Science.gov

Sample records for fast kinetic ligands

  1. Spatial kinetics in fast reactors

    NASA Astrophysics Data System (ADS)

    Seleznev, E. F.; Belov, A. A.; Panova, I. S.; Matvienko, I. P.; Zhukov, A. M.

    2013-12-01

    The analysis of the solution to the spatial nonstationary equation of neutron transport is presented by the example of a fast reactor. Experiments in spatial kinetics conducted recently at the complex of critical assemblies (fast physical stand) and computations of their data using the TIMER code (for solving the nonstationary equation in multidimensional diffusion approximation for direct and inverse problems of reactor kinetics) have shown that kinetics of fast reactors substantially differs from kinetics of thermal reactors. The difference is connected with influence of the delayed neutron spectrum on rates of the process in a fast reactor.

  2. Fast protein folding kinetics

    PubMed Central

    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

  3. On fast reactor kinetics studies

    SciTech Connect

    Seleznev, E. F.; Belov, A. A.; Matveenko, I. P.; Zhukov, A. M.; Raskach, K. F.

    2012-07-01

    The results and the program of fast reactor core time and space kinetics experiments performed and planned to be performed at the IPPE critical facility is presented. The TIMER code was taken as computation support of the experimental work, which allows transient equations to be solved in 3-D geometry with multi-group diffusion approximation. The number of delayed neutron groups varies from 6 to 8. The code implements the solution of both transient neutron transfer problems: a direct one, where neutron flux density and its derivatives, such as reactor power, etc, are determined at each time step, and an inverse one for the point kinetics equation form, where such a parameter as reactivity is determined with a well-known reactor power time variation function. (authors)

  4. (S)-5-(p-Nitrobenzyl)-PCTA, a Promising Bifunctional Ligand with Advantageous Metal Ion Complexation Kinetics

    PubMed Central

    Tircsó, Gyula; Benyó, Enikő Tircsóné; Suh, Eul Hyun; Jurek, Paul; Kiefer, Garry E.; Sherry, A. Dean; Kovács, Zoltán

    2009-01-01

    A bifunctional version of PCTA (3,6,9,15-tetraazabicyclo[9.3.1]pentadeca-1(15),11,13-triene-3,6,9,-triacetic acid) that exhibits fast complexation kinetics with the trivalent lanthanide(III) ions was synthesized in reasonable yields starting from N, N′, N″-tristosyl-(S)-2-(p-nitrobenzyl)-diethylenetriamine. pH-potentiometric studies showed that the basicities of p-nitrobenzyl-PCTA and the parent ligand PCTA were similar. The stability of M(NO2-Bn-PCTA) (M = Mg2+, Ca2+, Cu2+, Zn2+) complexes was similar to that of the corresponding PCTA complexes while the stability of Ln3+ complexes of the bifunctional ligand is somewhat lower than that of PCTA chelates. The rate of complex formation of Ln(NO2-Bn-PCTA) complexes was found to be quite similar to that of PCTA, a ligand known to exhibit the fastest formation rates among all lanthanide macrocyclic ligand complexes studied to date. The acid catalyzed decomplexation kinetic studies of the selected Ln(NO2-Bn-PCTA) complexes showed that the kinetic inertness of the complexes was comparable to that of Ln(DOTA) chelates making the bifunctional ligand NO2-Bn-PCTA suitable for labeling biological vectors with radioisotopes for nuclear medicine applications. PMID:19220012

  5. Exchange Kinetics of a Hydrophobic Ligand Binding Protein

    NASA Astrophysics Data System (ADS)

    Vaughn, Jeff; Stone, Martin

    2002-03-01

    Conformational fluctuations of proteins are thought to be important for determining the functional roles in biological activity. In some cases, the rates of these conformational changes may be directly correlated to, for example, the rates of catalysis or ligand binding. We are studying the role of conformational fluctuations in the binding of small volatile hydrophobic pheromones by the mouse major urinary proteins (MUPs). Communication among mice occurs, in part, with the MUP-1 protein. This urinary protein binds pheromones as a way to increase the longevity of the pheromone in an extracellular environment. Of interest is that the crystal structure of MUP-1 with a pheromone ligand shows the ligand to be completely occluded from the solvent with no obvious pathway to enter or exit. This suggests that conformational exchange of the protein may be required for ligand binding and release to occur. We hypothesize that the rate of conformational exchange may be a limiting factor determining the rate of ligand association and dissociation. By careful measurement of the on- and off-rates of ligand binding and the rates of conformational changes of the protein, a more defined picture of the interplay between protein structure and function can be obtained. To this end, heteronuclear saturation transfer, ^15N-exchange and ^15N dynamics experiments have been employed to probe the kinetics of ligand binding to MUP-1.

  6. Adsorption kinetic process of thiol ligands on gold nanocrystals.

    PubMed

    Cheng, Hao; Yang, Lina; Jiang, Yong; Huang, Yuanyuan; Sun, Zhihu; Zhang, Jing; Hu, Tiandou; Pan, Zhiyun; Pan, Guoqiang; Yao, Tao; Bian, Qing; Wei, Shiqiang

    2013-12-01

    Understanding the kinetic mechanism during ligand adsorption on gold nanocrystals is important for designing and fine-tuning their properties and implications. Here, we report a kinetic study on the adsorption process of dodecanethiol ligands on Au nanocrystals of 3.3 nm by an in situ time-resolved X-ray absorption fine structure technique. A two-step process of dodecanethiol adsorption on Au NC surfaces is proposed based on the obtained ligand coverage, which shows a quick increase from 0 to 0.40 within the first 20 min, followed by a much slower increase to the limiting value of 0.94. In-depth analysis suggests that the first stage involves the quick adsorption of dodecanethiol to the corner and edge sites of Au NCs surfaces, leading to remarkable surface Au-Au bond length relaxation (from 2.79 to 2.81 Å) and pronounced gold-to-ligand charge transfer. The second step that corresponds to the much slower adsorption process to the surface facets could be described by the Langmuir kinetics equation with an adsorption rate constant of 0.0132 min(-1) and an initial coverage of 0.41, in good agreement with the initially preferable adsorption of thiols to the most favorable sites. PMID:24122096

  7. Biphasic binding kinetics between FepA and its ligands.

    PubMed

    Payne, M A; Igo, J D; Cao, Z; Foster, S B; Newton, S M; Klebba, P E

    1997-08-29

    The Escherichia coli FepA protein is an energy- and TonB-dependent, ligand-binding porin that functions as a receptor for the siderophore ferric enterobactin and colicins B and D. We characterized the kinetic and thermodynamic parameters associated with the initial, energy-independent steps in ligand binding to FepA. In vivo experiments produced Kd values of 24, 185, and 560 nM for ferric enterobactin, colicin B, and colicin D, respectively. The siderophore and colicin B bound to FepA with a 1:1 stoichiometry, but colicin D bound to a maximum level that was 3-fold lower. Preincubation with ferric enterobactin prevented colicin B binding, and preincubation with colicin B prevented ferric enterobactin binding. Colicin B release from FepA was unexpectedly slow in vivo, about 10-fold slower than ferric enterobactin release. This slow dissociation of the colicin B.FepA complex facilitated the affinity purification of FepA and FepA mutants with colicin B-Sepharose. Analysis of a fluorescent FepA derivative showed that ferric enterobactin and colicin B adsorbed with biphasic kinetics, suggesting that both ligands bind in at least two distinct steps, an initial rapid stage and a subsequent slower step, that presumably establishes a transport-competent complex. PMID:9268330

  8. Solvent fluctuations in hydrophobic cavity–ligand binding kinetics

    PubMed Central

    Setny, Piotr; Baron, Riccardo; Michael Kekenes-Huskey, Peter; McCammon, J. Andrew; Dzubiella, Joachim

    2013-01-01

    Water plays a crucial part in virtually all protein–ligand binding processes in and out of equilibrium. Here, we investigate the role of water in the binding kinetics of a ligand to a prototypical hydrophobic pocket by explicit-water molecular dynamics (MD) simulations and implicit diffusional approaches. The concave pocket in the unbound state exhibits wet/dry hydration oscillations whose magnitude and time scale are significantly amplified by the approaching ligand. In turn, the ligand’s stochastic motion intimately couples to the slow hydration fluctuations, leading to a sixfold-enhanced friction in the vicinity of the pocket entrance. The increased friction considerably decelerates association in the otherwise barrierless system, indicating the importance of molecular-scale hydrodynamic effects in cavity–ligand binding arising due to capillary fluctuations. We derive and analyze the diffusivity profile and show that the mean first passage time distribution from the MD simulation can be accurately reproduced by a standard Brownian dynamics simulation if the appropriate position-dependent friction profile is included. However, long-time decays in the water–ligand (random) force autocorrelation demonstrate violation of the Markovian assumption, challenging standard diffusive approaches for rate prediction. Remarkably, the static friction profile derived from the force correlations strongly resembles the profile derived on the Markovian assumption apart from a simple shift in space, which can be rationalized by a time–space retardation in the ligand’s downhill dynamics toward the pocket. The observed spatiotemporal hydrodynamic coupling may be of biological importance providing the time needed for conformational receptor–ligand adjustments, typical of the induced-fit paradigm. PMID:23297241

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

    PubMed Central

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

    2016-01-01

    By monitoring the effect of deuterium decoupling on the decay of transverse 15N magnetization in D–15N spin pairs during multiple-refocusing echo sequences, we have determined fast D–D exchange rates k D and compared them with fast H–H exchange rates k H in tryptophan to determine the kinetic isotope effect as a function of pH and temperature. PMID:27009684

  10. Kinetics of a Fast Moving Partial Dislocation

    NASA Astrophysics Data System (ADS)

    Daphalapurkar, Nitin; Ramesh, K. T.

    2013-03-01

    Plastic deformation in materials under extreme stresses requires a kinetic description of moving dislocations. The velocities with which the partial dislocations can propagate under an applied stress has implications for plasticity at high strain rates, specifically, the rate of plastic deformation and the rate-sensitivity. In this work, we focus our attention on motion of a twinning partial dislocation in a face-centered cubic (FCC) material, Ni. We use molecular dynamics simulations to simulate the velocity of a propagating twinning partial dislocation and investigate the effect of applied shear stress. Results suggest a limiting value for the speeds of a propagating partial dislocation. The material speeds based on the nonlinear part (under high stresses) of the stress-strain curve are shown to have an influence on the velocity with which a partial dislocation can propagate. Predicted velocities from simulations will be related to observations from high rate impact experiments. Supported by Hopkins Extreme Materials Institute

  11. Quantitative Imaging in Laboratory: Fast Kinetics and Fluorescence Quenching

    ERIC Educational Resources Information Center

    Cumberbatch, Tanya; Hanley, Quentin S.

    2007-01-01

    The process of quantitative imaging, which is very commonly used in laboratory, is shown to be very useful for studying the fast kinetics and fluorescence quenching of many experiments. The imaging technique is extremely cheap and hence can be used in many absorption and luminescence experiments.

  12. Fast Kinetics of Calcium Signaling and Sensor Design

    PubMed Central

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

    2015-01-01

    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. PMID:26151819

  13. Fast algorithm for calculating chemical kinetics in turbulent reacting flow

    NASA Technical Reports Server (NTRS)

    Radhakrishnan, K.; Pratt, D. T.

    1986-01-01

    This paper addresses the need for a fast batch chemistry solver to perform the kinetics part of a split operator formulation of turbulent reacting flows, with special attention focused on the solution of the ordinary differential equations governing a homogeneous gas-phase chemical reaction. For this purpose, a two-part predictor-corrector algorithm which incorporates an exponentially fitted trapezoidal method was developed. The algorithm performs filtering of ill-posed initial conditions, automatic step-size selection, and automatic selection of Jacobi-Newton or Newton-Raphson iteration for convergence to achieve maximum computational efficiency while observing a prescribed error tolerance. The new algorithm, termed CREK1D (combustion reaction kinetics, one-dimensional), compared favorably with the code LSODE when tested on two representative problems drawn from combustion kinetics, and is faster than LSODE.

  14. Comparison of the kinetics of different Markov models for ligand binding under varying conditions

    SciTech Connect

    Martini, Johannes W. R.; Habeck, Michael

    2015-03-07

    We recently derived a Markov model for macromolecular ligand binding dynamics from few physical assumptions and showed that its stationary distribution is the grand canonical ensemble [J. W. R. Martini, M. Habeck, and M. Schlather, J. Math. Chem. 52, 665 (2014)]. The transition probabilities of the proposed Markov process define a particular Glauber dynamics and have some similarity to the Metropolis-Hastings algorithm. Here, we illustrate that this model is the stochastic analog of (pseudo) rate equations and the corresponding system of differential equations. Moreover, it can be viewed as a limiting case of general stochastic simulations of chemical kinetics. Thus, the model links stochastic and deterministic approaches as well as kinetics and equilibrium described by the grand canonical ensemble. We demonstrate that the family of transition matrices of our model, parameterized by temperature and ligand activity, generates ligand binding kinetics that respond to changes in these parameters in a qualitatively similar way as experimentally observed kinetics. In contrast, neither the Metropolis-Hastings algorithm nor the Glauber heat bath reflects changes in the external conditions correctly. Both converge rapidly to the stationary distribution, which is advantageous when the major interest is in the equilibrium state, but fail to describe the kinetics of ligand binding realistically. To simulate cellular processes that involve the reversible stochastic binding of multiple factors, our pseudo rate equation model should therefore be preferred to the Metropolis-Hastings algorithm and the Glauber heat bath, if the stationary distribution is not of only interest.

  15. Comparison of the kinetics of different Markov models for ligand binding under varying conditions.

    PubMed

    Martini, Johannes W R; Habeck, Michael

    2015-03-01

    We recently derived a Markov model for macromolecular ligand binding dynamics from few physical assumptions and showed that its stationary distribution is the grand canonical ensemble [J. W. R. Martini, M. Habeck, and M. Schlather, J. Math. Chem. 52, 665 (2014)]. The transition probabilities of the proposed Markov process define a particular Glauber dynamics and have some similarity to the Metropolis-Hastings algorithm. Here, we illustrate that this model is the stochastic analog of (pseudo) rate equations and the corresponding system of differential equations. Moreover, it can be viewed as a limiting case of general stochastic simulations of chemical kinetics. Thus, the model links stochastic and deterministic approaches as well as kinetics and equilibrium described by the grand canonical ensemble. We demonstrate that the family of transition matrices of our model, parameterized by temperature and ligand activity, generates ligand binding kinetics that respond to changes in these parameters in a qualitatively similar way as experimentally observed kinetics. In contrast, neither the Metropolis-Hastings algorithm nor the Glauber heat bath reflects changes in the external conditions correctly. Both converge rapidly to the stationary distribution, which is advantageous when the major interest is in the equilibrium state, but fail to describe the kinetics of ligand binding realistically. To simulate cellular processes that involve the reversible stochastic binding of multiple factors, our pseudo rate equation model should therefore be preferred to the Metropolis-Hastings algorithm and the Glauber heat bath, if the stationary distribution is not of only interest. PMID:25747058

  16. Comparison of the kinetics of different Markov models for ligand binding under varying conditions

    NASA Astrophysics Data System (ADS)

    Martini, Johannes W. R.; Habeck, Michael

    2015-03-01

    We recently derived a Markov model for macromolecular ligand binding dynamics from few physical assumptions and showed that its stationary distribution is the grand canonical ensemble [J. W. R. Martini, M. Habeck, and M. Schlather, J. Math. Chem. 52, 665 (2014)]. The transition probabilities of the proposed Markov process define a particular Glauber dynamics and have some similarity to the Metropolis-Hastings algorithm. Here, we illustrate that this model is the stochastic analog of (pseudo) rate equations and the corresponding system of differential equations. Moreover, it can be viewed as a limiting case of general stochastic simulations of chemical kinetics. Thus, the model links stochastic and deterministic approaches as well as kinetics and equilibrium described by the grand canonical ensemble. We demonstrate that the family of transition matrices of our model, parameterized by temperature and ligand activity, generates ligand binding kinetics that respond to changes in these parameters in a qualitatively similar way as experimentally observed kinetics. In contrast, neither the Metropolis-Hastings algorithm nor the Glauber heat bath reflects changes in the external conditions correctly. Both converge rapidly to the stationary distribution, which is advantageous when the major interest is in the equilibrium state, but fail to describe the kinetics of ligand binding realistically. To simulate cellular processes that involve the reversible stochastic binding of multiple factors, our pseudo rate equation model should therefore be preferred to the Metropolis-Hastings algorithm and the Glauber heat bath, if the stationary distribution is not of only interest.

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

    SciTech Connect

    Lanza-Jacoby, S.; Tabares, A. )

    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.

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

    PubMed

    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. PMID:27591598

  19. Kinetics of Fast Atoms in the Terrestrial Atmosphere

    NASA Technical Reports Server (NTRS)

    Kharchenko, Vasili A.; Dalgarno, A.; Mellott, Mary (Technical Monitor)

    2002-01-01

    This report summarizes our investigations performed under NASA Grant NAG5-8058. The three-year research supported by the Geospace Sciences SR&T program (Ionospheric, Thermospheric, and Mesospheric Physics) has been designed to investigate fluxes of energetic oxygen and nitrogen atoms in the terrestrial thermosphere. Fast atoms are produced due to absorption of the solar radiation and due to coupling between the ionosphere and the neutral thermospheric gas. We have investigated the impact of hot oxygen and nitrogen atoms on the thermal balance, chemistry and radiation properties of the terrestrial thermosphere. Our calculations have been focused on the accurate quantitative description of the thermalization of O and N energetic atoms in collisions with atom and molecules of the ambient neutral gas. Upward fluxes of oxygen and nitrogen atoms, the rate of atmospheric heating by hot oxygen atoms, and the energy input into translational and rotational-vibrational degrees of atmospheric molecules have been evaluated. Altitude profiles of hot oxygen and nitrogen atoms have been analyzed and compared with available observational data. Energetic oxygen atoms in the terrestrial atmosphere have been investigated for decades, but insufficient information on the kinetics of fast atmospheric atoms has been a main obstacle for the interpretation of observational data and modeling of the hot geocorona. The recent development of accurate computational methods of the collisional kinetics is seen as an important step in the quantitative description of hot atoms in the thermosphere. Modeling of relaxation processes in the terrestrial atmosphere has incorporated data of recent observations, and theoretical predictions have been tested by new laboratory measurements.

  20. Microdroplet fusion mass spectrometry for fast reaction kinetics

    PubMed Central

    Lee, Jae Kyoo; Kim, Samuel; Nam, Hong Gil; Zare, Richard N.

    2015-01-01

    We investigated the fusion of high-speed liquid droplets as a way to record the kinetics of liquid-phase chemical reactions on the order of microseconds. Two streams of micrometer-size droplets collide with one another. The droplets that fused (13 μm in diameter) at the intersection of the two streams entered the heated capillary inlet of a mass spectrometer. The mass spectrum was recorded as a function of the distance x between the mass spectrometer inlet and the droplet fusion center. Fused droplet trajectories were imaged with a high-speed camera, revealing that the droplet fusion occurred approximately within a 500-μm radius from the droplet fusion center and both the size and the speed of the fused droplets remained relatively constant as they traveled from the droplet fusion center to the mass spectrometer inlet. Evidence is presented that the reaction effectively stops upon entering the heated inlet of the mass spectrometer. Thus, the reaction time was proportional to x and could be measured and manipulated by controlling the distance x. Kinetic studies were carried out in fused water droplets for acid-induced unfolding of cytochrome c and hydrogen–deuterium exchange in bradykinin. The kinetics of the former revealed the slowing of the unfolding rates at the early stage of the reaction within 50 μs. The hydrogen–deuterium exchange revealed the existence of two distinct populations with fast and slow exchange rates. These studies demonstrated the power of this technique to detect reaction intermediates in fused liquid droplets with microsecond temporal resolution. PMID:25775573

  1. Measuring Fast and Slow Enzyme Kinetics in Stationary Droplets.

    PubMed

    Fradet, Etienne; Bayer, Christopher; Hollfelder, Florian; Baroud, Charles N

    2015-12-01

    We present a new microfluidic platform for the study of enzymtatic reactions using static droplets on demand. This allows us to monitor both fast and slow reactions with the same device and minute amounts of reagents. The droplets are produced and displaced using confinement gradients, which allows the experiments to be performed without having any mean flow of the external phase. Our device is used to produce six different pairs of drops, which are placed side by side in the same microfluidic chamber. A laser pulse is then used to trigger the fusion of each pair, thus initiating a chemcial reaction. Imaging is used to monitor the time evolution of enzymatic reactions. In the case of slow reactions, the reagents are completely mixed before any reaction is detected. This allows us to use standard Michaelis-Menten theory to analyze the time evolution. In the case of fast reactions, the time evolution takes place through a reaction-diffusion process, for which we develop a model that incorporates enzymatic reactions in the reaction terms. The theoretical predictions from this model are then compared to experiments in order to provide measurements of the chemical kinetics. The approach of producing droplets through confinement gradients and analyzing reactions within stationary drops provides an ultralow consumption platform. The physical principles are simple and robust, which suggests that the platform can be automated to reach large throughput analyses of enzymes. PMID:26524082

  2. Photoperturbation-relaxation approach to the kinetics of cooperative ligand binding by heme proteins

    SciTech Connect

    Schuresko, D.D.

    1983-05-01

    A small perturbation technique for measuring the ligand photodissociation and recombination kinetics of heme proteins has been developed. The Photodissociation Perturbation Relaxation (PPR) method involves perturbing the photodissociation rates of ligand-heme systems maintained at photointensity-dependent, nonequilibrium photostationary states. The theoretical and experimental datails of the PPR method are presented herein. A formalism for computing PPR amplitudes and time constants for complex reaction mechanisms for the eigenvectors and eigenvalues of the appropriate linear rate equations is derived; a FORTRAN code embodying this formalism is presented. PPR kinetics measurements obtained for the carbon monoxide derivatives of sperm whale myoglobin and human hemoglobin are presented. CO-hemoglobin combination rate constants and photodissociation quantum efficiencies, determined via fitting model-derived relaxation eigenmodes to PPR transients are presented.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    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. Enhanced kinetic stability of [Pd2L4](4+) cages through ligand substitution.

    PubMed

    Preston, Dan; McNeill, Samantha M; Lewis, James E M; Giles, Gregory I; Crowley, James D

    2016-05-10

    There is considerable interest in exploiting metallosupramolecular cages as drug delivery vectors. Recently, we developed a [Pd2L4](4+) cage capable of binding two molecules of cisplatin. Unfortunately, this first generation cage was rapidly decomposed by common biologically relevant nucleophiles. In an effort to improve the kinetic stability of these cage architectures here we report the synthesis of two amino substituted tripyridyl 2,6-bis(pyridin-3-ylethynyl)pyridine () ligands (with amino groups either in the 2-() or 3-() positions of the terminal pyridines) and their respective [Pd2()4](4+) cages. These systems have been characterised by (1)H, (13)C and DOSY NMR spectroscopies, high resolution electrospray mass spectrometry, elemental analysis and, in one case, by X-ray crystallography. It was established, using model palladium(ii) N-heterocyclic carbene (NHC) probe complexes, that the amino substituted compounds were stronger donor ligands than the parent system ( > > ). Competition experiments with a range of nucleophiles showed that these substitutions lead to more kinetically robust cage architectures, with [Pd2()4](4+) proving the most stable. Biological testing on the three ligands and cages against A549 and MDA-MB-231 cell lines showed that only [Pd2()4](4+) exhibited any appreciable cytotoxicity, with a modest IC50 of 36.4 ± 1.9 μM against the MDA-MB-231 cell line. Unfortunately, the increase in kinetic stability of the [Pd2()4](4+) cages was accompanied by loss of cisplatin-binding ability. PMID:27074828

  5. Fast O2 Binding at Dicopper Complexes Containing Schiff-Base Dinucleating Ligands

    PubMed Central

    Company, Anna; Gómez, Laura; Mas-Ballesté, Rubén; Korendovych, Ivan V.; Ribas, Xavi; Poater, Albert; Parella, Teodor; Fontrodona, Xavier; Benet-Buchholz, Jordi; Solà, Miquel; Que, Lawrence; Rybak-Akimova, Elena; Costas, Miquel

    2008-01-01

    A new family of dicopper(I) complexes [CuI2RL](X)2, (R = H, 1X, R = tBu, 2X and R = NO2, 3X, X = CF3SO3, ClO4, SbF6 or BArF, BArF = [B{3,5-(CF3)2-C6H3}4]−), where RL is a Schiff-base ligand containing two tridentate binding sites linked by a xylyl spacer have been prepared, characterized, and their reaction with O2 studied. The complexes were designed with the aim of reproducing structural aspects of the active site of type 3 dicopper proteins; they contain two three-coordinate copper sites and a rather flexible podand ligand backbone. The solid state structures of 1ClO4, 2CF3SO3, 2ClO4 and 3BArF·CH3CN have been established by single crystal X-ray diffraction analysis. 1ClO4 adopts a polymeric structure in solution while 2CF3SO3, 2ClO4 and 3BArF·CH3CN are monomeric. The complexes have been studied in solution by means of 1H and 19F NMR spectroscopy, which put forward the presence of dynamic processes in solution. 1-3BArF and 1-3CF3SO3 in acetone react rapidly with O2 to generate metaestable [CuIII2(μ-O)2(RL)]2+ 1-3(O2) and [CuIII2(μ-O)2(CF3SO3)(RL)]+ 1-3(O2)(CF3SO3) species, respectively that have been characterized by UV-vis spectroscopy and resonance Raman analysis. Instead, reaction of 1-3BArF with O2 in CH2Cl2 results in intermolecular O2 binding. DFT methods have been used to study the chemical identities and structural parameters of the O2 adducts, and the relative stability of the CuIII2(μ-O)2 form with respect to the CuII2(μ-η2: η2-peroxo) isomer. The reaction of 1X, X = CF3SO3 and BArF with O2 in acetone has been studied by stopped-flow exhibiting an unexpected very fast reaction rate (k = 3.82(4) × 103 M−1s−1, ΔH‡ = 4.9 ± 0.5 kJ·mol−1, ΔS‡ = −148 ± 5 J·K−1·mol−1), nearly three orders of magnitude faster than in the parent [CuI2(m-XYLMeAN)]2+. Thermal decomposition of 1-3(O2) does not result in aromatic hydroxylation. The mechanism and kinetics of O2 binding to 1X (X = CF3SO3 and BArF) is discussed and compared with those

  6. Recyclable Ligands for the Non-Enzymatic Dynamic Kinetic Resolution of Challenging α-Amino Acids.

    PubMed

    Nian, Yong; Wang, Jiang; Zhou, Shengbin; Wang, Shuni; Moriwaki, Hiroki; Kawashima, Aki; Soloshonok, Vadim A; Liu, Hong

    2015-10-26

    Structurally simple and inexpensive chiral tridentate ligands were employed for substantially advancing the purely chemical dynamic kinetic resolution (DKR) of unprotected racemic tailor-made α-amino acids (TM-α-AAs), enabling the first DKR of TM-α-AAs bearing tertiary alkyl chains as well as multiple unprotected functional groups. Owing to the operationally convenient conditions, virtually complete stereoselectivity, and full recyclability of the source of chirality, this method should find wide applications for the preparation of TM-α-AAs, especially on large scale. PMID:26367134

  7. Resolving the Fast Kinetics of Cooperative Binding: Ca2+ Buffering by Calretinin

    PubMed Central

    Faas, Guido C; Schwaller, Beat; Vergara, Julio L; Mody, Istvan

    2007-01-01

    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+ using a fast

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

    PubMed

    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. PMID:18660437

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

    PubMed

    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. PMID:27391254

  10. Scaling of Kinetic Instability Induced Fast Ion Losses in NSTX

    SciTech Connect

    E.D. Fredrickson; D. Darrow; S. Medley; J. Menard; H. Park; L. Roquemore; D. Stutman; K. Tritz; S. Kubota; K.C. Lee

    2005-06-24

    During neutral beam injection (NBI) in the National Spherical Torus Experiment (NSTX), a wide variety of fast ion driven instabilities is excited by the large ratio of fast ion velocity to Alfven velocity, together with the relatively high fast ion beta, beta(sub)f. The fast ion instabilities have frequencies ranging from a few kilohertz to the ion cyclotron frequency. The modes can be divided roughly into three categories, starting with Energetic Particle Modes (EPM) in the lowest frequency range (0 to 120 kHz), the Toroidal Alfven Eigenmodes (TAE) in the intermediate frequency range (50 to 200 kHz) and the Compressional and Global Alfven Eigenmodes (CAE and GAE, respectively) from approximately equal to 300 kHz up to the ion cyclotron frequency. Each of these categories of modes exhibits a wide range of behavior, including quasi-continuous oscillation, bursting, chirping and, except for the lower frequency range, turbulence.

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

    PubMed

    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

  12. Determination of Multivalent Protein–Ligand Binding Kinetics by Second-Harmonic Correlation Spectroscopy

    PubMed Central

    2015-01-01

    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) × 106 M–1·s–1 at 0.43 μM PnA to (1.1 ± 0.1) × 105 M–1·s–1 at 12 μM PnA. CTB–GM1 exhibited a similar trend, decreasing from (1.0 ± 0.1) × 109 M–1·s–1 at 0.5 nM CTB to (3.5 ± 0.2) × 106 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) × 109 M–1 and (2.8 ± 0.5) × 1013 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. PMID:25314127

  13. Role of water and steric constraints in the kinetics of cavity–ligand unbinding

    PubMed Central

    Tiwary, Pratyush; Mondal, Jagannath; Morrone, Joseph A.; Berne, B. J.

    2015-01-01

    A key factor influencing a drug’s efficacy is its residence time in the binding pocket of the host protein. Using atomistic computer simulation to predict this residence time and the associated dissociation process is a desirable but extremely difficult task due to the long timescales involved. This gets further complicated by the presence of biophysical factors such as steric and solvation effects. In this work, we perform molecular dynamics (MD) simulations of the unbinding of a popular prototypical hydrophobic cavity–ligand system using a metadynamics-based approach that allows direct assessment of kinetic pathways and parameters. When constrained to move in an axial manner, the unbinding time is found to be on the order of 4,000 s. In accordance with previous studies, we find that the cavity must pass through a region of sharp wetting transition manifested by sudden and high fluctuations in solvent density. When we remove the steric constraints on ligand, the unbinding happens predominantly by an alternate pathway, where the unbinding becomes 20 times faster, and the sharp wetting transition instead becomes continuous. We validate the unbinding timescales from metadynamics through a Poisson analysis, and by comparison through detailed balance to binding timescale estimates from unbiased MD. This work demonstrates that enhanced sampling can be used to perform explicit solvent MD studies at timescales previously unattainable, to our knowledge, obtaining direct and reliable pictures of the underlying physiochemical factors including free energies and rate constants. PMID:26371312

  14. Bio-layer interferometry for measuring kinetics of protein-protein interactions and allosteric ligand effects.

    PubMed

    Shah, Naman B; Duncan, Thomas M

    2014-01-01

    We describe the use of Bio-layer Interferometry to study inhibitory interactions of subunit ε with the catalytic complex of Escherichia coli ATP synthase. Bacterial F-type ATP synthase is the target of a new, FDA-approved antibiotic to combat drug-resistant tuberculosis. Understanding bacteria-specific auto-inhibition of ATP synthase by the C-terminal domain of subunit ε could provide a new means to target the enzyme for discovery of antibacterial drugs. The C-terminal domain of ε undergoes a dramatic conformational change when the enzyme transitions between the active and inactive states, and catalytic-site ligands can influence which of ε's conformations is predominant. The assay measures kinetics of ε's binding/dissociation with the catalytic complex, and indirectly measures the shift of enzyme-bound ε to and from the apparently nondissociable inhibitory conformation. The Bio-layer Interferometry signal is not overly sensitive to solution composition, so it can also be used to monitor allosteric effects of catalytic-site ligands on ε's conformational changes. PMID:24638157

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

    PubMed

    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. PMID:26460790

  16. Fast algorithms for combustion kinetics calculations: A comparison

    NASA Technical Reports Server (NTRS)

    Radhakrishnan, K.

    1984-01-01

    To identify the fastest algorithm currently available for the numerical integration of chemical kinetic rate equations, several algorithms were examined. Findings to date are summarized. The algorithms examined include two general-purpose codes EPISODE and LSODE and three special-purpose (for chemical kinetic calculations) codes CHEMEQ, CRK1D, and GCKP84. In addition, an explicit Runge-Kutta-Merson differential equation solver (IMSL Routine DASCRU) is used to illustrate the problems associated with integrating chemical kinetic rate equations by a classical method. Algorithms were applied to two test problems drawn from combustion kinetics. These problems included all three combustion regimes: induction, heat release and equilibration. Variations of the temperature and species mole fraction are given with time for test problems 1 and 2, respectively. Both test problems were integrated over a time interval of 1 ms in order to obtain near-equilibration of all species and temperature. Of the codes examined in this study, only CREK1D and GCDP84 were written explicitly for integrating exothermic, non-isothermal combustion rate equations. These therefore have built-in procedures for calculating the temperature.

  17. The kinetic isotopic effect, bridge ligand, and mechanisms of oxidation of alkanes in solutions

    SciTech Connect

    Rudakov, E.S

    1982-10-01

    The purpose of this article was to call attention to a new and striking fact: the kinetic isotopic effect of hydrogen (KIE) in oxidative homolysis, in a first approximation, is independent of the central atom-oxidizing agent M/sup n/ and is determined exclusively by the bridge ligand, which is a quantitative criterion for the selection of the bridge. Most of the data were obtained recently in a study of the first step of the oxidation of alkanes in sulfuric acid and aqueous media by reagents which, as has been suggested, include sulfate (OSO/sub 2/O-) or oxo (O=) bridges. The structures of the reagents were selected considering data on the kinetics, selectivity, and KIE. For the reactions of RH with CF/sub 3/-COOH, HOCl(Cl/sub 2/ + H/sub 2/O), H/sub 2/SO/sub 5/ (H/sub 2/O/sub 2/-90% H/sub 2/SO/sub 4/) and HNO/sub 3/-Pt/sup IV/-Cl/sup -/-H/sub 2/O, structures with OH bridges were assumed. The values of the KIE are the same for tert- and sec-C-H bonds; the reproducibility is usually within +/- 15%.

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

    PubMed Central

    2009-01-01

    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. PMID:20298519

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

    PubMed

    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. PMID:25314127

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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. PMID:25974546

  2. Anticooperative ligand binding properties of recombinant ferric Vitreoscilla homodimeric hemoglobin: a thermodynamic, kinetic and X-ray crystallographic study.

    PubMed

    Bolognesi, M; Boffi, A; Coletta, M; Mozzarelli, A; Pesce, A; Tarricone, C; Ascenzi, P

    1999-08-20

    Thermodynamics and kinetics for cyanide, azide, thiocyanate and imidazole binding to recombinant ferric Vitreoscilla sp. homodimeric hemoglobin (Vitreoscilla Hb) have been determined at pH 6.4 and 7.0, and 20.0 degrees C, in solution and in the crystalline state. Moreover, the three-dimensional structures of the diligated thiocyanate and imidazole derivatives of recombinant ferric Vitreoscilla Hb have been determined by X-ray crystallography at 1.8 A (Rfactor=19.9%) and 2.1 A (Rfactor=23.8%) resolution, respectively. Ferric Vitreoscilla Hb displays an anticooperative ligand binding behaviour in solution. This very unusual feature can only be accounted for by assuming ligand-linked conformational changes in the monoligated species, which lead to the observed 300-fold decrease in the affinity of cyanide, azide, thiocyanate and imidazole for the monoligated ferric Vitreoscilla Hb with respect to that of the fully unligated homodimer. In the crystalline state, thermodynamics for azide and imidazole binding to ferric Vitreoscilla Hb may be described as a simple process with an overall ligand affinity for the homodimer corresponding to that for diligation in solution. These data suggest that the ligand-free homodimer, observed in the crystalline state, is constrained in a low affinity conformation whose ligand binding properties closely resemble those of the monoligated species in solution. From the kinetic viewpoint, anticooperativity is reflected by the 300-fold decrease of the second-order rate constant for cyanide and imidazole binding to the monoligated ferric Vitreoscilla Hb with respect to that for ligand association to the ligand-free homodimer in solution. On the other hand, values of the first-order rate constant for cyanide and imidazole dissociation from the diligated and monoligated derivatives of ferric Vitreoscilla Hb in solution are closely similar. As a whole, ligand binding and structural properties of ferric Vitreoscilla Hb appear to be unique among

  3. Binding kinetics and multi-bond: Finding correlations by synthesizing interactions between ligand-coated bionanoparticles and receptor surfaces.

    PubMed

    Wang, Wenjing; Voigt, Andreas; Wolff, Michael W; Reichl, Udo; Sundmacher, Kai

    2016-07-15

    The number of bonds formed between one single bionanoparticle and many surface receptors is an important subject to be studied but is seldom quantitatively investigated. A new evaluation of the correlation between binding kinetics and number of bonds is presented by varying ligand density and receptor density. An experimental system was developed using measurements with surface plasmon resonance spectroscopy. A corresponding multi-site adsorption model elucidated the correlation. The results show that with the increase of the receptor density, the adsorption rate first decreased when the number of bonds was below a maximum value and then increased when the number of bonds stayed at this maximum value. The investigation on ligand density variation suggests that the coating density on top of the bionanoparticle surface may have a particular value below which more ligand will accelerate the adsorption rate. The ratio of ligand amount bound by the receptors to the total ligand amount associated with a single bionanoparticle will remain constant even if one attaches more ligands to a bionanoparticle. We envision that the bionanoparticle desorption will not depend on density changes from either ligand or receptor when the number of bonds reaches a specific efficient value. PMID:27108189

  4. 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.

    PubMed

    Sun, Bingbing; Mu, Xiaoyu; Qi, Li

    2014-04-22

    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(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. PMID:24703219

  5. Kinetic limitations in measuring stabilities of metal complexes by competitive ligand exchange-adsorptive stripping voltammetry (CLE-AdSV).

    PubMed

    Van Leeuwen, Herman P; Town, Raewyn M

    2005-09-15

    The kinetic limitations of Competitive Ligand Exchange-Adsorptive Stripping Voltammetry, CLE-AdSV, for the determination of very stable metal complexes are explained in detail. For a given type of metal, from a certain lower limit of the complex stability constant, K, the usual simple equilibrium interpretation of CLE-AdSV measurements is not generally valid. By critical assessment of data for natural waters we show that in many cases the reported stability constants appearto derive from nonequilibrium conditions in the bulk sample and hence overestimate the real values. Fe(II) is a special case due to the particular kinetic features of hydroxide as a ligand. Our results call for validation of such data by analysis on the basis of the kinetics involved and/or by independent kinetic-free experimental approaches. Earlier speculations from CLE-AdSV results on very strong ligands and derived features such as the potential bioavailability of trace metals in natural waters require reconsideration. PMID:16201651

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

    PubMed Central

    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-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. PMID:26236747

  7. Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations

    PubMed Central

    Mollica, Luca; Decherchi, Sergio; Zia, Syeda Rehana; Gaspari, Roberto; Cavalli, Andrea; Rocchia, Walter

    2015-01-01

    Drug discovery is expensive and high-risk. Its main reasons of failure are lack of efficacy and toxicity of a drug candidate. Binding affinity for the biological target has been usually considered one of the most relevant figures of merit to judge a drug candidate along with bioavailability, selectivity and metabolic properties, which could depend on off-target interactions. Nevertheless, affinity does not always satisfactorily correlate with in vivo drug efficacy. It is indeed becoming increasingly evident that the time a drug spends in contact with its target (aka residence time) can be a more reliable figure of merit. Experimental kinetic measurements are operatively limited by the cost and the time needed to synthesize compounds to be tested, to express and purify the target, and to setup the assays. We present here a simple and efficient molecular-dynamics-based computational approach to prioritize compounds according to their residence time. We devised a multiple-replica scaled molecular dynamics protocol with suitably defined harmonic restraints to accelerate the unbinding events while preserving the native fold. Ligands are ranked according to the mean observed scaled unbinding time. The approach, trivially parallel and easily implementable, was validated against experimental information available on biological systems of pharmacological relevance. PMID:26103621

  8. New insights into the kinetic target-guided synthesis of protein ligands.

    PubMed

    Oueis, Emilia; Sabot, Cyrille; Renard, Pierre-Yves

    2015-08-01

    The kinetic target-guided synthesis (KTGS) strategy is an unconventional discovery approach that takes advantage of the presence of the biological target itself in order to irreversibly assemble the best inhibitors from an array of building blocks. This strategy has grown over the last two decades notably after the introduction of the in situ click chemistry concept by Sharpless and colleagues in the early 2000s based on the use of the Huisgen cycloaddition between terminal alkynes and azides. KTGS is a captivating area of research offering an unprecedented and powerful strategy to probe the macromolecular complexity and dynamics of biological targets. After a brief introduction listing all chemical ligation reactions reported to date in KTGS, this review focuses on the last five years' progress to expand the repertoire of the click or "click-like" tool box targeting proteins, as well as to overcome limitations arising in particular from false negatives, i.e. potent ligands that are not formed, or formed in undetectable trace amounts. Furthermore, we wish to analyze the new twists and novelties described in some of these applications in order to better understand the conditions that govern this strategy and the extent to which it can be developed and generalized for a more efficient process. PMID:26144842

  9. Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Mollica, Luca; Decherchi, Sergio; Zia, Syeda Rehana; Gaspari, Roberto; Cavalli, Andrea; Rocchia, Walter

    2015-06-01

    Drug discovery is expensive and high-risk. Its main reasons of failure are lack of efficacy and toxicity of a drug candidate. Binding affinity for the biological target has been usually considered one of the most relevant figures of merit to judge a drug candidate along with bioavailability, selectivity and metabolic properties, which could depend on off-target interactions. Nevertheless, affinity does not always satisfactorily correlate with in vivo drug efficacy. It is indeed becoming increasingly evident that the time a drug spends in contact with its target (aka residence time) can be a more reliable figure of merit. Experimental kinetic measurements are operatively limited by the cost and the time needed to synthesize compounds to be tested, to express and purify the target, and to setup the assays. We present here a simple and efficient molecular-dynamics-based computational approach to prioritize compounds according to their residence time. We devised a multiple-replica scaled molecular dynamics protocol with suitably defined harmonic restraints to accelerate the unbinding events while preserving the native fold. Ligands are ranked according to the mean observed scaled unbinding time. The approach, trivially parallel and easily implementable, was validated against experimental information available on biological systems of pharmacological relevance.

  10. Fast and slow activation kinetics of voltage-gated sodium channels in molluscan neurons.

    PubMed

    Gilly, W F; Gillette, R; McFarlane, M

    1997-05-01

    Whole cell patch-clamp recordings of Na current (I(Na)) were made under identical experimental conditions from isolated neurons from cephalopod (Loligo, Octopus) and gastropod (Aplysia, Pleurobranchaea, Doriopsilla) species to compare properties of activation gating. Voltage dependence of peak Na conductance (gNa) is very similar in all cases, but activation kinetics in the gastropod neurons studied are markedly slower. Kinetic differences are very pronounced only over the voltage range spanned by the gNa-voltage relation. At positive and negative extremes of voltage, activation and deactivation kinetics of I(Na) are practically indistinguishable in all species studied. Voltage-dependent rate constants underlying activation of the slow type of Na channel found in gastropods thus appear to be much more voltage dependent than are the equivalent rates in the universally fast type of channel that predominates in cephalopods. Voltage dependence of inactivation kinetics shows a similar pattern and is representative of activation kinetics for the two types of Na channels. Neurons with fast Na channels can thus make much more rapid adjustments in the number of open Na channels at physiologically relevant voltages than would be possible with only slow Na channels. This capability appears to be an adaptation that is highly evolved in cephalopods, which are well known for their high-speed swimming behaviors. Similarities in slow and fast Na channel subtypes in molluscan and mammalian neurons are discussed. PMID:9163364

  11. An instrument to measure fast gas phase radical kinetics at high temperatures and pressures.

    PubMed

    Stone, Daniel; Blitz, Mark; Ingham, Trevor; Onel, Lavinia; Medeiros, Diogo J; Seakins, Paul W

    2016-05-01

    Fast radical reactions are central to the chemistry of planetary atmospheres and combustion systems. Laser-induced fluorescence is a highly sensitive and selective technique that can be used to monitor a number of radical species in kinetics experiments, but is typically limited to low pressure systems owing to quenching of fluorescent states at higher pressures. The design and characterisation of an instrument are reported using laser-induced fluorescence detection to monitor fast radical kinetics (up to 25 000 s(-1)) at high temperatures and pressures by sampling from a high pressure reaction region to a low pressure detection region. Kinetics have been characterised at temperatures reaching 740 K and pressures up to 2 atm, with expected maximum operational conditions of up to ∼900 K and ∼5 atm. The distance between the point of sampling from the high pressure region and the point of probing within the low pressure region is critical to the measurement of fast kinetics. The instrumentation described in this work can be applied to the measurement of kinetics relevant to atmospheric and combustion chemistry. PMID:27250442

  12. Affinity interactions of human immunoglobulin G with short peptides: role of ligand spacer on binding, kinetics, and mass transfer.

    PubMed

    Shen, Fei; Rojas, Orlando J; Genzer, Jan; Gurgel, Patrick V; Carbonell, Ruben G

    2016-03-01

    The interaction affinity between human IgG and a short peptide ligand (hexameric HWRGWV) was investigated by following the shifts in frequency and energy dissipation in a quartz crystal microbalance (QCM). HWRGWV was immobilized by means of poly(ethylene glycol) tethered on QCM sensors coated with silicon oxide, which enhanced the accessibility of the peptide to hIgG and also passivated the surface. Ellipsometry and ToF-SIMS were employed for surface characterization. The peptide ligand density was optimized to 0.88 chains nm(-2), which enabled the interaction of each hIgG molecule with at least one ligand. The maximum binding capacity was found to be 4.6 mg m(-2), corresponding to a monolayer of hIgG, similar to the values for chromatographic resins. Dissociation constants were lower than those obtained from resins, possibly due to overestimation of bound mass by QCM. Equilibrium thermodynamic and kinetic parameters were determined, shedding light on interfacial effects important for detection and bioseparation. Graphical Abstract The interaction affinity between human IgG and a short peptide ligand was investigated by using quartz crystal microgravimetry, ellipsometry and ToF-SIMS. Equilibrium thermodynamic and kinetics parameters were determined, shedding light on interfacial effects important for detection and bioseparation. PMID:26549116

  13. Simultaneous determination of kinetic and thermodynamic parameters from fast-reaction kinetic measurements.

    PubMed

    Trimm, H H; Ushio, H; Patel, R C

    1981-10-01

    A combined stopped-flow temperature-jump apparatus interfaced with a dedicated microcomputer has been used to study the complexation reaction of iron(III) with thiocyanate in aqueous solution. Kinetic rate-constants (k(f) = 143 l.mole(-1) .sec(-1) from T-jump, k(f) = 150 l.mole(-1) .sec(-1) from stopped flow), equilibrium constants (K = 143 from T-jump, K = 150 from stopped flow) and the thermodynamic enthalpy change (DeltaH(c) = -6.7 kJ/mole) could be independently determined from the simultaneous application of the two techniques. PMID:18962997

  14. Ultra-fast dynamic compression technique to study kinetics of phase transformations in Bismuth

    SciTech Connect

    Smith, R F; Kane, J O; Eggert, J H; Saculla, M D; Jankowski, A F; Bastea, M; Hicks, D G; Collins, G W

    2007-12-28

    Pre-heated Bi was ramp compressed within 30 ns to a peak stress of {approx}11 GPa to explore structural phase transformation kinetics under dynamic loading conditions. Under these ultra-fast compression time-scales the equilibrium Bi I-II phase boundary is overpressurized by {Delta}P {approx} 0.8 GPa. {Delta}P is observed to increase logarithmically with strain rate, {var_epsilon}, above 10{sup 6} s{sup -1}. Estimates from a kinetics model predict that the Bi I phase is fully transformed within 3 ns.

  15. Kinetics and computational studies of ligand migration in nitrophorin 7 and its Δ1-3 mutant.

    PubMed

    Oliveira, Ana; Allegri, Alessandro; Bidon-Chanal, Axel; Knipp, Markus; Roitberg, Adrian E; Abbruzzetti, Stefania; Viappiani, Cristiano; Luque, F Javier

    2013-09-01

    Nitrophorins (NPs) are nitric oxide (NO)-carrying heme proteins found in the saliva of the blood-sucking insect Rhodnius prolixus. Though NP7 exhibits a large sequence resemblance with other NPs, two major differential features are the ability to interact with negatively charged cell surfaces and the presence of a specific N-terminus composed of three extra residues (Leu1-Pro2-Gly3). The aim of this study is to examine the influence of the N-terminus on the ligand binding, and the topological features of inner cavities in closed and open states of NP7, which can be associated to the protein structure at low and high pH, respectively. Laser flash photolysis measurements of the CO rebinding kinetics to NP7 and its variant NP7(Δ1-3), which lacks the three extra residues at the N-terminus, exhibit a similar pattern and support the existence of a common kinetic mechanism for ligand migration and binding. This is supported by the existence of a common topology of inner cavities, which consists of two docking sites in the heme pocket and a secondary site at the back of the protein. The ligand exchange between these cavities is facilitated by an additional site, which can be transiently occupied by the ligand in NP7, although it is absent in NP4. These features provide a basis to explain the enhanced internal gas hosting capacity found experimentally in NP7 and the absence of ligand rebinding from secondary sites in NP4. The current data allow us to speculate that the processes of docking to cell surfaces and NO release may be interconnected in NP7, thereby efficiently releasing NO into a target cell. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins. PMID:23624263

  16. Effect of carboxylic and thiol ligands (oxalate, cysteine) on the kinetics of desorption of Hg(II) from kaolinite

    SciTech Connect

    Senevirathna, W. U.; Zhang, Hong; Gu, Baohua

    2010-01-01

    Sorption and desorption of Hg(II) on clay minerals can impact the biogeochemical cycle and bio-uptake of Hg in the environment. We studied the kinetics of the desorption of Hg(II) from kaolinite as affected by oxalate and cysteine, representing the ligands with carboxylic and thiol groups of different affinities for Hg(II). The effects of pH (3, 5, and 7), ligand concentration (0.25 and 1.0 mM), and temperature (15 C, 25 C, and 35 C) on the Hg(II) desorption were investigated through desorption kinetics. Our study showed that the Hg(II) desorption was pH dependent. In the absence of any organic ligand, >90% of the previously adsorbed Hg(II) desorbed at pH 3 within 2 h, compared to <10% at pH 7. Similar results were observed in the presence of oxalate, showing that it hardly affected the Hg(II) desorption. Cysteine inhibited the Hg(II) desorption significantly at all the pH tested, especially in the first 80 min with the desorption less than 20%, but the inhibition of the desorption appeared to be less prominent afterwards. The effect of the ligand concentration on the Hg(II) desorption was small, especially in the presence of oxalate. The effect of temperature on the Hg(II) desorption was nearly insignificant. The effect of the organic acids on the Hg(II) sorption and desorption is explained by the formation of the ternary surface complexes involving the mineral, ligand, and Hg(II). The competition for Hg(II) between the cysteine molecules adsorbed on the particle surfaces and in the solution phase probably can also affect the Hg(II) desorption.

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

    PubMed

    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. PMID:26927234

  18. Global solution for a kinetic chemotaxis model with internal dynamics and its fast adaptation limit

    NASA Astrophysics Data System (ADS)

    Liao, Jie

    2015-12-01

    A nonlinear kinetic chemotaxis model with internal dynamics incorporating signal transduction and adaptation is considered. This paper is concerned with: (i) the global solution for this model, and, (ii) its fast adaptation limit to Othmer-Dunbar-Alt type model. This limit gives some insight to the molecular origin of the chemotaxis behaviour. First, by using the Schauder fixed point theorem, the global existence of weak solution is proved based on detailed a priori estimates, under quite general assumptions. However, the Schauder theorem does not provide uniqueness, so additional analysis is required to be developed for uniqueness. Next, the fast adaptation limit of this model is derived by extracting a weak convergence subsequence in measure space. For this limit, the first difficulty is to show the concentration effect on the internal state. Another difficulty is the strong compactness argument on the chemical potential, which is essential for passing the nonlinear kinetic equation to the weak limit.

  19. Reversible dioxygen binding and arene hydroxylation reactions: Kinetic and thermodynamic studies involving ligand electronic and structural variations

    PubMed Central

    Karlin, Kenneth D.; Zhang, Christiana Xin; Rheingold, Arnold L.; Galliker, Benedikt; Kaderli, Susan; Zuberbühler, Andreas D.

    2012-01-01

    Copper-dioxygen interactions are of intrinsic importance in a wide range of biological and industrial processes. Here, we present detailed kinetic/thermodynamic studies on the O2-binding and arene hydroxylation reactions of a series of xylyl-bridged binuclear copper(I) complexes, where the effects of ligand electronic and structural elements on these reactions are investigated. Ligand 4-pyridyl substituents influence the reversible formation of side-on bound μ-η2:η2-peroxodicopper(II) complexes, with stronger donors leading to more rapid formation and greater thermodynamic stability of product complexes [CuII2(RXYL)(O22−)]2+. An interaction of the latter with the xylyl π-system is indicated. Subsequent peroxo electrophilic attack on the arene leads to C–H activation and oxygenation with hydroxylated products [CuII2(RXYLO2−)(−OH)]2+ being formed. A related unsymmetrical binucleating ligand was also employed. Its corresponding O2-adduct [CuII2(UN)(O22−)]2+ is more stable, but primarily because the subsequent decay by hydroxylation is in a relative sense slower. The study emphasizes how ligand electronic effects can and do influence and tune copper(I)–dioxygen complex formation and subsequent reactivity. PMID:23420124

  20. Kinetic and Thermodynamic Characterization of Dihydrotestosterone-Induced Conformational Perturbations in Androgen Receptor Ligand-Binding Domain

    PubMed Central

    Jasuja, Ravi; Ulloor, Jagadish; Yengo, Christopher M.; Choong, Karen; Istomin, Andrei Y.; Livesay, Dennis R.; Jacobs, Donald J.; Swerdloff, Ronald S.; Mikšovská, Jaroslava; Larsen, Randy W.; Bhasin, Shalender

    2009-01-01

    Ligand-induced conformational perturbations in androgen receptor (AR) are important in coactivator recruitment and transactivation. However, molecular rearrangements in AR ligand-binding domain (AR-LBD) associated with agonist binding and their kinetic and thermodynamic parameters are poorly understood. We used steady-state second-derivative absorption and emission spectroscopy, pressure and temperature perturbations, and 4,4′-bis-anilinonaphthalene 8-sulfonate (bis-ANS) partitioning to determine the kinetics and thermodynamics of the conformational changes in AR-LBD after dihydrotestosterone (DHT) binding. In presence of DHT, the second-derivative absorption spectrum showed a red shift and a change in peak-to-peak distance. Emission intensity increased upon DHT binding, and center of spectral mass was blue shifted, denoting conformational changes resulting in more hydrophobic environment for tyrosines and tryptophans within a more compact DHT-bound receptor. In pressure perturbation calorimetry, DHT-induced energetic stabilization increased the Gibbs free energy of unfolding to 8.4 ± 1.3 kcal/mol from 3.5 ± 1.6 kcal/mol. Bis-ANS partitioning studies revealed that upon DHT binding, AR-LBD underwent biphasic rearrangement with a high activation energy (13.4 kcal/mol). An initial, molten globule-like burst phase (k ∼30 sec−1) with greater solvent accessibility was followed by rearrangement (k ∼0.01 sec−1), leading to a more compact conformation than apo-AR-LBD. Molecular simulations demonstrated unique sensitivity of tyrosine and tryptophan residues during pressure unfolding with rearrangement of residues in the coactivator recruitment surfaces distant from the ligand-binding pocket. In conclusion, DHT binding leads to energetic stabilization of AR-LBD domain and substantial rearrangement of residues distant from the ligand-binding pocket. DHT binding to AR-LBD involves biphasic receptor rearrangement including population of a molten globule

  1. Kinetic evidence for the existence of a rate-limiting step in the reaction of ferric hemoproteins with anionic ligands.

    PubMed

    Coletta, M; Angeletti, M; De Sanctis, G; Cerroni, L; Giardina, B; Amiconi, G; Ascenzi, P

    1996-01-15

    The kinetics of azide and fluroide binding to various monomeric and tetrameric ferric hemoproteins (sperm whale Mb, isolated alpha and beta chains of human Hb reacted with p-chloromercuribenzoate, dromeday, ox and human Hb) has been investigated (at pH 6.5 and 20 degrees C over a large range (20 microM to 2 M) of ligand concentration. It has been observed that the pseuo-first-order rate constant for azide binding to the hemoproteins investigated does not increase linearly with ligand concentration, but tends to level off toward an asymptomatic concentration-independent value typical for each hemoprotein. This behavior, which has been detected only by an investigation covering an unusually large range of ligand concentrations appears to be independent of the ionic strength, and it underlies the existence of a rate-limiting step in the dynamic pathway of azide binding to ferric hemoproteins, which is detectable whenever the observed pseudo- first-order rate constant becomes faster than a given value characteristic of the specific hemoprotein. Such a behavior is not observed in the case of fluroide binding probably because the pesudo- first-order rate constant for this ligand is much slower and never attains a value faster than that of the rate-limiting step. In general terms, this feature should involve a conformational equilibrium between at least two forms (possibly related to the interaction of H2O with distal histidine and its exchange with the bulk solvent) which modulates the access of the anionic ligand into the heme pocket and its reaction with the ferric iron. PMID:8631366

  2. A Fast-Start Pacing Strategy Speeds Pulmonary Oxygen Uptake Kinetics and Improves Supramaximal Running Performance

    PubMed Central

    Turnes, Tiago; Salvador, Amadeo Félix; Lisbôa, Felipe Domingos; de Aguiar, Rafael Alves; Cruz, Rogério Santos de Oliveira; Caputo, Fabrizio

    2014-01-01

    The focus of the present study was to investigate the effects of a fast-start pacing strategy on running performance and pulmonary oxygen uptake () 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 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 response time is faster when a fast-start is adopted. PMID:25360744

  3. Gd3TCAS2: An Aquated Gd(3+)-Thiacalix[4]arene Sandwich Cluster with Extremely Slow Ligand Substitution Kinetics.

    PubMed

    Iki, Nobuhiko; Boros, Eszter; Nakamura, Mami; Baba, Ryo; Caravan, Peter

    2016-04-18

    In aqueous solution, Gd(3+) and thiacalix[4]arene-p-tetrasulfonate (TCAS) form the complex [Gd3TCAS2](7-), in which a trinuclear Gd(3+) core is sandwiched by two TCAS ligands. Acid-catalyzed dissociation reactions, as well as transmetalation and ligand exchange with physiological concentrations of Zn(2+) and phosphate, showed [Gd3TCAS2](7-) to be extremely inert compared to other Gd complexes. Luminescence lifetime measurements of the Tb analogue Tb3TCAS2 allowed estimation of the mean hydration number q to be 2.4 per Tb ion. The longitudinal relaxivity of [Gd3TCAS2](7-) (per Gd(3+)) was r1 = 5.83 mM(-1) s(-1) at 20 Hz (37 °C, pH 7.4); however, this relaxivity was limited by an extremely slow water exchange rate that was 5 orders of magnitude slower than the Gd(3+) aqua ion. Binding to serum albumin resulted in no relaxivity increase owing to the extremely slow water exchange kinetics. The slow dissociation and water exchange kinetics of [Gd3TCAS2](7-) can be attributed to the very rigid coordination geometry. PMID:27018719

  4. Electrical Detection of Fast Reaction Kinetics in Nanochannels with an Induced Flow

    PubMed Central

    Schoch, Reto B.; Cheow, Lih Feng; Han, Jongyoon

    2008-01-01

    Nanofluidic channels can be used to enhance surface binding reactions, since the target molecules are closely confined to the surfaces that are coated with specific binding partners. Moreover, diffusion-limited binding can be significantly enhanced if the molecules are steered into the nanochannels via either pressure-driven or electrokinetic flow. By monitoring the nanochannel impedance, which is sensitive to surface binding, low analyte concentrations have been detected electrically in nanofluidic channels within response times of 1–2 hours. This represents a ~54 fold reduction in the response time using convective flow compared to diffusion-limited binding. At high flow velocities the presented method of reaction kinetics enhancement is potentially limited by force-induced dissociations of the receptor-ligand bonds. Optimization of this scheme could be useful for label-free, electrical detection of biomolecule binding reactions within nanochannels on a chip. PMID:17997589

  5. KINETIC PLASMA TURBULENCE IN THE FAST SOLAR WIND MEASURED BY CLUSTER

    SciTech Connect

    Roberts, O. W.; Li, X.; Li, B.

    2013-05-20

    The k-filtering technique and wave polarization analysis are applied to Cluster magnetic field data to study plasma turbulence at the scale of the ion gyroradius in the fast solar wind. Waves are found propagating in directions nearly perpendicular to the background magnetic field at such scales. The frequencies of these waves in the solar wind frame are much smaller than the proton gyrofrequency. After the wavevector k is determined at each spacecraft frequency f{sub sc}, wave polarization property is analyzed in the plane perpendicular to k. Magnetic fluctuations have {delta}B > {delta}B{sub Parallel-To} (here the Parallel-To and refer to the background magnetic field B{sub 0}). The wave magnetic field has right-handed polarization at propagation angles {theta}{sub kB} < 90 Degree-Sign and >90 Degree-Sign . The magnetic field in the plane perpendicular to B{sub 0}, however, has no clear sense of a dominant polarization but local rotations. We discuss the merits and limitations of linear kinetic Alfven waves (KAWs) and coherent Alfven vortices in the interpretation of the data. We suggest that the fast solar wind turbulence may be populated with KAWs, small-scale current sheets, and Alfven vortices at ion kinetic scales.

  6. Characterization of Kinetic Binding Properties of Unlabeled Ligands via a Preincubation Endpoint Binding Approach.

    PubMed

    Shimizu, Yuji; Ogawa, Kazumasa; Nakayama, Masaharu

    2016-08-01

    The dissociation rates of unlabeled drugs have been well studied by kinetic binding analyses. Since kinetic assays are laborious, we developed a simple method to determine the kinetic binding parameters of unlabeled competitors by a preincubation endpoint assay. The probe binding after preincubation of a competitor can be described by a single equation as a function of time. Simulations using the equation revealed the degree of IC50 change induced by preincubation of a competitor depended on the dissociation rate koff of the competitor but not on the association rate kon To validate the model, an in vitro binding assay was performed using a smoothened receptor (SMO) and [(3)H]TAK-441, a SMO antagonist. The equilibrium dissociation constants (KI) and koff of SMO antagonists determined by globally fitting the model to the concentration-response curves obtained with and without 24 h preincubation correlated well with those determined by other methods. This approach could be useful for early-stage optimization of drug candidates by enabling determination of binding kinetics in a high-throughput manner because it does not require kinetic measurements, an intermediate washout step during the reaction, or prior determination of competitors' KI values. PMID:27270099

  7. Excitation of kinetic Alfvén waves by fast electron beams

    SciTech Connect

    Chen, L.; Wu, D. J.; Zhao, G. Q.; Tang, J. F.; Huang, J. E-mail: djwu@pmo.ac.cn E-mail: jftang@xao.ac.cn

    2014-09-20

    Energetic electron beams, which are ubiquitous in a large variety of active phenomena in space and astrophysical plasmas, are one of the most important sources that drive plasma instabilities. In this paper, taking account of the return-current effect of fast electron beams, kinetic Alfvén wave (KAW) instability driven by a fast electron beam is investigated in a finite-β plasma of Q < β < 1 (where β is the kinetic-to-magnetic pressure ratio and Q ≡ m{sub e} /m{sub i} is the mass ratio of electrons to ions). The results show that the kinetic resonant interaction of beam electrons is the driving source for KAW instability, unlike the case driven by a fast ion beam, where both the kinetic resonant interaction of beam ions and the return-current are the driving source for the KAW instability. KAW instability has a nonzero growth rate in the range of the perpendicular wave number, 0

  8. Fast dissociation kinetics between individual E-cadherin fragments revealed by flow chamber analysis

    PubMed Central

    Perret, Emilie; Benoliel, Anne-Marie; Nassoy, Pierre; Pierres, Anne; Delmas, Véronique; Thiery, Jean-Paul; Bongrand, Pierre; Feracci, Hélène

    2002-01-01

    E-cadherin is the predominant adhesion molecule of epithelia. The interaction between extracellular segments of E-cadherin in the membrane of opposing cells is homophilic and calcium dependent. Whereas it is widely accepted that the specificity of the adhesive interaction is localized to the N-terminal domain, the kinetics of the recognition process are unknown. We report the first quantitative data describing the dissociation kinetics of individual E-cadherin interactions. Aggregation assays indicate that the two outermost domains of E-cadherin (E/EC1–2) retain biological activity when chemically immobilized on glass beads. Cadherin fragment trans-interaction was analysed using a flow chamber technique. Transient tethers had first-order kinetics, suggesting a unimolecular interaction. The unstressed lifetime of individual E-cadherin interactions was as brief as 2 s. A fast off rate and the low tensile strength of the E-cadherin bond may be necessary to support the high selectivity and plasticity of epithelial cell interactions. PMID:12032067

  9. Thermodynamics and Kinetics of Ligand Binding to Vitamin B-12a: A Laboratory Experiment

    ERIC Educational Resources Information Center

    Sweigart, D. A.

    1975-01-01

    Describes an open-ended experiment involving a bioinorganic system that provides the student a direct link between thermodynamics and kinetics. It utilizes a rapid reaction technique and requires one to clearly understand the relationship of experimental observable (absorbance) to a mechanism. (GS)

  10. Effect of Fluorescently Labeling Protein Probes on Kinetics of Protein-Ligand Reactions

    PubMed Central

    Sun, Y.S.; Landry, J.P.; Fei, Y.Y.; Luo, J.T.; Wang, X.B.; Lam, K.S.

    2009-01-01

    We studied the effect of fluorescently labeling proteins on protein-ligand reactions. Un-labeled ligands (streptavidin-binding peptides and rabbit immunoglobulin G (IgG) as antigen targets) are immobilized on epoxy-functionalized glass slides. Unlabeled and Cy3-labeled protein probes from the same batch (streptavidin and goat antibodies) subsequently react with the surface-immobilized targets. By monitoring in situ the surface mass density change using an oblique-incidence reflectivity difference scanning microscope (a label-free detector), we measured kon and koff for streptavidin-peptide reactions and antibody-antigen reaction. We found that (1) equilibrium dissociation constants, defined as KD = koff/kon, for streptavidin-peptide reactions increases by a factor of 3 ~ 4 when the solution-phase streptavidin is labeled with Cy3 dye; and (2) KD for reactions of solution-phase goat anti-rabbit antibodies with rabbit IgG targets also change significantly when the goat antibodies are labeled with Cy3 dye. PMID:18991423

  11. Effect of fluorescently labeling protein probes on kinetics of protein-ligand reactions.

    PubMed

    Sun, Y S; Landry, J P; Fei, Y Y; Zhu, X D; Luo, J T; Wang, X B; Lam, K S

    2008-12-01

    We studied the effect of fluorescently labeling proteins on protein-ligand reactions. Unlabeled ligands (streptavidin-binding peptides and rabbit immunoglobulin G (IgG) as antigen targets) are immobilized on epoxy-functionalized glass slides. Unlabeled and Cy3-labeled protein probes from the same batch (streptavidin and goat antibodies) subsequently react with the surface-immobilized targets. By monitoring in situ the surface mass density change using an oblique-incidence reflectivity difference scanning microscope (a label-free detector), we measured k(on) and k(off) for streptavidin-peptide reactions and antibody-antigen reaction. We found that (1) equilibrium dissociation constants, defined as K(D) = k(off)/k(on), for streptavidin-peptide reactions increases by a factor of 3-4 when the solution-phase streptavidin is labeled with Cy3 dye and (2) K(D) for reactions of solution-phase goat anti-rabbit antibodies with rabbit IgG targets also change significantly when the goat antibodies are labeled with Cy3 dye. PMID:18991423

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

    PubMed

    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. PMID:24908607

  13. A quantitative kinetic model for the fast and isothermal hydrothermal liquefaction of Nannochloropsis sp.

    PubMed

    Hietala, David C; Faeth, Julia L; Savage, Phillip E

    2016-08-01

    Hydrothermal liquefaction (HTL) is a technology for converting algal biomass into biocrude oil and high-value products. To elucidate the underlying kinetics for this process, we conducted isothermal and non-isothermal reactions over a broad range of holding times (10s-60min), temperatures (100-400°C), and average heating rates (110-350°Cmin(-1)). Biocrude reached high yields (⩾37wt%) within 2min for heat-source set-point temperatures of 350°C or higher. We developed a microalgal HTL kinetic model valid from 10s to 60min, including significantly shorter timescales (10s-10min) than any previous model. The model predicts that up to 46wt% biocrude yields are achievable at 400°C and 1min, reaffirming the utility of short holding times and "fast" HTL. We highlight potential trade-offs between maximizing biocrude quantity and facilitating aqueous phase recovery, which may improve biocrude quality. PMID:27128195

  14. Kinetic modeling of solid yields formation in the fast pyrolysis of mahogany wood

    NASA Astrophysics Data System (ADS)

    Wijayanti, W.; Sasongko, M. N.

    2016-03-01

    There have been many research of biomass pyrolysis not only in heat transfer point of view but also in chemical reaction point of view. In the present study, the rate of reaction (kinetic rate) formation of solid yield was calculated by varying the pyrolysis temperature that gives a chance of 250 °C, 350 °C, 450 °C, 500 °C, 600 °C, 700 °C, until 800°C with heating rate around 700 °C/hour. The heating rate used was the fast pyrolysis in which the heating rate for heating furnaces takes place quickly. Pyrolysis was accomplished by direct pyrolysis process in which each process was conducted at the certain pyrolysis temperature variation that took over 3 hours. Biomass used was mahogany wood, while the inert gas used to hold in order to avoid combustion was nitrogen gas. The decreasing of solid yields formation obtained was used to calculate the kinetic rate of the pyrolysis process. It was calculated by using the similar Arrhenius equation that considering the temperature changes during the process and the decreasing mass of solid yield formation occurred. The kinetic rate results showed the decomposition of biomass occurs tended in two stages, namely a stage of water evaporation and degradation of biomass solid yield coal followed by a stage of constant formation. The decomposition is expressed by the magnitude of the rate of reaction at 25˚C-517˚C temperature range with a reaction rate constant k1 = 2151.67 exp (-2141/Tp). While at pyrolysis temperatures above 517˚C, the reaction rate constant is expressed with k2 = 32.20 exp (-127.8 / Tp).

  15. FAST TRACK COMMUNICATION Tuning the spin state of iron phthalocyanine by ligand adsorption

    NASA Astrophysics Data System (ADS)

    Isvoranu, C.; Wang, B.; Schulte, K.; Ataman, E.; Knudsen, J.; Andersen, J. N.; Bocquet, M. L.; Schnadt, J.

    2010-12-01

    The future use of single-molecule magnets in applications will require the ability to control and manipulate the spin state and magnetization of the magnets by external means. There are different approaches to this control, one being the modification of the magnets by adsorption of small ligand molecules. In this paper we use iron phthalocyanine supported by an Au(111) surface as a model compound and demonstrate, using x-ray photoelectron spectroscopy and density functional theory, that the spin state of the molecule can be tuned to different values (S ~ 0, \\case {1}{2} , 1) by adsorption of ammonia, pyridine, carbon monoxide or nitric oxide on the iron ion. The interaction also leads to electronic decoupling of the iron phthalocyanine from the Au(111) support.

  16. Scintillation proximity assay (SPA) as a new approach to determine a ligand's kinetic profile. A case in point for the adenosine A1 receptor.

    PubMed

    Xia, Lizi; de Vries, Henk; IJzerman, Ad P; Heitman, Laura H

    2016-03-01

    Scintillation proximity assay (SPA) is a radio-isotopic technology format used to measure a wide range of biological interactions, including drug-target binding affinity studies. The assay is homogeneous in nature, as it relies on a "mix and measure" format. It does not involve a filtration step to separate bound from free ligand as is the case in a traditional receptor-binding assay. For G protein-coupled receptors (GPCRs), it has been shown that optimal binding kinetics, next to a high affinity of a ligand, can result in more desirable pharmacological profiles. However, traditional techniques to assess kinetic parameters tend to be cumbersome and laborious. We thus aimed to evaluate whether SPA can be an alternative platform for real-time receptor-binding kinetic measurements on GPCRs. To do so, we first validated the SPA technology for equilibrium binding studies on a prototypic class A GPCR, the human adenosine A1 receptor (hA1R). Differently to classic kinetic studies, the SPA technology allowed us to study binding kinetic processes almost real time, which is impossible in the filtration assay. To demonstrate the reliability of this technology for kinetic purposes, we performed the so-called competition association experiments. The association and dissociation rate constants (k on and k off) of unlabeled hA1R ligands were reliably and quickly determined and agreed very well with the same parameters from a traditional filtration assay performed simultaneously. In conclusion, SPA is a very promising technique to determine the kinetic profile of the drug-target interaction. Its robustness and potential for high-throughput may render this technology a preferred choice for further kinetic studies. PMID:26647040

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

    PubMed

    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

  18. Kinetic and spectral properties of isovaleryl-CoA dehydrogenase and interaction with ligands.

    PubMed

    Mohsen, Al-Walid A; Vockley, Jerry

    2015-01-01

    Isovaleryl-CoA dehydrogenase (IVD) catalyzes the conversion of isovaleryl-CoA to 3-methylcrotonyl-CoA and the transfer of electrons to the electron transfer flavoprotein (ETF). Recombinant human IVD purifies with bound CoA-persulfide. A modified purification protocol was developed to isolate IVD without bound CoA-persulfide and to protect the protein thiols from oxidation. The CoA-persulfide-free IVD specific activity was 112.5 μmol porcine ETF min(-)(1) mg(-)(1), which was ∼20-fold higher than that of its CoA-persulfide bound form. The Km and catalytic efficiency (kcat/Km) for isovaleryl-CoA were 1.0 μM and 4.3 × 10(6) M(-1) s(-1) per monomer, respectively, and its Km for ETF was 2.0 μM. Anaerobic titration of isovaleryl-CoA into an IVD solution resulted in a stable blue complex with increased absorbance at 310 nm, decreased absorbance at 373 and 447 nm, and the appearance of the charge transfer complex band at 584 nm. The apparent dissociation constant (KDapp) determined spectrally for isovaleryl-CoA was 0.54 μM. Isovaleryl-CoA, acetoacetyl-CoA, methylenecyclopropyl-acetyl-CoA, and ETF induced CD spectral changes at the 250-500 nm region while isobutyryl-CoA did not, suggesting conformational changes occur at the flavin ring that are ligand specific. Replacement of the IVD Trp166 with a Phe did not block IVD interaction with ETF, indicating that its indole ring is not essential for electron transfer to ETF. A twelve amino acid synthetic peptide that matches the sequence of the ETF docking peptide competitively inhibited the enzyme reaction when ETF was used as the electron acceptor with a Ki of 1.5 mM. PMID:25450250

  19. Kinetic and Spectral Properties of Isovaleryl-CoA Dehydrogenase and Interaction with Ligands

    PubMed Central

    Mohsen, Al-Walid A.; Vockley, Jerry

    2014-01-01

    Isovaleryl-CoA dehydrogenase (IVD) catalyzes the conversion of isovaleryl-CoA to 3-methylcrotonyl-CoA and the transfer of electrons to the electron transfer flavoprotein (ETF). Recombinant human IVD purifies with bound CoA-persulfide. A modified purification protocol was developed to isolate IVD without bound CoA-persulfide and to protect the protein thiols from oxidation. The CoA-persulfide-free IVD specific activity was 112.5 µmol porcine ETF•min−1•mg−1, which was ~20-fold higher than that of its CoA-persulfide bound form. The Km and catalytic efficiency (kcat/Km) for isovaleryl-CoA were 1.0 µM and 4.3 × 106•M−1•sec−1 per monomer, respectively, and its Km for ETF was 2.0 µM. Anaerobic titration of isovaleryl-CoA into an IVD solution resulted in a stable blue complex with increased absorbance at 310 nm, decreased absorbance at 373 and 447 nm, and the appearance of the charge transfer complex band at 584 nm. The apparent dissociation constant (KD app) determined spectrally for isovaleryl-CoA was 0.54 µM. Isovaleryl-CoA, acetoacetyl-CoA, methylenecyclopropylacetyl-CoA, and ETF induced CD spectral changes at the 250–500 nm region while isobutyryl-CoA did not, suggesting conformational changes occur at the flavin ring that are ligand specific. Replacement of the IVD Trp166 with a Phe did not block IVD interaction with ETF, indicating that its indole ring is not essential for electron transfer to ETF. A twelve amino acid synthetic peptide that matches the sequence of the ETF docking peptide competitively inhibited the enzyme reaction when ETF was used as the electron acceptor with a Ki of 1.5 mM. PMID:25450250

  20. Migration kinetics of primary aromatic amines from polyamide kitchenware: Easy and fast screening procedure using fluorescence.

    PubMed

    Sanllorente, S; Sarabia, L A; Ortiz, M C

    2016-11-01

    Primary aromatic amines, PAAs, and their derivatives constitute a health risk and control of their migration from food contact materials is the subject of permanent attention by the authorities. 25.1% of notifications made by Rapid Alert System for Food and Feed in the European Union between 2010 and 2015 concerned PAAs, polyamide cooking utensils being a common source. It is thus useful to have fast and efficient analytical methods for their control. In this work a non-separative, easy, fast and inexpensive spectrofluorimetric method based on the second order calibration of excitation-emission fluorescence matrices (EEMs) was proposed for the determination of aniline (ANL), 2,4-diaminotoluene (2,4-TDA) and 4,4'-methylenedianiline (4,4'-MDA) in polyamide cooking utensils. The procedure made it possible to identify unequivocally each analyte. Trilinearity of the data tensor guarantees the uniqueness of the solution obtained through parallel factor analysis (PARAFAC), so the factors of the decomposition match up with the analytes. The three analytes were unequivocally identified by the correlation between the pure spectra and the PARAFAC excitation and emission spectral loadings. The recovery percentages found were, 82.6%, 112.7% and 84.4% for ANL, 2,4-TDA and 4,4'-MDA respectively. The proposed method was applied to carry out a migration test from polyamide cooking utensils, using a 3% (w/v) acetic acid in aqueous solution as food simulant. Detectable levels of 4,4'-MDA were found in food simulant from some of the investigated cooking utensils. Finally, a kinetic model for the migration of 4,4'-MDA has been fitted to experimental data obtained in the migration test. Thanks to the selectivity of PARAFAC calibration, which greatly simplifies sample treatment avoiding the use of toxic solvents, the developed method follows most green analytical chemistry principles. PMID:27591586

  1. Predicting properties of gas and solid streams by intrinsic kinetics of fast pyrolysis of wood

    SciTech Connect

    Klinger, Jordan; Bar-Ziv, Ezra; Shonnard, David; Westover, Tyler; Emerson, Rachel

    2015-12-12

    Pyrolysis has the potential to create a biocrude oil from biomass sources that can be used as fuel or as feedstock for subsequent upgrading to hydrocarbon fuels or other chemicals. The product distribution/composition, however, is linked to the biomass source. This work investigates the products formed from pyrolysis of woody biomass with a previously developed chemical kinetics model. Different woody feedstocks reported in prior literature are placed on a common basis (moisture, ash, fixed carbon free) and normalized by initial elemental composition through ultimate analysis. Observed product distributions over the full devolatilization range are explored, reconstructed by the model, and verified with independent experimental data collected with a microwave-assisted pyrolysis system. These trends include production of permanent gas (CO, CO2), char, and condensable (oil, water) species. Elementary compositions of these streams are also investigated. As a result, close agreement between literature data, model predictions, and independent experimental data indicate that the proposed model/method is able to predict the ideal distribution from fast pyrolysis given reaction temperature, residence time, and feedstock composition.

  2. Predicting properties of gas and solid streams by intrinsic kinetics of fast pyrolysis of wood

    DOE PAGESBeta

    Klinger, Jordan; Bar-Ziv, Ezra; Shonnard, David; Westover, Tyler; Emerson, Rachel

    2015-12-12

    Pyrolysis has the potential to create a biocrude oil from biomass sources that can be used as fuel or as feedstock for subsequent upgrading to hydrocarbon fuels or other chemicals. The product distribution/composition, however, is linked to the biomass source. This work investigates the products formed from pyrolysis of woody biomass with a previously developed chemical kinetics model. Different woody feedstocks reported in prior literature are placed on a common basis (moisture, ash, fixed carbon free) and normalized by initial elemental composition through ultimate analysis. Observed product distributions over the full devolatilization range are explored, reconstructed by the model, andmore » verified with independent experimental data collected with a microwave-assisted pyrolysis system. These trends include production of permanent gas (CO, CO2), char, and condensable (oil, water) species. Elementary compositions of these streams are also investigated. As a result, close agreement between literature data, model predictions, and independent experimental data indicate that the proposed model/method is able to predict the ideal distribution from fast pyrolysis given reaction temperature, residence time, and feedstock composition.« less

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

    ERIC Educational Resources Information Center

    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. SPOT-Ligand: Fast and effective structure-based virtual screening by binding homology search according to ligand and receptor similarity.

    PubMed

    Yang, Yuedong; Zhan, Jian; Zhou, Yaoqi

    2016-07-01

    Structure-based virtual screening usually involves docking of a library of chemical compounds onto the functional pocket of the target receptor so as to discover novel classes of ligands. However, the overall success rate remains low and screening a large library is computationally intensive. An alternative to this "ab initio" approach is virtual screening by binding homology search. In this approach, potential ligands are predicted based on similar interaction pairs (similarity in receptors and ligands). SPOT-Ligand is an approach that integrates ligand similarity by Tanimoto coefficient and receptor similarity by protein structure alignment program SPalign. The method was found to yield a consistent performance in DUD and DUD-E docking benchmarks even if model structures were employed. It improves over docking methods (DOCK6 and AUTODOCK Vina) and has a performance comparable to or better than other binding-homology methods (FINDsite and PoLi) with higher computational efficiency. The server is available at http://sparks-lab.org. © 2016 Wiley Periodicals, Inc. PMID:27074979

  5. Effects of organic ligands and temperature variations on the kinetics of olivine carbonation and the formation of associated secondary phases

    NASA Astrophysics Data System (ADS)

    Sissmann, O.; Daval, D.; Martinez, I.; Brunet, F.; Verlaguet, A.; Pinquier, Y.; Guyot, F. J.

    2011-12-01

    The slow dissolution kinetics of Mg-rich silicates has become a critical issue for the geologic CO2 sequestration in basic rocks. Previous batch carbonation studies on San Carlos olivine [1] performed in CO2 saturated water (at 90°C and P CO2 = 280 bar) have focused on the role that secondary phases, such as amorphous silica layers (SiO2 (am)), have on the transport of reactants from and to the reactive surfaces. The fluid composition remained roughly constant over the duration of the experiment, close to saturation with respect to amorphous silica and with a [Mg2+]/[SiO2 (aq)] ratio close to stoechiometric release, suggesting a passivation of the olivine surface by the silica layer. In order to accelerate the dissolution process, organic ligands such as citrate and acetate were added to the solutions and tested at 1M and 0.1M concentrations in similar batch experiments. An intrinsic increase of the dissolution rate of olivine was expected [2], [3] prior to the formation of a passivating silica layer. Preliminary results confirm this idea since Mg was released in non-stoechimoetric proportions with respect to SiO2 (aq) (found to be in equilibrium with SiO2 (am)). Similarly, a slight increase of temperature (from 90°C to 120°C) accelerated the reaction kinetics as well, possibly impacting the textural properties of SiO2 (am). Current TEM investigations are directed to confirming a possible link between the observed increase of the rate and textural properties of secondary phases. In addition, because carbonate minerals have a retrograde solubility, thermodynamical modelling suggests that this temperature increase should allow the fluid to reach saturation with respect to carbonates before reaching saturation with respect to SiO2 (am). Enough Mg can therefore be released to initiate the formation of carbonates before the silica precipitates and passivates the olivine surface. [1] Daval et al (2011), Chemical Geology, v.284, p.193-209 [2] Grandstaff, D.E. (1986) In

  6. Dependence of cancer cell adhesion kinetics on integrin ligand surface density measured by a high-throughput label-free resonant waveguide grating biosensor

    NASA Astrophysics Data System (ADS)

    Orgovan, Norbert; Peter, Beatrix; Bősze, Szilvia; Ramsden, Jeremy J.; Szabó, Bálint; Horvath, Robert

    2014-02-01

    A novel high-throughput label-free resonant waveguide grating (RWG) imager biosensor, the Epic® BenchTop (BT), was utilized to determine the dependence of cell spreading kinetics on the average surface density (vRGD) of integrin ligand RGD-motifs. vRGD was tuned over four orders of magnitude by co-adsorbing the biologically inactive PLL-g-PEG and the RGD-functionalized PLL-g-PEG-RGD synthetic copolymers from their mixed solutions onto the sensor surface. Using highly adherent human cervical tumor (HeLa) cells as a model system, cell adhesion kinetic data of unprecedented quality were obtained. Spreading kinetics were fitted with the logistic equation to obtain the spreading rate constant (r) and the maximum biosensor response (Δλmax), which is assumed to be directly proportional to the maximum spread contact area (Amax). r was found to be independent of the surface density of integrin ligands. In contrast, Δλmax increased with increasing RGD surface density until saturation at high densities. Interpreting the latter behavior with a simple kinetic mass action model, a 2D dissociation constant of 1753 +/- 243 μm-2 (corresponding to a 3D dissociation constant of ~30 μM) was obtained for the binding between RGD-specific integrins embedded in the cell membrane and PLL-g-PEG-RGD. All of these results were obtained completely noninvasively without using any labels.

  7. Dependence of cancer cell adhesion kinetics on integrin ligand surface density measured by a high-throughput label-free resonant waveguide grating biosensor

    PubMed Central

    Orgovan, Norbert; Peter, Beatrix; Bősze, Szilvia; Ramsden, Jeremy J.; Szabó, Bálint; Horvath, Robert

    2014-01-01

    A novel high-throughput label-free resonant waveguide grating (RWG) imager biosensor, the Epic® BenchTop (BT), was utilized to determine the dependence of cell spreading kinetics on the average surface density (vRGD) of integrin ligand RGD-motifs. vRGD was tuned over four orders of magnitude by co-adsorbing the biologically inactive PLL-g-PEG and the RGD-functionalized PLL-g-PEG-RGD synthetic copolymers from their mixed solutions onto the sensor surface. Using highly adherent human cervical tumor (HeLa) cells as a model system, cell adhesion kinetic data of unprecedented quality were obtained. Spreading kinetics were fitted with the logistic equation to obtain the spreading rate constant (r) and the maximum biosensor response (Δλmax), which is assumed to be directly proportional to the maximum spread contact area (Amax). r was found to be independent of the surface density of integrin ligands. In contrast, Δλmax increased with increasing RGD surface density until saturation at high densities. Interpreting the latter behavior with a simple kinetic mass action model, a 2D dissociation constant of 1753 ± 243 μm−2 (corresponding to a 3D dissociation constant of ~30 μM) was obtained for the binding between RGD-specific integrins embedded in the cell membrane and PLL-g-PEG-RGD. All of these results were obtained completely noninvasively without using any labels. PMID:24503534

  8. Effects of particle size and ligand density on the kinetics of receptor-mediated endocytosis of nanoparticles

    NASA Astrophysics Data System (ADS)

    Yuan, Hongyan; Zhang, Sulin

    2010-01-01

    We elucidate, from thermodynamic arguments, the governing factors of receptor-mediated endocytosis of nanoparticles (NPs). We show that the endocytic energetics specifies a minimal particle size and a minimal ligand density below which endocytosis is not possible. Due to the entropic penalty involved in ligand-receptor binding, endocytosis may occur with a large fraction of ligands unbound with receptors. Our analyses suggest that the endocytic time depends interrelatedly on the particle size and ligand density. There exists an optimal condition at which the endocytic time minimizes. These findings may provide valuable guidance to the rational designs of NP-based biomarkers and anticancer bioagents.

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

    NASA Astrophysics Data System (ADS)

    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.

  10. Fluorescence Biomembrane Force Probe: Concurrent Quantitation of Receptor-ligand Kinetics and Binding-induced Intracellular Signaling on a Single Cell.

    PubMed

    Chen, Yunfeng; Liu, Baoyu; Ju, Lining; Hong, Jinsung; Ji, Qinghua; Chen, Wei; Zhu, Cheng

    2015-01-01

    Membrane receptor-ligand interactions mediate many cellular functions. Binding kinetics and downstream signaling triggered by these molecular interactions are likely affected by the mechanical environment in which binding and signaling take place. A recent study demonstrated that mechanical force can regulate antigen recognition by and triggering of the T-cell receptor (TCR). This was made possible by a new technology we developed and termed fluorescence biomembrane force probe (fBFP), which combines single-molecule force spectroscopy with fluorescence microscopy. Using an ultra-soft human red blood cell as the sensitive force sensor, a high-speed camera and real-time imaging tracking techniques, the fBFP is of ~1 pN (10(-12) N), ~3 nm and ~0.5 msec in force, spatial and temporal resolution. With the fBFP, one can precisely measure single receptor-ligand binding kinetics under force regulation and simultaneously image binding-triggered intracellular calcium signaling on a single live cell. This new technology can be used to study other membrane receptor-ligand interaction and signaling in other cells under mechanical regulation. PMID:26274371

  11. Structural basis for a hand-like site in the calcium sensor CatchER with fast kinetics

    SciTech Connect

    Zhang, Ying; Reddish, Florence; Tang, Shen; Zhuo, You; Wang, Yuan-Fang; Yang, Jenny J.; Weber, Irene T.

    2013-12-01

    High-resolution crystal structures of the designed calcium sensor CatchER revealed snapshots of calcium and gadolinium ions binding within the designed site in agreement with its fast kinetics. Calcium ions, which are important signaling molecules, can be detected in the endoplasmic reticulum by an engineered mutant of green fluorescent protein (GFP) designated CatchER with a fast off-rate. High resolution (1.78–1.20 Å) crystal structures were analyzed for CatchER in the apo form and in complexes with calcium or gadolinium to probe the binding site for metal ions. While CatchER exhibits a 1:1 binding stoichiometry in solution, two positions were observed for each of the metal ions bound within the hand-like site formed by the carboxylate side chains of the mutated residues S147E, S202D, Q204E, F223E and T225E that may be responsible for its fast kinetic properties. Comparison of the structures of CatchER, wild-type GFP and enhanced GFP confirmed that different conformations of Thr203 and Glu222 are associated with the two forms of Tyr66 of the chromophore which are responsible for the absorbance wavelengths of the different proteins. Calcium binding to CatchER may shift the equilibrium for conformational population of the Glu222 side chain and lead to further changes in its optical properties.

  12. QALE analysis of CO dissociative kinetics of Ru(CO)4L (L = P-donor ligands): accelerating effects of hydrogen in PHnR(3 - n) ligands (n = 1-2).

    PubMed

    Babij, Claudia; Chen, Lezhan; Koshevoy, Igor O; Poë, Anthony J

    2004-03-01

    Studies of CO-dissociative substitution reactions of the complexes Ru(CO)4L (L = a wide variety of P-donor ligands) have been extended and analysis of the results by the QALE methodology has been refined (QALE = quantitative analysis of ligand effects). Rates increase substantially with increasing size of L, mainly as a consequence of increasingly favourable activation entropies. These can be associated with increasing Ru-CO bond breaking that is compensated enthalpically by increasing Ru-P bond making allowed by release of steric strain. Explicit allowance for pi-acidity shows that these effects are just significant while sigma-donor and aryl effects are negligible. However, pendent hydrogen atoms, attached directly to the phosphorus atoms, have a pronounced and unique positive effect on the rates, with significant kinetic isotope effects (KIE). This is associated with the novel occurrence of direct Ru-H or incipient Ru-(eta2-P-H) agostic bond making as the CO ligand departs. PMID:15252507

  13. Edge-bridging and face-capping coordination of alkenyl ligands in triruthenium carbonyl cluster complexes derived from hydrazines: synthetic, structural, theoretical, and kinetic studies.

    PubMed

    Cabeza, Javier A; del Río, Ignacio; Fernández-Colinas, José M; García-Granda, Santiago; Martínez-Méndez, Lorena; Pérez-Carreño, Enrique

    2004-12-01

    The reactions of the triruthenium cluster complex [Ru3(mu-H)(mu3-eta2-HNNMe2)(CO)9] (1; H2NNMe2=1,1-dimethylhydrazine) with alkynes (PhC triple bond CPh, HC triple bond CH, MeO2CC triple bond CCO2Me, PhC triple bond CH, MeO2CC triple bond CH, HOMe2CC triple bond CH, 2-pyC triple bond CH) give trinuclear complexes containing edge-bridging and/or face-capping alkenyl ligands. Whereas the edge-bridged products are closed triangular species (three Ru-Ru bonds), the face-capped products are open derivatives (two Ru-Ru bonds). For terminal alkynes, products containing gem (RCCH2) and/or trans (RHCCH) alkenyl ligands have been identified in both edge-bridging and face-capping positions, except for the complex [Ru3(mu3-eta2-HNNMe2)(mu3-eta3-HCCH-2-py)(mu-CO)(CO)7], which has the two alkenyl H atoms in a cis arrangement. Under comparable reaction conditions (1:1 molar ratio, THF at reflux, time required for the consumption of complex 1), some reactions give a single product, but most give mixtures of isomers (not all the possible ones), which were separated. To determine the effect of the hydrazido ligand, the reactions of [Ru3(mu-H)(mu3-eta2-MeNNHMe)(CO)9] (2; HMeNNHMe=1,2-dimethylhydrazine) with PhC triple bond CPh, PhC triple bond CH, and HC triple bond CH were also studied. For edge-bridged alkenyl complexes, the Ru--Ru edge that is spanned by the alkenyl ligand depends on the position of the methyl groups on the hydrazido ligand. For face-capped alkenyl complexes, the relative orientation of the hydrazido and alkenyl ligands also depends on the position of the methyl groups on the hydrazido ligand. A kinetic analysis of the reaction of 1 with PhC[triple chemical bond]CPh revealed that the reaction follows an associative mechanism, which implies that incorporation of the alkyne in the cluster is rate-limiting and precedes the release of a CO ligand. X-ray diffraction, IR and NMR spectroscopy, and calculations of minimum-energy structures by DFT methods were used to

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  15. Integrated kinetic simulation of laser-plasma interactions, fast-electron generation, and transport in fast ignition

    SciTech Connect

    Kemp, A. J.; Cohen, B. I.; Divol, L.

    2010-05-15

    We present new results on the physics of short-pulse laser-matter interaction of kilojoule-picosecond pulses at full spatial and temporal scale using a new approach that combines a three-dimensional collisional electromagnetic particle-in-cell code with a magnetohydrodynamic-hybrid model of high-density plasma. In the latter, collisions damp out plasma waves, and an Ohm's law with electron inertia effects neglected determines the electric field. In addition to yielding orders of magnitude in speed-up while avoiding numerical instabilities, this allows us to model the whole problem in a single unified framework: the laser-plasma interaction at subcritical densities, energy deposition at relativistic critical densities, and fast- electron transport in solid densities. Key questions such as the multipicosecond temporal evolution of the laser energy conversion into hot electrons, the impact of return currents on the laser-plasma interaction, and the effect of self-generated electric and magnetic fields on electron transport will be addressed. We will report applications to current experiments.

  16. Integrated Kinetic Simulation of Laser-Plasma Interactions, Fast-Electron Generation and Transport in Fast Ignition

    SciTech Connect

    Kemp, A; Cohen, B; Divol, L

    2009-11-16

    We present new results on the physics of short-pulse laser-matter interaction of kilojoule-picosecond pulses at full spatial and temporal scale, using a new approach that combines a 3D collisional electromagnetic Particle-in-Cell code with an MHD-hybrid model of high-density plasma. In the latter, collisions damp out plasma waves, and an Ohm's law with electron inertia effects neglected determines the electric field. In addition to yielding orders of magnitude in speed-up while avoiding numerical instabilities, this allows us to model the whole problem in a single unified framework: the laser-plasma interaction at sub-critical densities, energy deposition at relativistic critical densities, and fast-electron transport in solid densities. Key questions such as the multi-picosecond temporal evolution of the laser energy conversion into hot electrons, the impact of return currents on the laser-plasma interaction, and the effect of self-generated electric and magnetic fields on electron transport will be addressed. We will report applications to current experiments.

  17. A Simple and Fast Kinetic Assay for the Determination of Fructan Exohydrolase Activity in Perennial Ryegrass (Lolium perenne L.)

    PubMed Central

    Gasperl, Anna; Morvan-Bertrand, Annette; Prud’homme, Marie-Pascale; Roitsch, Thomas

    2015-01-01

    Despite the fact that fructans are the main constituent of water-soluble carbohydrates in forage grasses and cereal crops of temperate climates, little knowledge is available on the regulation of the enzymes involved in fructan metabolism. The analysis of enzyme activities involved in this process has been hampered by the low affinity of the fructan enzymes for sucrose and fructans used as fructosyl donor. Further, the analysis of fructan composition and enzyme activities is restricted to specialized labs with access to suited HPLC equipment and appropriate fructan standards. The degradation of fructan polymers with high degree of polymerization (DP) by fructan exohydrolases (FEHs) to fructosyloligomers is important to liberate energy in the form of fructan, but also under conditions where the generation of low DP polymers is required. Based on published protocols employing enzyme coupled endpoint reactions in single cuvettes, we developed a simple and fast kinetic 1-FEH assay. This assay can be performed in multi-well plate format using plate readers to determine the activity of 1-FEH against 1-kestotriose, resulting in a significant time reduction. Kinetic assays allow an optimal and more precise determination of enzyme activities compared to endpoint assays, and enable to check the quality of any reaction with respect to linearity of the assay. The enzyme coupled kinetic 1-FEH assay was validated in a case study showing the expected increase in 1-FEH activity during cold treatment. This assay is cost effective and could be performed by any lab with access to a plate reader suited for kinetic measurements and readings at 340 nm, and is highly suited to assess temporal changes and relative differences in 1-FEH activities. Thus, this enzyme coupled kinetic 1-FEH assay is of high importance both to the field of basic fructan research and plant breeding. PMID:26734049

  18. Kinetic-energy release in CO dissociation caused by fast F4+ impact

    NASA Astrophysics Data System (ADS)

    Ben-Itzhak, I.; Ginther, S. G.; Krishnamurthi, Vidhya; Carnes, K. D.

    1995-01-01

    The dissociation of CO caused by 1-MeV/amu F4+ impact has been studied using the coincidence time-of-flight technique. The kinetic energy released during the dissociation of COQ+ into ion pairs Cq1+ and Oq+2 was determined from the measured difference in the times of flight of the two charged fragments. The kinetic-energy distributions of CO2+ dissociating into C+ and O+ as a result of different impinging projectiles have been compared. These distributions shift towards higher kinetic-energy release values with increasing strength of interaction. A single Gaussian kinetic-energy distribution is in good agreement with the highly charged CO dissociation, while for doubly and triply charged CO, additional Gaussians are needed. While the Coulomb-explosion model approximately predicts the most likely value of a measured distribution, the widths of all distributions are grossly underestimated by the model. The measured widths of the distributions can be explained only by invoking the existence of potential-energy curves of the multiply charged ions that have steeper and shallower slopes as compared to the Coulombic curve. The reflection method was used to calculate the kinetic-energy release for F4++CO-->CO2+* transitions to all known CO2+ states. The final kinetic-energy distribution was then fitted to the data in order to evaluate the weights of the different transitions. The calculated fit is in fair agreement with the measured one, although the high-energy tail of the measured distribution could not be accounted for, indicating that contributions from highly excited dissociating states or from curve crossings need to be included.

  19. Unchanged content of oxidative enzymes in fast-twitch muscle fibers and kinetics after intensified training in trained cyclists

    PubMed Central

    Christensen, Peter M; Gunnarsson, Thomas P; Thomassen, Martin; Wilkerson, Daryl P; Nielsen, Jens Jung; Bangsbo, Jens

    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 () response during intense (INT), but not moderate (MOD), exercise and reduce the slow component and muscle metabolic perturbation during INT. Pulmonary kinetics was determined in eight trained male cyclists (-max: 59 ± 4 (means ± SD) mL min−1 kg−1) during MOD (205 ± 12 W ∼65% -max) and INT (286 ± 17 W ∼85% -max) exercise before and after a 7-week HIT period (30-sec sprints and 4-min intervals) with a 50% reduction in volume. Both before and after HIT the content in fast-twitch fibers of CS (P < 0.05) and COX-4 (P < 0.01) was lower, whereas PFK was higher (P < 0.001) than in slow-twitch fibers. Content of CS, COX-4, and PFK in homogenate and fast-twitch fibers was unchanged with HIT. Maximal activity (μmol g 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. kinetics was unchanged with HIT and the speed of the primary response did not differ 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 < 0.05) after compared to before HIT. A period of intensified training with a volume reduction did not increase the content of oxidative enzymes in fast-twitch fibers, and did not change kinetics. PMID:26152692

  20. Kinetic effects in the conversion of fast waves in pre-heated, low aspect ratio tokamak plasmas

    NASA Astrophysics Data System (ADS)

    Kommoshvili, K.; Cuperman, S.; Bruma, C.

    2003-03-01

    Kinetic effects in the conversion of fast waves to Alfvèn waves and their subsequent deposition in low aspect ratio (spherical) tokamaks (LARTs) have been investigated theoretically. More specifically, we have considered the consequences of incorporation of kinetic effects in the electron parallel (to the ambient magnetic field) dynamics derived by following the drift-tearing mode analysis of Chen et al (Chen L, Rutherford P H and Tang W M 1977 Phys. Rev. Lett. 39 460), and particle-conserving Krook collision operator for the passing electrons involved (Mett R R and Mahajan S M 1992 Phys. Fluids B 4 2885). The perpendicular plasma dynamics is described by a quite general resistive two-fluid (2F) model based dielectric tensor-operator (Cuperman S, Bruma C and Komoshvili K 2002 Solution of the resistive 2F wave equations for Alfvènic modes in spherical tokamak plasmas J. Plasma Phys. accepted for publication). The full-wave electromagnetic equations, formulated in terms of the vector and scalar potentials, have been solved by the aid of an advanced finite elements numerical code (Sewell G 1993 Adv. Eng. Software 17 105). Detailed solutions of the full-wave equations are obtained and compared with those corresponding to a pure resistive 2F model, this, for the illustrative pre-heated START-type device (Sykes 1994). Our results quantitatively confirm the general theory of the conversion of fast waves with subsequent power dissipation for the conditions of spherical tokamaks thus providing the required auxilliary energy source for the succesful operation of LARTs. Moreover, these results indicate the absolute necessity of using a full model for the parallel electron dynamics, i.e. including both kinetic and collisional effects.

  1. A fast kinetics study of the modes of action of some different radiosensitizers in bacteria.

    PubMed Central

    Michael, B. D.; Harrop, H. A.; Maughan, R. L.; Patel, K. B.

    1978-01-01

    Using a fast mixing a irradiation technique, the gas explosion method, with Serratia marcescents, the decay of oxygen-dependent damage is found to consist of a fast and a slow stage, each of which is associated with a sub-component of this damage. In the present work, the interactions of these components with radiosensitizers are examined. At low concentrations O2, TAN (a nitroxyl) and misonidazole all preferentially sensitize the slow-stage damage. At higher concentrations, O2 and TAN sensitize the fast-stage damage by a fixation reaction that competes with its repair; in contrast, misonidazole appears mainly to operate by reaction with an earlier, ever shorter form of oxygen-dependent damage. PMID:354678

  2. CO and O2 Binding to Pseudo-Tetradentate Ligand-Copper(I)-Complexes with a Variable N-Donor Moiety: Kinetic/Thermodynamic Investigation Reveals Ligand Induced Changes in Reaction Mechanism

    PubMed Central

    Lucas, Heather R.; Meyer, Gerald J.; Karlin, Kenneth D.

    2010-01-01

    The kinetics, thermodynamics, and coordination dynamics for O2 and CO 1:1 binding to a series of pseudo-tetradentate ligand-copper(I)-complexes (DLCuI) to give CuI/O2 and CuI/CO product species are reported. The DLCuI series possess an identical tridentate core structure where the cuprous ion binds to the bispicolylamine (L) fragment. DL also contains a fourth variable N-donor moiety {D = benzyl (Bz); pyridyl (Py); imidazolyl (Im); dimethylamino (NMe2-); tert-butylphenyl pyridyl (TBP); quinolyl (Q)}. The structural characteristics of DLCuI-CO and DLCuI are detailed, with X-ray crystal structures reported for TBPLCuI-CO, BzLCuI-CO, and QLCuI. Infrared studies (solution and solid-state) confirm that DLCuI-CO possess the same four-coordinate core structure in solution with the variable D moiety ‘dangling’, i.e. not coordinated to the copper(I) ion. Other trends observed for the present series appear to derive from the degree to which the D-group interacts with the cuprous ion center. Electrochemical studies reveal close similarities of behavior for ImLCuI and NMe2LCuI (as well as for TBPLCuI and QLCuI), which relate to the O2-binding kinetics and thermodynamics. Equilibrium CO binding data (KCO, ΔH°, ΔS°) were obtained by conducting UV-visible spectrophotometric CO titrations, while CO binding kinetics and thermodynamics (kCO ; ΔH‡, ΔS‡) were measured through variable temperature (193 K – 293 K) transient absorbance laser flash photolysis experiments, λex = 355 nm. Carbon monoxide dissociation rate constants (k−CO) and corresponding activation parameters (ΔH‡, ΔS‡) have also been obtained. CO binding to DLCuI follows an associative mechanism with the increased donation from D leading to higher kCO values. Unlike that seen in previous work, the KCO values increased as the kCO and k−CO values declines; the latter decreased at a faster rate. By using the ‘flash-and-trap’ method (λex = 355 nm ; 188 K – 218 K), the kinetics and

  3. Resonance elastic light scattering (RELS) spectroscopy of fast non-Langmuirian ligand-exchange in glutathione-induced gold nanoparticle assembly.

    PubMed

    Stobiecka, Magdalena; Coopersmith, Kaitlin; Hepel, Maria

    2010-10-01

    The interactions of a biomolecule glutathione (GSH) with citrate-capped gold nanoparticles (AuNP) have been investigated to evaluate the viability of a rapid GSH-capture by gold nanoparticle carriers, as a model system for applications ranging from designing nanoparticle-enhanced functional biosensor interfaces to nanomedicine. The measurements, performed using resonance elastic light scattering (RELS) spectroscopy, have shown a strong dependence of GSH-induced scattering cross-section on gold nanoparticle size. A large increase in RELS intensity after injection of GSH, in a short reaction time (tau=60 s), has been observed for small AuNP (5nm dia.) and ascribed to the fast ligand-exchange followed by AuNP assembly. The unexpected non-Langmuirian concentration dependence of scattering intensity for AuNP (5 nm) indicates on a 2D nucleation and growth mechanism of the ligand-exchange process. The ligand-exchange and small nanoparticle ensemble formation followed by relaxation have been observed in long term (10 h) monitoring of GSH-AuNP interactions by RELS. The results of molecular dynamics and quantum mechanical calculations corroborate the mechanism of the formation of hydrogen-bonded GSH-linkages and interparticle interactions and show that the assembly is driven by multiple H-bonding between GSH-capped AuNP and electrostatic zwitterionic interactions. The RELS spectroscopy has been found as a very sensitive tool for studying interparticle interactions. The application of RELS can be expanded to monitor reactivities and assembly of other monolayer-protected metal clusters, especially in very fast processes which cannot be followed by other techniques. PMID:20591439

  4. Characterizing the micro structure and kinetics of fast changing samples by simultaneous polarization measurements

    NASA Astrophysics Data System (ADS)

    Liao, Ran; He, Honghui; Zeng, Nan; Ma, Hui

    2015-03-01

    Taking accurate measurements of the state of polarization (SOP) is the key for the success of polarization sensitive techniques which can provide rich information on the microstructure of complex scattering media, such as biological tissues. For static or slow varying samples, SOP measurements can be achieved by time-sequential recoding of different polarization components controlled by rotating polarizers and wave plates or temporal modulation devices such as photoelastic modulators or liquid crystal variable retarders. When the sample is moving or changing its status quickly, polarization components recoded at different time may correspond to different SOPs, which can lead to significant errors in the final results. Simultaneous polarization measurements are necessary for probing such dynamic samples. In this paper, using the simultaneously recorded polarization components, we are able to mimic time sequential polarization schemes and evaluate the errors. The results show that the kinetics of the sample will affect the systematic error and an increase in the statistical errors of the measured degree of polarization (DOP). We change the kinetics of samples with different stirring speed, which is indicated by the characteristic time of the auto-correlation function. It is also demonstrated that the simultaneously recorded polarization components reveals additional information on the orientation of fibrous scatterers as well as their translation and rotation kinetics.

  5. Kinetic and electrochemical studies of the oxidative addition of demanding organic halides to Pd(0): the efficiency of polyphosphane ligands in low palladium loading cross-couplings decrypted.

    PubMed

    Zinovyeva, Veronika A; Mom, Sophal; Fournier, Sophie; Devillers, Charles H; Cattey, Hélène; Doucet, Henri; Hierso, Jean-Cyrille; Lucas, Dominique

    2013-10-21

    Oxidative addition (OA) of organic halides to palladium(0) species is a fundamental reaction step which initiates the C-C bond formation catalytic processes typical of Pd(0)/Pd(II) chemistry. The use of structurally congested polyphosphane ligands in palladium-catalyzed C-C bond formation has generated very high turnover numbers (TONs) in topical reactions such as Heck, Suzuki, Sonogashira couplings, and direct sp(2)C-H functionalization. Herein, the OA of aryl bromides to Pd(0) complexes stabilized by ferrocenylpolyphosphane ligands L1 (tetraphosphane), L2 (triphosphane), and L3 (diphosphane) is considered. The investigation of kinetic constants for the addition of Ph-Br to Pd(0) intermediates (generated by electrochemical reduction of Pd(II) complexes coordinated by L1-L3) is reported. Thus, in the OA of halides to the Pd(0) complex coordinated by L1 the series of rate constants kapp is found (mol(-1) L s(-1)): kapp(Ph-Br) = 0.48 > kapp(ClCH2-Cl) = 0.25 ≫ kapp(p-MeC6H4-Br) = 0.08 ≈ kapp(o-MeC6H4-Br) = 0.07 ≫ kapp(Ph-Cl). Kinetic measurements clarify the influence that the presence of four, three, or two phosphorus atoms in the coordination sphere of Pd has on OA. The presence of supplementary phosphorus atoms in L1 and L2 unambiguously stabilizes Pd(0) species and thus slows down the OA of Ph-Br to Pd(0) of about 2 orders of magnitude compared to the diphosphane L3. The electrosynthesis of the complexes resulting from the OA of organic halides to [Pd(0)/L] is easily performed and show the concurrent OA to Pd(0) of the sp(3)C-Cl bond of dichloromethane solvent. The resulting unstable Pd/alkyl complex is characterized by NMR and single crystal X-ray structure. We additionally observed the perfect stereoselectivity of the OA reactions which is induced by the tetraphosphane ligand L1. Altogether, a clearer picture of the general effects of congested polydentate ligands on the OA of organic halides to Pd(0) is given. PMID:24107007

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

    PubMed Central

    2010-01-01

    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 Licence and available on

  7. The fast-off hypothesis revisited: A functional kinetic study of antipsychotic antagonism of the dopamine D2 receptor.

    PubMed

    Sahlholm, Kristoffer; Zeberg, Hugo; Nilsson, Johanna; Ögren, Sven Ove; Fuxe, Kjell; Århem, Peter

    2016-03-01

    Newer, "atypical" antipsychotics carry a lower risk of motor side-effects than older, "typical" compounds. It has been proposed that a ~100-fold faster dissociation from the dopamine D2 receptor (D2R) distinguishes atypical from typical antipsychotics. Furthermore, differing antipsychotic D2R affinities have been suggested to reflect differences in dissociation rate constants (koff), while association rate constants (kon) were assumed to be similar. However, it was recently demonstrated that lipophilic accumulation of ligand in the cell interior and/or membrane can cause underestimation of koff, and as high-affinity D2R antagonists are frequently lipophilic, this may have been a confounding factor in previous studies. In the present work, a functional electrophysiology assay was used to measure the recovery of dopamine-mediated D2R responsivity from antipsychotic antagonism, using elevated concentrations of dopamine to prevent the potential bias of re-binding of lipophilic ligands. The variability of antipsychotic kon was also reexamined, capitalizing on the temporal resolution of the assay. kon was estimated from the experimental recordings using a simple mathematical model assumed to describe the binding process. The time course of recovery from haloperidol (typical antipsychotic) was only 6.4- to 2.5-fold slower than that of the atypical antipsychotics, amisulpride, clozapine, and quetiapine, while antipsychotic kons were found to vary more widely than previously suggested. Finally, affinities calculated using our kon and koff estimates correlated well with functional potency and with affinities reported from radioligand binding studies. In light of these findings, it appears unlikely that typical and atypical antipsychotics are primarily distinguished by their D2R binding kinetics. PMID:26811292

  8. Effect of pH and organic ligands on the kinetics of smectite dissolution at 25 °C

    NASA Astrophysics Data System (ADS)

    Golubev, Sergey V.; Bauer, Andreas; Pokrovsky, Oleg S.

    2006-09-01

    Forward dissolution rates of Na-Montmorillonite (Wyoming) SWy-2 smectite (Ca 0.06Na 0.56)[Al 3.08Fe(III) 0.38Mg 0.54] [Si 7.93 Al 0.07]O 20(OH) 4 were measured at 25 °C in a mixed-flow reactor equipped with interior dialysis compartment (6-8 kDa membrane) as a function of pH (1-12), dissolved carbonate (0.5-10 mM), phosphate (10 -5 to 0.03 M), and nine organic ligands (acetate, oxalate, citrate, EDTA, alginate, glucuronic acid, 3,4-dihydroxybenzoic acid, gluconate, and glucosamine) in the concentration range from 10 -5 to 0.03 M. In organic-free solutions, the Si-based rates decrease with increasing pH at 1 ⩽ pH ⩽ 8 with a slope close to -0.2. At 9 ⩽ pH ⩽ 12, the Si-based rates increase with a slope of ˜0.3. In contrast, non-stoichiometric Mg release weakly depends on pH at 1 ⩽ pH ⩽ 12 and decreases with increasing pH. The empirical expression describing Si-release rates [ R, mol/cm 2/s] obtained in the present study at 25 °C, I = 0.01 M is given by R=2.2·10-17·aH0.21+1.0·10-20+6·10-17·aOH0.33 At circum-neutral pH, the Si-release-based dissolution is promoted by the addition of the following ligands ranked by decreasing effectiveness: EDTA > 3,4-DHBA > citrate ⩾ oxalate. Phosphate, glucuronate, glucosamine, gluconate, alginate, and acetate act as inhibitors of dissolution and HCO 3-, CO 32- exhibit no effect on dissolution rate. Non-stoichiometric, non-steady-state Mg release was very weakly affected by the presence of ligands. Analysis of reacted solid products using XRD, FT-IR, and XPS revealed no major change in structure, surface chemical composition or specific surface area as a function of pH, ligand concentration, and duration of experiments. Ligand-affected rates re-calculated to constant pH were interpreted using a phenomenological equation which postulates the Langmurian adsorption of a ligand on surface sites. Overall, results of this study demonstrate that very high concentrations (0.001-0.01 M) of organic ligands, whether they are

  9. Computational studies of the first order kinetic reactions for mononuclear copper(II) complexes having a hard-soft NS donor ligand

    NASA Astrophysics Data System (ADS)

    Zaky, R. R.; Yousef, T. A.; Abdelghany, A. M.

    2014-09-01

    The chelation behaviour of 4-((E)-2-(1-(thiophen-2-yl)ethylidene)hydrazinyl)-1-(4-methoxyphenyl)-1H-pyrrole-3-carbonitrile (HL) towards Cu(II) ions has been investigated. These Cu(II) complexes are characterized by elemental analyses, molar-solid conductance, ESR, FTIR and electronic spectral studies. Also, the kinetic and thermodynamic parameters (Ea, A, ΔH, ΔS, ΔG) for all thermal decomposition steps have been evaluated using Coats-Redfern and Horowitz-Metzger methods. Furthermore, antimicrobial activity of the ligand and its complexes were studied against Gram-negative bacteria: Escherichia coli, Gram-positive Bacillus cereus, Bacillus subtilis and pathogenic fungi Pseudomonas aeruginosa by using minimum inhibitory concentrations (MICs) method.

  10. Computational studies of the first order kinetic reactions for mononuclear copper(II) complexes having a hard-soft NS donor ligand.

    PubMed

    Zaky, R R; Yousef, T A; Abdelghany, A M

    2014-09-15

    The chelation behaviour of 4-((E)-2-(1-(thiophen-2-yl)ethylidene)hydrazinyl)-1-(4-methoxyphenyl)-1H-pyrrole-3-carbonitrile (HL) towards Cu(II) ions has been investigated. These Cu(II) complexes are characterized by elemental analyses, molar-solid conductance, ESR, FTIR and electronic spectral studies. Also, the kinetic and thermodynamic parameters (Ea, A, ΔH, ΔS, ΔG) for all thermal decomposition steps have been evaluated using Coats-Redfern and Horowitz-Metzger methods. Furthermore, antimicrobial activity of the ligand and its complexes were studied against Gram-negative bacteria: Escherichia coli, Gram-positive Bacillus cereus, Bacillus subtilis and pathogenic fungi Pseudomonas aeruginosa by using minimum inhibitory concentrations (MICs) method. PMID:24785091

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

    PubMed Central

    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. PMID:26844298

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

    PubMed

    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. PMID:26844298

  13. Steady-state dissolution kinetics of aluminum-goethite in the presence of desferrioxamine-B and oxalate ligands.

    PubMed

    Cervini-Silva, Javiera; Sposito, Garrison

    2002-02-01

    This paper reports steady-state dissolution rates of synthetic low-substitution Al-goethites (mol % Al < 10) at pH 5 in the presence of the trihydroxamate siderophore, desferrioxamine B (DFO-B), and the common biological ligand, oxalate. The siderophore-promoted Fe release rate increased both with the level of Al substitution and with DFO-B concentration up to about 100 microM, after which a plateau occurred, suggesting a saturation effect from DFO-B adsorption as a precursor to dissolution. At concentrations above 200 microM, oxalate also enhanced the Fe release rate, which however was not influenced by Al substitution. For Al-goethites with mol % Al < 4, the Fe release rate in the presence of 40 microM DFO-B together with varying concentrations of oxalate was typically greater than the corresponding sum of dissolution rates in the presence of the two ligands alone. This synergism may be the combined result of the ability of oxalate to adsorb strongly at the goethite surface, thus promoting Fe release, and of the high selectivity of DFO for Fe(III). Ferric oxalate complexes formed during dissolution will likely lose Fe3+ by ligand substitution with DFO-B, leading to the production of Fe(HDFO-B)+ and uncomplexed oxalate, the latter of which, in turn, could adsorb to the goethite surface again. For Al-goethites with mol % Al > 4, synergism was not apparent, which may signal the effect of a decreased surface density of Fe-OH sites associated with Al for Fe substitution. The oxalate-promoted release rates of Al did not scale with those of Fe, indicating incongruent dissolution. However, Al release rates in the presence of DFO-B did scale approximately with those of Fe but were not affected by the concentration of siderophore. These results are consistent with the presence of Al(OH)3 inclusions in Al-goethite. PMID:11871546

  14. Compartmental analysis of technetium-99m-teboroxime kinetics employing fast dynamic SPECT at rest and stress

    SciTech Connect

    Chiao, P.C.; Ficaro, E.P.; Dayaniki, F.

    1994-08-01

    The authors have examined the feasibility of compartmental analysis of {sup 99m}Tc-teboroxime kinetics in measuring physiological changes in response to adenosine-induced coronary vasodilation. To evaluate the effect of tracer recirculation on {sup 99m}Tc-teboroxime kinetics in the myocardium, they also compared compartmental analysis with washout analysis (monoexponertial fitting), which does not account for this effect. Eight healthy male volunteers were imaged using fast dynamic SPECT protocols (5 sec per tomographic image) at rest and during adenosine infusion. A two-compartment model was used and compartmental parameters K1 and k2 (characterizing the diffusion of {sup 99m}Tc-teboroxime from the blood to the myocardium and from the myocardium to the blood, respectively) were fitted from myocardial time-activity curves and left ventricular input functions. Both K1 and washout estimates for the whole left ventricular myocardium changed significantly in response to coronary vasodilation. Mean stress-to-rest (S/R) ratios were almost two times higher for K1 (S/R = 2.7 {plus_minus} 1.1) than for washout estimates (S/R = 1.5 {plus_minus} 0.3). Estimation of K1 for all local regions, except the septal wall, is feasible because variations in K1 estimates for all local regions, except the septum during stress, are comparable with those for the global region. The authors conclude that quantitative compartmental analysis of {sup 99m}Tc-teboroxime kinetics provides a sensitive indicator for changes in response to adenosine-induced coronary vasodilation. 39 refs., 7 figs., 1 tab.

  15. Fast and slow crystal growth kinetics in glass-forming melts

    NASA Astrophysics Data System (ADS)

    Orava, J.; Greer, A. L.

    2014-06-01

    Published values of crystal growth rates are compared for supercooled glass-forming liquids undergoing congruent freezing at a planar crystal-liquid interface. For the purposes of comparison pure metals are considered to be glass-forming systems, using data from molecular-dynamics simulations. For each system, the growth rate has a maximum value Umax at a temperature Tmax that lies between the glass-transition temperature Tg and the melting temperature Tm. A classification is suggested, based on the lability (specifically, the propensity for fast crystallization), of the liquid. High-lability systems show "fast" growth characterized by a high Umax, a low Tmax / Tm, and a very broad peak in U vs. T / Tm. In contrast, systems showing "slow" growth have a low Umax, a high Tmax / Tm, and a sharp peak in U vs. T / Tm. Despite the difference of more than 11 orders of magnitude in Umax seen in pure metals and in silica, the range of glass-forming systems surveyed fit into a common pattern in which the lability increases with lower reduced glass-transition temperature (Tg / Tm) and higher fragility of the liquid. A single parameter, a linear combination of Tg / Tm and fragility, can show a good correlation with Umax. For all the systems, growth at Umax is coupled to the atomic/molecular mobility in the liquid. It is found that, across the diversity of glass-forming systems, Tmax / Tg = 1.48 ± 0.15.

  16. Fast ignition in system Dynamic Hohlraum with Monte-Carlo simulations of fusion kinetic and radiation processes

    NASA Astrophysics Data System (ADS)

    Andreev, Alexander A.; Platonov, Konstantin Y.; Zacharov, Sergey V.; Gus'kov, Sergei Y.; Rozanov, Vladimir B.; Il'in, Dmitrii V.; Levkovskii, Aleksey A.; Sherman, Vladimir E.

    2004-06-01

    The scheme of fast ignition by super-intense laser of DT target placed at a cavity of the radiate plasma liner, created in a "dynamic-hohlraum" system is considered. It is shown that this scheme can supply effective TN fusion. The process of compression and preheating of DT fuel of shell target by X-ray radiation of Dynamic Hohlraum is simulated by the code TRITON with parameters of Z-generator of Sandia National Laboratory. The optimum parameters of target are obtained. The mechanism of ignitor creation by protons, accelerated by ultra-shot laser radiation is considered and corresponding laser parameters are evaluated. The mathematical simulation of the following thermonuclear (TN) burn wave propagation in DT target is carried out with the use of TERA code based upon the direct statistical simulation of kinetics of fast charged particles and quantum of thermal radiation on each time step of hydrodynamics. The released TN energy is obtained as a function of ignition energy. The theoretical explanations of obtained dependencies are presented. The laser parameters necessary to produce G>>1 are determined.

  17. Structural basis for a hand-like site in the calcium sensor CatchER with fast kinetics

    PubMed Central

    Zhang, Ying; Reddish, Florence; Tang, Shen; Zhuo, You; Wang, Yuan-Fang; Yang, Jenny J.; Weber, Irene T.

    2013-01-01

    Calcium ions, which are important signaling molecules, can be detected in the endoplasmic reticulum by an engineered mutant of green fluorescent protein (GFP) designated CatchER with a fast off-rate. High resolution (1.78–1.20 Å) crystal structures were analyzed for CatchER in the apo form and in complexes with calcium or gadolinium to probe the binding site for metal ions. While CatchER exhibits a 1:1 binding stoichiometry in solution, two positions were observed for each of the metal ions bound within the hand-like site formed by the carboxylate side chains of the mutated residues S147E, S202D, Q204E, F223E and T225E that may be responsible for its fast kinetic properties. Comparison of the structures of CatchER, wild-type GFP and enhanced GFP confirmed that different conformations of Thr203 and Glu222 are associated with the two forms of Tyr66 of the chromophore which are responsible for the absorbance wavelengths of the different proteins. Calcium binding to CatchER may shift the equilibrium for conformational population of the Glu222 side chain and lead to further changes in its optical properties. PMID:24311573

  18. PLASMA EFFECTS ON FAST PAIR BEAMS. II. REACTIVE VERSUS KINETIC INSTABILITY OF PARALLEL ELECTROSTATIC WAVES

    SciTech Connect

    Schlickeiser, R.; Krakau, S.; Supsar, M. E-mail: steffen.krakau@rub.de

    2013-11-01

    The interaction of TeV gamma-rays from distant blazars with the extragalactic background light produces relativistic electron-positron pair beams by the photon-photon annihilation process. Using the linear instability analysis in the kinetic limit, which properly accounts for the longitudinal and the small but finite perpendicular momentum spread in the pair momentum distribution function, the growth rate of parallel propagating electrostatic oscillations in the intergalactic medium is calculated. Contrary to the claims of Miniati and Elyiv, we find that neither the longitudinal nor the perpendicular spread in the relativistic pair distribution function significantly affect the electrostatic growth rates. The maximum kinetic growth rate for no perpendicular spread is even about an order of magnitude greater than the corresponding reactive maximum growth rate. The reduction factors in the maximum growth rate due to the finite perpendicular spread in the pair distribution function are tiny and always less than 10{sup –4}. We confirm earlier conclusions by Broderick et al. and our group that the created pair beam distribution function is quickly unstable in the unmagnetized intergalactic medium. Therefore, there is no need to require the existence of small intergalactic magnetic fields to scatter the produced pairs, so that the explanation (made by several authors) for the Fermi non-detection of the inverse Compton scattered GeV gamma-rays by a finite deflecting intergalactic magnetic field is not necessary. In particular, the various derived lower bounds for the intergalactic magnetic fields are invalid due to the pair beam instability argument.

  19. Fast and slow crystal growth kinetics in glass-forming melts.

    PubMed

    Orava, J; Greer, A L

    2014-06-01

    Published values of crystal growth rates are compared for supercooled glass-forming liquids undergoing congruent freezing at a planar crystal-liquid interface. For the purposes of comparison pure metals are considered to be glass-forming systems, using data from molecular-dynamics simulations. For each system, the growth rate has a maximum value U(max) at a temperature T(max) that lies between the glass-transition temperature T(g) and the melting temperature T(m). A classification is suggested, based on the lability (specifically, the propensity for fast crystallization), of the liquid. High-lability systems show "fast" growth characterized by a high U(max), a low T(max)/T(m), and a very broad peak in U vs. T/T(m). In contrast, systems showing "slow" growth have a low U(max), a high T(max)/T(m), and a sharp peak in U vs. T/T(m). Despite the difference of more than 11 orders of magnitude in U(max) seen in pure metals and in silica, the range of glass-forming systems surveyed fit into a common pattern in which the lability increases with lower reduced glass-transition temperature (T(g)/T(m)) and higher fragility of the liquid. A single parameter, a linear combination of T(g)/T(m) and fragility, can show a good correlation with U(max). For all the systems, growth at U(max) is coupled to the atomic/molecular mobility in the liquid. It is found that, across the diversity of glass-forming systems, T(max)/T(g) = 1.48 ± 0.15. PMID:24908023

  20. Ultrasonic relaxation and fast chemical kinetics of some carbohydrate aqueous solutions

    SciTech Connect

    Behrends, R. |; Cowman, M.K.; Majewski, J.; Petrucci, S.; Eggers, F.; Richmann, K.H.; Eyring, E.M.; Riech, M.; Kaatze, U.

    1997-03-05

    Molecular relaxation properties of the monosaccharides (a) D-glucose, (b) methyl {beta}-D-glucopyranoside, (c) methyl {alpha}-D-mannopyranoside, (d) D-xylose, (e) D-arabinose, (f) methyl {beta}-D-xylopyranoside, (g) methyl {beta}-D-arabinopyranoside, (h) methyl {alpha}-L-(6-deoxy)mannopyranoside, and (i) 1,6-anhydro-{beta}-D-glucopyranoside, all in aqueous solution, have been studied using broad band ultrasonic spectrometry in the frequency range 0.2-2000 MHz. Ultrasonic excess absorption with relaxation characteristics near 80 MHz was found for glucose and the methyl glucosides of D-glucose and D-mannose, but no relaxation process was detected for the other monosaccharides in the same frequency range. From structural aspects it is deduced that the most likely process causing the observed relaxation is the rotation of the exocyclic -CH{sub 2}OH group, placing rotational isomerization on the nanosecond time scale. Relaxation parameters for D-glucose and methyl {beta}-D-glucopyranoside solutions were further investigated as a function of concentration and temperature, in order to confirm the assignment of the relaxation process, and to determine some of its thermodynamic and kinetic parameters. 19 refs., 7 figs., 1 tab.

  1. Linear and nonlinear thermodynamics of a kinetic heat engine with fast transformations

    NASA Astrophysics Data System (ADS)

    Cerino, Luca; Puglisi, Andrea; Vulpiani, Angelo

    2016-04-01

    We investigate a kinetic heat engine model composed of particles enclosed in a box where one side acts as a thermostat and the opposite side is a piston exerting a given pressure. Pressure and temperature are varied in a cyclical protocol of period τ : their relative excursions, δ and ɛ , respectively, constitute the thermodynamic forces dragging the system out of equilibrium. The analysis of the entropy production of the system allows us to define the conjugated fluxes, which are proportional to the extracted work and the consumed heat. In the limit of small δ and ɛ the fluxes are linear in the forces through a τ -dependent Onsager matrix whose off-diagonal elements satisfy a reciprocal relation. The dynamics of the piston can be approximated, through a coarse-graining procedure, by a Klein-Kramers equation which—in the linear regime—yields analytic expressions for the Onsager coefficients and the entropy production. A study of the efficiency at maximum power shows that the Curzon-Ahlborn formula is always an upper limit which is approached at increasing values of the thermodynamic forces, i.e., outside of the linear regime. In all our analysis the adiabatic limit τ →∞ and the the small-force limit δ ,ɛ →0 are not directly related.

  2. "Adapted Linear Interaction Energy": A Structure-Based LIE Parametrization for Fast Prediction of Protein-Ligand Affinities.

    PubMed

    Linder, Mats; Ranganathan, Anirudh; Brinck, Tore

    2013-02-12

    We present a structure-based parametrization of the Linear Interaction Energy (LIE) method and show that it allows for the prediction of absolute protein-ligand binding energies. We call the new model "Adapted" LIE (ALIE) because the α and β coefficients are defined by system-dependent descriptors and do therefore not require any empirical γ term. The best formulation attains a mean average deviation of 1.8 kcal/mol for a diverse test set and depends on only one fitted parameter. It is robust with respect to additional fitting and cross-validation. We compare this new approach with standard LIE by Åqvist and co-workers and the LIE + γSASA model (initially suggested by Jorgensen and co-workers) against in-house and external data sets and discuss their applicabilities. PMID:26588766

  3. Prolonged depolarization promotes fast gating kinetics of L-type Ca2+ channels in mouse skeletal myotubes

    PubMed Central

    O’Connell, Kristen M S; Dirksen, Robert T

    2000-01-01

    The effects of prolonged conditioning depolarizations on the activation kinetics of skeletal L-type calcium currents (L-currents) were characterized in mouse myotubes using the whole-cell patch clamp technique. The sum of two exponentials was required to adequately fit L-current activation and enabled determination of both the amplitudes (Afast and Aslow) and time constants (τfast and τslow) of each component comprising the macroscopic current. Prepulses sufficient to activate (200 ms) or inactivate (10 s) L-channels did not alter τfast, τslow, or the fractional contribution of either the fast (Afast/(Afast + Aslow)) or slow (Aslow/(Afast + Aslow)) amplitudes of subsequently activated L-currents. Prolonged depolarizations (60 s to +40 mV) resulted in the conversion of skeletal L-current to a fast gating mode following brief repriming intervals (3-10 s at -80 mV). Longer repriming intervals (30-60 s at -80 mV) restored L-channels to a predominantly slow gating mode. Accelerated L-currents originated from L-type calcium channels since they were completely blocked by a dihydropyridine antagonist (3 μM nifedipine) and exhibited a voltage dependence of activation similar to that observed in the absence of conditioning prepulses. The degree of L-current acceleration produced following prolonged depolarization was voltage dependent. For test potentials between +10 and +50 mV, the fractional contribution of Afast to the total current decreased exponentially with the test voltage (e-fold ∼38 mV). Thus, L-current acceleration was most significant at more negative test potentials (e.g. +10 mV). Prolonged depolarization also accelerated L-currents recorded from myotubes derived from RyR1-knockout (dyspedic) mice. These results indicate that L-channel acceleration occurs even in the absence of RyR1, and is therefore likely to represent an intrinsic property of skeletal L-channels. The results describe a novel experimental protocol used to demonstrate that slowly

  4. Coherent Events and Spectral Shape at Ion Kinetic Scales in the Fast Solar Wind Turbulence

    NASA Astrophysics Data System (ADS)

    Lion, Sonny; Alexandrova, Olga; Zaslavsky, Arnaud

    2016-06-01

    In this paper we investigate spectral and phase coherence properties of magnetic fluctuations in the vicinity of the spectral transition from large, magnetohydrodynamic to sub-ion scales using in situ measurements of the Wind spacecraft in a fast stream. For the time interval investigated by Leamon et al. (1998) the phase coherence analysis shows the presence of sporadic quasi-parallel Alfvén ion cyclotron (AIC) waves as well as coherent structures in the form of large-amplitude, quasi-perpendicular Alfvén vortex-like structures and current sheets. These waves and structures importantly contribute to the observed power spectrum of magnetic fluctuations around ion scales; AIC waves contribute to the spectrum in a narrow frequency range whereas the coherent structures contribute to the spectrum over a wide frequency band from the inertial range to the sub-ion frequency range. We conclude that a particular combination of waves and coherent structures determines the spectral shape of the magnetic field spectrum around ion scales. This phenomenon provides a possible explanation for a high variability of the magnetic power spectra around ion scales observed in the solar wind.

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

    NASA Astrophysics Data System (ADS)

    Yasuda, Kazuhiro; Kinoshita, Chiken; Fukuda, Korehisa; Garner, Frank A.

    2000-12-01

    Thermal stability of interstitial-type dislocation loops and cavities in single crystals of MgAl 2O 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 2O 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.

  6. Surface Interrogation Scanning Electrochemical Microscopy of Ni(1-x)Fe(x)OOH (0 < x < 0.27) Oxygen Evolving Catalyst: Kinetics of the "fast" Iron Sites.

    PubMed

    Ahn, Hyun S; Bard, Allen J

    2016-01-13

    Nickel-iron mixed metal oxyhydroxides have attracted significant attention as an oxygen evolution reaction (OER) catalyst for solar fuel renewable energy applications. Here, we performed surface-selective and time-dependent redox titrations to directly measure the surface OER kinetics of Ni(IV) and Fe(IV) in NiOOH, FeOOH, and Ni(1-x)Fe(x)OOH (0 < x < 0.27) electrodes. Most importantly, two types of surface sites exhibiting "fast" and "slow" kinetics were found, where the fraction of "fast" sites in Ni(1-x)Fe(x)OOH matched the iron atom content in the film. This finding provides experimental support to the theory-proposed model of active sites in Ni(1-x)Fe(x)OOH. The OER rate constant of the "fast" site was 1.70 s(-1) per atom. PMID:26645678

  7. Kinetic electro membrane extraction under stagnant conditions--fast isolation of drugs from untreated human plasma.

    PubMed

    Eibak, Lars Erik Eng; Gjelstad, Astrid; Rasmussen, Knut Einar; Pedersen-Bjergaard, Stig

    2010-07-30

    Amitriptyline, citalopram, fluoxetine, and fluvoxamine were isolated by electro membrane extraction (EME) from 70microl of untreated plasma (pH 7.4), through a supported liquid membrane (SLM) of 1-ethyl-2-nitrobenzene immobilized in the pores of a porous polypropylene hollow fiber, and into 30microl of 10mM HCOOH as acceptor solution inside the lumen of the hollow fiber. The driving force of the extraction was a 9V potential sustained over the SLM with a common battery, with the positive electrode placed in the plasma sample and the negative electrode placed in the acceptor solution. Extractions were performed under totally stagnant conditions with a very simple device for 1min (kinetic regime), and subsequently the acceptor solution was analyzed directly by liquid chromatography-mass spectrometry (LC-MS). Recoveries were 12, 13, 22, and 17% for fluoxetine, amitriptyline, citalopram, and fluvoxamine, respectively. Sample clean-up was comparable to reversed-phase solid-phase extraction (SPE), but EME required substantially less time than SPE. The time advantage of EME was further improved by parallel extraction of three samples (for 1min) with the same 9V battery. EME from plasma combined with LC-MS provided limits of quantification (S/N=10) in the range 0.4-2.3ng/ml, linearity in the range 1-1000ng/ml with r(2)-values of 0.998-0.999, and repeatability in the range 3.2-8.9% RSD in the mid-therapeutic window (100ng/ml). PMID:20591437

  8. Fast and slow crystal growth kinetics in glass-forming melts

    SciTech Connect

    Orava, J.; Greer, A. L.

    2014-06-07

    Published values of crystal growth rates are compared for supercooled glass-forming liquids undergoing congruent freezing at a planar crystal-liquid interface. For the purposes of comparison pure metals are considered to be glass-forming systems, using data from molecular-dynamics simulations. For each system, the growth rate has a maximum value U{sub max} at a temperature T{sub max} that lies between the glass-transition temperature T{sub g} and the melting temperature T{sub m}. A classification is suggested, based on the lability (specifically, the propensity for fast crystallization), of the liquid. High-lability systems show “fast” growth characterized by a high U{sub max}, a low T{sub max} / T{sub m}, and a very broad peak in U vs. T / T{sub m}. In contrast, systems showing “slow” growth have a low U{sub max}, a high T{sub max} / T{sub m}, and a sharp peak in U vs. T / T{sub m}. Despite the difference of more than 11 orders of magnitude in U{sub max} seen in pure metals and in silica, the range of glass-forming systems surveyed fit into a common pattern in which the lability increases with lower reduced glass-transition temperature (T{sub g} / T{sub m}) and higher fragility of the liquid. A single parameter, a linear combination of T{sub g} / T{sub m} and fragility, can show a good correlation with U{sub max}. For all the systems, growth at U{sub max} is coupled to the atomic/molecular mobility in the liquid. It is found that, across the diversity of glass-forming systems, T{sub max} / T{sub g} = 1.48 ± 0.15.

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

    PubMed Central

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

    2009-01-01

    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. PMID:19154569

  10. Quantitative analysis of protein-ligand interactions by NMR.

    PubMed

    Furukawa, Ayako; Konuma, Tsuyoshi; Yanaka, Saeko; Sugase, Kenji

    2016-08-01

    Protein-ligand interactions have been commonly studied through static structures of the protein-ligand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein-ligand interactions both for fundamental understanding of the underlying mechanisms and for drug development. NMR is a versatile and powerful tool, especially because it provides site-specific quantitative information. NMR has widely been used to determine the dissociation constant (KD), in particular, for relatively weak interactions. The simplest NMR method is a chemical-shift titration experiment, in which the chemical-shift changes of a protein in response to ligand titration are measured. There are other quantitative NMR methods, but they mostly apply only to interactions in the fast-exchange regime. These methods derive the dissociation constant from population-averaged NMR quantities of the free and bound states of a protein or ligand. In contrast, the recent advent of new relaxation-based experiments, including R2 relaxation dispersion and ZZ-exchange, has enabled us to obtain kinetic information on protein-ligand interactions in the intermediate- and slow-exchange regimes. Based on R2 dispersion or ZZ-exchange, methods that can determine the association rate, kon, dissociation rate, koff, and KD have been developed. In these approaches, R2 dispersion or ZZ-exchange curves are measured for multiple samples with different protein and/or ligand concentration ratios, and the relaxation data are fitted to theoretical kinetic models. It is critical to choose an appropriate kinetic model, such as the two- or three-state exchange model, to derive the correct kinetic information. The R2 dispersion and ZZ-exchange methods are suitable for the analysis of protein-ligand interactions with a micromolar or sub-micromolar dissociation constant but not for very weak interactions, which are typical in very fast exchange. This contrasts with the NMR methods that are used

  11. GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution

    PubMed Central

    Kinjo, Akira R.; Nakamura, Haruki

    2012-01-01

    Comparison and classification of protein structures are fundamental means to understand protein functions. Due to the computational difficulty and the ever-increasing amount of structural data, however, it is in general not feasible to perform exhaustive all-against-all structure comparisons necessary for comprehensive classifications. To efficiently handle such situations, we have previously proposed a method, now called GIRAF. We herein describe further improvements in the GIRAF protein structure search and alignment method. The GIRAF method achieves extremely efficient search of similar structures of ligand binding sites of proteins by exploiting database indexing of structural features of local coordinate frames. In addition, it produces refined atom-wise alignments by iterative applications of the Hungarian method to the bipartite graph defined for a pair of superimposed structures. By combining the refined alignments based on different local coordinate frames, it is made possible to align structures involving domain movements. We provide detailed accounts for the database design, the search and alignment algorithms as well as some benchmark results.

  12. A fast transient potassium current in thalamic relay neurons: kinetics of activation and inactivation.

    PubMed

    Huguenard, J R; Coulter, D A; Prince, D A

    1991-10-01

    1. Whole-cell voltage-clamp techniques were used to record K+ currents in relay neurons (RNs) that had been acutely isolated from rat thalamic ventrobasal complex and maintained at 23 degrees C in vitro. Tetrodoxin (TTX; 0.5 microM) was used to block Na+ currents, and reduced extracellular levels of Ca2+ (1 mM) were used to minimize contributions from Ca2+ current (ICa). 2. In RNs, depolarizing commands activate K+ currents characterized by a substantial rapidly inactivating (time constant approximately 20 ms) component, the features of which correspond to those of the transient K+ current (IA) in other preparations, and by a smaller, more slowly activating K+ current, "IK". IA was reversibly blocked by 4-aminopyridine (4-AP, 5 mM), and the reversal potential varied with [K+]o as predicted by the Nernst equation. 3. IA was relatively insensitive to blockade by tetraethylammonium [TEA; 50%-inhibitory concentration (IC50) much much greater than 20 mM]; however, two components of IK were blocked with IC50S of 30 microM and 3 mM. Because 20 mM TEA blocked 90% of the sustained current while reducing IA by less than 10%, this concentration was routinely used in experiments in which IA was isolated and characterized. To further minimize contamination by other conductances, 4-AP was added to TEA-containing solutions and the 4-AP-sensitive current was obtained by subtraction. 4. Voltage-dependent steady-state inactivation of peak IA was described by a Boltzman function with a slope factor (k) of -6.5 and half-inactivation (V1/2) occurring at -75 mV. Activation of IA was characterized by a Boltzman curve with V1/2 = -35 mV and k = 10.8. 5. IA activation and inactivation kinetics were best fitted by the Hodgkin-Huxley m4h formalism. The rate of activation was voltage dependent, with tau m decreasing from 2.3 ms at -40 mV to 0.5 ms at +50 mV. Inactivation was relatively voltage independent and nonexponential. The rate of inactivation was described by two exponential decay

  13. Ligand-Binding Affinity at the Insulin Receptor Isoform-A and Subsequent IR-A Tyrosine Phosphorylation Kinetics are Important Determinants of Mitogenic Biological Outcomes

    PubMed Central

    Rajapaksha, Harinda; Forbes, Briony E.

    2015-01-01

    The insulin receptor (IR) is a tyrosine kinase receptor that can mediate both metabolic and mitogenic biological actions. The IR isoform-A (IR-A) arises from alternative splicing of exon 11 and has different ligand binding and signaling properties compared to the IR isoform-B. The IR-A not only binds insulin but also insulin-like growth factor-II (IGF-II) with high affinity. IGF-II acting through the IR-A promotes cancer cell proliferation, survival, and migration by activating some unique signaling molecules compared to those activated by insulin. This observation led us to investigate whether the different IR-A signaling outcomes in response to IGF-II and insulin could be attributed to phosphorylation of a different subset of IR-A tyrosine residues or to the phosphorylation kinetics. We correlated IR-A phosphorylation to activation of molecules involved in mitogenic and metabolic signaling (MAPK and Akt) and receptor internalization rates (related to mitogenic signaling). We also extended this study to incorporate two ligands that are known to promote predominantly mitogenic [(His4, Tyr15, Thr49, Ile51) IGF-I, qIGF-I] or metabolic (S597 peptide) biological actions, to see if common mechanisms can be used to define mitogenic or metabolic signaling through the IR-A. The threefold lower mitogenic action of IGF-II compared to insulin was associated with a decreased potency in activation of Y960, Y1146, Y1150, Y1151, Y1316, and Y1322, in MAPK phosphorylation and in IR-A internalization. With the poorly mitogenic S597 peptide, it was a decreased rate of tyrosine phosphorylation rather than potency that was associated with a low mitogenic potential. We conclude that both decreased affinity of IR-A binding and kinetics of IR-A phosphorylation can independently lead to a lower mitogenic activity. None of the studied parameters could account for the lower metabolic activity of qIGF-I. PMID:26217307

  14. Constructing Kinetic Network Models to Elucidate Mechanisms of Functional Conformational Changes of Enzymes and Their Recognition with Ligands.

    PubMed

    Zhang, L; Jiang, H; Sheong, F K; Pardo-Avila, F; Cheung, P P-H; Huang, X

    2016-01-01

    Enzymes are biological macromolecules that catalyze complex reactions in life. In order to perform their functions effectively and efficiently, enzymes undergo conformational changes between different functional states. Therefore, elucidating the dynamics between these states is essential to understand the molecular mechanisms of enzymes. Although experimental methods such as X-ray crystallography and cryoelectron microscopy can produce high-resolution structures, the detailed conformational dynamics of many enzymes still remain obscure. While molecular dynamics (MD) simulations are able to complement the experiments by providing structure-based dynamics at atomic resolution, it is usually difficult for them to reach the biologically relevant timescales (hundreds of microseconds or longer). Kinetic network models (KNMs), in particular Markov state models (MSMs), hold great promise to overcome this challenge because they can bridge the timescale gap between MD simulations and experimental observations. In this chapter, we review the procedure of constructing KNMs to elucidate the molecular mechanisms of enzymes. First, we will give a general introduction of MSMs, including the methods to construct and validate MSMs. Second, we will present the applications of KNMs to study two important enzymes: the human Argonaute protein and the RNA polymerase II. We conclude by discussing the future perspectives regarding the potential of KNMs to investigate the dynamics of enzymes' functional conformational changes. PMID:27497174

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

    SciTech Connect

    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.

  16. A chiral ligand exchange CE essay with zinc(II)-L-valine complex for determining enzyme kinetic constant of L-amino acid oxidase.

    PubMed

    Qi, Li; Yang, Gengliang; Zhang, Haizhi; Qiao, Juan

    2010-06-15

    A new strategy for the enantioseparation of D,L-amino acids employing the principle of ligand exchange capillary electrophoresis with Zn(II)-L-valine complex as a chiral selecting system in the presence of beta-cyclodextrin has been designed. Successful enantioseparation of label free and labeled amino acids have been achieved with a buffer of 100.0mM boric acid, 5.0mM ammonium acetate, 4.0mM beta-cyclodextrin, 4.0mM ZnSO(4) and 8.0mM L-valine at pH 8.1. This new method was shown to be applicable to the quantitative analysis of label free D- and L-aromatic amino acids. Furthermore, the expanding enzymatic use of L-amino acid oxidase to incubate with different L-amino acids has allowed understanding of the substrate's specificity. An on-column incubation assay has been developed to study the L-amino acid oxidase's catalytic efficiency. It was demonstrated that the enzyme kinetic constant could be determined by using this new method. PMID:20441938

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

    PubMed

    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. PMID:12099878

  18. A voltage-dependent outward current with fast kinetics in single smooth muscle cells isolated from rabbit portal vein.

    PubMed

    Beech, D J; Bolton, T B

    1989-05-01

    1. Single smooth muscle cells were isolated enzymatically from the rabbit portal vein. They were voltage-clamped at room temperature using the whole-cell configuration of the patch-clamp technique. 2. When cells were bathed in physiological salt solution, depolarization from a holding potential of -70 mV elicited a time-dependent outward current which reached a maximum within 0.2-0.5 s, but when a more negative holding potential was used, an additional outward current could be activated. The current (Ifo) developed rapidly, was transient and seemed to be carried by potassium ions (K+). 3. The steady-state inactivation plot for Ifo was steeply voltage-dependent between -90 and -60 mV, current being 50% inactivated at -78 mV. The activation threshold was around -65 mV. The activation and inactivation kinetics were fast and voltage-dependent. When the test potential was -35 mV, peak current occurred after about 15 ms and the decay was complete within 250 ms. Recovery from inactivation was maximal after 1 s at -100 mV but was about five times slower at -70 mV. 4. The outward current Ifo was blocked completely by 4-aminopyridine (5 mM) or phencyclidine (0.1 mM), but was insensitive to tetraethylammonium ions (32 mM), apamin (0.1 microM), charybdotoxin from the venom of Leiurus quinquestriatus (0.1 microM), toxin-I from the venom of Dendroaspis polylepis (1 microM) or the putative K+ channel opener, cromakalim (10 microM). 5. The steady-state inactivation range and activation threshold, kinetics of activation and inactivation all showed a marked dependence on the concentration of divalent cations in the bathing solution. This effect was consistent with the hypothesis that Ifo was affected by membrane surface potential. The current did not seem to be Ca2+-activated. 6. Ifo closely resembled the A-current which has been described previously in neurones but not in smooth muscle. PMID:2600838

  19. An instrument for time resolved monitoring of fast chemical transitions: Application to the kinetics of refolding of a globular protein

    NASA Astrophysics Data System (ADS)

    Ratner, Vladimir; Haas, Elisha

    1998-05-01

    The dynamics of kinetic intermediates of protein folding can be studied by time resolved measurements of nonradiative excitation energy transfer, in site-specific labeled protein derivatives, combined with fast mixing experiments. A new device based on the single pulse approach was developed. This experiment is performed over two time scales: the "chemical time scale" of the conformational changes (milliseconds), defined by the rates of changes of conformations in the sample, and the "spectroscopic time scale" (nanoseconds) defined by the lifetimes of the excited states of the fluorescent probes. The chemical process was synchronized by means of a fast mixing stopped flow device. The low cost laser used here is suitable for use with dyes with excitation wavelengths of 337 nm and higher. Up to 20 fluorescence decay curves per second, can be measured within a single stopped flow run. Each fluorescence decay curve is recorded within 250 ns or more. The time resolution (of the spectroscopic time scale) was 0.5 ns. The noise level is low enough to estimate distance distributions from energy transfer experiments, provided that the shortest changeable lifetime component of the fluorescence decay of the donor probes would not be lower than ˜4 ns. The amount of double labeled protein which should be used for each experiment in order to obtain a full data set, with time resolution of 10 ms during protein transition, is only fourfold more than the amount needed for a stopped flow study with steady state fluorescence monitoring. The results obtained for refolding of α-lactalbumin in the presence of 1,8-anilino-naphthalene sulfonic acid from the GuHCl induced denatured state, support the model in which the probe has two states. The first state, is characterized by a fluorescence lifetime of 14.2±0.5 ns and the second by a fluorescence lifetime of 0.5±0.4 ns or less. During refolding the dye is transferred from the first state to the second, at a rate that coincides with the

  20. Measurement of blood protease kinetic parameters with self-assembled monolayer ligand binding assays and label-free MALDI-TOF MS.

    PubMed

    Patrie, Steven M; Roth, Michael J; Plymire, Daniel A; Maresh, Erica; Zhang, Junmei

    2013-11-01

    We report novel ligand binding assay (LBA) surface modalities that permit plasma protease catalytic efficiency (kcat/km) determination by MALDI-TOF MS without the use of liquid chromatography or internal standards such as chemical or metalized labels. Two model LBAs were constructed on planar self-assembled monolayers (SAMs) and used to evaluate the clinically relevant metalloprotease ADAMTS-13 kinetics in plasma. The SAM chemistries were designed to improve biosampling efficiency by minimization of nonspecific adsorption of abundant proteins present at ~100,000× the concentration of the endogenous enzyme. In the first protocol, in-solution digestion of the ADAMTS-13 substrate (vWFh) was performed with immunoaffinity enrichment of the reaction substrate and product to SAM arrays. The second configuration examined protease kcat/km via a surface digestion modality where different substrates were covalently immobilized to the SAM at controlled surface density for optimized protease screens. The results show the MALDI-TOF MS LBA platforms provide limits of quantitation to ~1% protease activity (~60 pM enzyme concentration) in <1 h analysis time, a ~16× improvement over other MS-based LBA formats. Implementation of a vacuum-sublimed MALDI matrix provided good MALDI-TOF MS intra- and interday repeatability, ~1.2 and ~6.6% RSD, respectively. Platform reliability permitted kcat/km determination without internal standards with observed values ~10× improved versus conventional fluorophoric assays. Application of the assays to 12 clinical plasma samples demonstrated proof-of-concept for clinical applications. Overall, this work demonstrates that rationally designed surface chemistries for MALDI-TOF MS may serve as an alternative, label-free methodology with potential for a wide range of biotechnology applications related to targeted enzyme molecular diagnostics. PMID:24107006

  1. Dynamics of methionine ligand rebinding in cytochrome c.

    PubMed

    Zhang, Ping; Małolepsza, Edyta; Straub, John E

    2012-06-14

    Geminate recombination of the methionine ligand to the heme iron in ferrous cytochrome c protein following photodissociation displays rich kinetics. It is of particular interest to develop an understanding of fast and slow rebinding time scales, observed in experimental studies, in terms of features of the underlying complex energy landscape. The classical empirical force field in the heme pocket has been extended by incorporating ab initio potential energy surface calculations representing the ground singlet state and quintet state associated with methionine bond breaking and rebinding. An algorithm based on the Landau-Zener nonadiabatic transition theory has been employed to model the electronic surface hopping between two spin states during the process of ligand dissociation and recombination. Multiple conformational substates of the dissociated methionine ligand are found to participate in the reaction dynamics. Varying time scales for interconversion between substates lead to a mechanism elucidating the fast and slow rebinding time scales. The reaction system may be understood in terms of a two-dimensional reaction coordinate distinctly separated from the coupled bath of surrounding protein and solvent degrees of freedom. Insights into the reaction dynamics provided by this study lead to suggestions for future experiments to further probe the role of dynamic heterogeneity in the kinetics of ligand-protein binding. PMID:22432601

  2. Kinetic analysis of the interactions of complement receptor 2 (CR2, CD21) with its ligands C3d, iC3b, and the EBV glycoprotein gp350/220.

    PubMed

    Sarrias, M R; Franchini, S; Canziani, G; Argyropoulos, E; Moore, W T; Sahu, A; Lambris, J D

    2001-08-01

    The molecular mechanisms involved in the interaction of complement receptor 2 (CR2) with its natural ligands iC3b and C3d are still not well understood. In addition, studies regarding the binding site(s) of the receptor on C3 as well as the affinities of the C3 fragments for CR2 have produced contradictory results. In the present study, we have used surface plasmon resonance technology to study the interaction of CR2 with its ligands C3d, iC3b, and the EBV surface glycoprotein gp350/220. We measured the kinetics of binding of the receptor to its ligands, examined the influence of ionic contacts on these interactions, and assessed whether immobilized and soluble iC3b bound with similar kinetics to CR2. Our results indicate that 1) gp350 binding to CR2 follows a simple 1:1 interaction, whereas that of the C3 fragments is more complex and involves more than one intramolecular component; 2) kinetic differences exist between the binding of C3d and iC3b to CR2, which may be due to an additional binding site found on the C3c region of iC3b; and 3) iC3b binds to CR2 with different kinetics, depending on whether the iC3b is in solution or immobilized on the surface. These findings suggest that binding of CR2 to iC3b and C3d is more complex than previously thought. PMID:11466369

  3. Structural and theoretical basis for ligand exchange on thiolate monolayer protected gold nanoclusters.

    PubMed

    Heinecke, Christine L; Ni, Thomas W; Malola, Sami; Mäkinen, Ville; Wong, O Andrea; Häkkinen, Hannu; Ackerson, Christopher J

    2012-08-15

    Ligand exchange reactions are widely used for imparting new functionality on or integrating nanoparticles into devices. Thiolate-for-thiolate ligand exchange in monolayer protected gold nanoclusters has been used for over a decade; however, a firm structural basis of this reaction has been lacking. Herein, we present the first single-crystal X-ray structure of a partially exchanged Au(102)(p-MBA)(40)(p-BBT)(4) (p-MBA = para-mercaptobenzoic acid, p-BBT = para-bromobenzene thiol) with p-BBT as the incoming ligand. The crystal structure shows that 2 of the 22 symmetry-unique p-MBA ligand sites are partially exchanged to p-BBT under the initial fast kinetics in a 5 min timescale exchange reaction. Each of these ligand-binding sites is bonded to a different solvent-exposed Au atom, suggesting an associative mechanism for the initial ligand exchange. Density functional theory calculations modeling both thiol and thiolate incoming ligands postulate a mechanistic pathway for thiol-based ligand exchange. The discrete modification of a small set of ligand binding sites suggests Au(102)(p-MBA)(44) as a powerful platform for surface chemical engineering. PMID:22816317

  4. The V499G/Y501H Mutation Impairs Fast Motor Kinetics of Prestin and Has Significance for Defining Functional Independence of Individual Prestin Subunits*

    PubMed Central

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

    2013-01-01

    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. PMID:23212912

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

    ERIC Educational Resources Information Center

    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…

  6. Recognition of some lanthanides, actinides, and transition- and heavy-metal cations by N-donor ligands: thermodynamic and kinetic aspects.

    PubMed

    Hubscher-Bruder, Véronique; Haddaoui, Jaouad; Bouhroum, Saliha; Arnaud-Neu, Françoise

    2010-02-15

    The remarkable actinide(III) selectivity of the polyaromatic N-donors bis-triazine-pyridines (BTPs), hemi-bis-triazine-pyridines (hemi-BTPs) and bis-triazine-bipyridines (BTBPs) make these ligands the most promising candidates in partitioning and transmutation processes developed so far to better manage nuclear waste. The interactions of n-Pr-BTP, C(5)-hemi-BTP, and the two most extensively investigated BTBPs (C(5)-BTBP and CyMe(4)-BTBP) have been studied with some representative lanthanide(III), uranyl, thorium, and transition- and other heavy-metal cations in methanol. The formation of complexes of different stoichiometries, the stability of which depended on both the ligands and the cations, was shown using UV absorption spectrophotometry. Study of the complexation reactions of La(3+), Eu(3+) and Yb(3+) with these four ligands by stopped-flow spectrophotometry allowed determination of the rate constants and postulation of possible complexation mechanisms. PMID:20055507

  7. LIGKA: A linear gyrokinetic code for the description of background kinetic and fast particle effects on the MHD stability in tokamaks

    SciTech Connect

    Lauber, Ph. Guenter, S.; Koenies, A.; Pinches, S.D.

    2007-09-10

    In a plasma with a population of super-thermal particles generated by heating or fusion processes, kinetic effects can lead to the additional destabilisation of MHD modes or even to additional energetic particle modes. In order to describe these modes, a new linear gyrokinetic MHD code has been developed and tested, LIGKA (linear gyrokinetic shear Alfven physics) [Ph. Lauber, Linear gyrokinetic description of fast particle effects on the MHD stability in tokamaks, Ph.D. Thesis, TU Muenchen, 2003; Ph. Lauber, S. Guenter, S.D. Pinches, Phys. Plasmas 12 (2005) 122501], based on a gyrokinetic model [H. Qin, Gyrokinetic theory and computational methods for electromagnetic perturbations in tokamaks, Ph.D. Thesis, Princeton University, 1998]. A finite Larmor radius expansion together with the construction of some fluid moments and specification to the shear Alfven regime results in a self-consistent, electromagnetic, non-perturbative model, that allows not only for growing or damped eigenvalues but also for a change in mode-structure of the magnetic perturbation due to the energetic particles and background kinetic effects. Compared to previous implementations [H. Qin, mentioned above], this model is coded in a more general and comprehensive way. LIGKA uses a Fourier decomposition in the poloidal coordinate and a finite element discretisation in the radial direction. Both analytical and numerical equilibria can be treated. Integration over the unperturbed particle orbits is performed with the drift-kinetic HAGIS code [S.D. Pinches, Ph.D. Thesis, The University of Nottingham, 1996; S.D. Pinches et al., CPC 111 (1998) 131] which accurately describes the particles' trajectories. This allows finite-banana-width effects to be implemented in a rigorous way since the linear formulation of the model allows the exchange of the unperturbed orbit integration and the discretisation of the perturbed potentials in the radial direction. Successful benchmarks for toroidal Alfven

  8. Simultaneous Measurements of Fast Optical and Proton Current Kinetics in the Bacteriorhodopsin Photocycle using an Enhanced Spectrophotometer

    PubMed Central

    Kakareka, John W.; Smith, Paul D.; Pohida, Thomas J.; Hendler, Richard W.

    2008-01-01

    A one-of-a-kind high speed optical multichannel spectrometer was designed and built at NIH and described in this journal in 1997 [Cole et al. Vol 35, pages 161–174]. The most unique aspect of this instrument was the ability to follow an entire time course from a single activation using a single sample. The instrument has been used to study rapid kinetic processes in the photon-driven bacteriorhodopsin photocycle and electron transport from cytochrome c to cytochrome aa3 and from cytochrome aa3 to oxygen. The present paper describes a second generation instrument with a number of important enhancements which significantly improve its capabilities for multichannel kinetic studies. An example application is presented in which the kinetics of photon-induced proton flow across the biological membrane is measured simultaneously with the individual steps of the photocycle determined optically. Matching the time constants for the two processes indicates which molecular transformations are associated with major proton movements. PMID:18160131

  9. Stopped-flow kinetics of pH-responsive polyamine latexes: how fast is the latex-to-microgel transition?

    PubMed

    Morse, A J; Armes, S P; Mills, P; Swart, R

    2013-12-10

    Four poly(ethylene glycol)-stabilized polyamine latexes, namely, poly(2-vinylpyridine) (P2VP), poly(2-(tert-butylamino)ethyl methacrylate) (PTBAEMA), poly(2-(diethylamino)ethyl methacrylate) (PDEA), and poly(2-(diisopropylamino)ethyl methacrylate) (PDPA) were prepared via emulsion copolymerization using divinylbenzene (DVB) as a cross-linker at 0.80 mol % for all formulations. According to dynamic light scattering studies, the resulting latexes were near-monodisperse and had approximately constant hydrodynamic diameters of 205-220 nm at pH 10; a latex-to-microgel transition was observed at around the respective pKa of each polyamine on addition of acid. The kinetics of swelling of each latex was investigated by the pH-jump method using a commercial stopped-flow instrument. The most rapid swelling was observed for the P2VP latex, which exhibited a characteristic swelling time (t*) of 5 ms. The corresponding t* values for PTBAEMA and PDEA were 25 and 35 ms, respectively, whereas the PDPA particles exhibited significantly slower swelling kinetics (t* = 180 ms). These t* values could not be correlated with either the latex Tg or the polyamine pKa. However, there is a positive correlation between t* and the repeat unit mass of the amine monomer, which suggests that the cationic charge density of the protonated polymer chains may influence the kinetics of swelling. Alternatively, the observed differences in swelling kinetics may simply reflect subtle differences in the DVB cross-link density, with more uniformly cross-linked latexes being capable of responding more quickly to a pH jump. The kinetics of deswelling for the corresponding microgel-to-latex transition was also briefly investigated for the PTBAEMA and P2VP particles. In both cases, much slower rates of deswelling were observed. This suggests that a latexlike "skin" is formed on the outer surface of the microgel particles during their deprotonation, which significantly retards the excretion of both salt and

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

    NASA Technical Reports Server (NTRS)

    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.

  11. Ligand Migration and Binding in Myoglobin Mutant L29W

    NASA Astrophysics Data System (ADS)

    Nienhaus, G. Ulrich; Waschipky, Robert; Nienhaus, Karin; Minkow, Oleksandr; Ostermann, Andreas; Parak, Fritz G.

    2001-09-01

    Myoglobin, a small globular heme protein that binds gaseous ligands such as O2, CO, and NO reversibly at the heme iron, has for many years been a paradigm for studying the effects of structure and dynamics on protein reactions. Time-resolved spectroscopic measurements after photodissociation of the ligand reveal a complex ligand binding reaction with multiple kinetic intermediates, resulting from protein relaxation and movements of the ligand within the protein. To observe structural changes induced by ligand dissociation, we have investigated carbonmonoxy myoglobin (MbCO) mutant L29W using time-resolved infrared spectroscopy in combination with x-ray crystallography. The presence of two distinct infrared stretch bands of the bound CO, AI at 1945 cm-1 and AII at 1955 cm-1, implies that L29W MbCO assumes two different conformations at neutral pH. Low-temperature flash photolysis experiments with monitoring of the absorption changes in the individual CO lines reveal markedly different rebinding properties. While recombination in AII is conceptually simple and well described by a two-state transition involving a distribution of enthalpy barriers, recombination in AI is more complicated: Besides a fast kinetic component, a second, slower kinetic component appears; its population grows with increasing temperature. X-ray crystallography of crystals illuminated below 180 K to photodissociate the CO reveals that the slow component arises from ligands that have migrated from their initial docking site to a remote site within the distal heme pocket. This process occurs in an essentially immobilized, frozen protein. Subsequently, ligands rebind by thermal activation over a barrier that is much higher than the barrier for recombination from the initial docking site. Upon photodissociation above 180 K, ligands escape from the distal pocket, aided by protein fluctuations that transiently open exit channels. The x-ray structure shows a large proportion of ligands in a cavity on

  12. Coherent anti-Stokes Raman scattering microspectroscopic kinetic study of fast hydrogen bond formation in microfluidic devices.

    PubMed

    Oshovsky, Gennady V; Rago, Gianluca; Day, James P R; Soudijn, Maarten L; Rock, William; Parekh, Sapun H; Ciancaleoni, Gianluca; Reek, Joost N H; Bonn, Mischa

    2013-10-01

    The kinetics of a key noncovalent, hydrogen bonding interaction was studied in situ using coherent anti-stokes Raman scattering (CARS) microspectroscopy in a microfluidic device. The association of model compounds, pyridine and hexafluoroisopropanol, was quantitatively monitored with submicrometer resolution. Lower limits for the very high formation and dissociation rate constants of the model 1:1 pyridine-hexafluoroisopropanol hydrogen bonded complex in dichloromethane-d2 were determined to be k1 > 10(5) M(-1)s(-1) and k-1 > 333.3 s(-1), respectively. PMID:23987583

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

    NASA Astrophysics Data System (ADS)

    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.

  14. In Situ TEM Observations of Sn-Containing Silicon Nanowires Undergoing Reversible Pore Formation Due to Fast Lithiation/Delithiation Kinetics

    SciTech Connect

    Lu, Xiaotang; Bogart, Timothy D.; Gu, Meng; Wang, Chong M.; Korgel, Brian

    2015-09-03

    In situ transmission electron microscopy (TEM) studies were carried out to observe directly in real time the lithiation and delithiation of silicon (Si) nanowires with significant amounts of tin (Sn). The incorporation of Sn significantly enhances the lithiation rate compared to typical Si nanowires. For instance, surface diffusion is enhanced by two orders of magnitude and the bulk lithiation rate by one order of magnitude, resulting in a sequential surface-then-core lithiation mechanism. Pore formation was observed in the nanowires during delithiation, most likely as a result of the fast delithiation kinetics of the nanowires. Pore formation was reversible and the pores disappeared during subsequent lithiation. When an amorphous Si shell was applied to the nanowires, pore formation was not observed during the in situ TEM experimences. Ex situ TEM analysis of Sn-containing Si nanowires cycled in coin cell batteries also showed that the application of an a-Si shell significantly retards pore formation in these nanowires.

  15. Fast Prediction of HCCI and PCCI Combustion with an Artificial Neural Network-Based Chemical Kinetic Model

    SciTech Connect

    Piggott, W T; Aceves, S M; Flowers, D L; Chen, J Y

    2007-09-26

    We have added the capability to look at in-cylinder fuel distributions using a previously developed ignition model within a fluid mechanics code (KIVA3V) that uses an artificial neural network (ANN) to predict ignition (The combined code: KIVA3V-ANN). KIVA3V-ANN was originally developed and validated for analysis of Homogeneous Charge Compression Ignition (HCCI) combustion, but it is also applicable to the more difficult problem of Premixed Charge Compression Ignition (PCCI) combustion. PCCI combustion refers to cases where combustion occurs as a nonmixing controlled, chemical kinetics dominated, autoignition process, where the fuel, air, and residual gas mixtures are not necessarily as homogeneous as in HCCI combustion. This paper analyzes the effects of introducing charge non-uniformity into a KIVA3V-ANN simulation. The results are compared to experimental results, as well as simulation results using a more physically representative and computationally intensive code (KIVA3V-MPI-MZ), which links a fluid mechanics code to a multi-zone detailed chemical kinetics solver. The results indicate that KIVA3V-ANN produces reasonable approximations to the more accurate KIVA3V-MPI-MZ at a much reduced computational cost.

  16. Fast self-assembly kinetics of alkanethiols on gold nanoparticles: simulation and characterization by localized surface plasmon resonance spectroscopy

    NASA Astrophysics Data System (ADS)

    Asiaei, Sasan; Denomme, Ryan C.; Marr, Chelsea; Nieva, Patricia M.; Vijayan, Mathilakath M.

    2012-03-01

    This study demonstrates improved kinetics for the formation of self-assembled monolayers (SAMs) of alkanethiols on gold nanoparticle substrates. A computational model was developed to predict SAM growth kinetics. Based on the predictions from the model, SAMs of 11-mercaptoundecanoic acid (11-MUA) and 1-octanethiol (1-OT) were formed by incubation of gold nanoparticle chips in an ethanolic 10 mM solution within 20 min. The performance of this novel rapid SAM formation protocol was compared with a conventional 24 hour incubation protocol. Binding capacity of the alkanethiol SAM was investigated for a 20 min incubation protocol using biotin-streptavidin. For this purpose, the SAM loaded gold nanoparticle chips were modified with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) to allow attachment of EZ-Link amine PEG3 biotin to the 11-MUA molecules. Binding reactions were monitored in real time using localized surface plasmon resonance (LSPR) spectroscopy. The resulting LSPR absorbance peak shift was comparable to the experimental results for biotin-streptavidin reported in literature. Results of this study suggest that formation of a high quality alkanethiol SAM within 20 min on gold nanoparticles surfaces is possible and could greatly reduce the time and cost compared to conventional 24 h incubation protocols.

  17. Crystal structures and DFT calculations of new chlorido-dimethylsulfoxide-M(III) (M = Ir, Ru, Rh) complexes with the N-pyrazolyl pyrimidine donor ligand: kinetic vs. thermodynamic isomers.

    PubMed

    Cánaves, María M; Cabra, María I; Bauzá, Antonio; Cañellas, Pablo; Sánchez, Kika; Orvay, Francisca; García-Raso, Angel; Fiol, Juan J; Terrón, Angel; Barceló-Oliver, Miquel; Ballester, Pablo; Mata, Ignasi; Molins, Elies; Hussain, Firasat; Frontera, Antonio

    2014-05-01

    New chlorido-dimethylsulfoxide-iridium(III), ruthenium(III) and rhodium(III) complexes with the 2-(1H-pyrazol-1-yl)-pyrimidine (pyrapyr) ligand (OC-6-N1)-[Rh(III)Cl3(DMSO-κS)(pyrapyr)] (1a, N = 3 and 1b, N = 4); (OC-6-N1)-[Ru(III)Cl3(DMSO-κS)(pyrapyr)] (2a, N = 3 and 2b, N = 4) and (OC-6-N1)-[Ir(III)Cl3(DMSO-κS)(pyrapyr)] (3a, N = 3 and 3b, N = 4) have been synthesized and characterized by spectroscopic techniques and by single crystal X-ray diffraction studies (1a, 1b, 2a, 2b, a disordered crystal 3a/3b and a cocrystal 3a·3b). In all cases, the metal centers show octahedral geometry coordinated to three chloride ligands and one S coordinated dimethylsulfoxide (DMSO-κS). The coordination sphere of the metal is completed by the pyrapyr molecule. Two different coordination modes are observed: (i) the DMSO-κS is opposite to the pyrimidinic N atom (IUPAC nomenclature is OC-6-31 denoted herein as trans); (ii) DMSO-κS is opposite to the pyrazolic N atom (IUPAC nomenclature is OC-6-41 denoted as cis). For Rh(III) the kinetic product (cis) yields the thermodynamic (trans) upon heating a solution of the kinetic product and both isomers have been X-ray characterized. Conversely for Ru(III), both kinetic and thermodynamic complexes have been obtained by using different procedures. Both isomers have been characterized by X-ray crystallography and the kinetic product does not yield the thermodynamic upon heating a solution of the former. Furthermore, the Ir(III) behaves differently, since both isomers are energetically equivalent and both isomers co-crystallize in the solid state. The kinetic/thermodynamic mechanism that yields the different isomers has been studied by using theoretical DFT calculations for each metal. Finally, two Ru(II) complexes (OC-6-N1)-[Ru(II)Cl2(DMSO-κS)2(pyrapyr)] (1a, N = 3 and 4b, N = 4) are also described and X-ray characterized. They were obtained as minor products during the synthesis of 2a. PMID:24599509

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

    PubMed

    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. PMID:26632764

  19. Monte-Carlo simulation of the kinetics of nuclear and radiative processes upon fast ignition of the fusion target in a `double liner' system

    NASA Astrophysics Data System (ADS)

    Andreev, Aleksandr A.; Gus'kov, Sergei Yu; Zakharov, S. V.; Il'in, Dmitrii V.; Levkovskii, Aleksei A.; Platonov, Konstantin Yu; Rozanov, Vladislav B.; Sherman, Vladimir E.

    2004-05-01

    A laser ignition scheme is considered for a fusion target placed in the cavity of a radiating plasma liner produced in a `double liner' system. It is shown that this scheme can be employed to realise an efficient thermonuclear burst. The precompression and heating of a deuterium — tritium target with an iron shell by a thermal radiation pulse was simulated using the TRITON mathematical code for the parameters of the Z-generator at the Sandia National Laboratories (USA). Laser and target parameters were optimised for the ignition of the deuterium — tritium fuel by protons accelerated by laser radiation. The propagation of the thermonuclear burning wave during the fast ignition was calculated employing the TERA mathematical code, which involves Monte-Carlo simulation of the kinetics of fast thermonuclear particles and hard gamma-ray quanta at each time step of hydrodynamic calculations. The dependence of the fusion energy gain G on the ignition energy is theoretically explained. The laser parameters required to obtain G gg 1 are determined.

  20. Kinetic Energy Release of the Singly and Doubly Charged Methylene Chloride Molecule: The Role of Fast Dissociation.

    PubMed

    Alcantara, K F; Rocha, A B; Gomes, A H A; Wolff, W; Sigaud, L; Santos, A C F

    2016-09-01

    The center of mass kinetic energy release distribution (KERD) spectra of selected ionic fragments, formed through dissociative single and double photoionization of CH2Cl2 at photon energies around the Cl 2p edge, were extracted from the shape and width of the experimentally obtained time-of-flight (TOF) distributions. The KERD spectra exhibit either smooth profiles or structures, depending on the moiety and photon energy. In general, the heavier the ionic fragments, the lower their average KERDs are. In contrast, the light H(+) fragments are observed with kinetic energies centered around 4.5-5.5 eV, depending on the photon energy. It was observed that the change in the photon energy involves a change in the KERDs, indicating different processes or transitions taking place in the breakup process. In the particular case of double ionization with the ejection of two charged fragments, the KERDs present have characteristics compatible with the Coulombic fragmentation model. Intending to interpret the experimental data, singlet and triplet states at Cl 2p edge of the CH2Cl2 molecule, corresponding to the Cl (2p → 10a1*) and Cl (2p → 4b1*) transitions, were calculated at multiconfigurational self-consistent field (MCSCF) level and multireference configuration interaction (MRCI). These states were selected to form the spin-orbit coupling matrix elements, which after diagonalization result in a spin-orbit manifold. Minimum energy pathways for dissociation of the molecule were additionally calculated aiming to give support to the presence of the ultrafast dissociation mechanism in the molecular breakup. PMID:27523328

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

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

    2016-01-01

    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. PMID:27321702

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

    PubMed Central

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

    2016-01-01

    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. PMID:27321702

  4. Spectrophotometric method for fast quantification of ascorbic acid and dehydroascorbic acid in simple matrix for kinetics measurements.

    PubMed

    Gómez Ruiz, Braulio; Roux, Stéphanie; Courtois, Francis; Bonazzi, Catherine

    2016-11-15

    A simple, rapid and reliable method was developed for quantifying ascorbic (AA) and dehydroascorbic (DHAA) acids and validated in 20mM malate buffer (pH 3.8). It consists in a spectrophotometric measurement of AA, either directly on the solution added with metaphosphoric acid or after reduction of DHAA into AA by dithiothreitol. This method was developed with real time measurement of reactions kinetics in bulk reactors in mind, and was checked in terms of linearity, limits of detection and quantification, fidelity and accuracy. The linearity was found satisfactory on the range of 0-6.95mM with limits of detection and quantification of 0.236mM and 0.467mM, respectively. The method was found acceptable in terms of fidelity and accuracy with a coefficient of variation for repeatability and reproducibility below 6% for AA and below 15% for DHAA, and with a recovery range of 97-102% for AA and 88-112% for DHAA. PMID:27283671

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

    PubMed

    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

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

    NASA Astrophysics Data System (ADS)

    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

  7. Kinetic isotope effect studies on the de novo rate of chromophore formation in fast- and slow-maturing GFP variants†

    PubMed Central

    Pouwels, Lauren J.; Zhang, Liping; Chan, Nam H.; Dorrestein, Pieter C.; Wachter, Rebekka M.

    2009-01-01

    The maturation process of green fluorescent protein (GFP) entails a protein oxidation reaction triggered by spontaneous backbone condensation. The chromophore is generated by full conjugation of the Tyr66 phenolic group with the heterocycle, a process that requires C-H bond scission at the benzylic carbon. We have prepared isotope-enriched protein bearing tyrosine residues deuterated at the beta carbon, and have determined kinetic isotope effects (KIEs) on the GFP self-processing reaction. Progress curves for the production of H2O2 and the mature chromophore were analyzed by global curve fitting to a three-step mechanism describing pre-oxidation, oxidation and post-oxidation events. Although a KIE for protein oxidation could not be discerned (kH/kD = 1.1 ± 0.2), a full primary KIE of 5.9 (± 2.8) was extracted for the post-oxidation step. Therefore, the exocyclic carbon is not involved in the reduction of molecular oxygen. Rather, C-H bond cleavage proceeds from the oxidized cyclic imine form, and is the rate-limiting event of the final step. Substantial pH-dependence of maturation was observed upon substitution of the catalytic glutamate (E222Q), indicating an apparent pKa of 9.4 (± 0.1) for the base catalyst. For this variant, a KIE of 5.8 (± 0.4) was determined for the intrinsic time constant that is thought to describe the final step, as supported by ultra-high resolution mass spectrometric results. The data are consistent with general base catalysis of the post-oxidation events yielding green color. Structural arguments suggest a mechanism in which the highly conserved Arg96 serves as catalytic base in proton abstraction from the Tyr66-derived beta carbon. PMID:18759496

  8. Kinetic isotope effect studies on the de novo rate of chromophore formation in fast- and slow-maturing GFP variants.

    PubMed

    Pouwels, Lauren J; Zhang, Liping; Chan, Nam H; Dorrestein, Pieter C; Wachter, Rebekka M

    2008-09-23

    The maturation process of green fluorescent protein (GFP) entails a protein oxidation reaction triggered by spontaneous backbone condensation. The chromophore is generated by full conjugation of the Tyr66 phenolic group with the heterocycle, a process that requires C-H bond scission at the benzylic carbon. We have prepared isotope-enriched protein bearing tyrosine residues deuterated at the beta carbon, and have determined kinetic isotope effects (KIEs) on the GFP self-processing reaction. Progress curves for the production of H 2O 2 and the mature chromophore were analyzed by global curve fitting to a three-step mechanism describing preoxidation, oxidation and postoxidation events. Although a KIE for protein oxidation could not be discerned ( k H/ k D = 1.1 +/- 0.2), a full primary KIE of 5.9 (+/-2.8) was extracted for the postoxidation step. Therefore, the exocyclic carbon is not involved in the reduction of molecular oxygen. Rather, C-H bond cleavage proceeds from the oxidized cyclic imine form, and is the rate-limiting event of the final step. Substantial pH-dependence of maturation was observed upon substitution of the catalytic glutamate (E222Q), indicating an apparent p K a of 9.4 (+/-0.1) for the base catalyst. For this variant, a KIE of 5.8 (+/-0.4) was determined for the intrinsic time constant that is thought to describe the final step, as supported by ultra-high resolution mass spectrometric results. The data are consistent with general base catalysis of the postoxidation events yielding green color. Structural arguments suggest a mechanism in which the highly conserved Arg96 serves as catalytic base in proton abstraction from the Tyr66-derived beta carbon. PMID:18759496

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

    PubMed

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

    2016-04-14

    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. PMID:26984451

  10. Role of the Fast Kinetics of Pyroglutamate-Modified Amyloid-β Oligomers in Membrane Binding and Membrane Permeability

    PubMed Central

    2015-01-01

    Membrane permeability to ions and small molecules is believed to be a critical step in the pathology of Alzheimer’s disease (AD). Interactions of oligomers formed by amyloid-β (Aβ) peptides with the plasma cell membrane are believed to play a fundamental role in the processes leading to membrane permeability. Among the family of Aβs, pyroglutamate (pE)-modified Aβ peptides constitute the most abundant oligomeric species in the brains of AD patients. Although membrane permeability mechanisms have been studied for full-length Aβ1–40/42 peptides, these have not been sufficiently characterized for the more abundant AβpE3–42 fragment. Here we have compared the adsorbed and membrane-inserted oligomeric species of AβpE3–42 and Aβ1–42 peptides. We find lower concentrations and larger dimensions for both species of membrane-associated AβpE3–42 oligomers. The larger dimensions are attributed to the faster self-assembly kinetics of AβpE3–42, and the lower concentrations are attributed to weaker interactions with zwitterionic lipid headgroups. While adsorbed oligomers produced little or no significant membrane structural damage, increased membrane permeabilization to ionic species is understood in terms of enlarged membrane-inserted oligomers. Membrane-inserted AβpE3–42 oligomers were also found to modify the mechanical properties of the membrane. Taken together, our results suggest that membrane-inserted oligomers are the primary species responsible for membrane permeability. PMID:24950761

  11. Kinetics of complex formation by macrocyclic polyaza polycarboxylate ligands: Detection and characterization of an intermediate in the Eu{sup 3+}-dota system by laser-excited luminescence

    SciTech Connect

    Wu, Shu Ling; Horrocks, W.DeW. Jr.

    1995-07-05

    The reaction of Eu{sup 3+} with 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetate was followed by luminescence of the Eu{sup 3+} center. Reaction kinetics for the formation of intermediates and the final product, [Eu(dota)H{sub 2}O]{sup {minus}}, are reported. The rate limiting step is found to be the rearrangement of EuHdotato from the final product.

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

    PubMed Central

    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. PMID:23982332

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

    PubMed

    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. PMID:26964888

  14. Real-time investigation of human topoisomerase I reaction kinetics using an optical sensor: a fast method for drug screening and determination of active enzyme concentrations

    NASA Astrophysics Data System (ADS)

    Kristoffersen, Emil L.; Jørgensen, Line A.; Franch, Oskar; Etzerodt, Michael; Frøhlich, Rikke; Bjergbæk, Lotte; Stougaard, Magnus; Ho, Yi-Ping; Knudsen, Birgitta R.

    2015-05-01

    Human DNA topoisomerase I (hTopI) is a nuclear enzyme that catalyzes relaxation of super helical tension that arises in the genome during essential DNA metabolic processes. This is accomplished through a common reaction mechanism shared among the type IB topoisomerase enzymes, including eukaryotic and poxvirus topoisomerase I. The mechanism of hTopI is specifically targeted in cancer treatment using camptothecin derivatives. These drugs convert the hTopI activity into a cellular poison, and hence the cytotoxic effects of camptothecin derivatives correlate with the hTopI activity. Therefore, fast and reliable techniques for high throughput measurements of hTopI activity are of high clinical interest. Here we demonstrate potential applications of a fluorophore-quencher based DNA sensor designed for measurement of hTopI cleavage-ligation activities, which are the catalytic steps affected by camptothecin. The kinetic analysis of the hTopI reaction with the DNA sensor exhibits a characteristic burst profile. This is the result of a two-step ping-pong reaction mechanism, where a fast first reaction, the one creating the signal, is followed by a slower second reaction necessary for completion of the catalytic cycle. Hence, the burst profile holds information about two reactions in the enzymatic mechanism. Moreover, it allows the amount of active enzyme in the reaction to be determined. The presented results pave the way for future high throughput drug screening and the potential of measuring active hTopI concentrations in clinical samples for individualized treatment.Human DNA topoisomerase I (hTopI) is a nuclear enzyme that catalyzes relaxation of super helical tension that arises in the genome during essential DNA metabolic processes. This is accomplished through a common reaction mechanism shared among the type IB topoisomerase enzymes, including eukaryotic and poxvirus topoisomerase I. The mechanism of hTopI is specifically targeted in cancer treatment using

  15. A DFT study to unravel the ligand exchange kinetics and thermodynamics of Os(VIII) oxo/hydroxido/aqua complexes in aqueous matrices.

    PubMed

    van Niekerk, Daniel M E; Gerber, Wilhelmus J; Koch, Klaus R

    2016-04-19

    The Os(VIII) oxo/hydroxido complexes that are abundant in mild to relatively concentrated basic aqueous solutions are Os(VIII)O4, [Os(VIII)O4(OH)](-) and two cis-[Os(VIII)O4(OH)2](2-) species. Os(VIII) complexes that contain water ligands are thermodynamically unfavoured w.r.t. the abovementioned species. Os(VIII)O4 reacts with hydroxide in two, consecutive, elementary coordination sphere expansion steps to form the [Os(VIII)O4(OH)](-) complex and then the cis-[Os(VIII)O4(OH)2](2-) species. The Gibbs energy of activation for both reactions, in the forward and reverse direction, are in the range of 6-12 kcal mol(-1) and are relatively close to diffusion-controlled. The thermodynamic driving force of the first reaction is the bonding energy of the Os(VIII)-OH metal-hydroxido ligand, while of the second reaction it is the relatively large hydration energy of the doubly-charged cis-[Os(VIII)O4(OH)2](2-) product compared to the singly-charged reactants. The DFT-calculated (PBE-D3 functional) in the simulated aqueous phase (COSMO) is -2.4 kcal mol(-1) for the first reaction and -0.6 kcal mol(-1) for the second reaction and agree to within 1 kcal mol(-1) with reported experimental values, at -2.7 and 0.3 kcal mol(-1) respectively. From QTAIM and EDA analyses it is deduced that the Os(VIII)[double bond, length as m-dash]O bonding interactions are ionic (closed-shell) and that Os(VIII)-OH bonding interactions are polar covalent (dative). In contrast to QTAIM, NCI analysis allowed for the identification of relatively weak intramolecular hydrogen bonding interactions between neighbouring oxo and hydroxido ligands in both [Os(VIII)O4(OH)](-) and cis-[Os(VIII)O4(OH)2](2-) complexes. PMID:26991070

  16. Kinetic Growth of Ultralong Metastable Zincblende MnSe Nanowires Catalyzed by a Fast Ionic Conductor via a Solution-Solid-Solid Mechanism.

    PubMed

    Zhang, Li; Yang, Qing

    2016-07-13

    The metastable semiconductor phase allows for the exploration of unusual properties and functionalities of abnormal structures, although it is often difficult to prevent thermodynamic transformations to lower energy structures from higher, unfavored energy states. Here, we show for the first time the preparation of high-quality ultralong metastable zincblende (ZB)-MnSe nanowires with a four-coordinate structure via solution-solid-solid (SSS) growth in a mild solution-phase synthetic environment (120-220 °C) in the presence of a trace amount of Ag(I). The metastable ZB-MnSe nanowires are stabilized kinetically due to the catalysis of early formed body-centered cubic (bcc) fast-ionic (superionic) Ag2Se nanocrystals from the Ag(I) source, and the ZB-MnSe nanowires grow epitaxially along the ⟨110⟩ axis rather than the ⟨111⟩ axis, as commonly observed for typical four-coordinate Grimm-Sommerfeld bonding solids. Our method provides a new route for the growth of metastable nanostructures. PMID:27254244

  17. Frizzleds and WNT/β-catenin signaling--The black box of ligand-receptor selectivity, complex stoichiometry and activation kinetics.

    PubMed

    Schulte, Gunnar

    2015-09-15

    The lipoglycoproteins of the mammalian WNT family induce β-catenin-dependent signaling through interaction with members of the Class Frizzled receptors and LDL receptor-related protein 5/6 (LRP5/6) albeit with unknown selectivity. The 10 mammalian Frizzleds (FZDs) are seven transmembrane (7TM) spanning receptors and have recently been classified as G protein-coupled receptors (GPCRs). This review summarizes the current knowledge about WNT/FZD selectivity and functional selectivity, the role of co-receptors for signal specification, the formation of receptor complexes as well as the kinetics and mechanisms of signal initiation with focus on WNT/β-catenin signaling. In order to exploit the true therapeutic potential of WNT/FZD signaling to treat human disease, it is clear that substantial progress in the understanding of receptor complex formation and signal specification has to precede a mechanism-based drug design targeting WNT receptors. PMID:26003275

  18. Mechanistic insights from resolving ligand-dependent kinetics of conformational changes at ATP-gated P2X1R ion channels.

    PubMed

    Fryatt, Alistair G; Dayl, Sudad; Cullis, Paul M; Schmid, Ralf; Evans, Richard J

    2016-01-01

    Structural studies of P2X receptors show a novel U shaped ATP orientation following binding. We used voltage clamp fluorometry (VCF) and molecular dynamics (MD) simulations to investigate agonist action. For VCF the P2X1 receptor (P2X1R) K190C mutant (adjacent to the agonist binding pocket) was labelled with the fluorophore MTS-TAMRA and changes in fluorescence on agonist treatment provided a real time measure of conformational changes. Studies with heteromeric channels incorporating a key lysine mutation (K68A) in the ATP binding site demonstrate that normally three molecules of ATP activate the receptor. The time-course of VCF responses to ATP, 2'-deoxy ATP, 3'-deoxy ATP, Ap5A and αβmeATP were agonist dependent. Comparing the properties of the deoxy forms of ATP demonstrated the importance of the 2' hydroxyl group on the ribose ring in determining agonist efficacy consistent with MD simulations showing that it forms a hydrogen bond with the γ-phosphate oxygen stabilizing the U-shaped conformation. Comparison of the recovery of fluorescence on agonist washout, with channel activation to a second agonist application for the partial agonists Ap5A and αβmeATP, showed a complex relationship between conformational change and desensitization. These results highlight that different agonists induce distinct conformational changes, kinetics and recovery from desensitization at P2X1Rs. PMID:27616669

  19. Kinetic aspects for the reduction of CO₂ and CS₂ with mixed-ligand ruthenium(II) hydride complexes containing phosphine and bipyridine.

    PubMed

    Huang, Jing; Chen, Jinzhu; Gao, Hui; Chen, Limin

    2014-09-15

    A new water-soluble ruthenium hydride complex [Ru(H)(bpy)2(PTA)]PF6 (bpy = 2,2'-bipyridine, PTA = 1,3,5-triaza-7-phosphaadamantane) (1a) was prepared. 1a reacted with CO2 and CS2 to give the corresponding formate and dithioformate complexes, respectively. Both the insertions of CO2 and CS2 into the Ru-H bond of 1a followed second-order kinetics. The second-order rate constant (k2) of CO2 insertion reaction varied from (9.40 ± 0.41) × 10(-4) M(-1) s(-1) in acetone to (1.13 ± 0.08) × 10(-1) M(-1) s(-1) in methanol; moreover, the ln(k2) is in good linear relationship with the acceptor number (AN) of the solvent used. Although, the k2 of CS2 insertion reaction ranged from (3.43 ± 0.10) M(-1) s(-1) in methanol to (24.0 ± 0.5) M(-1) s(-1) in N,N-dimethylformamide, which is 1000 times faster than CO2 insertion. Generally, the k2 of CS2 insertion increased with the static dielectric constant (D(s)) of the reaction medium investigated. For comparison purposes, we further investigated the reactivity of [Ru(H)(bpy)2(PPh3)]PF6 (PPh3 = triphenylphosphine) (1b) with CO2 and CS2. 1b reacted with CO2 slowly in the methanol with a k2 of (1.46 ± 0.09) × 10(-3) M(-1) s(-1), yielding a formate complex [Ru(η(1)-OC(H)═O)(bpy)2(PPh3)]PF6 (2b). The reaction of 1b with CS2 is 1000 times faster than that of CO2. The structures of 1a, 1b, and 2b were determined by X-ray crystallographic analysis. PMID:25167462

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

    SciTech Connect

    Hammond, J.R. )

    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.

  1. Determination of trace amounts of mercury(II) in water samples using a novel kinetic catalytic ligand substitution reaction of hexacyanoruthenate(II)

    NASA Astrophysics Data System (ADS)

    Naik, Radhey M.; Agarwal, Abhinav; Prasad, Surendra

    2009-11-01

    A simple, sensitive, selective and rapid kinetic catalytic method has been developed for the determination of Hg(II) ions at micro-level. This method is based on the catalytic effect of Hg(II) ion on the rate of substitution of cyanide in hexacyanoruthenate(II) with nitroso-R-salt (NRS) in aqueous medium and provides good accuracy and precision. The concentration of Hg(II) catalyst varied from 4.0 to 10.0 × 10 -6 M and the progress of reaction was followed spectrophotometrically at 525 nm ( λmax of purple-red complex [Ru(CN) 5NRS] 3-, ɛ = 3.1 × 10 3 M -1 s -1) under the optimized reaction conditions; 8.75 × 10 -5 M [Ru(CN) 64-], 3.50 × 10 -4 M [nitroso-R-salt], pH 7.00 ± 0.02, ionic strength, I = 0.1 M (KCl), temp 45.0 ± 0.1 °C. The linear calibration curves, i.e. calibration equations between the absorbance at fixed times ( t = 15, 20 and 25 min) versus concentration of Hg(II) ions were established under the optimized experimental conditions. The detection limit was found to be 1.0 × 10 -7 M of Hg(II). The effect of various foreign ions on the proposed method has also been studied and discussed. The method has been applied to the determination of mercury(II) in aqueous solutions.

  2. SU-8-Induced Strong Bonding of Polymer Ligands to Flexible Substrates via in Situ Cross-Linked Reaction for Improved Surface Metallization and Fast Fabrication of High-Quality Flexible Circuits.

    PubMed

    Hu, Mingjun; Guo, Qiuquan; Zhang, Tengyuan; Zhou, Shaolin; Yang, Jun

    2016-02-01

    On account of in situ cross-linked reaction of epoxy SU-8 with poly(4-vinylpyridine) (P4VP) and its strong reactive bonding ability with different pretreated substrates, we developed a simple universal one-step solution-based coating method for fast surface modification of various objects. Through this method, a layer of P4VP molecules with controllable thickness can be tethered tightly onto substrates with the assistance of SU-8. P4VP molecules possess a lot of pyridine ligands to immobilize transitional metal ions that can behave as the catalyst of electroless copper plating for surface metallization while functioning as the adhesion-promoting layer between the substrate and deposited metal. Attributed to interpenetrated entanglement of P4VP molecules and as-deposited metal, ultrathick (>7 μm) strongly adhesive high-quality copper layer can be formed on flexible substrates without any delamination. Then through laser printer to print toner mask, a variety of designed circuits can be easily fabricated on modified flexible PET substrate. PMID:26844943

  3. Kinetics of gravity-induced amyloplast sedimentation in statocytes of cress roots grown under fast clino-rotation, 1 g and after 180° inversion

    NASA Astrophysics Data System (ADS)

    Svegzdiene, D.; Rakleviciene, D.; Gaina, V.

    In order to detail the relation between the initial positioning of statoliths and root graviresponsiveness, the movement of amyloplasts within root statocytes of cress ( Lepidium sativum L.) seedlings grown under fast clino-rotation (50 rpm) and vertically at 1 g or 180° inverted after growth at 1 g has been analyzed during a subsequent 6-min period of lateral (reoriented 90°) gravistimulation. The main parameters of statolith motion kinetics such as relative positions and motion velocities in transverse and longitudinal directions have been evaluated taking linear measurements of organelle position with respect to the lower longitudinal and distal wall in the cells of the 2nd-5th columella storeys. A significant discrepancy in the direction and velocity of statolith movement has been determined within the first and second minutes of root horizontal placement. Centrally or proximally located statoliths in clino-rotated or inverted root statocytes moved transversely to the lower longitudinal cell wall more quickly as compared with distally located ones in 1- g root cells. At the same time, the longitudinal displacement of proximally located statoliths towards the cell center has been determined, while this displacement of distally located plastids was significantly more pronounced. The longitudinal motion of amyloplasts grouped in the central cell part was negligible within this 2-min period. After the 6th minute of stimulation, the total downward shift of the mean relative position of statoliths amounted to 16.3% from the total cell width in clino-rotated root statocytes and 17.1% in the cells of inverted roots, while it equalled 13.3% in 1- g root statocytes. The total change of the relative longitudinal position of amyloplasts with respect to the distal cell wall remained almost unchanged in roots grown on the clinostat. In inverted roots, the initial longitudinal position of 56.2% from the total cell length has been shifted significantly to 47.8% and from 27

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

    PubMed

    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. PMID:26916610

  5. O2 reduction reaction by biologically relevant anionic ligand bound iron porphyrin complexes.

    PubMed

    Samanta, Subhra; Das, Pradip Kumar; Chatterjee, Sudipta; Sengupta, Kushal; Mondal, Biswajit; Dey, Abhishek

    2013-11-18

    Iron porphyrin complex with a covalently attached thiolate ligand and another with a covalently attached phenolate ligand has been synthesized. The thiolate bound complex shows spectroscopic features characteristic of P450, including the hallmark absorption spectrum of the CO adduct. Electrocatalytic O2 reduction by this complex, which bears a terminal alkyne group, is investigated by both physiabsorbing on graphite surfaces (fast electron transfer rates) and covalent attachment to azide terminated self-assembled monolayer (physiologically relevant electron transfer rates) using the terminal alkyne group. Analysis of the steady state electrochemical kinetics reveals that this catalyst can selectively reduce O2 to H2O with a second-order k(cat.) ~10(7) M(-1 )s(-1) at pH 7. The analogous phenolate bound iron porphyrin complex reduces O2 with a second-order rate constant of 10(5) M(-1) s(-1) under the same conditions. The anionic ligand bound iron porphyrin complexes catalyze oxygen reduction reactions faster than any known synthetic heme porphyrin analogues. The kinetic parameters of O2 reduction of the synthetic thiolate bound complex, which is devoid of any second sphere effects present in protein active sites, provide fundamental insight into the role of the protein environment in tuning the reactivity of thiolate bound iron porphyrin containing metalloenzymes. PMID:24171513

  6. Efficient Estimation of Rare-Event Kinetics

    NASA Astrophysics Data System (ADS)

    Trendelkamp-Schroer, Benjamin; Noé, Frank

    2016-01-01

    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 process occurs more rapidly than its reverse, making the approach especially attractive for downhill processes such as folding and binding in biomolecules. Our method is implemented in the PyEMMA software.

  7. Kinetic Modeling and Fitting Software for Inter-connected Reaction Schemes: VisKin

    PubMed Central

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

    2007-01-01

    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. In order to determine rate constants from experimental data, fitting algorithms using the Levenberg-Marquardt algorithm or using Broyden-Fletcher-Goldfarb-Shanno (BFGS) methods were implemented that adjust rate constants to fit the model to imported data. 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. PMID:17207764

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

    PubMed

    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. PMID:17207764

  9. Protein-ligand-based pharmacophores: generation and utility assessment in computational ligand profiling.

    PubMed

    Meslamani, Jamel; Li, Jiabo; Sutter, Jon; Stevens, Adrian; Bertrand, Hugues-Olivier; Rognan, Didier

    2012-04-23

    Ligand profiling is an emerging computational method for predicting the most likely targets of a bioactive compound and therefore anticipating adverse reactions, side effects and drug repurposing. A few encouraging successes have already been reported using ligand 2-D similarity searches and protein-ligand docking. The current study describes the use of receptor-ligand-derived pharmacophore searches as a tool to link ligands to putative targets. A database of 68,056 pharmacophores was first derived from 8,166 high-resolution protein-ligand complexes. In order to limit the number of queries, a maximum of 10 pharmacophores was generated for each complex according to their predicted selectivity. Pharmacophore search was compared to ligand-centric (2-D and 3-D similarity searches) and docking methods in profiling a set of 157 diverse ligands against a panel of 2,556 unique targets of known X-ray structure. As expected, ligand-based methods outperformed, in most of the cases, structure-based approaches in ranking the true targets among the top 1% scoring entries. However, we could identify ligands for which only a single method was successful. Receptor-ligand-based pharmacophore search is notably a fast and reliable alternative to docking when few ligand information is available for some targets. Overall, the present study suggests that a workflow using the best profiling method according to the protein-ligand context is the best strategy to follow. We notably present concrete guidelines for selecting the optimal computational method according to simple ligand and binding site properties. PMID:22480372

  10. Ligand-Dependent Conformational Dynamics of Dihydrofolate Reductase

    PubMed Central

    Reddish, Michael J.; Vaughn, Morgan B.; Fu, Rong; Dyer, R. Brian

    2016-01-01

    Enzymes are known to change among several conformational states during turnover. The role of such dynamic structural changes in catalysis is not fully understood. The influence of dynamics in catalysis can be inferred, but not proven, by comparison of equilibrium structures of protein variants and protein–ligand complexes. A more direct way to establish connections between protein dynamics and the catalytic cycle is to probe the kinetics of specific protein motions in comparison to progress along the reaction coordinate. We have examined the enzyme model system dihydrofolate reductase (DHFR) from Escherichia coli with tryptophan fluorescence-probed temperature-jump spectroscopy. We aimed to observe the kinetics of the ligand binding and ligand-induced conformational changes of three DHFR complexes to establish the relationship among these catalytic steps. Surprisingly, in all three complexes, the observed kinetics do not match a simple sequential two-step process. Through analysis of the relationship between ligand concentration and observed rate, we conclude that the observed kinetics correspond to the ligand binding step of the reaction and a noncoupled enzyme conformational change. The kinetics of the conformational change vary with the ligand's identity and presence but do not appear to be directly related to progress along the reaction coordinate. These results emphasize the need for kinetic studies of DHFR with highly specific spectroscopic probes to determine which dynamic events are coupled to the catalytic cycle and which are not. PMID:26901612

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

    NASA Astrophysics Data System (ADS)

    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.

  12. Ultrafast ligand rebinding in the heme domain of the oxygen sensors FixL and Dos: general regulatory implications for heme-based sensors.

    PubMed

    Liebl, Ursula; Bouzhir-Sima, Latifa; Negrerie, Michel; Martin, Jean-Louis; Vos, Marten H

    2002-10-01

    Heme-based oxygen sensors are part of ligand-specific two-component regulatory systems, which have both a relatively low oxygen affinity and a low oxygen-binding rate. To get insight into the dynamical aspects underlying these features and the ligand specificity of the signal transduction from the heme sensor domain, we used femtosecond spectroscopy to study ligand dynamics in the heme domains of the oxygen sensors FixL from Bradyrhizobium japonicum (FixLH) and Dos from Escherichia coli (DosH). The heme coordination with different ligands and the corresponding ground-state heme spectra of FixLH are similar to myoglobin (Mb). After photodissociation, the excited-state properties and ligand-rebinding kinetics are qualitatively similar for FixLH and Mb for CO and NO as ligands. In contrast to Mb, the transient spectra of FixLH after photodissociation of ligands are distorted compared with the ground-state difference spectra, indicating differences in the heme environment with respect to the unliganded state. This distortion is particularly marked for O(2). Strikingly, heme-O(2) recombination occurs with efficiency unprecedented for heme proteins, in approximately 5 ps for approximately 90% of the dissociated O(2). For DosH-O(2), which shows 60% sequence similarity to FixLH, but where signal detection and transmission presumably are quite different, a similarly fast recombination was found with an even higher yield. Altogether these results indicate that in these sensors the heme pocket acts as a ligand-specific trap. The general implications for the functioning of heme-based ligand sensors are discussed in the light of recent studies on heme-based NO and CO sensors. PMID:12271121

  13. Ligand migration in nonsymbiotic hemoglobin AHb1 from Arabidopsis thaliana.

    PubMed

    Abbruzzetti, Stefania; Grandi, Elena; Bruno, Stefano; Faggiano, Serena; Spyrakis, Francesca; Mozzarelli, Andrea; Cacciatori, Elena; Dominici, Paola; Viappiani, Cristiano

    2007-11-01

    AHb1 is a hexacoordinated type 1 nonsymbiotic hemoglobin recently discovered in Arabidopsis thaliana. To gain insight into the ligand migration inside the protein, we studied the CO rebinding kinetics of AHb1 encapsulated in silica gels, in the presence of glycerol. The CO rebinding kinetics after nanosecond laser flash photolysis exhibits complex ligand migration patterns, consistent with the existence of discrete docking sites in which ligands can temporarily be stored before rebinding to the heme at different times. This finding may be of relevance to the physiological NO dioxygenase activity of this protein, which requires sequential binding of two substrates, NO and O2, to the heme. PMID:17924689

  14. Beyond radio-displacement techniques for Identification of CB1 Ligands: The First Application of a Fluorescence-quenching Assay

    PubMed Central

    Bruno, Agostino; Lembo, Francesca; Novellino, Ettore; Stornaiuolo, Mariano; Marinelli, Luciana

    2014-01-01

    Cannabinoid type 1 Receptor (CB1) belongs to the GPCR family and it has been targeted, so far, for the discovery of drugs aimed at the treatment of neuropathic pain, nausea, vomit, and food intake disorders. Here, we present the development of the first fluorescent assay enabling the measurement of kinetic binding constants for CB1orthosteric ligands. The assay is based on the use of T1117, a fluorescent analogue of AM251. We prove that T1117 binds endogenous and recombinant CB1 receptors with nanomolar affinity. Moreover, T1117 binding to CB1 is sensitive to the allosteric ligand ORG27569 and thus it is applicable to the discovery of new allosteric drugs. The herein presented assay constitutes a sustainable valid alternative to the expensive and environmental impacting radiodisplacement techniques and paves the way for an easy, fast and cheap high-throughput drug screening toward CB1 for identification of new orthosteric and allosteric modulators. PMID:24441508

  15. Beyond radio-displacement techniques for identification of CB1 ligands: the first application of a fluorescence-quenching assay.

    PubMed

    Bruno, Agostino; Lembo, Francesca; Novellino, Ettore; Stornaiuolo, Mariano; Marinelli, Luciana

    2014-01-01

    Cannabinoid type 1 Receptor (CB1) belongs to the GPCR family and it has been targeted, so far, for the discovery of drugs aimed at the treatment of neuropathic pain, nausea, vomit, and food intake disorders. Here, we present the development of the first fluorescent assay enabling the measurement of kinetic binding constants for CB1 orthosteric ligands. The assay is based on the use of T1117, a fluorescent analogue of AM251. We prove that T1117 binds endogenous and recombinant CB1 receptors with nanomolar affinity. Moreover, T1117 binding to CB1 is sensitive to the allosteric ligand ORG27569 and thus it is applicable to the discovery of new allosteric drugs. The herein presented assay constitutes a sustainable valid alternative to the expensive and environmental impacting radiodisplacement techniques and paves the way for an easy, fast and cheap high-throughput drug screening toward CB1 for identification of new orthosteric and allosteric modulators. PMID:24441508

  16. Cell-free synthesis of isotopically labelled peptide ligands for the functional characterization of G protein-coupled receptors.

    PubMed

    Joedicke, Lisa; Trenker, Raphael; Langer, Julian D; Michel, Hartmut; Preu, Julia

    2016-01-01

    Cell-free systems exploit the transcription and translation machinery of cells from different origins to produce proteins in a defined chemical environment. Due to its open nature, cell-free protein production is a versatile tool to introduce specific labels such as heavy isotopes, non-natural amino acids and tags into the protein while avoiding cell toxicity. In particular, radiolabelled peptides and proteins are valuable tools for the functional characterization of protein-protein interactions and for studying binding kinetics. In this study we evaluated cell-free protein production for the generation of radiolabelled ligands for G protein-coupled receptors (GPCRs). These receptors are seven-transmembrane-domain receptors activated by a plethora of extracellular stimuli including peptide ligands. Many GPCR peptide ligands contain disulphide bonds and are thus inherently difficult to produce in bacterial expression hosts or in Escherichia coli-based cell-free systems. Here, we established an adapted E. coli-based cell-free translation system for the production of disulphide bond-containing GPCR peptide ligands and specifically introduce tritium labels for detection. The bacterial oxidoreductase DsbA is used as a chaperone to favour the formation of disulphide bonds and to enhance the yield of correctly folded proteins and peptides. We demonstrate the correct folding and formation of disulphide bonds and show high-affinity ligand binding of the produced radio peptide ligands to the respective receptors. Thus, our system allows the fast, cost-effective and reliable synthesis of custom GPCR peptide ligands for functional and structural studies. PMID:27047736

  17. 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

    SciTech Connect

    Duke, Dana Lynn

    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.

  18. Kinetic Study of OH Reactions With n-Octane and n-Decane Using Relative Rate Combining with Discharge Fast Flow and Mass Spectrometer Technique

    SciTech Connect

    Li, Zhuangjie

    2004-03-31

    The combination of the relative rate method with the discharge fast flow/mass spectrometer technique (RR/DF/MS) has been developed to measure the rate constants for gas phase reactions involving OH radicals. The RR/DF/MS technique was used to measure the rate constant for reactions of the OH radical with n-octane (k3) and cyclohexane (k5) using 1,4-dioxane as a reference compound and with n-decane (k6) using n-octane and 1,4-dioxane as reference compounds. At 298 K, these rate constants were determined to be k3=(8.88 {+-} 0.31) x 10-12, k5=(6.95 {+-} 0.20) x 10-12 and k6=(1.38 {+-} 0.08) x 10-11 cm3 molecule-1 s-1, respectively, which are in very good agreement with those measured using different techniques. The features of the RR/DF/MS technique are discussed.

  19. High-temperature fast-flow-reactor kinetics study of the reaction AlO + CO/sub 2/. -->. AlO/sub 2/ + CO. Thermochemical implications

    SciTech Connect

    Rogowski, D.F.; English, A.J.; Fontijn, A.

    1986-04-10

    The title reaction has been studied in a high-temperature fast-flow reactor (HTFFR) at temperatures from 500 to 1300 K. Laser-induced fluorescence was used to monitor relative (AlO). k(T) was determined to be (2.5 +/- 1.3) x 10/sup -14/ exp((400 +/- 280)/T) cm/sup 3/ molecule/sup -1/ s/sup -1/ (confidence level > 95%). The reaction probably proceeds via an intermediate complex which preferentially dissociates to the reactants. The negative activation energy implies D(O-AlO) greater than or equal to D(O-CO) = 127 kcal mol/sup -1/, which is incompatible with the O-AlO dissociation energy obtained for AlO/sub 2/ from Al/sub 2/O/sub 3/ evaporation-mass spectrometry studies. It is argued that the latter AlO/sub 2/ may have a different structure from that of the present work. 19 references, 3 figures, 1 table.

  20. Kinetic recognition of the retinoblastoma tumor suppressor by a specific protein target.

    PubMed

    Chemes, Lucía B; Sánchez, Ignacio E; de Prat-Gay, Gonzalo

    2011-09-16

    The retinoblastoma tumor suppressor (Rb) plays a key role in cell cycle control and is linked to various types of human cancer. Rb binds to the LxCxE motif, present in a number of cellular and viral proteins such as AdE1A, SV40 large T-antigen and human papillomavirus (HPV) E7, all instrumental in revealing fundamental mechanisms of tumor suppression, cell cycle control and gene expression. A detailed kinetic study of RbAB binding to the HPV E7 oncoprotein shows that an LxCxE-containing E7 fragment binds through a fast two-state reaction strongly favored by electrostatic interactions. Conversely, full-length E7 binds through a multistep process involving a pre-equilibrium between E7 conformers, a fast electrostatically driven association step guided by the LxCxE motif and a slow conformational rearrangement. This kinetic complexity arises from the conformational plasticity and intrinsically disordered nature of E7 and from multiple interaction surfaces present in both proteins. Affinity differences between E7N domains from high- and low-risk types are explained by their dissociation rates. In fact, since Rb is at the center of a large protein interaction network, fast and tight recognition provides an advantage for disruption by the viral proteins, where the balance of physiological and pathological interactions is dictated by kinetic ligand competition. The localization of the LxCxE motif within an intrinsically disordered domain provides the fast, diffusion-controlled interaction that allows viral proteins to outcompete physiological targets. We describe the interaction mechanism of Rb with a protein ligand, at the same time an LxCxE-containing model target, and a paradigmatic intrinsically disordered viral oncoprotein. PMID:21787785

  1. Kinetics of Gravity-induced Amyloplast Sedimentation in Cress Root Statocytes Formed under 1 g and on Fast-rotating Clinostat

    NASA Astrophysics Data System (ADS)

    Svegzdiene, D.; Rakleviciene, D.; Gaina, V.

    The aim of the sudy was to compare the motion of a statolith complex in statocytes of roots grown vertically under 1 g and simulated weightlessness by fast-clinorotation (50 rpm) during lateral stimulation by the gravity vector; the experiments with cress (Lepidium sativum L.) on a centrifuge-clinostat device have been performed. Before gravistimulation, the statoliths are grouped in the distal region of 1g-root statocytes and at the center of statocytes in clino-rotated roots. Then roots were placed horizontally for increasing periods of time (1, 2, 4 or 6 min) and chemically fixed. Quantitative analysis of amyloplast movement in side-to-side and distal-to-proximal directions within statocytes of the 2nd to 5th statenchyma storeys was accomplished by light and electron microscopy. After the first minute of gravistimulation, the position of statolith complex in the 1g-statocytes has been changed by about 12.2% in side-to-side and 18.3% in distal-to-proximal direction versus its initial position. In roots grown on the clinostat, the plastids changed their initial position by 22.5% toward the lower longitudinal wall of the statocyte and negligibly (2.4%) -- toward the proximal cell wall during this stimulation period. Later, up to 2 min, the statoliths continued to displace following the alike trajectory in side-to-side by 36.6% as well as in distal-to-proximal direction by 34.4% in 1g-root statocytes versus their position occupied at 1 min, while they remained approximately at the same position in statocytes of clinostat-grown roots. During the period from 2 to 6 min, in the former roots a significant further shift (15.1%) parallel to the gravity vector and otherwise a reversible movement (- 13.3%) toward the distal wall of statolith complex were observed. However, within the same period of gravistimulation the statolith positioning in clinorotated-roots changed only slightly in side-to-side (4.8%) as well as in distal-to-proximal (2.1%) directions. The obtained

  2. Stretchable Self-Healing Polymeric Dielectrics Cross-Linked Through Metal-Ligand Coordination.

    PubMed

    Rao, Ying-Li; Chortos, Alex; Pfattner, Raphael; Lissel, Franziska; Chiu, Yu-Cheng; Feig, Vivian; Xu, Jie; Kurosawa, Tadanori; Gu, Xiaodan; Wang, Chao; He, Mingqian; Chung, Jong Won; Bao, Zhenan

    2016-05-11

    A self-healing dielectric elastomer is achieved by the incorporation of metal-ligand coordination as cross-linking sites in nonpolar polydimethylsiloxane (PDMS) polymers. The ligand is 2,2'-bipyridine-5,5'-dicarboxylic amide, while the metal salts investigated here are Fe(2+) and Zn(2+) with various counteranions. The kinetically labile coordination between Zn(2+) and bipyridine endows the polymer fast self-healing ability at ambient condition. When integrated into organic field-effect transistors (OFETs) as gate dielectrics, transistors with FeCl2 and ZnCl2 salts cross-linked PDMS exhibited increased dielectric constants compared to PDMS and demonstrated hysteresis-free transfer characteristics, owing to the low ion conductivity in PDMS and the strong columbic interaction between metal cations and the small Cl(-) anions which can prevent mobile anions drifting under gate bias. Fully stretchable transistors with FeCl2-PDMS dielectrics were fabricated and exhibited ideal transfer characteristics. The gate leakage current remained low even after 1000 cycles at 100% strain. The mechanical robustness and stable electrical performance proved its suitability for applications in stretchable electronics. On the other hand, transistors with gate dielectrics containing large-sized anions (BF4(-), ClO4(-), CF3SO3(-)) displayed prominent hysteresis due to mobile anions drifting under gate bias voltage. This work provides insights on future design of self-healing stretchable dielectric materials based on metal-ligand cross-linked polymers. PMID:27099162

  3. Ligand-grafted biomaterials for adsorptive separations of uranium in solution

    SciTech Connect

    Hu, M.Z.C.; Reeves, M.

    1999-11-01

    Many organic molecules, particularly biologicals, contain functional groups (ligands) that actively interact with metal ions in solution by adsorption, ion exchange, or chelation/coordination/complexation. Water-soluble organics have limitations as reagents for metal-ion separations from aqueous solutions. However, if the ligand molecule(s) are grafted on to an insoluble matrix, the resulting ligand(s)-containing product becomes useful for separations applications related to metal recovery or remediation. It was discovered that biomolecules containing a primary amino group, secondary amino group, or hydroxyl group could be grafted into a polyurethane polymeric network via in situ polymerization reactions. With carboxyl groups, grafted material showed good selectivity among a group of divalent metal cations, and a uranium-binding capacity of more than 10 mg/g of polymer. The material can be regenerated by sodium bicarbonate or sodium carbonate solution and reused. Data from a stirred-tank reactor showed fast uranium-binding kinetics, and breakthrough-elution studies with a packed-column reactor indicated promising process behavior.

  4. Spectroscopic, computational, and kinetic studies of the mu4-sulfide-bridged tetranuclear CuZ cluster in N2O reductase: pH effect on the edge ligand and its contribution to reactivity.

    PubMed

    Ghosh, Somdatta; Gorelsky, Serge I; George, Serena DeBeer; Chan, Jeannine M; Cabrito, Inês; Dooley, David M; Moura, José J G; Moura, Isabel; Solomon, Edward I

    2007-04-01

    A combination of spectroscopy and density functional theory (DFT) calculations has been used to evaluate the pH effect at the CuZ site in Pseudomonas nautica (Pn) nitrous oxide reductase (N2OR) and Achromobacter cycloclastes (Ac) N2OR and its relevance to catalysis. Absorption, magnetic circular dichroism, and electron paramagnetic resonance with sulfur K-edge X-ray absorption spectra of the enzymes at high and low pH show minor changes. However, resonance Raman (rR) spectroscopy of PnN2OR at high pH shows that the 415 cm-1 Cu-S vibration (observed at low pH) shifts to higher frequency, loses intensity, and obtains a 9 cm-1 18O shift, implying significant Cu-O character, demonstrating the presence of a OH- ligand at the CuICuIV edge. From DFT calculations, protonation of either the OH- to H2O or the mu4-S2- to mu4-SH- would produce large spectral changes which are not observed. Alternatively, DFT calculations including a lysine residue at an H-bonding distance from the CuICuIV edge ligand show that the position of the OH- ligand depends on the protonation state of the lysine. This would change the coupling of the Cu-(OH) stretch with the Cu-S stretch, as observed in the rR spectrum. Thus, the observed pH effect (pKa approximately 9.2) likely reflects protonation equilibrium of the lysine residue, which would both raise E degrees and provide a proton for lowering the barrier for the N-O cleavage and for reduction of the [Cu4S(im)7OH]2+ to the fully reduced 4CuI active form for turnover. PMID:17352474

  5. Ammonia formation by metal-ligand cooperative hydrogenolysis of a nitrido ligand

    NASA Astrophysics Data System (ADS)

    Askevold, Bjorn; Nieto, Jorge Torres; Tussupbayev, Samat; Diefenbach, Martin; Herdtweck, Eberhardt; Holthausen, Max C.; Schneider, Sven

    2011-07-01

    Bioinspired hydrogenation of N2 to ammonia at ambient conditions by stepwise nitrogen protonation/reduction with metal complexes in solution has experienced remarkable progress. In contrast, the highly desirable direct hydrogenation with H2 remains difficult. In analogy to the heterogeneously catalysed Haber-Bosch process, such a reaction is conceivable via metal-centred N2 splitting and unprecedented hydrogenolysis of the nitrido ligands to ammonia. We report the synthesis of a ruthenium(IV) nitrido complex. The high nucleophilicity of the nitrido ligand is demonstrated by unusual N-C coupling with π-acidic CO. Furthermore, the terminal nitrido ligand undergoes facile hydrogenolysis with H2 at ambient conditions to produce ammonia in high yield. Kinetic and quantum chemical examinations of this reaction suggest cooperative behaviour of a phosphorus-nitrogen-phosphorus pincer ligand in rate-determining heterolytic hydrogen splitting.

  6. Ammonia formation by metal-ligand cooperative hydrogenolysis of a nitrido ligand.

    PubMed

    Askevold, Bjorn; Nieto, Jorge Torres; Tussupbayev, Samat; Diefenbach, Martin; Herdtweck, Eberhardt; Holthausen, Max C; Schneider, Sven

    2011-07-01

    Bioinspired hydrogenation of N(2) to ammonia at ambient conditions by stepwise nitrogen protonation/reduction with metal complexes in solution has experienced remarkable progress. In contrast, the highly desirable direct hydrogenation with H(2) remains difficult. In analogy to the heterogeneously catalysed Haber-Bosch process, such a reaction is conceivable via metal-centred N(2) splitting and unprecedented hydrogenolysis of the nitrido ligands to ammonia. We report the synthesis of a ruthenium(IV) nitrido complex. The high nucleophilicity of the nitrido ligand is demonstrated by unusual N-C coupling with π-acidic CO. Furthermore, the terminal nitrido ligand undergoes facile hydrogenolysis with H(2) at ambient conditions to produce ammonia in high yield. Kinetic and quantum chemical examinations of this reaction suggest cooperative behaviour of a phosphorus-nitrogen-phosphorus pincer ligand in rate-determining heterolytic hydrogen splitting. PMID:21697873

  7. Characterization of the molecular species of glycerophospholipids from rabbit kidney: an alternative approach to the determination of the fatty acyl chain position by negative ion fast atom bombardment combined with mass-analysed ion kinetic energy analysis.

    PubMed

    Chen, S; Curcuruto, O; Catinella, S; Traldi, P; Menon, G

    1992-12-01

    An alternative approach to identifying fatty acid chain position in the molecular species of glycerophospholipids has been studied and developed. The fatty acyl groups esterified to the glycerol backbone in isomeric glycerophosphatidyl-choline, -serine and -ethanolamine as well as glycerophosphatidic acid can be detected by the presence of a pair of anions derived from phosphatidic acid parent ions (M minus the polar head groups in glycerophospholipids), designed to be [M--polar head--R2COOH]- and [M--polar head--R2CO--H]-, produced by negative ion fast atom bombardment combined with mass-analysed ion kinetic energy analysis. Because of the significant abundance of [M--polar head--R2COOH]- anion, fatty acid chains differing by 2 Da can be distinguished by accurate measurements of the electrostatic voltage related to this ion. Three-volt differences can be evidenced. Using this approach, the molecular species of glycerophosphatidyl-choline, -serine, -ethanolamine and -inositol from rabbit kidney were characterized after the separation of both class and species by normal and reversed-phase high-performance liquid chromatography, respectively. We identified 11 arachidonoyl-containing molecular species of glycerophospholipids and the other 17 lipid molecules in this biological material. A couple of 1- alkenyl-2-arachidonoyl-sn-glycerol-3-phosphoethanolamine species, identified as plasmalogen GPE 16:0-20:4 and plasmalogen GPE 18:0-20:4, were found for the first time in rabbit kidney. PMID:1477110

  8. Metal-ligand cooperation.

    PubMed

    Khusnutdinova, Julia R; Milstein, David

    2015-10-12

    Metal-ligand cooperation (MLC) has become an important concept in catalysis by transition metal complexes both in synthetic and biological systems. MLC implies that both the metal and the ligand are directly involved in bond activation processes, by contrast to "classical" transition metal catalysis where the ligand (e.g. phosphine) acts as a spectator, while all key transformations occur at the metal center. In this Review, we will discuss examples of MLC in which 1) both the metal and the ligand are chemically modified during bond activation and 2) bond activation results in immediate changes in the 1st coordination sphere involving the cooperating ligand, even if the reactive center at the ligand is not directly bound to the metal (e.g. via tautomerization). The role of MLC in enabling effective catalysis as well as in catalyst deactivation reactions will be discussed. PMID:26436516

  9. Kinetic Demonstration.

    ERIC Educational Resources Information Center

    Burgardt, Erik D.; Ryan, Hank

    1996-01-01

    Presents a unit on chemical reaction kinetics that consists of a predemonstration activity, the demonstration, and a set of postdemonstration activities that help students transfer the concepts to actual chemical reactions. Simulates various aspects of chemical reaction kinetics. (JRH)

  10. Kinetic Atom.

    ERIC Educational Resources Information Center

    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)

  11. Spectroscopic, Computational, and Kinetic Studies of the Mu-Sulfide-Bridged Tetranuclear CuZ Cluster in N(2)O Reductase: PH Effect on the Edge Ligand and its Contribution to Reactivity

    SciTech Connect

    Ghosh, S.; Gorelsky, S.I.; George, S.DeBeer; Chan, J.M.; Cabrito, I.; Dooley, D.M.; Moura, J.J.G.; Moura, I.; Solomon, E.I.

    2011-11-29

    A combination of spectroscopy and density functional theory (DFT) calculations has been used to evaluate the pH effect at the Cu{sub Z} site in Pseudomonas nautica (Pn) nitrous oxide reductase (N{sub 2}OR) and Achromobacter cycloclastes (Ac) N{sub 2}OR and its relevance to catalysis. Absorption, magnetic circular dichroism, and electron paramagnetic resonance with sulfur K-edge X-ray absorption spectra of the enzymes at high and low pH show minor changes. However, resonance Raman (rR) spectroscopy of PnN{sub 2}OR at high pH shows that the 415 cm{sup -1} Cu-S vibration (observed at low pH) shifts to higher frequency, loses intensity, and obtains a 9 cm{sup -1} {sup 18}O shift, implying significant Cu-O character, demonstrating the presence of a OH{sup -} ligand at the Cu{sub I}Cu{sub IV} edge. From DFT calculations, protonation of either the OH{sup -} to H{sub 2}O or the {mu}{sub 4}-S{sup 2-} to {mu}{sub 4}-SH{sup -} would produce large spectral changes which are not observed. Alternatively, DFT calculations including a lysine residue at an H-bonding distance from the Cu{sub I}Cu{sub IV} edge ligand show that the position of the OH{sup -} ligand depends on the protonation state of the lysine. This would change the coupling of the Cu-(OH) stretch with the Cu-S stretch, as observed in the rR spectrum. Thus, the observed pH effect (pK{sub a} {approx} 9.2) likely reflects protonation equilibrium of the lysine residue, which would both raise E{sup o} and provide a proton for lowering the barrier for the N-O cleavage and for reduction of the [Cu{sub 4}S(im){sub 7}OH]{sup 2+} to the fully reduced 4Cu{sup I} active form for turnover.

  12. Empirical potentials for recombination reactions of photo-dissociated ligands. Final report

    SciTech Connect

    Elber, R.

    1998-12-01

    The aim of this research was to design an appropriate potential and simulation methodology to describe the effect of radiation on ligands bound to metal-proteins. As model systems the authors investigated myoglobin, hemoglobin and their mutants. The great advantage of the globins as a target for theoretical studies is the wealth of experimental data available for them. They focused on studies that combine fast spectroscopy with mutation experiments. The mutations make it possible to examine detailed changes in the kinetic curves with atomically detailed information. The first spectroscopy, which is in the same time scale as of ordinary molecular dynamics (sub nanoseconds), makes it possible to compare the results of the computations to raw experimental data.

  13. Enzyme Kinetics.

    ERIC Educational Resources Information Center

    Moe, Owen; Cornelius, Richard

    1988-01-01

    Conveys an appreciation of enzyme kinetic analysis by using a practical and intuitive approach. Discusses enzyme assays, kinetic models and rate laws, the kinetic constants (V, velocity, and Km, Michaels constant), evaluation of V and Km from experimental data, and enzyme inhibition. (CW)

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

    NASA Astrophysics Data System (ADS)

    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

  15. Gating Kinetics of the Cyclic-GMP-Activated Channel of Retinal Rods: Flash Photolysis and Voltage-Jump Studies

    NASA Astrophysics Data System (ADS)

    Karpen, Jeffrey W.; Zimmerman, Anita L.; Stryer, Lubert; Baylor, Denis A.

    1988-02-01

    The gating kinetics of the cGMP-activated cation channel of salamander retinal rods have been studied in excised membrane patches. Relaxations in patch current were observed after two kinds of perturbation: (i) fast jumps of cGMP concentration, generated by laser flash photolysis of a cGMP ester (``caged'' cGMP), and (ii) membrane voltage jumps, which perturb activation of the channel by cGMP. In both methods the speed of activation increased with the final cGMP concentration. The results are explained by a simple kinetic model in which activation involves three sequential cGMP binding steps with bimolecular rate constants close to the diffusion-controlled limit; fully liganded channels undergo rapid open-closed transitions. Voltage perturbs activation by changing the rate constant for channel closing, which increases with hyperpolarization. Intramolecular transitions of the fully liganded channel limit the kinetics of activation at high cGMP concentrations (>50 μ M), whereas at physiological cGMP concentrations (<5 μ M), the kinetics of activation are limited by the third cGMP binding step. The channel appears to be optimized for rapid responses to changes in cytoplasmic cGMP concentration.

  16. Nuclear magnetic resonance study of the kinetics of ligand-exchange reactions in uranyl complexes. Part 5. Exchange reaction of acetylacetonate in bis(acetylacetonato)(dimethyl sulfoxide)dioxouranium(VI)

    SciTech Connect

    Ikeda, Y.; Tomiyasu, H.; Fukutomi, H.

    1984-09-26

    The kinetics of the exchange reaction of acac in UO/sub 2/(acac)/sub 2/Me/sub 2/SO (acac = acetylacetonate, Me/sub 2/SO = dimethyl sulfoxide) has been studied in o-C/sub 6/H/sub 4/Cl/sub 2/ by means of /sup 1/H NMR. The exchange rate depends on the concentration of the enol isomer of acetylacetone in its low region and approaches to the limiting value in its high region. The rate-determining step seems to be ring opening for one of two coordinated acac ions. The kinetic parameters of this step at 25/sup 0/C were found to be: equilibrium constant = 2.04 sec/sup -1/, enthalpy = 66.4 +/- 8.4 kJ mol/sup -1/, and entropy = 17.1 +/- 28.6 J K/sup -1/ mol/sup -1/. It was found that the exchange rate is decreased by addition of free Me/sub 2/SO. This is explained by considering the competition of Me/sub 2/SO with the enol isomer in attacking the four-coordinated intermediate in the equatorial plane or the outer-sphere complex formation between UO/sub 2/(acac)/sub 2/Me/sub 2/SO and free Me/sub 2/SO.

  17. Ligand Release Pathways Obtained with WExplore: Residence Times and Mechanisms.

    PubMed

    Dickson, Alex; Lotz, Samuel D

    2016-06-23

    The binding of ligands with their molecular receptors is of tremendous importance in biology. Although much emphasis has been placed on characterizing binding sites and bound poses that determine the binding thermodynamics, the pathway by which a ligand binds importantly determines the binding kinetics. The computational study of entire unbiased ligand binding and release pathways is still an emerging field, made possible only recently by advances in computational hardware and sampling methodologies. We have developed one such method (WExplore) that is based on a weighted ensemble of trajectories, which we apply to ligand release for the first time, using a set of three previously characterized interactions between low-affinity ligands and the protein FKBP-12 (FK-506 binding protein). WExplore is found to be more efficient that conventional sampling, even for the nanosecond-scale unbinding events observed here. From a nonequilibrium ensemble of unbinding trajectories, we obtain ligand residence times and release pathways without using biasing forces or a Markovian assumption of transitions between regions. We introduce a set of analysis tools for unbinding transition pathways, including using von Mises-Fisher distributions to model clouds of ligand exit points, which provide a quantitative proxy for ligand surface diffusion. Differences between the transition pathway ensembles of the three ligands are identified and discussed. PMID:27231969

  18. Control and recognition of anionic ligands in myoglobin.

    PubMed

    Cutruzzolà, F; Allocatelli, C T; Ascenzi, P; Bolognesi, M; Sligar, S G; Brunori, M

    1991-05-01

    Equilibrium and kinetic experiments on site-directed mutants of a synthetic sperm whale myoglobin (Mb) gene have been performed. Results on the reactivity on both ferric and ferrous wild type and mutants Mb's are presented. Analysis of ligand binding to His (E7) Val and His (E7) Val-Thr (E10) Arg mutants compared to wild-type sperm whale, horse and Aplysia limacina Mb's, shows that the introduction of an arginyl residue at the topological position E10 greatly enhances the stability of the various Mg:heme ligand adducts. Alternative mechanisms of ligand stabilization may therefore be operative in Mb's lacking the distal histidine. PMID:2037047

  19. Ligand-based reactivity of a platinum bisdithiolene: double diene addition yields a new C2-chiral chelate ligand.

    PubMed

    Kerr, Mitchell J; Harrison, Daniel J; Lough, Alan J; Fekl, Ulrich

    2009-10-01

    The reaction of Pt(tfd)(2) [tfd = S(2)C(2)(CF(3))(2)] with excess 2,3-dimethyl-1,3-butadiene initially yields the expected 1:1 adduct, in which the diene has added across two sulfur atoms on separate tfd ligands. However, within 1 day at 50 degrees C, this kinetic product quantitatively converts into a thermodynamic product where two dienes have added to one tfd ligand via unprecedented addition across the dithiolene CS bonds. The new reaction is highly selective for the C(2)-symmetric diastereomer. A new chiral bisthioether chelate ligand has formed in the product, which has been characterized crystallographically. PMID:19634863

  20. Ligand modeling and design

    SciTech Connect

    Hay, B.P.

    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.

  1. Kinetic regulation mechanism of pbuE riboswitch

    NASA Astrophysics Data System (ADS)

    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.

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

    SciTech Connect

    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.

  3. electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation

    PubMed Central

    Moriarty, Nigel W.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.

    2009-01-01

    The electronic Ligand Builder and Optimization Workbench (eLBOW) is a program module of the PHENIX suite of computational crystallographic software. It is designed to be a flexible procedure that uses 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 the attainment of a number of diverse goals including geometry optimization and generation of restraints. PMID:19770504

  4. Ligand modeling and design

    SciTech Connect

    Hay, B.

    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.

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

    PubMed

    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. PMID:22669908

  6. Controlling the Dissociation of Ligands from the Adenosine A2A Receptor through Modulation of Salt Bridge Strength.

    PubMed

    Segala, Elena; Guo, Dong; Cheng, Robert K Y; Bortolato, Andrea; Deflorian, Francesca; Doré, Andrew S; Errey, James C; Heitman, Laura H; IJzerman, Adriaan P; Marshall, Fiona H; Cooke, Robert M

    2016-07-14

    The association and dissociation kinetics of ligands binding to proteins vary considerably, but the mechanisms behind this variability are poorly understood, limiting their utilization for drug discovery. This is particularly so for G protein-coupled receptors (GPCRs) where high resolution structural information is only beginning to emerge. Engineering the human A2A adenosine receptor has allowed structures to be solved in complex with the reference compound ZM241385 and four related ligands at high resolution. Differences between the structures are limited, with the most pronounced being the interaction of each ligand with a salt bridge on the extracellular side of the receptor. Mutagenesis experiments confirm the role of this salt bridge in controlling the dissociation kinetics of the ligands from the receptor, while molecular dynamics simulations demonstrate the ability of ligands to modulate salt bridge stability. These results shed light on a structural determinant of ligand dissociation kinetics and identify a means by which this property may be optimized. PMID:27312113

  7. Macromolecular Crowding Modulates Actomyosin Kinetics.

    PubMed

    Ge, Jinghua; Bouriyaphone, Sherry D; Serebrennikova, Tamara A; Astashkin, Andrei V; Nesmelov, Yuri E

    2016-07-12

    Actomyosin kinetics is usually studied in dilute solutions, which do not reflect conditions in the cytoplasm. In cells, myosin and actin work in a dense macromolecular environment. High concentrations of macromolecules dramatically reduce the amount of free space available for all solutes, which results in an effective increase of the solutes' chemical potential and protein stabilization. Moreover, in a crowded solution, the chemical potential depends on the size of the solute, with larger molecules experiencing a larger excluded volume than smaller ones. Therefore, since myosin interacts with two ligands of different sizes (actin and ATP), macromolecular crowding can modulate the kinetics of individual steps of the actomyosin ATPase cycle. To emulate the effect of crowding in cells, we studied actomyosin cycle reactions in the presence of a high-molecular-weight polymer, Ficoll70. We observed an increase in the maximum velocity of the actomyosin ATPase cycle, and our transient-kinetics experiments showed that virtually all individual steps of the actomyosin cycle were affected by the addition of Ficoll70. The observed effects of macromolecular crowding on the myosin-ligand interaction cannot be explained by the increase of a solute's chemical potential. A time-resolved Förster resonance energy transfer experiment confirmed that the myosin head assumes a more compact conformation in the presence of Ficoll70 than in a dilute solution. We conclude that the crowding-induced myosin conformational change plays a major role in the changed kinetics of actomyosin ATPase. PMID:27410745

  8. Kinetic study on biomass gasification

    SciTech Connect

    Bingyan, X.; Chuangzhi, W.; Zhengfen, L.; Guang, Z.X. )

    1992-09-01

    An experimental apparatus, with the features of fast heating rate and continuous record of reaction parameters, was developed to study kinetics of fast pyrolysis. The temperature effects, at a range of 400 C to 900 C, on pyrolysis rate, products profile, gas quality and quantity, and so on, were studied and the results are listed and analyzed. The effect of secondary reaction of gas phase at 700 C was tested and the regression result is expressed in an experimental formula. Based on the experimental results, the three-stage-reaction mechanism module is suggested. The kinetic expression to calculate gas formation rate is concluded as: d{alpha}/dt = A exp({minus}E/RT)(1 {minus} {alpha}){sup n}. The kinetic parameters of A, E, and n at different temperatures are given in the paper.

  9. Inverse Kinetics

    Energy Science and Technology Software Center (ESTSC)

    2000-03-20

    Given the space-independent, one energy group reactor kinetics equations and the initial conditions, this prgram determines the time variation of reactivity required to produce the given input of flux-time data.

  10. Pathways of ligand clearance in acetylcholinesterase by multiple copy sampling.

    PubMed

    Van Belle, D; De Maria, L; Iurcu, G; Wodak, S J

    2000-05-12

    somewhat different electrostatic potentials during their migration, because they explore different microscopic routes. The potential along the clearance route of a cation such as methylammonium displays two clear minima at the active and peripheral anionic site. We find moreover that the electrostatic energy barrier that the cation needs to overcome when moving between these two sites is small in both directions, being of the order of the ligand kinetic energy. The peripheral site thus appears to play a role in trapping inbound cationic ligands as well as in cation clearance, and hence in product release. PMID:10788331

  11. Conformational dynamics and thermodynamics of protein-ligand binding studied by NMR relaxation.

    PubMed

    Akke, Mikael

    2012-04-01

    Protein conformational dynamics can be critical for ligand binding in two ways that relate to kinetics and thermodynamics respectively. First, conformational transitions between different substates can control access to the binding site (kinetics). Secondly, differences between free and ligand-bound states in their conformational fluctuations contribute to the entropy of ligand binding (thermodynamics). In the present paper, I focus on the second topic, summarizing our recent results on the role of conformational entropy in ligand binding to Gal3C (the carbohydrate-recognition domain of galectin-3). NMR relaxation experiments provide a unique probe of conformational entropy by characterizing bond-vector fluctuations at atomic resolution. By monitoring differences between the free and ligand-bound states in their backbone and side chain order parameters, we have estimated the contributions from conformational entropy to the free energy of binding. Overall, the conformational entropy of Gal3C increases upon ligand binding, thereby contributing favourably to the binding affinity. Comparisons with the results from isothermal titration calorimetry indicate that the conformational entropy is comparable in magnitude to the enthalpy of binding. Furthermore, there are significant differences in the dynamic response to binding of different ligands, despite the fact that the protein structure is virtually identical in the different protein-ligand complexes. Thus both affinity and specificity of ligand binding to Gal3C appear to depend in part on subtle differences in the conformational fluctuations that reflect the complex interplay between structure, dynamics and ligand interactions. PMID:22435823

  12. Kinetic titration series with biolayer interferometry.

    PubMed

    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. PMID:25229647

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

    PubMed

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

    2015-03-11

    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

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

    PubMed Central

    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

  15. Influence of process parameters on the reaction kinetics of the chromium-catalyzed trimerization of ethylene.

    PubMed

    Wöhl, Anina; Müller, Wolfgang; Peitz, Stephan; Peulecke, Normen; Aluri, Bhaskar R; Müller, Bernd H; Heller, Detlef; Rosenthal, Uwe; Al-Hazmi, Mohammed H; Mosa, Fuad M

    2010-07-12

    In this paper we report the results of an extensive experimental kinetic study carried out on the novel ethylene trimerization catalyst system, comprising the chromium source [CrCl(3)(thf)(3)] (thf=tetrahydrofuran), a Ph(2)P-N(iPr)-P(Ph)-N(iPr)H (PNPNH) ligand (Ph=phenyl, iPr=isopropyl), and triethylaluminum (AlEt(3)) as activator. It could be shown that the initial activity shows a first-order dependency on the ethylene concentration. Also, a first-order dependency was found for the catalyst concentration. The initial activity follows a typical Arrhenius behavior with an experimentally determined activation energy of 52.6 kJ mol(-1). At elevated temperatures (ca. 80 degrees C), a significant deactivation was observed, which can be tentatively traced back to a ligand rearrangement in the presence of AlEt(3). After a fast initial phase, a pronounced 'kink' in the ethylene-uptake curve is observed, followed by a slow, almost linear, further increase of the total ethylene consumption. The catalyst composition, in particular the ligand/chromium and the cocatalyst/chromium molar ratio, has a strong impact on the catalytic performance of the trimerization of ethylene. PMID:20512824

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

    ERIC Educational Resources Information Center

    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…

  17. Effect of surface ligands on the optical properties of aqueous soluble CdTe quantum dots

    PubMed Central

    2012-01-01

    We investigate systematically the influence of the nature of thiol-type capping ligands on the optical and structural properties of highly luminescent CdTe quantum dots synthesized in aqueous media, comparing mercaptopropionic acid (MPA), thioglycolic acid (TGA), 1-thioglycerol (TGH), and glutathione (GSH). The growth rate, size distribution, and quantum yield strongly depend on the type of surface ligand used. While TGH binds too strongly to the nanocrystal surface inhibiting growth, the use of GSH results in the fastest growth kinetics. TGA and MPA show intermediate growth kinetics, but MPA yields a much lower initial size distribution than TGA. The obtained fluorescence quantum yields range from 38% to 73%. XPS studies unambiguously put into evidence the formation of a CdS shell on the CdTe core due to the thermal decomposition of the capping ligands. This shell is thicker when GSH is used as ligand, as compared with TGA ligands. PMID:23017183

  18. LigandRNA: computational predictor of RNA–ligand interactions

    PubMed Central

    Philips, Anna; Milanowska, Kaja; Łach, Grzegorz; Bujnicki, Janusz M.

    2013-01-01

    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. PMID:24145824

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

    DOEpatents

    Von Dreele, Robert B.

    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.

  20. EGF receptor ligands: recent advances

    PubMed Central

    Singh, Bhuminder; Carpenter, Graham; Coffey, Robert J.

    2016-01-01

    Seven ligands bind to and activate the mammalian epidermal growth factor (EGF) receptor (EGFR/ERBB1/HER1): EGF, transforming growth factor-alpha (TGFA), heparin-binding EGF-like growth factor (HBEGF), betacellulin (BTC), amphiregulin (AREG), epiregulin (EREG), and epigen (EPGN). Of these, EGF, TGFA, HBEGF, and BTC are thought to be high-affinity ligands, whereas AREG, EREG, and EPGN constitute low-affinity ligands. This focused review is meant to highlight recent studies related to actions of the individual EGFR ligands, the interesting biology that has been uncovered, and relevant advances related to ligand interactions with the EGFR.

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

    NASA Astrophysics Data System (ADS)

    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" (<10ps) response with and without the magnetic field application (the amplitude changes from ˜55% at 0 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

  2. Reduction of persulfate ion by carbon monoxide in alkaline medium: the effect of stoichiometric and astoichiometric components on the reaction Kinetics

    SciTech Connect

    Abilov, M.T.; Golodov, V.A.

    1986-06-01

    The effect of the concentration of oxidant, cadalyst, and various ligands on the kinetics of the oxidation of CO have been studied kinetically, potentiometrically, and spectrometrically, and a general mechanism for the process is proposed.

  3. Fast valve

    DOEpatents

    Van Dyke, W.J.

    1992-04-07

    A fast valve is disclosed that can close on the order of 7 milliseconds. It is closed by the force of a compressed air spring with the moving parts of the valve designed to be of very light weight and the valve gate being of wedge shaped with O-ring sealed faces to provide sealing contact without metal to metal contact. The combination of the O-ring seal and an air cushion create a soft final movement of the valve closure to prevent the fast air acting valve from having a harsh closing. 4 figs.

  4. Fast valve

    DOEpatents

    Van Dyke, William J.

    1992-01-01

    A fast valve is disclosed that can close on the order of 7 milliseconds. It is closed by the force of a compressed air spring with the moving parts of the valve designed to be of very light weight and the valve gate being of wedge shaped with O-ring sealed faces to provide sealing contact without metal to metal contact. The combination of the O-ring seal and an air cushion create a soft final movement of the valve closure to prevent the fast air acting valve from having a harsh closing.

  5. Exploring the mechanism of general anesthesia: kinetic analysis of GABAA receptor electrophysiology.

    PubMed

    Lee, Daniel K; Albershardt, Daniel J; Cantor, Robert S

    2015-03-10

    A kinetic model of the effect of agonist and anesthetics on ligand-gated ion channels, developed in earlier work, is further refined and used to predict traces observed in fast-perfusion electrophysiological studies on recombinant GABAA receptors under a wide range of agonist and/or anesthetic concentrations. The model incorporates only three conformational states (resting, open, and desensitized) but allows for the modulation of the conformational free energy landscape connecting these states resulting from adsorption of agonist and/or anesthetic to the bilayer in which the protein is embedded. The model is shown to reproduce the diverse and complex features of experimental traces remarkably well, including both anesthetic-induced and agonist-induced traces, as well as the modulation of agonist-induced traces by anesthetic, either coapplied or continuously present. The solutions to the kinetic equations, which give the time-dependence of each of the nine protein states (three ligation states for each of the three conformations), describe the flow of probability among these states and thus reveal the kinetic underpinnings of the traces. Many of the parameters in the model, such as the desorption rate constants of anesthetic and agonist, are directly related to model-independent experimental measurements and thus can serve as a definitive test of its validity. PMID:25762320

  6. Spectra Library: An Assumption-Free In Situ Method to Access the Kinetics of Catechols Binding to Colloidal ZnO Quantum Dots.

    PubMed

    Lin, Wei; Haderlein, Michael; Walter, Johannes; Peukert, Wolfgang; Segets, Doris

    2016-01-18

    Assumption-free and in situ resolving of the kinetics of ligand binding to colloidal nanoparticles (NPs) with high time resolution is still a challenge in NP research. A unique concept of using spectra library and stopped-flow together with a "search best-match" Matlab algorithm to access the kinetics of ligand binding in colloidal systems is reported. Instead of deconvoluting superimposed spectra using assumptions, species absorbance contributions (ligand@ZnO NPs and ligand in solution) are obtained by offline experiments. Therefrom, a library of well-defined targets with known ligand distribution between particle surface and solution is created. Finally, the evolution of bound ligand is derived by comparing in situ spectra recorded by stopped-flow and the library spectra with the algorithm. Our concept is a widely applicable strategy for kinetic studies of ligand adsorption to colloidal NPs and a big step towards deep understanding of surface functionalization kinetics. PMID:26636565

  7. Subnanometer Control of Mean Core Size during Mesofluidic Synthesis of Small (D(core) < 10 nm) Water-Soluble, Ligand-Stabilized Gold Nanoparticles.

    PubMed

    Elliott, Edward W; Haben, Patrick M; Hutchison, James E

    2015-11-01

    A convenient, single-step synthesis is reported that produces ligand-stabilized, water-soluble gold nanoparticles (AuNPs) with subnanometer-level precision of the mean core diameter over a range of 2-9 nm for a series of desired surface chemistries. The synthesis involves the reduction of a Au(III) species with sodium borohydride in the presence of a functionalized alkyl thiosulfate (Bunte salt) to yield thiolate-protected AuNPs. A key advantage of this synthesis is that simply adjusting the pH of the gold salt solution leads to control over the AuNP core size. The speciation of Au(III), and therefore the kinetics for its reduction and the core size produced, depends upon pH. The use of pH as the sole variable to control core size is a more reliable and convenient method than traditional approaches that rely on adjusting the concentrations and ratios of ligand, metal salt, and reducing agent. The average core size increased as the pH was raised for each ligand studied. Because the influence of pH was different for each of the ligands, working curves were plotted for each ligand to identify conditions to synthesize particles with specific, targeted core diameters. Using this approach, reaction conditions can be rapidly optimized using a combination of a mesofluidic reactor and small-angle X-ray scattering (SAXS) size analysis. The use of the mesofluidic reactor was needed to ensure fast mixing given the rapid kinetics for core formation. Using the reactor, it is possible to obtain reproducible sizes across multiple syntheses (<1-2% core size variation) and subnanometer control of the mean core dimensions. The synthetic method demonstrated here provides an attractive alternative to two-step syntheses involving ligand exchange because it is more efficient and eliminates the possibility of nanoparticle core size changes during exchange steps. This approach enables the development of "size ladders" of particles with the same surface chemistry for investigations of

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

    SciTech Connect

    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.

  9. New efficient ligand for sub-mol % copper-catalyzed C-N cross-coupling reactions running under air.

    PubMed

    Larsson, Per-Fredrik; Astvik, Peter; Norrby, Per-Ola

    2012-01-01

    A new efficient ligand, N,N''-dimethyldiethylene triamine (DMDETA), has been synthesized and evaluated for sub-mol % copper-catalyzed C-N cross-coupling reactions. The efficiency of the ligand was determined by kinetic methods. DMDETA proved to display efficiency similar to DMEDA and, in addition, the resulting catalyst was tolerant to air. PMID:23209530

  10. New efficient ligand for sub-mol % copper-catalyzed C–N cross-coupling reactions running under air

    PubMed Central

    Larsson, Per-Fredrik; Astvik, Peter

    2012-01-01

    Summary A new efficient ligand, N,N’’-dimethyldiethylene triamine (DMDETA), has been synthesized and evaluated for sub-mol % copper-catalyzed C–N cross-coupling reactions. The efficiency of the ligand was determined by kinetic methods. DMDETA proved to display efficiency similar to DMEDA and, in addition, the resulting catalyst was tolerant to air. PMID:23209530