevant collection of supplemental materials, such as papers, figures, maps, photos, thin section images, etc.; and, (3) Field-Based Exercises enhancing the learning opportunities afforded by field-based exercises by supporting data analysis and interpretation, while still in the context in which the data was gathered. This IT-based approach to field education utilizes standard, off-the-shelf hardware and software, and provides students with experience using tools that are increasingly relevant to their future academic or professional careers. Furthermore, this approach is generally applicable to education and research in many traditionally non-IT-savvy science domains, in addition to geology, such as archeology, biology, sociology, and natural resources.

  16. S1 Pocket of a Bacterially Derived Subtilisin-like Protease Underpins Effective Tissue Destruction*

    Science.gov (United States)

    Wong, Wilson; Wijeyewickrema, Lakshmi C.; Kennan, Ruth M.; Reeve, Shane B.; Steer, David L.; Reboul, Cyril; Smith, A. Ian; Pike, Robert N.; Rood, Julian I.; Whisstock, James C.; Porter, Corrine J.

    2011-01-01

    The ovine footrot pathogen, Dichelobacter nodosus, secretes three subtilisin-like proteases that play an important role in the pathogenesis of footrot through their ability to mediate tissue destruction. Virulent and benign strains of D. nodosus secrete the basic proteases BprV and BprB, respectively, with the catalytic domain of these enzymes having 96% sequence identity. At present, it is not known how sequence variation between these two putative virulence factors influences their respective biological activity. We have determined the high resolution crystal structures of BprV and BprB. These data reveal that that the S1 pocket of BprV is more hydrophobic but smaller than that of BprB. We show that BprV is more effective than BprB in degrading extracellular matrix components of the host tissue. Mutation of two residues around the S1 pocket of BprB to the equivalent residues in BprV dramatically enhanced its proteolytic activity against elastin substrates. Application of a novel approach for profiling substrate specificity, the Rapid Endopeptidase Profiling Library (REPLi) method, revealed that both enzymes prefer cleaving after hydrophobic residues (and in particular P1 leucine) but that BprV has more restricted primary substrate specificity than BprB. Furthermore, for P1 Leu-containing substrates we found that BprV is a significantly more efficient enzyme than BprB. Collectively, these data illuminate how subtle changes in D. nodosus proteases may significantly influence tissue destruction as part of the ovine footrot pathogenesis process. PMID:21990366

  17. Coregulator control of androgen receptor action by a novel nuclear receptor-binding motif.

    Science.gov (United States)

    Jehle, Katja; Cato, Laura; Neeb, Antje; Muhle-Goll, Claudia; Jung, Nicole; Smith, Emmanuel W; Buzon, Victor; Carbó, Laia R; Estébanez-Perpiñá, Eva; Schmitz, Katja; Fruk, Ljiljana; Luy, Burkhard; Chen, Yu; Cox, Marc B; Bräse, Stefan; Brown, Myles; Cato, Andrew C B

    2014-03-28

    The androgen receptor (AR) is a ligand-activated transcription factor that is essential for prostate cancer development. It is activated by androgens through its ligand-binding domain (LBD), which consists predominantly of 11 α-helices. Upon ligand binding, the last helix is reorganized to an agonist conformation termed activator function-2 (AF-2) for coactivator binding. Several coactivators bind to the AF-2 pocket through conserved LXXLL or FXXLF sequences to enhance the activity of the receptor. Recently, a small compound-binding surface adjacent to AF-2 has been identified as an allosteric modulator of the AF-2 activity and is termed binding function-3 (BF-3). However, the role of BF-3 in vivo is currently unknown, and little is understood about what proteins can bind to it. Here we demonstrate that a duplicated GARRPR motif at the N terminus of the cochaperone Bag-1L functions through the BF-3 pocket. These findings are supported by the fact that a selective BF-3 inhibitor or mutations within the BF-3 pocket abolish the interaction between the GARRPR motif(s) and the BF-3. Conversely, amino acid exchanges in the two GARRPR motifs of Bag-1L can impair the interaction between Bag-1L and AR without altering the ability of Bag-1L to bind to chromatin. Furthermore, the mutant Bag-1L increases androgen-dependent activation of a subset of AR targets in a genome-wide transcriptome analysis, demonstrating a repressive function of the GARRPR/BF-3 interaction. We have therefore identified GARRPR as a novel BF-3 regulatory sequence important for fine-tuning the activity of the AR.

  18. TEPITOPEpan: extending TEPITOPE for peptide binding prediction covering over 700 HLA-DR molecules.

    Directory of Open Access Journals (Sweden)

    Lianming Zhang

    Full Text Available MOTIVATION: Accurate identification of peptides binding to specific Major Histocompatibility Complex Class II (MHC-II molecules is of great importance for elucidating the underlying mechanism of immune recognition, as well as for developing effective epitope-based vaccines and promising immunotherapies for many severe diseases. Due to extreme polymorphism of MHC-II alleles and the high cost of biochemical experiments, the development of computational methods for accurate prediction of binding peptides of MHC-II molecules, particularly for the ones with few or no experimental data, has become a topic of increasing interest. TEPITOPE is a well-used computational approach because of its good interpretability and relatively high performance. However, TEPITOPE can be applied to only 51 out of over 700 known HLA DR molecules. METHOD: We have developed a new method, called TEPITOPEpan, by extrapolating from the binding specificities of HLA DR molecules characterized by TEPITOPE to those uncharacterized. First, each HLA-DR binding pocket is represented by amino acid residues that have close contact with the corresponding peptide binding core residues. Then the pocket similarity between two HLA-DR molecules is calculated as the sequence similarity of the residues. Finally, for an uncharacterized HLA-DR molecule, the binding specificity of each pocket is computed as a weighted average in pocket binding specificities over HLA-DR molecules characterized by TEPITOPE. RESULT: The performance of TEPITOPEpan has been extensively evaluated using various data sets from different viewpoints: predicting MHC binding peptides, identifying HLA ligands and T-cell epitopes and recognizing binding cores. Among the four state-of-the-art competing pan-specific methods, for predicting binding specificities of unknown HLA-DR molecules, TEPITOPEpan was roughly the second best method next to NETMHCIIpan-2.0. Additionally, TEPITOPEpan achieved the best performance in

  19. Crystallographically mapped ligand binding differs in high and low IgE binding isoforms of birch pollen allergen bet v 1.

    Science.gov (United States)

    Kofler, Stefan; Asam, Claudia; Eckhard, Ulrich; Wallner, Michael; Ferreira, Fátima; Brandstetter, Hans

    2012-09-07

    The ability of pathogenesis-related proteins of family 10 to bind a broad spectrum of ligands is considered to play a key role for their physiological and pathological functions. In particular, Bet v 1, an archetypical allergen from birch pollen, is described as a highly promiscuous ligand acceptor. However, the detailed recognition mechanisms, including specificity factors discriminating binding properties of naturally occurring Bet v 1 variants, are poorly understood. Here, we report crystal structures of Bet v 1 variants in complex with an array of ligands at a resolution of up to 1.2 Å. Residue 30 within the hydrophobic pocket not only discriminates in high and low IgE binding Bet v 1 isoforms but also induces a drastic change in the binding mode of the model ligand deoxycholate. Ternary crystal structure complexes of Bet v 1 with several ligands together with the fluorogenic reporter 1-anilino-8-naphthalene sulfonate explain anomalous fluorescence binding curves obtained from 1-anilino-8-naphthalene sulfonate displacement assays. The structures reveal key interaction residues such as Tyr83 and rationalize both the binding specificity and promiscuity of the so-called hydrophobic pocket in Bet v 1. The intermolecular interactions of Bet v 1 reveal an unexpected complexity that will be indispensable to fully understand its roles within the physiological and allergenic context.

  20. A Disease-Causing Variant in PCNA Disrupts a Promiscuous Protein Binding Site.

    Science.gov (United States)

    Duffy, Caroline M; Hilbert, Brendan J; Kelch, Brian A

    2016-03-27

    The eukaryotic DNA polymerase sliding clamp, proliferating cell nuclear antigen or PCNA, is a ring-shaped protein complex that surrounds DNA to act as a sliding platform for increasing processivity of cellular replicases and for coordinating various cellular pathways with DNA replication. A single point mutation, Ser228Ile, in the human PCNA gene was recently identified to cause a disease whose symptoms resemble those of DNA damage and repair disorders. The mutation lies near the binding site for most PCNA-interacting proteins. However, the structural consequences of the S228I mutation are unknown. Here, we describe the structure of the disease-causing variant, which reveals a large conformational change that dramatically transforms the binding pocket for PCNA client proteins. We show that the mutation markedly alters the binding energetics for some client proteins, while another, p21(CIP1), is only mildly affected. Structures of the disease variant bound to peptides derived from two PCNA partner proteins reveal that the binding pocket can adjust conformation to accommodate some ligands, indicating that the binding site is dynamic and pliable. Our work has implications for the plasticity of the binding site in PCNA and reveals how a disease mutation selectively alters interactions to a promiscuous binding site that is critical for DNA metabolism.

  1. Redefining the structure-activity relationships of 2,6-methano-3-benzazocines. 5. Opioid receptor binding properties of N-((4'-phenyl)-phenethyl) analogues of 8-CAC.

    Science.gov (United States)

    VanAlstine, Melissa A; Wentland, Mark P; Cohen, Dana J; Bidlack, Jean M

    2007-12-01

    A series of aryl-containing N-monosubstituted analogues of the lead compound 8-[N-((4'-phenyl)-phenethyl)]-carboxamidocyclazocine were synthesized and evaluated to probe a putative hydrophobic binding pocket of opioid receptors. Very high binding affinity to the mu opioid receptor was achieved though the N-(2-(4'-methoxybiphenyl-4-yl)ethyl) analogue of 8-CAC. High binding affinity to mu and very high binding affinity to kappa opioid receptors was observed for the N-(3-bromophenethyl) analogue of 8-CAC. High binding affinity to all three opioid receptors were observed for the N-(2-naphthylethyl) analogue of 8-CAC.

  2. Functional identification and characterization of sodium binding sites in Na symporters.

    Science.gov (United States)

    Loo, Donald D F; Jiang, Xuan; Gorraitz, Edurne; Hirayama, Bruce A; Wright, Ernest M

    2013-11-19

    Sodium cotransporters from several different gene families belong to the leucine transporter (LeuT) structural family. Although the identification of Na(+) in binding sites is beyond the resolution of the structures, two Na(+) binding sites (Na1 and Na2) have been proposed in LeuT. Na2 is conserved in the LeuT family but Na1 is not. A biophysical method has been used to measure sodium dissociation constants (Kd) of wild-type and mutant human sodium glucose cotransport (hSGLT1) proteins to identify the Na(+) binding sites in hSGLT1. The Na1 site is formed by residues in the sugar binding pocket, and their mutation influences sodium binding to Na1 but not to Na2. For the canonical Na2 site formed by two -OH side chains, S392 and S393, and three backbone carbonyls, mutation of S392 to cysteine increased the sodium Kd by sixfold. This was accompanied by a dramatic reduction in the apparent sugar and phlorizin affinities. We suggest that mutation of S392 in the Na2 site produces a structural rearrangement of the sugar binding pocket to disrupt both the binding of the second Na(+) and the binding of sugar. In contrast, the S393 mutations produce no significant changes in sodium, sugar, and phlorizin affinities. We conclude that the Na2 site is conserved in hSGLT1, the side chain of S392 and the backbone carbonyl of S393 are important in the first Na(+) binding, and that Na(+) binding to Na2 promotes binding to Na1 and also sugar binding.

  3. Co-current air-water flow in downward sloping pipes: Transport of capacity reducing gas pockets in wastewater mains

    NARCIS (Netherlands)

    Pothof, I.W.M.

    2011-01-01

    Air-water flow is an undesired condition in many systems for the transportation of water or wastewater. Air in storm water tunnels may get trapped and negatively affect the system. Air pockets in hydropower tunnels or sewers may cause blow-back events and inadmissible pressure spikes. Water pipes an

  4. Calibration of polydimethylsiloxane and XAD-Pocket passive air samplers (PAS) for measuring gas- and particle-phase SVOCs

    Science.gov (United States)

    Okeme, Joseph O.; Saini, Amandeep; Yang, Congqiao; Zhu, Jiping; Smedes, Foppe; Klánová, Jana; Diamond, Miriam L.

    2016-10-01

    Polydimethylsiloxane (PDMS) has seen wide use as the stationary phase of gas chromatographic columns, a passive sampler in water, and recently as a personal exposure sampler, while styrene divinyl-benzene copolymer (XAD) has been used extensively as a passive air sampler outdoors and indoors. We have introduced PDMS and XAD-Pocket as new indoor passive air samplers (PASs). The XAD-Pocket was designed to maximize the surface area-to-volume ratio of XAD and to minimize obstruction of air flow by the sampler housing. Methods were developed to expedite the use of these PASs for measuring phthalates, novel brominated flame-retardants (NFRs) and polybrominated diphenyl ethers (PBDEs) indoors. Sampling rates, Rs, (m3 day-1), were measured during a 7-week calibration study. Variability within and between analyte groups was not statistically significant. As a result, generic values of 0.8 ± 0.4 and 0.5 ± 0.3 m3 day-1 dm-2 are recommended for PDMS and XAD-Pocket for a 50-day deployment time, respectively. PDMS has a higher uptake rate and is easier to use than XAD-Pocket.

  5. The financial burden of out-of-pocket patient payments in the European Union and accession countries: Results of a systematic literature review

    NARCIS (Netherlands)

    Moser, K.; Pavlova, M.; Groot, W.

    2014-01-01

    A major issue for public health policy is to reduce the poverty and catastrophic effects of out-of-pocket payments. This paper reviews empirical studies that analyze the financial burden of out-of-pocket payments and factors that are associated with this burden for households in the EU and accession

  6. Validity of a Smartphone-Based Fall Detection Application on Different Phones Worn on a Belt or in a Trouser Pocket.

    Science.gov (United States)

    Vermeulen, Joan; Willard, Sarah; Aguiar, Bruno; De Witte, Luc P

    2015-01-01

    The objective of this study was to evaluate the sensitivity and specificity of a smartphone-based fall detection application when different smartphone models are worn on a belt or in a trouser pocket. Eight healthy adults aged between 18 and 24 years old simulated 10 different types of true falls, 5 different types of falls with recovery, and 11 daily activities, five consecutive times. Participants wore one smartphone in a pocket that was attached to their belt and another one in their trouser pocket. All smartphones were equipped with a built-in accelerometer and the fall detection application. Four participants tested the application on a Samsung S3 and four tested the application on a Samsung S3 mini. Sensitivity scores were .75 (Samsung S3 belt), .88 (Samsung S3 mini trouser pocket), and .90 (Samsung S3 mini belt/Samsung S3 trouser pocket). Specificity scores were .87 (Samsung S3 trouser pocket), .91 (Samsung S3 mini trouser pocket), .97 (Samsung S3 belt), and .99 (Samsung S3 mini belt). These results suggest that an application on a smartphone can generate valid fall alarms when worn on a belt or in a trouser pocket. However, sensitivity should be improved before implementation of the application in practice.

  7. Anchorage-independent growth of pocket protein-deficient murine fibroblasts requires bypass of G2 arrest and can be accomplished by expression of TBX2

    NARCIS (Netherlands)

    Vormer, Tinke L; Foijer, Floris; Wielders, Camiel L C; te Riele, Hein

    2008-01-01

    Mouse embryonic fibroblasts (MEFs) deficient for pocket proteins (i.e., pRB/p107-, pRB/p130-, or pRB/p107/p130-deficient MEFs) have lost proper G(1) control and are refractory to Ras(V12)-induced senescence. However, pocket protein-deficient MEFs expressing Ras(V12) were unable to exhibit anchorage-

  8. The evaluation of chorionic membrane in guided tissue regeneration for periodontal pocket therapy: a clinical and radiographic study.

    Science.gov (United States)

    Kothiwale, Shaila V

    2014-03-01

    Periodontal regenerative therapy is aimed at reconstruction and to restore the architecture and function of lost or injured tissues. Melcher (J Periodontol 47(5):256-260, 1976) introduced the concept of guided tissue regeneration (GTR) for osseous reconstructive surgery. The aim of the present innovative clinical and radiographic study was to evaluate the effect of chorionic membrane (CM) in GTR in periodontal pocket therapy. Ten patients with moderate to severe periodontitis were selected in the single blind randomized controlled clinical trial. Patients were treated with periodontal pocket therapy along with CM in study sites and the control sites were treated with periodontal pocket therapy alone. The clinical parameters were recorded at baseline and 12 months. The radiographic parameters were recorded at baseline, 6 and 12 months. Clinical parameters included gingival index (GI), plaque index (PI), pocket probing depth (PPD) and relative attachment level (RAL). Digital images were analysed for bone gain (BG) and density. Data were evaluated using t test. Statistical significant differences were found in both sites at 12 months for GI, PI, PPD and RAL. Highly significant reduction was seen in GI 0.40 ± 0.08 (p = 0.0001), PI (0.41 ± 0.18), PPD 2.50 ± 0.53 mm (p = 0.0431) and increased BG 0.86 ± 0.18 (p < 0.0001) were observed in study sites. This shows that CM when used with pocket therapy can have influence on clinical parameters. Radiographic findings from this study demonstrated significant BG and density in sites treated with CM as compared to control sites.

  9. Quantitative evaluaiton of porphyromonas gingivalis before and after non- surgical periodontal treatment in deep pockets of patients with aggressive periodontitis

    Directory of Open Access Journals (Sweden)

    Kadkhoda Z.

    2004-08-01

    Full Text Available Statement of Problem: Elimination of porphyromonas gingivalis (p.g from subgingival area in order to successfully treatment out comes in patients with Aggressive periodntitis AP is necessary. Purpose: The aim of this study was the evaluation of non-surgical treatment efficacy in reduction of bacterial population in deep pockets. Materials and Methods: In this randomized clinical trial study we evaluated the result of non- surgical therapy on reduction of p.g count from deep pockets of patients with aggressive periodontitis that had at least one (p.g plus deep pocket (>5mm in each quadrant. At first stage of non-surgical treatment intra pocket irrigation with chlorhexidin was done after scaling and root planning for all patients. In second stage (one week later antibiotics including amoxicillin- metronidazol prescribed for ten days. At base line, one, six and twelve weeks after beginning of therapy, microbial samples, plaque index, bleeding on probing index and probing pocket index were recorded. Result: There was statistically important difference between one and six weeks after treatment with base line in colony count of p.g and all of clinical indices. But in 12 weeks after therapy just, PI and PPD had statistical difference with base line. In this stage, colony count and BOP was reduced but this reduction had not statistically important difference with base line. Conclusion: Thus in present study our non- surgical strategy in elimination of p.g and clinical improvement was successful in short time but three month after therapy recurrence of disease happened in some patients.

  10. Recent trends in the probability of high out-of-pocket medical expenses in the United States

    Directory of Open Access Journals (Sweden)

    Katherine E Baird

    2016-09-01

    Full Text Available Objective: This article measures the probability that out-of-pocket expenses in the United States exceed a threshold share of income. It calculates this probability separately by individuals’ health condition, income, and elderly status and estimates changes occurring in these probabilities between 2010 and 2013. Data and Method: This article uses nationally representative household survey data on 344,000 individuals. Logistic regressions estimate the probabilities that out-of-pocket expenses exceed 5% and alternatively 10% of income in the two study years. These probabilities are calculated for individuals based on their income, health status, and elderly status. Results: Despite favorable changes in both health policy and the economy, large numbers of Americans continue to be exposed to high out-of-pocket expenditures. For instance, the results indicate that in 2013 over a quarter of nonelderly low-income citizens in poor health spent 10% or more of their income on out-of-pocket expenses, and over 40% of this group spent more than 5%. Moreover, for Americans as a whole, the probability of spending in excess of 5% of income on out-of-pocket costs increased by 1.4 percentage points between 2010 and 2013, with the largest increases occurring among low-income Americans; the probability of Americans spending more than 10% of income grew from 9.3% to 9.6%, with the largest increases also occurring among the poor. Conclusion: The magnitude of out-of-pocket’s financial burden and the most recent upward trends in it underscore a need to develop good measures of the degree to which health care policy exposes individuals to financial risk, and to closely monitor the Affordable Care Act’s success in reducing Americans’ exposure to large medical bills.

  11. Recent trends in the probability of high out-of-pocket medical expenses in the United States

    Science.gov (United States)

    Baird, Katherine E

    2016-01-01

    Objective: This article measures the probability that out-of-pocket expenses in the United States exceed a threshold share of income. It calculates this probability separately by individuals’ health condition, income, and elderly status and estimates changes occurring in these probabilities between 2010 and 2013. Data and Method: This article uses nationally representative household survey data on 344,000 individuals. Logistic regressions estimate the probabilities that out-of-pocket expenses exceed 5% and alternatively 10% of income in the two study years. These probabilities are calculated for individuals based on their income, health status, and elderly status. Results: Despite favorable changes in both health policy and the economy, large numbers of Americans continue to be exposed to high out-of-pocket expenditures. For instance, the results indicate that in 2013 over a quarter of nonelderly low-income citizens in poor health spent 10% or more of their income on out-of-pocket expenses, and over 40% of this group spent more than 5%. Moreover, for Americans as a whole, the probability of spending in excess of 5% of income on out-of-pocket costs increased by 1.4 percentage points between 2010 and 2013, with the largest increases occurring among low-income Americans; the probability of Americans spending more than 10% of income grew from 9.3% to 9.6%, with the largest increases also occurring among the poor. Conclusion: The magnitude of out-of-pocket’s financial burden and the most recent upward trends in it underscore a need to develop good measures of the degree to which health care policy exposes individuals to financial risk, and to closely monitor the Affordable Care Act’s success in reducing Americans’ exposure to large medical bills. PMID:27651901

  12. Out-of-pocket cost of managing sick newborns in Enugu, southeast Nigeria

    Directory of Open Access Journals (Sweden)

    Ekwochi U

    2014-01-01

    Full Text Available Uchenna Ekwochi,1 D Chidiebere Osuorah,3 Ikenna K Ndu,1 Osita U Ezenwosu,2 Ogechukwu F Amadi,1 Ikenna C Nwokoye,1 O Israel Odetunde2 1Department of Pediatrics, Enugu State University Teaching Hospital, Parklane, Nigeria; 2Department of Pediatrics, University of Nigeria Teaching Hospital, Enugu, Nigeria; 3Child Survival Unit, Medical Research Council (UK, The Gambia unit, Fajara, The Gambia Background: Neonatal illnesses usually require long hospital stays and specialized care and/or facilities, which usually results in huge medical bills. With more than 70% of people in Nigeria living on less than US$2 per day, these bills are not affordable to many families' livelihoods. Aim: This study aims to determine the average cost of managing neonatal illnesses in Enugu in southeast Nigeria and the proportion of family income spent on these illnesses. It further seeks to ascertain the cost of various components in the management of neonatal diseases. Methods: This is a longitudinal and descriptive study involving 106 newborns admitted to the sick baby unit of the Enugu State University Teaching Hospital and the out-of-pocket medical expenditure in the management of their illnesses. Results: A hundred and six newborns participated in the study. All (100% medical bills were out-of-pocket payments, and 103 (97.2% of these were catastrophic health expenditure (more than 10% of total family monthly income. The average duration of hospital stay and cost of managing a neonatal illness was 12.86±8.81 days and ₦36,382±19,389.72 (US$223±119, respectively. This expenditure amounted to 157%, 71%, and 25% of total monthly family income for the low, middle, and upper socioeconomic class families, respectively, with a mean percentage of 85%. Families with a total monthly income of less than ₦10,000 (US$61, ₦10,000–49,999 (US$61–306, and ₦50,000–100,000 (US$306–612 and more than ₦100,000 (US$612 on average spent 683%, 108%, 54%, and 20% of their

  13. Isothermal titration calorimetric and computational studies on the binding of chitooligosaccharides to pumpkin (Cucurbita maxima) phloem exudate lectin.

    Science.gov (United States)

    Narahari, Akkaladevi; Singla, Hitesh; Nareddy, Pavan Kumar; Bulusu, Gopalakrishnan; Surolia, Avadhesha; Swamy, Musti J

    2011-04-14

    The interaction of chitooligosaccharides [(GlcNAc)(2-6)] with pumpkin phloem exudate lectin (PPL) was investigated by isothermal titration calorimetry and computational methods. The dimeric PPL binds to (GlcNAc)(3-5) with binding constants of 1.26-1.53 × 10(5) M(-1) at 25 °C, whereas chitobiose exhibits approximately 66-fold lower affinity. Interestingly, chitohexaose shows nearly 40-fold higher affinity than chitopentaose with a binding constant of 6.16 × 10(6) M(-1). The binding stoichiometry decreases with an increase in the oligosaccharide size from 2.26 for chitobiose to 1.08 for chitohexaose. The binding reaction was essentially enthalpy driven with negative entropic contribution, suggesting that hydrogen bonds and van der Waals' interactions are the main factors that stabilize PPL-saccharide association. The three-dimensional structure of PPL was predicted by homology modeling, and binding of chitooligosaccharides was investigated by molecular docking and molecular dynamics simulations, which showed that the protein binding pocket can accommodate up to three GlcNAc residues, whereas additional residues in chitotetraose and chitopentaose did not exhibit any interactions with the binding pocket. Docking studies with chitohexaose indicated that the two triose units of the molecule could interact with different protein binding sites, suggesting formation of higher order complexes by the higher oligomers of GlcNAc by their simultaneous interaction with two protein molecules.

  14. Evaluating the binding efficiency of pheromone binding protein with its natural ligand using molecular docking and fluorescence analysis

    Science.gov (United States)

    Ilayaraja, Renganathan; Rajkumar, Ramalingam; Rajesh, Durairaj; Muralidharan, Arumugam Ramachandran; Padmanabhan, Parasuraman; Archunan, Govindaraju

    2014-06-01

    Chemosignals play a crucial role in social and sexual communication among inter- and intra-species. Chemical cues are bound with protein that is present in the pheromones irrespective of sex are commonly called as pheromone binding protein (PBP). In rats, the pheromone compounds are bound with low molecular lipocalin protein α2u-globulin (α2u). We reported farnesol is a natural endogenous ligand (compound) present in rat preputial gland as a bound volatile compound. In the present study, an attempt has been made through computational method to evaluating the binding efficiency of α2u with the natural ligand (farnesol) and standard fluorescent molecule (2-naphthol). The docking analysis revealed that the binding energy of farnesol and 2-naphthol was almost equal and likely to share some binding pocket of protein. Further, to extrapolate the results generated through computational approach, the α2u protein was purified and subjected to fluorescence titration and binding assay. The results showed that the farnesol is replaced by 2-naphthol with high hydrophobicity of TYR120 in binding sites of α2u providing an acceptable dissociation constant indicating the binding efficiency of α2u. The obtained results are in corroboration with the data made through computational approach.

  15. STARD4 Membrane Interactions and Sterol Binding.

    Science.gov (United States)

    Iaea, David B; Dikiy, Igor; Kiburu, Irene; Eliezer, David; Maxfield, Frederick R

    2015-08-01

    The steroidogenic acute regulatory protein-related lipid transfer (START) domain family is defined by a conserved 210-amino acid sequence that folds into an α/β helix-grip structure. Members of this protein family bind a variety of ligands, including cholesterol, phospholipids, sphingolipids, and bile acids, with putative roles in nonvesicular lipid transport, metabolism, and cell signaling. Among the soluble START proteins, STARD4 is expressed in most tissues and has previously been shown to transfer sterol, but the molecular mechanisms of membrane interaction and sterol binding remain unclear. In this work, we use biochemical techniques to characterize regions of STARD4 and determine their role in membrane interaction and sterol binding. Our results show that STARD4 interacts with anionic membranes through a surface-exposed basic patch and that introducing a mutation (L124D) into the Omega-1 (Ω1) loop, which covers the sterol binding pocket, attenuates sterol transfer activity. To gain insight into the attenuating mechanism of the L124D mutation, we conducted structural and biophysical studies of wild-type and L124D STARD4. These studies show that the L124D mutation reduces the conformational flexibility of the protein, resulting in a diminished level of membrane interaction and sterol transfer. These studies also reveal that the C-terminal α-helix, and not the Ω1 loop, partitions into the membrane bilayer. On the basis of these observations, we propose a model of STARD4 membrane interaction and sterol binding and release that requires dynamic movement of both the Ω1 loop and membrane insertion of the C-terminal α-helix.

  16. A Novel, ;Double-Clamp; Binding Mode for Human Heme Oxygenase-1 Inhibition

    Energy Technology Data Exchange (ETDEWEB)

    Rahman, Mona N.; Vlahakis, Jason Z.; Vukomanovic, Dragic; Lee, Wallace; Szarek, Walter A.; Nakatsu, Kanji; Jia, Zongchao (Queens)

    2012-08-01

    The development of heme oxygenase (HO) inhibitors is critical in dissecting and understanding the HO system and for potential therapeutic applications. We have established a program to design and optimize HO inhibitors using structure-activity relationships in conjunction with X-ray crystallographic analyses. One of our previous complex crystal structures revealed a putative secondary hydrophobic binding pocket which could be exploited for a new design strategy by introducing a functional group that would fit into this potential site. To test this hypothesis and gain further insights into the structural basis of inhibitor binding, we have synthesized and characterized 1-(1H-imidazol-1-yl)-4,4-diphenyl-2-butanone (QC-308). Using a carbon monoxide (CO) formation assay on rat spleen microsomes, the compound was found to be {approx}15 times more potent (IC{sub 50} = 0.27{+-}0.07 {mu}M) than its monophenyl analogue, which is already a potent compound in its own right (QC-65; IC{sub 50} = 4.0{+-}1.8 {mu}M). The crystal structure of hHO-1 with QC-308 revealed that the second phenyl group in the western region of the compound is indeed accommodated by a definitive secondary proximal hydrophobic pocket. Thus, the two phenyl moieties are each stabilized by distinct hydrophobic pockets. This 'double-clamp' binding offers additional inhibitor stabilization and provides a new route for improvement of human heme oxygenase inhibitors.

  17. Solution NMR characterization of chemokine CXCL8/IL-8 monomer and dimer binding to glycosaminoglycans: structural plasticity mediates differential binding interactions.

    Science.gov (United States)

    Joseph, Prem Raj B; Mosier, Philip D; Desai, Umesh R; Rajarathnam, Krishna

    2015-11-15

    Chemokine CXCL8/interleukin-8 (IL-8) plays a crucial role in directing neutrophils and oligodendrocytes to combat infection/injury and tumour cells in metastasis development. CXCL8 exists as monomers and dimers and interaction of both forms with glycosaminoglycans (GAGs) mediate these diverse cellular processes. However, very little is known regarding the structural basis underlying CXCL8-GAG interactions. There are conflicting reports on the affinities, geometry and whether the monomer or dimer is the high-affinity GAG ligand. To resolve these issues, we characterized the binding of a series of heparin-derived oligosaccharides [heparin disaccharide (dp2), heparin tetrasaccharide (dp4), heparin octasaccharide (dp8) and heparin 14-mer (dp14)] to the wild-type (WT) dimer and a designed monomer using solution NMR spectroscopy. The pattern and extent of binding-induced chemical shift perturbation (CSP) varied between dimer and monomer and between longer and shorter oligosaccharides. NMR-based structural models show that different interaction modes coexist and that the nature of interactions varied between monomer and dimer and oligosaccharide length. MD simulations indicate that the binding interface is structurally plastic and provided residue-specific details of the dynamic nature of the binding interface. Binding studies carried out under conditions at which WT CXCL8 exists as monomers and dimers provide unambiguous evidence that the dimer is the high-affinity GAG ligand. Together, our data indicate that a set of core residues function as the major recognition/binding site, a set of peripheral residues define the various binding geometries and that the structural plasticity of the binding interface allows multiplicity of binding interactions. We conclude that structural plasticity most probably regulates in vivo CXCL8 monomer/dimer-GAG interactions and function.

  18. Positive versus negative modulation of different endogenous chemokines for CC-chemokine receptor 1 by small molecule agonists through allosteric versus orthosteric binding

    DEFF Research Database (Denmark)

    Jensen, Pia C; Thiele, Stefanie; Ulven, Trond

    2008-01-01

    5 and not CCL3 activation is affected by substitutions in the main ligand binding pocket including the conserved GluVII:06 anchor point. A series of metal ion chelator complexes were found to act as full agonists on CCR1 and to be critically affected by the same substitutions in the main ligand...

  19. In silico docking of forchlorfenuron (FCF to septins suggests that FCF interferes with GTP binding.

    Directory of Open Access Journals (Sweden)

    Dimitrios Angelis

    Full Text Available Septins are GTP-binding proteins that form cytoskeleton-like filaments, which are essential for many functions in eukaryotic organisms. Small molecule compounds that disrupt septin filament assembly are valuable tools for dissecting septin functions with high temporal control. To date, forchlorfenuron (FCF is the only compound known to affect septin assembly and functions. FCF dampens the dynamics of septin assembly inducing the formation of enlarged stable polymers, but the underlying mechanism of action is unknown. To investigate how FCF binds and affects septins, we performed in silico simulations of FCF docking to all available crystal structures of septins. Docking of FCF with SEPT2 and SEPT3 indicated that FCF interacts preferentially with the nucleotide-binding pockets of septins. Strikingly, FCF is predicted to form hydrogen bonds with residues involved in GDP-binding, mimicking nucleotide binding. FCF docking with the structure of SEPT2-GppNHp, a nonhydrolyzable GTP analog, and SEPT7 showed that FCF may assume two alternative non-overlapping conformations deeply into and on the outer side of the nucleotide-binding pocket. Surprisingly, FCF was predicted to interact with the P-loop Walker A motif GxxxxGKS/T, which binds the phosphates of GTP, and the GTP specificity motif AKAD, which interacts with the guanine base of GTP, and highly conserved amino acids including a threonine, which is critical for GTP hydrolysis. Thus, in silico FCF exhibits a conserved mechanism of binding, interacting with septin signature motifs and residues involved in GTP binding and hydrolysis. Taken together, our results suggest that FCF stabilizes septins by locking them into a conformation that mimics a nucleotide-bound state, preventing further GTP binding and hydrolysis. Overall, this study provides the first insight into how FCF may bind and stabilize septins, and offers a blueprint for the rational design of FCF derivatives that could target septins with

  20. Analyzing binding data.

    Science.gov (United States)

    Motulsky, Harvey J; Neubig, Richard R

    2010-07-01

    Measuring the rate and extent of radioligand binding provides information on the number of binding sites, and their affinity and accessibility of these binding sites for various drugs. This unit explains how to design and analyze such experiments.

  1. Structural insights into human peroxisome proliferator activated receptor delta (PPAR-delta selective ligand binding.

    Directory of Open Access Journals (Sweden)

    Fernanda A H Batista

    Full Text Available Peroxisome proliferator activated receptors (PPARs δ, α and γ are closely related transcription factors that exert distinct effects on fatty acid and glucose metabolism, cardiac disease, inflammatory response and other processes. Several groups developed PPAR subtype specific modulators to trigger desirable effects of particular PPARs without harmful side effects associated with activation of other subtypes. Presently, however, many compounds that bind to one of the PPARs cross-react with others and rational strategies to obtain highly selective PPAR modulators are far from clear. GW0742 is a synthetic ligand that binds PPARδ more than 300-fold more tightly than PPARα or PPARγ but the structural basis of PPARδ:GW0742 interactions and reasons for strong selectivity are not clear. Here we report the crystal structure of the PPARδ:GW0742 complex. Comparisons of the PPARδ:GW0742 complex with published structures of PPARs in complex with α and γ selective agonists and pan agonists suggests that two residues (Val312 and Ile328 in the buried hormone binding pocket play special roles in PPARδ selective binding and experimental and computational analysis of effects of mutations in these residues confirms this and suggests that bulky substituents that line the PPARα and γ ligand binding pockets as structural barriers for GW0742 binding. This analysis suggests general strategies for selective PPARδ ligand design.

  2. Effect of DNA binding on geminate CO recombination kinetics in CooA

    Science.gov (United States)

    Benabbas, Abdelkrim; Karunakaran, Venugopal; Youn, Hwan; Poulos, Thomas; Champion, Paul

    2012-02-01

    CooA proteins are heme-based CO-sensing transcription factors. Here we study the ultrafast dynamics of geminate CO rebinding to RrCooA. The effects of DNA binding and the truncation of the DNA binding domain on the CO geminate recombination kinetics were investigated. The CO rebinding kinetics in these CooA complexes takes place on ultrafast timescales but remains non-exponential over many decades in time. We show that this non-exponential kinetic response is due to a quenched enthalpic barrier distribution resulting from a distribution of heme geometries that is frozen or slowly evolving on the timescale of CO rebinding. We also show that, upon CO binding, the distal pocket of the heme in RrCooA relaxes to form a very efficient hydrophobic trap for CO. DNA binding further tightens the narrow distal pocket and slightly weakens the iron-proximal histidine bond. Analysis of our data reveals that the uncomplexed and inherently flexible DNA binding domain adds additional structural heterogeneity to the heme doming coordinate. When CooA forms a complex with DNA, the flexibility of the DNA-binding domain decreases and the distribution of the conformations available in the heme domain becomes restricted.

  3. Pocket atlas of sectional anatomy: computed tomography and magnetic resonance imaging. Vol. 3. Spine, extremities, joints

    Energy Technology Data Exchange (ETDEWEB)

    Moeller, T.B.; Reif, E. [Caritas Hospital, Dillingen (Germany). Dept. of Radiology

    2007-07-01

    Magnetic resonance imaging (MRI) of the musculoskeletal system is an established and important component in the diagnosis of diseases of the joints, soft tissues, bones, and bone marrow. We are therefore pleased to collect together images of the joints and the spinal column in a separate volume on the musculoskeletal system. Demonstrating the growing importance of new developments in MRI in recent years, with ever-increasing resolution, many images were acquired with 3-tesla units. We are deeply grateful to the manufacturers, Siemens and Philips, for making this possible. We believe that colored atlases are the ideal medium to represent the highly detailed images achieved nowadays with improved resolution techniques. Volume 3 of the Pocket Atlas of Sectional Anatomay provides a color illustration facing each magnetic resonance image, as in the preceding volumes on the skull, thorax, and abdomen. To ensure the greatest possible precision in details, we still produce these illustrations ourselves. Each is accompanied by a sectional image and an orientation aid. Uniform color schemes ensure optimal clarity, as similar structures, such as arteries, veins, nerves, tendons, etc., are consistently represented in the same color. Individual muscle groups are represented uniformly, but differentiated from other muscle groups, so that classification is possible even when numerous groups of muscles are shown in the same image. Maximal lucidity prevails even in highly detailed representations. This is made possible by the high quality of the production and printing process that are characteristic of Thieme International. (orig.)

  4. Heterogeneity in the smoking response to health shocks by out-of-pocket spending risk.

    Science.gov (United States)

    Richards, Michael R; Marti, Joachim

    2014-10-01

    An existing literature demonstrates that adverse changes to health can lead to improvements in health behaviors. Although the exact explanations for these empirical findings are debated, some posit that individuals learn about their true health risks through health shocks. Updated health risk information can then induce changes in health behaviors. While we follow a learning framework, we argue that past work has neglected the role of health insurance and medically related financial risk within this decision making context. Using longitudinal data from 11 European countries, we investigate the impact of a new cardiovascular (CV) health shock on smoking decisions among older adults and examine whether personal exposure to medical spending risk influences the smoking response. We then explore two potential mechanisms for this link: larger updates to health risk beliefs and higher medical expenditures to incentivize behavior change. We find that CV shocks impact the propensity to smoke, with relatively more impact among individuals with high financial risk exposure to medical spending. We also see larger increases in out-of-pocket expenditures following a shock for this group--consistent with the latter mechanism for behavior change.

  5. A High Performance Pocket-Size System for Evaluations in Acoustic Signal Processing

    Directory of Open Access Journals (Sweden)

    Steeger Gerhard H

    2001-01-01

    Full Text Available Custom-made hardware is attractive for sophisticated signal processing in wearable electroacoustic devices, but has a high initial cost overhead. Thus, signal processing algorithms should be tested thoroughly in real application environments by potential end users prior to the hardware implementation. In addition, the algorithms should be easily alterable during this test phase. A wearable system which meets these requirements has been developed and built. The system is based on the high performance signal processor Motorola DSP56309. This device also includes high quality stereo analog-to-digital-(ADC- and digital-to-analog-(DAC-converters with 20 bit word length each. The available dynamic range exceeds 88 dB. The input and output gains can be adjusted by digitally controlled potentiometers. The housing of the unit is small enough to carry it in a pocket (dimensions 150 × 80 × 25 mm. Software tools have been developed to ease the development of new algorithms. A set of configurable Assembler code modules implements all hardware dependent software routines and gives easy access to the peripherals and interfaces. A comfortable fitting interface allows easy control of the signal processing unit from a PC, even by assistant personnel. The device has proven to be a helpful means for development and field evaluations of advanced new hearing aid algorithms, within interdisciplinary research projects. Now it is offered to the scientific community.

  6. Heading Estimation for Indoor Pedestrian Navigation Using a Smartphone in the Pocket

    Directory of Open Access Journals (Sweden)

    Zhi-An Deng

    2015-08-01

    Full Text Available Heading estimation is a central problem for indoor pedestrian navigation using the pervasively available smartphone. For smartphones placed in a pocket, one of the most popular device positions, the essential challenges in heading estimation are the changing device coordinate system and the severe indoor magnetic perturbations. To address these challenges, we propose a novel heading estimation approach based on a rotation matrix and principal component analysis (PCA. Firstly, through a related rotation matrix, we project the acceleration signals into a reference coordinate system (RCS, where a more accurate estimation of the horizontal plane of the acceleration signal is obtained. Then, we utilize PCA over the horizontal plane of acceleration signals for local walking direction extraction. Finally, in order to translate the local walking direction into the global one, we develop a calibration process without requiring noisy compass readings. Besides, a turn detection algorithm is proposed to improve the heading estimation accuracy. Experimental results show that our approach outperforms the traditional uDirect and PCA-based approaches in terms of accuracy and feasibility.

  7. Transcriptional control of stem cell fate by E2Fs and Pocket Proteins

    Directory of Open Access Journals (Sweden)

    Lisa Marie Julian

    2015-04-01

    Full Text Available E2F transcription factors and their regulatory partners, the pocket proteins (PPs, have emerged as essential regulators of stem cell fate control in a number of lineages. In mammals, this role extends from both pluripotent stem cells to those encompassing all embryonic germ layers, as well as extra-embryonic lineages. E2F/PP-mediated regulation of stem cell decisions is highly evolutionarily conserved, and is likely a pivotal biological mechanism underlying stem cell homeostasis. This has immense implications for organismal development, tissue maintenance and regeneration. In this article, we discuss the roles of E2F factors and PPs in stem cell populations, focusing on mammalian systems. We discuss emerging findings that position the E2F and PP families as widespread and dynamic epigenetic regulators of cell fate decisions. Additionally, we focus on the ever expanding landscape of E2F/PP target genes, and explore the possibility that E2Fs are not simply regulators of general ‘multi-purpose’ cell fate genes but can execute tissue- and cell type-specific gene regulatory programs.

  8. Out-of-pocket costs and burden among rural breast cancer survivors.

    Science.gov (United States)

    Pisu, Maria; Azuero, Andres; Benz, Rachel; McNees, Patrick; Meneses, Karen

    2017-03-01

    Little is known about out-of-pocket (OOP) costs incurred for medical and health needs by rural breast cancer survivors and what factors may be associated with higher OOP costs and the associated economic burden. Data were examined for 432 survivors participating in the Rural Breast Cancer Survivor Intervention trial. OOP costs were collected using the Work and Finances Inventory survey at baseline and four assessments every 3 months. Mean and median OOP costs and burden (percent of monthly income spent on OOP costs) were reported and factors associated with OOP costs and burden identified with generalized linear models fitted with over-dispersed gamma distributions and logarithmic links (OOP costs) and with beta distributions with logit link (OOP burden). OOP costs per month since the end of treatment were on average $232.7 (median $95.6), declined at the next assessment point to $186.5 (median $89.1), and thereafter remained at that level. Mean OOP burden was 9% at baseline and between 7% and 8% at the next assessments. Factors suggestive of contributing to higher OOP costs and OOP burden were the following: younger age, lower income, time in survivorship from diagnosis, and use of supportive services. OOP costs burden rural breast cancer survivors, particularly those who are younger and low income. Research should investigate the impact of OOP costs and interventions to reduce economic burden.

  9. [Textual research on circulation of the Ming edition of Li Heng's Xiu zhen fang (Pocket Formulary)].

    Science.gov (United States)

    Yang, Jinping; Liu, Peng; Lu, Mingjing; Lu, Xing; Li, Shaolin; Jin, Xiumei

    2015-03-01

    Xiu zhen fang (Pocket Formulary) is a recipe book of the Ming Dynasty, inspired and managed by Zhu Su, compiled by Li Heng of liangyisuo (good physician house) in Zhou wangfu (Zhou's royal palace). The book was compiled and published twice during the reigns of the Hongwu and Yongle Emperors of the Ming Dynasty. Because of its high practicability, there were some editions in circulation, and the book was published several times only in the Ming Dynasty. At present, the earliest extanteditionwas the little character version of Yongle, and the version in the 4(th) year of Zhengde Emperor of the Ming Dynasty was a reprinting edition based on the Yongle edition, sharingthe same edition system. Most of the editions appeared after the reign of Zhengtong Emperor of the Ming Dynasty, titled by "kui ben (head version)" and "da quan (complete edition)" were the editionspublished in the local bookshops, which had rather distinct differences from the Yongle edition system not only in the its format but also in its contents.

  10. Performance investigations of novel dual-material gate(DMG) MOSFET with dielectric pockets(DP)

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Dual-material gate MOSFET with dielectric pockets (DMGDP MOSFET) is proposed to eliminate the potential weakness of the DP MOSFET for CMOS scaling toward the 32 nm gate length and beyond. The short-channel effects (SCE) can be effectively suppressed by the insulator near the source/drain regions. And the suppression capability can be even better than the DP MOSFET due to the drain bias absorbed by the screen gate. The speed performance and electronic characteristics of the DMGDP MOSFET are comprehensively studied. Compared to the experimental data from Jurczak et al., the DMGDP PMOSFET exhibits good subthreshold characteristics and the on-state current is almost the twice that of the DP PMOSFET. The intrinsic delay of the NMOS reaches 21% greater than the DP MOSFET for 32 nm node. The higher fT of 390 GHz is achieved, which is a 32% enhancement in comparison with the DP MOSFET when the gate length is 50 nm. Finally, the design guideline and the optimal regions of the DMGDP MOSFET are discussed.

  11. Performance investigations of novel dual-material gate (DMG)MOSFET with dielectric pockets(DP)

    Institute of Scientific and Technical Information of China (English)

    LUAN SuZhen; LIU HongXia; JIA RenXu

    2009-01-01

    Dual-material gate MOSFET with dielectric pockets(DMGDP MOSFET)is proposed to eliminate the potential weakness of the DP MOSFET for CMOS scaling toward the 32 nm gate length and beyond.The short-channel effects(SCE)can be effectively suppressed by the insulator near the source/drain regions.And the suppression capability can be even better than the DP MOSFET due to the drain bias absorbed by the screen gate.The speed performance and electronic characteristics of the DMGDP MOSFET are comprehensively studied.Compared to the experimental data from Jurczak et al.,the DMGDP PMOSFET exhibits good subthreshold characteristics and the on-state current is almost the twice that of the DP PMOSFET.The intrinsic delay of the NMOS reaches 21% greater than the DP MOSFET for 32 nm node.The higher fT of 390 GHz is achieved,which is a 32% enhancement in comparison with the DP MOSFET when the gate length is 50 nm.Finally,the design guideline and the opUmal regions of the DMGDP MOSFET are discussed.

  12. Location of the Antidepressant Binding Site in the Serotonin Transporter IMPORTANCE OF SER-438 IN RECOGNITION OF CITALOPRAM AND TRICYCLIC ANTIDEPRESSANTS

    DEFF Research Database (Denmark)

    Andersen, Jacob; Taboureau, Olivier; Hansen, Kasper B.

    2009-01-01

    The serotonin transporter (SERT) regulates extracellular levels of serotonin (5-hydroxytryptamine, 5HT) in the brain by transporting 5HT into neurons and glial cells. The human SERT (hSERT) is the primary target for drugs used in the treatment of emotional disorders, including depression. h......-function relationships. However, the precise structural mechanism by which antidepressants inhibit hSERT and the location of their binding pockets are still elusive. We have identified a residue (Ser-438) located within the 5HT-binding pocket in hSERT to be a critical determinant for the potency of several......- and inhibitor-binding sites in hSERT suggesting that antidepressants function by a mechanism that involves direct occlusion of the 5HT-binding site....

  13. Early Effect of Amyloid β-Peptide on Hippocampal and Serum Metabolism in Rats Studied by an Integrated Method of NMR-Based Metabolomics and ANOVA-Simultaneous Component Analysis.

    Science.gov (United States)

    Du, Yao; Zheng, Hong; Xia, Huanhuan; Zhao, Liangcai; Hu, Wenyi; Bai, Guanghui; Yan, Zhihan; Gao, Hongchang

    2017-01-01

    Amyloid β (Aβ) deposition has been implicated in the pathogenesis of Alzheimer's disease. However, the early effect of Aβ deposition on metabolism remains unclear. In the present study, thus, we explored the metabolic changes in the hippocampus and serum during first 2 weeks of Aβ25-35 injection in rats by using an integrated method of NMR-based metabolomics and ANOVA-simultaneous component analysis (ASCA). Our results show that Aβ25-35 injection, time, and their interaction had statistically significant effects on the hippocampus and serum metabolome. Furthermore, we identified key metabolites that mainly contributed to these effects. After Aβ25-35 injection from 1 to 2 weeks, the levels of lactate, N-acetylaspartate, creatine, and taurine were decreased in rat hippocampus, while an increase in lactate and decreases in LDL/VLDL and glucose were observed in rat serum. Therefore, we suggest that the reduction in energy and lipid metabolism as well as an increase in anaerobic glycolysis may occur at the early stage of Aβ25-35 deposition.

  14. Early Effect of Amyloid β-Peptide on Hippocampal and Serum Metabolism in Rats Studied by an Integrated Method of NMR-Based Metabolomics and ANOVA-Simultaneous Component Analysis

    Science.gov (United States)

    Du, Yao; Xia, Huanhuan; Zhao, Liangcai; Hu, Wenyi; Bai, Guanghui

    2017-01-01

    Amyloid β (Aβ) deposition has been implicated in the pathogenesis of Alzheimer's disease. However, the early effect of Aβ deposition on metabolism remains unclear. In the present study, thus, we explored the metabolic changes in the hippocampus and serum during first 2 weeks of Aβ25–35 injection in rats by using an integrated method of NMR-based metabolomics and ANOVA-simultaneous component analysis (ASCA). Our results show that Aβ25–35 injection, time, and their interaction had statistically significant effects on the hippocampus and serum metabolome. Furthermore, we identified key metabolites that mainly contributed to these effects. After Aβ25–35 injection from 1 to 2 weeks, the levels of lactate, N-acetylaspartate, creatine, and taurine were decreased in rat hippocampus, while an increase in lactate and decreases in LDL/VLDL and glucose were observed in rat serum. Therefore, we suggest that the reduction in energy and lipid metabolism as well as an increase in anaerobic glycolysis may occur at the early stage of Aβ25–35 deposition.

  15. Icariin reverses corticosterone-induced depression-like behavior, decrease in hippocampal brain-derived neurotrophic factor (BDNF) and metabolic network disturbances revealed by NMR-based metabonomics in rats.

    Science.gov (United States)

    Gong, Meng-Juan; Han, Bin; Wang, Shu-mei; Liang, Sheng-wang; Zou, Zhong-jie

    2016-05-10

    Previously published reports have revealed the antidepressant-like effects of icariin in a chronic mild stress model of depression and in a social defeat stress model in mice. However, the therapeutic effect of icariin in an animal model of glucocorticoid-induced depression remains unclear. This study aimed to investigate antidepressant-like effect and the possible mechanisms of icariin in a rat model of corticosterone (CORT)-induced depression by using a combination of behavioral and biochemical assessments and NMR-based metabonomics. The depression model was established by subcutaneous injections of CORT for 21 consecutive days in rats, as evidenced by reduced sucrose intake and hippocampal brain-derived neurotrophic factor (BDNF) levels, together with an increase in immobility time in a forced swim test (FST). Icariin significantly increased sucrose intake and hippocampal BDNF level and decreased the immobility time in FST in CORT-induced depressive rats, suggesting its potent antidepressant activity. Moreover, metabonomic analysis identified eight, five and three potential biomarkers associated with depression in serum, urine and brain tissue extract, respectively. These biomarkers are primarily involved in energy metabolism, lipid metabolism, amino acid metabolism and gut microbe metabolism. Icariin reversed the pathological process of CORT-induced depression, partially via regulation of the disturbed metabolic pathways. These results provide important mechanistic insights into the protective effects of icariin against CORT-induced depression and metabolic dysfunction.

  16. Crystal structure of ATP-binding subunit of an ABC transporter from Geobacillus kaustophilus.

    Science.gov (United States)

    Manjula, M; Pampa, K J; Kumar, S M; Mukherjee, S; Kunishima, N; Rangappa, K S; Lokanath, N K

    2015-03-27

    The ATP binding cassette (ABC) transporters, represent one of the largest superfamilies of primary transporters, which are very essential for various biological functions. The crystal structure of ATP-binding subunit of an ABC transporter from Geobacillus kaustophilus has been determined at 1.77 Å resolution. The crystal structure revealed that the protomer has two thick arms, (arm I and II), which resemble 'L' shape. The ATP-binding pocket is located close to the end of arm I. ATP molecule is docked into the active site of the protein. The dimeric crystal structure of ATP-binding subunit of ABC transporter from G. kaustophilus has been compared with the previously reported crystal structure of ATP-binding subunit of ABC transporter from Salmonella typhimurium.

  17. Effects of water models on binding affinity: evidence from all-atom simulation of binding of tamiflu to A/H5N1 neuraminidase.

    Science.gov (United States)

    Nguyen, Trang Truc; Viet, Man Hoang; Li, Mai Suan

    2014-01-01

    The influence of water models SPC, SPC/E, TIP3P, and TIP4P on ligand binding affinity is examined by calculating the binding free energy ΔG(bind) of oseltamivir carboxylate (Tamiflu) to the wild type of glycoprotein neuraminidase from the pandemic A/H5N1 virus. ΔG(bind) is estimated by the Molecular Mechanic-Poisson Boltzmann Surface Area method and all-atom simulations with different combinations of these aqueous models and four force fields AMBER99SB, CHARMM27, GROMOS96 43a1, and OPLS-AA/L. It is shown that there is no correlation between the binding free energy and the water density in the binding pocket in CHARMM. However, for three remaining force fields ΔG(bind) decays with increase of water density. SPC/E provides the lowest binding free energy for any force field, while the water effect is the most pronounced in CHARMM. In agreement with the popular GROMACS recommendation, the binding score obtained by combinations of AMBER-TIP3P, OPLS-TIP4P, and GROMOS-SPC is the most relevant to the experiments. For wild-type neuraminidase we have found that SPC is more suitable for CHARMM than TIP3P recommended by GROMACS for studying ligand binding. However, our study for three of its mutants reveals that TIP3P is presumably the best choice for CHARMM.

  18. Exploring Protein-Peptide Binding Specificity through Computational Peptide Screening.

    Directory of Open Access Journals (Sweden)

    Arnab Bhattacherjee

    2013-10-01

    Full Text Available The binding of short disordered peptide stretches to globular protein domains is important for a wide range of cellular processes, including signal transduction, protein transport, and immune response. The often promiscuous nature of these interactions and the conformational flexibility of the peptide chain, sometimes even when bound, make the binding specificity of this type of protein interaction a challenge to understand. Here we develop and test a Monte Carlo-based procedure for calculating protein-peptide binding thermodynamics for many sequences in a single run. The method explores both peptide sequence and conformational space simultaneously by simulating a joint probability distribution which, in particular, makes searching through peptide sequence space computationally efficient. To test our method, we apply it to 3 different peptide-binding protein domains and test its ability to capture the experimentally determined specificity profiles. Insight into the molecular underpinnings of the observed specificities is obtained by analyzing the peptide conformational ensembles of a large number of binding-competent sequences. We also explore the possibility of using our method to discover new peptide-binding pockets on protein structures.

  19. Predicting where small molecules bind at protein-protein interfaces.

    Directory of Open Access Journals (Sweden)

    Peter Walter

    Full Text Available Small molecules that bind at protein-protein interfaces may either block or stabilize protein-protein interactions in cells. Thus, some of these binding interfaces may turn into prospective targets for drug design. Here, we collected 175 pairs of protein-protein (PP complexes and protein-ligand (PL complexes with known three-dimensional structures for which (1 one protein from the PP complex shares at least 40% sequence identity with the protein from the PL complex, and (2 the interface regions of these proteins overlap at least partially with each other. We found that those residues of the interfaces that may bind the other protein as well as the small molecule are evolutionary more conserved on average, have a higher tendency of being located in pockets and expose a smaller fraction of their surface area to the solvent than the remaining protein-protein interface region. Based on these findings we derived a statistical classifier that predicts patches at binding interfaces that have a higher tendency to bind small molecules. We applied this new prediction method to more than 10,000 interfaces from the protein data bank. For several complexes related to apoptosis the predicted binding patches were in direct contact to co-crystallized small molecules.

  20. Computer simulation study of the binding of an antiviral agent to a sensitive and a resistant human rhinovirus

    Science.gov (United States)

    Lybrand, Terry P.; McCammon, J. Andrew

    1989-01-01

    Molecular dynamics simulations have been used to study the free energy of binding of an antiviral agent to the human rhinovirus HRV-14 and to a mutant in which a valine residue in the antiviral binding pocket is replaced by leucine. The simulations predict that the antiviral should bind to the two viruses with similar affinity, in apparent disagreement with experimental results. Possible origins of this discrepancy are outlined. Of particular importance is the apparent need for methods to systematically sample all significant conformations of the leucine side chain.

  1. Deciphering the molecular basis of multidrug recognition: crystal structures of the Staphylococcus aureus multidrug binding transcription regulator QacR.

    Science.gov (United States)

    Schumacher, Maria A; Brennan, Richard G

    2003-03-01

    Multidrug transporters and their transcriptional regulators are key components of bacterial multidrug resistance (MDR). How these multidrug binding proteins can recognize such chemically disparate compounds represents a fascinating question from a structural standpoint and an important question in future drug development efforts. The Staphylococcus aureus multidrug binding regulator, QacR, is soluble and recognizes an especially wide range of structurally dissimilar compounds, properties making it an ideal model system for deciphering the molecular basis of multidrug recognition. Recent structures of QacR have afforded the first view of any MDR protein bound to multiple drugs, revealing key structural features of multidrug recognition, including a multisite binding pocket.

  2. The Bisphenol A analogue Bisphenol S binds to K-Ras4B--implications for 'BPA-free' plastics.

    Science.gov (United States)

    Schöpel, Miriam; Herrmann, Christian; Scherkenbeck, Jürgen; Stoll, Raphael

    2016-02-01

    K-Ras4B is a small GTPase that belongs to the Ras superfamily of guanine nucleotide-binding proteins. GTPases function as molecular switches in cells and are key players in intracellular signalling. Ras has been identified as an oncogene and is mutated in more than 20% of human cancers. Here, we report that Bisphenol S binds into a binding pocket of K-Ras4B previously identified for various low molecular weight compounds. Our results advocate for more comprehensive safety studies on the toxicity of Bisphenol S, as it is frequently used for Bisphenol A-free food containers.

  3. Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove

    DEFF Research Database (Denmark)

    McMurtrey, Curtis; Trolle, Thomas; Sansom, Tiffany

    2016-01-01

    N-terminal binding core yet exhibit a C-terminal extension of 1-30 amino acids. Structural analysis demonstrates that binding of extended peptides opens the HLA class I F' pocket, allowing the C-terminal extension to protrude through one end of the binding groove. In summary, we demonstrate...... cells and characterize the peptide ligands using LCMS. We identify 195 T. gondii encoded ligands originating from both secreted and cytoplasmic proteins. Surprisingly, T. gondii ligands are significantly longer than uninfected host ligands, and these longer pathogen derived peptides maintain a canonical...

  4. Development and evaluation of a new dental model at Tokyo Medical and Dental University for the practice of periodontal pocket probing.

    Science.gov (United States)

    Sunaga, Masayo; Kondo, Keiko; Adachi, Toshiko; Miura, Yoshiko; Kinoshita, Atsuhiro

    2013-09-01

    Dental and dental hygiene students must acquire the skill of measuring periodontal pockets and learn to identify the bottom of a pocket, especially of deep periodontal pockets. A new dental model that would enable students to practice measuring deep periodontal pockets was developed at the Tokyo Medical and Dental University. The purpose of this study was to evaluate the feasibility and effectiveness of this model. Twenty dental hygiene students in their third year at the school and twenty-four instructors or dental hygienists of the University Hospital measured periodontal pockets on the newly designed dental model. Feasibility and effectiveness of the model were evaluated based on periodontal probing by the students and instructors, as well as results of a questionnaire. The results demonstrated an intraexaminer agreement (within ±1 mm) averaging 91 percent. The mean percentages of correct answers of the students and instructors were 82 percent and 80 percent, respectively. More than 90 percent of the instructors and students reported that the new model would be suitable for pocket probing training. In the questionnaire, they responded that this practice using the new model would contribute to students' future and that they wanted to try other dental models with various probing depths. The new dental model designed for periodontal pocket probing training was reported to be feasible and effective for student practice.

  5. Pyrazole-based cathepsin S inhibitors with arylalkynes as P1 binding elements

    Energy Technology Data Exchange (ETDEWEB)

    Ameriks, Michael K.; Axe, Frank U.; Bembenek, Scott D.; Edwards, James P.; Gu, Yin; Karlsson, Lars; Randal, Mike; Sun, Siquan; Thurmond, Robin L.; Zhu, Jian; (J& J-PRD); (Sunesis)

    2010-01-12

    A crystal structure of 1 bound to a Cys25Ser mutant of cathepsin S helped to elucidate the binding mode of a previously disclosed series of pyrazole-based CatS inhibitors and facilitated the design of a new class of arylalkyne analogs. Optimization of the alkyne and tetrahydropyridine portions of the pharmacophore provided potent CatS inhibitors (IC{sub 50} = 40-300 nM), and an X-ray structure of 32 revealed that the arylalkyne moiety binds in the S1 pocket of the enzyme.

  6. Equity and accessibility in health? Out-of-pocket expenditures on health care in middle income countries: evidence from Mexico

    Directory of Open Access Journals (Sweden)

    Armando Arredondo

    Full Text Available This study analyzes the results of a cross-sectional survey which set out to determine the costs to patients of searching for and receiving health care in public and private institutions. The information analyzed was obtained from the study population of the Mexican National Health Survey. The dependent variable was the out-of-pocket users' costs and the independent variables were the insurance conditions, type of institution and income. The empirical findings suggest that there is a need for a more detailed analysis of user costs in middle income countries in general, where the health system is based on social security, public assistance and private institutions. This study shows that the out of pocket costs faced by users are inequitable and fall disproportionately upon socially and economically marginalized populations.

  7. The influence of closed brine pockets and permeable brine channels on the thermo-elastic properties of saline ice.

    Science.gov (United States)

    Marchenko, Aleksey; Lishman, Ben

    2017-02-13

    A model of the thermo-elastic behaviour of saline ice is formulated, and model solutions describing thermo-elastic waves (TEW) propagating into a half-space of the ice are investigated. The model is based on a proposal that saline ice is a matrix, which encompasses both closed brine pockets and permeable channels filled with brine. Experiments on the thermal expansion of saline ice samples, and on TEW in saline ice, have been performed in the cold laboratories of the University Centre in Svalbard and in University College London. The experimental data are compared with theoretical conclusions. The experimental data support our hypothesis that the brine in saline ice is divided between closed pockets and open, permeable channels.This article is part of the themed issue 'Microdynamics of ice'.

  8. Optimasi Proses Pemesinan Milling Fitur Pocket Material Baja Karbon Rendah Menggunakan Response Surface Methodology

    Directory of Open Access Journals (Sweden)

    The Jaya Suteja

    2008-01-01

    Full Text Available Milling process is one of machining process mostly used to manufacture a component. In machining a component, to achieve higher production capacity, machining time should be minimized by increasing material rate removal. However, higher material rate removal will cause higher surface roughness. For that reason, machining parameter of milling process must be optimized. This research aims to develop mathematical model which can describe the relation between step over and depth of cut with surface roughness and machining time for two cut types. Subsequently, the purpose of this research is to find the combination of step over and depth of cut which resulting the maximum material rate removal and the minimum surface roughness. Milling process in this research is performed to machine a pocket feature of low carbon steel with dimension of 20 mm x 20 mm x 1 mm. To find the optimum milling parameter, the response surface methodology is used. Based on the optimization results, recommended step over and depth of cut is 6.7582 mm and 0.22 mm. By implementing this parameter, the achieved material rate removal and surface roughness for zig-zag cut type is 9.619 mm³/s and 1.5124 μm. Meanwhile, for spiral cut type the achieved material rate removal and surface roughness is 8.981 mm³/s dan 1.3824 μm. Abstract in Bahasa Indonesia: Proses pemesinan milling merupakan salah satu proses pemesinan yang banyak digunakan untuk pembuatan suatu komponen. Dalam proses pemesinan milling waktu yang dibutuhkan untuk membuat komponen harus seminimal mungkin agar tercapai kapasitas produksi yang tinggi. Parameter proses pemotongan yang maksimum akan menghasilkan laju pemakanan material (MRR yang tinggi namun juga mengakibatkan kekasaran permukaan (Ra yang tinggi pula. Oleh karena itu, parameter proses pemesinan milling yang optimum perlu untuk diketahui. Penelitian ini bertujuan untuk mendapatkan model matematis yang dapat menggambarkan hubungan antara kedalaman pemotongan

  9. Household out-of-pocket payments for illness: Evidence from Vietnam

    Directory of Open Access Journals (Sweden)

    Janlert Urban

    2006-11-01

    Full Text Available Abstract Background In Vietnam, illnesses create high out-of-pocket health care expenditures for households. In this study, the burden of illness in the Bavi district, Vietnam is measured based upon individual household health expenditures for communicable and non-communicable illnesses. The focus of the paper is on the relative effect of different illnesses on the total economic burden of health care on households in general and on households that have catastrophic health care spending in particular. Methods The study was performed by twelve monthly follow-up interviews of 621 randomly selected households. The households are part of the FilaBavi project sample – Health System Research Project. The heads of household were interviewed at monthly intervals from July 2001 to June 2002. Results For the population in the Bavi district, communicable illnesses predominate among the episodes of illness and are the reason for most household health care expenditure. This is the case for almost all groups within the study and for the study population as a whole. However, communicable illnesses are more dominant in the poor population compared to the rich population, and are more dominant in households that have very large, or catastrophic, health care expenditure, compared to those without such expenditures. Conclusion The main findings indicate that catastrophic health care spending for a household is not usually the result of one single disastrous event, but rather a series of events and is related more to "every-day illnesses" in a developing country context than to more spectacular events such as injuries or heart illnesses.

  10. In vitro phosphorylation and acetylation of the murine pocket protein Rb2/p130.

    Directory of Open Access Journals (Sweden)

    Muhammad Saeed

    Full Text Available The retinoblastoma protein (pRb and the related proteins Rb2/p130 and 107 represent the "pocket protein" family of cell cycle regulators. A key function of these proteins is the cell cycle dependent modulation of E2F-regulated genes. The biological activity of these proteins is controlled by acetylation and phosphorylation in a cell cycle dependent manner. In this study we attempted to investigate the interdependence of acetylation and phosphorylation of Rb2/p130 in vitro. After having identified the acetyltransferase p300 among several acetyltransferases to be associated with Rb2/p130 during S-phase in NIH3T3 cells in vivo, we used this enzyme and the CDK4 protein kinase for in vitro modification of a variety of full length Rb2/p130 and truncated versions with mutations in the acetylatable lysine residues 1079, 128 and 130. Mutation of these residues results in the complete loss of Rb2/p130 acetylation. Replacement of lysines by arginines strongly inhibits phosphorylation of Rb2/p130 by CDK4; the inhibitory effect of replacement by glutamines is less pronounced. Preacetylation of Rb2/p130 strongly enhances CDK4-catalyzed phosphorylation, whereas deacetylation completely abolishes in vitro phosphorylation. In contrast, phosphorylation completely inhibits acetylation of Rb2/p130 by p300. These results suggest a mutual interdependence of modifications in a way that acetylation primes Rb2/p130 for phosphorylation and only dephosphorylated Rb2/p130 can be subject to acetylation. Human papillomavirus 16-E7 protein, which increases acetylation of Rb2/p130 by p300 strongly reduces phosphorylation of this protein by CDK4. This suggests that the balance between phosphorylation and acetylation of Rb2/p130 is essential for its biological function in cell cycle control.

  11. Lead-dependent infective endocarditis and pocket infection – similarities and differences

    Directory of Open Access Journals (Sweden)

    Anna Polewczyk

    2016-01-01

    Full Text Available Introduction : Infectious complications in patients with implanted pacemakers are divided into infections of the generator pocket (PI and lead-dependent infective endocarditis (LDIE. Aim of the research: Identification of risk factors for developing different types of infections and evaluation of the extent of infectious complications. Material and methods : We compared two groups of patients with infectious complications, who underwent transvenous lead extraction (TLE in the Reference Centre between March 2006 and July 2013. The groups consisted of 414 patients with LDIE and 205 with PI. We analysed risk factors, clinical manifestations, inflammatory markers, microbiology, and echocardiography results. Results : The coexistence of LDIE and PI was observed in 62.1% patients. There were no significant differences in the presence of host-dependent risk factors. Patients with LDIE significantly more frequently had abrasion of leads (35.1.% vs. 21.0%; p = 0.0001 connected with other procedural risk factors: a larger number of the leads (2.2 vs. 2.0; p = 0.004 lead loops (24.6% vs. 13.2%; p = 0.001, and longer time interval from the last procedure prior to TLE (28.7 vs. 22.6 months; p = 0.005. Fever and pulmonary infections, higher level of erythrocyte sedimentation rate, C-reactive protein, procalcitonin, vegetation presence, and higher pulmonary systolic pressure were also revealed in patients with LDIE. Positive blood and leads culture were observed in 34.5% and 46.4% patients with LDIE. Conclusions: The frequent coexistence of LDIE and PI confirms their common pathogenesis, but the phenomenon of abrasion suggests also another mechanism for the development of LDIE. Intensity of clinical syndromes, high inflammatory parameters, echocardiography, and microbiology findings are helpful in assessment of the extensity of the infection.

  12. Helicobacter Pylori in periodontal pockets of chronic periodontitis patients with and without type II diabetes mellitus: a randomized controlled trial

    Directory of Open Access Journals (Sweden)

    Savita Sambashivaiah

    2011-09-01

    Full Text Available This randomized controlled study evaluated the association of Helicobacter pylori (H. pylori with chronic periodontitis patients with and without type II Diabetes Mellitus. H. pylori is considered to be a pathogen responsible for gastritis, peptic ulcers and a risk factor for gastric cancer. The aim of the present study was to evaluate the association of H. pylori with chronic periodontitis patients with and without type II diabetes mellitus before and after treatment. The prevalence of H. pylori in periodontal pockets was determined by rapid urease test in a 36 patients, which were grouped as Group 1 (Healthy subjects, Group II (chronic periodontitis patients and Group III (Chronic periodontitis patients with Type II Diabetes Mellitus, 12 in each group before treatment by collecting plaque samples. After treatment, 12 plaque samples were collected and prevalence H. pylori was detected. Group II and Group III had a significantly higher rate of positive results for H. pylori compared to healthy subjects before treatment. After treatment, H. pylori were not detected in Group II and in Group III Only one of 12 chronic periodontitis patients with Type II diabetes mellitus had H. pylori in the periodontal pocket. The prevalence of H. pylori did not differ significantly between the chronic periodontitis patients with and without type II diabetes mellitus. Meticulous scaling and root planning will reduce the prevalence of H. pylori in periodontal pockets.

  13. Damage reduction to ponderosa pine seedlings from northern pocket gophers by vegetation management through grass seeding and herbicide treatment

    Science.gov (United States)

    Engeman, Richard M.; Barnes, V.G.; Anthony, R.M.; Krupa, Heather W.

    1998-01-01

    2,4-D herbicide treatment was applied to 2 treatment units to remove the forbs that are the preferred food of pocket gophers. One of these units also was seeded with grasses prior to the 2,4-D treatment. The effect of 2,4-D and grass seeding plus 2,4-D treatments were compared to an untreated control unit. Long-term monitoring (7 yr) was conducted on the 3 units for vegetative cover (7 yr), pocket gopher activity, and individual survival times and time until gopher damage for 2 cohorts of seedlings (5 and 6 yrs). The 2,4-D treatments greatly reduced vegetative cover of the forbs and seeding increased grass cover on the unit receiving that treatment. Pocket gopher activity was reduced somewhat on the unit receiving only the 2,4-D treatment and more so on the unit receiving grass seeding and 2,4-D, although gophers remained active to some degree throughout the study. Both cohorts of seedlings for both treatments units showed greater average times until gopher damage over seedlings on the control unit. However, seedling survival from all sources of mortality was not positively affected by the treatments for the first cohort of seedlings. The 2,4-D treatment appeared to have killed some of the seedlings; however, seedlings that survived the treatment were in a situation where they were less likely to be damaged by gophers and seemed to have improved growth rates.

  14. Antibiotic susceptibility of Staphylococcus aureus isolates in oral mucosa and pockets of patients with gingivitis-periodontitis.

    Science.gov (United States)

    Cuesta, Alicia I; Jewtuchowicz, Virginia M; Brusca, María I; Mujica, María T; Rosa, Alcira C

    2011-01-01

    Both oral cavity and subgingival pocket are ecological niches conducive to hosting microorganisms that may act as opportunistic pathogens, such as Staphylococcus aureus and especially methicillin-resistant Staphylococcus aureus (MRSA). Early detection of MRSA is a matter of concern to Public Health. The aim of our study was to determine phenotypic and genotypic detection of methicillin resistance of S. aureus in oral mucosa and subgingival pocket in 102 patients with gingivitis-periodontitis. The prevalence of S. aureus was 10.8% (n = 11) in subgingival pocket and 19.6% (n = 20) in oral mucosa. We obtained 31 isolates of S. aureus of which 13 were mecA positive and 18 were mecA negative. Detection of mecA gene by PCR was used as the reference method to compare the results of phenotypic methods to determine methicillin resistance. Early, accurate detection of S. aureus through phenotyping and genotyping methods is crucial for assessing the colonization and preventing the spread of MRSA.

  15. Lead isotope ratios in tree bark pockets: An indicator of past air pollution in the Czech Republic

    Energy Technology Data Exchange (ETDEWEB)

    Conkova, M. [Charles University, Faculty of Natural Sciences, Benatska 8, Prague 1 (Czech Republic)], E-mail: conkova@chmi.cz; Kubiznakova, J. [Czech Hydrometeorogical Institute, Na Sabatce 17, Prague 4 (Czech Republic)], E-mail: kubiznakova@chmi.cz

    2008-10-15

    Tree bark pockets were collected at four sites in the Czech Republic with differing levels of lead (Pb) pollution. The samples, spanning 1923-2005, were separated from beech (Fagus sylvatica) and spruce (Picea abies). Elevated Pb content (0.1-42.4 {mu}g g{sup -1}) reflected air pollution in the city of Prague. The lowest Pb content (0.3-2.6 {mu}g g{sup -1}) was found at the Kosetice EMEP 'background pollution' site. Changes in {sup 206}Pb/{sup 207}Pb and {sup 208}Pb/{sup 206}Pb isotope ratios were in agreement with operation times of the Czech main anthropogenic Pb sources. Shortly after the Second World War, the {sup 206}Pb/{sup 207}Pb isotope ratio in bark pockets decreased from 1.17 to 1.14 and the {sup 208}Pb/{sup 206}Pb isotope ratio increased from 2.12 to 2.16. Two dominant emission sources responsible for these changes, lignite and leaded petrol combustion, contributed to the shifts in Pb isotope ratios. Low-radiogenic petrol Pb ({sup 206}Pb/{sup 207}Pb of 1.11) lead to lower {sup 206}Pb/{sup 207}Pb in bark pockets over time. High-radiogenic lignite-derived Pb ({sup 206}Pb/{sup 207}Pb of 1.18 to 1.19) was detected in areas affected by coal combustion rather than by traffic.

  16. NMR-Based Diffusion Lattice Imaging

    CERN Document Server

    Laun, Frederik Bernd

    2013-01-01

    Nuclear magnetic resonance (NMR) diffusion experiments are widely employed as they yield information about structures hindering the diffusion process, e.g. about cell membranes. While it has been shown in recent articles, that these experiments can be used to determine the exact shape of closed pores averaged over a volume of interest, it is still an open question how much information can be gained in open systems. In this theoretical work, we show that the full structure information of periodic open systems is accessible. To this end, the so-called 'SEquential Rephasing by Pulsed field-gradient Encoding N Time-intervals' (SERPENT) sequence is used, which employs several diffusion weighting gradient pulses with different amplitudes. The structural information is obtained by an iterative technique relying on a Gaussian envelope model of the diffusion propagator. Two solid matrices that are surrounded by an NMR-visible medium are considered: a hexagonal lattice of cylinders and a cubic lattice of triangles.

  17. Insights into ligand binding to PreQ1 Riboswitch Aptamer from molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Zhou Gong

    Full Text Available Riboswitches play roles in transcriptional or translational regulation through specific ligand binding of their aptamer domains. Although a number of ligand-bound aptamer complex structures have been solved, it is important to know ligand-free conformations of the aptamers in order to understand the mechanism of specific binding by ligands. In this paper, preQ1 riboswitch aptamer domain from Bacillus subtilis is studied by overall 1.5 μs all-atom molecular dynamics simulations We found that the ligand-free aptamer has a stable state with a folded P1-L3 and open binding pocket. The latter forms a cytosine-rich pool in which the nucleotide C19 oscillates between close and open positions, making it a potential conformation for preQ1 entrance. The dynamic picture further suggests that the specific recognition of preQ1 by the aptamer domain is not only facilitated by the key nucleotide C19 but also aided and enhanced by other cytosines around the binding pocket. These results should help to understand the details of preQ1 binding.

  18. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.

    Directory of Open Access Journals (Sweden)

    John A Capra

    2009-12-01

    Full Text Available Identifying a protein's functional sites is an important step towards characterizing its molecular function. Numerous structure- and sequence-based methods have been developed for this problem. Here we introduce ConCavity, a small molecule binding site prediction algorithm that integrates evolutionary sequence conservation estimates with structure-based methods for identifying protein surface cavities. In large-scale testing on a diverse set of single- and multi-chain protein structures, we show that ConCavity substantially outperforms existing methods for identifying both 3D ligand binding pockets and individual ligand binding residues. As part of our testing, we perform one of the first direct comparisons of conservation-based and structure-based methods. We find that the two approaches provide largely complementary information, which can be combined to improve upon either approach alone. We also demonstrate that ConCavity has state-of-the-art performance in predicting catalytic sites and drug binding pockets. Overall, the algorithms and analysis presented here significantly improve our ability to identify ligand binding sites and further advance our understanding of the relationship between evolutionary sequence conservation and structural and functional attributes of proteins. Data, source code, and prediction visualizations are available on the ConCavity web site (http://compbio.cs.princeton.edu/concavity/.

  19. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.

    Science.gov (United States)

    Capra, John A; Laskowski, Roman A; Thornton, Janet M; Singh, Mona; Funkhouser, Thomas A

    2009-12-01

    Identifying a protein's functional sites is an important step towards characterizing its molecular function. Numerous structure- and sequence-based methods have been developed for this problem. Here we introduce ConCavity, a small molecule binding site prediction algorithm that integrates evolutionary sequence conservation estimates with structure-based methods for identifying protein surface cavities. In large-scale testing on a diverse set of single- and multi-chain protein structures, we show that ConCavity substantially outperforms existing methods for identifying both 3D ligand binding pockets and individual ligand binding residues. As part of our testing, we perform one of the first direct comparisons of conservation-based and structure-based methods. We find that the two approaches provide largely complementary information, which can be combined to improve upon either approach alone. We also demonstrate that ConCavity has state-of-the-art performance in predicting catalytic sites and drug binding pockets. Overall, the algorithms and analysis presented here significantly improve our ability to identify ligand binding sites and further advance our understanding of the relationship between evolutionary sequence conservation and structural and functional attributes of proteins. Data, source code, and prediction visualizations are available on the ConCavity web site (http://compbio.cs.princeton.edu/concavity/).

  20. Characterization of the Binding Site of Aspartame in the Human Sweet Taste Receptor.

    Science.gov (United States)

    Maillet, Emeline L; Cui, Meng; Jiang, Peihua; Mezei, Mihaly; Hecht, Elizabeth; Quijada, Jeniffer; Margolskee, Robert F; Osman, Roman; Max, Marianna

    2015-10-01

    The sweet taste receptor, a heterodimeric G protein-coupled receptor comprised of T1R2 and T1R3, binds sugars, small molecule sweeteners, and sweet proteins to multiple binding sites. The dipeptide sweetener, aspartame binds in the Venus Flytrap Module (VFTM) of T1R2. We developed homology models of the open and closed forms of human T1R2 and human T1R3 VFTMs and their dimers and then docked aspartame into the closed form of T1R2's VFTM. To test and refine the predictions of our model, we mutated various T1R2 VFTM residues, assayed activity of the mutants and identified 11 critical residues (S40, Y103, D142, S144, S165, S168, Y215, D278, E302, D307, and R383) in and proximal to the binding pocket of the sweet taste receptor that are important for ligand recognition and activity of aspartame. Furthermore, we propose that binding is dependent on 2 water molecules situated in the ligand pocket that bridge 2 carbonyl groups of aspartame to residues D142 and L279. These results shed light on the activation mechanism and how signal transmission arising from the extracellular domain of the T1R2 monomer of the sweet receptor leads to the perception of sweet taste.