Science.gov

Sample records for fast kinetic ligands

  1. Kinetics of ligand binding to nucleic acids.

    PubMed

    Arakelyan, V B; Babayan, S Y; Tairyan, V I; Arakelyan, A V; Parsadanyan, M A; Vardevanyan, P O

    2006-02-01

    Ligand binding to nucleic acids (NA) is considered as a stationary Markov process. It is shown that the probabilistic description of ligand-NA binding allows one to describe not only the kinetics of the change of number of bound ligands at arbitrary fillings but also to calculate stationary values of the number of bound ligands and its dispersion. The general analysis of absorption isotherms and kinetics of ligand binding to NA make it possible to determine of rate constants of ligand-NA complex formation and dissociation.

  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. Adsorption and Exchange Kinetics of Hydrophilic and Hydrophobic Phosphorus Ligands on Gold Surface

    NASA Astrophysics Data System (ADS)

    Zhuge, X. Q.; Bian, Z. C.; Luo, Z. H.; Mu, Y. Y.; Luo, K.

    2017-02-01

    The adsorption kinetics process of hydrophobic ligand (triphenylphosphine, PPh3) and hydrophilic ligand (tris(hydroxymethyl)phosphine oxide, THPO) on the surface of gold electrode were estimated by using electrical double layer capacitance (EDLC). Results showed that the adsorption process of both ligands included fast and slow adsorption processes, and the fast adsorption process could fit the first order kinetic equation of Langmuir adsorption isotherm. During the slow adsorption process, the surface coverage (θ) of PPh3 was higher than that of THPO due to the larger adsorption kinetic constant of PPh3 than that of THPO, which implied that PPh3 could replace THPO on the gold electrode. The exchange process of both ligands on the surface of gold electrode proved that PPh3 take the place of THPO by testing the variation of EDLC which promote the preparation of Janus gold, and the theoretic simulation explained the reason of ligands exchange from the respect of energy..

  4. [Kinetics of ligand binding to nucleic acids at random fillings].

    PubMed

    Arakelian, V B; Babaian, S Iu; Tairian, V I; Arakelian, A V; Parsadanian, M A; Vardevanian, P O

    2006-01-01

    Ligand binding with nucleic acids is described in frames of the theory of random processes. It is shown that the probabilistic description of binding of a ligand to nucleic acid allows one to describe not only the kinetics of changes in the number of bound ligands at arbitrary fillings but also to calculate stationary values of the number of bound ligands and its dispersion. A general analysis of absorption isotherms and the kinetics of ligand binding with nucleic acids allows one to determine the rate constants of formation and decomposition of the ligand-nucleic acid complex. A comparison of the results obtained with the case of low fillings is conducted.

  5. A PET imaging agent with fast kinetics: synthesis and in vivo evaluation of the serotonin transporter ligand [11C]2-[2-dimethylaminomethylphenylthio)]-5-fluorophenylamine ([11C]AFA).

    PubMed

    Huang, Yiyun; Narendran, Raj; Bae, Sung-A; Erritzoe, David; Guo, Ningning; Zhu, Zhihong; Hwang, Dah-Ren; Laruelle, Marc

    2004-08-01

    A new serotonin transporter (SERT) ligand, [11C]2-[2-(dimethylaminomethylphenylthio)]-5-fluorophenylamine (10, [11C]AFA), was synthesized and evaluated as a candidate PET radioligand in pharmacological and pharmacokinetic studies. As a PET radioligand, AFA (8) can be labeled with either C-11 or F-18. In vitro, AFA displayed high affinity for SERT (Ki 1.46 +/- 0.15 nM) and lower affinity for norepinephrine transporter (NET, Ki 141.7 +/- 47.4 nM) or dopamine transporter (DAT, Ki > 10,000 nM). [11C]AFA (10) was prepared from its monomethylamino precursor 9 by reaction with high specific activity [11C]methyl iodide. Radiochemical yield was 43 +/- 20% based on [11C]methyl iodide at end of bombardment (EOB, n = 10) and specific activity was 2,129 +/- 1,369 Ci/mmol at end of synthesis (EOS, n = 10). Biodistribution studies in rats indicated that [11C]AFA accumulated in brain regions known to contain high concentrations of SERT. Binding in SERT-rich brain regions was reduced significantly by pretreatment with either the cold compound 8 or with the selective serotonin reuptake inhibitor (SSRI) citalopram, but not by the selective norepinephrine reuptake inhibitor nisoxetine, thus underlining its in vivo binding selectivity and specificity for SERT. Imaging experiments in baboons demonstrated that the uptake pattern of [11C]AFA in the baboon brain is consistent with the known distribution of SERT, with highest activity levels in the midbrain and thalamus, followed by striatum, hippocampus, and cortical regions. Activity levels in the baboon brain peaked at 15-40 min after radioligand injection, indicating a fast uptake kinetics for [11C]AFA. Pretreatment of the baboon with citalopram (4 mg/kg) significantly reduced the specific binding of [11C]AFA in all SERT-containing brain regions. Kinetic analysis revealed that the regional equilibrium specific to non-specific partition coefficients (V3") of [11C]AFA are similar to those of [11C]McN5652, but lower than those of [11C

  6. (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

  7. (S)-5-(p-nitrobenzyl)-PCTA, a promising bifunctional ligand with advantageous metal ion complexation kinetics.

    PubMed

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

    2009-03-18

    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(NO(2)-Bn-PCTA) (M = Mg(2+), Ca(2+), Cu(2+), Zn(2+)) complexes was similar to that of the corresponding PCTA complexes, while the stability of Ln(3+) complexes of the bifunctional ligand is somewhat lower than that of PCTA chelates. The rate of complex formation of Ln(NO(2)-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(NO(2)-Bn-PCTA) complexes showed that the kinetic inertness of the complexes was comparable to that of Ln(DOTA) chelates making the bifunctional ligand NO(2)-Bn-PCTA suitable for labeling biological vectors with radioisotopes for nuclear medicine applications.

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

    PubMed

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

    2016-04-21

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

  9. Active biopolymers confer fast reorganization kinetics.

    PubMed

    Swanson, Douglas; Wingreen, Ned S

    2011-11-18

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

  10. 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.

  11. Estimation of kinetic and thermodynamic ligand-binding parameters using computational strategies.

    PubMed

    Deganutti, Giuseppe; Moro, Stefano

    2017-03-31

    Kinetic and thermodynamic ligand-protein binding parameters are gaining growing importance as key information to consider in drug discovery. The determination of the molecular structures, using particularly x-ray and NMR techniques, is crucial for understanding how a ligand recognizes its target in the final binding complex. However, for a better understanding of the recognition processes, experimental studies of ligand-protein interactions are needed. Even though several techniques can be used to investigate both thermodynamic and kinetic profiles for a ligand-protein complex, these procedures are very often laborious, time consuming and expensive. In the last 10 years, computational approaches have enormous potential in providing insights into each of the above effects and in parsing their contributions to the changes in both kinetic and thermodynamic binding parameters. The main purpose of this review is to summarize the state of the art of computational strategies for estimating the kinetic and thermodynamic parameters of a ligand-protein binding.

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

    PubMed

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

    2008-05-15

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

  15. Kinetics of binding of fluorescent ligands to enzymes with engineered access tunnels.

    PubMed

    Kaushik, Shubhangi; Prokop, Zbynek; Damborsky, Jiri; Chaloupkova, Radka

    2017-01-01

    Molecular recognition mechanisms and kinetics of binding of ligands to buried active sites via access tunnels are not well understood. Fluorescence polarization enables rapid and non-destructive real-time quantification of the association between small fluorescent ligands and large biomolecules. In this study, we describe analysis of binding kinetics of fluorescent ligands resembling linear halogenated alkanes to haloalkane dehalogenases. Dehalogenases possess buried active sites connected to the surrounding solvent by access tunnels. Modification of these tunnels by mutagenesis has emerged as a novel strategy to tailor the enzyme properties. We demonstrate that the fluorescence polarization method can sense differences in binding kinetics originating from even single mutations introduced to the tunnels. The results show, strikingly, that the rate constant of the dehalogenase variants varied across seven orders of magnitude, and the type of ligand used strongly affected the binding kinetics of the enzyme. Furthermore, fluorescence polarization could be applied to cell-free extracts instead of purified proteins, extending the method's application to medium-throughput screening of enzyme variant libraries generated in directed evolution experiments. The method can also provide in-depth kinetic information about the rate-determining step in binding kinetics and reveals the bottlenecks of enzyme accessibility. Assuming availability of appropriate fluorescent ligand, the method could be applied for analysis of accessibility of tunnels and buried active sites of enzymes forming a covalent alkyl-enzyme intermediate during their catalytic cycle, such as α/β-hydrolases containing > 100 000 protein sequences based on the Pfam database.

  16. 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.

  17. A kinetic description of ligand binding to sperm whale myoglobin.

    PubMed

    Gibson, Q H; Olson, J S; McKinnie, R E; Rohlfs, R J

    1986-08-05

    Nanosecond recombination time courses were measured by photolyzing O2, NO, CO, methyl, ethyl, n-propyl, n-butyl, and tert-butyl isocyanide complexes of sperm whale myoglobin with a 30-ns laser pulse at pH 7, 20 degrees C. Absorbance was measured both during and after the excitation pulse and as a function of laser light intensity. The results were analyzed quantitatively in terms of a three-step reaction scheme, MbX in equilibrium B in equilibrium C in equilibrium Mb + X, where Mb is myoglobin, B represents a geminate state in which the ligand is present in the distal pocket but not covalently bound to the iron atom, and C, a state in which the ligand is still embedded in the protein but further away from the heme group. The fitted rate parameters were required to be consistent with the observed overall quantum yield, Q, which had been measured independently using much longer (approximately 0.5 ms) xenon flash pulses. Three major conclusions were derived from these analyses. First, the overall quantum yield of the ligand complex is determined primarily by the competition between the rate of iron-ligand bond formation from the initial photoproduct, kB----MbX, and the rate of migration away from state B, kB----C. For example, kB----C approximately equal to 30-100 microseconds-1 for all three gaseous ligands, whereas both Q and kB----MbX vary over 3 orders of magnitude (i.e. NO, Q = 0.001, kB----MbX approximately equal to 16,000 microseconds-1; O2, Q = 0.1, kB----MbX approximately equal to 500 microseconds-1; CO, Q = 1.0, kB----MbX approximately equal to 2 microseconds-1). Second, for NO, O2, and the isonitriles, the rate-limiting step in the overall association reaction starting from ligand in solution is the formation of state B. The rate constant for this process varies from 2 X 10(7) M-1 s-1 for the gaseous ligands to 0.02-1.4 X 10(5) M-1 s-1 for the isonitriles. In contrast, the B to MbX transition is limiting for CO binding. Third, for all the ligands except CO

  18. 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.

  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. Copper(II) complexes of quinoline polyazamacrocyclic scorpiand-type ligands: X-ray, equilibrium and kinetic studies.

    PubMed

    Castillo, Carmen E; Angeles Máñez, M; Basallote, Manuel G; Paz Clares, M; Blasco, Salvador; García-España, Enrique

    2012-05-14

    The formation of Cu(II) complexes with two isomeric quinoline-containing scorpiand-type ligands has been studied. The ligands have a tetraazapyridinophane core appended with an ethylamino tail including 2-quinoline (L1) or 4-quinoline (L2) functionalities. Potentiometric studies indicate the formation of stable CuL(2+) species with both ligands, the L1 complex being 3-4 log units more stable than the L2 complex. The crystal structure of [Cu(L1)](ClO(4))(2)·H(2)O shows that the coordination geometry around the Cu(2+) ions is distorted octahedral with significant axial elongation; the four Cu-N distances in the equatorial plane vary from 1.976 to 2.183 Å, while the axial distances are of 2.276 and 2.309 Å. The lower stability of the CuL2(2+) complex and its capability of forming protonated and hydroxo complexes suggest a penta-dentate coordination of the ligand, in agreement with the type of substitution at the quinoline ring. Kinetic studies on complex formation can be interpreted by considering that initial coordination of L1 and L2 takes place through the nitrogen atom in the quinoline ring. This is followed by coordination of the remaining nitrogen atoms, in a process that is faster in the L1 complex probably because substitution at the quinoline ring facilitates the reorganization. Kinetic studies on complex decomposition provide clear evidence on the occurrence of the molecular motion typical of scorpiands in the case of the L2 complex, for which decomposition starts with a very fast process (sub-millisecond timescale) that involves a shift in the absorption band from 643 to 690 nm.

  1. Kinetics of Denitrifying Growth by Fast-Growing Cowpea Rhizobia

    PubMed Central

    El Hassan, G. A.; Zablotowicz, R. M.; Focht, D. D.

    1985-01-01

    Two fast-growing strains of cowpea rhizobia (A26 and A28) were found to grow anaerobically at the expense of NO3−, NO2−, and N2O as terminal electron acceptors. The two major differences between aerobic and denitrifying growth were lower yield coefficients (Y) and higher saturation constants (Ks) with nitrogenous oxides as electron acceptors. When grown aerobically, A26 and A28 adhered to Monod kinetics, respectively, as follows: Ks, 3.4 and 3.8 μM; Y, 16.0 and 14.0 g · cells eq−1; μmax, 0.41 and 0.33 h−1. Yield coefficients for denitrifying growth ranged from 40 to 70% of those for aerobic growth. Only A26 adhered to Monod kinetics with respect to growth on all three nitrogenous oxides. The apparent Ks values were 41, 270, and 460 μM for nitrous oxide, nitrate, and nitrite, respectively; the Ks for A28 grown on nitrate was 250 μM. The results are kinetically and thermodynamically consistent in explaining why O2 is the preferred electron acceptor. Although no definitive conclusions could be drawn regarding preferential utilization of nitrogenous oxides, nitrite was inhibitory to both strains and effected slower growth. However, growth rates were identical (μmax, 0.41 h−1) when A26 was grown with either O2 or NO3− as an electron acceptor and were only slightly reduced when A28 was grown with NO3− (0.25 h−1) as opposed to O2 (0.33 h−1). PMID:16346745

  2. 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

  3. Kinetics of membrane adhesion mediated by ligand-receptor interaction studied with a biomimetic system.

    PubMed Central

    Boulbitch, A; Guttenberg, Z; Sackmann, E

    2001-01-01

    We report the first measurement of the kinetics of adhesion of a single giant vesicle controlled by the competition between membrane-substrate interaction mediated by ligand-receptor interaction, gravitation, and Helfrich repulsion. To model the cell-tissue interaction, we doped the vesicles with lipid-coupled polymers (mimicking the glycocalix) and the reconstituted ligands selectively recognized by alpha(IIb)beta(3) integrin-mediating specific attraction forces. The integrin was grafted on glass substrates to act as a target cell. The adhesion of the vesicle membrane to the integrin-covered surface starts with the spontaneous formation of a small (approximately 200 nm) domain of tight adhesion, which then gradually grows until the whole adhesion area is in the state of tight adhesion. The time of adhesion varies from few tens of seconds to about one hour depending on the ligand and lipopolymer concentration. At small ligand concentrations, we observed the displacement xi of the front of tight adhesion following the square root law xi approximately t(1/2), whereas, at high concentrations, we found a linear law xi approximately t. We show both experimentally and theoretically that the t(1/2)-regime is dominated by diffusion of ligands, and the xi approximately t-regime by the kinetics of ligands-receptors association. PMID:11606287

  4. Ligand-receptor binding kinetics in surface plasmon resonance cells: a Monte Carlo analysis

    NASA Astrophysics Data System (ADS)

    Carroll, Jacob; Raum, Matthew; Forsten-Williams, Kimberly; Täuber, Uwe C.

    2016-12-01

    Surface plasmon resonance (SPR) chips are widely used to measure association and dissociation rates for the binding kinetics between two species of chemicals, e.g., cell receptors and ligands. It is commonly assumed that ligands are spatially well mixed in the SPR region, and hence a mean-field rate equation description is appropriate. This approximation however ignores the spatial fluctuations as well as temporal correlations induced by multiple local rebinding events, which become prominent for slow diffusion rates and high binding affinities. We report detailed Monte Carlo simulations of ligand binding kinetics in an SPR cell subject to laminar flow. We extract the binding and dissociation rates by means of the techniques frequently employed in experimental analysis that are motivated by the mean-field approximation. We find major discrepancies in a wide parameter regime between the thus extracted rates and the known input simulation values. These results underscore the crucial quantitative importance of spatio-temporal correlations in binary reaction kinetics in SPR cell geometries, and demonstrate the failure of a mean-field analysis of SPR cells in the regime of high Damköhler number {{Da}}\\gt 0.1, where the spatio-temporal correlations due to diffusive transport and ligand-receptor rebinding events dominate the dynamics of SPR systems.

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

    PubMed

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

    2013-01-01

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

  6. Gompertz kinetics model of fast chemical neurotransmission currents.

    PubMed

    Easton, Dexter M

    2005-10-01

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

  7. Laminar-flow fluid mixer for fast fluorescence kinetics studies.

    PubMed Central

    Pabit, Suzette A; Hagen, Stephen J

    2002-01-01

    The ability to mix aqueous liquids on microsecond time scales, while consuming minimal amounts of sample and maintaining UV-visible optical access to the mixing region, is highly desirable for a range of biophysical studies of fast protein and nucleic acid interactions and folding. We have constructed a laminar coaxial jet mixer that allows the measurement of UV-excited fluorescence from nanoliter and microliter quantities of material, mixed at microsecond rates. The mixer injects a narrow cylindrical stream (radius a < 1 microm) of fluorescent sample into a larger flow of diluting buffer that moves through a capillary (100 microm i.d.) at a speed approximately 20 cm/s, under laminar flow conditions (Re approximately equal to 14). Construction from a fused silica capillary allows the laser excitation (at 266 nm) and detection (at 350 nm) of tryptophan fluorescence at reasonably low working concentrations, without interference from background fluorescence. Using this mixer we have measured sub-millisecond fluorescence quenching kinetics while consuming fluorescent sample at rates no greater than 6 nl/s. Consumption of the diluting buffer is also very modest (approximately 1-3 microl/s) in comparison with other rapid mixer designs. PMID:12414719

  8. 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.

  9. Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models

    PubMed Central

    Plattner, Nuria; Noé, Frank

    2015-01-01

    Understanding the structural mechanisms of protein–ligand binding and their dependence on protein sequence and conformation is of fundamental importance for biomedical research. Here we investigate the interplay of conformational change and ligand-binding kinetics for the serine protease Trypsin and its competitive inhibitor Benzamidine with an extensive set of 150 μs molecular dynamics simulation data, analysed using a Markov state model. Seven metastable conformations with different binding pocket structures are found that interconvert at timescales of tens of microseconds. These conformations differ in their substrate-binding affinities and binding/dissociation rates. For each metastable state, corresponding solved structures of Trypsin mutants or similar serine proteases are contained in the protein data bank. Thus, our wild-type simulations explore a space of conformations that can be individually stabilized by adding ligands or making suitable changes in protein sequence. These findings provide direct evidence of conformational plasticity in receptors. PMID:26134632

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

    PubMed

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

    2015-12-28

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

  11. Impact of human galectin-1 binding to saccharide ligands on dimer dissociation kinetics and structure.

    PubMed

    Romero, Juan M; Trujillo, Madia; Estrin, Darío A; Rabinovich, Gabriel A; Di Lella, Santiago

    2016-12-01

    Endogenous lectins can control critical biological responses, including cell communication, signaling, angiogenesis and immunity by decoding glycan-containing information on a variety of cellular receptors and the extracellular matrix. Galectin-1 (Gal-1), a prototype member of the galectin family, displays only one carbohydrate recognition domain and occurs in a subtle homodimerization equilibrium at physiologic concentrations. Such equilibrium critically governs the function of this lectin signaling by allowing tunable interactions with a preferential set of glycosylated receptors. Here, we used a combination of experimental and computational approaches to analyze the kinetics and mechanisms connecting Gal-1 ligand unbinding and dimer dissociation processes. Kinetic constants of both processes were found to differ by an order of magnitude. By means of steered molecular dynamics simulations, the ligand unbinding process was followed monitoring water occupancy changes. By determining the water sites in a carbohydrate binding place during the unbinding process, we found that rupture of ligand-protein interactions induces an increase in energy barrier while ligand unbinding process takes place, whereas the entry of water molecules to the binding groove and further occupation of their corresponding water sites contributes to lowering of the energy barrier. Moreover, our findings suggested local asymmetries between the two subunits in the dimer structure detected at a nanosecond timescale. Thus, integration of experimental and computational data allowed a more complete understanding of lectin ligand binding and dimerization processes, suggesting new insights into the relationship between Gal-1 structure and function and renewing the discussion on the biophysics and biochemistry of lectin-ligand lattices.

  12. Ligand recombination and a hierarchy of solvent slaved dynamics: the origin of kinetic phases in hemeproteins.

    PubMed

    Samuni, Uri; Dantsker, David; Roche, Camille J; Friedman, Joel M

    2007-08-15

    Ligand recombination studies play a central role both for characterizing different hemeproteins and their conformational states but also for probing fundamental biophysical processes. Consequently, there is great importance to providing a foundation from which one can understand the physical processes that give rise to and modulate the large range of kinetic patterns associated with ligand recombination in myoglobins and hemoglobins. In this work, an overview of cryogenic and solution phase recombination phenomena for COMb is first reviewed and then a new paradigm is presented for analyzing the temperature and viscosity dependent features of kinetic traces in terms of multiple phases that reflect which tier(s) of solvent slaved protein dynamics is (are) operative on the photoproduct population during the time course of the measurement. This approach allows for facile inclusion of both ligand diffusion among accessible cavities and conformational relaxation effects. The concepts are illustrated using kinetic traces and MEM populations derived from the CO recombination process for wild type and mutant myoglobins either in sol-gel matrices bathed in glycerol or in trehalose-derived glassy matrices.

  13. Theory of Kinetics of Multistep Ligand-Receptor Assembly in Dissipating and Fluctuating Environments

    NASA Astrophysics Data System (ADS)

    Teslenko, Victor I.; Kapitanchuk, Oleksiy L.

    2013-09-01

    Multistep kinetic processes play a key role in physics (excitation transfer, energy degradation), chemistry (ligand-receptor assembly, radical reactions) and biology (signal perception, molecular recognition). While a phenomenological thermodynamic approach for modeling the elementary acts of transitions underlying the maintaining of a system's stationary and equilibrium states is now well recognized, a more satisfying microscopic description based on the consistent understanding of dissipation and fluctuation processes accompanying the multistep relaxations remains elusive. In this paper, a microscopic theory of kinetics of a few-state system exhibited the energy fluctuations and coupled to a condensed medium is developed. The theory is formulated such as of being an example of the case of irreversible multistep ligand-receptor assembly in a dissipating environment. We first derive general expression for the probability of transitions between the system states valid on the whole timescale and then reduce this expression to the effectively slow times by making it an average over both the steady-state fluctuations of a system's energies and the equilibrium vibrations of the environment. Further, we calculate the populations of states for the sequence of cases of the three-to-two-to-single-step assemblage in dependence on the temperature, viscosity and ligand concentration. Finally, we discuss the results obtained with reference to the case of "negative" cooperativity emerging by virtue of the irreversibility of the last kinetic step.

  14. Oriented attachment kinetics for ligand capped nanocrystals: coarsening of thiol-PbS nanoparticles.

    PubMed

    Zhang, Jing; Wang, Yonghao; Zheng, Jinsheng; Huang, Feng; Chen, Dagui; Lan, Youzhao; Ren, Guoqiang; Lin, Zhang; Wang, Chen

    2007-02-15

    In this work, the growth kinetics of thiol-capped PbS nanoparticles was studied. Two-stage growth process was observed, which was controlled first by oriented attachment (OA) mechanism and then by the hybrid Ostwald ripening (OR) and OA mechanism. Different from the NaOH-ZnS system, where OA will occur between any two multilevel nanoparticles, an OA kinetic model only considering the attachment related to original particles was fitted well with the experimental results. Analysis reveals that this model may be a universal one to describe the OA crystal growth process of nanocrystals capped with easily destroyed ligands, such as thiol-ZnS in the previous report. The OA crystal growth characteristics determined by the surface agent were discussed and compared. We propose that with stronger surface capping, the OR growth of nanocrystals is hindered, which facilitates the size controlling via OA kinetics during nanosynthesis.

  15. 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

  16. Measuring two-dimensional receptor-ligand binding kinetics by micropipette.

    PubMed Central

    Chesla, S E; Selvaraj, P; Zhu, C

    1998-01-01

    We report a novel method for measuring forward and reverse kinetic rate constants, kf0 and kr0, for the binding of individual receptors and ligands anchored to apposing surfaces in cell adhesion. Not only does the method examine adhesion between a single pair of cells; it also probes predominantly a single receptor-ligand bond. The idea is to quantify the dependence of adhesion probability on contact duration and densities of the receptors and ligands. The experiment was an extension of existing micropipette protocols. The analysis was based on analytical solutions to the probabilistic formulation of kinetics for small systems. This method was applied to examine the interaction between Fc gamma receptor IIIA (CD16A) expressed on Chinese hamster ovary cell transfectants and immunoglobulin G (IgG) of either human or rabbit origin coated on human erythrocytes, which were found to follow a monovalent biomolecular binding mechanism. The measured rate constants are Ackf0 = (2.6 +/- 0.32) x 10(-7) micron 4 s-1 and kr0 = (0.37 +/- 0.055) s-1 for the CD16A-hIgG interaction and Ackf0 = (5.7 +/- 0.31) X 10(-7) micron 4 s-1 and kr0 = (0.20 +/- 0.042) s-1 for the CD16A-rIgG interaction, respectively, where Ac is the contact area, estimated to be a few percent of 3 micron 2. PMID:9726957

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

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

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

    PubMed

    Korzeniewski, Bernard; Zoladz, Jerzy A

    2013-09-01

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

  19. 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.

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

    PubMed

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

    2006-06-09

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

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

    PubMed

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

    2016-02-07

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

  2. 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.

  3. Kinetic theory of ligand recombination of myoglobin: a model for a combination of entropic and enthalpic effects

    NASA Astrophysics Data System (ADS)

    Yang, Dah-Yen; Sheu, Wen-Shyan; Sheu, Sheh-Yi; Lin, S. H.

    A kinetic theory of ligand recombination of myoglobin is obtained through a microscopic model. The macroscopic time dependent rate constant is obtained by the first passage time distribution random walk method. When the ligand is outside the haem pocket, it diffuses in a continuum space. In this process, this rate corresponds to a Smoluchowski rate constant times the concentration of myoglobin. After penetrating through the hydration shell, the ligand waits in front of the gate or diffuses on the myoglobin surface for entering the gate. This waiting time refers to a large scale fluctuation of protein to open the gate. When the ligand is inside the pocket, the motion of the ligand ranges from a ballistic to a diffusive limit. To cover the whole range of friction, it is necessary to solve exactly a finite area random walk model with periodic gating in one- and two-dimensional finite lattices with slippery boundary conditions. Protein dynamics influence the ligand motion indirectly through the collision between the ligand and the heme pocket well. The first step corresponds to an adiabatic dissociation process. A branching diagram method is used to show a detailed pathway analysis of the adiabaticity by introducing intermediate states in the quintet states for the CO ligand binding. The rate theories of ligand recombination of myoglobin are a combination of entropic and enthalpic effects.

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

    PubMed

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

    2017-02-24

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

  6. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

    The effect of ionic strength (I) on the ligand exchange reaction between a mononuclear ferric citrate complex and the siderophore, desferrioxamine B (DFB), was examined in the NaCl concentration range of 0.01-0.5 M, particularly focusing on the kinetics and mechanism of ligand exchange under environmentally relevant conditions. Overall ligand exchange rate constants were determined by spectrophotometrically measuring the time course of ferrioxamine B formation at a water temperature of 25 °C, pH 8.0, and citrate/Fe molar ratios of 500-5000. The overall ligand exchange rate decreased by 2-11-fold (depending on the citrate/Fe molar ratios) as I increased from approximately 0.01 to 0.5 M. In particular, a relatively large decrease was observed at lower I (<0.1 M). A ligand exchange model describing the effect of I on the ligand exchange rate via disjunctive and adjunctive pathways was developed by considering the pseudo-equilibration of ferric citrate complexes and subsequent ferrioxamine formation on the basis of the Eigen-Wilkins metal-ligand complexation theory. The model and experimental data consistently suggest that the adjunctive pathway (i.e., direct association of DFB with ferric mono- and di-citrate complexes following dissociation of citrate from the parent complexes) dominates in ferrioxamine formation under the experimental conditions used. The model also predicts that the higher rate of ligand exchange at lower I is associated with the decrease in the ferric dicitrate complex stability because of the relatively high electrical repulsion between ferric monocitrate and free citrate at lower I (note that the reactivity of ferric dicitrate with DFB is smaller than that for the monocitrate complex). Overall, the findings of this study contribute to the understanding of the potential effect of I on ligand exchange kinetics in natural waters and provide fundamental knowledge on iron transformation and bioavailability.

  8. Kinetics and Mechanism of the Ligand Exchange Reaction Between Tetraaza Macrocycle Ligand and Cu(II) Tetradentate Amine-Amide Complexes.

    PubMed

    Vafazadeh, Rasoul; Zare-Sadrabadi, Ghasem

    2015-01-01

    The kinetics of the ligand exchange reaction of tetraaza macrocycle, teazma (teazmais 5,7,7,12,14,14-hexamethyl-1,4,8,11-tetraazacyclotetradeca-4,11-diene dihydrogen perchlorate) with Cu(bcen)(2+) and Cu(bctn)(2+), where bcen and bctn are N,N'-bis(β-carbamoylethyl) ethylendiamine) and N,N'-bis(β-carbamoylethyl) propylendiamine), respectively, have been studied by visible spectrophotometry in dimethylformamide, DMF, solvent at 25 ± 0.2°C. In the system of Cu(bctn)(2+)/teazma,the ligand exchange reaction proceeds in a two-step-consecutive manner, with two rate constants k(bctn)(obsd)(1) and k(bctn)(obsd)(2). The first reaction step was dependent on the concentration of teazma macrocycle, while the second reaction step was independent. However, it is found that the ligand exchange reaction in Cu(bcen)(2+)/teazma proceeds in an one-step with the rate constant k(bcen)(obsd). The rate constant is dependent on [teazma] macrocycle. The ligand exchange reaction in the system of Cu(bcen)(2+)/teazma is not complete and after some progress, the reaction reaches equilibrium. On the basis of results, a reaction mechanism is proposed and discussed for the ligand exchange rate.

  9. The use of kinetic modelling as a fast way to screen thermal endurance of space materials

    NASA Astrophysics Data System (ADS)

    Moser, M.; Heltzel, S.; Semprimoschnig, C.; Garcia Martin, G.

    2003-09-01

    Currently planned missions of ESA (European Space Agency) to the inner part of the solar system will require the use of materials at an extreme radiation and temperature environment. A major concern regarding the selection of these materials is the thermal behaviour and the thermal stability. In this paper two kinetic models, the one following the ASTM E 1641 and ASTM E 1877 standards and the other following the Model Free Kinetics (MFK) approach, are presented. These models allow an easy and fast way to screen the thermal endurance of organic materials by running Thermo Gravimetric Analyses (TGA) temperature scans.

  10. 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.

  11. 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.

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

    PubMed

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

    2017-04-01

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

  13. 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.

  14. Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®

    NASA Astrophysics Data System (ADS)

    Morley, S. David; Afshar, Mohammad

    2004-03-01

    We report the design and validation of a fast empirical function for scoring RNA-ligand interactions, and describe its implementation within RiboDock®, a virtual screening system for automated flexible docking. Building on well-known protein-ligand scoring function foundations, features were added to describe the interactions of common RNA-binding functional groups that were not handled adequately by conventional terms, to disfavour non-complementary polar contacts, and to control non-specific charged interactions. The results of validation experiments against known structures of RNA-ligand complexes compare favourably with previously reported methods. Binding modes were well predicted in most cases and good discrimination was achieved between native and non-native ligands for each binding site, and between native and non-native binding sites for each ligand. Further evidence of the ability of the method to identify true RNA binders is provided by compound selection (`enrichment factor') experiments based around a series of HIV-1 TAR RNA-binding ligands. Significant enrichment in true binders was achieved amongst high scoring docking hits, even when selection was from a library of structurally related, positively charged molecules. Coupled with a semi-automated cavity detection algorithm for identification of putative ligand binding sites, also described here, the method is suitable for the screening of very large databases of molecules against RNA and RNA-protein interfaces, such as those presented by the bacterial ribosome. Abbreviations: ACD - Available Chemicals Directory; AMP - adenosine monophosphate; EF - enrichment factor; FMN - flavin mononucleotide; FRET - fluorescence resonance energy transfer; RMSD - root mean square deviation; TAR - trans-activation response element; Tat - transcriptional activator protein.

  15. Synthesis, characterization, dynamics and reactivity toward amination of η3-allyl palladium complexes bearing mixed ancillary ligands. Evaluation of the electronic characteristics of the ligands from kinetic data.

    PubMed

    Canovese, Luciano; Visentin, Fabiano; Levi, Carlo; Dolmella, Alessandro

    2011-01-28

    On the basis of an original protocol, we have synthesized several complexes of the type [Pd(η(3)-C(3)H(3)R(2))(LL')]ClO(4) (R = H, Me; L, L' = PPh(3), P(OEt)(3), 2,6-dimethylphenylisocyanide, t-butylisocyanide, 1,3-dimesitylimidazolidine, 1,3-dimesitylimidazol-2-ylidene). The complexes, some of which are completely new species, were fully characterized and their behaviour in solution was studied by means of (1)H NMR. The reactions of the complexes bearing the symmetric allyl moiety [Pd(η(3)-C(3)H(5))(LL')]ClO(4) with piperidine in the presence of the olefin dimethylfumarate were followed under kinetically controlled conditions. Formation of allyl-amine and of the palladium(0) derivatives [Pd(η(2)-dmfu)(LL'] was observed. The reaction rates k(2) proved to be strongly dependent on the ancillary ligand nature and allowed a direct comparison among the electronic characteristics of the ligands. The reactivity trend determined appears to be mainly influenced by the capability of the ancillary ligands in transferring electron density to the metal centre and consequently on the allyl fragment.

  16. Nanosecond Pulse Discharges and Fast Ionization Wave Discharges: Fundamental Kinetic Processes and Applications

    NASA Astrophysics Data System (ADS)

    Adamovich, Igor

    2011-10-01

    Over the last two decades, nanosecond pulse discharges and Fast Ionization Wave (FIW) discharges have been studied extensively, both theoretically and experimentally. Current interest in characterization of these discharges is driven mainly by their potential for applications such as plasma chemical fuel reforming, plasma-assisted combustion, high-speed flow control, pumping of electric discharge excited lasers, and generation of high-energy electrons. A unique capability of FIW discharges to generate significant ionization and high concentrations of excited species at high pressures and over large distances, before ionization instabilities have time to develop, is very attractive for these applications. Recent advances in laser optical diagnostics offer an opportunity of making non-intrusive, spatially and time-resolved measurements of electron density and electric field distributions in high-speed ionization wave discharges, on nanosecond time scale. Insight into FIW formation and propagation dynamics also requires development of predictive kinetic models, and their experimental validation. Although numerical kinetic models may incorporate detailed kinetics of charged and neutral species in the propagating ionization wave front (including non-local electron kinetics), analytic models are also attractive due to their capability of elucidating fundamental trends of discharge development. The talk gives an overview of recent progress in experimental characterization and kinetic modeling of nanosecond pulse and fast ionization wave discharges in nitrogen and air over a wide range of pulse repetition rates, 0.1-40 kHz. FIW discharge plasmas sustained at high pulse repetition rates are diffuse and volume filling, with most of the power coupled to the plasma behind the wave, at E/N = 200-300 Td and energy loading of 1-2 meV/molecule/pulse. The results demonstrate significant potential of large volume, diffuse, high pulse repetition rate FIW discharges for novel plasma

  17. 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.

  18. Probing fast ribozyme reactions under biological conditions with rapid quench-flow kinetics.

    PubMed

    Bingaman, Jamie L; Messina, Kyle J; Bevilacqua, Philip C

    2017-03-14

    Reaction kinetics on the millisecond timescale pervade the protein and RNA fields. To study such reactions, investigators often perturb the system with abiological solution conditions or substrates in order to slow the rate to timescales accessible by hand mixing; however, such perturbations can change the rate-limiting step and obscure key folding and chemical steps that are found under biological conditions. Mechanical methods for collecting data on the millisecond timescale, which allow these perturbations to be avoided, have been developed over the last few decades. These methods are relatively simple and can be conducted on affordable and commercially available instruments. Here, we focus on using the rapid quench-flow technique to study the fast reaction kinetics of RNA enzymes, or ribozymes, which often react on the millisecond timescale under biological conditions. Rapid quench of ribozymes is completely parallel to the familiar hand-mixing approach, including the use of radiolabeled RNAs and fractionation of reactions on polyacrylamide gels. We provide tips on addressing and preventing common problems that can arise with the rapid-quench technique. Guidance is also offered on ensuring the ribozyme is properly folded and fast-reacting. We hope that this article will facilitate the broader use of rapid-quench instrumentation to study fast-reacting ribozymes under biological reaction conditions.

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

    PubMed

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

    2015-05-15

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

  20. 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

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

    PubMed

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

  2. Protein-ligand recognition using spherical harmonic molecular surfaces: towards a fast and efficient filter for large virtual throughput screening.

    PubMed

    Cai, Wensheng; Shao, Xueguang; Maigret, Bernard

    2002-01-01

    Molecular surfaces are important because surface-shape complementarity is often a necessary condition in protein-ligand interactions and docking studies. We have previously described a fast and efficient method to obtain triangulated surface-meshes by topologically mapping ellipsoids on molecular surfaces. In this paper, we present an extension of our work to spherical harmonic surfaces in order to approximate molecular surfaces of both ligands and receptor-cavities and to easily check the surface-shape complementarity. The method consists of (1) finding lobes and holes on both ligand and cavity surfaces using contour maps of radius functions with spherical harmonic expansions, (2) superposing the surfaces around a given binding site by minimizing the distance between their respective expansion coefficients. This docking procedure capabilities was demonstrated by application to 35 protein-ligand complexes of known crystal structures. The method can also be easily and efficiently used as a filter to detect in a large conformational sampling the possible conformations presenting good complementarity with the receptor site, and being, therefore, good candidates for further more elaborate docking studies. This "virtual screening" was demonstrated on the platelet thrombin receptor.

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

    PubMed

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

    2014-11-18

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

  4. Fast electron energy deposition in a magnetized plasma: Kinetic theory and particle-in-cell simulation

    SciTech Connect

    Robiche, J.; Rax, J.-M.; Bonnaud, G.; Gremillet, L.

    2010-03-15

    The collisional dynamics of a relativistic electron jet in a magnetized plasma are investigated within the framework of kinetic theory. The relativistic Fokker-Planck equation describing slowing down, pitch angle scattering, and cyclotron rotation is derived and solved. Based on the solution of this Fokker-Planck equation, an analytical formula for the root mean square spot size transverse to the magnetic field is derived and this result predicts a reduction in radial transport. Some comparisons with particle-in-cell simulation are made and confirm striking agreement between the theory and the simulation. For fast electron with 1 MeV typical kinetic energy interacting with a solid density hydrogen plasma, the energy deposition density in the transverse direction increases by a factor 2 for magnetic field of the order of 1 T. Along the magnetic field, the energy deposition profile is unaltered compared with the field-free case.

  5. Method of experimental determination of the kinetic constants in fast polymerization reactions in nonisothermal diffusion conditions

    SciTech Connect

    Prochukhan, Yu.A.; Berlin, A.A.; Enikolopyan, N.S.

    1986-09-01

    A new method for the experimental determination of the kinetic constants k/sub p/ and k/sub t/ in fast polymerization reactions on the example of cationic (under the effect of AlCl/sub 3/, BF/sub 3/, and other catalysts) liquid phase polymerization of isobutylene in a flow was suggested. The study of the macrokinetic features of low-temperature polymerization of isobutylene revealed the specific conditions of the occurrence of the process (quasi-ideal displacement) which are characterized by the relative constancy and uniformity of the distribution of the concentrations of the reacting substances along the flow section.

  6. Isocyanide binding kinetics to monomeric hemoproteins. A study on the ligand partition between solvent and heme pocket.

    PubMed Central

    Di Iorio, E E; Winterhalter, K H; Giacometti, G M

    1987-01-01

    The kinetics of methyl-, ethyl-, iso-propyl-, and ter-butyl-isocyanide binding to Aplysia limacina myoglobin (distal His----Lys) and the isolated beta chains from hemoglobin Zurich (distal His----Arg) have been investigated by flash photolysis at various temperatures above 0 degrees C. Sperm whale (Physter catodon) myoglobin and the isolated beta chains from normal adult hemoglobin have been used as references. In most reaction systems investigated the apparent extent of photolysis increases with temperature. For sperm whale myoglobin and the normal beta chains the increase is of the same magnitude and not correlated to the type of ligand used. On the contrary, for the two proteins lacking the distal histidine, the phenomenon is dependent on the size of the alkyl side chain of the ligand. The results, analyzed on the basis of the multibarrier model (Austin, R.H., K.W. Beeson, L. Eisenstein, H. Frauenfelder, and I.C. Gunsalus, 1975, Biochemistry, 16:5355-5373), suggest that the partition of the ligand molecules between the solvent and the heme pocket, occurring during the photolysis process, is primarily determined by interactions between the ligand and residues in the heme cavity rather than by diffusion through the protein matrix. PMID:3567310

  7. 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.

  8. A simple and fast kinetic assay for phytases using phytic acid-protein complex as substrate.

    PubMed

    Tran, Thuy Thi; Hatti-Kaul, Rajni; Dalsgaard, Søren; Yu, Shukun

    2011-03-15

    Phytase (EC 3.1.3.-) hydrolyzes phytate (IP(6)) present in cereals and grains to release inorganic phosphate (P(i)), thereby making it bioavailable. The most commonly used method to assay phytase, developed nearly a century ago, measures the P(i) liberated from IP(6). This traditional endpoint assay is time-consuming and well known for its cumbersomeness in addition to requiring extra caution for handling the toxic regents used. This article reports a simple, fast, and nontoxic kinetic method adaptable for high throughput for assaying phytase using IP(6)-lysozyme as a substrate. The assay is based on the principle that IP(6) forms stable turbid complexes with positively charged lysozyme in a wide pH range, and hydrolysis of the IP(6) in the complex is accompanied by a decrease in turbidity monitored at 600 nm. The turbidity decrease correlates well to the released P(i) from IP(6). This kinetic method was found to be useful in assaying histidine acid phytases, including 3- and 6-phytases, a class representing all commercial phytases, and alkaline β-propeller phytase from Bacillus sp. The influences of temperature, pH, phosphate, and other salts on the kinetic assay were examined. All salts, including NaCl, CaCl(2), and phosphate, showed a concentration-dependent interference.

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

    PubMed

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

    2006-12-01

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

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

    PubMed

    Andruchov, Oleg; Galler, Stefan

    2008-03-01

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

  11. Bifunctional cyclam-based ligands with phosphorus acid pendant moieties for radiocopper separation: thermodynamic and kinetic studies.

    PubMed

    Paúrová, Monika; Havlíčková, Jana; Pospíšilová, Aneta; Vetrík, Miroslav; Císařová, Ivana; Stephan, Holger; Pietzsch, Hans-Jürgen; Hrubý, Martin; Hermann, Petr; Kotek, Jan

    2015-03-16

    Two macrocyclic ligands based on cyclam with trans-disposed N-methyl and N-(4-aminobenzyl) substituents as well as two methylphosphinic (H2L1) or methylphosphonic (H4L2) acid pendant arms were synthesised and investigated in solution. The ligands form stable complexes with transition metal ions. Both ligands show high thermodynamic selectivity for divalent copper over nickel(II) and zinc(II)-K(CuL) is larger than K(Ni/ZnL) by about seven orders of magnitude. Complexation is significantly faster for the phosphonate ligand H4L2, probably due to the stronger coordination ability of the more basic phosphonate groups, which efficiently bind the metal ion in an "out-of-cage" complex and thus accelerate its "in-cage" binding. The rate of Cu(II) complexation by the phosphinate ligand H2L1 is comparable to that of cyclam itself and its derivatives with non-coordinating substituents. Acid-assisted decomplexation of the copper(II) complexes is relatively fast (τ1/2 = 44 and 42 s in 1 M aq. HClO4 at 25 °C for H2L1 and H4L2, respectively). This combination of properties is convenient for selective copper removal/purification. Thus, the title ligands were employed in the preparation of ion-selective resins for radiocopper(II) separation. Glycidyl methacrylate copolymer beads were modified with the ligands through a diazotisation reaction. The separation ability of the modified polymers was tested with cold copper(II) and non-carrier-added (64)Cu in the presence of a large excess of both nickel(II) and zinc(II). The experiments exhibited high overall separation efficiency leading to 60-70% recovery of radiocopper with high selectivity over the other metal ions, which were originally present in 900-fold molar excess. The results showed that chelating resins with properly tuned selectivity of their complexing moieties can be employed for radiocopper separation.

  12. 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.

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

    PubMed

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

    2013-09-01

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

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

    PubMed

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

    2010-06-01

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

  15. 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)

  16. Fast Photochemical Oxidation of Proteins (FPOP) for Comparing Structures of Protein/Ligand Complexes: The Calmodulin-peptide Model System

    PubMed Central

    Zhang, Hao; Gau, Brian C.; Jones, Lisa M.; Vidavsky, Ilan; Gross, Michael L.

    2010-01-01

    Fast Photochemical Oxidation of Proteins (FPOP) is a mass-spectrometry-based protein footprinting method that modifies proteins on the microsecond time scale. Highly reactive •OH, produced by laser photolysis of hydrogen peroxide, oxidatively modifies the side chains of approximately one half the common amino acids on this time scale. Owing to the short labeling exposure, only solvent-accessible residues are sampled. Quantification of the modification extent for the apo and holo states of a protein-ligand complex should provide structurally sensitive information at the amino-acid level to compare the structures of unknown protein complexes with known ones. We report here the use of FPOP to monitor the structural changes of calmodulin in its established binding to M13 of the skeletal muscle myosin light chain kinase. We use the outcome to establish the unknown structures resulting from binding with melittin and mastoparan. The structural comparison follows from a comprehensive examination of the extent of FPOP modifications as measured by proteolysis and LC-MS/MS for each protein-ligand equilibrium. The results not only show that the three calmodulin-peptide complexes have similar structures but also reveal those regions of the protein that became more or less solvent-accessible upon binding. This approach has the potential for relatively high throughput, information-dense characterization of a series of protein-ligand complexes in biochemistry and drug discovery when the structure of one reference complex is known, as is the case for calmodulin and M13 of the skeletal muscle myosin light chain kinase, and the structures of related complexes are not,. PMID:21142124

  17. Effects of various competing ligands on the kinetics of trace metal complexes of Laurentian Fulvic Acid in model solutions and natural waters.

    PubMed

    Yapici, Tahir; Fasfous, Ismail I; Zhao, Jiujiang; Chakrabarti, Chuni L

    2009-03-16

    The objective of this work was to study the effects of the following Ligands: Chelex-100, Dowex MAC-3 and Dowex 50WX-8 using Competing Ligand Exchange Method. This objective was achieved by investigating complex dissociation kinetics of trace metals: Co(II), Ni(II), Cu(II), Zn(II), Cd(II), Mn(II) and Pb(II) of a well-characterized Laurentian Fulvic Acid (LFA) in model solutions and in a natural waters of Lake Heva (Québec, Canada). The effects of variation in the competing ligands (including their quantities) on the complex dissociation kinetics were quantitatively characterized by their first-order dissociation rate coefficients. The kinetic lability of the metal complexes varied with the metal-to-LFA ratio, as expected from the theory of metal complexes of the chemically and physically heterogeneous complexants, LFA. The general trend in the metal-binding by the above competing ligands was: Dowex 50WX-8>Chelex-100>Dowex MAC-3. However, no difference was found between the Dowex 50WX-8 and Chelex-100 for Cd(II), Zn(II), and Co(II). The results revealed the importance of the quantity of Chelex-100 as a competing ligand in the metal(II)-LFA complexation, on the dissociation kinetics of these complexes in model solutions. By developing Competing Ligand Exchange Method as an analytical technique, for studying the relative affinities of the above competing ligands for metals complexation in natural waters this work has made a substantial contribution to analytical chemistry.

  18. Nanohole-based SPR Instruments with Improved Spectral Resolution Quantify a Broad Range of Antibody-Ligand Binding Kinetics

    PubMed Central

    Im, Hyungsoon; Sutherland, Jamie N.; Maynard, Jennifer A.; Oh, Sang-Hyun

    2012-01-01

    We demonstrate an affordable low-noise SPR instrument based on extraordinary optical transmission (EOT) in metallic nanohole arrays and quantify a broad range of antibody-ligand binding kinetics with equilibrium dissociation constants ranging from 200 pM to 40 nM. This nanohole-based SPR instrument is straightforward to construct, align, and operate, since it is built around a standard microscope and a portable fiber-optic spectrometer. The measured refractive index resolution of this platform is 3.1 × 10−6 without on-chip cooling, which is among the lowest reported for SPR sensors based on EOT. This is accomplished via rapid full-spectrum acquisition in 10 milliseconds followed by frame averaging of the EOT spectra, which is made possible by the production of template-stripped gold nanohole arrays with homogeneous optical properties over centimeter-sized areas. Sequential SPR measurements are performed using a 12-channel microfluidic flow cell after optimizing surface modification protocols and antibody injection conditions to minimize mass-transport artifacts. The immobilization of a model ligand, the protective antigen of anthrax on the gold surface, is monitored in real-time with a signal-to-noise ratio of ~860. Subsequently, real-time binding kinetic curves were measured quantitatively between the antigen and a panel of small, 25 kDa single-chain antibodies at concentrations down to 1 nM. These results indicate that nanohole-based SPR instruments have potential for quantitative antibody screening and as a general-purpose platform for integrating SPR sensors with other bioanalytical tools. PMID:22235895

  19. Kinetic theory for neuronal networks with fast and slow excitatory conductances driven by the same spike train.

    PubMed

    Rangan, Aaditya V; Kovacic, Gregor; Cai, David

    2008-04-01

    We present a kinetic theory for all-to-all coupled networks of identical, linear, integrate-and-fire, excitatory point neurons in which a fast and a slow excitatory conductance are driven by the same spike train in the presence of synaptic failure. The maximal-entropy principle guides us in deriving a set of three (1+1) -dimensional kinetic moment equations from a Boltzmann-like equation describing the evolution of the one-neuron probability density function. We explain the emergence of correlation terms in the kinetic moment and Boltzmann-like equations as a consequence of simultaneous activation of both the fast and slow excitatory conductances and furnish numerical evidence for their importance in correctly describing the coarse-grained dynamics of the underlying neuronal network.

  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.

  1. Basic residue at position 14 is not required for fast assembly and disassembly kinetics in neural cadherin.

    PubMed

    Vunnam, Nagamani; Hammer, Nathan I; Pedigo, Susan

    2015-01-27

    In spite of their structural similarities, epithelial (E-) and neural (N-) cadherin are expressed at different types of synapses and differ significantly in their dimerization kinetics. Recent studies proposed a transient intermediate in E-cadherin as the key requirement for rapid disassembly kinetics of the adhesive dimer. This E-cadherin intermediate comprises four intermolecular ionic and H-bonding interactions between adhesive partners. These interactions are not preserved in N-cadherin except for a basic residue at the 14th position, which could stabilize the intermediate through either H-bonding or ionic interactions with the partner protomer. To investigate the origin of the rapid dimerization kinetics of N-cadherin in the presence of calcium, studies reported here systematically test the role of ionic and H-bonding interactions in dimerization kinetics using R14S, R14A, and R14E mutants of N-cadherin. Analytical size-exclusion chromatographic and bead aggregation studies showed two primary results. First, N-cadherin/R14S and N-cadherin/R14A mutants showed fast assembly and disassembly kinetics in the calcium-saturated state similar to that of wild-type N-cadherin. These results indicate that the fast disassembly of the calcium-saturated dimer of N-cadherin does not require a basic residue at the 14th position. Second, the dimerization kinetics of N-cadherin/R14E were slow in the calcium-saturated state, indicating that negative charge destabilizes the intermediate state. Taken together, these results indicate that the basic residue at the 14th position does not promote rapid dimerization kinetics but that an acidic amino acid in that position significantly impairs dimerization kinetics.

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

    DOE PAGES

    Klinger, Jordan; Bar-Ziv, Ezra; Shonnard, David; ...

    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. 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.

  4. Kinetics of brucite dissolution at 25°C in the presence of organic and inorganic ligands and divalent metals

    NASA Astrophysics Data System (ADS)

    Pokrovsky, Oleg S.; Schott, Jacques; Castillo, Alain

    2005-02-01

    Brucite (Mg(OH) 2) dissolution rate was measured at 25°C in a mixed-flow reactor at various pH (5 to 11) and ionic strengths (0.01 to 0.03 M) as a function of the concentration of 15 organic and 5 inorganic ligands and 8 divalent metals. At neutral and weakly alkaline pH, the dissolution is promoted by the addition of the following ligands ranked by decreasing effectiveness: EDTA ≥ H 2PO 4- > catechol ≥ HCO 3- > ascorbate > citrate > oxalate > acetate ˜ lactate and it is inhibited by boric acid. At pH >10.5, it decreases in the presence of PO 43-, CO 32-, F -, oxine, salicylate, lactate, acetate, 4-hydroxybenzoate, SO 42- and B(OH) 4- with orthophosphate and borate being the strongest and the weakest inhibitor, respectively. Xylose (up to 0.1 M), glycine (up to 0.05 M), formate (up to 0.3 M) and fulvic and humic acids (up to 40 mg/L DOC) have no effect on brucite dissolution kinetics. Fluorine inhibits dissolution both in neutral and alkaline solutions. From F sorption experiments in batch and flow-through reactors and the analysis of reacted surfaces using X-ray Photoelectron Spectroscopy (XPS), it is shown that fluorine adsorption is followed by its incorporation in brucite lattice likely via isomorphic substitution with OH. The effect of eight divalent metals (Sr, Ba, Ca, Pb, Mn, Fe, Co and Ni) studied at pH 4.9 and 0.01 M concentration revealed brucite dissolution rates to be correlated with the water molecule exchange rates in the first hydration sphere of the corresponding cation. The effect of investigated ligands on brucite dissolution rate can be modelled within the framework of the surface coordination approach taking into account the adsorption of ligands on dissolution-active sites and the molecular structure of the surface complexes they form. The higher the value of the ligand sorption constant, the stronger will be its catalyzing or inhibiting effect. As for Fe and Al oxides, bi- or multidentate mononuclear surface complexes, that labilize Mg

  5. Probability description of ligand-receptor interactions. Evaluation of reliability of events with small and supersmall doses. I. Kinetics of ligand-receptor interactions.

    PubMed

    Gurevich, K G; Varfolomeev, S D

    1999-09-01

    We have developed mathematical methods for describing ligand-receptor interactions (LRI) using Markov chains. Under some conditions, the mean value of ligand-receptor complexes obtained using Markov chains coincides with that obtained from the law of mass action. Using the calculated ratio of standard deviation to mean number of ligand-receptor complexes, we show that with small concentrations of ligand-receptor complexes LRI must be described using probability methods. Using data from the literature, we show that LRI description using the mass-action law under these conditions can cause significant errors in interpretation of experimental data.

  6. 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

  7. Water-soluble Mo3S4 clusters bearing hydroxypropyl diphosphine ligands: synthesis, crystal structure, aqueous speciation, and kinetics of substitution reactions.

    PubMed

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

    2012-06-18

    The [Mo(3)S(4)Cl(3)(dhprpe)(3)](+) (1(+)) cluster cation has been prepared by reaction between Mo(3)S(4)Cl(4)(PPh(3))(3) (solvent)(2) and the water-soluble 1,2-bis(bis(hydroxypropyl)phosphino)ethane (dhprpe, L) ligand. The crystal structure of [1](2)[Mo(6)Cl(14)] has been determined by X-ray diffraction methods and shows the typical incomplete cuboidal structure with a capping and three bridging sulfides. The octahedral coordination around each metal center is completed with a chlorine and two phosphorus atoms of the diphosphine ligand. Depending on the pH, the hydroxo group of the functionalized diphosphine can substitute the chloride ligands and coordinate to the cluster core to give new clusters with tridentate deprotonated dhprpe ligands of formula [Mo(3)S(4)(dhprpe-H)(3)](+) (2(+)). A detailed study based on stopped-flow, (31)P{(1)H} NMR, and electrospray ionization mass spectrometry techniques has been carried out to understand the behavior of acid-base equilibria and the kinetics of interconversion between the 1(+) and the 2(+) forms. Both conversion of 1(+) to 2(+) and its reverse process occur in a single kinetic step, so that reactions proceed at the three metal centers with statistically controlled kinetics. The values of the rate constants under different conditions are used to discuss on the mechanisms of opening and closing of the chelate rings with coordination or dissociation of chloride.

  8. 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…

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

    PubMed

    Galler, S

    1999-10-01

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

  10. Kinetics of Ligand-Receptor Interaction Reveals an Induced-Fit Mode of Binding in a Cyclic Nucleotide-Activated Protein

    PubMed Central

    Peuker, Sebastian; Cukkemane, Abhishek; Held, Martin; Noé, Frank; Kaupp, U. Benjamin; Seifert, Reinhard

    2013-01-01

    Many receptors and ion channels are activated by ligands. One key question concerns the binding mechanism. Does the ligand induce conformational changes in the protein via the induced-fit mechanism? Or does the protein preexist as an ensemble of conformers and the ligand selects the most complementary one, via the conformational selection mechanism? Here, we study ligand binding of a tetrameric cyclic nucleotide-gated channel from Mesorhizobium loti and of its monomeric binding domain (CNBD) using rapid mixing, mutagenesis, and structure-based computational biology. Association rate constants of ∼107 M−1 s−1 are compatible with diffusion-limited binding. Ligand binding to the full-length CNG channel and the isolated CNBD differ, revealing allosteric control of the CNBD by the effector domain. Finally, mutagenesis of allosteric residues affects only the dissociation rate constant, suggesting that binding follows the induced-fit mechanism. This study illustrates the strength of combining mutational, kinetic, and computational approaches to unravel important mechanistic features of ligand binding. PMID:23332059

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

    PubMed

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

    2016-09-02

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

  12. Kinetic-MHD hybrid simulation of fishbone modes excited by fast ions on the experimental advanced superconducting tokamak (EAST)

    NASA Astrophysics Data System (ADS)

    Pei, Youbin; Xiang, Nong; Hu, Youjun; Todo, Y.; Li, Guoqiang; Shen, Wei; Xu, Liqing

    2017-03-01

    Kinetic-MagnetoHydroDynamic hybrid simulations are carried out to investigate fishbone modes excited by fast ions on the Experimental Advanced Superconducting Tokamak. The simulations use realistic equilibrium reconstructed from experiment data with the constraint of the q = 1 surface location (q is the safety factor). Anisotropic slowing down distribution is used to model the distribution of the fast ions from neutral beam injection. The resonance condition is used to identify the interaction between the fishbone mode and the fast ions, which shows that the fishbone mode is simultaneously in resonance with the bounce motion of the trapped particles and the transit motion of the passing particles. Both the passing and trapped particles are important in destabilizing the fishbone mode. The simulations show that the mode frequency chirps down as the mode reaches the nonlinear stage, during which there is a substantial flattening of the perpendicular pressure of fast ions, compared with that of the parallel pressure. For passing particles, the resonance remains within the q = 1 surface, while, for trapped particles, the resonant location moves out radially during the nonlinear evolution. In addition, parameter scanning is performed to examine the dependence of the linear frequency and growth rate of fishbones on the pressure and injection velocity of fast ions.

  13. Genetically encoded fluorescent voltage sensors using the voltage-sensing domain of Nematostella and Danio phosphatases exhibit fast kinetics.

    PubMed

    Baker, Bradley J; Jin, Lei; Han, Zhou; Cohen, Lawrence B; Popovic, Marko; Platisa, Jelena; Pieribone, Vincent

    2012-07-15

    A substantial increase in the speed of the optical response of genetically encoded fluorescent protein voltage sensors (FP voltage sensors) was achieved by using the voltage-sensing phosphatase genes of Nematostella vectensis and Danio rerio. A potential N. vectensis voltage-sensing phosphatase was identified in silico. The voltage-sensing domain (S1-S4) of the N. vectensis homolog was used to create an FP voltage sensor called Nema. By replacing the phosphatase with a cerulean/citrine FRET pair, a new FP voltage sensor was synthesized with fast off kinetics (Tau(off)<5ms). However, the signal was small (ΔF/F=0.4%/200mV). FP voltage sensors using the D. rerio voltage-sensing phosphatase homolog, designated Zahra and Zahra 2, exhibited fast on and off kinetics within 2ms of the time constants observed with the organic voltage-sensitive dye, di4-ANEPPS. Mutagenesis of the S4 region of the Danio FP voltage sensor shifted the voltage dependence to more negative potentials but did not noticeably affect the kinetics of the optical signal.

  14. A survey of the cusp ion outflow's kinetic energy flux measured by Polar and FAST during conjunction events

    NASA Astrophysics Data System (ADS)

    Tian, S.; Wygant, J. R.; Cattell, C. A.; Scudder, J. D.; McFadden, J. P.; Mozer, F.; Russell, C. T.

    2014-12-01

    Polar and FAST conjunction events are selected from Polar cusp crossings in 1997. These conjunction events reveal a common pattern in which Polar observed significant ion kinetic energy flux in the upward direction at mid-altitudes (below 6 Re). Depending on the magnetic activity level, the maximum ion kinetic energy flux is on the order of 10-100 mW/m^2, when mapped to the ionosphere. It is an order of magnitude or more larger than the ion kinetic energy flux observed by FAST in conjunction at altitudes of <1 Re. Therefore, the ion outflows are significantly energized within the mid-latitude cusp. Also shown in the conjunction events is that the downward Poynting flux has enough wave energy to power the ion energization. The observed pattern suggests that the cusp at ionosphere altitudes is not a simple mapping of higher altitude particles. Instead, the mid-latitude cusp receives significant downward Poynting flux from higher altitude due to the solar wind/magnetosphere coupling. Within the mid-altitude cusp, the Poynting flux then supplies energy to power the ionosphere/magnetosphere coupling. Ion outflows are triggered and energized, forming a planetary wind that feeds the magnetosphere with ionospheric ions. During southward IMF, the wind convects anti-sunward and can affect the tail lobe, the nightside auroral region and the nightside plasma sheet.

  15. 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.

  16. Kinetic analysis of aptazyme-regulated gene expression in a cell-free translation system: modeling of ligand-dependent and -independent expression.

    PubMed

    Kobori, Shungo; Ichihashi, Norikazu; Kazuta, Yasuaki; Matsuura, Tomoaki; Yomo, Tetsuya

    2012-08-01

    Aptazymes are useful as RNA-based switches of gene expression responsive to several types of compounds. One of the most important properties of the switching ability is the signal/noise (S/N) ratio, i.e., the ratio of gene expression in the presence of ligand to that in the absence of ligand. The present study was performed to gain a quantitative understanding of how the aptazyme S/N ratio is determined by factors involved in gene expression, such as transcription, RNA self-cleavage, RNA degradation, protein translation, and their ligand dependencies. We performed switching of gene expression using two on-switch aptazymes with different properties in a cell-free translation system, and constructed a kinetic model that quantitatively describes the dynamics of RNA and protein species involved in switching. Both theoretical and experimental analyses consistently demonstrated that factors determining both the absolute value and the dynamics of the S/N ratio are highly dependent on the routes of translation in the absence of ligand: translation from the ligand-independently cleaved RNA or leaky translation from the noncleaved RNA. The model obtained here is useful to assess the factors that restrict the S/N ratio and to improve aptazymes more efficiently.

  17. Unanimous Model for Describing the Fast Bioluminescence Kinetics of Ca(2+) -regulated Photoproteins of Different Organisms.

    PubMed

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

    2017-03-01

    Upon binding their metal ion cofactors, Ca(2+) -regulated photoproteins display a rapid increase of light signal, which reaches its peak within milliseconds. In the present study, we investigate bioluminescence kinetics of the entire photoprotein family. All five recombinant hydromedusan Ca(2+) -regulated photoproteins-aequorin from Aequorea victoria, clytin from Clytia gregaria, mitrocomin from Mitrocoma cellularia and obelins from Obelia longissima and Obelia geniculata-demonstrate the same bioluminescent kinetics pattern. Based on these findings, for the first time we propose a unanimous kinetic model describing the bioluminescence mechanism of Ca(2+) -regulated photoproteins.

  18. 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.

  19. 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.

  20. 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.

  1. An active learning mammalian skeletal muscle lab demonstrating contractile and kinetic properties of fast- and slow-twitch muscle.

    PubMed

    Head, S I; Arber, M B

    2013-12-01

    The fact that humans possess fast- and slow-twitch muscle in the ratio of ∼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 properties of fast- and slow-twitch mammalian skeletal muscle. This laboratory illustrates the major differences in contractile properties and fatigue profiles exhibited by the two muscle types. Students compare and contrast twitch kinetics, fused tetanus characteristics, force-frequency relationships, and fatigue properties of fast- and slow-twitch muscles. Examples of results collected by students during class are used to illustrate the type of data collected and analysis performed. During the laboratory, students are encouraged to connect factual information from their skeletal muscle lectures to their laboratory findings. This enables student learning in an active fashion; in particular, the isolated muscle preparation demonstrates that much of what makes muscle fast or slow is myogenic and not the product of the nervous or circulatory systems. This has far-reaching implications for motor control and exercise behavior and therefore is a crucial element in exercise science, with its focus on power and endurance sport activities. To measure student satisfaction with this active learning technique, a questionnaire was administered after the laboratory; 96% of the comments were positive in their support of active versus passive learning strategies.

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

    PubMed

    Gasperl, Anna; Morvan-Bertrand, Annette; Prud'homme, Marie-Pascale; van der Graaff, Eric; 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.

  3. 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

  4. Compartmental analysis of (11C)flumazenil kinetics for the estimation of ligand transport rate and receptor distribution using positron emission tomography

    SciTech Connect

    Koeppe, R.A.; Holthoff, V.A.; Frey, K.A.; Kilbourn, M.R.; Kuhl, D.E. )

    1991-09-01

    The in vivo kinetic behavior of (11C)flumazenil ((11C)FMZ), a non-subtype-specific central benzodiazepine antagonist, is characterized using compartmental analysis with the aim of producing an optimized data acquisition protocol and tracer kinetic model configuration for the assessment of (11C)FMZ binding to benzodiazepine receptors (BZRs) in human brain. The approach presented is simple, requiring only a single radioligand injection. Dynamic positron emission tomography data were acquired on 18 normal volunteers using a 60- to 90-min sequence of scans and were analyzed with model configurations that included a three-compartment, four-parameter model, a three-compartment, three-parameter model, with a fixed value for free plus nonspecific binding; and a two-compartment, two-parameter model. Statistical analysis indicated that a four-parameter model did not yield significantly better fits than a three-parameter model. Goodness of fit was improved for three- versus two-parameter configurations in regions with low receptor density, but not in regions with moderate to high receptor density. Thus, a two-compartment, two-parameter configuration was found to adequately describe the kinetic behavior of (11C)FMZ in human brain, with stable estimates of the model parameters obtainable from as little as 20-30 min of data. Pixel-by-pixel analysis yields functional images of transport rate (K1) and ligand distribution volume (DV), and thus provides independent estimates of ligand delivery and BZR binding.

  5. Drosophila Ebony: a novel type of nonribosomal peptide synthetase related enzyme with unusually fast peptide bond formation kinetics.

    PubMed

    Hartwig, Silvia; Dovengerds, Christine; Herrmann, Christian; Hovemann, Bernhard T

    2014-11-01

    Drosophila Ebony is a β-alanyl biogenic amine synthetase with proven function in cuticle and in glia of the nervous system. It is closely related to nonribosomal peptide synthetases (NRPSs), which typically consist of at least an adenylation, a peptidyl carrier protein and a peptide bond forming condensation domain. Besides its role in cuticle formation, Ebony is in most glia of the brain thought to convert biogenic amines to β-alanyl conjugates. If the metabolization of the neurotransmitter histamine to β-alanyl histamine requires a fast reaction in visual signal transduction, Ebony must be able to fulfill this requirement. Since NRPSs are in general slowly acting multi-modular protein machineries, the enigma of how Ebony quickly facilitates this inactivation remains a key question for understanding its role in vision. To quantitatively analyze the reaction kinetics, we used phosphopantetheinylated holo-Ebony prepared from Baculovirus infected Sf9 cells. Kinetic parameters for the loading reaction, e.g. the formation of β-alanyl-Ebony thioester, complied with those of slow NRPSs. In contrast, single-turnover analysis of the last reaction step, peptide bond formation between pre-activated β-alanyl Ebony thioester and histamine, revealed a very rapid conjugation reaction. This biphasic nature of activity identifies Ebony as a novel type of NRPS related molecule that combines a slow amino acid activation phase with a very fast product formation step.

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

    NASA Astrophysics Data System (ADS)

    Krasikov, E.; Nikolaenko, V.

    2017-01-01

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

  7. Adaptation of acyl-enzyme kinetic theory and an experimental method for evaluating the kinetics of fast-acting, irreversible protease inhibitors.

    PubMed

    Leytus, S P; Peltz, S W; Mangel, W F

    1983-01-26

    The theory of acyl-enzyme kinetics (Bender, M.L., Kézdy, F.J. and Wedler, F.C. (1967) J. Chem. Educ. 44, 84-88) has been adapted for use in evaluating the kinetics of inhibition of serine proteases by both natural and synthetic irreversible inhibitors. The new theory is based upon formal analysis of the case of an irreversible, active-site-directed inhibitor competing with an irreversible, active-site-directed substrate for the active site of a serine protease. From this theory, an experimentally simple and accurate method is described to obtain a second-order rate constant that is characteristic of the efficiency with which an irreversible inhibitor reacts. The experimental method is particularly useful for characterizing fast-acting, irreversible inhibitors. The theory and method which are applicable to a wide variety of enzymes are verified by analysis of the inhibition of bovine trypsin by three model inhibitors, p-nitrophenyl p'-guanidinobenzoate, soybean trypsin inhibitor and alpha-1-proteinase inhibitor as well as by human antithrombin III in the presence of heparin and by bovine pancreatic trypsin inhibitor.

  8. Efficient removal of organic ligands from supported nanocrystals by fast thermal annealing enables catalytic studies on well-defined active phases.

    PubMed

    Cargnello, Matteo; Chen, Chen; Diroll, Benjamin T; Doan-Nguyen, Vicky V T; Gorte, Raymond J; Murray, Christopher B

    2015-06-03

    A simple yet efficient method to remove organic ligands from supported nanocrystals is reported for activating uniform catalysts prepared by colloidal synthesis procedures. The method relies on a fast thermal treatment in which ligands are quickly removed in air, before sintering can cause changes in the size and shape of the supported nanocrystals. A short treatment at high temperatures is found to be sufficient for activating the systems for catalytic reactions. We show that this method is widely applicable to nanostructures of different sizes, shapes, and compositions. Being rapid and effective, this procedure allows the production of monodisperse heterogeneous catalysts for studying a variety of structure-activity relationships. We show here results on methane steam reforming, where the particle size controls the CO/CO2 ratio on alumina-supported Pd, demonstrating the potential applications of the method in catalysis.

  9. 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

  10. 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.

  11. 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

    2004-12-03

    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

  12. Site specific ligand substitution in cubane-type Mo3FeS(4)(4+) clusters: kinetics and mechanism of reaction and isolation of mixed ligand Cl/SPh complexes.

    PubMed

    Algarra, Andrés G; Basallote, Manuel G; Fernandez-Trujillo, M J; Llusar, Rosa; Pino-Chamorro, Jose A; Sorribes, Ivan; Vicent, Cristian

    2010-04-21

    The synthesis, crystal structure and solution characterization of the cubane-type [Mo(3)(FeCl)S(4)(dmpe)(3)Cl(3)] (1) (dmpe = 1,2-bis(dimethylphophane-ethane)) cluster are reported and the ligand substitution processes of chloride by thiophenolate investigated. The kinetics and the intimate mechanism of these substitutions reveal that compound 1 undergoes a number of Fe and Mo site specific ligand substitution reactions in acetonitrile solutions. In particular, PhS(-) coordination at the tetrahedral Fe site proceeds in a single resolved kinetic step whereas such substitutions at the Mo sites proceed more slowly. The effect of the presence of acids in the reaction media is also investigated and reveals that an acid excess hinders substitution reactions both at the Fe and Mo sites; however, an acid-promoted solvolysis of the Fe-Cl bonds is observed. Electrospray ionization (ESI) and tandem (ESI-MS/MS) mass spectrometry allow the identification of all the reaction intermediates proposed on the basis of stopped-flow measurements. The distinctive site specific reactivity made it possible to isolate two new clusters of the Mo(3)FeS(4)(4+) family featuring mixed chlorine/thiophenolate ligands, namely Mo(3)S(4)(FeSPh)(dmpe)(3)Cl(3) (2) and [Mo(3)S(4)(FeSPh)(dmpe)(3)(SPh)(3)] (3). A detailed computational study has also been carried out to understand the details of the mechanism of substitution at the M-Cl (M = Mo and Fe) bonds as well as the solvolysis at the Fe-Cl sites, with particular emphasis on the role of acids on the substitution process. The results of the calculations are in agreement with the experimental observations, thus justifying the non-existence of an accelerating effect of acids on the thiophenolate substitution reaction, which differs from previous proposals for the Fe(4)S(4) and MoFe(3)S(4) clusters and some related compounds.

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

    PubMed

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

    2017-02-14

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

  14. 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.

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

    PubMed

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

    2016-05-01

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

  16. 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

  17. The derivative assay--an analysis of two fast components of DNA rejoining kinetics

    SciTech Connect

    Sandstroem, B.E. )

    1989-11-01

    The DNA rejoining kinetics of human U-118 MG cells were studied after gamma-irradiation with 4 Gy. The analysis of the sealing rate of the induced DNA strand breaks was made with a modification of the DNA unwinding technique. The modification meant that rather than just monitoring the number of existing breaks at each time of analysis, the velocity, at which the rejoining process proceeded, was determined. Two apparent first-order components of single-strand break repair could be identified during the 25 min of analysis. The half-times for the two components were 1.9 and 16 min, respectively.

  18. Comparison of the kinetic performance of different columns for fast liquid chromatography, emphasizing the contributions of column end structure.

    PubMed

    Lambert, Nándor; Miyazaki, Shota; Ohira, Masayoshi; Tanaka, Nobuo; Felinger, Attila

    2016-11-18

    The kinetic performance of five chromatographic columns designed for fast liquid chromatography with different column packing materials - including fully porous (2.0 and 1.9μm particles), core-shell (2.6μm particles) or monolithic packings - with identical column dimensions (2.1×50mm) was tested. Since the tested monolithic column showed systematically better efficiency for early eluting compounds than the packed columns, an additional band broadening effect was suspected for the packed columns. The effects of the presence of the frits and the bed heterogeneity of the columns near the frits were characterized by a column-reversal method. It has been shown that significant differences - even 20-25% difference in efficiency - can exist between the two ends of the packed columns, while the monolithic column shows rather similar performance at either column end.

  19. Kinetics of CO binding to the haem domain of murine inducible nitric oxide synthase: differential effects of haem domain ligands.

    PubMed Central

    Stevenson, T H; Gutierrez, A F; Alderton, W K; Lian , L; Scrutton, N S

    2001-01-01

    The binding of CO to the murine inducible nitric oxide synthase (iNOS) oxygenase domain has been studied by laser flash photolysis. The effect of the (6R)-5,6,7,8-tetrahydro-L-biopterin (BH(4)) cofactor L-arginine and several Type I L-arginine analogues/ligands on the rates of CO rebinding has been evaluated. The presence of BH(4) in the iNOS active site has little effect on the rebinding of protein-caged haem-CO pairs (geminate recombination), but decreases the bimolecular association rates 2-fold. Addition of L-arginine to the BH(4)-bound complex completely abolishes geminate recombination and results in a further 80-fold decrease in the overall rate of bimolecular association. Three of the Type I ligands, S-ethylisothiourea, L-canavanine and 2,5-lutidine, displaced the CO from the haem iron upon addition to the iNOS oxygenase domain. The Type I ligands significantly decreased the rate of bimolecular binding of CO to the haem iron after photolysis. Most of these ligands also completely abolished geminate recombination. These results are consistent with a relatively open distal pocket that allows CO to bind unhindered in the active site of murine iNOS in the absence of L-arginine or BH(4). In the presence of BH(4) and L-arginine, however, the enzyme adopts a more closed structure that can greatly reduce ligand access to the haem iron. These observations are discussed in terms of the known structure of iNOS haem domain and solution studies of ligand binding in iNOS and neuronal NOS isoenzymes. PMID:11485568

  20. In situ and in silico kinetic analyses of the Programmed Cell Death 1, Programmed Cell Death-Ligands, and B7-1 interaction network.

    PubMed

    Li, Kaitao; Cheng, Xiaoxiao; Tilevik, Andreas; Davis, Simon J; Zhu, Cheng

    2017-03-06

    Programmed cell death-1 (PD-1) is an inhibitory receptor with an essential role in maintaining peripheral tolerance, and among the most promising immunotherapeutic targets for treating cancer, autoimmunity, and infectious diseases. A complete understanding of the consequences of PD-1 engagement by its ligands, PD-L1 and PD-L2, and of PD-L1 binding to B7-1, requires quantitative analysis of their interactions at the cell surface. We present here the first complete in situ kinetic analysis of the PD-1/PD-1 ligands/B7-1 system. Consistent with previous solution measurements, we observed higher in situ affinities for human (h) than murine (m) PD-1 interactions, stronger binding of hPD-1 to hPD-L2 than hPD-L1, and comparable binding of mPD-1 to both ligands. However, in contrast to the relatively weak solution affinities, the in situ affinities of PD-1 are as high as those of the TCR for agonist pMHC and of LFA-1 for ICAM-1, but significantly lower than that of the B7-1-CTLA-4 interaction, suggesting a distinct basis for PD-1 versus CTLA-4 mediated inhibition. Notably, the in situ interactions of PD-1 are much stronger than that of B7-1 with PD-L1. Overall, the in situ affinity ranking greatly depends on the on-rate instead of the off-rate. In silico simulations predict that PD-1-PD-L1 interactions dominate at interfaces between activated T cells and mature dendritic cells, and that these interactions will be highly sensitive to the dynamics of PD-L1 and PD-L2 expression. Our results provide a kinetic framework for better understanding inhibitory PD-1 activity in health and disease.

  1. 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

  2. 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.

  3. 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.

  4. 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.

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

    PubMed

    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(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.

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

    PubMed

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

    2014-07-15

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

  7. Total Kinetic Energy Release in the Fast Neutron Induced Fission of 235U

    NASA Astrophysics Data System (ADS)

    Loveland, Walter; Yanez, Ricardo

    2016-09-01

    We have measured the total kinetic energy (TKE) release, its variance and associated fission product mass distributions for the neutron induced fission of 235U for En = 2-90 MeV using the 2E method. The neutron energies were determined,event by event, by time of flight measurements with the white spectrum neutron beam from LANSCE. The TKE decreases with increasing neutron energy. This TKE decrease is due to increasing symmetric fission (and decreasing asymmetric fission)with increasing neutron energy, in accord with Brosa model predictions. Our measurement of the TKE release for 235U(nth,f) is in excellent agreement with the known value, indicating our measurements are absolute measurements. The TKE variances are sensitive indicators of nth chance fission. Due to the occurrence of nth chance fission and pre-fission neutron emission, the average fissioning system and its excitation energy is a complex function of the incident neutron energy. Detailed comparisons of our data with previous measurements will be made. This work was supported, in part, by the Director, Office of Energy Research, Division of Nuclear Physics of the Office of High Energy and Nuclear Physics of the U.S. Department of Energy under Grant DE-SC0014380.

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  9. A FRET-facilitated photoswitching using an orange fluorescent protein with the fast photoconversion kinetics

    PubMed Central

    Subach, Oksana M.; Entenberg, David; Condeelis, John S.; Verkhusha, Vladislav V.

    2012-01-01

    Fluorescent proteins photoswitchable with non-cytotoxic light irradiation and spectrally distinct from multiple available photoconvertible green-to-red probes are in high demand. We have developed a monomeric fluorescent protein, called PSmOrange2, which is photoswitchable with blue light from an orange (ex./em. at 546 nm/561 nm) to a far-red (ex./em. at 619 nm/651 nm) form. Compared to another orange-to-far-red photoconvertable variant, PSmOrange2 has blue-shifted photoswitching action spectrum, 9-fold higher photoconversion contrast, and up to 10-fold faster photoswitching kinetics. This results in the 4-fold more PSmOrange2 molecules being photoconverted in mammalian cells. Compared to common orange fluorescent proteins, such as mOrange, the orange form of PSmOrange has substantially higher photostability allowing its use in multicolor imaging applications to track dynamics of multiple populations of intracellular objects. The PSmOrange2 photochemical properties allow its efficient photoswitching with common two-photon lasers and, moreover, via Förster resonance energy transfer (FRET) from green fluorescent donors. We have termed the latter effect a FRET-facilitated photoswitching and demonstrated it using several sets of interacting proteins. The enhanced photoswitching properties of PSmOrange2 make it a superior photoconvertable protein tag for flow cytometry, conventional microscopy, and two-photon imaging of live cells. PMID:22900938

  10. 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.

  11. BioRef II-Neutron reflectometry with relaxed resolution for fast, kinetic measurements at HZB.

    PubMed

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

    2016-10-01

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

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

    NASA Astrophysics Data System (ADS)

    Beke, D. L.; Erdélyi, Z.

    2006-01-01

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

  13. Rational Design of Thermodynamic and Kinetic Binding Profiles by Optimizing Surface Water Networks Coating Protein-Bound Ligands.

    PubMed

    Krimmer, Stefan G; Cramer, Jonathan; Betz, Michael; Fridh, Veronica; Karlsson, Robert; Heine, Andreas; Klebe, Gerhard

    2016-12-08

    A previously studied congeneric series of thermolysin inhibitors addressing the solvent-accessible S2' pocket with different hydrophobic substituents showed modulations of the surface water layers coating the protein-bound inhibitors. Increasing stabilization of water molecules resulted in an enthalpically more favorable binding signature, overall enhancing affinity. Based on this observation, we optimized the series by designing tailored P2' substituents to improve and further stabilize the surface water network. MD simulations were applied to predict the putative water pattern around the bound ligands. Subsequently, the inhibitors were synthesized and characterized by high-resolution crystallography, microcalorimetry, and surface plasmon resonance. One of the designed inhibitors established the most pronounced water network of all inhibitors tested so far, composed of several fused water polygons, and showed 50-fold affinity enhancement with respect to the original methylated parent ligand. Notably, the inhibitor forming the most perfect water network also showed significantly prolonged residence time compared to the other tested inhibitors.

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

    PubMed

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

    2015-05-01

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

  15. 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

  16. Does a fast nuclear magnetic resonance spectroscopy- and X-ray crystallography hybrid approach provide reliable structural information of ligand-protein complexes? A case study of metalloproteinases.

    PubMed

    Isaksson, Johan; Nyström, Susanne; Derbyshire, Dean; Wallberg, Hans; Agback, Tatiana; Kovacs, Helena; Bertini, Ivano; Giachetti, Andrea; Luchinat, Claudio

    2009-03-26

    A human matrix metalloproteinase (MMP) hydroxamic acid inhibitor (CGS27023A) was cross-docked into 15 MMP-12, MMP-13, MMP-9, and MMP-1 cocrystal structures. The aim was to validate a fast protocol for ligand binding conformation elucidation and to probe the feasibility of using inhibitor-protein NMR contacts to dock an inhibitor into related MMP crystal structures. Such an approach avoids full NMR structure elucidation, saving both spectrometer- and analysis time. We report here that for the studied MMPs, one can obtain docking results well within 1 A compared to the corresponding reference X-ray structure, using backbone amide contacts only. From the perspective of the pharmaceutical industry, these results are relevant for the binding studies of inhibitor series to a common target and have the potential advantage of obtaining information on protein-inhibitor complexes that are difficult to crystallize.

  17. 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.

  18. 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.

  19. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  1. "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.

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

    PubMed

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

    2016-10-21

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

  3. A "stripping" ligand tactic for use with the kinetic locking-on strategy: its use in the resolution and bioaffinity chromatographic purification of NAD(+)-dependent dehydrogenases.

    PubMed

    O'Flaherty, M; O'Carra, P; McMahon, M; Mulcahy, P

    1999-08-01

    The kinetic locking-on strategy utilizes soluble analogues of the target enzymes' specific substrate to promote selective adsorption of individual NAD(+)-dependent dehydrogenases on their complementary immobilized cofactor derivative. Application of this strategy to the purification of NAD(+)-dependent dehydrogenases from crude extracts has proven that it can yield bioaffinity systems capable of producing one-chromatographic-step purifications with yields approaching 100%. However, in some cases the purified enzyme preparation was found to be contaminated with other proteins weakly bound to the immobilized cofactor derivative through binary complex formation and/or nonspecific interactions, which continuously "dribbled" off the matrix during the chromatographic procedure. The fact that this problem can be overcome by including a short pulse of 5'-AMP (stripping ligand) in the irrigant a couple of column volumes prior to the discontinuation of the specific substrate analogue (locking-on ligand) is clear from the results presented in this report. The general effectiveness of this auxiliary tactic has been assessed using model studies and through incorporation into an actual purification from a crude cellular extract. The results confirm the usefulness of the stripping-ligand tactic for the resolution and purification of NAD(+)-dependent dehydrogenases when using the locking-on strategy. These studies have been carried out using bovine liver glutamate dehydrogenase (GDH, EC 1.4.1.3), yeast alcohol dehydrogenase (YADH, EC 1.1.1.1), porcine heart mitochondrial malate dehydrogenase (mMDH, EC 1.1.1.37), and bovine heart L-lactate dehydrogenase (l-LDH, EC 1.1.1.27).

  4. Equivalence of on-Lattice Stochastic Chemical Kinetics with the Well-Mixed Chemical Master Equation in the Limit of Fast Diffusion.

    PubMed

    Stamatakis, Michail; Vlachos, Dionisios G

    2011-12-14

    Well-mixed and lattice-based descriptions of stochastic chemical kinetics have been extensively used in the literature. Realizations of the corresponding stochastic processes are obtained by the Gillespie stochastic simulation algorithm and lattice kinetic Monte Carlo algorithms, respectively. However, the two frameworks have remained disconnected. We show the equivalence of these frameworks whereby the stochastic lattice kinetics reduces to effective well-mixed kinetics in the limit of fast diffusion. In the latter, the lattice structure appears implicitly, as the lumped rate of bimolecular reactions depends on the number of neighbors of a site on the lattice. Moreover, we propose a mapping between the stochastic propensities and the deterministic rates of the well-mixed vessel and lattice dynamics that illustrates the hierarchy of models and the key parameters that enable model reduction.

  5. A kinetic, mechanistic, and molecular mechanics investigation of olefin insertion into organoactinide-hydride bonds. Metal, olefin, ancillary ligand, and diastereoselection effects

    SciTech Connect

    Lin, Zerong; Marks, T.J. )

    1990-07-04

    This contribution reports a kinetic/mechanistic/stereochemical/molecular mechanics study of olefin insertion into the actinide-hydrogen bonds of Cp{prime}{sub 2}An(H)(OR) complexes (Cp{prime} = {eta}{sup 5}-(CH{sub 3}){sub 5}C{sub 5}; An = Th, U; R = achiral or chiral alkyl group). For the reaction Cp{prime}{sub 2}An(H)(O-t-Bu) + cyclohexene (An = Th), the rate law is first order in organoactinide and first order in olefin. For Cp{prime}{sub 2}Th(H)(OCH(t-Bu){sub 2}) + 1-hexene, k{sub Th{minus}H}/k{sub Th{minus}D} = 1.3 (2). A molecular mechanics/ molecular graphics analysis suggests that the sterically most favorable direction of olefin approach toward the actinide center is between the U-H and U-O bonds rather than from the side. These results provide additional insight into ancillary ligand effects on the kinetics of organo-f-element-catalyzed olefin hydrogenation.

  6. Dissolution Kinetics of Arsenopyrite in the Presence of Iron(III)-Sequestering Biogenic Ligands at pH 5.

    NASA Astrophysics Data System (ADS)

    Cornejo-Garrido, H.; Fernandez-Lomelin, P.; Guzman-Mendoza, J.; Sedov, S.; Cervini-Silva, J.

    2007-05-01

    Arsenopyrite is one of the most important natural sources of Arsenic on Earth. Arsenopyrite is relatively insoluble in pure water. That is not the case if it is exposed to environmental conditions. Notably, arsenopyrite surfaces exposed to biological activity undergo changes in lattice energy, surface morphology, particle size, and other properties, typical of mineral dissolution. Iron biogeochemical cycling is pivotal to electron transferring in nature. Therein, the need to further scrutinize on the mechanism of arsenopyrite dissolution induced by biological activity. In oxic environments, such as highly weathered soils or surficial seawater, microorganisms and higher plants produce biogenic ligands such as siderophores to mobilize Fe that otherwise would be unavailable. Siderophores ligands facilitate the dissolution of natural particles that represent a primary reservoir of iron. In this paper we study the stability of arsenopyrite in the presence of desferrioxamine (DFO-B), a common siderophore ligand, at pH 5. Arsenopyrite specimens from mines from Panasqueira, Portugal, were used for this study. Batch dissolution experiments of arsenopyrite (1 g L-1) in the presence of DFO-B ([DFO-B]0 - 200 ?M) were conducted for 7 days. The initial pH was adjusted to 5. Samples were stirred at 150 rpm. Sieving was conducted to homogeneized the particle size 0.149-0.1mm before conducting the dissolution experiments. Corresponding experiments in the absence of DFO-B for the purpose of comparison were also conducted. Analyses for soluble metals were conducted by AA and ICP-AES. Surface characterization was conducted by XRD and SEM-EDX. Incrustations of Pb(0) were detected in the arsenopyrite samples used for this study. In the presence of DFO-B, releases of Fe, As, and Pb showed positive trends with time. A shallower dependency was observed for release of Fe, As, and Pb in the presence of water only under similar experimental conditions. Detected concentrations of Fe, As, and

  7. How Fast Is Fast?

    ERIC Educational Resources Information Center

    Korn, Abe

    1994-01-01

    Presents an activity that enables students to answer for themselves the question of how fast a body must travel before the nonrelativistic expression must be replaced with the correct relativistic expression by deciding on the accuracy required in describing the kinetic energy of a body. (ZWH)

  8. Amplification of a fast wave by extracting both the kinetic energy and electrostatic potential energy of a large-orbit relativistic electron beam in a coaxial electrostatic wiggler

    SciTech Connect

    Zhang Shichang

    2010-05-15

    Nonlinear model and simulation technique of the interaction and energy transfer between a fast wave and a large-orbit relativistic electron beam in a coaxial electrostatic wiggler are presented. Unlike the situations in a magnetostatic-wiggler free-electron laser (MWFEL) and in an electron cyclotron maser (ECM), the electrostatic potential of the electrons plays an important role and participates in the energy exchange between the wave and the electron beam. Compared to MWFEL and ECM, the coaxial electrostatic-wiggler configuration has a distinguishing peculiarity that besides the electron-beam's kinetic energy, its electrostatic potential energy can be effectively transferred to the fast wave. Simulation shows that wave could be amplified with ultrahigh gain by extracting both the kinetic energy and electrostatic potential energy of the electron beam.

  9. A macrocyclic ligand able to bind gallium(III) by preorganized pendant arms; coordination and kinetic studies.

    PubMed

    Ambrosi, Gianluca; Boggioni, Alessia; Formica, Mauro; Fusi, Vieri; Giorgi, Luca; Lucarini, Simone; Micheloni, Mauro; Secco, Fernando; Venturini, Marcella; Zappia, Giovanni

    2005-02-07

    The equilibria and kinetics of the binding of gallium(III) to 4-(N),10-(N)-bis[2-(3-hydroxo-2-oxo-2-H-pyridine-1-y1)acetamido]-1,7-dimethyl-1,4,7,10-tetraazacyclododecane (L) were investigated in acidic medium at ionic strength 1 M (NaClO4). Spectrophotometric titrations in the UV region revealed that L is able to bind Ga3+ also at high H+ concentration. The kinetic (stopped-flow) experiments are interpreted on the basis of three parallel reaction paths (i) M3+ + H2L2+ = M(H2L)5+ where M(H2L)5+ is in a steady state, (ii) M(OH)2+ + H2L2+ = M(HL)4+ + H2O and (iii) M(OH)2+ + HL+ = ML3+ + H2O. The first-order rate constants for conversion of the outer-sphere into the inner-sphere complexes are similar to those of the Ga(III)/tropolone system which is known to react according to the dissociative Id mechanism and to the relevant rate constants for water exchange at the metal ion. The effects of pH on the UV-Vis absorption, fluorescence emission properties and NMR spectral features on the Ga(III)/L system were also investigated. Spectrophotometric titrations in the UV region reveal that, in acid medium the prevailing species is M(HL)4+ whereas the chelate ML3+ prevails for [H+] < 0.01 M. The results indicate metal coordination at the oxygen atoms of the 3-hydroxo-2-oxopyridine residues.

  10. 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

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

    2010-09-22

    The kinetics, thermodynamics, and coordination dynamics are reported for O(2) and CO 1:1 binding to a series of pseudo-tetradentate ligand-copper(I) complexes ((D)LCu(I)) to give Cu(I)/O(2) and Cu(I)/CO product species. Members of the (D)LCu(I) series possess an identical tridentate core structure where the cuprous ion binds to the bispicolylamine (L) fragment. (D)L also contains a fourth variable N-donor moiety {D = benzyl (Bz); pyridyl (Py); imidazolyl (Im); dimethylamino (NMe(2)); (tert-butylphenyl)pyridyl (TBP); quinolyl (Q)}. The structural characteristics of (D)LCu(I)-CO and (D)LCu(I) are detailed, with X-ray crystal structures reported for (TBP)LCu(I)-CO, (Bz)LCu(I)-CO, and (Q)LCu(I). Infrared studies (solution and solid-state) confirm that (D)LCu(I)-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 (Im)LCu(I) and (NMe(2))LCu(I) (as well as for (TBP)LCu(I) and (Q)LCu(I)), which relate to the O(2) binding kinetics and thermodynamics. Equilibrium CO binding data (K(CO), ΔH°, ΔS°) were obtained by conducting UV-visible spectrophotometric CO titrations, while CO binding kinetics and thermodynamics (k(CO), ΔH(double dagger), ΔS(double dagger)) were measured through variable-temperature (193-293 K) transient absorbance laser flash photolysis experiments, λ(ex) = 355 nm. Carbon monoxide dissociation rate constants (k(-CO)) and corresponding activation parameters (ΔH(double dagger), ΔS(double dagger)) have also been obtained. CO binding to (D)LCu(I) follows an associative mechanism, with the increased donation from D leading to higher k(CO) values. Unlike observations from previous work, the K(CO) values increased as the k(CO) and k(-CO) values declined; the

  11. Kinetic Models of Fast Solar Wind Driven by Imbalanced Ion Cyclotron Dissipation - What Will Solar Probe See?

    NASA Astrophysics Data System (ADS)

    Isenberg, P. A.; Vasquez, B. J.

    2012-12-01

    In previous work (e.g. Isenberg & Vasquez, ApJ, 731, 88, 2011), we have shown that resonant dissipation of a turbulently maintained power-law spectrum of ion cyclotron waves can produce a reasonable fast solar wind flow. Kinetic modeling of this ion heating in the expanding collisionless coronal hole must also take into account the effects of gravity, charge-separation electric field, mirror force, inertial force in the accelerating plasma, and ponderomotive Alfvén wave pressure. The combined action of all these processes leads to a characteristic evolution of the proton distribution function, some aspects of which may be independent of the actual mechanism for the perpendicular heating. Our previous model used resonant wave intensities that were "balanced" in that we took the power in outward-propagating waves and sunward-propagating waves to be equal. We also were limited by computational considerations to heliocentric radial positions < 6 Rs. Here, we consider imbalanced cases where the outward-propagating intensities of resonant waves are larger than the sunward intensities, as would be expected from reflection models of turbulent evolution in the solar atmosphere. We also extend our computations to beyond the Alfvenic critical point, into the radial range to be explored by Solar Probe Plus. We will present model results for the solar wind speeds and temperatures as functions of heliocentric radius for various ratios of sunward-to-outward wave intensities. We will also show detailed shapes of the proton distribution function and discuss their radial evolution with particular emphasis on the region accessible to the planned Solar Probe Plus mission.

  12. 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

  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. N-Substituted Benztropine Analogs: Selective Dopamine Transporter Ligands with a Fast Onset of Action and Minimal Cocaine-Like Behavioral Effects

    PubMed Central

    Li, Su-Min; Kopajtic, Theresa A.; O'Callaghan, Matthew J.; Agoston, Gregory E.; Cao, Jianjing; Newman, Amy Hauck

    2011-01-01

    Previous studies suggested that differences between the behavioral effects of cocaine and analogs of benztropine were related to the relatively slow onset of action of the latter compounds. Several N-substituted benztropine analogs with a relatively fast onset of effects were studied to assess whether a fast onset of effects would render the effects more similar to those of cocaine. Only one of the compounds increased locomotor activity, and the increases were modest compared with those of 10 to 20 mg/kg cocaine. In rats trained to discriminate 10 mg/kg cocaine from saline none of the compounds produced more than 40% cocaine-like responds up to 2 h after injection. None of the compounds produced place-conditioning when examined up to 90 min after injection, indicating minimal abuse liability. The compounds had 5.6 to 30 nM affinities at the dopamine transporter (DAT), with uniformly lower affinities at norepinephrine and serotonin transporters (from 490-4600 and 1420–7350 nM, respectively). Affinities at muscarinic M1 receptors were from 100- to 300-fold lower than DAT affinities, suggesting minimal contribution of those sites to the behavioral effects of the compounds. Affinities at histaminic H1 sites were from 11- to 43-fold lower than those for the DAT. The compounds also had affinity for sigma, 5-hydroxytryptamine1 (5-HT1), and 5-HT2 receptors that may have contributed to their behavioral effects. Together, the results indicate that a slow onset of action is not a necessary condition for reduced cocaine-like effects of atypical DAT ligands and suggest several mechanisms that may contribute to the reduced cocaine-like efficacy of these compounds. PMID:21088247

  15. The SH2 domains of inositol polyphosphate 5-phosphatases SHIP1 and SHIP2 have similar ligand specificity but different binding kinetics.

    PubMed

    Zhang, Yanyan; Wavreille, Anne-Sophie; Kunys, Andrew R; Pei, Dehua

    2009-11-24

    SH2 domain-containing inositol 5-phosphatases 1 (SHIP1) and 2 (SHIP2) are structurally similar proteins that catalyze the degradation of lipid secondary messenger phosphatidylinositol 3,4,5-triphosphate to produce phosphatidylinositol 3,4-diphosphate. Despite their high sequence identity (51%), SHIP1 and SHIP2 share little overlap in their in vivo functions. In this work, the sequence specificity of the SHIP2 SH2 domain was systematically defined through the screening of a combinatorial pY peptide library. Comparison of its specificity profile with that of the SHIP1 SH2 domain showed that the two SH2 domains have similar specificities, both recognizing pY peptides of the consensus sequence pY[S/Y][L/Y/M][L/M/I/V], although there are also subtle differences such as the tolerance of an arginine at the pY + 1 position by the SHIP2 but not SHIP1 SH2 domain. Surface plasmon resonance analysis of their interaction with various pY peptides suggested that the two domains have similar binding affinities but dramatically different binding kinetics, with the SHIP1 SH2 domain having fast association and dissociation rates while the SHIP2 domain showing apparent slow-binding behavior. Site-directed mutagenesis and kinetic studies indicated that the SHIP2 SH2 domain exists as a mixture of two conformational isomers. The major, inactive isomer apparently contains two cis peptidyl-prolyl bonds at positions 88 and 105, whereas the minor, active isomer has both proline residues in their trans configuration. Cis-trans isomerization of the peptidyl-prolyl bonds may provide a potential mechanism for regulating the interaction between SHIP2 and pY proteins. These data suggest that a combination of tissue distribution, specificity, and kinetic differences is likely responsible for their in vivo functional differences.

  16. Kinetic and ligand binding evidence for two heme A-based terminal oxidases in plasma membranes from Bacillus subtilis.

    PubMed

    Hill, B C; Vo, L; Albanese, J

    1993-02-15

    Detergent-solubilized plasma membranes from Bacillus subtilis have been characterized for their cytochrome oxidase content. Triton X-100-solubilized membranes show high O2 turnover with ascorbate plus TMPD. Reduced-oxidized difference spectroscopy of ascorbate-TMPD-reduced membranes reveals the presence of cytochrome c and cytochrome a. An additional, b-type cytochrome appears when the membranes are reduced with dithionite. Time-resolved difference spectra taken during reduction by ascorbate-TMPD reveal two kinetic forms of heme A-containing cytochromes. There is a high-turnover form that is rapidly reduced upon anaerobiosis, and a second type which is only slowly reduced upon anaerobiosis. The slowly reduced oxidase is distinguished by an alpha-band blue-shifted to 600 nm relative to the 603-nm position observed for high-turnover oxidase. Addition of CO to ascorbate-TMPD-reduced membranes gives a spectrum typical of ferrocytochrome a3-CO, and the intensity corresponds to the total ferrocytochrome a3 concentration. Photolysis of ascorbate-TMPD-reduced, CO-bound membranes indicates that both species are photosensitive with similar rates of recombination. Addition of CO to dithionite-reduced membranes shows an additional CO reactive center that has a spectrum characteristic of cytochrome o. Cyanide blocks complete reduction of high-turnover oxidase by ascorbate plus TMPD, but does not appear to effect slowly reduced oxidase. These results indicate the presence of two different types of cytochrome aa3 oxidase in plasma membranes of B. subtilis.

  17. 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.

  18. Kinetics of binding of dihydropyridine calcium channel ligands to skeletal muscle membranes: Evidence for low-affinity sites and for the involvement of G proteins

    SciTech Connect

    Dunn, S.M.J.; Bladen, C. )

    1991-06-11

    Detailed kinetic studies of the binding of the calcium channel antagonist (+)-({sup 3}H)PN200-110 to membrane preparations form rabbit skeletal muscle have demonstrated that, in addition to the high-affinity sites that are readily measured in equilibrium and kinetic experiments, there are also dihydropyridine binding sites with much lower affinities. These sites were detected by the ability of micromolar concentrations of several dihydropyridines to accelerate the rate of dissociation of (+)-({sup 3}H)PN200-110 from its high-affinity sites. The observed increase in rate was dependent on the concentration of competing ligand, and half-maximal effects occurred at approximately 10 {mu}M for the agonist ({plus minus})-Bay K8644 and for the antagonists nifedipine, ({plus minus})-nitrendipine, and (+)-PN200-110. The low-affinity sites appear to be stereospecific since ({minus})-PN200-110 (1-200 {mu}M) did not affect the dissociation rate. The possible involvement of guanine nucleotide binding proteins in dihydropyridine binding has been investigated by studying the effects of guanosine 5'-O-(3-thiotriphosphate) (GTP{gamma}S) and guanosine 5'-O-(2-thiodiphosphate) (GDP{beta}S) on binding parameters. GTP{gamma}S did increase the ability of ({plus minus})-({sup 3}H)PN200-110. These results suggest that skeletal muscle dihydropyridine receptors have low-affinity binding sites that may be involved in the regulation of calcium channel function and that activation of a guanine nucleotide binding protein may modulate the binding of agonists but not of antagonists to these sites.

  19. Thermo-kinetic analysis space expansion for cyclophilin-ligand interactions - identification of a new nonpeptide inhibitor using Biacore™ T200.

    PubMed

    Wear, Martin A; Nowicki, Matthew W; Blackburn, Elizabeth A; McNae, Iain W; Walkinshaw, Malcolm D

    2017-04-01

    We have established a refined methodology for generating surface plasmon resonance sensor surfaces of recombinant his-tagged human cyclophilin-A. Our orientation-specific stabilisation approach captures his-tagged protein under 'physiological conditions' (150 mm NaCl, pH 7.5) and covalently stabilises it on Ni(2+)-nitrilotriacetic acid surfaces, very briefly activated for primary amine-coupling reactions, producing very stable and active surfaces (≥ 95% specific activity) of cyclophilin-A. Variation in protein concentration with the same contact time allows straightforward generation of variable density surfaces, with essentially no loss of activity, making the protocol easily adaptable for studying numerous interactions; from very small fragments, ~ 100 Da, to large protein ligands. This new method results in an increased stability and activity of the immobilised protein and allowed us to expand the thermo-kinetic analysis space, and to determine accurate and robust thermodynamic parameters for the cyclophilin-A-cyclosporin-A interaction. Furthermore, the increased sensitivity of the surface allowed identification of a new nonpeptide inhibitor of cyclophilin-A, from a screen of a fragment library. This fragment, 2,3-diaminopyridine, bound specifically with a mean affinity of 248 ± 60 μm. The X-ray structure of this 109-Da fragment bound in the active site of cyclophilin-A was solved to a resolution of 1.25 Å (PDB: 5LUD), providing new insight into the molecular details for a potential new series of nonpeptide cyclophilin-A inhibitors.

  20. Evidence of kinetic control of ligand binding and staged product release in MurA (enolpyruvyl UDP-GlcNAc synthase)-catalyzed reactions .

    PubMed

    Jackson, Sean G; Zhang, Fuzhong; Chindemi, Paul; Junop, Murray S; Berti, Paul J

    2009-12-15

    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(cat)/K(M) of 520 M(-1) s(-1), was far slower than the normal reaction, and 3 x 10(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.ligand ion pairs, and three intraprotein hydrogen bonds helping hold the active site loop closed. These were replaced with only two MurA.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.

  1. Electrostatically-driven fast association and perdeuteration allow detection of transferred cross-relaxation for G protein-coupled receptor ligands with equilibrium dissociation constants in the high-to-low nanomolar range.

    PubMed

    Catoire, Laurent J; Damian, Marjorie; Baaden, Marc; Guittet, Eric; Banères, Jean-Louis

    2011-07-01

    The mechanism of signal transduction mediated by G protein-coupled receptors is a subject of intense research in pharmacological and structural biology. Ligand association to the receptor constitutes a critical event in the activation process. Solution-state NMR can be amenable to high-resolution structure determination of agonist molecules in their receptor-bound state by detecting dipolar interactions in a transferred mode, even with equilibrium dissociation constants below the micromolar range. This is possible in the case of an inherent ultra-fast diffusive association of charged ligands onto a highly charged extracellular surface, and by slowing down the (1)H-(1)H cross-relaxation by perdeuterating the receptor. Here, we demonstrate this for two fatty acid molecules in interaction with the leukotriene BLT2 receptor, for which both ligands display a submicromolar affinity.

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

    PubMed

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

    2015-07-01

    The present study examined if high intensity training (HIT) could increase the expression of oxidative enzymes in fast-twitch muscle fibers causing a faster oxygen uptake (V˙O2) response during intense (INT), but not moderate (MOD), exercise and reduce the V˙O2 slow component and muscle metabolic perturbation during INT. Pulmonary V˙O2 kinetics was determined in eight trained male cyclists (V˙O2-max: 59 ± 4 (means ± SD) mL min(-1) kg(-1)) during MOD (205 ± 12 W ~65% V˙O2-max) and INT (286 ± 17 W ~85% V˙O2-max) exercise before and after a 7-week HIT period (30-sec sprints and 4-min intervals) with a 50% 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. V˙O2 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 V˙O2 kinetics.

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

    PubMed

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

    2015-11-27

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

  4. 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…

  5. 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.

  6. 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.

  7. 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.

  8. Similar mitochondrial activation kinetics in wild-type and creatine kinase-deficient fast-twitch muscle indicate significant Pi control of respiration.

    PubMed

    Jeneson, Jeroen A L; ter Veld, Frank; Schmitz, Joep P J; Meyer, Ronald A; Hilbers, Peter A J; Nicolay, Klaas

    2011-06-01

    Past simulations of oxidative ATP metabolism in skeletal muscle have predicted that elimination of the creatine kinase (CK) reaction should result in dramatically faster oxygen consumption dynamics during transitions in ATP turnover rate. This hypothesis was investigated. Oxygen consumption of fast-twitch (FT) muscle isolated from wild-type (WT) and transgenic mice deficient in the myoplasmic (M) and mitochondrial (Mi) CK isoforms (MiM CK(-/-)) were measured at 20°C at rest and during electrical stimulation. MiM CK(-/-) muscle oxygen consumption activation kinetics during a step change in contraction rate were 30% faster than WT (time constant 53 ± 3 vs. 69 ± 4 s, respectively; mean ± SE, n = 8 and 6, respectively). MiM CK(-/-) muscle oxygen consumption deactivation kinetics were 380% faster than WT (time constant 74 ± 4 s vs. 264 ± 4 s, respectively). Next, the experiments were simulated using a computational model of the oxidative ATP metabolic network in FT muscle featuring ADP and Pi feedback control of mitochondrial respiration (J. A. L. Jeneson, J. P. Schmitz, N. A. van den Broek, N. A. van Riel, P. A. Hilbers, K. Nicolay, J. J. Prompers. Am J Physiol Endocrinol Metab 297: E774-E784, 2009) that was reparameterized for 20°C. Elimination of Pi control via clamping of the mitochondrial Pi concentration at 10 mM reproduced past simulation results of dramatically faster kinetics in CK(-/-) muscle, while inclusion of Pi control qualitatively explained the experimental observations. On this basis, it was concluded that previous studies of the CK-deficient FT muscle phenotype underestimated the contribution of Pi to mitochondrial respiratory control.

  9. Measurement of kinetic energy release in CO fragmentation by charge-changing collisions of fast heavy ions

    SciTech Connect

    Mizuno, T.; Yamada, T.; Tsuchida, H.; Itoh, A.; Nakai, Y.

    2010-01-15

    We study ionization and fragmentation of CO in electron loss and capture collisions of B{sup 2+}, O{sup 2+}, and Si{sup 2+} ions at an energy of 71.4 keV/u (v=1.69 a.u.). Coincidence measurements of fragment ions from CO and charge-selected ions were performed by means of a momentum three-dimensional imaging technique. Production cross sections of CO{sup r+} and branching ratios into various fragmentation channels were obtained for r=1-4. We also measured kinetic energy release (KER) in individual fragmentation channels. The KER spectra for r<=2 are found to be different for electron loss and capture collisions, while the difference becomes small for r>=3. As a measure of the degree of molecular fragmentation, the magnitude of the binding energy of the relevant electronic states seems the important parameter both in loss and capture collisions.

  10. Remobilizing surfactant retarded fluid particle interfaces. I. Stress-free conditions at the interfaces of micellar solutions of surfactants with fast sorption kinetics

    NASA Astrophysics Data System (ADS)

    Stebe, Kathleen J.; Lin, Shi-Yow; Maldarelli, Charles

    1991-01-01

    Surfactant molecules adsorb onto the interfaces of moving fluid particles and are convected to regions in which the surface flow converges. Accumulation of surfactant in these regions creates interfacial tension gradients that retard the surface flow. In this study it is argued theoretically and demonstrated experimentally that fluid movement on the surface of a drop or bubble can remain unhindered in the presence of a single adsorbed surfactant if, relative to the convective rate of transport of adsorbed surfactant along the surface, desorption is fast, and the bulk concentration is high enough so that diffusion away from the particle is fast. For this circumstance, a uniform surface concentration of surfactant is maintained, and no gradients in surface tension arise to retard the surface velocity. The fluid particle flow behaves as it would in the absence of surfactant save that it has a reduced, uniform surface tension. The remobilization of surfactant-laden interfaces of fluid particles is demonstrated experimentally in a three-phase periodic slug flow in a capillary tube in which a train of alternating air and aqueous slugs ride on an annular wetting film of fluorocarbon oil. Surfactant, dissolved in the aqueous slug phase, adsorbs onto and retards the aqueous-oil interface. The hydrodynamics of this flow is such that small changes in the mobility of this interface create large shear rates in the oil layer. This significantly increases the pressure drop required to drive the slug train at constant velocity. Three surface adsorbers are used to demonstrate surface remobilization: The polyethoxy, nonionic surfactants Triton X-100 and Brij-35, which have fast desorption kinetics and do not retard the surface flow at high concentrations and, as a counter example, the desorption hindered protein bovine serum albumin, which is shown to be unable to remobilize an interface even at high concentration.

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

    PubMed

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

    2017-02-24

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

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

    PubMed

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

    2013-08-05

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

  13. 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

    2016-06-20

    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.

  14. 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.

  15. 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.

  16. 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

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

    SciTech Connect

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

    2016-01-29

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

  18. 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

  19. 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

  20. 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.

  1. 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

    2014-05-07

    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.

  2. Hybrid Steered Molecular Dynamics Approach to Computing Absolute Binding Free Energy of Ligand-Protein Complexes: A Brute Force Approach That Is Fast and Accurate.

    PubMed

    Chen, Liao Y

    2015-04-14

    Computing the free energy of binding a ligand to a protein is a difficult task of essential importance for which purpose various theoretical/computational approaches have been pursued. In this paper, we develop a hybrid steered molecular dynamics (hSMD) method capable of resolving one ligand–protein complex within a few wall-clock days with high enough accuracy to compare with the experimental data. This hSMD approach is based on the relationship between the binding affinity and the potential of mean force (PMF) in the established literature. It involves simultaneously steering n (n = 1, 2, 3, ...) centers of mass of n selected segments of the ligand using n springs of infinite stiffness. Steering the ligand from a single initial state chosen from the bound state ensemble to the corresponding dissociated state, disallowing any fluctuations of the pulling centers along the way, one can determine a 3n-dimensional PMF curve connecting the two states by sampling a small number of forward and reverse pulling paths. This PMF constitutes a large but not the sole contribution to the binding free energy. Two other contributors are (1) the partial partition function containing the equilibrium fluctuations of the ligand at the binding site and the deviation of the initial state from the PMF minimum and (2) the partial partition function containing rotation and fluctuations of the ligand around one of the pulling centers that is fixed at a position far from the protein. We implement this hSMD approach for two ligand–protein complexes whose structures were determined and whose binding affinities were measured experimentally: caprylic acid binding to bovine β-lactoglobulin and glutathione binding to Schistosoma japonicum glutathione S-transferase tyrosine 7 to phenylalanine mutant. Our computed binding affinities agree with the experimental data within a factor of 1.5. The total time of computation for these two all-atom model systems (consisting of 96K and 114K atoms

  3. The fast and slow kinetics of chlorophyll a fluorescence induction in plants, algae and cyanobacteria: a viewpoint.

    PubMed

    Papageorgiou, George C; Tsimilli-Michael, Merope; Stamatakis, Kostas

    2007-01-01

    The light-induced/dark-reversible changes in the chlorophyll (Chl) a fluorescence of photosynthetic cells and membranes in the mus-to-several min time window (fluorescence induction, FI; or Kautsky transient) reflect quantum yield changes (quenching/de-quenching) as well as changes in the number of Chls a in photosystem II (PS II; state transitions). Both relate to excitation trapping in PS II and the ensuing photosynthetic electron transport (PSET), and to secondary PSET effects, such as ion translocation across thylakoid membranes and filling or depletion of post-PS II and post-PS I pools of metabolites. In addition, high actinic light doses may depress Chl a fluorescence irreversibly (photoinhibitory lowering; q(I)). FI has been studied quite extensively in plants an algae (less so in cyanobacteria) as it affords a low resolution panoramic view of the photosynthesis process. Total FI comprises two transients, a fast initial (OPS; for Origin, Peak, Steady state) and a second slower transient (SMT; for Steady state, Maximum, Terminal state), whose details are characteristically different in eukaryotic (plants and algae) and prokaryotic (cyanobacteria) oxygenic photosynthetic organisms. In the former, maximal fluorescence output occurs at peak P, with peak M lying much lower or being absent, in which case the PSMT phases are replaced by a monotonous PT fluorescence decay. In contrast, in phycobilisome (PBS)-containing cyanobacteria maximal fluorescence occurs at M which lies much higher than peak P. It will be argued that this difference is caused by a fluorescence lowering trend (state 1 --> 2 transition) that dominates the FI pattern of plants and algae, and correspondingly by a fluorescence increasing trend (state 2 --> 1 transition) that dominates the FI of PBS-containing cyanobacteria. Characteristically, however, the FI pattern of the PBS-minus cyanobacterium Acaryochloris marina resembles the FI patterns of algae and plants and not of the PBS

  4. 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

  5. Fast quantitative ROS detection based on dual-color single rare-earth nanoparticle imaging reveals signaling pathway kinetics in living cells.

    PubMed

    Abdesselem, M; Ramodiharilafy, R; Devys, L; Gacoin, T; Alexandrou, A; Bouzigues, C I

    2017-01-05

    Reactive oxygen species (ROS), and notably hydrogen peroxide H2O2, are cellular second messengers that are known to control a variety of signaling processes. They can finely regulate the dynamics of signal transduction, cell response and ultimately tissue function. However, there are very few local, quantitative and time-resolved descriptions of their cellular organization at the scale of molecular reactions, due to the lack of efficient sensors. We thus developed a novel nanoprobe-based ROS detection system using the simultaneous imaging of single lanthanide nanoparticles (YAG:Ce and chemically reduced Gd0.6Eu0.4VO4). We reveal that both particle luminescence signals are controlled by their H2O2 local environment. By simultaneously tracking their luminescence, we devised a new approach providing a quantitative (0.5 μM accuracy in the 1-10 μM range) H2O2 measurement with a 500 ms time resolution, surpassing all existing methods by two orders of magnitude, and revealing previously inaccessible molecular events controlling ROS concentration. We used this nanoprobe in living cells to track fast signaling pathways, by measuring the dynamics of H2O2 intracellular concentrations, induced by endothelin-1 (ET-1) stimulation. We thus revealed the mechanisms controlling ROS production, notably the activity modulation of the ROS-producing enzyme NADPH oxidase by fast (<10 s) EGFR transactivation, and measured quantitatively their kinetic parameters through a minimal analytical model. Altogether, these results illustrate how lanthanide nanoparticle-based sensors are a powerful tool to dynamically probe molecular mechanisms shaping the oxidative cell response.

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

    NASA Astrophysics Data System (ADS)

    McMillen, Laura M.; Vavylonis, Dimitrios

    2016-12-01

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

  7. 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.

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

    PubMed

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

    2015-09-28

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

  9. Sigma-1 receptor alters the kinetics of Kv1.3 voltage gated potassium channels but not the sensitivity to receptor ligands.

    PubMed

    Kinoshita, Maho; Matsuoka, Yoshikazu; Suzuki, Takeshi; Mirrielees, Jennifer; Yang, Jay

    2012-05-03

    Sigma1 receptors (Sigma1R) are intracellular chaperone proteins that bind psychotropic drugs and also clinically used drugs such as ketamine and haloperidol. Co-expression of the Sigma1R has been reported to enhance the sensitivity of several voltage-gated ion channels to Sigma1R ligands. Kv1.3 is the predominant voltage-gated potassium channel expressed in T lymphocytes with a documented role in immune activation. To gain a better understanding of Sigma1R modulation of Kv ion channels, we investigated the effects of Sigma1R co-expression on Kv1.3 physiology and pharmacology in ion channels expressed in Xenopus oocytes. We also explored the protein domains of Kv1.3 necessary for protein:protein interaction between Kv1.3 and Sigma1R through co-immunoprecipitation studies. Slowly inactivating outward-going currents consistent with Kv1.3 expression were elicited on step depolarizations. The current characterized by E(rev), V(1/2), and slope factor remained unchanged when co-expressed with Sigma1R. Analysis of inactivation time constant revealed a faster Kv1.3 current decay when co-expressed with Sigma1R. However the sensitivity to Sigma1R ligands remained unaltered when co-expressed with the Sigma1R in contrast to the previously reported modulation of ligand sensitivity in closely related Kv1.4 and Kv1.5 voltage gated potassium channels. Co-immunoprecipitation assays of various Kv1.3 truncation constructs indicated that the transmembrane domain of the Kv1.3 protein was responsible for the protein:protein interaction with the Sigma1R. Sigma1R likely interacts with different domains of Kv ion channel family proteins resulting in distinct modulation of different channels.

  10. Monofunctional chorismate mutase from Bacillus subtilis: Kinetic and sup 13 C NMR studies on the interactions of the enzyme with its ligands

    SciTech Connect

    Gray, J.V.; Eren, D.; Knowles, J.R. )

    1990-09-18

    The interaction of the monofuctional chorismate mutase from Bacillus subtilis with chorismate and prephenate has been studied kinetically and by NMR spectroscopy with {sup 13}C specifically labeled substrates. Prephenate dominates the population of enzyme-bound species, and the off rate constant obtained from line-broadening experiments is close to the value of k{sub cat} for chorismate determined kinetically. The calculated on rate constant for prephenate is similar to the value of k{sub cat}/K{sub m} for chorismate. The kinetic parameters of the Bacillus mutase are remarkably insensitive to pH over a wide range and display no solvent isotope effect. These results suggest that the enzyme-catalyzed reaction may be encounter controlled (slowed from the diffusion limit by some feature of the enzyme's active site) and the k{sub cat} for chorismate is determined by the product off rate. There is now no evidence to suggest that the skeletal rearrangement on the enzyme surface occurs by a pathway other than a pericyclic process.

  11. Flow cytometry-based TCR-ligand Koff -rate assay for fast avidity screening of even very small antigen-specific T cell populations ex vivo.

    PubMed

    Nauerth, Magdalena; Stemberger, Christian; Mohr, Fabian; Weißbrich, Bianca; Schiemann, Matthias; Germeroth, Lothar; Busch, Dirk H

    2016-09-01

    High epitope-specific sensitivity of CD8(+) T cells is required for optimal immune protection against intracellular pathogens as well as certain malignancies. The quality of antigen recognition of CD8(+) T cells is usually described as "avidity" to its cognate peptide MHCI complex. T cell avidity is mainly dependent on the structural qualities of the T cell receptor (TCR), as convincingly demonstrated by recombinant TCR re-expression experiments. Based on reversible MHCI multimer staining and koff -rate measurements of monomeric peptide MHCI complexes, we recently established a microscopic assay for determining the structural avidity of individual CD8(+) T cells. Here we demonstrate that this assay can be adapted for rapid flow-cytometric avidity screening of epitope-specific T cell populations. Furthermore, we show that-in combination with conventional nonreversible MHCI multimer staining-even very small epitope-specific CD8(+) T cell populations can be analyzed directly ex vivo without the need for previous TCR cloning or T cell sorting. This simplified approach provides highly accurate mean TCR-ligand koff -rate values for poly- or oligoclonal T cell populations and is ideally suited for high-throughput applications in basic research as well as clinical settings. © 2016 International Society for Advancement of Cytometry.

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

    SciTech Connect

    Yeston, Jake Simon

    2001-01-01

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

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

    PubMed Central

    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

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

    PubMed

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

    2014-03-01

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

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

    PubMed

    Clausen, Thomas Mandel; Pereira, Marina Ayres; Oo, Htoo Zarni; Resende, Mafalda; Gustavson, Tobias; Mao, Yang; Sugiura, Nobuo; Liew, Janet; Fazli, Ladan; Theander, Thor G; Daugaard, Mads; Salanti, Ali

    2016-07-01

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

  16. 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.

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

    PubMed

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

    2009-02-02

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

  19. 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.

  20. Stability, water exchange, and anion binding studies on lanthanide(III) complexes with a macrocyclic ligand based on 1,7-diaza-12-crown-4: extremely fast water exchange on the Gd3+ complex.

    PubMed

    Pálinkás, Zoltán; Roca-Sabio, Adrián; Mato-Iglesias, Marta; Esteban-Gómez, David; Platas-Iglesias, Carlos; de Blas, Andrés; Rodríguez-Blas, Teresa; Tóth, Eva

    2009-09-21

    The picolinate-derivative ligand based on the 1,7-diaza-12-crown-4 platform (bp12c4(2-)) forms stable Ln(3+) complexes with stability constants increasing from the early to the middle lanthanides, then being relatively constant for the rest of the series (logK(LnL) = 16.81(0.06), 18.82(0.01), and 18.08(0.05) for Ln = La, Gd, and Yb, respectively). The complex formation is fast, allowing for direct potentiometric titrations to assess the stability constants. In the presence of Zn(2+), the dissociation of [Gd(bp12c4)](+) proceeds both via proton- and metal-assisted pathways, and in this respect, this system is intermediate between DTPA-type and macrocyclic, DOTA-type chelates, for which the dissociation is predominated by metal- or proton-assisted pathways, respectively. The Cu(2+) exchange shows an unexpected pH dependency, with the observed rate constants decreasing with increasing proton concentration. The rate of water exchange, assessed by (17)O NMR, is extremely high on the [Gd(bp12c4)(H(2)O)(q)](+) complex (k(ex)(298) = (2.20 +/- 0.15) x 10(8) s(-1)), and is in the same order of magnitude as for the Gd(3+) aqua ion (k(ex)(298) = 8.0 x 10(8) s(-1)). In aqueous solution, the [Gd(bp12c4)(H(2)O)(q)](+) complex is present in hydration equilibrium between nine-coordinate, monohydrated, and ten-coordinate, bishydrated species. We attribute the fast exchange to the hydration equilibrium and to the flexible nature of the inner coordination sphere. The large negative value of the activation entropy (DeltaS = -35 +/- 8 J mol(-1) K(-1)) points to an associative character for the water exchange and suggests that water exchange on the nine-coordinate, monohydrated species is predominant in the overall exchange. Relaxometric and luminescence measurements on the Gd(3+) and Eu(3+) analogues, respectively, indicate strong binding of endogenous anions such as citrate, hydrogencarbonate, or phosphate to [Ln(bp12c4)](+) complexes (K(aff) = 280 +/- 20 M(-1), 630 +/- 50 M(-1), and

  1. {sup 237}Np: Oxidation state in vivo and chelation by multidentate catecholat and hydroxypyridinonate ligands

    SciTech Connect

    Durbin, P.W.; Kullgren, B.; Allen, P.G.; Bucher, J.J.; Edelstein, N.M.; Shuh, D.K.; Xu, J.; Raymond, K.N. |

    1998-07-01

    Chemically, {sup 237}Np(V) is as toxic as U(VI), and radiologically, about as toxic as {sup 239}Pu. Depending on redox conditions in vivo, {sup 237}Np exists as weakly complexing Np(V) (NpO{sub 2}{sup +}) or as Np(IV), which forms complexes as stable as those of Pu(IV). Ten multidentate catecholate (CAM) and hydroxypyridinonate (HOPO) ligands with great affinity for Pu(IV) were compared with CaNa{sub 3}-DTPA for in vivo chelation of {sup 237}Np. Mice were injected intravenously with {sup 237}NpO{sub 2}Cl: those in a kinetic study were killed 1 to 2,880 min; in ligand studies, fed mice were injected intraperitoneally with a ligand 5, 60, or 1,440 min after {sup 237}Np(V), mice fasted for 16 h were gastrically intubated with a ligand 3 min after {sup 237}Np(V), and all were killed 24 h after ligand administration; tissues and excreta were radioanalyzed. Rapid plasma clearance and urinary excretion of {sup 237}Np(V) resemble U(VI); deposition and early retention in skeleton and liver resemble Pu(IV). The x-ray absorption near edge structure spectroscopy (XANES) spectra of femora of {sup 237}Np(V)-injected mice, compared with spectra of Np(V) and Np(IV) from reference solids, showed predominantly Np(IV). Significant in vivo {sup 237}Np chelation was obtained with all of the HOPO and CAM ligands injected at molar ratio 22; the HOPO ligands reduced {sup 237}Np in skeleton, liver, and other soft tissue, on average, to 72, 25, and 25% of control, respectively, while CaNa{sub 3}-DTPA was ineffective.

  2. Rational optimization of reprogramming culture conditions for the generation of induced pluripotent stem cells with ultra-high efficiency and fast kinetics

    PubMed Central

    Chen, Jiekai; Liu, Jing; Chen, You; Yang, Jiaqi; Chen, Jing; Liu, He; Zhao, Xiangjie; Mo, Kunlun; Song, Hong; Guo, Lin; Chu, Shilong; Wang, Deping; Ding, Ke; Pei, Duanqing

    2011-01-01

    The ectopic expression of several transcription factors can restore embryonic cell fate to cultured somatic cells and generate induced pluripotent stem cells (iPSCs), revealing a previously unknown pathway to pluripotency. However, this technology is currently limited by low efficiency, slow kinetics and multi-factorial requirement. Here we show that reprogramming can be improved and dramatically accelerated by optimizing culture conditions. First, we developed an optimized defined medium, iCD1, which allows Oct4/Sox2/Klf4 (OSK)-mediated reprogramming to achieve ultra-high efficiency (∼10% at day 8). We also found that this optimized condition renders both Sox2 and Klf4 dispensable, although the elimination of these two factors leads to lower efficiency and slower kinetics. Our studies define a shortened route, both in timing and factor requirement, toward pluripotency. This new paradigm not only provides a rationale to further improve iPSC generation but also simplifies the conceptual understanding of reprogramming by defined factors. PMID:21445094

  3. Early postnatal kinetics of colostral immunoglobulin G absorption in fed and fasted piglets and developmental expression of the intestinal immunoglobulin G receptor.

    PubMed

    Cabrera, R; Lin, X; Ashwell, M; Moeser, A; Odle, J

    2013-01-01

    The transport of IgG across the epithelial barrier and into the circulation is achieved in part by the neonatal Fc receptor (FcRn), and this provides passive immunity to the neonate. The objective of this study was to determine the effect of time and feeding state on IgG absorption, intestinal morphology, and expression of IgG receptors in the first 24 h postbirth. Twenty newborn pigs were obtained immediately after birth and fitted with umbilical arterial catheters. Colostrum was manually collected from 12 lactating sows and centrifuged to produce defatted colostrum. Piglets were orally gavaged with 32 mL defatted colostrum per kilogram of BW (given in 2 doses 1 h apart) either at birth (0 h) or at 12 h postbirth under either fed (milk replacer) or fasted (saline solution) condition (n=5 per treatment). A fifth reference group (n=5) was euthanized at birth. Blood was collected every hour for the first 2 h immediately after the catheter was inserted and then every 4 h until 12 h (i.e., 0, 1, 2, 4, 8, and 12 h) for the treatment in which the defatted colostrum was given right after birth. For the treatment gavaged at 12 h postbirth, the sampling schedule was at 12, 13, 14, 16, 20, and 24 h. At 12 h postgavage, pigs were euthanized and jejunum tissues were collected for measurement of villi height, width, crypt depth, and gene expression of FcRn and β2-microglobulin (β2M) via reverse transcription PCR. Pig serum IgG concentration was determined by radial immunodiffusion. Data were analyzed according to a 2×2 factorial arrangement of treatments (0 h-fed, 0 h-fasted, 12 h-fed, and 12 h-fasted). There was no interaction between the time (age) of offering defatted colostrum (0 vs. 12 h) and nutritional state (fed vs. fasted) for any of the measurements, and there were no differences between fed and fasted pigs. Serum IgG concentrations increased progressively with time. Piglets offered defatted colostrum at 0 h had greater (P<0.05) overall IgG absorption and greater

  4. 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

  5. Kinetic method for the large-scale analysis of the binding mechanism of histone deacetylase inhibitors.

    PubMed

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

    2014-09-01

    Performing kinetic studies on protein ligand interactions provides important information on complex formation and dissociation. Beside kinetic parameters such as association rates and residence times, kinetic experiments also reveal insights into reaction mechanisms. Exploiting intrinsic tryptophan fluorescence a parallelized high-throughput Förster resonance energy transfer (FRET)-based reporter displacement assay with very low protein consumption was developed to enable the large-scale kinetic characterization of the binding of ligands to recombinant human histone deacetylases (HDACs) and a bacterial histone deacetylase-like amidohydrolase (HDAH) from Bordetella/Alcaligenes. For the binding of trichostatin A (TSA), suberoylanilide hydroxamic acid (SAHA), and two other SAHA derivatives to HDAH, two different modes of action, simple one-step binding and a two-step mechanism comprising initial binding and induced fit, were verified. In contrast to HDAH, all compounds bound to human HDAC1, HDAC6, and HDAC8 through a two-step mechanism. A quantitative view on the inhibitor-HDAC systems revealed two types of interaction, fast binding and slow dissociation. We provide arguments for the thesis that the relationship between quantitative kinetic and mechanistic information and chemical structures of compounds will serve as a valuable tool for drug optimization.

  6. Thermodynamics and high-pressure kinetics of a fast carbon dioxide fixation reaction by a (2,6-pyridinedicarboxamidato-hydroxo)nickel(II) complex.

    PubMed

    Troeppner, O; Huang, D; Holm, R H; Ivanović-Burmazović, I

    2014-04-14

    The previously reported carbon dioxide fixation reaction by the planar terminal hydroxide complex [Ni(pyN2(Me2))(OH)](1-) in DMF has been further characterized by determination of the equilibrium constants K(eq)²⁹⁸ = 2.4 ± 0.2 × 10(5) M(-1) and K(eq)²²³ = 1.3 ± 0.1 × 10(7) M(-1), as well as the volume of activation for the CO2 binding (ΔV(on)(≠223) = -21 ± 3 cm(3) mol(-1)) and back decarboxylation (ΔV(off)(≠223) = -13 ± 1 cm(3) mol(-1)) by high-pressure kinetics. The data are consistent with an earlier DFT computation, including the probable nature of the transition state, and support designating the reaction as one of the most completely investigated carbon dioxide fixation reactions of any type.

  7. Probing the structure of the ligand binding cavity of lipocalins by fluorescence spectroscopy.

    PubMed

    Patel, R C; Lange, D; McConathy, W J; Patel, Y C; Patel, S C

    1997-06-01

    The lipocalin superfamily constitutes a phylogenetically conserved group of more than 40 proteins that function in the binding and transport of a variety of physiologically important ligands. Members of this family subserve diverse functions as carriers of retinoids (retinol binding protein), odorants (odorant binding proteins), chromophores (insecticyanin, INS), pheromones (aphrodisin) and sterols (apolipoprotein D, apoD). Despite the pivotal importance of the ligand binding function of these proteins, a suitable approach for characterizing the molecular determinants of such binding has not been available. In studies using three homogeneously purified lipocalins INS, beta-lactoglobulin (BLG) and human apoD, we find that the fluorescence reporter BIS (1,1'-bi(4-anilino) naphthalene-5,5'-disulfonic acid) is an ideal candidate for use in rapid kinetic experiments and in fluorescence resonance energy transfer (FRET). These methods require only small amounts of reagents and yield molecular coordinates of the ligand binding cavity of lipocalins in solution that are in remarkably close agreement to those obtained from crystallographic work with solids. Extremely fast ligand binding dynamics is indicated.

  8. 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.

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

    PubMed

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

    2014-12-01

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

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

    DOEpatents

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

    2017-02-21

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

  11. 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.

  12. 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.

  13. The Positive Effects of Priming Exercise on Oxygen Uptake Kinetics and High-Intensity Exercise Performance Are Not Magnified by a Fast-Start Pacing Strategy in Trained Cyclists

    PubMed Central

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

    2014-01-01

    The purpose of this study was to determine both the independent and additive effects of prior heavy-intensity exercise and pacing strategies on the VO2 kinetics and performance during high-intensity exercise. Fourteen endurance cyclists (VO2max  = 62.8±8.5 mL.kg−1.min−1) volunteered to participate in the present study with the following protocols: 1) incremental test to determine lactate threshold and VO2max; 2) four maximal constant-load tests to estimate critical power; 3) six bouts of exercise, using a fast-start (FS), even-start (ES) or slow-start (SS) pacing strategy, with and without a preceding heavy-intensity exercise session (i.e., 90% critical power). In all conditions, the subjects completed an all-out sprint during the final 60 s of the test as a measure of the performance. For the control condition, the mean response time was significantly shorter (p<0.001) for FS (27±4 s) than for ES (32±5 s) and SS (32±6 s). After the prior exercise, the mean response time was not significantly different among the paced conditions (FS = 24±5 s; ES = 25±5 s; SS = 26±5 s). The end-sprint performance (i.e., mean power output) was only improved (∼3.2%, p<0.01) by prior exercise. Thus, in trained endurance cyclists, an FS pacing strategy does not magnify the positive effects of priming exercise on the overall VO2 kinetics and short-term high-intensity performance. PMID:24740278

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

    PubMed

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

    2015-09-09

    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.

  15. Kinetic mechanism of putrescine oxidase from Rhodococcus erythropolis.

    PubMed

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

    2014-10-01

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

  16. Reversible sequential-binding probe receptor-ligand interactions in single cells.

    PubMed

    Schreiter, Christoph; Gjoni, Marinela; Hovius, Ruud; Martinez, Karen L; Segura, Jean-Manuel; Vogel, Horst

    2005-12-01

    With the reversible sequential (ReSeq) binding assay,we present a novel approach for the ultrasensitive profiling of receptor function in single living cells. This assay is based on the repetitive application of fluorescent ligands that have fast association-dissociation kinetics. We chose the nicotinic-acetylcholine receptor (nAChR) as a prototypical example and performed ReSeq equilibrium, kinetic, and competition-binding assays using fluorescent derivatives of the antagonist alpha-conotoxin GI (alpha-CnTx). Thereby, we determined the binding constants of unlabeled alpha-CnTx and d-tubocurarine. The high selectivity of alpha-CnTx for muscle-type nAChR made it possible to observe specific binding even in the presence of other nAChR subtypes. Imaging of individual nAChRs and ligand-binding cycles to single cells in microfluidic devices demonstrated the ultimate miniaturization and accuracy of ReSeq-binding assays even at low receptor-expression levels. We expect our approach to be of generic importance for functional screening of compounds or membrane receptors, and for the detailed characterization of rare primary cells.

  17. Efficient chemoenzymatic synthesis of chiral pincer ligands.

    PubMed

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

    2009-05-01

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

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

    PubMed

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

    2015-09-14

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

  19. 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)

  20. Zinc Coordination Geometry and Ligand Binding Affinity: The Structural and Kinetic Analysis of the Second-Shell Serine 228 Residue and the Methionine 180 Residue of the Aminopeptidase from Vibrio proteolyticus

    SciTech Connect

    Ataie, Niloufar J.; Hoang, Quyen Q.; Zahniser, Megan P.D.; Tu, Yupeng; Milne, Amy; Petsko, Gregory A.; Ringe, Dagmar

    2008-07-28

    The chemical properties of zinc make it an ideal metal to study the role of coordination strain in enzymatic rate enhancement. The zinc ion and the protein residues that are bound directly to the zinc ion represent a functional charge/dipole complex, and polarization of this complex, which translates to coordination distortion, may tune electrophilicity, and hence, reactivity. Conserved protein residues outside of the charge/dipole complex, such as second-shell residues, may play a role in supporting the electronic strain produced as a consequence of functional polarization. To test the correlation between charge/dipole polarity and ligand binding affinity, structure?function studies were carried out on the dizinc aminopeptidase from Vibrio proteolyticus. Alanine substitutions of S228 and M180 resulted in catalytically diminished enzymes whose crystal structures show very little change in the positions of the metal ions and the protein residues. However, more detailed inspections of the crystal structures show small positional changes that account for differences in the zinc ion coordination geometry. Measurements of the binding affinity of leucine phosphonic acid, a transition state analogue, and leucine, a product, show a correlation between coordination geometry and ligand binding affinity. These results suggest that the coordination number and polarity may tune the electrophilicity of zinc. This may have provided the evolving enzyme with the ability to discriminate between reaction coordinate species.

  1. 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.

  2. 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)

  3. Kinetic protein crystallography: a tool to watch proteins in action

    SciTech Connect

    Bourgeois, D.; Weik, M.

    2009-04-14

    Many proteins function in the crystalline state, making crystallography a tool that, beside structure, can address mechanism. By initiating biological turnover in the crystal, transient structural species form, which may be filmed 'on the fly' by Laue diffraction or captured by trapping methods. These strategies are jointly referred to as 'kinetic crystallography'. In this article, we review the general concepts of kinetic crystallography in the context of the conformational energy landscape of a protein. Whereas Laue diffraction is best suited to the investigation of cyclic, ultra-fast and light-triggered reactions, trapping approaches, on the other hand, are applicable to a wider range of biological systems but require care to avoid artefacts. Complementary methods - mainly UV/visible single-crystal spectroscopy - have proven essential to design, interpret and validate kinetic crystallography experiments. Achievements in the field as well as remaining puzzling questions are considered through the examination of recently published work: real-time-resolved crystallography of dimeric haemoglobin based on pump-probe Laue diffraction, temperature-trapping crystallography of acetylcholinesterase based on photo- and radio-induced ligand cleavage, and lattice-trapping crystallography of superoxide reductase based on product soaking and the combined use of X-ray diffraction and Raman spectroscopy.

  4. 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.

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

    PubMed

    Bhardwaj, Vimal K; Singh, Ajnesh

    2014-10-06

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

  6. 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.

  7. Fast Reactors

    NASA Astrophysics Data System (ADS)

    Esposito, S.; Pisanti, O.

    The following sections are included: * Elementary Considerations * The Integral Equation to the Neutron Distribution * The Critical Size for a Fast Reactor * Supercritical Reactors * Problems and Exercises

  8. 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

  9. Water network perturbation in ligand binding: adenosine A(2A) antagonists as a case study.

    PubMed

    Bortolato, Andrea; Tehan, Ben G; Bodnarchuk, Michael S; Essex, Jonathan W; Mason, Jonathan S

    2013-07-22

    Recent efforts in the computational evaluation of the thermodynamic properties of water molecules have resulted in the development of promising new in silico methods to evaluate the role of water in ligand binding. These methods include WaterMap, SZMAP, GRID/CRY probe, and Grand Canonical Monte Carlo simulations. They allow the prediction of the position and relative free energy of the water molecule in the protein active site and the analysis of the perturbation of an explicit water network (WNP) as a consequence of ligand binding. We have for the first time extended these approaches toward the prediction of kinetics for small molecules and of relative free energy of binding with a focus on the perturbation of the water network and application to large diverse data sets. Our results support a qualitative correlation between the residence time of 12 related triazine adenosine A(2A) receptor antagonists and the number and position of high energy trapped solvent molecules. From a quantitative viewpoint, we successfully applied these computational techniques as an implicit solvent alternative, in linear combination with a molecular mechanics force field, to predict the relative ligand free energy of binding (WNP-MMSA). The applicability of this linear method, based on the thermodynamics additivity principle, did not extend to 375 diverse A(2A) receptor antagonists. However, a fast but effective method could be enabled by replacing the linear approach with a machine learning technique using probabilistic classification trees, which classified the binding affinity correctly for 90% of the ligands in the training set and 67% in the test set.

  10. Hysteresis of ligand binding in CNGA2 ion channels

    PubMed Central

    Nache, Vasilica; Eick, Thomas; Schulz, Eckhard; Schmauder, Ralf; Benndorf, Klaus

    2013-01-01

    Tetrameric cyclic nucleotide-gated (CNG) channels mediate receptor potentials in olfaction and vision. The channels are activated by the binding of cyclic nucleotides to a binding domain embedded in the C terminus of each subunit. Here using a fluorescent cGMP derivative (fcGMP), we show for homotetrameric CNGA2 channels that ligand unbinding is ~50 times faster at saturating than at subsaturating fcGMP. Analysis with complex Markovian models reveals two pathways for ligand unbinding; the partially liganded open channel unbinds its ligands from closed states only, whereas the fully liganded channel reaches a different open state from which it unbinds all four ligands rapidly. Consequently, the transition pathways for ligand binding and activation of a fully liganded CNGA2 channel differ from that of ligand unbinding and deactivation, resulting in pronounced hysteresis of the gating mechanism. This concentration-dependent gating mechanism allows the channels to respond to changes in the cyclic nucleotide concentration with different kinetics. PMID:24287615

  11. 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.

  12. Group IV organometallic compounds based on dianionic "pincer" ligands: synthesis, characterization, and catalytic activity in intramolecular hydroamination reactions.

    PubMed

    Luconi, Lapo; Rossin, Andrea; Motta, Alessandro; Tuci, Giulia; Giambastiani, Giuliano

    2013-04-08

    Neutral Zr(IV) and Hf(IV) diamido complexes stabilized by unsymmetrical dianionic N,C,N' pincer ligands have been prepared through the simplest and convenient direct metal-induced Caryl-H bond activation. Simple ligand modification has contributed to highlight the non-innocent role played by the donor atom set in the control of the cyclometallation kinetics. The as-prepared bis-amido catalysts were found to be good candidates for the intramolecular hydroamination/cyclization of primary aminoalkenes. The ability of these compounds to promote such a catalytic transformation efficiently (by providing, in some cases, fast and complete substrate conversion at room temperature) constitutes a remarkable step forward toward catalytic systems that can operate at relatively low catalyst loading and under milder reaction conditions. Kinetic studies and substrate-scope investigations, in conjunction with preliminary DFT calculations on the real systems, were used to elucidate the effects of the substrate substitution on the catalyst performance and to support the most reliable mechanistic path operative in the hydroamination reaction.

  13. 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.

  14. Fast CRCs

    DTIC Science & Technology

    2009-10-01

    Detecting Codes: General Theory and Their Application in Feedback Communication Systems. Kluwer Academic, 1995. [8] D.E. Knuth , The Art of Computer ... computation . Index Terms—Fast CRC, low-complexity CRC, checksum, error-detection code, Hamming code, period of polynomial, fast software implementation...simulations, and performance analysis of systems and networks. CRC implementation in software is desirable, because many computers do not have hardware

  15. 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.

  16. 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.

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

    PubMed

    Atkins, William M

    2005-01-01

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

  18. Diffusion modifies the connectivity of kinetic schemes for multisite binding and catalysis.

    PubMed

    Gopich, Irina V; Szabo, Attila

    2013-12-03

    The simplest way to describe the influence of the relative diffusion of the reactants on the time course of bimolecular reactions is to modify or renormalize the phenomenological rate constants that enter into the rate equations of conventional chemical kinetics. However, for macromolecules with multiple inequivalent reactive sites, this is no longer sufficient, even in the low concentration limit. The physical reason is that an enzyme (or a ligand) that has just modified (or dissociated from) one site can bind to a neighboring site rather than diffuse away. This process is not described by the conventional chemical kinetics, which is only valid in the limit that diffusion is fast compared with reaction. Using an exactly solvable many-particle reaction-diffusion model, we show that the influence of diffusion on the kinetics of multisite binding and catalysis can be accounted for by not only scaling the rates, but also by introducing new connections into the kinetic scheme. The rate constants that describe these new transitions or reaction channels turn out to have a transparent physical interpretation: The chemical rates are scaled by the appropriate probabilities that a pair of reactants, which are initially in contact, bind rather than diffuse apart. The theory is illustrated by application to phosphorylation of a multisite substrate.

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

    PubMed Central

    Kantardjiev, Alexander A.

    2012-01-01

    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 pKa 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

  20. 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.

  1. New approach to a novel axially chiral ligand showing spontaneous enrichment of axial chirality.

    PubMed

    Hasegawa, Tomokuni; Omote, Masaaki; Sato, Kazuyuki; Ando, Akira; Kumadaki, Itsumaro

    2003-03-01

    We have synthesized novel axially chiral ligand with two chiral centers, (R)-(R)(2)- and (S)-(S)(2)-2,2'-bis(2,2,2-trifluoro-1-hydroxyethyl)biphenyl (1), which showed a high asymmetric induction when used as ligand. Here, another new approach to 1 by kinetic and thermodynamic resolution is presented which gave these ligands in a much shorter steps, in a higher yield, and in a higher enantiomeric excess.

  2. Equilibrium and kinetic studies on complex formation and decomposition and the movement of Cu(2+)metal ions within polytopic receptors.

    PubMed

    Castillo, Carmen Ester; González-García, Jorge; Llinares, José M; Máñez, M Angeles; Jimenez, Hermas R; García-España, Enrique; Basallote, Manuel G

    2013-05-07

    Potentiometric studies carried out on the interaction of two tritopic double-scorpiand receptors in which two equivalent 5-(2-aminoethyl)-2,5,8-triaza[9]-(2,6)-pyridinophane moieties are linked with 2,9-dimethylphenanthroline (L1) and 2,6-dimethylpyridine (L2) establish the formation of mono-, bi- and trinuclear Cu(2+) complexes. The values of the stability constants and paramagnetic (1)H NMR studies permit one to infer the most likely coordination modes of the various complexes formed. Kinetic studies on complex formation and decomposition have also been carried out. Complex formation occurs with polyphasic kinetics for both receptors, although a significant difference is found between both ligands with respect to the relative values of the rate constants for the metal coordination steps and the structural reorganizations following them. Complex decomposition occurs with two separate kinetic steps, the first one being so fast that it occurs within the stopped-flow mixing time, whereas the second one is slow enough to allow kinetic studies using a conventional spectrophotometer. As a whole, the kinetic experiments also provide information about the movement of the metal ion within the receptors. The differences observed between the different receptors can be interpreted in terms of changes in the network of hydrogen bonds formed in the different species.

  3. Kinetics of excitation in TL and OSL detectors

    NASA Astrophysics Data System (ADS)

    Mandowski, A.; Orzechowski, J.; Mandowska, E.

    2010-10-01

    Kinetic equations for the semi-localized transitions (SLT) model are presented describing charge carrier's kinetics for the excitation and fast relaxation stages. The formulation allows for dose dependence studies of thermoluminescence (TL) and optically stimulated luminescence (OSL) detectors based on the SLT model. The sets of equations were solved numerically demonstrating temporal evolution of all variables of the SLT model during excitation and fast relaxation. The influence of the dose rate on excitation kinetics is shown.

  4. [Kinetics of conformational changes of methemoglobin complexed with liposomes].

    PubMed

    Gorbenko, G P

    1998-01-01

    Kinetics of methemoglobin structural changes in the complex with liposomes composed of phosphatidylcholine and its mixtures with cardiolipin has been studied. The amplitudes and rate constants of the two observed kinetic phases are determined. The fast kinetic phase is attributed to the formation of the unstable intermediate protein form, while the slow one is assumed to reflect dissociation of the heme--globin complex.

  5. 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.

  6. 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.

  7. 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.

  8. Determining enzyme kinetics via isothermal titration calorimetry.

    PubMed

    Demarse, Neil A; Killian, Marie C; Hansen, Lee D; Quinn, Colette F

    2013-01-01

    Isothermal titration calorimetry (ITC) has emerged as a powerful tool for determining the thermodynamic properties of chemical or physical equilibria such as protein-protein, ligand-receptor, and protein-DNA binding interactions. The utility of ITC for determining kinetic information, however, has not been fully recognized. Methods for collecting and analyzing data on enzyme kinetics are discussed here. The step-by-step process of converting the raw heat output rate into the kinetic parameters of the Michaelis-Menten equation is explicitly stated. The hydrolysis of sucrose by invertase is used to demonstrate the capability of the instrument and method.

  9. Project FAST.

    ERIC Educational Resources Information Center

    Essexville-Hampton Public Schools, MI.

    Described are components of Project FAST (Functional Analysis Systems Training) a nationally validated project to provide more effective educational and support services to learning disordered children and their regular elementary classroom teachers. The program is seen to be based on a series of modules of delivery systems ranging from mainstream…

  10. 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.

  11. 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

  12. Lipid metabolism during fasting.

    PubMed

    Jensen, M D; Ekberg, K; Landau, B R

    2001-10-01

    These studies were conducted to understand the relationship between measures of systemic free fatty acid (FFA) reesterification and regional FFA, glycerol, and triglyceride metabolism during fasting. Indirect calorimetry was used to measure fatty acid oxidation in six men after a 60-h fast. Systemic and regional (splanchnic, renal, and leg) FFA ([(3)H]palmitate) and glycerol ([(3)H]glycerol) kinetics, as well as splanchnic triglyceride release, were measured. The rate of systemic FFA reesterification was 366 +/- 93 micromol/min, which was greater (P < 0.05) than splanchnic triglyceride fatty acid output (64 +/- 6 micromol/min), a measure of VLDL triglyceride fatty acid export. The majority of glycerol uptake occurred in the splanchnic and renal beds, although some leg glycerol uptake was detected. Systemic FFA release was approximately double that usually present in overnight postabsorptive men, yet the regional FFA release rates were of the same proportions previously observed in overnight postabsorptive men. In conclusion, FFA reesterification at rest during fasting far exceeds splanchnic triglyceride fatty acid output. This indicates that nonhepatic sites of FFA reesterification are important, and that peripheral reesterification of FFA exceeds the rate of simultaneous intracellular triglyceride fatty acid oxidation.

  13. 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…

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

    PubMed

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

    2015-08-03

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

  15. Revealing equilibrium and rate constants of weak and fast noncovalent interactions.

    PubMed

    Mironov, Gleb G; Okhonin, Victor; Gorelsky, Serge I; Berezovski, Maxim V

    2011-03-15

    Rate and equilibrium constants of weak noncovalent molecular interactions are extremely difficult to measure. Here, we introduced a homogeneous approach called equilibrium capillary electrophoresis of equilibrium mixtures (ECEEM) to determine k(on), k(off), and K(d) of weak (K(d) > 1 μM) and fast kinetics (relaxation time, τ < 0.1 s) in quasi-equilibrium for multiple unlabeled ligands simultaneously in one microreactor. Conceptually, an equilibrium mixture (EM) of a ligand (L), target (T), and a complex (C) is prepared. The mixture is introduced into the beginning of a capillary reactor with aspect ratio >1000 filled with T. Afterward, differential mobility of L, T, and C along the reactor is induced by an electric field. The combination of differential mobility of reactants and their interactions leads to a change of the EM peak shape. This change is a function of rate constants, so the rate and equilibrium constants can be directly determined from the analysis of the EM peak shape (width and symmetry) and propagation pattern along the reactor. We proved experimentally the use of ECEEM for multiplex determination of kinetic parameters describing weak (3 mM > K(d) > 80 μM) and fast (0.25 s ≥ τ ≥ 0.9 ms) noncovalent interactions between four small molecule drugs (ibuprofen, S-flurbiprofen, salicylic acid and phenylbutazone) and α- and β-cyclodextrins. The affinity of the drugs was significantly higher for β-cyclodextrin than α-cyclodextrin and mostly determined by the rate constant of complex formation.

  16. Ligand fitting with CCP4

    PubMed Central

    2017-01-01

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

  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

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

    2013-12-01

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

  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. 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

  1. 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. PMID:27635238

  2. 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

    2015-11-03

    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

  3. Ligand Binding Mechanism in Steroid Receptors: From Conserved Plasticity to Differential Evolutionary Constraints.

    PubMed

    Edman, Karl; Hosseini, Ali; Bjursell, Magnus K; Aagaard, Anna; Wissler, Lisa; Gunnarsson, Anders; Kaminski, Tim; Köhler, Christian; Bäckström, Stefan; Jensen, Tina J; Cavallin, Anders; Karlsson, Ulla; Nilsson, Ewa; Lecina, Daniel; Takahashi, Ryoji; Grebner, Christoph; Geschwindner, Stefan; Lepistö, Matti; Hogner, Anders C; Guallar, Victor

    2015-12-01

    Steroid receptor drugs have been available for more than half a century, but details of the ligand binding mechanism have remained elusive. We solved X-ray structures of the glucocorticoid and mineralocorticoid receptors to identify a conserved plasticity at the helix 6-7 region that extends the ligand binding pocket toward the receptor surface. Since none of the endogenous ligands exploit this region, we hypothesized that it constitutes an integral part of the binding event. Extensive all-atom unbiased ligand exit and entrance simulations corroborate a ligand binding pathway that gives the observed structural plasticity a key functional role. Kinetic measurements reveal that the receptor residence time correlates with structural rearrangements observed in both structures and simulations. Ultimately, our findings reveal why nature has conserved the capacity to open up this region, and highlight how differences in the details of the ligand entry process result in differential evolutionary constraints across the steroid receptors.

  4. Kinetics of Social Contagion

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  5. 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.

  6. Tolrestat kinetics

    SciTech Connect

    Hicks, D.R.; Kraml, M.; Cayen, M.N.; Dubuc, J.; Ryder, S.; Dvornik, D.

    1984-10-01

    The kinetics of tolrestat, a potent inhibitor of aldose reductase, were examined. Serum concentrations of tolrestat and of total /sup 14/C were measured after dosing normal subjects and subjects with diabetes with /sup 14/C-labeled tolrestat. In normal subjects, tolrestat was rapidly absorbed and disappearance from serum was biphasic. Distribution and elimination t 1/2s were approximately 2 and 10 to 12 hr, respectively, after single and multiple doses. Unchanged tolrestat accounted for the major portion of /sup 14/C in serum. Radioactivity was rapidly and completely excreted in urine and feces in an approximate ratio of 2:1. Findings were much the same in subjects with diabetes. In normal subjects, the kinetics of oral tolrestat were independent of dose in the 10 to 800 mg range. Repetitive dosing did not result in unexpected cumulation. Tolrestat was more than 99% bound to serum protein; it did not compete with warfarin for binding sites but was displaced to some extent by high concentrations of tolbutamide or salicylate.

  7. Ligand binding analysis and screening by chemical denaturation shift.

    PubMed

    Schön, Arne; Brown, Richard K; Hutchins, Burleigh M; Freire, Ernesto

    2013-12-01

    The identification of small molecule ligands is an important first step in drug development, especially drugs that target proteins with no intrinsic activity. Toward this goal, it is important to have access to technologies that are able to measure binding affinities for a large number of potential ligands in a fast and accurate way. Because ligand binding stabilizes the protein structure in a manner dependent on concentration and binding affinity, the magnitude of the protein stabilization effect elicited by binding can be used to identify and characterize ligands. For example, the shift in protein denaturation temperature (Tm shift) has become a popular approach to identify potential ligands. However, Tm shifts cannot be readily transformed into binding affinities, and the ligand rank order obtained at denaturation temperatures (≥60°C) does not necessarily coincide with the rank order at physiological temperature. An alternative approach is the use of chemical denaturation, which can be implemented at any temperature. Chemical denaturation shifts allow accurate determination of binding affinities with a surprisingly wide dynamic range (high micromolar to sub nanomolar) and in situations where binding changes the cooperativity of the unfolding transition. In this article, we develop the basic analytical equations and provide several experimental examples.

  8. Rate constants of agonist binding to muscarinic receptors in rat brain medulla. Evaluation by competition kinetics

    SciTech Connect

    Schreiber, G.; Henis, Y.I.; Sokolovsky, M.

    1985-07-25

    The method of competition kinetics, which measures the binding kinetics of an unlabeled ligand through its effect on the binding kinetics of a labeled ligand, was employed to investigate the kinetics of muscarinic agonist binding to rat brain medulla pons homogenates. The agonists studied were acetylcholine, carbamylcholine, and oxotremorine, with N-methyl-4-(TH)piperidyl benzilate employed as the radiolabeled ligand. Our results suggested that the binding of muscarinic agonists to the high affinity sites is characterized by dissociation rate constants higher by 2 orders of magnitude than those of antagonists, with rather similar association rate constants. Our findings also suggest that isomerization of the muscarinic receptors following ligand binding is significant in the case of antagonists, but not of agonists. Moreover, it is demonstrated that in the medulla pons preparation, agonist-induced interconversion between high and low affinity bindings sites does not occur to an appreciable extent.

  9. Kinetic buffers.

    PubMed

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

    2015-01-12

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

  10. Ligand binding and proton exchange dynamics in site-specific mutants of human myoglobin

    SciTech Connect

    Lambright, D.G.

    1992-01-01

    Site specific mutagenesis was used to make substitutions of four residues in the distal heme pocket of human myoglobin: Val68, His64, Lys45, and Asp60. Strongly diffracting crystals of the conservative mutation K45R in the met aquo form were grown in the trigonal space group P3[sub 2]21 and the X-ray crystal structure determined at 1.6 [angstrom] resolution. The overall structure is similar to that of sperm whale met aquo myoglobin. Several of the mutant proteins were characterized by 2-D NMR spectroscopy. The NMR data suggest the structural changes are localized to the region of the mutation. The dynamics of ligand binding to myoglobin mutants were studied by transient absorption spectroscopy following photolysis of the CO complexes. Transient absorption kinetics and spectra on the ns to ms timescale were measured in aqueous solution from 280 K to 310 K and in 75% glycerol: water from 250 K to 310 K. Two significant basis spectra were obtained from singular value decomposition of the matrix of time dependent spectra. The information was used to obtain approximations for the extent of ligand rebinding and the kinetics of conformational relaxation. Except for K45R, substitutions at Lys45 or Asp60 produce changes in the kinetics for ligand rebinding. Replacement of Lys45 with Arg increases the rate of ligand rebinding from the protein matrix by a factor of 2, but does not alter the rates for ligand escape or entry into the protein or the dynamics of the conformational relaxation. Substitutions at His64 and Val68 influence the kinetics of ligand rebinding and the dynamics of conformational relaxation. The results do not support the hypothesis that ligand migration between the heme pocket and solvent is determined solely by fluctuations of Arg45 and His64 between open and closed conformations of the heme pocket but can be rationalized if ligand diffusion through the protein matrix involves multiple competing pathways.

  11. EDTA modified LDHs as Cu2+ scavengers: removal kinetics and sorbent stability.

    PubMed

    Rojas, Ricardo; Perez, M Rosario; Erro, Eustaquio M; Ortiz, Patricia I; Ulibarri, Maria Angeles; Giacomelli, Carla E

    2009-03-15

    EDTA modified layered double hydroxides (LDHs) were investigated as potential sorbents to remediate heavy metals pollution. The polidentate ligand was introduced by an exchange method in a Zn-Al-LDH, which takes place with partial erosion of the layers, causing the intercalation of [Zn(EDTA)](2-) complex instead of the ligand. [Cu(H(2)O)(6)](2+) cation was selected as a model cation to study the uptake mechanism, exploring the elimination kinetics from the first minutes up to the steady state. A flow injection analysis system coupled to an amperometric detector (FIA-AM) was applied to perform fast and reliable [Cu(H(2)O)(6)](2+) determinations in monodisperse solid-aqueous solution systems. Furthermore, the sorbent stability was determined as a function of the pH and the nitrate concentration. The [Cu(H(2)O)(6)](2+) elimination is produced by an exchange reaction with [Zn(EDTA)](2-) anions placed either in the solid interlayer or in the aqueous solution, this last being released from the sorbent. Additional [Cu(H(2)O)(6)](2+) removal is produced by Cu(OH)(2) precipitation at high copper concentrations due to the LDHs high pH buffering capacity. The sorbent removes [Cu(H(2)O)(6)](2+) with high affinity in a wide concentration range. The elimination process reaches equilibrium in less than 30 min and leaves metal cation concentrations lower than 0.05 ppm in the supernatants.

  12. Melatonin: functions and ligands.

    PubMed

    Singh, Mahaveer; Jadhav, Hemant R

    2014-09-01

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

  13. Fluorescence‐ and bioluminescence‐based approaches to study GPCR ligand binding

    PubMed Central

    Stoddart, Leigh A; White, Carl W; Nguyen, Kim; Hill, Stephen J

    2015-01-01

    Ligand binding is a vital component of any pharmacologist's toolbox and allows the detailed investigation of how a molecule binds to its receptor. These studies enable the experimental determination of binding affinity of labelled and unlabelled compounds through kinetic, saturation (Kd) and competition (Ki) binding assays. Traditionally, these studies have used molecules labelled with radioisotopes; however, more recently, fluorescent ligands have been developed for this purpose. This review will briefly cover receptor ligand binding theory and then discuss the use of fluorescent ligands with some of the different technologies currently employed to examine ligand binding. Fluorescent ligands can be used for direct measurement of receptor‐associated fluorescence using confocal microscopy and flow cytometry as well as in assays such as fluorescence polarization, where ligand binding is monitored by changes in the free rotation when a fluorescent ligand is bound to a receptor. Additionally, fluorescent ligands can act as donors or acceptors for fluorescence resonance energy transfer (FRET) with the development of assays based on FRET and time‐resolved FRET (TR‐FRET). Finally, we have recently developed a novel bioluminescence resonance energy transfer (BRET) ligand binding assay utilizing a small (19 kDa), super‐bright luciferase subunit (NanoLuc) from a deep sea shrimp. In combination with fluorescent ligands, measurement of RET now provides an array of methodologies to study ligand binding. While each method has its own advantages and drawbacks, binding studies using fluorescent ligands are now a viable alternative to the use of radioligands. Linked Articles This article is part of a themed section on Molecular Pharmacology of G Protein‐Coupled Receptors. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v173.20/issuetoc PMID:26317175

  14. Ligand binding to a high-energy partially unfolded protein.

    PubMed

    Kasper, Joseph R; Park, Chiwook

    2015-01-01

    The conformational energy landscape of a protein determines populations of all possible conformations of the protein and also determines the kinetics of the conversion between the conformations. Interaction with ligands influences the conformational energy landscapes of proteins and shifts populations of proteins in different conformational states. To investigate the effect of ligand binding on partial unfolding of a protein, we use Escherichia coli dihydrofolate reductase (DHFR) and its functional ligand NADP(+) as a model system. We previously identified a partially unfolded form of DHFR that is populated under native conditions. In this report, we determined the free energy for partial unfolding of DHFR at varying concentrations of NADP(+) and found that NADP(+) binds to the partially unfolded form as well as the native form. DHFR unfolds partially without releasing the ligand, though the binding affinity for NADP(+) is diminished upon partial unfolding. Based on known crystallographic structures of NADP(+) -bound DHFR and the model of the partially unfolded protein we previously determined, we propose that the adenosine-binding domain of DHFR remains folded in the partially unfolded form and interacts with the adenosine moiety of NADP(+) . Our result demonstrates that ligand binding may affect the conformational free energy of not only native forms but also high-energy non-native forms.

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

    PubMed Central

    Du, Xing; Li, Yi; Xia, Yuan-Ling; Ai, Shi-Meng; Liang, Jing; Sang, Peng; Ji, Xing-Lai; Liu, Shu-Qun

    2016-01-01

    Molecular recognition, which is the process of biological macromolecules interacting with each other or various small molecules with a high specificity and affinity to form a specific complex, constitutes the basis of all processes in living organisms. Proteins, an important class of biological macromolecules, realize their functions through binding to themselves or other molecules. A detailed understanding of the protein–ligand interactions is therefore central to understanding biology at the molecular level. Moreover, knowledge of the mechanisms responsible for the protein-ligand recognition and binding will also facilitate the discovery, design, and development of drugs. In the present review, first, the physicochemical mechanisms underlying protein–ligand binding, including the binding kinetics, thermodynamic concepts and relationships, and binding driving forces, are introduced and rationalized. Next, three currently existing protein-ligand binding models—the “lock-and-key”, “induced fit”, and “conformational selection”—are described and their underlying thermodynamic mechanisms are discussed. Finally, the methods available for investigating protein–ligand binding affinity, including experimental and theoretical/computational approaches, are introduced, and their advantages, disadvantages, and challenges are discussed. PMID:26821017

  16. Formation of very stable and selective Cu(II) complexes with a non-macrocyclic ligand: can basicity rival pre-organization?

    PubMed

    Abada, Sabah; Lecointre, Alexandre; Elhabiri, Mourad; Charbonnière, Loïc J

    2010-10-14

    The synthesis of ligand L based on a 2,6-bis[(N,N-bis(methylene phosphonic acid)aminomethyl] pyridine scaffold is described. Potentiometry combined with UV-Vis absorption spectrophotometric titrations were used to determine the protonation constants of the ligand and the stability constants of its corresponding Cu(II), Ni(II), Zn(II) and Ga(III) cations (0.1 M NaClO(4), 25.0 °C). The physico-chemical approach revealed very large stability constants for Cu(II) complexation (logK(CuL) = 22.71(7)) reflected in a very high pCu(II) value of ∼ 15.5 (pH = 7.4, [L](tot) = 10(-5) M, [Cu](tot) = 10(-6) M), close to those measured for the strong methylphosphonate functionalized cyclen chelators. Based on a literature survey, a correlation is proposed between the pK values of branched polyamine ligands and their stability constants for Cu(II) complexation, allowing for an estimation of the latter on the basis of the protonation constants of L. Ligand L was also shown to be very selective towards Cu(II) compared to the other cations studied (ΔlogK > 4). UV-Vis spectroscopy and kinetic measurements indicated that the formation of the cupric complexes with L is very fast, which, in combination with all other properties, makes it an excellent non-cyclic target for Cu(II) radiopharmaceutical within the frame of (64)Cu positron emission tomography imaging and radiotherapy.

  17. A miniaturized technique for assessing protein thermodynamics and function using fast determination of quantitative cysteine reactivity.

    PubMed

    Isom, Daniel G; Marguet, Philippe R; Oas, Terrence G; Hellinga, Homme W

    2011-04-01

    Protein thermodynamic stability is a fundamental physical characteristic that determines biological function. Furthermore, alteration of thermodynamic stability by macromolecular interactions or biochemical modifications is a powerful tool for assessing the relationship between protein structure, stability, and biological function. High-throughput approaches for quantifying protein stability are beginning to emerge that enable thermodynamic measurements on small amounts of material, in short periods of time, and using readily accessible instrumentation. Here we present such a method, fast quantitative cysteine reactivity, which exploits the linkage between protein stability, sidechain protection by protein structure, and structural dynamics to characterize the thermodynamic and kinetic properties of proteins. In this approach, the reaction of a protected cysteine and thiol-reactive fluorogenic indicator is monitored over a gradient of temperatures after a short incubation time. These labeling data can be used to determine the midpoint of thermal unfolding, measure the temperature dependence of protein stability, quantify ligand-binding affinity, and, under certain conditions, estimate folding rate constants. Here, we demonstrate the fQCR method by characterizing these thermodynamic and kinetic properties for variants of Staphylococcal nuclease and E. coli ribose-binding protein engineered to contain single, protected cysteines. These straightforward, information-rich experiments are likely to find applications in protein engineering and functional genomics.

  18. Bifunctional DTPA-type ligand

    SciTech Connect

    Gansow, O.A.; Brechbiel, M.W.

    1990-03-26

    The subject matter of the invention relates to bifunctional cyclohexyl DTPA ligands and methods of using these compounds. Specifically, such ligands are useful for radiolabeling proteins with radioactive metals, and can consequently be utilized with respect to radioimmunoimaging and/or radioimmunotherapy.

  19. Navigating ligand protein binding free energy landscapes: universality and diversity of protein folding and molecular recognition mechanisms

    NASA Astrophysics Data System (ADS)

    Verkhivker, Gennady M.; Rejto, Paul A.; Bouzida, Djamal; Arthurs, Sandra; Colson, Anthony B.; Freer, Stephan T.; Gehlhaar, Daniel K.; Larson, Veda; Luty, Brock A.; Marrone, Tami; Rose, Peter W.

    2001-03-01

    Thermodynamic and kinetic aspects of ligand-protein binding are studied for the methotrexate-dihydrofolate reductase system from the binding free energy profile constructed as a function of the order parameter. Thermodynamic stability of the native complex and a cooperative transition to the unique native structure suggest the nucleation kinetic mechanism at the equilibrium transition temperature. Structural properties of the transition state ensemble and the ensemble of nucleation conformations are determined by kinetic simulations of the transmission coefficient and ligand-protein association pathways. Structural analysis of the transition states and the nucleation conformations reconciles different views on the nucleation mechanism in protein folding.

  20. Analytical model for fast-shock ignition

    SciTech Connect

    Ghasemi, S. A. Farahbod, A. H.; Sobhanian, S.

    2014-07-15

    A model and its improvements are introduced for a recently proposed approach to inertial confinement fusion, called fast-shock ignition (FSI). The analysis is based upon the gain models of fast ignition, shock ignition and considerations for the fast electrons penetration into the pre-compressed fuel to examine the formation of an effective central hot spot. Calculations of fast electrons penetration into the dense fuel show that if the initial electron kinetic energy is of the order ∼4.5 MeV, the electrons effectively reach the central part of the fuel. To evaluate more realistically the performance of FSI approach, we have used a quasi-two temperature electron energy distribution function of Strozzi (2012) and fast ignitor energy formula of Bellei (2013) that are consistent with 3D PIC simulations for different values of fast ignitor laser wavelength and coupling efficiency. The general advantages of fast-shock ignition in comparison with the shock ignition can be estimated to be better than 1.3 and it is seen that the best results can be obtained for the fuel mass around 1.5 mg, fast ignitor laser wavelength ∼0.3  micron and the shock ignitor energy weight factor about 0.25.

  1. Ligand Lone-Pair Influence on Hydrocarbon C-H Activation. A Computational Perspective

    SciTech Connect

    Ess, Daniel H.; Gunnoe, T. Brent; Cundari, Thomas R.; Goddard, William A.; Periana, Roy A.

    2010-12-03

    Mid to late transition metal complexes that break hydrocarbon C-H bonds by transferring the hydrogen to a heteroatom ligand while forming a metal-alkyl bond offer a promising strategy for C-H activation. Here we report a density functional (B3LYP, M06, and X3LYP) analysis of cis-(acac)2MX and TpM(L)X (M = Ir, Ru, Os, and Rh; acac = acetylacetonate, Tp = tris(pyrazolyl)borate; X = CH3, OH, OMe, NH2, and NMe2) systems for methane C-H bond activation reaction kinetics and thermodynamics. We address the importance of whether a ligand lone pair provides an intrinsic kinetic advantage through possible electronic dπ-pπ repulsions for M-OR and M-NR2 systems versus M-CH3 systems. This involves understanding the energetic impact of the X ligand group on ligand loss, C-H bond coordination, and C-H bond cleavage steps as well as understanding how the nucleophilicity of the ligand X group, the electrophilicity of the transition metal center, and cis-ligand stabilization effect influence each of these steps. We also explore how spectator ligands and second- versus third-row transition metal centers impact the energetics of each of these C-H activation steps.

  2. Protein-Ligand Docking Based on Beta-Shape

    NASA Astrophysics Data System (ADS)

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

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

  3. Distribution kinetics of dietary methylmercury in the arctic charr (Salvelinus alpinus)

    SciTech Connect

    Ribeiro, C.A.O.; Rouleau, C.; Pelletier, E.; Audet, C.; Tjaelve, H.

    1999-03-15

    The authors fed immature 1+ arctic charr with a single dose of methyl[{sup 203}Hg]mercury (MeHg) and quantified distribution kinetics with a new and simple three-compartment caternary model having well-perfused viscera and blood as the central compartment (VB), whereas gut (G) and the rest of body (R) constituted the peripheral compartments. The model accurately described distribution kinetics of MeHg in the fish, using either data of MeHg content in compartments or blood concentration data. Despite the known fast translocation of MeHg between binding sites at the molecular level, its translocation rate between compartments was surprisingly slow, 27 days being needed to complete 95% of the transfer from gut to blood and 48 days for the subsequent transfer to compartment R. This probably results from a limitation of the stepwise transfer rate of MeHg from red blood cells, which contain most of blood MeHg, to plasma and then to tissues due to low plasmatic concentration of small mobile sulfhydryl ligands. The model presented is a convenient tool that could be used to compare the fate of MeHg and other organometals, such as butyltins and alkylleads, in various aquatic and terrestrial animal species.

  4. Triple bioaffinity mass spectrometry concept for thyroid transporter ligands.

    PubMed

    Aqai, Payam; Fryganas, Christos; Mizuguchi, Mineyuki; Haasnoot, Willem; Nielen, Michel W F

    2012-08-07

    For the analysis of thyroid transporter ligands, a triple bioaffinity mass spectrometry (BioMS) concept was developed, with the aim at three different analytical objectives: rapid screening of any ligand, confirmation of known ligands in accordance with legislative requirements, and identification of emerging yet unknown ligands. These three purposes share the same biorecognition element, recombinant thyroid transport protein transthyretin (rTTR), and dedicated modes of liquid chromatography-mass spectrometry (LC-MS). For screening, a rapid and radiolabel-free competitive inhibition MS binding assay was developed with fast ultrahigh performance-liquid chromatography-electrospray ionization-triple-quadrupole-MS (UPLC-QqQ-MS) as the readout system. It uses the nonradioactive stable isotopic thyroid hormone (13)C(6)-L-thyroxine as the label of which the binding to rTTR is inhibited by any ligand such as thyroid drugs and thyroid endocrine disrupting chemicals (EDCs). To this end, rTTR is either used in solution or immobilized on paramagnetic microbeads. The concentration-dependent inhibition of the label by the natural thyroid hormone l-thyroxine (T4), as a model analyte, is demonstrated in water at part-per-trillion and in urine at part-per-billion level. For confirmation of identity of known ligands, rTTR was used for bioaffinity purification for confirmation of naturally present free T4 in urine. As a demonstrator for identification of unknown ligands, the same rTTR was used again but in combination with nano-UPLC-quadrupole time-of-flight-MS (nLC-Q-TOF-MS) and urine samples spiked with the model "unknown" EDCs triclosan and tetrabromobisphenol-A. This study highlights the potential of BioMS using one affinity system, both for rapid screening and for confirmation and identification of known and unknown emerging thyroid EDCs.

  5. Conformational kinetics reveals affinities of protein conformational states.

    PubMed

    Daniels, Kyle G; Suo, Yang; Oas, Terrence G

    2015-07-28

    Most biological reactions rely on interplay between binding and changes in both macromolecular structure and dynamics. Practical understanding of this interplay requires detection of critical intermediates and determination of their binding and conformational characteristics. However, many of these species are only transiently present and they have often been overlooked in mechanistic studies of reactions that couple binding to conformational change. We monitored the kinetics of ligand-induced conformational changes in a small protein using six different ligands. We analyzed the kinetic data to simultaneously determine both binding affinities for the conformational states and the rate constants of conformational change. The approach we used is sufficiently robust to determine the affinities of three conformational states and detect even modest differences in the protein's affinities for relatively similar ligands. Ligand binding favors higher-affinity conformational states by increasing forward conformational rate constants and/or decreasing reverse conformational rate constants. The amounts by which forward rate constants increase and reverse rate constants decrease are proportional to the ratio of affinities of the conformational states. We also show that both the affinity ratio and another parameter, which quantifies the changes in conformational rate constants upon ligand binding, are strong determinants of the mechanism (conformational selection and/or induced fit) of molecular recognition. Our results highlight the utility of analyzing the kinetics of conformational changes to determine affinities that cannot be determined from equilibrium experiments. Most importantly, they demonstrate an inextricable link between conformational dynamics and the binding affinities of conformational states.

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

    NASA Astrophysics Data System (ADS)

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

    2002-10-01

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

  7. Ligand Docking and Virtual Screening in Structure-based Drug Discovery

    NASA Astrophysics Data System (ADS)

    Cavasotto, Claudio N.

    2006-08-01

    As the number of high-resolution three-dimensional protein and nucleic acid structures continues to grow, ligand-docking—based virtual screening of chemical libraries to a receptor are playing a critical role in the drug discovery process by identifying new `drug-candidates'. The capability to correctly predict ligand-protein interaction is fundamental to any accurate docking algorithm and the necessary starting point for any reliable virtual screening protocol. Furthermore, explicit consideration of receptor flexibility in computational ligand docking is emerging in many cases as crucial for an accurate prediction of the orientation and interactions of ligands within the binding pocket. The combination of ligand docking with a fast scoring algorithm that can account for the thermodynamics of binding, and discriminate between potential active/inactive compounds, can greatly reduced the number of compounds to be tested experimentally, while predicting a detailed structure of hits bound to the receptor useful enough to help the synthetic elaboration of leads.

  8. Validity of ligand efficiency metrics.

    PubMed

    Murray, Christopher W; Erlanson, Daniel A; Hopkins, Andrew L; Keserü, György M; Leeson, Paul D; Rees, David C; Reynolds, Charles H; Richmond, Nicola J

    2014-06-12

    A recent viewpoint article (Improving the plausibility of success with inefficient metrics. ACS Med. Chem. Lett. 2014, 5, 2-5) argued that the standard definition of ligand efficiency (LE) is mathematically invalid. In this viewpoint, we address this criticism and show categorically that the definition of LE is mathematically valid. LE and other metrics such as lipophilic ligand efficiency (LLE) can be useful during the multiparameter optimization challenge faced by medicinal chemists.

  9. Ligand Identification Scoring Algorithm (LISA)

    PubMed Central

    Zheng, Zheng; Merz, Kenneth M.

    2011-01-01

    A central problem in de novo drug design is determining the binding affinity of a ligand with a receptor. A new scoring algorithm is presented that estimates the binding affinity of a protein-ligand complex given a three-dimensional structure. The method, LISA (Ligand Identification Scoring Algorithm), uses an empirical scoring function to describe the binding free energy. Interaction terms have been designed to account for van der Waals (VDW) contacts, hydrogen bonding, desolvation effects and metal chelation to model the dissociation equilibrium constants using a linear model. Atom types have been introduced to differentiate the parameters for VDW, H-bonding interactions and metal chelation between different atom pairs. A training set of 492 protein-ligand complexes was selected for the fitting process. Different test sets have been examined to evaluate its ability to predict experimentally measured binding affinities. By comparing with other well known scoring functions, the results show that LISA has advantages over many existing scoring functions in simulating protein-ligand binding affinity, especially metalloprotein-ligand binding affinity. Artificial Neural Network (ANN) was also used in order to demonstrate that the energy terms in LISA are well designed and do not require extra cross terms. PMID:21561101

  10. Ligand Identification Scoring Algorithm (LISA).

    PubMed

    Zheng, Zheng; Merz, Kenneth M

    2011-06-27

    A central problem in de novo drug design is determining the binding affinity of a ligand with a receptor. A new scoring algorithm is presented that estimates the binding affinity of a protein-ligand complex given a three-dimensional structure. The method, LISA (Ligand Identification Scoring Algorithm), uses an empirical scoring function to describe the binding free energy. Interaction terms have been designed to account for van der Waals (VDW) contacts, hydrogen bonding, desolvation effects, and metal chelation to model the dissociation equilibrium constants using a linear model. Atom types have been introduced to differentiate the parameters for VDW, H-bonding interactions, and metal chelation between different atom pairs. A training set of 492 protein-ligand complexes was selected for the fitting process. Different test sets have been examined to evaluate its ability to predict experimentally measured binding affinities. By comparing with other well-known scoring functions, the results show that LISA has advantages over many existing scoring functions in simulating protein-ligand binding affinity, especially metalloprotein-ligand binding affinity. Artificial Neural Network (ANN) was also used in order to demonstrate that the energy terms in LISA are well designed and do not require extra cross terms.

  11. Mechanism of activation of a hafnium pyridyl-amide olefin polymerization catalyst: ligand modification by monomer.

    PubMed

    Froese, Robert D J; Hustad, Phillip D; Kuhlman, Roger L; Wenzel, Timothy T

    2007-06-27

    . Experimental evidence for aryl-insertion products is obtained from reactions of ethylene (13C2H4 NMR studies) or 4-methyl-1-pentene (4M1P) using relatively low monomer/catalyst ratios. Quantitative generation of monomer-inserted products is complicated by slow initiation kinetics followed by fast polymerization kinetics. However, NMR evidence for reaction with 13C2H4 was observed in situ at low temperature, and the attachment of monomer to ligand was confirmed by GC/MS and 13C NMR after quenching. Furthermore, a 4M1P-appended ligand was isolated from a polymerization reaction (50:1 monomer:catalyst) by column chromatography followed by multiple recrystallizations. One isomer was characterized by X-ray crystallography, which unequivocally shows a 4-methylpentyl substituent at the 2-position of the naphthyl, consistent with 1,2-insertion into the Hf-aryl bond. NMR suggests a second diastereomer (not isolated) is formed from a 1,2-insertion of opposite stereoselectivity.

  12. Coupled hydro-neutronic calculations for fast burst reactor accidents

    SciTech Connect

    Paternoster, R.; Kimpland, R.; Jaegers, P.; McGhee, J.

    1994-01-01

    Methods are described for determining the fully coupled neutronic/hydrodynamic response of fast burst reactors (FBR) under disruptive accident conditions. Two code systems, PAD (1 -D Lagrangian) and NIKE-PAGOSA (3-D Eulerian) were used to accomplish this. This is in contrast to the typical methodology that computes these responses by either single point kinetics or in a decoupled manner. This methodology is enabled by the use of modem supercomputers (CM-200). Two examples of this capability are presented: an unreflected metal fast burst assembly, and a reflected fast burst assembly typical of the Skua or SPR-III class of fast burst reactor.

  13. Comparison of ligand migration and binding in heme proteins of the globin family

    NASA Astrophysics Data System (ADS)

    Karin, Nienhaus; Ulrich Nienhaus, G.

    2015-12-01

    The binding of small diatomic ligands such as carbon monoxide or dioxygen to heme proteins is among the simplest biological processes known. Still, it has taken many decades to understand the mechanistic aspects of this process in full detail. Here, we compare ligand binding in three heme proteins of the globin family, myoglobin, a dimeric hemoglobin, and neuroglobin. The combination of structural, spectroscopic, and kinetic experiments over many years by many laboratories has revealed common properties of globins and a clear mechanistic picture of ligand binding at the molecular level. In addition to the ligand binding site at the heme iron, a primary ligand docking site exists that ensures efficient ligand binding to and release from the heme iron. Additional, secondary docking sites can greatly facilitate ligand escape after its dissociation from the heme. Although there is only indirect evidence at present, a preformed histidine gate appears to exist that allows ligand entry to and exit from the active site. The importance of these features can be assessed by studies involving modified proteins (via site-directed mutagenesis) and comparison with heme proteins not belonging to the globin family.

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

    ERIC Educational Resources Information Center

    Roecker, Lee

    2008-01-01

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

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

    PubMed

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

    2016-05-17

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

  16. Using chemical shift perturbation to characterise ligand binding.

    PubMed

    Williamson, Mike P

    2013-08-01

    Chemical shift perturbation (CSP, chemical shift mapping or complexation-induced changes in chemical shift, CIS) follows changes in the chemical shifts of a protein when a ligand is added, and uses these to determine the location of the binding site, the affinity of the ligand, and/or possibly the structure of the complex. A key factor in determining the appearance of spectra during a titration is the exchange rate between free and bound, or more specifically the off-rate koff. When koff is greater than the chemical shift difference between free and bound, which typically equates to an affinity Kd weaker than about 3μM, then exchange is fast on the chemical shift timescale. Under these circumstances, the observed shift is the population-weighted average of free and bound, which allows Kd to be determined from measurement of peak positions, provided the measurements are made appropriately. (1)H shifts are influenced to a large extent by through-space interactions, whereas (13)Cα and (13)Cβ shifts are influenced more by through-bond effects. (15)N and (13)C' shifts are influenced both by through-bond and by through-space (hydrogen bonding) interactions. For determining the location of a bound ligand on the basis of shift change, the most appropriate method is therefore usually to measure (15)N HSQC spectra, calculate the geometrical distance moved by the peak, weighting (15)N shifts by a factor of about 0.14 compared to (1)H shifts, and select those residues for which the weighted shift change is larger than the standard deviation of the shift for all residues. Other methods are discussed, in particular the measurement of (13)CH3 signals. Slow to intermediate exchange rates lead to line broadening, and make Kd values very difficult to obtain. There is no good way to distinguish changes in chemical shift due to direct binding of the ligand from changes in chemical shift due to allosteric change. Ligand binding at multiple sites can often be characterised, by

  17. Chemical and Biological Kinetics

    NASA Astrophysics Data System (ADS)

    Emanuel', N. M.

    1981-10-01

    Examples of the application of the methods and ideas of chemical kinetics in various branches of chemistry and biology are considered and the results of studies on the kinetics and mechanisms of autoxidation and inhibited and catalysed oxidation of organic substances in the liquid phase are surveyed. Problems of the kinetics of the ageing of polymers and the principles of their stabilisation are discussed and certain trends in biological kinetics (kinetics of tumour growth, kinetic criteria of the effectiveness of chemotherapy, problems of gerontology, etc.) are considered. The bibliography includes 281 references.

  18. Scintillation Proximity Radioimmunoassay Utilizing 125I-Labeled Ligands

    NASA Astrophysics Data System (ADS)

    Udenfriend, Sidney; Diekmann Gerber, Louise; Brink, Larry; Spector, Sydney

    1985-12-01

    A unique type of radioimmunoassay is described that does not require centrifugation or separation. Microbeads containing a fluorophor are covalently linked to antibody. When an 125I-labeled antigen is added it binds to the beads and, by its proximity, the emitted short-range electrons of the 125I excite the fluorophor in the beads. The light emitted can be measured in a standard scintillation counter. Addition of unlabeled antigen from tissue extracts displaces the labeled ligand and diminishes the fluorescent signal. Application of scintillation proximity immunoassay to tissue enkephalins, serum thyroxin, and urinary morphine is described. Applications of the principle to study the kinetics of interaction between receptors and ligands are discussed.

  19. Scintillation proximity radioimmunoassay utilizing 125I-labeled ligands

    SciTech Connect

    Udenfriend, S.; Gerber, L.D.; Brink, L.; Spector, S.

    1985-12-01

    A unique type of radioimmunoassay is described that does not require centrifugation or separation. Microbeads containing a fluorophor are covalently linked to antibody. When an /sup 125/I-labeled antigen is added it binds to the beads and, by its proximity, the emitted short-range electrons of the /sup 125/I excite the fluorophor in the beads. The light emitted can be measured in a standard scintillation counter. Addition of unlabeled antigen from tissue extracts displaces the labeled ligand and diminishes the fluorescent signal. Application of scintillation proximity immunoassay to tissue enkephalins, serum thyroxin, and urinary morphine is described. Applications of the principle to study the kinetics of interaction between receptors and ligands are discussed.

  20. Ligand-Gated Ion Channels: Permeation and Activation1

    NASA Astrophysics Data System (ADS)

    Lynch, Joseph W.; Barry, Peter H.

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

  1. Budded baculoviruses as a tool for a homogeneous fluorescence anisotropy-based assay of ligand binding to G protein-coupled receptors: the case of melanocortin 4 receptors.

    PubMed

    Veiksina, Santa; Kopanchuk, Sergei; Rinken, Ago

    2014-01-01

    We present here the implementation of budded baculoviruses that display G protein-coupled receptors on their surfaces for the investigation of ligand-receptor interactions using fluorescence anisotropy (FA). Melanocortin 4 (MC4) receptors and the fluorescent ligand Cy3B-NDP-α-MSH were used as the model system. The real-time monitoring of reactions and the high assay quality allow the application of global data analysis with kinetic mechanistic models that take into account the effect of nonspecific interactions and the depletion of the fluorescent ligand during the reaction. The receptor concentration, affinity and kinetic parameters of fluorescent ligand binding as well as state anisotropies for different fluorescent ligand populations were determined. At low Cy3B-NDP-α-MSH concentrations, a one-site receptor-ligand binding model described the processes, whereas divergence from this model was observed at higher ligand concentrations, which indicated a more complex mechanism of interactions similar to those mechanisms that have been found in experiments with radioactive ligands. The information obtained from our kinetic experiments and the inherent flexibility of FA assays also allowed the estimation of binding parameters for several MC4 receptor-specific unlabelled compounds. In summary, the FA assay that was developed with budded baculoviruses led the experimental data to a level that would solve complex models of receptor-ligand interactions also for other receptor systems and would become as a valuable tool for the screening of pharmacologically active compounds.

  2. Kinetics of actinide complexation reactions

    SciTech Connect

    Nash, K.L.; Sullivan, J.C.

    1997-09-01

    Though the literature records extensive compilations of the thermodynamics of actinide complexation reactions, the kinetics of complex formation and dissociation reactions of actinide ions in aqueous solutions have not been extensively investigated. In light of the central role played by such reactions in actinide process and environmental chemistry, this situation is somewhat surprising. The authors report herein a summary of what is known about actinide complexation kinetics. The systems include actinide ions in the four principal oxidation states (III, IV, V, and VI) and complex formation and dissociation rates with both simple and complex ligands. Most of the work reported was conducted in acidic media, but a few address reactions in neutral and alkaline solutions. Complex formation reactions tend in general to be rapid, accessible only to rapid-scan and equilibrium perturbation techniques. Complex dissociation reactions exhibit a wider range of rates and are generally more accessible using standard analytical methods. Literature results are described and correlated with the known properties of the individual ions.

  3. Fast food (image)

    MedlinePlus

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

  5. Is fast food addictive?

    PubMed

    Garber, Andrea K; Lustig, Robert H

    2011-09-01

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

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

    PubMed

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

    2016-01-14

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

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

    PubMed Central

    2015-01-01

    A series of selective androgen receptor modulators (SARMs) containing the 1-(trifluoromethyl)benzyl alcohol core have been optimized for androgen receptor (AR) potency and drug-like properties. We have taken advantage of the lipophilic ligand efficiency (LLE) parameter as a guide to interpret the effect of structural changes on AR activity. Over the course of optimization efforts the LLE increased over 3 log units leading to a SARM 43 with nanomolar potency, good aqueous kinetic solubility (>700 μM), and high oral bioavailability in rats (83%). PMID:26819671

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

    DTIC Science & Technology

    2013-08-13

    to be a facile and ambient synthesis of cyclic azines (6). 2.e) Identifying catalyst arrest mechanisms in a Ruthenium -catalyzed hydroxylation...active catalyst molecules in a ruthenium catalyzed hydroxylation reaction 6 3. Monitoring Catalytic Processes on Electrode Surfaces in Real-Time

  9. Why mercury prefers soft ligands

    SciTech Connect

    Riccardi, Demian M; Guo, Hao-Bo; Gu, Baohua; Parks, Jerry M; Summers, Anne; Miller, S; Liang, Liyuan; Smith, Jeremy C

    2013-01-01

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

  10. What are Nuclear Receptor Ligands?

    PubMed Central

    Sladek, Frances M.

    2010-01-01

    Nuclear receptors (NRs) are a family of highly conserved transcription factors that regulate transcription in response to small lipophilic compounds. They play a role in every aspect of development, physiology and disease in humans. They are also ubiquitous in and unique to the animal kingdom suggesting that they may have played an important role in their evolution. In contrast to the classical endocrine receptors that originally defined the family, recent studies suggest that the first NRs might have been sensors of their environment, binding ligands that were external to the host organism. The purpose of this review is to provide a broad perspective on NR ligands and address the issue of exactly what constitutes a NR ligand from historical, biological and evolutionary perspectives. This discussion will lay the foundation for subsequent reviews in this issue as well as pose new questions for future investigation. PMID:20615454

  11. Molecular Recognition and Ligand Association

    NASA Astrophysics Data System (ADS)

    Baron, Riccardo; McCammon, J. Andrew

    2013-04-01

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

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

    PubMed

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

    1996-09-01

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

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

    PubMed Central

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

    1996-01-01

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

  14. Evidence for dynamics in proteins as a mechanism for ligand dissociation

    PubMed Central

    Carroll, Mary J.; Mauldin, Randall V.; Gromova, Anna V.; Singleton, Scott F.; Collins, Edward J.; Lee, Andrew L.

    2011-01-01

    Signal transduction, regulatory processes, and pharmaceutical responses are highly dependent upon ligand residence times. Gaining insight into how physical factors influence residence times, or koff, should enhance our ability to manipulate biological interactions. We report experiments that yield structural insight into koff for a series of eight 2,4-diaminopyrimidine inhibitors of dihydrofolate reductase that vary by six orders of magnitude in binding affinity. NMR relaxation dispersion experiments revealed a common set of residues near the binding site that undergo a concerted, millisecond-timescale switching event to a previously unidentified conformation. The rate of switching from ground to excited conformations correlates exponentially with Ki and koff, suggesting that protein dynamics serves as a mechanical initiator of ligand dissociation within this series and potentially for other macromolecule-ligand systems. Although kconf,forward is faster than koff, use of the ligand series allowed for connections to be drawn between kinetic events on different timescales. PMID:22246400

  15. Acetylcholine receptors and cholinergic ligands: biochemical and genetic aspects in Torpedo californica and Drosophila melanogaster

    SciTech Connect

    Rosenthal, L.S.

    1987-01-01

    This study evaluates the biochemical and genetic aspects of the acetylcholine receptor proteins and cholinergic ligands in Drosophila melanogaster and Torpedo californica. Included are (1) a comparative study of nicotinic ligand-induced cation release from acetylcholine receptors isolated from Torpedo californica and from Drosophila melanogaster, (2) solution studies of the cholinergic ligands, nikethamide and ethamivan, aimed at measuring internal molecular rotational barriers in solvents of different polarity; and (3) the isolation and characterization of the gene(s) for the acetylcholine receptor in Drosophila melasogaster. Acetylcholine receptor proteins isolated from Drosphila melanogaster heads were found to behave kinetically similar (with regards to cholinergic ligand-induced /sup 155/Eu:/sup 3 +/ displacement from prelabeled proteins) to receptor proteins isolated from Torpedo californica electric tissue, providing additional biochemical evidence for the existence of a Drosophila acetylcholine receptor.

  16. Gadolinium(III) complexes as MRI contrast agents: ligand design and properties of the complexes.

    PubMed

    Hermann, Petr; Kotek, Jan; Kubícek, Vojtech; Lukes, Ivan

    2008-06-21

    Magnetic resonance imaging is a commonly used diagnostic method in medicinal practice as well as in biological and preclinical research. Contrast agents (CAs), which are often applied are mostly based on Gd(III) complexes. In this paper, the ligand types and structures of their complexes on one side and a set of the physico-chemical parameters governing properties of the CAs on the other side are discussed. The solid-state structures of lanthanide(III) complexes of open-chain and macrocyclic ligands and their structural features are compared. Examples of tuning of ligand structures to alter the relaxometric properties of gadolinium(III) complexes as a number of coordinated water molecules, their residence time (exchange rate) or reorientation time of the complexes are given. Influence of the structural changes of the ligands on thermodynamic stability and kinetic inertness/lability of their lanthanide(III) complexes is discussed.

  17. Kinetic partitioning mechanism of HDV ribozyme folding.

    PubMed

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

    2014-01-14

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

  18. Kinetic partitioning mechanism of HDV ribozyme folding

    SciTech Connect

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

    2014-01-14

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

  19. Kinetic partitioning mechanism of HDV ribozyme folding

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

  20. Evaluation of H2CHXdedpa, H2dedpa- and H2CHXdedpa-N,N'-propyl-2-NI ligands for (64)Cu(ii) radiopharmaceuticals.

    PubMed

    Ramogida, Caterina F; Boros, Eszter; Patrick, Brian O; Zeisler, Stefan K; Kumlin, Joel; Adam, Michael J; Schaffer, Paul; Orvig, Chris

    2016-08-16

    The chiral acyclic "pa" ligand (pa = picolinic acid) H2CHXdedpa (N4O2) and two NI-containing dedpa analogues (H2CHXdedpa-N,N'-propyl-2-NI, H2dedpa-N,N'-propyl-2-NI, NI = nitroimidazole) were studied as chelators for copper radiopharmaceuticals (CHX = cyclohexyl, H2dedpa = 1,2-[[carboxypyridin-2-yl]methylamino]ethane). The hexadentate ligand H2CHXdedpa was previously established as a superb system for (67/68)Ga radiochemistry. The solid state X-ray crystal structures of [Cu(CHXdedpa-N,N'-propyl-2-NI)] and [Cu(dedpa-N,N'-propyl-2-NI)] reveal the predicted hexadentate, distorted octahedral binding of the copper(ii) ion. Cyclic voltammetry of [Cu(dedpa-N,N'-propyl-2-NI)] shows that there is one reversible couple associated with the NI redox, and one irreversible but reproducible couple attributed to the Cu(ii)/Cu(i) redox cycle. Quantitative radiolabeling (>99%) of CHXdedpa(2-) and (dedpa-N,N'-propyl-2-NI)(2-) with (64)Cu was achieved under fast and efficient labeling conditions (10 min, RT, 0.5 M sodium acetate buffer, pH 5.5) at ligand concentrations as low as 10(-6) M. In vitro kinetic inertness studies of the (64)Cu labelled complexes were studied in human serum at 37 °C over 24 hours; [(64)Cu(CHXdedpa)] was found to be 98% stable compared to previously investigated [(64)Cu(dedpa)] which was only 72% intact after 24 hours.

  1. Thermodynamics and kinetics of adaptive binding in the malachite green RNA aptamer.

    PubMed

    Da Costa, Jason B; Andreiev, Aurelia I; Dieckmann, Thorsten

    2013-09-24

    Adaptive binding, the ability of molecules to fold themselves around the structure of a ligand and thereby incorporating it into their three-dimensional fold, is a key feature of most RNA aptamers. The malachite green aptamer (MGA) has been shown to bind several closely related triphenyl dyes with planar and nonplanar structures in this manner. Competitive binding studies using isothermal titration calorimetry and stopped flow kinetics have been conducted with the aim of understanding the adaptive nature of RNA-ligand interaction. The results of these studies reveal that binding of one ligand can reduce the ability of the aptamer pocket to adapt to another ligand, even if this second ligand has a significantly higher affinity to the free aptamer. A similar effect is observed in the presence of Mg(2+) ions which stabilize the binding pocket in a more ligand bound-like conformation.

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

    PubMed

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

    2001-09-13

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

  3. Ligand-induced Epitope Masking

    PubMed Central

    Mould, A. Paul; Askari, Janet A.; Byron, Adam; Takada, Yoshikazu; Jowitt, Thomas A.; Humphries, Martin J.

    2016-01-01

    We previously demonstrated that Arg-Gly-Asp (RGD)-containing ligand-mimetic inhibitors of integrins are unable to dissociate pre-formed integrin-fibronectin complexes (IFCs). These observations suggested that amino acid residues involved in integrin-fibronectin binding become obscured in the ligand-occupied state. Because the epitopes of some function-blocking anti-integrin monoclonal antibodies (mAbs) lie near the ligand-binding pocket, it follows that the epitopes of these mAbs may become shielded in the ligand-occupied state. Here, we tested whether function-blocking mAbs directed against α5β1 can interact with the integrin after it forms a complex with an RGD-containing fragment of fibronectin. We showed that the anti-α5 subunit mAbs JBS5, SNAKA52, 16, and P1D6 failed to disrupt IFCs and hence appeared unable to bind to the ligand-occupied state. In contrast, the allosteric anti-β1 subunit mAbs 13, 4B4, and AIIB2 could dissociate IFCs and therefore were able to interact with the ligand-bound state. However, another class of function-blocking anti-β1 mAbs, exemplified by Lia1/2, could not disrupt IFCs. This second class of mAbs was also distinguished from 13, 4B4, and AIIB2 by their ability to induce homotypic cell aggregation. Although the epitope of Lia1/2 was closely overlapping with those of 13, 4B4, and AIIB2, it appeared to lie closer to the ligand-binding pocket. A new model of the α5β1-fibronectin complex supports our hypothesis that the epitopes of mAbs that fail to bind to the ligand-occupied state lie within, or very close to, the integrin-fibronectin interface. Importantly, our findings imply that the efficacy of some therapeutic anti-integrin mAbs could be limited by epitope masking. PMID:27484800

  4. Multifunctional Ligands in Transition Metal Catalysis

    SciTech Connect

    Crabtree, Robert H

    2011-01-01

    Sophisticated ligands are now being designed that do far more than just fulfil their traditional spectator roles by binding to the metal and providing a sterically-defined binding pocket for the substrate in homogeneous transition metal catalysis. This Focus review emphasizes selected cases in which ligands carry additional functional groups that change the properties of the ligand as a result of an external stimulus or undergo catalytically-relevant ligand-based reactivity. These include proton responsive ligands capable of gaining or losing one or more protons, ligands having a hydrogen bonding function, electroresponsive ligands capable of gaining or losing one or more electrons, and photoresponsive ligands capable of undergoing a useful change of properties upon irradiation. Molecular recognition ligands and proton coupled electron transfer (PCET) are briefly discussed.

  5. Integrative Physiology of Fasting.

    PubMed

    Secor, Stephen M; Carey, Hannah V

    2016-03-15

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

  6. Ligand and proton exchange dynamics in recombinant human myoglobin mutants.

    PubMed

    Lambright, D G; Balasubramanian, S; Boxer, S G

    1989-05-05

    Site-specific mutants of human myoglobin have been prepared in which lysine 45 is replaced by arginine (K45R) and aspartate 60 by glutamate (D60E), in order to examine the influence of these residues and their interaction on the dynamics of the protein. These proteins were studied by a variety of methods, including one and two-dimensional proton nuclear magnetic resonance spectroscopy, exchange kinetics for the distal and proximal histidine NH protons as a function of pH in the met cyano forms, flash photolysis of the CO forms, and ligand replacement kinetics. The electronic absorption and proton nuclear magnetic resonance spectra of the CO forms of these proteins are virtually identical, indicating that the structure of the heme pocket is unaltered by these mutations. There are, however, substantial changes in the dynamics of both CO binding and proton exchange for the mutant K45R, whereas the mutant D60E exhibits behavior indistinguishable from the reference human myoglobin. K45R has a faster CO bimolecular recombination rate and slower CO off-rate relative to the reference. The kinetics for CO binding are independent of pH (6.5 to 10) as well as ionic strength (0 to 1 M-NaCl). The exchange rate for the distal histidine NH is substantially lower for K45R than the reference, whereas the proximal histidine NH exchange rate is unaltered. The exchange behavior of the human proteins is similar to that reported for a comparison of the exchange rates for myoglobins having lysine at position 45 with sperm whale myoglobin, which has arginine at this position. This indicates that the differences in exchange rates reflects largely the Lys----Arg substitution. The lack of a simple correlation for the CO kinetics with this substitution means that these are sensitive to other factors as well. Specific kinetic models, whereby substitution of arginine for lysine at position 45 can affect ligand binding dynamics, are outlined. These experiments demonstrate that a relatively

  7. Constitutive and ligand-induced nuclear localization of oxytocin receptor.

    PubMed

    Kinsey, Conan G; Bussolati, Gianni; Bosco, Martino; Kimura, Tadashi; Pizzorno, Marie C; Chernin, Mitchell I; Cassoni, Paola; Novak, Josef F

    2007-01-01

    Oxytocin receptor (OTR) is a membrane protein known to mediate oxytocin (OT) effects, in both normal and neoplastic cells. We report here that human osteosarcoma (U2OS, MG63, OS15 and SaOS2), breast cancer (MCF7), and primary human fibroblastic cells (HFF) all exhibit OTR not only on the cell membrane, but also in the various nuclear compartments including the nucleolus. Both an OTR-GFP fusion protein and the native OTR appear to be localized to the nucleus as detected by transfection and/or confocal immunofluorescence, respectively. Treatment with oxytocin causes internalization of OTR and the resulting vesicles accumulate in the vicinity of the nucleus and some of the perinuclear OTR enters the nucleus. Western blots indicate that OTR in the nucleus and on the plasma membrane are likely to be the same biochemical and immunological entities. It appears that OTR is first visible in the nucleoli and subsequently disperses within the nucleus into 4-20 spots while some of the OTR diffuses throughout the nucleoplasm. The behaviour and kinetics of OTR-GFP and OTR are different, indicating interference by GFP in both OTR entrance into the nucleus and subsequent relocalization of OTR within the nucleus. There are important differences among the tested cells, such as the requirement of a ligand for transfer of OTR in nuclei. A constitutive internalization of OTR was found only in osteosarcoma cells, while the nuclear localization in all other tested cells was dependent on ligand binding. The amount of OTR-positive material within and in the vicinity of the nucleus increased following a treatment with oxytocin in both constitutive and ligand-dependent type of cells. The evidence of OTR compartmentalization at the cell nucleus (either ligand-dependent or constitutive) in different cell types suggests still unknown biological functions of this protein or its ligand and adds this G-protein-coupled receptor to other heptahelical receptors displaying this atypical and unexpected

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2012-12-01

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

  11. One-Step Ligand Immobilization and Single Sample Injection for Regeneration-Free Surface Plasmon Resonance Measurements of Biomolecular Interactions.

    PubMed

    Wang, Xiaoying; Li, Zhiqiang; Ly, Nguyen; Zhou, Feimeng

    2017-03-21

    Surface plasmon resonance (SPR) has been well established as a method of choice for label-free kinetic measurements of biomolecular interactions. The conventional approach involves multiple injections of an analyte of different concentrations into a fluidic channel covered with a fixed ligand density. Optimization of the experimental conditions and assessment of the data quality can be complicated by issues such as disruption of the ligand structure by the regeneration step and the limited availability of the sample solution. By sequentially closing fluidic channels on a five-channel SPR instrument, different densities of a ligand can be immobilized and determined in one step. With a subsequent injection of a single sample solution, SPR sensorgrams can be simultaneously collected to yield binding and dissociation rate constants (ka and kd) and dissociation constant (KD) between the ligand and analyte. For biomolecular interactions that obey the Langmuir isotherm, we show that the fidelity of the kinetic data can only be reliably confirmed when there exists a strong linear correlation between the SPR signals and the ligand densities. The use of a multichannel SPR instrument also obviates the regeneration step, allowing the binding kinetics between the green fluorescent protein and its antibody to be measured. In comparison to the conventional approach, the method simplifies the experimental procedure, reduces costs associated with sensor chips and biological samples, expedites kinetic measurements, and allows affinity constants to be determined more straightforwardly.

  12. Multicoordinate ligands for actinide/lanthanide separations.

    PubMed

    Dam, Henk H; Reinhoudt, David N; Verboom, Willem

    2007-02-01

    In nuclear waste treatment processes there is a need for improved ligands for the separation of actinides (An(III)) and lanthanides (Ln(III)). Several research groups are involved in the design and synthesis of new An(III) ligands and in the confinement of these and existing An(III) ligands onto molecular platforms giving multicoordinate ligands. The preorganization of ligands considerably improves the An(III) extraction properties, which are largely dependent on the solubility and rigidity of the platform. This tutorial review summarizes the most important An(III) ligands with emphasis on the preorganization strategy using (macrocyclic) platforms.

  13. Application of Photoacoustic Effect to Chemical Kinetics in Solution.

    NASA Astrophysics Data System (ADS)

    Cheng, Huy-Zu.

    The application of the pulsed photoacoustic technique (PA) to the study of chemical kinetics in very dilute solutions is demonstrated with three different reactions: A bidental ligand substitution of 1,2-bi(diphenylphosphino) ethane on the five-coordinate cobalt dithiolene complex, a nucleophilic addition of tributyl phosphite to (p-(dimethylamino)triphenyl)methyl cation, and an enzyme catalyzed reduction of nicotinamide adenine dinucleotide by glucose-6-phosphate. Photoacoustic detection is shown to be 100 times more sensitive than spectrophotometric detection. As a consequence, it allows one to use lower reactant concentrations so that the time scale for the corresponding fast reactions can be lengthened. The pulsed PA technique also provides an alternative method for the direct determination of reverse rate constants and equilibrium constants of reactions. Moreover, Michaelis constants of biochemical reactions, especially for enzymes whose K_{rm m} values is below 1.0 muM, can be measured more accurately using photoacoustic detection than using spectrophotometric detection. Additionally, the pulsed PA method can be very valuable for the study of reactions that are restricted by the low solubility, availability, or high cost of reactants. The sensitivity of the PA method is found to be limited by the background signal resulting from solvents. Photoacoustic signals generated in strongly absorbing media are also studied and results are in agreement with the theory developed by G. J. Diebold. From the time profile of the acoustic signal, the absorption coefficient of strongly absorbing medium can be determined provided the sound speed is known. Since the pulse shape of the acoustic transient depends upon the relative density and the acoustic velocity of the transparent and the strongly absorbing media, the physical properties of the transparent medium can also be determined with the use of the PA technique.

  14. Fluorescent Approaches for Understanding Interactions of Ligands with G Protein Coupled Receptors

    PubMed Central

    Sridharan, Rajashri; Zuber, Jeffrey; Connelly, Sara M.; Mathew, Elizabeth; Dumont, Mark E.

    2014-01-01

    G Protein Coupled Receptors (GPCRs) are responsible for a wide variety of signaling responses in diverse cell types. Despite major advances in the determination of structures of this class of receptors, the underlying mechanisms by which binding of different types of ligands specifically elicits particular signaling responses remains unclear. The use of fluorescence spectroscopy can provide important information about the process of ligand binding and ligand dependent conformational changes in receptors, especially kinetic aspects of these processes, that can be difficult to extract from x-ray structures. We present an overview of the extensive array of fluorescent ligands that have been used in studies of GPCRs and describe spectroscopic approaches for assaying binding and probing the environment of receptor-bound ligands with particular attention to examples involving yeast pheromone receptors. In addition, we discuss the use of fluorescence spectroscopy for detecting and characterizing conformational changes in receptors induced by the binding of ligands. Such studies have provided strong evidence for diversity of receptor conformations elicited by different ligands, consistent with the idea that GPCRs are not simple on and off switches. This diversity of states constitutes an underlying mechanistic basis for biased agonism, the observation that different stimuli can produce different responses from a single receptor. It is likely that continued technical advances will allow fluorescence spectroscopy to play an important role in continued probing of structural transitions in GPCRs. PMID:24055822

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

    PubMed Central

    Yang, Guang; Hallinan, Daniel T.

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Yang, Guang; Hallinan, Daniel T.

    2016-10-01

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

  17. Biotic ligand model does not predict the bioavailability of rare Earth elements in the presence of organic ligands.

    PubMed

    Zhao, Chun-Mei; Wilkinson, Kevin J

    2015-02-17

    Due to their distinct physicochemical properties, rare earth elements (REEs) are critical to high-tech and clean-energy industries; however, their bioavailability is still largely unexplored. In this paper, the bioavailability of several REEs has been carefully examined for the freshwater alga, Chlamydomonas reinhardtii. In the presence of organic ligands (L), the biouptake of REEs was much higher than that predicted by the biotic ligand model (BLM). Enhancement of the biouptake flux was observed for six ligands (metal = thulium) and six REEs (ligand = citric acid), indicating that this could be a common feature for these metals. In order to explore the mechanism for the enhanced uptake, Tm internalization was carefully evaluated. The Tm internalization flux (Jint) followed first-order (Michaelis-Menten) kinetics with a calculated maximum internalization flux (Jmax) of (1.1 ± 0.08) × 10(-14) mol · cm(-2) · s(-1) and an affinity constant for the reaction of the metal with the transport sites (KTm-R) of 10(7.1) M(-1). In the presence of citric acid, malic acid, or NTA, the Jint for Tm was more than 1 order of magnitude higher than that predicted by the BLM when algae were exposed to a constant 10(-9) M Tm(3+). The bioavailability of the metal complexes could not be explained by a piggyback internalization (through an anion channel) or the contribution of labile complexes. The enhanced biouptake was attributed to the formation of a ternary Tm complex {L-Tm-R} at the metal transport site. In the natural environment where organic ligands are ubiquitous, classic models are unlikely to predict the bioavailability of REEs to aquatic organisms.

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

    PubMed Central

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  20. Real-Time Ligand Binding Pocket Database Search Using Local Surface Descriptors

    PubMed Central

    Chikhi, Rayan; Sael, Lee; Kihara, Daisuke

    2010-01-01

    Due to the increasing number of structures of unknown function accumulated by ongoing structural genomics projects, there is an urgent need for computational methods for characterizing protein tertiary structures. As functions of many of these proteins are not easily predicted by conventional sequence database searches, a legitimate strategy is to utilize structure information in function characterization. Of a particular interest is prediction of ligand binding to a protein, as ligand molecule recognition is a major part of molecular function of proteins. Predicting whether a ligand molecule binds a protein is a complex problem due to the physical nature of protein-ligand interactions and the flexibility of both binding sites and ligand molecules. However, geometric and physicochemical complementarity is observed between the ligand and its binding site in many cases. Therefore, ligand molecules which bind to a local surface site in a protein can be predicted by finding similar local pockets of known binding ligands in the structure database. Here, we present two representations of ligand binding pockets and utilize them for ligand binding prediction by pocket shape comparison. These representations are based on mapping of surface properties of binding pockets, which are compactly described either by the two dimensional pseudo-Zernike moments or the 3D Zernike descriptors. These compact representations allow a fast real-time pocket searching against a database. Thorough benchmark study employing two different datasets show that our representations are competitive with the other existing methods. Limitations and potentials of the shape-based methods as well as possible improvements are discussed. PMID:20455259

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

    PubMed

    Miyabe, Kanji

    2014-08-22

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

  2. Fast wave current drive

    SciTech Connect

    Goree, J.; Ono, M.; Colestock, P.; Horton, R.; McNeill, D.; Park, H.

    1985-07-01

    Fast wave current drive is demonstrated in the Princeton ACT-I toroidal device. The fast Alfven wave, in the range of high ion-cyclotron harmonics, produced 40 A of current from 1 kW of rf power coupled into the plasma by fast wave loop antenna. This wave excites a steady current by damping on the energetic tail of the electron distribution function in the same way as lower-hybrid current drive, except that fast wave current drive is appropriate for higher plasma densities.

  3. fast-matmul

    SciTech Connect

    Grey Ballard, Austin Benson

    2014-11-26

    This software provides implementations of fast matrix multiplication algorithms. These algorithms perform fewer floating point operations than the classical cubic algorithm. The software uses code generation to automatically implement the fast algorithms based on high-level descriptions. The code serves two general purposes. The first is to demonstrate that these fast algorithms can out-perform vendor matrix multiplication algorithms for modest problem sizes on a single machine. The second is to rapidly prototype many variations of fast matrix multiplication algorithms to encourage future research in this area. The implementations target sequential and shared memory parallel execution.

  4. Molecular modeling and ligand docking for Solute Carrier (SLC) transporters

    PubMed Central

    Schlessinger, Avner; Khuri, Natalia; Giacomini, Kathleen M.; Sali, Andrej

    2014-01-01

    Solute Carrier (SLC) transporters are membrane proteins that transport solutes, such as ions, metabolites, peptides, and drugs, across biological membranes, using diverse energy coupling mechanisms. In human, there are 386 SLC transporters, many of which contribute to the absorption, distribution, metabolism, and excretion of drugs and/or can be targeted directly by therapeutics. Recent atomic structures of SLC transporters determined by X-ray crystallography and NMR spectroscopy have significantly expanded the applicability of structure-based prediction of SLC transporter ligands, by enabling both comparative modeling of additional SLC transporters and virtual screening of small molecules libraries against experimental structures as well as comparative models. In this review, we begin by describing computational tools, including sequence analysis, comparative modeling, and virtual screening, that are used to predict the structures and functions of membrane proteins such as SLC transporters. We then illustrate the applications of these tools to predicting ligand specificities of select SLC transporters, followed by experimental validation using uptake kinetic measurements and other assays. We conclude by discussing future directions in the discovery of the SLC transporter ligands. PMID:23578028

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

    PubMed

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

    2015-08-28

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

  6. Glyconanomaterials: synthesis, characterization, and ligand presentation.

    PubMed

    Wang, Xin; Ramström, Olof; Yan, Mingdi

    2010-05-04

    Glyconanomaterials, nanomaterials carrying surface-tethered carbohydrate ligands, have emerged and demonstrated increasing potential in biomedical imaging, therapeutics, and diagnostics. These materials combine the unique properties of nanometer-scale objects with the ability to present multiple copies of carbohydrate ligands, greatly enhancing the weak affinity of individual ligands to their binding partners. Critical to the performance of glyconanomaterials is the proper display of carbohydrate ligands, taking into consideration of the coupling chemistry, the type and length of the spacer linkage, and the ligand density. This article provides an overview of the coupling chemistry for attaching carbohydrate ligands to nanomaterials, and discusses the need for thorough characterization of glyconanomaterials, especially quantitative analyses of the ligand density and binding affinities. Using glyconanoparticles synthesized by a versatile photocoupling chemistry, methods for determining the ligand density by colorimetry and the binding affinity with lectins by a fluorescence competition assay are determined. The results show that the multivalent presentation of carbohydrate ligands significantly enhances the binding affinity by several orders of magnitude in comparison to the free ligands in solution. The effect is sizeable even at low surface ligand density. The type and length of the spacer linkage also affect the binding affinity, with the longer linkage promoting the association of bound ligands with the corresponding lectins.

  7. Glyconanomaterials: Synthesis, Characterization, and Ligand Presentation

    PubMed Central

    Wang, Xin

    2010-01-01

    Glyconanomaterials, nanomaterials carrying surface-tethered carbohydrate ligands, have emerged and demonstrated increasing potential in biomedical imaging, therapeutics, and diagnostics. These materials combine the unique properties of nanometer-scale objects with the ability to present multiple copies of carbohydrate ligands, greatly enhancing the weak affinity of individual ligands to their binding partners. Critical to the performance of glyconanomaterials is the proper display of carbohydrate ligands, taking into consideration of the coupling chemistry, the type and length of the spacer linkage, and the ligand density. This article provides an overview of the coupling chemistry for attaching carbohydrate ligands to nanomaterials, and discusses the need for thorough characterization of glyconanomaterials, especially quantitative analyses of the ligand density and binding affinities. Using glyconanoparticles synthesized by a versatile photocoupling chemistry, methods for determining the ligand density by colorimetry and the binding affinity with lectins by a fluorescence competition assay are determined. The results show that the multivalent presentation of carbohydrate ligands significantly enhances the binding affinity by several orders of magnitude in comparison to the free ligands in solution. The effect is sizeable even at low surface ligand density. The type and length of the spacer linkage also affect the binding affinity, with the longer linkage promoting the association of bound ligands with the corresponding lectins. PMID:20301131

  8. Influence of mixed-ligand complexes on retention and distribution of radioniobium in mice

    SciTech Connect

    Gachalyi, A.; Namenyi, J.; Szegedi, I.; Varga, L.P.

    1987-11-01

    The individual effects of desferrioxamine B (DFOA), Na3Ca diethylenetriaminepentaacetic acid (DTPA), Na-salicylate, DL-penicillamine, and 2-aminoethylisothiouronium bromide hydrobromide, as well as the effect of mixed-ligand treatment on the retention and elimination of /sup 95/Nb in mice have been examined. It was found that /sup 95/Nb could easily be mobilized by a single dose of DFOA, but the best result was obtained with the DFOA and DTPA combination. Mixed-ligand treatment did not change the deposition characteristics and translocation kinetics of /sup 95/Nb.

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

    PubMed

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

    2015-02-13

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

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

    PubMed

    Xie, Yuling; Hamann, Thomas W

    2013-01-17

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

  11. Synthesis and NMR characterization of ligand-capped metal and metal-oxide nanoparticles

    NASA Astrophysics Data System (ADS)

    Sharma, Ramesh

    Ligand-capped metal and metal-oxide nanoparticles (NPs) have some interesting and useful physical properties that are not present in their respective bulk materials. These properties are of research interest in many applications such as catalysis, drug delivery, biological imaging, and plasmonics. In such applications, it is critical to understand the surface structure of NPs and the roles played by the surface bound ligands. To characterize surface environment, ligand dynamics, and exchange kinetics, ligand-capped metal and metal-oxide NPs are synthesized and studied by multinuclear NMR. Phosphines and phosphonic acids are used to passivate metal (gold and silver) and metal-oxide (tin dioxide) NPs in different sizes (1-5 nm) by following published procedures or original synthesis methods. In both solution and solid state NMR, the 31P chemical shift of surface-bound ligands are distinctly different from those observed for free ligands. Additionally, NMR line widths in surface-bound ligands are highly broadened compared to those of free ligands. The lines are broadened due to both homogeneous and inhomogeneous broadening mechanisms, determined through hole burning NMR and spin-spin relaxation measurements. In small particles (< 2 nm), the main source of line broadening is inhomogeneous and originates due to structural heterogeneity and underlying chemical shift distributions. In large particles (> 2 nm), both inhomogeneous and homogeneous line broadening mechanisms are present. When the particles' sizes increase from small to large, the homogeneous broadening mechanism becomes dominant due to strong nuclear-electron interaction and reintroduction of residual dipolar coupling as shown by a combination of 1H, 13C and 31P NMR. Results from a series of ligand exchange experiments in silver and gold NPs further indicate the presence of Au(I) and Ag(I) on the particle surfaces.

  12. Characterization of aqueous lead removal by phosphatic clay: equilibrium and kinetic studies.

    PubMed

    Singh, S P; Ma, L Q; Hendry, M J

    2006-08-25

    Immobilization of heavy metals from contaminated environments is an emerging field of interest from both resource conservation and environmental remediation points of view. This study investigated the feasibility of using phosphatic clay, a waste by-product of the phosphate mining industry, as an effective sorbent for Pb from aqueous effluents. The major parameters controlling aqueous Pb removal, viz. initial metal ion concentrations, solution pH, sorbent amounts, ionic strength and presence of both inorganic and organic ligands were evaluated using batch experiments. Results demonstrated that aqueous Pb removal efficiency of phosphatic clay is controlled mainly by dissolution of phosphatic clay associated fluoroapatite [Ca(10)(PO(4))(5)CaCO(3)(F,Cl,OH)(2)], followed by subsequent precipitation of geochemically stable pyromorphite [Pb(10)(PO(4))(6)(F,Cl,OH)(2)], which was confirmed by both X-ray diffraction (XRD) and scanning electron microscopic (SEM) analysis. Lead removal efficiency of phosphatic clay increased with increasing pH, sorbent amount and decreasing ionic strength. It also depends on the nature of complexing ligands. Formation of insoluble calcium oxalate and lead oxalate in the presence of oxalic acid explained high uptake of Pb by phosphatic clay from aqueous solution. However, Pb sorption kinetics onto phosphatic clay were biphasic, with initially fast reactions followed by slow and continuous Pb removal reactions. The slow reactions may include surface sorption, co-precipitation and diffusion. The exceptional capability of phosphatic clay to remove aqueous Pb demonstrated its potential as a cost effective way to remediate Pb-contaminated water, soils and sediments.

  13. Ligand chain length conveys thermochromism.

    PubMed

    Ganguly, Mainak; Panigrahi, Sudipa; Chandrakumar, K R S; Sasmal, Anup Kumar; Pal, Anjali; Pal, Tarasankar

    2014-08-14

    Thermochromic properties of a series of non-ionic copper compounds have been reported. Herein, we demonstrate that Cu(II) ion with straight-chain primary amine (A) and alpha-linolenic (fatty acid, AL) co-jointly exhibit thermochromic properties. In the current case, we determined that thermochromism becomes ligand chain length-dependent and at least one of the ligands (A or AL) must be long chain. Thermochromism is attributed to a balanced competition between the fatty acids and amines for the copper(II) centre. The structure-property relationship of the non-ionic copper compounds Cu(AL)2(A)2 has been substantiated by various physical measurements along with detailed theoretical studies based on time-dependent density functional theory. It is presumed from our results that the compound would be a useful material for temperature-sensor applications.

  14. Presentation of Ligands on Hydroxylapatite

    NASA Technical Reports Server (NTRS)

    Chu, Barbara C. F.; Orgel, Leslie E.

    1997-01-01

    Conjugates of biotin with the decamer of glutamic acid (glu(sub 10)) and the trimer of D,L-2-amino-5-phosphonovaleric acid (I) have been synthesized, and it has been shown that they mediate the binding of avidin to hydroxylapatite. In a similar way a conjugate of methotrexate with glu(sub 10) mediates the binding of dihydrofolate reductase to the mineral. The presentation of ligands on the hydroxylapatite component of bone may find applications in clinical medicine.

  15. Fast and effective?

    PubMed

    Trueland, Jennifer

    2013-12-18

    The 5.2 diet involves two days of fasting each week. It is being promoted as the key to sustained weight loss, as well as wider health benefits, despite the lack of evidence on the long-term effects. Nurses need to support patients who wish to try intermittent fasting.

  16. fastKDE

    SciTech Connect

    O'Brien, Travis A.; Kashinath, Karthik

    2015-05-22

    This software implements the fast, self-consistent probability density estimation described by O'Brien et al. (2014, doi: ). It uses a non-uniform fast Fourier transform technique to reduce the computational cost of an objective and self-consistent kernel density estimation method.

  17. Fast optical pyrometry

    NASA Technical Reports Server (NTRS)

    Cezairliyan, Ared

    1988-01-01

    Design and operation of accurate millisecond and microsecond resolution optical pyrometers developed at the National Bureau of Standards during the last two decades are described. Results of tests are presented and estimates of uncertainties in temperature measurements are given. Calibration methods are discussed and examples of applications of fast pyrometry are given. Ongoing research in developing fast multiwavelength and spatial scanning pyrometers are summarized.

  18. Tumor Targeting via Integrin Ligands

    PubMed Central

    Marelli, Udaya Kiran; Rechenmacher, Florian; Sobahi, Tariq Rashad Ali; Mas-Moruno, Carlos; Kessler, Horst

    2013-01-01

    Selective and targeted delivery of drugs to tumors is a major challenge for an effective cancer therapy and also to overcome the side-effects associated with current treatments. Overexpression of various receptors on tumor cells is a characteristic structural and biochemical aspect of tumors and distinguishes them from physiologically normal cells. This abnormal feature is therefore suitable for selectively directing anticancer molecules to tumors by using ligands that can preferentially recognize such receptors. Several subtypes of integrin receptors that are crucial for cell adhesion, cell signaling, cell viability, and motility have been shown to have an upregulated expression on cancer cells. Thus, ligands that recognize specific integrin subtypes represent excellent candidates to be conjugated to drugs or drug carrier systems and be targeted to tumors. In this regard, integrins recognizing the RGD cell adhesive sequence have been extensively targeted for tumor-specific drug delivery. Here we review key recent examples on the presentation of RGD-based integrin ligands by means of distinct drug-delivery systems, and discuss the prospects of such therapies to specifically target tumor cells. PMID:24010121

  19. Synthesis and Comparative Biological Evalution of Bifunctional Ligands for Radiotherapy Applications of 90Y and 177Lu

    PubMed Central

    Chong, Hyun-Soon; Sun, Xiang; Chen, Yunwei; Sin, Inseok; Kang, Chi Soo; Lewis, Michael R.; Liu, Dijie; Ruthengael, Varyanna C.; Zhong, Yongliang; Wu, Ningjie; Song, Hyun A

    2015-01-01

    Zevalin® is an antibody-drug conjugate radiolabeled with a cytotoxic radioisotope (90Y) that was approved for radioimmunotherapy (RIT) of B-cell non-Hodgkin’s lymphoma. A bifunctional ligand that displays favorable complexation kinetics and in vivo stability is required for effective RIT. New bifunctional ligands 3p-C-DE4TA and 3p-C-NE3TA for potential use in RIT were efficiently prepared by the synthetic route based on regiospecific ring opening of aziridinium ions with prealkylated triaza- or tetraaza-backboned macrocycles. The new bifunctional ligands 3p-C-DE4TA and 3p-C-NE3TA along with the known bimodal ligands 3p-C-NETA and 3p-C-DEPA were comparatively evaluated for potential use in targeted radiotherapy using β-emitting radionuclides 90Y and 177Lu. The bifunctional ligands were evaluated for radiolabeling kinetics with 90Y and 177Lu, and the corresponding 90Y or 177Lu-radiolabeled complexes were studied for in vitro stability in human serum and in vivo biodistribution in mice. The results of the comparative complexation kinetic and stability studies indicate that size of macrocyclic cavity, ligand denticity, and bimodality of donor groups have a substantial impact on complexation of the bifunctional ligands with the radiolanthanides. The new promising bifunctional chelates in the DE4TA and NE3TA series were rapid in binding 90Y and 177Lu, and the corresponding 90Y- and 177Lu-radiolabeled complexes remained inert in human serum or in mice. The in vitro and in vivo data show that 3p-C-DE4TA and 3p-C-NE3TA are promising bifunctional ligands for targeted radiotherapy applications of 90Y and 177Lu. PMID:25648683

  20. Tools for ligand validation in Coot

    PubMed Central

    Emsley, Paul

    2017-01-01

    Coot is a molecular-graphics program primarily aimed at model building using X-ray data. Recently, tools for the manipulation and representation of ligands have been introduced. Here, these new tools for ligand validation and comparison are described. Ligands in the wwPDB have been scored by density-fit, distortion and atom-clash metrics. The distributions of these scores can be used to assess the relative merits of the particular ligand in the protein–ligand complex of interest by means of ‘sliders’ akin to those now available for each accession code on the wwPDB websites. PMID:28291755

  1. Thermodynamics and kinetics of protein folding: an evolutionary perspective.

    PubMed

    Demetrius, Lloyd

    2002-08-07

    This article appeals to an evolutionary model which postulates that primordial proteins were described by small polypeptide chains which (i) lack disulfide bridges, and (ii) display slow folding rates with multi-state kinetics, to determine relations between structural properties of proteins and their folding kinetics. We parameterize the energy landscape of proteins in terms of thermodynamic activation variables. The model studies evolutionary changes in these thermodynamic parameters, and we invoke relations between these activation variables and structural properties of the protein to predict the following correspondence between protein structure and folding kinetics. 1. Proteins with inter- and intra-chain disulfide bridges: large variability in both folding rates and stability of intermediates, multi-state kinetics. 2. Proteins which lack inter and intra-chain disulfide bridges. 2.1 Single-domain chains: fast folding rates; unstable intermediates; two-state kinetics. 2.2 Multi-domain monomers: intermediate rates; metastable intermediates; multi-state kinetics. 2.3 Multi-domain oligomers: slow rates; metastable intermediates; multi-state kinetics. The evolutionary model thus provides a kinetic characterization of one important subfamily of proteins which we describe by the following properties: Folding dynamics of single-domain proteins which lack disulfide bridges are described by two-state kinetics. Folding rate of this class of proteins is positively correlated with the thermodynamic stability of the folded state.

  2. Bivalent kinetic binding model to surface plasmon resonance studies of antigen-antibody displacement reactions.

    PubMed

    Gelinsky-Wersing, Dagmar; Wersing, Wolfram; Pompe, Wolfgang

    2017-02-01

    Molecular and functional analysis of small molecule binding to protein can provoke insights into cellular signaling and regulatory systems as well as facilitate pharmaceutical drug discovery. In label free small molecule detection the displacement assay format can be applied. This is beneficial because displacement of high molecular weight receptors is detected instead of low molecular weight ligand as in classical binding analysis. Thus, detection limit is potentially lowered. Using the influenza haemagglutinin (HA) peptide binding to mono or bivalent anti-haemagglutinin peptide antibody displacement assay formats could be established. The exact time resolved analysis of binding and dissolution of ligand HA and anti-Haemagglutinin peptide antibody was achieved with surface plasmon resonance (SPR) spectroscopy. Mathematical models could be developed from kinetic equations of ligand binding to mono or bivalent antibodies. With this, an accurate simulation of the SPR results was reached. The simulation plot had to be exactly adjusted to the SPR results to determine all kinetic rate constants defining ligand and receptor binding kinetics. Large variations in receptor concentration gave almost identical rate constants in binding. It became obvious that rebinding is in any case not necessary to understand the binding kinetics of our model system HA/anti-HA. Maximum decline of SPR response could be used to determine ligand concentrations in analyte.

  3. Ligand identification using electron-density mapcorrelations

    SciTech Connect

    Terwilliger, Thomas C.; Adams, Paul D.; Moriarty, Nigel W.; Cohn,Judith D.

    2006-12-01

    A procedure for the identification of ligands bound incrystal structuresof macromolecules is described. Two characteristics ofthe density corresponding to a ligand are used in the identificationprocedure. One is the correlation of the ligand density with each of aset of test ligands after optimization of the fit of that ligand to thedensity. The other is the correlation of a fingerprint of the densitywith the fingerprint of model density for each possible ligand. Thefingerprints consist of an ordered list of correlations of each the testligands with the density. The two characteristics are scored using aZ-score approach in which the correlations are normalized to the mean andstandard deviation of correlations found for a variety of mismatchedligand-density pairs, so that the Z scores are related to the probabilityof observing a particular value of the correlation by chance. Theprocedure was tested with a set of 200 of the most commonly found ligandsin the Protein Data Bank, collectively representing 57 percent of allligands in the Protein Data Bank. Using a combination of these twocharacteristics of ligand density, ranked lists of ligand identificationswere made for representative (F-o-F-c) exp(i phi(c)) difference densityfrom entries in the Protein Data Bank. In 48 percent of the 200 cases,the correct ligand was at the top of the ranked list of ligands. Thisapproach may be useful in identification of unknown ligands in newmacromolecular structures as well as in the identification of whichligands in a mixture have bound to a macromolecule.

  4. NKG2D ligands as therapeutic targets

    PubMed Central

    Spear, Paul; Wu, Ming-Ru; Sentman, Marie-Louise; Sentman, Charles L.

    2013-01-01

    The Natural Killer Group 2D (NKG2D) receptor plays an important role in protecting the host from infections and cancer. By recognizing ligands induced on infected or tumor cells, NKG2D modulates lymphocyte activation and promotes immunity to eliminate ligand-expressing cells. Because these ligands are not widely expressed on healthy adult tissue, NKG2D ligands may present a useful target for immunotherapeutic approaches in cancer. Novel therapies targeting NKG2D ligands for the treatment of cancer have shown preclinical success and are poised to enter into clinical trials. In this review, the NKG2D receptor and its ligands are discussed in the context of cancer, infection, and autoimmunity. In addition, therapies targeting NKG2D ligands in cancer are also reviewed. PMID:23833565

  5. Preparation of poly(ethylene glycol) protected nanoparticles with variable bioconjugate ligand density.

    PubMed

    Gindy, Marian E; Ji, Shengxiang; Hoye, Thomas R; Panagiotopoulos, Athanassios Z; Prud'homme, Robert K

    2008-10-01

    Maleimide-functional poly(ethylene glycol)-b-poly(epsilon-caprolactone) nanoparticles (NPs) were prepared via the Flash NanoPrecipitation technique. Subsequent reaction with a model ligand, bovine serum albumin (BSA), was conducted using thiol-maleimide conjugation. Reaction of up to 22% of NP surface maleimide-PEG tethers was obtained, with the percent conversion being essentially independent of the ratio of maleimide-PEG to methyl-PEG over the range 30-100%, respectively. At the highest surface coverage, BSA is calculated to essentially cover the NP surface area. Reaction parameters (reaction order and docking constant) describing the extent of ligand conjugation were determined. The reaction order is applicable to the conjugation of ligands presenting free thiol functionalities, while the value of the docking constant is ligand-dependent and accounts for physical and dynamic properties of the ligand-PEG interaction. Jointly, the particle formation process, using block copolymer-directed kinetically controlled assembly and surface functionalization represent a versatile new platform for the preparation of bioconjugated NPs with accurate control of ligand density and minimal processing steps.

  6. Cyclic voltammetry of fast conducting electrocatalytic films.

    PubMed

    Costentin, Cyrille; Savéant, Jean-Michel

    2015-07-15

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

  7. Are superhalogens without halogen ligand capable of transcending traditional halogen-based superhalogens? Ab initio case study of binuclear anions based on pseudohalogen ligand

    SciTech Connect

    Li, Jin-Feng; Sun, Yin-Yin; Li, Miao-Miao; Li, Jian-Li; Yin, Bing; Bai, Hongcun

    2015-06-15

    The superhalogen properties of polynuclear structures without halogen ligand are theoretically explored here for several [M{sub 2}(CN){sub 5}]{sup −1} (M =  Ca, Be) clusters. At CCSD(T) level, these clusters have been confirmed to be superhalogens due to their high vertical electron detachment energies (VDE). The largest one is 9.70 eV for [Ca{sub 2}(CN){sub 5}]{sup −1} which is even higher than those of corresponding traditional structures based on fluorine or chlorine ligands. Therefore the superhalogens stronger than the traditional halogen-based structures could be realized by ligands other than halogen atoms. Compared with CCSD(T), outer valence Green’s function (OVGF) method either overestimates or underestimates the VDEs for different structures while MP2 results are generally consistent in the aspect of relative values. The extra electrons of the highest VDE anions here aggregate on the bridging CN units with non-negligible distribution occurring on other CN units too. These two features lower both the potential and kinetic energies of the extra electron respectively and thus lead to high VDE. Besides superhalogen properties, the structures, relative stabilities and thermodynamic stabilities with respect to the detachment of cyanide ligand were also investigated. The sum of these results identifies the potential of polynuclear structures with pseudohalogen ligand as suitable candidates with enhanced superhalogens properties.

  8. Kinetic theory for interacting Luttinger liquids

    NASA Astrophysics Data System (ADS)

    Buchhold, Michael; Diehl, Sebastian

    2015-10-01

    We derive a closed set of equations for the kinetics and non-equilibrium dynamics of interacting Luttinger Liquids with cubic resonant interactions. In the presence of these interactions, the Luttinger phonons become dressed but still well defined quasi-particles, characterized by a life-time much larger then the inverse energy. This enables the separation of forward time dynamics and relative time dynamics into slow and fast dynamics and justifies the so-called Wigner approximation, which can be seen as a "local-time approximation" for the relative dynamics. Applying field theoretical methods in the Keldysh framework, i.e. kinetic and Dyson-Schwinger equations, we derive a closed set of dynamic equations, describing the kinetics of normal and anomalous phonon densities, the phonon self-energy and vertex corrections for a Gaussian non-equilibrium initial state. In the limit of low phonon densities, the results from self-consistent Born approximation are recaptured, including Andreev's scaling solution for the quasi-particle life-time in a thermal state. As an application, we compute the relaxation of an excited state to its thermal equilibrium. While the intermediate time dynamics displays exponentially fast relaxation, the last stages of thermalization are governed by algebraic laws. This can be traced back to the importance of energy and momentum conservation at the longest times, which gives rise to dynamical slow modes.

  9. Protein Fibrillation Lag Times During Kinetic Inhibition

    PubMed Central

    Pagano, Rodrigo S.; López Medus, Máximo; Gómez, Gabriela E.; Couto, Paula M.; Labanda, María S.; Landolfo, Lucas; D’Alessio, Cecilia; Caramelo, Julio J.

    2014-01-01

    Protein aggregation is linked to more than 30 human pathologies, including Alzheimer’s and Parkinson’s diseases. Since small oligomers that form at the beginning of the fibrillation process probably are the most toxic elements, therapeutic strategies involving fibril fragmentation could be detrimental. An alternative approach, named kinetic inhibition, aims to prevent fibril formation by using small ligands that stabilize the parent protein. The factors that govern fibrillation lag times during kinetic inhibition are largely unknown, notwithstanding their importance for designing effective long-term therapies. Inhibitor-bound species are not likely to be incorporated into the core of mature fibrils, although their presence could alter the kinetics of the fibrillation process. For instance, inhibitor-bound species may act as capping elements that impair the nucleation process and/or fibril growth. Here, we address this issue by studying the effect of two natural inhibitors on the fibrillation behavior of lysozyme at neutral pH. We analyzed a set of 79 fibrillation curves obtained in lysozyme alone and a set of 37 obtained in the presence of inhibitors. We calculated the concentrations of the relevant species at the beginning of the curves using the inhibitor-binding constants measured under the same experimental conditions. We found that inhibitor-bound protein species do not affect fibrillation onset times, which are mainly determined by the concentration of unbound protein species present in equilibrium. In this system, knowledge of the fibrillation kinetics and inhibitor affinities suffices to predict the effect of kinetic inhibitors on fibrillation lag times. In addition, we developed a new methodology to better estimate fibrillation lag times from experimental curves. PMID:25099810

  10. Gyrokinetic particle simulation of fast-electron driven beta-induced Aflvén eigenmode

    NASA Astrophysics Data System (ADS)

    Cheng, Junyi; Zhang, Wenlu; Lin, Zhihong; Holod, Ihor; Li, Ding; Chen, Yang; Cao, Jintao

    2016-05-01

    The fast-electron driven beta-induced Alfvén eigenmode (e-BAE) in toroidal plasmas is investigated for the first time using global gyrokinetic particle simulations, where the fast electron is described by the drift kinetic equation. The simulation shows that the e-BAE propagates in the fast electron diamagnetic direction and its polarization is close to an ideal MHD mode. The phase space structure shows that only the fast electron processional resonance is responsible for the e-BAE excitations while fast-ion driven BAE can be excited through all the channels, including transit, bounce, and processional resonance.

  11. Kinetic barriers to the folding of horse cytochrome C in the reduced state.

    PubMed

    Bhuyan, Abani K; Kumar, Rajesh

    2002-10-22

    To determine the kinetic barrier in the folding of horse cytochrome c, a CO-liganded derivative of cytochrome c, called carbonmonoxycytochrome c, has been prepared by exploiting the thermodynamic reversibility of ferrocytochrome c unfolding induced by guanidinium hydrochloride (GdnHCl), pH 7. The CO binding properties of unfolded ferrocytochrome c, studied by 13C NMR and optical spectroscopy, are remarkably similar to those of native myoglobin and isolated chains of human hemoglobin. Equilibrium unfolding transitions of ferrocytochrome c in the presence and the absence of CO observed by both excitation energy transfer from the lone tryptophan to the ferrous heme and far-UV circular dichroism (CD) indicate no accumulation of structural intermediates to a detectable level. Values of thermodynamic parameters obtained by two-state analysis of fluorescence transitions are DeltaG(H2O) = 11.65(+/-1.13) kcal x mol(-1) and C(m) = 3.9(+/-0.1) M GdnHCl in the presence of CO, and DeltaG(H2O)=19.3(+/-0.5) kcal x mol(-1) and C(m) = 5.1(+/-0.1) M GdnHCl in the absence of CO, indicating destabilization of ferrocytochrome c by approximately 7.65 kcal x mol(-1) due to CO binding. The native states of ferrocytochrome c and carbonmonoxycytochrome c are nearly identical in terms of structure and conformation except for the Fe2+-M80 --> Fe2+-CO replacement. Folding and unfolding kinetics as a function of GdnHCl, studied by stopped-flow fluorescence, are significantly different for the two proteins. Both refold fast, but carbonmonoxycytochrome c refolds 2-fold faster (tau = 1092 micros at 10 degrees C) than ferrocytochrome c. Linear extrapolation of the folding rates to the ordinate of the chevron plot projects this value of tau to 407 micros. The unfolding rate of the former in water, estimated by extrapolation, is faster by more than 10 orders of magnitude. Significant differences are also observed in rate-denaturant gradients in the chevron. Formation and disruption of the Fe2+-M80

  12. Nonisothermal Analysis of Solution Kinetics by Spreadsheet Simulation

    ERIC Educational Resources Information Center

    de Levie, Robert

    2012-01-01

    A fast and generally applicable alternative solution to the problem of determining the useful shelf life of medicinal solutions is described. It illustrates the power and convenience of the combination of numerical simulation and nonlinear least squares with a practical pharmaceutical application of chemical kinetics and thermodynamics, validated…

  13. Advanced plastic scintillators for fast neutron discrimination

    SciTech Connect

    Feng, Patrick L; Anstey, Mitchell; Doty, F. Patrick; Mengesha, Wondwosen

    2014-09-01

    The present work addresses the need for solid-state, fast neutron discriminating scintillators that possess higher light yields and faster decay kinetics than existing organic scintillators. These respective attributes are of critical importance for improving the gamma-rejection capabilities and increasing the neutron discrimination performance under high-rate conditions. Two key applications that will benefit from these improvements include large-volume passive detection scenarios as well as active interrogation search for special nuclear materials. Molecular design principles were employed throughout this work, resulting in synthetically tailored materials that possess the targeted scintillation properties.

  14. Reusable fast opening switch

    DOEpatents

    Van Devender, J.P.; Emin, D.

    1983-12-21

    A reusable fast opening switch for transferring energy, in the form of a high power pulse, from an electromagnetic storage device such as an inductor into a load. The switch is efficient, compact, fast and reusable. The switch comprises a ferromagnetic semiconductor which undergoes a fast transition between conductive and metallic states at a critical temperature and which undergoes the transition without a phase change in its crystal structure. A semiconductor such as europium rich europhous oxide, which undergoes a conductor to insulator transition when it is joule heated from its conductor state, can be used to form the switch.

  15. Reusable fast opening switch

    DOEpatents

    Van Devender, John P.; Emin, David

    1986-01-01

    A reusable fast opening switch for transferring energy, in the form of a high power pulse, from an electromagnetic storage device such as an inductor into a load. The switch is efficient, compact, fast and reusable. The switch comprises a ferromagnetic semiconductor which undergoes a fast transition between conductive and insulating states at a critical temperature and which undergoes the transition without a phase change in its crystal structure. A semiconductor such as europium rich europhous oxide, which undergoes a conductor to insulator transition when it is joule heated from its conductor state, can be used to form the switch.

  16. Fast Breeder Reactor studies

    SciTech Connect

    Till, C.E.; Chang, Y.I.; Kittel, J.H.; Fauske, H.K.; Lineberry, M.J.; Stevenson, M.G.; Amundson, P.I.; Dance, K.D.

    1980-07-01

    This report is a compilation of Fast Breeder Reactor (FBR) resource documents prepared to provide the technical basis for the US contribution to the International Nuclear Fuel Cycle Evaluation. The eight separate parts deal with the alternative fast breeder reactor fuel cycles in terms of energy demand, resource base, technical potential and current status, safety, proliferation resistance, deployment, and nuclear safeguards. An Annex compares the cost of decommissioning light-water and fast breeder reactors. Separate abstracts are included for each of the parts.

  17. FAST Construction Progress

    NASA Astrophysics Data System (ADS)

    Nan, R. D.; Zhang, H. Y.; Zhang, Y.; Yang, L.; Cai, W. J.; Liu, N.; Xie, J. T.; Zhang, S. X.

    2016-11-01

    The Five-hundred-meter Aperture Spherical radio Telescope (FAST) is a Chinese mega-science project to build the largest single dish radio telescope in the world. A unique karst depression in Guizhou province has been selected as the site to build an active reflector radio telescope with a diameter of 500 m and three outstanding aspects, which enables FAST to have a large sky coverage and the ability of observing astronomical targets with a high precision. Chinese Academy of Sciences and Guizhou province are in charge of FAST construction. The first light of the telescope was expected on September 25, 2016.

  18. Fast magnetic reconnection with large guide fields

    DOE PAGES

    Stanier, A.; Simakov, Andrei N.; Chacón, L.; ...

    2015-01-09

    We domonstrate, using two-fluid simulations, that low-βmagnetic reconnection remains fast, regardless of the presence of fast dispersive waves, which have been previously suggested to play a critical role. In order to understand these results, a discrete model is constructed that offers scaling relationships for the reconnection rate and dissipation region (DR) thickness in terms of the upstream magnetic field and DR length. Moreover, we verify these scalings numerically and show how the DR self-adjusts to process magnetic flux at the same rate that it is supplied to a larger region where two-fluid effects become important. The rate is therefore independentmore » of the DR physics and is in good agreement with kinetic results.« less

  19. Novel Ligands for a Purine Riboswitch Discovered by RNA-Ligand Docking

    PubMed Central

    Daldrop, Peter; Reyes, Francis E.; Robinson, David A.; Hammond, Colin M.; Lilley, David M.; Batey, Robert T.; Brenk, Ruth

    2011-01-01

    Summary The increasing number of RNA crystal structures enables a structure-based approach to the discovery of new RNA-binding ligands. To develop the poorly explored area of RNA-ligand docking, we have conducted a virtual screening exercise for a purine riboswitch to probe the strengths and weaknesses of RNA-ligand docking. Using a standard protein-ligand docking program with only minor modifications, four new ligands with binding affinities in the micromolar range were identified, including two compounds based on molecular scaffolds not resembling known ligands. RNA-ligand docking performed comparably to protein-ligand docking indicating that this approach is a promising option to explore the wealth of RNA structures for structure-based ligand design. PMID:21439477

  20. Metabotropic glutamate receptor ligands as potential therapeutics for addiction

    PubMed Central

    Olive, M. F.

    2009-01-01

    There is now compelling evidence that the excitatory amino acid neurotransmitter glutamate plays a pivotal role in drug addiction and alcoholism. As a result, there has been increasing interest in developing glutamate-based therapies for the treatment of addictive disorders. Receptors for glutamate are primarily divided into two classes: ionotropic glutamate receptors (iGluRs) that mediate fast excitatory glutamate transmission, and metabotropic glutamate receptors (mGluRs), which are G-protein coupled receptors that mediate slower, modulatory glutamate transmission. Most iGluR antagonists, while showing some efficacy in animal models of addiction, exhibit serious side effects when tested in humans. mGluR ligands, on the other hand, which have been advanced to testing in clinical trials for various medical conditions, have demonstrated the ability to reduce drug reward, reinforcement, and relapse-like behaviors in animal studies. mGluR ligands that have been shown to be primarily effective are Group I (mGluR1 and mGluR5) negative allosteric modulators and Group II (mGluR2 and mGluR3) orthosteric presynaptic autoreceptor agonists. In this review, we will summarize findings from animal studies suggesting that these mGluR ligands may be of potential benefit in reducing on-going drug self-administration and may aid in the prevention of relapse. The neuroanatomical distribution of mGluR1, mGluR2/3, and mGluR5 receptors and the pharmacological properties of Group I negative allosteric modulators and Group II agonists will also be overviewed. Finally, we will discuss the current status of mGluR ligands in human clinical trials. PMID:19630739

  1. Tellurium-containing polymer micelles: competitive-ligand-regulated coordination responsive systems.

    PubMed

    Cao, Wei; Gu, Yuwei; Meineck, Myriam; Li, Tianyu; Xu, Huaping

    2014-04-02

    Nanomaterials capable of achieving tunable cargo release kinetics are of significance in a fundamental sense and various biological or medical applications. We report a competitive coordination system based on a novel tellurium-containing polymer and its ligand-regulated release manners. Tellurium was introduced to water-soluble polymers for the first time as drug delivery vehicles. The coordination chemistry between platinum and tellurium was designed to enable the load of platinum-based drugs. Through the competitive coordination of biomolecules, the drugs could be released in a controlled manner. Furthermore, the release kinetics could be modulated by the competitive ligands involved due to their different coordination ability. This tellurium-containing polymer may enrich the family of delivery systems and provide a new platform for future biomedical nanotechnologies.

  2. Syntheses, X-ray crystal structures, and ligand substitution kinetics of the carbon-bonded chromium(III) complexes trans-(CrR(acac)/sub 2/(L)) (R = CH/sub 2/Cl, CHCl/sub 2/; L = H/sub 2/O, CH/sub 3/OH, pyridine)

    SciTech Connect

    Ogino, H.; Shoji, M.; Abe, Y.; Shimura, M.; Shimoi, M.

    1987-07-29

    The alkylchromium(III) complexes trans-(CrR(acac)/sub 2/(H/sub 2/O)) (a) (R = CHCl/sub 2/, CH/sub 2/Cl; Hacac = 2,4-pentanedione) were prepared by the reaction of (CrR(H/sub 2/O)/sub 5/)/sup 2 +/ with Hacac and triethylamine. Synthetic methods reported previously for (CrR(H/sub 2/O)/sub 5/)/sup 2 +/ (R = CHCl/sub 2/, CH/sub 2/Cl) were improved to give approximately quantitative yields. The complexes trans-(CrR(acac)/sub 2/L) (L = CH/sub 3/OH, pyridine) were derived by replacing a coordinated water molecule in a with L. The X-ray crystal structure analyses of trans-(CrR(acac)/sub 2/(py)) (R = CHCl/sub 2/, CH/sub 2/Cl) have been performed. The carbon-bonded ligands CHCl/sub 2/ and CH/sub 2/Cl lengthen specifically the Cr-N bond trans to the Cr-C bond in trans-(Cr(CHCl/sub 2/)(acac)/sub 2/(py)) (b; Cr-N = 2.154 (7) A) as well as in trans-(Cr-(CH/sub 2/Cl)(acac)/sub 2/(py)) (c; Cr-N = 2.201(4) A). The elongation of the Cr-N bonds in b and c is reflected in substantial labilization of the ligand substitution reactions at the position trans to R: trans-(CrR(acac)/sub 2/(CH/sub 3/OH)) + L reversible trans-(CrR(acac)/sub 2/L) + CH/sub 3/OH. The rate constants (M/sup -1/ s/sup -1/) at 25 /sup 0/C in methanol for the formation of trans-(CrR(acac)/sub 2/L) are 85 +/- 2 (R = CHCl/sub 2/, L = py), 98 +/- 1 (R = CHCl/sub 2/, L = 4-methylpyridine), 57 +/- 1 (R = CHCl/sub 2/, L = isonicotinamide), and (1.2 +/- 0.5) x 10/sup 3/ (R = CH/sub 2/Cl, L = py), and the rate constants (s/sup -1/) for the backward reaction at 25 /sup 0/C are 15 +/- 1 (R = CHCl/sub 2/, L = py), 11 +/- 1 (R = CHCl/sub 2/, L = 4-methylpyridine), 33 +/- 1 (R = CHCl/sub 2/, L = isonicotinamide), and (5 +/- 2) x 10/sup 2/ (R = CH/sub 2/Cl, L = py).

  3. Ligand placement based on prior structures: the guided ligand-replacement method

    SciTech Connect

    Klei, Herbert E.; Moriarty, Nigel W. Echols, Nathaniel; Terwilliger, Thomas C.; Baldwin, Eric T.; Pokross, Matt; Posy, Shana; Adams, Paul D.

    2014-01-01

    A new module, Guided Ligand Replacement (GLR), has been developed in Phenix to increase the ease and success rate of ligand placement when prior protein-ligand complexes are available. The process of iterative structure-based drug design involves the X-ray crystal structure determination of upwards of 100 ligands with the same general scaffold (i.e. chemotype) complexed with very similar, if not identical, protein targets. In conjunction with insights from computational models and assays, this collection of crystal structures is analyzed to improve potency, to achieve better selectivity and to reduce liabilities such as absorption, distribution, metabolism, excretion and toxicology. Current methods for modeling ligands into electron-density maps typically do not utilize information on how similar ligands bound in related structures. Even if the electron density is of sufficient quality and resolution to allow de novo placement, the process can take considerable time as the size, complexity and torsional degrees of freedom of the ligands increase. A new module, Guided Ligand Replacement (GLR), was developed in Phenix to increase the ease and success rate of ligand placement when prior protein–ligand complexes are available. At the heart of GLR is an algorithm based on graph theory that associates atoms in the target ligand with analogous atoms in the reference ligand. Based on this correspondence, a set of coordinates is generated for the target ligand. GLR is especially useful in two situations: (i) modeling a series of large, flexible, complicated or macrocyclic ligands in successive structures and (ii) modeling ligands as part of a refinement pipeline that can automatically select a reference structure. Even in those cases for which no reference structure is available, if there are multiple copies of the bound ligand per asymmetric unit GLR offers an efficient way to complete the model after the first ligand has been placed. In all of these applications, GLR

  4. Utilization of extracellular information before ligand-receptor binding reaches equilibrium expands and shifts the input dynamic range

    PubMed Central

    Ventura, Alejandra C.; Bush, Alan; Vasen, Gustavo; Goldín, Matías A.; Burkinshaw, Brianne; Bhattacharjee, Nirveek; Folch, Albert; Brent, Roger; Chernomoretz, Ariel; Colman-Lerner, Alejandro

    2014-01-01

    Cell signaling systems sense and respond to ligands that bind cell surface receptors. These systems often respond to changes in the concentration of extracellular ligand more rapidly than the ligand equilibrates with its receptor. We demonstrate, by modeling and experiment, a general “systems level” mechanism cells use to take advantage of the information present in the early signal, before receptor binding reaches a new steady state. This mechanism, pre-equilibrium sensing and signaling (PRESS), operates in signaling systems in which the kinetics of ligand-receptor binding are slower than the downstream signaling steps, and it typically involves transient activation of a downstream step. In the systems where it operates, PRESS expands and shifts the input dynamic range, allowing cells to make different responses to ligand concentrations so high as to be otherwise indistinguishable. Specifically, we show that PRESS applies to the yeast directional polarization in response to pheromone gradients. Consideration of preexisting kinetic data for ligand-receptor interactions suggests that PRESS operates in many cell signaling systems throughout biology. The same mechanism may also operate at other levels in signaling systems in which a slow activation step couples to a faster downstream step. PMID:25172920

  5. A comparison of various optimization algorithms of protein-ligand docking programs by fitness accuracy.

    PubMed

    Guo, Liyong; Yan, Zhiqiang; Zheng, Xiliang; Hu, Liang; Yang, Yongliang; Wang, Jin

    2014-07-01

    In protein-ligand docking, an optimization algorithm is used to find the best binding pose of a ligand against a protein target. This algorithm plays a vital role in determining the docking accuracy. To evaluate the relative performance of different optimization algorithms and provide guidance for real applications, we performed a comparative study on six efficient optimization algorithms, containing two evolutionary algorithm (EA)-based optimizers (LGA, DockDE) and four particle swarm optimization (PSO)-based optimizers (SODock, varCPSO, varCPSO-ls, FIPSDock), which were implemented into the protein-ligand docking program AutoDock. We unified the objective functions by applying the same scoring function, and built a new fitness accuracy as the evaluation criterion that incorporates optimization accuracy, robustness, and efficiency. The varCPSO and varCPSO-ls algorithms show high efficiency with fast convergence speed. However, their accuracy is not optimal, as they cannot reach very low energies. SODock has the highest accuracy and robustness. In addition, SODock shows good performance in efficiency when optimizing drug-like ligands with less than ten rotatable bonds. FIPSDock shows excellent robustness and is close to SODock in accuracy and efficiency. In general, the four PSO-based algorithms show superior performance than the two EA-based algorithms, especially for highly flexible ligands. Our method can be regarded as a reference for the validation of new optimization algorithms in protein-ligand docking.

  6. Sliding tethered ligands add topological interactions to the toolbox of ligand–receptor design

    PubMed Central

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

    2015-01-01

    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. PMID:26350224

  7. Calculations of distance distributions and probabilities of binding by ligands between parallel plane membranes comprising receptors

    NASA Astrophysics Data System (ADS)

    Plante, Ianik; Devroye, Luc; Cucinotta, Francis A.

    2014-03-01

    Cell communication through biochemical signaling pathways is a key determinant of tissue responses to radiation. Several molecules, such as the transforming growth factor β (TGFβ), are implicated in radiation-induced signaling between cells. Brownian Dynamics (BD) algorithms have recently been used to simulate the interaction of ligands with receptors and to elucidate signal transduction and autocrine loops in ligand-receptors systems. In this paper, we discuss the simulation of particle diffusion and binding kinetics in a space bounded by two parallel plane membranes, using an exact algorithm to sample the propagator (Green’s function) of a particle located between 2 membranes. We also show that the simulation results are independent of the number of time steps used, in accordance with time discretization equations. These simulations could be used to simulate the motion and binding of ligand molecules in a cell culture, and possibly in neuronal synapses.

  8. Simple phosphinate ligands access zinc clusters identified in the synthesis of zinc oxide nanoparticles

    NASA Astrophysics Data System (ADS)

    Pike, Sebastian D.; White, Edward R.; Shaffer, Milo S. P.; Williams, Charlotte K.

    2016-10-01

    The bottom-up synthesis of ligand-stabilized functional nanoparticles from molecular precursors is widely applied but is difficult to study mechanistically. Here we use 31P NMR spectroscopy to follow the trajectory of phosphinate ligands during the synthesis of a range of ligated zinc oxo clusters, containing 4, 6 and 11 zinc atoms. Using an organometallic route, the clusters interconvert rapidly and self-assemble in solution based on thermodynamic equilibria rather than nucleation kinetics. These clusters are also identified in situ during the synthesis of phosphinate-capped zinc oxide nanoparticles. Unexpectedly, the ligand is sequestered to a stable Zn11 cluster during the majority of the synthesis and only becomes coordinated to the nanoparticle surface, in the final step. In addition to a versatile and accessible route to (optionally doped) zinc clusters, the findings provide an understanding of the role of well-defined molecular precursors during the synthesis of small (2-4 nm) nanoparticles.

  9. FAST joins Breakthrough programme

    NASA Astrophysics Data System (ADS)

    Banks, Michael

    2016-11-01

    The 180m Five-hundred-meter Aperture Spherical radio Telescope (FAST) - the world's largest single-aperture radio receiver - has become part of the Breakthrough Listen programme, which launched in July 2015 to look for intelligent life beyond Earth.

  10. Pneumococcal Disease Fast Facts

    MedlinePlus

    ... Home About Pneumococcal Types of Infection Risk Factors & Transmission Symptoms & Complications Diagnosis & Treatment Prevention Photos Fast Facts Pneumococcal Vaccination For Clinicians Streptococcus pneumoniae Transmission Clinical Features Risk Factors Diagnosis & Management Prevention For ...

  11. Calorie count - Fast food

    MedlinePlus

    ... count - fast food FOOD ITEM SERVING SIZE CALORIES Breakfast Foods Dunkin Donuts Egg White Veggie Wrap 1 ... Cheese Biscuit Sandwich 1 sandwich 510 BK Ultimate Breakfast Platter 1 platter 1190 McDonalds Fruit 'n Yogurt ...

  12. Caged Naloxone Reveals Opioid Signaling Deactivation Kinetics

    PubMed Central

    Banghart, Matthew R.; Shah, Ruchir C.; Lavis, Luke D.

    2013-01-01

    The spatiotemporal dynamics of opioid signaling in the brain remain poorly defined. Photoactivatable opioid ligands provide a means to quantitatively measure these dynamics and their underlying mechanisms in brain tissue. Although activation kinetics can be assessed using caged agonists, deactivation kinetics are obscured by slow clearance of agonist in tissue. To reveal deactivation kinetics of opioid signaling we developed a caged competitive antagonist that can be quickly photoreleased in sufficient concentrations to render agonist dissociation effectively irreversible. Carboxynitroveratryl-naloxone (CNV-NLX), a caged analog of the competitive opioid antagonist NLX, was readily synthesized from commercially available NLX in good yield and found to be devoid of antagonist activity at heterologously expressed opioid receptors. Photolysis in slices of rat locus coeruleus produced a rapid inhibition of the ionic currents evoked by multiple agonists of the μ-opioid receptor (MOR), but not of α-adrenergic receptors, which activate the same pool of ion channels. Using the high-affinity peptide agonist dermorphin, we established conditions under which light-driven deactivation rates are independent of agonist concentration and thus intrinsic to the agonist-receptor complex. Under these conditions, some MOR agonists yielded deactivation rates that are limited by G protein signaling, whereas others appeared limited by agonist dissociation. Therefore, the choice of agonist determines which feature of receptor signaling is unmasked by CNV-NLX photolysis. PMID:23960100

  13. Ultrafast Spectroscopy Evidence for Picosecond Ligand Exchange at the Binding Site of a Heme Protein: Heme-Based Sensor YddV.

    PubMed

    Lambry, Jean-Christophe; Stranava, Martin; Lobato, Laura; Martinkova, Marketa; Shimizu, Toru; Liebl, Ursula; Vos, Marten H

    2016-01-07

    An important question for the functioning of heme proteins is whether different ligands present within the protein moiety can readily exchange with heme-bound ligands. Studying the dynamics of the heme domain of the Escherichia coli sensor protein YddV upon dissociation of NO from the ferric heme by ultrafast spectroscopy, we demonstrate that when the hydrophobic leucine residue in the distal heme pocket is mutated to glycine, in a substantial fraction of the protein water replaces NO as an internal ligand in as fast as ∼4 ps. This process, which is near-barrierless and occurs orders of magnitude faster than the corresponding process in myoglobin, corresponds to a ligand swap of NO with a water molecule present in the heme pocket, as corroborated by molecular dynamics simulations. Our findings provide important new insight into ligand exchange in heme proteins that functionally interact with different external ligands.

  14. Discovery with FAST

    NASA Astrophysics Data System (ADS)

    Wilkinson, P.

    2016-02-01

    FAST offers "transformational" performance well-suited to finding new phenomena - one of which might be polarised spectral transients. But discoveries will only be made if "the system" provides its users with the necessary opportunities. In addition to designing in as much observational flexibility as possible, FAST should be operated with a philosophy which maximises its "human bandwidth". This band includes the astronomers of tomorrow - many of whom not have yet started school or even been born.

  15. A universal rule for organic ligand exchange.

    PubMed

    You, Hongjun; Wang, Wenjin; Yang, Shengchun

    2014-11-12

    Most synthetic routes to high-quality nanocrystals with tunable morphologies predominantly employ long hydro-carbon molecules as ligands, which are detrimental for electronic and catalytic applications. Here, a rule is found that the adsorption energy of an organic ligand is related to its carbon-chain length. Using the density functional theory method, the adsorption energies of some commonly used ligand molecules with different carbon-chain lengths are calculated, including carboxylate, hydroxyl, and amine molecules adsorbed on metal or metal oxide crystal surface. The results indicate that the adsorption energy of the ligand molecule with a long carbon chain is weaker than that of a smaller molecule with same functional group. This rule provides a theoretical support for a new kind of ligand exchange method in which large organic ligand molecules can be exchanged by small molecules with same functional group to improve the catalytic properties.

  16. Ligand Migration in the Apolar Tunnel of Cerebratulus lacteus Mini-Hemoglobin*

    PubMed Central

    Pesce, Alessandra; Nardini, Marco; Dewilde, Sylvia; Capece, Luciana; Martí, Marcelo A.; Congia, Sonia; Salter, Mallory D.; Blouin, George C.; Estrin, Darío A.; Ascenzi, Paolo; Moens, Luc; Bolognesi, Martino; Olson, John S.

    2011-01-01

    The large apolar tunnel traversing the mini-hemoglobin from Cerebratulus lacteus (CerHb) has been examined by x-ray crystallography, ligand binding kinetics, and molecular dynamic simulations. The addition of 10 atm of xenon causes loss of diffraction in wild-type (wt) CerHbO2 crystals, but Leu-86(G12)Ala CerHbO2, which has an increased tunnel volume, stably accommodates two discrete xenon atoms: one adjacent to Leu-86(G12) and another near Ala-55(E18). Molecular dynamics simulations of ligand migration in wt CerHb show a low energy pathway through the apolar tunnel when Leu or Ala, but not Phe or Trp, is present at the 86(G12) position. The addition of 10–15 atm of xenon to solutions of wt CerHbCO and L86A CerHbCO causes 2–3-fold increases in the fraction of geminate ligand recombination, indicating that the bound xenon blocks CO escape. This idea was confirmed by L86F and L86W mutations, which cause even larger increases in the fraction of geminate CO rebinding, 2–5-fold decreases in the bimolecular rate constants for ligand entry, and large increases in the computed energy barriers for ligand movement through the apolar tunnel. Both the addition of xenon to the L86A mutant and oxidation of wt CerHb heme iron cause the appearance of an out Gln-44(E7) conformer, in which the amide side chain points out toward the solvent and appears to lower the barrier for ligand escape through the E7 gate. However, the observed kinetics suggest little entry and escape (≤25%) through the E7 pathway, presumably because the in Gln-44(E7) conformer is thermodynamically favored. PMID:21147768

  17. Insights into an original pocket-ligand pair classification: a promising tool for ligand profile prediction.

    PubMed

    Pérot, Stéphanie; Regad, Leslie; Reynès, Christelle; Spérandio, Olivier; Miteva, Maria A; Villoutreix, Bruno O; Camproux, Anne-Claude

    2013-01-01

    Pockets are today at the cornerstones of modern drug discovery projects and at the crossroad of several research fields, from structural biology to mathematical modeling. Being able to predict if a small molecule could bind to one or more protein targets or if a protein could bind to some given ligands is very useful for drug discovery endeavors, anticipation of binding to off- and anti-targets. To date, several studies explore such questions from chemogenomic approach to reverse docking methods. Most of these studies have been performed either from the viewpoint of ligands or targets. However it seems valuable to use information from both ligands and target binding pockets. Hence, we present a multivariate approach relating ligand properties with protein pocket properties from the analysis of known ligand-protein interactions. We explored and optimized the pocket-ligand pair space by combining pocket and ligand descriptors using Principal Component Analysis and developed a classification engine on this paired space, revealing five main clusters of pocket-ligand pairs sharing specific and similar structural or physico-chemical properties. These pocket-ligand pair clusters highlight correspondences between pocket and ligand topological and physico-chemical properties and capture relevant information with respect to protein-ligand interactions. Based on these pocket-ligand correspondences, a protocol of prediction of clusters sharing similarity in terms of recognition characteristics is developed for a given pocket-ligand complex and gives high performances. It is then extended to cluster prediction for a given pocket in order to acquire knowledge about its expected ligand profile or to cluster prediction for a given ligand in order to acquire knowledge about its expected pocket profile. This prediction approach shows promising results and could contribute to predict some ligand properties critical for binding to a given pocket, and conversely, some key pocket

  18. CB receptor ligands from plants.

    PubMed

    Woelkart, Karin; Salo-Ahen, Outi M H; Bauer, Rudolf

    2008-01-01

    Advances in understanding the physiology and pharmacology of the endogenous cannabinoid system have potentiated the interest of cannabinoid receptors as potential therapeutic targets. Cannabinoids have been shown to modulate a variety of immune cell functions and have therapeutic implications on central nervous system (CNS) inflammation, chronic inflammatory conditions such as arthritis, and may be therapeutically useful in treating autoimmune conditions such as multiple sclerosis. Many of these drug effects occur through cannabinoid receptor signalling mechanisms and the modulation of cytokines and other gene products. Further, endocannabinoids have been found to have many physiological and patho-physiological functions, including mood alteration and analgesia, control of energy balance, gut motility, motor and co-ordination activities, as well as alleviation of neurological, psychiatric and eating disorders. Plants offer a wide range of chemical diversity and have been a growing domain in the search for effective cannabinoid ligands. Cannabis sativa L. with the known plant cannabinoid, Delta(9-)tetrahydrocannabinol (THC) and Echinacea species with the cannabinoid (CB) receptor-binding lipophilic alkamides are the best known herbal cannabimimetics. This review focuses on the state of the art in CB ligands from plants, as well their possible therapeutic and immunomodulatory effects.

  19. Imaging neurotransmitter release kinetics in living cells

    SciTech Connect

    Tan, Weihong; Yeung, E.S.; Haydon, P.G.

    1996-12-31

    A new UV-laser based optical microscope and CCD detection system has been developed to image neurotransmitter in living biological cells. We demonstrate the detection of serotonin that has been taken up into and released from individual living glial cells (astrocytes) based on its native fluorescence. The detection methodology has high sensitivity, low limit of detection and does not require coupling to fluorescence dyes. We have studied serotonin uptake kinetics and its release dynamics in single glial cells. Different regions of a glial cell have taken up different amounts of serotonin with a variety of kinetics. Similarly, different serotonin release mechanisms have been observed in different astrocyte cell regions. The temporal resolution of this detection system is as fast as 50 ms, and the spatial resolution is diffraction limited. We will also report on single enzyme molecule reaction studies and single metal ion detection based on CCD imaging of pL reaction vials formed by micromachining on fused silica.

  20. Kinetics of noradrenaline released by sympathetic nerves.

    PubMed

    Gonon, F; Msghina, M; Stjärne, L

    1993-10-01

    At the skeletal neuromuscular junction the released neurotransmitter, acetylcholine, is eliminated within some milliseconds. This time course is known with great precision through the electrical response of target cells. At the sympathetic neuroeffector junction the fast electrical response is not mediated by noradrenaline but by a cotransmitter: ATP. The slow electrical response and the slow component of smooth muscle contraction are principally mediated by noradrenaline. These responses are two orders of magnitude slower than the electrical response to ATP. Therefore, great uncertainty remains regarding the kinetics of noradrenaline appearance and elimination. Here, the local noradrenaline concentration at the surface of the isolated rat tail artery was electrochemically monitored in real time using a carbon fibre electrode. We have shown that the time course of the neurogenically released noradrenaline is at least one order of magnitude faster than the resulting contraction. The kinetics of noradrenaline inactivation by neuronal reuptake were also precisely measured.

  1. PL-PatchSurfer: A Novel Molecular Local Surface-Based Method for Exploring Protein-Ligand Interactions

    PubMed Central

    Hu, Bingjie; Zhu, Xiaolei; Monroe, Lyman; Bures, Mark G.; Kihara, Daisuke

    2014-01-01

    Structure-based computational methods have been widely used in exploring protein-ligand interactions, including predicting the binding ligands of a given protein based on their structural complementarity. Compared to other protein and ligand representations, the advantages of a surface representation include reduced sensitivity to subtle changes in the pocket and ligand conformation and fast search speed. Here we developed a novel method named PL-PatchSurfer (Protein-Ligand PatchSurfer). PL-PatchSurfer represents the protein binding pocket and the ligand molecular surface as a combination of segmented surface patches. Each patch is characterized by its geometrical shape and the electrostatic potential, which are represented using the 3D Zernike descriptor (3DZD). We first tested PL-PatchSurfer on binding ligand prediction and found it outperformed the pocket-similarity based ligand prediction program. We then optimized the search algorithm of PL-PatchSurfer using the PDBbind dataset. Finally, we explored the utility of applying PL-PatchSurfer to a larger and more diverse dataset and showed that PL-PatchSurfer was able to provide a high early enrichment for most of the targets. To the best of our knowledge, PL-PatchSurfer is the first surface patch-based method that treats ligand complementarity at protein binding sites. We believe that using a surface patch approach to better understand protein-ligand interactions has the potential to significantly enhance the design of new ligands for a wide array of drug-targets. PMID:25167137

  2. Measurement of protein-ligand complex formation.

    PubMed

    Lowe, Peter N; Vaughan, Cara K; Daviter, Tina

    2013-01-01

    Experimental approaches to detect, measure, and quantify protein-ligand binding, along with their theoretical bases, are described. A range of methods for detection of protein-ligand interactions is summarized. Specific protocols are provided for a nonequilibrium procedure pull-down assay, for an equilibrium direct binding method and its modification into a competition-based measurement and for steady-state measurements based on the effects of ligands on enzyme catalysis.

  3. The Kinetics of Formation and Decomposition of Austenite in Relation to Carbide Morphology

    NASA Astrophysics Data System (ADS)

    Alvarenga, Henrique Duarte; Van Steenberge, Nele; Sietsma, Jilt; Terryn, Herman

    2017-02-01

    The effect of the carbide morphology on the kinetics of austenite formation and its decomposition was investigated by a combination of measurements of austenite fraction by dilatometry and metallography. These measurements show that coarse carbide morphology is generated by fast cooling through the early stages of eutectoid transformation, enabling fast precipitation of pro-eutectoid ferrite, followed by slow cooling during the final stages of transformation, during the precipitation of carbides. Additionally, a strong influence of the morphology of carbides on the kinetics of austenite formation is observed. The presence of coarse carbides can determine the rate of austenite formation during intercritical annealing as a result of its slow dissolution kinetics.

  4. Fast repetition rate (FRR) flasher

    DOEpatents

    Kolber, Z.; Falkowski, P.

    1997-02-11

    A fast repetition rate (FRR) flasher is described suitable for high flash photolysis including kinetic chemical and biological analysis. The flasher includes a power supply, a discharge capacitor operably connected to be charged by the power supply, and a flash lamp for producing a series of flashes in response to discharge of the discharge capacitor. A triggering circuit operably connected to the flash lamp initially ionizes the flash lamp. A current switch is operably connected between the flash lamp and the discharge capacitor. The current switch has at least one insulated gate bipolar transistor for switching current that is operable to initiate a controllable discharge of the discharge capacitor through the flash lamp. Control means connected to the current switch for controlling the rate of discharge of the discharge capacitor thereby to effectively keep the flash lamp in an ionized state between successive discharges of the discharge capacitor. Advantageously, the control means is operable to discharge the discharge capacitor at a rate greater than 10,000 Hz and even up to a rate greater than about 250,000 Hz. 14 figs.

  5. Fast repetition rate (FRR) flasher

    DOEpatents

    Kolber, Zbigniew; Falkowski, Paul

    1997-02-11

    A fast repetition rate (FRR) flasher suitable for high flash photolysis including kinetic chemical and biological analysis. The flasher includes a power supply, a discharge capacitor operably connected to be charged by the power supply, and a flash lamp for producing a series of flashes in response to discharge of the discharge capacitor. A triggering circuit operably connected to the flash lamp initially ionizes the flash lamp. A current switch is operably connected between the flash lamp and the discharge capacitor. The current switch has at least one insulated gate bipolar transistor for switching current that is operable to initiate a controllable discharge of the discharge capacitor through the flash lamp. Control means connected to the current switch for controlling the rate of discharge of the discharge capacitor thereby to effectively keep the flash lamp in an ionized state between Successive discharges of the discharge capacitor. Advantageously, the control means is operable to discharge the discharge capacitor at a rate greater than 10,000 Hz and even up to a rate greater than about 250,000 Hz.

  6. Chemical Kinetics Database

    National Institute of Standards and Technology Data Gateway

    SRD 17 NIST Chemical Kinetics Database (Web, free access)   The NIST Chemical Kinetics Database includes essentially all reported kinetics results for thermal gas-phase chemical reactions. The database is designed to be searched for kinetics data based on the specific reactants involved, for reactions resulting in specified products, for all the reactions of a particular species, or for various combinations of these. In addition, the bibliography can be searched by author name or combination of names. The database contains in excess of 38,000 separate reaction records for over 11,700 distinct reactant pairs. These data have been abstracted from over 12,000 papers with literature coverage through early 2000.

  7. A "Stationery" Kinetics Experiment.

    ERIC Educational Resources Information Center

    Hall, L.; Goberdhansingh, A.

    1988-01-01

    Describes a simple redox reaction that occurs between potassium permanganate and oxalic acid that can be used to prepare an interesting disappearing ink for demonstrating kinetics for introductory chemistry. Discusses laboratory procedures and factors that influence disappearance times. (CW)

  8. Thermal kinetic inductance detector

    DOEpatents

    Cecil, Thomas; Gades, Lisa; Miceli, Antonio; Quaranta, Orlando

    2016-12-20

    A microcalorimeter for radiation detection that uses superconducting kinetic inductance resonators as the thermometers. The detector is frequency-multiplexed which enables detector systems with a large number of pixels.

  9. Asymmetric catalysis with chiral ferrocene ligands.

    PubMed

    Dai, Li-Xin; Tu, Tao; You, Shu-Li; Deng, Wei-Ping; Hou, Xue-Long

    2003-09-01

    Chiral ferrocene ligands have been widely used in asymmetric catalysis. The advantages of using ferrocene as a scaffold for chiral ligands are described, particularly those regarding planar chirality, rigid bulkiness, and ease of derivatization. The role of planar chirality in 1,2- and 1,1'-disubstituted ferrocene systems is discussed. By using a bulky ferrocene fragment, novel ferrocene ligands were designed, and high enantioselectivity and regioselectivity were achieved in the allylic substitution reaction of monosubstituted allyl substrates. Using the tunable electronic properties of a diphosphine-oxazoline ferrocenyl ligand, the regioselectivity of the intermolecular asymmetric Heck reaction was also examined.

  10. Kinetics of human sperm acrosomal exocytosis.

    PubMed

    Sosa, C M; Pavarotti, M A; Zanetti, M N; Zoppino, F C M; De Blas, G A; Mayorga, L S

    2015-03-01

    The acrosome reaction is a unique event in the lifespan of sperm characterized by the exocytosis of the acrosomal content and the release of hybrid vesicles formed by patches of the outer acrosomal membrane and the plasma membrane. This unique regulated exocytosis is mediated by essentially the same membrane fusion machinery present in neuroendocrine cells. However, whereas secretion in neuroendocrine cells occurs in less than a second, the acrosome reaction is normally assessed after several minutes of incubation with inducers. In this report, we measured the kinetics of human sperm exocytosis triggered by two stimuli (calcium ionophore and progesterone) by using electron microscopy and three different approaches based on the incorporation of fluorescent Pisum sativum agglutinin into the acrosome upon opening of fusion pores connecting the extracellular medium with the acrosomal lumen. The results with the different methods are consistent with a slow kinetics (t½ = 14 min). We also manipulated the system to measure different steps of the process. We observed that cytosolic calcium increased with a relatively fast kinetics (t½ = 0.1 min). In contrast, the swelling of the acrosomal granule that precedes exocytosis was a slow process (t½ = 13 min). When swelling was completed, the fusion pore opening was fast (t½ = 0.2 min). The results indicate that acrosomal swelling is the slowest step and it determines the kinetics of the acrosome reaction. After the swelling is completed, the efflux of calcium from intracellular stores triggers fusion pores opening and the release of hybrid vesicles in seconds.

  11. Fast Collisional Lipid Transfer Among Polymer-Bounded Nanodiscs

    PubMed Central

    Cuevas Arenas, Rodrigo; Danielczak, Bartholomäus; Martel, Anne; Porcar, Lionel; Breyton, Cécile; Ebel, Christine; Keller, Sandro

    2017-01-01

    Some styrene/maleic acid (SMA) copolymers solubilise membrane lipids and proteins to form polymer-bounded nanodiscs termed SMA/lipid particles (SMALPs). Although SMALPs preserve a lipid-bilayer core, they appear to be more dynamic than other membrane mimics. We used time-resolved Förster resonance energy transfer and small-angle neutron scattering to determine the kinetics and the mechanisms of phospholipid transfer among SMALPs. In contrast with vesicles or protein-bounded nanodiscs, SMALPs exchange lipids not only by monomer diffusion but also by fast collisional transfer. Under typical experimental conditions, lipid exchange occurs within seconds in the case of SMALPs but takes minutes to days in the other bilayer particles. The diffusional and second-order collisional exchange rate constants for SMALPs at 30 °C are kdif = 0.287 s−1 and kcol = 222 M−1s−1, respectively. Together with the fast kinetics, the observed invariability of the rate constants with probe hydrophobicity and the moderate activation enthalpy of ~70 kJ mol−1 imply that lipids exchange through a “hydrocarbon continuum” enabled by the flexible nature of the SMA belt surrounding the lipid-bilayer core. Owing to their fast lipid-exchange kinetics, SMALPs represent highly dynamic equilibrium rather than kinetically trapped membrane mimics, which has important implications for studying protein/lipid interactions in polymer-bounded nanodiscs. PMID:28378790

  12. Fundamentals of enzyme kinetics.

    PubMed

    Seibert, Eleanore; Tracy, Timothy S

    2014-01-01

    This chapter provides a general introduction to the kinetics of enzyme-catalyzed reactions, with a focus on drug-metabolizing enzymes. A prerequisite to understanding enzyme kinetics is having a clear grasp of the meanings of "enzyme" and "catalysis." Catalysts are reagents that can increase the rate of a chemical reaction without being consumed in the reaction. Enzymes are proteins that form a subset of catalysts. These concepts are further explored below.

  13. Incorporation of aqueous reaction and sorption kinetics andbiodegradation into TOUGHREACT

    SciTech Connect

    Xu, Tianfu

    2006-04-17

    The needs for considering aqueous and sorption kinetics and microbiological processes arises in many subsurface problems, such as environmental and acid mine remediation. A general rate expression has been implemented into TOUGHREACT, which considers multiple mechanisms(pathways) and includes multiple product, Monod, and inhibition terms. In this paper, the formulation for incorporating kinetic rates among primary species into the mass balance equations is presented. A batch sulfide oxidation problem is simulated. The resulting concentrations are consistent with simple hand calculations. A 1-D reactive transport problem with kinetic biodegradation and sorption was investigated, which models the processes when a pulse of water containing NTA (nitrylotriacetate) and cobalt is injected into a column. The problem has several interacting chemical processes that are common to many environmental problems: biologically-mediated degradation of an organic substrate, bacterial cell growth and decay, metal sorption and aqueous speciation including metal-ligand complexation. The TOUGHREACT simulation results agree very well with those obtained with other simulators.

  14. Integrated ligand based pharmacophore model derived from diverse FAAH covalent ligand classes.

    PubMed

    Shen, Lingling; Huang, Hongwei; Makriyannis, Alexandros; Fisher, Luke S

    2012-12-01

    3D pharmacophore modeling is an important computational methodology for ligand-enzyme binding interactions in drug discovery. More specifically, a consensus pharmacophore model derived from diverse ligands is a key determinant upon which the prediction power of computational models is based for designing novel ligands. In this work, by merging the important pharmacophore features based on four classes of covalent FAAH ligands, and then integrating the exclusion volume spheres derived from the crystal structure, we created for the first time an integrated FAAH pharmacophore model to describe the ligand-enzyme binding interactions. This new integrated FAAH pharmacophore model can correctly predict the covalent ligand binding mode, which correlates with the SAR data. The study is expected to provide insights into novel covalent ligand-FAAH binding interactions, and facilitate the design of covalent ligands against FAAH.

  15. Catalytic and mechanistic studies into the epoxidation of styrenes using manganese complexes of structurally similar polyamine ligands.

    PubMed

    Ilyashenko, Gennadiy; De Faveri, Giorgio; Follier, Thomas; Al-Safadi, Rawan; Motevalli, Majid; Watkinson, Michael

    2014-02-21

    Two structurally similar polyamine ligands (7 and 8) have been prepared, which differ only by the presence of either a secondary or tertiary nitrogen donor within their N5 donor set. The ligands, in combination with iron and manganese salts, have been screened for their efficacy as catalysts for the epoxidation of styrene, using both hydrogen peroxide and peracetic acid as oxidants. Clear differences in activity between the two systems were observed, with 7 proving most effective in the presence of MnSO4 with H2O2, whereas ligand 8 proved to be effective with Mn(OTf)2, MnCl2 and Mn(ClO4)2 using peracetic acid as the oxidant. A Hammett analysis of the initial rate kinetics of the optimal systems, combined with analysis by UV-vis spectroscopy, indicates that the small structural differences in the ligands elicit profound changes in the nature of the active species formed.

  16. Equilibrium and kinetic behavior of Fe(CN)6(3-/4-) and cytochrome c in direct electrochemistry using a film electrode thin-layer transmission cell.

    PubMed

    Dai, Yingrui; Zheng, Yi; Swain, Greg M; Proshlyakov, Denis A

    2011-01-15

    We report on the design and performance of a thin-layer electrochemical cell optimized for use with optically transparent film electrodes in combination with UV/vis and IR transmission spectroscopic measurements. The cell allows for measurements under both aerobic and anaerobic conditions. The direct, unmediated electron transfer, as assessed by the current transient, and the corresponding optical response observed for the Fe(CN)(6)(3-/4-) couple were in good agreement with theoretical predictions for voltammetry and optical absorption by an analyte confined in a thin layer. Chronoamperometric and spectroscopic measurements of Fe(CN)(6)(3-/4-) on gold mesh electrode revealed fast kinetics strongly influenced by the electrolyte concentration. Maximal apparent rates exceeding 2 s(-1) in 1 M KCl were observed optically. The direct kinetic and thermodynamic behavior of cytochrome c was compared with several electrode materials using the cell. The results showed heme ligand-dependent changes in the protein-electrode interactions. Mid-UV/visible spectral changes upon redox transitions in native cytochrome c and its cyanide derivative, as well as dissociation of the ferrous cytochrome c-CN complex, are reported.

  17. Computational protein-ligand docking and virtual drug screening with the AutoDock suite

    PubMed Central

    Forli, Stefano; Huey, Ruth; Pique, Michael E.; Sanner, Michel; Goodsell, David S.; Olson, Arthur J.

    2016-01-01

    Computational docking can be used to predict bound conformations and free energies of binding for small molecule ligands to macromolecular targets. Docking is widely used for the study of biomolecular interactions and mechanisms, and is applied to structure-based drug design. The methods are fast enough to allow virtual screening of ligand libraries containing tens of thousands of compounds. This protocol covers the docking and virtual screening methods provided by the AutoDock suite of programs, including a basic docking of a drug molecule with an anticancer target, a virtual screen of this target with a small ligand library, docking with selective receptor flexibility, active site prediction, and docking with explicit hydration. The entire protocol will require approximately 5 hours. PMID:27077332

  18. Targeting Ligand-Dependent and Ligand-Independent Androgen Receptor Signaling in Prostate Cancer

    DTIC Science & Technology

    2013-10-01

    sub 10nM range efficacy. Our primary objective was to establish a series of compounds blocking the AR ligand-dependent and ligand-independent gene ...of AR driven genes to be more comprehensive and more in line with what is currently known about AR-driven signaling in prostate cancer. We have...developed a robust panel of genes for AR signaling that is reflective of the clinical findings in both ligand dependent and ligand-independent androgen

  19. Fast wave current drive

    NASA Astrophysics Data System (ADS)

    Goree, J.; Ono, M.; Colestock, P.; Horton, R.; McNeill, D.; Park, H.

    1985-07-01

    Experiments on the fast wave in the range of high ion cyclotron harmonics in the ACT-1 device show that current drive is possible with the fast wave just as it is for the lower hybrid wave, except that it is suitable for higher plasma densities. A 140° loop antenna launched the high ion cyclotron harmonic fast wave [ω/Ω=O(10)] into a He+ plasma with ne≂4×1012 cm-3 and B=4.5 kG. Probe and magnetic loop diagnostics and FIR laser scattering confirmed the presence of the fast wave, and the Rogowski loop indicated that the circulating plasma current increased by up to 40A with 1 kW of coupled power, which is comparable to lower hybrid current drive in the same device with the same unidirectional fast electron beam used as the target for the rf. A phased antenna array would be used for FWCD in a tokamak without the E-beam.

  20. Thermal, spectroscopic, and solvent influence studies on mixed-ligand copper(II) complexes containing the bulky ligand: Bis[N-(p-tolyl)imino]acenaphthene.

    PubMed

    El-Ayaan, Usama; Gabr, I M

    2007-05-01

    Four mixed-ligand copper(II) complexes containing the rigid bidentate nitrogen ligand bis[N-(p-tolyl)imino]acenaphthene (abb. p-Tol-BIAN) ligand are reported. These complexes, namely [Cu(p-Tol-BIAN)(2)](ClO(4))(2)1, [Cu(p-Tol-BIAN)(acac)](ClO(4)) 2, [Cu(p-Tol-BIAN)Cl(2)] 3 and [Cu(p-Tol-BIAN)(AcOH)(2)](ClO(4))(2)4 (where acac, acetylacetonate and AcOH, acetic acid) have been prepared and characterized by elemental analysis, spectroscopic, magnetic and molar conductance measurements. ESR spectra suggest a square planar geometry for complexes 1 and 2. In complexes 3 and 4, a distorted tetrahedral arrangement around copper(II) centre was suggested. Solvatochromic behavior of all studied complexes indicates strong solvatochromism of their solutions. The observed solvatochromism is mainly due to the solute-solvent interaction between the chelate cation and the solvent molecules. Thermal properties and decomposition kinetics of all complexes are investigated. The kinetic parameters (E, A, Delta H, Delta S and Delta G) of all thermal decomposition stages have been calculated using the Coats-Redfern and other standard equations.

  1. Determinants of gallbladder kinetics in obesity.

    PubMed

    Mathus-Vliegen, E M H; Van Ierland-Van Leeuwen, M L; Terpstra, A

    2004-01-01

    Obese subjects are at risk of developing gallstones both by being overweight and by reducing their body weight. The aim of the present study was to investigate factors related to disturbances in gallbladder emptying measured by ultrasound. Detailed information about weight loss attempts, age at onset of obesity, parity, presence of menopause, use of contraceptive or hormonal replacement drugs, and phase of menstrual cycle was obtained. Smoking habits, alcohol use, dietary intake, and physical activity were recorded. Body composition and fat distribution were assessed by anthropometry. Blood samples were taken for CCK, lipids, glucose, and insulin. Mean (SD) fasting gallbladder volume was 30.0 (12.6) ml. The residual volume was 12.5 (9.8) ml 90 min after a test meal. CCK levels increased from a basal 1.64 (0.8) pM to a peak value of 2.9 (1.0) pM. Fasting gallbladder volumes were closely related to residual and ejection volumes. Body weight and fasting insulin levels explained 35.2% of the variance in fasting volume, lean body mass and insulin explained 28.1% of the residual volume, and waist circumference 23.6% of the ejection volume. None of the other factors were related to gallbladder emptying. Subjects with the largest fasting gallbladders had the largest residual and least emptying gallbladders, scored the highest in every aspect of body size, composition, and fat distribution, and also had the highest insulin levels. Body weight, lean body mass, central fat distribution, and insulin levels were the main determinants of gallbladder kinetics. Fasting and residual gallbladder volumes were closely related and both determined by obesity and its metabolic complication of hyperinsulinemia.

  2. Cis-interactions between Notch and its ligands block ligand-independent Notch activity

    PubMed Central

    Palmer, William Hunt; Jia, Dongyu; Deng, Wu-Min

    2014-01-01

    The Notch pathway is integrated into numerous developmental processes and therefore is fine-tuned on many levels, including receptor production, endocytosis, and degradation. Notch is further characterized by a twofold relationship with its Delta-Serrate (DSL) ligands, as ligands from opposing cells (trans-ligands) activate Notch, whereas ligands expressed in the same cell (cis-ligands) inhibit signaling. We show that cells without both cis- and trans-ligands can mediate Notch-dependent developmental events during Drosophila oogenesis, indicating ligand-independent Notch activity occurs when the receptor is free of cis- and trans-ligands. Furthermore, cis-ligands can reduce Notch activity in endogenous and genetically induced situations of elevated trans-ligand-independent Notch signaling. We conclude that cis-expressed ligands exert their repressive effect on Notch signaling in cases of trans-ligand-independent activation, and propose a new function of cis-inhibition which buffers cells against accidental Notch activity. DOI: http://dx.doi.org/10.7554/eLife.04415.001 PMID:25486593

  3. A Generalized Kinetic Model for Heterogeneous Gas-Solid Reactions

    SciTech Connect

    Xu, Zhijie; Sun, Xin; Khaleel, Mohammad A.

    2012-08-15

    We present a generalized kinetic model for gas-solid heterogeneous reactions taking place at the interface between two phases. The model studies the reaction kinetics by taking into account the reactions at the interface, as well as the transport process within the product layer. The standard unreacted shrinking core model relies on the assumption of quasi-static diffusion that results in a steady-state concentration profile of gas reactant in the product layer. By relaxing this assumption and resolving the entire problem, general solutions can be obtained for reaction kinetics, including the reaction front velocity and the conversion (volume fraction of reacted solid). The unreacted shrinking core model is shown to be accurate and in agreement with the generalized model for slow reaction (or fast diffusion), low concentration of gas reactant, and small solid size. Otherwise, a generalized kinetic model should be used.

  4. Explicit integration with GPU acceleration for large kinetic networks

    DOE PAGES

    Brock, Benjamin; Belt, Andrew; Billings, Jay Jay; ...

    2015-09-15

    In this study, we demonstrate the first implementation of recently-developed fast explicit kinetic integration algorithms on modern graphics processing unit (GPU) accelerators. Taking as a generic test case a Type Ia supernova explosion with an extremely stiff thermonuclear network having 150 isotopic species and 1604 reactions coupled to hydrodynamics using operator splitting, we demonstrate the capability to solve of order 100 realistic kinetic networks in parallel in the same time that standard implicit methods can solve a single such network on a CPU. In addition, this orders-of-magnitude decrease in computation time for solving systems of realistic kinetic networks implies thatmore » important coupled, multiphysics problems in various scientific and technical fields that were intractable, or could be simulated only with highly schematic kinetic networks, are now computationally feasible.« less

  5. Explicit integration with GPU acceleration for large kinetic networks

    SciTech Connect

    Brock, Benjamin; Belt, Andrew; Billings, Jay Jay; Guidry, Mike W.

    2015-09-15

    In this study, we demonstrate the first implementation of recently-developed fast explicit kinetic integration algorithms on modern graphics processing unit (GPU) accelerators. Taking as a generic test case a Type Ia supernova explosion with an extremely stiff thermonuclear network having 150 isotopic species and 1604 reactions coupled to hydrodynamics using operator splitting, we demonstrate the capability to solve of order 100 realistic kinetic networks in parallel in the same time that standard implicit methods can solve a single such network on a CPU. In addition, this orders-of-magnitude decrease in computation time for solving systems of realistic kinetic networks implies that important coupled, multiphysics problems in various scientific and technical fields that were intractable, or could be simulated only with highly schematic kinetic networks, are now computationally feasible.

  6. Explicit integration with GPU acceleration for large kinetic networks

    SciTech Connect

    Brock, Benjamin; Belt, Andrew; Billings, Jay Jay; Guidry, Mike

    2015-12-01

    We demonstrate the first implementation of recently-developed fast explicit kinetic integration algorithms on modern graphics processing unit (GPU) accelerators. Taking as a generic test case a Type Ia supernova explosion with an extremely stiff thermonuclear network having 150 isotopic species and 1604 reactions coupled to hydrodynamics using operator splitting, we demonstrate the capability to solve of order 100 realistic kinetic networks in parallel in the same time that standard implicit methods can solve a single such network on a CPU. This orders-of-magnitude decrease in computation time for solving systems of realistic kinetic networks implies that important coupled, multiphysics problems in various scientific and technical fields that were intractable, or could be simulated only with highly schematic kinetic networks, are now computationally feasible.

  7. Ligand binding by PDZ domains.

    PubMed

    Chi, Celestine N; Bach, Anders; Strømgaard, Kristian; Gianni, Stefano; Jemth, Per

    2012-01-01

    The postsynaptic density protein-95/disks large/zonula occludens-1 (PDZ) protein domain family is one of the most common protein-protein interaction modules in mammalian cells, with paralogs present in several hundred human proteins. PDZ domains are found in most cell types, but neuronal proteins, for example, are particularly rich in these domains. The general function of PDZ domains is to bring proteins together within the appropriate cellular compartment, thereby facilitating scaffolding, signaling, and trafficking events. The many functions of PDZ domains under normal physiological as well as pathological conditions have been reviewed recently. In this review, we focus on the molecular details of how PDZ domains bind their protein ligands and their potential as drug targets in this context.

  8. Removal of Zinc Form Carbonic Anhydrase: A Kinetics Experiment for Upper-Level Chemistry Laboratories

    ERIC Educational Resources Information Center

    Williams, Kathryn R.; Adhyaru, Bhavin

    2004-01-01

    An experiment on kinetics of deactivation of carbonic anhydrase by removal of zinc is demonstrated. Carbonic anhydrase, the enzyme that catalyzes the interconversion of carbon dioxide and bicarbonate, requires on Zn(II) ion in its active site, and removal of the zinc cofactor by complexion to another ligand leaves the apoenzyme, which is totally…

  9. An Analogy Using Pennies and Dimes to Explain Chemical Kinetics Concepts

    ERIC Educational Resources Information Center

    Cortes-Figueroa, Jose E.; Perez, Wanda I.; Lopez, Jose R.; Moore-Russo, Deborah A.

    2011-01-01

    In this article, the authors present an analogy that uses coins and graphical analysis to teach kinetics concepts and resolve pseudo-first-order rate constants related to transition-metal complexes ligand-solvent exchange reactions. They describe an activity that is directed to upper-division undergraduate and graduate students. The activity…

  10. Catalytic water oxidation by mononuclear Ru complexes with an anionic ancillary ligand.

    PubMed

    Tong, Lianpeng; Inge, A Ken; Duan, Lele; Wang, Lei; Zou, Xiaodong; Sun, Licheng

    2013-03-04

    Mononuclear Ru-based water oxidation catalysts containing anionic ancillary ligands have shown promising catalytic efficiency and intriguing properties. However, their insolubility in water restricts a detailed mechanism investigation. In order to overcome this disadvantage, complexes [Ru(II)(bpc)(bpy)OH2](+) (1(+), bpc = 2,2'-bipyridine-6-carboxylate, bpy = 2,2'-bipyridine) and [Ru(II)(bpc)(pic)3](+) (2(+), pic = 4-picoline) were prepared and fully characterized, which features an anionic tridentate ligand and has enough solubility for spectroscopic study in water. Using Ce(IV) as an electron acceptor, both complexes are able to catalyze O2-evolving reaction with an impressive rate constant. On the basis of the electrochemical and kinetic studies, a water nucleophilic attack pathway was proposed as the dominant catalytic cycle of the catalytic water oxidation by 1(+), within which several intermediates were detected by MS. Meanwhile, an auxiliary pathway that is related to the concentration of Ce(IV) was also revealed. The effect of anionic ligand regarding catalytic water oxidation was discussed explicitly in comparison with previously reported mononuclear Ru catalysts carrying neutral tridentate ligands, for example, 2,2':6',2″-terpyridine (tpy). When 2(+) was oxidized to the trivalent state, one of its picoline ligands dissociated from the Ru center. The rate constant of picoline dissociation was evaluated from time-resolved UV-vis spectra.

  11. Corneal graft rejection occurs despite Fas ligand expression and apoptosis of infiltrating cells

    PubMed Central

    Williams, K A; Standfield, S D; Smith, J R; Coster, D J

    2005-01-01

    Background/aims: Constitutive expression of Fas ligand (CD95L) protects the eye against cell mediated immune responses by inducing apoptosis in infiltrating Fas bearing T cells. This study was designed to examine Fas ligand expression on acutely rejecting rat corneal grafts and to investigate the kinetics of induction of apoptosis in infiltrating leucocytes. Methods: Orthotopic penetrating corneal transplantation was performed between genetically disparate inbred rats. Fas ligand expression and the phenotype of infiltrating leucocytes were examined by immunohistochemistry. Apoptotic nuclei were visualised in sections of normal rat cornea, rejecting allografts, and time matched isografts by terminal deoxynucleotidyl transferase mediated dUTP biotin nick end labelling (TUNEL) and quantified by video image analysis. Staining with Hoechst dye 33258 was used to confirm the presence of apoptotic nuclei. Results: Fas ligand was expressed on corneal endothelial and epithelial cells during acute corneal graft rejection. At all time points examined, including as early as the fifth postoperative day, the cells infiltrating both corneal isografts and allografts were TUNEL positive. By the 15th postoperative day, over 90% of all nuclei, many of which were T cells, were apoptotic. Conclusion: Expression of Fas ligand is not downregulated on the cornea during allograft rejection and infiltrating leucocytes in both isografts and allografts die rapidly in situ. Despite the death of the cells believed to be responsible for rejection, isografts survive indefinitely whereas allografts are irreparably damaged. PMID:15834099

  12. Can ligand addition to soil enhance Cd phytoextraction? A mechanistic model study.

    PubMed

    Lin, Zhongbing; Schneider, André; Nguyen, Christophe; Sterckeman, Thibault

    2014-11-01

    Phytoextraction is a potential method for cleaning Cd-polluted soils. Ligand addition to soil is expected to enhance Cd phytoextraction. However, experimental results show that this addition has contradictory effects on plant Cd uptake. A mechanistic model simulating the reaction kinetics (adsorption on solid phase, complexation in solution), transport (convection, diffusion) and root absorption (symplastic, apoplastic) of Cd and its complexes in soil was developed. This was used to calculate plant Cd uptake with and without ligand addition in a great number of combinations of soil, ligand and plant characteristics, varying the parameters within defined domains. Ligand addition generally strongly reduced hydrated Cd (Cd(2+)) concentration in soil solution through Cd complexation. Dissociation of Cd complex ([Formula: see text]) could not compensate for this reduction, which greatly lowered Cd(2+) symplastic uptake by roots. The apoplastic uptake of [Formula: see text] was not sufficient to compensate for the decrease in symplastic uptake. This explained why in the majority of the cases, ligand addition resulted in the reduction of the simulated Cd phytoextraction. A few results showed an enhanced phytoextraction in very particular conditions (strong plant transpiration with high apoplastic Cd uptake capacity), but this enhancement was very limited, making chelant-enhanced phytoextraction poorly efficient for Cd.

  13. Electronic coupling between ligand and core energy states in dithiolate-monothiolate stabilized Au clusters.

    PubMed

    Ahuja, Tarushee; Wang, Dengchao; Tang, Zhenghua; Robinson, Donald A; Padelford, Jonathan W; Wang, Gangli

    2015-07-15

    Electron transfer activities of metal clusters are fundamentally significant and have promising potential in catalysis, charge or energy storage, sensing, biomedicine and other applications. Strong resonance coupling between the metal core energy states and the ligand molecular orbitals has not been established experimentally, albeit exciting progress has been achieved in the composition and structure determination of these types of nanomaterials recently. In this report, the coupling between core and ligand energy states is demonstrated by the rich electron transfer activities of Au130 clusters. Quantized electron transfers to the core and multi-electron transfers involving the durene-dithiolate ligands were observed at lower and higher potentials, respectively, in voltammetric studies. After a facile multi-electron oxidation from +1.34 to +1.40 V, several reversal reduction processes at more negative potentials, i.e. +0.91 V, +0.18 V and -0.34 V, were observed in an electrochemically irreversible fashion or with sluggish kinetics. The number of electrons and the shifts of the respective reduction potentials in the reversal process were attributed to the electronic coupling or energy relaxation processes. The electron transfer activities and subsequent relaxation processes are drastically reduced at lower temperatures. The time- and temperature-dependent relaxation, involving multiple energy states in the reversal reduction processes upon the oxidation of ligands, reveals the coupling between core and ligand energy states.

  14. Osmolyte-induced folding of an intrinsically disordered protein: folding mechanism in the absence of ligand.

    PubMed

    Chang, Yu-Chu; Oas, Terrence G

    2010-06-29

    Understanding the interconversion between thermodynamically distinguishable states present in a protein folding pathway provides not only the kinetics and energetics of protein folding but also insights into the functional roles of these states in biological systems. The protein component of the bacterial RNase P holoenzyme from Bacillus subtilis (P protein) was previously shown to be unfolded in the absence of its cognate RNA or other anionic ligands. P protein was used in this study as a model system to explore general features of intrinsically disordered protein (IDP) folding mechanisms. The use of trimethylamine N-oxide (TMAO), an osmolyte that stabilizes the unliganded folded form of the protein, enabled us to study the folding process of P protein in the absence of ligand. Transient stopped-flow kinetic traces at various final TMAO concentrations exhibited multiphasic kinetics. Equilibrium "cotitration" experiments were performed using both TMAO and urea during the titration to produce a urea-TMAO titration surface of P protein. Both kinetic and equilibrium studies show evidence of a previously undetected intermediate state in the P protein folding process. The intermediate state is significantly populated, and the folding rate constants are relatively slow compared to those of intrinsically folded proteins similar in size and topology. The experiments and analysis described serve as a useful example for mechanistic folding studies of other IDPs.

  15. A Fast Hermite Transform.

    PubMed

    Leibon, Gregory; Rockmore, Daniel N; Park, Wooram; Taintor, Robert; Chirikjian, Gregory S

    2008-12-17

    We present algorithms for fast and stable approximation of the Hermite transform of a compactly supported function on the real line, attainable via an application of a fast algebraic algorithm for computing sums associated with a three-term relation. Trade-offs between approximation in bandlimit (in the Hermite sense) and size of the support region are addressed. Numerical experiments are presented that show the feasibility and utility of our approach. Generalizations to any family of orthogonal polynomials are outlined. Applications to various problems in tomographic reconstruction, including the determination of protein structure, are discussed.

  16. Kinetic mechanism of L-α-glycerophosphate oxidase from Mycoplasma pneumoniae.

    PubMed

    Maenpuen, Somchart; Watthaisong, Pratchaya; Supon, Pacharee; Sucharitakul, Jeerus; Parsonage, Derek; Karplus, P Andrew; Claiborne, Al; Chaiyen, Pimchai

    2015-08-01

    L-α-glycerophosphate oxidase is an FAD-dependent enzyme that catalyzes the oxidation of L-α-glycerophosphate (Glp) by molecular oxygen to generate dihydroxyacetone phosphate (DHAP) and hydrogen peroxide (H2O2). The catalytic properties of recombinant His6-GlpO from Mycoplasma pneumoniae (His6-MpGlpO) were investigated through transient and steady-state kinetics and ligand binding studies. The results indicate that the reaction mechanism of His6-MpGlpO follows a ping-pong model. Double-mixing mode stopped-flow experiments show that, after flavin-mediated substrate oxidation, DHAP leaves rapidly prior to the oxygen reaction. The values determined for the individual rate constants and kcat (4.2 s(-1) at 4 °C), in addition to the finding that H2 O2 binds to the oxidized enzyme, suggest that H2O2 release is the rate-limiting step for the overall reaction. The results indicate that His6 -MpGlpO contains mixed populations of fast- and slow-reacting species. It is predominantly the fast-reacting species that participates in turnover. In contrast to other GlpO enzymes previously described, His6-MpGlpO is able to catalyze the reverse reaction of reduced enzyme and DHAP. This result may be explained by the standard reduction potential value of His6-MpGlpO (-167 ± 1 mV), which is lower than those of GlpO from other species. We found that D,L-glyceraldehyde 3-phosphate (GAP) may be used as a substrate in the His6-MpGlpO reaction, although it exhibited an approximately 100-fold lower kcat value in comparison with the reaction of Glp. These results also imply involvement of GlpO in glycolysis, as well as in lipid and glycerol metabolism. The kinetic models and distinctive properties of His6-MpGlpO reported here should be useful for future drug development against Mycoplasma pneumoniae infection.

  17. Ligand placement based on prior structures: the guided ligand-replacement method

    PubMed Central

    Klei, Herbert E.; Moriarty, Nigel W.; Echols, Nathaniel; Terwilliger, Thomas C.; Baldwin, Eric T.; Pokross, Matt; Posy, Shana; Adams, Paul D.

    2014-01-01

    The process of iterative structure-based drug design involves the X-ray crystal structure determination of upwards of 100 ligands with the same general scaffold (i.e. chemotype) complexed with very similar, if not identical, protein targets. In conjunction with insights from computational models and assays, this collection of crystal structures is analyzed to improve potency, to achieve better selectivity and to reduce liabilities such as absorption, distribution, metabolism, excretion and toxicology. Current methods for modeling ligands into electron-density maps typically do not utilize information on how similar ligands bound in related structures. Even if the electron density is of sufficient quality and resolution to allow de novo placement, the process can take considerable time as the size, complexity and torsional degrees of freedom of the ligands increase. A new module, Guided Ligand Replacement (GLR), was developed in Phenix to increase the ease and success rate of ligand placement when prior protein–ligand complexes are available. At the heart of GLR is an algorithm based on graph theory that associates atoms in the target ligand with analogous atoms in the reference ligand. Based on this correspondence, a set of coordinates is generated for the target ligand. GLR is especially useful in two situations: (i) modeling a series of large, flexible, complicated or macrocyclic ligands in successive structures and (ii) modeling ligands as part of a refinement pipeline that can automatically select a reference structure. Even in those cases for which no reference structure is available, if there are multiple copies of the bound ligand per asymmetric unit GLR offers an efficient way to complete the model after the first ligand has been placed. In all of these applications, GLR leverages prior knowledge from earlier structures to facilitate ligand placement in the current structure. PMID:24419386

  18. Ligand Exchange Reaction of Au(I) R-N-Heterocyclic Carbene Complexes with Cysteine.

    PubMed

    Dos Santos, H F; Vieira, M A; Sánchez Delgado, G Y; Paschoal, D

    2016-04-14

    The chemotherapy with gold complexes has been attempted since the 90s after the clinical success of auranofin, a gold(I) coordination complex. Currently, the organometallics compounds have shown promise in cancer therapy, mainly in those complexes containing N-heterocylic carbenes (NHC) as a ligand. The present study shows a kinetic analysis of the reaction of six alkyl-substituted NHC with cysteine (Cys), which is taken as an important bionucleophile representative. The first and second ligand exchange processes were analyzed with the complete description of the mechanism and energy profiles. For the first reaction step, which is the rate-limiting step of the whole substitution reaction, the activation enthalpy follows the order 1/Me2 < 2/Me,Et < 4/n-Bu2 < 3/i-Pr2 < 6/Cy2 < 5/t-Bu2, which is fully explained by steric and electronic features. From a steric point of view, the previous reactivity order is correlated with the r(Au-S) calculated for the transition state structures where S is the sulfur ligand from the Cys entering group. This means that longer r(Au-S) leads to higher activation enthalpy and is consistent with the effectiveness of gold shielding from nucleophile attack by bulkier alkyl-substituted NHC ligand. When electronic effect was addressed we found that higher activation barrier was predicted for strongly electron-donating NHC ligand, represented by the eigenvalue of σ-HOMO orbital of the free ligands. The molecular interpretation of the electronic effects is that strong donating NHC forms strong metal-ligand bond. For the second reaction step, similar structure-reactivity relationships were obtained, however the activation energies are less sensitive to the structure.

  19. Flexible ligand docking using a genetic algorithm

    NASA Astrophysics Data System (ADS)

    Oshiro, C. M.; Kuntz, I. D.; Dixon, J. Scott

    1995-04-01

    Two computational techniques have been developed to explore the orientational and conformational space of a flexible ligand within an enzyme. Both methods use the Genetic Algorithm (GA) to generate conformationally flexible ligands in conjunction with algorithms from the DOCK suite of programs to characterize the receptor site. The methods are applied to three enzyme-ligand complexes: dihydrofolate reductase-methotrexate, thymidylate synthase-phenolpthalein and HIV protease-thioketal haloperidol. Conformations and orientations close to the crystallographically determined structures are obtained, as well as alternative structures with low energy. The potential for the GA method to screen a database of compounds is also examined. A collection of ligands is evaluated simultaneously, rather than docking the ligands individually into the enzyme.

  20. Biomimetic affinity ligands for protein purification.

    PubMed

    Sousa, Isabel T; Taipa, M Angela

    2014-01-01

    The development of sophisticated molecular modeling software and new bioinformatic tools, as well as the emergence of data banks containing detailed information about a huge number of proteins, enabled the de novo intelligent design of synthetic affinity ligands. Such synthetic compounds can be tailored to mimic natural biological recognition motifs or to interact with key surface-exposed residues on target proteins and are designated as "biomimetic ligands." A well-established methodology for generating biomimetic or synthetic affinity ligands integrates rational design with combinatorial solid-phase synthesis and screening, using the triazine scaffold and analogues of amino acids side chains to create molecular diversity.Triazine-based synthetic ligands are nontoxic, low-cost, highly stable compounds that can replace advantageously natural biological ligands in the purification of proteins by affinity-based methodologies.

  1. Interactions of the c-di-GMP riboswitch with its second messenger ligand

    PubMed Central

    Smith, Kathryn D.; Strobel, Scott A.

    2013-01-01

    The c-di-GMP riboswitch is a macromolecular target in the c-di-GMP second messenger signaling pathway. It regulates many genes related to c-di-GMP metabolism as well as genes involved in bacterial motility, virulence and biofilm formation. The riboswitch makes asymmetric contacts to the bases and phosphate backbone of this symmetric dinucleotide. The phylogenetics suggested and mutagenesis has confirmed that this is a flexible motif where variants can make alternative interactions with each of the guanine bases of c-di-GMP. A mutant riboswitch has been designed that can bind a related molecule, c-di-AMP, confirming the most important contacts made to the ligand. The binding kinetics reveal that this is a kinetically controlled riboswitch and mutations to the riboswitch lead to increases in the off-rate. This riboswitch is therefore flexible in sequence as well as kinetic properties. PMID:21428955

  2. Multiple alternative substrate kinetics.

    PubMed

    Anderson, Vernon E

    2015-11-01

    The specificity of enzymes for their respective substrates has been a focal point of enzyme kinetics since the initial characterization of metabolic chemistry. Various processes to quantify an enzyme's specificity using kinetics have been utilized over the decades. Fersht's definition of the ratio kcat/Km for two different substrates as the "specificity constant" (ref [7]), based on the premise that the important specificity existed when the substrates were competing in the same reaction, has become a consensus standard for enzymes obeying Michaelis-Menten kinetics. The expansion of the theory for the determination of the relative specificity constants for a very large number of competing substrates, e.g. those present in a combinatorial library, in a single reaction mixture has been developed in this contribution. The ratio of kcat/Km for isotopologs has also become a standard in mechanistic enzymology where kinetic isotope effects have been measured by the development of internal competition experiments with extreme precision. This contribution extends the theory of kinetic isotope effects to internal competition between three isotopologs present at non-tracer concentrations in the same reaction mix. This article is part of a special issue titled: Enzyme Transition States from Theory and Experiment.

  3. Evidence for proximal control of ligand specificity in hemeproteins: Absorption and Raman studies of cryogenically trapped photoproducts of ligand bound myoglobins

    NASA Astrophysics Data System (ADS)

    Ahmed, A. M.; Campbell, B. F.; Caruso, D.; Chance, M. R.; Chavez, M. D.; Courtney, S. H.; Friedman, J. M.; Iben, I. E. T.; Ondrias, M. R.; Yang, M.

    1991-12-01

    The absorption and resonance Raman spectra of cryogenically trapped photoproducts of oxy and carboxy derivatives of myoglobin (Mb) are compared and analyzed in an attempt to understand the structural basis for ligand specificity in hemeproteins. Pulsed and cw excitations over a wide temperature range are used in order to differentiate between kinetic hole burning (KHB), optical pumping of structural relaxation, and spontaneous relaxation effects. Using these techniques, we are able to correlate changes in the absorption spectrum (band III at ≈ 760 nm) with low-frequency Raman bands. Based on these correlations we are able to determine which proximal heme pocket parameters are participating in KHB and optical pumping phenomena. Differences in the spectra of the ligand specific photoproducts have revealed differences in the populations of conformational substates (CS) that participate in the geminate recombination (process I) at cryogenic temperatures. A model is presented that relates the ligand specific spectral differences to structural and functional differences in the bound protein. What emerges is evidence that Mb and hemoglobin (Hb) can differentiate between O 2 and CO based on proximal control of the bond forming step between the ligand and the iron.

  4. High-throughput identification of telomere-binding ligands based on the fluorescence regulation of DNA-copper nanoparticles.

    PubMed

    Yang, Luzhu; Wang, Yanjun; Li, Baoxin; Jin, Yan

    2017-01-15

    Formation of the G-quadruplex in the human telomeric DNA is an effective way to inhibit telomerase activity. Therefore, screening ligands of G-quadruplex has potential applications in the treatment of cancer by inhibit telomerase activity. Although several techniques have been explored for screening of telomeric G-quadruplexes ligands, high-throughput screening method for fast screening telomere-binding ligands from the large compound library is still urgently needed. Herein, a label-free fluorescence strategy has been proposed for high-throughput screening telomere-binding ligands by using DNA-copper nanoparticles (DNA-CuNPs) as a signal probe. In the absence of ligands, human telomeric DNA (GDNA) hybridized with its complementary DNA (cDNA) to form double stranded DNA (dsDNA) which can act as an efficient template for the formation of DNA-CuNPs, leading to the high fluorescence of DNA-CuNPs. In the presence of ligands, GDNA folded into G-quadruplex. Single-strdanded cDNA does not support the formation of DNA-CuNP, resulting in low fluorescence of DNA-CuNPs. Therefore, telomere-binding ligands can be high-throughput screened by monitoring the change in the fluorescence of DNA-CuNPs. Thirteen traditional chinese medicines were screened. Circular dichroism (CD) measurements demonstrated that the selected ligands could induce single-stranded telomeric DNA to form G-quadruplex. The telomere repeat amplification protocol (TRAP) assay demonstrated that the selected ligands can effectively inhibit telomerase activity. Therefore, it offers a cost-effective, label-free and reliable high-throughput way to identify G-quadruplex ligands, which holds great potential in discovering telomerase-targeted anticancer drugs.

  5. Qualification of a free ligand assay in the presence of anti-ligand antibody Fab fragments.

    PubMed

    Hansen, Ryan J; Brown, Robin M; Lu, Jirong; Wroblewski, Victor J

    2013-01-01

    The aim of this work was to develop and characterize an ELISA to measure free ligand concentrations in rat serum in the presence of a Fab to the same ligand. A variety of experiments were conducted to understand optimal assay conditions and to verify that only free ligand was detected. The parameters explored included sample incubation time on plate, the initial concentrations of Fab and ligand, and the pre-incubation time required for the Fab-ligand complex concentrations to reach equilibrium. We found the optimal experimental conditions to include a 10-minute on-plate incubation of ligand-containing samples, with a 24-hour pre-incubation time for test samples of Fab and ligand to reach equilibrium. An alternative approach, involving removal of Fab-ligand complexes from the solution prior to measuring concentrations of the ligand, was also used to verify that the assay only measured free ligand. Rats were dosed subcutaneously with Fab and the assay was used to demonstrate dose-dependent suppression of endogenous free ligand levels in vivo.

  6. Chiral Bidentate NHC Ligands Based on the 1,1'-Binaphthyl Scaffold: Synthesis and Application in Transition-Metal-Catalyzed Asymmetric Reactions.

    PubMed

    Xu, Qin; Gu, Peng; Jiang, Hanchun; Wei, Yin; Shi, Min

    2016-12-01

    The use of the chiral 1,1'-binaphthyl scaffold to construct chiral ligands can be traced back for a long time. However, the development of bidentate NHC ligands based on the same backbone has only appeared recently. In this account, we describe the design and synthesis of a new family of chiral NHC ligands based on the 1,1'-binaphthyl scaffold and demonstrate the applications of these chiral NHC-metal complexes in the catalyzed oxidative kinetic resolution of secondary alcohols, asymmetric carbon-carbon bond formations, hydrosilylations, and cyclizations of 1,6-enynes. The chiral NHC ligands containing the 1,1'-binaphthyl backbone can be synthesized in good yields from enantiomerically pure 1,1'-binaphthyl-2,2'-diamine. These transition metals coordinated with chiral bidentate NHC ligands exhibit high catalytic activities and good enantioselectivities for a wide range of metal-catalyzed asymmetric reactions.

  7. Fast ForWord.

    ERIC Educational Resources Information Center

    Education Commission of the States, Denver, CO.

    This paper provides an overview of Fast ForWord, a CD-ROM and Internet-based training program for children (pre-K to grade 8) with language and reading problems that helps children rapidly build oral language comprehension and other critical skills necessary for learning to read or becoming a better reader. With the help of computers, speech…

  8. The Integral Fast Reactor

    SciTech Connect

    Till, C.E.; Chang, Y.I. ); Lineberry, M.J. )

    1990-01-01

    Argonne National Laboratory, since 1984, has been developing the Integral Fast Reactor (IFR). This paper will describe the way in which this new reactor concept came about; the technical, public acceptance, and environmental issues that are addressed by the IFR; the technical progress that has been made; and our expectations for this program in the near term. 5 refs., 3 figs.

  9. Integral Fast Reactor concept

    SciTech Connect

    Till, C.E.; Chang, Y.I.

    1986-01-01

    The Integral Fast Reactor (IFR) is an innovative LMR concept, being developed at Argonne National Laboratory, that fully exploits the inherent properties of liquid metal cooling and metallic fuel to achieve breakthroughs in economics and inherent safety. This paper describes key features and potential advantages of the IFR concept, technology development status, fuel cycle economics potential, and future development path.

  10. Relativistic Chiral Kinetic Theory

    NASA Astrophysics Data System (ADS)

    Stephanov, Mikhail

    2016-12-01

    This very brief review of the recent progress in chiral kinetic theory is based on the results of Refs. [J.-Y. Chen, D. T. Son, M. A. Stephanov, H.-U. Yee, Y. Yin, Lorentz Invariance in Chiral Kinetic Theory, Phys. Rev. Lett. 113 (18) (2014) 182302. doi:10.1103/PhysRevLett.113.182302; J.-Y. Chen, D. T. Son, M. A. Stephanov, Collisions in Chiral Kinetic Theory, Phys. Rev. Lett. 115 (2) (2015) 021601. doi: 10.1103/PhysRevLett.115.021601; M. A. Stephanov, H.-U. Yee, The no-drag frame for anomalous chiral fluid, Phys. Rev. Lett. 116 (12) (2016) 122302. doi: 10.1103/PhysRevLett.116.122302].

  11. Microstructure design for fast oxygen conduction

    DOE PAGES

    Aidhy, Dilpuneet S.; Weber, William J.

    2015-11-11

    Research from the last decade has shown that in designing fast oxygen conducting materials for electrochemical applications has largely shifted to microstructural features, in contrast to material-bulk. In particular, understanding oxygen energetics in heterointerface materials is currently at the forefront, where interfacial tensile strain is being considered as the key parameter in lowering oxygen migration barriers. Nanocrystalline materials with high densities of grain boundaries have also gathered interest that could possibly allow leverage over excess volume at grain boundaries, providing fast oxygen diffusion channels similar to those previously observed in metals. In addition, near-interface phase transformations and misfit dislocations aremore » other microstructural phenomenon/features that are being explored to provide faster diffusion. In this review, the current understanding on oxygen energetics, i.e., thermodynamics and kinetics, originating from these microstructural features is discussed. Moreover, our experimental observations, theoretical predictions and novel atomistic mechanisms relevant to oxygen transport are highlighted. In addition, the interaction of dopants with oxygen vacancies in the presence of these new microstructural features, and their future role in the design of future fast-ion conductors, is outlined.« less

  12. Microstructure design for fast oxygen conduction

    SciTech Connect

    Aidhy, Dilpuneet S.; Weber, William J.

    2015-11-11

    Research from the last decade has shown that in designing fast oxygen conducting materials for electrochemical applications has largely shifted to microstructural features, in contrast to material-bulk. In particular, understanding oxygen energetics in heterointerface materials is currently at the forefront, where interfacial tensile strain is being considered as the key parameter in lowering oxygen migration barriers. Nanocrystalline materials with high densities of grain boundaries have also gathered interest that could possibly allow leverage over excess volume at grain boundaries, providing fast oxygen diffusion channels similar to those previously observed in metals. In addition, near-interface phase transformations and misfit dislocations are other microstructural phenomenon/features that are being explored to provide faster diffusion. In this review, the current understanding on oxygen energetics, i.e., thermodynamics and kinetics, originating from these microstructural features is discussed. Moreover, our experimental observations, theoretical predictions and novel atomistic mechanisms relevant to oxygen transport are highlighted. In addition, the interaction of dopants with oxygen vacancies in the presence of these new microstructural features, and their future role in the design of future fast-ion conductors, is outlined.

  13. Emergence of ion channel modal gating from independent subunit kinetics

    PubMed Central

    Bicknell, Brendan A.

    2016-01-01

    Many ion channels exhibit a slow stochastic switching between distinct modes of gating activity. This feature of channel behavior has pronounced implications for the dynamics of ionic currents and the signaling pathways that they regulate. A canonical example is the inositol 1,4,5-trisphosphate receptor (IP3R) channel, whose regulation of intracellular Ca2+ concentration is essential for numerous cellular processes. However, the underlying biophysical mechanisms that give rise to modal gating in this and most other channels remain unknown. Although ion channels are composed of protein subunits, previous mathematical models of modal gating are coarse grained at the level of whole-channel states, limiting further dialogue between theory and experiment. Here we propose an origin for modal gating, by modeling the kinetics of ligand binding and conformational change in the IP3R at the subunit level. We find good agreement with experimental data over a wide range of ligand concentrations, accounting for equilibrium channel properties, transient responses to changing ligand conditions, and modal gating statistics. We show how this can be understood within a simple analytical framework and confirm our results with stochastic simulations. The model assumes that channel subunits are independent, demonstrating that cooperative binding or concerted conformational changes are not required for modal gating. Moreover, the model embodies a generally applicable principle: If a timescale separation exists in the kinetics of individual subunits, then modal gating can arise as an emergent property of channel behavior. PMID:27551100

  14. Multiresolution imaging of in-vivo ligand-receptor interactions

    NASA Astrophysics Data System (ADS)

    Thevenaz, Philippe; Millet, Philippe

    2001-05-01

    The aim of this study is to obtain voxel-by-voxel images of binding parameters between [11C]-flumazenil and benzodiazepine receptors using positron emission tomography (PET). We estimate five local parameters (k1, k2, B'max, kon/VR, koff) by fitting a three- compartment ligand-receptor model for each voxel of a PET time series. It proves difficult to fit the ligand-receptor model to the data. We trade noise and spatial resolution to get better results. Our strategy is based on the use of a multiresolution pyramid. It is much easier to solve the problem at coarse resolution because there are fewer data to process. To increase resolution, we expand the parameter maps to the next finer level and use them as initial solution to further optimization, which then proceeds at a fast pace and is more likely to escape false local minima. For this approach to work optimally, the residue between data at a given pyramid level and data at the next level must be as small as possible. We satisfy this constraint by working with spline-based least- squares pyramids. To achieve speed, the optimizer must be efficient, particularly when it is nearing the solution. To that effect, we have developed a Marquardt-Levenberg algorithm that exhibits superlinear convergence properties.

  15. Quantifying high-affinity binding of hydrophobic ligands by isothermal titration calorimetry.

    PubMed

    Krainer, Georg; Broecker, Jana; Vargas, Carolyn; Fanghänel, Jörg; Keller, Sandro

    2012-12-18

    A fast and reliable quantification of the binding thermodynamics of hydrophobic high-affinity ligands employing a new calorimetric competition experiment is described. Although isothermal titration calorimetry is the method of choice for a quantitative characterization of intermolecular interactions in solution, a reliable determination of a dissociation constant (K(D)) is typically limited to the range 100 μM > K(D) > 1 nM. Interactions displaying higher or lower K(D) values can be assessed indirectly, provided that a suitable competing ligand is available whose K(D) falls within the directly accessible affinity window. This established displacement assay, however, requires the high-affinity ligand to be soluble at high concentrations in aqueous buffer and, consequently, poses serious problems in the study of protein binding involving small-molecule ligands dissolved in organic solvents--a familiar case in many drug-discovery projects relying on compound libraries. The calorimetric competition assay introduced here overcomes this limitation, thus allowing for a detailed thermodynamic description of high-affinity receptor-ligand interactions involving poorly water-soluble compounds. Based on a single titration of receptor into a dilute mixture of the two competing ligands, this competition assay provides accurate and precise values for the dissociation constants and binding enthalpies of both high- and moderate-affinity ligands. We discuss the theoretical background underlying the approach, demonstrate its practical application to metal ion chelation and high-affinity protein-inhibitor interactions, and explore its potential and limitations with the aid of simulations and statistical analyses.

  16. The Usefulness of Serum CXCR3 Ligands for Evaluating the Early Treatment Response in Tuberculosis: A Longitudinal Cohort Study.

    PubMed

    Chung, Wou Young; Yoon, Dukyong; Lee, Keu Sung; Jung, Yun Jung; Kim, Young Sun; Sheen, Seung Soo; Park, Kwang Joo

    2016-04-01

    Cell-mediated immunity plays an important role in the pathobiology of tuberculosis (TB). The ligands for CXC chemokine receptor 3 (CXCR3) activate the T-helper type 1 lymphocyte pathway. The CXCR3 ligands are reportedly useful clinical markers for the diagnosis and follow-up of TB. The objective of this study was to assess the utility of CXCR3 ligands for evaluating early treatment responses in TB.We recruited 88 patients who underwent antituberculous chemotherapy. The serum levels of interferon (IFN)-γ and the CXCR3 ligands CXCL9 (monokine induced by IFN-γ [MIG]), CXCL10 (IFN-γ-inducible 10-kDa protein [IP-10]), and CXCL11 (IFN-inducible T-cell α chemoattractant [I-TAC]) were measured before and 2 months after the start of treatment. Treatment responses were divided into "fast" and "slow" based on the clinical, radiological, and bacteriological improvement at 2 months. A change in level of 20% or more at 2 months was defined as "significant."In patients with treatment success, 58 patients exhibited a fast response and 20 patients exhibited a slow response. Treatment failure occurred in 5 patients, and the diagnoses were changed to non-TB diseases in 5 patients. The levels of all CXCR3 ligands significantly decreased in the fast-response group (P < 0.01) but did not decrease in the other groups. IFN-γ levels showed no significant changes. The ability of significant decreases in marker levels to predict a fast response was evaluated. CXCL9 showed a sensitivity of 83%, and CXCL10 showed a specificity of 100%. Use of various combinations of CXCR3 ligands resulted in improvements in sensitivity (88%-93%), while specificity (92%-96%) was similar to that using single CXCR3 ligands. The decreases in CXCR3 ligand levels were less marked in the 2-month Mycobacterium tuberculosis culture-positive group than in the culture-negative group. There were significant differences in treatment outcomes in terms of 2-month culture positivity (P < 0.001), the significance

  17. Limiting Energy Dissipation Induces Glassy Kinetics in Single-Cell High-Precision Responses

    PubMed Central

    Das, Jayajit

    2016-01-01

    Single cells often generate precise responses by involving dissipative out-of-thermodynamic-equilibrium processes in signaling networks. The available free energy to fuel these processes could become limited depending on the metabolic state of an individual cell. How does limiting dissipation affect the kinetics of high-precision responses in single cells? I address this question in the context of a kinetic proofreading scheme used in a simple model of early-time T cell signaling. Using exact analytical calculations and numerical simulations, I show that limiting dissipation qualitatively changes the kinetics in single cells marked by emergence of slow kinetics, large cell-to-cell variations of copy numbers, temporally correlated stochastic events (dynamic facilitation), and ergodicity breaking. Thus, constraints in energy dissipation, in addition to negatively affecting ligand discrimination in T cells, can create a fundamental difficulty in determining single-cell kinetics from cell-population results. PMID:26958894

  18. Chemistry of Marine Ligands and Siderophores

    NASA Astrophysics Data System (ADS)

    Vraspir, Julia M.; Butler, Alison

    2009-01-01

    Marine microorganisms are presented with unique challenges to obtain essential metal ions required to survive and thrive in the ocean. The production of organic ligands to complex transition metal ions is one strategy to both facilitate uptake of specific metals, such as iron, and to mitigate the potential toxic effects of other metal ions, such as copper. A number of important trace metal ions are complexed by organic ligands in seawater, including iron, cobalt, nickel, copper, zinc, and cadmium, thus defining the speciation of these metal ions in the ocean. In the case of iron, siderophores have been identified and structurally characterized. Siderophores are low molecular weight iron-binding ligands produced by marine bacteria. Although progress has been made toward the identity of in situ iron-binding ligands, few compounds have been identified that coordinate the other trace metals. Deciphering the chemical structures and production stimuli of naturally produced organic ligands and the organisms they come from is fundamental to understanding metal speciation and bioavailability. The current evidence for marine ligands, with an emphasis on siderophores, and discussion of the importance and implications of metal-binding ligands in controlling metal speciation and cycling within the world's oceans are presented.

  19. Cooperative thermodynamic control of selectivity in the self-assembly of rare earth metal-ligand helices.

    PubMed

    Johnson, Amber M; Young, Michael C; Zhang, Xing; Julian, Ryan R; Hooley, Richard J

    2013-11-27

    Metal-selective self-assembly with rare-earth cations is possible with suitable rigid, symmetrical bis-tridentate ligands. Kinetically controlled formation is initially observed, with smaller cations preferentially incorporated. Over time, the more thermodynamically favorable complexes with larger metals are formed. This thermodynamic control is a cooperative supramolecular phenomenon and only occurs upon multiple-metal-based self-assembly: single-metal ML3 analogues do not show reversible selectivity. The selectivity is dependent on small variations in lanthanide ionic radius and occurs despite identical coordination-ligand coordination geometries and minor size differences in the rare-earth metals.

  20. γ-Sultam-cored N,N-ligands in the ruthenium(ii)-catalyzed asymmetric transfer hydrogenation of aryl ketones.

    PubMed

    Rast, Slavko; Modec, Barbara; Stephan, Michel; Mohar, Barbara

    2016-02-14

    The synthesis of new enantiopure syn- and anti-3-(α-aminobenzyl)-benzo-γ-sultam ligands 6 and their application in the ruthenium(ii)-catalyzed asymmetric transfer hydrogenation (ATH) of ketones using formic acid/triethylamine is described. In particular, benzo-fused cyclic ketones afforded excellent enantioselectivities in reasonable time employing a low loading of the syn ligand-containing catalyst. A never-before-seen dynamic kinetic resolution (DKR) during reduction of a γ-keto carboxylic ester (S7) derivative of 1-indanone is realized leading as well to excellent induction.

  1. Binding Kinetics versus Affinities in BRD4 Inhibition.

    PubMed

    Kuang, Ming; Zhou, Jingwei; Wang, Laiyou; Liu, Zhihong; Guo, Jiao; Wu, Ruibo

    2015-09-28

    Bromodomains (BRDs) are protein modules that selectively recognize histones as a "reader" by binding to an acetylated lysine substrate. The human BRD4 has emerged as a promising drug target for a number of disease pathways, and several potent BRD inhibitors have been discovered experimentally recently. However, the detailed inhibition mechanism especially for the inhibitor binding kinetics is not clear. Herein, by employing classical molecular dynamics (MD) and state-of-the-art density functional QM/MM MD simulations, the dynamic characteristics of ZA-loop in BRD4 are revealed. And then the correlation between binding pocket size and ZA-loop motion is elucidated. Moreover, our simulations found that the compound (-)-JQ1 could be accommodated reasonably in thermodynamics whereas it is infeasible in binding kinetics against BRD4. Its racemate (+)-JQ1 proved to be both thermodynamically reasonable and kinetically achievable against BRD4, which could explain the previous experimental results that (+)-JQ1 shows a high inhibitory effect toward BRD4 (IC50 is 77 nM) while (-)-JQ1 is inactive (>10 μM). Furthermore, the L92/L94/Y97 in the ZA-loop and Asn140 in the BC-loop are identified to be critical residues in (+)-JQ1 binding/releasing kinetics. All these findings shed light on further selective inhibitor design toward BRD family, by exploiting the non-negligible ligand binding kinetics features and flexible ZA-loop motions of BRD, instead of only the static ligand-protein binding affinity.

  2. Mini-ISES identifies promising carbafructopyranose-based salens for asymmetric catalysis: Tuning ligand shape via the anomeric effect

    PubMed Central

    Karukurichi, Kannan R.; Fei, Xiang; Swyka, Robert A.; Broussy, Sylvain; Shen, Weijun; Dey, Sangeeta; Roy, Sandip K.; Berkowitz, David B.

    2015-01-01

    This study introduces new methods of screening for and tuning chiral space and in so doing identifies a promising set of chiral ligands for asymmetric synthesis. The carbafructopyranosyl-1,2-diamine(s) and salens constructed therefrom are particularly compelling. It is shown that by removing the native anomeric effect in this ligand family, one can tune chiral ligand shape and improve chiral bias. This concept is demonstrated by a combination of (i) x-ray crystallographic structure determination, (ii) assessment of catalytic performance, and (iii) consideration of the anomeric effect and its underlying dipolar basis. The title ligands were identified by a new mini version of the in situ enzymatic screening (ISES) procedure through which catalyst-ligand combinations are screened in parallel, and information on relative rate and enantioselectivity is obtained in real time, without the need to quench reactions or draw aliquots. Mini-ISES brings the technique into the nanomole regime (200 to 350 nmol catalyst/20 μl organic volume) commensurate with emerging trends in reaction development/process chemistry. The best-performing β-d-carbafructopyranosyl-1,2-diamine–derived salen ligand discovered here outperforms the best known organometallic and enzymatic catalysts for the hydrolytic kinetic resolution of 3-phenylpropylene oxide, one of several substrates examined for which the ligand is “matched.” This ligand scaffold defines a new swath of chiral space, and anomeric effect tunability defines a new concept in shaping that chiral space. Both this ligand set and the anomeric shape-tuning concept are expected to find broad application, given the value of chiral 1,2-diamines and salens constructed from these in asymmetric catalysis. PMID:26501130

  3. Physical characterization of the Skua fast burst assembly

    SciTech Connect

    Paternoster, R.; Bounds, J.; Sanchez, R.; Miko, D.

    1994-08-01

    In this paper we discuss the system design and ongoing efforts to characterize the machine physics and operating properties of the Skua fast burst assembly. The machine is currently operating up to prompt critical while we await approval for super-prompt burst operations. Efforts have centered on characterizing neutron kinetic properties, comparing calculated and measured temperature coefficients and power distributions, improving the burst reproducibility, examining the site-wide dose characteristics, and fitting the machine with cooling and filtration systems.

  4. Kinetic tetrazolium microtiter assay

    NASA Technical Reports Server (NTRS)

    Pierson, Duane L. (Inventor); Stowe, Raymond P. (Inventor); Koeing, David W. (Inventor)

    1992-01-01

    A method for conducting an in vitro cell assay using a tetrazolium indicator is disclosed. The indicator includes a nonionic detergent which solubilizes a tetrazolium reduction product in vitro and has low toxicity for the cells. The incubation of test cells in the presence of zolium bromide and octoxynol (TRITON X-100) permits kinetics of the cell metabolism to be determined.

  5. Applications of kinetic theory

    SciTech Connect

    Gidaspow, D.

    1992-01-01

    The overall objective of this investigation is to develop experimentally verified models for circulating fluidized bed (CFB) combustors. This report presents the author's derivation of analytical solutions useful in understanding the operation of a CFB. The report is in a form of a chapter that reviews the kinetic theory applications.

  6. Kinetics and Catalysis Demonstrations.

    ERIC Educational Resources Information Center

    Falconer, John L.; Britten, Jerald A.

    1984-01-01

    Eleven videotaped kinetics and catalysis demonstrations are described. Demonstrations include the clock reaction, oscillating reaction, hydrogen oxidation in air, hydrogen-oxygen explosion, acid-base properties of solids, high- and low-temperature zeolite reactivity, copper catalysis of ammonia oxidation and sodium peroxide decomposition, ammonia…

  7. Oxidative desulfurization: kinetic modelling.

    PubMed

    Dhir, S; Uppaluri, R; Purkait, M K

    2009-01-30

    Increasing environmental legislations coupled with enhanced production of petroleum products demand, the deployment of novel technologies to remove organic sulfur efficiently. This work represents the kinetic modeling of ODS using H(2)O(2) over tungsten-containing layered double hydroxide (LDH) using the experimental data provided by Hulea et al. [V. Hulea, A.L. Maciuca, F. Fajula, E. Dumitriu, Catalytic oxidation of thiophenes and thioethers with hydrogen peroxide in the presence of W-containing layered double hydroxides, Appl. Catal. A: Gen. 313 (2) (2006) 200-207]. The kinetic modeling approach in this work initially targets the scope of the generation of a superstructure of micro-kinetic reaction schemes and models assuming Langmuir-Hinshelwood (LH) and Eley-Rideal (ER) mechanisms. Subsequently, the screening and selection of above models is initially based on profile-based elimination of incompetent schemes followed by non-linear regression search performed using the Levenberg-Marquardt algorithm (LMA) for the chosen models. The above analysis inferred that Eley-Rideal mechanism describes the kinetic behavior of ODS process using tungsten-containing LDH, with adsorption of reactant and intermediate product only taking place on the catalyst surface. Finally, an economic index is presented that scopes the economic aspects of the novel catalytic technology with the parameters obtained during regression analysis to conclude that the cost factor for the catalyst is 0.0062-0.04759 US $ per barrel.

  8. Fast electrochemical actuator

    NASA Astrophysics Data System (ADS)

    Uvarov, I. V.; Postnikov, A. V.; Svetovoy, V. B.

    2016-03-01

    Lack of fast and strong microactuators is a well-recognized problem in MEMS community. Electrochemical actuators can develop high pressure but they are notoriously slow. Water electrolysis produced by short voltage pulses of alternating polarity can overcome the problem of slow gas termination. Here we demonstrate an actuation regime, for which the gas pressure is relaxed just for 10 μs or so. The actuator consists of a microchamber filled with the electrolyte and covered with a flexible membrane. The membrane bends outward when the pressure in the chamber increases. Fast termination of gas and high pressure developed in the chamber are related to a high density of nanobubbles in the chamber. The physical processes happening in the chamber are discussed so as problems that have to be resolved for practical applications of this actuation regime. The actuator can be used as a driving engine for microfluidics.

  9. "Fast" Capitalism and "Fast" Schools: New Realities and New Truths.

    ERIC Educational Resources Information Center

    Robertson, Susan L.

    This paper locates the phenomenon of self-managing schools within the framework of "fast capitalism" and identifies themes of organization central to fast capitalism, which are argued to also underpin the self-managing schools. "Fast capitalism" refers to the rapidly intensified integration of regionalized productive activities into the global…

  10. PHENIX Fast TOF

    SciTech Connect

    Soha, Aria; Chiu, Mickey; Mannel, Eric; Stoll, Sean; Lynch, Don; Boose, Steve; Northacker, Dave; Alfred, Marcus; Lindesay, James; Chujo, Tatsuya; Inaba, Motoi; Nonaka, Toshihiro; Sato, Wataru; Sakatani, Ikumi; Hirano, Masahiro; Choi, Ihnjea

    2014-01-15

    This is a technical scope of work (TSW) between the Fermi National Accelerator Laboratory (Fermilab) and the experimenters of PHENIX Fast TOF group who have committed to participate in beam tests to be carried out during the FY2014 Fermilab Test Beam Facility program. The goals for this test beam experiment are to verify the timing performance of the two types of time-of-flight detector prototypes.

  11. The Integral Fast Reactor

    SciTech Connect

    Chang, Y.I.

    1988-01-01

    The Integral Fast Reactor (IFR) is an innovative liquid metal reactor concept being developed at Argonne National Laboratory. It seeks to specifically exploit the inherent properties of liquid metal cooling and metallic fuel in a way that leads to substantial improvements in the characteristics of the complete reactor system. This paper describes the key features and potential advantages of the IFR concept, with emphasis on its safety characteristics. 3 refs., 4 figs., 1 tab.

  12. Fast tracking hospital construction.

    PubMed

    Quirk, Andrew

    2013-03-01

    Hospital leaders should consider four factors in determining whether to fast track a hospital construction project: Expectations of project length, quality, and cost. Whether decisions can be made quickly as issues arise. Their own time commitment to the project, as well as that of architects, engineers, construction managers, and others. The extent to which they are willing to share with the design and construction teams how and why decisions are being made.

  13. Application of the Principle of Linked Functions to ATP-Driven Ion Pumps: Kinetics of Activation by ATP

    NASA Astrophysics Data System (ADS)

    Reynolds, Jacqueline A.; Johnson, Edward A.; Tanford, Charles

    1985-06-01

    If a ligand binds with unequal affinity to two distinct states of a protein, then the equilibrium between the two states becomes a function of the concentration of the ligand. A necessary consequence is that the ligand must also affect the forward and/or reverse rate constants for transition between the two states. For an enzyme or transport protein with such a transition as a slow step in the catalytic cycle, the overall rate also becomes a function of ligand concentration. These conclusions are independent of whether or not the ligand is a direct participant in the reaction. If it is a direct partitipant, then the kinetic effect arising from the principle of linked functions is distinct from the direct catalytic effect. These principles suffice to account for the biphasic response of the hydrolytic activity of ATP-driven ion pumps to the concentration of ATP, without the need to invoke more than one ATP binding site per catalytic center.

  14. ProPose: steered virtual screening by simultaneous protein-ligand docking and ligand-ligand alignment.

    PubMed

    Seifert, Markus H J

    2005-01-01

    The 'model-free' screening engine ProPose implements a general method for performing simultaneous protein-ligand docking, ligand-ligand alignment, pharmacophore queries-and combinations thereof-in order to incorporate a priori information into screening protocols. In this manuscript we describe a case study on herpes simplex virus thymidine kinase, an important antiviral drug target, where we evaluate different approaches for handling a specific type of a priori information, i.e., multiple target structures. We demonstrate that a simultaneous alignment on two target structures--in conjunction with logic operations on interactions and docking constraints derived from protein structure--is an effective means of (i) improving the enrichment of chemical substructures that are compatible with the a priori known ligands, (ii) ensuring the steric fit into the target protein, and (iii) handling target flexibility. The combination of ligand- and receptor-based methods steers the virtual screening by ranking molecules according to the similarity of their interaction pattern with known ligands, thereby--to some extent--outweighing the deficiencies of simple scoring functions often used in initial virtual screening.

  15. Fasting - the ultimate diet?

    PubMed

    Johnstone, A M

    2007-05-01

    Adult humans often undertake acute fasts for cosmetic, religious or medical reasons. For example, an estimated 14% of US adults have reported using fasting as a means to control body weight and this approach has long been advocated as an intermittent treatment for gross refractory obesity. There are unique historical data sets on extreme forms of food restriction that give insight into the consequences of starvation or semi-starvation in previously healthy, but usually non-obese subjects. These include documented medical reports on victims of hunger strike, famine and prisoners of war. Such data provide a detailed account on how the body adapts to prolonged starvation. It has previously been shown that fasting for the biblical period of 40 days and 40 nights is well within the overall physiological capabilities of a healthy adult. However, the specific effects on the human body and mind are less clearly documented, either in the short term (hours) or in the longer term (days). This review asks the following three questions, pertinent to any weight-loss therapy, (i) how effective is the regime in achieving weight loss, (ii) what impact does it have on psychology? and finally, (iii) does it work long-term?

  16. Fast Track Study

    NASA Technical Reports Server (NTRS)

    1996-01-01

    The NASA Fast Track Study supports the efforts of a Special Study Group (SSG) made up of members of the Advanced Project Management Class number 23 (APM-23) that met at the Wallops Island Management Education Center from April 28 - May 8, 1996. Members of the Class expressed interest to Mr. Vem Weyers in having an input to the NASA Policy Document (NPD) 7120.4, that will replace NASA Management Institute (NMI) 7120.4, and the NASA Program/Project Management Guide. The APM-23 SSG was tasked with assisting in development of NASA policy on managing Fast Track Projects, defined as small projects under $150 million and completed within three years. 'Me approach of the APM-23 SSG was to gather data on successful projects working in a 'Better, Faster, Cheaper' environment, within and outside of NASA and develop the Fast Track Project section of the NASA Program/Project Management Guide. Fourteen interviews and four other data gathering efforts were conducted by the SSG, and 16 were conducted by Strategic Resources, Inc. (SRI), including five interviews at the Jet Propulsion Laboratory (JPL) and one at the Applied Physics Laboratory (APL). The interviews were compiled and analyzed for techniques and approaches commonly used to meet severe cost and schedule constraints.

  17. Mechanistic insights into the chemistry of RuII complexes containing Cl and DMSO ligands.

    PubMed

    Mola, Joaquim; Romero, Isabel; Rodríguez, Montserrat; Bozoglian, Fernando; Poater, Albert; Solà, Miquel; Parella, Teodor; Benet-Buchholz, Jordi; Fontrodona, Xavier; Llobet, Antoni

    2007-12-10

    Two new isomers trans,mer-[RuIICl2(bpea)(DMSO)], 2a, and cis,fac-[RuIICl2(bpea)(DMSO)], 2b, (bpea = N,N-bis(2-pyridylmethyl)ethylamine), as well as the bis-DMSO complex trans,fac-[RuIICl(bpea)(DMSO)2]Cl, 3, have been synthesized and characterized by cyclic voltammetry and UV-vis and 1D and 2D NMR spectroscopy in solution. Their solid-state structure has also been solved by means of single-crystal X-ray diffraction analysis. All the three complexes display a ruthenium metal center possessing a distorted-octahedral type of coordination, where the bpea ligand is coordinated in a meridional fashion in 2a and in a facial fashion in 2b and 3. The isomer 2a is the kinetically favored and thus can be thermally converted into 2b, that is the thermodynamically favored one. A thorough kinetic analysis strongly points toward a dissociative mechanism, where in the first step a chloro ligand is removed from the metal coordination sphere, followed by a geometric rearrangement before the chloro ligand coordinates again, generating the final complex. DFT calculations agree with the experimental data for the proposed mechanism and allow us to further characterize the mechanism of the 2a --> 2b rearrangement by obtaining the intermediates and transition state.

  18. Simulating complex ion channel kinetics with IonChannelLab

    PubMed Central

    Covarrubias, Manuel; Sánchez-Rodríguez, Jorge E; Perez-Cornejo, Patricia; Arreola, Jorge

    2010-01-01

    In-silico simulation based on Markov chains is a powerful way to describe and predict the activity of many transport proteins including ion channels. However, modeling and simulation using realistic models of voltage- or ligand-gated ion channels exposed to a wide range of experimental conditions require building complex kinetic schemes and solving complicated differential equations. To circumvent these problems, we developed IonChannelLab a software tool that includes a user-friendly Graphical User Interface and a simulation library. This program supports channels with Ohmic or Goldman-Hodgkin-Katz behavior and can simulate the time-course of ionic and gating currents, single channel behavior and steady-state conditions. The program allows the simulation of experiments where voltage, ligand and ionic concentration are varied independently or simultaneously. PMID:20935453

  19. Neighborhood fast food availability and fast food consumption

    PubMed Central

    Oexle, Nathalie; Barnes, Timothy L; Blake, Christine E; Bell, Bethany A; Liese, Angela D

    2015-01-01

    Recent nutritional and public health research has focused on how the availability of various types of food in a person’s immediate area or neighborhood influences his or her food choices and eating habits. It has been theorized that people living in areas with a wealth of unhealthy fast-food options may show higher levels of fast-food consumption, a factor that often coincides with being overweight or obese. However, measuring food availability in a particular area is difficult to achieve consistently: there may be differences in the strict physical locations of food options as compared to how individuals perceive their personal food availability, and various studies may use either one or both of these measures. The aim of this study was to evaluate the association between weekly fast-food consumption and both a person’s perceived availability of fast-food and an objective measure of fast-food presence—Geographic Information Systems (GIS)—within that person’s neighborhood. A randomly selected population-based sample of eight counties in South Carolina was used to conduct a cross-sectional telephone survey assessing self-report fast-food consumption and perceived availability of fast food. GIS was used to determine the actual number of fast-food outlets within each participant’s neighborhood. Using multinomial logistic regression analyses, we found that neither perceived availability nor GIS-based presence of fast-food was significantly associated with weekly fast-food consumption. Our findings indicate that availability might not be the dominant factor influencing fast-food consumption. We recommend using subjective availability measures and considering individual characteristics that could influence both perceived availability of fast food and its impact on fast-food consumption. If replicated, our findings suggest that interventions aimed at reducing fast-food consumption by limiting neighborhood fast-food availability might not be completely

  20. Neighborhood fast food availability and fast food consumption.

    PubMed

    Oexle, Nathalie; Barnes, Timothy L; Blake, Christine E; Bell, Bethany A; Liese, Angela D

    2015-09-01

    Recent nutritional and public health research has focused on how the availability of various types of food in a person's immediate area or neighborhood influences his or her food choices and eating habits. It has been theorized that people living in areas with a wealth of unhealthy fast-food options may show higher levels of fast-food consumption, a factor that often coincides with being overweight or obese. However, measuring food availability in a particular area is difficult to achieve consistently: there may be differences in the strict physical locations of food options as compared to how individuals perceive their personal food availability, and various studies may use either one or both of these measures. The aim of this study was to evaluate the association between weekly fast-food consumption and both a person's perceived availability of fast-food and an objective measure of fast-food presence - Geographic Information Systems (GIS) - within that person's neighborhood. A randomly selected population-based sample of eight counties in South Carolina was used to conduct a cross-sectional telephone survey assessing self-report fast-food consumption and perceived availability of fast food. GIS was used to determine the actual number of fast-food outlets within each participant's neighborhood. Using multinomial logistic regression analyses, we found that neither perceived availability nor GIS-based presence of fast-food was significantly associated with weekly fast-food consumption. Our findings indicate that availability might not be the dominant factor influencing fast-food consumption. We recommend using subjective availability measures and considering individual characteristics that could influence both perceived availability of fast food and its impact on fast-food consumption. If replicated, our findings suggest that interventions aimed at reducing fast-food consumption by limiting neighborhood fast-food availability might not be completely effective.

  1. Ligand engineering of nanoparticle solar cells

    NASA Astrophysics Data System (ADS)

    Voros, Marton

    Semiconductor nanoparticles (NP) are promising materials to build cheap and efficient solar cells. One of the key challenges in their utilization for solar energy conversion is the control of NP surfaces and ligand-NP interfaces. Recent experiments have shown that by carefully choosing the ligands terminating the NPs, one can tailor electronic and optical absorption properties of NP assemblies, along with their transport properties. By using density functional theory based methods, we investigated how the opto-electronic properties of lead chalcogenide NPs may be tuned by using diverse organic and inorganic ligands. We interpreted experiments, and we showed that an essential prerequisite to avoid detrimental trap states is to ensure charge balance at the ligand-NP interface, possibly with the help of hydrogen treatment Work supported by the Center for Advanced Solar Photophysics, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences.

  2. Automated design of ligands to polypharmacological profiles

    PubMed Central

    Besnard, Jérémy; Ruda, Gian Filippo; Setola, Vincent; Abecassis, Keren; Rodriguiz, Ramona M.; Huang, Xi-Ping; Norval, Suzanne; Sassano, Maria F.; Shin, Antony I.; Webster, Lauren A.; Simeons, Frederick R.C.; Stojanovski, Laste; Prat, Annik; Seidah, Nabil G.; Constam, Daniel B.; Bickerton, G. Richard; Read, Kevin D.; Wetsel, William C.; Gilbert, Ian H.; Roth, Bryan L.; Hopkins, Andrew L.

    2012-01-01

    The clinical efficacy and safety of a drug is determined by its activity profile across multiple proteins in the proteome. However, designing drugs with a specific multi-target profile is both complex and difficult. Therefore methods to rationally design drugs a priori against profiles of multiple proteins would have immense value in drug discovery. We describe a new approach for the automated design of ligands against profiles of multiple drug targets. The method is demonstrated by the evolution of an approved acetylcholinesterase inhibitor drug into brain penetrable ligands with either specific polypharmacology or exquisite selectivity profiles for G-protein coupled receptors. Overall, 800 ligand-target predictions of prospectively designed ligands were tested experimentally, of which 75% were confirmed correct. We also demonstrate target engagement in vivo. The approach can be a useful source of drug leads where multi-target profiles are required to achieve either selectivity over other drug targets or a desired polypharmacology. PMID:23235874

  3. Ligand inducible assembly of a DNA tetrahedron.

    PubMed

    Dohno, Chikara; Atsumi, Hiroshi; Nakatani, Kazuhiko

    2011-03-28

    Here we show that a small synthetic ligand can be used as a key building component for DNA nanofabrication. Using naphthyridinecarbamate dimer (NCD) as a molecular glue for DNA hybridization, we demonstrate NCD-triggered formation of a DNA tetrahedron.

  4. Advanced Organic Ligands for Protecting Metal Nanoparticles

    NASA Astrophysics Data System (ADS)

    Yu, Jonathan Ka-Wing

    Organic monolayer protected metal nanoparticles have been utilized in many different fields such as catalysis, drug delivery, and sensor chemistry. However, these nanomaterials are prone to increase in size consequently losing its function at the nanoscale. The stability these nanoparticles have been a great interest of research. This thesis focuses on the synthesis of a novel cross-linkable ligand for the protection of metal nanoparticles. Chapter 1 reviews key concepts of nanoparticles, its usefulness in applications, some of the stabilizing strategies employed, and the scope of the thesis project. Chapter 2 describes the synthetic attempts and optimization of the novel cross-linkable ligand. In addition, its characterization data is also included. Section 2.8 also highlights another fully synthesized novel hydrophobic ligand. Chapter 3 contains the summary of the work and closing remarks. Future works is also included to describe the prospects of the synthesis of the novel ligand. Chapter 4 entails the experimental data and supplementary information.

  5. GW-501516 GlaxoSmithKline/Ligand.

    PubMed

    Pelton, Patricia

    2006-04-01

    GlaxoSmithKline and Ligand are developing GW-501516, a peroxisome proliferator-activator receptor-delta agonist for the potential treatment of dyslipidemia. Phase II clinical trials of this compound are ongoing.

  6. The Retinoid X Receptors and Their Ligands

    PubMed Central

    Dawson, Marcia I.; Xia, Zebin

    2014-01-01

    This chapter presents an overview of the current status of studies on the structural and molecular biology of the retinoid X receptor subtypes α, β, and γ (RXRs, NR2B1–3), their nuclear and cytoplasmic functions, post-transcriptional processing, and recently reported ligands. Points of interest are the different changes in the ligand-binding pocket induced by variously shaped agonists, the communication of the ligand–bound pocket with the coactivator binding surface and the heterodimerization interface, and recently identified ligands that are natural products, those that function as environmental toxins or drugs that had been originally designed to interact with other targets, as well as those that were deliberately designed as RXR-selective transcriptional agonists, synergists, or antagonists. Of these synthetic ligands, the general trend in design appears to be away from fully aromatic rigid structures to those containing partial elements of the flexible tetraene side chain of 9-cis-retinoic acid. PMID:22020178

  7. Localized Control of Ligand Binding in Hemoglobin: Effect of Tertiary Structure on Picosecond Geminate Recombination

    NASA Astrophysics Data System (ADS)

    Friedman, J. M.; Scott, T. W.; Fisanick, G. J.; Simon, S. R.; Findsen, E. W.; Ondrias, M. R.; MacDonald, V. W.

    1985-07-01

    The picosecond geminate rebinding of molecular oxygen was monitored in a variety of different human, reptilian, and fish hemoglobins. The fast (100 to 200 picoseconds) component of the rebinding is highly sensitive to protein structure. Both proximal and distal perturbations of the heme affect this rebinding process. The rebinding yield for the fast process correlates with the frequency of the stretching motion of the iron-proximal histidine mode (vFe-His) observed in the transient Raman spectra of photodissociated ligated hemoglobins. The high-affinity R-state species exhibit the highest values for vFe-His and the highest yields for fast rebinding, whereas low affinity R-state species and T-state species exhibit lower values of vFe-His and correspondingly reduced yields for this geminate process. These findings link protein control of ligand binding with events at the heme.

  8. LLNL Chemical Kinetics Modeling Group

    SciTech Connect

    Pitz, W J; Westbrook, C K; Mehl, M; Herbinet, O; Curran, H J; Silke, E J

    2008-09-24

    The LLNL chemical kinetics modeling group has been responsible for much progress in the development of chemical kinetic models for practical fuels. The group began its work in the early 1970s, developing chemical kinetic models for methane, ethane, ethanol and halogenated inhibitors. Most recently, it has been developing chemical kinetic models for large n-alkanes, cycloalkanes, hexenes, and large methyl esters. These component models are needed to represent gasoline, diesel, jet, and oil-sand-derived fuels.

  9. Cationic cure kinetics of a polyoxometalate loaded epoxy nanocomposite

    SciTech Connect

    Anderson, Benjamin J.

    2012-08-06

    The reaction cure kinetics of a novel polyoxometalate (POM) loaded epoxy nanocomposite is described. The POM is dispersed in the epoxy resin up to volume fractions of 0.1. Differential scanning calorimetry measurements show the cure of the epoxy resin to be sensitive to the POM loading. A kinetics study of the cure exotherm confirms that POM acts as a catalyst promoting cationic homopolymerization of the epoxy resin. The cure reaction is shown to propagate through two cure regimes. A fast cure at short time is shown to be propagation by the activated chain end (ACE) mechanism. A slow cure at long time is shown to be propagation by the activated monomer (AM) mechanism. The activation energies for the fast and slow cure regimes agree well with other epoxy based systems that have been confirmed to propagate by the ACE and AM mechanisms.

  10. Origin of fast catalysis in allylic amination reactions catalyzed by Pd-Ti heterobimetallic complexes.

    PubMed

    Walker, Whitney K; Kay, Benjamin M; Michaelis, Scott A; Anderson, Diana L; Smith, Stacey J; Ess, Daniel H; Michaelis, David J

    2015-06-17

    Experiments and density functional calculations were used to quantify the impact of the Pd-Ti interaction in the cationic heterobimetallic Cl2Ti(N(t)BuPPh2)2Pd(η(3)-methallyl) catalyst 1 used for allylic aminations. The catalytic significance of the Pd-Ti interaction was evaluated computationally by examining the catalytic cycle for catalyst 1 with a conformation where the Pd-Ti interaction is intact versus one where the Pd-Ti interaction is severed. Studies were also performed on the relative reactivity of the cationic monometallic (CH2)2(N(t)BuPPh2)2Pd(η(3)-methallyl) catalyst 2 where the Ti from catalyst 1 was replaced by an ethylene group. These computational and experimental studies revealed that the Pd-Ti interaction lowers the activation barrier for turnover-limiting amine reductive addition and accelerates catalysis up to 10(5). The Pd-Ti distance in 1 is the result of the N(t)Bu groups enforcing a boat conformation that brings the two metals into close proximity, especially in the transition state. The turnover frequency of classic Pd π allyl complexes was compared to that of 1 to determine the impact of P-Pd-P coordination angle and ligand electronic properties on catalysis. These experiments identified that cationic (PPh3)2Pd(η(3)-CH2C(CH3)CH2) catalyst 3 performs similarly to 1 for allylic aminations with diethylamine. However, computations and experiment reveal that the apparent similarity in reactivity is due to very fast reaction kinetics. The higher reactivity of 1 versus 3 was confirmed in the reaction of methallyl chloride and 2,2,6,6-tetramethylpiperidine (TMP). Overall, experiments and calculations demonstrate that the Pd-Ti interaction induces and is responsible for significantly lower barriers and faster catalysis for allylic aminations.

  11. Affinity Electrophoresis Using Ligands Attached To Polymers

    NASA Technical Reports Server (NTRS)

    Van Alstine, James M.; Snyder, Robert S.; Harris, J. M.; Brooks, D. E.

    1990-01-01

    In new technique, reduction of electrophoretic mobilities by addition of polyethylene glycol to ligands increases electrophoretic separabilities. In immuno-affinity electrophoresis, modification of ligands extends specificity of electrophoretic separation to particles having surface electric-charge structures otherwise making them electrophoretically inseparable. Modification of antibodies by polyethylene glycol greatly reduces ability to aggregate while enhancing ability to affect electrophoretic mobilities of cells. In hydrophobic-affinity electrophoresis, addition of polyethylene glycol reduces tendency toward aggregation of cells or macromolecules.

  12. Modelling of trace metal uptake by roots taking into account complexation by exogenous organic ligands

    NASA Astrophysics Data System (ADS)

    Jean-Marc, Custos; Christian, Moyne; Sterckeman, Thibault

    2010-05-01

    The context of this study is phytoextraction of soil trace metals such as Cd, Pb or Zn. Trace metal transfer from soil to plant depends on physical and chemical processes such as minerals alteration, transport, adsorption/desorption, reactions in solution and biological processes including the action of plant roots and of associated micro-flora. Complexation of metal ions by organic ligands is considered to play a role on the availability of trace metals for roots in particular in the event that synthetic ligands (EDTA, NTA, etc.) are added to the soil to increase the solubility of the contaminants. As this role is not clearly understood, we wanted to simulate it in order to quantify the effect of organic ligands on root uptake of trace metals and produce a tool which could help in optimizing the conditions of phytoextraction.We studied the effect of an aminocarboxilate ligand on the absorption of the metal ion by roots, both in hydroponic solution and in soil solution, for which we had to formalize the buffer power for the metal. We assumed that the hydrated metal ion is the only form which can be absorbed by the plants. Transport and reaction processes were modelled for a system made up of the metal M, a ligand L and the metal complex ML. The Tinker-Nye-Barber model was adapted to describe the transport of solutes M, L and ML in the soil and absorption of M by the roots. This allowed to represent the interactions between transport, chelating reactions, absorption of the solutes at the root surface, root growth with time, in order to simulate metal uptake by a whole root system.Several assumptions were tested such as i) absorption of the metal by an infinite sink and according to a Michaelis-Menten kinetics, solutes transport by diffusion with and without ii) mass flow and iii) soil buffer power for the ligand L. In hydroponic solution (without soil buffer power), ligands decreased the trace metal flux towards roots, as they reduced the concentration of hydrated

  13. Rifampicin-Independent Interactions between the Pregnane X Receptor Ligand Binding Domain and Peptide Fragments of Coactivator and Corepressor Proteins

    PubMed Central

    Navaratnarajah, Punya; Steele, Bridgett L.; Redinbo, Matthew R.; Thompson, Nancy L.

    2015-01-01

    The pregnane X receptor (PXR), a member of the nuclear receptor superfamily, regulates the expression of drug-metabolizing enzymes in a ligand-dependent manner. The conventional view of nuclear receptor action is that ligand binding enhances the receptor’s affinity for coactivator proteins, while decreasing its affinity for corepressors. To date, however, no known rigorous biophysical studies have been conducted to investigate the interaction among PXR, its coregulators, and ligands. In this work, steady-state total internal reflection fluorescence microscopy (TIRFM) and total internal reflection with fluorescence recovery after photobleaching were used to measure the thermodynamics and kinetics of the interaction between the PXR ligand binding domain and a peptide fragment of the steroid receptor coactivator-1 (SRC-1) in the presence and absence of the established PXR agonist, rifampicin. Equilibrium dissociation and dissociation rate constants of ~5 μM and ~2 s−1, respectively, were obtained in the presence and absence of rifampicin, indicating that the ligand does not enhance the affinity of the PXR and SRC-1 fragments. Additionally, TIRFM was used to examine the interaction between PXR and a peptide fragment of the corepressor protein, the silencing mediator for retinoid and thyroid receptors (SMRT). An equilibrium dissociation constant of ~70 μM was obtained for SMRT in the presence and absence of rifampicin. These results strongly suggest that the mechanism of ligand-dependent activation in PXR differs significantly from that seen in many other nuclear receptors. PMID:22185585

  14. Characterizing dissolved Cu and Cd uptake in terms of the biotic ligand and biodynamics using enriched stable isotopes

    USGS Publications Warehouse

    Croteau, M.-N.; Luoma, S.N.

    2007-01-01

    The biotic ligand model considers the biological and geochemical complexities that affect metal exposure. It relates toxicity to the fraction of physiological active sites impacted by reactive metal species. The biodynamic model is a complementary construct that predicts bioaccumulation and assumes that toxicity occurs when influx rates exceed rates of loss and detoxification. In this paper we presume that metal influx rates are mechanistically the resulting processes that characterize transmembrane transport. We use enriched stable isotopes to characterize, both in terms of the biotic ligand and biodynamics, dissolved metal uptake by a freshwater snail at water hardness varying up to 180-fold. Upon 24 h exposure, metal uptake was linear over a range encompassing most environmental concentrations; although saturation kinetics were observed at higher concentrations. Cadmium influx rates correlate with changes in the affinity of the biotic ligand, whereas those of Cu correlate with changes in both site affinity and capacity. A relationship between metal influx rate and ligand character asks whether toxicity is the result of accumulation at the biotic ligand or the rate at which metal is transported by that ligand.

  15. An Introductory Level Kinetics Investigation.

    ERIC Educational Resources Information Center

    McGarvey, J. E. B.; Knipe, A. C.

    1980-01-01

    Provides a list of the reactions commonly used for introductory kinetics studies. These reactions illustrate the kinetics concepts of rate law, rate constant, and reaction order. Describes a kinetic study of the hydrolysis of 3-bromo-3-phenylpropanoic acid which offers many educational advantages. (CS)

  16. Semiconductor Quantum Dots with Photoresponsive Ligands.

    PubMed

    Sansalone, Lorenzo; Tang, Sichen