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Sample records for fast kinetic ligands

  1. Fast protein folding kinetics

    Science.gov (United States)

    Gelman, Hannah; Gruebele, Martin

    2014-01-01

    Fast folding proteins have been a major focus of computational and experimental study because they are accessible to both techniques: they are small and fast enough to be reasonably simulated with current computational power, but have dynamics slow enough to be observed with specially developed experimental techniques. This coupled study of fast folding proteins has provided insight into the mechanisms which allow some proteins to find their native conformation well less than 1 ms and has uncovered examples of theoretically predicted phenomena such as downhill folding. The study of fast folders also informs our understanding of even “slow” folding processes: fast folders are small, relatively simple protein domains and the principles that govern their folding also govern the folding of more complex systems. This review summarizes the major theoretical and experimental techniques used to study fast folding proteins and provides an overview of the major findings of fast folding research. Finally, we examine the themes that have emerged from studying fast folders and briefly summarize their application to protein folding in general as well as some work that is left to do. PMID:24641816

  2. Fast protein folding kinetics.

    Science.gov (United States)

    Gelman, Hannah; Gruebele, Martin

    2014-05-01

    Fast-folding proteins have been a major focus of computational and experimental study because they are accessible to both techniques: they are small and fast enough to be reasonably simulated with current computational power, but have dynamics slow enough to be observed with specially developed experimental techniques. This coupled study of fast-folding proteins has provided insight into the mechanisms, which allow some proteins to find their native conformation well fast folders also informs our understanding of even 'slow' folding processes: fast folders are small; relatively simple protein domains and the principles that govern their folding also govern the folding of more complex systems. This review summarizes the major theoretical and experimental techniques used to study fast-folding proteins and provides an overview of the major findings of fast-folding research. Finally, we examine the themes that have emerged from studying fast folders and briefly summarize their application to protein folding in general, as well as some work that is left to do.

  3. Mechanics, thermodynamics, and kinetics of ligand binding to biopolymers.

    Science.gov (United States)

    Jarillo, Javier; Morín, José A; Beltrán-Heredia, Elena; Villaluenga, Juan P G; Ibarra, Borja; Cao, Francisco J

    2017-01-01

    Ligands binding to polymers regulate polymer functions by changing their physical and chemical properties. This ligand regulation plays a key role in many biological processes. We propose here a model to explain the mechanical, thermodynamic, and kinetic properties of the process of binding of small ligands to long biopolymers. These properties can now be measured at the single molecule level using force spectroscopy techniques. Our model performs an effective decomposition of the ligand-polymer system on its covered and uncovered regions, showing that the elastic properties of the ligand-polymer depend explicitly on the ligand coverage of the polymer (i.e., the fraction of the polymer covered by the ligand). The equilibrium coverage that minimizes the free energy of the ligand-polymer system is computed as a function of the applied force. We show how ligands tune the mechanical properties of a polymer, in particular its length and stiffness, in a force dependent manner. In addition, it is shown how ligand binding can be regulated applying mechanical tension on the polymer. Moreover, the binding kinetics study shows that, in the case where the ligand binds and organizes the polymer in different modes, the binding process can present transient shortening or lengthening of the polymer, caused by changes in the relative coverage by the different ligand modes. Our model will be useful to understand ligand-binding regulation of biological processes, such as the metabolism of nucleic acid. In particular, this model allows estimating the coverage fraction and the ligand mode characteristics from the force extension curves of a ligand-polymer system.

  4. Ligand Exchange Kinetics of Environmentally Relevant Metals

    Energy Technology Data Exchange (ETDEWEB)

    Panasci, Adele Frances [Univ. of California, Davis, CA (United States)

    2014-07-15

    The interactions of ground water with minerals and contaminants are of broad interest for geochemists but are not well understood. Experiments on the molecular scale can determine reaction parameters (i.e. rates of ligand exchange, activation entropy, activation entropy, and activation volume) that can be used in computations to gain insight into reactions that occur in natural groundwaters. Experiments to determine the rate of isotopic ligand exchange for three environmentally relevant metals, rhodium (Rh), iron (Fe), and neptunium (Np), are described. Many environmental transformations of metals (e.g. reduction) in soil occur at trivalent centers, Fe(III) in particular. Contaminant ions absorb to mineral surfaces via ligand exchange, and the reversal of this reaction can be dangerous, releasing contaminants into the environment. Ferric iron is difficult to study spectroscopically because most of its complexes are paramagnetic and are generally reactive toward ligand exchange; therefore, Rh(III), which is diamagnetic and less reactive, was used to study substitution reactions that are analogous to those that occur on mineral oxide surfaces. Studies on both Np(V) and Np(VI) are important in their own right, as 237Np is a radioactive transuranic element with a half-life of 2 million years.

  5. Kinetics of Receptor-Ligand Interactions in Immune Responses

    Institute of Scientific and Technical Information of China (English)

    Mian Long; Shouqin Lü; Ganyun Sun

    2006-01-01

    Receptor-ligand interactions in blood flow are crucial to initiate the biological processes as inflammatory cascade,platelet thrombosis, as well as tumor metastasis. To mediate cell adhesions, the interacting receptors and ligands must be anchored onto two apposing surfaces of two cells or a cell and a substratum, i.e., the two-dimensional (2D) binding, which is different from the binding of a soluble ligand in fluid phase to a receptor, i.e., three-dimensional (3D) binding. While numerous works have been focused on 3D kinetics of receptor-ligand interactions in immune systems, 2D kinetics and its regulations have less been understood, since no theoretical framework and experimental assays have been established until 1993. Not only does the molecular structure dominate 2D binding kinetics, but the shear force in blood flow also regulates cell adhesions mediated by interacting receptors and ligands. Here we provided the overview of current progresses in 2D bindings and regulations. Relevant issues of theoretical frameworks, experimental measurements, kinetic rates and binding affinities, and force regulations,were discussed.

  6. Kinetic isotope effects for fast deuterium and proton exchange rates.

    Science.gov (United States)

    Canet, Estel; Mammoli, Daniele; Kadeřávek, Pavel; Pelupessy, Philippe; Bodenhausen, Geoffrey

    2016-04-21

    By monitoring the effect of deuterium decoupling on the decay of transverse (15)N magnetization in D-(15)N spin pairs during multiple-refocusing echo sequences, we have determined fast D-D exchange rates kD and compared them with fast H-H exchange rates kH in tryptophan to determine the kinetic isotope effect as a function of pH and temperature.

  7. Active biopolymers confer fast reorganization kinetics.

    Science.gov (United States)

    Swanson, Douglas; Wingreen, Ned S

    2011-11-18

    Many cytoskeletal biopolymers are "active," consuming energy in large quantities. In this Letter, we identify a fundamental difference between active polymers and passive, equilibrium polymers: for equal mean lengths, active polymers can reorganize faster than equilibrium polymers. We show that equilibrium polymers are intrinsically limited to linear scaling between mean lifetime (or mean first-passage time, or MFPT) and mean length, MFPT∼, by analogy to 1D Potts models. By contrast, we present a simple active-polymer model that improves upon this scaling, such that MFPT∼(1/2). Since, to be biologically useful, structural biopolymers must typically be many monomers long yet respond dynamically to the needs of the cell, the difference in reorganization kinetics may help to justify the active polymers' greater energy cost.

  8. Active Polymers Confer Fast Reorganization Kinetics

    CERN Document Server

    Swanson, Douglas

    2011-01-01

    Many cytoskeletal biopolymers are "active," consuming energy in large quantities. In this Letter, we identify a fundamental difference between active polymers and passive, equilibrium polymers: for equal mean lengths, active polymers can reorganize faster than equilibrium polymers. We show that equilibrium polymers are intrinsically limited to linear scaling between mean lifetime and mean length, MFPT ~ , by analogy to 1-d Potts models. By contrast, we present a simple active-polymer model that improves upon this scaling, such that MFPT ~ ^{1/2}. Since to be biologically useful, structural biopolymers must typically be many monomers long, yet respond dynamically to the needs of the cell, the difference in reorganization kinetics may help to justify active polymers' greater energy cost. PACS numbers: 87.10.Ed, 87.16.ad, 87.16.Ln

  9. Fast kinetics of calcium signaling and sensor design.

    Science.gov (United States)

    Tang, Shen; Reddish, Florence; Zhuo, You; Yang, Jenny J

    2015-08-01

    Fast calcium signaling is regulated by numerous calcium channels exhibiting high spatiotemporal profiles which are currently measured by fluorescent calcium sensors. There is still a strong need to improve the kinetics of genetically encoded calcium indicators (sensors) to capture calcium dynamics in the millisecond time frame. In this review, we summarize several major fast calcium signaling pathways and discuss the recent developments and application of genetically encoded calcium indicators to detect these pathways. A new class of genetically encoded calcium indicators designed with site-directed mutagenesis on the surface of beta-barrel fluorescent proteins to form a pentagonal bipyramidal-like calcium binding domain dramatically accelerates calcium binding kinetics. Furthermore, novel genetically encoded calcium indicators with significantly increased fluorescent lifetime change are advantageous in deep-field imaging with high light-scattering and notable morphology change.

  10. Impact of ligand protonation on higher-order metal complexation kinetics in aqueous systems

    NARCIS (Netherlands)

    Town, R.M.; Leeuwen, van H.P.

    2008-01-01

    The impact of ligand protonation on the complexation kinetics of higher-order complexes is quantitatively described. The theory is formulated on the basis of the usual situation for metal complex formation in aqueous systems in which the exchange of water for the ligand in the inner coordination sph

  11. Impact of ligand protonation on higher-order metal complexation kinetics in aqueous systems

    NARCIS (Netherlands)

    Town, R.M.; Leeuwen, van H.P.

    2008-01-01

    The impact of ligand protonation on the complexation kinetics of higher-order complexes is quantitatively described. The theory is formulated on the basis of the usual situation for metal complex formation in aqueous systems in which the exchange of water for the ligand in the inner coordination sph

  12. The kinetics of the hydrogen/deuterium exchange of epidermal growth factor receptor ligands.

    Science.gov (United States)

    Iloro, Ibon; Narváez, Daniel; Guillén, Nancy; Camacho, Carlos M; Guillén, Lalisse; Cora, Elsa; Pastrana-Ríos, Belinda

    2008-05-15

    Five highly homologous epidermal growth factor receptor ligands were studied by mass spectral analysis, hydrogen/deuterium (H/D) exchange via attenuated total reflectance Fourier transform-infrared spectroscopy, and two-dimensional correlation analysis. These studies were performed to determine the order of events during the exchange process, the extent of H/D exchange, and associated kinetics of exchange for a comparative analysis of these ligands. Furthermore, the secondary structure composition of amphiregulin (AR) and heparin-binding-epidermal growth factor (HB-EGF) was determined. All ligands were found to have similar contributions of 3(10)-helix and random coil with varying contributions of beta-sheets and beta-turns. The extent of exchange was 40%, 65%, 55%, 65%, and 98% for EGF, transforming growth factor-alpha (TGF-alpha), AR, HB-EGF, and epiregulin (ER), respectively. The rate constants were determined and classified as fast, intermediate, and slow: for EGF the 0.20 min(-1) (Tyr), 0.09 min(-1) (Arg, beta-turns), and 1.88 x 10(-3) min(-1) (beta-sheets and 3(10)-helix); and for TGF-alpha 0.91 min(-1) (Tyr), 0.27 min(-1) (Arg, beta-turns), and 1.41 x 10(-4) min(-1) (beta-sheets). The time constants for AR 0.47 min(-1) (Tyr), 0.04 min(-1) (Arg), and 1.00 x 10(-4) min(-1) (buried 3(10)-helix, beta-turns, and beta-sheets); for HB-EGF 0.89 min(-1) (Tyr), 0.14 min(-1) (Arg and 3(10)-helix), and 1.00 x 10(-3) min(-1) (buried 3(10)-helix, beta-sheets, and beta-turns); and for epiregulin 0.16 min(-1) (Tyr), 0.03 min(-1) (Arg), and 1.00 x 10(-4) min(-1) (3(10)-helix and beta-sheets). These results provide essential information toward understanding secondary structure, H/D exchange kinetics, and solvation of these epidermal growth factor receptor ligands in their unbound state.

  13. 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...

  14. Triglyceride kinetics in fasted and fed E. coli septic rats

    Energy Technology Data Exchange (ETDEWEB)

    Lanza-Jacoby, S.; Tabares, A. (Jefferson Medical Coll., Philadelphia, PA (United States))

    1990-02-26

    The mechanism for the development of hypertriglyceridemia during gram-negative sepsis was studies by examining the liver production and clearance of very-low-density lipoprotein (VLDL) triglyceride (TG). To assess the liver output and peripheral clearance the kinetics of VLDL-TG were determined by a constant intravenous infusion of (2-{sup 3}H) glycerol-labeled VLDL in fasted control, fasted E. coli-treated, fed control, and fed E.coli-treated rats. Lewis inbred rats, 275-300 g, were made septic with 8 {times} 10{sup 7} live E.coli colonies per 100 g body weight. Twenty-four hours following E.coli injection serum TG of fasted E.coli-treated rats was elevated by 170% which was attributed to a 67% decrease in the clearance rate of VLDL-TG in fasted E.coli-treated rats compared with their fasted controls. The secretion of VLDL-TG declined by 31% in the livers of the fasted E.coli-treated rats which was accompanied by a 2-fold increase in the composition of liver TG. In a second series of experiments control and E.coli-treated rats were fed intragastrically (IG) a balanced solution containing glucose plus fat as the sources of nonprotein calories. Serum TG were 26% lower in the fed E.coli-treated rats because the clearance rate increased by 86%. The secretion of TG in the fed septic rats increased by 40% but this difference was not significant. In the septic rat the ability to clear triglycerides from the plasma depends upon the nutritional state.

  15. Thermo-Kinetic Investigation of Comparative Ligand Effect on Cysteine Iron Redox Reaction

    Directory of Open Access Journals (Sweden)

    Masood Ahmad Rizvi

    2015-03-01

    Full Text Available Transition metal ions in their free state bring unwanted biological oxidations generating oxidative stress. The ligand modulated redox potential can be indispensable in prevention of such oxidative stress by blocking the redundant bio-redox reactions. In this study we investigated the comparative ligand effect on the thermo-kinetic aspects of biologically important cysteine iron (III redox reaction using spectrophotometric and potentiometric methods. The results were corroborated with the complexation effect on redox potential of iron(III-iron(II redox couple. The selected ligands were found to increase the rate of cysteine iron (III redox reaction in proportion to their stability of iron (II complex (EDTA < terpy < bipy < phen. A kinetic profile and the catalytic role of copper (II ions by means of redox shuttle mechanism for the cysteine iron (III redox reaction in presence of 1,10-phenanthroline (phen ligand is also reported.

  16. Ligand-receptor binding kinetics in surface plasmon resonance cells: A Monte Carlo analysis

    CERN Document Server

    Carroll, Jacob; Forsten-Williams, Kimberly; Täuber, Uwe C

    2016-01-01

    Surface plasmon resonance (SPR) chips are widely used to measure association and dissociation rates for the binding kinetics between two species of chemicals, e.g., cell receptors and ligands. It is commonly assumed that ligands are spatially well mixed in the SPR region, and hence a mean-field rate equation description is appropriate. This approximation however ignores the spatial fluctuations as well as temporal correlations induced by multiple local rebinding events, which become prominent for slow diffusion rates and high binding affinities. We report detailed Monte Carlo simulations of ligand binding kinetics in an SPR cell subject to laminar flow. We extract the binding and dissociation rates by means of the techniques frequently employed in experimental analysis that are motivated by the mean-field approximation. We find major discrepancies in a wide parameter regime between the thus extracted rates and the known input simulation values. These results underscore the crucial quantitative importance of s...

  17. Kinetic Studies of the Coordination of Mono- and Ditopic Ligands with First Row Transition Metal Ions.

    Science.gov (United States)

    Munzert, Stefanie Martina; Schwarz, Guntram; Kurth, Dirk G

    2016-03-01

    The reactions of the ditopic ligand 1,4-bis(2,2':6',2″-terpyridin-4'-yl)benzene (1) as well as the monotopic ligands 4'-phenyl-2,2':6',2″-terpyridine (2) and 2,2':6',2″-terpyridine (3) with Fe(2+), Co(2+), and Ni(2+) in solution are studied. While the reaction of 1 with Fe(2+), Co(2+), and Ni(2+) results in metallo-supramolecular coordination polyelectrolytes (MEPEs), ligands 2 and 3 give mononuclear complexes. All compounds are analyzed by UV/vis and fluorescence spectroscopy. Fluorescence spectroscopy indicates that protonation as well as coordination to Zn(2+) leads to an enhanced fluorescence of the terpyridine ligands. In contrast, Fe(2+), Co(2+), or Ni(2+) quench the fluorescence of the ligands. The kinetics of the reactions are studied by stopped-flow fluorescence spectroscopy. Analysis of the measured data is presented and the full kinetic rate laws for the coordination of the terpyridine ligands 1, 2, and 3 to Fe(2+), Co(2+), and Ni(2+) are presented. The coordination occurs within a few seconds, and the rate constant increases in the order Ni(2+) < Co(2+) < Fe(2+). With the rate constants at hand, the polymer growth of Ni-MEPE is computed.

  18. Simple and fast screening of G-quadruplex ligands with electrochemical detection system.

    Science.gov (United States)

    Fan, Qiongxuan; Li, Chao; Tao, Yaqin; Mao, Xiaoxia; Li, Genxi

    2016-11-01

    Small molecules that may facilitate and stabilize the formation of G-quadruplexes can be used for cancer treatments, because the G-quadruplex structure can inhibit the activity of telomerase, an enzyme over-expressed in many cancer cells. Therefore, there is considerable interest in developing a simple and high-performance method for screening small molecules binding to G-quadruplex. Here, we have designed a simple electrochemical approach to screen such ligands based on the fact that the formation and stabilization of G-quadruplex by ligand may inhibit electron transfer of redox species to electrode surface. As a proof-of-concept study, two types of classical G-quadruplex ligands, TMPyP4 and BRACO-19, are studied in this work, which demonstrates that this method is fast and robust and it may be applied to screen G-quadruplex ligands for anticancer drugs testing and design in the future.

  19. Modulation of fast synaptic transmission by presynaptic ligand-gated cation channels.

    Science.gov (United States)

    Khakh, B S; Henderson, G

    2000-07-01

    There is now considerable evidence demonstrating that ligand-gated cation channels (i.e., P2X, nicotinic, kainate, NMDA, AMPA and 5-HT(3) receptors), in addition to mediating fast excitatory neurotransmission, may be located presynaptically on nerve terminals in the peripheral and central nervous systems where they function to modulate neurotransmitter release. This modulation can be facilitation, inhibition or both. In this article, we first outline the multiple mechanisms by which activation of presynaptic ligand-gated cation channels can modulate spontaneous and evoked neurotransmitter release, before reviewing in detail published electrophysiological studies of presynaptic P2X, nicotinic, kainate, NMDA, AMPA and 5-HT(3) receptors.

  20. Impact of ligand protonation on higher-order metal complexation kinetics in aqueous systems.

    Science.gov (United States)

    Town, Raewyn M; Leeuwen, Herman P van

    2008-03-27

    The impact of ligand protonation on the complexation kinetics of higher-order complexes is quantitatively described. The theory is formulated on the basis of the usual situation for metal complex formation in aqueous systems in which the exchange of water for the ligand in the inner coordination sphere is rate-determining (Eigen mechanism). We derive expressions for the general case of lability of ML(n) species that account for the contributions from all outer-sphere complexes to the rate of complex formation. For dynamic complexes, dissociation of ML is usually the rate-determining step in the overall process ML(n) --> M. Under such conditions, it is the role of ligand protonation in the step ML --> M that is relevant for the kinetic flux. 1:2 complexes of Cd(II) with pyridine-2,6-dicarboxylic acid fall into this category, and their lability at a microelectrode is reasonably well predicted by the differentiated approach. For non-dynamic systems, the kinetic flux arising from dissociation of higher-order complexes contributes to the rate-determining step. In this case, the weighted contribution of protonated and unprotonated outer-sphere complexes in all contributing dissociation reactions must be taken into account. The kinetic flux arising from the dissociation of 1:2 complexes of Ni(II) with bicine at a conventional electrode was quite well described by this combined approach. The results establish the generic role of ligand protonation within the overall framework of metal complexation kinetics in which complexes may be dynamic to an extent that depends on the operational time scale of the measurement technique.

  1. Gompertz kinetics model of fast chemical neurotransmission currents.

    Science.gov (United States)

    Easton, Dexter M

    2005-10-01

    At a chemical synapse, transmitter molecules ejected from presynaptic terminal(s) bind reversibly with postsynaptic receptors and trigger an increase in channel conductance to specific ions. This paper describes a simple but accurate predictive model for the time course of the synaptic conductance transient, based on Gompertz kinetics. In the model, two simple exponential decay terms set the rates of development and decline of transmitter action. The first, r, triggering conductance activation, is surrogate for the decelerated rate of growth of conductance, G. The second, r', responsible for Y, deactivation of the conductance, is surrogate for the decelerated rate of decline of transmitter action. Therefore, the differential equation for the net conductance change, g, triggered by the transmitter is dg/dt=g(r-r'). The solution of that equation yields the product of G(t), representing activation, and Y(t), which defines the proportional decline (deactivation) of the current. The model fits, over their full-time course, published records of macroscopic ionic current associated with fast chemical transmission. The Gompertz model is a convenient and accurate method for routine analysis and comparison of records of synaptic current and putative transmitter time course. A Gompertz fit requiring only three independent rate constants plus initial current appears indistinguishable from a Markov fit using seven rate constants.

  2. Macroscopic kinetics of pentameric ligand gated ion channels: comparisons between two prokaryotic channels and one eukaryotic channel.

    Science.gov (United States)

    Laha, Kurt T; Ghosh, Borna; Czajkowski, Cynthia

    2013-01-01

    Electrochemical signaling in the brain depends on pentameric ligand-gated ion channels (pLGICs). Recently, crystal structures of prokaryotic pLGIC homologues from Erwinia chrysanthemi (ELIC) and Gloeobacter violaceus (GLIC) in presumed closed and open channel states have been solved, which provide insight into the structural mechanisms underlying channel activation. Although structural studies involving both ELIC and GLIC have become numerous, thorough functional characterizations of these channels are still needed to establish a reliable foundation for comparing kinetic properties. Here, we examined the kinetics of ELIC and GLIC current activation, desensitization, and deactivation and compared them to the GABAA receptor, a prototypic eukaryotic pLGIC. Outside-out patch-clamp recordings were performed with HEK-293T cells expressing ELIC, GLIC, or α1β2γ2L GABAA receptors, and ultra-fast ligand application was used. In response to saturating agonist concentrations, we found both ELIC and GLIC current activation were two to three orders of magnitude slower than GABAA receptor current activation. The prokaryotic channels also had slower current desensitization on a timescale of seconds. ELIC and GLIC current deactivation following 25 s pulses of agonist (cysteamine and pH 4.0 buffer, respectively) were relatively fast with time constants of 24.9 ± 5.1 ms and 1.2 ± 0.2 ms, respectively. Surprisingly, ELIC currents evoked by GABA activated very slowly with a time constant of 1.3 ± 0.3 s and deactivated even slower with a time constant of 4.6 ± 1.2 s. We conclude that the prokaryotic pLGICs undergo similar agonist-mediated gating transitions to open and desensitized states as eukaryotic pLGICs, supporting their use as experimental models. Their uncharacteristic slow activation, slow desensitization and rapid deactivation time courses are likely due to differences in specific structural elements, whose future identification may help uncover mechanisms underlying p

  3. Binding kinetics of membrane-anchored receptors and ligands: Molecular dynamics simulations and theory.

    Science.gov (United States)

    Hu, Jinglei; Xu, Guang-Kui; Lipowsky, Reinhard; Weikl, Thomas R

    2015-12-28

    The adhesion of biological membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. Central questions are how the binding kinetics of these proteins is affected by the membranes and by the membrane anchoring of the proteins. In this article, we (i) present detailed data for the binding of membrane-anchored proteins from coarse-grained molecular dynamics simulations and (ii) provide a theory that describes how the binding kinetics depends on the average separation and thermal roughness of the adhering membranes and on the anchoring, lengths, and length variations of the proteins. An important element of our theory is the tilt of bound receptor-ligand complexes and transition-state complexes relative to the membrane normals. This tilt results from an interplay of the anchoring energy and rotational entropy of the complexes and facilitates the formation of receptor-ligand bonds at membrane separations smaller than the preferred separation for binding. In our simulations, we have considered both lipid-anchored and transmembrane receptor and ligand proteins. We find that the binding equilibrium constant and binding on-rate constant of lipid-anchored proteins are considerably smaller than the binding constant and on-rate constant of rigid transmembrane proteins with identical binding domains.

  4. Synthesis and Thermal Decomposition Kinetics of La(Ⅲ) Complex with Unsymmetrical Schiff Base Zwitterion Ligand

    Institute of Scientific and Technical Information of China (English)

    Bi Caifeng; Xiao Yan; Fan Yuhua; Xie Sitan; Xu Jiakun

    2007-01-01

    A new unsymmetrical solid Schiff base (LLi) was synthesized using L-lysine. o-vanillin and 2-hydroxy-l-naph-thaldehyde. Solid La (Ⅲ) complex of this ligand [LaL(NO3)](NO3)·2H2O was prepared and characterized by elemental analyses, IR, UV and molar conductance. The thermal decomposition kinetics of the complex for the second stage were studied under non-isothermal condition by TG and DTG methods. The kinetic equation may be expressed as: dα/dt=A·e-E/RT·(1-α)2. The kinetic parameters (E, A), activation entropy ΔS≠ and activation free-energy ΔG≠ were also gained.

  5. Resolving the fast kinetics of cooperative binding: Ca2+ buffering by calretinin.

    Directory of Open Access Journals (Sweden)

    Guido C Faas

    2007-11-01

    Full Text Available Cooperativity is one of the most important properties of molecular interactions in biological systems. It is the ability to influence ligand binding at one site of a macromolecule by previous ligand binding at another site of the same molecule. As a consequence, the affinity of the macromolecule for the ligand is either decreased (negative cooperativity or increased (positive cooperativity. Over the last 100 years, O2 binding to hemoglobin has served as the paradigm for cooperative ligand binding and allosteric modulation, and four practical models were developed to quantitatively describe the mechanism: the Hill, the Adair-Klotz, the Monod-Wyman-Changeux, and the Koshland-Némethy-Filmer models. The predictions of these models apply under static conditions when the binding reactions are at equilibrium. However, in a physiological setting, e.g., inside a cell, the timing and dynamics of the binding events are essential. Hence, it is necessary to determine the dynamic properties of cooperative binding to fully understand the physiological implications of cooperativity. To date, the Monod-Wyman-Changeux model was applied to determine the kinetics of cooperative binding to biologically active molecules. In this model, cooperativity is established by postulating two allosteric isoforms with different binding properties. However, these studies were limited to special cases, where transition rates between allosteric isoforms are much slower than the binding rates or where binding and unbinding rates could be measured independently. For all other cases, the complex mathematical description precludes straightforward interpretations. Here, we report on calculating for the first time the fast dynamics of a cooperative binding process, the binding of Ca2+ to calretinin. Calretinin is a Ca2+-binding protein with four cooperative binding sites and one independent binding site. The Ca2+ binding to calretinin was assessed by measuring the decay of free Ca2

  6. Slow VO2 off-kinetics in skeletal muscle is associated with fast PCr off-kinetics--and inversely.

    Science.gov (United States)

    Korzeniewski, Bernard; Zoladz, Jerzy A

    2013-09-01

    The computer model of the bioenergetic system in skeletal muscle, developed previously, was used to study the effect of the characteristic decay time of the parallel activation of oxidative phosphorylation [τ(OFF)] during muscle recovery on the muscle oxygen consumption rate (Vo2) and phosphocreatine (PCr) work-to-rest transition (off)-kinetics and on the relationship between the Vo2 and PCr rest-to-work transition (on)- and off-kinetics in moderate and heavy exercise. An increase in τ(OFF) slows down the initial phase of the muscle Vo2 off-kinetics and accelerates the PCr off-kinetics. As a result, the relationship between the initial phase of the Vo2 off-kinetics (lasting approximately 3-60 s in computer simulations) and the PCr off-kinetics is inverse: the slower the former, the faster the latter. A faster initial phase of the Vo2 off-kinetics is associated with a slower late phase of the Vo2 off-kinetics, and as a result, the integral of Vo2 above baseline during recovery, representing the oxygen debt, is identical in all cases [values of τ(OFF)] for a given PCr decrease. Depending on τ(OFF), the muscle Vo2 on-kinetics was either equally fast or slower than the Vo2 off-kinetics in moderate exercise and always slower in heavy exercise. PCr on-kinetics was always faster than PCr off-kinetics. This study clearly demonstrates that τ(OFF) has a pronounced impact on the mutual relations between the muscle Vo2 and PCr on- and off-kinetics.

  7. Equilibrium and kinetic studies on ligand substitution reactions of chloromethyl(aquo)cobaloxime with aromatic and aliphatic N-donor ligands

    Indian Academy of Sciences (India)

    D Sudarshan Reddy; S Satyanarayana

    2003-06-01

    Equilibria and kinetics of the reactions of chloromethyl(aquo)cobaloxime with histamine, histidine, glycine and ethyl glycine ester were studied as a function of pH at 25°C, 1.0 M ionic strength (KCl) by spectrophotometric techniques. Comparison of equilibrium constants and rate constants tells that the order is Hisdn > Hiamn > Gly > EtGlyest. The rate of substitution of H2O varies with the p of the incoming ligand and nucleophilic participation of the ligand in the transition state. The rate constants and equilibrium constants are correlated to the hardness and softness of the ligands and the Co(III) of cobaloxime.

  8. Combination of isothermal titration calorimetry and time-resolved luminescence for high affinity antibody-ligand interaction thermodynamics and kinetics

    Science.gov (United States)

    Aweda, Tolulope A.; Meares, Claude F.

    2011-01-01

    For experiments using synthetic ligands as probes for biological experiments, it is useful to determine the specificity and affinity of the ligands for their receptors. As ligands with higher affinities are developed (KA >108 M−1; KD calorimetry measures heat produced or consumed during ligand binding, and also provides the equilibrium binding constant. However, as normally practiced, its range is limited. Displacement titration, where a competing weaker ligand is used to lower the apparent affinity of the stronger ligand, can be used to determine the binding affinity as well as the complete thermodynamic data for ligand-antibody complexes with very high affinity. These equilibrium data have been combined with kinetic measurements to yield the rate constants as well. We describe this methodology, using as an example antibody 2D12.5, which captures yttrium S-2-(4-aminobenzyl)-1, 4, 7, 10-tetraazacyclododecanetetraacetate. PMID:21964396

  9. Fast pulling of ligand approach for the design of β-secretase 1 inhibitors

    Science.gov (United States)

    Truong, Duc Toan; Nguyen, Minh Tung; Vu, Van V.; Ngo, Son Tung

    2017-03-01

    The fast pulling of ligand (FPL) method, which evaluates the relative ligand-protein binding affinity with low CPU usage and high accuracy, was applied for the first time to determine the affinity of β-secretase 1 (BACE1) and its inhibitors using steered-molecular dynamics simulations. The total non-bonded interaction energy difference ΔEtotal is a highly appropriate criterion to predict the relative BACE1-inhibitor binding affinity with strong correlation to experimental data (R = 0.92) and small deviation (δEtotal = 7 %). The van der Waals interaction and electrostatic interaction contribute 56% and 44% to the total non-bonded interaction energy between BACE1 and its inhibitors.

  10. Species-specific kinetics and zonation of hepatic DNA synthesis induced by ligands of PPARalpha.

    Science.gov (United States)

    Al Kholaifi, Abdullah; Amer, Abeer; Jeffery, Brett; Gray, Tim J B; Roberts, Ruth A; Bell, David R

    2008-07-01

    Peroxisome proliferator-activated receptor alpha (PPARalpha) ligands evoke a profound mitogenic response in rodent liver, and the aim of this study was to characterize the kinetics of induction of DNA synthesis. The CAR ligand, 1,4-bis[2-(3,5-dichoropyridyloxy)]benzene, caused induction of hepatocyte DNA synthesis within 48 h in 129S4/SvJae mice, but the potent PPARalpha ligand, ciprofibrate, induced hepatocyte DNA synthesis only after 3 or 4 days dosing; higher or lower doses did not hasten the DNA synthesis response. This contrasted with the rapid induction (24 h) reported by Styles et al., 1988, Carcinogenesis 9, 1647-1655. C57BL/6 and DBA/2J mice showed significant induction of DNA synthesis after 4, but not 2, days ciprofibrate treatment. Alderley Park and 129S4/SvJae mice dosed with methylclofenapate induced hepatocyte DNA synthesis at 4, but not 2, days after dosing and proved that inconsistency with prior work was not due to a difference in mouse strain or PPARalpha ligand. Ciprofibrate-induced liver DNA synthesis and growth was absent in PPARalpha-null mice and are PPARalpha dependent. In the Fisher344 rat, hepatocyte DNA synthesis was induced at 24 h after dosing, with a second peak at 48 h. Lobular localization of hepatocyte DNA synthesis showed preferential periportal induction of DNA synthesis in rat but panlobular zonation of hepatocyte DNA synthesis in mouse. These results characterize a markedly later hepatic induction of panlobular DNA synthesis by PPARalpha ligands in mouse, compared to rapid induction of periportal DNA synthesis in rat.

  11. Macroscopic kinetics of pentameric ligand gated ion channels: comparisons between two prokaryotic channels and one eukaryotic channel.

    Directory of Open Access Journals (Sweden)

    Kurt T Laha

    Full Text Available Electrochemical signaling in the brain depends on pentameric ligand-gated ion channels (pLGICs. Recently, crystal structures of prokaryotic pLGIC homologues from Erwinia chrysanthemi (ELIC and Gloeobacter violaceus (GLIC in presumed closed and open channel states have been solved, which provide insight into the structural mechanisms underlying channel activation. Although structural studies involving both ELIC and GLIC have become numerous, thorough functional characterizations of these channels are still needed to establish a reliable foundation for comparing kinetic properties. Here, we examined the kinetics of ELIC and GLIC current activation, desensitization, and deactivation and compared them to the GABAA receptor, a prototypic eukaryotic pLGIC. Outside-out patch-clamp recordings were performed with HEK-293T cells expressing ELIC, GLIC, or α1β2γ2L GABAA receptors, and ultra-fast ligand application was used. In response to saturating agonist concentrations, we found both ELIC and GLIC current activation were two to three orders of magnitude slower than GABAA receptor current activation. The prokaryotic channels also had slower current desensitization on a timescale of seconds. ELIC and GLIC current deactivation following 25 s pulses of agonist (cysteamine and pH 4.0 buffer, respectively were relatively fast with time constants of 24.9 ± 5.1 ms and 1.2 ± 0.2 ms, respectively. Surprisingly, ELIC currents evoked by GABA activated very slowly with a time constant of 1.3 ± 0.3 s and deactivated even slower with a time constant of 4.6 ± 1.2 s. We conclude that the prokaryotic pLGICs undergo similar agonist-mediated gating transitions to open and desensitized states as eukaryotic pLGICs, supporting their use as experimental models. Their uncharacteristic slow activation, slow desensitization and rapid deactivation time courses are likely due to differences in specific structural elements, whose future identification may help uncover

  12. Unanimous Model for Describing the Fast Bioluminescence Kinetics of Ca

    NARCIS (Netherlands)

    Eremeeva, Elena V.; Bartsev, Sergey I.; Berkel, van Willem J.H.; Vysotski, Eugene S.

    2017-01-01

    Upon binding their metal ion cofactors, Ca2+-regulated photoproteins display a rapid increase of light signal, which reaches its peak within milliseconds. In the present study, we investigate bioluminescence kinetics of the entire photoprotein family. All five recombinant hydromedusan Ca2+-regulated

  13. Roles of cell and microvillus deformation and receptor-ligand binding kinetics in cell rolling.

    Science.gov (United States)

    Pawar, Parag; Jadhav, Sameer; Eggleton, Charles D; Konstantopoulos, Konstantinos

    2008-10-01

    Polymorphonuclear leukocyte (PMN) recruitment to sites of inflammation is initiated by selectin-mediated PMN tethering and rolling on activated endothelium under flow. Cell rolling is modulated by bulk cell deformation (mesoscale), microvillus deformability (microscale), and receptor-ligand binding kinetics (nanoscale). Selectin-ligand bonds exhibit a catch-slip bond behavior, and their dissociation is governed not only by the force but also by the force history. Whereas previous theoretical models have studied the significance of these three "length scales" in isolation, how their interplay affects cell rolling has yet to be resolved. We therefore developed a three-dimensional computational model that integrates the aforementioned length scales to delineate their relative contributions to PMN rolling. Our simulations predict that the catch-slip bond behavior and to a lesser extent bulk cell deformation are responsible for the shear threshold phenomenon. Cells bearing deformable rather than rigid microvilli roll slower only at high P-selectin site densities and elevated levels of shear (>or=400 s(-1)). The more compliant cells (membrane stiffness=1.2 dyn/cm) rolled slower than cells with a membrane stiffness of 3.0 dyn/cm at shear rates >50 s(-1). In summary, our model demonstrates that cell rolling over a ligand-coated surface is a highly coordinated process characterized by a complex interplay between forces acting on three distinct length scales.

  14. Force-Mediated Kinetics of Single P-Selectin/Ligand Complexes Observed by Atomic Force Microscopy

    Science.gov (United States)

    Fritz, Jurgen; Katopodis, Andreas G.; Kolbinger, Frank; Anselmetti, Dario

    1998-10-01

    Leukocytes roll along the endothelium of postcapillary venules in response to inflammatory signals. Rolling under the hydrodynamic drag forces of blood flow is mediated by the interaction between selectins and their ligands across the leukocyte and endothelial cell surfaces. Here we present force-spectroscopy experiments on single complexes of P-selectin and P-selectin glycoprotein ligand-1 by atomic force microscopy to determine the intrinsic molecular properties of this dynamic adhesion process. By modeling intermolecular and intramolecular forces as well as the adhesion probability in atomic force microscopy experiments we gain information on rupture forces, elasticity, and kinetics of the P-selectin/P-selectin glycoprotein ligand-1 interaction. The complexes are able to withstand forces up to 165 pN and show a chain-like elasticity with a molecular spring constant of 5.3 pN nm-1 and a persistence length of 0.35 nm. The dissociation constant (off-rate) varies over three orders of magnitude from 0.02 s-1 under zero force up to 15 s-1 under external applied forces. Rupture force and lifetime of the complexes are not constant, but directly depend on the applied force per unit time, which is a product of the intrinsic molecular elasticity and the external pulling velocity. The high strength of binding combined with force-dependent rate constants and high molecular elasticity are tailored to support physiological leukocyte rolling.

  15. Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain.

    Science.gov (United States)

    Gilbert, Sunny D; Stoddard, Colby D; Wise, Sarah J; Batey, Robert T

    2006-06-09

    Riboswitches are cis-acting genetic regulatory elements found commonly in bacterial mRNAs that consist of a metabolite-responsive aptamer domain coupled to a regulatory switch. Purine riboswitches respond to intracellular concentrations of either adenine or guanine/hypoxanthine to control gene expression. The aptamer domain of the purine riboswitch contains a pyrimidine residue (Y74) that forms a Watson-Crick base-pairing interaction with the bound purine nucleobase ligand that discriminates between adenine and guanine. We sought to understand the structural basis of this specificity and the mechanism of ligand recognition by the purine riboswitch. Here, we present the 2,6-diaminopurine-bound structure of a C74U mutant of the xpt-pbuX guanine riboswitch, along with a detailed thermodynamic and kinetic analysis of nucleobase recognition by both the native and mutant riboswitches. These studies demonstrate clearly that the pyrimidine at position 74 is the sole determinant of purine riboswitch specificity. In addition, the mutant riboswitch binds adenine and adenine derivatives well compared with the guanine-responsive riboswitch. Under our experimental conditions, 2,6-diaminopurine binds the RNA with DeltaH=-40.3 kcal mol(-1), DeltaS=-97.6 cal mol(-1)K(-1), and DeltaG=-10.73 kcal mol(-1). A kinetic determination of the slow rate (0.15 x 10(5)M(-1)s(-1) and 2.1 x 10(5)mM(-1)s(-1) for 2-aminopurine binding the adenine-responsive mutant riboswitch and 7-deazaguanine-binding guanine riboswitch, respectively) of association under varying experimental conditions allowed us to propose a mechanism for ligand recognition by the purine riboswitch. A conformationally dynamic unliganded state for the binding pocket is stabilized first by the Watson-Crick base pairing between the ligand and Y74, and by the subsequent ordering of the J2/3 loop, enclosing the ligand within the three-way junction.

  16. Copper(II) complexes with peptides based on the second cell binding site of fibronectin: metal coordination and ligand exchange kinetics.

    Science.gov (United States)

    Pizzanelli, Silvia; Forte, Claudia; Pinzino, Calogero; Magrì, Antonio; La Mendola, Diego

    2016-02-07

    Copper(ii) complexes with short peptides based on the second cell binding site of fibronectin, PHSFN and PHSEN, have been characterized by potentiometric, UV-vis, CD, EPR and NMR spectroscopic methods. The histidine imidazole nitrogen is the anchoring site for the metal ion binding. Thermodynamic and spectroscopic evidence is given that the side chain oxygen donor atom of glutamyl residue in Ac-PHSEN-NH2 is also involved in the binding up to physiological pH. To determine ligand exchange kinetic parameters after the imidazole nitrogen anchoring, proton relaxation enhancement NMR data have been collected for the two hydrogen atoms of the imidazole ring in the temperature range 293-315 K at pH 5.2 and globally treated within different kinetic models for ligand exchange. The best fitting model involves two steps. In the first one, which is slow, a water molecule disengages a carbonyl or a carboxylate group coordinated to the metal ion in the complex formed by PHSFN or PHSEN, respectively. This stage is one order of magnitude slower for PHSEN, due to entropic effects. In the second step, which is fast, the complex just formed exchanges with the ligand. In this step, no appreciable differences are found for the two cases examined.

  17. Kinetic models for historical processes of fast invasion and aggression

    Science.gov (United States)

    Aristov, Vladimir V.; Ilyin, Oleg V.

    2015-04-01

    In the last few decades many investigations have been devoted to theoretical models in new areas concerning description of different biological, sociological, and historical processes. In the present paper we suggest a model of the Nazi Germany invasion of Poland, France, and the USSR based on kinetic theory. We simulate this process with the Cauchy boundary problem for two-element kinetic equations. The solution of the problem is given in the form of a traveling wave. The propagation velocity of a front line depends on the quotient between initial forces concentrations. Moreover it is obtained that the general solution of the model can be expressed in terms of quadratures and elementary functions. Finally it is shown that the front-line velocities agree with the historical data.

  18. Equilibria and kinetics for pH-dependent axial ligation of bromomethyl(aquo)cobaloxime by aliphatic amine ligands

    Indian Academy of Sciences (India)

    M Bhoopal; N Ravi Kumar Reddy; S Satyanarayana

    2003-04-01

    Kinetics and equilibria of axial ligation of bromomethyl(aquo) cobaloxime by a series of straight chain primary amines (methylamine, ethylamine, propylamine, butylamine, pentylamine, hexylamine), cycloamines (cyclopentylamine, cyclohexylamine, cycloheptylamine) and secondary amines (N,N-dimethylamine, N,N-diethylamine) have been measured as functions of pH by spectrophotometric technique in aqueous solution, ionic strength 1 M (KCl) at 25°C. The rate of substitution of H2O varies with the Ka of incoming ligand, thus establishing nucleophilic participation of the ligand in the transition state. Binding and kinetic data are interpreted based on the basicity and steric influence of the entering ligand. To compare the rate constants of the entering ligands, pH independent second-order rate constants (on) are calculated.

  19. Cyclam Derivatives with a Bis(phosphinate) or a Phosphinato-Phosphonate Pendant Arm: Ligands for Fast and Efficient Copper(II) Complexation for Nuclear Medical Applications.

    Science.gov (United States)

    David, Tomáš; Kubíček, Vojtěch; Gutten, Ondrej; Lubal, Přemysl; Kotek, Jan; Pietzsch, Hans-Jürgen; Rulíšek, Lubomír; Hermann, Petr

    2015-12-21

    Cyclam derivatives bearing one geminal bis(phosphinic acid), -CH2PO2HCH2PO2H2 (H2L(1)), or phosphinic-phosphonic acid, -CH2PO2HCH2PO3H2 (H3L(2)), pendant arm were synthesized and studied as potential copper(II) chelators for nuclear medical applications. The ligands showed good selectivity for copper(II) over zinc(II) and nickel(II) ions (log KCuL = 25.8 and 27.7 for H2L(1) and H3L(2), respectively). Kinetic study revealed an unusual three-step complex formation mechanism. The initial equilibrium step leads to out-of-cage complexes with Cu(2+) bound by the phosphorus-containing pendant arm. These species quickly rearrange to an in-cage complex with cyclam conformation II, which isomerizes to another in-cage complex with cyclam conformation I. The first in-cage complex is quantitatively formed in seconds (pH ≈5, 25 °C, Cu:L = 1:1, cM ≈ 1 mM). At pH >12, I isomers undergo nitrogen atom inversion, leading to III isomers; the structure of the III-[Cu(HL(2))] complex in the solid state was confirmed by X-ray diffraction analysis. In an alkaline solution, interconversion of the I and III isomers is mutual, leading to the same equilibrium isomeric mixture; such behavior has been observed here for the first time for copper(II) complexes of cyclam derivatives. Quantum-chemical calculations showed small energetic differences between the isomeric complexes of H3L(2) compared with analogous data for isomeric complexes of cyclam derivatives with one or two methylphosphonic acid pendant arm(s). Acid-assisted dissociation proved the kinetic inertness of the complexes. Preliminary radiolabeling of H2L(1) and H3L(2) with (64)Cu was fast and efficient, even at room temperature, giving specific activities of around 70 GBq of (64)Cu per 1 μmol of the ligand (pH 6.2, 10 min, ca. 90 equiv of the ligand). These specific activities were much higher than those of H3nota and H4dota complexes prepared under identical conditions. The rare combination of simple ligand synthesis, very

  20. Molecular Dynamics Simulations and Kinetic Measurements to Estimate and Predict Protein-Ligand Residence Times.

    Science.gov (United States)

    Mollica, Luca; Theret, Isabelle; Antoine, Mathias; Perron-Sierra, Françoise; Charton, Yves; Fourquez, Jean-Marie; Wierzbicki, Michel; Boutin, Jean A; Ferry, Gilles; Decherchi, Sergio; Bottegoni, Giovanni; Ducrot, Pierre; Cavalli, Andrea

    2016-08-11

    Ligand-target residence time is emerging as a key drug discovery parameter because it can reliably predict drug efficacy in vivo. Experimental approaches to binding and unbinding kinetics are nowadays available, but we still lack reliable computational tools for predicting kinetics and residence time. Most attempts have been based on brute-force molecular dynamics (MD) simulations, which are CPU-demanding and not yet particularly accurate. We recently reported a new scaled-MD-based protocol, which showed potential for residence time prediction in drug discovery. Here, we further challenged our procedure's predictive ability by applying our methodology to a series of glucokinase activators that could be useful for treating type 2 diabetes mellitus. We combined scaled MD with experimental kinetics measurements and X-ray crystallography, promptly checking the protocol's reliability by directly comparing computational predictions and experimental measures. The good agreement highlights the potential of our scaled-MD-based approach as an innovative method for computationally estimating and predicting drug residence times.

  1. Carbon nanoparticle-modified multi-wall carbon nanotubes with fast adsorption kinetics for water treatment

    Science.gov (United States)

    Wang, Guan; Ren, Wei; Tan, Hui Ru; Liu, Ye

    2017-02-01

    Carbon nanoparticle-modified multi-wall carbon nanotubes were prepared using a dehydration of carbohydrate compound method. The structural change was characterized by transmission electron microscopy, Raman spectroscopy, and Brunauer, Emmett and Teller measurement. Fast adsorption kinetics was observed for multi-wall carbon nanotubes with modification, as demonstrated by the adsorption of the model compound methylene blue. This work provides a novel facile engineering strategy to equip multi-wall carbon nanotubes with fast adsorption kinetics, which is promising for efficient water purification.

  2. Fast synthesis of dopamine-coated Fe3O4 nanoparticles through ligand-exchange method

    Institute of Scientific and Technical Information of China (English)

    Peng An; Fang Zuo; Yuan Peng Wu; Jun Hua Zhang; Zhao Hui Zheng; Xiao Bin Ding; Yu Xing Peng

    2012-01-01

    A fast approach was described for the synthesis of water-dispersible monodisperse dopamine-coated Fe3O4 nanoparticles (DA-Fe3O4) with uniform size and shape via ligand-exchange of oleic acid on Fe3O4 using only 2 min.The prepared DA-Fe3O4 nanoparticles were characterized by transmission electron microscopy,Fourier transform infrared spectrometry,and vibrating sample magnetometer.The results indicated that the resulting DA-Fe3O4 nanoparticles had an average diameter of about 19.2 nm.The magnetic saturation value of the prepared DA-Fe3O4 nanoparticles was determined to be 72.87 emu/g,which indicating a wellestablished superparamagnetic property.

  3. Fast automated placement of polar hydrogen atoms in protein-ligand complexes

    Directory of Open Access Journals (Sweden)

    Lippert Tobias

    2009-08-01

    Full Text Available Abstract Background Hydrogen bonds play a major role in the stabilization of protein-ligand complexes. The ability of a functional group to form them depends on the position of its hydrogen atoms. An accurate knowledge of the positions of hydrogen atoms in proteins is therefore important to correctly identify hydrogen bonds and their properties. The high mobility of hydrogen atoms introduces several degrees of freedom: Tautomeric states, where a hydrogen atom alters its binding partner, torsional changes where the position of the hydrogen atom is rotated around the last heavy-atom bond in a residue, and protonation states, where the number of hydrogen atoms at a functional group may change. Also, side-chain flips in glutamine and asparagine and histidine residues, which are common crystallographic ambiguities must be identified before structure-based calculations can be conducted. Results We have implemented a method to determine the most probable hydrogen atom positions in a given protein-ligand complex. Optimality of hydrogen bond geometries is determined by an empirical scoring function which is used in molecular docking. This allows to evaluate protein-ligand interactions with an established model. Also, our method allows to resolve common crystallographic ambiguities such as as flipped amide groups and histidine residues. To ensure high speed, we make use of a dynamic programming approach. Conclusion Our results were checked against selected high-resolution structures from an external dataset, for which the positions of the hydrogen atoms have been validated manually. The quality of our results is comparable to that of other programs, with the advantage of being fast enough to be applied on-the-fly for interactive usage or during score evaluation.

  4. Kinetic consequences of introducing a proximal selenocysteine ligand into cytochrome P450cam.

    Science.gov (United States)

    Vandemeulebroucke, An; Aldag, Caroline; Stiebritz, Martin T; Reiher, Markus; Hilvert, Donald

    2015-11-10

    The structural, electronic, and catalytic properties of cytochrome P450cam are subtly altered when the cysteine that coordinates to the heme iron is replaced with a selenocysteine. To map the effects of the sulfur-to-selenium substitution on the individual steps of the catalytic cycle, we conducted a comparative kinetic analysis of the selenoenzyme and its cysteine counterpart. Our results show that the more electron-donating selenolate ligand has only negligible effects on substrate, product, and oxygen binding, electron transfer, catalytic turnover, and coupling efficiency. Off-pathway reduction of oxygen to give superoxide is the only step significantly affected by the mutation. Incorporation of selenium accelerates this uncoupling reaction approximately 50-fold compared to sulfur, but because the second electron transfer step is much faster, the impact on overall catalytic turnover is minimal. Density functional theory calculations with pure and hybrid functionals suggest that superoxide formation is governed by a delicate interplay of spin distribution, spin state, and structural effects. In light of the remarkably similar electronic structures and energies calculated for the sulfur- and selenium-containing enzymes, the ability of the heavier atom to enhance the rate of spin crossover may account for the experimental observations. Because the selenoenzyme closely mimics wild-type P450cam, even at the level of individual steps in the reaction cycle, selenium represents a unique mechanistic probe for analyzing the role of the proximal ligand and spin crossovers in P450 chemistry.

  5. Effect of Global ATGL Knockout on Murine Fasting Glucose Kinetics

    Directory of Open Access Journals (Sweden)

    Margarida Coelho

    2015-01-01

    Full Text Available Mice deficient in adipose triglyceride lipase (ATGL−/− present elevated ectopic lipid levels but are paradoxically glucose-tolerant. Measurement of endogenous glucose production (EGP and Cori cycle activity provide insights into the maintenance of glycemic control in these animals. These parameters were determined in 7 wild-type (ATGL+/− and 6 ATGL−/− mice by a primed-infusion of [U-13C6]glucose followed by LC-MS/MS targeted mass-isotopomer analysis of blood glucose. EGP was quantified by isotope dilution of [U-13C6]glucose while Cori cycling was estimated by analysis of glucose triose 13C-isotopomers. Fasting plasma free fatty-acids were significantly lower in ATGL−/− versus control mice (0.43 ± 0.05 mM versus 0.73 ± 0.11 mM, P<0.05. Six-hour fasting EGP rates were identical for both ATGL−/− and control mice (79 ± 11 versus 71 ± 7 μmol/kg/min, resp.. Peripheral glucose metabolism was dominated by Cori cycling (80 ± 2% and 82 ± 7% of glucose disposal for ATGL−/− and control mice, resp. indicating that peripheral glucose oxidation was not significantly upregulated in ATGL−/− mice under these conditions. The glucose 13C-isotopomer distributions in both ATGL−/− and control mice were consistent with extensive hepatic pyruvate recycling. This suggests that gluconeogenic outflow from the Krebs cycle was also well compensated in ATGL−/− mice.

  6. Kinetics of circulating endogenous insulin, C-peptide, and proinsulin in fasting nondiabetic man

    DEFF Research Database (Denmark)

    Henriksen, J H; Tronier, B; Bülow, J B

    1987-01-01

    Plasma concentrations of insulin, C-peptide, and proinsulin were measured in different vascular beds in order to determine renal, hepatic, and systemic kinetics of the endogenous peptides in the fasting condition. Nineteen nondiabetic subjects were studied, two were normal, nine had minor vascular...

  7. Cascade ultrafiltration and competing ligand exchange for kinetic speciation of aluminium, iron, and nickel in fresh water.

    Science.gov (United States)

    Hassan, Nouri M; Murimboh, John D; Sekaly, Amina L R; Mandal, Rupasri; Chakrabarti, Chuni L; Grégoire, D Conrad

    2006-04-01

    Kinetic speciation of nickel, aluminium, and iron in fresh water has been investigated by cascade ultrafiltration followed by competing ligand exchange of the ultrafiltered fractions. Graphite furnace atomic absorption spectrometry was used to measure the kinetics of metal complex dissociation. Dissolved metal species were fractionated by cascade ultrafiltration. Metal speciation in each ultrafiltered fraction was then characterized as free metal ions, "labile" metal complexes (with dissociation rate constants >/=10(-3) s(-1)), "slowly labile" metal complexes (with dissociation rate constants >10(-6) s(-1)), and "inert" metal complexes (with dissociation rate constants measurement of dissociation kinetics alone.

  8. KINETIC MODEL OF ELECTRIC-DISCHARGE СО2-LASER WITH FAST FLOW

    Directory of Open Access Journals (Sweden)

    V. Nevdakh

    2013-01-01

    Full Text Available The paper presents a kinetic model of CW electric-discharge CO2-laser with fast flow. Expressions linking a non-saturated gain ratio, saturation intensity and output power of the fast-flow laser with excitation rates and relaxation times of laser levels have been obtained in the paper. The paper demonstrates that the higher excitation and flow rates or higher saturation intensity provide considerably higher specific output power of the fast-flow CO2-laser in comparison with a sealed-off CO2-laser. While maintaining a steady discharge the same output power of the fast-flow CO2-laser may be obtained under various discharge conditions and combinations of fast flow rate, gas mixture composition and active media temperature.

  9. MCNP5 study on kinetics parameters of coupled fast-thermal system HERBE

    Directory of Open Access Journals (Sweden)

    Pešić Milan P.

    2011-01-01

    Full Text Available New validation of the well-known Monte Carlo code MCNP5 against measured criticality and kinetics data for the coupled fast-thermal HERBE System at the Reactor B critical assembly is shown in this paper. Results of earlier calculations of these criticality and kinetics parameters, done by combination of transport and diffusion codes using two-dimension geometry model are compared to results of new calculations carried out by the MCNP5 code in three-dimension geometry. Satisfactory agreements in comparison of new results with experimental data, in spite complex heterogeneous composition of the HERBE core, are achieved confirming that MCNP5 code could apply successfully to study on HERBE kinetics parameters after uncertainties in impurities in material compositions and positions of fuel elements in fast zone were removed.

  10. Effect of Global ATGL Knockout on Murine Fasting Glucose Kinetics.

    Science.gov (United States)

    Coelho, Margarida; Nunes, Patricia; Mendes, Vera M; Manadas, Bruno; Heerschap, Arend; Jones, John G

    2015-01-01

    Mice deficient in adipose triglyceride lipase (ATGL(-/-)) present elevated ectopic lipid levels but are paradoxically glucose-tolerant. Measurement of endogenous glucose production (EGP) and Cori cycle activity provide insights into the maintenance of glycemic control in these animals. These parameters were determined in 7 wild-type (ATGL(+/-)) and 6 ATGL(-/-) mice by a primed-infusion of [U-(13)C6]glucose followed by LC-MS/MS targeted mass-isotopomer analysis of blood glucose. EGP was quantified by isotope dilution of [U-(13)C6]glucose while Cori cycling was estimated by analysis of glucose triose (13)C-isotopomers. Fasting plasma free fatty-acids were significantly lower in ATGL(-/-) versus control mice (0.43 ± 0.05 mM versus 0.73 ± 0.11 mM, P Cori cycling (80 ± 2% and 82 ± 7% of glucose disposal for ATGL(-/-) and control mice, resp.) indicating that peripheral glucose oxidation was not significantly upregulated in ATGL(-/-) mice under these conditions. The glucose (13)C-isotopomer distributions in both ATGL(-/-) and control mice were consistent with extensive hepatic pyruvate recycling. This suggests that gluconeogenic outflow from the Krebs cycle was also well compensated in ATGL(-/-) mice.

  11. Effect of ionic strength on ligand exchange kinetics between a mononuclear ferric citrate complex and siderophore desferrioxamine B

    Science.gov (United States)

    Ito, Hiroaki; Fujii, Manabu; Masago, Yoshifumi; Waite, T. David; Omura, Tatsuo

    2015-04-01

    The effect of ionic strength (I) on the ligand exchange reaction between a mononuclear ferric citrate complex and the siderophore, desferrioxamine B (DFB), was examined in the NaCl concentration range of 0.01-0.5 M, particularly focusing on the kinetics and mechanism of ligand exchange under environmentally relevant conditions. Overall ligand exchange rate constants were determined by spectrophotometrically measuring the time course of ferrioxamine B formation at a water temperature of 25 °C, pH 8.0, and citrate/Fe molar ratios of 500-5000. The overall ligand exchange rate decreased by 2-11-fold (depending on the citrate/Fe molar ratios) as I increased from approximately 0.01 to 0.5 M. In particular, a relatively large decrease was observed at lower I (dissociation of citrate from the parent complexes) dominates in ferrioxamine formation under the experimental conditions used. The model also predicts that the higher rate of ligand exchange at lower I is associated with the decrease in the ferric dicitrate complex stability because of the relatively high electrical repulsion between ferric monocitrate and free citrate at lower I (note that the reactivity of ferric dicitrate with DFB is smaller than that for the monocitrate complex). Overall, the findings of this study contribute to the understanding of the potential effect of I on ligand exchange kinetics in natural waters and provide fundamental knowledge on iron transformation and bioavailability.

  12. Determination of multivalent protein-ligand binding kinetics by second-harmonic correlation spectroscopy.

    Science.gov (United States)

    Sly, Krystal L; Conboy, John C

    2014-11-18

    Binding kinetics of the multivalent proteins peanut agglutinin (PnA) and cholera toxin B subunit (CTB) to a GM1-doped 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) lipid bilayer were investigated by both second-harmonic correlation spectroscopy (SHCS) and a traditional equilibrium binding isotherm. Adsorption and desorption rates, as well as binding affinity and binding free energy, for three bulk protein concentrations were determined by SHCS. For PnA binding to GM1, the measured adsorption rate decreased with increasing bulk PnA concentration from (3.7 ± 0.3) × 10(6) M(-1)·s(-1) at 0.43 μM PnA to (1.1 ± 0.1) × 10(5) M(-1)·s(-1) at 12 μM PnA. CTB-GM1 exhibited a similar trend, decreasing from (1.0 ± 0.1) × 10(9) M(-1)·s(-1) at 0.5 nM CTB to (3.5 ± 0.2) × 10(6) M(-1)·s(-1) at 240 nM CTB. The measured desorption rates in both studies did not exhibit any dependence on initial protein concentration. As such, 0.43 μM PnA and 0.5 nM CTB had the strongest measured binding affinities, (3.7 ± 0.8) × 10(9) M(-1) and (2.8 ± 0.5) × 10(13) M(-1), respectively. Analysis of the binding isotherm data suggests there is electrostatic repulsion between protein molecules when PnA binds GM1, while CTB-GM1 demonstrates positive ligand-ligand cooperativity. This study provides additional insight into the complex interactions between multivalent proteins and their ligands and showcases SHCS for examining these complex yet technologically important protein-ligand complexes used in biosensors, immunoassays, and other biomedical diagnostics.

  13. Development of new chiral ligand exchange capillary electrophoresis system with amino acid ionic liquids ligands and its application in studying the kinetics of L-amino acid oxidase

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Bingbing [Beijing National Laboratory for Molecular Sciences, Key Lab of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (China); College of Food Sciences and Engineering, Shandong Agricultural University, Tai’an, Shandong 271018 (China); Mu, Xiaoyu [Beijing National Laboratory for Molecular Sciences, Key Lab of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Qi, Li, E-mail: qili@iccas.ac.cn [Beijing National Laboratory for Molecular Sciences, Key Lab of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (China)

    2014-04-01

    Highlights: • Novel amino acid ionic liquids with pyridinium as cations and L-lysine as anion were synthesized. • These synthesized AAILs have been explored as the ligands coordinated with Zn(II) in CLE-CE system. • The developed CLE-CE method could be used for the enantioseparation of Dns-D, L-amino acids. • The kinetic contents of L-amino acid oxidase were investigated with the proposed CLE-CE system. - Abstract: New kinds of amino acid ionic liquids (AAILs) with pyridinium as cations and L-lysine (L-Lys) as anion have been developed as the available chiral ligands coordinated with Zn(II) in chiral ligand-exchange capillary electrophoresis (CLE-CE). Four kinds of AAILs, including [1-ethylpyridinium][L-lysine], 1-butylpyridinium][L-lysine], [1-hexylpyridinium][L-lysine] and 1-[octylpyridinium][L-lysine], were successfully synthesized and characterized by nuclear magnetic resonance and mass spectrometry. Compared with other AAILs, the best chiral separation of Dns-D, L-amino acids could be achieved when [1-ethylpyridinium][L-lysine] was chosen as the chiral ligand. It has been found that after investigating the influence of key factors on the separation efficiency, such as pH of buffer solution, the ratio of Zn(II) to ligand and complex concentration, eight pairs of Dns-D, L-AAs enantiomers could be baseline separated and three pairs were partly separated under the optimum conditions. The proposed CLE-CE method also exhibited favorable quantitative analysis property of Dns-D, L-Met with good linearity (r{sup 2} = 0.998) and favorable repeatability (RSD ≤ 1.5%). Furthermore, the CLE-CE system was applied in investigating the kinetic contents of L-amino acid oxidase, which implied that the proposed system has the potential in studying the enzymatic reaction mechanism.

  14. Insights into ligand binding to a glutathione S-transferase from mango: Structure, thermodynamics and kinetics.

    Science.gov (United States)

    Valenzuela-Chavira, Ignacio; Contreras-Vergara, Carmen A; Arvizu-Flores, Aldo A; Serrano-Posada, Hugo; Lopez-Zavala, Alonso A; García-Orozco, Karina D; Hernandez-Paredes, Javier; Rudiño-Piñera, Enrique; Stojanoff, Vivian; Sotelo-Mundo, Rogerio R; Islas-Osuna, Maria A

    2017-04-01

    We studied a mango glutathione S-transferase (GST) (Mangifera indica) bound to glutathione (GSH) and S-hexyl glutathione (GSX). This GST Tau class (MiGSTU) had a molecular mass of 25.5 kDa. MiGSTU Michaelis-Menten kinetic constants were determined for their substrates obtaining a Km, Vmax and kcat for CDNB of 0.792 mM, 80.58 mM min(-1) and 68.49 s(-1) respectively and 0.693 mM, 105.32 mM min(-1) and 89.57 s(-1), for reduced GSH respectively. MiGSTU had a micromolar affinity towards GSH (5.2 μM) or GSX (7.8 μM). The crystal structure of the MiGSTU in apo or bound to GSH or GSX generated a model that explains the thermodynamic signatures of binding and showed the importance of enthalpic-entropic compensation in ligand binding to Tau-class GST enzymes. Copyright © 2017 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  15. Computational fluid dynamics modelling of biomass fast pyrolysis in fluidised bed reactors, focusing different kinetic schemes.

    Science.gov (United States)

    Ranganathan, Panneerselvam; Gu, Sai

    2016-08-01

    The present work concerns with CFD modelling of biomass fast pyrolysis in a fluidised bed reactor. Initially, a study was conducted to understand the hydrodynamics of the fluidised bed reactor by investigating the particle density and size, and gas velocity effect. With the basic understanding of hydrodynamics, the study was further extended to investigate the different kinetic schemes for biomass fast pyrolysis process. The Eulerian-Eulerian approach was used to model the complex multiphase flows in the reactor. The yield of the products from the simulation was compared with the experimental data. A good comparison was obtained between the literature results and CFD simulation. It is also found that CFD prediction with the advanced kinetic scheme is better when compared to other schemes. With the confidence obtained from the CFD models, a parametric study was carried out to study the effect of biomass particle type and size and temperature on the yield of the products.

  16. Design, testing and kinetic analysis of bulky monodentate phosphorus ligands in the Mizoroki-Heck reaction

    NARCIS (Netherlands)

    Dodds, D.L.; Boele, M.D.K.; van Strijdonck, G.P.F.; de Vries, J.G.; van Leeuwen, P.W.N.M.; Kamer, P.C.J.

    2012-01-01

    A series of new monodentate phosphane ligands 2 have been evaluated in the Mizoroki-Heck arylation reaction of iodobenzene and styrene and compared with our previously reported ligands, 1, 3 and 4. The concept of rational ligand design is discussed, and we describe how the performance of this new li

  17. Design, Testing and Kinetic Analysis of Bulky Monodentate Phosphorus Ligands in the Mizoroki-Heck Reaction

    NARCIS (Netherlands)

    Dodds, Deborah L.; Boele, Maarten D. K.; van Strijdonck, Gino P. F.; de Vries, Johannes G.; van Leeuwen, Piet W. N. M.; Kamer, Paul C. J.

    2012-01-01

    A series of new monodentate phosphane ligands 2 have been evaluated in the MizorokiHeck arylation reaction of iodobenzene and styrene and compared with our previously reported ligands, 1, 3 and 4. The concept of rational ligand design is discussed, and we describe how the performance of this new lig

  18. Design, Testing and Kinetic Analysis of Bulky Monodentate Phosphorus Ligands in the Mizoroki-Heck Reaction

    NARCIS (Netherlands)

    Dodds, Deborah L.; Boele, Maarten D. K.; van Strijdonck, Gino P. F.; de Vries, Johannes G.; van Leeuwen, Piet W. N. M.; Kamer, Paul C. J.

    A series of new monodentate phosphane ligands 2 have been evaluated in the MizorokiHeck arylation reaction of iodobenzene and styrene and compared with our previously reported ligands, 1, 3 and 4. The concept of rational ligand design is discussed, and we describe how the performance of this new

  19. Design, testing and kinetic analysis of bulky monodentate phosphorus ligands in the Mizoroki-Heck reaction

    NARCIS (Netherlands)

    Dodds, D.L.; Boele, M.D.K.; van Strijdonck, G.P.F.; de Vries, J.G.; van Leeuwen, P.W.N.M.; Kamer, P.C.J.

    2012-01-01

    A series of new monodentate phosphane ligands 2 have been evaluated in the Mizoroki-Heck arylation reaction of iodobenzene and styrene and compared with our previously reported ligands, 1, 3 and 4. The concept of rational ligand design is discussed, and we describe how the performance of this new

  20. Gyro-Kinetic Electron and Fully-Kinetic Ion Simulations of Fast Magnetosonic Waves in the Magnetosphere

    Science.gov (United States)

    Gao, X.; Liu, K.; Wang, X.; Min, K.; Lin, Y.

    2016-12-01

    Two-dimensional simulations using a gyro-kinetic electron and fully-kinetic ion (GeFi) scheme are preformed to study the excitation of fast magnetosonic waves in the magnetosphere, which arise from the ion Bernstein instability driven by ring-like proton velocity distributions (with a positive slope with respect to the perpendicular velocity). Since both ion and electron kinetics are relevant, particle-in-cell (PIC) simulations have often been employed to study the wave excitation. However, such simulations are limited to reduced ion-to-electron mass ratio (mi/me) and light-to-Alfvén speed ratio (c/VA) due to the computationally expensive nature of PIC codes. The present study exploits a GeFi scheme that can break through these limitations and use larger/more realistic mi/me and c/VA. The capability of the GeFi code in simulating the ion Bernstein instability is first demonstrated by comparing a GeFi simulation using reduced mass ratio (mi/me=100) and speed ratio (c/VA=15) to a corresponding PIC simulation. A realistic speed ratio (c/VA=400) and a larger mass ratio (mi/me=400) are then adopted in the GeFi code to explore how the results vary. It is shown that the increased mi/me and c/VA lead to a larger lower hybrid frequency and allow waves to arise at more ion cyclotron harmonics, consistent with the general prediction of linear dispersion theory.

  1. Fast and sensitive optical toxicity bioassay based on dual wavelength analysis of bacterial ferricyanide reduction kinetics.

    Science.gov (United States)

    Pujol-Vila, F; Vigués, N; Díaz-González, M; Muñoz-Berbel, X; Mas, J

    2015-05-15

    Global urban and industrial growth, with the associated environmental contamination, is promoting the development of rapid and inexpensive general toxicity methods. Current microbial methodologies for general toxicity determination rely on either bioluminescent bacteria and specific medium solution (i.e. Microtox(®)) or low sensitivity and diffusion limited protocols (i.e. amperometric microbial respirometry). In this work, fast and sensitive optical toxicity bioassay based on dual wavelength analysis of bacterial ferricyanide reduction kinetics is presented, using Escherichia coli as a bacterial model. Ferricyanide reduction kinetic analysis (variation of ferricyanide absorption with time), much more sensitive than single absorbance measurements, allowed for direct and fast toxicity determination without pre-incubation steps (assay time=10 min) and minimizing biomass interference. Dual wavelength analysis at 405 (ferricyanide and biomass) and 550 nm (biomass), allowed for ferricyanide monitoring without interference of biomass scattering. On the other hand, refractive index (RI) matching with saccharose reduced bacterial light scattering around 50%, expanding the analytical linear range in the determination of absorbent molecules. With this method, different toxicants such as metals and organic compounds were analyzed with good sensitivities. Half maximal effective concentrations (EC50) obtained after 10 min bioassay, 2.9, 1.0, 0.7 and 18.3 mg L(-1) for copper, zinc, acetic acid and 2-phenylethanol respectively, were in agreement with previously reported values for longer bioassays (around 60 min). This method represents a promising alternative for fast and sensitive water toxicity monitoring, opening the possibility of quick in situ analysis.

  2. A fast-start pacing strategy speeds pulmonary oxygen uptake kinetics and improves supramaximal running performance.

    Directory of Open Access Journals (Sweden)

    Tiago Turnes

    Full Text Available The focus of the present study was to investigate the effects of a fast-start pacing strategy on running performance and pulmonary oxygen uptake (VO2 kinetics at the upper boundary of the severe-intensity domain. Eleven active male participants (28±10 years, 70±5 kg, 176±6 cm, 57±4 mL/kg/min visited the laboratory for a series of tests that were performed until exhaustion: 1 an incremental test; 2 three laboratory test sessions performed at 95, 100 and 110% of the maximal aerobic speed; 3 two to four constant speed tests for the determination of the highest constant speed (HS that still allowed achieving maximal oxygen uptake; and 4 an exercise based on the HS using a higher initial speed followed by a subsequent decrease. To predict equalized performance values for the constant pace, the relationship between time and distance/speed through log-log modelling was used. When a fast-start was utilized, subjects were able to cover a greater distance in a performance of similar duration in comparison with a constant-pace performance (constant pace: 670 m±22%; fast-start: 683 m±22%; P = 0.029; subjects also demonstrated a higher exercise tolerance at a similar average speed when compared with constant-pace performance (constant pace: 114 s±30%; fast-start: 125 s±26%; P = 0.037. Moreover, the mean VO2 response time was reduced after a fast start (constant pace: 22.2 s±28%; fast-start: 19.3 s±29%; P = 0.025. In conclusion, middle-distance running performances with a duration of 2-3 min are improved and VO2 response time is faster when a fast-start is adopted.

  3. Kinetics of Hg(II) exchange between organic ligands, goethite, and natural organic matter studied with an enriched stable isotope approach.

    Science.gov (United States)

    Jiskra, Martin; Saile, Damian; Wiederhold, Jan G; Bourdon, Bernard; Björn, Erik; Kretzschmar, Ruben

    2014-11-18

    The mobility and bioavailability of toxic Hg(II) in the environment strongly depends on its interactions with natural organic matter (NOM) and mineral surfaces. Using an enriched stable isotope approach, we investigated the exchange of Hg(II) between dissolved species (inorganically complexed or cysteine-, EDTA-, or NOM-bound) and solid-bound Hg(II) (carboxyl-/thiol-resin or goethite) over 30 days under constant conditions (pH, Hg and ligand concentrations). The Hg(II)-exchange was initially fast, followed by a slower phase, and depended on the properties of the dissolved ligands and sorbents. The results were described by a kinetic model allowing the simultaneous determination of adsorption and desorption rate coefficients. The time scales required to reach equilibrium with the carboxyl-resin varied greatly from 1.2 days for Hg(OH)2 to 16 days for Hg(II)-cysteine complexes and approximately 250 days for EDTA-bound Hg(II). Other experiments could not be described by an equilibrium model, suggesting that a significant fraction of total-bound Hg was present in a non-exchangeable form (thiol-resin and NOM: 53-58%; goethite: 22-29%). Based on the slow and incomplete exchange of Hg(II) described in this study, we suggest that kinetic effects must be considered to a greater extent in the assessment of the fate of Hg in the environment and the design of experimental studies, for example, for stability constant determination or metal isotope fractionation during sorption.

  4. Displacement of aqua ligands from the hydroxopentaaquarhodium(III) ion by 1-hydroxybenzotriazole (HOBt): A kinetic and mechanistic approach

    Indian Academy of Sciences (India)

    Biplab K Bera; Arup Mandal; Biswarup Maity; Sumon Ray; Parnajyoti Karmakar; Subala Mondal; Subhasis Mallick; Alak K Ghosh

    2012-07-01

    The kinetics of the reaction of HOBt with [Rh(H2O)5(OH)]2+ has been studied spectrophotometrically in aqueous medium as a function of [Rh(H2O)5OH2+], [HOBt], pH and temperature. At pH 4.3, the reaction proceeds via a rapid outer sphere association complex formation step followed by two consecutive steps. The first of these involves ligand-assisted anation, while the second involves chelation as the second aqua ligand is displaced. The association equilibrium constant for the outer sphere complex formation has been evaluated together with the rate constants for the two subsequent steps. The activation parameters for both steps have been evaluated using Eyrings equation. Thermodynamic parameters calculated from the temperature dependence of the outer sphere association equilibrium constants are also consistent with an associative mode of activation. The product of the reaction has been characterized by IR and ESI-mass spectroscopic analysis.

  5. Equilibria and kinetics for H-dependent axial ligation of alkyl(aquo) cobaloximes with aromatic and aliphatic N-donor ligands

    Indian Academy of Sciences (India)

    V Sridhar; D Sudarshan Reddy; N Ravikumar Reddy; S Satyanarayana

    2002-02-01

    Equilibria and kinetics of the reaction of bromomethyl(aquo) cobaloxime with histamine, histidine, glycine and ethyl glycine ester and iodomethyl(aquo) cobaloxime with cyanide, imidazole and substituted imidazoles were studied as a function of H at 25°C, 1.0 M ionic strength (KCl) by spectrophotometry technique. The rate of substitution of H2O varies with the of the incoming ligand, thus establishing the existence of nucleophilic participation of the ligand in the transition state. Dissociation kinetic reactions were also studied as a function of H. Binding and kinetic data were interpreted based on the basicity, steric crowd of the entering ligand and HSAB principle. To compare the rate constants of the entering ligands H independent second-order rate constants were calculated.

  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

    Full Text Available BACKGROUND: Nuclear Magnetic Resonance (NMR spectroscopy offers a variety of experiments to study protein-ligand interactions at atomic resolution. Among these experiments, 15N Heteronuclear Single Quantum Correlation (HSQCexperiment is simple, less time consuming and highly informative in mapping the binding site of the ligand. The interpretation of 15N HSQC becomes ambiguous when the chemical shift perturbations are caused by non-specific interactions like allosteric changes and local structural rearrangement. Under such cases, detailed chemical exchange analysis based on chemical shift perturbation will assist in locating the binding site accurately. METHODOLOGY/PRINCIPAL FINDINGS: We have automated the mapping of binding sites for fast chemical exchange systems using information obtained from 15N HSQC spectra of protein serially titrated with ligand of increasing concentrations. The automated program Auto-FACE (Auto-FAst Chemical Exchange analyzer determines the parameters, e.g. rate of change of perturbation, binding equilibrium constant and magnitude of chemical shift perturbation to map the binding site residues.Interestingly, the rate of change of perturbation at lower ligand concentration is highly sensitive in differentiating the binding site residues from the non-binding site residues. To validate this program, the interaction between the protein hBcl(XL and the ligand BH3I-1 was studied. Residues in the hydrophobic BH3 binding groove of hBcl(XL were easily identified to be crucial for interaction with BH3I-1 from other residues that also exhibited perturbation. The geometrically averaged equilibrium constant (3.0 x 10(4 calculated for the residues present at the identified binding site is consistent with the values obtained by other techniques like isothermal calorimetry and fluorescence polarization assays (12.8 x 10(4. Adjacent to the primary site, an additional binding site was identified which had an affinity of 3.8 times weaker

  7. Fast Palladium Catalyzed Arylation of Alkenes Using Bulky Monodentate Phosphorus Ligands

    NARCIS (Netherlands)

    Strijdonck, Gino P.F. van; Boele, Maarten D.K.; Kamer, Paul C.J.; Vries, Johannes G. de; Leeuwen, Piet W.N.M. van

    1999-01-01

    Complex 1b shows an unprecedented high activity in the Heck reaction. Kinetic studies show that in this system not the oxidative addition but the alkene coordination/migratory insertion is the rate determining step.

  8. Influence of fast and slow alkali myosin light chain isoforms on the kinetics of stretch-induced force transients of fast-twitch type IIA fibres of rat.

    Science.gov (United States)

    Andruchov, Oleg; Galler, Stefan

    2008-03-01

    This study contributes to understand the physiological role of slow myosin light chain isoforms in fast-twitch type IIA fibres of skeletal muscle. These isoforms are often attached to the myosin necks of rat type IIA fibres, whereby the slow alkali myosin light chain isoform MLC1s is much more frequent and abundant than the slow regulatory myosin light chain isoform MLC2s. In the present study, single-skinned rat type IIA fibres were maximally Ca(2+) activated and subjected to stepwise stretches for causing a perturbation of myosin head pulling cycles. From the time course of the resulting force transients, myosin head kinetics was deduced. Fibres containing MLC1s exhibited slower kinetics independently of the presence or absence of MLC2s. At the maximal MLC1s concentration of about 75%, the slowing was about 40%. The slowing effect of MLC1s is possibly due to differences in the myosin heavy chain binding sites of the fast and slow alkali MLC isoforms, which changes the rigidity of the myosin neck. Compared with the impact of myosin heavy chain isoforms in various fast-twitch fibre types, the influence of MLC1s on myosin head kinetics of type IIA fibres is much smaller. In conclusion, the physiological role of fast and slow MLC isoforms in type IIA fibres is a fine-tuning of the myosin head kinetics.

  9. High-speed gas chromatography in doping control: fast-GC and fast-GC/MS determination of beta-adrenoceptor ligands and diuretics.

    Science.gov (United States)

    Brunelli, Claudio; Bicchi, Carlo; Di Stilo, Antonella; Salomone, Alberto; Vincenti, Marco

    2006-12-01

    In official doping controls, about 300 drugs and metabolites have to be screened for each sample. Moreover, the number of determinations to be routinely processed increases continuously as the number of both samples and potential illicit drugs keeps growing. As a consequence, increasingly specific, sensitive, and, above all, fast methods for doping controls are needed. The present study presents an efficient fast-GC/MS approach to the routine screening of two different classes of doping agents, namely beta-adrenoceptor ligands and diuretics (belonging to the S3, P2, and S5 groups of the WADA list of prohibited substances). Narrow bore columns (100 mm id) of different lengths and coated with apolar stationary phases were successfully used to separate the derivatized analytes; preliminary experiments (results not shown) showed better performances with OV-1701 for the separation of beta-adrenoceptor ligands. On the same stationary phase some diuretics required too high a temperature or a long isothermal time for elution, in which case a DB1-MS column was preferred. Two methods of sample preparation, derivatization, and analysis were used on aqueous standard mixtures of, respectively, (i) eight beta-adrenoceptor ligands, including five beta-antagonists (acebutolol, alprenolol, atenolol, metoprolol, pindolol) and three beta2-agonists (salbutamol, clenbuterol, terbutaline) and (ii) seventeen diuretic drugs (acetazolamide, althiazide, bendroflumethiazide, bumethanide, canrenone, chlorothiazide, chlortalidone, clopamide, ethacrinic acid, furosemide, hydrochlorothiazide, hydroflumethiazide, indapamide, indomethacine, spironolactone, triamterene, trichloromethiazide) and one masking agent (probenecid). The mixture of beta-adrenoceptor ligand derivatives was efficiently separated in about 5.6 min, while the one of 18 diuretics and masking agents required less than 5 min for analysis. Limits of detection were from 1 microg/L for pindolol, ethacrinic acid, furosemide

  10. Ligand Binding Kinetics of the Quorum Sensing Regulator PqsR

    DEFF Research Database (Denmark)

    Welch, Martin; Hodgkinson, James T.; Gross, Jeremy;

    2013-01-01

    The Pseudomonas aeruginosa quinolone signal (PQS) is a quorum sensing molecule that plays an important role in regulating the virulence of this organism. We have purified the ligand binding domain of the receptor PqsRLBD for PQS and have used Förster resonance energy transfer fluorimetry...

  11. A kinetic and structural investigation of DNA-Based asymmetric catalysis using first-generation ligands

    NARCIS (Netherlands)

    Rosati, Fiora; Boersma, Arnold J.; Klijn, Jaap E.; Meetsma, Auke; Feringa, Ben L.; Roelfes, Gerard

    2009-01-01

    The recently developed concept of DNA-based asymmetric catalysis involves the transfer of chirality from the DNA double helix in reactions using a noncovalently bound catalyst. To date, two generations of DNA-based catalysts have been reported that differ in the design of the ligand for the metal. H

  12. Chronic impact of sulfamethoxazole on acetate utilization kinetics and population dynamics of fast growing microbial culture.

    Science.gov (United States)

    Kor-Bicakci, G; Pala-Ozkok, I; Rehman, A; Jonas, D; Ubay-Cokgor, E; Orhon, D

    2014-08-01

    The study evaluated the chronic impact of sulfamethoxazole on metabolic activities of fast growing microbial culture. It focused on changes induced on utilization kinetics of acetate and composition of the microbial community. The experiments involved a fill and draw reactor, fed with acetate and continuous sulfamethoxazole dosing of 50 mg/L. The evaluation relied on model evaluation of the oxygen uptake rate profiles, with parallel assessment of microbial community structure by 454-pyrosequencing. Continuous sulfamethoxazole dosing inflicted a retardation effect on acetate utilization in a way commonly interpreted as competitive inhibition, blocked substrate storage and accelerated endogenous respiration. A fraction of acetate was utilized at a much lower rate with partial biodegradation of sulfamethoxazole. Results of pyrosequencing with a replacement mechanism within a richer more diversified microbial culture, through inactivation of vulnerable fractions in favor of species resistant to antibiotic, which made them capable of surviving and competing even with a slower metabolic response. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. Lipoproteins attenuate TLR2 and TLR4 activation by bacteria and bacterial ligands with differences in affinity and kinetics.

    Science.gov (United States)

    van Bergenhenegouwen, Jeroen; Kraneveld, Aletta D; Rutten, Lieke; Garssen, Johan; Vos, Arjan P; Hartog, Anita

    2016-10-28

    The small intestine is a specialized compartment were close interactions take place between host, microbes, food antigens and dietary fatty acids. Dietary fats get absorbed by epithelial cells and processed into a range of lipoprotein particles after which they are basolaterally secreted and collected in the lymphatics. In contrast to the colon, the small intestine is covered only by a thin mucus coat that allows for intimate interactions between host-cells and microbes. Lipoproteins have long been recognized as protective factors in infectious diseases via the neutralization of bacterial toxins like lipopolysaccharides. Much less attention has been given to the potential role of lipoproteins as factors contributing to the maintenance of small intestinal immune homeostasis via modulating bacteria-induced immune responses. Lipoproteins VLDL, LDL and HDL were found to neutralize TLR responses towards specific TLR-ligands or a selection of gram-negative and gram-positive bacteria. Attenuation of TLR2 activity was acute and only slightly improved by longer pre-incubation times of ligands and lipoproteins with no differences between bacterial-lipopeptides or bacteria. In contrast, attenuation of TLR4 responses was only observed after extensive preincubation of lipoproteins and LPS. Preincubation of bacteria and lipoproteins led only to a modest attenuation of TLR4 activity. Moreover, compared to TLR2, TLR4 activity could only be attenuated by lipoproteins over a small ligand dose range. These results demonstrate the ability of lipoproteins VLDL, LDL and HDL to inhibit TLR responses towards bacterial-ligands and bacteria. Presence of lipoproteins was found to modulate the MAMP-induced cytokine release by primary human monocytes measured as changes in the release of IL-6, TNFα, GM-CSF and IFNγ. Using TLR2 and TLR4-reporter cells, lipoproteins were found to inhibit TLR responses with differences in affinity and kinetics. These data establish a role for lipoproteins as

  14. Kinetics of fast short-term depression are matched to spike train statistics to reduce noise.

    Science.gov (United States)

    Khanbabaie, Reza; Nesse, William H; Longtin, Andre; Maler, Leonard

    2010-06-01

    Short-term depression (STD) is observed at many synapses of the CNS and is important for diverse computations. We have discovered a form of fast STD (FSTD) in the synaptic responses of pyramidal cells evoked by stimulation of their electrosensory afferent fibers (P-units). The dynamics of the FSTD are matched to the mean and variance of natural P-unit discharge. FSTD exhibits switch-like behavior in that it is immediately activated with stimulus intervals near the mean interspike interval (ISI) of P-units (approximately 5 ms) and recovers immediately after stimulation with the slightly longer intervals (>7.5 ms) that also occur during P-unit natural and evoked discharge patterns. Remarkably, the magnitude of evoked excitatory postsynaptic potentials appear to depend only on the duration of the previous ISI. Our theoretical analysis suggests that FSTD can serve as a mechanism for noise reduction. Because the kinetics of depression are as fast as the natural spike statistics, this role is distinct from previously ascribed functional roles of STD in gain modulation, synchrony detection or as a temporal filter.

  15. Ligand-rebinding kinetics of 2/2 hemoglobin from the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125.

    Science.gov (United States)

    Russo, Roberta; Giordano, Daniela; di Prisco, Guido; Hui Bon Hoa, Gaston; Marden, Michael C; Verde, Cinzia; Kiger, Laurent

    2013-09-01

    Kinetic studies were performed on ligand rebinding to a cold-adapted globin of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 (Ph-2/2HbO). This 2/2 hemoglobin displays a rapid spectroscopic phase that is independent of CO concentration, followed by the standard bimolecular recombination. While the geminate recombination usually occurs on a ns timescale, Ph-2/2HbO displays a component of about 1μs that accounts for half of the geminate phase at 8°C, indicative of a relatively slow internal ligand binding. The O2 binding kinetics were measured in competition with CO to allow a short-time exposure of the deoxy hemes to O2 before CO replacement. Indeed Ph-2/2HbO is readily oxidised in the presence of O2, probably due to a superoxide character of the FeO2 bond induced by of a hydrogen-bond donor amino-acid residue. Upon O2 release or iron oxidation a distal residue (probably Tyr) is able to reversibly bind to the heme and as such to compete for binding with an external ligand. The transient hexacoordinated ferrous His-Fe-Tyr conformation after O2 dissociation could initiate the electron transfer from the iron toward its final acceptor, molecular O2 under our conditions. The hexacoordination via the distal Tyr is only partial, indicating a weak interaction between Tyr and the heme under atmospheric pressure. Hydrostatic high pressure enhances the hexacoordination indicating a flexible globin that allows structural changes. The O2 binding affinity for Ph-2/2HbO, poorly affected by the competition with Tyr, is about 1Torr at 8°C, pH7.0, which is compatible for an in vivo O2 binding function; however, this globin is more likely involved in a redox reaction associating diatomic ligands and their derived oxidative species. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.

  16. Frequency Activated Fast Power Reserve for Wind Power Plant Delivered from Stored Kinetic Energy in the Wind Turbine Inertia

    DEFF Research Database (Denmark)

    Knüppel, Thyge; Thuring, P.; Kumar, S

    2011-01-01

    is proposed that delivers a short-term power reserve from the kinetic energy in the wind turbine (WT) inertia, while considering the inherent characteristics of a wind power plant. The aim is to contribute with a fast power reserve to stabilize the frequency drop during large and sudden production deficits...

  17. Spherical polystyrene-supported chitosan thin film of fast kinetics and high capacity for copper removal

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Wei, E-mail: jiangwei@nju.edu.cn; Chen, Xubin; Pan, Bingcai; Zhang, Quanxing; Teng, Long; Chen, Yufan; Liu, Lu

    2014-07-15

    Graphical abstract: - Highlights: • Sub-micron-sized polystyrene supported chitosan thin-film was synthesized. • Absorbents exhibited fast kinetics and high capacity for Cu(II) removal from water. • Absorbents could be employed for repeated use for Cu(II) removal after regeneration. - Abstract: In order to accelerate the kinetics and improve the utilization of the surface active groups of chitosan (CS) for heavy metal ion removal, sub-micron-sized polystyrene supported chitosan thin-film was synthesized by the electrostatic assembly method. Glutaraldehyde was used as cross-linking agent. Chitosan thin-film was well coated onto the surface of the polystyrene (PS) beads characterized by scanning electron microscopy (SEM) and energy dispersive X-ray (EDX). Their adsorption toward Cu(II) ions was investigated as a function of solution pH, degree of cross-linking, equilibrium Cu(II) ions concentration and contact time. The maximum adsorptive capacity of PS–CS was 99.8 mg/g in the adsorption isotherm study. More attractively, the adsorption equilibrium was achieved in 10 min, which showed superior properties among similar adsorbents. Continuous adsorption–desorption cyclic results demonstrated that Cu(II)-loaded PS–CS can be effectively regenerated by a hydrochloric acid solution (HCl), and the regenerated composite beads could be employed for repeated use without significant capacity loss, indicating the good stability of the adsorbents. The XPS analysis confirmed that the adsorption process was due to surface complexes with atoms of chitosan. Generally, PS beads could be employed as a promising host to fabricate efficient composites that originated from chitosan or other bio-sorbents for environmental remediation.

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

    DEFF Research Database (Denmark)

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

    2010-01-01

    addressed the kinetic mechanism of interaction of such bivalent ligands. We have investigated the binding interaction of a recently identified potent plasma-stable dimeric pentapeptide and PDZ1-2 of postsynaptic density protein-95 (PSD-95) using protein engineering in combination with fluorescence...

  19. Oxygen equilibria and ligand binding kinetics of erythrocruorins from two burrowing polychaetes of different modes of life, Marphysa sanguinea and Diopatra cuprea

    DEFF Research Database (Denmark)

    Weber, Roy E.; Bonaventura, J.; Sullivan, B.;

    1978-01-01

    Oxygen equilibria, ligand-binding kinetics and some other physicochemical properties are reported for erythrocruorins of two intertidal polychaetes:Marphysa sanguinea, which inhabits simple, relatively stagnant burrows, andDiopatra cuprea, which inhabits impermeable, parchment-like tubes that are...

  20. A Pyridine-Based Ligand with Two Hydrazine Functions for Lanthanide Chelation: Remarkable Kinetic Inertness for a Linear, Bishydrated Complex.

    Science.gov (United States)

    Bonnet, Célia S; Laine, Sophie; Buron, Frédéric; Tircsó, Gyula; Pallier, Agnès; Helm, Lothar; Suzenet, Franck; Tóth, Éva

    2015-06-15

    To study the influence of hydrazine functions in the ligand skeleton, we designed the heptadentate HYD ligand (2,2',2″,2‴-(2,2'-(pyridine-2,6-diyl)bis(2-methylhydrazine-2,1,1-triyl)) tetraacetic acid) and compared the thermodynamic, kinetic, and relaxation properties of its Ln(3+) complexes to those of the parent pyridine (Py) analogues without hydrazine (Py = 2,6-pyridinebis(methanamine)-N,N,N',N'-tetraacetic acid). The protonation constants of HYD were determined by pH-potentiometric measurements, and assigned by a combination of UV-visible and NMR spectroscopies. The protonation sequence is rather unusual and illustrates that small structural changes can strongly influence ligand basicity. The first protonation step occurs on the pyridine nitrogen in the basic region, followed by two hydrazine nitrogens and the carboxylate groups at acidic pH. Contrary to Py, HYD self-aggregates through a pH-dependent process (from pH ca. 4). Thermodynamic stability constants have been obtained by pH-potentiometry and UV-visible spectrophotometry for various Ln(3+) and physiological cations (Zn(2+), Ca(2+), Cu(2+)). LnHYD stability constants show the same trend as those of LnDTPA complexes along the Ln(3+) series, with log K = 18.33 for Gd(3+), comparable to the Py analogue. CuHYD has a particularly high stability (log K > 19) preventing its determination from pH-potentiometric measurements. The stability constant of CuPy was also revisited and found to be underestimated in previous studies, highlighting that UV-visible spectrophotometry is often indispensable to obtain reliable stability constants for Cu(2+) chelates. The dissociation of GdL, assessed by studying the Cu(2+)-exchange reaction, occurs mainly via an acid-catalyzed process, with limited contribution from direct Cu(2+) attack. The kinetic inertness of GdHYD is remarkable for a linear bishydrated chelate; the 25-fold increase in the dissociation half-life with respect to the monohydrated commercial contrast agent

  1. Gyrokinetic electron and fully kinetic ion simulations of fast magnetosonic waves in the magnetosphere

    Science.gov (United States)

    Gao, Xiaotian; Liu, Kaijun; Wang, Xueyi; Min, Kyungguk; Lin, Yu; Wang, Xiaogang

    2017-06-01

    Two-dimensional simulations using a gyrokinetic electron and fully kinetic ion (GeFi) scheme are preformed to study the excitation of fast magnetosonic waves in the terrestrial magnetosphere, which arise from the ion Bernstein instability driven by proton velocity distributions with a positive slope with respect to the perpendicular velocity. Since both ion and electron kinetics are relevant, particle-in-cell (PIC) simulations have often been employed to study the wave excitation. However, the full particle-in-cell scheme is computationally expensive for simulating waves in the ion scale because the electron scale must be fully resolved. Therefore, such simulations are limited to reduced proton-to-electron mass ratio ( m p / m e) and light-to-Alfvén speed ratio ( c / v A). The present study exploits the GeFi scheme that can break through these limitations to some extent, so larger m p / m e and c / v A can be used. In the simulations presented, the ion Bernstein instability is driven by a proton velocity distribution composed of 10% energetic protons with a shell distribution and 90% relatively cool, background protons with a Maxwellian distribution. The capability of the GeFi code in simulating the ion Bernstein instability is first demonstrated by comparing a GeFi simulation using reduced mass ratio ( m p / m e = 100) and speed ratio ( c / v A = 15) to a corresponding PIC simulation as well as linear dispersion analysis. A realistic speed ratio ( c / v A = 400) and a larger mass ratio ( m p / m e = 400) are then adopted in the GeFi code to explore how the results vary. It is shown that, as the increased m p / m e and c / v A lead to a larger lower hybrid frequency, ion Bernstein waves are excited at more ion cyclotron harmonics, consistent with the general prediction of linear dispersion theory. On the other hand, the GeFi simulations also revealed some interesting features after the instability saturation, which are likely related to nonlinear wave

  2. Ca2+_, Sr2+_force relationships and kinetic properties of fast-twitch rat leg muscle fibre subtypes.

    Science.gov (United States)

    Galler, S

    1999-10-01

    Force generation of fast-twitch and slow-twitch fibres exhibits large differences in its sensitivity to Ca2+ and Sr2+ (e.g. Fink et al. 1986). Little is known about fast-twitch fibre subtypes. Thus, a variety of mechanical measurements on segments of rehydrated freeze-dried fast-twitch rat leg muscle fibres were executed in this study. Among these, the Ca2+- and Sr2+-force relationship and the unloaded shortening velocity were determined. The fibres were classified into subtypes according to their kinetics of stretch activation (Galler et al. 1994). In all fibres, the maximal force under Sr2+ activation was about 0.9 of that under Ca2+ activation. The Ca2+- and Sr2+-force relationship exhibited a biphasic shape with a steeper part (Hill coefficient, n1) below 50% and a flatter part (Hill coefficient, n2) above 50% of maximal force. The difference between the Ca2+ - and Sr2+ -sensitivity was independent of the fibre subtypes. The Hill coefficients were only partially correlated with kinetic properties. The correlation was more pronounced for the unloaded shortening velocity than for the kinetics of stretch activation. The data are consistent with the idea that the Ca2+ and Sr2+ sensitivities of fast-twitch fibres are mainly determined by a single isoform of troponin C. Among several protein isoforms, the isoforms of the myosin light chains seem to be involved for determining the slope of the Ca2+- and Sr2+-force relationship of fast-twitch muscle fibres.

  3. Saturation-Transfer Difference (STD) NMR: A Simple and Fast Method for Ligand Screening and Characterization of Protein Binding

    Science.gov (United States)

    Viegas, Aldino; Manso, Joao; Nobrega, Franklin L.; Cabrita, Eurico J.

    2011-01-01

    Saturation transfer difference (STD) NMR has emerged as one of the most popular ligand-based NMR techniques for the study of protein-ligand interactions. The success of this technique is a consequence of its robustness and the fact that it is focused on the signals of the ligand, without any need of processing NMR information about the receptor…

  4. Saturation-Transfer Difference (STD) NMR: A Simple and Fast Method for Ligand Screening and Characterization of Protein Binding

    Science.gov (United States)

    Viegas, Aldino; Manso, Joao; Nobrega, Franklin L.; Cabrita, Eurico J.

    2011-01-01

    Saturation transfer difference (STD) NMR has emerged as one of the most popular ligand-based NMR techniques for the study of protein-ligand interactions. The success of this technique is a consequence of its robustness and the fact that it is focused on the signals of the ligand, without any need of processing NMR information about the receptor…

  5. One-Dimensional Biomass Fast Pyrolysis Model with Reaction Kinetics Integrated in an Aspen Plus Biorefinery Process Model

    Energy Technology Data Exchange (ETDEWEB)

    Humbird, David; Trendewicz, Anna; Braun, Robert; Dutta, Abhijit

    2017-01-27

    A biomass fast pyrolysis reactor model with detailed reaction kinetics and one-dimensional fluid dynamics was implemented in an equation-oriented modeling environment (Aspen Custom Modeler). Portions of this work were detailed in previous publications; further modifications have been made here to improve stability and reduce execution time of the model to make it compatible for use in large process flowsheets. The detailed reactor model was integrated into a larger process simulation in Aspen Plus and was stable for different feedstocks over a range of reactor temperatures. Sample results are presented that indicate general agreement with experimental results, but with higher gas losses caused by stripping of the bio-oil by the fluidizing gas in the simulated absorber/condenser. This integrated modeling approach can be extended to other well-defined, predictive reactor models for fast pyrolysis, catalytic fast pyrolysis, as well as other processes.

  6. Binding equilibrium and kinetics of membrane-anchored receptors and ligands in cell adhesion: Insights from computational model systems and theory.

    Science.gov (United States)

    Weikl, Thomas R; Hu, Jinglei; Xu, Guang-Kui; Lipowsky, Reinhard

    2016-09-02

    The adhesion of cell membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. In this article, we review recent results from simulations and theory that lead to novel insights on how the binding equilibrium and kinetics of these proteins is affected by the membranes and by the membrane anchoring and molecular properties of the proteins. Simulations and theory both indicate that the binding equilibrium constant [Formula: see text] and the on- and off-rate constants of anchored receptors and ligands in their 2-dimensional (2D) membrane environment strongly depend on the membrane roughness from thermally excited shape fluctuations on nanoscales. Recent theory corroborated by simulations provides a general relation between [Formula: see text] and the binding constant [Formula: see text] of soluble variants of the receptors and ligands that lack the membrane anchors and are free to diffuse in 3 dimensions (3D).

  7. Kinetics and mechanism of the ligand substitution reaction of di--hydroxobis(bipyridyl)dipalladium(II) ion with diethyldithiocarbamate anion in aqueous solution

    Indian Academy of Sciences (India)

    Subhasis Mallick; Biplab K Bera; Subala Mondal; Parnajyoti Karmakar; Arup Mandal; Alak K Ghosh

    2011-05-01

    The kinetics of the interaction between diethyldithiocarbamate (Et2DTC) and the title complex has been studied spectrophotometrically in aqueous medium as a function of nucleophile concentration, temperature and pH at constant ionic strength. The reaction is a two-step process in which the first step is liganddependent, but the second step is ligand-independent and is assigned to ring closure. The rate and activation parameters, conductivity studies and IR data were used to deduce a plausible mechanism.

  8. Equilibria and kinetics for pH-dependent axial ligation of ethylester and methylester(aquo)cobaloximes with aromatic and aliphatic N-donor ligands and a molecular mechanistic study of the Co-C bond

    Indian Academy of Sciences (India)

    J V Madhuri; V Malathi; S Satyanarayana

    2004-03-01

    Equilibrium constants are determined for the reaction of ethylester and methyl ester (aquo) cobaloximes with histamine, histidine, glycine and ethyl glycine ester as a function of pH at 25°C, using spectrophotometric technique. The functional dependence of p on the substitution rate of H2O varies with the p of the incoming ligand, establishing the existence of nucleophilic participation of the ligand in the transition state. This data is interpreted with the help of kinetic data where dissociation kinetic reactions were also studied as a function of pH. Binding and kinetic data were correlated based on the basicity, steric hindrance of the entering ligand and HSAB principle. To compare the rate constants of the entering ligands pH-independent second-order rate constants were calculated. The effect of incoming ligand on Co-C bond is studied using molecular mechanics.

  9. Physiologic growth hormone replacement improves fasting lipid kinetics in patients with HIV lipodystrophy syndrome

    Science.gov (United States)

    HIV lipodystrophy syndrome (HLS) is characterized by accelerated lipolysis, inadequate fat oxidation, increased hepatic reesterification, and a high frequency of growth hormone deficiency (GHD). The effect of growth hormone (GH) replacement on these lipid kinetic abnormalities is unknown. We aimed ...

  10. Kinetic identification of protein ligands in a 51,200 small-molecule library using microarrays and a label-free ellipsometric scanner

    Science.gov (United States)

    Landry, James P.; Proudian, Andrew P.; Malovichko, Galina; Zhu, Xiangdong

    2013-02-01

    Drug discovery begins by identifying protein-small molecule binding pairs. Afterwards, binding kinetics and biofunctional assays are performed, to reduce candidates for further development. High-throughput screening, typically employing fluorescence, is widely used to find protein ligands in small-molecule libraries, but is rarely used for binding kinetics measurement because: (1) attaching fluorophores to proteins can alter kinetics and (2) most label-free technologies for kinetics measurement are inherently low-throughput and consume expensive sensing surfaces. We addressed this need with polarization-modulated ellipsometric scanning microscopes, called oblique-incidence reflectivity difference (OI-RD). Label-free ligand screening and kinetics measurement are performed simultaneously on small-molecule microarrays printed on relatively inexpensive isocyanate-functionalized glass slides. As a microarray is reacted, an OI-RD microscope tracks the change in surface-bound macromolecule density in real-time at every spot. We report progress applying OI-RD to screen purified proteins and virus particles against a 51,200-compound library from the National Cancer Institute. Four microarrays, each containing 12,800 library compounds, are installed in four flow cells in an automated OI-RD microscope. The slides are reacted serially, each giving 12,800 binding curves with ~30 sec time resolution. The entire library is kinetically screened against a single probe in ~14 hours and multiple probes can be reacted sequentially under automation. Real-time binding detection identifies both high-affinity and low-affinity (transient binding) interactions; fluorescence endpoint images miss the latter. OI-RD and microarrays together is a powerful high-throughput tool for early stage drug discovery and development. The platform also has great potential for downstream steps such as in vitro inhibition assays.

  11. Fast pyrolysis of palm kernel cake in a closed-tubular reactor: product compositions and kinetic model.

    Science.gov (United States)

    Ngo, Thanh-An; Kim, Jinsoo; Kim, Seung-Soo

    2011-03-01

    In this study, fast pyrolysis of palm kernel cake (PKC) was carried out in a closed-tubular reactor over a temperature range of 550 to 750°C with various retention times. The pyrolyzing gas products mainly included CO, CO(2), and light hydrocarbons; it is noted that no hydrogen was detected in the product. In order to investigate the reaction pathway, the kinetic lump model of Liden was applied to verify and calculate all rate constants. The results obtained at different temperatures indicated that the rate constant increased with pyrolysis temperature. Furthermore, the experimental results were in good agreement with the proposed mechanism.

  12. Frequency Activated Fast Power Reserve for Wind Power Plant Delivered from Stored Kinetic Energy in the Wind Turbine Inertia

    DEFF Research Database (Denmark)

    Knüppel, Thyge; Thuring, P.; Kumar, S

    2011-01-01

    With increased penetration of converter interfaced generation, synchronous generators may start to be displaced to keep the overall power balance. As a consequence the resulting inertia in the system may decrease and make the power system more exposed to frequency excursions. Here, a control...... is proposed that delivers a short-term power reserve from the kinetic energy in the wind turbine (WT) inertia, while considering the inherent characteristics of a wind power plant. The aim is to contribute with a fast power reserve to stabilize the frequency drop during large and sudden production deficits...

  13. FAST

    DEFF Research Database (Denmark)

    Zuidmeer-Jongejan, Laurian; Fernandez-Rivas, Montserrat; Poulsen, Lars K.

    2012-01-01

    ABSTRACT: The FAST project (Food Allergy Specific Immunotherapy) aims at the development of safe and effective treatment of food allergies, targeting prevalent, persistent and severe allergy to fish and peach. Classical allergen-specific immunotherapy (SIT), using subcutaneous injections with aqu......ABSTRACT: The FAST project (Food Allergy Specific Immunotherapy) aims at the development of safe and effective treatment of food allergies, targeting prevalent, persistent and severe allergy to fish and peach. Classical allergen-specific immunotherapy (SIT), using subcutaneous injections...... with aqueous food extracts may be effective but has proven to be accompanied by too many anaphylactic side-effects. FAST aims to develop a safe alternative by replacing food extracts with hypoallergenic recombinant major allergens as the active ingredients of SIT. Both severe fish and peach allergy are caused...... in depth serological and cellular immune analyses will be performed, allowing identification of novel biomarkers for monitoring treatment efficacy. FAST aims at improving the quality of life of food allergic patients by providing a safe and effective treatment that will significantly lower their threshold...

  14. Disclosure of the oscillations in kinetics of the reactor pressure vessel steel damage at fast neutron intensity decreasing

    Science.gov (United States)

    Krasikov, E.; Nikolaenko, V.

    2017-01-01

    Fast neutron intensity influence on reactor materials radiation damage is a critically important question in the problem of the correct use of the accelerated irradiation tests data for substantiation of the materials workability in real irradiation conditions that is low neutron intensity. Investigations of the fast neutron intensity (flux) influence on radiation damage and experimental data scattering reveal the existence of non-monotonous sections in kinetics of the reactor pressure vessels (RPV) steel damage. Discovery of the oscillations as indicator of the self-organization processes presence give reasons for new ways searching on reactor pressure vessel (RPV) steel radiation stability increasing and attempt of the self-restoring metal elaboration. Revealing of the wavelike process in the form of non monotonous parts of the kinetics of radiation embrittlement testifies that periodic transformation of the structure take place. This fact actualizes the problem of more precise definition of the RPV materials radiation embrittlement mechanisms and gives reasons for search of the ways to manage the radiation stability (nanostructuring and so on to stimulate the radiation defects annihilation), development of the means for creating of more stableness self recovering smart materials.

  15. Kinetic analysis of the translocator protein positron emission tomography ligand [{sup 18}F]GE-180 in the human brain

    Energy Technology Data Exchange (ETDEWEB)

    Feeney, Claire [Imperial College London, Division of Brain Sciences, Hammersmith Hospital Campus, London (United Kingdom); Hammersmith Hospital, Computational, Cognitive and Clinical Neuroimaging Laboratory, London (United Kingdom); Scott, Gregory; Raffel, Joel; Roberts, S.; Coello, Christopher; Jolly, Amy; Searle, Graham; Goldstone, A.P.; Nicholas, Richard S.; Gunn, Roger N.; Sharp, David J. [Imperial College London, Division of Brain Sciences, Hammersmith Hospital Campus, London (United Kingdom); Brooks, David J. [Imperial College London, Division of Brain Sciences, Hammersmith Hospital Campus, London (United Kingdom); Aarhus University, Institute of Clinical Medicine, Aarhus (Denmark); Trigg, William [GE Healthcare Ltd, Amersham (United Kingdom)

    2016-11-15

    PET can image neuroinflammation by targeting the translocator protein (TSPO), which is upregulated in activated microglia. The high nonspecific binding of the first-generation TSPO radioligand [{sup 11}C]PK-11195 limits accurate quantification. [{sup 18}F]GE-180, a novel TSPO ligand, displays superior binding to [{sup 11}C]PK-11195 in vitro. Our objectives were to: (1) evaluate tracer characteristics of [{sup 18}F]GE-180 in the brains of healthy human subjects; and (2) investigate whether the TSPO Ala147Thr polymorphism influences outcome measures. Ten volunteers (five high-affinity binders, HABs, and five mixed-affinity binders, MABs) underwent a dynamic PET scan with arterial sampling after injection of [{sup 18}F]GE-180. Kinetic modelling of time-activity curves with one-tissue and two-tissue compartment models and Logan graphical analysis was applied to the data. The primary outcome measure was the total volume of distribution (V{sub T}) across various regions of interest (ROIs). Secondary outcome measures were the standardized uptake values (SUV), the distribution volume and SUV ratios estimated using a pseudoreference region. The two-tissue compartment model was the best model. The average regional delivery rate constant (K{sub 1}) was 0.01 mL cm{sup -3} min{sup -1} indicating low extraction across the blood-brain barrier (1 %). The estimated median V{sub T} across all ROIs was also low, ranging from 0.16 mL cm{sup -3} in the striatum to 0.38 mL cm{sup -3} in the thalamus. There were no significant differences in V{sub T} between HABs and MABs across all ROIs. A reversible two-tissue compartment model fitted the data well and determined that the tracer has a low first-pass extraction (approximately 1 %) and low V{sub T} estimates in healthy individuals. There was no observable dependency on the rs6971 polymorphism as compared to other second-generation TSPO PET tracers. Investigation of [{sup 18}F]GE-180 in populations with neuroinflammatory disease is needed

  16. Fast Fourier transform spectrometer readout for large arrays of microwave kinetic inductance detectors

    NARCIS (Netherlands)

    Yates, S. J. C.; Baryshev, A. M.; Baselmans, J. J. A.; Klein, B.; Guesten, R.

    2009-01-01

    Microwave kinetic inductance detectors have great potential for large, very sensitive detector arrays for use in, for example, submillimeter imaging. Being intrinsically readout in the frequency domain, they are particularly suited for frequency domain multiplexing allowing similar to 1000 s of devi

  17. Generalized Temporal Acceleration Scheme for Kinetic Monte Carlo Simulations of Surface Catalytic Processes by Scaling the Rates of Fast Reactions.

    Science.gov (United States)

    Dybeck, Eric Christopher; Plaisance, Craig Patrick; Neurock, Matthew

    2017-02-14

    A novel algorithm has been developed to achieve temporal acceleration during kinetic Monte Carlo (KMC) simulations of surface catalytic processes. This algorithm allows for the direct simulation of reaction networks containing kinetic processes occurring on vastly disparate timescales which computationally overburden standard KMC methods. Previously developed methods for temporal acceleration in KMC have been designed for specific systems and often require a priori information from the user such as identifying the fast and slow processes. In the approach presented herein, quasi-equilibrated processes are identified automatically based on previous executions of the forward and reverse reactions. Temporal acceleration is achieved by automatically scaling the intrinsic rate constants of the quasi-equilibrated processes, bringing their rates closer to the timescales of the slow kinetically relevant non-equilibrated processes. All reactions are still simulated directly, although with modified rate constants. Abrupt changes in the underlying dynamics of the reaction network are identified during the simulation and the reaction rate constants are rescaled accordingly. The algorithm has been utilized here to model the Fischer-Tropsch synthesis reaction over ruthenium nanoparticles. This reaction network has multiple timescale-disparate processes which would be intractable to simulate without the aid of temporal acceleration. The accelerated simulations are found to give reaction rates and selectivities indistinguishable from those calculated by an equivalent mean-field kinetic model. The computational savings of the algorithm can span many orders of magnitude in realistic systems and the computational cost is not limited by the magnitude of the timescale disparity in the system processes. Furthermore, the algorithm has been designed in a generic fashion and can easily be applied to other surface catalytic processes of interest.

  18. Influence of composition on setting kinetics of new injectable and/or fast setting tricalcium silicate cements.

    Science.gov (United States)

    Setbon, H M; Devaux, J; Iserentant, A; Leloup, G; Leprince, J G

    2014-12-01

    New commercial tricalcium silicate based cements were elaborated to improve handling properties and setting time. The goals of the present work were: (i) to determine the composition of the new injectable and/or fast setting calcium silicate based cements, and (ii) to investigate the impact of the differences in composition on their setting kinetics. The materials considered were Angelus MTA™, Biodentine™, MM-MTA™, MTA-Caps™, and ProRoot MTA™ as control. Elemental composition of materials was studied by Inductively Coupled Plasma-Atomic Emission Spectroscopy and X-ray Energy Dispersive analysis, whereas phases in presence were analyzed by Micro-Raman spectroscopy and X-ray Diffraction analysis and cement surface by Scanning Electron Microscope. Setting kinetics was evaluated using rheometry. Elemental analysis revealed, for all cements, the presence of three major components: calcium, silicon and oxygen. Chlorine was detected in MM-MTA, MTA-Caps and Biodentine. Different radio-opacifiers were identified: bismuth oxide in ProRoot MTA, Angelus MTA and MM-MTA, zirconium oxide in Biodentine and calcium tungstate (CaWO4) in MTA-Caps. All cements were composed of di- and tri-calcium silicate, except Biodentine for which only the latter was detected. Major differences in setting kinetics were observed: a modulus of 8×10(8)Pa is reached after 12min for Biodentine, 150min for MM-MTA, 230min for Angelus MTA and 320min for ProRoot MTA. The maximum modulus reached by MTA-Caps was 7×10(8)Pa after 150min. Even if these cements possess some common compounds, major differences in their composition were observed between them, which directly influence their setting kinetics. Copyright © 2014 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

  19. Mg-based nanocomposites with high capacity and fast kinetics for hydrogen storage.

    Science.gov (United States)

    Yao, Xiangdong; Wu, Chengzhang; Du, Aijun; Lu, Gao Qing; Cheng, Huiming; Smith, Sean C; Zou, Jin; He, Yinghe

    2006-06-22

    Magnesium and its alloys have shown a great potential in effective hydrogen storage due to their advantages of high volumetric/gravimetric hydrogen storage capacity and low cost. However, the use of these materials in fuel cells for automotive applications at the present time is limited by high hydrogenation temperature and sluggish sorption kinetics. This paper presents the recent results of design and development of magnesium-based nanocomposites demonstrating the catalytic effects of carbon nanotubes and transition metals on hydrogen adsorption in these materials. The results are promising for the application of magnesium materials for hydrogen storage, with significantly reduced absorption temperatures and enhanced ab/desorption kinetics. High level Density Functional Theory calculations support the analysis of the hydrogenation mechanisms by revealing the detailed atomic and molecular interactions that underpin the catalytic roles of incorporated carbon and titanium, providing clear guidance for further design and development of such materials with better hydrogen storage properties.

  20. Functional model of oxomolybdoenzymes: Synthesis and characterization of a molybdenum complex with sulphur and pterin ligands exhibiting saturation kinetics with pyridine N-oxide

    Indian Academy of Sciences (India)

    M D Afsar Ali; Parag S Roy

    2001-04-01

    Redox reaction between 6-acetonylisoxanthopterin (H2pte) and [MoVIO2(ssp)] [ssp = anion of 2-(salicylideneamino) benzenethiol] in CH3OH-C2H5OH medium produces a new mixed ligand compound [MoIV (ssp) (Hpte) (OCH3)] (1). It has been characterized by elemental analysis, ESMS data, UV-Vis, IR, 1H NMR (1D and 2D) spectroscopy and cyclic voltammetry. Kinetics of formation of this compound as well as that of its reaction with pyridine N-oxide have been followed spectrophotometrically. Both the reactions follow substrate saturation kinetics and involve metal-centred oxygen atom transfer process. Large negative values of entropy of activation indicate the operation of associative mechanism.

  1. KID - an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information of enzymes

    Directory of Open Access Journals (Sweden)

    Schomburg Dietmar

    2010-07-01

    Full Text Available Abstract Background The amount of available biological information is rapidly increasing and the focus of biological research has moved from single components to networks and even larger projects aiming at the analysis, modelling and simulation of biological networks as well as large scale comparison of cellular properties. It is therefore essential that biological knowledge is easily accessible. However, most information is contained in the written literature in an unstructured way, so that methods for the systematic extraction of knowledge directly from the primary literature have to be deployed. Description Here we present a text mining algorithm for the extraction of kinetic information such as KM, Ki, kcat etc. as well as associated information such as enzyme names, EC numbers, ligands, organisms, localisations, pH and temperatures. Using this rule- and dictionary-based approach, it was possible to extract 514,394 kinetic parameters of 13 categories (KM, Ki, kcat, kcat/KM, Vmax, IC50, S0.5, Kd, Ka, t1/2, pI, nH, specific activity, Vmax/KM from about 17 million PubMed abstracts and combine them with other data in the abstract. A manual verification of approx. 1,000 randomly chosen results yielded a recall between 51% and 84% and a precision ranging from 55% to 96%, depending of the category searched. The results were stored in a database and are available as "KID the KInetic Database" via the internet. Conclusions The presented algorithm delivers a considerable amount of information and therefore may aid to accelerate the research and the automated analysis required for today's systems biology approaches. The database obtained by analysing PubMed abstracts may be a valuable help in the field of chemical and biological kinetics. It is completely based upon text mining and therefore complements manually curated databases. The database is available at http://kid.tu-bs.de. The source code of the algorithm is provided under the GNU General Public

  2. Kinetic modeling of a high power fast-axial-flow CO2 laser with computational fluid dynamics method

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A new computational fluid dynamics (CFD) method for the simulation of fast-axial-flow CO2 laser is developed.The model which is solved by CFD software uses a set of dynamic differential equations to describe the dynamic process in one discharge tube.The velocity,temperature,pressure and turbulence energy distributions in discharge passage are presented.There is a good agreement between the theoretical prediction and the experimental results.This result indicates that the parameters of the laser have significant effect on the flow distribution in the discharge passage.It is helpful to optimize the output of high power CO2 laser by mastering its kinetic characteristics.

  3. ERENA: A fast and robust Jacobian-free integration method for ordinary differential equations of chemical kinetics

    Science.gov (United States)

    Morii, Youhi; Terashima, Hiroshi; Koshi, Mitsuo; Shimizu, Taro; Shima, Eiji

    2016-10-01

    We herein propose a fast and robust Jacobian-free time integration method named as the extended robustness-enhanced numerical algorithm (ERENA) to treat the stiff ordinary differential equations (ODEs) of chemical kinetics. The formulation of ERENA is based on an exact solution of a quasi-steady-state approximation that is optimized to preserve the mass conservation law through use of a Lagrange multiplier method. ERENA exhibits higher accuracy and faster performance in homogeneous ignition simulations compared to existing popular explicit and implicit methods for stiff ODEs such as VODE, MTS, and CHEMEQ2. We investigate the effects of user-specified threshold values in ERENA, to provide trade-off information between the accuracy and the computational cost.

  4. Competitive binding-based optical DNA mapping for fast identification of bacteria--multi-ligand transfer matrix theory and experimental applications on Escherichia coli.

    Science.gov (United States)

    Nilsson, Adam N; Emilsson, Gustav; Nyberg, Lena K; Noble, Charleston; Stadler, Liselott Svensson; Fritzsche, Joachim; Moore, Edward R B; Tegenfeldt, Jonas O; Ambjörnsson, Tobias; Westerlund, Fredrik

    2014-09-01

    We demonstrate a single DNA molecule optical mapping assay able to resolve a specific Escherichia coli strain from other strains. The assay is based on competitive binding of the fluorescent dye YOYO-1 and the AT-specific antibiotic netropsin. The optical map is visualized by stretching the DNA molecules in nanofluidic channels. We optimize the experimental conditions to obtain reproducible barcodes containing as much information as possible. We implement a multi-ligand transfer matrix method for calculating theoretical barcodes from known DNA sequences. Our method extends previous theoretical approaches for competitive binding of two types of ligands to many types of ligands and introduces a recursive approach that allows long barcodes to be calculated with standard computer floating point formats. The identification of a specific E. coli strain (CCUG 10979) is based on mapping of 50-160 kilobasepair experimental DNA fragments onto the theoretical genome using the developed theory. Our identification protocol introduces two theoretical constructs: a P-value for a best experiment-theory match and an information score threshold. The developed methods provide a novel optical mapping toolbox for identification of bacterial species and strains. The protocol does not require cultivation of bacteria or DNA amplification, which allows for ultra-fast identification of bacterial pathogens.

  5. Frequency-Dependent Modulation of Dopamine Release by Nicotine and Dopamine D1 Receptor Ligands: An In Vitro Fast Cyclic Voltammetry Study in Rat Striatum.

    Science.gov (United States)

    Goutier, W; Lowry, J P; McCreary, A C; O'Connor, J J

    2016-05-01

    Nicotine is a highly addictive drug and exerts this effect partially through the modulation of dopamine release and increasing extracellular dopamine in regions such as the brain reward systems. Nicotine acts in these regions on nicotinic acetylcholine receptors. The effect of nicotine on the frequency dependent modulation of dopamine release is well established and the purpose of this study was to investigate whether dopamine D1 receptor (D1R) ligands have an influence on this. Using fast cyclic voltammetry and rat corticostriatal slices, we show that D1R ligands are able to modulate the effect of nicotine on dopamine release. Nicotine (500 nM) induced a decrease in dopamine efflux at low frequency (single pulse or five pulses at 10 Hz) and an increase at high frequency (100 Hz) electrical field stimulation. The D1R agonist SKF-38393, whilst having no effect on dopamine release on its own or on the effect of nicotine upon multiple pulse evoked dopamine release, did significantly prevent and reverse the effect of nicotine on single pulse dopamine release. Interestingly similar results were obtained with the D1R antagonist SCH-23390. In this study we have demonstrated that the modulation of dopamine release by nicotine can be altered by D1R ligands, but only when evoked by single pulse stimulation, and are likely working via cholinergic interneuron driven dopamine release.

  6. Competitive binding-based optical DNA mapping for fast identification of bacteria - multi-ligand transfer matrix theory and experimental applications on Escherichia coli

    Science.gov (United States)

    Nilsson, Adam N.; Emilsson, Gustav; Nyberg, Lena K.; Noble, Charleston; Stadler, Liselott Svensson; Fritzsche, Joachim; Moore, Edward R. B.; Tegenfeldt, Jonas O.; Ambjörnsson, Tobias; Westerlund, Fredrik

    2014-01-01

    We demonstrate a single DNA molecule optical mapping assay able to resolve a specific Escherichia coli strain from other strains. The assay is based on competitive binding of the fluorescent dye YOYO-1 and the AT-specific antibiotic netropsin. The optical map is visualized by stretching the DNA molecules in nanofluidic channels. We optimize the experimental conditions to obtain reproducible barcodes containing as much information as possible. We implement a multi-ligand transfer matrix method for calculating theoretical barcodes from known DNA sequences. Our method extends previous theoretical approaches for competitive binding of two types of ligands to many types of ligands and introduces a recursive approach that allows long barcodes to be calculated with standard computer floating point formats. The identification of a specific E. coli strain (CCUG 10979) is based on mapping of 50–160 kilobasepair experimental DNA fragments onto the theoretical genome using the developed theory. Our identification protocol introduces two theoretical constructs: a P-value for a best experiment-theory match and an information score threshold. The developed methods provide a novel optical mapping toolbox for identification of bacterial species and strains. The protocol does not require cultivation of bacteria or DNA amplification, which allows for ultra-fast identification of bacterial pathogens. PMID:25013180

  7. Pd-catalyzed amidation of aryl chlorides using monodentate biaryl phosphine ligands: a kinetic, computational, and synthetic investigation.

    Science.gov (United States)

    Ikawa, Takashi; Barder, Timothy E; Biscoe, Mark R; Buchwald, Stephen L

    2007-10-31

    We present results on the amidation of aryl halides and sulfonates utilizing a monodentate biaryl phosphine-Pd catalyst. Our results are in accord with a previous report that suggests that the formation of kappa(2)-amidate complexes is deleterious to the effectiveness of a catalyst for this transformation and that their formation can be prevented by the use of appropriate bidentate ligands. We now provide data that suggest that the use of certain monodentate ligands can also prevent the formation of the kappa(2)-amidate complexes and thereby generate more stable catalysts for the amination of aryl chlorides. Furthermore, computational studies shed light on the importance of the key feature(s) of the biaryl phosphines (a methyl group ortho to the phosphorus center) that enable the coupling to occur. The use of ligands that possess a methyl group ortho to the phosphorus center allows a variety of aryl and heteroaryl chlorides with various amides to be coupled in high yield.

  8. Environmentally-friendly aqueous Li (or Na)-ion battery with fast electrode kinetics and super-long life.

    Science.gov (United States)

    Dong, Xiaoli; Chen, Long; Liu, Jingyuan; Haller, Servane; Wang, Yonggang; Xia, Yongyao

    2016-01-01

    Current rechargeable batteries generally display limited cycle life and slow electrode kinetics and contain environmentally unfriendly components. Furthermore, their operation depends on the redox reactions of metal elements. We present an original battery system that depends on the redox of I(-)/I3 (-) couple in liquid cathode and the reversible enolization in polyimide anode, accompanied by Li(+) (or Na(+)) diffusion between cathode and anode through a Li(+)/Na(+) exchange polymer membrane. There are no metal element-based redox reactions in this battery, and Li(+) (or Na(+)) is only used for charge transfer. Moreover, the components (electrolyte/electrode) of this system are environment-friendly. Both electrodes are demonstrated to have very fast kinetics, which gives the battery a supercapacitor-like high power. It can even be cycled 50,000 times when operated within the electrochemical window of 0 to 1.6 V. Such a system might shed light on the design of high-safety and low-cost batteries for grid-scale energy storage.

  9. A Plan for the Development of the Spatial Kinetics and the Detailed Reactivity Model for a Fast Reactor

    Energy Technology Data Exchange (ETDEWEB)

    Kwon, Y. M.; Jeong, H. Y.; Lee, Y. B.; Sim, Y. S

    2005-11-15

    The reactivity feedback effect of metallic fuel is determined by the fuel burnup characteristics, the configuration of core and fuel assembly, and the complicated interaction between the fuel assembly and core internal structures. Currently, a quite simple evaluation model is frequently applied for the calculation of reactivity feedback. The simple model usually induces some over-conservatism to compensate the simplification, which is an obstacle to take advantage of the positive characteristics of metallic fuel over the oxide fuel. Therefore, to develop a detailed reactivity feedback model and to remove the over-conservatism in the existing simple model would be the foundation to strengthen the economic and operational competitiveness of a liquid metal-cooled fast reactor. In the present study, the plan for the development of the detailed reactivity feedback model and the methodology to combine the spatial kinetics code with the thermal-hydraulic code have been set up, which are two prerequisites for the evaluation of the detailed reactivity feedback effect. The proposed detailed model is expected to be developed in short-term, thus, easily implemented in the SSC-K code. The development of the spatial kinetics code and the merging it to the detailed thermal-hydraulics code would be achieved in long-term, but finally minimize the uncertainty in the reactivity feedback evaluation by including the detailed thermal-hydraulic information in the reactivity calculation.

  10. Model of punctual kinetic for studies on fast reactor stability; Modelo de cinetica pontual para estudos de estabilidade de reatores rapidos

    Energy Technology Data Exchange (ETDEWEB)

    Rocamora, Francisco Dias Jr.; Rosa, Mauricio A. Pinheiro; Braz Filho, Francisco A.; Borges, Eduardo M.; Guimaraes, Lamartine

    1998-07-01

    The neutron kinetics equations are used to obtain the Zero Power Transfer Function which establishes a relationship between a reactor core reactivity perturbation and the corresponding reactor power response. This transfer function should be coupled with those obtained from the fuel element and coolant thermal-hydraulics models in order to study fast reactor stability 'in the small'. (author)

  11. Total kinetic energy release in the fast neutron-induced fission of $^{235}$U

    CERN Document Server

    Yanez, R; King, J; Barrett, J S; Fotiades, N; Lee, H Y

    2016-01-01

    We have measured the total kinetic energy (TKE) release for the $^{235}$U(n,f) reaction for $E_{n}$=2-100 MeV using the 2E method with an array of Si PIN diode detectors. The neutron energies were determined by time of flight measurements using the white spectrum neutron beam at the LANSCE facility. To benchmark the TKE measurement, the TKE release for $^{235}$U(n$_{th}$,f) was also measured using a thermal neutron beam from the Oregon State University TRIGA reactor, giving pre-neutron emission $E^*_{TKE}=170.7\\pm0.4$ MeV in good agreement with known values. Our measurements are thus absolute measurements. The TKE in $^{235}$U(n,f) decreases non-linearly from 169.0 MeV to 161.4 MeV for $E_{n}$=2-90 MeV. Comparison of the data with the multi-modal fission model of Brosa indicates the TKE decrease is a consequence of the growth of symmetric fission and the corresponding decrease of asymmetric fission with increasing neutron energy. The average TKE associated with the Brosa superlong, standard I and standard II ...

  12. Dry reforming of methane in a fast fluidized bed reactor catalysis and kinetics

    Energy Technology Data Exchange (ETDEWEB)

    El-Solh, T.

    2002-07-01

    A new methane reforming process based on fluidized catalysts is examined. Alpha-alumina catalysts, which were developed using a wetness technique that produces bulk nickel loadings, were tested under industrial operating conditions in a new Riser Simulator. Studies showed that for methane reforming, the nickel deposited in zeolites is a promising catalyst because it allows for close control of metal dispersion and re-dispersion. When the catalyst was exposed to repeated oxidation and reduction cycles, the nickel dispersions remained stable at 25 per cent for the NaY zeolite and at 15 per cent for the USY zeolite. The catalyst only offers limited use for steam reforming of methane because of the potential collapse of the zeolite structure under steam conditions. If steam reforming of methane is necessary, then nickel on alpha-alumina catalysts should be considered for maximum catalytic activity. The kinetics of dry reforming and steam reforming of methane on a fluidized Ni on Zeolite/alpha-alumina catalyst were studied in the CRED Riser Simulator reactor. Thermodynamic analysis indicates that it is possible to determine operating conditions for coke formation and the conversion of methane over nickel catalysts. The adsorption of both carbon dioxide and methane play a vital role in determining the observed rate dry reforming of methane in the CATFORMER reactor. All parameters were found to be important at the 95 per cent confidence level.

  13. Total kinetic energy release in the fast neutron-induced fission of $^{235}$U

    CERN Document Server

    Yanez, R; King, J; Barrett, J S; Fotiades, N; Lee, H Y

    2015-01-01

    We have measured the total kinetic energy (TKE) release for the $^{235}$U(n,f) reaction for $E_{n}$=2-100 MeV using the 2E method with an array of Si PIN diode detectors. The neutron energies were determined by time of flight measurements using the white spectrum neutron beam at the LANSCE facility. (To calibrate the apparatus, the TKE release for $^{235}$U(n$_{th}$,f) was also measured using a thermal neutron beam from the OSU TRIGA reactor). The TKE decreases non-linearly from 169.0 MeV to 161.4 MeV for $E_{n}$=2-90 MeV. The standard deviation of the TKE distribution is constant from $E_{n}$=20-90 MeV. Comparison of the data with the multi-modal fission model of Brosa indicates the TKE decrease is a consequence of the growth of symmetric fission and the corresponding decrease of asymmetric fission with increasing neutron energy. The average TKE associated with the Brosa superlong, standard I and standard II modes for a given mass is independent of neutron energy.

  14. Resolution of the diffusional paradox predicting infinitely fast kinetics on the nanoscale

    Science.gov (United States)

    Beke, D. L.; Erdélyi, Z.

    2006-01-01

    In our paper, we offer a natural resolution for a long-standing paradox in diffusion. We show that the growth rate of the diffusion zone (reaction layer) should not go to infinity with decreasing time (as 1/t ), just because the diffusion permeability of the interface is finite. Expression for the changeover thickness X* between the linear and parabolic regimes of the interface shift in phase separating binary A(B) systems is derived in the framework of a deterministic atomistic model for diffusion. X* lies typically between 0.01 and 300nm , depending on the composition dependence of the diffusion coefficient and the phase separation tendency of the alloy. While in ideal binary alloys with composition independent diffusivity, the deviation from the parabolic law practically cannot be observed, in real systems (where the diffusion coefficient can change several orders of magnitude with the composition), measurable deviations are expected as it was experimentally observed very recently in the Ni/Cu and Au/Ni systems. We also offer an atomistic explanation for the phenomenological interface transfer coefficient K . It measures the finite interface permeability (proportional to the jump frequency across the interface) and thus it controls the shift of the interface at short times (diffusion distances). Although it is almost exclusively accepted in the literature that linear growth kinetics are the result of interface reaction control, our results suggest that the linear or nonparabolic growth of a reaction layer on the nanoscale cannot be automatically interpreted by an interface reaction.

  15. BioRef II—Neutron reflectometry with relaxed resolution for fast, kinetic measurements at HZB

    Science.gov (United States)

    Trapp, M.; Steitz, R.; Kreuzer, M.; Strobl, M.; Rose, M.; Dahint, R.

    2016-10-01

    We present an upgrade to the time-of-flight neutron reflectometer BioRef at the research reactor BER II of the Helmholtz-Zentrum Berlin für Materialien und Energie (HZB). Through the integration of an additional chopper into the existing setup, the available wavelength resolution is significantly extended. Now two distinct operation modes can be used: a high resolution mode with Δλ/λ ranging from 1% to 5%, which allows for the investigation of thick films up to 4000 Å, and a high flux mode with Δλ/λ = 7%-11%. In the high flux mode, reflectivity curves from 0.007 Å-1 to 0.2 Å-1 with three angular settings can be recorded in 7 min. For a single angular setting and its respective window in Q-space, a time resolution of even less than 4 min is reached. The different configurations are documented by respective measurements (a) on a Ni-Ti multilayer and (b) the swelling kinetics of a solid-supported phospholipid coating upon incubation in a polyelectrolyte solution.

  16. Spherical polystyrene-supported chitosan thin film of fast kinetics and high capacity for copper removal.

    Science.gov (United States)

    Jiang, Wei; Chen, Xubin; Pan, Bingcai; Zhang, Quanxing; Teng, Long; Chen, Yufan; Liu, Lu

    2014-07-15

    In order to accelerate the kinetics and improve the utilization of the surface active groups of chitosan (CS) for heavy metal ion removal, sub-micron-sized polystyrene supported chitosan thin-film was synthesized by the electrostatic assembly method. Glutaraldehyde was used as cross-linking agent. Chitosan thin-film was well coated onto the surface of the polystyrene (PS) beads characterized by scanning electron microscopy (SEM) and energy dispersive X-ray (EDX). Their adsorption toward Cu(II) ions was investigated as a function of solution pH, degree of cross-linking, equilibrium Cu(II) ions concentration and contact time. The maximum adsorptive capacity of PS-CS was 99.8 mg/g in the adsorption isotherm study. More attractively, the adsorption equilibrium was achieved in 10 min, which showed superior properties among similar adsorbents. Continuous adsorption-desorption cyclic results demonstrated that Cu(II)-loaded PS-CS can be effectively regenerated by a hydrochloric acid solution (HCl), and the regenerated composite beads could be employed for repeated use without significant capacity loss, indicating the good stability of the adsorbents. The XPS analysis confirmed that the adsorption process was due to surface complexes with atoms of chitosan. Generally, PS beads could be employed as a promising host to fabricate efficient composites that originated from chitosan or other bio-sorbents for environmental remediation.

  17. Thermal stability and kinetics of defects in magnesium aluminate spinel irradiated with fast neutrons

    Energy Technology Data Exchange (ETDEWEB)

    Yasuda, Kazuhiro E-mail: yasudak@nucl.kyushu-u.ac.jp; Kinoshita, Chiken; Fukuda, Korehisa; Garner, Frank A

    2000-12-01

    Thermal stability of interstitial-type dislocation loops and cavities in single crystals of MgAl{sub 2}O{sub 4} was examined during isochronal and isothermal annealing. The specimens were irradiated with fast-neutrons in FFTF/MOTA at 658 and 1023 K up to 249 dpa. During the isochronal annealing, dislocation loops started to shrink around 1000 K and completely disappeared at 1470 K without changing their character. Cavities grew slightly around 1570 K, and above this temperature, cavities shrunk with increasing annealing temperature. The recovery stage of point defects in MgAl{sub 2}O{sub 4} was discussed in terms of the thermal stability of defect clusters; vacancy migration starts around 1000 K (corresponding to stage III), whereas vacancy clusters start to dissociate around 1570 K (corresponding to stage V). The vacancy migration energy for rate controlling species was estimated from the shrinkage process of interstitial-type dislocation loops to be 2.0 {+-} 0.7 eV.

  18. Nanosecond absorption study of kinetics associated with carbon monoxide rebinding to hemoglobin S and hemoglobin C following ligand photolysis.

    Science.gov (United States)

    Shapiro, D B; Paquette, S J; Esquerra, R M; Che, D; Goldbeck, R A; Hirsch, R E; Mohandas, N; Kliger, D S

    1994-11-30

    The absorption spectra of photolysis intermediates of the CO complex of hemoglobin S and hemoglobin C, in the tetramer form, have been measured between 10 ns and 200 ms after excitation. These data were analyzed using singular value decomposition (SVD) and global analysis to determine kinetic lifetimes associated with various processes involved in CO recombination. The results of this analysis show that, in the tetramer (non-aggregated) form, hemoglobin S and hemoglobin C exhibit the same kinetics associated with CO recombination as hemoglobin A.

  19. Effect of the competition of Cu(II) and Ni(II) on the kinetic and thermodynamic stabilities of Cr(III)-organic ligand complexes using competitive ligand exchange (EDTA).

    Science.gov (United States)

    Cunha, Graziele da Costa; Goveia, Danielle; Romão, Luciane Pimenta Cruz; de Oliveira, Luciana Camargo

    2015-05-01

    The effect of competition of Cu(II) and Ni(II) on the kinetic stability of Cr(III) complexed with natural organic matter (NOM) was characterized using EDTA exchange with single-stage tangential-flow ultrafiltration. For a water sample from Serra de Itabaiana, 3% of spiked Cr(III) was exchanged, while for a sample from the Itapanhaú River, 7, 10, 10, and 21% was exchanged in experiments using Cr(III) alone and in combination with Cu(II), Ni(II), or Cu(II) + Ni(II), respectively. Times required to reach exchange equilibrium with EDTA were less than 360 min. The influence of competition from Ni(II) and Cu(II) on the availability of complexed Cr(III) was low, demonstrating preference of the ligand sites for Cr(III). This was correlated with sample humification, as confirmed by EPR and (13)C NMR analyses. Exchange efficiency was in the order Cu > Ni > Cr, and the process could be readily described by first order kinetics, with average rate constants of 0.35-0.37 h(-1). Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Kinetics of expression of costimulatory molecules and their ligands in murine relapsing experimental autoimmune encephalomyelitis in vivo

    DEFF Research Database (Denmark)

    Issazadeh-Navikas, Shohreh; Navikas, V; Schaub, M;

    1998-01-01

    We studied the kinetics of expression of costimulatory molecules and cytokines in the central nervous system (CNS) in murine relapsing experimental autoimmune encephalomyelitis (EAE). During the natural course of EAE, B7-2 expression in the CNS correlated with clinical signs, while B7-1 was exclu...

  1. A P2X receptor from the tardigrade species Hypsibius dujardini with fast kinetics and sensitivity to zinc and copper.

    Science.gov (United States)

    Bavan, Selvan; Straub, Volko A; Blaxter, Mark L; Ennion, Steven J

    2009-01-20

    vertebrates and invertebrates. Furthermore, several characteristics of HdP2X including fast kinetics with low ATP sensitivity, potentiation by ivermectin in a channel with fast kinetics and distinct copper and zinc binding sites not dependent on histidines make HdP2X a useful model for comparative structure-function studies allowing a better understanding of P2X receptors in higher organisms.

  2. A P2X receptor from the tardigrade species Hypsibius dujardini with fast kinetics and sensitivity to zinc and copper

    Directory of Open Access Journals (Sweden)

    Blaxter Mark L

    2009-01-01

    to the split between vertebrates and invertebrates. Furthermore, several characteristics of HdP2X including fast kinetics with low ATP sensitivity, potentiation by ivermectin in a channel with fast kinetics and distinct copper and zinc binding sites not dependent on histidines make HdP2X a useful model for comparative structure-function studies allowing a better understanding of P2X receptors in higher organisms.

  3. Recombinant Escherichia coli GMP reductase: kinetic, catalytic and chemical mechanisms, and thermodynamics of enzyme-ligand binary complex formation.

    Science.gov (United States)

    Martinelli, Leonardo Krás Borges; Ducati, Rodrigo Gay; Rosado, Leonardo Astolfi; Breda, Ardala; Selbach, Bruna Pelegrim; Santos, Diógenes Santiago; Basso, Luiz Augusto

    2011-04-01

    Guanosine monophosphate (GMP) reductase catalyzes the reductive deamination of GMP to inosine monophosphate (IMP). GMP reductase plays an important role in the conversion of nucleoside and nucleotide derivatives of guanine to adenine nucleotides. In addition, as a member of the purine salvage pathway, it also participates in the reutilization of free intracellular bases. Here we present cloning, expression and purification of Escherichia coli guaC-encoded GMP reductase to determine its kinetic mechanism, as well as chemical and thermodynamic features of this reaction. Initial velocity studies and isothermal titration calorimetry demonstrated that GMP reductase follows an ordered bi-bi kinetic mechanism, in which GMP binds first to the enzyme followed by NADPH binding, and NADP(+) dissociates first followed by IMP release. The isothermal titration calorimetry also showed that GMP and IMP binding are thermodynamically favorable processes. The pH-rate profiles showed groups with apparent pK values of 6.6 and 9.6 involved in catalysis, and pK values of 7.1 and 8.6 important to GMP binding, and a pK value of 6.2 important for NADPH binding. Primary deuterium kinetic isotope effects demonstrated that hydride transfer contributes to the rate-limiting step, whereas solvent kinetic isotope effects arise from a single protonic site that plays a modest role in catalysis. Multiple isotope effects suggest that protonation and hydride transfer steps take place in the same transition state, lending support to a concerted mechanism. Pre-steady-state kinetic data suggest that product release does not contribute to the rate-limiting step of the reaction catalyzed by E. coli GMP reductase.

  4. A fast, open source implementation of adaptive biasing potentials uncovers a ligand design strategy for the chromatin regulator BRD4

    Science.gov (United States)

    Dickson, Bradley M.; de Waal, Parker W.; Ramjan, Zachary H.; Xu, H. Eric; Rothbart, Scott B.

    2016-10-01

    In this communication we introduce an efficient implementation of adaptive biasing that greatly improves the speed of free energy computation in molecular dynamics simulations. We investigated the use of accelerated simulations to inform on compound design using a recently reported and clinically relevant inhibitor of the chromatin regulator BRD4 (bromodomain-containing protein 4). Benchmarking on our local compute cluster, our implementation achieves up to 2.5 times more force calls per day than plumed2. Results of five 1 μs-long simulations are presented, which reveal a conformational switch in the BRD4 inhibitor between a binding competent and incompetent state. Stabilization of the switch led to a -3 kcal/mol improvement of absolute binding free energy. These studies suggest an unexplored ligand design principle and offer new actionable hypotheses for medicinal chemistry efforts against this druggable epigenetic target class.

  5. A fast, open source implementation of adaptive biasing potentials uncovers a ligand design strategy for the chromatin regulator BRD4

    CERN Document Server

    Dickson, Bradley M; Ramjan, Zachary H; Xu, H Eric; Rothbart, Scott B

    2016-01-01

    In this communication we introduce an efficient implementation of adaptive biasing that greatly improves the speed of free energy computation in molecular dynamics simulations. We investigated the use of accelerated simulations to inform on compound design using a recently reported and clinically relevant inhibitor of the chromatin regulator BRD4. Benchmarking on our local compute cluster, our implementation achieves up to 2.5 times more force calls per day than plumed2. Results of five 1{\\mu}second-long simulations are presented, which reveal a conformational switch in the BRD4 inhibitor between a binding competent and incompetent state. Stabilization of the switch led to a -3 kcal/mol improvement of absolute binding free energy. These studies suggest an unexplored ligand design principle and offer new actionable hypotheses for medicinal chemistry efforts against this druggable epigenetic target class.

  6. Substitution reactions of [Pd(bipy)(malonate)] explored with a different set of ligands: Kinetic and mechanistic interpretation in aqueous medium and at pH 7.4

    Indian Academy of Sciences (India)

    SUMON RAY; PARNAJYOTI KARMAKAR; ANIMESH CHATTOPADHYAY; DEBABRATA NANDI; SUSHOBHAN UKIL; ROSHNI SARKAR (SAIN); ALAK K GHOSH

    2016-08-01

    A brief overview of mechanistic studies of the reactions of Pd(II)-bipy-malonate complex with different set of ligands, viz., (N, S), (S, O) and (S) donor molecules is reported here. The kinetics of complex formation reactions of three sulphur containing bio-relevant ligands thioglycolic acid[L₁],thiourea[L₂] andthiosemicarbazide [L₃] were studied with innermetallic [Pd(bipy)(malonate)] complex at physiological condition. The effect of the nucleophilicity of the chosen nucleophiles was studied for the reactant complex under pseudo-first order conditions as a function of nucleophile concentration and temperature using stopped-flow technique. This article describes the results obtained for substitution reactions of bi-functional Pd(II) complex with different biomolecules, under varying experimental conditions. The kinetic studies showed that the malonate ring departs from the coordination zone of palladium centre via two-step mechanism. The first step depends on the concentration of the incoming ligand for all the ligands. But in the second step thiourea is ligand dependent where as other two are independent of the ligand concentration. Hence, it can be concluded that the second step is the chelation step for L₁ and L₃. The mechanism for the substitution of the coordinated malonate molecule is associative, as demonstrated by the negative values of ∆S=. Such type of complexes are less toxic than chloro-, which in turn hydrolyses to aqua or aqua complexes as they are prevented from oligomer formation at physiological pH.

  7. The extraordinary specificity of xanthine phosphoribosyltransferase from Bacillus subtilis elucidated by reaction kinetics, ligand binding, and crystallography

    DEFF Research Database (Denmark)

    Arent, Susan; Kadziola, Anders; Larsen, Sine

    2006-01-01

    (X)GPRTases with respect to sequence, PRPP binding motif, and oligomeric structure. They are more related with the PurR repressor of Gram-positive bacteria, the adenine PRTase, and orotate PRTase. The catalytic function and high specificity for xanthine of B. subtilis XPRTase were investigated by ligand binding studies...... related to a few key residues in the active site. Asn27 can in different orientations form hydrogen bonds to an amino group or an oxo group at the 2-position of the purine base, and Lys156 is positioned to make a hydrogen bond with N7. This and the absence of a catalytic carboxylate group near the N7......Xanthine phosphoribosyltransferase (XPRTase) from Bacillus subtilis is a representative of the highly xanthine specific XPRTases found in Gram-positive bacteria. These XPRTases constitute a distinct subclass of 6-oxopurine PRTases, which deviate strongly from the major class of H...

  8. Evidence of Kinetic Control of Ligand Binding and Staged Product Release in MurA (enolpyruvyl UDP-GlcNAc synthase)-catalyzed Reactions

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, S.; Zhang, F; Chindemi, P; Junop, M; Berti, P

    2009-01-01

    MurA (enolpyruvyl UDP-GlcNAc synthase) catalyzes the first committed step in peptidoglycan biosynthesis. In this study, MurA-catalyzed breakdown of its tetrahedral intermediate (THI), with a k{sub cat}/K{sub M} of 520 M{sup -1} s{sup -1}, was far slower than the normal reaction, and 3 x 10{sup 5}-fold slower than the homologous enzyme, AroA, reacting with its THI. This provided kinetic evidence of slow binding and a conformationally constrained active site. The MurA cocrystal structure with UDP-N-acetylmuramic acid (UDP-MurNAc), a potent inhibitor, and phosphite revealed a new 'staged' MurA conformation in which the Arg397 side chain tracked phosphite out of the catalytic site. The closed-to-staged transition involved breaking eight MurA {center_dot} ligand ion pairs, and three intraprotein hydrogen bonds helping hold the active site loop closed. These were replaced with only two MurA {center_dot} UDP-MurNAc ion pairs, two with phosphite, and seven new intraprotein ion pairs or hydrogen bonds. Cys115 appears to have an important role in forming the staged conformation. The staged conformation appears to be one step in a complex choreography of release of the product from MurA.

  9. Photochemical nitric oxide precursors: synthesis, photochemistry, and ligand substitution kinetics of ruthenium salen nitrosyl and ruthenium salophen nitrosyl complexes.

    Science.gov (United States)

    Works, Carmen F; Jocher, Christoph J; Bart, Gwen D; Bu, Xianhui; Ford, Peter C

    2002-07-15

    Described are syntheses, characterizations, and photochemical reactions of the nitrosyl complexes Ru(salen)(ONO)(NO) (I, salen = N,N'-ethylenebis(salicylideneiminato) dianion), Ru(salen)(Cl)(NO) (II), Ru((t)Bu(4)salen)(Cl)(NO) (III,(t)Bu(4)salen = N,N'-ethylenebis(3,5-di-tert-butylsalicylideneiminato) dianion), Ru((t)Bu(4)salen)(ONO)(NO) (IV), Ru((t)Bu(2)salophen)(Cl)(NO) (V, (t)Bu(2)salophen = N,N'-1,2-phenylenediaminebis(3-tert-butylsalicylideneiminato) dianion), and Ru((t)Bu(4)salophen)(Cl)(NO) (VI, (t)Bu(4)salophen = N,N'-1,2-phenylenebis(3,5-di-tert-butylsalicylideneiminato) dianion). Upon photolysis, these Ru(L)(X)(NO) compounds undergo NO dissociation to give the ruthenium(III) solvento products Ru(L)(X)(Sol). Quantum yields for 365 nm irradiation in acetonitrile solution fall in a fairly narrow range (0.055-0.13) but decreased at longer lambda(irr). The quantum yield (lambda(irr) = 365 nm) for NO release from the water soluble complex [Ru(salen)(H(2)O)(NO)]Cl (VII) was 0.005 in water. Kinetics of thermal back-reactions to re-form the nitrosyl complexes demonstrated strong solvent dependence with second-order rate constants k(NO) varying from 5 x 10(-4) M(-1) s(-1) for the re-formation of II in acetonitrile to 5 x 10(8) M(-1) s(-1) for re-formation of III in cyclohexane. Pressure and temperature effects on the back-reaction rates were also examined. These results are relevant to possible applications of photochemistry for nitric oxide delivery to biological targets, to the mechanisms by which NO reacts with metal centers to form metal-nitrosyl bonds, and to the role of photochemistry in activating similar compounds as catalysts for several organic transformations. Also described are the X-ray crystal structures of I and V.

  10. Fast kinetic studies of reduction of ferricytochrome c by a series of Fe(EDTA)-type complexes

    Institute of Scientific and Technical Information of China (English)

    黄仲贤; 周刚; 王韵华; 王霞

    1996-01-01

    The reductions of cytochrome c by a series of derivatives of Fe(EDTA)2- complex have been studied by a stopped-flow technique. The reactions of cytochrome c with Fe(EDTA)2-, Fe (CDTA)2- and Fe(IDA)22- present typical outer sphere mechanism, meanwhile the cytochrome c(III) and Fe(NTA)- system shows abnormal kinetic behavior, including the rate saturation, big negative entropy and lower overall charge and binding site charge calculated from the dependence of electron transfer rate on ionic strength. On the basis of these observations a semi-inner-sphere mechanism is proposed to illustrate the kinetics.

  11. The V499G/Y501H mutation impairs fast motor kinetics of prestin and has significance for defining functional independence of individual prestin subunits.

    Science.gov (United States)

    Homma, Kazuaki; Duan, Chongwen; Zheng, Jing; Cheatham, Mary Ann; Dallos, Peter

    2013-01-25

    Outer hair cells (OHCs) are a mammalian innovation for mechanically amplifying sound energy to overcome the viscous damping of the cochlear partition. Although the voltage-dependent OHC membrane motor, prestin, has been demonstrated to be essential for mammalian cochlear amplification, the molecular mechanism by which prestin converts electrical energy into mechanical displacement/force remains elusive. Identifying mutations that alter the motor function of prestin provides vital information for unraveling the energy transduction mechanism of prestin. We show that the V499G/Y501H mutation does not deprive prestin of its voltage-induced motor activity, but it does significantly impair the fast motor kinetics and voltage operating range. Furthermore, mutagenesis studies suggest that Val-499 is the primary site responsible for these changes. We also show that V499G/Y501H prestin forms heteromers with wild-type prestin and that the fast motor kinetics of wild-type prestin is not affected by heteromer formation with V499G/Y501H prestin. These results suggest that prestin subunits are individually functional within a given multimer.

  12. Nanosecond-time-resolved infrared spectroscopic study of fast relaxation kinetics of protein folding by means of laser-induced temperature-jump

    Institute of Scientific and Technical Information of China (English)

    Zhang Qing-Li; Wang Li; Weng Yu-Xiang; Qiu Xiang-Gang; Wang Wei-Chi; Yan Ji-Xiang

    2005-01-01

    Elucidating the initial kinetics of folding pathways is critical to the understanding of the protein folding mechanism. Transient infrared spectroscopy has proved a powerful tool to probe the folding kinetics. Herein we report the construction of a nanosecond laser-induced temperature-jump (T-jump) technique coupled to a nanosecond timeresolved transient mid-infrared (mid-IR) spectrometer system capable of investigating the protein folding kinetics with a temporal resolution of 50 ns after deconvolution of the instrumental response function. The mid-IR source is a liquid N2 cooled CO laser covering a spectral range of 5.0μm (2000 cm-1) ~ 6.5μm (1540 cm-1). The heating pulse was generated by a high pressure H2 Raman shifter at wavelength of 1.9μm. The maximum temperature-jump could reach as high as 26±1℃. The fast folding/unfolding dynamics of cytochrome C was investigated by the constructed system,providing an example.

  13. Fast-scan cyclic voltammetry reveals that L-Dopa produces regionally selective, bimodal influences on striatal dopamine kinetics in vivo

    Science.gov (United States)

    Harun, R; Munoz, M; Grassi, C; Hare, K; Brough, E; Torres, GE; Grace, AA; Wagner, AK

    2016-01-01

    Parkinson’s disease (PD) is a debilitating condition that is caused by a relatively specific degeneration of dopaminergic (DAergic) neurons of the substantia nigra pars compacta. Levodopa (L-Dopa) was introduced as a viable treatment option for PD over 40 years ago and still remains the most common and effective therapy for PD. Though the effects of L-Dopa to augment striatal DA production are well known, little is actually known about how L-Dopa alters the kinetics of DA neurotransmission that contribute to its beneficial and adverse effects. In this study, we examined the effects of L-Dopa administration (100mg/kg carbidopa/250mg/kg L-Dopa) on regional electrically stimulated DA response kinetics using fast-scan cyclic voltammetry (FSCV) in anesthetized rats. We demonstrate that L-Dopa enhances DA release in both the dorsal striatum (D-STR) and nucleus accumbens (NAc), but surprisingly causes a delayed inhibition of release in the D-STR, a finding that may be related to high-dose L-Dopa effects. In both regions, L-Dopa progressively attenuated reuptake kinetics through a decrease in Vmax and an increase in Km. This finding is consistent with recent clinical studies suggesting that L-Dopa chronically down-regulates the DA transporter (DAT), which may relate to the common development of L-Dopa induced dyskinesias (LID) in PD subjects. PMID:26611352

  14. Fast-scan cyclic voltammetry demonstrates that L-DOPA produces dose-dependent regionally selective, bimodal effects on striatal dopamine kinetics in vivo.

    Science.gov (United States)

    Harun, R; Hare, K M; Brough, M E; Munoz, M J; Grassi, C M; Torres, G E; Grace, A A; Wagner, A K

    2015-11-27

    Parkinson's disease (PD) is a debilitating condition that is caused by a relatively specific degeneration of dopaminergic (DAergic) neurons of the substantia nigra pars compacta. Levodopa (L-DOPA) was introduced as a viable treatment option for PD over 40 years ago and still remains the most common and effective therapy for PD. Though the effects of L-DOPA to augment striatal DA production are well known, little is actually known about how L-DOPA alters the kinetics of DA neurotransmission that contribute to its beneficial and adverse effects. In this study, we examined the effects of L-DOPA administration (50mg/kg carbidopa + 0, 100, and 250mg/kg L-DOPA) on regional electrically stimulated DA response kinetics using fast-scan cyclic voltammetry (FSCV) in anesthetized rats. We demonstrate that L-DOPA enhances DA release in both the dorsal striatum (D-STR) and nucleus accumbens (NAc), but surprisingly causes a delayed inhibition of release in the D-STR. In both regions, L-DOPA progressively attenuated reuptake kinetics, predominantly through a decrease in Vmax. These findings have important implications on understanding the pharmacodynamics of L-DOPA, which can be informative for understand its therapeutic effects and also common side effects like L-DOPA induced dyskinesias (LID). This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  15. An Active Learning Mammalian Skeletal Muscle Lab Demonstrating Contractile and Kinetic Properties of Fast- and Slow-Twitch Muscle

    Science.gov (United States)

    Head, S. I.; Arber, M. B.

    2013-01-01

    The fact that humans possess fast and slow-twitch muscle in the ratio of approximately 50% has profound implications for designing exercise training strategies for power and endurance activities. With the growth of exercise and sport science courses, we have seen the need to develop an undergraduate student laboratory that demonstrates the basic…

  16. An Active Learning Mammalian Skeletal Muscle Lab Demonstrating Contractile and Kinetic Properties of Fast- and Slow-Twitch Muscle

    Science.gov (United States)

    Head, S. I.; Arber, M. B.

    2013-01-01

    The fact that humans possess fast and slow-twitch muscle in the ratio of approximately 50% has profound implications for designing exercise training strategies for power and endurance activities. With the growth of exercise and sport science courses, we have seen the need to develop an undergraduate student laboratory that demonstrates the basic…

  17. Environmentally-friendly aqueous Li (or Na)-ion battery with fast electrode kinetics and super-long life

    OpenAIRE

    Dong, Xiaoli; Chen, Long; Liu, Jingyuan; Haller, Servane; Wang, Yonggang; Xia, Yongyao

    2016-01-01

    Current rechargeable batteries generally display limited cycle life and slow electrode kinetics and contain environmentally unfriendly components. Furthermore, their operation depends on the redox reactions of metal elements. We present an original battery system that depends on the redox of I−/I3 − couple in liquid cathode and the reversible enolization in polyimide anode, accompanied by Li+ (or Na+) diffusion between cathode and anode through a Li+/Na+ exchange polymer membrane. There are n...

  18. Angular distribution, kinetic energy distributions, and excitation functions of fast metastable oxygen fragments following electron impact of CO2

    Science.gov (United States)

    Misakian, M.; Mumma, M. J.; Faris, J. F.

    1975-01-01

    Dissociative excitation of CO2 by electron impact was studied using the methods of translational spectroscopy and angular distribution analysis. Earlier time of flight studies revealed two overlapping spectra, the slower of which was attributed to metastable CO(a3 pi) fragments. The fast peak is the focus of this study. Threshold energy, angular distribution, and improve time of flight measurements indicate that the fast peak actually consists of five overlapping features. The slowest of the five features is found to consist of metastable 0(5S) produced by predissociation of a sigma u + state of CO2 into 0(5S) + CO(a3 pi). Oxygen Rydberg fragments originating directly from a different sigma u + state are believed to make up the next fastest feature. Mechanisms for producing the three remaining features are discussed.

  19. Periodicity in tumor vasculature targeting kinetics of ligand-functionalized nanoparticles studied by dynamic contrast enhanced magnetic resonance imaging and intravital microscopy

    DEFF Research Database (Denmark)

    Hak, Sjoerd; Cebulla, Jana; Huuse, Else Marie

    2014-01-01

    kinetics. These kinetics will not only depend on nanoparticle characteristics, but also on receptor binding and recycling. In this study, we monitored the in vivo targeting kinetics of αvβ3-integrin specific nanoparticles with intravital microscopy and dynamic contrast enhanced magnetic resonance imaging...... in the accumulation kinetics of αvβ3-integrin targeted nanoparticles and hypothesize that this periodicity is caused by receptor binding, internalization and recycling dynamics. Taken together, this demonstrates that our experimental approach provides new insights in in vivo nanoparticle targeting, which may proof...

  20. A novel fast and flexible technique of radical kinetic behaviour investigation based on pallet for plasma evaluation structure and numerical analysis

    Science.gov (United States)

    Malinowski, Arkadiusz; Takeuchi, Takuya; Chen, Shang; Suzuki, Toshiya; Ishikawa, Kenji; Sekine, Makoto; Hori, Masaru; Lukasiak, Lidia; Jakubowski, Andrzej

    2013-07-01

    This paper describes a new, fast, and case-independent technique for sticking coefficient (SC) estimation based on pallet for plasma evaluation (PAPE) structure and numerical analysis. Our approach does not require complicated structure, apparatus, or time-consuming measurements but offers high reliability of data and high flexibility. Thermal analysis is also possible. This technique has been successfully applied to estimation of very low value of SC of hydrogen radicals on chemically amplified ArF 193 nm photoresist (the main goal of this study). Upper bound of our technique has been determined by investigation of SC of fluorine radical on polysilicon (in elevated temperature). Sources of estimation error and ways of its reduction have been also discussed. Results of this study give an insight into the process kinetics, and not only they are helpful in better process understanding but additionally they may serve as parameters in a phenomenological model development for predictive modelling of etching for ultimate CMOS topography simulation.

  1. Design Improvement of Iso-Kinetic Flow Sampling Device at Subchannel in a Wire-Wrapped 37-pin Fuel Assembly for a Sodium Cooled Fast Reactor

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Dong-Won; Kim, Hyungmo; Ko, Yung-Joo; Chang, Seok-Kyu; Choi, Hae Seob; Euh, Dong-kin; Lee, Hyeong-Yeon [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2014-10-15

    Securing the structural integrity of a fuel assembly during reactor operation is of utmost importance in order to prevent reactor severe accident like the Fukushima nuclear power plant through a flow characteristics tests with test assembly scaled down from a prototype reactor of a sodium-cooled fast reactor (SFR). To evaluate uncertainty is very important to ensure reliability at the results of the fuel assembly. Therefore the sub-channel analysis method is commonly used for the thermal hydraulic analysis of a SFR, a wire wrapped sub-channel type. In KAERI, two sub-channel analysis codes (SLTHEN, MATRA-LMR) are considered to utilize for the design of the prototype reactor. In this study, design improvement of iso-Kinetic flow sampling device at sub-channel in a wire-wrapped 37-pin fuel assembly for a sodium cooled fast reactor is conducted for decreasing misalignment sensitivity. The subchannel flow characteristics analysis method is commonly used for the thermal hydraulic analysis of a SFR, a wire wrapped subchannel type. In KAERI, two subchannel analysis codes are considered to be utilized for the design of the prototype reactor. In this study, the X-axis probe misalignment error is 2.5%, the Y-axis probe misalignment error is 0.9% and flowmeter and DA equipment error is 0.2%. As shown in above results, the misalignment error was the highest factor in uncertainty analysis. To solve the problem, design improvement of iso-kinetic flow sampling device at subchannel in a wire-wrapped 37-pin fuel assembly is practiced for decreasing misalignment sensitivity error.

  2. Ultrafine Nanocrystalline CeO2@C-Containing NaAlH4 with Fast Kinetics and Good Reversibility for Hydrogen Storage.

    Science.gov (United States)

    Zhang, Xin; Liu, Yongfeng; Wang, Ke; Li, You; Gao, Mingxia; Pan, Hongge

    2015-12-21

    A nanocrystalline CeO2@C-containing NaAlH4 composite is successfully synthesized in situ by hydrogenating a NaH-Al mixture doped with CeO2@C. Compared with NaAlH4 , the as-prepared CeO2@C-containing NaAlH4 composite, with a minor amount of excess Al, exhibits significantly improved hydrogen storage properties. The dehydrogenation onset temperature of the hydrogenated [NaH-Al-7 wt % CeO2@C]-0.04Al sample is 77 °C lower than that of the pristine sample because of a reduced kinetic barrier. More importantly, the dehydrogenated sample absorbs ∼4.7 wt % hydrogen within 35 min at 100°C and 10 MPa of hydrogen. Compositional and structural analyses reveal that CeO2 is converted to CeH2 during ball milling and that the newly formed CeH2 works with the excess of Al to synergistically improve the hydrogen storage properties of NaAlH4. Our findings will aid in the rational design of novel catalyst-doped complex hydride systems with low operating temperatures, fast kinetics, and long-term cyclability.

  3. Annealing Kinetic Model Using Fast and Slow Metastable Defects for Hydrogenated-Amorphous-Silicon-Based Solar Cells

    Directory of Open Access Journals (Sweden)

    Seung Yeop Myong

    2007-01-01

    Full Text Available The two-component kinetic model employing “fast” and “slow” metastable defects for the annealing behaviors in pin-type hydrogenated-amorphous-silicon- (a-Si:H- based solar cells is simulated using a normalized fill factor. Reported annealing data on pin-type a-Si:H-based solar cells are revisited and fitted using the model to confirm its validity. It is verified that the two-component model is suitable for fitting the various experimental phenomena. In addition, the activation energy for annealing of the solar cells depends on the definition of the recovery time. From the thermally activated and high electric field annealing behaviors, the plausible microscopic mechanism on the defect removal process is discussed.

  4. Mechanism for the formation of substituted manganese(V) cyanidonitrido complexes: crystallographic and kinetic study of the substitution reactions of trans-[MnN(H2O)(CN)4]2- with monodentate pyridine and bidentate pyridine-carboxylate ligands.

    Science.gov (United States)

    van der Westhuizen, Hendrik J; Meijboom, Reinout; Schutte, Marietjie; Roodt, Andreas

    2010-10-18

    Dissolution of [(CH(3))N](2)Na[MnN(CN)(5)]·H(2)O in water results in the rapid dissociation of the trans-CN(-) ligand to form trans-[MnN(H(2)O)(CN)(4)](2-)(aq), which reacts with monodentate pyridine ligands such as 3-methyl and 4-methyl pyridine to form the corresponding mono-substituted complexes, of which the molecular structures obtained from X-ray crystallography, trans-[MnN(3-pic)(CN)(4)](2-) and trans-[MnN(4-pic)(CN)(4)](2-), are reported. [MnN(H(2)O)(CN)(4)](2-)(aq) also reacts with bidentate nucleophiles such as pyridine-2-carboxylate (pico) and quinoline-2-carboxylate (quino), yielding the corresponding [MnN(η(2)-pico)(CN)(3)](2-) and [MnN(η(2)-quino)(CN)(3)](2-) complexes as determined by X-ray crystallography. The formation kinetics of pyridine-2-carboxylate and three different pyridine-2,x-dicarboxylate ligands (x = 3, 4, 5) are reported, and two consecutive reaction steps are proposed, defined as the formation of the [MnN(η(1)-pico)(CN)(4)](3-) and [MnN(η(2)-pico)(CN)(3)](3-) complexes, respectively. Only the second steps could be spectrophotometrically observed and kinetically investigated. The first reaction is attributed to the rapid aqua substitution of [MnN(H(2)O)(CN)(4)](2-), thermodynamically unfavored and too fast to observe by conventional rapid third generation stopped-flow techniques. The second, slower reaction is attributed to cyanido substitution, with overall formation rate constants (25 °C; k(1)'; M(-1) s(-1)) and corresponding activation parameters (ΔH(k1')(double dagger), kJ mol(-1), ΔS(k1')(double dagger), J K(-1) mol(-1)) for the following entering bidentate nucleophiles: pyridine-2-carboxylate: (1.15 ± 0.04) × 10(-3), 102 ± 1, and 48 ± 3; pyridine-2,3-dicarboxylate: (1.1 ± 0.1) × 10(-3), 93 ± 2, and 20 ± 4; pyridine-2,4-dicarboxylate (8.5 ± 0.5) × 10(-4), 123 ± 5, and 115 ± 14; pyridine-2,5-dicarboxylate: (1.08 ± 0.04) × 10(-3), 106 ± 1, and 60 ± 2. A dissociative activation for the cyanido substitution

  5. Kv3.1/Kv3.2 channel positive modulators enable faster activating kinetics and increase firing frequency in fast-spiking GABAergic interneurons.

    Science.gov (United States)

    Boddum, Kim; Hougaard, Charlotte; Xiao-Ying Lin, Julie; von Schoubye, Nadia Lybøl; Jensen, Henrik Sindal; Grunnet, Morten; Jespersen, Thomas

    2017-02-24

    Due to their fast kinetic properties, Kv3.1 voltage gated potassium channels are important in setting and controlling firing frequency in neurons and pivotal in generating high frequency firing of interneurons. Pharmacological activation of Kv3.1 channels may possess therapeutic potential for treatment of epilepsy, hearing disorders, schizophrenia and cognitive impairments. Here we thoroughly investigate the selectivity and positive modulation of the two small molecules, EX15 and RE01, on Kv3 channels. Selectivity studies, conducted in Xenopus laevis oocytes confirmed a positive modulatory effect of the two compounds on Kv3.1 and to a minor extent on Kv3.2 channels. RE01 had no effect on the Kv3.3 and Kv3.4 channels, whereas EX15 had an inhibitory impact on the Kv3.4 mediated current. Voltage-clamp experiments in monoclonal hKv3.1b/HEK293 cells (34 °C) revealed that the two compounds indeed induced larger currents and faster activation kinetics. They also decrease the speed of deactivation and shifted the voltage dependence of activation, to a more negative activation threshold. Application of action potential clamping and repetitive stimulation protocols of hKv3.1b expressing HEK293 cells revealed that EX15 and RE01 significantly increased peak amplitude, half width and decay time of Kv3.1 mediated currents, even during high-frequency action potential clamping (250 Hz). In rat hippocampal slices, EX15 and RE01 increased neuronal excitability in fast-spiking interneurons in dentate gyrus. Action potential frequency was prominently increased at minor depolarizing steps, whereas more marginal effects of EX15 and RE01 were observed after stronger depolarizations. In conclusion, our results suggest that EX15 and RE01 positive modulation of Kv3.1 and Kv3.2 currents facilitate increased firing frequency in fast-spiking GABAergic interneurons.

  6. Efficient estimation of rare-event kinetics

    CERN Document Server

    Trendelkamp-Schroer, Benjamin

    2014-01-01

    The efficient calculation of rare-event kinetics in complex dynamical systems, such as the rate and pathways of ligand dissociation from a protein, is a generally unsolved problem. Markov state models can systematically integrate ensembles of short simulations and thus effectively parallelize the computational effort, but the rare events of interest still need to be spontaneously sampled in the data. Enhanced sampling approaches, such as parallel tempering or umbrella sampling, can accelerate the computation of equilibrium expectations massively - but sacrifice the ability to compute dynamical expectations. In this work we establish a principle to combine knowledge of the equilibrium distribution with kinetics from fast "downhill" relaxation trajectories using reversible Markov models. This approach is general as it does not invoke any specific dynamical model, and can provide accurate estimates of the rare event kinetics. Large gains in sampling efficiency can be achieved whenever one direction of the proces...

  7. Influence of the ligand alkyl chain length on the solubility, aqueous speciation, and kinetics of substitution reactions of water-soluble M3S4 (M = Mo, W) clusters bearing hydroxyalkyl diphosphines.

    Science.gov (United States)

    Beltrán, Tomás F; Llusar, Rosa; Sokolov, Maxim; Basallote, Manuel G; Fernández-Trujillo, M Jesús; Pino-Chamorro, Jose Ángel

    2013-08-05

    Water-soluble [M3S4X3(dhbupe)3](+) diphosphino complexes (dhbupe = 1,2-bis(bis(hydroxybutyl)phosphino)ethane), 1(+) (M = Mo, X = Cl) and 2(+) (M = W; X = Br), have been synthesized by extending the procedure used for the preparation of their hydroxypropyl analogues by reaction of the M3S4(PPh3)3X4(solvent)x molecular clusters with the corresponding 1,2-bis(bishydroxyalkyl)diphosphine. The solid state structure of the [M3S4X3(dhbupe)3](+) cation possesses a C3 symmetry with a cuboidal M3S4 unit, and the outer positions are occupied by one halogen and two phosphorus atoms of the diphosphine ligand. At a basic pH, the halide ligands are substituted by hydroxo groups to afford the corresponding [Mo3S4(OH)3(dhbupe)3](+) (1OH(+)) and [W3S4(OH)3(dhbupe)3](+) (2OH(+)) complexes. This behavior is similar to that found in 1,2-bis(bis(hydroxymethyl)phosphino)ethane (dhmpe) complexes and differs from that observed for 1,2-bis(bis(hydroxypropyl)phosphino)ethane (dhprpe) derivatives. In the latter case, an alkylhydroxo group of the functionalized diphosphine replaces the chlorine ligands to afford Mo3S4 complexes in which the deprotonated dhprpe acts in a tridentate fashion. Detailed studies based on stopped-flow, (31)P{(1)H} NMR, and electrospray ionization mass spectrometry techniques have been carried out in order to understand the solution behavior and kinetics of interconversion between the different species formed in solution: 1 and 1OH(+) or 2 and 2OH(+). On the basis of the kinetic results, a mechanism with two parallel reaction pathways involving water and OH(-) attacks is proposed for the formal substitution of halides by hydroxo ligands. On the other hand, reaction of the hydroxo clusters with HX acids occurs with protonation of the OH(-) ligands followed by substitution of coordinated water by X(-).

  8. DKE: a fast numerical solver for the 3-D relativistic bounce-averaged electron drift kinetic equation

    Energy Technology Data Exchange (ETDEWEB)

    Decker, J.; Peysson, Y

    2004-12-01

    A new original code for solving the 3-D relativistic and bounce-averaged electron drift kinetic equation is presented. It designed for the current drive problem in tokamak with an arbitrary magnetic equilibrium. This tool allows self-consistent calculations of the bootstrap current in presence of other external current sources. RF current drive for arbitrary type of waves may be used. Several moments of the electron distribution function are determined, like the exact and effective fractions of trapped electrons, the plasma current, absorbed RF power, runaway and magnetic ripple loss rates and non-thermal Bremsstrahlung. Advanced numerical techniques have been used to make it the first fully implicit (reverse time) 3-D solver, particularly well designed for implementation in a chain of code for realistic current drive calculations in high {beta}{sub p} plasmas. All the details of the physics background and the numerical scheme are presented, as well a some examples to illustrate main code capabilities. Several important numerical points are addressed concerning code stability and potential numerical and physical limitations. (authors)

  9. Water-mediated cation intercalation of open-framework indium hexacyanoferrate with high voltage and fast kinetics

    Science.gov (United States)

    Chen, Liang; Shao, Hezhu; Zhou, Xufeng; Liu, Guoqiang; Jiang, Jun; Liu, Zhaoping

    2016-06-01

    Rechargeable aqueous metal-ion batteries made from non-flammable and low-cost materials offer promising opportunities in large-scale utility grid applications, yet low voltage and energy output, as well as limited cycle life remain critical drawbacks in their electrochemical operation. Here we develop a series of high-voltage aqueous metal-ion batteries based on `M+/N+-dual shuttles' to overcome these drawbacks. They utilize open-framework indium hexacyanoferrates as cathode materials, and TiP2O7 and NaTi2(PO4)3 as anode materials, respectively. All of them possess strong rate capability as ultra-capacitors. Through multiple characterization techniques combined with ab initio calculations, water-mediated cation intercalation of indium hexacyanoferrate is unveiled. Water is supposed to be co-inserted with Li+ or Na+, which evidently raises the intercalation voltage and reduces diffusion kinetics. As for K+, water is not involved in the intercalation because of the channel space limitation.

  10. Effects of hydraulic retention time on aerobic granulation and granule growth kinetics at steady state with a fast start-up strategy.

    Science.gov (United States)

    Liu, Yong-Qiang; Zhang, Xing; Zhang, Rui; Liu, Wen-Tso; Tay, Joo-Hwa

    2016-01-01

    A hydraulic retention time (HRT) of 4, 6, and 8 h was employed, respectively, in three reactors to study the effects of HRT on granulation with a newly developed fast granulation strategy, i.e., a strategy by combining strong hydraulic selection pressure with high organic loading rate (OLR). Granules with clear boundary appeared within 24 h after reactor start-up and all reactors reached a pseudo steady state after 6-day operation. A 4-h HRT resulted in a relatively higher increasing rate in terms of granule size during granule development period, i.e., 208 μm day(-1), and the bigger granule size and the higher sludge volume index at the pseudo steady state. For HRT of 6 or 8 h, no obvious difference was observed. However, it was found that HRT influenced sludge retention time (SRT) and kinetics significantly. A HRT changing from 4 to 8 h led to an increased SRT from 3 to 21 days, a decreased observed specific biomass growth rate (μ obs) and an decreased observed biomass yield (Y obs) of stable granules from 0.37 to 0.062 days(-1), and 0.177 to 0.055 g MLVSS g(-1) COD, respectively. Both μ obs and Y obs had a linear relationship with the reciprocal of HRT. In addition, the great difference of microbial community between seed sludge, sludge retained in the reactors, and sludge washed out indicated a strong microbial selection for fast granulation within 24 h. However, during the granule development period from day 1 to 6, no more microbial selection was observed except an adjustment of microbial community. Little influence of HRT on microbial population in granular sludge indicated a minor role of HRT played for granulation with the fast start-up strategy adopted in this study. The results demonstrated that hydraulic selection pressure for granulation was mainly from short settling time, which led to strong microbial selection during the granulation period. Meanwhile, although HRT did not affect granulation with the fast start-up strategy, it played an

  11. Germanium as a Sodium Ion Battery Material: In Situ TEM Reveals Fast Sodiation Kinetics with High Capacity

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Xiaotang; Adkins, Emily R.; He, Yang; Zhong, Li; Luo, Langli; Mao, Scott X.; Wang, Chong M.; Korgel, Brian A.

    2016-01-29

    Amorphous germanium (a-Ge) nanowires have great potential for application as anodes in Na-ion batteries. However, the Na-Ge reaction is much less studied and understood compared with other metal alloy anodes. Here, in situ transmission electron microscopy (TEM) is used to study the sodiation/desodiation behavior of a-Ge nanowires. Unexpectedly, our experiments revealed that a-Ge nanowires can be charged at a very fast rate and the final sodiation product, with over 300% volume expansion, is close to Na3Ge instead of NaGe which was considered as the ultimate sodiation state that Ge could achieve. Porous structure was observed in desodiation and, in contrast to delithiation, Na extraction is more likely to create pores in the nanowires due to the much larger radius of the Na ion. This porous structure has demonstrated excellent robustness upon cycling: it could recover flawlessly from the giant pores that were created during experimentation. These results show that the potential of a-Ge for Na-ion battery applications may have been previously underestimated.

  12. High quality reduced graphene oxide flakes by fast kinetically controlled and clean indirect UV-induced radical reduction

    Science.gov (United States)

    Flyunt, Roman; Knolle, Wolfgang; Kahnt, Axel; Halbig, Christian E.; Lotnyk, Andriy; Häupl, Tilmann; Prager, Andrea; Eigler, Siegfried; Abel, Bernd

    2016-03-01

    This work highlights a surprisingly simple and kinetically controlled highly efficient indirect method for the production of high quality reduced graphene oxide (rGO) flakes via UV irradiation of aqueous dispersions of graphene oxide (GO), in which the GO is not excited directly. While the direct photoexcitation of aqueous GO (when GO is the only light-absorbing component) takes several hours of reaction time at ambient temperature (4 h) leading only to a partial GO reduction, the addition of small amounts of isopropanol and acetone (2% and 1%) leads to a dramatically shortened reaction time by more than two orders of magnitude (2 min) and a very efficient and soft reduction of graphene oxide. This method avoids the formation of non-volatile species and in turn contamination of the produced rGO and it is based on the highly efficient generation of reducing carbon centered isopropanol radicals via the reaction of triplet acetone with isopropanol. While the direct photolysis of GO dispersions easily leads to degradation of the carbon lattice of GO and thus to a relatively low electric conductivity of the films of flakes, our indirect photoreduction of GO instead largely avoids the formation of defects, keeping the carbon lattice intact. Mechanisms of the direct and indirect photoreduction of GO have been elucidated and compared. Raman spectroscopy, XPS and conductivity measurements prove the efficiency of the indirect photoreduction in comparison with the state-of-the-art reduction method for GO (hydriodic acid/trifluoroacetic acid). The rapid reduction times and water solvent containing only small amounts of isopropanol and acetone may allow easy process up-scaling for technical applications and low-energy consumption.This work highlights a surprisingly simple and kinetically controlled highly efficient indirect method for the production of high quality reduced graphene oxide (rGO) flakes via UV irradiation of aqueous dispersions of graphene oxide (GO), in which the

  13. Kinetics and mechanism of interaction of some bioactive ligands with cis-diaqua(cis-1,2-diaminocyclohexane)platinum(II) in aqueous medium

    Indian Academy of Sciences (India)

    P Karmakar; S Ray; S Mallick; B K Bera; A Mandal; S Mondal; A K Ghosh

    2013-09-01

    The substitution reaction of cis-[Pt(cis-dach)(H2O)2]2+ (where `dach’ is cis-1,2-diaminocyclohexane) with 2-thiouracil (S, N), 1,2-cyclohexanedionedioxime (N, N) and acetylacetone (O, O) were studied in aqueous solution in 0.10 M NaClO4 under pseudo-first order conditions as a functions of concentration, pH and temperature using UV-Vis spectrophotometry. The substitution reaction proceeds via rapid outer sphere association complex formation, followed by two slow consecutive steps. The first of these involves ligand-assisted deaquation, while second involves chelation as the second aqua ligand is displaced. The association equilibrium constant (KE) for the outer sphere complex formation has been evaluated together with rate constants for the two subsequent steps. The rate constants increase with increasing ligand concentration and the evaluated activation parameters for all reactions suggest an associative substitution mechanism for both the aqua ligand substitution processes. The product of the reaction has been characterized by IR, NMR and ESI-MS spectral analysis; which throws more light on the mechanistic behaviour of platinum(II) antitumour complexes.

  14. Model of turnover kinetics in the lamellipodium: implications of slow- and fast- diffusing capping protein and Arp2/3 complex

    Science.gov (United States)

    McMillen, Laura M.; Vavylonis, Dimitrios

    2016-12-01

    Cell protrusion through polymerization of actin filaments at the leading edge of motile cells may be influenced by spatial gradients of diffuse actin and regulators. Here we study the distribution of two of the most important regulators, capping protein and Arp2/3 complex, which regulate actin polymerization in the lamellipodium through capping and nucleation of free barbed ends. We modeled their kinetics using data from prior single molecule microscopy experiments on XTC cells. These experiments have provided evidence for a broad distribution of diffusion coefficients of both capping protein and Arp2/3 complex. The slowly diffusing proteins appear as extended ‘clouds’ while proteins bound to the actin filament network appear as speckles that undergo retrograde flow. Speckle appearance and disappearance events correspond to assembly and dissociation from the actin filament network and speckle lifetimes correspond to the dissociation rate. The slowly diffusing capping protein could represent severed capped actin filament fragments or membrane-bound capping protein. Prior evidence suggests that slowly diffusing Apr2/3 complex associates with the membrane. We use the measured rates and estimates of diffusion coefficients of capping protein and Arp2/3 complex in a Monte Carlo simulation that includes particles in association with a filament network and diffuse in the cytoplasm. We consider two separate pools of diffuse proteins, representing fast and slowly diffusing species. We find a steady state with concentration gradients involving a balance of diffusive flow of fast and slow species with retrograde flow. We show that simulations of FRAP are consistent with prior experiments performed on different cell types. We provide estimates for the ratio of bound to diffuse complexes and calculate conditions where Arp2/3 complex recycling by diffusion may become limiting. We discuss the implications of slowly diffusing populations and suggest experiments to distinguish

  15. Ligand-substitution mode capillary electrophoretic reactor: extending capillary electrophoretic reactor toward measurement of slow dissociation kinetics with a half-life of hours.

    Science.gov (United States)

    Iki, Nobuhiko; Takahashi, Mariko; Takahashi, Toru; Hoshino, Hitoshi

    2009-09-15

    A method employing capillary electrophoresis (CE) was developed to determine the rate constant of the very slow spontaneous dissociation of a complex species. The method uses a CE reactor (CER) to electrophoretically separate components from a complex zone and, thus, spontaneously dissociate a complex. The dissociation is accelerated by ligand substitution (LS) involving a competing ligand added to the electrophoretic buffer. The LS-CER method is validated using the dissociation of a Ti(IV)-catechin complex and EDTA as a competing ligand. There is good agreement between the spontaneous dissociation rate constant (k(d) = (1.64 +/- 0.63) x 10(-4) s(-1)) and the rate constant obtained by a conventional batchwise LS reaction (k(d) = (1.43 +/- 0.04) x 10(-4) s(-1)). Furthermore, the usefulness of the method is demonstrated using a Ti(IV)-tiron complex, for which k(d) = (0.51 +/- 0.43) x 10(-4) s(-1), corresponding to a half-life (t(1/2)) of 3.8 h. Notably, a single run of LS-CER for the Ti(IV) complex is completed within 40 min, implying that LS-CER requires a considerably shorter measurement time (roughly equal to t(1/2)) than conventional CER. LS-CER can be widely applied to determine the spontaneous dissociation rates of inorganic diagnostic and therapeutic reagents as well as of biomolecular complexes.

  16. Unchanged content of oxidative enzymes in fast-twitch muscle fibers and V˙O2 kinetics after intensified training in trained cyclists

    DEFF Research Database (Denmark)

    Christensen, Peter Møller; Gunnarsson, Thomas Gunnar Petursson; Thomassen, Martin;

    2015-01-01

    The present study examined if high intensity training (HIT) could increase the expression of oxidative enzymes in fast-twitch muscle fibers causing a faster oxygen uptake (V˙O2) response during intense (INT), but not moderate (MOD), exercise and reduce the V˙O2 slow component and muscle metabolic...... perturbation during INT. Pulmonary V˙O2 kinetics was determined in eight trained male cyclists (V˙O2-max: 59 ± 4 (means ± SD) mL min(-1) kg(-1)) during MOD (205 ± 12 W ~65% V˙O2-max) and INT (286 ± 17 W ~85% V˙O2-max) exercise before and after a 7-week HIT period (30-sec sprints and 4-min intervals) with a 50...... between MOD and INT. Muscle creatine phosphate was lower (42 ± 15 vs. 66 ± 17 mmol kg DW(-1)) and muscle lactate was higher (40 ± 18 vs. 14 ± 5 mmol kg DW(-1)) at 6 min of INT (P training with a volume reduction did not increase the content...

  17. Fast and Efficient Fragment-Based Lead Generation by Fully Automated Processing and Analysis of Ligand-Observed NMR Binding Data.

    Science.gov (United States)

    Peng, Chen; Frommlet, Alexandra; Perez, Manuel; Cobas, Carlos; Blechschmidt, Anke; Dominguez, Santiago; Lingel, Andreas

    2016-04-14

    NMR binding assays are routinely applied in hit finding and validation during early stages of drug discovery, particularly for fragment-based lead generation. To this end, compound libraries are screened by ligand-observed NMR experiments such as STD, T1ρ, and CPMG to identify molecules interacting with a target. The analysis of a high number of complex spectra is performed largely manually and therefore represents a limiting step in hit generation campaigns. Here we report a novel integrated computational procedure that processes and analyzes ligand-observed proton and fluorine NMR binding data in a fully automated fashion. A performance evaluation comparing automated and manual analysis results on (19)F- and (1)H-detected data sets shows that the program delivers robust, high-confidence hit lists in a fraction of the time needed for manual analysis and greatly facilitates visual inspection of the associated NMR spectra. These features enable considerably higher throughput, the assessment of larger libraries, and shorter turn-around times.

  18. Decoding the Role of Water Dynamics in Ligand-Protein Unbinding: CRF1R as a Test Case.

    Science.gov (United States)

    Bortolato, Andrea; Deflorian, Francesca; Weiss, Dahlia R; Mason, Jonathan S

    2015-09-28

    The residence time of a ligand-protein complex is a crucial aspect in determining biological effect in vivo. Despite its importance, the prediction of ligand koff still remains challenging for modern computational chemistry. We have developed aMetaD, a fast and generally applicable computational protocol to predict ligand-protein unbinding events using a molecular dynamics (MD) method based on adiabatic-bias MD and metadynamics. This physics-based, fully flexible, and pose-dependent ligand scoring function evaluates the maximum energy (RTscore) required to move the ligand from the bound-state energy basin to the next. Unbinding trajectories are automatically analyzed and translated into atomic solvation factor (SF) values representing the water dynamics during the unbinding event. This novel computational protocol was initially tested on two M3 muscarinic receptor and two adenosine A2A receptor antagonists and then evaluated on a test set of 12 CRF1R ligands. The resulting RTscores were used successfully to classify ligands with different residence times. Additionally, the SF analysis was used to detect key differences in the degree of accessibility to water molecules during the predicted ligand unbinding events. The protocol provides actionable working hypotheses that are applicable in a drug discovery program for the rational optimization of ligand binding kinetics.

  19. Influence of equatorial and axial carboxylato ligands on the kinetic inertness of platinum(IV) complexes in the presence of ascorbate and cysteine and within DLD-1 cancer cells.

    Science.gov (United States)

    Chen, Catherine K J; Zhang, Jenny Z; Aitken, Jade B; Hambley, Trevor W

    2013-11-14

    The rapid and premature reduction of platinum(IV) complexes in vivo is a significant impediment to these complexes being successfully employed as anticancer prodrugs. This study investigates the influence of the platinum(IV) coordination sphere on the ease of reduction of the platinum center in various biological contexts. In the presence of the biological reductants, ascorbate and cysteine, platinum(IV) complexes with dicarboxylato equatorial ligands were observed to exhibit lower reduction potentials and slower reduction rates than analogous platinum(IV) complexes with dichlorido equatorial ligands. Diaminetetracarboxylatoplatinum(IV) complexes exhibited unusually long half-lives in the presence of excess reductants; however, the complexes exhibited moderate potency in vitro, indicative of rapid reduction within the intracellular environment. By use of XANES spectroscopy, trans-[Pt(OAc)2(ox)(en)] and trans-[PtCl2(OAc)2(en)] were observed to be reduced at a similar rate within DLD-1 cancer cells. This large variability in kinetic inertness of diaminetetracarboxylatoplatinum(IV) complexes in different biological contexts has significant implications for the design of platinum(IV) prodrugs.

  20. Periodicity in tumor vasculature targeting kinetics of ligand-functionalized nanoparticles studied by dynamic contrast enhanced magnetic resonance imaging and intravital microscopy.

    Science.gov (United States)

    Hak, Sjoerd; Cebulla, Jana; Huuse, Else Marie; Davies, Catharina de L; Mulder, Willem J M; Larsson, Henrik B W; Haraldseth, Olav

    2014-01-01

    In the past two decades advances in the development of targeted nanoparticles have facilitated their application as molecular imaging agents and targeted drug delivery vehicles. Nanoparticle-enhanced molecular imaging of the angiogenic tumor vasculature has been of particular interest. Not only because angiogenesis plays an important role in various pathologies, but also since endothelial cell surface receptors are directly accessible for relatively large circulating nanoparticles. Typically, nanoparticle targeting towards these receptors is studied by analyzing the contrast distribution on tumor images acquired before and at set time points after administration. Although several exciting proof-of-concept studies demonstrated qualitative assessment of relative target concentration and distribution, these studies did not provide quantitative information on the nanoparticle targeting kinetics. These kinetics will not only depend on nanoparticle characteristics, but also on receptor binding and recycling. In this study, we monitored the in vivo targeting kinetics of αvβ3-integrin specific nanoparticles with intravital microscopy and dynamic contrast enhanced magnetic resonance imaging, and using compartment modeling we were able to quantify nanoparticle targeting rates. As such, this approach can facilitate optimization of targeted nanoparticle design and it holds promise for providing more quantitative information on in vivo receptor levels. Interestingly, we also observed a periodicity in the accumulation kinetics of αvβ3-integrin targeted nanoparticles and hypothesize that this periodicity is caused by receptor binding, internalization and recycling dynamics. Taken together, this demonstrates that our experimental approach provides new insights in in vivo nanoparticle targeting, which may proof useful for vascular targeting in general.

  1. Equilibrium and kinetic aspects of protein-DNA recognition.

    Science.gov (United States)

    Livshitz, M A; Gursky, G V; Zasedatelev, A S; Volkenstein, M V

    1979-01-01

    The specificity of regulatory protein binding to DNA is due to a complementarity between the sequence of reaction centres on the protein and the base pair sequence in the specific DNA site allowing the formation of a number of specific noncovalent bonds between the interacting entities. In the present communication the thermodynamic and kinetic aspects of these interactions are considered. The extent of binding specificity is shown to increase with an increase of the bond stability constants and with an increase in the number of ligand reaction centres. Kinetic analysis is carried out assuming that association process is very fast and that dissociation of nonspecific complexes is a rate-limiting step in the recognition of a specific binding site on DNA. The calculations show that a ligand can recognize its specific binding site on DNA within a reasonably limited time interval if the number of its reaction centres and the corresponding stability constants are strongly limited.

  2. The Adsorption of Pb, Zn, Cu, Ni, and Cd by Modified Ligand in a Single Component Aqueous Solution: Equilibrium, Kinetic, Thermodynamic, and Desorption Studies

    Directory of Open Access Journals (Sweden)

    E. Igberase

    2017-01-01

    Full Text Available In this investigation, an amino functionalized adsorbent was developed by grafting 4-aminobenzoic acid onto the backbone of cross-linked chitosan beads. The 3 sets of beads including chitosan (CX, glutaraldehyde cross-linked chitosan (CCX, and 4-aminobenzoic acid grafted cross-linked chitosan (FGCX were characterized by FTIR, XRD, SEM, and TGA. The water content and amine concentration of FGCX were determined. The effect of adsorption parameters was studied and the optimum was used for further studies. Equilibrium data was obtained from the adsorption experiment carried out at different initial concentration; the data were applied in isotherm, thermodynamics, and kinetic studies. The Langmuir and Dubinin-Kaganer-Radushkevich (DKR models were successful in describing the isotherm data for the considered metal ions while the Freundlich and Temkin model fit some of the considered metal ions. Pseudo-second-order and intraparticle model described the kinetic data quite well. Thermodynamic parameters such as Gibb’s free energy change (ΔGo, enthalpy change (ΔHo, and entropy change (ΔSo were calculated and the results showed that the adsorption of Pb, Cu, Ni, Zn, and Cd ions onto FGCX is spontaneous and endothermic in nature. Regeneration of the spent adsorbent was efficient for the considered metal ions.

  3. Single molecule high-throughput footprinting of small and large DNA ligands.

    Science.gov (United States)

    Manosas, Maria; Camunas-Soler, Joan; Croquette, Vincent; Ritort, Felix

    2017-08-21

    Most DNA processes are governed by molecular interactions that take place in a sequence-specific manner. Determining the sequence selectivity of DNA ligands is still a challenge, particularly for small drugs where labeling or sequencing methods do not perform well. Here, we present a fast and accurate method based on parallelized single molecule magnetic tweezers to detect the sequence selectivity and characterize the thermodynamics and kinetics of binding in a single assay. Mechanical manipulation of DNA hairpins with an engineered sequence is used to detect ligand binding as blocking events during DNA unzipping, allowing determination of ligand selectivity both for small drugs and large proteins with nearly base-pair resolution in an unbiased fashion. The assay allows investigation of subtle details such as the effect of flanking sequences or binding cooperativity. Unzipping assays on hairpin substrates with an optimized flat free energy landscape containing all binding motifs allows determination of the ligand mechanical footprint, recognition site, and binding orientation.Mapping the sequence specificity of DNA ligands remains a challenge, particularly for small drugs. Here the authors develop a parallelized single molecule magnetic tweezers approach using engineered DNA hairpins that can detect sequence selectivity, thermodynamics and kinetics of binding for small drugs and large proteins.

  4. Real-time and label free determination of ligand binding-kinetics to primary cancer tissue specimens; a novel tool for the assessment of biomarker targeting

    DEFF Research Database (Denmark)

    Clausen, Thomas Mandel; Ayres Pereira, Marina; Oo, Htoo Zarni;

    2016-01-01

    In clinical oncology, diagnosis and evaluation of optimal treatment strategies are mostly based on histopathological examination combined with immunohistochemical (IHC) expression analysis of cancer-associated antigens in formalin fixed paraffin-embedded (FFPE) tissue biopsies. However, informative...... of epitopes available, this readout offers a quantitative and unbiased readout for in situ binding-avidity and amount of binding epitopes. In summary, this method adds a new and important dimension to classical IHC-based molecular pathology by adding information about the binding characteristics...... IHC analysis depends on both the specificity and affinity of the binding reagent, which are inherently difficult to quantify in situ. Here we describe a label-free method that allows for the direct and real-time assessment of molecular binding kinetics in situ on FFPE tissue specimens using quartz...

  5. Real time analysis of β2-adrenoceptor-mediated signaling kinetics in Human Primary Airway Smooth Muscle Cells reveals both ligand and dose dependent differences

    Directory of Open Access Journals (Sweden)

    Hall Ian P

    2011-07-01

    Full Text Available Abstract Background β2-adrenoceptor agonists elicit bronchodilator responses by binding to β2-adrenoceptors on airway smooth muscle (ASM. In vivo, the time between drug administration and clinically relevant bronchodilation varies significantly depending on the agonist used. Our aim was to utilise a fluorescent cyclic AMP reporter probe to study the temporal profile of β2-adrenoceptor-mediated signaling induced by isoproterenol and a range of clinically relevant agonists in human primary ASM (hASM cells by using a modified Epac protein fused to CFP and a variant of YFP. Methods Cells were imaged in real time using a spinning disk confocal system which allowed rapid and direct quantification of emission ratio imaging following direct addition of β2-adrenoceptor agonists (isoproterenol, salbutamol, salmeterol, indacaterol and formoterol into the extracellular buffer. For pharmacological comparison a radiolabeling assay for whole cell cyclic AMP formation was used. Results Temporal analysis revealed that in hASM cells the β2-adrenoceptor agonists studied did not vary significantly in the onset of initiation. However, once a response was initiated, significant differences were observed in the rate of this response with indacaterol and isoproterenol inducing a significantly faster response than salmeterol. Contrary to expectation, reducing the concentration of isoproterenol resulted in a significantly faster initiation of response. Conclusions We conclude that confocal imaging of the Epac-based probe is a powerful tool to explore β2-adrenoceptor signaling in primary cells. The ability to analyse the kinetics of clinically used β2-adrenoceptor agonists in real time and at a single cell level gives an insight into their possible kinetics once they have reached ASM cells in vivo.

  6. Thermal Thiocyanate Ligand Substitution Kinetics of the Solar Cell Dye N719 by Acetonitrile, 3-Methoxypropionitrile, and 4-tert-Butylpyridine

    DEFF Research Database (Denmark)

    Nguyen, Thai Hoang; Minh, Ha; Lund, Torben

    2007-01-01

    the same products as occur in the homogenous solutions; however, the reactions are approximately 10 times faster. For the reaction of a colloidal mixture of N719-dyed TiO2 particles in acetonitrile containing 0.5 M 4-TBP, a t1/2(het) of 120 h was calculated at 85°C. The N719-based DSSC cells...... in both homogenous solutions and colloidal mixtures of N719-dyed TiO2 nanocrystalline particles. Thiocyanate ligand substitution by the solvents (S) acetonitrile or 3-methoxypropionitrile in homogeneous solutions occurs at elevated temperatures (80-110°C) by means of a simple slow pseudo......-first-order reaction leading to the formation of the product [RuL2(NCS)(S)]+ with a half life time t1/2  ~ 2000 h of N719 at 80 ºC. If tert-butylpyridine (0.5 M) is added, the end product instead becomes [RuL2(NCS)(4-TBP)]+  with a t1/2 ~1000 h. When N719 is bound to TiO2 particles, the reactions with S and 4-TBP give...

  7. Flash kinetics in liquefied noble gases: Studies of alkane activation and ligand dynamics at rhodium carbonyl centers, and a search for xenon-carbene adducts

    Energy Technology Data Exchange (ETDEWEB)

    Yeston, Jake Simon [Univ. of California, Berkeley, CA (United States)

    2001-01-01

    A general introduction is given to place the subsequent chapters in context for the nonspecialist. Results are presented from a low temperature infrared (IR) flash kinetic study of C-H bond activation via photoinduced reaction of Cp*Rh(CO)2 (1) with linear and cyclic alkanes in liquid krypton and liquid xenon solution. No reaction was observed with methane; for all other hydrocarbons studied, the rate law supports fragmentation of the overall reaction into an alkane binding step followed by an oxidative addition step. For the binding step, larger alkanes within each series (linear and cyclic) interact more strongly than smaller alkanes with the Rh center. The second step, oxidative addition of the C-H bond across Rh, exhibits very little variance in the series of linear alkanes, while in the cyclic series the rate decreases with increasing alkane size. Results are presented from an IR flash kinetic study of the photoinduced chemistry of Tp*Rh(CO)2 (5; Tp* = hydridotris(3,5-dimethylpyrazolyl)borato) in liquid xenon solution at –50 °C. IR spectra of the solution taken 2 μs after 308 nm photolysis exhibit two transient bands at 1972-1980 cm-1 and 1992-2000 cm-1, respectively. These bands were assigned to (η3-Tp*)Rh(CO)•Xe and (η2-Tp*)Rh(CO)•Xe solvates on the basis of companion studies using Bp*Rh(CO)2 (9; Bp* = dihydridobis(3,5-dimethyl pyrazolyl)borato). Preliminary kinetic data for reaction of 5 with cyclohexane in xenon solution indicate that both transient bands still appear and that their rates of decay correlate with formation of the product Tp*Rh(CO)(C6H11)(H). The preparation and reactivity of the new complex Bp*Rh(CO)(pyridine) (11) are described. The complex reacts with CH3I to yield the novel Rh carbene hydride complex HB(Me2pz)2Rh(H)(I)(C5H5N)(C(O)Me) (12), resulting from formal addition of CH

  8. Non-bridging ligand effects on the kinetics of reduction of chloro- and azido-pentaamminecobalt(III by some polypyridyl complexes of ruthenium(II

    Directory of Open Access Journals (Sweden)

    Olayinka A. Oyetunji

    2006-12-01

    Full Text Available Pentaamminecobalt(III complexes, [Co(NH35X]2+ (X = Cl-, N3-, are reduced by [Ru(bipy3]2+ and [Ru(terpy(bipyCl] + in aqueous media at a constant ionic strength of 0.5 M (HCl/LiCl. At 308 K, the second order rate constants (M-1 s-1 are as follows: 17.9 for the reduction of the azidocobalt(III complex by [Ru(bipy3]2+, and 1.41 and 2.63 for the [Ru(terpy(bipyCl]+ reduction of the azido- and chlorocobalt(III complexes, respectively. Activation enthalpies (ΔH‡ and entropies (ΔS‡ were determined from temperature dependence measurements with the following results: ΔH‡= 72.1 kJ mol-1 and ΔS‡ = 13.3 J mol-1 K-1 for the [Ru(bipy3]2+ reduction of the azidocobalt(III complex, while for the reduction of the cobalt(III complexes by [Ru(terpy(bipyCl] +, ΔH‡ (N3- = 20.3 kJ mol-1, ΔH‡ (Cl- = 40.6 kJ mol-1, ΔS‡(N3- = -177 J mol-1 K-1, and ΔS‡ (Cl- = -106 J mol-1 K-1. The relative rates of electron transfer in the different reactions and the influence of π-acceptor ligands on the ruthenium(II reduction of the cobalt(III complexes are discussed.

  9. Urease and α-chymotrypsin inhibitory activities of transition metal complexes of new Schiff base ligand: Kinetic and thermodynamic studies of the synthesized complexes using TG–DTA pyrolysis

    Energy Technology Data Exchange (ETDEWEB)

    Ikram, Muhammad, E-mail: ikram.chemistry@suit.edu.pk [Department of Chemistry, Sarhad University of Science and Information Technology, Peshawar (Pakistan); Rehman, Sadia [Department of Chemistry, Sarhad University of Science and Information Technology, Peshawar (Pakistan); Institute of Chemical Sciences, University of Peshawar (Pakistan); Ali, Muhammad [Department of Biotechnology, Bacha Khan University Charsadda (Pakistan); Faridoon [Institute of Chemical Sciences, University of Peshawar (Pakistan); Schulzke, Carola [Institut für Biochemie, Ernst-Moritz-Arndt, Universität Greifswald, Felix-Hausdorff-Straße 4, 17487, Greifswald (Germany); Baker, Robert J. [School of Chemistry, University of Dublin, Trinity College, Dublin 2 (Ireland); Blake, Alexander J. [School of Chemistry, The University of Nottingham, Nottingham NG7 2RD (United Kingdom); Malook, Khan [Centralized Resource Laboratory, University of Peshawar (Pakistan); Wong, Henry [School of Chemistry, The University of Nottingham, Nottingham NG7 2RD (United Kingdom); Saeed-Ur-Rehman [Institute of Chemical Sciences, University of Peshawar (Pakistan)

    2013-06-20

    Graphical abstract: - Highlights: • Single crystal structural analysis of co-crystallized Schiff base ligand. • Urease and α-chymotrypsin inhibition activities of all the synthesized compounds. • TG–DTA studies of all the synthesized compounds under static air. • Kinetic and thermodynamic parameters evaluation using Horrowitz–Mettzger method. - Abstract: The Schiff base 2-[(E)-(quinolin-3-ylimino)methyl]phenol (H-QMP) was crystallized in Pc space group and complexed with Ni(II) and Co(II) in [M(QMP){sub 2}] and Cu(II) and Zn(II) in [M(QMP)(CH{sub 3}COO)]H{sub 2}O compositions. Elemental analyses, mass spectrometry, IR, UV–vis spectroscopy, conductance study and magnetic susceptibilities were used to characterize the complexes. The thermograms obtained in the range of 30–1000 °C were used for kinetic and thermodynamic calculations. The activation energies and order of pyrolysis were calculated using Horowitz–Metzger method. The calculated activation energies were subsequently used for the calculations of thermodynamic parameters including ΔS*, ΔH* and ΔG*. It was found that the thermal stability and activation energy follow the order Cu(II) > Ni(II) > Co(II) > Zn(II) and E{sub Ni}{sup *}>E{sub Cu}{sup *}>E{sub Co}{sup *}>E{sub Zn}{sup *}, respectively. All the compounds were also studied for their urease and α-chymotrypsin inhibition, showing medium to moderate activities for both the enzymes except nickel complex. Nickel complex shows IC{sub 50} = 9.9 ± 0.124 μM ± SEM, and the activity was rationalized by carrying out molecular modeling studies.

  10. Real-time and label free determination of ligand binding-kinetics to primary cancer tissue specimens; a novel tool for the assessment of biomarker targeting

    Directory of Open Access Journals (Sweden)

    Thomas Mandel Clausen

    2016-07-01

    Full Text Available In clinical oncology, diagnosis and evaluation of optimal treatment strategies are mostly based on histopathological examination combined with immunohistochemical (IHC expression analysis of cancer-associated antigens in formalin fixed paraffin-embedded (FFPE tissue biopsies. However, informative IHC analysis depends on both the specificity and affinity of the binding reagent, which are inherently difficult to quantify in situ. Here we describe a label-free method that allows for the direct and real-time assessment of molecular binding kinetics in situ on FFPE tissue specimens using quartz crystal microbalance (QCM enabled biosensor technology. We analysed the interaction between the rVAR2 protein and its placental-like chondroitin sulfate (pl-CS receptor in primary human placenta tissue and in breast and prostate tumour specimens in situ. rVAR2 interacted with FFPE human placenta and cancer tissue with an affinity in the nanomolar range, and showed no detectable interaction with pl-CS negative normal tissue. We further validated the method by including analysis with the androgen receptor N-20 antibody (anti-AR. As the KD value produced by this method is independent of the number of epitopes available, this readout offers a quantitative and unbiased readout for in situ binding-avidity and amount of binding epitopes. In summary, this method adds a new and important dimension to classical IHC-based molecular pathology by adding information about the binding characteristics in biologically relevant conditions. This can potentially be used to select optimal biologics for diagnostic and for therapeutic applications as well as guide the development of novel high affinity binding drugs.

  11. Kinetic analysis of ligand binding to the Ehrlich cell nucleoside transporter: Pharmacological characterization of allosteric interactions with the sup 3 Hnitrobenzylthioinosine binding site

    Energy Technology Data Exchange (ETDEWEB)

    Hammond, J.R. (Department of Pharmacology and Toxicology, University of Western Ontario, London (Canada))

    1991-06-01

    Kinetic analysis of the binding of {sup 3}Hnitrobenzylthioinosine ({sup 3}H NBMPR) to Ehrlich ascites tumor cell plasma membranes was conducted in the presence and absence of a variety of nucleoside transport inhibitors and substrates. The association of {sup 3}H NBMPR with Ehrlich cell membranes occurred in two distinct phases, possibly reflecting functional conformation changes in the {sup 3}HNBMPR binding site/nucleoside transporter complex. Inhibitors of the equilibrium binding of {sup 3}HNBMPR, tested at submaximal inhibitory concentrations, generally decreased the rate of association of {sup 3}HNBMPR, but the magnitude of this effect varied significantly with the agent tested. Adenosine and diazepam had relatively minor effects on the association rate, whereas dipyridamole and mioflazine slowed the rate dramatically. Inhibitors of nucleoside transport also decreased the rate of dissociation of {sup 3}HNBMPR, with an order of potency significantly different from their relative potencies as inhibitors of the equilibrium binding of {sup 3}HNBMPR. Dilazep, dipyridamole, and mioflazine were effective inhibitors of both {sup 3}HNBMPR dissociation and equilibrium binding. The lidoflazine analogue R75231, on the other hand, had no effect on the rate of dissociation of {sup 3}HNBMPR at concentrations below 300 microM, even though it was one of the most potent inhibitors of {sup 3}HNBMPR binding tested (Ki less than 100 nM). In contrast, a series of natural substrates for the nucleoside transport system enhanced the rate of dissociation of {sup 3}HNBMPR with an order of effectiveness that paralleled their relative affinities for the permeant site of the transporter. The most effective enhancers of {sup 3}HNBMPR dissociation, however, were the benzodiazepines diazepam, chlordiazepoxide, and triazolam.

  12. Thermodynamics of ligand binding to histone deacetylase like amidohydrolase from Bordetella/Alcaligenes.

    Science.gov (United States)

    Meyners, Christian; Baud, Matthias G J; Fuchter, Matthew J; Meyer-Almes, Franz-Josef

    2014-03-01

    Thermodynamic studies on ligand-protein binding have become increasingly important in the process of drug design. In combination with structural data and molecular dynamics simulations, thermodynamic studies provide relevant information about the mode of interaction between compounds and their target proteins and therefore build a sound basis for further drug optimization. Using the example of histone deacetylases (HDACs), particularly the histone deacetylase like amidohydrolase (HDAH) from Bordetella/Alcaligenes, a novel sensitive competitive fluorescence resonance energy transfer-based binding assay was developed and the thermodynamics of interaction of both fluorescent ligands and inhibitors to histone deacetylase like amidohydrolase were investigated. The assay consumes only small amounts of valuable target proteins and is suitable for fast kinetic and mechanistic studies as well as high throughput screening applications. Binding affinity increased with increasing length of aliphatic spacers (n = 4-7) between the hydroxamate moiety and the dansyl head group of ligand probes. Van't Hoff plots revealed an optimum in enthalpy contribution to the free energy of binding for the dansyl-ligand with hexyl spacer. The selectivity in the series of dansyl-ligands against human class I HDAC1 but not class II HDACs 4 and 6 increased with the ratio of ΔH(0)/ΔG(0). The data clearly emphasize the importance of thermodynamic signatures as useful general guidance for the optimization of ligands or rational drug design.

  13. Geometric isomerism in pentacoordinate Cu2+ complexes: equilibrium, kinetic, and density functional theory studies reveal the existence of equilibrium between square pyramidal and trigonal bipyramidal forms for a tren-derived ligand.

    Science.gov (United States)

    Algarra, Andrés G; Basallote, Manuel G; Castillo, Carmen E; Clares, M Paz; Ferrer, Armando; García-España, Enrique; Llinares, José M; Máñez, M Angeles; Soriano, Conxa

    2009-02-02

    A ligand (L1) (bis(aminoethyl)[2-(4-quinolylmethyl)aminoethyl]amine) containing a 4-quinolylmethyl group attached to one of the terminal amino groups of tris(2-aminoethyl)amine (tren) has been prepared, and its protonation constants and stability constants for the formation of Cu(2+) complexes have been determined. Kinetic studies on the formation of Cu(2+) complexes in slightly acidic solutions and on the acid-promoted complex decomposition strongly suggest that the Cu(2+)-L1 complex exists in solution as a mixture of two species, one of them showing a trigonal bipyramidal (tbp) coordination environment with an absorption maximum at 890 nm in the electronic spectrum, and the other one being square pyramidal (sp) with a maximum at 660 nm. In acidic solution only a species with tbp geometry is formed, whereas in neutral and basic solutions a mixture of species with tbp and sp geometries is formed. The results of density functional theory (DFT) calculations indicate that these results can be rationalized by invoking the existence of an equilibrium of hydrolysis of the Cu-N bond with the amino group supporting the quinoline ring so that CuL1(2+) would be actually a mixture of tbp [CuL1(H(2)O)](2+) and sp [CuL1(H(2)O)(2)](2+). As there are many Cu(2+)-polyamine complexes with electronic spectra that show two overlapping bands at wavelengths close to those observed for the Cu(2+)-L1 complex, the existence of this kind of equilibrium between species with two different geometries can be quite common in the chemistry of these compounds. A correlation found between the position of the absorption maximum and the tau parameter measuring the distortion from the idealized tbp and sp geometries can be used to estimate the actual geometry in solution of this kind of complex.

  14. Co(II), Ni(II), Cu(II) and Zn(II) complexes of tridentate ONO donor Schiff base ligand: Synthesis, characterization, thermal, non-isothermal kinetics and DFT calculations

    Science.gov (United States)

    Kusmariya, Brajendra S.; Mishra, A. P.

    2017-02-01

    We report here four mononuclear Co(II), Ni(II), Cu(II) and Zn(II) coordination compounds of general formula [M(L)2] {L = dcp; M = CoII, CuII & ZnII} and [M(L)(H2O)]·H2O {L = dcp; M = NiII} derived from tridentate 2,4-dichloro-6-{[(3-chloro-2-hydroxy-5-nitrophenyl)imino]methyl}phenol (dcp) ligand. These compounds were synthesized and characterized by elemental analysis, FT-IR, uv-vis, 1H NMR, molar conductance, magnetic moment, thermal, PXRD and SEM-EDX. The Powder X-ray Diffraction patterns and SEM analyses showed the crystalline nature of synthesized compounds. The peak broadening was explained in terms of crystallite size and the lattice strain using Scherrer and Williamson-Hall method. Thermogravimetric analysis was performed to determine the thermal stability of synthesized compounds under nitrogen atmosphere up to 820 K at 10 Kmin-1 heating rate. The kinetic and thermodynamic parameters of thermal decomposition were calculated using Coats-Redfern (C-R), Piloyan-Novikova (P-N) and Horowitz-Metzger (H-M) methods assuming first order degradation. The calculated optical band gap values of complexes were found to be in semiconducting range. To support the experimental findings, and derive some fruitful information viz. frequency calculations, HOMO-LUMO, energy gap (ΔE), molecular electrostatic potential (MEP), spin density, absorption spectra etc.; theoretical calculations by means of DFT and TD-DFT at B3LYP level were incorporated.

  15. Kinetic and Thermodynamic Stabilization of Metal Complexes by Introverted Coordination in a Calix[6]azacryptand.

    Science.gov (United States)

    Inthasot, Alex; Brunetti, Emilio; Lejeune, Manuel; Menard, Nicolas; Prangé, Thierry; Fusaro, Luca; Bruylants, Gilles; Reinaud, Olivia; Luhmer, Michel; Jabin, Ivan; Colasson, Benoit

    2016-03-24

    The Huisgen thermal reaction between an organic azide and an acetylene was employed for the selective monofunctionalization of a X6 -azacryptand ligand bearing a tren coordinating unit [X6 stands for calix[6]arene and tren for tris(2-aminoethyl)amine]. Supramolecular assistance, originating from the formation of a host-guest inclusion complex between the reactants, greatly accelerates the reaction while self-inhibition affords a remarkable selectivity. The new ligand possesses a single amino-leg appended at the large rim of the calixarene core and the corresponding Zn(2+) complex was characterized both in solution and in the solid state. The coordination of Zn(2+) not only involves the tren cap but also the introverted amino-leg, which locks the metal ion in the cavity. Compared with the parent ligand deprived of the amino-leg, the affinity of the new monofunctionalized X6 tren ligand 6 for Zn(2+) is found to have a 10-fold increase in DMSO, which is a very competitive solvent, and with an enhancement of at least three orders of magnitude in CDCl3 /CD3 OD (1:1, v/v). In strong contrast with the fast binding kinetics, decoordination of Zn(2+) as well as transmetallation appeared to be very slow processes. The monofunctionalized X6 tren ligand 6 fully protects the metal ion from the external medium thanks to the combination of a cavity and a closed coordination sphere, leading to greater thermodynamic and kinetic stabilities.

  16. Unchanged content of oxidative enzymes in fast-twitch muscle fibers and V˙O2 kinetics after intensified training in trained cyclists

    DEFF Research Database (Denmark)

    Christensen, Peter Møller; Gunnarsson, Thomas Gunnar Petursson; Thomassen, Martin;

    2015-01-01

    DW(-1) min(-1)) of CS (56 ± 8 post-HIT vs. 59 ± 10 pre-HIT), HAD (27 ± 6 vs. 29 ± 3) and PFK (340 ± 69 vs. 318 ± 105) and the capillary to fiber ratio (2.30 ± 0.16 vs. 2.38 ± 0.20) was unaltered following HIT. V˙O2 kinetics was unchanged with HIT and the speed of the primary response did not differ...

  17. Quantitative Characterization of E-selectin Interaction with Native CD44 and P-selectin Glycoprotein Ligand-1 (PSGL-1) Using a Real Time Immunoprecipitation-based Binding Assay

    KAUST Repository

    Abu Samra, Dina Bashir Kamil

    2015-06-29

    Selectins (E-, P-, and L-selectins) interact with glycoprotein ligands to mediate the essential tethering/rolling step in cell transport and delivery that captures migrating cells from the circulating flow. In this work, we developed a real time immunoprecipitation assay on a surface plasmon resonance chip that captures native glycoforms of two well known E-selectin ligands (CD44/hematopoietic cell E-/L-selectin ligand and P-selectin glycoprotein ligand-1) from hematopoietic cell extracts. Here we present a comprehensive characterization of their binding to E-selectin. We show that both ligands bind recombinant monomeric E-selectin transiently with fast on- and fast off-rates, whereas they bind dimeric E-selectin with remarkably slow onand off-rates. This binding requires the sialyl Lewis x sugar moiety to be placed on both O- and N-glycans, and its association, but not dissociation, is sensitive to the salt concentration. Our results suggest a mechanism through which monomeric selectins mediate initial fast on and fast off kinetics to help capture cells out of the circulating shear flow; subsequently, tight binding by dimeric/oligomeric selectins is enabled to significantly slow rolling. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  18. Exploring the Hydrolytic Behavior of the Platinum(IV) Complexes with Axial Acetato Ligands.

    Science.gov (United States)

    Zhao, Jian; Xu, Zichen; Lin, Jing; Gou, Shaohua

    2017-08-21

    Platinum(IV) complexes are generally thought to be kinetically inert, and are expected to be stable enough to resist premature aquation before entering the cancer cells. Nevertheless, in this work, complex 2 with axial acetato ligands can hydrolyze relatively quickly under biologically relevant conditions with a half-life of 91.7 min, resulting in the loss of the equatorial chlorido ligand. Further study indicated that the fast hydrolysis of complex 2 may be attributed to the strong σ-donor ability of N-isopropyl-1R,2R-diaminocyclohexane, and an increasing σ-donor ability of the amine group can promote the hydrolysis rate of the corresponding platinum(IV) complex. The experiment results were proven by the corresponding DFT calculation. Our study can help to re-evaluate the aqueous properties of the platinum(IV) complexes with axial acetate, which may be less inert to hydrolysis than expected under biologically relevant conditions.

  19. Slow-Equilibration Approximation in Kinetic Size Exclusion Chromatography.

    Science.gov (United States)

    Cherney, Leonid T; Krylov, Sergey N

    2016-04-05

    Kinetic size exclusion chromatography with mass spectrometry detection (KSEC-MS) is a solution-based label-free approach for studying kinetics of reversible binding of a small molecule to a protein. Extraction of kinetic data from KSEC-MS chromatograms is greatly complicated by the lack of separation between the protein and protein-small molecule complex. As a result, a sophisticated time-consuming numerical approach was used for the determination of rate constants in the proof-of-principle works on KSEC-MS. Here, we suggest the first non-numerical (analytical) approach for finding rate constants of protein-small molecule interaction from KSEC-MS data. The approach is based on the slow-equilibration approximation, which is applicable to KSEC-MS chromatograms that reveal two peaks. The analysis of errors shows that the slow-equilibration approximation guarantees that the errors in the rate constants are below 20% if the ratio between the characteristic separation and equilibration times does not exceed 0.1. The latter condition can typically be satisfied for specific interactions such as receptor-ligand or protein-drug. The suggested analytical solution equips analytical scientists with a simple and fast tool for processing KSEC-MS data. Moreover, a similar approach can be potentially developed for kinetic analysis of protein-small molecule binding by other kinetic-separation methods such as nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM).

  20. The positive effects of priming exercise on oxygen uptake kinetics and high-intensity exercise performance are not magnified by a fast-start pacing strategy in trained cyclists.

    Science.gov (United States)

    Caritá, Renato Aparecido Corrêa; Greco, Camila Coelho; Denadai, Benedito Sérgio

    2014-01-01

    The purpose of this study was to determine both the independent and additive effects of prior heavy-intensity exercise and pacing strategies on the VO2 kinetics and performance during high-intensity exercise. Fourteen endurance cyclists (VO2max  = 62.8 ± 8.5 mL.kg-1.min-1) volunteered to participate in the present study with the following protocols: 1) incremental test to determine lactate threshold and VO2max; 2) four maximal constant-load tests to estimate critical power; 3) six bouts of exercise, using a fast-start (FS), even-start (ES) or slow-start (SS) pacing strategy, with and without a preceding heavy-intensity exercise session (i.e., 90% critical power). In all conditions, the subjects completed an all-out sprint during the final 60 s of the test as a measure of the performance. For the control condition, the mean response time was significantly shorter (p positive effects of priming exercise on the overall VO2 kinetics and short-term high-intensity performance.

  1. Kinetic modeling and fitting software for interconnected reaction schemes: VisKin.

    Science.gov (United States)

    Zhang, Xuan; Andrews, Jared N; Pedersen, Steen E

    2007-02-15

    Reaction kinetics for complex, highly interconnected kinetic schemes are modeled using analytical solutions to a system of ordinary differential equations. The algorithm employs standard linear algebra methods that are implemented using MatLab functions in a Visual Basic interface. A graphical user interface for simple entry of reaction schemes facilitates comparison of a variety of reaction schemes. To ensure microscopic balance, graph theory algorithms are used to determine violations of thermodynamic cycle constraints. Analytical solutions based on linear differential equations result in fast comparisons of first order kinetic rates and amplitudes as a function of changing ligand concentrations. For analysis of higher order kinetics, we also implemented a solution using numerical integration. To determine rate constants from experimental data, fitting algorithms that adjust rate constants to fit the model to imported data were implemented using the Levenberg-Marquardt algorithm or using Broyden-Fletcher-Goldfarb-Shanno methods. We have included the ability to carry out global fitting of data sets obtained at varying ligand concentrations. These tools are combined in a single package, which we have dubbed VisKin, to guide and analyze kinetic experiments. The software is available online for use on PCs.

  2. Buprenorphine kinetics.

    Science.gov (United States)

    Bullingham, R E; McQuay, H J; Moore, A; Bennett, M R

    1980-11-01

    Buprenorphine kinetics was determined in surgical patients using radioimmunoassay. Buprenorphine was measured in the plasma of 24 patients who had received 0.3 mg buprenorphine intraoperatively. After 3 hr 10 of these patients then received a further 0.3 mg buprenorphine intravenously for postoperative pain relief, and 11 patients were given 0.3 mg intramuscularly; again, plasma levels were measured for 3 hr. The data fitted closely to a triexponential decay curve. There was a very fast initial phase, with a half-life (t1/2) of 2 min. The terminal t1/2 was slow, approximately 3 hr. Comparison of the kinetics of the same patient, awake and anesthetized, showed that the clearance was significantly lower in the anesthetized state. A notable feature of the drug given intramuscularly is rapid systemic availability, so that peaks are obtained in 2 to 5 min, and in 10 min the resulting levels are the same as for the intravenous and intramuscular routes.

  3. Fission Fragment Mass Distributions and Total Kinetic Energy Release of 235-Uranium and 238-Uranium in Neutron-Induced Fission at Intermediate and Fast Neutron Energies

    Energy Technology Data Exchange (ETDEWEB)

    Duke, Dana Lynn [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-11-12

    This Ph.D. dissertation describes a measurement of the change in mass distributions and average total kinetic energy (TKE) release with increasing incident neutron energy for fission of 235U and 238U. Although fission was discovered over seventy-five years ago, open questions remain about the physics of the fission process. The energy of the incident neutron, En, changes the division of energy release in the resulting fission fragments, however, the details of energy partitioning remain ambiguous because the nucleus is a many-body quantum system. Creating a full theoretical model is difficult and experimental data to validate existing models are lacking. Additional fission measurements will lead to higher-quality models of the fission process, therefore improving applications such as the development of next-generation nuclear reactors and defense. This work also paves the way for precision experiments such as the Time Projection Chamber (TPC) for fission cross section measurements and the Spectrometer for Ion Determination in Fission (SPIDER) for precision mass yields.

  4. A Xenon dielectric barrier discharge lamp (172nm) with a fast-pulse voltage driver: Influence of the voltage waveform on plasma kinetic issues and light output.

    Science.gov (United States)

    Carman, Robert; Ward, Barry; Mildren, Richard; Kane, Deborah

    2003-10-01

    An important class of vacuum-ultraviolet (VUV) excimer lamps based on high pressure rare-gas and rare-gas halogen mixtures utilize the dielectric barrier discharge (DBD) to generate a transient, non-equilibrium plasma that yields high electrical to VUV conversion efficiency. Recent interest has focussed on the use of pulsed voltage excitation techniques (rather than conventional AC sinusoidal waveforms) to alter the physical appearance of the DBD "micro-discharges" from filamentary (AC) to semi-diffuse, conical or homogeneous (pulsed), whilst at the same time dramatically improving the lamp performance and VUV efficiency^1,2. We report results from a combined experimental/computer modelling study of a short-pulse excited co-axial DBD Xe lamp to investigate the influence of the pulsed voltage waveform on the discharge structure, lamp performance, VUV output, and electrical efficiency. The underlying plasma kinetics issues relating to lamp performance, including parasitic collisional processes that act to quench key xenon species population densities, are examined in detail. ^1 Vollkommer F and Hitzschke, US patent 5604410 (1997) ^2 R.P.Mildren and R.J.Carman, J.Phys.D, 34, L1-L6 (2001)

  5. Bis(methylpyridine)-EDTA derivative as a potential ligand for PET imaging: synthesis, complexation, and biological evaluation.

    Science.gov (United States)

    Singh, Pooja; Aggarwal, Swati; Tiwari, Anjani K; Kumar, Vikas; Pratap, Ramendra; Chuttani, Krishna; Mishra, Anil K

    2014-12-01

    A novel transitional metal ligand derivatized from EDTA-conjugated 2-amino-4-methyl pyridine, an acyclic vehicle (EDTA-Mepy2 ) was designed, synthesized, and characterized for PET imaging with ⁶⁸Ga. The drug likeliness and appropriate lipophilicity were first analyzed by molecular docking studies which shows interactive property of ligand with serum albumin protein (HSA: PDB 1E78), at Lys199, Arg257, and His242 residues, which make it more appropriate in transportation as a specific ligand for PET imaging. As a confirmation, binding constant of the ligand with human serum albumin was calculated at λex = 350 nm which was found to be 4.9 × 10³ m⁻¹. The pharmacokinetics of (68) Ga-EDTA-Mepy2 was analyzed by blood kinetics (t(1/2) slow: 3 h 56 min and t(1/2) fast: 32 min) and biodistribution (maximum % ID/g was found in kidney at 1 h). Further the capability of this ligand was analyzed as optical marker also, by recording λex = 380 nm, RFU = 8000; 710 nm, RFU = 1000 units at fixed λem = 280 nm. Additionally, in physiological conditions where its stability was calculated, suggests 15-20 times selectivity over the endogenously present metal ions (KG aL /KZ nL = 14.3, KG aL /KC uL = 18.1).

  6. Development and Application of Ligand-Exchange Reaction Method ...

    African Journals Online (AJOL)

    Erah

    Methods: The method is based on ligand-exchange reaction. ... Clonazepam, Ligand-exchange reaction, Kinetic spectrometry, Validation, Pharmaceutical ... sensitive and selective analytical method for ... does not need sophisticated instruments or ..... of clonazepam in human serum ("Lytorol N) by standard addition method.

  7. Ligand-modified metal clusters for gas separation and purification

    Energy Technology Data Exchange (ETDEWEB)

    Okrut, Alexander; Ouyang, Xiaoying; Runnebaum, Ron; Gates, Bruce C.; Katz, Alexander

    2017-02-21

    Provided is an organic ligand-bound metal surface that selects one gaseous species over another. The species can be closely sized molecular species having less than 1 Angstrom difference in kinetic diameter. In one embodiment, the species comprise carbon monoxide and ethylene. Such organic ligand-bound metal surfaces can be successfully used in gas phase separations or purifications, sensing, and in catalysis.

  8. Sliding tethered ligands add topological interactions to the toolbox of ligand-receptor design

    Science.gov (United States)

    Bauer, Martin; Kékicheff, Patrick; Iss, Jean; Fajolles, Christophe; Charitat, Thierry; Daillant, Jean; Marques, Carlos M.

    2015-09-01

    Adhesion in the biological realm is mediated by specific lock-and-key interactions between ligand-receptor pairs. These complementary moieties are ubiquitously anchored to substrates by tethers that control the interaction range and the mobility of the ligands and receptors, thus tuning the kinetics and strength of the binding events. Here we add sliding anchoring to the toolbox of ligand-receptor design by developing a family of tethered ligands for which the spacer can slide at the anchoring point. Our results show that this additional sliding degree of freedom changes the nature of the adhesive contact by extending the spatial range over which binding may sustain a significant force. By introducing sliding tethered ligands with self-regulating length, this work paves the way for the development of versatile and reusable bio-adhesive substrates with potential applications for drug delivery and tissue engineering.

  9. Kinetic mechanism of putrescine oxidase from Rhodococcus erythropolis.

    Science.gov (United States)

    Kopacz, Malgorzata M; Heuts, Dominic P H M; Fraaije, Marco W

    2014-10-01

    Putrescine oxidase from Rhodococcus erythropolis (PuO) is a flavin-containing amine oxidase from the monoamine oxidase family that performs oxidative deamination of aliphatic diamines. In this study we report pre-steady-state kinetic analyses of the enzyme with the use of single- and double-mixing stopped-flow spectroscopy and putrescine as a substrate. During the fast and irreversible reductive half-reaction no radical intermediates were observed, suggesting a direct hydride transfer from the substrate to the FAD. The rate constant of flavin reoxidation depends on the ligand binding; when the imine product was bound to the enzyme the rate constant was higher than with free enzyme species. Similar results were obtained with product-mimicking ligands and this indicates that a ternary complex is formed during catalysis. The obtained kinetic data were used together with steady-state rate equations derived for ping-pong, ordered sequential and bifurcated mechanisms to explore which mechanism is operative. The integrated analysis revealed that PuO employs a bifurcated mechanism due to comparable rate constants of product release from the reduced enzyme and reoxidation of the reduced enzyme-product complex.

  10. Thermodynamic and kinetic studies of the equilibration reaction between the sulfur and carbon bonded forms of a cobalt(III) complex with the ligands 2-aminoethyl-3-aminopropylsulfide and 1,1,1-tris(aminomethyl)ethane

    DEFF Research Database (Denmark)

    Springborg, J.; Kjellerup, S.; Kofod, Pauli

    1996-01-01

    A thermodn. and kinetic study of the equilibration between the Co-S bonded complex Co(tame)(S-aeaps)3+ and the Co-C bonded complex Co(tame)(C-aeaps)2+ is reported (tame = 1,1,1-tris(aminomethyl)ethane, aeaps = 2-aminoethyl-3-aminopropyl sulfide = 3-thiahexane-1,6-diamine and C-aeaps = 1,6-diamine...... the Co-alkyl complex gave complete loss of D. From the kinetic data it is estd. that the carbanion reacts with H2O 170 times faster than it is captured by Co(III)....

  11. The physical chemistry of ligand-receptor binding identifies some limitations to the analysis of receptor images

    Energy Technology Data Exchange (ETDEWEB)

    Krohn, Kenneth A. E-mail: kkrohn@u.washington.edu

    2001-07-01

    The biophysical chemistry of ligand-receptor interactions imposes some restrictions on the characteristics of a radioligand if it is to be a useful tracer for accurately measuring the in vivo concentration of a specific cellular membrane receptor. This review discusses thermodynamic and kinetic rate constant considerations in selecting a ligand for radiolabeling and imaging. When radioligands of only modest specific activity are injected, one is able to use kinetic analysis to calculate the rate constant for the bimolecular binding reaction as well as the receptor concentration. Images of regional receptor density can be constructed from analysis of emission imaging data when the binding occurs at a rate that is slower than the collision frequency. A tracer that reacts with each collision cannot distinguish receptor density from blood flow. The theory of diffusion-limited reactions is reviewed and individual ligand-receptor examples are presented to demonstrate conditions where, even for very fast forward reactions, the binding of radioligand to receptor is controlled by local biochemistry rather than by the purely physical process of diffusion.

  12. Evaluation of several novel diamide based ligands for selective extraction of tetravalent plutonium

    Energy Technology Data Exchange (ETDEWEB)

    Sivaramakrishna, Mallampalli; Nayak, Shashikant K. [Heavy Water Board, V.S. Bhavan, Mumbai (India); Raut, Dhaval R.; Mohapatra, Prasanta K. [Bhabha Atomic Research Center, Mumbai (India). Radiochemistry Division; Nayak, Sandip K. [Bhabha Atomic Research Center, Mumbai (India). Bioorganic Division

    2017-06-01

    The present paper describes the selective extraction of tetravalent plutonium employing several diamide ligands containing aromatic spacer groups. The ligands containing two amide functional groups attached to a 2,4,6-tri-phenyl pyridine moiety with different substituents viz.; L{sub I} (iso-butyl), L{sub II}(n-butyl), L{sub III}(n-octyl), L{sub IV} (2-ethylhexyl) at the amidic nitrogen atom were evaluated for the extraction of Pu(IV) using their nitrobenzene solutions. The distribution ratio values of Pu(IV) with the diamide ligands followed the order: L{sub II}>L{sub I}>L{sub III}>L{sub IV} and were significantly higher than those of metal ions such as Cs(I), Sr(II), Am(III) and Eu(III). The distribution ratio values of U(VI) were about 2-3 orders magnitude lower than those of Pu(IV). The extraction and stripping kinetics were found to be moderately fast and it took less than 30 min (less than 5 min for L{sub I} and L{sub IV}) to obtain equilibrium D values. The extraction was found to be increasing with the aqueous phase nitric acid concentration conforming to a solvation mechanism of extraction. The extracted species contained two ligand molecules for L{sub I} and L{sub II} while monosolvates were observed for the other two extractants. The ligands showed good radiation stability up to an absorbed dose of 630 kGy.

  13. Efficient chemoenzymatic synthesis of chiral pincer ligands.

    Science.gov (United States)

    Felluga, Fulvia; Baratta, Walter; Fanfoni, Lidia; Pitacco, Giuliana; Rigo, Pierluigi; Benedetti, Fabio

    2009-05-01

    Chiral, nonracemic pincer ligands based on the 6-phenyl-2-aminomethylpyridine and 2-aminomethylbenzo[h]quinoline scaffolds were obtained by a chemoenzymatic approach starting from 2-pyridyl and 2-benzoquinolyl ethanone. In the enantiodifferentiating step, secondary alcohols of opposite absolute configuration were obtained by a baker's yeast reduction of the ketones and by lipase-mediated dynamic kinetic resolution of the racemic alcohols. Their transformation into homochiral 1-methyl-1-heteroarylethanamines occurred without loss of optical purity, giving access to pincer ligands used in enantioselective catalysis.

  14. Formation of Foam-like Microstructural Carbon Material by Carbonization of Porous Coordination Polymers through a Ligand-Assisted Foaming Process.

    Science.gov (United States)

    Kongpatpanich, Kanokwan; Horike, Satoshi; Fujiwara, Yu-Ichi; Ogiwara, Naoki; Nishihara, Hirotomo; Kitagawa, Susumu

    2015-09-14

    Porous carbon material with a foam-like microstructure has been synthesized by direct carbonization of porous coordination polymer (PCP). In situ generation of foaming agents by chemical reactions of ligands in PCP during carbonization provides a simple way to create lightweight carbon material with a foam-like microstructure. Among several substituents investigated, the nitro group has been shown to be the key to obtain the unique foam-like microstructure, which is due to the fast kinetics of gas evolution during carbonization. Foam-like microstructural carbon materials showed higher pore volume and specific capacitance compared to a microporous carbon.

  15. Kinetic Atom.

    Science.gov (United States)

    Wilson, David B.

    1981-01-01

    Surveys the research of scientists like Joule, Kelvin, Maxwell, Clausius, and Boltzmann as it comments on the basic conceptual issues involved in the development of a more precise kinetic theory and the idea of a kinetic atom. (Author/SK)

  16. Kinetic Typography

    DEFF Research Database (Denmark)

    van Leeuwen, Theo; Djonov, Emilia

    2014-01-01

    After discussing broad cultural drivers behind the development of kinetic typography, the chapter outlines an approach to analysing kinetic typography which is based on Halliday's theory of transitivity, as applied by Kress and Van Leeuwen to visual images.......After discussing broad cultural drivers behind the development of kinetic typography, the chapter outlines an approach to analysing kinetic typography which is based on Halliday's theory of transitivity, as applied by Kress and Van Leeuwen to visual images....

  17. Thermodynamic and kinetic studies of the equilibration reaction between the sulfur and carbon bonded forms of a cobalt(III) complex with the ligands 2-aminoethyl-3-aminopropylsulfide and 1,1,1-tris(aminomethyl)ethane

    DEFF Research Database (Denmark)

    Springborg, J.; Kjellerup, S.; Kofod, Pauli

    1996-01-01

    A thermodn. and kinetic study of the equilibration between the Co-S bonded complex Co(tame)(S-aeaps)3+ and the Co-C bonded complex Co(tame)(C-aeaps)2+ is reported (tame = 1,1,1-tris(aminomethyl)ethane, aeaps = 2-aminoethyl-3-aminopropyl sulfide = 3-thiahexane-1,6-diamine and C-aeaps = 1,6-diamine-3...

  18. Structural determinants of agonist-specific kinetics at the ionotropic glutamate receptor 2.

    Science.gov (United States)

    Holm, Mai Marie; Lunn, Marie-Louise; Traynelis, Stephen F; Kastrup, Jette S; Egebjerg, Jan

    2005-08-23

    Glutamate receptors (GluRs) are the most abundant mediators of the fast excitatory neurotransmission in the human brain. Agonists will, after activation of the receptors, induce different degrees of desensitization. The efficacy of agonists strongly correlates with the agonist-induced closure of the ligand-binding domain. However, the differences in desensitization properties are less well understood. By using high-resolution x-ray structure of the GluR2 flop (GluR2o) ligand-binding core protein in complex with the partial glutamate receptor agonist (S)-2-amino-3-(3-hydroxy-5-tert-butyl-4-isothiazolyl)propionic acid [(S)-thio-ATPA], we show that (S)-thio-ATPA induces an 18 degrees closure of the binding core similar to another partial agonist, (S)-2-amino-3-(4-bromo-3-hydroxy-5-isoxazolyl)propionic acid [(S)-Br-HIBO]. Despite the similar closure of the ligand-binding domain, we find in electrophysiological studies that (S)-thio-ATPA induced a 6.4-fold larger steady-state current than (RS)-Br-HIBO, and rapid agonist applications show that (S)-thio-ATPA induces a 3.6-fold higher steady-state/peak ratio and a 2.2-fold slower desensitization time constant than (RS)-Br-HIBO. Structural comparisons reveal that (S)-Br-HIBO, but not (S)-thio-ATPA, induces a twist of the ligand-binding core compared with the apostructure, and the agonist-specific conformation of Leu-650 correlates with the different kinetic profiles pointing at a key role in defining the desensitization kinetics. We conclude that, especially for intermediate efficacious agonists, the desensitization properties are influenced by additional ligand-induced factors beyond domain closure.

  19. Molecular Characterization of the Interactions between Vascular Selectins and Glycoprotein Ligands on Human Hematopoietic Stem/Progenitor Cells

    KAUST Repository

    Abusamra, Dina

    2016-12-01

    The human bone marrow vasculature constitutively expresses both E-selectin and P-selectin where they interact with the cell-surface glycan moiety, sialyl Lewis x, on circulating hematopoietic stem/progenitor cells (HSPCs) to mediate the essential tethering/rolling step. Although several E-selectin glycoprotein ligands (E-selLs) have been identified, the importance of each E-selL on human HSPCs is debatable and requires additional methodologies to advance their specific involvement. The first objective was to fill the knowledge gap in the in vitro characterization of the mechanisms used by selectins to mediate the initial step in the HSPCs homing by developing a real time immunoprecipitation-based assay on a surface plasmon resonance chip. This novel assay bypass the difficulties of purifying ligands, enables the use of natively glycosylated forms of selectin ligands from any model cell of interest and study its binding affinities under flow. We provide the first comprehensive quantitative binding kinetics of two well-documented ligands, CD44 and PSGL-1, with E-selectin. Both ligands bind monomeric E-selectin transiently with fast on- and off-rates while they bind dimeric E-selectin with remarkably slow on- and off-rates with the on-rate, but not the off-rate, is dependent on salt concentration. Thus, suggest a mechanism through which monomeric selectins mediate initial fast-on and -off binding to capture the circulating cells out of shear-flow; subsequently, tight binding by dimeric/oligomeric selectins is enabled to slow rolling significantly. The second objective is to fully identify and characterize E/P-selectin ligand candidates expressed on CD34+ HSPCs which cause enhanced migration after intravenous transplantation compared to their CD34- counterparts. CD34 is widely recognized marker of human HSPCs but its natural ligand and function on these cells remain elusive. Proteomics identified CD34 as an E-selL candidate on human HSPCs, whose binding to E

  20. Colloidal nanoparticle size control: experimental and kinetic modeling investigation of the ligand–metal binding role in controlling the nucleation and growth kinetics

    Energy Technology Data Exchange (ETDEWEB)

    Mozaffari, Saeed; Li, Wenhui; Thompson, Coogan B.; Ivanov, Sergei; Siefert, Soenke; Lee, Byeongdu; Kovarik, Libor; Karim, Ayman M.

    2017-09-04

    Despite the major advancements in colloidal metal nanoparticles synthesis, a quantitative mechanistic treatment of the ligand’s role in controlling the rates of nucleation and growth still remains elusive. In this work, we conducted a mechanistic investigation and kinetic modeling of the role of trioctylphosphine (TOP) in controlling the size of Pd nanoparticles in different solvents using in-situ small angle x-ray scattering (SAXS). In both pyridine and toluene, slow nucleation which overlapped fast growth was observed under various synthetic conditions demonstrating the significant deviation of the particle formation pathway from the classical LaMer mechanism. We developed a novel kinetic model that, for the first time, accounts for both the nucleation and growth events through simultaneous fitting of number of nanoparticles (nucleation event) and their diameter (increase in number of atoms in nanoparticles from both nucleation and growth events) measured from in-situ SAXS. We show that the binding of TOP to both the Pd precursor and surface of Pd nanoparticles controls the nucleation and growth rates and is necessary to capture the evolution of diameter and number of particles during synthesis. The kinetic model was used to predict the synthetic conditions to control the Pd nanoparticle size from 1.1 to 4.6 nm, and the experimental results showed an excellent quantitative agreement. Additionally, our model was used to quantitatively explain the effect of ligand/metal ratio on the final size of Pd and Au nanoparticles reported in the literature. More importantly, we demonstrate that the final nanoparticle size can be determined using a single unique kinetic descriptor: Growth-to-Nucleation rate ratio to the power of 1/3, which is model independent, and remarkably applies to all the conditions studied in this work and several results from the literature despite the very different ligands, solvents and concentrations used. Our kinetic model, while simple, can

  1. Comparative DNA binding abilities and phosphatase-like activities of mono-, di-, and trinuclear Ni(II) complexes: the influence of ligand denticity, metal-metal distance, and coordinating solvent/anion on kinetics studies.

    Science.gov (United States)

    Bhardwaj, Vimal K; Singh, Ajnesh

    2014-10-06

    Six novel Ni(II) complexes, namely, [Ni2(HL(1))(OAc)2] (1), [Ni3L(1)2]·H2O·2CH3CN (2), [Ni2(L(2))(L(3))(CH3CN)] (3), [Ni2(L(2))2(H2O)2] (4), [Ni2(L(2))2(DMF)2]2·2H2O (5), and [Ni(HL(2))2]·H2O (6), were synthesized by reacting nitrophenol-based tripodal (H3L(1)) and dipodal (H2L(2)) Schiff base ligands with Ni(II) metal salts at ambient conditions. All the complexes were fully characterized with different spectroscopic techniques such as elemental analyses, IR, UV-vis spectroscopy, and electrospray ionization mass spectrometry. The solid-state structures of 2, 3, 5, and 6 were determined using single-crystal X-ray crystallography. The compounds 1, 3, 4, and 5 are dinuclear complexes where the two Ni(II) centers have octahedral geometry with bridging phenoxo groups. Compound 2 is a trinuclear complex with two different types of Ni(II) centers. In compound 3 one of the Ni(II) centers has a coordinated acetonitrile molecule, whereas in compound 4, a water molecule has occupied one coordination site of each Ni(II) center. In complex 5, the coordinated water of complex 4 was displaced by the dimethylformamide (DMF) during its crystallization. Complex 6 is mononuclear with two amine-bis(phenolate) ligands in scissorlike fashion around the Ni(II) metal center. The single crystals of 1 and 4 could not be obtained; however, from the spectroscopic data and physicochemical properties (electronic and redox properties) it was assumed that the structures of these complexes are quite similar to other analogues. DNA binding abilities and phosphatase-like activities of all characterized complexes were also investigated. The ligand denticity, coordinated anions/solvents (such as acetate, acetonitrile, water, and DMF), and cooperative action of two metal centers play a significant role in the phosphate ester bond cleavage of 2-hydroxypropyl-p-nitropenylphosphate by transesterification mechanism. Complex 3 exhibits highest activity among complexes 1-6 with 3.86 × 10(5) times

  2. Ruthenium-based olefin metathesis catalysts bearing pH-responsive ligands: External control of catalyst solubility and activity

    Science.gov (United States)

    Balof, Shawna Lynn

    2011-12-01

    Sixteen novel, Ru-based olefin metathesis catalysts bearing pH responsive ligands were synthesized. The pH-responsive groups employed with these catalysts included dimethylamino (NMe2) modified NHC ligands as well as N-donor dimethylaminopyridine (DMAP) and 3-(o-pyridyl)propylidene ligands. These pH-responsive ligands provided the means by which the solubility and/or activity profiles of the catalysts produced could be controlled via acid addition. The main goal of this dissertation was to design catalyst systems capable of performing ring opening metathesis (ROMP) and ring closing metathesis (RCM) reactions in both organic and aqueous media. In an effort to quickly gain access to new catalyst structures, a template synthesis for functionalized NHC ligand precursors was designed, in addition to other strategies, to obtain ligand precursors with ancillary NMe2 groups. Kinetic studies for the catalysts produced from these precursors showed external control of catalyst solubility was afforded via protonation of the NMe2 groups of their NHC ligands. Additionally, this protonation afforded external control of catalyst propagation rates for several catalysts. This is the first known independent external control for the propagation rates of ROMP catalysts. The incorporation of pH-responsive N-donor ligands into catalyst structures also provided the means for the external control of metathesis activity, as the protonation of these ligands resulted in an increased initiation rate based on their fast and irreversible dissociation from the metal center. The enhanced external control makes these catalysts applicable to a wide range of applications, some of which have been explored by us and/or through collaboration. Three of the catalysts designed showed remarkable metathesis activity in aqueous media. These catalysts displayed comparable RCM activity in aqueous media to a class of water-soluble catalysts reported by Grubbs et al., considered to be the most active catalyst for

  3. Fast generation of dendritic cells

    DEFF Research Database (Denmark)

    Kvistborg, P; Bøgh, Marie; Claesson, M H

    2009-01-01

    we have developed fast DC protocol by comparing two different fast DC protocols with SDDC. DC were evaluated by FACS analysis, and the optimal profile was considered: CD14(low), CD80(high), CD83(high), CD86(high), CCR7(high), HLA class I and II(high). FACS profiles were used as the selection criteria...... together with yield and morphology. Two fast DC protocols fulfilled these criteria and were selected for functional analysis. Our results demonstrate that DC generated within 5days or 48h are comparable with SDDC both phenotypically and functionally. However, we found that 48h DC were more susceptible than...... SDDC to the IL-10 inducing stimulus of TLR ligands (R848 and LPS). Thus to determine the clinical relevance of fast DC protocols in cancer settings, small phase I trials should be conducted monitoring regulatory T cells carefully....

  4. Thermodynamic and kinetic studies of the equilibration reaction between the sulfur and carbon bonded forms of a cobalt(III) complex with the ligands 1,4,7-triazycyclononane and 1,4-diaza-7-thiacyclodecane

    DEFF Research Database (Denmark)

    Song, Y.S.; Becker, J.; Kofod, Pauli

    1996-01-01

    The new cyclic thioether 1,4-diaza-7-thiacyclodecane, dathicd, has been synthesized and used for the prepn. of the sulfur- and carbon-bonded cobalt(III) complexes: [Co(tacn)(S-dathicd)]Cl3.5H2O and [Co(tacn)(C-dathicd)](ClO4)2 (tacn, 1,4,7-triazacyclononane; C-dathicd, 1,4-diamino-7-thiacyclodecan......-8-ide anion). A thermodn. and kinetic study of the equilibration between these coordination compds. has been performed using UV-VIS absorption spectroscopy, IE-HPLC and 13C NMR ([OH-]=10-5-1.0 M, T=25.0 DegC, I=1.0 M). In basic soln. Co(tacn)(S-dathicd)3+ deprotonates at one of the coordinated amine...

  5. Thermodynamic and kinetic studies of the equilibration reaction between the sulfur and carbon bonded forms of a cobalt(III) complex with the ligands 1,4,7-triazycyclononane and 1,4-diaza-7-thiacyclodecane

    DEFF Research Database (Denmark)

    Song, Y.S.; Becker, J.; Kofod, Pauli

    1996-01-01

    -sulfur complex to form the alkyl complex gave 100% loss of deuterium. It is concluded that the labile methylene proton is bound to the carbon atom which in the alkyl complex is bound to cobalt(III). From the kinetic data it is estd. that the carbanion reacts with water 270 times faster than it is captured......The new cyclic thioether 1,4-diaza-7-thiacyclodecane, dathicd, has been synthesized and used for the prepn. of the sulfur- and carbon-bonded cobalt(III) complexes: [Co(tacn)(S-dathicd)]Cl3.5H2O and [Co(tacn)(C-dathicd)](ClO4)2 (tacn, 1,4,7-triazacyclononane; C-dathicd, 1,4-diamino-7-thiacyclodecan...

  6. Kinetic regulation mechanism of pbuE riboswitch

    Science.gov (United States)

    Gong, Sha; Wang, Yujie; Zhang, Wenbing

    2015-01-01

    Riboswitches are RNA residue segments located in untranslated regions of messenger RNAs. These folded segments directly bind ligands through shape complementarity and specific interactions in cells and alter the expression of genes at the transcriptional or translational level through conformation change. Using the recently developed systematic helix-based computational method to predict the cotranscription folding kinetics, we theoretically studied the cotranscription folding behavior of the Bacillus subtilis pbuE riboswitch in the absence and presence of the ligand. The ligand concentration, the transcription speed, and the transcription pausing are incorporated into the method. The results are in good agreement with the experimental results. We find that there are no obvious misfolded structures formed during the transcription and the formation of the ligand bound state is rate-limited by the association of the ligand and the RNA. For this kinetically driven riboswitch, the ligand concentration, the transcription speed, and the transcription pausing are coupled to perform regulatory activity.

  7. Ligand modeling and design

    Energy Technology Data Exchange (ETDEWEB)

    Hay, B.P. [Pacific Northwest National Lab., Richland, WA (United States)

    1997-10-01

    The purpose of this work is to develop and implement a molecular design basis for selecting organic ligands that would be used in the cost-effective removal of specific radionuclides from nuclear waste streams. Organic ligands with metal ion specificity are critical components in the development of solvent extraction and ion exchange processes that are highly selective for targeted radionuclides. The traditional approach to the development of such ligands involves lengthy programs of organic synthesis and testing, which in the absence of reliable methods for screening compounds before synthesis, results in wasted research effort. The author`s approach breaks down and simplifies this costly process with the aid of computer-based molecular modeling techniques. Commercial software for organic molecular modeling is being configured to examine the interactions between organic ligands and metal ions, yielding an inexpensive, commercially or readily available computational tool that can be used to predict the structures and energies of ligand-metal complexes. Users will be able to correlate the large body of existing experimental data on structure, solution binding affinity, and metal ion selectivity to develop structural design criteria. These criteria will provide a basis for selecting ligands that can be implemented in separations technologies through collaboration with other DOE national laboratories and private industry. The initial focus will be to select ether-based ligands that can be applied to the recovery and concentration of the alkali and alkaline earth metal ions including cesium, strontium, and radium.

  8. electronic Ligand Builder and Optimisation Workbench (eLBOW): A tool for ligand coordinate and restraint generation

    Energy Technology Data Exchange (ETDEWEB)

    Moriarty, Nigel; Grosse-Kunstleve, Ralf; Adams, Paul

    2009-07-01

    The electronic Ligand Builder and Optimisation Workbench (eLBOW) is a program module of the PHENIX suite of computational crystallographic software. It's designed to be a flexible procedure using simple and fast quantum chemical techniques to provide chemically accurate information for novel and known ligands alike. A variety of input formats and options allow for the attainment of a number of diverse goals including geometry optimisation and generation of restraints.

  9. Non-Michaelis-Menten kinetics in cytochrome P450-catalyzed reactions.

    Science.gov (United States)

    Atkins, William M

    2005-01-01

    The cytochrome P450 monooxygenases (CYPs) are the dominant enzyme system responsible for xenobiotic detoxification and drug metabolism. Several CYP isoforms exhibit non-Michaelis-Menten, or "atypical," steady state kinetic patterns. The allosteric kinetics confound prediction of drug metabolism and drug-drug interactions, and they challenge the theoretical paradigms of allosterism. Both homotropic and heterotropic ligand effects are now widely documented. It is becoming apparent that multiple ligands can simultaneously bind within the active sites of individual CYPs, and the kinetic parameters change with ligand occupancy. In fact, the functional effect of any specific ligand as an activator or inhibitor can be substrate dependent. Divergent approaches, including kinetic modeling and X-ray crystallography, are providing new information about how multiple ligand binding yields complex CYP kinetics.

  10. Kinetic Interface

    DEFF Research Database (Denmark)

    2009-01-01

    A kinetic interface for orientation detection in a video training system is disclosed. The interface includes a balance platform instrumented with inertial motion sensors. The interface engages a participant's sense of balance in training exercises.......A kinetic interface for orientation detection in a video training system is disclosed. The interface includes a balance platform instrumented with inertial motion sensors. The interface engages a participant's sense of balance in training exercises....

  11. Hg(Ⅱ)催化亚铁氰化钾配位交换番红花红T增敏显色动力学光度法测定痕量汞%Determination of trace mercury with Hg (Ⅱ) catalyzing the sensitization color of potassium ferrocyanide ligand exchanging safranine* T kinetic spectrophotometry

    Institute of Scientific and Technical Information of China (English)

    王洪福; 苏智先; 张素兰; 罗英; 冯秀君

    2011-01-01

    When heated in a dilute sulfuric acid medium, the color reaction of the potassium ferrocyanide-safranine T ligand can be enhanced by the activation agent thiourea. Also, Hg(II) catalyzing the color reaction of potassium ferrocyanide ligand exchanging safranine T can be greatly enhanced. Based on this, a new method for the determination of trace Mercury (Ⅱ) with ion catalyzing ligand exchange sensitized color kinetic spectrophotometry was established. The optimum experimental conditions were studied. The absorbency difference A A between non-catalytic reaction (absorbency A0) and catalytic reaction (absorbency A) remained good linear relationship with the mass concentration p of Hg(Ⅱ) in the range of 0.0055 ~2 50 ug/25 mL. The detection limit was 1.39 x 10-10g/mL. The kinetic parameters were determined, and the results showed that the reaction was the first order to Hg(II) and pseudo first order to the total reaction. The apparent rate constant was 4.32 × 10-4/s and the apparent activation energy was 57.4kJ/mol. This method has been applied to the determination of trace Hg( Ⅱ) in water samples and human hair with the recoveries of 98% -101% , which fulfilled the trace analysis requirements.%基于在H2SO4介质中及加热的条件下,加入活化剂硫脲对亚铁氰化钾-番红花红T配位显色反应具有增敏作用.痕量Hg(Ⅱ)催化亚铁氰化钾配位交换番红花红T增敏显色反应显著增强,据此,建立了离子催化配位交换增敏显色反应动力学光度法测定痕量汞(Hg)的新光度分析法.研究了反应的最佳实验条件.催化反应(吸光度A)与非催化反应(吸光度A0)吸光度差值△A与Hg(Ⅱ)的质量浓度在0.0055~2.50 μg/25 mL范围内呈良好的线性关系,检出限为1.39×10-10g/mL.测定了动力学参数,反应对Hg(Ⅱ)为一级反应,总反应为准一级反应.表现速率常数为4.32×10-4/s,表观活化能为57.4kJ/moL.该方法用于水样和人发中痕量汞Hg(

  12. Ligand modeling and design

    Energy Technology Data Exchange (ETDEWEB)

    Hay, B. [Pacific Northwest Lab., Richland, WA (United States)

    1996-10-01

    The purpose of this work is to develop and implement a molecular design basis for selecting organic ligands that would be used tin applications for the cost-effective removal of specific radionuclides from nuclear waste streams.

  13. Organotellurium ligands - designing and complexation reactions

    Indian Academy of Sciences (India)

    Ajai K Singh

    2002-08-01

    A variety of tellurium ligands has been designed and studied for their complexation reactions in the last decade. Of these hybrid telluroethers, halotellurium ligands and polytellurides are the most notable ones. RTe- and polytelluride ions have also been used to design clusters. Ligation of ditelluroethers and several hybrid telluroethers is extensively studied in our laboratories. The ditelluroether ligand RTeCH2TeR (where R = 4-MeOC6H4) (1), similar to dppm [1,2-bis(diphenylphosphino) methane], has been synthesized in good yield (∼80 %) by reacting CHCl3 with RTe- (generated in situ by borohydride reduction of R2Te2). Iodine reacts with 1 to give tetra-iodo derivative, which has intermolecular Te$\\cdots$I interactions resulting in a macro structure containing rectangular Te-I$\\cdots$Te bridges. 1 readily forms four membered rings with Pd(II) and Ru(II). On the formation of this chelate ring, the signal in 125Te NMR spectra shifts significantly upfield (50-60 ppm). The bridging mode of 1 has been shown in [Ru(-cymene)Cl2](-1)[Ru(-cymene)Cl2]. The hybrid telluroether ligands explored are of the types (Te, S), (Te, N) and (Te, O). The tellurium donor site has strong trans influence, which is manifested more strongly in square planar complexes of palladium(II). The morpholine N-donor site has been found to have weaker donor characteristics in (Te, N) ligands than pyridine and alkylamine donor sites of analogous ligands. The singlet oxygen readily oxidises the coordinated Te. This oxidation follows first order kinetics. The complexation reaction of RuCl3.H2O with N-[2-(4-methoxyphenyltelluro)ethyl]phthalimide (2) results in a novel (Te, N, O)-heterocycle, Te-chloro,Te-anisyl-1a-aza-4-oxa-3-tellura-1H, 2H, 4aH-9 fluorenone. The (Te, O) ligands can be used as hemilabile ligands, the oxygen atom temporarily protects the vacant coordination site before the arrival of the substrate. The chelate shifts observed in 125Te NMR spectra of metal complexes of Te-ligands have

  14. Quantum.Ligand.Dock: protein-ligand docking with quantum entanglement refinement on a GPU system.

    Science.gov (United States)

    Kantardjiev, Alexander A

    2012-07-01

    Quantum.Ligand.Dock (protein-ligand docking with graphic processing unit (GPU) quantum entanglement refinement on a GPU system) is an original modern method for in silico prediction of protein-ligand interactions via high-performance docking code. The main flavour of our approach is a combination of fast search with a special account for overlooked physical interactions. On the one hand, we take care of self-consistency and proton equilibria mutual effects of docking partners. On the other hand, Quantum.Ligand.Dock is the the only docking server offering such a subtle supplement to protein docking algorithms as quantum entanglement contributions. The motivation for development and proposition of the method to the community hinges upon two arguments-the fundamental importance of quantum entanglement contribution in molecular interaction and the realistic possibility to implement it by the availability of supercomputing power. The implementation of sophisticated quantum methods is made possible by parallelization at several bottlenecks on a GPU supercomputer. The high-performance implementation will be of use for large-scale virtual screening projects, structural bioinformatics, systems biology and fundamental research in understanding protein-ligand recognition. The design of the interface is focused on feasibility and ease of use. Protein and ligand molecule structures are supposed to be submitted as atomic coordinate files in PDB format. A customization section is offered for addition of user-specified charges, extra ionogenic groups with intrinsic pK(a) values or fixed ions. Final predicted complexes are ranked according to obtained scores and provided in PDB format as well as interactive visualization in a molecular viewer. Quantum.Ligand.Dock server can be accessed at http://87.116.85.141/LigandDock.html.

  15. Kinetic titration series with biolayer interferometry.

    Science.gov (United States)

    Frenzel, Daniel; Willbold, Dieter

    2014-01-01

    Biolayer interferometry is a method to analyze protein interactions in real-time. In this study, we illustrate the usefulness to quantitatively analyze high affinity protein ligand interactions employing a kinetic titration series for characterizing the interactions between two pairs of interaction patterns, in particular immunoglobulin G and protein G B1 as well as scFv IC16 and amyloid beta (1-42). Kinetic titration series are commonly used in surface plasmon resonance and involve sequential injections of analyte over a desired concentration range on a single ligand coated sensor chip without waiting for complete dissociation between the injections. We show that applying this method to biolayer interferometry is straightforward and i) circumvents problems in data evaluation caused by unavoidable sensor differences, ii) saves resources and iii) increases throughput if screening a multitude of different analyte/ligand combinations.

  16. Kinetic titration series with biolayer interferometry.

    Directory of Open Access Journals (Sweden)

    Daniel Frenzel

    Full Text Available Biolayer interferometry is a method to analyze protein interactions in real-time. In this study, we illustrate the usefulness to quantitatively analyze high affinity protein ligand interactions employing a kinetic titration series for characterizing the interactions between two pairs of interaction patterns, in particular immunoglobulin G and protein G B1 as well as scFv IC16 and amyloid beta (1-42. Kinetic titration series are commonly used in surface plasmon resonance and involve sequential injections of analyte over a desired concentration range on a single ligand coated sensor chip without waiting for complete dissociation between the injections. We show that applying this method to biolayer interferometry is straightforward and i circumvents problems in data evaluation caused by unavoidable sensor differences, ii saves resources and iii increases throughput if screening a multitude of different analyte/ligand combinations.

  17. Single-molecule kinetics and footprinting of DNA bis-intercalation: the paradigmatic case of Thiocoraline

    Science.gov (United States)

    Camunas-Soler, Joan; Manosas, Maria; Frutos, Silvia; Tulla-Puche, Judit; Albericio, Fernando; Ritort, Felix

    2015-01-01

    DNA bis-intercalators are widely used in molecular biology with applications ranging from DNA imaging to anticancer pharmacology. Two fundamental aspects of these ligands are the lifetime of the bis-intercalated complexes and their sequence selectivity. Here, we perform single-molecule optical tweezers experiments with the peptide Thiocoraline showing, for the first time, that bis-intercalation is driven by a very slow off-rate that steeply decreases with applied force. This feature reveals the existence of a long-lived (minutes) mono-intercalated intermediate that contributes to the extremely long lifetime of the complex (hours). We further exploit this particularly slow kinetics to determine the thermodynamics of binding and persistence length of bis-intercalated DNA for a given fraction of bound ligand, a measurement inaccessible in previous studies of faster intercalating agents. We also develop a novel single-molecule footprinting technique based on DNA unzipping and determine the preferred binding sites of Thiocoraline with one base-pair resolution. This fast and radiolabelling-free footprinting technique provides direct access to the binding sites of small ligands to nucleic acids without the need of cleavage agents. Overall, our results provide new insights into the binding pathway of bis-intercalators and the reported selectivity might be of relevance for this and other anticancer drugs interfering with DNA replication and transcription in carcinogenic cell lines. PMID:25690887

  18. Quartz crystal microbalance study of the kinetics of surface initiated polymerization

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Surface initiated polymerization (SIP) is a valuable tool in synthesizing functional polymer brushes,yet the kinetic understanding of SIP lags behind the development of its application. We apply quartz crystal microbalance (QCM) to address two issues that are not fully addressed yet play a central role in the rational design of functional polymer brushes,namely quantitative determination of the kinetics and the initiator efficiency (IE) of SIP. SIP are monitored online using QCM. Two quantitative frequencythickness (f-T) relations make the direct determination and comparison of the rate of polymerization possible even for different monomers. Based on the bi-termination model,the kinetics of SIP is simply described by two variables,which are related to two polymerization constants,namely a = 1/(kp,s,app-[M][R·]0) and b = kt,s,app/(kp,s,app[M]). Factors that could alter the kinetics of SIP are studied,including (i) the molecular weight of monomers,(ii) the solvent used,(iii) the initial density of the initiator,(iv) the concentration of monomer,[M],and (v) the catalyst system (ratio among the ingredients,metal,ligands,and additives). The dynamic nature of IE is also described by these two variables,IE = a/(a + bt). Instead of the molecular weight and the polydispersity,we suggest that film thickness,the two kinetic parameters (a and b),and the initial density of the initiator and IE be the parameters that characterize ultrathin polymer brushes. Besides the kinetics study of SIP,the reported method has many other applications,for example,in the fast screening of catalyst system for SIP and other polymerization systems.

  19. Kinetics and

    Directory of Open Access Journals (Sweden)

    Mojtaba Ahmadi

    2016-11-01

    Full Text Available The aqueous degradation of Reactive Yellow 84 (RY84 by potassium peroxydisulfate (K2S2O8 has been studied in laboratory scale experiments. The effect of the initial concentrations of potassium peroxydisulfate and RY84, pH and temperature on RY84 degradation were also examined. Experimental data were analyzed using first and second-order kinetics. The degradation kinetics of RY84 of the potassium peroxydisulfate process followed the second-order reaction kinetics. These rate constants have an extreme values similar to of 9.493 mM−1min−1 at a peroxydisulfate dose of 4 mmol/L. Thermodynamic parameters such as activation (Ea and Gibbs free energy (ΔG° were also evaluated. The negative value of ΔGo and Ea shows the spontaneous reaction natural conditions and exothermic nature.

  20. Gender dependent rate of metabolism of the opioid receptor-PET ligand [{sup 18}F]fluoroethyl-diprenorphine

    Energy Technology Data Exchange (ETDEWEB)

    Henriksen, G.; Spilker, M.E.; Hauser, A.I.; Boecker, H.; Schwaiger, M.; Wester, H.J. [Technische Univ. Muenchen, Garching (Germany). Dept. of Nuclear Medicine; Sprenger, T.; Platzer, S.; Toelle, T.R. [Technische Univ. Muenchen, Garching (Germany). Klinikum rechts der Isar, Neurology

    2006-07-01

    Aim: The morphinane-derivate 6-O-(2-[{sup 18}F]fluoroethyl)-6-O-desmethyldiprenorphine ([{sup 18}F]FDPN) is a non-selective opioid receptor ligand currently used in positron emission tomography (PET). Correction for plasma metabolites of the arterial input function is necessary for quantitative measurements of [{sup 18}]FDPN binding. A study was undertaken to investigate if there are gender dependent differences in the rate of metabolism of [{sup 18}F]FDPN. Methods: The rate of metabolism of [{sup 18}F]FDPN was mathematically quantified by fitting a bi-exponential function to each individual's dynamic metabolite data. Results: No statistically significant gender differences were found for age, weight, body mass index or dose. However, significant differences (p<0.01) in two of the four kinetic parameters describing the rate of metabolism were found between the two groups, with women metabolizing [{sup 18}F]FDPN faster than men. These differences were found in the contribution of the fast and slow kinetic components of the model describing the distribution of radioactive species in plasma, indicating a higher rate of enzyme-dependent degradation of [{sup 18}F]FDPN in women than in men. Conclusion: The findings reinforce the need for individualized metabolite correction during [{sup 18}F]FDPN-PET scans and also indicate that in certain cases, grouping according to gender could be performed in order to minimize methodological errors of the input function prior to kinetic analyses. (orig.)

  1. Steered molecular dynamics simulations of protein-ligand interactions

    Institute of Scientific and Technical Information of China (English)

    XU; Yechun; SHEN; Jianhua; LUO; Xiaomin; SHEN; Xu; CHEN; Ka

    2004-01-01

    Studies of protein-ligand interactions are helpful to elucidating the mechanisms of ligands, providing clues for rational drug design. The currently developed steered molecular dynamics (SMD) is a complementary approach to experimental techniques in investigating the biochemical processes occurring at microsecond or second time scale, thus SMD may provide dynamical and kinetic processes of ligand-receptor binding and unbinding, which cannot be accessed by the experimental methods. In this article, the methodology of SMD is described, and the applications of SMD simulations for obtaining dynamic insights into protein-ligand interactions are illustrated through two of our own examples. One is associated with the simulations of binding and unbinding processes between huperzine A and acetylcholinesterase, and the other is concerned with the unbinding process of α-APA from HIV-1 reverse transcriptase.

  2. Computational Exploration of a Protein Receptor Binding Space with Student Proposed Peptide Ligands

    Science.gov (United States)

    King, Matthew D.; Phillips, Paul; Turner, Matthew W.; Katz, Michael; Lew, Sarah; Bradburn, Sarah; Andersen, Tim; McDougal, Owen M.

    2016-01-01

    Computational molecular docking is a fast and effective "in silico" method for the analysis of binding between a protein receptor model and a ligand. The visualization and manipulation of protein to ligand binding in three-dimensional space represents a powerful tool in the biochemistry curriculum to enhance student learning. The…

  3. Multi-scale times and modes of fast and slow relaxation in solutions with coexisting spherical and cylindrical micelles according to the difference Becker-Döring kinetic equations

    Science.gov (United States)

    Babintsev, Ilya A.; Adzhemyan, Loran Ts.; Shchekin, Alexander K.

    2014-08-01

    The eigenvalues and eigenvectors of the matrix of coefficients of the linearized kinetic equations applied to aggregation in surfactant solution determine the full spectrum of characteristic times and specific modes of micellar relaxation. The dependence of these relaxation times and modes on the total surfactant concentration has been analyzed for concentrations in the vicinity and well above the second critical micelle concentration (cmc2) for systems with coexisting spherical and cylindrical micelles. The analysis has been done on the basis of a discrete form of the Becker-Döring kinetic equations employing the Smoluchowsky diffusion model for the attachment rates of surfactant monomers to surfactant aggregates with matching the rates for spherical aggregates and the rates for large cylindrical micelles. The equilibrium distribution of surfactant aggregates in solution has been modeled as having one maximum for monomers, another maximum for spherical micelles and wide slowly descending branch for cylindrical micelles. The results of computations have been compared with the analytical ones known in the limiting cases from solutions of the continuous Becker-Döring kinetic equation. They demonstrated a fair agreement even in the vicinity of the cmc2 where the analytical theory looses formally its applicability.

  4. Further Insight into the Lability of MeCN Ligands of Cytotoxic Cycloruthenated Compounds: Evidence for the Antisymbiotic Effect Trans to the Carbon Atom at the Ru Center.

    Science.gov (United States)

    Barbosa, Ana Soraya Lima; Werlé, Christophe; Colunga, Claudia Olivia Oliva; Rodríguez, Cecilia Franco; Toscano, Ruben Alfredo; Le Lagadec, Ronan; Pfeffer, Michel

    2015-08-03

    The two MeCN ligands in [Ru(2-C6H4-2'-Py-κC,N)(Phen, trans-C)(MeCN)2]PF6 (1), both trans to a sp(2) hybridized N atom, cannot be substituted by any other ligand. In contrast, the isomerized derivative [Ru(2-C6H4-2'-Py-κC,N)(Phen, cis-C)(MeCN)2]PF6 (2), in which one MeCN ligand is now trans to the C atom of the phenyl ring orthometalated to Ru, leads to fast and quantitative substitution reactions with several monodentate ligands. With PPh3, 2 affords [Ru(2-C6H4-2'-Py-κC,N)(Phen, cis-C)(PPh3)(MeCN)]PF6 (3), in which PPh3 is trans to the C σ bound to Ru. Compound 3 is not kinetically stable, because, under thermodynamic control, it leads to 4, in which the PPh3 is trans to a N atom of the Phen ligand. Dimethylsulfoxide (DMSO) can also substitute a MeCN ligand in 2, leading to 5, in which DMSO is coordinated to Ru via its S atom trans to the N atom of the Phen ligand, the isomer under thermodynamic control being the only compound observed. We also found evidence for the fast to very fast substitution of MeCN in 2 by water or a chloride anion by studying the electronic spectra of 2 in the presence of water or NBu4Cl, respectively. An isomerization related to that observed between 3 and 4 is also found for the known monophosphine derivative [Ru(2-C6H4-2'-Py-κC,N)(PPh3, trans-C)(MeCN)3]PF6 (10), in which the PPh3 is located trans to the C of the cyclometalated 2-phenylpyridine, since, upon treatment by refluxing MeCN, it leads to its isomer 11, [Ru(2-C6H4-2'-Py-κC,N)(PPh3, cis-C)(MeCN)3]PF6. Further substitutions are also observed on 11, whereby N^N chelates (N^N = 2,2'-bipyridine and phenanthroline) substitute two MeCN ligands, affording [Ru(2-C6H4-2'-Py-κC,N)(PPh3, cis-C)(N^N)(MeCN)]PF6 (12a and 12b). Altogether, the behavior of the obtained complexes by ligand substitution reactions can be rationalized by an antisymbiotic effect on the Ru center, trans to the C atom of the cyclometalated unit, leading to compounds having the least nucleophilic ligand trans to C

  5. Ligand fitting with CCP4

    Science.gov (United States)

    2017-01-01

    Crystal structures of protein–ligand complexes are often used to infer biology and inform structure-based drug discovery. Hence, it is important to build accurate, reliable models of ligands that give confidence in the interpretation of the respective protein–ligand complex. This paper discusses key stages in the ligand-fitting process, including ligand binding-site identification, ligand description and conformer generation, ligand fitting, refinement and subsequent validation. The CCP4 suite contains a number of software tools that facilitate this task: AceDRG for the creation of ligand descriptions and conformers, Lidia and JLigand for two-dimensional and three-dimensional ligand editing and visual analysis, Coot for density interpretation, ligand fitting, analysis and validation, and REFMAC5 for macromolecular refinement. In addition to recent advancements in automatic carbohydrate building in Coot (LO/Carb) and ligand-validation tools (FLEV), the release of the CCP4i2 GUI provides an integrated solution that streamlines the ligand-fitting workflow, seamlessly passing results from one program to the next. The ligand-fitting process is illustrated using instructive practical examples, including problematic cases such as post-translational modifications, highlighting the need for careful analysis and rigorous validation. PMID:28177312

  6. Physisorption kinetics

    CERN Document Server

    Kreuzer, Hans Jürgen

    1986-01-01

    This monograph deals with the kinetics of adsorption and desorption of molecules physisorbed on solid surfaces. Although frequent and detailed reference is made to experiment, it is mainly concerned with the theory of the subject. In this, we have attempted to present a unified picture based on the master equation approach. Physisorption kinetics is by no means a closed and mature subject; rather, in writing this monograph we intended to survey a field very much in flux, to assess its achievements so far, and to give a reasonable basis from which further developments can take off. For this reason we have included many papers in the bibliography that are not referred to in the text but are of relevance to physisorption. To keep this monograph to a reasonable size, and also to allow for some unity in the presentation of the material, we had to omit a number of topics related to physisorption kinetics. We have not covered to any extent the equilibrium properties of physisorbed layers such as structures, phase tr...

  7. Kinetic Biochemistry

    Directory of Open Access Journals (Sweden)

    Lorentz JÄNTSCHI

    2003-03-01

    Full Text Available Mathematics and computer programming have a major contribution to chemistry. Two directions can be identified: one that searches and tries (rich to explain the structural binding and shape of the chemical compounds [1] with major applications in QSPR/QSAR studies [2], and applied sciences such as engineering of materials or agriculture [3]; the second direction is to models the kinetic processes that are involved in chemical reactions [4]. Many such models are available here. The present paper describes three variants of well the known kinetic models and presents the mathematical equations associated with them. The differential equations are numerically solved and fitted with MathCad program. [1] Diudea M., Gutman I., Jäntschi L., Molecular Topology, Nova Science, Huntington, New York, 332 p., 2001, 2002. [2] Diudea M. V., Ed., QSPR / QSAR Studies by Molecular Descriptors, Nova Science, Huntington, New York, 438 p., 2001. [3] Jäntschi L., Microbiology and Toxicology. Phytochemistry Studies (in Romanian, Amici, Cluj-Napoca, 184 p., 2003. [4] Jäntschi L., Unguresan M., Physical Chemistry. Molecular Kinetic and Dynamic (in Romanian, Mediamira, Cluj-Napoca, 159 p., 2001.

  8. Investigations of ultrafast ligand rebinding to heme and heme proteins using temperature and strong magnetic field perturbations

    Science.gov (United States)

    Zhang, Zhenyu

    study the ligand recombination after photolysis. No magnetic field induced rate changes are observed in any of these ligand recombination processes within the experimental detection limit. A magnetic field dependent CO rebinding behavior is observed for the FePPIX-CO sample in 80%glycerol/20%water environment. Careful data analysis indicates that this magnetic field induced change is due to the amplitude difference of a "fast" (Tesla to ˜45% at 10 Tesla). Kinetics of CO rebinding to FePPIX in 80%glycerol at the extremes of the magnetic field intensities (0Tesla vs. 10 Tesla) can be decomposed into a ligand rebinding process plus two 5ps decays heme cooling with different amplitudes. It leads to suggest a magnetic field induced change of a short-lived heme cooling response after photolysis. Also, CO rebinding kinetics to different heme compounds demonstrates a wide range for the Arrhenius pre-factors. This work reveals that the "spin-selection rule" does not play a key role in the recombination process of CO to heme iron. In Appendix 1, the recombination of oxymyoglobin and its mutants is investigated in the temperature range from 275K to 318K, using a home-made cryostat. Quite surprisingly, the O2 molecule rebinds to heme iron inside myoglobin with dramatically different behavior as the temperature is varied, depending on the protein environment. It shows little dependence (Mb), no dependence (V68W Mb mutant) and large dependence (L29W Mb mutant) in this 40K temperature window. To expand this temperature window, since the motor inside the cryostat is capable to work as low as 230K, glycerol is introduced into the protein preparation. It is observed that protein samples in a glycerol/water mixture, even with only 20% glycerol (in weight), the temperature dependences of the O2 rebinding to heme iron are dramatically altered. The O 2 rebinding behavior also shows a high dependence on the glycerol concentration in the solution. In Appendix 2, the absorption spectra of Fe

  9. LigandRNA: computational predictor of RNA-ligand interactions.

    Science.gov (United States)

    Philips, Anna; Milanowska, Kaja; Lach, Grzegorz; Bujnicki, Janusz M

    2013-12-01

    RNA molecules have recently become attractive as potential drug targets due to the increased awareness of their importance in key biological processes. The increase of the number of experimentally determined RNA 3D structures enabled structure-based searches for small molecules that can specifically bind to defined sites in RNA molecules, thereby blocking or otherwise modulating their function. However, as of yet, computational methods for structure-based docking of small molecule ligands to RNA molecules are not as well established as analogous methods for protein-ligand docking. This motivated us to create LigandRNA, a scoring function for the prediction of RNA-small molecule interactions. Our method employs a grid-based algorithm and a knowledge-based potential derived from ligand-binding sites in the experimentally solved RNA-ligand complexes. As an input, LigandRNA takes an RNA receptor file and a file with ligand poses. As an output, it returns a ranking of the poses according to their score. The predictive power of LigandRNA favorably compares to five other publicly available methods. We found that the combination of LigandRNA and Dock6 into a "meta-predictor" leads to further improvement in the identification of near-native ligand poses. The LigandRNA program is available free of charge as a web server at http://ligandrna.genesilico.pl.

  10. Analysis of macromolecules, ligands and macromolecule-ligand complexes

    Science.gov (United States)

    Von Dreele, Robert B [Los Alamos, NM

    2008-12-23

    A method for determining atomic level structures of macromolecule-ligand complexes through high-resolution powder diffraction analysis and a method for providing suitable microcrystalline powder for diffraction analysis are provided. In one embodiment, powder diffraction data is collected from samples of polycrystalline macromolecule and macromolecule-ligand complex and the refined structure of the macromolecule is used as an approximate model for a combined Rietveld and stereochemical restraint refinement of the macromolecule-ligand complex. A difference Fourier map is calculated and the ligand position and points of interaction between the atoms of the macromolecule and the atoms of the ligand can be deduced and visualized. A suitable polycrystalline sample of macromolecule-ligand complex can be produced by physically agitating a mixture of lyophilized macromolecule, ligand and a solvent.

  11. Ligand-Receptor Interactions

    CERN Document Server

    Bongrand, Pierre

    2008-01-01

    The formation and dissociation of specific noncovalent interactions between a variety of macromolecules play a crucial role in the function of biological systems. During the last few years, three main lines of research led to a dramatic improvement of our understanding of these important phenomena. First, combination of genetic engineering and X ray cristallography made available a simultaneous knowledg of the precise structure and affinity of series or related ligand-receptor systems differing by a few well-defined atoms. Second, improvement of computer power and simulation techniques allowed extended exploration of the interaction of realistic macromolecules. Third, simultaneous development of a variety of techniques based on atomic force microscopy, hydrodynamic flow, biomembrane probes, optical tweezers, magnetic fields or flexible transducers yielded direct experimental information of the behavior of single ligand receptor bonds. At the same time, investigation of well defined cellular models raised the ...

  12. Therapeutic androgen receptor ligands

    OpenAIRE

    Allan, George F.; Sui, Zhihua

    2003-01-01

    In the past several years, the concept of tissue-selective nuclear receptor ligands has emerged. This concept has come to fruition with estrogens, with the successful marketing of drugs such as raloxifene. The discovery of raloxifene and other selective estrogen receptor modulators (SERMs) has raised the possibility of generating selective compounds for other pathways, including androgens (that is, selective androgen receptor modulators, or SARMs).

  13. Imidazoline receptors ligands

    Directory of Open Access Journals (Sweden)

    Agbaba Danica

    2012-01-01

    Full Text Available Extensive biochemical and pharmacological studies have determined three different subtypes of imidazoline receptors: I1-imidazoline receptors (I1-IR involved in central inhibition of sympathicus that produce hypotensive effect; I2-imidazoline receptors (I2-IR modulate monoamine oxidase B activity (MAO-B; I3-imidazoline receptors (I3-IR regulate insulin secretion from pancreatic β-cells. Therefore, the I1/I2/I3 imidazoline receptors are selected as new, interesting targets for drug design and discovery. Novel selective I1/I2/I3 agonists and antagonists have been recently developed. In the present review, we provide a brief update to the field of imidazoline research, highlighting some of the chemical diversity and progress made in the 2D-QSAR, 3D-QSAR and quantitative pharmacophore development studies of I1-IR and I2-IR imidazoline receptor ligands. Theoretical studies of I3-IR ligands are not yet performed because of insufficient number of synthesized I3-IR ligands.

  14. Kinetics of Social Contagion

    Science.gov (United States)

    Ruan, Zhongyuan; Iñiguez, Gerardo; Karsai, Márton; Kertész, János

    2015-11-01

    Diffusion of information, behavioral patterns or innovations follows diverse pathways depending on a number of conditions, including the structure of the underlying social network, the sensitivity to peer pressure and the influence of media. Here we study analytically and by simulations a general model that incorporates threshold mechanism capturing sensitivity to peer pressure, the effect of "immune" nodes who never adopt, and a perpetual flow of external information. While any constant, nonzero rate of dynamically introduced spontaneous adopters leads to global spreading, the kinetics by which the asymptotic state is approached shows rich behavior. In particular, we find that, as a function of the immune node density, there is a transition from fast to slow spreading governed by entirely different mechanisms. This transition happens below the percolation threshold of network fragmentation, and has its origin in the competition between cascading behavior induced by adopters and blocking due to immune nodes. This change is accompanied by a percolation transition of the induced clusters.

  15. Kinetics of Social Contagion

    CERN Document Server

    Ruan, Zhongyuan; Karsai, Marton; Kertesz, Janos

    2015-01-01

    Diffusion of information, behavioural patterns or innovations follows diverse pathways depending on a number of conditions, including the structure of the underlying social network, the sensitivity to peer pressure and the influence of media. Here we study analytically and by simulations a general model that incorporates threshold mechanism capturing sensitivity to peer pressure, the effect of `immune' nodes who never adopt, and a perpetual flow of external information. While any constant, non-zero rate of dynamically-introduced innovators leads to global spreading, the kinetics by which the asymptotic state is approached show rich behaviour. In particular we find that, as a function of the density of immune nodes, there is a transition from fast to slow spreading governed by entirely different mechanisms. This transition happens below the percolation threshold of fragmentation of the network, and has its origin in the competition between cascading behaviour induced by innovators and blocking of adoption due ...

  16. LASSO-ligand activity by surface similarity order: a new tool for ligand based virtual screening.

    Science.gov (United States)

    Reid, Darryl; Sadjad, Bashir S; Zsoldos, Zsolt; Simon, Aniko

    2008-01-01

    Virtual Ligand Screening (VLS) has become an integral part of the drug discovery process for many pharmaceutical companies. Ligand similarity searches provide a very powerful method of screening large databases of ligands to identify possible hits. If these hits belong to new chemotypes the method is deemed even more successful. eHiTS LASSO uses a new interacting surface point types (ISPT) molecular descriptor that is generated from the 3D structure of the ligand, but unlike most 3D descriptors it is conformation independent. Combined with a neural network machine learning technique, LASSO screens molecular databases at an ultra fast speed of 1 million structures in under 1 min on a standard PC. The results obtained from eHiTS LASSO trained on relatively small training sets of just 2, 4 or 8 actives are presented using the diverse directory of useful decoys (DUD) dataset. It is shown that over a wide range of receptor families, eHiTS LASSO is consistently able to enrich screened databases and provides scaffold hopping ability.

  17. INFLUENCE OF NATURAL AND SYNTHETIC ORGANIC LIGANDS ON THE STABILITY AND MOBILITY OF REDUCED TC(IV)

    Energy Technology Data Exchange (ETDEWEB)

    Nathalie A. Wall; Baohua Gu

    2012-12-20

    The primary objectives were (1) to quantify the interactions of organic ligands with Tc(IV) through the generation of thermodynamic (complexation) and kinetic parameters needed to assess and predict the mobility of reduced Tc(IV) at DOE contaminated sites; and (2) to determine the impact of organic ligands on the mobility and fate of reduced Tc(IV) under field geochemical conditions.

  18. Kinetic analysis of palladium(II) adsorption process on condensed-tannin gel based on redox reaction models.

    Science.gov (United States)

    Kim, Yeon-Ho; Ogata, Takeshi; Nakano, Yoshio

    2007-07-01

    We have developed a novel recovery system of palladium (Pd) from wastes such as spent catalysts or scraps, using tannin gel particles synthesized from condensed-tannin molecules. The Pd(II) ionic species are reduced to metallic Pd(0) on the network of the tannin gel: a two-electron transfer from the tannin gel to Pd(II). The kinetic study of the electron transfer was performed with a multiple reaction model containing an intermediate step (formation of a ligand-substituted Pd(II)-tannin inner sphere complex), resulting in a better fit with the experimental results than with the single reaction model (outer sphere redox reaction), which means that the inner sphere redox mechanism is an appropriate reaction model for the Pd(II) adsorption process. Because the intermediate is included in the adsorption amount, the adsorption process can be divided into two steps: fast adsorption by the ligand substitution at the initial stage and slow adsorption by the subsequent redox reaction after the ligand substitution reaches an equilibrium state, with different adsorption rates between the Pd(II) ionic species (PdCl(+)>PdCl(2)>PdCl(3)(-),PdCl(4)(2-)).

  19. AMPA receptor ligands

    DEFF Research Database (Denmark)

    Strømgaard, Kristian; Mellor, Ian

    2004-01-01

    Alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptors (AMPAR), subtype of the ionotropic glutamate receptors (IGRs), mediate fast synaptic transmission in the central nervous system (CNS), and are involved in many neurological disorders, as well as being a key player in the f......Alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptors (AMPAR), subtype of the ionotropic glutamate receptors (IGRs), mediate fast synaptic transmission in the central nervous system (CNS), and are involved in many neurological disorders, as well as being a key player...

  20. Bexarotene ligand pharmaceuticals.

    Science.gov (United States)

    Hurst, R E

    2000-12-01

    Bexarotene (LGD-1069), from Ligand, was the first retinoid X receptor (RXR)-selective, antitumor retinoid to enter clinical trials. The company launched the drug for the treatment of cutaneous T-cell lymphoma (CTCL), as Targretin capsules, in the US in January 2000 [359023]. The company filed an NDA for Targretin capsules in June 1999, and for topical gel in December 1999 [329011], [349982] specifically for once-daily oral administration for the treatment of patients with early-stage CTCL who have not tolerated other therapies, patients with refractory or persistent early stage CTCL and patients with refractory advanced stage CTCL. The FDA approved Targretin capsules at the end of December 1999 for once-daily oral treatment of all stages of CTCL in patients refractory to at least one prior systemic therapy, at an initial dose of 300 mg/m2/day. After an NDA was submitted in December 1999 for Targretin gel, the drug received Priority Review status for use as a treatment of cutaneous lesions in patients with stage IA, IB or IIA CTCL [354836]. The FDA issued an approvable letter in June 2000, and granted marketing clearance for CTCL in the same month [370687], [372768], [372769], [373279]. Ligand had received Orphan Drug designation for this indication [329011]. At the request of the FDA, Ligand agreed to carry out certain post-approval phase IV and pharmacokinetic studies [351604]. The company filed an MAA with the EMEA for Targretin Capsules to treat lymphoma in November 1999 [348944]. The NDA for Targretin gel is based on a multicenter phase III trial that was conducted in the US, Canada, Europe and Australia involving 50 patients and a multicenter phase I/II clinical program involving 67 patients. Targretin gel was evaluated for the treatment of patients with early stage CTCL (IA-IIA) who were refractory to, intolerant to, or reached a response plateau for at least 6 months on at least two prior therapies. Efficacy results exceeded the protocol-defined response

  1. Lipoteichoic acid induces unique inflammatory responses when compared to other toll-like receptor 2 ligands.

    Directory of Open Access Journals (Sweden)

    Elizabeth M Long

    Full Text Available Toll-like receptors (TLRs recognize evolutionarily-conserved molecular patterns originating from invading microbes. In this study, we were interested in determining if microbial ligands, which use distinct TLR2-containing receptor complexes, represent unique signals to the cell and can thereby stimulate unique cellular responses. Using the TLR2 ligands, R-FSL1, S-FSL1, Pam2CSK4, Pam3CSK4, and lipoteichoic acid (LTA, we demonstrate that these ligands activate NF-kappaB and MAP Kinase pathways with ligand-specific differential kinetics in murine macrophages. Most strikingly, LTA stimulation of these pathways was substantially delayed when compared with the other TLR2 ligands. These kinetics differences were associated with a delay in the LTA-induced expression of a subset of genes as compared with another TLR2 ligand, R-FSL1. However, this did not translate to overall differences in gene expression patterns four hours following stimulation with different TLR2 ligands. We extended this study to evaluate the in vivo responses to distinct TLR2 ligands using a murine model of acute inflammation, which employs intravital microscopy to monitor leukocyte recruitment into the cremaster muscle. We found that, although R-FSL1, S-FSL1, Pam2CSK4, and Pam3CSK4 were all able to stimulate robust leukocyte recruitment in vivo, LTA remained functionally inert in this in vivo model. Therefore distinct TLR2 ligands elicit unique cellular responses, as evidenced by differences in the kinetic profiles of signaling and gene expression responses in vitro, as well as the physiologically relevant differences in the in vivo responses to these ligands.

  2. Kinetic buffers.

    Science.gov (United States)

    Alibrandi, Giuseppe; Fabbrizzi, Luigi; Licchelli, Maurizio; Puglisi, Antonio

    2015-01-12

    This paper proposes a new type of molecular device that is able to act as an inverse proton sponge to slowly decrease the pH inside a reaction vessel. This makes the automatic monitoring of the concentration of pH-sensitive systems possible. The device is a composite formed of an alkyl chloride, which kinetically produces acidity, and a buffer that thermodynamically modulates the variation in pH value. Profiles of pH versus time (pH-t plots) have been generated under various experimental conditions by computer simulation, and the device has been tested by carrying out automatic spectrophotometric titrations, without using an autoburette. To underline the wide variety of possible applications, this new system has been used to realize and monitor HCl uptake by a di-copper(II) bistren complex in a single run, in a completely automatic experiment. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Effect of sorption kinetics on nickel toxicity in methanogenic granular sludge

    NARCIS (Netherlands)

    Bartacek, J.; Fermoso, F.G.; Catena, A.B.; Lens, P.N.L.

    2010-01-01

    This study investigates the effect of nickel speciation and its equilibrium kinetics on the nickel toxicity to methylotrophic methanogenic activity. Toxicity tests were done with anaerobic granular sludge in three different media containing variable concentrations of complexing ligands. A correlatio

  4. A Tunable Coarse-Grained Model for Ligand-Receptor Interaction

    Science.gov (United States)

    Guantes, Raúl; Miguez, David G.

    2013-01-01

    Cell-surface receptors are the most common target for therapeutic drugs. The design and optimization of next generation synthetic drugs require a detailed understanding of the interaction with their corresponding receptors. Mathematical approximations to study ligand-receptor systems based on reaction kinetics strongly simplify the spatial constraints of the interaction, while full atomistic ligand-receptor models do not allow for a statistical many-particle analysis, due to their high computational requirements. Here we present a generic coarse-grained model for ligand-receptor systems that accounts for the essential spatial characteristics of the interaction, while allowing statistical analysis. The model captures the main features of ligand-receptor kinetics, such as diffusion dependence of affinity and dissociation rates. Our model is used to characterize chimeric compounds, designed to take advantage of the receptor over-expression phenotype of certain diseases to selectively target unhealthy cells. Molecular dynamics simulations of chimeric ligands are used to study how selectivity can be optimized based on receptor abundance, ligand-receptor affinity and length of the linker between both ligand subunits. Overall, this coarse-grained model is a useful approximation in the study of systems with complex ligand-receptor interactions or spatial constraints. PMID:24244115

  5. Dynamics of catalytic resolution of 2-lithio-N-Boc-piperidine by ligand exchange.

    Science.gov (United States)

    Beng, Timothy K; Tyree, William S; Parker, Trent; Su, Chicheung; Williard, Paul G; Gawley, Robert E

    2012-10-10

    The dynamics of the racemization and catalytic and stoichiometric dynamic resolution of 2-lithio-N-Boc-piperidine (7) have been investigated. The kinetic order in tetramethylethylenediamine (TMEDA) for both racemization and resolution of the title compound and the kinetic orders in two resolving ligands have been determined. The catalytic dynamic resolution is second order in TMEDA and 0.5 and 0.265 order in chiral ligands 8 and 10, respectively. The X-ray crystal structure of ligand 10 shows it to be an octamer. Dynamic NMR studies of the resolution process were carried out. Some of the requirements for a successful catalytic dynamic resolution by ligand exchange have been identified.

  6. The kinetic mechanism of wild-type and mutant mouse dihydrofolate reductases.

    Science.gov (United States)

    Thillet, J; Adams, J A; Benkovic, S J

    1990-05-29

    A kinetic mechanism is presented for mouse dihydrofolate reductase that predicts all the steady-state parameters and full time-course kinetics. This mechanism was derived from association and dissociation rate constants and pre-steady-state transients by using stopped-flow fluorescence and absorbance measurements. The major features of this kinetic mechanism are as follows: (1) the two native enzyme conformers, E1 and E2, bind ligands with varying affinities although only one conformer, E1, can support catalysis in the forward direction, (2) tetrahydrofolate dissociation is the rate-limiting step under steady-state turnover at low pH, and (3) the pH-independent rate of hydride transfer from NADPH to dihydrofolate is fast (khyd = 9000 s-1) and favorable (Keq = 100). The overall mechanism is similar in form to the Escherichia coli kinetic scheme (Fierke et al., 1987), although several differences are observed: (1) substrates and products predominantly bind the same form of the E. coli enzyme, and (2) the hydride transfer rate from NADPH to either folate or dihydrofolate is considerably faster for the mouse enzyme. The role of Glu-30 (Asp-27 in E. coli) in mouse DHFR has also been examined by using site-directed mutagenesis as a potential source of these differences. While aspartic acid is strictly conserved in all bacterial DHFRs, glutamic acid is conserved in all known eucaryotes. The two major effects of substituting Asp for Glu-30 in the mouse enzyme are (1) a decreased rate of folate reduction and (2) an increased rate of hydride transfer from NADPH to dihydrofolate.(ABSTRACT TRUNCATED AT 250 WORDS)

  7. FAST: FAST Analysis of Sequences Toolbox.

    Science.gov (United States)

    Lawrence, Travis J; Kauffman, Kyle T; Amrine, Katherine C H; Carper, Dana L; Lee, Raymond S; Becich, Peter J; Canales, Claudia J; Ardell, David H

    2015-01-01

    FAST (FAST Analysis of Sequences Toolbox) provides simple, powerful open source command-line tools to filter, transform, annotate and analyze biological sequence data. Modeled after the GNU (GNU's Not Unix) Textutils such as grep, cut, and tr, FAST tools such as fasgrep, fascut, and fastr make it easy to rapidly prototype expressive bioinformatic workflows in a compact and generic command vocabulary. Compact combinatorial encoding of data workflows with FAST commands can simplify the documentation and reproducibility of bioinformatic protocols, supporting better transparency in biological data science. Interface self-consistency and conformity with conventions of GNU, Matlab, Perl, BioPerl, R, and GenBank help make FAST easy and rewarding to learn. FAST automates numerical, taxonomic, and text-based sorting, selection and transformation of sequence records and alignment sites based on content, index ranges, descriptive tags, annotated features, and in-line calculated analytics, including composition and codon usage. Automated content- and feature-based extraction of sites and support for molecular population genetic statistics make FAST useful for molecular evolutionary analysis. FAST is portable, easy to install and secure thanks to the relative maturity of its Perl and BioPerl foundations, with stable releases posted to CPAN. Development as well as a publicly accessible Cookbook and Wiki are available on the FAST GitHub repository at https://github.com/tlawrence3/FAST. The default data exchange format in FAST is Multi-FastA (specifically, a restriction of BioPerl FastA format). Sanger and Illumina 1.8+ FastQ formatted files are also supported. FAST makes it easier for non-programmer biologists to interactively investigate and control biological data at the speed of thought.

  8. FAST: FAST Analysis of Sequences Toolbox

    Directory of Open Access Journals (Sweden)

    Travis J. Lawrence

    2015-05-01

    Full Text Available FAST (FAST Analysis of Sequences Toolbox provides simple, powerful open source command-line tools to filter, transform, annotate and analyze biological sequence data. Modeled after the GNU (GNU’s Not Unix Textutils such as grep, cut, and tr, FAST tools such as fasgrep, fascut, and fastr make it easy to rapidly prototype expressive bioinformatic workflows in a compact and generic command vocabulary. Compact combinatorial encoding of data workflows with FAST commands can simplify the documentation and reproducibility of bioinformatic protocols, supporting better transparency in biological data science. Interface self-consistency and conformity with conventions of GNU, Matlab, Perl, BioPerl, R and GenBank help make FAST easy and rewarding to learn. FAST automates numerical, taxonomic, and text-based sorting, selection and transformation of sequence records and alignment sites based on content, index ranges, descriptive tags, annotated features, and in-line calculated analytics, including composition and codon usage. Automated content- and feature-based extraction of sites and support for molecular population genetic statistics makes FAST useful for molecular evolutionary analysis. FAST is portable, easy to install and secure thanks to the relative maturity of its Perl and BioPerl foundations, with stable releases posted to CPAN. Development as well as a publicly accessible Cookbook and Wiki are available on the FAST GitHub repository at https://github.com/tlawrence3/FAST. The default data exchange format in FAST is Multi-FastA (specifically, a restriction of BioPerl FastA format. Sanger and Illumina 1.8+ FastQ formatted files are also supported. FAST makes it easier for non-programmer biologists to interactively investigate and control biological data at the speed of thought.

  9. Melatonin: functions and ligands.

    Science.gov (United States)

    Singh, Mahaveer; Jadhav, Hemant R

    2014-09-01

    Melatonin is a chronobiotic substance that acts as synchronizer by stabilizing bodily rhythms. Its synthesis occurs in various locations throughout the body, including the pineal gland, skin, lymphocytes and gastrointestinal tract (GIT). Its synthesis and secretion is controlled by light and dark conditions, whereby light decreases and darkness increases its production. Thus, melatonin is also known as the 'hormone of darkness'. Melatonin and analogs that bind to the melatonin receptors are important because of their role in the management of depression, insomnia, epilepsy, Alzheimer's disease (AD), diabetes, obesity, alopecia, migraine, cancer, and immune and cardiac disorders. In this review, we discuss the mechanism of action of melatonin in these disorders, which could aid in the design of novel melatonin receptor ligands.

  10. The chemistry of separations ligand degradation by organic radical cations

    Energy Technology Data Exchange (ETDEWEB)

    Mezyk, S.P.; Horne, G.P. [California State University at Long Beach, Long Beach, CA 90840 (United States); Mincher, B.J.; Zalupski, P.R. [Idaho National Laboratory, Idaho Falls, ID 83415 (United States); Cook, A.R.; Wishart, J.F. [Chemistry Department, Brookhaven National Laboratory, New York, 11973 (United States)

    2016-07-01

    Solvent based extractions of used nuclear fuel use designer ligands in an organic phase extracting ligand complexed metal ions from an acidic aqueous phase. These extractions will be performed in highly radioactive environments, and the radiation chemistry of all these complexing agents and their diluents will play a major role in determining extraction efficiency, separation factors, and solvent-recycle longevity. Although there has been considerable effort in investigating ligand damage occurring in acidic water radiolysis conditions, only minimal fundamental kinetic and mechanistic data has been reported for the degradation of extraction ligands in the organic phase. Extraction solvent phases typically use normal alkanes such as dodecane, TPH, and kerosene as diluents. The radiolysis of such diluents produce a mixture of radical cations (R{sup .+}), carbon-centered radicals (R{sup .}), solvated electrons, and molecular products such as hydrogen. Typically, the radical species will preferentially react with the dissolved oxygen present to produce relatively inert peroxyl radicals. This isolates the alkane radical cation species, R{sup .+} as the major radiolytically-induced organic species that can react with, and degrade, extraction agents in this phase. Here we report on our recent studies of organic radical cation reactions with 2 ligands: CMPO and TODGA. Elucidating these parameters, and combining them with the known acidic aqueous phase chemistry, will allow a full, fundamental, understanding of the impact of radiation on solvent extraction based separation processes to be achieved. (authors)

  11. Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods

    Directory of Open Access Journals (Sweden)

    Xing Du

    2016-01-01

    Full Text Available Molecular recognition, which is the process of biological macromolecules interacting with each other or various small molecules with a high specificity and affinity to form a specific complex, constitutes the basis of all processes in living organisms. Proteins, an important class of biological macromolecules, realize their functions through binding to themselves or other molecules. A detailed understanding of the protein–ligand interactions is therefore central to understanding biology at the molecular level. Moreover, knowledge of the mechanisms responsible for the protein-ligand recognition and binding will also facilitate the discovery, design, and development of drugs. In the present review, first, the physicochemical mechanisms underlying protein–ligand binding, including the binding kinetics, thermodynamic concepts and relationships, and binding driving forces, are introduced and rationalized. Next, three currently existing protein-ligand binding models—the “lock-and-key”, “induced fit”, and “conformational selection”—are described and their underlying thermodynamic mechanisms are discussed. Finally, the methods available for investigating protein–ligand binding affinity, including experimental and theoretical/computational approaches, are introduced, and their advantages, disadvantages, and challenges are discussed.

  12. Protein ligand interactions. Part 5: Isoquinoline alkaloids as inhibitors of acetylcholinesterase from Electrophorus electricus.

    Science.gov (United States)

    Whiteley, C G; Daya, S

    1995-01-01

    Kinetic analysis has shown that papaverine, berberine and isoquinoline alkaloids acts as reversible competitive inhibitors of acetylcholinesterase with respect to the substrate, acetylthiocholine chloride. The inhibitor constants (Ki) vary from 3.5 microM to 88 microM. With time they act as irreversible covalent inhibitors with papaverine producing 85% inactivation after 40 min. Pseudo first-order kinetics are observed with the rate constant being proportional to the concentration of the ligand and the order of reaction being equal to one. Spectrophotometry was used to study the binding of the ligands with acetylcholinesterase and Scatchard analysis used to calculate the respective dissociation constants and the number of binding sites.

  13. Macrocyclic G-quadruplex ligands

    DEFF Research Database (Denmark)

    Nielsen, M C; Ulven, Trond

    2010-01-01

    G-quadruplex stabilizing compounds have recently received increased interest due to their potential application as anticancer therapeutics. A significant number of structurally diverse G-quadruplex ligands have been developed. Some of the most potent and selective ligands currently known are macr...

  14. Ligand fishing with functionalized magnetic nanoparticles coupled with mass spectrometry for herbal medicine analysis: Ligand fishing for herbal medicine analysis

    OpenAIRE

    Qing, Lin-Sen; XUE, YING; Deng, Wen-Long; Liao, Xun; XU, XUE-MIN; Li, Bo-Gang; Liu, Yi-Ming

    2010-01-01

    The chemical composition of herbal medicines is very complex, and their therapeutic effects are determined by multi-components with sophisticated synergistic and/or suppressive actions. Therefore, quality control of herbal medicines has been a formidable challenge. In this work, we describe a fast analytical method that can be used for quality assessment of herbal medicines. The method is based on ligand fishing using human-serum-albumin-functionalized magnetic nanoparticles (HSA-MNPs) and ma...

  15. Cloud computing approaches for prediction of ligand binding poses and pathways.

    Science.gov (United States)

    Lawrenz, Morgan; Shukla, Diwakar; Pande, Vijay S

    2015-01-22

    We describe an innovative protocol for ab initio prediction of ligand crystallographic binding poses and highly effective analysis of large datasets generated for protein-ligand dynamics. We include a procedure for setup and performance of distributed molecular dynamics simulations on cloud computing architectures, a model for efficient analysis of simulation data, and a metric for evaluation of model convergence. We give accurate binding pose predictions for five ligands ranging in affinity from 7 nM to > 200 μM for the immunophilin protein FKBP12, for expedited results in cases where experimental structures are difficult to produce. Our approach goes beyond single, low energy ligand poses to give quantitative kinetic information that can inform protein engineering and ligand design.

  16. Surface-Bound Ligands Modulate Chemoselectivity and Activity of a Bimetallic Nanoparticle Catalyst

    KAUST Repository

    Vu, Khanh B.

    2015-04-03

    "Naked" metal nanoparticles (NPs) are thermodynamically and kinetically unstable in solution. Ligands, surfactants, or polymers, which adsorb at a particle\\'s surface, can be used to stabilize NPs; however, such a mode of stabilization is undesirable for catalytic applications because the adsorbates block the surface active sites. The catalytic activity and the stability of NPs are usually inversely correlated. Here, we describe an example of a bimetallic (PtFe) NP catalyst stabilized by carboxylate surface ligands that bind preferentially to one of the metals (Fe). NPs stabilized by fluorous ligands were found to be remarkably competent in catalyzing the hydrogenation of cinnamaldehyde; NPs stabilized by hydrocarbon ligands were significantly less active. The chain length of the fluorous ligands played a key role in determining the chemoselectivity of the FePt NP catalysts. (Chemical Presented). © 2015 American Chemical Society.

  17. QE+QSS for Derivation of Kinetic Equations and Stiffness Removing

    CERN Document Server

    Gorban, A N

    2010-01-01

    We present the general formalism of the Quasiequilibrium approximation (QE) with the proof of the persistence of entropy production in the QE approximation. We demonstrate, how to apply this formalism to chemical kinetics and describe the difference between QE and Quasi--Steady--State (QSS) approximations. The celebrated QSS "Michaelis--Menten" kinetics is, as a matter of fact, the "Briggs-Haldane" kinetics. Michaelis and Menten used the QE assumption that all intermediate complexes are in fast equilibrium with free substrates and enzyme. Similar approach was developed by Stuekelberg (1952) for the Boltzmann kinetics. Following them, we combine the QE (fast equilibria) and the QSS (small amounts) approaches and study the general kinetics with fast intermediates present in small amount. We prove the representation of the rate of an elementary reaction as a product of the Boltzmann factor (purely thermodynamic) and the kinetic factor, and found the basic relations between kinetic factors. In the practice of mod...

  18. Fast pyrolysis of biomass at high temperatures

    DEFF Research Database (Denmark)

    Trubetskaya, Anna

    This Ph.D. thesis describes experimental and modeling investigations of fast high temperature pyrolysis of biomass. Suspension firing of biomass is widely used for power generation and has been considered as an important step in reduction of greenhouse gas emissions by using less fossil fuels. Fast...... pyrolysis at high temperatures plays a significant role in the overall combustion process since the biomass type, the reaction kinetics and heat transfer rates during pyrolysis influence the volatile gas release. The solid residue yield and its properties in suspension firing, including particle size...... and shape, composition, reactivity and burnout depend significantly on the operating conditions of the fast pyrolysis. Biomass fast pyrolysis experiments were performed in a laboratory-scale wire mesh reactor and bench scale atmospheric pressure drop tube / entrained flow reactors with the aim...

  19. DINC: a new AutoDock-based protocol for docking large ligands.

    Science.gov (United States)

    Dhanik, Ankur; McMurray, John S; Kavraki, Lydia E

    2013-01-01

    Using the popular program AutoDock, computer-aided docking of small ligands with 6 or fewer rotatable bonds, is reasonably fast and accurate. However, docking large ligands using AutoDock's recommended standard docking protocol is less accurate and computationally slow. In our earlier work, we presented a novel AutoDock-based incremental protocol (DINC) that addresses the limitations of AutoDock's standard protocol by enabling improved docking of large ligands. Instead of docking a large ligand to a target protein in one single step as done in the standard protocol, our protocol docks the large ligand in increments. In this paper, we present three detailed examples of docking using DINC and compare the docking results with those obtained using AutoDock's standard protocol. We summarize the docking results from an extended docking study that was done on 73 protein-ligand complexes comprised of large ligands. We demonstrate not only that DINC is up to 2 orders of magnitude faster than AutoDock's standard protocol, but that it also achieves the speed-up without sacrificing docking accuracy. We also show that positional restraints can be applied to the large ligand using DINC: this is useful when computing a docked conformation of the ligand. Finally, we introduce a webserver for docking large ligands using DINC. Docking large ligands using DINC is significantly faster than AutoDock's standard protocol without any loss of accuracy. Therefore, DINC could be used as an alternative protocol for docking large ligands. DINC has been implemented as a webserver and is available at http://dinc.kavrakilab.org. Applications such as therapeutic drug design, rational vaccine design, and others involving large ligands could benefit from DINC and its webserver implementation.

  20. Simulation of the kinetics of oxygen complexes in crystalline silicon

    Science.gov (United States)

    Joo Lee, Young; von Boehm, J.; Nieminen, R. M.

    2002-10-01

    The formation kinetics of thermal double donors (TDD's) is studied by a general kinetic model with parameters based on accurate ab initio total-energy calculations. The kinetic model includes all relevant association, dissociation, and restructuring processes. The simulated kinetics agrees qualitatively and in most cases quantitatively with the experimentally found consecutive kinetics of TDD's. It also supports our earlier assignments of the ring-type oxygen chains to TDD's [Pesola et al., Phys. Rev. Lett. 84, 5343 (2000)]. We demonstrate with the kinetic model that the most common assumption that only the O2 dimer acts as a fast diffusing species would lead to an unrealistic steady increase of the concentration of O3. The neglect of restructuring processes leads to an anomalous increase of oxygen dimers and negligible concentrations of TDD's. The capture of interstitial oxygens by diffusing oxygen chains and the escaping of interstitial oxygens from the chains fully dominate the formation kinetics.

  1. Protein-Ligand Docking Based on Beta-Shape

    Science.gov (United States)

    Kim, Chong-Min; Won, Chung-In; Kim, Jae-Kwan; Ryu, Joonghyun; Bhak, Jong; Kim, Deok-Soo

    Protein-ligand docking is to predict the location and orientation of a ligand with respect to a protein within its binding site, and has been known to be essential for the development of new drugs. The protein-ligand docking problem is usually formulated as an energy minimization problem to identify the docked conformation of the ligand. A ligand usually docks around a depressed region, called a pocket, on the surface of a protein. Presented in this paper is a docking method, called BetaDock, based on the newly developed geometric construct called the β-shape and the β-complex. To cope with the computational intractability, the global minimum of the potential energy function is searched using the genetic algorithm. The proposed algorithm first locates initial chromosomes at some locations within the pocket recognized according to the local shape of the β-shape. Then, the algorithm proceeds generations by taking advantage of powerful properties of the β-shape to achieve an extremely fast and good solution. We claim that the proposed method is much faster than other popular docking softwares including AutoDock.

  2. How hydrophobic drying forces impact the kinetics of molecular recognition.

    Science.gov (United States)

    Mondal, Jagannath; Morrone, Joseph A; Berne, B J

    2013-08-13

    A model of protein-ligand binding kinetics, in which slow solvent dynamics results from hydrophobic drying transitions, is investigated. Molecular dynamics simulations show that solvent in the receptor pocket can fluctuate between wet and dry states with lifetimes in each state that are long enough for the extraction of a separable potential of mean force and wet-to-dry transitions. We present a diffusive surface hopping model that is represented by a 2D Markovian master equation. One dimension is the standard reaction coordinate, the ligand-pocket separation, and the other is the solvent state in the region between ligand and binding pocket which specifies whether it is wet or dry. In our model, the ligand diffuses on a dynamic free-energy surface which undergoes kinetic transitions between the wet and dry states. The model yields good agreement with results from explicit solvent molecular dynamics simulation and an improved description of the kinetics of hydrophobic assembly. Furthermore, it is consistent with a "non-Markovian Brownian theory" for the ligand-pocket separation coordinate alone.

  3. Construction of the simplest model to explain complex receptor activation kinetics

    DEFF Research Database (Denmark)

    Bywater, RP; Sorensen, A; Røgen, Peter;

    2002-01-01

    We study the mathematical solutions to the kinetic equations arising from various simple ligand-reactor models. Focusing on the prediction of the various models for the activity vs. concentration curve, we find that solutions to the kinetic equations arising from the so-called dimer model exibit...

  4. Glutamate receptor ligands

    DEFF Research Database (Denmark)

    Guldbrandt, Mette; Johansen, Tommy N; Frydenvang, Karla Andrea;

    2002-01-01

    Homologation and substitution on the carbon backbone of (S)-glutamic acid [(S)-Glu, 1], as well as absolute stereochemistry, are structural parameters of key importance for the pharmacological profile of (S)-Glu receptor ligands. We describe a series of methyl-substituted 2-aminoadipic acid (AA......-ray crystallographic analyses, chemical correlation, and CD spectral analyses. The effects of the individual stereoisomers at ionotropic and metabotropic (S)-Glu receptors (iGluRs and mGluRs) were characterized. Compounds with S-configuration at the alpha-carbon generally showed mGluR2 agonist activity of similar...... limited effect on pharmacology. Structure-activity relationships at iGluRs in the rat cortical wedge preparation showed a complex pattern, some compounds being NMDA receptor agonists [e.g., EC(50) =110 microM for (2S,5RS)-5-methyl-AA (6a,b)] and some compounds showing NMDA receptor antagonist effects [e...

  5. Introduction to the neutron kinetics of nuclear power reactors

    CERN Document Server

    Tyror, J G; Grant, P J

    2013-01-01

    An Introduction to the Neutron Kinetics of Nuclear Power Reactors introduces the reader to the neutron kinetics of nuclear power reactors. Topics covered include the neutron physics of reactor kinetics, feedback effects, water-moderated reactors, fast reactors, and methods of plant control. The reactor transients following faults are also discussed, along with the use of computers in the study of power reactor kinetics. This book is comprised of eight chapters and begins with an overview of the reactor physics characteristics of a nuclear power reactor and their influence on system design and

  6. Synthesis and Base Hydrolysis of a Cobalt(III) Complex Coordinated by a Thioether Ligand

    Science.gov (United States)

    Roecker, Lee

    2008-01-01

    A two-week laboratory experiment for students in advanced inorganic chemistry is described. Students prepare and characterize a cobalt(III) complex coordinated by a thioether ligand during the first week of the experiment and then study the kinetics of Co-S bond cleavage in basic solution during the second week. The synthetic portion of the…

  7. Cooperation between lateral ligand mobility and accessibility for receptor recognition in selectin-induced cell rolling

    NARCIS (Netherlands)

    Bakowsky, U; Schumacher, G; Gege, C; Schmidt, RR; Rothe, U; Bendas, G

    2002-01-01

    Selectin-induced leukocyte rolling along the endothelial surface is an essential step in the immune response. Several in vitro studies showed that this cell rolling is a highly regulated adhesion phenomenon, controlled by the kinetics and forces of selectin-ligand interactions. In the flow chamber s

  8. Synthesis and Base Hydrolysis of a Cobalt(III) Complex Coordinated by a Thioether Ligand

    Science.gov (United States)

    Roecker, Lee

    2008-01-01

    A two-week laboratory experiment for students in advanced inorganic chemistry is described. Students prepare and characterize a cobalt(III) complex coordinated by a thioether ligand during the first week of the experiment and then study the kinetics of Co-S bond cleavage in basic solution during the second week. The synthetic portion of the…

  9. Predicting Electrophoretic Mobility of Protein-Ligand Complexes for Ligands from DNA-Encoded Libraries of Small Molecules.

    Science.gov (United States)

    Bao, Jiayin; Krylova, Svetlana M; Cherney, Leonid T; Hale, Robert L; Belyanskaya, Svetlana L; Chiu, Cynthia H; Shaginian, Alex; Arico-Muendel, Christopher C; Krylov, Sergey N

    2016-05-17

    Selection of target-binding ligands from DNA-encoded libraries of small molecules (DELSMs) is a rapidly developing approach in drug-lead discovery. Methods of kinetic capillary electrophoresis (KCE) may facilitate highly efficient homogeneous selection of ligands from DELSMs. However, KCE methods require accurate prediction of electrophoretic mobilities of protein-ligand complexes. Such prediction, in turn, requires a theory that would be applicable to DNA tags of different structures used in different DELSMs. Here we present such a theory. It utilizes a model of a globular protein connected, through a single point (small molecule), to a linear DNA tag containing a combination of alternating double-stranded and single-stranded DNA (dsDNA and ssDNA) regions of varying lengths. The theory links the unknown electrophoretic mobility of protein-DNA complex with experimentally determined electrophoretic mobilities of the protein and DNA. Mobility prediction was initially tested by using a protein interacting with 18 ligands of various combinations of dsDNA and ssDNA regions, which mimicked different DELSMs. For all studied ligands, deviation of the predicted mobility from the experimentally determined value was within 11%. Finally, the prediction was tested for two proteins and two ligands with a DNA tag identical to those of DELSM manufactured by GlaxoSmithKline. Deviation between the predicted and experimentally determined mobilities did not exceed 5%. These results confirm the accuracy and robustness of our model, which makes KCE methods one step closer to their practical use in selection of drug leads, and diagnostic probes from DELSMs.

  10. Highly selective ligand binding by Methylophilus methylotrophus cytochrome c''.

    Science.gov (United States)

    Quintas, Pedro O; Catarino, Teresa; Todorovic, Smilja; Turner, David L

    2011-06-28

    Cytochrome c'' (cyt c'') from Methylophilus methylotrophus is unusual insofar as the heme has two axial histidine ligands in the oxidized form but one is detached when the protein is reduced. Despite cyt c'' having an axial site available for binding small ligands, we show here that only NO binds readily to the ferrous cyt c''. Binding of CO, as well as CN(-), on the other hand requires considerable structural reorganization, or reduction of the disulfide bridge close to the heme. Standard free energies for the binding of NO and CO reveal high selectivity of the ferrous cyt c'' for NO, indicating its putative physiological role. In this work, we characterize in detail the kinetics of NO binding and the structural features of the Fe(2+)-NO adduct by stopped-flow and resonance Raman spectroscopy, respectively.

  11. Improved safety fast reactor with “reservoir” for delayed neutrons generating

    Science.gov (United States)

    Kulikov, G. G.; Apse, V. A.; Shmelev, A. N.; Kulikov, E. G.

    2017-01-01

    The paper considers the possibility to improve safety of fast reactors by using weak neutron absorber with large atomic weight as a material for external neutron reflector and for internal cavity in the reactor core (the neutron “reservoir”) where generation of some additional “delayed” neutron takes place. The effects produced by the external neutron reflector and the internal neutron “reservoir” on kinetic behavior of fast reactors are inter-compared. It is demonstrated that neutron kinetics of fast reactors with such external and internal zones becomes the quieter as compared with neutron kinetics of thermal reactors.

  12. Non-Isothermal Kinetics.

    Science.gov (United States)

    Brown, M. E.; Phillpotts, C. A. R.

    1978-01-01

    Discusses the principle of nonisothermal kinetics and some of the factors involved in such reactions, especially when considering the reliability of the kinetic parameters, compared to those of isothermal conditions. (GA)

  13. Monopicolinate cross-bridged cyclam combining very fast complexation with very high stability and inertness of its copper(II) complex.

    Science.gov (United States)

    Lima, Luís M P; Halime, Zakaria; Marion, Ronan; Camus, Nathalie; Delgado, Rita; Platas-Iglesias, Carlos; Tripier, Raphaël

    2014-05-19

    The synthesis of a new cross-bridged 1,4,8,11-tetraazacyclotetradecane (cb-cyclam) derivative bearing a picolinate arm (Hcb-te1pa) was achieved by taking advantage of the proton sponge properties of the starting constrained macrocycle. The structure of the reinforced ligand as well as its acid-base properties and coordination properties with Cu(2+) and Zn(2+) was investigated. The X-ray structure of the free ligand showed a completely preorganized conformation that lead to very fast copper(II) complexation under mild conditions (instantaneous at pH 7.4) or even in acidic pH (3 min at pH 5) at room temperature and that demonstrated high thermodynamic stability, which was measured by potentiometry (at 25 °C and 0.10 M in KNO3). The results also revealed that the complex exists as a monopositive copper(II) species in the intermediate pH range. A comparative study highlighted the important selectivity for Cu(2+) over Zn(2+). The copper(II) complex was synthesized and investigated in solution using different spectroscopic techniques and DFT calculations. The kinetic inertness of the copper(II) complex in acidic medium was evaluated by spectrophotometry, revealing the very slow dissociation of the complex. The half-life of 96 days, in 5 M HClO4, and 465 min, in 5 M HCl at 25 °C, show the high kinetic stability of the copper(II) chelate compared to that of the corresponding complexes of other macrocyclic ligands. Additionally, cyclic voltammetry experiments underlined the perfect electrochemical inertness of the complex as well as the quasi-reversible Cu(2+)/Cu(+) redox system. The coordination geometry of the copper center in the complex was established in aqueous solution from UV-vis and EPR spectroscopies.

  14. HCUP Fast Stats

    Data.gov (United States)

    U.S. Department of Health & Human Services — HCUP Fast Stats provides easy access to the latest HCUP-based statistics for health information topics. HCUP Fast Stats uses visual statistical displays in...

  15. Fast food (image)

    Science.gov (United States)

    Fast foods are quick, reasonably priced, and readily available alternatives to home cooking. While convenient and economical for a busy lifestyle, fast foods are typically high in calories, fat, saturated ...

  16. Fast food tips (image)

    Science.gov (United States)

    ... challenge to eat healthy when going to a fast food place. In general, avoiding items that are deep ... challenge to eat healthy when going to a fast food place. In general, avoiding items that are deep ...

  17. Ligand-Gated Ion Channels: Permeation and Activation1

    Science.gov (United States)

    Lynch, Joseph W.; Barry, Peter H.

    Ligand-gated ion channels (LGICs) are fast-responding channels in which the receptor, which binds the activating molecule (the ligand), and the ion channel are part of the same nanomolecular protein complex. This chapter will describe the properties and functions of the nicotinic acetylcholine LGIC superfamily, which play a critical role in the fast chemical transmission of electrical signals between nerve cells at synapses and between nerve and muscle cells at endplates. All the processing functions of the brain and the resulting behavioral output depend on chemical transmission across such neuronal interconnections. To describe the properties of the channels of this LGIC superfamily,we will mainly use two examples of this family of channels: the excitatory nicotinic acetylcholine receptor (nAChR) and the inhibitory glycine receptor (GlyR) channels. In the chemical transmission of electrical signals, the arrival of an electrical signal at the synaptic terminal of a nerve causes the release of a chemical signal—a neurotransmitter molecule (the ligand, also referred to as the agonist). The neurotransmitter rapidly diffuses across the very narrow 20-40 nm synaptic gap between the cells and binds to the LGIC receptors in the membrane of the target (postsynaptic) cell and generates a new electrical signal in that cell (e.g., Kandel et al., 2000). How this chemical signal is converted into an electrical one depends on the fundamental properties of LGICs and the ionic composition of the postsynaptic cell and its external solution.

  18. Bicarbonate kinetics in Indian males

    Indian Academy of Sciences (India)

    T Raj; R Kuriyan; A V Kurpad

    2006-06-01

    Measurement of rates of in vivo substrate oxidation such as that of glucose, fatty acids and amino acids, are based on tracer (14C or 13C) data, and often depend on the isotopic content of expired CO2. The recovery of tracer-labelled CO2 generated from the oxidation of 13C labelled substrates may not be 100% over short term. This can lead to underestimation of oxidation rate of substrates, and consequently a correction for the incomplete recovery of tracer has to be applied by the determination of the recovery of 13CO2 in the breath during tracer bicarbonate infusions. We have studied the recovery of tracer-labelled bicarbonate using a bolus administration model, and further characterized kinetics of bicarbonate using a three-compartment model, to assess which compartmental fluxes changed during the change from a fasted state to fed state. Recovery of bicarbonate was lower at 69% and 67% (fasted and fed state) than the value of 71% and 74% found during earlier longer term of continuous infusions. During feeding, there was a 20-fold increase in the flux of bicarbonate between the central compartment and the compartment that was equivalent to the viscera. This study shows that the difference between the fasted and fed state recovery of tracer bicarbonate similar to that obtained with continuous infusions, and that bicarbonate fluxes show large changes between different compartments in the body depending on metabolic state.

  19. Effect of Global ATGL Knockout on Murine Fasting Glucose Kinetics

    NARCIS (Netherlands)

    Coelho, M.; Nunes, P.; Mendes, V.M.; Manadas, B.; Heerschap, A.; Jones, J.G.

    2015-01-01

    Mice deficient in adipose triglyceride lipase (ATGL(-/-)) present elevated ectopic lipid levels but are paradoxically glucose-tolerant. Measurement of endogenous glucose production (EGP) and Cori cycle activity provide insights into the maintenance of glycemic control in these animals. These

  20. Use of Competition Kinetics with Fast Reactions of Grignard Reagents

    DEFF Research Database (Denmark)

    Holm, Torkil

    2000-01-01

    may account for almost all the product even when present as only 1 part in 100 parts of the competing agent. In this way allylmagnesium bromide is estimated to react with acetone, benzophenone, benzaldehyde, and diethylacetaldehyde ca. 1.5 x 105 times faster than does butylmagnesium bromide. The rates...... or effects of polar substituents with isotopically or otherwise substituted benzophenones. A recently reported a-deuterium secondary KIE for the reaction of benzaldehyde with allylmagnesium bromide was observed at -78 °C , but was absent at room temperature. It is suggested that the reaction of benzophenone...... and benzaldehyde with allylmagnesium bromide has a radical-concerted mechanism since no radical type products are produced and since no colour from an intermediate ketyl is observed even at -78 °C....

  1. Kinetic Studies of Reactions in Solution Using Fast Mass Spectrometry

    Science.gov (United States)

    2013-08-13

    REPORT Directorate of Chemistry and Materials Research NUMBER(S) AFOSR/RSA, 875 Randolph St., Suite 325, Rm 3112, Arlington, VA 222C 3 12...Mass Spectrometry to detect transient intermediates and decomposition products of catalyzed organometallic reactions Identifying intermediates is...in organometallic catalysis. HV N2 45o 5 mm 2 mm Reagent A Reagent B MS Secondary microdroplets Surface ~2-5 ms reaction time

  2. Effect of Global ATGL Knockout on Murine Fasting Glucose Kinetics

    NARCIS (Netherlands)

    Coelho, M.; Nunes, P.; Mendes, V.M.; Manadas, B.; Heerschap, A.; Jones, J.G.

    2015-01-01

    Mice deficient in adipose triglyceride lipase (ATGL(-/-)) present elevated ectopic lipid levels but are paradoxically glucose-tolerant. Measurement of endogenous glucose production (EGP) and Cori cycle activity provide insights into the maintenance of glycemic control in these animals. These paramet

  3. Methods of nonlinear kinetics

    OpenAIRE

    Gorban, A. N.; Karlin, I.V.

    2003-01-01

    Nonlinear kinetic equations are reviewed for a wide audience of specialists and postgraduate students in physics, mathematical physics, material science, chemical engineering and interdisciplinary research. Contents: The Boltzmann equation, Phenomenology and Quasi-chemical representation of the Boltzmann equation, Kinetic models, Discrete velocity models, Direct simulation, Lattice Gas and Lattice Boltzmann models, Minimal Boltzmann models for flows at low Knudsen number, Other kinetic equati...

  4. Is fast food addictive?

    Science.gov (United States)

    Garber, Andrea K; Lustig, Robert H

    2011-09-01

    Studies of food addiction have focused on highly palatable foods. While fast food falls squarely into that category, it has several other attributes that may increase its salience. This review examines whether the nutrients present in fast food, the characteristics of fast food consumers or the presentation and packaging of fast food may encourage substance dependence, as defined by the American Psychiatric Association. The majority of fast food meals are accompanied by a soda, which increases the sugar content 10-fold. Sugar addiction, including tolerance and withdrawal, has been demonstrated in rodents but not humans. Caffeine is a "model" substance of dependence; coffee drinks are driving the recent increase in fast food sales. Limited evidence suggests that the high fat and salt content of fast food may increase addictive potential. Fast food restaurants cluster in poorer neighborhoods and obese adults eat more fast food than those who are normal weight. Obesity is characterized by resistance to insulin, leptin and other hormonal signals that would normally control appetite and limit reward. Neuroimaging studies in obese subjects provide evidence of altered reward and tolerance. Once obese, many individuals meet criteria for psychological dependence. Stress and dieting may sensitize an individual to reward. Finally, fast food advertisements, restaurants and menus all provide environmental cues that may trigger addictive overeating. While the concept of fast food addiction remains to be proven, these findings support the role of fast food as a potentially addictive substance that is most likely to create dependence in vulnerable populations.

  5. Kinetic partitioning mechanism of HDV ribozyme folding

    Science.gov (United States)

    Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing

    2014-01-01

    RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.

  6. Kinetic partitioning mechanism of HDV ribozyme folding

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing, E-mail: wbzhang@whu.edu.cn [Department of Physics, Wuhan University, Wuhan, Hubei 430072 (China)

    2014-01-14

    RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.

  7. Ligand fishing with functionalized magnetic nanoparticles coupled with mass spectrometry for herbal medicine analysis: ligand fishing for herbal medicine analysis.

    Science.gov (United States)

    Qing, Lin-Sen; Xue, Ying; Deng, Wen-Long; Liao, Xun; Xu, Xue-Min; Li, Bo-Gang; Liu, Yi-Ming

    2011-01-01

    The chemical composition of herbal medicines is very complex, and their therapeutic effects are determined by multi-components with sophisticated synergistic and/or suppressive actions. Therefore, quality control of herbal medicines has been a formidable challenge. In this work, we describe a fast analytical method that can be used for quality assessment of herbal medicines. The method is based on ligand fishing using human-serum-albumin-functionalized magnetic nanoparticles (HSA-MNPs) and mass spectrometry. To demonstrate the applicability of the proposed method, eight samples of Dioscorea panthaica were analyzed. The sampled plants were of both wild and cultivated origins. They grew at different geographical locations and were harvested at different times. The ligands bound to HSA-MNPs were isolated from the plant extracts and detected by using direct infusion electrospray ionization mass spectrometry (DI-ESI-MS). Chemical identity has been confirmed for five of the ligands isolated. From more than 15 peaks in the ESI-MS spectrum, 11 common peaks were selected for calculating the correlation coefficient and cosine ratio. The values of correlation coefficient and cosine ratio were >0.9824 and >0.9988, respectively, for all the samples tested. The results indicated a high level of similarity among the eight D. panthaica samples. Compared with chromatographic fingerprint analysis, the proposed HSA-MNP-based DI-ESI-MS/MS approach was not only fast and easy to carry out but also biological-activity-oriented, promising a more effective data interpretation and thus reliable assessment conclusions.

  8. Visualization of Metal-to-Ligand and Ligand-to-Ligand Charge Transfer in Metal-Ligand Complexes

    Institute of Scientific and Technical Information of China (English)

    Yong Ding; Jian-xiu Guo; Xiang-si Wang; Sha-sha Liu; Feng-cai Ma

    2009-01-01

    Three methods including the atomic resolved density of state, charge difference density, and the transition density matrix are used to visualize metal to ligand charge transfer (MLCT) in ruthenium(Ⅱ) ammine complex. The atomic resolved density of state shows that there is density of Ru on the HOMOs. All the density is localized on the ammine, which reveals that the excited electrons in the Ru complex are delocalized over the ammine ligand. The charge difference density shows that all the holes are localized on the Ru and the electrons on the ammine. The localization explains the MLCT on excitation. The transition density matrix shows that there is electron-hole coherence between Ru and ammine. These methods are also used to examine the MLCT in Os(bpy)(p0p)Cl ("Osp0p"; bpy=2,2'-bipyridyl; p0p=4,4'-bipyridyl) and the ligand-to-ligand charge transfer (LLCT) in Alq3. The calculated results show that these methods are powerful to examine MLCT and LLCT in the metal-ligand system.

  9. Optimizing Ligand Efficiency of Selective Androgen Receptor Modulators (SARMs).

    Science.gov (United States)

    Handlon, Anthony L; Schaller, Lee T; Leesnitzer, Lisa M; Merrihew, Raymond V; Poole, Chuck; Ulrich, John C; Wilson, Joseph W; Cadilla, Rodolfo; Turnbull, Philip

    2016-01-14

    A series of selective androgen receptor modulators (SARMs) containing the 1-(trifluoromethyl)benzyl alcohol core have been optimized for androgen receptor (AR) potency and drug-like properties. We have taken advantage of the lipophilic ligand efficiency (LLE) parameter as a guide to interpret the effect of structural changes on AR activity. Over the course of optimization efforts the LLE increased over 3 log units leading to a SARM 43 with nanomolar potency, good aqueous kinetic solubility (>700 μM), and high oral bioavailability in rats (83%).

  10. Investigations on the conditional kinetic and thermodynamic stability of aquatic humic substance-metal complexes by means of EDTA exchange, ultrafiltration and atomic spectrometry.

    Science.gov (United States)

    Van den Bergh, J; Jakubowski, B; Burba, P

    2001-09-13

    The conditional metal availability and the kinetic stability of humic substance-metal species in humic-rich waters (e.g. bog water) was characterized by means of EDTA exchange. For this purpose a combined procedure consisting of time-controlled ligand exchange by EDTA, species differentiation by a fast single-stage tangential-flow ultrafiltration (TF-UF) technique (cut-off 1 kDa) and sensitive atomic spectrometry methods (e.g. AAS, ICP-OES, TXRF) was developed. The kinetics and the yield of the EDTA exchange served as operational parameters for assessing the kinetic stability and EDTA availability of HS-metal species, respectively. Considerable fractions of natural HS-metal species studied were shown to be EDTA-inert (e.g. 31% of the total Fe, 44% of the total Al) even after long reaction times (48 h), in contrast to artificial ones formed in solutions of isolated HS. Moreover, the conditional thermodynamic stability of HS-metal complexes formed by successive loading of an aquatic reference HS (HO14) with a number of heavy metal ions (e.g. Cr(III), Cu(II), Fe(III), Mn(II), Zn(II)) was also evaluated discriminating the free metal concentrations by means of TF-UF. In addition, from the loading isotherms obtained conditional complexation capacities could be derived for the studied HS exhibiting the order Fe(III)>Cu(II)>Cr(III)>Co(II)>Mn(II).

  11. Ligand binding to heme proteins. VI. Interconversion of taxonomic substates in carbonmonoxymyoglobin.

    Science.gov (United States)

    Johnson, J B; Lamb, D C; Frauenfelder, H; Müller, J D; McMahon, B; Nienhaus, G U; Young, R D

    1996-09-01

    The kinetic properties of the three taxonomic A substates of sperm whale carbonmonoxy myoglobin in 75% glycerol/buffer are studied by flash photolysis with monitoring in the infrared stretch bands of bound CO at nu(A0) approximately 1967 cm-1, nu(A1) approximately 1947 cm-1, and nu(A3) approximately 1929 cm-1 between 60 and 300 K. Below 160 K the photodissociated CO rebinds from the heme pocket, no interconversion among the A substates is observed, and rebinding in each A substate is nonexponential in time and described by a different temperature-independent distribution of enthalpy barriers with a different preexponential. Measurements in the electronic bands, e.g., the Soret, contain contributions of all three A substates and can, therefore, be only approximately modeled with a single enthalpy distribution and a single preexponential. The bond formation step at the heme is fastest for the A0 substate, intermediate for the A1 substate, and slowest for A3. Rebinding between 200 and 300 K displays several processes, including geminate rebinding, rebinding after ligand escape to the solvent, and interconversion among the A substates. Different kinetics are measured in each of the A bands for times shorter than the characteristic time of fluctuations among the A substates. At longer times, fluctuational averaging yields the same kinetics in all three A substates. The interconversion rates between A1 and A3 are determined from the time when the scaled kinetic traces of the two substates merge. Fluctuations between A1 and A3 are much faster than those between A0 and either A1 or A3, so A1 and A3 appear as one kinetic species in the exchange with A0. The maximum-entropy method is used to extract the distribution of rate coefficients for the interconversion process A0 A1 + A3 from the flash photolysis data. The temperature dependencies of the A substate interconversion processes are fitted with a non-Arrhenius expression similar to that used to describe relaxation

  12. Ramadan, fasting and pregnancy

    DEFF Research Database (Denmark)

    Ahmed, Urfan Zahoor; Lykke, Jacob Alexander

    2014-01-01

    In Islam, the month of Ramadan is a period of fasting lasting 29 or 30 days. Epidemiological studies among Muslims in Denmark have not been conducted, but studies show, that fasting among pregnant Muslim women is common. Fasting does not increase the risk of growth restriction or preterm delivery......, but there are reports of decreased foetal movements. Furthermore, the fasting may have long-term health consequences for the offspring, especially when they reach their middle age. According to Islam and the interpretation, pregnant and breast-feeding women are allowed to postpone the fasting of the month of Ramadan...

  13. Folding Kinetics of Riboswitch Transcriptional Terminators

    Science.gov (United States)

    Sauerwine, Benjamin; Widom, Michael

    2009-03-01

    Riboswitches control the expression of genes in bacteria by halting gene transcription or allowing it to proceed based on the presence of ligands in solution. A key feature of every riboswitch is a transcriptional terminator in which the messenger RNA folds into a secondary structure with the stem-loop structure of a hairpin. Through kinetic Monte Carlo simulation we show that terminators have been naturally selected to fold with high reliability on the time-scale of gene transcription. This efficient folding behavior is preserved among two classes of riboswitch and among two species of bacteria.

  14. Integrative Physiology of Fasting.

    Science.gov (United States)

    Secor, Stephen M; Carey, Hannah V

    2016-03-15

    Extended bouts of fasting are ingrained in the ecology of many organisms, characterizing aspects of reproduction, development, hibernation, estivation, migration, and infrequent feeding habits. The challenge of long fasting episodes is the need to maintain physiological homeostasis while relying solely on endogenous resources. To meet that challenge, animals utilize an integrated repertoire of behavioral, physiological, and biochemical responses that reduce metabolic rates, maintain tissue structure and function, and thus enhance survival. We have synthesized in this review the integrative physiological, morphological, and biochemical responses, and their stages, that characterize natural fasting bouts. Underlying the capacity to survive extended fasts are behaviors and mechanisms that reduce metabolic expenditure and shift the dependency to lipid utilization. Hormonal regulation and immune capacity are altered by fasting; hormones that trigger digestion, elevate metabolism, and support immune performance become depressed, whereas hormones that enhance the utilization of endogenous substrates are elevated. The negative energy budget that accompanies fasting leads to the loss of body mass as fat stores are depleted and tissues undergo atrophy (i.e., loss of mass). Absolute rates of body mass loss scale allometrically among vertebrates. Tissues and organs vary in the degree of atrophy and downregulation of function, depending on the degree to which they are used during the fast. Fasting affects the population dynamics and activities of the gut microbiota, an interplay that impacts the host's fasting biology. Fasting-induced gene expression programs underlie the broad spectrum of integrated physiological mechanisms responsible for an animal's ability to survive long episodes of natural fasting.

  15. Molecular Recognition and Ligand Association

    Science.gov (United States)

    Baron, Riccardo; McCammon, J. Andrew

    2013-04-01

    We review recent developments in our understanding of molecular recognition and ligand association, focusing on two major viewpoints: (a) studies that highlight new physical insight into the molecular recognition process and the driving forces determining thermodynamic signatures of binding and (b) recent methodological advances in applications to protein-ligand binding. In particular, we highlight the challenges posed by compensating enthalpic and entropic terms, competing solute and solvent contributions, and the relevance of complex configurational ensembles comprising multiple protein, ligand, and solvent intermediate states. As more complete physics is taken into account, computational approaches increase their ability to complement experimental measurements, by providing a microscopic, dynamic view of ensemble-averaged experimental observables. Physics-based approaches are increasingly expanding their power in pharmacology applications.

  16. Why mercury prefers soft ligands

    Energy Technology Data Exchange (ETDEWEB)

    Riccardi, Demian M [ORNL; Guo, Hao-Bo [ORNL; Gu, Baohua [ORNL; Parks, Jerry M [ORNL; Summers, Anne [University of Georgia, Athens, GA; Miller, S [University of California, San Francisco; Liang, Liyuan [ORNL; Smith, Jeremy C [ORNL

    2013-01-01

    Mercury (Hg) is a major global pollutant arising from both natural and anthropogenic sources. Defining the factors that determine the relative affinities of different ligands for the mercuric ion, Hg2+, is critical to understanding its speciation, transformation, and bioaccumulation in the environment. Here, we use quantum chemistry to dissect the relative binding free energies for a series of inorganic anion complexes of Hg2+. Comparison of Hg2+ ligand interactions in the gaseous and aqueous phases shows that differences in interactions with a few, local water molecules led to a clear periodic trend within the chalcogenide and halide groups and resulted in the well-known experimentally observed preference of Hg2+ for soft ligands such as thiols. Our approach establishes a basis for understanding Hg speciation in the biosphere.

  17. Sorption kinetics of ofloxacin in soils and mineral particles.

    Science.gov (United States)

    Pan, Bo; Wang, Peng; Wu, Min; Li, Jing; Zhang, Di; Xiao, Di

    2012-12-01

    The environmental behavior of antibiotics is not well known and the precise environmental risk assessment is not practical. This study investigated the sorption kinetics of ofloxacin, a widely used antibiotics, on soil particles with different organic carbon contents as well as soil components (a humic acid, ferric oxide and kaolinite). Two-compartment sorption kinetics were mathematically recognized (except ferric oxide because of its very fast sorption). The apparent sorption rate and the contribution of fast sorption compartment decreased with the increased organic carbon content with the exception of humic acid, suggesting that the slow sorption sites were partially located in organo-mineral complex. The OFL concentration-dependent sorption kinetics suggested that the slow sorption compartment was not controlled by diffusion process as indicated by slower sorption at higher OFL loading. The difference between OFL sorption kinetics and those of hydrophobic organic contaminants was discussed and possible mechanism of OFL two-compartment sorption was proposed.

  18. Luminescence from the ligand to metal charge transfer state of the neptunyl (V) ion and its complexes in solution

    Energy Technology Data Exchange (ETDEWEB)

    Bradshaw, Rebecca; Sykes, Daniel; Faulkner, Stephen [University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford (United Kingdom); Natrajan, Louise S; Livens, Francis R [Centre for Radiochemistry Research, School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL (United Kingdom); Taylor, Robin J, E-mail: Stephen.Faulkner@chem.ox.ac.uk [Central Laboratory, National Nuclear Laboratory, Sellafield, Seascale, Cumbria, CA20 1PG (United Kingdom)

    2010-03-15

    The photophysical properties of the neptunyl (V) ion in aqueous solution have been studied using time-resolved luminescence spectroscopy. While any f-f transitions in emission are too weak to detect using available technology, the ligand to metal charge transfer state is emissive in the visible part of the spectrum. Both the aquo ion and its complexes with bidentate ligands exhibit biexponential decay kinetics, which can be rationalised by slow exchange on the timescale of the experiment.

  19. Fast magnetic reconnection in laser-produced plasma bubbles

    OpenAIRE

    Fox, W.; Bhattacharjee, A.; Germaschewski, K.

    2011-01-01

    Recent experiments have observed magnetic reconnection in high-energy-density, laser-produced plasma bubbles, with reconnection rates observed to be much higher than can be explained by classical theory. Based on fully kinetic particle simulations we find that fast reconnection in these strongly driven systems can be explained by magnetic flux pile-up at the shoulder of the current sheet and subsequent fast reconnection via two-fluid, collisionless mechanisms. In the strong drive regime with ...

  20. FAST User Guide

    Science.gov (United States)

    Walatka, Pamela P.; Clucas, Jean; McCabe, R. Kevin; Plessel, Todd; Potter, R.; Cooper, D. M. (Technical Monitor)

    1994-01-01

    The Flow Analysis Software Toolkit, FAST, is a software environment for visualizing data. FAST is a collection of separate programs (modules) that run simultaneously and allow the user to examine the results of numerical and experimental simulations. The user can load data files, perform calculations on the data, visualize the results of these calculations, construct scenes of 3D graphical objects, and plot, animate and record the scenes. Computational Fluid Dynamics (CFD) visualization is the primary intended use of FAST, but FAST can also assist in the analysis of other types of data. FAST combines the capabilities of such programs as PLOT3D, RIP, SURF, and GAS into one environment with modules that share data. Sharing data between modules eliminates the drudgery of transferring data between programs. All the modules in the FAST environment have a consistent, highly interactive graphical user interface. Most commands are entered by pointing and'clicking. The modular construction of FAST makes it flexible and extensible. The environment can be custom configured and new modules can be developed and added as needed. The following modules have been developed for FAST: VIEWER, FILE IO, CALCULATOR, SURFER, TOPOLOGY, PLOTTER, TITLER, TRACER, ARCGRAPH, GQ, SURFERU, SHOTET, and ISOLEVU. A utility is also included to make the inclusion of user defined modules in the FAST environment easy. The VIEWER module is the central control for the FAST environment. From VIEWER, the user can-change object attributes, interactively position objects in three-dimensional space, define and save scenes, create animations, spawn new FAST modules, add additional view windows, and save and execute command scripts. The FAST User Guide uses text and FAST MAPS (graphical representations of the entire user interface) to guide the user through the use of FAST. Chapters include: Maps, Overview, Tips, Getting Started Tutorial, a separate chapter for each module, file formats, and system

  1. Optimization of enrichment for virtual ligand screening using an established FRED-Surflex approach

    NARCIS (Netherlands)

    Du, J.; Bleylevens, I.W.M.; Bitorina, A.V.; Nicolaes, G.A.F.

    2012-01-01

    Virtual ligand screening (VLS) is an in silico technology used for the productive and cost effective search for novel hit or lead compounds. VLS can be divided into rigid body docking (e.g. FRED) and flexible body docking (e.g. Surflex) procedures. Theoretically, rigid body docking VLS is fast but l

  2. Heterobifunctional crosslinkers for tethering single ligand molecules to scanning probes

    Energy Technology Data Exchange (ETDEWEB)

    Riener, Christian K.; Kienberger, Ferry; Hahn, Christoph D.; Buchinger, Gerhard M.; Egwim, Innocent O.C.; Haselgruebler, Thomas; Ebner, Andreas; Romanin, Christoph; Klampfl, Christian; Lackner, Bernd; Prinz, Heino; Blaas, Dieter; Hinterdorfer, Peter; Gruber, Hermann J

    2003-11-14

    Single molecule recognition force microscopy (SMRFM) is a versatile atomic force microscopy (AFM) method to probe specific interactions of cognitive molecules on the single molecule level. It allows insights to be gained into interaction potentials and kinetic barriers and is capable of mapping interaction sites with nm positional accuracy. These applications require a ligand to be attached to the AFM tip, preferably by a distensible poly(ethylene glycol) (PEG) chain between the measuring tip and the ligand molecule. The PEG chain greatly facilitates specific binding of the ligand to immobile receptor sites on the sample surface. The present study contributes to tip-PEG-ligand tethering in three ways: (i) a convenient synthetic route was found to prepare NH{sub 2}-PEG-COOH which is the key intermediate for long heterobifunctional crosslinkers; (ii) a variety of heterobifunctional PEG derivatives for tip-PEG-ligand linking were prepared from NH{sub 2}-PEG-COOH; (iii) in particular, a new PEG crosslinker with one thiol-reactive end and one terminal nitrilotriacetic acid (NTA) group was synthesized and successfully used to tether His{sub 6}-tagged protein molecules to AFM tips via noncovalent NTA-Ni{sup 2+}-His{sub 6} bridges. The new crosslinker was applied to link a recombinant His{sub 6}-tagged fragment of the very-low density lipoprotein receptor to the AFM tip whereupon specific docking to the capsid of human rhinovirus particles was observed by force microscopy. In a parallel study, the specific interaction of the small GTPase Ran with the nuclear import receptor importin {beta}1 was studied in detail by SMRFM, using the new crosslinker to link His{sub 6}-tagged Ran to the measuring tip [Nat. Struct. Biol. (2003), 10, 553-557].

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

    Directory of Open Access Journals (Sweden)

    Klaus B Nissen

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

  4. Toroidal Electromagnetic Particle-in-Cell Code with Gyro-kinetic Electron and Fully-kinetic ion

    Science.gov (United States)

    Lin, Jingbo; Zhang, Wenlu; Liu, Pengfei; Li, Ding

    2016-10-01

    A kinetic simulation model has been developed using gyro-kinetic electron and fully-kinetic ion by removing fast gyro motion of electrons using the Lie-transform perturbation theory. A particle-in-cell kinetic code is developed based on this model in general magnetic flux coordinate systems, which is particularly suitable for simulations of toroidally confined plasma. Single particle motion and field solver are successfully verified respectively. Integrated electrostatic benchmark, for example the lower-hybrid wave (LHW) and ion Bernstein wave (IBW), shows a good agreement with theoretical results. Preliminary electromagnetic benchmark of fast wave at lower hybrid frequency range is also presented. This code can be a first-principal tool to investigate high frequency nonlinear phenomenon, such as parametric decay instability, during lower-hybrid current drive (LHCD) and ion cyclotron radio frequency heating (ICRF) with complex geometry effect included. Supported by National Special Research Program of China For ITER and National Natural Science Foundation of China.

  5. Gold Nanoparticle Monolayers from Sequential Interfacial Ligand Exchange and Migration in a Three-Phase System

    Science.gov (United States)

    Yang, Guang; Hallinan, Daniel T.

    2016-10-01

    Using a three-phase system, centimeter-scale monolayer gold nanoparticle (Au NP) films have been prepared that have long-range order and hydrophobic ligands. The system contains an interface between an aqueous phase containing Au NPs and an oil phase containing one of various types of amine ligands, and a water/air interface. As the Au NPs diffuse to the water/oil interface, ligand exchange takes place which temporarily traps them at the water/oil interface. The ligand-exchanged particles then spontaneously migrate to the air/water interface, where they self-assemble, forming a monolayer under certain conditions. The spontaneous formation of the NP film at the air/water interface was due to the minimization of the system Helmholtz free energy. However, the extent of surface functionalization was dictated by kinetics. This decouples interfacial ligand exchange from interfacial self-assembly, while maintaining the simplicity of a single system. The interparticle center-to-center distance was dictated by the amine ligand length. The Au NP monolayers exhibit tunable surface plasma resonance and excellent spatial homogeneity, which is useful for surface-enhanced Raman scattering. The “air/water/oil” self-assembly method developed here not only benefits the fundamental understanding of NP ligand conformations, but is also applicable to the manufacture of plasmonic nanoparticle devices with precisely designed optical properties.

  6. Gold Nanoparticle Monolayers from Sequential Interfacial Ligand Exchange and Migration in a Three-Phase System

    Science.gov (United States)

    Yang, Guang; Hallinan, Daniel T.

    2016-01-01

    Using a three-phase system, centimeter-scale monolayer gold nanoparticle (Au NP) films have been prepared that have long-range order and hydrophobic ligands. The system contains an interface between an aqueous phase containing Au NPs and an oil phase containing one of various types of amine ligands, and a water/air interface. As the Au NPs diffuse to the water/oil interface, ligand exchange takes place which temporarily traps them at the water/oil interface. The ligand-exchanged particles then spontaneously migrate to the air/water interface, where they self-assemble, forming a monolayer under certain conditions. The spontaneous formation of the NP film at the air/water interface was due to the minimization of the system Helmholtz free energy. However, the extent of surface functionalization was dictated by kinetics. This decouples interfacial ligand exchange from interfacial self-assembly, while maintaining the simplicity of a single system. The interparticle center-to-center distance was dictated by the amine ligand length. The Au NP monolayers exhibit tunable surface plasma resonance and excellent spatial homogeneity, which is useful for surface-enhanced Raman scattering. The “air/water/oil” self-assembly method developed here not only benefits the fundamental understanding of NP ligand conformations, but is also applicable to the manufacture of plasmonic nanoparticle devices with precisely designed optical properties. PMID:27762394

  7. Multivalent ligand presentation as a central concept to study intricate carbohydrate-protein interactions.

    Science.gov (United States)

    Jayaraman, Narayanaswamy

    2009-12-01

    Studying the weak binding affinities between carbohydrates and proteins has been a central theme in sustained efforts to uncover intricate details of this class of biomolecular interaction. The amphiphilic nature of most carbohydrates, the competing nature of the surrounding water molecules to a given protein receptor site and the receptor binding site characteristics led to the realization that carbohydrates are required to exert favorable interactions, primarily through clustering of the ligands. The clustering of sugar ligands has been augmented using many different innovative molecular scaffolds. The synthesis of clustered ligands also facilitates fine-tuning of the spatial and topological proximities between the ligands, so as to allow the identification of optimal molecular features for significant binding affinity enhancements. The kinetic and thermodynamic parameters have been delineated in many instances, thereby allowing an ability to correlate the multivalent presentation and the observed ligand-receptor interaction profiles. This critical review presents various multivalent ligands, synthetic and semisynthetic, and mechanisms by which the weak binding affinities are overcome, and the ligand-receptor complexation leads to significantly enhanced binding affinities (157 references).

  8. Fluorinated Carbohydrates as Lectin Ligands: 19F-Based Direct STD Monitoring for Detection of Anomeric Selectivity

    Science.gov (United States)

    Ribeiro, João P.; Diercks, Tammo; Jiménez-Barbero, Jesús; André, Sabine; Gabius, Hans-Joachim; Cañada, Francisco Javier

    2015-01-01

    The characterization of the binding of reducing carbohydrates present as mixtures of anomers in solution to a sugar recepor (lectin) poses severe difficulties. In this situation, NMR spectroscopy enables the observation of signals for each anomer in the mixture by applying approaches based on ligand observation. Saturation transfer difference (STD) NMR allows fast and efficient screening of compound mixtures for reactivity to a receptor. Owing to the exceptionally favorable properties of 19F in NMR spectroscopy and the often complex 1H spectra of carbohydrates, 19F-containing sugars have the potential to be turned into versatile sensors for recognition. Extending the recently established 1H → 1H STDre19F-NMR technique, we here demonstrate its applicability to measure anomeric selectivity of binding in a model system using the plant lectin concanavalin A (ConA) and 2-deoxy-2-fluoro-d-mannose. Indeed, it is also possible to account for the mutual inhibition between the anomers on binding to the lectin by means of a kinetic model. The monitoring of 19F-NMR signal perturbation disclosed the relative activities of the anomers in solution and thus enabled the calculation of their binding affinity towards ConA. The obtained data show a preference for the α anomer that increases with temperature. This experimental approach can be extended to others systems of biomedical interest by testing human lectins with suitably tailored glycan derivatives. PMID:26580665

  9. Recent Results on Fast Flow Gas-Phase Partial Oxidation of Lower Alkanes

    Institute of Scientific and Technical Information of China (English)

    Vladimir S. Arutyunov

    2004-01-01

    Recent experimental results and kinetic modeling of fast flow gas-phase oxidation of methane and other lower alkanes to methanol and other oxygenates are discussed, alongside with prospects and possible areas for applications of the processes.

  10. A race for RAGE ligands.

    Science.gov (United States)

    Schleicher, Erwin D

    2010-08-01

    In experimental animals a causal involvement of the multiligand receptor for advanced glycation end products (RAGE) in the development of diabetic vascular complications has been demonstrated. However, the nature of RAGE ligands present in patients with diabetic nephropathy has not yet been defined; this leaves open the relevance of the RAGE system to the human disease.

  11. Moment equations for chromatography based on Langmuir type reaction kinetics.

    Science.gov (United States)

    Miyabe, Kanji

    2014-08-22

    Moment equations were derived for chromatography, in which the reaction kinetics between solute molecules and functional ligands on the stationary phase was represented by the Langmuir type rate equation. A set of basic equations of the general rate model of chromatography representing the mass balance, mass transfer rate, and reaction kinetics in the column were analytically solved in the Laplace domain. The moment equations for the first absolute moment and the second central moment in the real time domain were derived from the analytical solution in the Laplace domain. The moment equations were used for predicting the chromatographic behavior under hypothetical HPLC conditions. The influence of the parameters relating to the adsorption equilibrium and to the reaction kinetics on the chromatographic behavior was quantitatively evaluated. It is expected that the moment equations are effective for a detailed analysis of the influence of the mass transfer rates and of the Langmuir type reaction kinetics on the column efficiency.

  12. Kinetics of methane fermentation

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Y. R.; Hashimoto, A. G.

    1978-01-01

    The kinetics on methane fermentation are described using published data for livestock residue, sewage sludge, and municipal refuse. Methods are presented to determine the kinetic constants and the finally attainable methane production using steady-state methane production data. The effects of temperature, loading rate, and influent substrate concentration on methane fermentation kinetics are discussed. These relationships were used to predict the rate of methane production of a pilot-scale fermentor with excellent results.

  13. Structure-kinetics relationships of Capadenoson derivatives as adenosine A1 receptor agonists.

    Science.gov (United States)

    Louvel, Julien; Guo, Dong; Soethoudt, Marjolein; Mocking, Tamara A M; Lenselink, Eelke B; Mulder-Krieger, Thea; Heitman, Laura H; IJzerman, Adriaan P

    2015-08-28

    We report the synthesis and biological evaluation of new derivatives of Capadenoson, a former drug candidate that was previously advanced to phase IIa clinical trials. 19 of the 20 ligands show an affinity below 100 nM at the human adenosine A1 receptor (hA1AR) and display a wide range of residence times at this target (from approx. 5 min (compound 10) up to 132 min (compound 5)). Structure-affinity and structure-kinetics relationships were established, and computational studies of a homology model of the hA1AR revealed crucial interactions for both the affinity and dissociation kinetics of this family of ligands. These results were also combined with global metrics (Ligand Efficiency, cLogP), showing the importance of binding kinetics as an additional way to better select a drug candidate amongst seemingly similar leads.

  14. Absorption kinetics of oral sotalol combined with cisapride and sublingual sotalol in healthy subjects

    NARCIS (Netherlands)

    Deneer, V.; A Lie, Huen; Proost, Hans; Kelder, J.C; Brouwers, J.R.B.J.; Kingma, J.H.

    1998-01-01

    Aims To study the absorption kinetics of sotalol following administration of different formulations. A formulation which results in fast absorption might be useful in the episodic treatment of paroxysmal supraventricular tachycardia (SVT), atrial fibrillation (Afib) or atrial flutter (Afl). Methods

  15. Introduction to chemical kinetics

    CERN Document Server

    Soustelle, Michel

    2013-01-01

    This book is a progressive presentation of kinetics of the chemical reactions. It provides complete coverage of the domain of chemical kinetics, which is necessary for the various future users in the fields of Chemistry, Physical Chemistry, Materials Science, Chemical Engineering, Macromolecular Chemistry and Combustion. It will help them to understand the most sophisticated knowledge of their future job area. Over 15 chapters, this book present the fundamentals of chemical kinetics, its relations with reaction mechanisms and kinetic properties. Two chapters are then devoted to experimental re

  16. Principles of chemical kinetics

    CERN Document Server

    House, James E

    2007-01-01

    James House's revised Principles of Chemical Kinetics provides a clear and logical description of chemical kinetics in a manner unlike any other book of its kind. Clearly written with detailed derivations, the text allows students to move rapidly from theoretical concepts of rates of reaction to concrete applications. Unlike other texts, House presents a balanced treatment of kinetic reactions in gas, solution, and solid states. The entire text has been revised and includes many new sections and an additional chapter on applications of kinetics. The topics covered include quantitative rela

  17. Fast Low-Spin Cobalt Complex Redox Shuttles for Dye-Sensitized Solar Cells.

    Science.gov (United States)

    Xie, Yuling; Hamann, Thomas W

    2013-01-17

    A low-spin cobalt(II) complex, cobalt bis(trithiacyclononane), [Co(ttcn)2](3+/2+), was investigated for use as a redox shuttle in dye-sensitized solar cells, DSSCs. This unique cobalt complex redox shuttle is stable, transparent, and easy to synthesize from commercial ligands and has attractive energetic and kinetic features for use in DSSCs. Initial results indicate that the overall performance is limited by recombination. Variation of the sensitizer and deposition of an ultrathin coating of alumina on nanoparticle-based TiO2 DSSC photoanodes reduced recombination, which resulted in significantly improved quantum yields. The photovoltaic behavior was compared to the current record efficiency cobalt tris-bipyridine, [Co(bpy)3](3+/2+), redox shuttle and produced similar results. Further use of high extinction organic sensitizers with only ∼200 mV of driving force for regeneration was examined, which produced efficiencies of over 2%; importantly, regeneration is not rate-limiting in this system, thus demonstrating the promise of using such fast redox shuttles.

  18. A comparative study of kinetics of nuclear reactors

    Directory of Open Access Journals (Sweden)

    Obaidurrahman Khalilurrahman

    2009-01-01

    Full Text Available The paper deals with the study of reactivity initiated transients to investigate major differences in the kinetics behavior of various reactor systems under different operating conditions. The article also states guidelines to determine the safety limits on reactivity insertion rates. Three systems, light water reactors (pressurized water reactors, heavy water reactors (pressurized heavy water reactors, and fast breeder reactors are considered for the sake of analysis. The upper safe limits for reactivity insertion rate in these reactor systems are determined. The analyses of transients are performed by a point kinetics computer code, PKOK. A simple but accurate method for accounting total reactivity feedback in kinetics calculations is suggested and used. Parameters governing the kinetics behavior of the core are studied under different core states. A few guidelines are discussed to project the possible kinetics trends in the next generation reactors.

  19. Coupling of disulfide bond and distal histidine dissociation in human ferrous cytoglobin regulates ligand binding.

    Science.gov (United States)

    Beckerson, Penny; Reeder, Brandon J; Wilson, Michael T

    2015-02-13

    Earlier kinetics studies on cytoglobin did not assign functional properties to specific structural forms. Here, we used defined monomeric and dimeric forms and cysteine mutants to show that an intramolecular disulfide bond (C38-C83) alters the dissociation rate constant of the intrinsic histidine (H81) (∼1000 fold), thus controlling binding of extrinsic ligands. Through time-resolved spectra we have unequivocally assigned CO binding to hexa- and penta-coordinate forms and have made direct measurement of histidine rebinding following photolysis. We present a model that describes how the cysteine redox state of the monomer controls histidine dissociation rate constants and hence extrinsic ligand binding.

  20. Influence of ligands in metal nanoparticle electrophoresis for the fabrication of biofunctional coatings

    Energy Technology Data Exchange (ETDEWEB)

    Streich, Carmen; Koenen, Sven [Technical Chemistry I, University of Duisburg-Essen and Center for Nanointegration Duisburg-Essen (CENIDE), Universitaetsstr. 7, 45141 Essen (Germany); Lelle, Marco; Peneva, Kalina [Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany); Barcikowski, Stephan, E-mail: stephan.barcikowski@uni-due.de [Technical Chemistry I, University of Duisburg-Essen and Center for Nanointegration Duisburg-Essen (CENIDE), Universitaetsstr. 7, 45141 Essen (Germany)

    2015-09-01

    Graphical abstract: - Highlights: • Particle mobility measurements quantify how ligand size and charge influence particle electrophoresis. • Although negatively-charged ligands enhance particle mobility, ultimate deposition is suppressed. • Laser-generated metal nanoparticles can serve as model materials in electrophoretic deposition because they are ligand-free, hard colloidal spheres. • Only bare nanoparticles feature a high electrophoretic mobility and a constant deposition rate with no barrier formation. • Bioactive implant coatings may result from depositing nanoparticles functionalized with cell-penetrating peptides. - Abstract: Electrophoretic deposition of colloidal nanoparticles shows great promise for the fabrication of nanostructured surfaces, especially relevant for the surface modification of three dimensional medical implants. Here, the role of small and bulky, chemisorbent and physisorbent ligands on metal (gold, platinum) nanoparticle deposition dynamics are systematically investigated. To be able to compare ligand-coated to ligand-free nanoparticles, pulsed laser ablation in liquid is employed as nanoparticle fabrication method. Nanoparticles’ electrophoretic properties are assessed via zeta potential measurements and nanoparticle tracking analysis, while online-UV–vis spectroscopy provides information about the deposition dynamics. Electron micrographs and contact angle measurements are employed to characterize the deposit. We show that ligand-free nanoparticles feature a high electrophoretic mobility and linear deposition kinetics, representing an excellent model material for controlled electrophoretic deposition. In contrast, the electrophoretic mobility of surface-modified nanoparticles is altered due to the surrounding ligand layer, resulting in less efficient deposition. Notably, electrophoretic mobility is not solely governed by the ligand's charge and does not correlate to the zeta potential values directly. Finally

  1. Fast growth in control

    NARCIS (Netherlands)

    Z. Rico (Zulay)

    2009-01-01

    textabstractThe focus of this paper is on the influence of the fast growth of organizations on the design process of management control systems. What are the management accounting and control problems that a fast growth organization encounters that can be ascribed to this growth. What are the circum

  2. Ramadan, faste og graviditet

    DEFF Research Database (Denmark)

    Ahmed, Urfan Zahoor; Lykke, Jacob Alexander

    2014-01-01

    , but there are reports of decreased foetal movements. Furthermore, the fasting may have long-term health consequences for the offspring, especially when they reach their middle age. According to Islam and the interpretation, pregnant and breast-feeding women are allowed to postpone the fasting of the month of Ramadan...

  3. Fast ejendom III

    DEFF Research Database (Denmark)

    Munk-Hansen, Carsten

    Bogen er det tredje bind af tre planlagte bind om fast ejendom: I Overdragelsen, II Bolighandlen og III Ejerbeføjelsen. Fremstillingens giver et grundigt overblik over centrale områder af en omfattende regulering af fast ejendom, med angivelse af litteratur, hvor læseren kan søge yderligere...... oplysning. En ejer af fast ejendom er på særdeles mange områder begrænset i sin råden sammenlignet med ejeren af et formuegode i almindelighed. Fremstillingen tager udgangspunkt i ejerens perspektiv (fremfor samfundets eller myndighedernes). Både den privatretlige og offentligretlige regulering behandles......, eksempelvis ejendomsdannelsen, servitutter, naboretten, hævd, zoneinddelingen, den fysiske planlægning, beskyttelse af natur, beskyttelse af kultur, forurening fra fast ejendom, erstatning for forurening, jordforurening, ekspropriation, byggeri og adgang til fast ejendom....

  4. Islamic Fasting and Diabetes

    Directory of Open Access Journals (Sweden)

    Fereidoun Azizi

    2013-07-01

    Full Text Available The aim of this article is to review health-related aspects of Ramadan fasting in normal individuals and diabetics. During fasting days of Ramadan, glucose homeostasis is maintained by meal taken bepore dawn and by liver glycogen stores. Changes in serum lipids are variable and defend on the quality and quantity of food consumption and changes in weight. Compliant, well controlled type 2 diabetics may observe Ramadan fasting; but fasting is not recommended for type 1, non complaint, poorly controlled and pregnant diabetics. Although Ramadan fasting is safe for all healthy individuals and well controlled diabetics, those with uncontrolled diabetics and diabetics with complications should consult physicians and follow scientific recommendations.

  5. Fast Spectrum Reactors

    CERN Document Server

    Todd, Donald; Tsvetkov, Pavel

    2012-01-01

    Fast Spectrum Reactors presents a detailed overview of world-wide technology contributing to the development of fast spectrum reactors. With a unique focus on the capabilities of fast spectrum reactors to address nuclear waste transmutation issues, in addition to the well-known capabilities of breeding new fuel, this volume describes how fast spectrum reactors contribute to the wide application of nuclear power systems to serve the global nuclear renaissance while minimizing nuclear proliferation concerns. Readers will find an introduction to the sustainable development of nuclear energy and the role of fast reactors, in addition to an economic analysis of nuclear reactors. A section devoted to neutronics offers the current trends in nuclear design, such as performance parameters and the optimization of advanced power systems. The latest findings on fuel management, partitioning and transmutation include the physics, efficiency and strategies of transmutation, homogeneous and heterogeneous recycling, in addit...

  6. Controlled-deactivation cannabinergic ligands.

    Science.gov (United States)

    Sharma, Rishi; Nikas, Spyros P; Paronis, Carol A; Wood, Jodianne T; Halikhedkar, Aneetha; Guo, Jason Jianxin; Thakur, Ganesh A; Kulkarni, Shashank; Benchama, Othman; Raghav, Jimit Girish; Gifford, Roger S; Järbe, Torbjörn U C; Bergman, Jack; Makriyannis, Alexandros

    2013-12-27

    We report an approach for obtaining novel cannabinoid analogues with controllable deactivation and improved druggability. Our design involves the incorporation of a metabolically labile ester group at the 2'-position on a series of (-)-Δ(8)-THC analogues. We have sought to introduce benzylic substituents α to the ester group which affect the half-lives of deactivation through enzymatic activity while enhancing the affinities and efficacies of individual ligands for the CB1 and CB2 receptors. The 1'-(S)-methyl, 1'-gem-dimethyl, and 1'-cyclobutyl analogues exhibit remarkably high affinities for both CB receptors. The novel ligands are susceptible to enzymatic hydrolysis by plasma esterases in a controllable manner, while their metabolites are inactive at the CB receptors. In further in vitro and in vivo experiments key analogues were shown to be potent CB1 receptor agonists and to exhibit CB1-mediated hypothermic and analgesic effects.

  7. Privileged chiral ligands and catalysts

    CERN Document Server

    Zhou, Qi-Lin

    2011-01-01

    This ultimate ""must have"" and long awaited reference for every chemist working in the field of asymmetric catalysis starts with the core structure of the catalysts, explaining why a certain ligand or catalyst is so successful. It describes in detail the history, the basic structural characteristics, and the applications of these ""privileged catalysts"". A novel concept that gives readers a much deeper insight into the topic.

  8. Tumor targeting via integrin ligands

    Directory of Open Access Journals (Sweden)

    Udaya Kiran eMarelli

    2013-08-01

    Full Text Available Selective and targeted delivery of drugs to tumors is a major challenge for an effective cancer therapy and also to overcome the side effects associated with current treatments. Overexpression of various receptors on tumor cells is a characteristic structural and biochemical aspect of tumors and distinguishes them from physiologically normal cells. This abnormal feature is therefore suitable for selectively directing anticancer molecules to tumors by using ligands that can preferentially recognize such receptors. Several subtypes of integrin receptors that are crucial for cell adhesion, cell signaling, cell viability and motility have been shown to have an upregulated expression on cancer cells. Thus, ligands that recognize specific integrin subtypes represent excellent candidates to be conjugated to drugs or drug carrier systems and be targeted to tumors. In this regard, integrins recognizing the RGD cell adhesive sequence have been extensively targeted for tumor specific drug delivery. Here we review key recent examples on the presentation of RGD-based integrin ligands by means of distinct drug delivery systems, and discuss the prospects of such therapies to specifically target tumor cells.

  9. Cyclic voltammetry of fast conducting electrocatalytic films.

    Science.gov (United States)

    Costentin, Cyrille; Savéant, Jean-Michel

    2015-07-15

    In the framework of contemporary energy challenges, cyclic voltammetry is a particularly useful tool for deciphering the kinetics of catalytic films. The case of fast conducting films is analyzed, whether conduction is of the ohmic type or proceeds through rapid electron hopping. The rate-limiting factors are then the diffusion of the substrate in solution and through the film as well as the catalytic reaction itself. The dimensionless combination of the characteristics of these factors allows reducing the number of actual parameters to a maximum of two. The kinetics of the system may then be fully analyzed with the help of a kinetic zone diagram. Observing the variations of the current-potential responses with operational parameters such as film thickness, the potential scan rate and substrate concentration allows a precise assessment of the interplay between these factors and of the values of the rate controlling factors. A series of thought experiments is described in order to render the kinetic analysis more palpable.

  10. Transient impairment of the adaptive response to fasting in FXR-deficient mice

    NARCIS (Netherlands)

    Cariou, B; van Harmelen, K; Duran-Sandoval, D; van Dijk, T; Grefhorst, A; Bouchaert, E; Fruchart, JC; Gonzalez, FJ; Kuipers, F; Staels, B

    2005-01-01

    The farnesoid X receptor (FXR) has been suggested to play a role in gluconeogenesis. To determine whether FXR modulates the response to fasting in vivo, FXR-deficient (FXR-/-) and wild-type mice were submitted to fasting for 48 h. Our results demonstrate that FXR modulates the kinetics of alteration

  11. Transient impairment of the adaptive response to fasting in FXR-deficient mice

    NARCIS (Netherlands)

    Cariou, B; van Harmelen, K; Duran-Sandoval, D; van Dijk, T; Grefhorst, A; Bouchaert, E; Fruchart, JC; Gonzalez, FJ; Kuipers, F; Staels, B

    2005-01-01

    The farnesoid X receptor (FXR) has been suggested to play a role in gluconeogenesis. To determine whether FXR modulates the response to fasting in vivo, FXR-deficient (FXR-/-) and wild-type mice were submitted to fasting for 48 h. Our results demonstrate that FXR modulates the kinetics of

  12. Biomass fast pyrolysis in fluidized bed : product cleaning by in-situ filtration

    NARCIS (Netherlands)

    Wang, Xiaoquan

    2006-01-01

    This thesis is dedicated to the subject of fast pyrolysis in a fluid bed reactor. A large part of the work is related to reactor design aspects of fast pyrolysis, a subject that has not been considered sufficiently. Past research efforts were focussed mainly on the kinetics of wood pyrolysis and the

  13. New method for the determination of precipitation kinetics using a laminar jet reactor

    NARCIS (Netherlands)

    Al-Tarazi, Mousa; Heesink, A. Bert M.; Versteeg, Geert F.

    2005-01-01

    In this paper a new experimental method for determining the kinetics of fast precipitation reactions is introduced. Use is made of a laminar jet reactor, which is also frequently applied to determine the kinetics of homogeneous gas-liquid reactions. The liquid containing one or more of the precipita

  14. New method for the determination of precipitation kinetics using a laminar jet reactor

    NARCIS (Netherlands)

    Al-Tarazi, Mousa; Heesink, A. Bert M.; Versteeg, Geert F.

    2005-01-01

    In this paper a new experimental method for determining the kinetics of fast precipitation reactions is introduced. Use is made of a laminar jet reactor, which is also frequently applied to determine the kinetics of homogeneous gas–liquid reactions. The liquid containing one or more of the precipita

  15. Structural determinants of ligand migration in Mycobacterium tuberculosis truncated hemoglobin O.

    Science.gov (United States)

    Boechi, Leonardo; Martí, Marcelo A; Milani, Mario; Bolognesi, Martino; Luque, F Javier; Estrin, Darío A

    2008-11-01

    Mycobacterium tuberculosis is the causative agent of human tuberculosis, one of the most prevalent infectious diseases in the world. Its genome hosts the glbN and glbO genes coding for two proteins, truncated hemoglobin N (trHbN) and truncated hemoglobin O (trHbO), that belong to different groups (I and II, respectively) of the recently discovered trHb family of hemeproteins. The different expression pattern and kinetics rates constants for ligand association and NO oxidation rate suggest different functions for these proteins. Previous experimental and theoretical studies showed that, in trHbs, ligand migration along the internal tunnel cavity system is a key issue in determining the ligand-binding characteristics. The X-ray structure of trHbO has been solved and shows several internal cavities and secondary-docking sites. In this work, we present an extensive investigation of the tunnel/cavity system ofM. tuberculosis trHbO by means of computer-simulation techniques. We have computed the free-energy profiles for ligand migration along three found tunnels in the oxy and deoxy w.t. and mutant trHbO proteins. Our results show that multiple-ligand migration paths are possible and that several conserved residues such as TrpG8 play a key role in the ligand-migration regulation.

  16. Are superhalogens without halogen ligand capable of transcending traditional halogen-based superhalogens? Ab initio case study of binuclear anions based on pseudohalogen ligand

    Science.gov (United States)

    Li, Jin-Feng; Sun, Yin-Yin; Bai, Hongcun; Li, Miao-Miao; Li, Jian-Li; Yin, Bing

    2015-06-01

    The superhalogen properties of polynuclear structures without halogen ligand are theoretically explored here for several [M2(CN)5]-1 (M = Ca, Be) clusters. At CCSD(T) level, these clusters have been confirmed to be superhalogens due to their high vertical electron detachment energies (VDE). The largest one is 9.70 eV for [Ca2(CN)5]-1 which is even higher than those of corresponding traditional structures based on fluorine or chlorine ligands. Therefore the superhalogens stronger than the traditional halogen-based structures could be realized by ligands other than halogen atoms. Compared with CCSD(T), outer valence Green's function (OVGF) method either overestimates or underestimates the VDEs for different structures while MP2 results are generally consistent in the aspect of relative values. The extra electrons of the highest VDE anions here aggregate on the bridging CN units with non-negligible distribution occurring on other CN units too. These two features lower both the potential and kinetic energies of the extra electron respectively and thus lead to high VDE. Besides superhalogen properties, the structures, relative stabilities and thermodynamic stabilities with respect to the detachment of cyanide ligand were also investigated. The sum of these results identifies the potential of polynuclear structures with pseudohalogen ligand as suitable candidates with enhanced superhalogens properties.

  17. Are superhalogens without halogen ligand capable of transcending traditional halogen-based superhalogens? Ab initio case study of binuclear anions based on pseudohalogen ligand

    Energy Technology Data Exchange (ETDEWEB)

    Li, Jin-Feng; Sun, Yin-Yin; Li, Miao-Miao; Li, Jian-Li; Yin, Bing, E-mail: rayinyin@nwu.edu.cn [MOE Key Laboratory of Synthetic and Natural Functional Molecule Chemistry, Shaanxi Key Laboratory of Physico-Inorganic Chemistry, College of Chemistry and Materials Science, Northwest University, Xi’an 710069 (China); Bai, Hongcun [Key Laboratory of Energy Source and Chemical Engineering, Ningxia University, Yinchuan, Ningxia 750021 (China)

    2015-06-15

    The superhalogen properties of polynuclear structures without halogen ligand are theoretically explored here for several [M{sub 2}(CN){sub 5}]{sup −1} (M =  Ca, Be) clusters. At CCSD(T) level, these clusters have been confirmed to be superhalogens due to their high vertical electron detachment energies (VDE). The largest one is 9.70 eV for [Ca{sub 2}(CN){sub 5}]{sup −1} which is even higher than those of corresponding traditional structures based on fluorine or chlorine ligands. Therefore the superhalogens stronger than the traditional halogen-based structures could be realized by ligands other than halogen atoms. Compared with CCSD(T), outer valence Green’s function (OVGF) method either overestimates or underestimates the VDEs for different structures while MP2 results are generally consistent in the aspect of relative values. The extra electrons of the highest VDE anions here aggregate on the bridging CN units with non-negligible distribution occurring on other CN units too. These two features lower both the potential and kinetic energies of the extra electron respectively and thus lead to high VDE. Besides superhalogen properties, the structures, relative stabilities and thermodynamic stabilities with respect to the detachment of cyanide ligand were also investigated. The sum of these results identifies the potential of polynuclear structures with pseudohalogen ligand as suitable candidates with enhanced superhalogens properties.

  18. Are superhalogens without halogen ligand capable of transcending traditional halogen-based superhalogens? Ab initio case study of binuclear anions based on pseudohalogen ligand

    Directory of Open Access Journals (Sweden)

    Jin-Feng Li

    2015-06-01

    Full Text Available The superhalogen properties of polynuclear structures without halogen ligand are theoretically explored here for several [M2(CN5]−1 (M =  Ca, Be clusters. At CCSD(T level, these clusters have been confirmed to be superhalogens due to their high vertical electron detachment energies (VDE. The largest one is 9.70 eV for [Ca2(CN5]−1 which is even higher than those of corresponding traditional structures based on fluorine or chlorine ligands. Therefore the superhalogens stronger than the traditional halogen-based structures could be realized by ligands other than halogen atoms. Compared with CCSD(T, outer valence Green’s function (OVGF method either overestimates or underestimates the VDEs for different structures while MP2 results are generally consistent in the aspect of relative values. The extra electrons of the highest VDE anions here aggregate on the bridging CN units with non-negligible distribution occurring on other CN units too. These two features lower both the potential and kinetic energies of the extra electron respectively and thus lead to high VDE. Besides superhalogen properties, the structures, relative stabilities and thermodynamic stabilities with respect to the detachment of cyanide ligand were also investigated. The sum of these results identifies the potential of polynuclear structures with pseudohalogen ligand as suitable candidates with enhanced superhalogens properties.

  19. Chaotic Fast Scrambling At Black Holes

    CERN Document Server

    Barbon, Jose L F

    2011-01-01

    Fast scramblers process information in characteristic times scaling logarithmically with the entropy, a behavior which has been conjectured for black hole horizons. In this note we use the AdS/CFT fold to argue that causality bounds on information flow only depend on the properties of a single thermal cell, and admit a geometrical interpretation in terms of the optical depth, i.e. the thickness of the Rindler region in the so-called optical metric. The spatial sections of the optical metric are well approximated by constant-curvature hyperboloids. We use this fact to propose an effective kinetic model of scrambling which can be assimilated to a compact hyperbolic billiard, furnishing a classic example of hard chaos. It is suggested that classical chaos at large N is a crucial ingredient in reconciling the notion of fast scrambling with the required saturation of causality.

  20. FAST Construction Progress

    Science.gov (United States)

    Nan, R. D.; Zhang, H. Y.; Zhang, Y.; Yang, L.; Cai, W. J.; Liu, N.; Xie, J. T.; Zhang, S. X.

    2016-11-01

    The Five-hundred-meter Aperture Spherical radio Telescope (FAST) is a Chinese mega-science project to build the largest single dish radio telescope in the world. A unique karst depression in Guizhou province has been selected as the site to build an active reflector radio telescope with a diameter of 500 m and three outstanding aspects, which enables FAST to have a large sky coverage and the ability of observing astronomical targets with a high precision. Chinese Academy of Sciences and Guizhou province are in charge of FAST construction. The first light of the telescope was expected on September 25, 2016.

  1. Fast Breeder Reactor studies

    Energy Technology Data Exchange (ETDEWEB)

    Till, C.E.; Chang, Y.I.; Kittel, J.H.; Fauske, H.K.; Lineberry, M.J.; Stevenson, M.G.; Amundson, P.I.; Dance, K.D.

    1980-07-01

    This report is a compilation of Fast Breeder Reactor (FBR) resource documents prepared to provide the technical basis for the US contribution to the International Nuclear Fuel Cycle Evaluation. The eight separate parts deal with the alternative fast breeder reactor fuel cycles in terms of energy demand, resource base, technical potential and current status, safety, proliferation resistance, deployment, and nuclear safeguards. An Annex compares the cost of decommissioning light-water and fast breeder reactors. Separate abstracts are included for each of the parts.

  2. Gas cooled fast reactor

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1972-06-01

    Although most of the development work on fast breeder reactors has been devoted to the use of liquid metal cooling, interest has been expressed for a number of years in alternative breeder concepts using other coolants. One of a number of concepts in which interest has been retained is the Gas-Cooled Fast Reactor (GCFR). As presently envisioned, it would operate on the uranium-plutonium mixed oxide fuel cycle, similar to that used in the Liquid Metal Fast Breeder Reactor (LMFBR), and would use helium gas as the coolant.

  3. Structure and stability of hexadentate complexes of ligands based on AAZTA for efficient PET labelling with gallium-68.

    Science.gov (United States)

    Waldron, Bradley P; Parker, David; Burchardt, Carsten; Yufit, Dmitry S; Zimny, Melanie; Roesch, Frank

    2013-01-21

    Pre-organised tricarboxylate ligands based on 6-amino-perhydro-1,4-diazepine bind (68)Ga rapidly and selectively in acetate buffer at pH 4 to 7, forming kinetically stable complexes suitable for use in PET imaging.

  4. Superparamagnetic Ironoxide Nanoparticles via Ligand Exchange Reactions: Organic 1,2-Diols as Versatile Building Blocks for Surface Engineering

    Directory of Open Access Journals (Sweden)

    Robert Sachsenhofer

    2008-09-01

    Full Text Available A method for the preparation of ligand-covered superparamagnetic iron oxide nanoparticles via exchange reactions is described. 1,2-diol-ligands are used to provide a stable binding of the terminally modified organic ligands onto the surface of γ-Fe2O3-nanoparticles (r∼4 nm. The 1,2-diol-ligands are equipped with variable terminal functional groups (i.e., hydrogen bonding moieties, azido- bromo-, fluorescent moieties and can be easily prepared via osmium tetroxide-catalyzed 1,2-dihydroxylation reactions of the corresponding terminal alkenes. Starting from octylamine-covered Î��-Fe2O3-nanoparticles, ligand exchange was effected at 50∘C over 24–48 hours, whereupon complete ligand exchange is taking place as proven by thermogravimetric (TGA- and IR-spectroscopic measurements. A detailed kinetic analysis of the ligand exchange reaction was performed via TGA analysis, demonstrating a complete ligand exchange after 24 hours. The method offers a simple approach for the generation of various γ-Fe2O3-nanoparticles with functional organic shells in a one-step procedure.

  5. Kinetics of reduction of Fe(III) complexes by outer membrane cytochromes MtrC and OmcA of Shewanella oneidensis MR-1.

    Science.gov (United States)

    Wang, Zheming; Liu, Chongxuan; Wang, Xuelin; Marshall, Matthew J; Zachara, John M; Rosso, Kevin M; Dupuis, Michel; Fredrickson, James K; Heald, Steve; Shi, Liang

    2008-11-01

    Because of their cell surface locations, the outer membrane c-type cytochromes MtrC and OmcA of Shewanella oneidensis MR-1 have been suggested to be the terminal reductases for a range of redox-reactive metals that form poorly soluble solids or that do not readily cross the outer membrane. In this work, we determined the kinetics of reduction of a series of Fe(III) complexes with citrate, nitrilotriacetic acid (NTA), and EDTA by MtrC and OmcA using a stopped-flow technique in combination with theoretical computation methods. Stopped-flow kinetic data showed that the reaction proceeded in two stages, a fast stage that was completed in less than 1 s, followed by a second, relatively slower stage. For a given complex, electron transfer by MtrC was faster than that by OmcA. For a given cytochrome, the reaction was completed in the order Fe-EDTA > Fe-NTA > Fe-citrate. The kinetic data could be modeled by two parallel second-order bimolecular redox reactions with second-order rate constants ranging from 0.872 microM(-1) s(-1) for the reaction between MtrC and the Fe-EDTA complex to 0.012 microM(-1) s(-1) for the reaction between OmcA and Fe-citrate. The biphasic reaction kinetics was attributed to redox potential differences among the heme groups or redox site heterogeneity within the cytochromes. The results of redox potential and reorganization energy calculations showed that the reaction rate was influenced mostly by the relatively large reorganization energy. The results demonstrate that ligand complexation plays an important role in microbial dissimilatory reduction and mineral transformation of iron, as well as other redox-sensitive metal species in nature.

  6. Kinetics of Reduction of Fe(III) Complexes by Outer Membrane Cytochromes MtrC and OmcA of Shewanella oneidensis MR-1▿

    Science.gov (United States)

    Wang, Zheming; Liu, Chongxuan; Wang, Xuelin; Marshall, Matthew J.; Zachara, John M.; Rosso, Kevin M.; Dupuis, Michel; Fredrickson, James K.; Heald, Steve; Shi, Liang

    2008-01-01

    Because of their cell surface locations, the outer membrane c-type cytochromes MtrC and OmcA of Shewanella oneidensis MR-1 have been suggested to be the terminal reductases for a range of redox-reactive metals that form poorly soluble solids or that do not readily cross the outer membrane. In this work, we determined the kinetics of reduction of a series of Fe(III) complexes with citrate, nitrilotriacetic acid (NTA), and EDTA by MtrC and OmcA using a stopped-flow technique in combination with theoretical computation methods. Stopped-flow kinetic data showed that the reaction proceeded in two stages, a fast stage that was completed in less than 1 s, followed by a second, relatively slower stage. For a given complex, electron transfer by MtrC was faster than that by OmcA. For a given cytochrome, the reaction was completed in the order Fe-EDTA > Fe-NTA > Fe-citrate. The kinetic data could be modeled by two parallel second-order bimolecular redox reactions with second-order rate constants ranging from 0.872 μM−1 s−1 for the reaction between MtrC and the Fe-EDTA complex to 0.012 μM−1 s−1 for the reaction between OmcA and Fe-citrate. The biphasic reaction kinetics was attributed to redox potential differences among the heme groups or redox site heterogeneity within the cytochromes. The results of redox potential and reorganization energy calculations showed that the reaction rate was influenced mostly by the relatively large reorganization energy. The results demonstrate that ligand complexation plays an important role in microbial dissimilatory reduction and mineral transformation of iron, as well as other redox-sensitive metal species in nature. PMID:18791025

  7. Irreversible processes kinetic theory

    CERN Document Server

    Brush, Stephen G

    2013-01-01

    Kinetic Theory, Volume 2: Irreversible Processes deals with the kinetic theory of gases and the irreversible processes they undergo. It includes the two papers by James Clerk Maxwell and Ludwig Boltzmann in which the basic equations for transport processes in gases are formulated, together with the first derivation of Boltzmann's ""H-theorem"" and a discussion of this theorem, along with the problem of irreversibility.Comprised of 10 chapters, this volume begins with an introduction to the fundamental nature of heat and of gases, along with Boltzmann's work on the kinetic theory of gases and s

  8. Unconventional ligands and modulators of nicotinic receptors

    National Research Council Canada - National Science Library

    Pereira, Edna F.R; Hilmas, Corey; Santos, Mariton D; Alkondon, Manickavasagom; Maelicke, Alfred; Albuquerque, Edson X

    2002-01-01

    .... In the mammalian brain, neuronal nAChRs, in addition to mediating fast synaptic transmission, modulate fast synaptic transmission mediated by the major excitatory and inhibitory neurotransmitters...

  9. FAST joins Breakthrough programme

    Science.gov (United States)

    Banks, Michael

    2016-11-01

    The 180m Five-hundred-meter Aperture Spherical radio Telescope (FAST) - the world's largest single-aperture radio receiver - has become part of the Breakthrough Listen programme, which launched in July 2015 to look for intelligent life beyond Earth.

  10. CMS Fast Facts

    Data.gov (United States)

    U.S. Department of Health & Human Services — CMS has developed a new quick reference statistical summary on annual CMS program and financial data. CMS Fast Facts includes summary information on total program...

  11. Kinetic Scale Structure of Low-frequency Waves and Fluctuations

    Science.gov (United States)

    López, Rodrigo A.; Viñas, Adolfo F.; Araneda, Jaime A.; Yoon, Peter H.

    2017-08-01

    The dissipation of solar wind turbulence at kinetic scales is believed to be important for the heating of the corona and for accelerating the wind. The linear Vlasov kinetic theory is a useful tool for identifying various wave modes, including kinetic Alfvén, fast magnetosonic/whistler, and ion-acoustic (or kinetic slow), and their possible roles in the dissipation. However, the kinetic mode structure in the vicinity of ion-cyclotron modes is not clearly understood. The present paper aims to further elucidate the structure of these low-frequency waves by introducing discrete particle effects through hybrid simulations and Klimontovich formalism of spontaneous emission theory. The theory and simulation of spontaneously emitted low-frequency fluctuations are employed to identify and distinguish the detailed mode structures associated with ion-Bernstein modes versus quasi-modes. The spontaneous emission theory and simulation also confirm the findings of the Vlasov theory in that the kinetic Alfvén waves can be defined over a wide range of frequencies, including the proton cyclotron frequency and its harmonics, especially for high-beta plasmas. This implies that these low-frequency modes may play predominant roles even in the fully kinetic description of kinetic scale turbulence and dissipation despite the fact that cyclotron harmonic and Bernstein modes may also play important roles in wave-particle interactions.

  12. Sorption kinetics and its effects on retention and leaching.

    Science.gov (United States)

    de Wilde, Tineke; Mertens, Jan; Spanoghe, Pieter; Ryckeboer, Jaak; Jaeken, Peter; Springael, Dirk

    2008-06-01

    Sorption of pesticides to substrates used in biopurification systems is important as it controls the system's efficiency. Ideally, pesticide sorption should occur fast so that leaching of the pesticide in the biopurification system is minimized. Although modeling of pesticide transport commonly assumes equilibrium, this may not always be true in practice. Sorption kinetics have to be taken into account. This study investigated the batch sorption kinetics of linuron, isoproturon, metalaxyl, isoxaben and lenacil on substrates commonly used in a biopurification system, i.e. cow manure, straw, willow chopping, sandy loam soil, coconut chips, garden waste compost and peat mix. The first-order sorption kinetics model was fitted to the observed pesticide concentrations versus time resulting in an estimated kinetic rate constant alpha. Sorption appeared to be fast for the pesticides linuron and isoxaben, pesticides which were classified as immobile, while less mobile pesticides displayed an overall slower sorption. However, the substrate does not seem to be the main parameter influencing the sorption kinetics. Coconut chips, which is a substrate with a high organic matter content showed slow sorption for most of the pesticides. The effect of different estimated alpha values on the breakthrough of pesticides through a biopurification system was evaluated using the HYDRUS 1D model. Significant differences in leaching behavior were observed as a result of the obtained differences in sorption kinetics.

  13. FAST Maser Surveys

    Indian Academy of Sciences (India)

    J. S. Zhang

    2014-09-01

    FAST, the Five-hundred meter Aperture Spherical radio Telescope, will become the largest operating single-dish telescope in the coming years. It has many advantages: much better sensitivity for its largest collecting area; large sky coverage due to its innovative design of the active primary surface; extremely radio quiet from its unique location, etc. In this work, I will highlight the future capabilities of FAST to discover and observe both galactic and extragalactic masers.

  14. Utilization of extracellular information before ligand-receptor binding reaches equilibrium expands and shifts the input dynamic range

    Science.gov (United States)

    Ventura, Alejandra C.; Bush, Alan; Vasen, Gustavo; Goldín, Matías A.; Burkinshaw, Brianne; Bhattacharjee, Nirveek; Folch, Albert; Brent, Roger; Chernomoretz, Ariel; Colman-Lerner, Alejandro

    2014-01-01

    Cell signaling systems sense and respond to ligands that bind cell surface receptors. These systems often respond to changes in the concentration of extracellular ligand more rapidly than the ligand equilibrates with its receptor. We demonstrate, by modeling and experiment, a general “systems level” mechanism cells use to take advantage of the information present in the early signal, before receptor binding reaches a new steady state. This mechanism, pre-equilibrium sensing and signaling (PRESS), operates in signaling systems in which the kinetics of ligand-receptor binding are slower than the downstream signaling steps, and it typically involves transient activation of a downstream step. In the systems where it operates, PRESS expands and shifts the input dynamic range, allowing cells to make different responses to ligand concentrations so high as to be otherwise indistinguishable. Specifically, we show that PRESS applies to the yeast directional polarization in response to pheromone gradients. Consideration of preexisting kinetic data for ligand-receptor interactions suggests that PRESS operates in many cell signaling systems throughout biology. The same mechanism may also operate at other levels in signaling systems in which a slow activation step couples to a faster downstream step. PMID:25172920

  15. Ligand placement based on prior structures: the guided ligand-replacement method

    Energy Technology Data Exchange (ETDEWEB)

    Klei, Herbert E. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Bristol-Myers Squibb, Princeton, NJ 08543-4000 (United States); Moriarty, Nigel W., E-mail: nwmoriarty@lbl.gov; Echols, Nathaniel [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Terwilliger, Thomas C. [Los Alamos National Laboratory, Los Alamos, NM 87545-0001 (United States); Baldwin, Eric T. [Bristol-Myers Squibb, Princeton, NJ 08543-4000 (United States); Natural Discovery LLC, Princeton, NJ 08542-0096 (United States); Pokross, Matt; Posy, Shana [Bristol-Myers Squibb, Princeton, NJ 08543-4000 (United States); Adams, Paul D. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); University of California at Berkeley, Berkeley, CA 94720-1762 (United States)

    2014-01-01

    A new module, Guided Ligand Replacement (GLR), has been developed in Phenix to increase the ease and success rate of ligand placement when prior protein-ligand complexes are available. The process of iterative structure-based drug design involves the X-ray crystal structure determination of upwards of 100 ligands with the same general scaffold (i.e. chemotype) complexed with very similar, if not identical, protein targets. In conjunction with insights from computational models and assays, this collection of crystal structures is analyzed to improve potency, to achieve better selectivity and to reduce liabilities such as absorption, distribution, metabolism, excretion and toxicology. Current methods for modeling ligands into electron-density maps typically do not utilize information on how similar ligands bound in related structures. Even if the electron density is of sufficient quality and resolution to allow de novo placement, the process can take considerable time as the size, complexity and torsional degrees of freedom of the ligands increase. A new module, Guided Ligand Replacement (GLR), was developed in Phenix to increase the ease and success rate of ligand placement when prior protein–ligand complexes are available. At the heart of GLR is an algorithm based on graph theory that associates atoms in the target ligand with analogous atoms in the reference ligand. Based on this correspondence, a set of coordinates is generated for the target ligand. GLR is especially useful in two situations: (i) modeling a series of large, flexible, complicated or macrocyclic ligands in successive structures and (ii) modeling ligands as part of a refinement pipeline that can automatically select a reference structure. Even in those cases for which no reference structure is available, if there are multiple copies of the bound ligand per asymmetric unit GLR offers an efficient way to complete the model after the first ligand has been placed. In all of these applications, GLR

  16. Fasting and Urinary Stones

    Directory of Open Access Journals (Sweden)

    Ali Shamsa

    2013-11-01

    Full Text Available Introduction: Fasting is considered as one of the most important practices of Islam, and according to Prophet Mohammad, fasting is obligatory upon Muslims. The aim of this study is to evaluate the effects of fasting on urinary stones. Materials and Methods: Very few studies have been carried out on urinary stones and the effect of Ramadan fasting. The sources of the present study are Medline and articles presented by local and Muslim researchers. Meanwhile, since we are acquainted with three well-known researchers in the field of urology, we contacted them via email and asked for their professional opinions. Results: The results of studies about the relationship of urinary stones and their incidence in Ramadan are not alike, and are even sometimes contradictory. Some believe that increased incidence of urinary stones in Ramadan is related not to fasting, but to the rise of weather temperature in hot months, and an increase in humidity. Conclusion: Numerous biological and behavioral changes occur in people who fast in Ramadan and some researchers believe that urinary stone increases during this month.

  17. Fasting and urinary stones

    Directory of Open Access Journals (Sweden)

    Ali Shamsa

    2013-12-01

    Full Text Available Introduction: Fasting is considered as one of the most important practices of Islam, and according to Prophet Mohammad, fasting is obligatory upon Muslims. The aim of this study is to evaluate the effects of fasting on urinary stones. Materials and Methods:Very few studies have been carried out on urinary stones and the effect of Ramadan fasting. The sources of the present study are Medline and articles presented by local and Muslim researchers. Meanwhile, since we are acquainted with three well-known researchers in the field  of urology, we contacted them via email and asked for their professional opinions. Results:The results of studies about the relationship of urinary stones and their incidence in Ramadan are not alike, and are even sometimes contradictory. Some believe that increased incidence of urinary stones in Ramadan is related not to fasting, but to the rise of weather temperature in hot months, and an increase in humidity. Conclusion: Numerous biological and behavioral changes occur in people who fast in Ramadan and some researchers believe that urinary stone increases during this month.

  18. Stochastic description of the ligand-receptor interaction of biologically active substances at extremely low doses.

    Science.gov (United States)

    Gurevich, Konstantin G; Agutter, Paul S; Wheatley, Denys N

    2003-04-01

    Signalling molecules can be effective at extraordinarily low concentrations (down to attomolar levels). To handle such cases, probabilistic methods have been used to describe the formal kinetics of action of biologically active substances in these low doses, although it has been necessary to review what is meant by such a term. The mean numbers of transformed/degraded molecules and their dispersions were calculated for the possible range of ligand-receptor binding schemes. We used both analytical equations and numerical simulations to calculate the coefficients of variation (ratio of standard deviation to mean) and demonstrated that the distribution of the coefficient is highly dependent on the reaction scheme. It may, therefore, be used as an additional factor for discriminating between cooperative and noncooperative models of ligand-receptor interaction over extreme ranges of ligand dilution. The relevance to signalling behaviour is discussed.

  19. A comparison of various optimization algorithms of protein-ligand docking programs by fitness accuracy.

    Science.gov (United States)

    Guo, Liyong; Yan, Zhiqiang; Zheng, Xiliang; Hu, Liang; Yang, Yongliang; Wang, Jin

    2014-07-01

    In protein-ligand docking, an optimization algorithm is used to find the best binding pose of a ligand against a protein target. This algorithm plays a vital role in determining the docking accuracy. To evaluate the relative performance of different optimization algorithms and provide guidance for real applications, we performed a comparative study on six efficient optimization algorithms, containing two evolutionary algorithm (EA)-based optimizers (LGA, DockDE) and four particle swarm optimization (PSO)-based optimizers (SODock, varCPSO, varCPSO-ls, FIPSDock), which were implemented into the protein-ligand docking program AutoDock. We unified the objective functions by applying the same scoring function, and built a new fitness accuracy as the evaluation criterion that incorporates optimization accuracy, robustness, and efficiency. The varCPSO and varCPSO-ls algorithms show high efficiency with fast convergence speed. However, their accuracy is not optimal, as they cannot reach very low energies. SODock has the highest accuracy and robustness. In addition, SODock shows good performance in efficiency when optimizing drug-like ligands with less than ten rotatable bonds. FIPSDock shows excellent robustness and is close to SODock in accuracy and efficiency. In general, the four PSO-based algorithms show superior performance than the two EA-based algorithms, especially for highly flexible ligands. Our method can be regarded as a reference for the validation of new optimization algorithms in protein-ligand docking.

  20. Ligand conjugation to bimodal poly(ethylene glycol) brush layers on microbubbles.

    Science.gov (United States)

    Chen, Cherry C; Borden, Mark A

    2010-08-17

    Using microbubbles as model systems, we examined molecular diffusion and binding to colloidal surfaces in bimodal poly(ethylene glycol) (PEG) brush layers. A microbubble is a gaseous colloidal particle with a diameter of less than 10 mum, of which the surface comprises amphiphilic phospholipids self-assembled to form a lipid monolayer shell. Due to the compressible gas core, microbubbles provide a sensitive acoustic response and are currently used as ultrasound contrast agents. Similar to the design of long circulating liposomes, PEG chains are typically incorporated into the shell of microbubbles to form a steric barrier against coalescence and adsorption of macromolecules to the microbubble surface. We introduced a buried-ligand architecture (BLA) design where the microbubble surface was coated with a bimodal PEG brush. After microbubbles were generated, fluorescent ligands with different molecular weights were conjugated to the tethered functional groups on the shorter PEG chains, while the longer PEG chains served as a shield to protect these ligands from exposure to the surrounding environment. BLA microbubbles reduced the binding of macromolecules (>10 kDa) to the tethers due to the steric hindrance of the PEG overbrush while allowing the uninhibited attachment of small molecules (microbubbles compared to exposed-ligand architecture (ELA) microbubbles. The binding of SA-FITC to BLA microbubbles suggested a possible phase separation between the lipid species on the surface leading to populations of revealed and concealed ligands. Ligand conjugation kinetics was independent of microbubble size, regardless of ligand size or microbubble architecture. We observed, for the first time, streptavidin-induced surface structure formation for ELA microbubbles and proposed that this phenomenon may be correlated to flow cytometry scattering measurements. We therefore demonstrated the feasibility of postlabeling for small-molecule ligands to BLA microbubbles to generate

  1. The Kinetics of Formation and Decomposition of Austenite in Relation to Carbide Morphology

    Science.gov (United States)

    Alvarenga, Henrique Duarte; Van Steenberge, Nele; Sietsma, Jilt; Terryn, Herman

    2017-02-01

    The effect of the carbide morphology on the kinetics of austenite formation and its decomposition was investigated by a combination of measurements of austenite fraction by dilatometry and metallography. These measurements show that coarse carbide morphology is generated by fast cooling through the early stages of eutectoid transformation, enabling fast precipitation of pro-eutectoid ferrite, followed by slow cooling during the final stages of transformation, during the precipitation of carbides. Additionally, a strong influence of the morphology of carbides on the kinetics of austenite formation is observed. The presence of coarse carbides can determine the rate of austenite formation during intercritical annealing as a result of its slow dissolution kinetics.

  2. Kinetic equations: computation

    CERN Document Server

    Pareschi, Lorenzo

    2013-01-01

    Kinetic equations bridge the gap between a microscopic description and a macroscopic description of the physical reality. Due to the high dimensionality the construction of numerical methods represents a challenge and requires a careful balance between accuracy and computational complexity.

  3. Thermal kinetic inductance detector

    Energy Technology Data Exchange (ETDEWEB)

    Cecil, Thomas; Gades, Lisa; Miceli, Antonio; Quaranta, Orlando

    2016-12-20

    A microcalorimeter for radiation detection that uses superconducting kinetic inductance resonators as the thermometers. The detector is frequency-multiplexed which enables detector systems with a large number of pixels.

  4. Chemical Kinetics Database

    Science.gov (United States)

    SRD 17 NIST Chemical Kinetics Database (Web, free access)   The NIST Chemical Kinetics Database includes essentially all reported kinetics results for thermal gas-phase chemical reactions. The database is designed to be searched for kinetics data based on the specific reactants involved, for reactions resulting in specified products, for all the reactions of a particular species, or for various combinations of these. In addition, the bibliography can be searched by author name or combination of names. The database contains in excess of 38,000 separate reaction records for over 11,700 distinct reactant pairs. These data have been abstracted from over 12,000 papers with literature coverage through early 2000.

  5. Ultrafast Spectroscopy Evidence for Picosecond Ligand Exchange at the Binding Site of a Heme Protein: Heme-Based Sensor YddV.

    Science.gov (United States)

    Lambry, Jean-Christophe; Stranava, Martin; Lobato, Laura; Martinkova, Marketa; Shimizu, Toru; Liebl, Ursula; Vos, Marten H

    2016-01-07

    An important question for the functioning of heme proteins is whether different ligands present within the protein moiety can readily exchange with heme-bound ligands. Studying the dynamics of the heme domain of the Escherichia coli sensor protein YddV upon dissociation of NO from the ferric heme by ultrafast spectroscopy, we demonstrate that when the hydrophobic leucine residue in the distal heme pocket is mutated to glycine, in a substantial fraction of the protein water replaces NO as an internal ligand in as fast as ∼4 ps. This process, which is near-barrierless and occurs orders of magnitude faster than the corresponding process in myoglobin, corresponds to a ligand swap of NO with a water molecule present in the heme pocket, as corroborated by molecular dynamics simulations. Our findings provide important new insight into ligand exchange in heme proteins that functionally interact with different external ligands.

  6. Kinetics of methane and carbon dioxide sorption and sorption–induced expansion of coal – kinetic equations assessment

    Directory of Open Access Journals (Sweden)

    Czerw Katarzyna

    2016-01-01

    Full Text Available The aim of this study was to investigate the ability of kinetic equations to describe the sorption kinetics and expansion rate of solid coal samples. In order to address his issue the sorption kinetics of methane and carbon dioxide on bituminous coals were studied. At the same time, the changes occurring in the sample’s overall dimensions, which accompanied sorption processes, were monitored. Experiments were carried out at high pressure by means of the volumetric method on a cubicoid solid samples. Several literature-based modeling approaches and equations are proposed to fit the kinetic curves of gas deposition, as well as the adequate kinetics of coal swelling. First equation represents the traditional approach to interpret experimental data in terms of fast and slow sorption process and consider the combination of two first-order rate functions. The other empirical kinetic equations are: the pseudo-second-order kinetic equation (PSOE, Elovich equation and the stretched exponential equation (SE. Two of the four equations are suitable to describe the kinetics of methane and carbon dioxide sorption and have been successfully used to quantify the observed dilatometric phenomena rates. The stretched exponential equation gave the best fit to the experimental data.

  7. Kinetics of human sperm acrosomal exocytosis.

    Science.gov (United States)

    Sosa, C M; Pavarotti, M A; Zanetti, M N; Zoppino, F C M; De Blas, G A; Mayorga, L S

    2015-03-01

    The acrosome reaction is a unique event in the lifespan of sperm characterized by the exocytosis of the acrosomal content and the release of hybrid vesicles formed by patches of the outer acrosomal membrane and the plasma membrane. This unique regulated exocytosis is mediated by essentially the same membrane fusion machinery present in neuroendocrine cells. However, whereas secretion in neuroendocrine cells occurs in less than a second, the acrosome reaction is normally assessed after several minutes of incubation with inducers. In this report, we measured the kinetics of human sperm exocytosis triggered by two stimuli (calcium ionophore and progesterone) by using electron microscopy and three different approaches based on the incorporation of fluorescent Pisum sativum agglutinin into the acrosome upon opening of fusion pores connecting the extracellular medium with the acrosomal lumen. The results with the different methods are consistent with a slow kinetics (t½ = 14 min). We also manipulated the system to measure different steps of the process. We observed that cytosolic calcium increased with a relatively fast kinetics (t½ = 0.1 min). In contrast, the swelling of the acrosomal granule that precedes exocytosis was a slow process (t½ = 13 min). When swelling was completed, the fusion pore opening was fast (t½ = 0.2 min). The results indicate that acrosomal swelling is the slowest step and it determines the kinetics of the acrosome reaction. After the swelling is completed, the efflux of calcium from intracellular stores triggers fusion pores opening and the release of hybrid vesicles in seconds.

  8. Electrochemical kinetics theoretical aspects

    CERN Document Server

    Vetter, Klaus J

    1967-01-01

    Electrochemical Kinetics: Theoretical Aspects focuses on the processes, methodologies, reactions, and transformations in electrochemical kinetics. The book first offers information on electrochemical thermodynamics and the theory of overvoltage. Topics include equilibrium potentials, concepts and definitions, electrical double layer and electrocapillarity, and charge-transfer, diffusion, and reaction overvoltage. Crystallization overvoltage, total overvoltage, and resistance polarization are also discussed. The text then examines the methods of determining electrochemical reaction mechanisms

  9. CB receptor ligands from plants.

    Science.gov (United States)

    Woelkart, Karin; Salo-Ahen, Outi M H; Bauer, Rudolf

    2008-01-01

    Advances in understanding the physiology and pharmacology of the endogenous cannabinoid system have potentiated the interest of cannabinoid receptors as potential therapeutic targets. Cannabinoids have been shown to modulate a variety of immune cell functions and have therapeutic implications on central nervous system (CNS) inflammation, chronic inflammatory conditions such as arthritis, and may be therapeutically useful in treating autoimmune conditions such as multiple sclerosis. Many of these drug effects occur through cannabinoid receptor signalling mechanisms and the modulation of cytokines and other gene products. Further, endocannabinoids have been found to have many physiological and patho-physiological functions, including mood alteration and analgesia, control of energy balance, gut motility, motor and co-ordination activities, as well as alleviation of neurological, psychiatric and eating disorders. Plants offer a wide range of chemical diversity and have been a growing domain in the search for effective cannabinoid ligands. Cannabis sativa L. with the known plant cannabinoid, Delta(9-)tetrahydrocannabinol (THC) and Echinacea species with the cannabinoid (CB) receptor-binding lipophilic alkamides are the best known herbal cannabimimetics. This review focuses on the state of the art in CB ligands from plants, as well their possible therapeutic and immunomodulatory effects.

  10. Ligand photo-isomerization triggers conformational changes in iGluR2 ligand binding domain.

    Directory of Open Access Journals (Sweden)

    Tino Wolter

    Full Text Available Neurological glutamate receptors bind a variety of artificial ligands, both agonistic and antagonistic, in addition to glutamate. Studying their small molecule binding properties increases our understanding of the central nervous system and a variety of associated pathologies. The large, oligomeric multidomain membrane protein contains a large and flexible ligand binding domains which undergoes large conformational changes upon binding different ligands. A recent application of glutamate receptors is their activation or inhibition via photo-switchable ligands, making them key systems in the emerging field of optochemical genetics. In this work, we present a theoretical study on the binding mode and complex stability of a novel photo-switchable ligand, ATA-3, which reversibly binds to glutamate receptors ligand binding domains (LBDs. We propose two possible binding modes for this ligand based on flexible ligand docking calculations and show one of them to be analogues to the binding mode of a similar ligand, 2-BnTetAMPA. In long MD simulations, it was observed that transitions between both binding poses involve breaking and reforming the T686-E402 protein hydrogen bond. Simulating the ligand photo-isomerization process shows that the two possible configurations of the ligand azo-group have markedly different complex stabilities and equilibrium binding modes. A strong but slow protein response is observed after ligand configuration changes. This provides a microscopic foundation for the observed difference in ligand activity upon light-switching.

  11. PL-PatchSurfer: A Novel Molecular Local Surface-Based Method for Exploring Protein-Ligand Interactions

    Directory of Open Access Journals (Sweden)

    Bingjie Hu

    2014-08-01

    Full Text Available Structure-based computational methods have been widely used in exploring protein-ligand interactions, including predicting the binding ligands of a given protein based on their structural complementarity. Compared to other protein and ligand representations, the advantages of a surface representation include reduced sensitivity to subtle changes in the pocket and ligand conformation and fast search speed. Here we developed a novel method named PL-PatchSurfer (Protein-Ligand PatchSurfer. PL-PatchSurfer represents the protein binding pocket and the ligand molecular surface as a combination of segmented surface patches. Each patch is characterized by its geometrical shape and the electrostatic potential, which are represented using the 3D Zernike descriptor (3DZD. We first tested PL-PatchSurfer on binding ligand prediction and found it outperformed the pocket-similarity based ligand prediction program. We then optimized the search algorithm of PL-PatchSurfer using the PDBbind dataset. Finally, we explored the utility of applying PL-PatchSurfer to a larger and more diverse dataset and showed that PL-PatchSurfer was able to provide a high early enrichment for most of the targets. To the best of our knowledge, PL-PatchSurfer is the first surface patch-based method that treats ligand complementarity at protein binding sites. We believe that using a surface patch approach to better understand protein-ligand interactions has the potential to significantly enhance the design of new ligands for a wide array of drug-targets.

  12. Measurement of protein-ligand complex formation.

    Science.gov (United States)

    Lowe, Peter N; Vaughan, Cara K; Daviter, Tina

    2013-01-01

    Experimental approaches to detect, measure, and quantify protein-ligand binding, along with their theoretical bases, are described. A range of methods for detection of protein-ligand interactions is summarized. Specific protocols are provided for a nonequilibrium procedure pull-down assay, for an equilibrium direct binding method and its modification into a competition-based measurement and for steady-state measurements based on the effects of ligands on enzyme catalysis.

  13. Explicit Integration with GPU Acceleration for Large Kinetic Networks

    CERN Document Server

    Brock, Benjamin; Billings, Jay Jay; Guidry, Mike

    2014-01-01

    We demonstrate the first implementation of recently-developed fast explicit kinetic integration algorithms on modern graphics processing unit (GPU) accelerators. Taking as a generic test case a Type Ia supernova explosion with an extremely stiff thermonuclear network having 150 isotopic species and 1604 reactions coupled to hydrodynamics using operator splitting, we demonstrate the capability to solve of order 100 realistic kinetic networks in parallel in the same time that standard implicit methods can solve a single such network on a CPU. This orders-of-magnitude decrease in compute time for solving systems of realistic kinetic networks implies that important coupled, multiphysics problems in various scientific and technical fields that were intractible, or could be simulated only with highly schematic kinetic networks, are now computationally feasible.

  14. The Szilard-Chalmers effect in macrocyclic ligands to increase the specific activity of reactor-produced radiolanthanides. Experiments and explanations

    Energy Technology Data Exchange (ETDEWEB)

    Zhernosekov, K.P.; Roesch, F. [Mainz Univ. (Germany). Inst. of Nuclear Chemistry; Filosofov, D.V. [Laboratory of Nuclear Problems, Dubna (Russian Federation). Joint Inst. of Nuclear Research

    2012-07-01

    Successful utilization of medical isotopes in the radiolabeling reactions to a significant degree depends on the technically achievable specific activity. In this respect, the Szilard-Chalmers effect is considered in detail as a radiochemical tool to increase the specific activity of radionuclides produced by direct nuclear reactions. In the present study, a physico-chemical model is described utilizing the specific aspects of thermodynamically and kinetically stabilised metal-ligand complexes. The approach is applied as a proof-of-principle study to increase the specific activity of {sup 166}Ho, produced via the (n,{gamma}) nuclear reaction. As a target material, {sup 165}Ho-DOTA is used. In this case, {sup 166}Ho, the product nucleus of the neutron capture reaction, is obtained chemically as non-complexed cationic {sup 166}Ho{sup III} species in situ. Consequently, it can effectively and quantitatively be separated from the inactive {sup 165}Ho-DOTA target material by means of fast and simple chromatographic, column-based methods. We were able to verify the physico-chemical model by the experimentally obtained data. For the first time we quantitatively describe the interaction of the ligand-framework of the target material (e.g. the Ho-DOTA complex) with the radiation field of the nuclear reactor. The analysis of the experimental data allows to assume that radionuclides with half-lives of T{sub 1/2} < 64 h can be produced at a TRIGA II nuclear reactor via the Szilard-Chalmers effect with specific activities higher than in the case of direct irradiation of common target materials such as oxides. (orig.)

  15. Computational protein-ligand docking and virtual drug screening with the AutoDock suite.

    Science.gov (United States)

    Forli, Stefano; Huey, Ruth; Pique, Michael E; Sanner, Michel F; Goodsell, David S; Olson, Arthur J

    2016-05-01

    Computational docking can be used to predict bound conformations and free energies of binding for small-molecule ligands to macromolecular targets. Docking is widely used for the study of biomolecular interactions and mechanisms, and it is applied to structure-based drug design. The methods are fast enough to allow virtual screening of ligand libraries containing tens of thousands of compounds. This protocol covers the docking and virtual screening methods provided by the AutoDock suite of programs, including a basic docking of a drug molecule with an anticancer target, a virtual screen of this target with a small ligand library, docking with selective receptor flexibility, active site prediction and docking with explicit hydration. The entire protocol will require ∼5 h.

  16. Thermal, spectroscopic, and solvent influence studies on mixed-ligand copper(II) complexes containing the bulky ligand: Bis[ N-( p-tolyl)imino]acenaphthene

    Science.gov (United States)

    El-Ayaan, Usama; Gabr, I. M.

    2007-05-01

    Four mixed-ligand copper(II) complexes containing the rigid bidentate nitrogen ligand bis[ N-( p-tolyl)imino]acenaphthene (abb. p-Tol-BIAN) ligand are reported. These complexes, namely [Cu( p-Tol-BIAN) 2](ClO 4) 21, [Cu( p-Tol-BIAN)(acac)](ClO 4) 2, [Cu( p-Tol-BIAN)Cl 2] 3 and [Cu( p-Tol-BIAN)(AcOH) 2](ClO 4) 24 (where acac, acetylacetonate and AcOH, acetic acid) have been prepared and characterized by elemental analysis, spectroscopic, magnetic and molar conductance measurements. ESR spectra suggest a square planar geometry for complexes 1 and 2. In complexes 3 and 4, a distorted tetrahedral arrangement around copper(II) centre was suggested. Solvatochromic behavior of all studied complexes indicates strong solvatochromism of their solutions. The observed solvatochromism is mainly due to the solute-solvent interaction between the chelate cation and the solvent molecules. Thermal properties and decomposition kinetics of all complexes are investigated. The kinetic parameters ( E, A, Δ H, Δ S and Δ G) of all thermal decomposition stages have been calculated using the Coats-Redfern and other standard equations.

  17. An Analogy Using Pennies and Dimes to Explain Chemical Kinetics Concepts

    Science.gov (United States)

    Cortes-Figueroa, Jose E.; Perez, Wanda I.; Lopez, Jose R.; Moore-Russo, Deborah A.

    2011-01-01

    In this article, the authors present an analogy that uses coins and graphical analysis to teach kinetics concepts and resolve pseudo-first-order rate constants related to transition-metal complexes ligand-solvent exchange reactions. They describe an activity that is directed to upper-division undergraduate and graduate students. The activity…

  18. The fast code

    Energy Technology Data Exchange (ETDEWEB)

    Freeman, L.N.; Wilson, R.E. [Oregon State Univ., Dept. of Mechanical Engineering, Corvallis, OR (United States)

    1996-09-01

    The FAST Code which is capable of determining structural loads on a flexible, teetering, horizontal axis wind turbine is described and comparisons of calculated loads with test data are given at two wind speeds for the ESI-80. The FAST Code models a two-bladed HAWT with degrees of freedom for blade bending, teeter, drive train flexibility, yaw, and windwise and crosswind tower motion. The code allows blade dimensions, stiffnesses, and weights to differ and models tower shadow, wind shear, and turbulence. Additionally, dynamic stall is included as are delta-3 and an underslung rotor. Load comparisons are made with ESI-80 test data in the form of power spectral density, rainflow counting, occurrence histograms, and azimuth averaged bin plots. It is concluded that agreement between the FAST Code and test results is good. (au)

  19. A fast friend

    Institute of Scientific and Technical Information of China (English)

    高怡

    2010-01-01

    我们都知道fast food的意思是“快餐”。那fast friend能解释为“快速或速成的朋友”吗?也许你会说:“什么是速成朋友呀?It doesn’t make sense.”没错,交朋友怎么会有速成的呢?原来;fast还有一个意思是“忠实的、牢固的”,所以a fast friend的真正意思是“可靠、忠实的朋友”。

  20. Fast Distributed Gradient Methods

    CERN Document Server

    Jakovetic, Dusan; Moura, Jose M F

    2011-01-01

    The paper proposes new fast distributed optimization gradient methods and proves convergence to the exact solution at rate O(\\log k/k), much faster than existing distributed optimization (sub)gradient methods with convergence O(1/\\sqrt{k}), while incurring practically no additional communication nor computation cost overhead per iteration. We achieve this for convex (with at least one strongly convex,) coercive, three times differentiable and with Lipschitz continuous first derivative (private) cost functions. Our work recovers for distributed optimization similar convergence rate gains obtained by centralized Nesterov gradient and fast iterative shrinkage-thresholding algorithm (FISTA) methods over ordinary centralized gradient methods. We also present a constant step size distributed fast gradient algorithm for composite non-differentiable costs. A simulation illustrates the effectiveness of our distributed methods.

  1. Fast ejendom II

    DEFF Research Database (Denmark)

    Munk-Hansen, Carsten

    Fremstillingen påviser, at lov om forbrugerbeskyttelse ved erhvervelse af fast ejendom mv. lider af en række svagheder og at ankenævnspraksis bevæger sig væk fra retspraksis på en række områder.......Fremstillingen påviser, at lov om forbrugerbeskyttelse ved erhvervelse af fast ejendom mv. lider af en række svagheder og at ankenævnspraksis bevæger sig væk fra retspraksis på en række områder....

  2. Moms og fast ejendom

    DEFF Research Database (Denmark)

    Edlund, Hans Henrik

    1999-01-01

    I artiklen gives et overblik over, hvorledes fast ejendom behandles momsmæssigt. Derfor findes en kort skitsering af reglerne for moms på byggearbejder, afgrænsningen mellem momspligtig og momsfri udlejning, muligheden for frivillig registrering af udlejning samt opgørelse af reguleringsforpligte......I artiklen gives et overblik over, hvorledes fast ejendom behandles momsmæssigt. Derfor findes en kort skitsering af reglerne for moms på byggearbejder, afgrænsningen mellem momspligtig og momsfri udlejning, muligheden for frivillig registrering af udlejning samt opgørelse af...

  3. Fast Josephson vortex

    Energy Technology Data Exchange (ETDEWEB)

    Malishevskii, A.S.; Silin, V.P.; Uryupin, S.A

    2002-12-30

    For the magnetically coupled waveguide and long Josephson junction we gave the analytic description of two separate velocity domains where the free motion of traveling vortex (2{pi}-kink) exists. The role of the mutual influence of waveguide and long Josephson junction is discussed. It is shown the possibility of the fast vortex motion with the velocity much larger than Swihart velocity of Josephson junction and close to the speed of light in the waveguide. The excitation of motion of such fast Josephson vortex is described.

  4. ATLAS fast physics monitoring

    Indian Academy of Sciences (India)

    Karsten Köneke; on behalf of the ATLAS Collaboration

    2012-11-01

    The ATLAS experiment at the Large Hadron Collider is recording data from proton–proton collisions at a centre-of-mass energy of 7 TeV since the spring of 2010. The integrated luminosity has grown nearly exponentially since then and continues to rise fast. The ATLAS Collaboration has set up a framework to automatically process the rapidly growing dataset and produce performance and physics plots for the most interesting analyses. The system is designed to give fast feedback. The histograms are produced within hours of data reconstruction (2–3 days after data taking). Hints of potentially interesting physics signals obtained this way are followed up by physics groups.

  5. Multiple alternative substrate kinetics.

    Science.gov (United States)

    Anderson, Vernon E

    2015-11-01

    The specificity of enzymes for their respective substrates has been a focal point of enzyme kinetics since the initial characterization of metabolic chemistry. Various processes to quantify an enzyme's specificity using kinetics have been utilized over the decades. Fersht's definition of the ratio kcat/Km for two different substrates as the "specificity constant" (ref [7]), based on the premise that the important specificity existed when the substrates were competing in the same reaction, has become a consensus standard for enzymes obeying Michaelis-Menten kinetics. The expansion of the theory for the determination of the relative specificity constants for a very large number of competing substrates, e.g. those present in a combinatorial library, in a single reaction mixture has been developed in this contribution. The ratio of kcat/Km for isotopologs has also become a standard in mechanistic enzymology where kinetic isotope effects have been measured by the development of internal competition experiments with extreme precision. This contribution extends the theory of kinetic isotope effects to internal competition between three isotopologs present at non-tracer concentrations in the same reaction mix. This article is part of a special issue titled: Enzyme Transition States from Theory and Experiment.

  6. Onsager reciprocity principle for kinetic models and kinetic schemes

    CERN Document Server

    Mahendra, Ajit Kumar

    2013-01-01

    Boltzmann equation requires some alternative simpler kinetic model like BGK to replace the collision term. Such a kinetic model which replaces the Boltzmann collision integral should preserve the basic properties and characteristics of the Boltzmann equation and comply with the requirements of non equilibrium thermodynamics. Most of the research in development of kinetic theory based methods have focused more on entropy conditions, stability and ignored the crucial aspect of non equilibrium thermodynamics. The paper presents a new kinetic model formulated based on the principles of non equilibrium thermodynamics. The new kinetic model yields correct transport coefficients and satisfies Onsager's reciprocity relationship. The present work also describes a novel kinetic particle method and gas kinetic scheme based on this linkage of non-equilibrium thermodynamics and kinetic theory. The work also presents derivation of kinetic theory based wall boundary condition which complies with the principles of non-equili...

  7. Catalytic water oxidation by mononuclear Ru complexes with an anionic ancillary ligand.

    Science.gov (United States)

    Tong, Lianpeng; Inge, A Ken; Duan, Lele; Wang, Lei; Zou, Xiaodong; Sun, Licheng

    2013-03-04

    Mononuclear Ru-based water oxidation catalysts containing anionic ancillary ligands have shown promising catalytic efficiency and intriguing properties. However, their insolubility in water restricts a detailed mechanism investigation. In order to overcome this disadvantage, complexes [Ru(II)(bpc)(bpy)OH2](+) (1(+), bpc = 2,2'-bipyridine-6-carboxylate, bpy = 2,2'-bipyridine) and [Ru(II)(bpc)(pic)3](+) (2(+), pic = 4-picoline) were prepared and fully characterized, which features an anionic tridentate ligand and has enough solubility for spectroscopic study in water. Using Ce(IV) as an electron acceptor, both complexes are able to catalyze O2-evolving reaction with an impressive rate constant. On the basis of the electrochemical and kinetic studies, a water nucleophilic attack pathway was proposed as the dominant catalytic cycle of the catalytic water oxidation by 1(+), within which several intermediates were detected by MS. Meanwhile, an auxiliary pathway that is related to the concentration of Ce(IV) was also revealed. The effect of anionic ligand regarding catalytic water oxidation was discussed explicitly in comparison with previously reported mononuclear Ru catalysts carrying neutral tridentate ligands, for example, 2,2':6',2″-terpyridine (tpy). When 2(+) was oxidized to the trivalent state, one of its picoline ligands dissociated from the Ru center. The rate constant of picoline dissociation was evaluated from time-resolved UV-vis spectra.

  8. Screening of Small Molecule Microarrays for Ligands Targeted to the Extracellular Epitopes of Living Cells

    Directory of Open Access Journals (Sweden)

    Jeong Heon Lee

    2015-02-01

    Full Text Available The screening of living cells using high-throughput microarrays is technically challenging. Great care must be taken in the chemical presentation of potential ligands and the number of collisions that cells make with them. To overcome these issues, we have developed a glass slide-based microarray system to discover small molecule ligands that preferentially bind to one cell type over another, including when the cells differ by only a single receptor. Chemical spots of 300 ± 10 µm in diameter are conjugated covalently to glass slides using an arraying robot, and novel near-infrared fluorophores with peak emission at 700 nm and 800 nm are used to label two different cell types. By carefully optimizing incubation conditions, including cell density, motion, kinetics, detection, etc. we demonstrate that cell-ligand binding occurs, and that the number of cells bound per chemical spot correlates with ligand affinity and specificity. This screening system lays the foundation for high-throughput discovery of novel ligands to the cell surface.

  9. Ligand-assisted, copper(II) acetate-accelerated azide-alkyne cycloaddition.

    Science.gov (United States)

    Michaels, Heather A; Zhu, Lei

    2011-10-04

    Polytriazole ligands such as the widely used tris[(1-benzyl-1H-1,2,3-triazol-4-yl)methyl]amine (TBTA), are shown to assist copper(II) acetate-mediated azide-alkyne cycloaddition (AAC) reactions that involve nonchelating azides. Tris(2-{4-[(dimethylamino)methyl]-1H-1,2,3-traizol-1-yl}ethyl)amine (DTEA) outperforms TBTA in a number of reactions. The satisfactory solubility of DTEA in a wide range of polar and nonpolar solvents, including water and toluene, renders it advantageous under copper(II) acetate-mediated conditions. The copper(II) acetate-mediated formation of the three triazolyl groups in a tris(triazolyl)-based ligand occurs sequentially with an inhibitory effect in the last step. The kinetic investigations of the ligand-assisted reactions reveal an interesting mechanistic dependence on the relative affinity of azide and alkyne to copper (II). In addition to expanding the scope of the copper(II) acetate-mediated AAC reactions to include nonchelating azides, this work offers evidence for the mechanistic synergy between the title reaction and the alkyne oxidative homocoupling reaction. The elucidation of the structural details of the polytriazole-ligand-bound reactive species in copper(I/II)-mediated AAC reactions, however, awaits further characterization of the metal coordination chemistry of polytriazole ligands. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Integrating folding kinetics and protein function: biphasic kinetics and dual binding specificity in a WW domain.

    Science.gov (United States)

    Karanicolas, John; Brooks, Charles L

    2004-03-09

    Because of the association of beta-sheet formation with the initiation and propagation of amyloid diseases, model systems have been sought to further our understanding of this process. WW domains have been proposed as one such model system. Whereas the folding of the WW domains from human Yes-associated protein (YAP) and Pin have been shown to obey single-exponential kinetics, the folding of the WW domain from formin-binding protein (FBP) 28 has been shown to proceed via biphasic kinetics. From an analysis of free-energy landscapes from atomic-level molecular dynamics simulations, the biphasic folding kinetics observed in the FBP WW domain may be traced to the ability of this WW domain to adopt two slightly different forms of packing in its hydrophobic core. This conformational change is propagated along the peptide backbone and affects the position of a tryptophan residue shown in other WW domains to play a key role in binding. The WW domains of Pin and YAP do not support more than one type of packing each, leading to monophasic folding kinetics. The ability of the FBP WW domain to assume two different types of packing may, in turn, explain the capacity of this WW domain to bind two classes of ligand, a property that is not shared by other WW domains. These findings lead to the hypothesis that lability with respect to conformations separated by an observable barrier as a requirement for function is incompatible with the ability of a protein to fold via single-exponential kinetics.

  11. Enzyme-catalyzed and binding reaction kinetics determined by titration calorimetry.

    Science.gov (United States)

    Hansen, Lee D; Transtrum, Mark K; Quinn, Colette; Demarse, Neil

    2016-05-01

    Isothermal calorimetry allows monitoring of reaction rates via direct measurement of the rate of heat produced by the reaction. Calorimetry is one of very few techniques that can be used to measure rates without taking a derivative of the primary data. Because heat is a universal indicator of chemical reactions, calorimetry can be used to measure kinetics in opaque solutions, suspensions, and multiple phase systems and does not require chemical labeling. The only significant limitation of calorimetry for kinetic measurements is that the time constant of the reaction must be greater than the time constant of the calorimeter which can range from a few seconds to a few minutes. Calorimetry has the unique ability to provide both kinetic and thermodynamic data. This article describes the calorimetric methodology for determining reaction kinetics and reviews examples from recent literature that demonstrate applications of titration calorimetry to determine kinetics of enzyme-catalyzed and ligand binding reactions. A complete model for the temperature dependence of enzyme activity is presented. A previous method commonly used for blank corrections in determinations of equilibrium constants and enthalpy changes for binding reactions is shown to be subject to significant systematic error. Methods for determination of the kinetics of enzyme-catalyzed reactions and for simultaneous determination of thermodynamics and kinetics of ligand binding reactions are reviewed. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Erbium hydride decomposition kinetics.

    Energy Technology Data Exchange (ETDEWEB)

    Ferrizz, Robert Matthew

    2006-11-01

    Thermal desorption spectroscopy (TDS) is used to study the decomposition kinetics of erbium hydride thin films. The TDS results presented in this report are analyzed quantitatively using Redhead's method to yield kinetic parameters (E{sub A} {approx} 54.2 kcal/mol), which are then utilized to predict hydrogen outgassing in vacuum for a variety of thermal treatments. Interestingly, it was found that the activation energy for desorption can vary by more than 7 kcal/mol (0.30 eV) for seemingly similar samples. In addition, small amounts of less-stable hydrogen were observed for all erbium dihydride films. A detailed explanation of several approaches for analyzing thermal desorption spectra to obtain kinetic information is included as an appendix.

  13. Equilibrium and kinetic selectivity profiling on the human adenosine receptors.

    Science.gov (United States)

    Guo, Dong; Dijksteel, Gabrielle S; van Duijl, Tirsa; Heezen, Maxime; Heitman, Laura H; IJzerman, Adriaan P

    2016-04-01

    Classical evaluation of target selectivity is usually undertaken by measuring the binding affinity of lead compounds against a number of potential targets under equilibrium conditions, without considering the kinetics of the ligand-receptor interaction. In the present study we propose a combined strategy including both equilibrium- and kinetics-based selectivity profiling. The adenosine receptor (AR) was chosen as a prototypical drug target. Six in-house AR antagonists were evaluated in a radioligand displacement assay for their affinity and in a competition association assay for their binding kinetics on three AR subtypes. One of the compounds with a promising kinetic selectivity profile was also examined in a [(35)S]-GTPγS binding assay for functional activity. We found that XAC and LUF5964 were kinetically more selective for the A1R and A3R, respectively, although they are non-selective in terms of their affinity. In comparison, LUF5967 displayed a strong equilibrium-based selectivity for the A1R over the A2AR, yet its kinetic selectivity thereon was less pronounced. In a GTPγS assay, LUF5964 exhibited insurmountable antagonism on the A3R while having a surmountable effect on the A1R, consistent with its kinetic selectivity profile. This study provides evidence that equilibrium and kinetic selectivity profiling can both be important in the early phases of the drug discovery process. Our proposed combinational strategy could be considered for future medicinal chemistry efforts and aid the design and discovery of different or even better leads for clinical applications.

  14. Cofactor-Controlled Chirality of Tropoisomeric Ligand

    NARCIS (Netherlands)

    Théveau, L.; Bellini, R.; Dydio, P.; Szabo, Z.; van der Werf, A.; Sander, R.A.; Reek, J.N.H.; Moberg, C.

    2016-01-01

    A new tropos ligand with an integrated anion receptor receptor site has been prepared. Chiral carboxylate and phosphate anions that bind in the anion receptor unit proved capable of stabilizing chiral conformations of the achiral flexible bidentate biaryl phosphite ligand, as shown by variable

  15. Flexible Ligand Docking Using Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Thomsen, Rene

    2003-01-01

    The docking of ligands to proteins can be formulated as a computational problem where the task is to find the most favorable energetic conformation among the large space of possible protein–ligand complexes. Stochastic search methods such as evolutionary algorithms (EAs) can be used to sample large...

  16. Flexible Ligand Docking Using Differential Evolution

    DEFF Research Database (Denmark)

    Thomsen, René

    2003-01-01

    the most favorable energetic conformation among the large space of possible protein-ligand complexes. Stochastic search methods, such as evolutionary algorithms (EAs), can be used to sample large search spaces effectively and is one of the preferred methods for flexible ligand docking. The differential...

  17. Rhodium olefin complexes of diiminate type ligands

    NARCIS (Netherlands)

    Willems, Sander Theodorus Hermanus

    2003-01-01

    The mono-anionic beta-diiminate ligand (ArNC(CH3)CHC(CH3)NAr) on several previous occasions proved useful in stabilising low coordination numbers for both early and late transition metals. In this thesis the reactivity of the rhodium olefin complexes of one of these beta-diiminate ligands (Ar = 2,6-

  18. Ligand sphere conversions in terminal carbide complexes

    DEFF Research Database (Denmark)

    Morsing, Thorbjørn Juul; Reinholdt, Anders; Sauer, Stephan P. A.

    2016-01-01

    Metathesis is introduced as a preparative route to terminal carbide complexes. The chloride ligands of the terminal carbide complex [RuC(Cl)2(PCy3)2] (RuC) can be exchanged, paving the way for a systematic variation of the ligand sphere. A series of substituted complexes, including the first exam...

  19. Fast magnetic reconnection in laser-produced plasma bubbles.

    Science.gov (United States)

    Fox, W; Bhattacharjee, A; Germaschewski, K

    2011-05-27

    Recent experiments have observed magnetic reconnection in high-energy-density, laser-produced plasma bubbles, with reconnection rates observed to be much higher than can be explained by classical theory. Based on fully kinetic particle simulations we find that fast reconnection in these strongly driven systems can be explained by magnetic flux pileup at the shoulder of the current sheet and subsequent fast reconnection via two-fluid, collisionless mechanisms. In the strong drive regime with two-fluid effects, we find that the ultimate reconnection time is insensitive to the nominal system Alfvén time.

  20. Handel med fast ejendom

    DEFF Research Database (Denmark)

    Edlund, Hans Henrik

    Bogen tilstræber at give et overblik over nogle af de vigtigste generelle problemområder på markedet for ejendomshandel, der jo bliver mere og mere kompliceret. Værket er opdelt i følgende hovedafsnit: Ejendomsbegrebet. Indgåelse af aftale om salg af fast ejendom. Begrænsninger i adgangen til...

  1. Not so fast

    DEFF Research Database (Denmark)

    Marras, Stefano; Noda, Takuji; Steffensen, John Fleng

    2015-01-01

    , it is an open question whether such supposedly very fast swimmers do use high-speed bursts when feeding on evasive prey, in addition to using their bill for slashing prey. Here, we measured the swimming behavior of sailfish by using high-frequency accelerometry and high-speed video observations during predator...

  2. Fast Passenger Tracks Network

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    China’s fast passenger tracks network consists of four parts:express rail- way with speeds between 300km/h and 350 kin/h,passenger rail lines with speeds between 200 km/h and 250 km/h,intercity high-speed railways that run

  3. Integral Fast Reactor concept

    Energy Technology Data Exchange (ETDEWEB)

    Till, C.E.; Chang, Y.I.

    1986-01-01

    The Integral Fast Reactor (IFR) is an innovative LMR concept, being developed at Argonne National Laboratory, that fully exploits the inherent properties of liquid metal cooling and metallic fuel to achieve breakthroughs in economics and inherent safety. This paper describes key features and potential advantages of the IFR concept, technology development status, fuel cycle economics potential, and future development path.

  4. Fast Air Temperature Sensors

    DEFF Research Database (Denmark)

    Hendricks, Elbert

    1998-01-01

    The note documents briefly work done on a newly developed sensor for making fast temperature measurements on the air flow in the intake ports of an SI engine and in the EGR input line. The work reviewed has been carried out in close cooperation with Civ. Ing. Michael Føns, the author (IAU...

  5. Parallel Fast Legendre Transform

    NARCIS (Netherlands)

    Alves de Inda, M.; Bisseling, R.H.; Maslen, D.K.

    2001-01-01

    We discuss a parallel implementation of a fast algorithm for the discrete polynomial Legendre transform We give an introduction to the DriscollHealy algorithm using polynomial arithmetic and present experimental results on the eciency and accuracy of our implementation The algorithms were implemente

  6. Foinaven fast track flowlines

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, L.H.; Mair, J.

    1996-12-31

    The decision by British Petroleum to develop offshore fields west of the Shetlands in water depths exceeding 500 meters within three and a half years of discovery posed a unique submarine pipeline installation challenge. This paper summarizes the salient features of a fast track program to install a diverless subsea pipeline system using rigid reeled pipe technology in an offshore frontier area.

  7. Fast food tips

    Science.gov (United States)

    ... Order smaller servings when you can. Split some fast-food items to reduce calories and fat. Ask for a "doggy bag." You can also leave the extra food on your plate. Your food choices can teach your children how to eat healthy, too. Choosing a variety ...

  8. Fast Fourier Orthogonalization

    NARCIS (Netherlands)

    Ducas, L.; Prest, T.; Abramov, S.A.; Zima, E.V.; Gao, X-S.

    2016-01-01

    The classical fast Fourier transform (FFT) allows to compute in quasi-linear time the product of two polynomials, in the {\\em circular convolution ring} R[x]/(x^d−1) --- a task that naively requires quadratic time. Equivalently, it allows to accelerate matrix-vector products when the matrix is *circ

  9. Tachycardia | Fast Heart Rate

    Science.gov (United States)

    ... SA) node --- the heart's natural pacemaker - sends out electrical signals faster than usual. The heart rate is fast, but the heart beats properly. Causes of sinus tachycardia A rapid heartbeat may be your body's response to common conditions such as: Fever Anxiety ...

  10. Quantum kinetic theory

    CERN Document Server

    Bonitz, Michael

    2016-01-01

    This book presents quantum kinetic theory in a comprehensive way. The focus is on density operator methods and on non-equilibrium Green functions. The theory allows to rigorously treat nonequilibrium dynamics in quantum many-body systems. Of particular interest are ultrafast processes in plasmas, condensed matter and trapped atoms that are stimulated by rapidly developing experiments with short pulse lasers and free electron lasers. To describe these experiments theoretically, the most powerful approach is given by non-Markovian quantum kinetic equations that are discussed in detail, including computational aspects.

  11. Asymmetric catalysis based on tropos ligands.

    Science.gov (United States)

    Aikawa, Kohsuke; Mikami, Koichi

    2012-11-21

    All enantiopure atropisomeric (atropos) ligands essentially require enantiomeric resolution or synthetic transformation from a chiral pool. In sharp contrast, the use of tropos (chirally flexible) ligands, which are highly modular, versatile, and easy to synthesize without enantiomeric resolution, has recently been the topic of much interest in asymmetric catalysis. Racemic catalysts bearing tropos ligands can be applied to asymmetric catalysis through enantiomeric discrimination by the addition of a chiral source, which preferentially transforms one catalyst enantiomer into a highly activated catalyst enantiomer. Additionally, racemic catalysts bearing tropos ligands can also be utilized as atropos enantiopure catalysts obtained via the control of chirality by a chiral source followed by the memory of chirality. In this feature article, our results on the asymmetric catalysis via the combination of various central metals and tropos ligands are summarized.

  12. Emergence of ion channel modal gating from independent subunit kinetics.

    Science.gov (United States)

    Bicknell, Brendan A; Goodhill, Geoffrey J

    2016-09-06

    Many ion channels exhibit a slow stochastic switching between distinct modes of gating activity. This feature of channel behavior has pronounced implications for the dynamics of ionic currents and the signaling pathways that they regulate. A canonical example is the inositol 1,4,5-trisphosphate receptor (IP3R) channel, whose regulation of intracellular Ca(2+) concentration is essential for numerous cellular processes. However, the underlying biophysical mechanisms that give rise to modal gating in this and most other channels remain unknown. Although ion channels are composed of protein subunits, previous mathematical models of modal gating are coarse grained at the level of whole-channel states, limiting further dialogue between theory and experiment. Here we propose an origin for modal gating, by modeling the kinetics of ligand binding and conformational change in the IP3R at the subunit level. We find good agreement with experimental data over a wide range of ligand concentrations, accounting for equilibrium channel properties, transient responses to changing ligand conditions, and modal gating statistics. We show how this can be understood within a simple analytical framework and confirm our results with stochastic simulations. The model assumes that channel subunits are independent, demonstrating that cooperative binding or concerted conformational changes are not required for modal gating. Moreover, the model embodies a generally applicable principle: If a timescale separation exists in the kinetics of individual subunits, then modal gating can arise as an emergent property of channel behavior.

  13. High-throughput identification of telomere-binding ligands based on the fluorescence regulation of DNA-copper nanoparticles.

    Science.gov (United States)

    Yang, Luzhu; Wang, Yanjun; Li, Baoxin; Jin, Yan

    2017-01-15

    Formation of the G-quadruplex in the human telomeric DNA is an effective way to inhibit telomerase activity. Therefore, screening ligands of G-quadruplex has potential applications in the treatment of cancer by inhibit telomerase activity. Although several techniques have been explored for screening of telomeric G-quadruplexes ligands, high-throughput screening method for fast screening telomere-binding ligands from the large compound library is still urgently needed. Herein, a label-free fluorescence strategy has been proposed for high-throughput screening telomere-binding ligands by using DNA-copper nanoparticles (DNA-CuNPs) as a signal probe. In the absence of ligands, human telomeric DNA (GDNA) hybridized with its complementary DNA (cDNA) to form double stranded DNA (dsDNA) which can act as an efficient template for the formation of DNA-CuNPs, leading to the high fluorescence of DNA-CuNPs. In the presence of ligands, GDNA folded into G-quadruplex. Single-strdanded cDNA does not support the formation of DNA-CuNP, resulting in low fluorescence of DNA-CuNPs. Therefore, telomere-binding ligands can be high-throughput screened by monitoring the change in the fluorescence of DNA-CuNPs. Thirteen traditional chinese medicines were screened. Circular dichroism (CD) measurements demonstrated that the selected ligands could induce single-stranded telomeric DNA to form G-quadruplex. The telomere repeat amplification protocol (TRAP) assay demonstrated that the selected ligands can effectively inhibit telomerase activity. Therefore, it offers a cost-effective, label-free and reliable high-throughput way to identify G-quadruplex ligands, which holds great potential in discovering telomerase-targeted anticancer drugs. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Ligand binding mechanics of maltose binding protein.

    Science.gov (United States)

    Bertz, Morten; Rief, Matthias

    2009-11-13

    In the past decade, single-molecule force spectroscopy has provided new insights into the key interactions stabilizing folded proteins. A few recent studies probing the effects of ligand binding on mechanical protein stability have come to quite different conclusions. While some proteins seem to be stabilized considerably by a bound ligand, others appear to be unaffected. Since force acts as a vector in space, it is conceivable that mechanical stabilization by ligand binding is dependent on the direction of force application. In this study, we vary the direction of the force to investigate the effect of ligand binding on the stability of maltose binding protein (MBP). MBP consists of two lobes connected by a hinge region that move from an open to a closed conformation when the ligand maltose binds. Previous mechanical experiments, where load was applied to the N and C termini, have demonstrated that MBP is built up of four building blocks (unfoldons) that sequentially detach from the folded structure. In this study, we design the pulling direction so that force application moves the two MBP lobes apart along the hinge axis. Mechanical unfolding in this geometry proceeds via an intermediate state whose boundaries coincide with previously reported MBP unfoldons. We find that in contrast to N-C-terminal pulling experiments, the mechanical stability of MBP is increased by ligand binding when load is applied to the two lobes and force breaks the protein-ligand interactions directly. Contour length measurements indicate that MBP is forced into an open conformation before unfolding even if ligand is bound. Using mutagenesis experiments, we demonstrate that the mechanical stabilization effect is due to only a few key interactions of the protein with its ligand. This work illustrates how varying the direction of the applied force allows revealing important details about the ligand binding mechanics of a large protein.

  15. The binding of quinone to the photosynthetic reaction centers: kinetics and thermodynamics of reactions occurring at the QB-site in zwitterionic and anionic liposomes.

    Science.gov (United States)

    Mavelli, Fabio; Trotta, Massimo; Ciriaco, Fulvio; Agostiano, Angela; Giotta, Livia; Italiano, Francesca; Milano, Francesco

    2014-07-01

    Liposomes represent a versatile biomimetic environment for studying the interaction between integral membrane proteins and hydrophobic ligands. In this paper, the quinone binding to the QB-site of the photosynthetic reaction centers (RC) from Rhodobacter sphaeroides has been investigated in liposomes prepared with either the zwitterionic phosphatidylcholine (PC) or the negatively charged phosphatidylglycerol (PG) to highlight the role of the different phospholipid polar heads. Quinone binding (K Q) and interquinone electron transfer (L AB) equilibrium constants in the two type of liposomes were obtained by charge recombination reaction of QB-depleted RC in the presence of increasing amounts of ubiquinone-10 over the temperature interval 6-35 °C. The kinetic of the charge recombination reactions has been fitted by numerically solving the ordinary differential equations set associated with a detailed kinetic scheme involving electron transfer reactions coupled with quinone release and uptake. The entire set of traces at each temperature was accurately fitted using the sole quinone release constants (both in a neutral and a charge separated state) as adjustable parameters. The temperature dependence of the quinone exchange rate at the QB-site was, hence, obtained. It was found that the quinone exchange regime was always fast for PC while it switched from slow to fast in PG as the temperature rose above 20 °C. A new method was introduced in this paper for the evaluation of constant K Q using the area underneath the charge recombination traces as the indicator of the amount of quinone bound to the QB-site.

  16. Limiting Energy Dissipation Induces Glassy Kinetics in Single-Cell High-Precision Responses.

    Science.gov (United States)

    Das, Jayajit

    2016-03-08

    Single cells often generate precise responses by involving dissipative out-of-thermodynamic-equilibrium processes in signaling networks. The available free energy to fuel these processes could become limited depending on the metabolic state of an individual cell. How does limiting dissipation affect the kinetics of high-precision responses in single cells? I address this question in the context of a kinetic proofreading scheme used in a simple model of early-time T cell signaling. Using exact analytical calculations and numerical simulations, I show that limiting dissipation qualitatively changes the kinetics in single cells marked by emergence of slow kinetics, large cell-to-cell variations of copy numbers, temporally correlated stochastic events (dynamic facilitation), and ergodicity breaking. Thus, constraints in energy dissipation, in addition to negatively affecting ligand discrimination in T cells, can create a fundamental difficulty in determining single-cell kinetics from cell-population results. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  17. Kinetic modeling of the Townsend breakdown in argon

    Science.gov (United States)

    Macheret, S. O.; Shneider, M. N.

    2013-10-01

    Kinetic modeling of the Townsend breakdown in argon was performed in the "forward-back" approximation. The kinetic model was found to adequately describe the left branch of the Paschen curve, and the important role of ionization by fast ions and atoms near the cathode, as well as the increase in secondary emission coefficient in strong electric fields described in the literature, was confirmed. The modeling also showed that the electron energy distribution function develops a beam of high-energy electrons and that the runaway effect, i.e., the monotonic increase of the mean electron energy with the distance from the cathode, occurs at the left branch of the Paschen curve.

  18. Enhanced charge transport kinetics in anisotropic, stratified photoanodes.

    Science.gov (United States)

    Yazdani, Nuri; Bozyigit, Deniz; Utke, Ivo; Buchheim, Jakob; Youn, Seul Ki; Patscheider, Jörg; Wood, Vanessa; Park, Hyung Gyu

    2014-02-12

    The kinetics of charge transport in mesoporous photoanodes strongly constrains the design and power conversion efficiencies of dye sensitized solar cells (DSSCs). Here, we report a stratified photoanode design with enhanced kinetics achieved through the incorporation of a fast charge transport intermediary between the titania and charge collector. Proof of concept photoanodes demonstrate that the inclusion of the intermediary not only enhances effective diffusion coefficients but also significantly suppresses charge recombination, leading to diffusion lengths two orders of magnitude greater than in standard mesoporous titania photoanodes. The intermediary concept holds promise for higher-efficiency DSSCs.

  19. The ligand binding domain controls glucocorticoid receptor dynamics independent of ligand release.

    Science.gov (United States)

    Meijsing, Sebastiaan H; Elbi, Cem; Luecke, Hans F; Hager, Gordon L; Yamamoto, Keith R

    2007-04-01

    Ligand binding to the glucocorticoid receptor (GR) results in receptor binding to glucocorticoid response elements (GREs) and the formation of transcriptional regulatory complexes. Equally important, these complexes are continuously disassembled, with active processes driving GR off GREs. We found that co-chaperone p23-dependent disruption of GR-driven transcription depended on the ligand binding domain (LBD). Next, we examined the importance of the LBD and of ligand dissociation in GR-GRE dissociation in living cells. We showed in fluorescence recovery after photobleaching studies that dissociation of GR from GREs is faster in the absence of the LBD. Furthermore, GR interaction with a target promoter revealed ligand-specific exchange rates. However, using covalently binding ligands, we demonstrated that ligand dissociation is not required for receptor dissociation from GREs. Overall, these studies showed that activities impinging on the LBD regulate GR exchange with GREs but that the dissociation of GR from GREs is independent from ligand dissociation.

  20. Ligand-induced type II interleukin-4 receptor dimers are sustained by rapid re-association within plasma membrane microcompartments

    Science.gov (United States)

    Richter, David; Moraga, Ignacio; Winkelmann, Hauke; Birkholz, Oliver; Wilmes, Stephan; Schulte, Markos; Kraich, Michael; Kenneweg, Hella; Beutel, Oliver; Selenschik, Philipp; Paterok, Dirk; Gavutis, Martynas; Schmidt, Thomas; Garcia, K. Christopher; Müller, Thomas D.; Piehler, Jacob

    2017-07-01

    The spatiotemporal organization of cytokine receptors in the plasma membrane is still debated with models ranging from ligand-independent receptor pre-dimerization to ligand-induced receptor dimerization occurring only after receptor uptake into endosomes. Here, we explore the molecular and cellular determinants governing the assembly of the type II interleukin-4 receptor, taking advantage of various agonists binding the receptor subunits with different affinities and rate constants. Quantitative kinetic studies using artificial membranes confirm that receptor dimerization is governed by the two-dimensional ligand-receptor interactions and identify a critical role of the transmembrane domain in receptor dimerization. Single molecule localization microscopy at physiological cell surface expression levels, however, reveals efficient ligand-induced receptor dimerization by all ligands, largely independent of receptor binding affinities, in line with the similar STAT6 activation potencies observed for all IL-4 variants. Detailed spatiotemporal analyses suggest that kinetic trapping of receptor dimers in actin-dependent microcompartments sustains robust receptor dimerization and signalling.

  1. Functional group based Ligand binding affinity scoring function at atomic environmental level

    Science.gov (United States)

    Varadwaj, Pritish Kumar; Lahiri, Tapobrata

    2009-01-01

    Use of knowledge based scoring function (KBSF) for virtual screening and molecular docking has become an established method for drug discovery. Lack of a precise and reliable free energy function that describes several interactions including water-mediated atomic interaction between amino-acid residues and ligand makes distance based statistical measure as the only alternative. Till now all the distance based scoring functions in KBSF arena use atom singularity concept, which neglects the environmental effect of the atom under consideration. We have developed a novel knowledge-based statistical energy function for protein-ligand complexes which takes atomic environment in to account hence functional group as a singular entity. The proposed knowledge based scoring function is fast, simple to construct, easy to use and moreover it tackle the existing problem of handling molecular orientation in active site pocket. We have designed and used Functional group based Ligand retrieval (FBLR) system which can identify and detect the orientation of functional groups in ligand. This decoy searching was used to build the above KBSF to quantify the activity and affinity of high resolution protein-ligand complexes. We have proposed the probable use of these decoys in molecular build-up as a de-novo drug designing approach. We have also discussed the possible use of the said KSBF in pharmacophore fragment detection and pseudo center based fragment alignment procedure. PMID:19255647

  2. An ELISA Based Binding and Competition Method to Rapidly Determine Ligand-receptor Interactions.

    Science.gov (United States)

    Syedbasha, Mohameedyaseen; Linnik, Janina; Santer, Deanna; O'Shea, Daire; Barakat, Khaled; Joyce, Michael; Khanna, Nina; Tyrrell, D Lorne; Houghton, Michael; Egli, Adrian

    2016-01-01

    A comprehensive understanding of signaling pathways requires detailed knowledge regarding ligand-receptor interaction. This article describes two fast and reliable point-by-point protocols of enzyme-linked immunosorbent assays (ELISAs) for the investigation of ligand-receptor interactions: the direct ligand-receptor interaction assay (LRA) and the competition LRA. As a case study, the ELISA based analysis of the interaction between different lambda interferons (IFNLs) and the alpha subunit of their receptor (IL28RA) is presented: the direct LRA is used for the determination of dissociation constants (KD values) between receptor and IFN ligands, and the competition LRA for the determination of the inhibitory capacity of an oligopeptide, which was designed to compete with the IFNLs at their receptor binding site. Analytical steps to estimate KD and half maximal inhibitory concentration (IC50) values are described. Finally, the discussion highlights advantages and disadvantages of the presented method and how the results enable a better molecular understanding of ligand-receptor interactions.

  3. Oxidative desulfurization: kinetic modelling.

    Science.gov (United States)

    Dhir, S; Uppaluri, R; Purkait, M K

    2009-01-30

    Increasing environmental legislations coupled with enhanced production of petroleum products demand, the deployment of novel technologies to remove organic sulfur efficiently. This work represents the kinetic modeling of ODS using H(2)O(2) over tungsten-containing layered double hydroxide (LDH) using the experimental data provided by Hulea et al. [V. Hulea, A.L. Maciuca, F. Fajula, E. Dumitriu, Catalytic oxidation of thiophenes and thioethers with hydrogen peroxide in the presence of W-containing layered double hydroxides, Appl. Catal. A: Gen. 313 (2) (2006) 200-207]. The kinetic modeling approach in this work initially targets the scope of the generation of a superstructure of micro-kinetic reaction schemes and models assuming Langmuir-Hinshelwood (LH) and Eley-Rideal (ER) mechanisms. Subsequently, the screening and selection of above models is initially based on profile-based elimination of incompetent schemes followed by non-linear regression search performed using the Levenberg-Marquardt algorithm (LMA) for the chosen models. The above analysis inferred that Eley-Rideal mechanism describes the kinetic behavior of ODS process using tungsten-containing LDH, with adsorption of reactant and intermediate product only taking place on the catalyst surface. Finally, an economic index is presented that scopes the economic aspects of the novel catalytic technology with the parameters obtained during regression analysis to conclude that the cost factor for the catalyst is 0.0062-0.04759 US $ per barrel.

  4. Kinetics and Catalysis Demonstrations.

    Science.gov (United States)

    Falconer, John L.; Britten, Jerald A.

    1984-01-01

    Eleven videotaped kinetics and catalysis demonstrations are described. Demonstrations include the clock reaction, oscillating reaction, hydrogen oxidation in air, hydrogen-oxygen explosion, acid-base properties of solids, high- and low-temperature zeolite reactivity, copper catalysis of ammonia oxidation and sodium peroxide decomposition, ammonia…

  5. Kinetic Gravity Separation

    NARCIS (Netherlands)

    Van Kooy, L.; Mooij, M.; Rem, P.

    2004-01-01

    Separations by density, such as the separation of non-ferrous scrap into light and heavy alloys, are often realized by means of heavy media. In principle, kinetic gravity separations in water can be faster and cheaper, because they do not rely on suspensions or salt solutions of which the density

  6. Correcting ligands, metabolites, and pathways

    Directory of Open Access Journals (Sweden)

    Vriend Gert

    2006-11-01

    Full Text Available Abstract Background A wide range of research areas in bioinformatics, molecular biology and medicinal chemistry require precise chemical structure information about molecules and reactions, e.g. drug design, ligand docking, metabolic network reconstruction, and systems biology. Most available databases, however, treat chemical structures more as illustrations than as a datafield in its own right. Lack of chemical accuracy impedes progress in the areas mentioned above. We present a database of metabolites called BioMeta that augments the existing pathway databases by explicitly assessing the validity, correctness, and completeness of chemical structure and reaction information. Description The main bulk of the data in BioMeta were obtained from the KEGG Ligand database. We developed a tool for chemical structure validation which assesses the chemical validity and stereochemical completeness of a molecule description. The validation tool was used to examine the compounds in BioMeta, showing that a relatively small number of compounds had an incorrect constitution (connectivity only, not considering stereochemistry and that a considerable number (about one third had incomplete or even incorrect stereochemistry. We made a large effort to correct the errors and to complete the structural descriptions. A total of 1468 structures were corrected and/or completed. We also established the reaction balance of the reactions in BioMeta and corrected 55% of the unbalanced (stoichiometrically incorrect reactions in an automatic procedure. The BioMeta database was implemented in PostgreSQL and provided with a web-based interface. Conclusion We demonstrate that the validation of metabolite structures and reactions is a feasible and worthwhile undertaking, and that the validation results can be used to trigger corrections and improvements to BioMeta, our metabolite database. BioMeta provides some tools for rational drug design, reaction searches, and

  7. Quantifying high-affinity binding of hydrophobic ligands by isothermal titration calorimetry.

    Science.gov (United States)

    Krainer, Georg; Broecker, Jana; Vargas, Carolyn; Fanghänel, Jörg; Keller, Sandro

    2012-12-18

    A fast and reliable quantification of the binding thermodynamics of hydrophobic high-affinity ligands employing a new calorimetric competition experiment is described. Although isothermal titration calorimetry is the method of choice for a quantitative characterization of intermolecular interactions in solution, a reliable determination of a dissociation constant (K(D)) is typically limited to the range 100 μM > K(D) > 1 nM. Interactions displaying higher or lower K(D) values can be assessed indirectly, provided that a suitable competing ligand is available whose K(D) falls within the directly accessible affinity window. This established displacement assay, however, requires the high-affinity ligand to be soluble at high concentrations in aqueous buffer and, consequently, poses serious problems in the study of protein binding involving small-molecule ligands dissolved in organic solvents--a familiar case in many drug-discovery projects relying on compound libraries. The calorimetric competition assay introduced here overcomes this limitation, thus allowing for a detailed thermodynamic description of high-affinity receptor-ligand interactions involving poorly water-soluble compounds. Based on a single titration of receptor into a dilute mixture of the two competing ligands, this competition assay provides accurate and precise values for the dissociation constants and binding enthalpies of both high- and moderate-affinity ligands. We discuss the theoretical background underlying the approach, demonstrate its practical application to metal ion chelation and high-affinity protein-inhibitor interactions, and explore its potential and limitations with the aid of simulations and statistical analyses.

  8. Physical characterization of the Skua fast burst assembly

    Energy Technology Data Exchange (ETDEWEB)

    Paternoster, R.; Bounds, J.; Sanchez, R.; Miko, D.

    1994-08-01

    In this paper we discuss the system design and ongoing efforts to characterize the machine physics and operating properties of the Skua fast burst assembly. The machine is currently operating up to prompt critical while we await approval for super-prompt burst operations. Efforts have centered on characterizing neutron kinetic properties, comparing calculated and measured temperature coefficients and power distributions, improving the burst reproducibility, examining the site-wide dose characteristics, and fitting the machine with cooling and filtration systems.

  9. Effect of inorganic and organic ligands on the sorption/desorption of arsenate on/from Al-Mg and Fe-Mg layered double hydroxides

    Science.gov (United States)

    Caporale, A. G.; Pigna, M.; Dynes, J. J.; Cozzolino, V.; Zhu, J.; Violante, A.

    2012-04-01

    In recent decades, a class of anionic clays known as layered double hydroxides (LDHs) has attracted substantial attention due to the potential use in many applications, such as photochemistry, electrochemistry, polymerization, magnetization and biomedical science. There has also been considerable interest in using LDHs as adsorbents to remove environmental contaminants due to their large surface area, high anion exchange capacity and good thermal stability. We studied the sorption of arsenate on Al-Mg and Fe-Mg layered double hydroxides (easily reproducible at low-cost) as affected by pH and varying concentrations of inorganic (nitrate, nitrite, phosphate, selenite and sulphate) and organic (oxalate and tartrate) ligands, ii) the effect of residence time on the arsenate desorption by these ligands, and iii) the kinetics of arsenate desorption by phosphate. The Fe-Mg-LDH sorbed nearly twice the amount of arsenate compared to the Al-Mg-LDH, due, in part, to its greater surface area and lower degree of crystallinity. Moreover, the Fe-Mg-LDH sorbed more arsenate than phosphate, in contrast to the Al-Mg-LDH, which adsorbed more phosphate than arsenate, probably because of the greater affinity of arsenate than phosphate for Fe sites and, vice versa, the greater affinity of phosphate than arsenate for Al sites. Arsenate sorption onto samples decreased by increasing pH, due, maybe, to the high affinity of hydroxyl ions for LDHs and/or to the value of zero point charge of two sorbents. The rate of decline in the amount of arsenate sorbed was, however, relatively constant, decreasing the fastest for the Fe-Mg-LDH compared to the Al-Mg-LDH. The capacity of ligands to inhibit the fixation of arsenate followed the sequence: nitrate tartrate tartrate anions have a stronger affinity for Fe than Al and for the presence in Fe-Mg-LDH of short-range-ordered materials on which arsenate forms very strong inner-sphere complexes not easily desorbable by competing ligands. The longer the

  10. Multicomponent mixtures for cryoprotection and ligand solubilization

    Directory of Open Access Journals (Sweden)

    Lidia Ciccone

    2015-09-01

    Full Text Available Mixed cryoprotectants have been developed for the solubilization of ligands for crystallization of protein–ligand complexes and for crystal soaking. Low affinity lead compounds with poor solubility are problematic for structural studies. Complete ligand solubilization is required for co-crystallization and crystal soaking experiments to obtain interpretable electron density maps for the ligand. Mixed cryo-preserving compounds are needed prior to X-ray data collection to reduce radiation damage at synchrotron sources. Here we present dual-use mixes that act as cryoprotectants and also promote the aqueous solubility of hydrophobic ligands. Unlike glycerol that increases protein solubility and can cause crystal melting the mixed solutions of cryo-preserving compounds that include precipitants and solubilizers, allow for worry-free crystal preservation while simultaneously solubilizing relatively hydrophobic ligands, typical of ligands obtained in high-throughput screening. The effectiveness of these mixture has been confirmed on a human transthyretin crystals both during crystallization and in flash freezing of crystals.

  11. Coordinate unsaturation with fluorinated ligands

    Energy Technology Data Exchange (ETDEWEB)

    Rack, J.L.; Hurlburt, P.K.; Anderson, O.P.; Strauss, S.H. [Colorado State Univ., Ft. Collins, CO (United States)

    1993-12-31

    The preparation and characterization of Zn(OTeF{sub 5}){sub 2} has resulted in a model compound with which to explore the concept of coordinative unsaturation. The coordination of solvents of varying donicity and dielectric constant to the Zn(II) ions in Zn(OTeF{sub 5}){sub 2} was studied by vapor phase monometry, NMR and IR spectroscopy, conductimetry, and X-Ray crystallography. The structures of [Zn(C{sub 6}H{sub 5}NO{sub 2}){sub 2}(OTeF{sub 5})2]2 and Zn(C{sub 6}H{sub 5}NO{sub 2}){sub 3}(OTEF{sub 5}){sub 2} demonstrate the electronic flexibility of some weakly coordinating solvents in that nitrobenzene can function as either an {eta}{sup 1}O or {eta}{sup 2}O,O`-ligand. The dependence of the number of bound solvent molecules and the degree of OTeF{sub 5}{minus} dissociation on solvent donor number and dielectric constant will be presented.

  12. Beyond Fast Mapping

    OpenAIRE

    Carey, Susan

    2010-01-01

    Since the seminal 1957 studies of word learning by Roger Brown, most experimental studies of lexical acquisition have concerned fast mapping: the process through which a new lexical entry is established, and through which representations of the linguistic context of a newly heard word interact with representations of its nonlinguistic context to fix an initial partial meaning. Here I focus on the subsequent extended process through which the adult meaning is approximated. Two factors lead to ...

  13. Fast Radio Bursts

    Indian Academy of Sciences (India)

    Akshaya Rane; Duncan Lorimer

    2017-09-01

    We summarize our current state of knowledge of fast radio bursts (FRBs) which were first discovered a decade ago. Following an introduction to radio transients in general, including pulsars and rotating radio transients, we discuss the discovery of FRBs. We then discuss FRB follow-up observations in the context of repeat bursts before moving on to review propagation effects on FRB signals, FRB progenitor models and an outlook on FRBs as potential cosmological tools.

  14. PHENIX Fast TOF

    Energy Technology Data Exchange (ETDEWEB)

    Soha, Aria [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Chiu, Mickey [Brookhaven National Lab. (BNL), Upton, NY (United States); Mannel, Eric [Brookhaven National Lab. (BNL), Upton, NY (United States); Stoll, Sean [Brookhaven National Lab. (BNL), Upton, NY (United States); Lynch, Don [Brookhaven National Lab. (BNL), Upton, NY (United States); Boose, Steve [Brookhaven National Lab. (BNL), Upton, NY (United States); Northacker, Dave [Brookhaven National Lab. (BNL), Upton, NY (United States); Alfred, Marcus [Howard Univ., Washington, DC (United States); Lindesay, James [Howard Univ., Washington, DC (United States); Chujo, Tatsuya [Univ. of Tsukuba (Japan); Inaba, Motoi [Univ. of Tsukuba (Japan); Nonaka, Toshihiro [Univ. of Tsukuba (Japan); Sato, Wataru [Univ. of Tsukuba (Japan); Sakatani, Ikumi [Univ. of Tsukuba (Japan); Hirano, Masahiro [Univ. of Tsukuba (Japan); Choi, Ihnjea [Univ. of Illinois, Urbana-Champaign, IL (United States)

    2014-01-15

    This is a technical scope of work (TSW) between the Fermi National Accelerator Laboratory (Fermilab) and the experimenters of PHENIX Fast TOF group who have committed to participate in beam tests to be carried out during the FY2014 Fermilab Test Beam Facility program. The goals for this test beam experiment are to verify the timing performance of the two types of time-of-flight detector prototypes.

  15. Fast Air Temperature Sensors

    DEFF Research Database (Denmark)

    Hendricks, Elbert

    1998-01-01

    The note documents briefly work done on a newly developed sensor for making fast temperature measurements on the air flow in the intake ports of an SI engine and in the EGR input line. The work reviewed has been carried out in close cooperation with Civ. Ing. Michael Føns, the author (IAU......) and Spencer C. Sorenson (ET). The theory which decribes in detail the overall dynamic chracteristics of the sensor was developed at IAU, DTU....

  16. ADT fast losses MD

    CERN Document Server

    Priebe, A; Dehning, B; Redaelli, S; Salvachua Ferrando, BM; Sapinski, M; Solfaroli Camillocci, M; Valuch, D

    2013-01-01

    The fast beam losses in the order of 1 ms are expected to be a potential major luminosity limitation for higher beam energies after the LHC long shutdown (LS1). Therefore a Quench Test is planned in the winter 2013 to estimate the quench limit in this timescale and revise the current models. This experiment was devoted to determination the LHC Transverse Damper (ADT) as a system for fast losses induction. A non-standard operation of the ADT was used to develop the beam oscillation instead of suppressing them. The sign flip method had allowed us to create the fast losses within several LHC turns at 450 GeV during the previous test (26th March 2012). Thus, the ADT could be potentially used for the studies of the UFO ("Unidentied Falling Object") impact on the cold magnets. Verification of the system capability and investigations of the disturbed beam properties were the main objectives of this MD. During the experiment, the pilot bunches of proton beam were excited independently in the horizontal and vertical ...

  17. Fast Light Optical Gyroscopes

    Science.gov (United States)

    Smith, David D.

    2015-01-01

    Next-generation space missions are currently constrained by existing spacecraft navigation systems which are not fully autonomous. These systems suffer from accumulated dead-reckoning errors and must therefore rely on periodic corrections provided by supplementary technologies that depend on line-of-sight signals from Earth, satellites, or other celestial bodies for absolute attitude and position determination, which can be spoofed, incorrectly identified, occluded, obscured, attenuated, or insufficiently available. These dead-reckoning errors originate in the ring laser gyros themselves, which constitute inertial measurement units. Increasing the time for standalone spacecraft navigation therefore requires fundamental improvements in gyroscope technologies. One promising solution to enhance gyro sensitivity is to place an anomalous dispersion or fast light material inside the gyro cavity. The fast light essentially provides a positive feedback to the gyro response, resulting in a larger measured beat frequency for a given rotation rate as shown in figure 1. Game Changing Development has been investing in this idea through the Fast Light Optical Gyros (FLOG) project, a collaborative effort which began in FY 2013 between NASA Marshall Space Flight Center (MSFC), the U.S. Army Aviation and Missile Research, Development, and Engineering Center (AMRDEC), and Northwestern University. MSFC and AMRDEC are working on the development of a passive FLOG (PFLOG), while Northwestern is developing an active FLOG (AFLOG). The project has demonstrated new benchmarks in the state of the art for scale factor sensitivity enhancement. Recent results show cavity scale factor enhancements of approx.100 for passive cavities.

  18. Ligand-induced changes in estrogen receptor conformation as measured by site-directed spin labeling.

    Science.gov (United States)

    Hurth, Kyle M; Nilges, Mark J; Carlson, Kathryn E; Tamrazi, Anobel; Belford, R Linn; Katzenellenbogen, John A

    2004-02-24

    Site-directed spin labeling (SDSL), the site-specific incorporation of nitroxide spin-labels into a protein, has allowed us to investigate ligand-induced conformational changes in the ligand-binding domain of human estrogen receptor alpha (hERalpha-LBD). EPR (electron paramagnetic resonance) spectroscopy of the nitroxide probe attached to ER produces different spectra depending upon the identity of the bound ligand; these differences are indicative of changes in the type and degree of motional character of the spin-label induced by different ligand-induced conformations of labeled ER. Visual inspection of EPR spectra, construction of B versus C cross-correlation plots, and cross-comparison of spectral pairs using a relative squared difference (RSD) calculation allowed receptor-ligand complexes to be profiled according to their conformational character. Plotting B and C parameters allowed us to evaluate the liganded receptor according to the motional characteristics of the attached spin-label, and they were particularly illustrative for the receptor labeled at position 530, which had motion between the fast and intermediate regimes. RSD analysis allowed us to directly compare the similarity or difference between two different spectra, and these comparisons produced groupings that paralleled those seen in B versus C cross-correlation plots, again relating meaningfully with the pharmacological nature of the bound ligand. RSD analysis was also particularly useful for qualifying differences seen with the receptor labeled at position 417, which had motion between the intermediate and slow motional regimes. This work demonstrates that B and C formulas from EPR line shape theory are useful for qualitative analysis of spectra with differences subtler than those that are often analyzed by EPR spectroscopists. This work also provides evidence that the ER can exist in a range of conformations, with specific conformations resulting from preferential stabilization of ER by the

  19. Distribution of unselectively bound ligands along DNA.

    Science.gov (United States)

    Lando, Dmitri Y; Nechipurenko, Yury D

    2008-10-01

    Unselective and reversible adsorption of ligands on DNA for a model of binding proposed by Zasedatelev, Gursky, and Volkenshtein is considered. In this model, the interaction between neighboring ligands located at the distance of i binding centers is characterized by the statistical weight ai. Each ligand covers L binding centers. For this model, expressions for binding averages are represented in a new simple form. This representation is convenient for the calculation of the fraction of inter-ligand distances of i binding centers fd(i) and the fraction of binding centers included in the distances of i binding centers fbc(i) for various types of interaction between bound ligands. It is shown that, for non-cooperative binding, contact cooperativity and long-range cooperativity, the fraction of the zero inter-ligand distance fd(0) is maximal at any relative concentration of bound ligands (r). Calculations demonstrate that, at low r, fd(0) approximately r.ao, and fd(i) approximately r at 11/r-L, then fd(i) rapidly decreases with i at any r for all types of inter-ligand interaction. At high ligand concentration (r is close to rmax=L(-1)), fd(0) is close to unity and fd(i) rapidly decreases with i for any type of inter-ligand interaction. For strong contact cooperativity, fd(0) is close to unity in a much lager r interval ((0.5-1).rmax), and fd(1) approximately ao(-1) at r approximately 0.5.rmax. In the case of long-range interaction between bound ligands, the dependence fd(i) is more complex and has a maximum at i approximately (1/r-L)1/2 for anti-cooperative binding. fbc(i) is maximal at i approximately 1/r-L for all types of binding except the contact cooperativity. A strong asymmetry in the influence of contact cooperativity and anticooperativity on the ligand distribution along DNA is demonstrated.

  20. Metabolic Effects of Intermittent Fasting.

    Science.gov (United States)

    Patterson, Ruth E; Sears, Dorothy D

    2017-08-21

    The objective of this review is to provide an overview of intermittent fasting regimens, summarize the evidence on the health benefits of intermittent fasting, and discuss physiological mechanisms by which intermittent fasting might lead to improved health outcomes. A MEDLINE search was performed using PubMed and the terms "intermittent fasting," "fasting," "time-restricted feeding," and "food timing." Modified fasting regimens appear to promote weight loss and may improve metabolic health. Several lines of evidence also support the hypothesis that eating patterns that reduce or eliminate nighttime eating and prolong nightly fasting intervals may result in sustained improvements in human health. Intermittent fasting regimens are hypothesized to influence metabolic regulation via effects on (a) circadian biology, (b) the gut microbiome, and (c) modifiable lifestyle behaviors, such as sleep. If proven to be efficacious, these eating regimens offer promising nonpharmacological approaches to improving health at the population level, with multiple public health benefits.

  1. Kinetics of Laser-Assisted Carbon Nanotube Growth

    CERN Document Server

    van de Burgt, Yoeri; Mandamparambil, Rajesh

    2014-01-01

    Laser-assisted chemical vapour deposition (CVD) growth is an attractive mask-less process for growing locally aligned carbon nanotubes (CNTs) in selected places on temperature sensitive substrates. The nature of the localized process results in fast carbon nanotube growth with high experimental throughput. Here, we report on detailed investigation of growth kinetics related to physical and chemical process characteristics. Specifically, the growth kinetics is investigated by monitoring the dynamical changes of reflected laser beam intensity during growth. Benefiting from the fast growth and high experimental throughput, we investigate a wide range of experimental conditions and propose several growth regimes. Rate-limiting steps are determined using rate equations linked to the proposed growth regimes, which are further characterized by Raman spectroscopy and Scanning Electron Microscopy (SEM), therefore directly linking growth regimes to the structural quality of the CNTs. Activation energies for the differe...

  2. Neighborhood fast food availability and fast food consumption.

    Science.gov (United States)

    Oexle, Nathalie; Barnes, Timothy L; Blake, Christine E; Bell, Bethany A; Liese, Angela D

    2015-09-01

    Recent nutritional and public health research has focused on how the availability of various types of food in a person's immediate area or neighborhood influences his or her food choices and eating habits. It has been theorized that people living in areas with a wealth of unhealthy fast-food options may show higher levels of fast-food consumption, a factor that often coincides with being overweight or obese. However, measuring food availability in a particular area is difficult to achieve consistently: there may be differences in the strict physical locations of food options as compared to how individuals perceive their personal food availability, and various studies may use either one or both of these measures. The aim of this study was to evaluate the association between weekly fast-food consumption and both a person's perceived availability of fast-food and an objective measure of fast-food presence - Geographic Information Systems (GIS) - within that person's neighborhood. A randomly selected population-based sample of eight counties in South Carolina was used to conduct a cross-sectional telephone survey assessing self-report fast-food consumption and perceived availability of fast food. GIS was used to determine the actual number of fast-food outlets within each participant's neighborhood. Using multinomial logistic regression analyses, we found that neither perceived availability nor GIS-based presence of fast-food was significantly associated with weekly fast-food consumption. Our findings indicate that availability might not be the dominant factor influencing fast-food consumption. We recommend using subjective availability measures and considering individual characteristics that could influence both perceived availability of fast food and its impact on fast-food consumption. If replicated, our findings suggest that interventions aimed at reducing fast-food consumption by limiting neighborhood fast-food availability might not be completely effective.

  3. Kinetics of hole nucleation in biomembrane rupture

    Energy Technology Data Exchange (ETDEWEB)

    Evans, Evan [Biomedical Engineering, Boston University, Boston, MA 02215 (United States); Smith, Benjamin A, E-mail: evanse@bu.edu [Departments of Physics and Pathology, University of British Columbia, Vancouver, BC, V6T 2A6 (Canada)

    2011-09-15

    The core component of a biological membrane is a fluid-lipid bilayer held together by interfacial-hydrophobic and van der Waals interactions, which are balanced for the most part by acyl chain entropy confinement. If biomembranes are subjected to persistent tensions, an unstable (nanoscale) hole will emerge at some time to cause rupture. Because of the large energy required to create a hole, thermal activation appears to be requisite for initiating a hole and the activation energy is expected to depend significantly on mechanical tension. Although models exist for the kinetic process of hole nucleation in tense membranes, studies of membrane survival have failed to cover the ranges of tension and lifetime needed to critically examine nucleation theory. Hence, rupturing giant ({approx}20 {mu}m) membrane vesicles ultra-slowly to ultra-quickly with slow to fast ramps of tension, we demonstrate a method to directly quantify kinetic rates at which unstable holes form in fluid membranes, at the same time providing a range of kinetic rates from <0.01 to >100 s{sup -1}. Measuring lifetimes of many hundreds of vesicles, each tensed by precision control of micropipette suction, we have determined the rates of failure for vesicles made from several synthetic phospholipids plus 1:1 mixtures of phospho- and sphingo-lipids with cholesterol, all of which represent prominent constituents of eukaryotic cell membranes. Plotted on a logarithmic scale, the failure rates for vesicles are found to rise dramatically with an increase in tension. Converting the experimental profiles of kinetic rates into changes of activation energy versus tension, we show that the results closely match expressions for thermal activation derived from a combination of meso-scale theory and molecular-scale simulations of hole formation. Moreover, we demonstrate a generic approach to transform analytical fits of activation energies obtained from rupture experiments into energy landscapes characterizing the

  4. Relationships of ligand binding, redox properties, and protonation in Coprinus cinereus peroxidase.

    Science.gov (United States)

    Ciaccio, Chiara; Rosati, Antonella; De Sanctis, Giampiero; Sinibaldi, Federica; Marini, Stefano; Santucci, Roberto; Ascenzi, Paolo; Welinder, Karen G; Coletta, Massimo

    2003-05-23

    The pH dependence of the redox potentials and kinetics for CO association and dissociation was determined between pH 3.0 and 13.0 at 25 degrees C for the wild-type Coprinus cinereus fungal peroxidase and for a site-directed mutant in which Asp245, which is H-bonded to N delta of the imidazole of the proximal His183, was substituted with Asn. The determination of these functional properties allowed this information to be merged in a self-consistent fashion and to formulate for the first time a complete scheme employing the minimum number of groups required to describe the whole proton-linked behavior of both redox and ligand binding properties. The overall pH dependence can be accounted for by four redox- and ligand-linked groups. The proximal H-bond, which is strictly conserved in all peroxidases, will still be present in the site-specific mutant, but will no longer have an ionic character, and this event will bring about an alteration of redox equilibria and CO binding kinetics, envisaging a relevant role played by this H-bond also in modulating redox properties and ligand binding equilibria.

  5. Sulfated ligands for the copper(I)-catalyzed azide-alkyne cycloaddition.

    Science.gov (United States)

    Wang, Wei; Hong, Senglian; Tran, Andrew; Jiang, Hao; Triano, Rebecca; Liu, Yi; Chen, Xing; Wu, Peng

    2011-10-04

    The copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC), the prototypical reaction of click chemistry, is accelerated by tris(triazolylmethyl)amine-based ligands. Herein, we compare two new ligands in this family--3-[4-({bis[(1-tert-butyl-1H-1,2,3-triazol-4-yl)methyl]amino}methyl)-1H-1,2,3-triazol-1-yl]propanol (BTTP) and the corresponding sulfated ligand 3-[4-({bis[(1-tert-butyl-1H-1,2,3-triazol-4-yl)methyl]amino}methyl)-1H-1,2,3-triazol-1-yl]propyl hydrogen sulfate (BTTPS)--for three bioconjugation applications: 1) labeling of alkyne-tagged glycoproteins in crude cell lysates, 2) labeling of alkyne- or azide-tagged glycoproteins on the surface of live mammalian cells, and 3) labeling of azides in surface proteins of live Escherichia coli. Although BTTPS exhibits faster kinetics than BTTP in accelerating the CuAAC reaction in in vitro kinetic measurements, its labeling efficiency is slightly lower than BTTP in modifying biomolecules with a significant amount of negative charges due to electrostatic repulsion. Nevertheless, the negative charge conferred by the sulfate at physiological conditions significantly reduced the cellular internalization of the coordinated copper(I), thus making BTTPS-Cu(I) a better choice for live-cell labeling. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Simulation of chemical kinetics in sodium-concrete interactions

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Sodium-concrete interaction is a key safety-related issue in safety analysis of liquid metal cooled fast breeder reactors (LMFBRs). The chemical kinetics model is a key component of the sodium-concrete interaction model. Conservation equations integrated in sodium-concrete interaction model cannot be solved without a set of relationships that couple the equations together, and this may be done by the chemical kinetics model. Simultaneously,simulation of chemical kinetics is difficult due to complexity of the mechanism of chemical reactions between sodium and concrete. This paper describes the chemical kinetics simulation under some hypotheses. The chemical kinetics model was integrated with the conservation equations to form a computer code. Penetration depth, penetration rate,hydrogen flux, reaction heat, etc. can be provided by this code. Theoretical models and computational procedure were recounted in detail. Good agreements of an overall transient behavior were obtained in a series of sodium-concrete interaction experiment analysis. Comparison between analytical and experimental results showed that the chemical kinetics model presented in this paper was creditable and reasonable for simulating the sodium-concrete interactions.

  7. Serum Lipid Profile: Fasting or Non-fasting?

    OpenAIRE

    Nigam, P. K.

    2010-01-01

    Serum lipid profile has now become almost a routine test. It is usually done in fasting state due to certain limitations in non-fasting serum sample. In the recent past efforts have been made to simplify blood sampling by replacing fasting lipid profile with non-fasting lipid profile. However, fasting specimen is preferred if cardiovascular risk assessment is based on total cholesterol, LDL cholesterol or non-HDL cholesterol. A lot has yet to be done in this area. Till then we have to believe...

  8. Serum Lipid Profile: Fasting or Non-fasting?

    OpenAIRE

    Nigam, P. K.

    2010-01-01

    Serum lipid profile has now become almost a routine test. It is usually done in fasting state due to certain limitations in non-fasting serum sample. In the recent past efforts have been made to simplify blood sampling by replacing fasting lipid profile with non-fasting lipid profile. However, fasting specimen is preferred if cardiovascular risk assessment is based on total cholesterol, LDL cholesterol or non-HDL cholesterol. A lot has yet to be done in this area. Till then we have to believe...

  9. Role of fast ignitor in fast-shock ignition concept

    Directory of Open Access Journals (Sweden)

    S. A. Ghasemi

    2014-03-01

    Full Text Available This paper deals with the role of fast ignitor in fast-shock ignition (FSI concept. The semi-analytical model indicates that the FSI target gain is a function of fast ignitor laser wavelength. If the energy of fast ignitor driver is and the laser wavelength is less than 0.53 micron, then with a fuel mass about 2 mg the FSI has a considerable advantage over pure shock ignition and the figure of merit is better than 1.2. When the wavelength of fast ignitor becomes shorter, the approaches , and for wavelengths shorter than 0.25 micron no additional is advantage is obtained.

  10. Hispanics in Fast Food Jobs.

    Science.gov (United States)

    Charner, Ivan; Fraser, Bryna Shore

    A study examined the employment of Hispanics in the fast-food industry. Data were obtained from a national survey of employees at 279 fast-food restaurants from seven companies in which 194 (4.2 percent) of the 4,660 respondents reported being Hispanic. Compared with the total sample, Hispanic fast-food employees were slightly less likely to be…

  11. Energy dissipation in magnetic null points at kinetic scales

    OpenAIRE

    Olshevsky, Vyacheslav; Divin, Andrey; Eriksson, Elin; Markidis, Stefano; Lapenta, Giovanni

    2015-01-01

    We use kinetic particle-in-cell and MHD simulations supported by an observational data set to investigate magnetic reconnection in clusters of null points in space plasma. The magnetic configuration under investigation is driven by fast adiabatic flux rope compression that dissipates almost half of the initial magnetic field energy. In this phase powerful currents are excited producing secondary instabilities, and the system is brought into a state of "intermittent turbulence" within a few io...

  12. Luminescence kinetics of phosphors after excitation by electron beam

    OpenAIRE

    Ваганов, Виталий; Полисадова, Елена Фёдоровна; Мархабаева, А. А.

    2016-01-01

    The luminescence decay of industrial phosphors based on yttrium-aluminum garnet has beeninvestigated at the excitation by an electron beam. The ratio of slow and fast component amplitude in the kinetics of luminescence decay was estimated. It is shown that the luminescence decay time depends on the composition of the phosphor. The luminescence decay time can be used for analysis of the phosphors, to determine their quality.

  13. Kinetic Damage from Meteorites

    Science.gov (United States)

    Cooke, W.; Brown, P.; Matney, M.

    2017-01-01

    Comparing the natural meteorite flux at the Earth's surface to that of space debris, re-entering debris is 2 orders of magnitude less of a kinetic hazard at all but the very largest (and therefore rarest) sizes compared to natural impactors. Debris re-entries over several metric tonnes are roughly as frequent as natural impactors, but the survival fraction is expected to be much higher. Kinetic hazards from meteorites are very small, with only one recorded (indirect) injury reported. We expect fatalities to be even more rare, on the order of one person killed per several millennia. That several reports exist of small fragments/sand hitting people during meteorite falls is consistent with our prediction that this should occur every decade or so.

  14. Kinetic Actviation Relaxation Technique

    CERN Document Server

    Béland, Laurent Karim; El-Mellouhi, Fedwa; Joly, Jean-François; Mousseau, Normand

    2011-01-01

    We present a detailed description of the kinetic Activation-Relaxation Technique (k-ART), an off-lattice, self-learning kinetic Monte Carlo algorithm with on-the-fly event search. Combining a topological classification for local environments and event generation with ART nouveau, an efficient unbiased sampling method for finding transition states, k-ART can be applied to complex materials with atoms in off-lattice positions or with elastic deformations that cannot be handled with standard KMC approaches. In addition to presenting the various elements of the algorithm, we demonstrate the general character of k-ART by applying the algorithm to three challenging systems: self-defect annihilation in c-Si, self-interstitial diffusion in Fe and structural relaxation in amorphous silicon.

  15. Photon kinetics in plasmas

    Directory of Open Access Journals (Sweden)

    V.G. Morozov

    2009-01-01

    Full Text Available We present a kinetic theory of radiative processes in many-component plasmas with relativistic electrons and nonrelativistic heavy particles. Using the non-equilibrium Green's function technique in many-particle QED, we show that the transverse field correlation functions can be naturally decomposed into sharply peaked (non-Lorentzian parts that describe resonant (propagating photons and off-shell parts corresponding to virtual photons in the medium. Analogous decompositions are obtained for the longitudinal field correlation functions and the correlation functions of relativistic electrons. We derive a kinetic equation for the resonant photons with a finite spectral width and show that the off-shell parts of the particle and field correlation functions are essential to calculate the local radiating power in plasmas and recover the results of vacuum QED. The plasma effects on radiative processes are discussed.

  16. Kinetic Tetrazolium Microtiter Assay

    Science.gov (United States)

    Pierson, Duane L.; Stowe, Raymond; Koenig, David

    1993-01-01

    Kinetic tetrazolium microtiter assay (KTMA) involves use of tetrazolium salts and Triton X-100 (or equivalent), nontoxic, in vitro color developer solubilizing colored metabolite formazan without injuring or killing metabolizing cells. Provides for continuous measurement of metabolism and makes possible to determine rate of action of antimicrobial agent in real time as well as determines effective inhibitory concentrations. Used to monitor growth after addition of stimulatory compounds. Provides for kinetic determination of efficacy of biocide, greatly increasing reliability and precision of results. Also used to determine relative effectiveness of antimicrobial agent as function of time. Capability of generating results on day of test extremely important in treatment of water and waste, disinfection of hospital rooms, and in pharmaceutical, agricultural, and food-processing industries. Assay also used in many aspects of cell biology.

  17. Automated design of ligands to polypharmacological profiles

    Science.gov (United States)

    Besnard, Jérémy; Ruda, Gian Filippo; Setola, Vincent; Abecassis, Keren; Rodriguiz, Ramona M.; Huang, Xi-Ping; Norval, Suzanne; Sassano, Maria F.; Shin, Antony I.; Webster, Lauren A.; Simeons, Frederick R.C.; Stojanovski, Laste; Prat, Annik; Seidah, Nabil G.; Constam, Daniel B.; Bickerton, G. Richard; Read, Kevin D.; Wetsel, William C.; Gilbert, Ian H.; Roth, Bryan L.; Hopkins, Andrew L.

    2012-01-01

    The clinical efficacy and safety of a drug is determined by its activity profile across multiple proteins in the proteome. However, designing drugs with a specific multi-target profile is both complex and difficult. Therefore methods to rationally design drugs a priori against profiles of multiple proteins would have immense value in drug discovery. We describe a new approach for the automated design of ligands against profiles of multiple drug targets. The method is demonstrated by the evolution of an approved acetylcholinesterase inhibitor drug into brain penetrable ligands with either specific polypharmacology or exquisite selectivity profiles for G-protein coupled receptors. Overall, 800 ligand-target predictions of prospectively designed ligands were tested experimentally, of which 75% were confirmed correct. We also demonstrate target engagement in vivo. The approach can be a useful source of drug leads where multi-target profiles are required to achieve either selectivity over other drug targets or a desired polypharmacology. PMID:23235874

  18. Ligand inducible assembly of a DNA tetrahedron.

    Science.gov (United States)

    Dohno, Chikara; Atsumi, Hiroshi; Nakatani, Kazuhiko

    2011-03-28

    Here we show that a small synthetic ligand can be used as a key building component for DNA nanofabrication. Using naphthyridinecarbamate dimer (NCD) as a molecular glue for DNA hybridization, we demonstrate NCD-triggered formation of a DNA tetrahedron.

  19. Flocculation Kinetics of Chitosan

    Institute of Scientific and Technical Information of China (English)

    陈亮; 林志艳; 陈东辉

    2003-01-01

    Under the various conditions, the experiments of flocculation of bentonite solution with chitosan were carried out. And the flocculation kinetics was studied by the changes of floc size along with time. The results show that hydraulic gradient G (s-1) plays a key role in growing up of floc size and both of molecular weight and initial turbidity of bentonite solution influence the floc size in steady state and the time needed for steady floc size.

  20. Fast beam studies of free radical photodissociation

    Energy Technology Data Exchange (ETDEWEB)

    Neumark, D.M. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01

    The authors have developed a novel technique for studying the photodissociation spectroscopy and dynamics of free radicals. In these experiments, radicals are generated by laser photodetachment of a fast (6-8 keV) mass-selected negative ion beam. The resulting radicals are photodissociated with a second laser, and the photofragments are collected and detected with high efficiency using a microchannel plate detector. The overall process is: ABC{sup -} {yields} ABC + e{sup -} {yields} A + BC, AB + C. Two types of fragment detection schemes are used. To map out the photodissociation cross-section of the radical, the photodissociation laser is scanned and the total photofragment yield is measured as a function of wavelength. In other experiments, the photodissociation frequency is fixed and the photofragment masses, kinetic energy release, and scattering angle is determined for each photodissociation event.

  1. Secondary ionization and heating by fast electrons

    CERN Document Server

    Furlanetto, Steven

    2009-01-01

    We examine the fate of fast electrons (with energies E>10 eV) in a thermal gas of primordial composition. To follow their interactions with the background gas, we construct a Monte Carlo model that includes: (1) electron-electron scattering (which transforms the electron kinetic energy into heat), (2) collisional ionization of hydrogen and helium (which produces secondary electrons that themselves scatter through the medium), and (3) collisional excitation (which produces secondary photons, whose fates we also follow approximately). For the last process, we explicitly include all transitions to upper levels n<=4, together with a well-motivated extrapolation to higher levels. In all cases, we use recent calculated cross-sections at E<1 keV and the Bethe approximation to extrapolate to higher energies. We compute the fractions of energy deposited as heat, ionization (tracking HI and the helium species separately), and excitation (tracking HI Lyman-alpha separately) under a broad range of conditions approp...

  2. Modelling of trace metal uptake by roots taking into account complexation by exogenous organic ligands

    Science.gov (United States)

    Jean-Marc, Custos; Christian, Moyne; Sterckeman, Thibault

    2010-05-01

    The context of this study is phytoextraction of soil trace metals such as Cd, Pb or Zn. Trace metal transfer from soil to plant depends on physical and chemical processes such as minerals alteration, transport, adsorption/desorption, reactions in solution and biological processes including the action of plant roots and of associated micro-flora. Complexation of metal ions by organic ligands is considered to play a role on the availability of trace metals for roots in particular in the event that synthetic ligands (EDTA, NTA, etc.) are added to the soil to increase the solubility of the contaminants. As this role is not clearly understood, we wanted to simulate it in order to quantify the effect of organic ligands on root uptake of trace metals and produce a tool which could help in optimizing the conditions of phytoextraction.We studied the effect of an aminocarboxilate ligand on the absorption of the metal ion by roots, both in hydroponic solution and in soil solution, for which we had to formalize the buffer power for the metal. We assumed that the hydrated metal ion is the only form which can be absorbed by the plants. Transport and reaction processes were modelled for a system made up of the metal M, a ligand L and the metal complex ML. The Tinker-Nye-Barber model was adapted to describe the transport of solutes M, L and ML in the soil and absorption of M by the roots. This allowed to represent the interactions between transport, chelating reactions, absorption of the solutes at the root surface, root growth with time, in order to simulate metal uptake by a whole root system.Several assumptions were tested such as i) absorption of the metal by an infinite sink and according to a Michaelis-Menten kinetics, solutes transport by diffusion with and without ii) mass flow and iii) soil buffer power for the ligand L. In hydroponic solution (without soil buffer power), ligands decreased the trace metal flux towards roots, as they reduced the concentration of hydrated

  3. Nye ligander for Pt-MOF strukturer

    OpenAIRE

    Jakobsen, Søren

    2006-01-01

    Metalorganic frameworks (MOFs) are a new type of compounds which have been intensely investigated during the last few years. They have been synthesized using a wide variety of metals and ligands constructing a vast number of 1, 2 and 3 dimensional structures, some of which possess zeolite-type physics and chemistry. Our approach is to incorporate platinum metal sites into the structures making them bimetallic and potentially catalytically active. Therefore a number of N-N-type ligands (dii...

  4. SnapShot: GPCR-Ligand Interactions.

    Science.gov (United States)

    Ghosh, Eshan; Nidhi, Kumari; Shukla, Arun K

    2014-12-18

    G-protein-coupled receptors enable cells to recognize numerous external stimuli and to transmit corresponding signals across the plasma membrane to trigger appropriate cellular responses. Crystal structures of a number of these receptors have now been determined in inactive and active conformations bound to chemically and functionally distinct ligands. These crystal structures illustrate overall receptor organization and atomic details of ligand-receptor interactions. Copyright © 2014 Elsevier Inc. All rights reserved.

  5. Cell surface receptors for signal transduction and ligand transport: a design principles study.

    Directory of Open Access Journals (Sweden)

    Harish Shankaran

    2007-06-01

    Full Text Available Receptors constitute the interface of cells to their external environment. These molecules bind specific ligands involved in multiple processes, such as signal transduction and nutrient transport. Although a variety of cell surface receptors undergo endocytosis, the systems-level design principles that govern the evolution of receptor trafficking dynamics are far from fully understood. We have constructed a generalized mathematical model of receptor-ligand binding and internalization to understand how receptor internalization dynamics encodes receptor function and regulation. A given signaling or transport receptor system represents a particular implementation of this module with a specific set of kinetic parameters. Parametric analysis of the response of receptor systems to ligand inputs reveals that receptor systems can be characterized as being: i avidity-controlled where the response control depends primarily on the extracellular ligand capture efficiency, ii consumption-controlled where the ability to internalize surface-bound ligand is the primary control parameter, and iii dual-sensitivity where both the avidity and consumption parameters are important. We show that the transferrin and low-density lipoprotein receptors are avidity-controlled, the vitellogenin receptor is consumption-controlled, and the epidermal growth factor receptor is a dual-sensitivity receptor. Significantly, we show that ligand-induced endocytosis is a mechanism to enhance the accuracy of signaling receptors rather than merely serving to attenuate signaling. Our analysis reveals that the location of a receptor system in the avidity-consumption parameter space can be used to understand both its function and its regulation.

  6. T cell receptor signaling can directly enhance the avidity of CD28 ligand binding.

    Directory of Open Access Journals (Sweden)

    Mariano Sanchez-Lockhart

    Full Text Available T cell activation takes place in the context of a spatial and kinetic reorganization of cell surface proteins and signaling molecules at the contact site with an antigen presenting cell, termed the immunological synapse. Coordination of the activation, recruitment, and signaling from T cell receptor (TCR in conjunction with adhesion and costimulatory receptors regulates both the initiation and duration of signaling that is required for T cell activation. The costimulatory receptor, CD28, is an essential signaling molecule that determines the quality and quantity of T cell immune responses. Although the functional consequences of CD28 engagement are well described, the molecular mechanisms that regulate CD28 function are largely unknown. Using a micropipet adhesion frequency assay, we show that TCR signaling enhances the direct binding between CD28 and its ligand, CD80. Although CD28 is expressed as a homodimer, soluble recombinant CD28 can only bind ligand monovalently. Our data suggest that the increase in CD28-CD28 binding is mediated through a change in CD28 valency. Molecular dynamic simulations and in vitro mutagenesis indicate that mutations at the base of the CD28 homodimer interface, distal to the ligand-binding site, can induce a change in the orientation of the dimer that allows for bivalent ligand binding. When expressed in T cells, this mutation allows for high avidity CD28-CD80 interactions without TCR signaling. Molecular dynamic simulations also suggest that wild type CD28 can stably adopt a bivalent conformation. These results support a model whereby inside-out signaling from the TCR can enhance CD28 ligand interactions by inducing a change in the CD28 dimer interface to allow for bivalent ligand binding and ultimately the transduction of CD28 costimulatory signals that are required for T cell activation.

  7. A versatile dinucleating ligand containing sulfonamide groups

    DEFF Research Database (Denmark)

    Sundberg, Jonas; Witt, Hannes; Cameron, Lisa

    2014-01-01

    Copper, iron, and gallium coordination chemistries of the new pentadentate bis-sulfonamide ligand 2,6-bis(N-2-pyridylmethylsulfonamido)-4-methylphenol (psmpH3) were investigated. PsmpH3 is capable of varying degrees of deprotonation, and notably, complexes containing the fully trideprotonated...... ligand can be prepared in aqueous solutions using only divalent metal ions. Two of the copper(II) complexes, [Cu2(psmp)(OH)] and [Cu2(psmp)(OAc)2]-, demonstrate the anticipated 1:2 ligand/metal stoichiometry and show that the dimetallic binding site created for exogenous ligands possesses high inherent...... flexibility since additional one- and three-atom bridging ligands bridge the two copper(II) ions in each complex, respectively. This gives rise to a difference of 0.4 Å in the Cu···Cu distances. Complexes with 2:3 and 2:1 ligand/metal stoichiometries for the divalent and trivalent metal ions, respectively...

  8. Designer TGFβ superfamily ligands with diversified functionality.

    Directory of Open Access Journals (Sweden)

    George P Allendorph

    Full Text Available Transforming Growth Factor--beta (TGFβ superfamily ligands, including Activins, Growth and Differentiation Factors (GDFs, and Bone Morphogenetic Proteins (BMPs, are excellent targets for protein-based therapeutics because of their pervasiveness in numerous developmental and cellular processes. We developed a strategy termed RASCH (Random Assembly of Segmental Chimera and Heteromer, to engineer chemically-refoldable TGFβ superfamily ligands with unique signaling properties. One of these engineered ligands, AB208, created from Activin-βA and BMP-2 sequences, exhibits the refolding characteristics of BMP-2 while possessing Activin-like signaling attributes. Further, we find several additional ligands, AB204, AB211, and AB215, which initiate the intracellular Smad1-mediated signaling pathways more strongly than BMP-2 but show no sensitivity to the natural BMP antagonist Noggin unlike natural BMP-2. In another design, incorporation of a short N-terminal segment from BMP-2 was sufficient to enable chemical refolding of BMP-9, without which was never produced nor refolded. Our studies show that the RASCH strategy enables us to expand the functional repertoire of TGFβ superfamily ligands through development of novel chimeric TGFβ ligands with diverse biological and clinical values.

  9. Comparison of linear modes in kinetic plasma models

    CERN Document Server

    Camporeale, Enrico

    2016-01-01

    We compare, in an extensive and systematic way, linear theory results obtained with the hybrid (ion-kinetic and electron-fluid), the gyrokinetic and the fully-kinetic plasma models. We present a test case with parameters that are relevant for solar wind turbulence at small scales, which is a topic now recognized to need a kinetic treatment, to a certain extent. We comment on the comparison of low-frequency single modes (Alfv\\'{e}n/ion-cyclotron, ion-acoustic, and fast modes) for a wide range of propagation angles, and on the overall spectral properties of the linear operators, for quasi-perpendicular propagation. The methodology and the results presented in this paper will be valuable when choosing which model should be used in regimes where the assumptions of each model are not trivially satisfied.

  10. Adsorption and desorption kinetics of carbofuran in acid soils.

    Science.gov (United States)

    Bermúdez-Couso, Alipio; Fernández-Calviño, David; Pateiro-Moure, Miriam; Nóvoa-Muñoz, Juan Carlos; Simal-Gándara, Jesús; Arias-Estévez, Manuel

    2011-06-15

    Carbofuran adsorption and desorption were investigated in batch and stirred flow chamber (SFC) tests. The carbofuran adsorption capacity of the soils was found to be low and strongly dependent on their clay and organic carbon contents. Carbofuran sorption was due mainly (>80%) to fast adsorption processes governed by intraparticle diffusion. The adsorption kinetic constant for the pesticide ranged from 0.047 to 0.195 min(-1) and was highly correlated with constant n in the Freundlich equation (r=0.965, Pcarbofuran desorption to be highly variable and negatively correlated with eCEC and the clay content. The SFC tests showed that soil organic carbon (C) plays a key role in the irreversibility of carbofuran adsorption. Carbofuran desorption increased rapidly at C contents below 4%. The desorption kinetic constant for the compound (0.086-0.195 min(-1)) was generally higher than its adsorption kinetic constant; therefore, carbofuran is more rapidly desorbed than it is adsorbed in soil.

  11. LigandRFs: random forest ensemble to identify ligand-binding residues from sequence information alone

    KAUST Repository

    Chen, Peng

    2014-12-03

    Background Protein-ligand binding is important for some proteins to perform their functions. Protein-ligand binding sites are the residues of proteins that physically bind to ligands. Despite of the recent advances in computational prediction for protein-ligand binding sites, the state-of-the-art methods search for similar, known structures of the query and predict the binding sites based on the solved structures. However, such structural information is not commonly available. Results In this paper, we propose a sequence-based approach to identify protein-ligand binding residues. We propose a combination technique to reduce the effects of different sliding residue windows in the process of encoding input feature vectors. Moreover, due to the highly imbalanced samples between the ligand-binding sites and non ligand-binding sites, we construct several balanced data sets, for each of which a random forest (RF)-based classifier is trained. The ensemble of these RF classifiers forms a sequence-based protein-ligand binding site predictor. Conclusions Experimental results on CASP9 and CASP8 data sets demonstrate that our method compares favorably with the state-of-the-art protein-ligand binding site prediction methods.

  12. Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand.

    Directory of Open Access Journals (Sweden)

    Samuel DeLuca

    Full Text Available RosettaLigand has been successfully used to predict binding poses in protein-small molecule complexes. However, the RosettaLigand docking protocol is comparatively slow in identifying an initial starting pose for the small molecule (ligand making it unfeasible for use in virtual High Throughput Screening (vHTS. To overcome this limitation, we developed a new sampling approach for placing the ligand in the protein binding site during the initial 'low-resolution' docking step. It combines the translational and rotational adjustments to the ligand pose in a single transformation step. The new algorithm is both more accurate and more time-efficient. The docking success rate is improved by 10-15% in a benchmark set of 43 protein/ligand complexes, reducing the number of models that typically need to be generated from 1000 to 150. The average time to generate a model is reduced from 50 seconds to 10 seconds. As a result we observe an effective 30-fold speed increase, making RosettaLigand appropriate for docking medium sized ligand libraries. We demonstrate that this improved initial placement of the ligand is critical for successful prediction of an accurate binding position in the 'high-resolution' full atom refinement step.

  13. Methods of Fast Exponentiation

    Directory of Open Access Journals (Sweden)

    Mohammed A. Maitah

    2010-01-01

    Full Text Available Problem statement: Modular exponentiation constitutes the basis of many well-known and widely used public key cryptosystems. Approach: A fast portable modular exponentiation algorithm considerably enhanced the speed and applicability of these systems, also an efficient implementation of this algorithm was the key to high performance of such system. Results: In this study, two main approaches for solving this problem were proposed. The proposed approaches involved calculations without usage of extra operational memory for saving constants and calculations with usage of preliminary calculated constants. Conclusion/Recommendations: The estimation of complexity of the speedup and effectiveness of proposed approaches for the data were presented.

  14. FAST NEUTRONIC REACTOR

    Science.gov (United States)

    Snell, A.H.

    1957-12-01

    This patent relates to a reactor and process for carrying out a controlled fast neutron chain reaction. A cubical reactive mass, weighing at least 920 metric tons, of uranium metal containing predominantly U/sup 238/ and having a U/sup 235/ content of at least 7.63% is assembled and the maximum neutron reproduction ratio is limited to not substantially over 1.01 by insertion and removal of a varying amount of boron, the reactive mass being substantially freed of moderator.

  15. Impaired Insulin Suppression of VLDL-Triglyceride Kinetics in Non-alcoholic Fatty Liver Disease

    DEFF Research Database (Denmark)

    Poulsen, Marianne K; Nellemann, Birgitte; Stødkilde-Jørgensen, Hans;

    2016-01-01

    CONTEXT: Non-alcoholic fatty liver disease (NAFLD) is associated with glucose and lipid metabolic abnormalities. However, insulin suppression of VLDL-triglyceride (VLDL-TG) kinetics is not fully understood. OBJECTIVE: To determine VLDL-TG, glucose and palmitate kinetics during fasting and hyperin......CONTEXT: Non-alcoholic fatty liver disease (NAFLD) is associated with glucose and lipid metabolic abnormalities. However, insulin suppression of VLDL-triglyceride (VLDL-TG) kinetics is not fully understood. OBJECTIVE: To determine VLDL-TG, glucose and palmitate kinetics during fasting...... and hyperinsulinemia in men with (NAFLD+) and without NAFLD (NAFLD-). DESIGN: 27 non-diabetic, upper-body obese (WHR >0.9, BMI >28 kg/m(2)) men, 18 NAFLD+ and 9 NAFLD- determined by magnetic resonance spectroscopy, were enrolled.(14)C-labeled VLDL-TG and (3)H-labeled glucose and palmitate tracers were applied...... metabolic abnormalities associated with NAFLD and presumably diabetes....

  16. Light-Induced Copper(II) Coordination by a Bicyclic Tetraaza Chelator through a Ligand-to-Metal Charge-Transfer Reaction

    DEFF Research Database (Denmark)

    Holm-Jørgensen, Jacob Rørdam; Jensen, Mikael; Bjerrum, Morten J.

    2011-01-01

    To enable utilization of the broad potential of copper isotopes in nuclear medicine, rapid and robust chelation of the copper is required. Bowl adamanzanes (bicyclic tetraaza ligands) can form kinetically stable copper complexes, but they are usually formed at low rates unless high pH values...

  17. Catalytic C-H imidation of aromatic cores of functional molecules: ligand-accelerated Cu catalysis and application to materials- and biology-oriented aromatics.

    Science.gov (United States)

    Kawakami, Takahiro; Murakami, Kei; Itami, Kenichiro

    2015-02-25

    Versatile imidation of aromatic C-H bonds was accomplished. In the presence of copper bromide and 6,6'-dimethyl-2,2'-bipyridyl, a range of aromatics, such as polycyclic aromatic hydrocarbons, aromatic bowls, porphyrins, heteroaromatics, and natural products, can be imidated by N-fluorobenzenesulfonimide. A dramatic ligand-accelerated copper catalysis and an interesting kinetic profile were uncovered.

  18. Combining on-chip synthesis of a focused combinatorial library with computational target prediction reveals imidazopyridine GPCR ligands.

    Science.gov (United States)

    Reutlinger, Michael; Rodrigues, Tiago; Schneider, Petra; Schneider, Gisbert

    2014-01-07

    Using the example of the Ugi three-component reaction we report a fast and efficient microfluidic-assisted entry into the imidazopyridine scaffold, where building block prioritization was coupled to a new computational method for predicting ligand-target associations. We identified an innovative GPCR-modulating combinatorial chemotype featuring ligand-efficient adenosine A1/2B and adrenergic α1A/B receptor antagonists. Our results suggest the tight integration of microfluidics-assisted synthesis with computer-based target prediction as a viable approach to rapidly generate bioactivity-focused combinatorial compound libraries with high success rates.

  19. Nonequilibrium sensing and its analogy to kinetic proofreading

    CERN Document Server

    Hartich, David; Seifert, Udo

    2015-01-01

    For a paradigmatic model of chemotaxis, we analyze the effect how a nonzero affinity driving receptors out of equilibrium affects sensitivity. This affinity arises whenever changes in receptor activity involve ATP hydrolysis. The sensitivity integrated over a ligand concentration range is shown to be enhanced by the affinity, providing a measure of how much energy consumption improves sensing. With this integrated sensitivity we can establish an intriguing analogy between sensing with nonequilibrium receptors and kinetic proofreading: the increase in integrated sensitivity is equivalent to the decrease of the error in kinetic proofreading. The influence of the occupancy of the receptor on the phosphorylation and dephosphorylation reaction rates is shown to be crucial for the relation between integrated sensitivity and affinity. This influence can even lead to a regime where a nonzero affinity decreases the integrated sensitivity, which corresponds to anti-proofreading.

  20. Fasting and sport: an introduction.

    Science.gov (United States)

    Maughan, R J

    2010-06-01

    Most humans observe an overnight fast on a daily basis, and the human body copes well with short duration fasting. Periodic fasting is widely practised for cultural, religious or health reasons. Fasting may take many different forms. Prolonged restriction of food and fluid is harmful to health and performance, and it is often automatically assumed that intermittent fasting will lead to decrements in exercise performance. Athletes who choose to fast during training or competitions may therefore be at a disadvantage. The available evidence does not entirely support this view, but there is little or no information on the effects on elite athletes competing in challenging environments. Prolonged periods of training in the fasted state may not allow optimum adaptation of muscles and other tissues. Further research on a wide range of athletes with special nutrition needs is urgently required. In events where performance might be affected, other strategies to eliminate or minimise any effects must be sought.

  1. Molecular Dynamics Simulations Reveal the Mechanisms of Allosteric Activation of Hsp90 by Designed Ligands.

    Science.gov (United States)

    Vettoretti, Gerolamo; Moroni, Elisabetta; Sattin, Sara; Tao, Jiahui; Agard, David A; Bernardi, Anna; Colombo, Giorgio

    2016-04-01

    Controlling biochemical pathways through chemically designed modulators may provide novel opportunities to develop therapeutic drugs and chemical tools. The underlying challenge is to design new molecular entities able to act as allosteric chemical switches that selectively turn on/off functions by modulating the conformational dynamics of their target protein. We examine the origins of the stimulation of ATPase and closure kinetics in the molecular chaperone Hsp90 by allosteric modulators through atomistic molecular dynamics (MD) simulations and analysis of protein-ligand interactions. In particular, we focus on the cross-talk between allosteric ligands and protein conformations and its effect on the dynamic properties of the chaperone's active state. We examine the impact of different allosteric modulators on the stability, structural and internal dynamics properties of Hsp90 closed state. A critical aspect of this study is the development of a quantitative model that correlates Hsp90 activation to the presence of a certain compound, making use of information on the dynamic adaptation of protein conformations to the presence of the ligand, which allows to capture conformational states relevant in the activation process. We discuss the implications of considering the conformational dialogue between allosteric ligands and protein conformations for the design of new functional modulators.

  2. TonB-dependent ligand trapping in the BtuB transporter.

    Science.gov (United States)

    Mills, Allan; Le, Hai-Tuong; Duong, Franck

    2016-12-01

    TonB-dependent transporters are β-barrel outer membrane proteins occluded by a plug domain. Upon ligand binding, these transporters extend a periplasmic motif termed the TonB box. The TonB box permits the recruitment of the inner membrane protein complex TonB-ExbB-ExbD, which drives import of ligands in the cell periplasm. It is unknown precisely how the plug domain is moved aside during transport nor have the intermediate states between TonB recruitment and plug domain movement been characterized biochemically. Here we employ nanodiscs, native gel electrophoresis, and scintillation proximity assays to determine the binding kinetics of vitamin B12 to BtuB. The results show that ligand-bound BtuB recruits a monomer of TonB (TonB∆1-31), which in turn increases retention of vitamin B12 within the transporter. The TonB box and the extracellular residue valine 90 that forms part of the vitamin B12 binding site are essential for this event. These results identify a novel step in the TonB-dependent transport process. They show that TonB binding to BtuB trap the ligand, possibly until the ExbB-ExbD complex is activated or recruited to ensure subsequent transport. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Fast dynamics perturbation analysis for prediction of protein functional sites

    Directory of Open Access Journals (Sweden)

    Cohn Judith D

    2008-01-01

    Full Text Available Abstract Background We present a fast version of the dynamics perturbation analysis (DPA algorithm to predict functional sites in protein structures. The original DPA algorithm finds regions in proteins where interactions cause a large change in the protein conformational distribution, as measured using the relative entropy Dx. Such regions are associated with functional sites. Results The Fast DPA algorithm, which accelerates DPA calculations, is motivated by an empirical observation that Dx in a normal-modes model is highly correlated with an entropic term that only depends on the eigenvalues of the normal modes. The eigenvalues are accurately estimated using first-order perturbation theory, resulting in a N-fold reduction in the overall computational requirements of the algorithm, where N is the number of residues in the protein. The performance of the original and Fast DPA algorithms was compared using protein structures from a standard small-molecule docking test set. For nominal implementations of each algorithm, top-ranked Fast DPA predictions overlapped the true binding site 94% of the time, compared to 87% of the time for original DPA. In addition, per-protein recall statistics (fraction of binding-site residues that are among predicted residues were slightly better for Fast DPA. On the other hand, per-protein precision statistics (fraction of predicted residues that are among binding-site residues were slightly better using original DPA. Overall, the performance of Fast DPA in predicting ligand-binding-site residues was comparable to that of the original DPA algorithm. Conclusion Compared to the original DPA algorithm, the decreased run time with comparable performance makes Fast DPA well-suited for implementation on a web server and for high-throughput analysis.

  4. Fast Fourier transform telescope

    Science.gov (United States)

    Tegmark, Max; Zaldarriaga, Matias

    2009-04-01

    We propose an all-digital telescope for 21 cm tomography, which combines key advantages of both single dishes and interferometers. The electric field is digitized by antennas on a rectangular grid, after which a series of fast Fourier transforms recovers simultaneous multifrequency images of up to half the sky. Thanks to Moore’s law, the bandwidth up to which this is feasible has now reached about 1 GHz, and will likely continue doubling every couple of years. The main advantages over a single dish telescope are cost and orders of magnitude larger field-of-view, translating into dramatically better sensitivity for large-area surveys. The key advantages over traditional interferometers are cost (the correlator computational cost for an N-element array scales as Nlog⁡2N rather than N2) and a compact synthesized beam. We argue that 21 cm tomography could be an ideal first application of a very large fast Fourier transform telescope, which would provide both massive sensitivity improvements per dollar and mitigate the off-beam point source foreground problem with its clean beam. Another potentially interesting application is cosmic microwave background polarization.

  5. Fast SCR Thyratron Driver

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, M.N.; /SLAC

    2007-06-18

    As part of an improvement project on the linear accelerator at SLAC, it was necessary to replace the original thyratron trigger generator, which consisted of two chassis, two vacuum tubes, and a small thyratron. All solid-state, fast rise, and high voltage thyratron drivers, therefore, have been developed and built for the 244 klystron modulators. The rack mounted, single chassis driver employs a unique way to control and generate pulses through the use of an asymmetric SCR, a PFN, a fast pulse transformer, and a saturable reactor. The resulting output pulse is 2 kV peak into 50 {Omega} load with pulse duration of 1.5 {mu}s FWHM at 180 Hz. The pulse risetime is less than 40 ns with less than 1 ns jitter. Various techniques are used to protect the SCR from being damaged by high voltage and current transients due to thyratron breakdowns. The end-of-line clipper (EOLC) detection circuit is also integrated into this chassis to interrupt the modulator triggering in the event a high percentage of line reflections occurred.

  6. Synthesis and characterization of mixed ligand chiral nanoclusters

    KAUST Repository

    Guven, Zekiye P.

    2016-06-22

    Chiral mixed ligand silver nanoclusters were synthesized in the presence of a chiral and an achiral ligand. While the chiral ligand led mostly to the formation of nanoparticles, the presence of the achiral ligand drastically increased the yield of nanoclusters with enhanced chiral properties. © 2016 The Royal Society of Chemistry.

  7. Long-lived charge-separated states in ligand-stabilized silver clusters

    KAUST Repository

    Pelton, Matthew

    2012-07-25

    Recently developed synthesis methods allow for the production of atomically monodisperse clusters of silver atoms stabilized in solution by aromatic thiol ligands, which exhibit intense absorption peaks throughout the visible and near-IR spectral regions. Here we investigated the time-dependent optical properties of these clusters. We observed two kinetic processes following ultrafast laser excitation of any of the absorption peaks: a rapid decay, with a time constant of 1 ps or less, and a slow decay, with a time constant that can be longer than 300 ns. Both time constants decrease as the polarity of the solvent increases, indicating that the two processes correspond to the formation and recombination, respectively, of a charge-separated state. The long lifetime of this state and the broad optical absorption spectrum mean that the ligand-stabilized silver clusters are promising materials for solar energy harvesting. © 2012 American Chemical Society.

  8. Protein–ligand interactions investigated by thermal shift assays (TSA) and dual polarization interferometry (DPI)

    Energy Technology Data Exchange (ETDEWEB)

    Grøftehauge, Morten K., E-mail: m.k.groftehauge@durham.ac.uk; Hajizadeh, Nelly R. [Durham University, South Road, Durham DH1 3LE (United Kingdom); Swann, Marcus J. [Biolin Scientific, 62 Wellington Road South, Stockport, Cheshire SK1 3SU (United Kingdom); Pohl, Ehmke, E-mail: m.k.groftehauge@durham.ac.uk [Durham University, South Road, Durham DH1 3LE (United Kingdom)

    2015-01-01

    The biophysical characterization of protein–ligand interactions in solution using techniques such as thermal shift assay, or on surfaces using, for example, dual polarization interferometry, plays an increasingly important role in complementing crystal structure determinations. Over the last decades, a wide range of biophysical techniques investigating protein–ligand interactions have become indispensable tools to complement high-resolution crystal structure determinations. Current approaches in solution range from high-throughput-capable methods such as thermal shift assays (TSA) to highly accurate techniques including microscale thermophoresis (MST) and isothermal titration calorimetry (ITC) that can provide a full thermodynamic description of binding events. Surface-based methods such as surface plasmon resonance (SPR) and dual polarization interferometry (DPI) allow real-time measurements and can provide kinetic parameters as well as binding constants. DPI provides additional spatial information about the binding event. Here, an account is presented of new developments and recent applications of TSA and DPI connected to crystallography.

  9. The influence of ligand valency on aggregation mechanisms for inhibiting bacterial toxins.

    Science.gov (United States)

    Sisu, Cristina; Baron, Andrew J; Branderhorst, Hilbert M; Connell, Simon D; Weijers, Carel A G M; de Vries, Renko; Hayes, Edward D; Pukin, Aliaksei V; Gilbert, Michel; Pieters, Roland J; Zuilhof, Han; Visser, Gerben M; Turnbull, W Bruce

    2009-01-26

    Divalent and tetravalent analogues of ganglioside GM1 are potent inhibitors of cholera toxin and Escherichia coli heat-labile toxin. However, they show little increase in inherent affinity when compared to the corresponding monovalent carbohydrate ligand. Analytical ultracentrifugation and dynamic light scattering have been used to demonstrate that the multivalent inhibitors induce protein aggregation and the formation of space-filling networks. This aggregation process appears to arise when using ligands that do not match the valency of the protein receptor. While it is generally accepted that multivalency is an effective strategy for increasing the activity of inhibitors, here we show that the valency of the inhibitor also has a dramatic effect on the kinetics of aggregation and the stability of intermediate protein complexes. Structural studies employing atomic force microscopy have revealed that a divalent inhibitor induces head-to-head dimerization of the protein toxin en route to higher aggregates.

  10. Hydrophobic side chain dynamics of a glutamate receptor ligand binding domain.

    Science.gov (United States)

    Maltsev, Alexander S; Oswald, Robert E

    2010-03-26

    Ionotropic glutamate receptors are ligand-gated ion channels that mediate much of the fast excitatory neurotransmission in the central nervous system. The extracellular ligand binding core (S1S2) of the GluR2 subtype of ionotropic glutamate receptors can be produced as a soluble protein with properties essentially identical to the corresponding domain in the intact, membrane-bound protein. Using a variety of biophysical techniques, much has been learned about the structure and dynamics of S1S2 and the relationship between its ligand-induced conformational changes and the function of the receptor. It is clear that dynamic processes are essential to the function of ionotropic glutamate receptors. We have isotopically labeled side chain methyls of GluR2 S1S2 and used NMR spectroscopy to study their dynamics on the ps-ns and mus-ms time scales. Increased disorder is seen in regions that are part of the key dimer interface in the intact protein. When glutamate is bound, the degree of ps-ns motion is less than that observed with other ligands, suggesting that the physiological agonist binds to a preformed binding site. At the slower time scales, the degree of S1S2 flexibility induced by ligand binding is greatest for willardiine partial agonists, least for antagonists, and intermediate for full agonists. Notable differences among bound ligands are in the region of the protein that forms a hinge between two lobes that close upon agonist binding, and along the beta-sheet in Lobe 2. These motions provide clues as to the functional properties of partial agonists and to the conformational changes associated with lobe closure and channel activation.

  11. Ligand- and drug-binding studies of membrane proteins revealed through circular dichroism spectroscopy.

    Science.gov (United States)

    Siligardi, Giuliano; Hussain, Rohanah; Patching, Simon G; Phillips-Jones, Mary K

    2014-01-01

    A great number of membrane proteins have proven difficult to crystallise for use in X-ray crystallographic structural determination or too complex for NMR structural studies. Circular dichroism (CD) is a fast and relatively easy spectroscopic technique to study protein conformational behaviour. In this review examples of the applications of CD and synchrotron radiation CD (SRCD) to membrane protein ligand binding interaction studies are discussed. The availability of SRCD has been an important advancement in recent progress, most particularly because it can be used to extend the spectral region in the far-UV region (important for increasing the accuracy of secondary structure estimations) and for working with membrane proteins available in only small quantities for which SRCD has facilitated molecular recognition studies. Such studies have been accomplished by probing in the near-UV region the local tertiary structure of aromatic amino acid residues upon addition of chiral or non-chiral ligands using long pathlength cells of small volume capacity. In particular, this review describes the most recent use of the technique in the following areas: to obtain quantitative data on ligand binding (exemplified by the FsrC membrane sensor kinase receptor); to distinguish between functionally similar drugs that exhibit different mechanisms of action towards membrane proteins (exemplified by secretory phospholipase A2); and to identify suitable detergent conditions to observe membrane protein-ligand interactions using stabilised proteins (exemplified by the antiseptic transporter SugE). Finally, the importance of characterising in solution the conformational behaviour and ligand binding properties of proteins in both far- and near-UV regions is discussed. This article is part of a Special Issue entitled: Structural and biophysical characterisation of membrane protein-ligand binding. © 2013.

  12. Rigidified Clicked Dimeric Ligands for Studying the Dynamics of the PDZ1-2 Supramodule of PSD-95

    DEFF Research Database (Denmark)

    Eildal, Jonas N N; Bach, Anders; Dogan, Jakob

    2015-01-01

    PSD-95 is a scaffolding protein of the MAGUK protein family, and engages in several vital protein-protein interactions in the brain with its PDZ domains. It has been suggested that PSD-95 is composed of two supramodules, one of which is the PDZ1-2 tandem domain. Here we have developed rigidified...... high-affinity dimeric ligands that target the PDZ1-2 supramodule, and established the biophysical parameters of the dynamic PDZ1-2/ligand interactions. By employing ITC, protein NMR, and stopped-flow kinetics this study provides a detailed insight into the overall conformational energetics...... of the interaction between dimeric ligands and tandem PDZ domains. Our findings expand our understanding of the dynamics of PSD-95 with potential relevance to its biological role in interacting with multivalent receptor complexes and development of novel drugs....

  13. Ligand Conformation Dictates Membrane and Endosomal Trafficking of Arginine-Glycine-Aspartate (RGD)-Functionalized Mesoporous Silica Nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Fang, I-Ju; Slowing, Igor I; Wu, Kevin C.W.; Lin, Victor S.Y.; Trewyn, Brian

    2012-05-15

    Recent breakthrough research on mesoporous silica nanoparticle (MSN) materials has illustrated their significant potential in biological applications due to their excellent drug delivery and endocytotic behavior. We set out to determine if MSN, covalently functionalized with conformation specific bioactive molecules (either linear or cyclic RGD ligands), behave towards mammalian cells in a similar manner as the free ligands. We discovered that RGD immobilized on the MSN surface did not influence the integrity of the porous matrix and improved the endocytosis efficiency of the MSN materials. Through competition experiments with free RGD ligands, we also discovered a conformation specific receptor–integrin association. The interaction between RGD immobilized on the MSN surface and integrins plays an important role in endosome trafficking, specifically dictating the kinetics of endosomal escape. Thus, covalent functionalization of biomolecules on MSN assists in the design of a system for controlling the interface with cancer cells.

  14. Design, synthesis and evaluation of 4,7-diamino-1,10-phenanthroline G-quadruplex ligands

    DEFF Research Database (Denmark)

    Nielsen, Mads Corvinius; Borch, Jonas; Ulven, Trond

    2009-01-01

    the central ionic column. Introduction of positively charged side chains results in compounds with appreciable G-quadruplex stabilizing properties and high aqueous solubility, with the longer side chains giving more potent compounds. Ligands carrying guanidine side chains in general show higher quadruplex...... stabilizing activity and distinctly slower kinetic properties than their amino and dimethylamino analogues, possibly due to specific hydrogen bond interactions with the G-quadruplex loops....

  15. Kinetic distance and kinetic maps from molecular dynamics simulation

    CERN Document Server

    Noe, Frank

    2015-01-01

    Characterizing macromolecular kinetics from molecular dynamics (MD) simulations requires a distance metric that can distinguish slowly-interconverting states. Here we build upon diffusion map theory and define a kinetic distance for irreducible Markov processes that quantifies how slowly molecular conformations interconvert. The kinetic distance can be computed given a model that approximates the eigenvalues and eigenvectors (reaction coordinates) of the MD Markov operator. Here we employ the time-lagged independent component analysis (TICA). The TICA components can be scaled to provide a kinetic map in which the Euclidean distance corresponds to the kinetic distance. As a result, the question of how many TICA dimensions should be kept in a dimensionality reduction approach becomes obsolete, and one parameter less needs to be specified in the kinetic model construction. We demonstrate the approach using TICA and Markov state model (MSM) analyses for illustrative models, protein conformation dynamics in bovine...

  16. Glucagon receptors: effect of exercise and fasting.

    Science.gov (United States)

    Lavoie, Carole

    2005-06-01

    One paradox of hormonal regulation during exercise is the maintenance of glucose homeostasis after endurance training despite a lower increase in plasma glucagon. One explanation could be that liver sensitivity to glucagon is increased by endurance training. Glucagon exerts its effect through a 62 KDa glycoprotein receptor, member of the G protein-coupled receptor. To determine whether changes with exercise in glucagon sensitivity occurred at the level of the glucagon receptor (GR), binding characteristics of hepatic glucagon receptors were ascertained in rat purified plasma membranes. Saturation kinetics indicated no difference in the dissociation constant or affinity of glucagon receptor, but a significantly higher glucagon receptor binding density in liver in endurance trained compared to untrained animals. Along with endurance training, it appears that fasting also changes GR binding characteristics. In animals fasting 24 hrs, a significant increase in glucagon receptor density was also reported. Although the exact mechanism remains unknown, there is no doubt that the liver can adapt to physiological stress through modulation of GR binding characteristics to enhance the hepatic glucose production responsiveness to glucagon.

  17. Fast Food Jobs. National Study of Fast Food Employment.

    Science.gov (United States)

    Charner, Ivan; Fraser, Bryna Shore

    A study examined employment in the fast-food industry. The national survey collected data from employees at 279 fast-food restaurants from seven companies. Female employees outnumbered males by two to one. The ages of those fast-food employees in the survey sample ranged from 14 to 71, with fully 70 percent being in the 16- to 20-year-old age…

  18. Islamic fasting and multiple sclerosis

    Science.gov (United States)

    2014-01-01

    Background Month-long daytime Ramadan fasting pose s major challenges to multiple sclerosis (MS) patients in Muslim countries. Physicians should have practical knowledge on the implications of fasting on MS. We present a summary of database searches (Cochrane Database of Systematic Reviews, PubMed) and a mini-symposium on Ramadan fasting and MS. In this symposium, we aimed to review the effect of fasting on MS and suggest practical guidelines on management. Discussion In general, fasting is possible for most stable patients. Appropriate amendment of drug regimens, careful monitoring of symptoms, as well as providing patients with available evidence on fasting and MS are important parts of management. Evidence from experimental studies suggests that calorie restriction before disease induction reduces inflammation and subsequent demyelination and attenuates disease severity. Fasting does not appear to have unfavorable effects on disease course in patients with mild disability (Expanded Disability Status Scale (EDSS) score ≤3). Most experts believed that during fasting (especially in summer), some MS symptoms (fatigue, fatigue perception, dizziness, spasticity, cognitive problems, weakness, vision, balance, gait) might worsen but return to normal levels during feasting. There was a general consensus that fasting is not safe for patients: on high doses of anti-convulsants, anti-spastics, and corticosteroids; with coagulopathy or active disease; during attacks; with EDSS score ≥7. Summary These data suggest that MS patients should have tailored care. Fasting in MS patients is a challenge that is directly associated with the spiritual belief of the patient. PMID:24655543

  19. Ramadan fasting, pregnancy and lactation

    Directory of Open Access Journals (Sweden)

    Mohsen Khoshniat Nikoo

    2014-04-01

    Full Text Available Background: Fasting and malnutrition during pregnancy is associated with deleterious consequences such as hypoglycemia, ketonemia, impaired fetal IQ, low birth weight and even abortion. Comparison of pregnancy length and year duration shows that about 75% of pregnancies coincided with Ramadan. Also, fasting during Ramadan is not equivalent to hunger and malnutrition, however, knowledge of the effects of Ramadan fasting on pregnancy outcome is important. In this review, the results of all studies related to the possible effects of Ramadan fasting in pregnancy and lactation have been collected. Material and Methods: Keywords such as "Ramadan", "Ramadan Fasting", "Islamic Fasting", "Fasting in Ramadan "and Fasting with words Pregnancy, Birth Weight, Lactation, Preterm, Milk Composition, Breast Milk were searched in PubMed Database, SID (Scientific Information Database, and some regional journals and 40 related articles (descriptive cross - sectional, cohort, clinical trial and review articles from 1968 to 2010 were studied. Results: Based on available information, if the maternal nutrition during Ramadan is good, the normal process of pregnancy will be maintained and Ramadan fasting would not have deleterious effects on fetal physical and mental growth. Conclusion: Considering nutritional tips, nursing mothers could also fast during Ramadan.

  20. Kinetics of tetrataenite disordering

    Energy Technology Data Exchange (ETDEWEB)

    Dos Santos, E., E-mail: edisanfi@cbpf.br [Centro Brasileiro de Pesquisas Físicas, Rio de Janeiro (Brazil); Gattacceca, J.; Rochette, P. [Centre Européen de Recherche et d’Enseignement des Géosciences de l’Environnement, UM34, CNRS/Aix-Marseille University, Aix-en-Provence (France); Fillion, G. [Laboratoire National des Champs Magnétiques Intenses (LNCMI), CNRS, UJF, 38042 Grenoble (France); Scorzelli, R.B. [Centro Brasileiro de Pesquisas Físicas, Rio de Janeiro (Brazil)

    2015-02-01

    Tetrataenite is a chemically ordered L1{sub 0}-type Fe{sub 50}Ni{sub 50} alloy detected for the first time in 1977 by {sup 57}Fe Mössbauer spectroscopy studies in iron meteorites. The thermal history of meteorites, in particular short thermal events like those associated to hypervelocity impacts, can be constrained by tracing the presence of tetrataenite or its disordering into taenite. The knowledge of the disordering kinetics of tetrataenite, that is associated with changes in its magnetic properties, is still very fragmentary so that the time–temperature history of these meteorites cannot be constrained in details. Furthermore, knowledge of disordering kinetics is important due to potential technological application of tetrataenite as a rare-earth free strong magnet. Thus, this work provides the first time–temperature data for disordering reaction of tetrataenite. We have shown that disordering is not an instantaneous process but is a kinetic limited reaction. It was shown that disordering may take place at any temperature above the order–disorder transition for L{sub 10} superstructure phase (∼320 °C) when the appropriate time-scale is considered. This result means that the apparent Curie point for tetrataenite is not an absolute property in the sense that any estimate of this parameter should be referred to a given time-scale. - Highlights: • The first time–temperature data for tetrataenite disordering reaction is provided. • Previous works does not give a complete picture of tetrataenite disordering. • Apparent Curie temperature of tetrataenite should be referred to a time-scale. • Tetrataenite can be used as a probe to detect thermal/shock events recorded in meteorites.