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Sample records for affinity dissociation constant

  1. Inhibition of ionotropic neurotransmitter receptors by antagonists: strategy to estimate the association and the dissociation rate constant of antagonists with very strong affinity to the receptors.

    PubMed

    Aoshima, H; Inoue, Y; Hori, K

    1992-10-01

    Since binding of an agonist to an ionotropic neurotransmitter receptor causes not only channel opening, but also desensitization of the receptor, inhibition of the receptor by the antagonist sometimes becomes very complicated. The transient state kinetics of ligand association and dissociation, and desensitization of the receptor were considered on the basis of the minimal model proposed by Hess' group, and the following possibilities were proposed. 1) When an agonist is simultaneously applied to the receptor with an antagonist whose affinity to the receptor is extremely strong and different from that of the agonist, it is usually impossible to estimate the real inhibition constant exactly from the responses because desensitization of the receptor proceeds before the equilibrium of the ligand binding. Simultaneous addition of the antagonist with strong affinity to the receptor may apparently accelerate inactivation (desensitization) of the receptor. The association rate constant of the antagonist can be estimated by analyses of the rate of the inactivation in the presence and the absence of the antagonist. 2) A preincubated antagonist with a slow dissociation rate constant, i.e., a very effective inhibitor, may cause apparent noncompetitive inhibition of the receptor, since the receptor is desensitized by an agonist as soon as the antagonist dissociates from the receptor and the dissociation of the antagonist from the receptor becomes the rate-determining step. A nicotinic acetylcholine receptor (nAChR) was expressed in Xenopus oocytes by injecting mRNA prepared from Electrophorus electricus electroplax and used for the experiments on inhibition by an antagonist.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:1337082

  2. Automatic gesture analysis using constant affine velocity.

    PubMed

    Cifuentes, Jenny; Boulanger, Pierre; Pham, Minh Tu; Moreau, Richard; Prieto, Flavio

    2014-01-01

    Hand human gesture recognition has been an important research topic widely studied around the world, as this field offers the ability to identify, recognize, and analyze human gestures in order to control devices or to interact with computer interfaces. In particular, in medical training, this approach is an important tool that can be used to obtain an objective evaluation of a procedure performance. In this paper, some obstetrical gestures, acquired by a forceps, were studied with the hypothesis that, as the scribbling and drawing movements, they obey the one-sixth power law, an empirical relationship which connects path curvature, torsion, and euclidean velocity. Our results show that obstetrical gestures have a constant affine velocity, which is different for each type of gesture and based on this idea this quantity is proposed as an appropriate classification feature in the hand human gesture recognition field. PMID:25570332

  3. The dissociation constant of water at extreme conditions

    NASA Astrophysics Data System (ADS)

    Gonzalez-Vazquez, Otto; Giacomazzi, Luigi; Pinilla, C.; Scandolo, Sandro

    2013-06-01

    Only one out of 107 water molecules is dissociated in liquid water at ambient conditions, but the concentration of dissociated molecules increases with pressure ad temperature, and water eventually reaches a fully dissociated state when pressure exceeds 50-100 GPa and temperature reaches a few thousand Kelvin. The behavior of the dissociation constant of water (pKa) at conditions intermediate between ambient and the fully dissociated state is poorly known. Yet, the water pKa is a parameter of primary importance in the aqueous geochemistry as it controls the solubility of ions in geological fluids. We present results of molecular dynamics calculations of the pKa water at extreme conditions. Free-energy differences between the undissociated and the dissociated state are calculated by thermodynamic integration along the dissociation path. The calculations are based on a recently developed all-atom polarizable force-field for water, parametrized on density-functional theory calculations.

  4. Radioligand Binding Assays for Determining Dissociation Constants of Phytohormone Receptors.

    PubMed

    Hellmuth, Antje; Calderón Villalobos, Luz Irina A

    2016-01-01

    In receptor-ligand interactions, dissociation constants provide a key parameter for characterizing binding. Here, we describe filter-based radioligand binding assays at equilibrium, either varying ligand concentrations up to receptor saturation or outcompeting ligand from its receptor with increasing concentrations of ligand analogue. Using the auxin coreceptor system, we illustrate how to use a saturation binding assay to determine the apparent dissociation constant (K D (') ) for the formation of a ternary TIR1-auxin-AUX/IAA complex. Also, we show how to determine the inhibitory constant (K i) for auxin binding by the coreceptor complex via a competition binding assay. These assays can be applied broadly to characterize a one-site binding reaction of a hormone to its receptor. PMID:27424743

  5. MEASUREMENT OF DRUG-PROTEIN DISSOCIATION RATES BY HIGH-PERFORMANCE AFFINITY CHROMATOGRAPHY AND PEAK PROFILING

    PubMed Central

    Schiel, John E.; Ohnmacht, Corey M.; Hage, David S.

    2012-01-01

    The rate at which a drug or other small solute interacts with a protein is important in understanding the biological and pharmacokinetic behavior of these agents. One approach that has been developed for examining these rates involves the use of high-performance affinity chromatography (HPAC) and estimates of band-broadening through peak profiling. Previous work with this method has been based on a comparison of the statistical moments for a retained analyte versus non-retained species at a single, high flow rate to obtain information on stationary phase mass transfer. In this study an alternative approach was created that allows a broad range of flow rates to be used for examining solute-protein dissociation rates. Chromatographic theory was employed to derive equations that could be used with this approach on a single column, as well as with multiple columns to evaluate and correct for the impact of stagnant mobile phase mass transfer. The interaction of L-tryptophan with human serum albumin was used as a model system to test this method. A dissociation rate constant of 2.7 (± 0.2) s−1 was obtained by this approach at pH 7.4 and 37°C, which was in good agreement with previous values determined by other methods. The techniques described in this report can be applied to other biomolecular systems and should be valuable for the determination of drug-protein dissociation rates. PMID:19422253

  6. Semiclassical Calculation of Reaction Rate Constants for Homolytical Dissociations

    NASA Technical Reports Server (NTRS)

    Cardelino, Beatriz H.

    2002-01-01

    There is growing interest in extending organometallic chemical vapor deposition (OMCVD) to III-V materials that exhibit large thermal decomposition at their optimum growth temperature, such as indium nitride. The group III nitrides are candidate materials for light-emitting diodes and semiconductor lasers operating into the blue and ultraviolet regions. To overcome decomposition of the deposited compound, the reaction must be conducted at high pressures, which causes problems of uniformity. Microgravity may provide the venue for maintaining conditions of laminar flow under high pressure. Since the selection of optimized parameters becomes crucial when performing experiments in microgravity, efforts are presently geared to the development of computational OMCVD models that will couple the reactor fluid dynamics with its chemical kinetics. In the present study, we developed a method to calculate reaction rate constants for the homolytic dissociation of III-V compounds for modeling OMCVD. The method is validated by comparing calculations with experimental reaction rate constants.

  7. New (alpha-Hydroxyalkyl)phosphorus Amphiphiles: Synthesis and Dissociation Constants.

    PubMed

    Albouy, Dominique; Brun, Alice; Munoz, Aurelio; Etemad-Moghadam, Guita

    1998-10-16

    Direct synthesis of free (alpha-hydroxyalkyl)phosphinic acid amphiphiles 1 can be readily realized by sonication of the heterogeneous mixture of 50% aqueous hypophosphorous acid and long-chain aldehydes in the presence of catalytic amounts of hydrochloric acid. Oxidation of these phosphinic acids by DMSO in the presence of catalytic amounts of iodine quantitatively leads to the corresponding phosphonic acids 3. IR spectra of the phosphinic acids 1 in the condensed phase and in solution reveal the presence of intra- and intermolecular associations. Dissociation constants of the phosphorus acids 1 and 3 determined by potentiometric and (31)P NMR titrations show a good correlation between the two methods. The phosphinic acid amphiphiles 1 are slightly stronger than the corresponding phosphonic acids 3. (alpha-Hydroxyalkyl)phosphonium chlorides are prepared in good yields from the phosphine PH(3) and long-chain aldehydes in acidic media.

  8. Determination of thermodynamic values of acidic dissociation constants and complexation constants of profens and their utilization for optimization of separation conditions by Simul 5 Complex.

    PubMed

    Riesová, Martina; Svobodová, Jana; Ušelová, Kateřina; Tošner, Zdeněk; Zusková, Iva; Gaš, Bohuslav

    2014-10-17

    In this paper we determine acid dissociation constants, limiting ionic mobilities, complexation constants with β-cyclodextrin or heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin, and mobilities of resulting complexes of profens, using capillary zone electrophoresis and affinity capillary electrophoresis. Complexation parameters are determined for both neutral and fully charged forms of profens and further corrected for actual ionic strength and variable viscosity in order to obtain thermodynamic values of complexation constants. The accuracy of obtained complexation parameters is verified by multidimensional nonlinear regression of affinity capillary electrophoretic data, which provides the acid dissociation and complexation parameters within one set of measurements, and by NMR technique. A good agreement among all discussed methods was obtained. Determined complexation parameters were used as input parameters for simulations of electrophoretic separation of profens by Simul 5 Complex. An excellent agreement of experimental and simulated results was achieved in terms of positions, shapes, and amplitudes of analyte peaks, confirming the applicability of Simul 5 Complex to complex systems, and accuracy of obtained physical-chemical constants. Simultaneously, we were able to demonstrate the influence of electromigration dispersion on the separation efficiency, which is not possible using the common theoretical approaches, and predict the electromigration order reversals of profen peaks. We have shown that determined acid dissociation and complexation parameters in combination with tool Simul 5 Complex software can be used for optimization of separation conditions in capillary electrophoresis.

  9. NON-COMPETITIVE PEAK DECAY ANALYSIS OF DRUG-PROTEIN DISSOCIATION BY HIGH-PERFORMANCE AFFINITY CHROMATOGRAPHY

    PubMed Central

    Chen, Jianzhong; Schiel, John E.; Hage, David S.

    2009-01-01

    The peak decay method is an affinity chromatographic technique that has been used to examine the dissociation of solutes from immobilized ligands in the presence of excess displacing agent. However, it can be difficult to find a displacing agent that does not interfere with detection of the eluting analyte. In this study, a non-competitive peak decay method was developed in which no displacing agent was required for analyte elution. This method was evaluated for the study of drug-protein interactions by using it along with high-performance affinity chromatography to measure the dissociation rate constants for R- and S-warfarin from columns containing immobilized human serum albumin (HSA). Several factors were considered in the optimization of this method, including the amount of applied analyte, the column size, and the flow rate. The dissociation rate constants for R- and S-warfarin from HSA were measured at several temperatures by this approach, giving values of 0.56 (± 0.01) and 0.66 (± 0.01) s−1 at pH 7.4 and 37°C. These results were in good agreement with previous values obtained by other methods. This approach is not limited to warfarin and HSA but could be employed in studying additional drug-protein interactions or other systems with weak-to-moderate binding. PMID:19472288

  10. Determination of proton affinities and acidity constants of sugars.

    PubMed

    Feng, Shuting; Bagia, Christina; Mpourmpakis, Giannis

    2013-06-20

    Proton transfer reactions play a key role in the conversion of biomass derived sugars to chemicals. In this study, we employ high level ab initio theoretical methods, in tandem with solvation effects to calculate the proton affinities (PA) and acidity constants (pKa) of various d-glucose and d-fructose tautomers (protonation-deprotonation processes). In addition, we compare the theoretically derived pH values of sugar solutions against experimentally measured pH values in our lab. Our results demonstrate that the protonation of any of the O atoms of the sugars is thermodynamically preferred without any significant variation in the PA values. Intramolecular hydrogen transfers, dehydration reactions, and ring-opening processes were observed, resulting from the protonation of specific hydroxyl groups on the sugars. Regarding the deprotonation processes (pKa), we found that the sugars' anomeric hydroxyls exhibit the highest acidity. The theoretically calculated pH values of sugar solutions are in excellent agreement with experimental pH measurements at low sugar concentrations. At higher sugar concentrations the calculations predict less acidic solutions than the experiments. In this case, we expect the sugars to act as solvents increasing the proton solvation energy and the acidity of the solutions. We demonstrated through linear relationships that the pKa values are correlated with the relative stability of the conjugate bases. The latter is related to hydrogen bonding and polarization of the C-O(-) bond. A plausible explanation for the good performance of the direct method in calculating the pKa values of sugars can be the presence of intramolecular hydrogen bonds on the conjugate base. Both theory and experiments manifest that fructose is a stronger acid than glucose, which is of significant importance in self-catalyzed biomass-relevant dehydration reactions. PMID:23706015

  11. Bayesian Estimation of the Active Concentration and Affinity Constants Using Surface Plasmon Resonance Technology.

    PubMed

    Feng, Feng; Kepler, Thomas B

    2015-01-01

    Surface plasmon resonance (SPR) has previously been employed to measure the active concentration of analyte in addition to the kinetic rate constants in molecular binding reactions. Those approaches, however, have a few restrictions. In this work, a Bayesian approach is developed to determine both active concentration and affinity constants using SPR technology. With the appropriate prior probabilities on the parameters and a derived likelihood function, a Markov Chain Monte Carlo (MCMC) algorithm is applied to compute the posterior probability densities of both the active concentration and kinetic rate constants based on the collected SPR data. Compared with previous approaches, ours exploits information from the duration of the process in its entirety, including both association and dissociation phases, under partial mass transport conditions; do not depend on calibration data; multiple injections of analyte at varying flow rates are not necessary. Finally the method is validated by analyzing both simulated and experimental datasets. A software package implementing our approach is developed with a user-friendly interface and made freely available. PMID:26098764

  12. Simulations of dissociation constants in low pressure supercritical water

    NASA Astrophysics Data System (ADS)

    Halstead, S. J.; An, P.; Zhang, S.

    2014-09-01

    This article reports molecular dynamics simulations of the dissociation of hydrochloric acid and sodium hydroxide in water from ambient to supercritical temperatures at a fixed pressure of 250 atm. Corrosion of reaction vessels is known to be a serious problem of supercritical water, and acid/base dissociation can be a significant contributing factor to this. The SPC/e model was used in conjunction with solute models determined from density functional calculations and OPLSAA Lennard-Jones parameters. Radial distribution functions were calculated, and these show a significant increase in solute-solvent ordering upon forming the product ions at all temperatures. For both dissociations, rapidly decreasing entropy of reaction was found to be the controlling thermodynamic factor, and this is thought to arise due to the ions produced from dissociation maintaining a relatively high density and ordered solvation shell compared to the reactants. The change in entropy of reaction reaches a minimum at the critical temperature. The values of pKa and pKb were calculated and both increased with temperature, in qualitative agreement with other work, until a maximum value at 748 K, after which there was a slight decrease.

  13. Determination of Acid Dissociation Constant of Pravastatin under Degraded Conditions by Capillary Zone Electrophoresis.

    PubMed

    Takayanagi, Toshio; Amiya, Mika; Shimakami, Natsumi; Yabutani, Tomoki

    2015-01-01

    The acid dissociation constant of pravastatin was determined under degraded conditions. Pravastatin was degraded in an acidic solution (pH = 2.0) for 5 h, and the degradation solution was subjected to the measurement of the effective electrophoretic mobility by capillary zone electrophoresis. Although the amount of pravastatin decreased by the acid degradation, its acid dissociation constant was successfully determined with the residual pravastatin through its effective electrophoretic mobility. The determined acid dissociation constant value agreed well with the one obtained with freshly prepared solution and with some reported values.

  14. High Throughput pharmacokinetic modeling using computationally predicted parameter values: dissociation constants (TDS)

    EPA Science Inventory

    Estimates of the ionization association and dissociation constant (pKa) are vital to modeling the pharmacokinetic behavior of chemicals in vivo. Methodologies for the prediction of compound sequestration in specific tissues using partition coefficients require a parameter that ch...

  15. The fundamental constants of orthotropic affine plate/slab equations

    NASA Technical Reports Server (NTRS)

    Brunelle, E. J.

    1984-01-01

    The global constants associated with orthotropic slab/plate equations are discussed, and the rotational behavior of the modulus/compliance components associated with orthotropic slabs/plates are addressed. It is concluded that one cluster constant is less than or equal to unity for all physically possible materials. Rotationally anomalous behavior is found in two materials, and a simple inequality which can be used to identify regular or anomalous behavior is presented and discussed in detail.

  16. Specific allowance for antibody bivalence in the determination of dissociation constants by kinetic exclusion assay.

    PubMed

    Winzor, Donald J

    2011-07-15

    Theory that takes rigorous account of antibody bivalence in the characterization of immunospecific reactions by kinetic exclusion assay is presented. In addition to reinforcing the basic correctness of quantitative expressions currently being used for the determination of dissociation constants (K(d)) by this method, the current study highlights a requirement for conformity of the system with critical assumptions/approximations therein. Published results for the interaction between the extracellular domain of human insulin-like growth factor (hIGFR) and anti-hIGFR are used to illustrate aspects of the theoretical predictions for a system to which those assumptions/approximations may well apply; and those for a cadmium-ethylenediaminetetraacetic acid (Cd-EDTA) antibody interaction to emphasize the consequences of adopting the same analytical procedure in a situation where one of those assumptions does not apply. The major weakness of current protocols for the characterization of antigen-antibody interactions by kinetic exclusion assay is an absence of any check on the likely magnitude of the probability of antibody capture by the affinity beads--a parameter that needs to be 5% or lower for validity of the quantitative expression on which the analysis is based. PMID:21443855

  17. Determination of Dissociation Constants in Living Zebrafish Embryos with Single Wavelength Fluorescence Cross-Correlation Spectroscopy

    PubMed Central

    Shi, Xianke; Foo, Yong Hwee; Sudhaharan, Thankiah; Chong, Shang-Wei; Korzh, Vladimir; Ahmed, Sohail; Wohland, Thorsten

    2009-01-01

    Abstract The quantification of biological interactions is very important in life sciences. Here we report for the first time, to our knowledge, the determination of a biomolecular dissociation constant (KD) in living zebrafish embryos at physiological protein expression levels. For that purpose, we extend the application of single wavelength fluorescence cross-correlation spectroscopy into small organisms and measure the interaction of Cdc42, a small Rho-GTPase, and IQGAP1, an actin-binding scaffolding protein. Cdc42 and IQGAP1 were labeled with monomeric red fluorescent protein and enhanced green fluorescent protein, respectively. Both fluorophores were excited at a single wavelength of 514 nm, simplifying the fluorescence spectroscopy measurements and allowing quantification. For the determination of the interaction, we used two Cdc42 mutants, the constitutively active Cdc42G12V which is in a predominantly GTP-bound form and the dominant-negative GDP-bound Cdc42T17N. While Cdc42G12V binds to IQGAP1 with an apparent KD of ∼100 nM, Cdc42T17N has at least a one-order-of-magnitude lower affinity for the same protein. As a comparison, we measure the same protein-protein interactions in Chinese hamster ovary cell cultures but observe significant differences in protein mobility and KD from the zebrafish measurements, supporting the notion that bimolecular interactions depend on the biological system under investigation and are best performed under physiologically relevant conditions. PMID:19619483

  18. Determination of dissociation constants of flavonoids by capillary electrophoresis.

    PubMed

    Herrero-Martínez, José M; Sanmartin, Meritxell; Rosés, Martí; Bosch, Elisabeth; Ràfols, Clara

    2005-05-01

    Ionization constants of some flavanols (catechin and epicatechin) and flavonols (kaempherol, fisetin, morin, and quercetin) are determined by capillary zone electrophoresis (CZE). This technique allows the determination of pK(a) values until about 12. The pK(a) values obtained are compared with those calculated by the SPARC computational program. This program predicts the microscopic and macroscopic pK(a) values and the order of deprotonation of the different -OH groups. While for catechin and epicatechin the first ionizable OH group occurs in ring 1 and the second ionizable group in ring 2, in flavonols the first deprotonation occurs in ring 2 and the second in ring 1.

  19. Dissociation constant measurement using combination tapered fiber optic biosensor (CTFOB) dip-probes

    NASA Astrophysics Data System (ADS)

    Wang, Chun-Wei; Kapoor, Rakesh

    2010-02-01

    The document reports a novel method of measuring dissociation constant (kD) of antibody-antigen interaction using evanescent wave based combination tapered fiber-optic biosensor (CTFOB) dip-probes. The method was demonstrated by measuring the dissociation constant of human Interleukin-6 (IL-6) and anti-IL-6 interaction. Sandwich immunoassay was used to generate fluorescence signal proportional to antigen-antibody conjugate pairs. A portable CCD based spectrometer setup was used to record spectral profile of the fluorescence signal. The measured value of dissociation constant kD for IL-6 and capture anti-IL-6 (clone MQ2-13A5) antibodies at room temperature is588 +/-19 pM .

  20. Understanding selenocysteine through conformational analysis, proton affinities, acidities and bond dissociation energies

    NASA Astrophysics Data System (ADS)

    Kaur, Damanjit; Sharma, Punita; Bharatam, Prasad V.; Kaur, Mondeep

    Density functional methods have been employed to characterize the gas phase conformations of selenocysteine. The 33 stable conformers of selenocysteine have been located on the potential energy surface using density functional B3LYP/6-31+G* method. The conformers are analyzed in terms of intramolecular hydrogen bonding interactions. The proton affinity, gas phase acidities, and bond dissociation energies have also been evaluated for different reactive sites of selenocysteine for the five lowest energy conformers at B3LYP/6-311++G*//B3LYP/6-31+G* level. Evaluation of these intrinsic properties reflects the antioxidant activity of selenium in selenocysteine.0

  1. Determination of chromatographic and spectrophotometric dissociation constants of some beta lactam antibiotics.

    PubMed

    Demiralay, Ebru Çubuk; Koç, Duygu; Daldal, Y Doğan; Cakır, Cansel

    2012-12-01

    In this work, dissociation constants values of seven beta lactam antibiotics in water and acetonitrile-water mixtures using spectrophotometric and reversed phase liquid chromatography methods were determined. The dissociation constant values of these compounds were calculated by NLREG and STAR programs. Aqueous pK(a) values of beta lactam antibiotics were calculated with extrapolation by means of the Yasuda-Shedlovsky and mole fraction equations. Finally, application of the different techniques was compared to the determination of aqueous pK(a) values of investigated compounds.

  2. The vibrational dependence of dissociative recombination: Rate constants for N{sub 2}{sup +}

    SciTech Connect

    Guberman, Steven L.

    2014-11-28

    Dissociative recombination rate constants are reported with electron temperature dependent uncertainties for the lowest 5 vibrational levels of the N{sub 2}{sup +} ground state. The rate constants are determined from ab initio calculations of potential curves, electronic widths, quantum defects, and cross sections. At 100 K electron temperature, the rate constants overlap with the exception of the third vibrational level. At and above 300 K, the rate constants for excited vibrational levels are significantly smaller than that for the ground level. It is shown that any experimentally determined total rate constant at 300 K electron temperature that is smaller than 2.0 × 10{sup −7} cm{sup 3}/s is likely to be for ions that have a substantially excited vibrational population. Using the vibrational level specific rate constants, the total rate constant is in very good agreement with that for an excited vibrational distribution found in a storage ring experiment. It is also shown that a prior analysis of a laser induced fluorescence experiment is quantitatively flawed due to the need to account for reactions with unknown rate constants. Two prior calculations of the dissociative recombination rate constant are shown to be inconsistent with the cross sections upon which they are based. The rate constants calculated here contribute to the resolution of a 30 year old disagreement between modeled and observed N{sub 2}{sup +} ionospheric densities.

  3. DISSOCIATION OF ARSENITE-PEPTIDE COMPLEXES: TRIPHASIC NATURE, RATE CONSTANTS, HALF LIVES AND BIOLOGICAL IMPORTANCE

    EPA Science Inventory

    We determined the number and the dissociation rate constants of different complexes formed from arsenite and two peptides containing either one (RV AVGNDYASGYHYGV for peptide 20) or three cysteines (LE AWQGK VEGTEHLYSMK K for peptide 10) via radioactive 73As labeled arsenite and ...

  4. Analysis of agonist dissociation constants as assessed by functional antagonism in guinea pig left atria

    SciTech Connect

    Molenaar, P.; Malta, E.

    1986-04-01

    In electrically driven guinea pig left atria, positive inotropic responses to (-)-isoprenaline and the selective beta 1-adrenoceptor agonist RO363 were obtained in the absence and in the presence of the functional antagonists adenosine, carbachol, gallopamil, nifedipine, and Ro 03-7894. Each of the functional antagonists reduced the maximum response to both agonists and produced nonparallel rightward shifts in the cumulative concentration effect curves. For both agonists, dissociation constants (KA) were calculated using the equation described by Furchgott (1966) for irreversible antagonism. For RO363, which is a partial agonist with high agonist activity, the equations outlined for functional interaction by Mackay (1981) were also employed to calculate KA values. The KA values obtained by each method were compared with the dissociation constants (KD) for the two agonists determined from their ability to displace the radioligand (-)-(/sup 125/I)iodocyanopindolol from beta 1-adrenoceptors in guinea pig left atrial membrane preparations. The estimates of KA varied substantially from KD values. The KD values were taken as more accurate estimates of the true values for the dissociation constants because a high degree of correlation exists between pKD and pD2 values for a number of other beta-adrenoceptor agonists that behave as partial agonists and between pKD and pKB values for a number of beta-adrenoceptor antagonists. Thus, it appears that there are serious limitations in the current theory for using functional antagonism as a means of obtaining agonist dissociation constants.

  5. Energy-dependent dissociation of ATP from high affinity catalytic sites of beef heart mitochondrial adenosine triphosphatase

    SciTech Connect

    Penefsky, H.S.

    1985-11-05

    Incubation of (gamma-TSP)ATP with a molar excess of the membrane-bound form of mitochondrial ATPase (F1) results in binding of the bulk of the radioactive nucleotide in high affinity catalytic sites (Ka = 10(12) M-1). Subsequent initiation of respiration by addition of succinate or NADH is accompanied by a profound decrease in the affinity for ATP. About one-third of the bound radioactive ATP appears to dissociate, that is, the (gamma-TSP)ATP becomes accessible to hexokinase. The NADH-stimulated dissociation of (gamma-TSP)ATP is energy-dependent since the stimulation is inhibited by uncouplers of oxidative phosphorylation and is prevented by respiratory chain inhibitors. The rate of the energy-dependent dissociation of ATP that occurs in the presence of NADH, ADP, and Pi is commensurate with the measured initial rate of ATP synthesis in NADH-supported oxidative phosphorylation catalyzed by the same submitochondrial particles. Thus, the rate of dissociation of ATP from the high affinity catalytic site of submitochondrial particles meets the criterion of kinetic competency under the conditions of oxidative phosphorylation. These experiments provide evidence in support of the argument that energy conserved during the oxidation of substrates by the respiratory chain can be utilized to reduce the very tight binding of product ATP in high affinity catalytic sites and to promote dissociation of the nucleotide.

  6. Determination of Henry's constant, the dissociation constant, and the buffer capacity of the bicarbonate system in ruminal fluid.

    PubMed

    Hille, Katharina T; Hetz, Stefan K; Rosendahl, Julia; Braun, Hannah-Sophie; Pieper, Robert; Stumpff, Friederike

    2016-01-01

    Despite the clinical importance of ruminal acidosis, ruminal buffering continues to be poorly understood. In particular, the constants for the dissociation of H2CO3 and the solubility of CO2 (Henry's constant) have never been stringently determined for ruminal fluid. The pH was measured in parallel directly in the rumen and the reticulum in vivo, and in samples obtained via aspiration from 10 fistulated cows on hay- or concentrate-based diets. The equilibrium constants of the bicarbonate system were measured at 38°C both using the Astrup technique and a newly developed method with titration at 2 levels of partial pressure of CO2 (pCO2; 4.75 and 94.98 kPa), yielding mean values of 0.234 ± 0.005 mmol ∙ L(-1) ∙ kPa(-1) and 6.11 ± 0.02 for Henry's constant and the dissociation constant, respectively (n/n = 31/10). Both reticular pH and the pH of samples measured after removal were more alkalic than those measured in vivo in the rumen (by ΔpH = 0.87 ± 0.04 and 0.26 ± 0.04). The amount of acid or base required to shift the pH of ruminal samples to 6.4 or 5.8 (base excess) differed between the 2 feeding groups. Experimental results are compared with the mathematical predictions of an open 2-buffer Henderson-Hasselbalch equilibrium model. Because pCO2 has pronounced effects on ruminal pH and can decrease rapidly in samples removed from the rumen, introduction of a generally accepted protocol for determining the acid-base status of ruminal fluid with standard levels of pCO2 and measurement of base excess in addition to pH should be considered.

  7. Determination of Henry's constant, the dissociation constant, and the buffer capacity of the bicarbonate system in ruminal fluid.

    PubMed

    Hille, Katharina T; Hetz, Stefan K; Rosendahl, Julia; Braun, Hannah-Sophie; Pieper, Robert; Stumpff, Friederike

    2016-01-01

    Despite the clinical importance of ruminal acidosis, ruminal buffering continues to be poorly understood. In particular, the constants for the dissociation of H2CO3 and the solubility of CO2 (Henry's constant) have never been stringently determined for ruminal fluid. The pH was measured in parallel directly in the rumen and the reticulum in vivo, and in samples obtained via aspiration from 10 fistulated cows on hay- or concentrate-based diets. The equilibrium constants of the bicarbonate system were measured at 38°C both using the Astrup technique and a newly developed method with titration at 2 levels of partial pressure of CO2 (pCO2; 4.75 and 94.98 kPa), yielding mean values of 0.234 ± 0.005 mmol ∙ L(-1) ∙ kPa(-1) and 6.11 ± 0.02 for Henry's constant and the dissociation constant, respectively (n/n = 31/10). Both reticular pH and the pH of samples measured after removal were more alkalic than those measured in vivo in the rumen (by ΔpH = 0.87 ± 0.04 and 0.26 ± 0.04). The amount of acid or base required to shift the pH of ruminal samples to 6.4 or 5.8 (base excess) differed between the 2 feeding groups. Experimental results are compared with the mathematical predictions of an open 2-buffer Henderson-Hasselbalch equilibrium model. Because pCO2 has pronounced effects on ruminal pH and can decrease rapidly in samples removed from the rumen, introduction of a generally accepted protocol for determining the acid-base status of ruminal fluid with standard levels of pCO2 and measurement of base excess in addition to pH should be considered. PMID:26519978

  8. A Unified Kinetics and Equilibrium Experiment: Rate Law, Activation Energy, and Equilibrium Constant for the Dissociation of Ferroin

    ERIC Educational Resources Information Center

    Sattar, Simeen

    2011-01-01

    Tris(1,10-phenanthroline)iron(II) is the basis of a suite of four experiments spanning 5 weeks. Students determine the rate law, activation energy, and equilibrium constant for the dissociation of the complex ion in acid solution and base dissociation constant for phenanthroline. The focus on one chemical system simplifies a daunting set of…

  9. Analysis of Biochemical Equilibria Relevant to the Immune Response: Finding the Dissociation Constants.

    PubMed

    Cummings, L J; Perez-Castillejos, R; Mack, E T

    2012-02-01

    This paper analyzes the biochemical equilibria between bivalent receptors, homo-bifunctional ligands, monovalent inhibitors, and their complexes. Such reaction schemes arise in the immune response, where immunoglobulins (bivalent receptors) bind to pathogens or allergens. The equilibria may be described by an infinite system of algebraic equations, which accounts for complexes of arbitrary size n (n being the number of receptors present in the complex). The system can be reduced to just 3 algebraic equations for the concentrations of free (unbound) receptor, free ligand and free inhibitor. Concentrations of all other complexes can be written explicitly in terms of these variables. We analyze how concentrations of key (experimentally-measurable) quantities vary with system parameters. Such measured quantities can furnish important information about dissociation constants in the system, which are difficult to obtain by other means. We provide analytical expressions and suggest specific experiments that could be used to determine the dissociation constants.

  10. Electron-ion dissociative recombination rate constants relevant to the Titan atmosphere and the Interstellar Medium

    SciTech Connect

    Osborne, David; Lawson, Patrick; Adams, Nigel

    2014-01-21

    Following the arrival of Cassini at Titan in 2004, the Titan atmosphere has been shown to contain large complex polycyclic-aromatic hydrocarbons. Since Cassini has provided a great deal of data, there exists a need for kinetic rate data to help with modeling this atmosphere. One type of kinetic data needed is electron-ion dissociative recombination (e-IDR) rate constants. These data are not readily available for larger compounds, such as naphthalene, or oxygen containing compounds, such as 1,4 dioxane or furan. Here, the rate constants for naphthalene, 1,4 dioxane, and furan have been measured and their temperature dependencies are determined when possible, using the University of Georgia's Variable Temperature Flowing Afterglow. The rate constants are compared with those previously published for other compounds; these show trends which illustrate the effects which multi-rings and oxygen heteroatoms substitutions have upon e-IDR rate constants.

  11. Determination of the kinetic rate constant of cyclodextrin supramolecular systems by high-performance affinity chromatography.

    PubMed

    Zhang, Jiwen; Li, Haiyan; Sun, Lixin; Wang, Caifen

    2015-01-01

    The kinetics of the association and dissociation are fundamental kinetic processes for the host-guest interactions (such as the drug-target and drug-excipient interactions) and the in vivo performance of supramolecules. With advantages of rapid speed, high precision and ease of automation, the high-performance affinity chromatography (HPAC) is one of the best techniques to measure the interaction kinetics of weak to moderate affinities, such as the typical host-guest interactions of drug and cyclodextrins by using a cyclodextrin-immobilized column. The measurement involves the equilibration of the cyclodextrin column, the upload and elution of the samples (non-retained substances and retained solutes) at different flow rates on the cyclodextrin and control column, and data analysis. It has been indicated that cyclodextrin-immobilized chromatography is a cost-efficient high-throughput tool for the measurement of (small molecule) drug-cyclodextrin interactions as well as the dissociation of other supramolecules with relatively weak, fast, and extensive interactions. PMID:25749964

  12. Increased precision for analysis of protein-ligand dissociation constants determined from chemical shift titrations.

    PubMed

    Markin, Craig J; Spyracopoulos, Leo

    2012-06-01

    NMR is ideally suited for the analysis of protein-protein and protein ligand interactions with dissociation constants ranging from ~2 μM to ~1 mM, and with kinetics in the fast exchange regime on the NMR timescale. For the determination of dissociation constants (K ( D )) of 1:1 protein-protein or protein-ligand interactions using NMR, the protein and ligand concentrations must necessarily be similar in magnitude to the K ( D ), and nonlinear least squares analysis of chemical shift changes as a function of ligand concentration is employed to determine estimates for the parameters K ( D ) and the maximum chemical shift change (Δδ(max)). During a typical NMR titration, the initial protein concentration, [P (0)], is held nearly constant. For this condition, to determine the most accurate parameters for K ( D ) and Δδ(max) from nonlinear least squares analyses requires initial protein concentrations that are ~0.5 × K ( D ), and a maximum concentration for the ligand, or titrant, of ~10 × [P (0)]. From a practical standpoint, these requirements are often difficult to achieve. Using Monte Carlo simulations, we demonstrate that co-variation of the ligand and protein concentrations during a titration leads to an increase in the precision of the fitted K ( D ) and Δδ(max) values when [P (0)] > K ( D ). Importantly, judicious choice of protein and ligand concentrations for a given NMR titration, combined with nonlinear least squares analyses using two independent variables (ligand and protein concentrations) and two parameters (K ( D ) and Δδ(max)) is a straightforward approach to increasing the accuracy of measured dissociation constants for 1:1 protein-ligand interactions.

  13. Binding of ionic species: a general approach to measuring binding constants and assessing affinities.

    PubMed

    Roelens, Stefano; Vacca, Alberto; Venturi, Chiara

    2009-03-01

    Bound together: The association of receptors with ionic species cannot be assimilated to the binding of neutral guests. When dealing with salts, both ion pairing and binding to the free and the ion-paired ionic guest determine the actual association pattern (see figure). The general issue of measuring association constants and assessing affinities for ions is addressed and validated in two cases of anion binding.A general approach to the largely underestimated issue of measuring binding constants and assessing affinities in the binding of ionic species is described. The approach is based on a rigorous, nongraphical determination of binding constants in multiequilibrium systems by nonlinear regression of chemical shift data from NMR titrations and on the use of the BC(50) descriptor for assessing affinities and ranking the binding ability of receptors on a common scale. The approach has been validated with two tripodal anion-binding receptors, namely, a ureidic (1) and a pyrrolic (2) receptor, binding to tetramethylammonium chloride in CDCl(3)/CD(3)CN (80:20). A set of five and six formation constants could be measured for 1 and 2, respectively, including, in addition to the ion pair, complexes of the free and the ion-paired anion. The BC(50) values calculated from the measured constants allowed a quantitative assessment of each receptor's binding affinity towards the chloride anion, the pyrrolic receptor showing a 15-fold larger affinity over the ureidic receptor, a figure that quantifies the improvement obtained by replacing the amido-pyrrolic for ureidic binding groups on the tripodal scaffold of the receptor. The results have shown that, in contrast to common practice, neither of the two systems could be appropriately described by a 1:1 association with the anion only, but required the ion-pairing and ion-pair binding equilibria to be taken into account because these contribute substantially to the complexation process. The BC(50) descriptor has also been shown

  14. Shock Tube Measurement for the Dissociation Rate Constant of Acetaldehyde Using Sensitive CO Diagnostics.

    PubMed

    Wang, Shengkai; Davidson, David F; Hanson, Ronald K

    2016-09-01

    The rate constant of acetaldehyde thermal dissociation, CH3CHO = CH3 + HCO, was measured behind reflected shock waves at temperatures of 1273-1618 K and pressures near 1.6 and 0.34 atm. The current measurement utilized sensitive CO diagnostics to track the dissociation of CH3CHO via oxygen atom balance and inferred the title rate constant (k1) from CO time histories obtained in pyrolysis experiments of 1000 and 50 ppm of CH3CHO/Ar mixtures. By using dilute test mixtures, the current study successfully suppressed the interferences from secondary reactions and directly determined the title rate constant as k1(1.6 atm) = 1.1 × 10(14) exp(-36 700 K/T) s(-1) over 1273-1618 K and k1(0.34 atm) = 5.5 × 10(12) exp(-32 900 K/T) s(-1) over 1377-1571 K, with 2σ uncertainties of approximately ±30% for both expressions. Example simulations of existing reaction mechanisms updated with the current values of k1 demonstrated substantial improvements with regards to the acetaldehyde pyrolysis chemistry. PMID:27523494

  15. Acid-base titration curves for acids with very small ratios of successive dissociation constants.

    PubMed

    Campbell, B H; Meites, L

    1974-02-01

    The shapes of the potentiometric acid-base titration curves obtained in the neutralizations of polyfunctional acids or bases for which each successive dissociation constant is smaller than the following one are examined. In the region 0 < < 1 (where is the fraction of the equivalent volume of reagent that has been added) the slope of the titration curve decreases as the number j of acidic or basic sites increases. The difference between the pH-values at = 0.75 and = 0.25 has (1 j)log 9 as the lower limit of its maximum value.

  16. Determination of stability constants of complexes of neutral analytes with charged cyclodextrins by affinity capillary electrophoresis.

    PubMed

    Beneš, Martin; Zusková, Iva; Svobodová, Jana; Gaš, Bohuslav

    2012-03-01

    A novel procedure for the determination of stability constants in systems with neutral analytes and charged complexation agents by affinity capillary electrophoresis was established. This procedure involves all necessary corrections to achieve precise and reliable data. Temperature, ionic strength, and viscosity corrections were applied. Based on the conductivity measurements, the average temperature of the background electrolyte in the capillary was kept at the constant value of 25°C by decreasing the temperature of the cooling medium. The viscosity correction was performed using the viscosity ratio determined by an external viscosimeter. The electrophoretical measurements were performed, at first, at constant ionic strength. In this case, the increase of ionic strength caused by increasing complexation agent concentration was compensated by changing of the running buffer concentration. Subsequently the dependence of the analyte effective mobility on the complexation agent concentration was measured without the ionic strength compensation (at variable ionic strength). The new procedure for determination of the stability constants even from such data was established. These stability constants are in a very good agreement with those obtained at the constant ionic strength. The established procedure was applied for determination of the thermodynamic stability constants of (R, R)-(+)- and (S, S)-(-)-hydrobenzoin and R- and S-(3-bromo-2-methylpropan-1-ol) complexing with 6-monodeoxy-6-mono(3-hydroxy)propylamino-β-cyclodextrin hydrochloride.

  17. Spectrophotometric determination of the dissociation constants of methyl yellow in mixed protic solvents.

    PubMed

    Fan, J; Shen, X; Wang, J

    1999-07-12

    The concentration dissociation constants (pK(a)) of methyl yellow, MY (H(+)In) in mixed aqueous solvents of methanol, ethanol, iso-propanol, tert-butanol have been accurately determined from spectrophotometric measurements at 25 degrees C and a constant ionic strength of 0.1 mol l(-1). It has been shown that in these solvents, the pK(a) values decrease with increasing composition of the organic co-solvent. A linear relationship between pK(a) and the mole fraction (x(2)) of the co-solvent was observed in a limited range of the compositions for each of the solvent systems. The results have been discussed in the light of transfer thermodynamic properties of the species existing in the dissociation equilibrium, solvent basicity and solute-solvent interactions. Furthermore, it was also observed that with the change of the solvents, the absorption spectra of MY shifted apparently and the color transition changed accordingly. The solvent effect on the spectra has been attributed to the isomerization equilibria of MY. A simple application of MY was also shown to the sodium acetate-hydrochloric acid titrations in the mixed solvents.

  18. Determination of the dissociation constants of sulfonated azo dyes by capillary zone electrophoresis and spectrophotometry methods.

    PubMed

    Pérez-Urquiza, M; Beltrán, J L

    2001-05-11

    The dissociation constants of 10 sulfonated azo dyes, six of the most common food colours used as additives (Food Yellow 4, Food Yellow 3, Food Red 9, Food Red 7, Food Red 17 and Food Blue 5), and four commonly used as textile dyes (Acid Orange 7, Acid Orange 12, Acid Red 26 and Acid Red 88), have been determined by two different systems, one by using capillary electrophoresis (CE) with diode array detection and the other by using UV-visible absorption spectrophotometry, which has been used as reference method to obtain the pKa values. The pKa values obtained by CE were determined in two ways, first on the basis of the electrophoretic mobilities (calculated from the migration times), and after we propose a new methodology, in which the dissociation constants are determined from the spectra corresponding to the maxima of electrophoretic peaks. The pKa values obtained by using these CE methods have been compared with those obtained by using the spectrophotometric method. The results show that the pKa values obtained by the CE proposed method are in general closer to the reference values than those obtained from the electrophoretic mobilities. Moreover, the proposed method retains the advantages of CE, as the possibility of working with small amounts of sample, despite its purity.

  19. Determination of the dissociation constants for recombinant c-Myc, Max, and DNA complexes: The inhibitory effect of linoleic acid on the DNA-binding step

    SciTech Connect

    Jung, Kyung Chae; Rhee, Ho Sung; Park, Chi Hoon; Yang, Chul-Hak . E-mail: chulyang@plaza.snu.ac.kr

    2005-08-19

    c-Myc, the protein product of protooncogene c-myc, functions in cell proliferation, differentiation, and neoplastic disease. In this study, recombinant c-Myc and Max proteins, encompassing DNA binding (basic region) and dimerization (helix-loop-helix/leucine zipper) domain of human origin, were expressed in bacteria as Myc87 and Max85. Myc87 was purified under denatured conditions and was renatured again. The dissociation constant for the protein dimers and for dimer/DNA complexes were not detectable by isothermal titration calorimetry because of the low degree of solubility of Myc87 and Max85. Therefore, we set up equations which were used to determine the dissociation constants from the proportion of protein-DNA complexes. The dimer dissociation constants in TBS were 5.90({+-}0.54) x 10{sup -7} M for Max85/Max85 homodimer, 6.85({+-}0.25) x 10{sup -3} M for Myc87/Myc87 homodimer, and 2.55({+-}0.29) x 10{sup -8} M for Myc87/Max85 heterodimer, and the DNA-binding dissociation constants in TBS were 1.33({+-}0.21) x 10{sup -9} M for Max85/Max85/DNA, 2.27({+-}0.08) x 10{sup -12} M for Myc87/Myc87/DNA, and 4.43({+-}0.37) x 10{sup -10} M for Myc87/Max85/DNA. In addition, we revealed that linoleic acid which is known as an inhibitor for the formation of Max/Max/DNA complex reduced the affinity of Max homodimer for DNA. This result indicates that linoleic acid may bind to the DNA-binding region of Max homodimer.

  20. Using electrophoretic mobility shift assays to measure equilibrium dissociation constants: GAL4-p53 binding DNA as a model system.

    PubMed

    Heffler, Michael A; Walters, Ryan D; Kugel, Jennifer F

    2012-01-01

    An undergraduate biochemistry laboratory experiment is described that will teach students the practical and theoretical considerations for measuring the equilibrium dissociation constant (K(D) ) for a protein/DNA interaction using electrophoretic mobility shift assays (EMSAs). An EMSA monitors the migration of DNA through a native gel; the DNA migrates more slowly when bound to a protein. To determine a K(D) the amount of unbound and protein-bound DNA in the gel is measured as the protein concentration increases. By performing this experiment, students will be introduced to making affinity measurements and gain experience in performing quantitative EMSAs. The experiment describes measuring the K(D) for the interaction between the chimeric protein GAL4-p53 and its DNA recognition site; however, the techniques are adaptable to other DNA binding proteins. In addition, the basic experiment described can be easily expanded to include additional inquiry-driven experimentation. © 2012 by The International Union of Biochemistry and Molecular Biology.

  1. Determination of acid dissociation constants of warfarin and hydroxywarfarins by capillary electrophoresis.

    PubMed

    Nowak, Paweł; Olechowska, Paulina; Mitoraj, Mariusz; Woźniakiewicz, Michał; Kościelniak, Paweł

    2015-08-10

    In this work the acid dissociation constants--pKa of warfarin and its all important oxidative metabolites have been determined by capillary electrophoresis-based methods. It has resulted in a complete description of two acid-base dissociation equilibria, yet not investigated experimentally for phase I metabolites of warfarin. The capillary electrophoresis (CE) method based on the relation between effective electrophoretic mobilities and pH has proven to be a suitable tool for pKa determination, while the spectrophotometric (CE-DAD) and the internal standard methods (IS-CE), have appeared to be promising alternative approaches. The CE-DAD approach based on the change in absorbance spectra between the acidic and basic forms is a combination between capillary electrophoresis and spectrophotometric titration, and yields very consistent values of pKa1 with CE. The IS-CE, in turn, enables an estimation of pKa1 and pKa2 from only two analytical runs, however, less accurate than CE and CE-DAD. The Debye-Hückel model has been confirmed experimentally as a good predictor of pKa values at various ionic strengths. Therefore, it has been used in determination of thermodynamic pKa1 and pKa2, referring to the zero ionic strength. The results are important from the analytical, pharmacological, and theoretical points of view.

  2. Determination of acid dissociation constants of warfarin and hydroxywarfarins by capillary electrophoresis.

    PubMed

    Nowak, Paweł; Olechowska, Paulina; Mitoraj, Mariusz; Woźniakiewicz, Michał; Kościelniak, Paweł

    2015-08-10

    In this work the acid dissociation constants--pKa of warfarin and its all important oxidative metabolites have been determined by capillary electrophoresis-based methods. It has resulted in a complete description of two acid-base dissociation equilibria, yet not investigated experimentally for phase I metabolites of warfarin. The capillary electrophoresis (CE) method based on the relation between effective electrophoretic mobilities and pH has proven to be a suitable tool for pKa determination, while the spectrophotometric (CE-DAD) and the internal standard methods (IS-CE), have appeared to be promising alternative approaches. The CE-DAD approach based on the change in absorbance spectra between the acidic and basic forms is a combination between capillary electrophoresis and spectrophotometric titration, and yields very consistent values of pKa1 with CE. The IS-CE, in turn, enables an estimation of pKa1 and pKa2 from only two analytical runs, however, less accurate than CE and CE-DAD. The Debye-Hückel model has been confirmed experimentally as a good predictor of pKa values at various ionic strengths. Therefore, it has been used in determination of thermodynamic pKa1 and pKa2, referring to the zero ionic strength. The results are important from the analytical, pharmacological, and theoretical points of view. PMID:25968611

  3. Measuring Kinetic Dissociation/Association Constants Between Lactococcus lactis Bacteria and Mucins Using Living Cell Probes

    PubMed Central

    Le, Doan Thanh Lam; Guérardel, Yann; Loubière, Pascal; Mercier-Bonin, Muriel; Dague, Etienne

    2011-01-01

    In this work we focused on quantifying adhesion between Lactococcus lactis, the model for lactic acid bacteria (LAB) and mucins. Interactions between two strains of L. lactis (IBB477 and MG1820 as control) and pig gastric mucin–based coating were measured and compared with the use of atomic force microscopy. Analysis of retraction force-distance curves shed light on the differential contributions of nonspecific and specific forces. An increased proportion of specific adhesive events was obtained for IBB477 (20% vs. 5% for the control). Blocking assays with free pig gastric mucin and its O-glycan moiety showed that oligosaccharides play a major (but not exclusive) role in L. lactis-mucins interactions. Specific interactions were analyzed in terms of kinetic constants. An increase in the loading rate of atomic force microscope tip led to a higher force between interacting biological entities, which was directly linked to the kinetic dissociation constant (Koff). Enhancing the contact time between the tip and the sample allowed an increase in the interaction probability, which can be related to the kinetic association constant (Kon). Variations in the loading rate and contact time enabled us to determine Kon (3.3 × 102 M−1·s−1) and Koff (0.46 s−1), and the latter was consistent with values given in the literature for sugar-protein interactions. PMID:22261074

  4. Spectroscopic determination of acid dissociation constants of N-substituted-6-acylbenzothiazolone derivatives.

    PubMed

    Sıdır, Yadigar Gülseven; Sıdır, Isa; Berber, Halil

    2011-05-26

    The acid dissociation constants of twelve novel drug precursor N-substituted-6-acylbenzothiazolone derivatives were determined by using the UV-vis spectroscopic technique. The protonation and deprotonation behaviors of the investigated molecules were researched from the super basic to super acid regions (i.e., 8 mol·L(-1) KOH to 98% H(2)SO(4)) including the pH region. It is observed that all of the molecules are protonated in the super acidic region. The calculated relative stability values of possible tautomer structures indicate that the keto form of investigated molecules is favored over the enol form. It was predicted that protonation occurs at the amide (oxo) group found in the keto form.

  5. Determination of dissociation constants of pharmacologically active xanthones by capillary zone electrophoresis with diode array detection.

    PubMed

    Wu, Xiaomu; Gong, Suxuan; Bo, Tao; Liao, Yiping; Liu, Huwei

    2004-12-24

    In this article, the dissociation constants (pKa) of 10 pharmacologically active xanthones isolated from herbal medicine Securidaca inappendiculata were determined by capillary zone electrophoresis with diode array detection. The pKa values determined by the method based on the electrophoretic mobilities (calculated from migration times) have been proved by the method based on UV absorbance calculated from the online spectra corresponding peaks. No conspicuous difference was observed between the two methods with acceptable reproducibility. Two pKa values (pKa1 and pKa2) were found for four xanthones while generally the 10 compounds possess the pKa values ranging from 6.4 to 9.2. PMID:15641365

  6. Simultaneous determination of equivalence volumes and acid dissociation constants from potentiometric titration data.

    PubMed

    Papanastasiou, G; Ziogas, I

    1995-06-01

    New iterative methods for analysis of potentiometric titration data of (a) mixtures of weak monoprotic acids with their conjugate bases, (b) solutions of polyprotic (di- and triprotic) acids, and (c) mixtures of two diprotic acids are presented. These methods, using data exclusively resulting from the acidic region of the titration curve permits the accurate determination of the analytical concentration of one or more acids even if the titration is stopped well before the end point of the titration. For the titration of a solution containing a conjugate acid/base pair, the proposed procedure enables the extraction of the initial composition of the mixture, as well as the dissociation constant of the concerned acid. Thus, it is possible by this type of analysis to distinguish whether a weak acid has been contaminated by a strong base and define the extent of the contamination. On the other hand, for the titration of polyprotic acids, the proposed approach enables the extraction of the accurate values of the equivalence volume and the dissociation constants K(i) even when the ionization stages overlap. Finally, for the titration of a mixture of two diprotic acids the proposed procedure enables the determination of the composition of the mixture even if the sum of the concentrations of the acids is not known. This method can be used in the analysis of solutions containing two diastereoisomeric forms of a weak diprotic acid. The test of the proposed procedures by means of ideal and Monte Carlo simulated data revealed that these methods are fairly applicable even when the titration data are considerably obscured by 'noise' or contain an important systematic error. The proposed procedures were also successfully applied to experimental titration data.

  7. Determination of acid dissociation constants of triazole fungicides by pressure assisted capillary electrophoresis.

    PubMed

    Konášová, Renáta; Dytrtová, Jana Jaklová; Kašička, Václav

    2015-08-21

    Pressure assisted capillary electrophoresis was applied to determination of acid dissociation constants (pKa) of six widely used triazole fungicides (cyproconazole, epoxiconazole, flusilazole, tebuconazole, penconazole and propiconazole) in aqueous medium. The pKa values were determined from the dependence of effective electrophoretic mobility of the triazole fungicides on p[H(+)] of the background electrolyte (BGE) using non-linear regression analysis. The p[H(+)] was used instead of pH to reflect the increased ionic strength of the strongly acidic BGEs (pH<1.75) as compared to the BGEs at pH equal to or greater than 1.75. Prior to the pKa calculation, the measured effective electrophoretic mobilities were corrected to the reference temperature (25°C) and constant ionic strength (25mM). The regression function was modified to allow the determination of pKa in the BGEs of varying ionic strength. The electrophoretic measurements showed that the above triazole fungicides are very weak bases - their pKa values were found to be in the range 1.05-1.97 and were in a good agreement with the values calculated by SPARC online pKa calculator.

  8. The universal statistical distributions of the affinity, equilibrium constants, kinetics and specificity in biomolecular recognition.

    PubMed

    Zheng, Xiliang; Wang, Jin

    2015-04-01

    We uncovered the universal statistical laws for the biomolecular recognition/binding process. We quantified the statistical energy landscapes for binding, from which we can characterize the distributions of the binding free energy (affinity), the equilibrium constants, the kinetics and the specificity by exploring the different ligands binding with a particular receptor. The results of the analytical studies are confirmed by the microscopic flexible docking simulations. The distribution of binding affinity is Gaussian around the mean and becomes exponential near the tail. The equilibrium constants of the binding follow a log-normal distribution around the mean and a power law distribution in the tail. The intrinsic specificity for biomolecular recognition measures the degree of discrimination of native versus non-native binding and the optimization of which becomes the maximization of the ratio of the free energy gap between the native state and the average of non-native states versus the roughness measured by the variance of the free energy landscape around its mean. The intrinsic specificity obeys a Gaussian distribution near the mean and an exponential distribution near the tail. Furthermore, the kinetics of binding follows a log-normal distribution near the mean and a power law distribution at the tail. Our study provides new insights into the statistical nature of thermodynamics, kinetics and function from different ligands binding with a specific receptor or equivalently specific ligand binding with different receptors. The elucidation of distributions of the kinetics and free energy has guiding roles in studying biomolecular recognition and function through small-molecule evolution and chemical genetics. PMID:25885453

  9. The Universal Statistical Distributions of the Affinity, Equilibrium Constants, Kinetics and Specificity in Biomolecular Recognition

    PubMed Central

    Zheng, Xiliang; Wang, Jin

    2015-01-01

    We uncovered the universal statistical laws for the biomolecular recognition/binding process. We quantified the statistical energy landscapes for binding, from which we can characterize the distributions of the binding free energy (affinity), the equilibrium constants, the kinetics and the specificity by exploring the different ligands binding with a particular receptor. The results of the analytical studies are confirmed by the microscopic flexible docking simulations. The distribution of binding affinity is Gaussian around the mean and becomes exponential near the tail. The equilibrium constants of the binding follow a log-normal distribution around the mean and a power law distribution in the tail. The intrinsic specificity for biomolecular recognition measures the degree of discrimination of native versus non-native binding and the optimization of which becomes the maximization of the ratio of the free energy gap between the native state and the average of non-native states versus the roughness measured by the variance of the free energy landscape around its mean. The intrinsic specificity obeys a Gaussian distribution near the mean and an exponential distribution near the tail. Furthermore, the kinetics of binding follows a log-normal distribution near the mean and a power law distribution at the tail. Our study provides new insights into the statistical nature of thermodynamics, kinetics and function from different ligands binding with a specific receptor or equivalently specific ligand binding with different receptors. The elucidation of distributions of the kinetics and free energy has guiding roles in studying biomolecular recognition and function through small-molecule evolution and chemical genetics. PMID:25885453

  10. The universal statistical distributions of the affinity, equilibrium constants, kinetics and specificity in biomolecular recognition.

    PubMed

    Zheng, Xiliang; Wang, Jin

    2015-04-01

    We uncovered the universal statistical laws for the biomolecular recognition/binding process. We quantified the statistical energy landscapes for binding, from which we can characterize the distributions of the binding free energy (affinity), the equilibrium constants, the kinetics and the specificity by exploring the different ligands binding with a particular receptor. The results of the analytical studies are confirmed by the microscopic flexible docking simulations. The distribution of binding affinity is Gaussian around the mean and becomes exponential near the tail. The equilibrium constants of the binding follow a log-normal distribution around the mean and a power law distribution in the tail. The intrinsic specificity for biomolecular recognition measures the degree of discrimination of native versus non-native binding and the optimization of which becomes the maximization of the ratio of the free energy gap between the native state and the average of non-native states versus the roughness measured by the variance of the free energy landscape around its mean. The intrinsic specificity obeys a Gaussian distribution near the mean and an exponential distribution near the tail. Furthermore, the kinetics of binding follows a log-normal distribution near the mean and a power law distribution at the tail. Our study provides new insights into the statistical nature of thermodynamics, kinetics and function from different ligands binding with a specific receptor or equivalently specific ligand binding with different receptors. The elucidation of distributions of the kinetics and free energy has guiding roles in studying biomolecular recognition and function through small-molecule evolution and chemical genetics.

  11. A new sensitive method of dissociation constants determination based on the isohydric solutions principle.

    PubMed

    Michałowski, Tadeusz; Pilarski, Bogusław; Asuero, Agustin G; Dobkowska, Agnieszka

    2010-10-15

    The paper provides a new formulation and analytical proposals based on the isohydric solutions concept. It is particularly stated that a mixture formed, according to titrimetric mode, from a weak acid (HX, C(0)mol/L) and a strong acid (HB, Cmol/L) solutions, assumes constant pH, independently on the volumes of the solutions mixed, provided that the relation C(0)=C+C(2)·10(pK(1)) is valid, where pK(1)=-log K(1), K(1) the dissociation constant for HX. The generalized formulation, referred to the isohydric solutions thus obtained, was extended also to more complex acid-base systems. Particularly in the (HX, HB) system, the titration occurs at constant ionic strength (I) value, not resulting from presence of a basal electrolyte. This very advantageous conjunction of the properties provides, among others, a new, very sensitive method for verification of pK(1) value. The new method is particularly useful for weak acids HX characterized by low pK(1) values. The method was tested experimentally on four acid-base systems (HX, HB), in aqueous and mixed-solvent media and compared with the literature data. Some useful (linear and hyperbolic) correlations were stated and applied for validation of pK(1) values. Finally, some practical applications of analytical interest of the isohydricity (pH constancy) principle as one formulated in this paper were enumerated, proving the usefulness of such a property which has its remote roots in the Arrhenius concept.

  12. Enrichment and Analysis of Nonenzymatically Glycated Peptides: Boronate Affinity Chromatography Coupled with Electron-Transfer Dissociation Mass Spectrometry

    SciTech Connect

    Zhang, Qibin; Tang, Ning; Brock, Jonathan W.; Mottaz, Heather M.; Ames, Jennifer M.; Baynes, John; Smith, Richard D.; Metz, Thomas O.

    2007-06-01

    Non-enzymatic glycation of peptides and proteins by D-glucose has important implications in the pathogenesis of diabetes mellitus, particularly in the development of diabetic complications. However, no effective high-throughput methods exist for identifying proteins containing this low abundance post-translational modification in bottom-up proteomic studies. In this report, phenylboronate affinity chromatography was used in a two-step enrichment scheme to selectively isolate first glycated proteins and then glycated, tryptic peptides from human serum glycated in vitro. Enriched peptides were subsequently analyzed by alternating electron transfer dissociation (ETD) and collision induced dissociation (CID) tandem mass spectrometry. It was observed that ETD fragmentation mode resulted in a significantly higher number of glycated peptide identifications (87.6% of all identified peptides) versus CID mode (17.0% of all identified peptides), when utilizing dual glycation enrichment on both the protein and peptide level. This study illustrates that phenylboronate affinity chromatography coupled with LC-MS/MS with ETD as the fragmentation mode is an efficient approach for analyses of glycated proteins and can have broad applications in studies of diabetes mellitus.

  13. Interpolation constants for calculation of transmittance and rate of dissociation of molecular oxygen in the mesosphere and lower thermosphere

    NASA Technical Reports Server (NTRS)

    Hudson, R. D.; Mahle, S. H.

    1972-01-01

    Values of band oscillator strengths and rotational line widths for the Schumann-Runge band system have been used to derive interpolation constants from which the transmittance and rate of dissociation of molecular oxygen can be calculated. These constants, valid for temperatures between 150 and 300 K and for column densities between 1 x 10 to the 17th power/cm sq and 7 x 10 to the 24th power/cm sq, cover the wavelength range 1750 and 2050A.

  14. Using Electrophoretic Mobility Shift Assays to Measure Equilibrium Dissociation Constants: GAL4-p53 Binding DNA as a Model System

    ERIC Educational Resources Information Center

    Heffler, Michael A.; Walters, Ryan D.; Kugel, Jennifer F.

    2012-01-01

    An undergraduate biochemistry laboratory experiment is described that will teach students the practical and theoretical considerations for measuring the equilibrium dissociation constant (K[subscript D]) for a protein/DNA interaction using electrophoretic mobility shift assays (EMSAs). An EMSA monitors the migration of DNA through a native gel;…

  15. SK&F 97426-A: a novel bile acid sequestrant with higher affinities and slower dissociation rates for bile acids in vitro than cholestyramine.

    PubMed

    Benson, G M; Alston, D R; Hickey, D M; Jaxa-Chamiec, A A; Whittaker, C M; Haynes, C; Glen, A; Blanchard, S; Cresswell, S R; Suckling, K E

    1997-01-01

    SK&F 97426-A is a novel bile acid sequestrant that is threefold more potent than cholestyramine at increasing bile acid excretion in the hamster. SK&F 97426-A is a quaternary alkylammonium polymethacrylate that was selected for comparison with cholestyramine in vivo because of its superior in vitro bile acid binding properties. Association, dissociation, affinity, and capacity experiments were performed under physiologically relevant conditions with the most abundant bile acids found in human bile. The bile acids came to equilibrium with SK&F 97426-A and cholestyramine within approximately 30 min and 6 min, respectively. SK&F 97426-A and cholestyramine had similar capacities for all the bile acids (between 2.5 and 4 mmol/g) and both had similar, very high affinities and slow dissociation rates for the dihydroxy bile acids. However, SK&F 97426-A had much higher affinities for the trihydroxy bile acids glycocholic acid and taurocholic acid than did cholestyramine. Dissociation of glycocholic acid and taurocholic acid from SK&F 97426-A was also much slower (27 and 25%, respectively, dissociated after 60 min) than from cholestyramine (89 and 84%, respectively, dissociated after 60 min). The higher affinities and slower dissociation rates of the trihydroxy bile acids for and from SK&F 97426-A probably account for the increased potency of SK&F 97426-A over cholestyramine in vivo.

  16. Determination of acid-base dissociation constants of azahelicenes by capillary zone electrophoresis.

    PubMed

    Ehala, Sille; Mísek, Jirí; Stará, Irena G; Starý, Ivo; Kasicka, Václav

    2008-08-01

    CZE was employed to determine acid-base dissociation constants (pK(a)) of ionogenic groups of azahelicenes in methanol (MeOH). Azahelicenes are unique 3-D aromatic systems, which consist of ortho-fused benzene/pyridine units and exhibit helical chirality. The pK(a) values of pyridinium groups of the studied azahelicenes were determined from the dependence of their effective electrophoretic mobility on pH by a nonlinear regression analysis. The effective mobilities of azahelicenes were determined by CZE at pH range between 2.1 and 10.5. Thermodynamic pK(a) values of monobasic 1-aza[6]helicene and 2-aza[6]helicene in MeOH were determined to be 4.94 +/- 0.05 and 5.68 +/- 0.05, respectively, and pK(a) values of dibasic 1,14-diaza[5]helicene were found to be equal to 7.56 +/- 0.38 and 8.85 +/- 0.26. From these values, the aqueous pK(a) of these compounds was estimated.

  17. Chromatographic determination of aqueous dissociation constants of some water-insoluble nonsteroidal antiinflammatory drugs.

    PubMed

    Oumada, Fadoua Z; Ràfols, Clara; Rosés, Martí; Bosch, Elisabeth

    2002-04-01

    The purpose of this work is to propose a new, useful, and easy chromatographic method to determine accurately the aqueous dissociation constant of drugs sparingly soluble in water. The method uses the rigorous intersolvental pH scale, (w)(s)pH, i.e., the pH measurements are made in the mobile phase after mixing the aqueous buffer with methanol by a combined glass electrode previously standardised with common aqueous buffers. The measured pK allows the determination of the drug's pK(a) in the mobile phase, (w)(s)pK(a), which can be easily converted in the aqueous pK(a), (w)(w)pK(a), by means of previously established equations. A series of nonsteroidal carboxylic acids with antiinflammatory properties were selected to test the method because their aqueous pK(a) values, (w)(w)pK(a), had been previously evaluated from different approaches that gave consistent results. The comparison of the aqueous pK(a) values obtained by means of the proposed procedure with those of literature allows the accurate evaluation of this new methodology. The results obtained show very good precision and accuracy.

  18. A rigorous multiple independent binding site model for determining cell-based equilibrium dissociation constants.

    PubMed

    Drake, Andrew W; Klakamp, Scott L

    2007-01-10

    A new 4-parameter nonlinear equation based on the standard multiple independent binding site model (MIBS) is presented for fitting cell-based ligand titration data in order to calculate the ligand/cell receptor equilibrium dissociation constant and the number of receptors/cell. The most commonly used linear (Scatchard Plot) or nonlinear 2-parameter model (a single binding site model found in commercial programs like Prism(R)) used for analysis of ligand/receptor binding data assumes only the K(D) influences the shape of the titration curve. We demonstrate using simulated data sets that, depending upon the cell surface receptor expression level, the number of cells titrated, and the magnitude of the K(D) being measured, this assumption of always being under K(D)-controlled conditions can be erroneous and can lead to unreliable estimates for the binding parameters. We also compare and contrast the fitting of simulated data sets to the commonly used cell-based binding equation versus our more rigorous 4-parameter nonlinear MIBS model. It is shown through these simulations that the new 4-parameter MIBS model, when used for cell-based titrations under optimal conditions, yields highly accurate estimates of all binding parameters and hence should be the preferred model to fit cell-based experimental nonlinear titration data. PMID:17141800

  19. Determination of dissociation constant of the NFκB p50/p65 heterodimer using fluorescence cross-correlation spectroscopy in the living cell

    SciTech Connect

    Tiwari, Manisha; Mikuni, Shintaro; Muto, Hideki; Kinjo, Masataka

    2013-07-05

    Highlights: •We used two-laser-beam FCCS to determine the dissociation constant (K{sub d}) of IPT domain of p50/p65 heterodimer in living cell. •Interaction of p50 and p65 was analyzed in the cytoplasm and nucleus of single living cell. •Binding affinity of p50/p65 heterodimer is higher in cytoplasm than that of nucleus. -- Abstract: Two-laser-beam fluorescence cross-correlation spectroscopy (FCCS) is promising technique that provides quantitative information about the interactions of biomolecules. The p50/p65 heterodimer is the most abundant and well understood of the NFκB dimers in most cells. However, the quantitative value of affinity, namely the K{sub d}, for the heterodimer in living cells is not known yet. To quantify the heterodimerization of the IPT domain of p50/p65 in the living cell, we used two-laser-beam FCCS. The K{sub d} values of mCherry{sub 2}- and EGFP-fused p50 and p65 were determined to be 0.46 μM in the cytoplasm and 1.06 μM in the nucleus of the living cell. These results suggest the different binding affinities of the p50/p65 heterodimer in the cytoplasm and nucleus of the living cell and different complex formation in each region.

  20. High kinetic stability of Zn(II) coordinated by the tris(histidine) unit of carbonic anhydrase towards solvolytic dissociation studied by affinity capillary electrophoresis.

    PubMed

    Sato, Yosuke; Hoshino, Hitoshi; Iki, Nobuhiko

    2016-08-01

    Solvolytic dissociation rate constants (kd) of bovine carbonic anhydrase II (CA) and its metallovariants (M-CAs, M=Co(II), Ni(II), Cu(II), Zn(II), and Cd(II)) were estimated by a ligand substitution reaction, which was monitored by affinity capillary electrophoresis to selectively detect the undissociated CAs in the reaction mixture. Using EDTA as the competing ligand for Zn-CA, the dissociation followed the unimolecular nucleophilic substitution (SN1) mechanism with kd=1.0×10(-7)s(-1) (pH7.4, 25°C). The corresponding solvolysis half-life (t1/2) was 80days, showing the exceptionally high kinetic stability of t Zn-CA, in contrast to the highly labile [Zn(II)(H2O)6](2+), where the water exchange rate (kex) is high. This behavior is attributed to the tetrahedral coordination geometry supported by the tris(histidine) unit (His3) of CA. In the case of Co-CA, it showed a somewhat larger kd value (5.7×10(-7)s(-1), pH7.4, 25°C) even though it shares the same tetrahedral coordination environment with Zn-CA, suggesting that the d(7) electronic configuration of Co(II) in the transition state of the dissociation is stabilized by the ligand field. Among M-CAs, only Ni-CA showed a bimolecular nucleophilic substitution (SN2) reaction path in its reaction with EDTA, implying that the large coordination number (6) of Ni(II) in Ni-CA allows EDTA to form an EDTA-Ni-CA intermediate. Overall, kd values roughly correlated with kex values among M-CAs, with the kd value of Zn-CA deviating strongly from the trend and highlighting the exceptionally high kinetic stabilization of Zn-CA by the His3 unit. PMID:27235274

  1. MR Imaging-derived Oxygen-Hemoglobin Dissociation Curves and Fetal-Placental Oxygen-Hemoglobin Affinities.

    PubMed

    Avni, Reut; Golani, Ofra; Akselrod-Ballin, Ayelet; Cohen, Yonni; Biton, Inbal; Garbow, Joel R; Neeman, Michal

    2016-07-01

    Purpose To generate magnetic resonance (MR) imaging-derived, oxygen-hemoglobin dissociation curves and to map fetal-placental oxygen-hemoglobin affinity in pregnant mice noninvasively by combining blood oxygen level-dependent (BOLD) T2* and oxygen-weighted T1 contrast mechanisms under different respiration challenges. Materials and Methods All procedures were approved by the Weizmann Institutional Animal Care and Use Committee. Pregnant mice were analyzed with MR imaging at 9.4 T on embryonic days 14.5 (eight dams and 58 fetuses; imprinting control region ICR strain) and 17.5 (21 dams and 158 fetuses) under respiration challenges ranging from hyperoxia to hypoxia (10 levels of oxygenation, 100%-10%; total imaging time, 100 minutes). A shorter protocol with normoxia to hyperoxia was also performed (five levels of oxygenation, 20%-100%; total imaging time, 60 minutes). Fast spin-echo anatomic images were obtained, followed by sequential acquisition of three-dimensional gradient-echo T2*- and T1-weighted images. Automated registration was applied to align regions of interest of the entire placenta, fetal liver, and maternal liver. Results were compared by using a two-tailed unpaired Student t test. R1 and R2* values were derived for each tissue. MR imaging-based oxygen-hemoglobin dissociation curves were constructed by nonlinear least square fitting of 1 minus the change in R2*divided by R2*at baseline as a function of R1 to a sigmoid-shaped curve. The apparent P50 (oxygen tension at which hemoglobin is 50% saturated) value was derived from the curves, calculated as the R1 scaled value (x) at which the change in R2* divided by R2*at baseline scaled (y) equals 0.5. Results The apparent P50 values were significantly lower in fetal liver than in maternal liver for both gestation stages (day 14.5: 21% ± 5 [P = .04] and day 17.5: 41% ± 7 [P < .0001]). The placenta showed a reduction of 18% ± 4 in mean apparent P50 values from day 14.5 to day 17.5 (P = .003

  2. SARS CoV main proteinase: The monomer-dimer equilibrium dissociation constant.

    PubMed

    Graziano, Vito; McGrath, William J; Yang, Lin; Mangel, Walter F

    2006-12-12

    The SARS coronavirus main proteinase (SARS CoV main proteinase) is required for the replication of the severe acute respiratory syndrome coronavirus (SARS CoV), the virus that causes SARS. One function of the enzyme is to process viral polyproteins. The active form of the SARS CoV main proteinase is a homodimer. In the literature, estimates of the monomer-dimer equilibrium dissociation constant, KD, have varied more than 65,0000-fold, from <1 nM to more than 200 microM. Because of these discrepancies and because compounds that interfere with activation of the enzyme by dimerization may be potential antiviral agents, we investigated the monomer-dimer equilibrium by three different techniques: small-angle X-ray scattering, chemical cross-linking, and enzyme kinetics. Analysis of small-angle X-ray scattering data from a series of measurements at different SARS CoV main proteinase concentrations yielded KD values of 5.8 +/- 0.8 microM (obtained from the entire scattering curve), 6.5 +/- 2.2 microM (obtained from the radii of gyration), and 6.8 +/- 1.5 microM (obtained from the forward scattering). The KD from chemical cross-linking was 12.7 +/- 1.1 microM, and from enzyme kinetics, it was 5.2 +/- 0.4 microM. While each of these three techniques can present different, potential limitations, they all yielded similar KD values.

  3. (/sup 3/H)dihydroergotamine as a high-affinity, slowly dissociating radioligand for 5-HT1B binding sites in rat brain membranes: evidence for guanine nucleotide regulation of agonist affinity states

    SciTech Connect

    Hamblin, M.W.; Ariani, K.; Adriaenssens, P.I.; Ciaranello, R.D.

    1987-12-01

    (/sup 3/H)Dihydroergotamine (DE) labels a population of binding sites in rat brain membranes with an affinity of approximately 70 pM in both hippocampus (maximal binding at saturation (Bmax) = 340 fmol/mg of protein) and cerebral cortex (Bmax = 250 fmol/mg of protein). Specific binding typically comprises about 97% of total binding at the Kd of the radioligand when nonspecific binding is determined in the presence of 100 nM unlabeled DE. Association kinetics at 37 degrees C are consistent with a uniform association rate constant for all sites labeled. Specific binding is completely reversible with addition of excess unlabeled DE, but dissociation does not proceed with simple first-order kinetics, suggesting the presence of more than one discrete binding site. Competition studies with selective drugs reveal alpha adrenergic, 5-HT1A and 5-HT1B components of (/sup 3/H)DE specific binding. When phentolamine (500 nM) is included to block alpha receptors and DPAT (100 nM) or spiroxatrine (500 nM) is included to block 5-HT1A receptors, specific binding is exclusively to sites with drug affinities characteristic of 5-HT1B receptors. Under these 5-HT1B-selective conditions, (/sup 3/H)DE binding is about 90% specific, with a Kd of about 50 to 60 pM and a Bmax of 96 fmol/mg of protein in hippocampus and 77 fmol/mg of protein in cortex. (/sup 3/H)DE binding to 5-HT1B sites is very slowly dissociable, with a T1/2 of greater than 2 h at 37 degrees C. 5-HT1B antagonists and DE itself yield competition curves at (/sup 3/H)DE-labeled 5-HT1B sites that are adequately fit assuming a single site in nonlinear regression analysis. Addition of 100 microM guanylyl 5'-imidodiphosphate appears to convert nearly all 5-HT1B sites to those having low affinity for agonists while having a much smaller effect on the binding of (/sup 3/H)DE.

  4. Thermodynamic dissociation constant studies of caffeine at different temperatures and in organic water solvent mixture.

    PubMed

    Saeeduddin; Khanzada, A W K

    2004-01-01

    Thermodynamic dissociation studies have been carried out potentiometrically at various temperatures from 25 to 50 degrees C and in 10, 20, 30 and 40% v/v dioxane-water solvent mixture at 25 degrees C. The influence of temperature and nature of solvent on dissociation equilibria of caffeine is being investigated. A computer program in GW-BASIC has been used to calculate the pK values.

  5. Determination of the dissociation constants of the cephalosporins cefepime and cefpirome using UV spectrometry and pH potentiometry.

    PubMed

    Evagelou, Vassilis; Tsantili-Kakoulidou, Anna; Koupparis, Michael

    2003-04-10

    UV spectrometry and pH potentiometry were used for the determination and direct characterization of the dissociation constants of cefepime (Cef) and cefpirome. The absorbance/pH profiles at two analytical wavelengths and different conditions were assessed and found to conform to those of diprotic acids. The titration curves indicated a triprotic acid profile with two overlapping dissociation constants. The comparison of the results of both techniques permitted the direct attribution of the three dissociation constants to the carboxylic group at position 4 of the Delta-3 cephem nucleus, the aminothiazole group and the amide group at position 7 of the Delta-3 cephem nucleus. Stability studies of Cef in alkaline solutions were also performed in order to evaluate the accuracy of the measurements carried out for the determination of the third pK(a) value. The experimental pK(a) values were compared to the corresponding predicted values derived by PALLAS/PKALC and Advanced Chemical Development (ACD) software packages.

  6. A comparative study of capillary zone electrophoresis and pH-potentiometry for determination of dissociation constants.

    PubMed

    Andrasi, Melinda; Buglyo, Peter; Zekany, Laszlo; Gaspar, Attila

    2007-09-01

    Acidity constants of six cephalosporin antibiotics, cefalexin, cefaclor, cefadroxil, cefotaxim, cefoperazon and cefoxitin are determined using capillary zone electrophoresis (CZE) and pH-potentiometric titrations. Since CZE is a separation method, it is not necessary for the samples to be of high purity and known concentration because only mobilities are measured. The effect on determination of dissociation constants of different matrices (serum, 0.9% NaCl, fermentation matrix) was examined. The advantages of CZE can be utilized in those fields where potentiometry has limitations (sample quantity, solubility, purity, simultaneous determinations), although pK(a) values that are close to each other can be determined by potentiometry with more accuracy.

  7. Somatostatin analogs. Dissociation of brain receptor binding affinities and pituitary actions in the rat.

    PubMed

    Srikant, C B; Patel, Y C

    1981-01-01

    We have recently demonstrated the presence of specific receptors for somatostatin (SRIF) in rat brain synaptosomal membranes which appear to mediate its action. Using this system as a radioreceptor assay, we have examined the ability of a wide range of SRIF analogs to interact with these receptors. Although structural modifications in the Trp8 moiety of SRIF resulted in significant enhancement of affinity for binding to the brain SRIF receptors, the different relative specificities of des AA1,2,4,5,12,13 D-Trp8 SRIF (oligo D-Trp8 SRIF), D-Trp8 SRIF and D-5-Br-Trp8 SRIF in the pituitary and the central nervous system (CNS) suggest that basic differences exist between SRIF receptors present in the brain and the pituitary.

  8. Simulations of acid dissociation constants of polyprotic acids in near-critical and supercritical water.

    PubMed

    Halstead, Simon J; An, Pengna

    2013-12-01

    This paper reports a molecular dynamics study on the dissociation of sulfuric acid and phosphoric acid in near-critical and supercritical water. pK(a) is known to vary as the temperature and pressure vary, and this variation has important implications for corrosion in supercritical water reaction vessels. This work uses the SPC/E water model and solutes based upon DFT calculations to examine both structural and thermodynamic properties of the dissociation processes. An increase in solute-solvent ordering is observed for larger charges, and this also corresponds to a lower rate of diffusion. All dissociation reactions become less favored with increasing temperature except pK(a1) for sulfuric acid which becomes significantly more favored until 748 K.

  9. General equation for calculating the dissociation constants of polyprotic acids and bases from measured retention factors in high-performance liquid chromatography.

    PubMed

    Jano, I; Hardcastle, J E; Zhao, K; Vermillion-Salsbury, R

    1997-02-21

    A general equation relating the observed retention factor to the pH of the mobile phase, the dissociation constants, and the retention factors of the different ionic species has been derived. This equation is applicable to polyprotic weak acid and base dissociation events, that is, the secondary equilibria existing in the HPLC mobile phase. It is written as: [formula: see text] where the kr values are the retention factors of the dissociated species, and Ka(r), the product of the first r-dissociation constants, [formula: see text] is related to the pH of the mobile phase: x = 2.303.pH. The derived equation was used to calculate three dissociation constants of leukotriene E4. Also, a formula is established for calculating the range of pH values where an ionic species is most likely to be predominant in the mobile phase.

  10. Comparison of three distinct ELLA protocols for determination of apparent affinity constants between Con A and glycoproteins.

    PubMed

    Mislovičová, D; Katrlík, J; Paulovičová, E; Gemeiner, P; Tkac, J

    2012-06-01

    A procedure for determination of apparent affinity constants K(D)(app) between Concanavalin A (Con A) and naturally d-mannose containing glycoproteins using enzyme-linked lectin assay (ELLA) is reported. Three distinct ELLA protocols are compared to each other with 3 different fitting models used (Liliom, Hill with and without a cooperativity factor). The glycoproteins were physisorbed on a highly charged polystyrene solid surface of immunoassay plates and the amount of lectin bound to the glycoproteins was determined by photometry. The interactions of Con A with five mannose-containing glycoproteins, invertase (INV), glucoamylase (GA), glucose oxidase (GOx), ovalbumin (OVA), and transferrin (TRF) were quantified with apparent affinity constant being in the range 2×10(-7) to 9×10(-6)M. The strength of interaction between Con A and glycoproteins is discussed on the basis of glycan structure/exposure on the protein backbone for each glycoprotein.

  11. Determination of acid-base dissociation constants of amino- and guanidinopurine nucleotide analogs and related compounds by capillary zone electrophoresis.

    PubMed

    Solínová, Veronika; Kasicka, Václav; Koval, Dusan; Cesnek, Michal; Holý, Antonín

    2006-03-01

    CZE has been applied for determination of acid-base dissociation constants (pKa) of ionogenic groups of newly synthesized amino- and (amino)guanidinopurine nucleotide analogs, such as acyclic nucleoside phosphonate, acyclic nucleoside phosphonate diesters and other related compounds. These compounds bear characteristic pharmacophores contained in various important biologically active substances, such as cytostatics and antivirals. The pKa values of ionogenic groups of the above compounds were determined by nonlinear regression analysis of the experimentally measured pH dependence of their effective electrophoretic mobilities. The effective mobilities were measured by CZE performed in series of BGEs in a broad pH range (3.50-11.25), at constant ionic strength (25 mM) and temperature (25 degrees C). pKa values were determined for the protonated guanidinyl group in (amino)guanidino 9-alkylpurines and in (amino)guanidinopurine nucleotide analogs, such as acyclic nucleoside phosphonates and acyclic nucleoside phosphonate diesters, for phosphonic acid to the second dissociation degree (-2) in acyclic nucleoside phosphonates of amino and (amino)guanidino 9-alkylpurines, and for protonated nitrogen in position 1 (N1) of purine moiety in acyclic nucleoside phosphonates of amino 9-alkylpurines. Thermodynamic pKa of protonated guanidinyl group was estimated to be in the range of 7.75-10.32, pKa of phosphonic acid to the second dissociation degree achieved values of 6.64-7.46, and pKa of protonated nitrogen in position 1 of purine was in the range of 4.13-4.89, depending on the structure of the analyzed compounds.

  12. Determination of dissociation constants of aristolochic acid I and II by capillary electrophoresis with carboxymethyl chitosan-coated capillary.

    PubMed

    Fu, Xiaofang; Liu, Yi; Li, Wei; Bai, Yu; Liao, Yiping; Liu, Huwei

    2011-07-15

    Aristolochic acid-I and aristolochic acid-II have been proved to be the main bioactive and toxic component in Aristolochia plants. As a result, the determination of their dissociation constants, which are important property parameters for weak acids, is highly desired for related pharmacological and toxicological studies. In this work, the dissociation constant values of aristolochic acid-I and aristolochic acid-II were determined by capillary electrophoresis using carboxymethyl chitosan-coated capillary, based on their electrophoretic mobilities by using nonlinear regression as well as linear regression, showing that the two models give comparable results. The data were also compared with those obtained by capillary electrophoresis with polybrene-coated capillary, and no conspicuous difference was observed. The correlation coefficients were all higher than 0.998 for both linear and nonlinear regression model. The pKa values were found to be 3.3±0.1 for aristolochic acid-I and 3.2±0.1 for aristolochic acid-II.

  13. Effect of selected calculation routines and dissociation constants on the determination of total carbon dioxide in seawater

    NASA Astrophysics Data System (ADS)

    Stoll, M. H. C.; Rommets, J. W.; de Baar, H. J. W.

    1993-06-01

    During the 1989 and 1990 JGOFS North Atlantic Pilot Study a comparison was made between the Coulometric and the acid titration method for determination of total carbon dioxide (TCO 2) in seawater. TCO 2 and alkalinity have been calculated from acid titration using either the modified Gran plot or the curve-fitting routine. Depth profiles showed fair agreement (on average 0.6% or about 12.5 μmol 1 -1) between the TCO 2 calculated from the acid titration method and the TCO 2 measured independently by Coulometry. It is shown that different data processing routines combined with the proper use of dissociation constants can influence the acid titration result considerably. There appears to be a slight offset between calculated and Coulometric data which is smallest when using the combined dissociation constants of HANSSON ( Deep-Sea Research, 20, 461-478, 1973) with GOYET and POISSON ( Deep-Sea Research, 36, 1635-1654, 1989). No statistically significant difference could be found between the two used calculation methods (Gran plot and curve-fitting). The agreement between the independent methods of Coulometry and acid titration is encouraging and furthermore independent of depth, for this dataset there is no reason for invoking the existence of interfering (organic) protolytes.

  14. Jacalin interaction with human immunoglobulin A1 and bovine immunoglobulin G1: affinity constant determined by piezoelectric biosensoring.

    PubMed

    Pedroso, Mariele M; Pesquero, Naira C; Thomaz, Sandra M O; Roque-Barreira, Maria C; Faria, Ronaldo C; Bueno, Paulo R

    2012-03-01

    The affinity of the D-galactose-binding lectin from Artocarpus heterophyllus lectin, known as jacalin, with immonuglobulins (Igs) was determined by biofunctionalization of a piezoelectric transducer. This piezoelectric biofunctionalized transducer was used as a mass-sensitive analytical tool, allowing the real-time binding analysis of jacalin-human immunoglobulin A1 (IgA(1)) and jacalin-bovine IgG(1) interactions from which the apparent affinity constant was calculated. The strategy was centered in immobilizing jacalin on the gold electrode's surface of the piezoelectric crystal resonator using appropriate procedures based on self-assembling of 11-mercaptoundecanoic acid and 2-mercaptoethanol thiol's mixture, a particular immobilization strategy by which it was possible to avoid cross-interaction between the proteins over electrode's surface. The apparent affinity constants obtained between jacalin-human IgA(1) and jacalin-bovine IgG(1) differed by 1 order of magnitude [(8.0 ± 0.9) 10(5) vs (8.3 ± 0.1) 10(6) L mol(-1)]. On the other hand, the difference found between human IgA(1) and human IgA(2) interaction with jacalin, eight times higher for IgA(1), was attributed to the presence of O-linked glycans in the IgA(1) hinge region, which is absent in IgA(2). Specific interaction of jacalin with O-glycans, proved to be present in the human IgA(1) and hypothetically present in bovine IgG(1) structures, is discussed as responsible for the obtained affinity values.

  15. Effect of surfactants on the dissociation constants of ascorbic and maleic acids.

    PubMed

    Jaiswal, P V; Ijeri, V S; Srivastava, A K

    2005-11-25

    The dissociation equilibria of ascorbic and maleic acids have been studied in certain cationic, anionic and non-ionic micellar media and their pK(a) values have been evaluated by the potentiometric, conductometric and spectrophotometric techniques. These pK(a) values have been found to shift in micellar media as compared to those in pure water. The differences in the values have been attributed to the solvent properties of the interfacial and bulk phases involving contribution from the micellar surface potential in the case of charged micelles. The values of the limiting molar conductance of the acids have been determined in the various surfactants and were found to be different in different surfactants. In case of the cationic surfactants the limiting molar conductance was found to increase with increase in surfactant concentration.

  16. Thermodynamics of Calcium binding to the Calmodulin N-terminal domain to evaluate site-specific affinity constants and cooperativity.

    PubMed

    Beccia, Maria Rosa; Sauge-Merle, Sandrine; Lemaire, David; Brémond, Nicolas; Pardoux, Romain; Blangy, Stéphanie; Guilbaud, Philippe; Berthomieu, Catherine

    2015-07-01

    Calmodulin (CaM) is an essential Ca(II)-dependent regulator of cell physiology. To understand its interaction with Ca(II) at a molecular level, it is essential to examine Ca(II) binding at each site of the protein, even if it is challenging to estimate the site-specific binding properties of the interdependent CaM-binding sites. In this study, we evaluated the site-specific Ca(II)-binding affinity of sites I and II of the N-terminal domain by combining site-directed mutagenesis and spectrofluorimetry. The mutations had very low impact on the protein structure and stability. We used these binding constants to evaluate the inter-site cooperativity energy and compared it with its lower limit value usually reported in the literature. We found that site I affinity for Ca(II) was 1.5 times that of site II and that cooperativity induced an approximately tenfold higher affinity for the second Ca(II)-binding event, as compared to the first one. We further showed that insertion of a tryptophan at position 7 of site II binding loop significantly increased site II affinity for Ca(II) and the intra-domain cooperativity. ΔH and ΔS parameters were studied by isothermal titration calorimetry for Ca(II) binding to site I, site II and to the entire N-terminal domain. They showed that calcium binding is mainly entropy driven for the first and second binding events. These findings provide molecular information on the structure-affinity relationship of the individual sites of the CaM N-terminal domain and new perspectives for the optimization of metal ion binding by mutating the EF-hand loops sequences.

  17. Photodetachment of an electron from selenide ion - The electron affinity and spin-orbit coupling constant for SeH.

    NASA Technical Reports Server (NTRS)

    Smyth, K. C.; Brauman, J. I.

    1972-01-01

    The relative cross section for the gas phase photodetachment of an electron from SeH(-) was determined in the wavelength region 428 to 578 nm. An ion cyclotron resonance spectrometer was used to generate, trap, and detect the negative ions, and a 1000-W xenon arc lamp with a grating monochromator was employed as the light source. The cross section exhibited two sharp thresholds, whose positions remained unchanged for the photodetachment of SeD(-). As a result of these thresholds, the electron affinity and the spin-orbit coupling constant were evaluated.

  18. Adding explicit solvent molecules to continuum solvent calculations for the calculation of aqueous acid dissociation constants.

    PubMed

    Kelly, Casey P; Cramer, Christopher J; Truhlar, Donald G

    2006-02-23

    Aqueous acid dissociation free energies for a diverse set of 57 monoprotic acids have been calculated using a combination of experimental and calculated gas and liquid-phase free energies. For ionic species, aqueous solvation free energies were calculated using the recently developed SM6 continuum solvation model. This model combines a dielectric continuum with atomic surface tensions to account for bulk solvent effects. For some of the acids studied, a combined approach that involves attaching a single explicit water molecule to the conjugate base (anion), and then surrounding the resulting anion-water cluster by a dielectric continuum, significantly improves the agreement between the calculated pK(a) value and experiment. This suggests that for some anions, particularly those concentrating charge on a single exposed heteroatom, augmenting implicit solvent calculations with a single explicit water molecule is required, and adequate, to account for strong short-range hydrogen bonding interactions between the anion and the solvent. We also demonstrate the effect of adding several explicit waters by calculating the pK(a) of bicarbonate (HCO(3)(-)) using as the conjugate base carbonate (CO(3)(2-)) bound by up to three explicit water molecules.

  19. Dissociation and rate constants of some human liver alcohol dehydrogenase isoenzymes.

    PubMed

    Pietruszko, R; de Zalenski, C; Theorell, H

    1976-01-01

    ADH from human liver forms binary complexes with NADH, associated with a blue shift of the peak of the fluorescence emission of NADH. The wavelength shift is the same for all isoenzymes but the accompanying intensification of the fluorescence is different. The fluorescence is further increased by the formation of the very tight ternary enzyme-NADH-isobutyramide complexes. These properties are similar to those for the horse liver ADH, as well as the molecular weight of E=40 000 per active site of the dimer molecule (EE). "Stopped-flow" determined velocity constants (ER in equilibrium E+R) were found to be in good agreement with ethanol activity constants previously determined by activity measurement, confirming the validity of the ordered ternary complex mechanism also for the human ADH. No single isoenzyme activity as high as that reported by Mourad and Woronick or Drum has been found. PMID:184631

  20. Enthalpies and constants of dissociation of several neutral and cationic acids in aqueous and methanol/water solutions at various temperatures.

    PubMed

    Shoghi, Elham; Romero, Lilian; Reta, Mario; Ràfols, Clara; Bosch, Elisabeth

    2009-05-01

    The acidic dissociation enthalpies and constants of anilinium, protonated tris(hydroxymethyl)aminomethane (HTris(+)), benzoic and acetic acids, have been determined at several temperatures in pure water and in methanol/water mixtures by potentiometry and by isothermal titration microcalorimetry (ITC). The pK(a) values determined by both techniques are in accordance when the dissociation process involves large amounts of heat. However, for the neutral acids the ITC technique gave slightly lower pK(a) values than those from potentiometry at the highest temperatures studied due to the small amounts of heat involved in the acidic dissociation. The dissociation enthalpies have been determined directly by calorimetry and the obtained values slightly decrease with the increase of temperature. Therefore, only a rough estimation of the dissociation enthalpies can be obtained from potentiometric pK(a) by means of the Van't Hoff approach.

  1. Enthalpies and constants of dissociation of several neutral and cationic acids in aqueous and methanol/water solutions at various temperatures.

    PubMed

    Shoghi, Elham; Romero, Lilian; Reta, Mario; Ràfols, Clara; Bosch, Elisabeth

    2009-05-01

    The acidic dissociation enthalpies and constants of anilinium, protonated tris(hydroxymethyl)aminomethane (HTris(+)), benzoic and acetic acids, have been determined at several temperatures in pure water and in methanol/water mixtures by potentiometry and by isothermal titration microcalorimetry (ITC). The pK(a) values determined by both techniques are in accordance when the dissociation process involves large amounts of heat. However, for the neutral acids the ITC technique gave slightly lower pK(a) values than those from potentiometry at the highest temperatures studied due to the small amounts of heat involved in the acidic dissociation. The dissociation enthalpies have been determined directly by calorimetry and the obtained values slightly decrease with the increase of temperature. Therefore, only a rough estimation of the dissociation enthalpies can be obtained from potentiometric pK(a) by means of the Van't Hoff approach. PMID:19261425

  2. Optimization of Electrospray Ionization by Statistical Design of Experiments and Response Surface Methodology: Protein-Ligand Equilibrium Dissociation Constant Determinations

    NASA Astrophysics Data System (ADS)

    Pedro, Liliana; Van Voorhis, Wesley C.; Quinn, Ronald J.

    2016-09-01

    Electrospray ionization mass spectrometry (ESI-MS) binding studies between proteins and ligands under native conditions require that instrumental ESI source conditions are optimized if relative solution-phase equilibrium concentrations between the protein-ligand complex and free protein are to be retained. Instrumental ESI source conditions that simultaneously maximize the relative ionization efficiency of the protein-ligand complex over free protein and minimize the protein-ligand complex dissociation during the ESI process and the transfer from atmospheric pressure to vacuum are generally specific for each protein-ligand system and should be established when an accurate equilibrium dissociation constant (KD) is to be determined via titration. In this paper, a straightforward and systematic approach for ESI source optimization is presented. The method uses statistical design of experiments (DOE) in conjunction with response surface methodology (RSM) and is demonstrated for the complexes between Plasmodium vivax guanylate kinase ( PvGK) and two ligands: 5'-guanosine monophosphate (GMP) and 5'-guanosine diphosphate (GDP). It was verified that even though the ligands are structurally similar, the most appropriate ESI conditions for KD determination by titration are different for each.

  3. Optimization of Electrospray Ionization by Statistical Design of Experiments and Response Surface Methodology: Protein-Ligand Equilibrium Dissociation Constant Determinations.

    PubMed

    Pedro, Liliana; Van Voorhis, Wesley C; Quinn, Ronald J

    2016-09-01

    Electrospray ionization mass spectrometry (ESI-MS) binding studies between proteins and ligands under native conditions require that instrumental ESI source conditions are optimized if relative solution-phase equilibrium concentrations between the protein-ligand complex and free protein are to be retained. Instrumental ESI source conditions that simultaneously maximize the relative ionization efficiency of the protein-ligand complex over free protein and minimize the protein-ligand complex dissociation during the ESI process and the transfer from atmospheric pressure to vacuum are generally specific for each protein-ligand system and should be established when an accurate equilibrium dissociation constant (KD) is to be determined via titration. In this paper, a straightforward and systematic approach for ESI source optimization is presented. The method uses statistical design of experiments (DOE) in conjunction with response surface methodology (RSM) and is demonstrated for the complexes between Plasmodium vivax guanylate kinase (PvGK) and two ligands: 5'-guanosine monophosphate (GMP) and 5'-guanosine diphosphate (GDP). It was verified that even though the ligands are structurally similar, the most appropriate ESI conditions for KD determination by titration are different for each. Graphical Abstract ᅟ.

  4. Evaluation of equilibrium constants for the interaction of lactate dehydrogenase isoenzymes with reduced nicotinamide-adenine dinucleotide by affinity chromatography.

    PubMed Central

    Brinkworth, R I; Masters, C J; Winzor, D J

    1975-01-01

    Rabbit muscle lactate dehydrogenase was subjected to frontal affinity chromatography on Sepharose-oxamate in the presence of various concentrations of NADH and sodium phosphate buffer (0.05 M, pH 6.8) containing 0.5 M-NaCl. Quantitative interpretation of the results yields an intrinsic association constant of 9.0 x 10 (4)M-1 for the interaction of enzyme with NADH at 5 degrees C, a value that is confirmed by equilibrium-binding measurements. In a second series of experiments, zonal affinity chromatography of a mouse tissue extract under the same conditions was used to evaluate assoication constants of the order 2 x 10(5)M-1, 3 x 10(5)M-1, 4 x 10(5)M-1, 7 x 10(5)M-1 and 2 x 10(6)M-1 for the interaction of NADH with the M4, M3H, M2H2, MH3 and H4 isoenzymes respectively of lactate dehydrogenase. PMID:175784

  5. SNAP-Tag Technology: A Useful Tool To Determine Affinity Constants and Other Functional Parameters of Novel Antibody Fragments.

    PubMed

    Niesen, Judith; Sack, Markus; Seidel, Melanie; Fendel, Rolf; Barth, Stefan; Fischer, Rainer; Stein, Christoph

    2016-08-17

    Antibody derivatives, such as the single chain fragment variable (scFv), can be developed as diagnostic and therapeutic tools in cancer research, especially in the form of fusion proteins. Such derivatives are easier to produce and modify than monoclonal antibodies (mAbs) and achieve better tissue/tumor penetration. The genetic modification of scFvs is also much more straightforward than the challenging chemical modification of mAbs. Therefore, we constructed two scFvs derived from the approved monoclonal antibodies cetuximab (scFv2112) and panitumumab (scFv1711), both of which are specific for the epidermal growth factor receptor (EGFR), a well-characterized solid tumor antigen. Both scFvs were genetically fused to the SNAP-tag, an engineered version of the human DNA repair enzyme O(6)-alkylguanine DNA alkyltransferase that allows the covalent coupling of benzylguanine (BG)-modified substrates such as fluorescent dyes. The SNAP-tag achieves controllable and irreversible protein modification and is an important tool for experimental studies in vitro and in vivo. The affinity constant of a scFv is a key functional parameter, especially in the context of a fusion protein. Therefore, we developed a method to define the affinity constants of scFv-SNAP fusion proteins by surface plasmon resonance (SPR) spectroscopy. We could confirm that both scFvs retained their functionality after fusion to the SNAP-tag in a variety of procedures and assays, including ELISA, flow cytometry, and confocal microscopy. The experimental procedures described herein, and the new protocol for affinity determination by SPR spectroscopy, are suitable for the preclinical evaluation of diverse antibody formats and derivatives. PMID:27391930

  6. Resolution of a Challenge for Solvation Modeling: Calculation of Dicarboxylic Acid Dissociation Constants Using Mixed Discrete-Continuum Solvation Models

    SciTech Connect

    Marenich, Aleksandr; Ding, Wendu; Cramer, Christopher J.; Truhlar, Donald G.

    2012-06-07

    First and second dissociation constants (pKa values) of oxalic acid, malonic acid, and adipic acid were computed by using a number of theoretical protocols based on density functional theory and using both continuum solvation models and mixed discrete-continuum solvation models. We show that fully implicit solvation models (in which the entire solvent is represented by a dielectric continuum) fail badly for dicarboxylic acids with mean unsigned errors averaged over six pKa values) of 2.4-9.0 log units, depending on the particular implicit model used. The use of water-solute clusters and accounting for multiple conformations in solution significantly improve the performance of both generalized Born solvation models and models that solve the nonhomogeneous dielectric Poisson equation for bulk electrostatics. The four most successful models have mean unsigned errors of only 0.6-0.8 log units.

  7. Determination of chromatographic dissociation constants of some carbapenem group antibiotics and quantification of these compounds in human urine.

    PubMed

    Çubuk Demiralay, Ebru; Koç, Duygu; Daldal, Y Doğan; Alsancak, Güleren; Ozkan, Sibel A

    2014-05-01

    The dissociation constant values (s (s) pKa ) of some carbapenem group drugs (ertapenem, meropenem, doripenem) in different percentages of methanol-water binary mixtures (18, 20 and 22%, v/v) were determined from the mobile phase pH dependence of their retention factor. Evaluation of these data was performed using the NLREG program. From calculated pKa values, the aqueous pKa values of these subtances were calculated by different approaches. Moreover, the correlation established between retention factor and the pH of the water-methanol mobile phase was used to determine the optimum separation conditions. In order to validate the optimized conditions, these drugs were studied in human urine. The chromatographic separation was realized using a Gemini NX C18 column (250 × 4.6 mm i.d., 5 µm particles) and UV detector set at 220 and 295 nm.

  8. Determination of residue-specific acid dissociation constants for peptides by band-selective homonuclear-decoupled (1)H NMR.

    PubMed

    Wang, Jing; Rabenstein, Dallas L

    2007-09-01

    Acid dissociation constants of side-chain acidic groups of amino acid residues in peptides can be determined by 1H NMR, provided resonances can be resolved for carbon-bonded reporter protons located near the acidic group. We report here that the increased resolution of the band-selective homonuclear-decoupled (BASHD) TOCSY experiment greatly extends the range of application of the NMR method for determination of residue-specific, side-chain acid dissociation constants of peptides that contain multiple residues of the same amino acid. Chemical shift-pH titration curves are obtained from cross-peaks for reporter protons in BASHD-TOCSY spectra measured as a function of pH. The method is based on using sequence-dependent differences in the chemical shifts of resonances for the backbone CalphaH protons and the increased resolution in BASHD-TOCSY spectra from collapse of CalphaH multiplets to singlets in the F1 dimension to resolve resonances for the side-chain reporter protons. Application of the method is demonstrated by determination of residue-specific pKA values for each of the side-chain ammonium groups of the six lysine residues in the hexadecapeptide Ac-SRGKAKVKAKVKDQTK-NH2. Chemical shift-pH titration curves were obtained for the lysine side-chain CepsilonH2 reporter protons from their resolved CalphaH-CepsilonH2 TOCSY cross-peaks in BASHD-TOCSY spectra. Relative acidities of the six ammonium groups were also determined from the residue specific chemical shift-pH titration data by a pH-independent method, and calculation of fractional concentrations of protonation microspecies using the residue-specific pKAs is also described.

  9. The estimation of affinity constants for the binding of model peptides to DNA by equilibrium dialysis.

    PubMed Central

    Standke, K C; Brunnert, H

    1975-01-01

    The binding of lysine model peptides of the type Lys-X-Lys, Lys-X-X-Lys and Lys-X-X-X-Lys (X = different aliphatic and aromatic amino acids) has been studied by equilibrium dialysis. It was shown that the strong electrostatic binding forces generated by protonated amino groups of lysine can be distinguished from the weak forces stemming from neutral and aromatic spacer amino acids. The overall binding strength of the lysine model peptides is modified by these weak binding forces and the apparent binding constants are influenced more by the hydrophobic character of the spacer amino acid side chains than by the chainlength of the spacers. PMID:1187347

  10. Estimation of apparent binding constant of complexes of selected acyclic nucleoside phosphonates with β-cyclodextrin by affinity capillary electrophoresis.

    PubMed

    Šolínová, Veronika; Mikysková, Hana; Kaiser, Martin Maxmilián; Janeba, Zlatko; Holý, Antonín; Kašička, Václav

    2016-01-01

    Affinity capillary electrophoresis (ACE) has been applied to estimation of apparent binding constant of complexes of (R,S)-enantiomers of selected acyclic nucleoside phosphonates (ANPs) with chiral selector β-cyclodextrin (βCD) in aqueous alkaline medium. The noncovalent interactions of five pairs of (R,S)-enantiomers of ANPs-based antiviral drugs and their derivatives with βCD were investigated in the background electrolyte (BGE) composed of 35 or 50 mM sodium tetraborate, pH 10.0, and containing variable concentration (0-25 mM) of βCD. The apparent binding constants of the complexes of (R,S)-enantiomers of ANPs with βCD were estimated from the dependence of effective electrophoretic mobilities of (R,S)-enantiomers of ANPs (measured simultaneously by ACE at constant reference temperature 25°C inside the capillary) on the concentration of βCD in the BGE using different nonlinear and linear calculation methodologies. Nonlinear regression analysis provided more precise and accurate values of the binding constants and a higher correlation coefficient as compared to the regression analysis of the three linearized plots of the effective mobility dependence on βCD concentration in the BGE. The complexes of (R,S)-enantiomers of ANPs with βCD have been found to be relatively weak - their apparent binding constants determined by the nonlinear regression analysis were in the range 13.3-46.4 L/mol whereas the values from the linearized plots spanned the interval 12.3-55.2 L/mol. PMID:26426398

  11. Determination of acid-base dissociation constants of very weak zwitterionic heterocyclic bases by capillary zone electrophoresis.

    PubMed

    Ehala, Sille; Grishina, Anastasiya A; Sheshenev, Andrey E; Lyapkalo, Ilya M; Kašička, Václav

    2010-12-17

    Thermodynamic acid-base dissociation (ionization) constants (pK(a)) of seven zwitterionic heterocyclic bases, first representatives of new heterocyclic family (2,3,5,7,8,9-hexahydro-1H-diimidazo[1,2-c:2',1'-f][1,3,2]diazaphosphinin-4-ium-5-olate 5-oxides), originally designed as chiral Lewis base catalysts for enantioselective reactions, were determined by capillary zone electrophoresis (CZE). The pK(a) values of the above very weak zwitterionic bases were determined from the dependence of their effective electrophoretic mobility on pH in strongly acidic background electrolytes (pH 0.85-2.80). Prior to pK(a) calculation by non-linear regression analysis, the CZE measured effective mobilities were corrected to reference temperature, 25°C, and constant ionic strength, 25 mM. Thermodynamic pK(a) values of the analyzed zwitterionic heterocyclic bases were found to be particularly low, in the range 0.04-0.32. Moreover, from the pH dependence of effective mobility of the bases, some other relevant characteristics, such as actual and absolute ionic mobilities and hydrodynamic radii of the acidic cationic forms of the bases were determined.

  12. Equilibrium and rate constants, and reaction mechanism of the HF dissociation in the HF(H2O)7 cluster by ab initio rare event simulations.

    PubMed

    Elena, Alin Marin; Meloni, Simone; Ciccotti, Giovanni

    2013-12-12

    We perform restrained hybrid Monte Carlo (MC) simulations to compute the equilibrium constant of the dissociation reaction of HF in HF(H2O)7. We find that the HF is a stronger acid in the cluster than in the bulk, and its acidity is higher at lower T. The latter phenomenon has a vibrational entropic origin, resulting from a counterintuitive balance of intra- and intermolecular terms. We find also a temperature dependence of the reactions mechanism. At low T (≤225 K) the dissociation reaction follows a concerted path, with the H atoms belonging to the relevant hydrogen bond chain moving synchronously. At higher T (300 K), the first two hydrogen atoms move together, forming an intermediate metastable state having the structure of an eigen ion (H9O4(+)), and then the third hydrogen migrates completing the reaction. We also compute the dissociation rate constant, kRP. At very low T (≤75 K) kRP depends strongly on the temperature, whereas it gets almost constant at higher T’s. With respect to the bulk, the HF dissociation in the HF(H2O)7 is about 1 order of magnitude faster. This is due to a lower free energy barrier for the dissociation in the cluster.

  13. The New Low Value for the Second Dissociation Constant for H2S: Its History, Its Best Value, and Its Impact on the Teaching of Sulfide Equilibria.

    ERIC Educational Resources Information Center

    Myers, Rollie J.

    1986-01-01

    Discusses the historical development of a new value of the second dissociation constant (K2) for hydrogen sulfide (H2S). Describes the differences between the traditional high values for K2. Suggests modification of teaching about sulfide equilibria in light of the new low value for K2. (TW)

  14. Determination of the acid dissociation constant of the biosurfactant monorhamnolipid in aqueous solution by potentiometric and spectroscopic methods.

    PubMed

    Lebrón-Paler, Ariel; Pemberton, Jeanne E; Becker, Bridget A; Otto, William H; Larive, Cynthia K; Maier, Raina M

    2006-11-15

    The acid dissociation constant in water for a monorhamnolipid mixture extracted from Pseudomonas aeruginosa ATCC 9027 has been determined using potentiometry and two spectroscopic approaches at concentrations below and above the critical micelle concentration (cmc). Potentiometric titrations resulted in pKa values ranging from 4.28 +/- 0.16 to 5.50 +/- 0.06 depending on concentration. 1H NMR spectrochemical titrations at concentrations below the cmc revealed a pKa value of 4.39 +/- 0.06. ATR-FT-IR spectrochemical titrations on solutions well above the cmc gave a pKa value of 4.84 +/- 0.05. The value of 4.28 for the free rhamnolipid molecule for concentrations below the cmc differs markedly from that reported previously. However, the pKa of 5.50 for surface-adsorbed and solution aggregates correlates closely to that previously reported. Differences in these pKa values are rationalized in terms of the pH- and concentration-dependent aggregation behavior of rhamnolipids in aqueous solution.

  15. Prediction of the dissociation constant pKa of organic acids from local molecular parameters of their electronic ground state.

    PubMed

    Yu, Haiying; Kühne, Ralph; Ebert, Ralf-Uwe; Schüürmann, Gerrit

    2011-09-26

    A quantum chemical method has been developed to estimate the dissociation constant pK(a) of organic acids from their neutral molecular structures by employing electronic structure properties. The data set covers 219 phenols (including 29 phenols with intramolecular H-bonding), 150 aromatic carboxylic acids, 190 aliphatic carboxylic acids, and 138 alcohols, with pK(a) varying by 16 units (0.38-16.80). Optimized ground-state geometries employing the semiempirical AM1 Hamiltonian have been used to quantify the site-specific molecular readiness to donate or accept electron charge in terms of both charge-associated energies and energy-associated charges, augmented by an ortho substitution indicator for aromatic compounds. The resultant regression models yield squared correlation coefficients (r(2)) from 0.82 to 0.90 and root-mean-square errors (rms) from 0.39 to 0.70 pK(a) units, corresponding to an overall (subset-weighted) r(2) of 0.86. Simulated external validation, leave-10%-out cross-validation and target value scrambling demonstrate the statistical robustness and prediction power of the derived model suite. The low intercorrelation with prediction errors from the commercial ACD package provides opportunity for a consensus model approach, offering a pragmatic way for further increasing the confidence in prediction significantly. Interestingly, inclusion of calculated free energies of aqueous solvation does not improve the prediction performance, probably because of the limited precision provided by available continuum-solvation models.

  16. Determination of acid dissociation constant of 20 coumarin derivatives by capillary electrophoresis using the amine capillary and two different methodologies.

    PubMed

    Nowak, Paweł Mateusz; Woźniakiewicz, Michał; Piwowarska, Monika; Kościelniak, Paweł

    2016-05-13

    In this work capillary electrophoresis has been used to determine acid dissociation constant of 20 structurally diverse coumarin derivatives. For a majority of compounds pKa value has been determined for the first time. The obtained values vary between 4.16-9.10pH unit, pointing to the interesting structure-acidity relationships. The amine permanently coated capillary has been applied for that purpose, because it has turned out to be more effective in pKa determination than the bare silica and other coated capillaries, ensuring good precision and shorter migration times. A traditional methodology relying on measurements in a broad pH range and fitting of a sigmoidal function has been compared to an alternative simplified approach, reported for the first time, where only two electrophoretic mobility values suffice for pKa estimation. The first value corresponds to the partially ionized form and it is measured experimentally, while the second one to the totally ionized form - it is measured experimentally (two-values method) or estimated directly from molecular mass (one-value method). We show that despite a limited measurements number, the alternative approach may be consistent with the traditional methodology, yielding the relatively low pKa deviation. Its reliability has also been confirmed by the analytical predictions, comprising resolution, migration order, migration times and peaks overlapping. Therefore, combination of the amine capillary with the simplified calculation method is an attractive tool for fast and reliable pKa estimation.

  17. Detection analysis of surface hydroxyl active sites and simulation calculation of the surface dissociation constants of aqueous diatomite suspensions

    NASA Astrophysics Data System (ADS)

    Ma, Shu-Cui; Wang, Zhi-Gang; Zhang, Ji-Lin; Sun, De-Hui; Liu, Gui-Xia

    2015-02-01

    The surface properties of the diatomite were investigated using nitrogen adsorption/deadsorption isotherms, TG-DSC, FTIR, and XPS, and surface protonation-deprotonation behavior was determined by continuous acid-base potentiometric titration technique. The diatomite sample with porous honeycomb structure has a BET specific surface area of 10.21 m2/g and large numbers of surface hydroxyl functional groups (i.e. tbnd Si-OH, tbnd Fe-OH, and tbnd Al-OH). These surface hydroxyls can be protonated or deprotonated depending on the pH of the suspension. The experimental potentiometric data in two different ionic strength solutions (0.1 and 0.05 mol/L NaCl) were fitted using ProtoFit GUI V2.1 program by applying diffuse double layer model (DLM) with three amphoteric sites and minimizing the sum of squares between a dataset derivative function and a model derivative function. The optimized surface parameters (i.e. surface dissociation constants (log K1, log K2) and surface site concentrations (log C)) of the sample were obtained. Based on the optimized surface parameters, the surface species distribution was calculated using Program-free PHREEQC 3.1.2. Thus, this work reveals considerable new information about surface protonation-deprotonation processes and surface adsorptive behaviors of the diatomite, which helps us to effectively use the cheap and cheerful diatomite clay adsorbent.

  18. Effects of alkyl chain length and solvents on thermodynamic dissociation constants of the ionic liquids with one carboxyl group in the alkyl chain of imidazolium cations.

    PubMed

    Chen, Yuehua; Wang, Huiyong; Wang, Jianji

    2014-05-01

    Thermodynamic dissociation constants of the Brønsted acidic ionic liquids (ILs) are important for their catalytic and separation applications. In this work, a series of imidazolium bromides with one carboxylic acid substitute group in their alkyl chain ([{(CH2)nCOOH}mim]Br, n = 1,3,5,7) have been synthesized, and their dissociation constants (pKa) at different ionic strengths have been determined in aqueous and aqueous organic solvents at 0.1 mole fraction (x) of ethanol, glycol, iso-propanol, and dimethyl sulfoxide by potentiometric titrations at 298.2 K. The standard thermodynamic dissociation constants (pKa(T)) of the ILs in these solvents were calculated from the extended Debye-Hückel equation. It was found that the pKa values increased with the increase of ionic strength of the media and of the addition of organic solvent in water. The pKa(T) values also increased with the increase of the alkyl chain length of cations of the ILs. In addition, the effect of solvent nature on pKa(T) values is interpreted from solvation of the dissociation components and their Gibbs energy of transfer from water to aqueous organic solutions. PMID:24720707

  19. Effects of alkyl chain length and solvents on thermodynamic dissociation constants of the ionic liquids with one carboxyl group in the alkyl chain of imidazolium cations.

    PubMed

    Chen, Yuehua; Wang, Huiyong; Wang, Jianji

    2014-05-01

    Thermodynamic dissociation constants of the Brønsted acidic ionic liquids (ILs) are important for their catalytic and separation applications. In this work, a series of imidazolium bromides with one carboxylic acid substitute group in their alkyl chain ([{(CH2)nCOOH}mim]Br, n = 1,3,5,7) have been synthesized, and their dissociation constants (pKa) at different ionic strengths have been determined in aqueous and aqueous organic solvents at 0.1 mole fraction (x) of ethanol, glycol, iso-propanol, and dimethyl sulfoxide by potentiometric titrations at 298.2 K. The standard thermodynamic dissociation constants (pKa(T)) of the ILs in these solvents were calculated from the extended Debye-Hückel equation. It was found that the pKa values increased with the increase of ionic strength of the media and of the addition of organic solvent in water. The pKa(T) values also increased with the increase of the alkyl chain length of cations of the ILs. In addition, the effect of solvent nature on pKa(T) values is interpreted from solvation of the dissociation components and their Gibbs energy of transfer from water to aqueous organic solutions.

  20. The proton dissociation constant of additive effect on self-assembly of poly(3-hexyl-thiophene) for organic solar cells

    NASA Astrophysics Data System (ADS)

    Wang, Po-Hsun; Lee, Hsu-Feng; Huang, Yi-Chiang; Jung, Yi-Jiun; Gong, Fang-Lin; Huang, Wen-Yao

    2014-07-01

    In the decision on the pros and cons of the optical and electrical properties of organic solar cells, the morphology has proven to be very important. Easy to change the morphology via adding a small amount of additive, because proton dissociation constant is the main reason for their application. In this study, the use of poly(3-hexylthiophene) and [6,6]-phenyl C 61-butyric acid methyl ester as the donor and acceptor materials, and were subsequently doped with different quantity of 4,4'-sulfonyldiphenol, 4,4'-dihydroxybiphenyl, biphenyl-4,4'-dithiol. When the proton dissociation constant is higher and lower respectively, the morphology reveals earthworms-like and fiber-like. For the reason that when the additive is biphenyl-4,4'-dithiol, it can improve the power conversion efficiency of about 27% and the incident photon-to-current conversion efficiency of about 12%.

  1. The dissociation constants of the cytostatic bosutinib by nonlinear least-squares regression of multiwavelength spectrophotometric and potentiometric pH-titration data.

    PubMed

    Meloun, Milan; Nečasová, Veronika; Javůrek, Milan; Pekárek, Tomáš

    2016-02-20

    Potentiometric and spectrophotometric pH-titration of the multiprotic cytostatics bosutinib for dissociation constants determination were compared. Bosutinib treats patients with positive chronic myeloid leukemia. Bosutinib exhibits four protonatable sites in a pH range from 2 to 11, where two pK are well separated (ΔpK>3), while the other two are near dissociation constants. In the neutral medium, bosutinib occurs in the slightly water soluble form LH that can be protonated to the soluble cation LH4(3+). The molecule LH can be dissociated to still difficultly soluble anion L(-). The set of spectra upon pH from 2 to 11 in the 239.3-375.0nm was divided into two absorption bands: the first one from 239.3 to 290.5nm and the second from 312.3 to 375.0nm, which differ in sensitivity of chromophores to a pH change. Estimates of pK of the entire set of spectra were compared with those of both absorption bands. Due to limited solubility of bosutinib the protonation in a mixed aqueous-methanolic medium was studied. In low methanol content of 3-6% three dissociation constants can be reliably determined with SPECFIT/32 and SQUAD(84) and after extrapolation to zero content of methanol they lead to pKc1=3.43(12), pKc2=4.54(10), pKc3=7.56(07) and pKc4=11.04(05) at 25°C and pKc1=3.44(06), pKc2=5.03(08) pKc3=7.33(05) and pKc4=10.92(06) at 37°C. With an increasing content of methanol in solvent the dissociation of bosutinib is suppressed and the percentage of LH3(2+) decreases and LH prevails. From the potentiometric pH-titration at 25°C the concentration dissociation constants were estimated with ESAB pKc1=3.51(02), pKc2=4.37(02), pKc3=7.97(02) and pKc4=11.05(03) and with HYPERQUAD: pKc1=3.29(12), pKc2=4.24(10), pKc3=7.95(07) and pKc4=11.29(05).

  2. The dissociation constants of the cytostatic bosutinib by nonlinear least-squares regression of multiwavelength spectrophotometric and potentiometric pH-titration data.

    PubMed

    Meloun, Milan; Nečasová, Veronika; Javůrek, Milan; Pekárek, Tomáš

    2016-02-20

    Potentiometric and spectrophotometric pH-titration of the multiprotic cytostatics bosutinib for dissociation constants determination were compared. Bosutinib treats patients with positive chronic myeloid leukemia. Bosutinib exhibits four protonatable sites in a pH range from 2 to 11, where two pK are well separated (ΔpK>3), while the other two are near dissociation constants. In the neutral medium, bosutinib occurs in the slightly water soluble form LH that can be protonated to the soluble cation LH4(3+). The molecule LH can be dissociated to still difficultly soluble anion L(-). The set of spectra upon pH from 2 to 11 in the 239.3-375.0nm was divided into two absorption bands: the first one from 239.3 to 290.5nm and the second from 312.3 to 375.0nm, which differ in sensitivity of chromophores to a pH change. Estimates of pK of the entire set of spectra were compared with those of both absorption bands. Due to limited solubility of bosutinib the protonation in a mixed aqueous-methanolic medium was studied. In low methanol content of 3-6% three dissociation constants can be reliably determined with SPECFIT/32 and SQUAD(84) and after extrapolation to zero content of methanol they lead to pKc1=3.43(12), pKc2=4.54(10), pKc3=7.56(07) and pKc4=11.04(05) at 25°C and pKc1=3.44(06), pKc2=5.03(08) pKc3=7.33(05) and pKc4=10.92(06) at 37°C. With an increasing content of methanol in solvent the dissociation of bosutinib is suppressed and the percentage of LH3(2+) decreases and LH prevails. From the potentiometric pH-titration at 25°C the concentration dissociation constants were estimated with ESAB pKc1=3.51(02), pKc2=4.37(02), pKc3=7.97(02) and pKc4=11.05(03) and with HYPERQUAD: pKc1=3.29(12), pKc2=4.24(10), pKc3=7.95(07) and pKc4=11.29(05). PMID:26730513

  3. Constant-atomic-final-state filtering of dissociative states in the O1s-->sigma* core excitation in O2.

    PubMed

    Hjelte, I; Björneholm, O; Carravetta, V; Angeli, C; Cimiraglia, R; Wiesner, K; Svensson, S; Piancastelli, M N

    2005-08-01

    The below-threshold region in core-excited O2 is very complex, consisting of a multitude of exchange-split states with mixed molecular orbital-Rydberg character. We have investigated the nature of these intermediate states by resonant Auger spectroscopy. In particular, we have obtained constant-atomic-final-state yield curves for several atomic peaks in the electron decay spectra which are stemming from ultrafast dissociation. The relative intensity of Auger decay leading to atomic final states is considered a signature of the relative weight of the sigma* character. This method allows one to "filter out" intermediate states with dissociative character. Extensive calculations have been performed by multi-reference configuration interaction at different interatomic distances in order to evaluate the potential curves of the core-excited states and propose a qualitative description of the dissociative molecular dynamics. The calculations show that the core-excited states have a relevant admixture of excitations to orbitals with Rydberg character and excitations to the sigma* orbital with different spin couplings. A diabatization of the adiabatic potential curves shows that the coupling between Rydberg and sigma* diabatic states is very different at the different crossing points and ultrafast dissociation occurs more easily on the lowest sigma* diabatic potential curve. As a consequence, the observation of atomic peaks only in the lower-energy region of the absorption curve is well justified.

  4. Determination by ultraviolet absorption spectrometry and theoretical calculation of dissociation constant of 1,2,3,9-tetrahydro-4H-carbazol-4-one.

    PubMed

    Zhang, Shufang; Zhang, Xiaoyan; Tang, Ke; Zhou, Zhengyu

    2009-08-15

    The dissociation constant of 1,2,3,9-tetrahydro-4H-carbazol-4-one was determined by ultraviolet absorption spectrometry method based on the absorption spectra of 1,2,3,9-tetrahydro-4H-carbazol-4-one at different pH in ethanol-water mixed solvents. The results show that the pK(b) was a good linear function of the volume fraction of ethanol in the concentration range studied. The dissociation constant of 1, 2, 3,9-tetrahydro-4H-carbazol-4-one in water were determined by extrapolation to be 14.04 under the condition of this experiment. The accurate pK(b) calculations of 1,2,3,9-tetrahydro-4H-carbazol-4-one have been investigated using the combination of the extended clusters-continuum model with the polarizable continuum solvation model (PCM). The calculations are performed at the B3LYP/6-31G levels. The formation of molecular clusters by means of the 1,2,3,9-tetrahydro-4H-carbazol-4-one wrapped up with water molecules leads to the weakness of the interaction between the polar solvents and the 1,2,3,9-tetrahydro-4H-carbazol-4-one, hence, the accuracy of pK(b) has been enhanced. The dissociation constant of 1,2,3,9-tetrahydro-4H-carbazol-4-one in water were calculated to be 14.10 and agreed well with experimental data.

  5. Formation and reactivity of a porphyrin iridium hydride in water: acid dissociation constants and equilibrium thermodynamics relevant to Ir-H, Ir-OH, and Ir-CH2- bond dissociation energetics.

    PubMed

    Bhagan, Salome; Wayland, Bradford B

    2011-11-01

    Aqueous solutions of group nine metal(III) (M = Co, Rh, Ir) complexes of tetra(3,5-disulfonatomesityl)porphyrin [(TMPS)M(III)] form an equilibrium distribution of aquo and hydroxo complexes ([(TMPS)M(III)(D(2)O)(2-n)(OD)(n)]((7+n)-)). Evaluation of acid dissociation constants for coordinated water show that the extent of proton dissociation from water increases regularly on moving down the group from cobalt to iridium, which is consistent with the expected order of increasing metal-ligand bond strengths. Aqueous (D(2)O) solutions of [(TMPS)Ir(III)(D(2)O)(2)](7-) react with dihydrogen to form an iridium hydride complex ([(TMPS)Ir-D(D(2)O)](8-)) with an acid dissociation constant of 1.8(0.5) × 10(-12) (298 K), which is much smaller than the Rh-D derivative (4.3 (0.4) × 10(-8)), reflecting a stronger Ir-D bond. The iridium hydride complex adds with ethene and acetaldehyde to form organometallic derivatives [(TMPS)Ir-CH(2)CH(2)D(D(2)O)](8-) and [(TMPS)Ir-CH(OD)CH(3)(D(2)O)](8-). Only a six-coordinate carbonyl complex [(TMPS)Ir-D(CO)](8-) is observed for reaction of the Ir-D with CO (P(CO) = 0.2-2.0 atm), which contrasts with the (TMPS)Rh-D analog which reacts with CO to produce an equilibrium with a rhodium formyl complex ([(TMPS)Rh-CDO(D(2)O)](8-)). Reactivity studies and equilibrium thermodynamic measurements were used to discuss the relative M-X bond energetics (M = Rh, Ir; X = H, OH, and CH(2)-) and the thermodynamically favorable oxidative addition of water with the (TMPS)Ir(II) derivatives.

  6. Dissociation constants of weak acids from ab initio molecular dynamics using metadynamics: influence of the inductive effect and hydrogen bonding on pKa values.

    PubMed

    Tummanapelli, Anil Kumar; Vasudevan, Sukumaran

    2014-11-26

    The theoretical estimation of the dissociation constant, or pKa, of weak acids continues to be a challenging field. Here, we show that ab initio Car-Parrinello molecular dynamics simulations in conjunction with metadynamics calculations of the free-energy profile of the dissociation reaction provide reasonable estimates of the pKa value. Water molecules, sufficient to complete the three hydration shells surrounding the acid molecule, were included explicitly in the computation procedure. The free-energy profiles exhibit two distinct minima corresponding to the dissociated and neutral states of the acid, and the difference in their values provides the estimate for pKa. We show for a series of organic acids that CPMD simulations in conjunction with metadynamics can provide reasonable estimates of pKa values. The acids investigated were aliphatic carboxylic acids, chlorine-substituted carboxylic acids, cis- and trans-butenedioic acid, and the isomers of hydroxybenzoic acid. These systems were chosen to highlight that the procedure could correctly account for the influence of the inductive effect as well as hydrogen bonding on pKa values of weak organic acids. In both situations, the CPMD metadynamics procedure faithfully reproduces the experimentally observed trend and the magnitudes of the pKa values.

  7. Determination of acid/base dissociation constants based on a rapid detection of the half equivalence point by feedback-based flow ratiometry.

    PubMed

    Tanaka, Hideji; Tachibana, Takahiro

    2004-06-01

    Acid dissociation constants (Ka) were determined through the rapid detection of the half equivalence point (EP1/2) based on a feedback-based flow ratiometry. A titrand, delivered at a constant flow rate, was merged with a titrant, whose flow rate was varied in response to a control voltage (Vc) from a controller. Downstream, the pH of the mixed solution was monitored. Initially, Vc was increased linearly. At the instance that the detector sensed EP1/2, the ramp direction of Vc changed downward. When EP1/2 was sensed again, Vc was increased again. This series of process was repeated automatically. The pH at EP1/2 was regarded as being pKa of the analyte after an activity correction. Satisfactory results were obtained for different acids in various matrices with good precision (RSD approximately 3%) at a throughput rate of 56 s/determination.

  8. Determination of the dissociation constants (pKa) of secondary and tertiary amines in organic media by capillary electrophoresis and their role in the electrophoretic mobility order inversion.

    PubMed

    Cantu, Marcelo Delmar; Hillebranda, Sandro; Carrilho, Emanuel

    2005-03-11

    Non-aqueous capillary electrophoresis (NACE) may provide a selectivity enhancement in separations since the analyte dissociation constants (pKa) in organic media are different from those in aqueous solutions. In this work, we have studied the inversion in mobility order observed in the separation of tertiary (imipramine (IMI) and amitryptiline (AMI)) and secondary amines (desipramine (DES) and nortryptiline (NOR)) in water, methanol, and acetonitrile. We have determined the pKa values in those solvents and the variation of dissociation constants with the temperature. From these data, and applying the Van't Hoff equation, we have calculated the thermodynamic parameters deltaH and deltaS. The pKa values found in methanol for DES, NOR, IMI, and AMI were 10.80, 10.79, 10.38, and 10.33, respectively. On the other hand, in acetonitrile an opposite relation was found since the values were 20.60, 20.67, 20.74, and 20.81 for DES, NOR, IMI, and AMI. This is the reason why a migration order inversion is observed in NACE for these solvents. The thermodynamic parameters were evaluated and presented a tendency that can be correlated with that observed for pKa values.

  9. Determination of binding constants by affinity capillary electrophoresis, electrospray ionization mass spectrometry and phase-distribution methods

    PubMed Central

    Chen, Zhi; Weber, Stephen G.

    2008-01-01

    Many methods for determining intermolecular interactions have been described in the literature in the past several decades. Chief among them are methods based on spectroscopic changes, particularly those based on absorption or nuclear magnetic resonance (NMR) [especially proton NMR (1H NMR)]. Recently, there have been put forward several new methods that are particularly adaptable, use very small quantities of material, and do not place severe requirements on the spectroscopic properties of the binding partners. This review covers new developments in affinity capillary electrophoresis, electrospray ionization mass spectrometry (ESI-MS) and phasetransfer methods. PMID:19802330

  10. Correct pK values for dissociation constant of carbonic acid lower the reported Km values of ribulose bisphosphate carboxylase to half. Presentation of a nomograph and an equation for determining the pK values.

    PubMed

    Yokota, A; Kitaoka, S

    1985-09-30

    In the assay of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) in vitro, the concentration of CO2, the substrate of the enzyme, has been calculated from the amount of sodium bicarbonate added to the assay mixture with a dissociation constant of carbonic acid in pure water, 6.35 to 6.37. However, Rubisco is generally assayed at ionic strength of 0.1 to 0.2 M, where the dissociation constant decreases up to 6.06. The decrease of this level of the constant reduces the calculated CO2 concentration in the assay mixture to about half and accordingly the Kms of Rubisco for CO2 reported so far are not correct. The present report presents a nomograph and an equation, from which dissociation constants of carbonic acid in the presence of various concentrations of salts can be easily calculated. PMID:3931642

  11. Label-Free Determination of the Dissociation Constant of Small Molecule-Aptamer Interaction by Isothermal Titration Calorimetry.

    PubMed

    Vogel, Marc; Suess, Beatrix

    2016-01-01

    Isothermal titration calorimetry (ITC) is a powerful label-free technique to determine the binding constant as well as thermodynamic parameters of a binding reaction and is therefore well suited for the analysis of small molecule-RNA aptamer interaction. We will introduce you to the method and present a protocol for sample preparation and the calorimetric measurement. A detailed note section will point out useful tips and pitfalls.

  12. Estimation of the acid dissociation constant of perfluoroalkyl carboxylic acids through an experimental investigation of their water-to-air transport.

    PubMed

    Vierke, Lena; Berger, Urs; Cousins, Ian T

    2013-10-01

    The acid dissociation constants (pKas) of perfluoroalkyl carboxylic acids (PFCAs) have been the subject of discussion in the literature; for example, values from -0.2 to 3.8 have been suggested for perfluorooctanoic acid (PFOA). The dissociated anionic conjugate bases of PFCAs have negligible air-water partition coefficients (KAWs) and do not volatilize from water. The neutral acids, however, have relatively high KAWs and volatilization from water has been demonstrated. The extent of volatilization of PFCAs in the environment will depend on the water pH and their pKa. Knowledge of the pKas of PFCAs is therefore vital for understanding their environmental transport and fate. We investigated the water-to-air transfer of PFCAs in a novel experimental setup. We used ∼1 μg L(-1) of PFCAs in water (above environmental background concentrations but below the concentration at which self-association occurs) at different water pH (pH 0.3 to pH 6.9) and sampled the PFCAs volatilized from water during a 2-day experiment. Our results suggest that the pKas of C4-11 PFCAs are <1.6. For PFOA, we derived a pKa of 0.5 from fitting the experimental measurements with a volatilization model. Perfluoroalkane sulfonic acids were not volatilized, suggesting that their pKas are below the investigated pH range (pKa <0.3).

  13. Dissociation constants and speciation in aqueous Li 2SO 4 and K 2SO 4 from measurements of electrical conductance to 673 K and 29 MPa

    NASA Astrophysics Data System (ADS)

    Sharygin, Andrei V.; Grafton, Brian K.; Xiao, Caibin; Wood, Robert H.; Balashov, Victor N.

    2006-10-01

    The electrical conductivities of aqueous solutions of Li 2SO 4 and K 2SO 4 have been measured at 523-673 K at 20-29 MPa in dilute solutions for molalities up to 2 × 10 -2 mol kg -1. These conductivities have been fitted to the conductance equation of Turq, Blum, Bernard, and Kunz with a consensus mixing rule and mean spherical approximation activity coefficients. In the temperature interval 523-653 K, where the dielectric constant, ɛ, is greater than 14, the electrical conductance data can be fitted by a solution model which includes ion association to form MSO4-, MSO40, and HSO4-, where M is Li or K. The adjustable parameters of this model are the first and second dissociation constants of the M 2SO 4. For the 673 K and 300 kg m -3 state point where the Coulomb interactions are the strongest (dielectric constant, ɛ = 5), models with more extensive association give good fits to the data. In the case of the Li 2SO 4 model, including the multi-ion associate, Li(SO)80, gave an extremely good fit to the conductance data.

  14. Determination of the dissociation constant of valine from acetohydroxy acid synthase by equilibrium partition in an aqueous two-phase system.

    PubMed

    Engel, S; Vyazmensky, M; Barak, Z; Chipman, D M; Merchuk, J C

    2000-06-23

    An aqueous polyethylene glycol/salt two-phase system was used to estimate the dissociation constant, K(dis), of the Escherichia coli isoenzyme AHAS III regulatory subunit, ilvH protein, from the feedback inhibitor valine. The amounts of the bound and free radioactive valine in the system were determined. A Scatchard plot of the data revealed a 1:1 valine-protein binding ratio and K(dis) of 133+/-14 microM. The protein did not bind leucine, and the ilvH protein isolated from a valine resistant mutant showed no valine binding. This method is very simple, rapid and requires only a small amounts of protein compared to the presently used equilibrium dialysis method.

  15. A survey of the reaction rate constants for the thermal dissociation and recombination of nitrogen and oxygen

    NASA Technical Reports Server (NTRS)

    Marraffa, Lionel; Dulikravich, George S.; Keeney, Timothy C.; Deiwert, George S.

    1988-01-01

    The objective of the present report is to survey the various values of forward and backward reaction rate constants used by investigators in the field of high-temperature (T greater than 2000 K) gas reactions involving nitrogen and oxygen only. The objective is to find those values that correlate well so that they can be used for the studies of hypersonic flow and supersonic combustion with reasonable confidence. Relatively good agreement among these various values is observed for temperatures lower than 10,000 K.

  16. Fractionation of oil sands-process affected water using pH-dependent extractions: a study of dissociation constants for naphthenic acids species.

    PubMed

    Huang, Rongfu; Sun, Nian; Chelme-Ayala, Pamela; McPhedran, Kerry N; Changalov, Mohamed; Gamal El-Din, Mohamed

    2015-05-01

    The fractionation of oil sands process-affected water (OSPW) via pH-dependent extractions was performed to quantitatively investigate naphthenic acids (NAs, CnH2n+ZO2) and oxidized NAs (Ox-NAs) species (CnH2n+ZO3 and CnH2n+ZO4) using ultra-performance liquid chromatography time-of-flight mass spectrometry (UPLC-TOFMS). A mathematical model was also developed to estimate the dissociation constant pKa for NAs species, considering the liquid-liquid extraction process and the aqueous layer acid-base equilibrium. This model provides estimated dissociation constants for compounds in water samples based on fractionation extraction and relative quantification. Overall, the sum of O2-, O3-, and O4-NAs species accounted for 33.6% of total extracted organic matter. Accumulative extracted masses at different pHs revealed that every oxygen atom added to NAs increases the pKa (i.e., O2-NAs

  17. Asymmetry in inward- and outward-affinity constant of transport explain unidirectional lysine flux in Saccharomyces cerevisiae.

    PubMed

    Bianchi, Frans; Klooster, Joury S van 't; Ruiz, Stephanie J; Luck, Katja; Pols, Tjeerd; Urbatsch, Ina L; Poolman, Bert

    2016-01-01

    The import of basic amino acids in Saccharomyces cerevisiae has been reported to be unidirectional, which is not typical of how secondary transporters work. Since studies of energy coupling and transport kinetics are complicated in vivo, we purified the major lysine transporter (Lyp1) of yeast and reconstituted the protein into lipid vesicles. We show that the Michaelis constant (KM) of transport from out-to-in is well in the millimolar range and at least 3 to 4-orders of magnitude higher than that of transport in the opposite direction, disfavoring the efflux of solute via Lyp1. We also find that at low values of the proton motive force, the transport by Lyp1 is comparatively slow. We benchmarked the properties of eukaryotic Lyp1 to that of the prokaryotic homologue LysP and find that LysP has a similar KM for transport from in-to-out and out-to-in, consistent with rapid influx and efflux. We thus explain the previously described unidirectional nature of lysine transport in S. cerevisiae by the extraordinary kinetics of Lyp1 and provide a mechanism and rationale for previous observations. The high asymmetry in transport together with secondary storage in the vacuole allow the cell to accumulate basic amino acids to very high levels. PMID:27550794

  18. Asymmetry in inward- and outward-affinity constant of transport explain unidirectional lysine flux in Saccharomyces cerevisiae

    PubMed Central

    Bianchi, Frans; Klooster, Joury S. van ‘t; Ruiz, Stephanie J.; Luck, Katja; Pols, Tjeerd; Urbatsch, Ina L.; Poolman, Bert

    2016-01-01

    The import of basic amino acids in Saccharomyces cerevisiae has been reported to be unidirectional, which is not typical of how secondary transporters work. Since studies of energy coupling and transport kinetics are complicated in vivo, we purified the major lysine transporter (Lyp1) of yeast and reconstituted the protein into lipid vesicles. We show that the Michaelis constant (KM) of transport from out-to-in is well in the millimolar range and at least 3 to 4-orders of magnitude higher than that of transport in the opposite direction, disfavoring the efflux of solute via Lyp1. We also find that at low values of the proton motive force, the transport by Lyp1 is comparatively slow. We benchmarked the properties of eukaryotic Lyp1 to that of the prokaryotic homologue LysP and find that LysP has a similar KM for transport from in-to-out and out-to-in, consistent with rapid influx and efflux. We thus explain the previously described unidirectional nature of lysine transport in S. cerevisiae by the extraordinary kinetics of Lyp1 and provide a mechanism and rationale for previous observations. The high asymmetry in transport together with secondary storage in the vacuole allow the cell to accumulate basic amino acids to very high levels. PMID:27550794

  19. Analysis of fast and slow acid dissociation equilibria of 3',3″,5',5″-tetrabromophenolphthalein and determination of its equilibrium constants by capillary zone electrophoresis.

    PubMed

    Takayanagi, Toshio

    2013-01-01

    Acid dissociation constants of 3',3″,5',5″-tetrabrompohenolphthalein (TBPP) were determined in an aqueous solution by capillary zone electrophoresis at an ionic strength of 0.01 mol/L. Two steps of the fast acid-dissociation equilibria including precipitable species of H2TBPP were analyzed at a weakly acidic pH region by using the change in effective electrophoretic mobility of TBPP with the pH of the separation buffer. On the other hand, an acid-dissociation reaction of TBPP at an alkaline pH region was reversible, but very slow to reach its equilibrium; the two TBPP species concerned with the equilibrium were detected as distinct signals in the electropherograms. After reaching its equilibrium, the acid-dissociation constant was determined with the signal height corresponding to its dianion form. Thus, three steps of the acid dissociation constants of TBPP were determined in an aqueous solution as pKa1 = 5.29 ± 0.06, pKa2 = 6.35 ± 0.02, and pKa3 = 11.03 ± 0.04.

  20. The influence of cooperativity on the determination of dissociation constants: examination of the Cheng-Prusoff equation, the Scatchard analysis, the Schild analysis and related power equations.

    PubMed

    Cheng, Hsien C

    2004-07-01

    Use of the Cheng-Prusoff equation for determination of the equilibrium dissociation constant, K(B), is based on an assumption that simple bi-molecular interaction kinetics are strictly followed. Under such circumstances, the slope parameters of the agonist concentration-response curve (K) and that of the inhibition curve (n) are unity. New equations are needed for calculating K(B) when slope parameters (K and n) deviate from unity. In this article, the slope parameters K and n are used as indexes of cooperativity. Thus, the following new equations are derived: (1) For calculation of K(B) from IC(50), the new equation which incorporates both cooperativity indexes is described as K(B) = (IC50)n/(1 + A(K)/K(A)) = (IC50)n/[1 + (A/EC50)K] where A is the concentration of the agonist against which the IC(50) is determined, and K(A) is the apparent equilibrium dissociation constant of the agonist. This new equation is applicable when the cooperativity indexes of K and n are less than, equal to, or greater than unity. This equation reduces to the Cheng-Prusoff equation when the cooperativity indexes K and n are unity. (2) For saturation binding assays, the enhanced Scatchard analysis is described by the equation: B/Fm = -B/K(D) + B(max)/K(D) where B and F are the concentrations of the bound and free ligand, respectively, and m is the cooperativity index of the ligand. A plot of B/F(m) versus B yields a straight line with a negative slope that equals 1/K(D), and an x-axis intercept that equals B(max). When m equals unity, the above analysis reduces to the traditional Scatchard analysis. (3) The importance of the slope parameters (K and n) on Schild analysis is illustrated by the equation: log(x(K) - 1) = log Bn - log K(B), where x is the concentration ratio, and B is the concentration of the antagonist. The modified pA(2) is now defined as the -logarithm of the molar concentration of the antagonist (B), power adjusted with the slope parameter (B(n)), that causes a two

  1. Label-free Growth Receptor-2 Detection and Dissociation Constant Assessment in Diluted Human Serum Using a Longitudinal Extension Mode of a Piezoelectric Microcantilever Sensor.

    PubMed

    Capobianco, Joseph A; Shih, Wan Y; Adams, Gregory P; Shih, Wei-Heng

    2011-12-15

    We have investigated real-time, label-free, in-situ detection of human epidermal growth factor receptor 2 (Her2) in diluted serum using the first longitudinal extension mode of a lead zirconate-lead titanate (PZT)/glass piezoelectric microcantilever sensor (PEMS) with H3 single-chain variable fragment (scFv) immobilized on the 3-mercaptopropyltrimethoxysilane (MPS) insulation layer of the PEMS surface. We showed that with the longitudinal extension mode, the PZT/glass PEMS consisting of a 1 mm long and 127 μm thick PZT layer bonded with a 75 μm thick glass layer with a 1.8 mm long glass tip could detect Her2 at a concentration of 6-60 ng/ml (or 0.06-0.6 nM) in diluted human serum, about 100 times lower than the concentration limit obtained using the lower-frequency flexural mode of a similar PZT/glass PEMS. We further showed that with the longitudinal mode, the PZT/glass PEMS determined the equilibrium H3-Her2 dissociation constant K(d) to be 3.3±0.3 × 10(-8) M consistent with the value, 3.2±0.28 ×10(-8) M deduced by the surface plasmon resonance method (BIAcore).

  2. Acid dissociation constants of uridine-5'-diphosphate compounds determined by 31phosphorus nuclear magnetic resonance spectroscopy and internal pH referencing.

    PubMed

    Jancan, Igor; Macnaughtan, Megan A

    2012-10-24

    The acid dissociation constant (pK(a)) of small, biological molecules is an important physical property used for investigating enzyme mechanisms and inhibitor design. For phosphorus-containing molecules, the (31)P nuclear magnetic resonance (NMR) chemical shift is sensitive to the local chemical environment, particularly to changes in the electronic state of the molecule. Taking advantage of this property, we present a (31)P NMR approach that uses inorganic phosphate buffer as an internal pH reference to determine the pK(a) values of the imide and second diphosphate of uridine-5'-diphosphate compounds, including the first reported values for UDP-GlcNAc and UDP-S-GlcNAc. New methods for using inorganic phosphate buffer as an internal pH reference, involving mathematical correction factors and careful control of the chemical shift reference sample, are illustrated. A comparison of the newly determined imide and diphosphate pK(a) values of UDP, UDP-GlcNAc, and UDP-S-GlcNAc with other nucleotide phosphate and thio-analogs reveals the significance of the monosaccharide and sulfur position on the pK(a) values.

  3. Effects of deuterium oxide on the rate and dissociation constants for saxitoxin and tetrodotoxin action. Voltage-clamp studies on frog myelinated nerve

    SciTech Connect

    Hahin, R.; Strichartz, G.

    1981-08-01

    The actions of tetrodotoxin (TTX) and saxitoxin (STX) in normal water and in deuterium oxide (D/sub 20/) have been studied in frog myelinated nerve. Substitution of D/sub 20/ for H/sub 20/ in normal Ringer's solution has no effect on the potency of TTX in blocking action potentials but increases the potency of STX by approximately 50%. Under voltage clamp, the steady-state inhibition of sodium currents by 1 nM STX is doubled in D/sub 20/ as a result of a halving of the rate of dissociation of STX from the sodium channel; the rate of block by STX is not measurably changed by D/sub 20/. Neither steady-state inhibition nor the on- or off-rate constants of TTX are changed by D/sub 20/ substitution. The isotopic effects on STX binding are observed less than 10 min after the toxin has been added to D/sub 20/, thus eliminating the possibility that slow-exchange (t 1/2 greater than 10 h) hydrogen-binding sites on STX are involved. The results are consistent with a hypothesis that attributes receptor-toxin stabilization to isotopic changes of hydrogen bonding; this interpretation suggests that hydrogen bonds contribute more to the binding of STX than to that of TTX at the sodium channel.

  4. Directed evolution of antibody fragments with monovalent femtomolar antigen-binding affinity.

    PubMed

    Boder, E T; Midelfort, K S; Wittrup, K D

    2000-09-26

    Single-chain antibody mutants have been evolved in vitro with antigen-binding equilibrium dissociation constant K(d) = 48 fM and slower dissociation kinetics (half-time > 5 days) than those for the streptavidin-biotin complex. These mutants possess the highest monovalent ligand-binding affinity yet reported for an engineered protein by over two orders of magnitude. Optimal kinetic screening of randomly mutagenized libraries of 10(5)-10(7) yeast surface-displayed antibodies enabled a >1,000-fold decrease in the rate of dissociation after four cycles of affinity mutagenesis and screening. The consensus mutations are generally nonconservative by comparison with naturally occurring mouse Fv sequences and with residues that do not contact the fluorescein antigen in the wild-type complex. The existence of these mutants demonstrates that the antibody Fv architecture is not intrinsically responsible for an antigen-binding affinity ceiling during in vivo affinity maturation.

  5. Application of chemometrics in determination of the acid dissociation constants (pKa) of several benzodiazepine derivatives as poorly soluble drugs in the presence of ionic surfactants.

    PubMed

    Shayesteh, Tavakol Heidary; Radmehr, Moojan; Khajavi, Farzad; Mahjub, Reza

    2015-03-10

    In this study, the acid dissociation constants (pKa) of some benzodiazepine derivatives including chlordiazepoxide, clonazepam, lorazepam, and oxazepam in aqueous micellar solution were determined spectrophotometrically at an ionic strength of 0.1M at 25°C. The effect of cetyl trimethylammonium bromide (CTAB) as a cationic and sodium n-dodecyl sulfate(SDS) as an anionic surfactant on the absorption spectra of benzodiazepine drugs at different pH values were studied. The acidity constants of all related species are estimated by considering the surfactant concept and the application of chemometric methods using the whole spectral fitting of the collected data to an established factor analysis model. DATAN® software (Ver. 5.0, Multid Analyses AB, and Goteborg, Sweden) was applied to determine the acidity constants. In this study, a simple and fast method to determine the ionization constant (pKa) of poorly soluble drugs was developed using surfactants. The acidity constant (i.e. pKa) for chlordiazepoxide, clonazepam, lorazepam, and oxazepam were reported as 4.62, pKa1 value of 1.52 and pKa2 value of 10.51, pKa1 value of 1.53 and pKa2 value of 10.92 and pKa1 value 1.63 and pKa2 value of 11.21 respectively. The results showed that the peak values in the spectrophotometric absorption spectra of drugs are influenced by the presence of anionic and cationic surfactants. According to the results, by changing the SDS concentration from 0 to 0.05M, the pKa of chlordiazepoxide was increased to 5.9, the pKa1 of lorazepam was decreased to 0.1 while the pKa2 was increased to 11.5. Increase in SDS concentration has not shown significant alteration in pKa of clonazepam and oxazepam. Results indicate that by Changing the CTAB concentration from 0 to 0.05M, the pKa of chlordiazepoxide was reduced to 4.4, the pKa1 of clonazepam was decreased to 0.1 and the pKa2 was decreased to 9.1, the pKa1 of lorazepam was decreased to 0.4 and the pKa2 was decreased to 9.4, the pKa1 of oxazepam was

  6. Structure-based model profiles affinity constant of drugs with hPEPT1 for rapid virtual screening of hPEPT1's substrate.

    PubMed

    Sun, L; Meng, S

    2016-08-01

    The human proton-coupled peptide transporter (hPEPT1) with broad substrates is an important route for improving the pharmacokinetic performance of drugs. Thus, it is essential to predict the affinity constant between drug molecule and hPEPT1 for rapid virtual screening of hPEPT1's substrate during lead optimization, candidate selection and hPEPT1 prodrug design. Here, a structure-based in silico model for 114 compounds was constructed based on eight structural parameters. This model was built by the multiple linear regression method and satisfied all the prerequisites of the regression models. For the entire data set, the r(2) and adjusted r(2) values were 0.74 and 0.72, respectively. Then, this model was used to perform substrate/non-substrate classification. For 29 drugs from DrugBank database, all were correctly classified as substrates of hPEPT1. This model was also used to perform substrate/non-substrate classification for 18 drugs and their prodrugs; this QSAR model also can distinguish between the substrate and non-substrate. In conclusion, the QSAR model in this paper was validated by a large external data set, and all results indicated that the developed model was robust, stable, and can be used for rapid virtual screening of hPEPT1's substrate in the early stage of drug discovery. PMID:27586363

  7. Identification of c-Type Heme-Containing Peptides Using Non-Activated Immobilized Metal Affinity Cchromatography Resin Enrichment and Higher-Energy Collisional Dissociation

    SciTech Connect

    Zhang, Haizhen; Yang, Feng; Qian, Weijun; Brown, Roslyn N.; Wang, Yuexi; Merkley, Eric D.; Park, Jea H.; Monroe, Matthew E.; Purvine, Samuel O.; Moore, Ronald J.; Shi, Liang; Fredrickson, Jim K.; Pasa-Tolic, Ljiljana; Smith, Richard D.; Lipton, Mary S.

    2011-10-01

    c-type cytochromes play essential roles in many biological activities of both prokaryotic and eukaryotic cells, including electron transfer, enzyme catalysis and induction of apoptosis. We report a novel enrichment strategy for identifying c-type heme-containing peptides that uses non-activated IMAC resin. The strategy demonstrated at least seven-fold enrichment for heme-containing peptides digested from a cytochrome c protein standard, and quantitative linear performance was also assessed for heme-containing peptide enrichment. Heme-containing peptides extracted from the periplasmic fraction of Shewanella oneidensis MR-1 were further identified using higher-energy collisional dissociation tandem mass spectrometry. The results demonstrated the applicability of this enrichment strategy to identify c-type heme-containing peptides from a highly complex biological sample, and at the same time, confirmed the periplasmic localization of heme-containing proteins during suboxic respiration activities of S. oneidensis MR-1.

  8. Thermodynamic mixing of molecular states of the epidermal growth factor receptor modulates macroscopic ligand binding affinity.

    PubMed Central

    Holbrook, M R; Slakey, L L; Gross, D J

    2000-01-01

    The epidermal growth factor receptor (EGFr), when expressed on the cell surface, has long been known to display two distinct affinities for epidermal growth factor (EGF) binding. In addition, the treatment of cells expressing the EGFr with phorbol esters has been shown to cause a loss of the high-affinity binding capacity of the receptor. In the present study, point mutations that alter acidic or phosphorylation sites have been made in an intracellular domain near Tyr-992 (residues 988-992) of the EGFr. Equilibrium (125)I-EGF binding studies demonstrate that the conversion of Tyr-992 into glutamate induces a 4-fold decrease in the EGFr apparent low-affinity dissociation constant, whereas the mutation of two acidic residues, Asp-988 and Glu-991, or the conversion of Tyr-992 into phenylalanine does not alter EGFr affinity. Phorbol ester treatment of EGFr-expressing Chinese hamster ovary cells results in a loss of high-affinity binding and an increase in the apparent low-affinity dissociation constant of the receptor, similar to the effect of a truncation mutant in which the C-terminal 190 residues are deleted. These results are examined in the context of a new model for regulation of the affinity of the EGFr for EGF in which a cytosolic particle stabilizes the high-affinity conformation of the EGFr and a rapid equilibrium exists between EGFr high-affinity and low-affinity conformations. This model demonstrates that the macroscopic affinities of the EGFr can differ from the affinities of individual EGFr molecules and provides a theoretical framework whereby the measured affinities of the EGFr are modulated by intracellular interactions. PMID:11062062

  9. Affinity purification of aprotinin from bovine lung.

    PubMed

    Xin, Yu; Liu, Lanhua; Chen, Beizhan; Zhang, Ling; Tong, Yanjun

    2015-05-01

    An affinity protocol for the purification of aprotinin from bovine lung was developed. To simulate the structure of sucrose octasulfate, a natural specific probe for aprotinin, the affinity ligand was composed of an acidic head and a hydrophobic stick, and was then linked with Sepharose. The sorbent was then subjected to adsorption analysis with pure aprotinin. The purification process consisted of one step of affinity chromatography and another step of ultrafiltration. Then purified aprotinin was subjected to sodium dodecyl sulfate polyacrylamide gel electrophoresis, trypsin inhibitor activity, gel-filtration, and thin-layer chromatography analysis. As calculated, the theoretical maximum adsorption (Qmax ) of the affinity sorbent was 25,476.0 ± 184.8 kallikrein inactivator unit/g wet gel; the dissociation constant of the complex "immobilized ligand-aprotinin" (Kd ) was 4.6 ± 0.1 kallikrein inactivator unit/mL. After the affinity separation of bovine lung aprotinin, reducing sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis and gel-filtration chromatography revealed that the protein was a single polypeptide, and the purities were ∼ 97 and 100%, respectively; the purified peptide was also confirmed with aprotinin standard by gel-filtration chromatography and thin-layer chromatography. After the whole purification process, protein, and bioactivity recoveries were 2.2 and 92.6%, respectively; and the specific activity was up to 15,907.1 ± 10.2 kallikrein inactivator unit/mg. PMID:25677462

  10. Interpolation method for accurate affinity ranking of arrayed ligand-analyte interactions.

    PubMed

    Schasfoort, Richard B M; Andree, Kiki C; van der Velde, Niels; van der Kooi, Alex; Stojanović, Ivan; Terstappen, Leon W M M

    2016-05-01

    The values of the affinity constants (kd, ka, and KD) that are determined by label-free interaction analysis methods are affected by the ligand density. This article outlines a surface plasmon resonance (SPR) imaging method that yields high-throughput globally fitted affinity ranking values using a 96-plex array. A kinetic titration experiment without a regeneration step has been applied for various coupled antibodies binding to a single antigen. Globally fitted rate (kd and ka) and dissociation equilibrium (KD) constants for various ligand densities and analyte concentrations are exponentially interpolated to the KD at Rmax = 100 RU response level (KD(R100)).

  11. Probing the affinity of polyanions for acidic fibroblast growth factor by unfolding kinetics.

    PubMed

    Mach, H; Middaugh, C R

    1994-02-15

    The relationship between ligand-protein affinity and the extent of protein stabilization induced by such interactions has been investigated using the binding of polyanions to acidic fibroblast growth factor (aFGF) as a model system. It was found that the experimentally observed unfolding rate constant of aFGF consists of two components: one equal to the unfolding rate constant of the aFGF-ligand complex and the other the product of the unfolding rate constant of free aFGF, the aFGF-ligand dissociation constant (Kd), and the reciprocal of the molar ligand concentration. This reflects the presence of two possible unfolding pathways: at high ligand excess dissociation is suppressed and slow unfolding of the aFGF-ligand complex itself prevails. When lower concentrations of ligand allows equilibrium-driven appearance of free aFGF, a more rapid unfolding of dissociated protein predominates. Existence of a steady state of dissociated aFGF undergoing unfolding was demonstrated by computer simulation of the elementary events, using experimentally determined rate constants. The potential applications of such simulations are outlined. An equation allowing estimation of dissociation constants from equilibrium denaturation curves obtained in the presence of a varying amount of ligand is also proposed. In addition, determination of initial unfolding rates in the presence of excess protein permits the the stoichiometry of the interaction to be determined.

  12. Two bradykinin binding sites with picomolar affinities

    SciTech Connect

    Manning, D.C.; Vavrek, R.; Stewart, J.M.; Snyder, S.H.

    1986-05-01

    Bradykinin (BK) and related peptides exert a wide range of effects on several organ systems. We have attempted to sort out these effects by studying the binding interaction of (/sup 3/H)BK at the membrane level with in vitro receptor binding techniques. High specific activity (/sup 3/H)BK and an enzyme inhibitor cocktail has enabled us to label two BK binding sites with different affinity and peptide specificity in several guinea-pig tissues. In the guinea-pig ileum the high-affinity site has an equilibrium dissociation constant (Kd) for (/sup 3/H)BK of 13 pM and a maximal number of binding sites of 8.3 pmol/g of tissue wet weight. The low-affinity guinea-pig ileum site displays a Kd of 910 pM, a maximum number of binding sites of 14 pmol/g of tissue wet weight and shows a greater selectivity for BK analogs over Lysyl-BK analogs. Two similar sites can also be discriminated in kidney and heart. The potencies of a series of BK analogs at the high-affinity guinea-pig ileum site correlate well with their potencies in contracting ileal smooth muscle. The binding of (/sup 3/H)BK in the guinea-pig ileum is inhibited by physiological concentrations of monovalent and divalent cations.

  13. Spectrophotometric determination of the protolytic dissociation constants of the new chromogenic reagent "palladiazo"-I Investigations with sodium hydroxide, perchloric acid and different aqueous buffer solutions.

    PubMed

    Pérez-Butsamante, J A; Burriel-Martí, F

    1971-02-01

    The "palladiazo" reagent has been subjected to a detailed spectrophotometric investigation in concentrated perchloric acid, different aqueous buffers and concentrated sodium hydroxide solutions. K(1)-K(10) and (1)-(10) values corresponding to the instability constants of the protolytic equilibria involved and to the molar absorptivities at 540 and 630 run of the different proton complex species of the system have been calculated by a number of analytical and graphical spectrophotometric methods. Special attention has been paid to the study of the complicated phenomena implied by the interaction of the reagent with perchloric acid, which has been shown to give rise to alteration of the initial isomeric composition of the reagent and to the formation of addition and/or oxidation products derived from side-reactions undergone by the reagent with the medium. All the instability constants and molar absorptivities, which have been determined by several methods, are tabulated for comparison.

  14. Structure of a human IgA1 Fab fragment at 1.55 Å resolution: potential effect of the constant domains on antigen-affinity modulation.

    PubMed

    Correa, Agustin; Trajtenberg, Felipe; Obal, Gonzalo; Pritsch, Otto; Dighiero, Guillermo; Oppezzo, Pablo; Buschiazzo, Alejandro

    2013-03-01

    Despite being the most abundant class of immunoglobulins in humans and playing central roles in the adaptive immune response, high-resolution structural data are still lacking for the antigen-binding region of human isotype A antibodies (IgAs). The crystal structures of a human Fab fragment of IgA1 in three different crystal forms are now reported. The three-dimensional organization is similar to those of other Fab classes, but FabA1 seems to be more rigid, being constrained by a hydrophobic core in the interface between the variable and constant domains of the heavy chain (VH-CH1) as well as by a disulfide bridge that connects the light and heavy chains, influencing the relative heavy/light-chain orientation. The crystal structure of the same antibody but with a G-isotype CH1 which is reported to display different antigen affinity has also been solved. The differential structural features reveal plausible mechanisms for constant/variable-domain long-distance effects whereby antibody class switching could alter antigen affinity.

  15. Predicting pressure-dependent unimolecular rate constants using variational transition state theory with multidimensional tunneling combined with system-specific quantum RRK theory: a definitive test for fluoroform dissociation.

    PubMed

    Bao, Junwei Lucas; Zhang, Xin; Truhlar, Donald G

    2016-06-22

    Understanding the falloff in rate constants of gas-phase unimolecular reaction rate constants as the pressure is lowered is a fundamental problem in chemical kinetics, with practical importance for combustion, atmospheric chemistry, and essentially all gas-phase reaction mechanisms. In the present work, we use our recently developed system-specific quantum RRK theory, calibrated by canonical variational transition state theory with small-curvature tunneling, combined with the Lindemann-Hinshelwood mechanism, to model the dissociation reaction of fluoroform (CHF3), which provides a definitive test for falloff modeling. Our predicted pressure-dependent thermal rate constants are in excellent agreement with experimental values over a wide range of pressures and temperatures. The present validation of our methodology, which is able to include variational transition state effects, multidimensional tunneling based on the directly calculated potential energy surface along the tunneling path, and torsional and other vibrational anharmonicity, together with state-of-the-art reaction-path-based direct dynamics calculations, is important because the method is less empirical than models routinely used for generating full mechanisms, while also being simpler in key respects than full master equation treatments and the full reduced falloff curve and modified strong collision methods of Troe. PMID:27273734

  16. Predicting pressure-dependent unimolecular rate constants using variational transition state theory with multidimensional tunneling combined with system-specific quantum RRK theory: a definitive test for fluoroform dissociation.

    PubMed

    Bao, Junwei Lucas; Zhang, Xin; Truhlar, Donald G

    2016-06-22

    Understanding the falloff in rate constants of gas-phase unimolecular reaction rate constants as the pressure is lowered is a fundamental problem in chemical kinetics, with practical importance for combustion, atmospheric chemistry, and essentially all gas-phase reaction mechanisms. In the present work, we use our recently developed system-specific quantum RRK theory, calibrated by canonical variational transition state theory with small-curvature tunneling, combined with the Lindemann-Hinshelwood mechanism, to model the dissociation reaction of fluoroform (CHF3), which provides a definitive test for falloff modeling. Our predicted pressure-dependent thermal rate constants are in excellent agreement with experimental values over a wide range of pressures and temperatures. The present validation of our methodology, which is able to include variational transition state effects, multidimensional tunneling based on the directly calculated potential energy surface along the tunneling path, and torsional and other vibrational anharmonicity, together with state-of-the-art reaction-path-based direct dynamics calculations, is important because the method is less empirical than models routinely used for generating full mechanisms, while also being simpler in key respects than full master equation treatments and the full reduced falloff curve and modified strong collision methods of Troe.

  17. Dissociative disorders.

    PubMed

    Kihlstrom, John F

    2005-01-01

    The dissociative disorders, including "psychogenic" or "functional" amnesia, fugue, dissociative identity disorder (DID, also known as multiple personality disorder), and depersonalization disorder, were once classified, along with conversion disorder, as forms of hysteria. The 1970s witnessed an "epidemic" of dissociative disorder, particularly DID, which may have reflected enthusiasm for the diagnosis more than its actual prevalence. Traditionally, the dissociative disorders have been attributed to trauma and other psychological stress, but the existing evidence favoring this hypothesis is plagued by poor methodology. Prospective studies of traumatized individuals reveal no convincing cases of amnesia not attributable to brain insult, injury, or disease. Treatment generally involves recovering and working through ostensibly repressed or dissociated memories of trauma; at present, there are few quantitative or controlled outcome studies. Experimental studies are few in number and have focused largely on state-dependent and implicit memory. Depersonalization disorder may be in line for the next "epidemic" of dissociation.

  18. Dissociative amnesia.

    PubMed

    Staniloiu, Angelica; Markowitsch, Hans J

    2014-08-01

    Dissociative amnesia is one of the most enigmatic and controversial psychiatric disorders. In the past two decades, interest in the understanding of its pathophysiology has surged. In this report, we review new data about the epidemiology, neurobiology, and neuroimaging of dissociative amnesia and show how advances in memory research and neurobiology of dissociation inform proposed pathogenetic models of the disorder. Dissociative amnesia is characterised by functional impairment. Additionally, preliminary data suggest that affected people have an increased and possibly underestimated suicide risk. The prevalence of dissociative amnesia differs substantially across countries and populations. Symptoms and disease course also vary, indicating a possibly heterogeneous disorder. The accompanying clinical features differ across cultural groups. Most dissociative amnesias are retrograde, with memory impairments mainly involving the episodic-autobiographical memory domain. Anterograde dissociative amnesia occurring without significant retrograde memory impairments is rare. Functional neuroimaging studies of dissociative amnesia with prevailing retrograde memory impairments show changes in the network that subserves autobiographical memory. At present, no evidence-based treatments are available for dissociative amnesia and no broad framework exists for its rehabilitation. Further research is needed into its neurobiology, course, treatment options, and strategies to improve differential diagnoses.

  19. Measurement of acid dissociation constants and ionic mobilities of 3-nitro-tyrosine and 3-chloro-tyrosine by capillary zone electrophoresis.

    PubMed

    Ren, Haixia; Wang, Licheng; Wang, Xusheng; Liu, Xia; Jiang, Shengxiang

    2013-04-15

    The ionization constant (pKa) and limiting ionic mobility of 3-chlorotyrosine (CT) and 3-nitrotyrosine (NT) were determined in capillary zone electrophoresis (CZE) in a wide pH range. Measurements were carried out in a poly(ionic liquid) (PIL) modified capillary at a low pH (1.80-4.00) and a bare fused capillary at an upper pH (3.00-11.00). Electrostatic interaction between analytes and inner wall was suppressed dramatically. Furthermore, parameters usually empirically assumed were calculated from a simple theoretical model. Besides pKa and limiting ionic mobility, diameter of the hydrated ion was calculated as well. The former were inserted into the database of Peakmaster software, whose predictions led to satisfactory agreement with experimental runs.

  20. Sodium chloride in supercritical water as a function of density: potentials of mean force and an equation for the dissociation constant from 723 to 1073 K and from 0 to 0.9 g/cm(3).

    PubMed

    Liu, Wenbin; Wood, Robert H; Doren, Douglas J

    2008-06-19

    The potential of mean force (PMF) of sodium chloride in water has been calculated by using the ab initio classical free-energy perturbation method at five state points: at 973 K with densities of 0.2796, 0.0935, and 0.0101 g/cm (3) and at 723 K with densities of 0.0897 and 0.0098 g/cm (3). The method is based on a QM-MM model in which Na-H 2O, Cl-H 2O, and Na-Cl interactions are calculated by ab initio methods. The water-water interactions are from the polarizable TIP4P-FQ model. The logarithm of the dissociation constant (log K c) has been calculated from the PMF. These predictions, together with experimental measurements, were used to derive an equation for log K c at densities from 0 to 0.9 g/cm (3) and temperatures from 723 to 1073 K, as well as from 600 to 1073 K for densities from 0.29 g/cm (3) to 0.9 g/cm (3). Extrapolation of the present equation below 723 K for densities less than 0.29 g/cm (3) does not fit the experimental results. This is attributed to long-range changes in the local dielectric constant due to the high compressibility. Comparisons with previous predictions and simulations are presented.

  1. Sodium chloride in supercritical water as a function of density: potentials of mean force and an equation for the dissociation constant from 723 to 1073 K and from 0 to 0.9 g/cm(3).

    PubMed

    Liu, Wenbin; Wood, Robert H; Doren, Douglas J

    2008-06-19

    The potential of mean force (PMF) of sodium chloride in water has been calculated by using the ab initio classical free-energy perturbation method at five state points: at 973 K with densities of 0.2796, 0.0935, and 0.0101 g/cm (3) and at 723 K with densities of 0.0897 and 0.0098 g/cm (3). The method is based on a QM-MM model in which Na-H 2O, Cl-H 2O, and Na-Cl interactions are calculated by ab initio methods. The water-water interactions are from the polarizable TIP4P-FQ model. The logarithm of the dissociation constant (log K c) has been calculated from the PMF. These predictions, together with experimental measurements, were used to derive an equation for log K c at densities from 0 to 0.9 g/cm (3) and temperatures from 723 to 1073 K, as well as from 600 to 1073 K for densities from 0.29 g/cm (3) to 0.9 g/cm (3). Extrapolation of the present equation below 723 K for densities less than 0.29 g/cm (3) does not fit the experimental results. This is attributed to long-range changes in the local dielectric constant due to the high compressibility. Comparisons with previous predictions and simulations are presented. PMID:18491938

  2. Picomolar affinity antibodies from a fully synthetic naive library selected and evolved by ribosome display.

    PubMed

    Hanes, J; Schaffitzel, C; Knappik, A; Plückthun, A

    2000-12-01

    Here we applied ribosome display to in vitro selection and evolution of single-chain antibody fragments (scFvs) from a large synthetic library (Human Combinatorial Antibody Library; HuCAL) against bovine insulin. In three independent ribosome display experiments different clusters of closely related scFvs were selected, all of which bound the antigen with high affinity and specificity. All selected scFvs had affinity-matured up to 40-fold compared to their HuCAL progenitors, by accumulating point mutations during the ribosome display cycles. The dissociation constants of the isolated scFvs were as low as 82 pM, which validates the design of the naïve library and the power of this evolutionary method. We have thus mimicked the process of antibody generation and affinity maturation with a synthetic library in a cell-free system in just a few days, obtaining molecules with higher affinities than most natural antibodies.

  3. Affinity Chromatography.

    ERIC Educational Resources Information Center

    Gray, Gary R.

    1980-01-01

    Presents selected recent advances in immobilization chemistry which have important connections to affinity chromatography. Discusses ligand immobilization and support modification. Cites 51 references. (CS)

  4. Increased Antibody Affinity Confers Broad In Vitro Protection against Escape Mutants of Severe Acute Respiratory Syndrome Coronavirus

    PubMed Central

    Rani, Mridula; Bolles, Meagan; Donaldson, Eric F.; Van Blarcom, Thomas; Baric, Ralph; Iverson, Brent

    2012-01-01

    Even though the effect of antibody affinity on neutralization potency is well documented, surprisingly, its impact on neutralization breadth and escape has not been systematically determined. Here, random mutagenesis and DNA shuffling of the single-chain variable fragment of the neutralizing antibody 80R followed by bacterial display screening using anchored periplasmic expression (APEx) were used to generate a number of higher-affinity variants of the severe acute respiratory syndrome coronavirus (SARS-CoV)-neutralizing antibody 80R with equilibrium dissociation constants (KD) as low as 37 pM, a >270-fold improvement relative to that of the parental 80R single-chain variable fragment (scFv). As expected, antigen affinity was shown to correlate directly with neutralization potency toward the icUrbani strain of SARS-CoV. Additionally, the highest-affinity antibody fragment displayed 10-fold-increased broad neutralization in vitro and completely protected against several SARS-CoV strains containing substitutions associated with antibody escape. Importantly, higher affinity also led to the suppression of viral escape mutants in vitro. Escape from the highest-affinity variant required reduced selective pressure and multiple substitutions in the binding epitope. Collectively, these results support the hypothesis that engineered antibodies with picomolar dissociation constants for a neutralizing epitope can confer escape-resistant protection. PMID:22696652

  5. Importin {beta}-type nuclear transport receptors have distinct binding affinities for Ran-GTP

    SciTech Connect

    Hahn, Silvia; Schlenstedt, Gabriel

    2011-03-18

    Highlights: {yields} Determination of binding properties of nuclear transport receptor/Ran-GTP complexes. {yields} Biosensor measurements provide constants for dissociation, on-rates, and off-rates. {yields} The affinity of receptors for Ran-GTP is widely divergent. {yields} Dissociation constants differ for three orders of magnitude. {yields} The cellular concentration of yeast Ran is not limiting. -- Abstract: Cargos destined to enter or leave the cell nucleus are typically transported by receptors of the importin {beta} family to pass the nuclear pore complex. The yeast Saccharomyces cerevisiae comprises 14 members of this protein family, which can be divided in importins and exportins. The Ran GTPase regulates the association and dissociation of receptors and cargos as well as the transport direction through the nuclear pore. All receptors bind to Ran exclusively in its GTP-bound state and this event is restricted to the nuclear compartment. We determined the Ran-GTP binding properties of all yeast transport receptors by biosensor measurements and observed that the affinity of importins for Ran-GTP differs significantly. The dissociation constants range from 230 pM to 270 nM, which is mostly based on a variability of the off-rate constants. The divergent affinity of importins for Ran-GTP suggests the existence of a novel mode of nucleocytoplasmic transport regulation. Furthermore, the cellular concentration of {beta}-receptors and of other Ran-binding proteins was determined. We found that the number of {beta}-receptors altogether about equals the amounts of yeast Ran, but Ran-GTP is not limiting in the nucleus. The implications of our results for nucleocytoplasmic transport mechanisms are discussed.

  6. [Cell-ELA-based determination of binding affinity of DNA aptamer against U87-EGFRvIII cell].

    PubMed

    Tan, Yan; Liang, Huiyu; Wu, Xidong; Gao, Yubo; Zhang, Xingmei

    2013-05-01

    A15, a DNA aptamer with binding specificity for U87 glioma cells stably overexpressing the epidermal growth factor receptor variant III (U87-EGFRvIII), was generated by cell systematic evolution of ligands by exponential enrichment (cell-SELEX) using a random nucleotide library. Subsequently, we established a cell enzyme-linked assay (cell-ELA) to detect the affinity of A15 compared to an EGFR antibody. We used A15 as a detection probe and cultured U87-EGFRvIII cells as targets. Our data indicate that the equilibrium dissociation constants (K(d)) for A15 were below 100 nmol/L and had similar affinity compared to an EGFR antibody for U87-EGFRvIII. We demonstrated that the cell-ELA was a useful method to determine the equilibrium dissociation constants (K(d)) of aptamers generated by cell-SELEX.

  7. Sperm in poor quality semen from bulls during heat stress have a lower affinity for binding hydrogen-3 heparin

    SciTech Connect

    Ax, R.L.; Gilbert, G.R.; Shook, G.E.

    1987-01-01

    Binding assays with (/sup 3/H) heparin were performed using spermatozoa collected prior to, during, and following summer heat stress to dairy bulls. Ejaculates collected in August 1983 after a period of ambient temperatures exceeding 29.4/sup 0/C exhibited a high frequency of abnormal sperm, and motility was reduced in some samples. Sperm in samples collected during heat stress possessed dissociation constants for binding (/sup 3/H) heparin ranging from 134.5 to 163.2 nmol. In contrast, sperm in semen collected prior to and after heat stress had significantly lower dissociation constants (higher affinity) for (/sup 3/H)heparin, 12.9 to 56.4 nmol. The number of binding sites for (/sup 3/H) heparin on sperm did not change among collection periods. It was concluded that the binding affinity for (/sup 3/H) heparin may reflect membrane integrity of bull sperm.

  8. Affinity screening using competitive binding with fluorine-19 hyperpolarized ligands.

    PubMed

    Kim, Yaewon; Hilty, Christian

    2015-04-13

    Fluorine-19 NMR and hyperpolarization form a powerful combination for drug screening. Under a competitive equilibrium with a selected fluorinated reporter ligand, the dissociation constant (K(D)) of other ligands of interest is measurable using a single-scan Carr-Purcell-Meiboom-Gill (CPMG) experiment, without the need for a titration. This method is demonstrated by characterizing the binding of three ligands with different affinities for the serine protease trypsin. Monte Carlo simulations show that the highest accuracy is obtained when about one-half of the bound reporter ligand is displaced in the binding competition. Such conditions can be achieved over a wide range of affinities, allowing for rapid screening of non-fluorinated compounds when a single fluorinated ligand for the binding pocket of interest is known.

  9. Km as an Apparent Dissociation Constant.

    ERIC Educational Resources Information Center

    Cohlberg, Jeffrey A.

    1979-01-01

    An approach to enzyme kinetics which emphasizes similarities between equilibrium binding and steady state kinetics is outlined. It is intended for use in teaching biochemistry to beginning students. (Author/SA)

  10. Microcantilever-Based Label-Free Characterization of Temperature-Dependent Biomolecular Affinity Binding

    PubMed Central

    Wang, Bin; Huang, Fengliang; Nguyen, ThaiHuu; Xu, Yong; Lin, Qiao

    2014-01-01

    This paper presents label-free characterization of temperature-dependent biomolecular affinity binding on solid surfaces using a microcantilever-based device. The device consists of a Parylene cantilever one side of which is coated with a gold film and functionalized with molecules as an affinity receptor to a target analyte. The cantilever is located in a poly(dimethylsiloxane) (PDMS) microfluidic chamber that is integrated with a transparent indium tin oxide (ITO) resistive temperature sensor on the underlying substrate. The ITO sensor allows for real-time measurements of the chamber temperature, as well as unobstructed optical access for reflection-based optical detection of the cantilever deflection. To test the temperature-dependent binding between the target and receptor, the temperature of the chamber is maintained at a constant setpoint, while a solution of unlabeled analyte molecules is continuously infused through the chamber. The measured cantilever deflection is used to determine the target-receptor binding characteristics. We demonstrate label-free characterization of temperature-dependent binding kinetics of the platelet-derived growth factor (PDGF) protein with an aptamer receptor. Affinity binding properties including the association and dissociation rate constants as well as equilibrium dissociation constant are obtained, and shown to exhibit significant dependencies on temperature. PMID:24723743

  11. High-affinity Cyclic Peptide Matriptase Inhibitors*

    PubMed Central

    Quimbar, Pedro; Malik, Uru; Sommerhoff, Christian P.; Kaas, Quentin; Chan, Lai Y.; Huang, Yen-Hua; Grundhuber, Maresa; Dunse, Kerry; Craik, David J.; Anderson, Marilyn A.; Daly, Norelle L.

    2013-01-01

    The type II transmembrane serine protease matriptase is a key activator of multiple signaling pathways associated with cell proliferation and modification of the extracellular matrix. Deregulated matriptase activity correlates with a number of diseases, including cancer and hence highly selective matriptase inhibitors may have therapeutic potential. The plant-derived cyclic peptide, sunflower trypsin inhibitor-1 (SFTI-1), is a promising drug scaffold with potent matriptase inhibitory activity. In the current study we have analyzed the structure-activity relationships of SFTI-1 and Momordica cochinchinensis trypsin inhibitor-II (MCoTI-II), a structurally divergent trypsin inhibitor from Momordica cochinchinensis that also contains a cyclic backbone. We show that MCoTI-II is a significantly more potent matriptase inhibitor than SFTI-1 and that all alanine mutants of both peptides, generated using positional scanning mutagenesis, have decreased trypsin affinity, whereas several mutations either maintain or result in enhanced matriptase inhibitory activity. These intriguing results were used to design one of the most potent matriptase inhibitors known to date with a 290 pm equilibrium dissociation constant, and provide the first indication on how to modulate affinity for matriptase over trypsin in cyclic peptides. This information might be useful for the design of more selective and therapeutically relevant inhibitors of matriptase. PMID:23548907

  12. Quantification of the affinities and kinetics of protein interactions using silicon nanowire biosensors

    PubMed Central

    Duan, Xuexin; Li, Yue; Rajan, Nitin K.; Routenberg, David A.; Modis, Yorgo; Reed, Mark A.

    2014-01-01

    Monitoring the binding affinities and kinetics of protein interactions is important in clinical diagnostics and drug development because such information is used to identify new therapeutic candidates. Surface plasmon resonance is at present the standard method used for such analysis, but this is limited by low sensitivity and low-throughput analysis. Here, we show that silicon nanowire field-effect transistors can be used as biosensors to measure protein–ligand binding affinities and kinetics with sensitivities down to femtomolar concentrations. Based on this sensing mechanism, we develop an analytical model to calibrate the sensor response and quantify the molecular binding affinities of two representative protein–ligand binding pairs. The rate constant of the association and dissociation of the protein–ligand pair is determined by monitoring the reaction kinetics, demonstrating that silicon nanowire field-effect transistors can be readily used as high-throughput biosensors to quantify protein interactions. PMID:22635097

  13. Recurrent Episodes of Dissociative Fugue

    PubMed Central

    Angothu, Hareesh; Pabbathi, Lokeswar Reddy

    2016-01-01

    Dissociative fugue is rare entity to encounter with possible differentials of epilepsy and malingering. It is one of the dissociative disorders rarely seen in clinical practice more often because of the short lasting nature of this condition. This might also be because of organized travel of the individuals during the episodes and return to their families after the recovery from episodes. This is a case description of a patient who has experienced total three episodes of dissociative fugue. The patient has presented during the third episode and two prior episodes were diagnosed as fugue episodes retrospectively based on the history. Planned travel in this case by the patient to a distant location was prevented because of early diagnosis and constant vigilance till the recovery. As in this case, it may be more likely that persons with Dissociative fugue may develop similar episodes if they encounter exceptional perceived stress. However, such conclusions may require follow-up studies. PMID:27114633

  14. Control of antibody-antigen binding or dissociation by electric field

    NASA Astrophysics Data System (ADS)

    Oldham, Philip B.; Asanov, Alexander N.

    1999-04-01

    The development of a biosensor with adequate sensitivity generally requires a biospecific interaction with high binding affinity. The affinity constants for most antibody- antigen interactions are determined largely by the dissociation constants, kd, with little variation observed in rates of associated. additionally, surface immobilization typically results in a reduced kd. In this case, the sensor binds analyte kinetically irreversibly preventing response to changes in analytic concentration or reuse. Regeneration of the sensor surface is difficult, at best. On the other hand, a higher dissociation rate which would lend itself to a linear and reusable sensor, results in lower affinity and poor sensitivity. Consequently, most biosensors are disposable devices and quantitation is obtained using multiple single-use sensors. In this work, a new reusable biosensor platform which provides simultaneous fluorescence detection and electrochemical control of biospecific binding has been developed. Biotin was covalently attached to a transparent indium tin oxide electrode, which also served as an integral part of a total internal reflection fluorescence (TIRF) flow cell. TIRF was used to monitor biospecific interactions while electrochemical polarization was employed to control the interactions. Two possible mechanisms of the electric field effect involving interactions with induced and permanent dipoles of proteins will be discussed.

  15. Quantification of the Effects of Ionic Strength, Viscosity, and Hydrophobicity on Protein–Ligand Binding Affinity

    PubMed Central

    2014-01-01

    In order to quantify the interactions between molecules of biological interest, the determination of the dissociation constant (Kd) is essential. Estimation of the binding affinity in this way is routinely performed in “favorable” conditions for macromolecules. Crucial data for ligand–protein binding elucidation is mainly derived from techniques (e.g., macromolecular crystallography) that require the addition of high concentration of salts and/or other additives. In this study we have evaluated the effect of temperature, ionic strength, viscosity, and hydrophobicity on the Kd of three previously characterized protein–ligand systems, based on variation in their binding sites, in order to provide insight into how these often overlooked unconventional circumstances impact binding affinity. Our conclusions are as follows: (1) increasing solvent viscosity in general is detrimental to ligand binding, (2) moderate increases in temperature have marginal effects on the dissociation constant, and (3) the degree of hydrophobicity of the ligand and the binding site determines the extent of the influence of cosolvents and salt concentration on ligand binding affinity. PMID:25147617

  16. A comparison of affinity constants for muscarine-sensitive acetylcholine receptors in guinea-pig atrial pacemaker cells at 29 degrees C and in ileum at 29 degrees C and 37 degrees C.

    PubMed Central

    Barlow, R B; Berry, K J; Glenton, P A; Nilolaou, N M; Soh, K S

    1976-01-01

    1 The affinity of 17 compounds for muscarine-sensitive acetylcholine receptors in atrial pacemaker cells and ileum of the guinea-pig has been measured at 29 degrees C in Ringer-Locke solution. Measurements were also made at 37 degrees C with 7 of them. 2 Some of the compounds had much higher affinity for the receptors in the ileum than for those in the atria. For the most selective compound, 4-diphenylacetoxy-N-methylpiperidine methiodide, the difference was approximately 20-fold. The receptors in the atria are therefore different the structure from those in the ileum. 3 The effect of temperature on affinity are not the same for all the compounds, tested indicating different enthalpies and entropies of adsorption and accounting for some of the difficulty experienced in predicting the affinity of new compounds. PMID:1000135

  17. Purification of muscarinic acetylcholine receptors by affinity chromatography.

    PubMed Central

    André, C; De Backer, J P; Guillet, J C; Vanderheyden, P; Vauquelin, G; Strosberg, A D

    1983-01-01

    Calf forebrain homogenates contain 2.8 pM muscarinic acetylcholine receptors per mg of protein. [3H]Antagonist saturation binding experiments under equilibrium conditions revealed a single class of sites with equilibrium dissociation constants of 0.82 nM for [3H]dexetimide and 0.095 nM for [3H]quinuclidinyl benzilate. Displacement binding studies with agonists revealed the presence of low and high affinity sites. Here we describe the solubilization of muscarinic acetylcholine receptors with digitonin and their purification by affinity chromatography using an affinity gel which consisted of dexetimide coupled to Affi-Gel 10 (i.e., carboxy N-hydroxysuccinimide esters linked via a 1 nm spacer arm to agarose beads). Purified proteins were obtained by specific elution with muscarinic drugs, i.e., the antagonist atropine and the irreversible ligand propylbenzilylcholine mustard. SDS-polyacrylamide gel electrophoresis of the radioiodinated purified preparations revealed a major 70-K protein. Images Fig. 3. PMID:6605245

  18. Analysis of free drug fractions in human serum by ultrafast affinity extraction and two-dimensional affinity chromatography.

    PubMed

    Zheng, Xiwei; Podariu, Maria; Matsuda, Ryan; Hage, David S

    2016-01-01

    Ultrafast affinity extraction and a two-dimensional high performance affinity chromatographic system were used to measure the free fractions for various drugs in serum and at typical therapeutic concentrations. Pooled samples of normal serum or serum from diabetic patients were utilized in this work. Several drug models (i.e., quinidine, diazepam, gliclazide, tolbutamide, and acetohexamide) were examined that represented a relatively wide range of therapeutic concentrations and affinities for human serum albumin (HSA). The two-dimensional system consisted of an HSA microcolumn for the extraction of a free drug fraction, followed by a larger HSA analytical column for the further separation and measurement of this fraction. Factors that were optimized in this method included the flow rates, column sizes, and column switching times that were employed. The final extraction times used for isolating the free drug fractions were 333-665 ms or less. The dissociation rate constants for several of the drugs with soluble HSA were measured during system optimization, giving results that agreed with reference values. In the final system, free drug fractions in the range of 0.7-9.5% were measured and gave good agreement with values that were determined by ultrafiltration. Association equilibrium constants or global affinities were also estimated by this approach for the drugs with soluble HSA. The results for the two-dimensional system were obtained in 5-10 min or less and required only 1-5 μL of serum per injection. The same approach could be adapted for work with other drugs and proteins in clinical samples or for biomedical research. PMID:26462924

  19. Comparative Study of Three Methods for Affinity Measurements: Capillary Electrophoresis Coupled with UV Detection and Mass Spectrometry, and Direct Infusion Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Mironov, Gleb G.; Logie, Jennifer; Okhonin, Victor; Renaud, Justin B.; Mayer, Paul M.; Berezovski, Maxim V.

    2012-07-01

    We present affinity capillary electrophoresis and mass spectrometry (ACE-MS) as a comprehensive separation technique for label-free solution-based affinity analysis. The application of ACE-MS for measuring affinity constants between eight small molecule drugs [ibuprofen, s-flurbiprofen, diclofenac, phenylbutazone, naproxen, folic acid, resveratrol, and 4,4'-(propane-1,3-diyl) dibenzoic acid] and β-cyclodextrin is described. We couple on-line ACE with MS to combine the separation and kinetic capability of ACE together with the molecular weight and structural elucidation of MS in one system. To understand the full potential of ACE-MS, we compare it with two other methods: Direct infusion mass spectrometry (DIMS) and ACE with UV detection (ACE-UV). After the evaluation, DIMS provides less reliable equilibrium dissociation constants than separation-based ACE-UV and ACE-MS, and cannot be used solely for the study of noncovalent interactions. ACE-MS determines apparent dissociation constants for all reacting small molecules in a mixture, even in cases when drugs overlap with each other during separation. The ability of ACE-MS to interact, separate, and rapidly scan through m/z can facilitate the simultaneous affinity analysis of multiple interacting pairs, potentially leading to the high-throughput screening of drug candidates.

  20. Glycan:glycan interactions: High affinity biomolecular interactions that can mediate binding of pathogenic bacteria to host cells

    PubMed Central

    Day, Christopher J.; Tran, Elizabeth N.; Semchenko, Evgeny A.; Tram, Greg; Hartley-Tassell, Lauren E.; Ng, Preston S. K.; King, Rebecca M.; Ulanovsky, Rachel; McAtamney, Sarah; Apicella, Michael A.; Tiralongo, Joe; Morona, Renato; Korolik, Victoria; Jennings, Michael P.

    2015-01-01

    Cells from all domains of life express glycan structures attached to lipids and proteins on their surface, called glycoconjugates. Cell-to-cell contact mediated by glycan:glycan interactions have been considered to be low-affinity interactions that precede high-affinity protein–glycan or protein–protein interactions. In several pathogenic bacteria, truncation of surface glycans, lipooligosaccharide (LOS), or lipopolysaccharide (LPS) have been reported to significantly reduce bacterial adherence to host cells. Here, we show that the saccharide component of LOS/LPS have direct, high-affinity interactions with host glycans. Glycan microarrays reveal that LOS/LPS of four distinct bacterial pathogens bind to numerous host glycan structures. Surface plasmon resonance was used to determine the affinity of these interactions and revealed 66 high-affinity host–glycan:bacterial–glycan pairs with equilibrium dissociation constants (KD) ranging between 100 nM and 50 µM. These glycan:glycan affinity values are similar to those reported for lectins or antibodies with glycans. Cell assays demonstrated that glycan:glycan interaction-mediated bacterial adherence could be competitively inhibited by either host cell or bacterial glycans. This is the first report to our knowledge of high affinity glycan:glycan interactions between bacterial pathogens and the host. The discovery of large numbers of glycan:glycan interactions between a diverse range of structures suggests that these interactions may be important in all biological systems. PMID:26676578

  1. Glycan:glycan interactions: High affinity biomolecular interactions that can mediate binding of pathogenic bacteria to host cells.

    PubMed

    Day, Christopher J; Tran, Elizabeth N; Semchenko, Evgeny A; Tram, Greg; Hartley-Tassell, Lauren E; Ng, Preston S K; King, Rebecca M; Ulanovsky, Rachel; McAtamney, Sarah; Apicella, Michael A; Tiralongo, Joe; Morona, Renato; Korolik, Victoria; Jennings, Michael P

    2015-12-29

    Cells from all domains of life express glycan structures attached to lipids and proteins on their surface, called glycoconjugates. Cell-to-cell contact mediated by glycan:glycan interactions have been considered to be low-affinity interactions that precede high-affinity protein-glycan or protein-protein interactions. In several pathogenic bacteria, truncation of surface glycans, lipooligosaccharide (LOS), or lipopolysaccharide (LPS) have been reported to significantly reduce bacterial adherence to host cells. Here, we show that the saccharide component of LOS/LPS have direct, high-affinity interactions with host glycans. Glycan microarrays reveal that LOS/LPS of four distinct bacterial pathogens bind to numerous host glycan structures. Surface plasmon resonance was used to determine the affinity of these interactions and revealed 66 high-affinity host-glycan:bacterial-glycan pairs with equilibrium dissociation constants (K(D)) ranging between 100 nM and 50 µM. These glycan:glycan affinity values are similar to those reported for lectins or antibodies with glycans. Cell assays demonstrated that glycan:glycan interaction-mediated bacterial adherence could be competitively inhibited by either host cell or bacterial glycans. This is the first report to our knowledge of high affinity glycan:glycan interactions between bacterial pathogens and the host. The discovery of large numbers of glycan:glycan interactions between a diverse range of structures suggests that these interactions may be important in all biological systems. PMID:26676578

  2. Development of a sensitive method for selection of affinity ligand for trypsin using quartz crystal microbalance sensor.

    PubMed

    Bayramoglu, Gulay; Yakup Arica, M

    2012-03-01

    In this work, a new methodology is developed for selection of affinity ligands towards the enzyme "trypsin" using quartz crystals microbalance (QCM) technique. To achieve this goal, the surface amination of gold plated QCM crystals was achieved in 13.56 MHz plasma polymerization system by using ethylenediamine. Three different ligands (i.e., 4-aminobenzamidine, 4-aminobenzoic acid, and phenylalanine) were immobilized on the aminated QCM crystals surface via glutaraldehyde coupling. All three ligand immobilized QCM crystals were characterized and compared under different experimental conditions. It was observed that the benzamidine ligand showed higher affinity to trypsin with a dissociation constant on the order of 1.76 × 10(-9) M, which is within the range of 10(-4)-10(-8) M for affinity ligands. Thus, its selectivity was suitable for purification of trypsin from biological fluids. PMID:21853329

  3. Complementary DNA display selection of high-affinity peptides binding the vacuolating toxin (VacA) of Helicobacter pylori.

    PubMed

    Hayakawa, Yumiko; Matsuno, Mitsuhiro; Tanaka, Makoto; Wada, Akihiro; Kitamura, Koichiro; Takei, Osamu; Sasaki, Ryuzo; Mizukami, Tamio; Hasegawa, Makoto

    2015-09-01

    Artificial peptides designed for molecular recognition of a bacterial toxin have been developed. Vacuolating cytotoxin A protein (VacA) is a major virulence factor of Helicobacter pylori, a gram-negative microaerophilic bacterium inhabiting the upper gastrointestinal tract, particularly the stomach. This study attempted to identify specific peptide sequences with high affinity for VacA using systematic directed evolution in vitro, a cDNA display method. A surface plasmon resonance-based biosensor and fluorescence correlation spectroscopy to examine binding of peptides with VacA identified a peptide (GRVNQRL) with high affinity. Cyclization of the peptide by attaching cysteine residues to both termini improved its binding affinity to VacA, with a dissociation constant (Kd ) of 58 nm. This study describes a new strategy for the development of artificial functional peptides, which are promising materials in biochemical analyses and medical applications.

  4. A global benchmark study using affinity-based biosensors.

    PubMed

    Rich, Rebecca L; Papalia, Giuseppe A; Flynn, Peter J; Furneisen, Jamie; Quinn, John; Klein, Joshua S; Katsamba, Phini S; Waddell, M Brent; Scott, Michael; Thompson, Joshua; Berlier, Judie; Corry, Schuyler; Baltzinger, Mireille; Zeder-Lutz, Gabrielle; Schoenemann, Andreas; Clabbers, Anca; Wieckowski, Sebastien; Murphy, Mary M; Page, Phillip; Ryan, Thomas E; Duffner, Jay; Ganguly, Tanmoy; Corbin, John; Gautam, Satyen; Anderluh, Gregor; Bavdek, Andrej; Reichmann, Dana; Yadav, Satya P; Hommema, Eric; Pol, Ewa; Drake, Andrew; Klakamp, Scott; Chapman, Trevor; Kernaghan, Dawn; Miller, Ken; Schuman, Jason; Lindquist, Kevin; Herlihy, Kara; Murphy, Michael B; Bohnsack, Richard; Andrien, Bruce; Brandani, Pietro; Terwey, Danny; Millican, Rohn; Darling, Ryan J; Wang, Liann; Carter, Quincy; Dotzlaf, Joe; Lopez-Sagaseta, Jacinto; Campbell, Islay; Torreri, Paola; Hoos, Sylviane; England, Patrick; Liu, Yang; Abdiche, Yasmina; Malashock, Daniel; Pinkerton, Alanna; Wong, Melanie; Lafer, Eileen; Hinck, Cynthia; Thompson, Kevin; Primo, Carmelo Di; Joyce, Alison; Brooks, Jonathan; Torta, Federico; Bagge Hagel, Anne Birgitte; Krarup, Janus; Pass, Jesper; Ferreira, Monica; Shikov, Sergei; Mikolajczyk, Malgorzata; Abe, Yuki; Barbato, Gaetano; Giannetti, Anthony M; Krishnamoorthy, Ganeshram; Beusink, Bianca; Satpaev, Daulet; Tsang, Tiffany; Fang, Eric; Partridge, James; Brohawn, Stephen; Horn, James; Pritsch, Otto; Obal, Gonzalo; Nilapwar, Sanjay; Busby, Ben; Gutierrez-Sanchez, Gerardo; Gupta, Ruchira Das; Canepa, Sylvie; Witte, Krista; Nikolovska-Coleska, Zaneta; Cho, Yun Hee; D'Agata, Roberta; Schlick, Kristian; Calvert, Rosy; Munoz, Eva M; Hernaiz, Maria Jose; Bravman, Tsafir; Dines, Monica; Yang, Min-Hsiang; Puskas, Agnes; Boni, Erica; Li, Jiejin; Wear, Martin; Grinberg, Asya; Baardsnes, Jason; Dolezal, Olan; Gainey, Melicia; Anderson, Henrik; Peng, Jinlin; Lewis, Mark; Spies, Peter; Trinh, Quyhn; Bibikov, Sergei; Raymond, Jill; Yousef, Mohammed; Chandrasekaran, Vidya; Feng, Yuguo; Emerick, Anne; Mundodo, Suparna; Guimaraes, Rejane; McGirr, Katy; Li, Yue-Ji; Hughes, Heather; Mantz, Hubert; Skrabana, Rostislav; Witmer, Mark; Ballard, Joshua; Martin, Loic; Skladal, Petr; Korza, George; Laird-Offringa, Ite; Lee, Charlene S; Khadir, Abdelkrim; Podlaski, Frank; Neuner, Phillippe; Rothacker, Julie; Rafique, Ashique; Dankbar, Nico; Kainz, Peter; Gedig, Erk; Vuyisich, Momchilo; Boozer, Christina; Ly, Nguyen; Toews, Mark; Uren, Aykut; Kalyuzhniy, Oleksandr; Lewis, Kenneth; Chomey, Eugene; Pak, Brian J; Myszka, David G

    2009-03-15

    To explore the variability in biosensor studies, 150 participants from 20 countries were given the same protein samples and asked to determine kinetic rate constants for the interaction. We chose a protein system that was amenable to analysis using different biosensor platforms as well as by users of different expertise levels. The two proteins (a 50-kDa Fab and a 60-kDa glutathione S-transferase [GST] antigen) form a relatively high-affinity complex, so participants needed to optimize several experimental parameters, including ligand immobilization and regeneration conditions as well as analyte concentrations and injection/dissociation times. Although most participants collected binding responses that could be fit to yield kinetic parameters, the quality of a few data sets could have been improved by optimizing the assay design. Once these outliers were removed, the average reported affinity across the remaining panel of participants was 620 pM with a standard deviation of 980 pM. These results demonstrate that when this biosensor assay was designed and executed appropriately, the reported rate constants were consistent, and independent of which protein was immobilized and which biosensor was used.

  5. AlGaN/GaN high electron mobility transistors for protein-peptide binding affinity study.

    PubMed

    Huang, Chih-Cheng; Lee, Geng-Yen; Chyi, Jen-Inn; Cheng, Hui-Teng; Hsu, Chen-Pin; Hsu, You-Ren; Hsu, Chia-Hsien; Huang, Yu-Fen; Sun, Yuh-Chang; Chen, Chih-Chen; Li, Sheng-Shian; Yeh, J Andrew; Yao, Da-Jeng; Ren, Fan; Wang, Yu-Lin

    2013-03-15

    Antibody-immobilized AlGaN/GaN high electron mobility transistors (HEMTs) were used to detect a short peptide consisting of 20 amino acids. One-binding-site model and two-binding-site model were used for the analysis of the electrical signals, revealing the number of binding sites on an antibody and the dissociation constants between the antibody and the short peptide. In the binding-site models, the surface coverage ratio of the short peptide on the sensor surface is relevant to the electrical signals resulted from the peptide-antibody binding on the HEMTs. Two binding sites on an antibody were observed and two dissociation constants, 4.404×10(-11) M and 1.596×10(-9) M, were extracted from the binding-site model through the analysis of the surface coverage ratio of the short peptide on the sensor surface. We have also shown that the conventional method to extract the dissociation constant from the linear regression of curve-fitting with Langmuir isotherm equation may lead to an incorrect information if the receptor has more than one binding site for the ligand. The limit of detection (LOD) of the sensor observed in the experimental result (~10 pM of the short peptide) is very close to the LOD (around 2.7-3.4 pM) predicted from the value of the smallest dissociation constants. The sensitivity of the sensor is not only dependent on the transistors, but also highly relies on the affinity of the ligand-receptor pair. The results demonstrate that the AlGaN/GaN HEMTs cannot only be used for biosensors, but also for the biological affinity study.

  6. Screening of high-affinity scFvs from a ribosome displayed library using BIAcore biosensor.

    PubMed

    Yuan, Qing; Wang, Zhongkang; Nian, Siji; Yin, Youping; Chen, Gang; Xia, Yuxian

    2009-02-01

    An experimental protocol was developed to screen high-affinity single-chain Fv antibody fragments (scFvs) from a Xanthomonas axonopodis pv. citri (Xac) immunized ribosome display library using BIAcore biosensor. The screening methods involved immobilizing antigen [lipopolysaccharides (LPS) of Xac] on sensor chip HPA and then unpurified expression products of scFvs flowing over the immobilized sensor chip. The affinity-improved scFvs were selected based on dissociation rate constants (k (d)). Thirty-five enzyme-linked immunosorbent assay-positive scFvs were analyzed by BIAcore, and three of those (scFv A1, B2, and C5) with lower k (d) were screened. To demonstrate the accuracy of the screening method, the three scFvs were expressed in Escherichia coli HB2151 and purified. The purified scFvs were subsequently further identified according to association rate and affinity constants. The results showed that the three scFvs (A1, B2, and C5) had high affinity for LPS of Xac (3.51 x 10(-11), 1.13 x 10(-10), 5.06 x 10(-10) M, respectively). Furthermore, the scFv B2 was highly specific for LPS of Xac and had no any cross-reactions with bovine serum albumin and LPS from Xac-related bacteria. This provided evidence that the information from the BIAcore screening assay could be accurate. PMID:18574567

  7. Selection is more intelligent than design: improving the affinity of a bivalent ligand through directed evolution.

    PubMed

    Ahmad, Kareem M; Xiao, Yi; Soh, H Tom

    2012-12-01

    Multivalent molecular interactions can be exploited to dramatically enhance the performance of an affinity reagent. The enhancement in affinity and specificity achieved with a multivalent construct depends critically on the effectiveness of the scaffold that joins the ligands, as this determines their positions and orientations with respect to the target molecule. Currently, no generalizable design rules exist for construction of an optimal multivalent ligand for targets with known structures, and the design challenge remains an insurmountable obstacle for the large number of proteins whose structures are not known. As an alternative to such design-based strategies, we report here a directed evolution-based method for generating optimal bivalent aptamers. To demonstrate this approach, we fused two thrombin aptamers with a randomized DNA sequence and used a microfluidic in vitro selection strategy to isolate scaffolds with exceptionally high affinities. Within five rounds of selection, we generated a bivalent aptamer that binds thrombin with an apparent dissociation constant (K(d)) <10 pM, representing a ∼200-fold improvement in binding affinity over the monomeric aptamers and a ∼15-fold improvement over the best designed bivalent construct. The process described here can be used to produce high-affinity multivalent aptamers and could potentially be adapted to other classes of biomolecules.

  8. On the binding affinity of macromolecular interactions: daring to ask why proteins interact

    PubMed Central

    Kastritis, Panagiotis L.; Bonvin, Alexandre M. J. J.

    2013-01-01

    Interactions between proteins are orchestrated in a precise and time-dependent manner, underlying cellular function. The binding affinity, defined as the strength of these interactions, is translated into physico-chemical terms in the dissociation constant (Kd), the latter being an experimental measure that determines whether an interaction will be formed in solution or not. Predicting binding affinity from structural models has been a matter of active research for more than 40 years because of its fundamental role in drug development. However, all available approaches are incapable of predicting the binding affinity of protein–protein complexes from coordinates alone. Here, we examine both theoretical and experimental limitations that complicate the derivation of structure–affinity relationships. Most work so far has concentrated on binary interactions. Systems of increased complexity are far from being understood. The main physico-chemical measure that relates to binding affinity is the buried surface area, but it does not hold for flexible complexes. For the latter, there must be a significant entropic contribution that will have to be approximated in the future. We foresee that any theoretical modelling of these interactions will have to follow an integrative approach considering the biology, chemistry and physics that underlie protein–protein recognition. PMID:23235262

  9. Single-experiment displacement assay for quantifying high-affinity binding by isothermal titration calorimetry.

    PubMed

    Krainer, Georg; Keller, Sandro

    2015-04-01

    Isothermal titration calorimetry (ITC) is the gold standard for dissecting the thermodynamics of a biomolecular binding process within a single experiment. However, reliable determination of the dissociation constant (KD) from a single titration is typically limited to the range 100 μM>KD>1 nM. Interactions characterized by a lower KD can be assessed indirectly by so-called competition or displacement assays, provided that a suitable competitive ligand is available whose KD falls within the directly accessible window. However, this protocol is limited by the fact that it necessitates at least two titrations to characterize one high-affinity inhibitor, resulting in considerable consumption of both sample material and time. Here, we introduce a fast and efficient ITC displacement assay that allows for the simultaneous characterization of both a high-affinity ligand and a moderate-affinity ligand competing for the same binding site on a receptor within a single experiment. The protocol is based on a titration of the high-affinity ligand into a solution containing the moderate-affinity ligand bound to the receptor present in excess. The resulting biphasic binding isotherm enables accurate and precise determination of KD values and binding enthalpies (ΔH) of both ligands. We discuss the theoretical background underlying the approach, demonstrate its practical application to metal ion chelation, explore its potential and limitations with the aid of simulations and statistical analyses, and elaborate on potential applications to protein-inhibitor interactions.

  10. A kinetic analysis using fractals of cellular analyte-receptor binding and dissociation.

    PubMed

    Sadana, A; Vo-Dinh, T

    2001-02-01

    A fractal analysis is presented for cellular analyte-receptor binding and dissociation kinetics using a biosensor. Data taken from the literature may be modelled, in the case of binding, using a single-fractal analysis or a dual-fractal analysis. The dual-fractal analysis represents a change in the binding mechanism as the reaction progresses on the surface. The predictive relationship developed for the equilibrium constant, K (affinity which is equal to k(d)/k(1or2)), as a function of the analyte concentration is of particular value since it provides a means by which the affinity may be manipulated. This should be of assistance in cell-surface reactions, drug-candidate optimization and for the design of immunodiagnostic devices. Relationships are also presented for the binding and dissociation rate coefficients as a function of their corresponding fractal dimension, D(f) or the degree of heterogeneity that exists on the surface, and the analyte concentration in solution. When analyte-receptor binding or dissociation is involved, an increase in the heterogeneity on the surface (increase in D(f) or D(fd) as the case may be) leads to an increase in the binding and the dissociation rate coefficients. It is suggested that an increase in the degree of heterogeneity on the surface leads to an increase in the turbulence on the surface owing to the irregularities on the surface. This turbulence promotes mixing, minimizes diffusional limitations and leads subsequently to an increase in the binding and the dissociation rate coefficients. The binding and dissociation rate coefficients are rather sensitive to the degree of heterogeneity, D(f) and D(fd), respectively, that exists on the biosensor surface. The heterogeneity on the surface in general affects the binding and dissociation rate coefficients differently. In general, the analyte concentration in solution has a mild affect on the fractal dimension for binding or the fractal dimension for dissociation. This is indicated

  11. Relationship of nonreturn rates of dairy bulls to binding affinity of heparin to sperm

    SciTech Connect

    Marks, J.L.; Ax, R.L.

    1985-08-01

    The binding of the glycosaminoglycan (3H) heparin to bull spermatozoa was compared with nonreturn rates of dairy bulls. Semen samples from five bulls above and five below an average 71% nonreturn rate were used. Samples consisted of first and second ejaculates on a single day collected 1 d/wk for up to 5 consecutive wk. Saturation binding assays using (TH) heparin were performed to quantitate the binding characteristics of each sample. Scatchard plot analyses indicated a significant difference in the binding affinity for (TH) heparin between bulls of high and low fertility. Dissociation constants were 69.0 and 119.3 pmol for bulls of high and low fertility, respectively. In contrast, the number of binding sites for (TH) heparin did not differ significantly among bulls. Differences in binding affinity of (TH) heparin to bull sperm might be used to predict relative fertility of dairy bulls.

  12. Structure-based Design of Peptides with High Affinity and Specificity to HER2 Positive Tumors

    PubMed Central

    Geng, Lingling; Wang, Zihua; Yang, Xiaoliang; Li, Dan; Lian, Wenxi; Xiang, Zhichu; Wang, Weizhi; Bu, Xiangli; Lai, Wenjia; Hu, Zhiyuan; Fang, Qiaojun

    2015-01-01

    To identify peptides with high affinity and specificity against human epidermal growth factor receptor 2 (HER2), a series of peptides were designed based on the structure of HER2 and its Z(HER2:342) affibody. By using a combination protocol of molecular dynamics modeling, MM/GBSA binding free energy calculations, and binding free energy decomposition analysis, two novel peptides with 27 residues, pep27 and pep27-24M, were successfully obtained. Immunocytochemistry and flow cytometry analysis verified that both peptides can specifically bind to the extracellular domain of HER2 protein at cellular level. The Surface Plasmon Resonance imaging (SPRi) analysis showed that dissociation constants (KD) of these two peptides were around 300 nmol/L. Furthermore, fluorescence imaging of peptides against nude mice xenografted with SKBR3 cells indicated that both peptides have strong affinity and high specificity to HER2 positive tumors. PMID:26284145

  13. Rate constants and branching ratios for the dissociative recombination of C{sub 3}D{sub 7}{sup +} and C{sub 4}D{sub 9}{sup +}

    SciTech Connect

    Larsson, M.; Ehlerding, A.; Geppert, W.D.; Hellberg, F.; Kalhori, S.; Thomas, R.D.; Djuric, N.; Oesterdahl, F.; Angelova, G.; Semaniak, J.; Novotny, O.; Arnold, S.T.; Viggiano, A.A.

    2005-04-15

    Product branching ratios and thermal rate coefficients for the dissociative recombination of C{sub 3}D{sub 7}{sup +} and C{sub 4}D{sub 9}{sup +} have been measured in the ion storage ring CRYRING. The results for C{sub 3}D{sub 7}{sup +} are believed to be slightly more accurate than those obtained earlier for C{sub 3}H{sub 7}{sup +}. Only the C-C bond breaking channels could be measured for C{sub 4}D{sub 9}{sup +} and were found to be in excellent agreement with earlier data.

  14. Dissociative phenomenology of dissociative identity disorder.

    PubMed

    Dell, Paul F

    2002-01-01

    The goal of this study was to investigate the dissociative phenomenology of dissociative identity disorder (DID). The Multidimensional Inventory of Dissociation (MID) was administered to 34 patients with DID, 23 patients with dissociative disorder not otherwise specified (DDNOS), 52 patients with mixed psychiatric disorders, and 58 normal individuals. DID patients obtained significantly higher scores than the other three groups on 27 dissociation-related variables. DDNOS patients had significantly higher scores than normals and mixed psychiatric patients on 17 and 15 dissociation-related variables, respectively. The findings of the present study are virtually identical to a large body of replicated findings about the dissociative phenomenology of DID. This broad range of dissociation-related phenomena, which routinely occurs in individuals with DID, is largely absent from the DSM-IV-TR account of DID. Factor analysis of the 11 dimensions of dissociation that are measured by the MID extracted only one factor that accounted for 85% of the variance. It was concluded that dissociation is a unifactorial taxon or natural type that has different aspects or epiphenomena (i.e., amnesia, depersonalization, voices, trance, etc.).

  15. Subunit dissociations in natural and recombinant hemoglobins.

    PubMed

    Manning, L R; Jenkins, W T; Hess, J R; Vandegriff, K; Winslow, R M; Manning, J M

    1996-04-01

    A precise and rapid procedure employing gel filtration on Superose-12 to measure the tetramer-dimer dissociation constants of some natural and recombinant hemoglobins in the oxy conformation is described. Natural sickle hemoglobin was chosen to verify the validity of the results by comparing the values with those reported using an independent method not based on gel filtration. Recombinant sickle hemoglobin, as well as a sickle double mutant with a substitution at the Val-6(beta) receptor site, had approximately the same dissociation constant as natural sickle hemoglobin. Of the two recombinant hemoglobins with amino acid replacements in the alpha 1 beta 2 subunit interface, one was found to be extensively dissociated and the other completely dissociated. In addition, the absence of an effect of the allosteric regulators DPG and IHP on the dissociation constant was demonstrated. Thus, a tetramer dissociation constant can now be determined readily and used together with other criteria for characterization of hemoglobins and their interaction with small regulatory molecules. PMID:8845768

  16. Metal-Mediated Affinity and Orientation Specificity in a Computationally Designed Protein Homodimer

    SciTech Connect

    Der, Bryan S.; Machius, Mischa; Miley, Michael J.; Mills, Jeffrey L.; Szyperski, Thomas; Kuhlman, Brian

    2015-10-15

    Computationally designing protein-protein interactions with high affinity and desired orientation is a challenging task. Incorporating metal-binding sites at the target interface may be one approach for increasing affinity and specifying the binding mode, thereby improving robustness of designed interactions for use as tools in basic research as well as in applications from biotechnology to medicine. Here we describe a Rosetta-based approach for the rational design of a protein monomer to form a zinc-mediated, symmetric homodimer. Our metal interface design, named MID1 (NESG target ID OR37), forms a tight dimer in the presence of zinc (MID1-zinc) with a dissociation constant <30 nM. Without zinc the dissociation constant is 4 {micro}M. The crystal structure of MID1-zinc shows good overall agreement with the computational model, but only three out of four designed histidines coordinate zinc. However, a histidine-to-glutamate point mutation resulted in four-coordination of zinc, and the resulting metal binding site and dimer orientation closely matches the computational model (C{alpha} rmsd = 1.4 {angstrom}).

  17. Influence of length and flexibility of spacers on the binding affinity of divalent ligands.

    PubMed

    Liese, Susanne; Netz, Roland R

    2015-01-01

    We present a quantitative model for the binding of divalent ligand-receptor systems. We study the influence of length and flexibility of the spacers on the overall binding affinity and derive general rules for the optimal ligand design. To this end, we first compare different polymeric models and determine the probability to simultaneously bind to two neighboring receptor binding pockets. In a second step the binding affinity of divalent ligands in terms of the IC50 value is derived. We find that a divalent ligand has the potential to bind more efficiently than its monovalent counterpart only, if the monovalent dissociation constant is lower than a critical value. This critical monovalent dissociation constant depends on the ligand-spacer length and flexibility as well as on the size of the receptor. Regarding the optimal ligand-spacer length and flexibility, we find that the average spacer length should be equal or slightly smaller than the distance between the receptor binding pockets and that the end-to-end spacer length fluctuations should be in the same range as the size of a receptor binding pocket.

  18. Influence of length and flexibility of spacers on the binding affinity of divalent ligands

    PubMed Central

    Liese, Susanne

    2015-01-01

    Summary We present a quantitative model for the binding of divalent ligand–receptor systems. We study the influence of length and flexibility of the spacers on the overall binding affinity and derive general rules for the optimal ligand design. To this end, we first compare different polymeric models and determine the probability to simultaneously bind to two neighboring receptor binding pockets. In a second step the binding affinity of divalent ligands in terms of the IC50 value is derived. We find that a divalent ligand has the potential to bind more efficiently than its monovalent counterpart only, if the monovalent dissociation constant is lower than a critical value. This critical monovalent dissociation constant depends on the ligand-spacer length and flexibility as well as on the size of the receptor. Regarding the optimal ligand-spacer length and flexibility, we find that the average spacer length should be equal or slightly smaller than the distance between the receptor binding pockets and that the end-to-end spacer length fluctuations should be in the same range as the size of a receptor binding pocket. PMID:26124882

  19. Single amino acid exchange in bacteriophage HK620 tailspike protein results in thousand-fold increase of its oligosaccharide affinity.

    PubMed

    Broeker, Nina K; Gohlke, Ulrich; Müller, Jürgen J; Uetrecht, Charlotte; Heinemann, Udo; Seckler, Robert; Barbirz, Stefanie

    2013-01-01

    Bacteriophage HK620 recognizes and cleaves the O-antigen polysaccharide of Escherichia coli serogroup O18A1 with its tailspike protein (TSP). HK620TSP binds hexasaccharide fragments with low affinity, but single amino acid exchanges generated a set of high-affinity mutants with submicromolar dissociation constants. Isothermal titration calorimetry showed that only small amounts of heat were released upon complex formation via a large number of direct and solvent-mediated hydrogen bonds between carbohydrate and protein. At room temperature, association was both enthalpy- and entropy-driven emphasizing major solvent rearrangements upon complex formation. Crystal structure analysis showed identical protein and sugar conformers in the TSP complexes regardless of their hexasaccharide affinity. Only in one case, a TSP mutant bound a different hexasaccharide conformer. The extended sugar binding site could be dissected in two regions: first, a hydrophobic pocket at the reducing end with minor affinity contributions. Access to this site could be blocked by a single aspartate to asparagine exchange without major loss in hexasaccharide affinity. Second, a region where the specific exchange of glutamate for glutamine created a site for an additional water molecule. Side-chain rearrangements upon sugar binding led to desolvation and additional hydrogen bonding which define this region of the binding site as the high-affinity scaffold.

  20. Subunit dissociation in fish hemoglobins.

    PubMed

    Edelstein, S J; McEwen, B; Gibson, Q H

    1976-12-10

    solutions containing guanidine hydrochloride indicated that there are changes in both the absolute rates and the proportions of the fast and slow components, which along with other factors complicated the analysis of the data in terms of dissociation constants. Measurements were also made in solutions containing urea to promote dissociation, but with this agent very high concentrations (about 6 M) were required to give measureable dissociation and the fish hemoglobins were unstable under these conditions, with appreciable loss of absorbance spectra in both the sedimentation and kinetic experiments. PMID:1002703

  1. Analytical high-performance affinity chromatography: evaluation by studies of neurophysin self-association and neurophysin-peptide hormone interaction using glass matrices

    SciTech Connect

    Swaisgood, H.E.; Chaiken, I.M.

    1986-07-01

    Bovine neurophysin II (BNP II) was covalently immobilized on both nonporous and porous (200-nm pore diameter) glass beads and incorporated in a high-performance liquid chromatograph to evaluate analytical high-performance affinity chromatography as a microscale method for characterizing biomolecular interactions. The self-association of neurophysin and its binding of the peptide hormone vasopressin were characterized by using a single chromatograhic column containing immobilized neurophysin predominantly in the monomer form. Both (/sup 3/H)(Arg/sup 8/)vasopressin (AVP) and /sup 125/I-BNP II were rapidly eluted (<25 min). The relatively symmetrical elution peaks obtained allowed calculation of both equilibrium dissociation constants and kinetic dissociation rate constants. In contrast to the agreement of chromatographic equilibrium binding constants with those measured in solution, the dissociation rate, k..sqrt../sub 3/, determined from the variance of the affinity chromatographic elution profile with nonporous beads, was several orders of magnitude smaller than the solution counterpart. This latter difference may reflect the probability of rebinding to contiguous sites immobilized on a surface, a feature which would be related to that for contiguous sites on a membrane.

  2. Diminazene or berenil, a classic duplex minor groove binder, binds to G-quadruplexes with low nanomolar dissociation constants and the amidine groups are also critical for G-quadruplex binding.

    PubMed

    Zhou, Jie; Le, Vu; Kalia, Dimpy; Nakayama, Shizuka; Mikek, Clinton; Lewis, Edwin A; Sintim, Herman O

    2014-10-01

    G-quadruplexes have shown great promise as chemotherapeutic targets, probably by inhibiting telomere elongation or downregulating oncogene expression. There have been many G-quadruplex ligands developed over the years but only a few have drug-like properties. Consequently only a few G-quadruplex ligands have entered clinical trials as cancer chemotherapeutic agents. The DNA minor groove ligand, berenil (diminazene aceturate or DMZ), is used to treat animal trypanosomiasis and hence its toxicological profile is already known, making it an ideal platform to engineer into new therapeutics. Herein, using a plethora of biophysical methods including UV, NMR, MS and ITC, we show that DMZ binds to several G-quadruplexes with a Kd of ∼1 nM. This is one of the strongest G-quadruplex binding affinities reported to date and is 10(3) tighter than the berenil affinity for an AT-rich duplex DNA. Structure-activity-relationship studies demonstrate that the two amidine groups on DMZ are important for binding to both G-quadruplex and duplex DNA. This work reveals that DMZ or berenil is not as selective for AT-rich duplexes as originally thought and that some of its biological effects could be manifested through G-quadruplex binding. The DMZ scaffold represents a good starting point to develop new G-quadruplex ligands for cancer cell targeting. PMID:25096593

  3. Phosphatidylserine Reversibly Binds Cu2+ with Extremely High Affinity

    PubMed Central

    Monson, Christopher F.; Cong, Xiao; Robison, Aaron; Pace, Hudson P.; Liu, Chunming; Poyton, Matthew F.; Cremer, Paul S.

    2012-01-01

    Phosphatidylserine (PS) embedded within supported lipid bilayers (SLBs) was found to bind Cu2+ from solution with extraordinarily high affinity. In fact, the equilibrium dissociation constant was in the femtomolar range. The resulting complex formed in a 1:2 Cu2+ to PS ratio and quenches a broad spectrum of lipid-bound fluorophores in a reversible and pH-dependent fashion. At acidic pH values, the fluorophores were almost completely unquenched, while at basic pH values significant quenching (85–90%) was observed. The pH at which the transition occurred was dependent on the PS concentration and ranged from approximately pH 5 to 8. The quenching kinetics was slow at low Cu2+ concentrations and basic values pH (up to several hours), while the unquenching reaction was orders of magnitude more rapid upon lowering the pH. This was consistent with diffusion limited complex formation at basic pH, but rapid dissociation under acidic conditions. The tight binding of Cu2+ to PS may have physiological consequences under certain circumstances. PMID:22548290

  4. Report: Affinity Chromatography.

    ERIC Educational Resources Information Center

    Walters, Rodney R.

    1985-01-01

    Supports, affinity ligands, immobilization, elution methods, and a number of applications are among the topics considered in this discussion of affinity chromatography. An outline of the basic principles of affinity chromatography is included. (JN)

  5. Dissociated Vertical Deviation

    MedlinePlus

    ... Eye Terms Conditions Frequently Asked Questions Español Condiciones Chinese Conditions Dissociated Vertical Deviation En Español Read in Chinese What is Dissociated Vertical Deviation (DVD)? DVD is ...

  6. Metals affect the structure and activity of human plasminogen activator inhibitor-1. II. Binding affinity and conformational changes

    PubMed Central

    Thompson, Lawrence C; Goswami, Sumit; Peterson, Cynthia B

    2011-01-01

    Human plasminogen activator inhibitor type 1 (PAI-1) is a serine protease inhibitor with a metastable active conformation. The lifespan of the active form of PAI-1 is modulated via interaction with the plasma protein, vitronectin, and various metal ions. These metal ions fall into two categories: Type I metals, including calcium, magnesium, and manganese, stabilize PAI-1 in the absence of vitronectin, whereas Type II metals, including cobalt, copper, and nickel, destabilize PAI-1 in the absence of vitronectin, but stabilize PAI-1 in its presence. To provide a mechanistic basis for understanding the unusual modulation of PAI-1 structure and activity, the binding characteristics and conformational effects of these two types of metals were further evaluated. Steady-state binding measurements using surface plasmon resonance indicated that both active and latent PAI-1 exhibit a dissociation constant in the low micromolar range for binding to immobilized nickel. Stopped-flow measurements of approach-to-equilibrium changes in intrinsic protein fluorescence indicated that the Type I and Type II metals bind in different modes that induce distinct conformational effects on PAI-1. Changes in the observed rate constants with varying concentrations of metal allowed accurate determination of binding affinities for cobalt, nickel, and copper, yielding dissociation constants of ∼40, 30, and 0.09 μM, respectively. Competition experiments that tested effects on PAI-1 stability were consistent with these measurements of affinity and indicate that copper binds tightly to PAI-1. PMID:21280128

  7. Spectroscopic constants and potential energy curve of the iodine weakly bound 1u state correlating with the I(2P1/2) + I(2P1/2) dissociation limit

    NASA Astrophysics Data System (ADS)

    Akopyan, M. E.; Baturo, V. V.; Lukashov, S. S.; Poretsky, S. A.; Pravilov, A. M.

    2015-01-01

    The stepwise three-step three-color laser population of the I2(β1g, νβ, Jβ) rovibronic states via the B0u+, νB, JB rovibronic states and rovibronic levels of the 1u(bb) and 0g+(bb) states mixed by hyperfine interaction is used for determination of rovibronic level energies of the weakly bound I2(1u(bb)) state. Dunham coefficients of the state, Yi0 (i = 0-3), Yi1 (i = 0-2), Y02 and Y12 for the {{v}{{1u}}} = 1-5, 8, 10, 15 and {{J}{{1u}}} ≈ 9-87 ranges, the dissociation energy of the state, De, and equilibrium I-I distance, Re, as well as the potential energy curve are determined. There are aperiodicities in the excitation spectrum corresponding to the β, νβ = 23, Jβ ← 1u(bb), ν1u = 4, 5, J1u progressions in the I2 + Rg = He, Ar mixture, namely, a great number of lines which do not coincide with the R or P line progressions. Their positions conflict with the ΔJ-even selection rule. Furthermore, they do not correspond to the ΔJ-odd progression.

  8. Dissociative recombination of molecular ions in the He-Ne plasma. Partial rate constants of atoms formation in the 2 p 53d and 2 p 54d configurations

    NASA Astrophysics Data System (ADS)

    Ivanov, V. A.; Petrovskaya, A. S.; Skoblo, Yu. E.

    2016-02-01

    A spectroscopic study of population processes was carried out for states of the neon atom of the 2 p 53 d configuration in the discharge afterglow in helium with a small admixture of neon ([Ne]/[He] ≈ 10-5) at a pressure of 38 Torr. Based on the comparative analysis of time dependences of the spectral line intensities of the Ne I 2 p 53 d → 2 p 53 d and 2 p 54 d → 2 p 53 d transitions and ratio of ion densities [Ne 2 + ]/[HeNe+], it has been found that the formation of excited Ne(2 p 53 d) atoms in the afterglow caused by two dissociative recombination processes: HeNe+ + e → Ne(2 p 53 d) + Ne and Ne 2 + + e → Ne(2 p 53 d) + Ne. Distributions of population fluxes of the 2 p 53 d levels Γ _{3{d_t}}^{HeN{e^ + }} and Γ _{3{d_t}}^{Ne_2^ + }—were obtained for each of these processes.

  9. Rationally Designing Aptamer Sequences with Reduced Affinity for Controlled Sensor Performance

    PubMed Central

    Schoukroun-Barnes, Lauren R.; White, Ryan J.

    2015-01-01

    The relative ease of predicting the secondary structure of nucleic acid sequences lends itself to the design of sequences to perform desired functions. Here, we combine the utility of nucleic acid aptamers with predictable control over the secondary structure to rationally design sequences with controlled affinity towards a target analyte when employed as the recognition element in an electrochemical sensor. Specifically, we present a method to modify an existing high-gain aptamer sequence to create sequences that, when employed in an electrochemical, aptamer-based sensor, exhibit reduced affinity towards a small molecule analyte tobramycin. Sensors fabricated with the high-gain parent sequence saturate at concentrations much below the therapeutic window for tobramycin (7–18 µM). Accordingly, the rationale behind modifying this high-gain sequence to reduce binding affinity was to tune sensor performance for optimal sensitivity in the therapeutic window. Using secondary structure predictions and analysis of the NMR structure of an aminoglycoside RNA aptamer bound to tobramycin, we are able to successfully modify the aptamer sequence to tune the dissociation constants of electrochemical aptamer-based sensors between 0.17 and 3 µM. The guidelines we present represent a general strategy to lessening binding affinity of sensors employing aptamer-modified electrodes. PMID:25835184

  10. Chemiluminescently labeled aptamers as the affinity probe for interaction analysis by capillary electrophoresis.

    PubMed

    Li, Hong-Yi; Deng, Qin-Pei; Zhang, De-Wen; Zhou, Ying-Lin; Zhang, Xin-Xiang

    2010-07-01

    Aptamers are nucleic acid oligonucleotides, which can recognize targets with high affinity and specificity. Fluorescently labeled aptamers have been used as affinity probes in CE for interaction analysis. In this study, a method of labeling aptamers chemiluminescently with isoluminol isothiocyanate (ILITC) through covalent bonds was proposed and realized. The ILITC-labeled aptamers were characterized by HPLC-MS and purified by HPLC. After desalination, the ILITC-labeled aptamers were employed as the affinity probe for interaction analysis in CE coupled with chemiluminescence detection (CE-CL) by interface of end column reaction mode, the apparatus of which was home-designed and setup. CE-CL experiment conditions, including buffer pH, concentrations of horseradish peroxidase and H(2)O(2), were optimized first. The system of thrombin and its 29-mer aptamer was chosen as the model. Binding parameters, namely the dissociation constant (K(d)) and the binding site number (n), were calculated. The K(d) obtained was 124.0+/-6.9 nM in agreement with the reported values. Thus, interaction analysis method based on chemiluminescently labeled aptamers as the affinity probe in CE-CL has been established. This method can be widely applied due to the ease and universality of the labeling method, simplicity of CE-CL apparatus and combination with aptamers for a wide range of targets.

  11. Characterization of a constant current charge detector.

    PubMed

    Mori, Masanobu; Chen, Yongjing; Ohira, Shin-Ichi; Dasgupta, Purnendu K

    2012-12-15

    Ion exchangers are ionic equivalents of doped semiconductors, where cations and anions are equivalents of holes and electrons as charge carriers in solid state semiconductors. We have previously demonstrated an ion exchange membrane (IEM) based electrolyte generator which behaves similar to a light-emitting diode and a charge detector (ChD) which behaves analogous to a p-i-n photodiode. The previous work on the charge detector, operated at a constant voltage, established its unique ability to respond to the charge represented by the analyte ions regardless of their redox properties, rather than to their conductivities. It also suggested that electric field induced dissociation (EFID) of water occurs at one or both ion exchange membranes. A logical extension is to study the behavior of the same device, operated in a constant current mode (ChD(i)). The evidence indicates that in the present operational mode the device also responds to the charge represented by the analytes and not their conductivity. Injection of a base into a charge detector operated in the constant voltage mode was not previously examined; in the constant current mode, base injection appears to inhibit EFID. The effects of applied current, analyte residence time and outer channel fluid composition were individually examined; analyte ions of different mobilities as well as affinities for the respective IEMs were used. While the exact behavior is somewhat dependent on the applied current, strong electrolytes, both acids and salts, respond the highest and in a near-uniform fashion, weak acids and their salts respond in an intermediate fashion and bases produce the lowest responses. A fundamentally asymmetric behavior is observed. Injected bases but not injected acids produce a poor response; the effects of incorporating a strong base as the electrolyte in the anion exchange membrane (AEM) compartment is far greater than incorporating an acid in the cation exchange membrane (CEM) compartment. These

  12. Coupling Isotachophoresis with Affinity Chromatography for Rapid and Selective Purification with High Column Utilization, Part 1: Theory

    PubMed Central

    2015-01-01

    We present a novel technique that couples isotachophoresis (ITP) with affinity chromatography (AC) to achieve rapid, selective purification with high column utilization. ITP simultaneously preconcentrates an analyte and purifies it, based on differences in mobility of sample components, excluding species that may foul or compete with the target at the affinity substrate. ITP preconcentration accelerates the affinity reaction, reducing assay time, improving column utilization, and allowing for capture of targets with higher dissociation constants. Furthermore, ITP-AC separates the target and contaminants into nondiffusing zones, thus achieving high resolution in a short distance and time. We present an analytical model for spatiotemporal dynamics of ITP-AC. We identify and explore the effect of key process parameters, including target distribution width and height, ITP zone velocity, forward and reverse reaction constants, and probe concentration on necessary affinity region length, assay time, and capture efficiency. Our analytical approach shows collapse of these variables to three nondimensional parameters. The analysis yields simple analytical relations for capture length and capture time in relevant ITP-AC regimes, and it demonstrates how ITP greatly reduces assay time and improves column utilization. In the second part of this two-part series, we will present experimental validation of our model and demonstrate ITP-AC separation of the target from 10,000-fold more-abundant contaminants. PMID:24937679

  13. Enhanced antigen-antibody binding affinity mediated by an anti-idiotypic antibody

    SciTech Connect

    Sawutz, D.G.; Koury, R.; Homcy, C.J.

    1987-08-25

    The authors previously described the production of four monoclonal antibodies to the ..beta..-adrenergic receptor antagonist alprenolol. One of these antibodies, 5B7 (IgG/sub 2a/, kappa), was used to raise anti-idiotypic antisera in rabbits. In contrast to the expected results, one of the anti-idiotypic antisera (R9) promotes (/sup 125/I)iodocyanopinodolol (ICYP) binding to antibody 5B7. In the presence of R9, the dissociation constant decreases 100-fold from 20 to 0.3 nM. This increase in binding affinity of antibody 5B7 for ICYP is not observed in the presence of preimmune, rabbit anti-mouse or anti-idiotypic antisera generated to a monoclonal antibody of a different specificity. Furthermore, R9 in the absence of 5B7 does not bind ICYP. The F(ab) fragments of 5B7 and T9 behaved in a similar manner, and the soluble complex responsible for the high-affinity interaction with ICYP can be identified by gel filtration chromatography. The elution position of the complex is consistent with a 5B7 F(ab)-R9 F(ab) dimer, indicating that polyvalency is not responsible for the enhanced ligand binding. Kinetic analysis of ICYP-5B7 binding revealed that the rate of ICYP dissociation from 5B7 in the presence of R9 is approximately 100 times slower than in the absence of R9, consistent with the 100-fold change in binding affinity of 5B7 for ICYP. The available data best fit a model in which an anti-idiotypic antibody binds at or near the binding site of the idiotype participating in the formation of a hybrid ligand binding site. This would allow increased contact of the ligand with the idiotype-anti-idiotype complex and result in an enhanced affinity of the ligand interaction.

  14. Differences in affinity of cardiac beta-adrenergic receptors for (3H)dihydroalprenolol

    SciTech Connect

    Muntz, K.H.; Calianos, T.A.; Vandermolen, D.T.; Willerson, J.T.; Buja, L.M.

    1986-03-01

    We performed quantitative light microscopic autoradiography of (3H)dihydroalprenolol (DHA) binding to frozen sections of canine myocardium to test the hypothesis that there are differences in the density or affinity of beta-adrenergic receptors on various tissue compartments. In one study, with concentrations of (3H)DHA from 0.34 to 5.1 nM, specific binding to cardiac myocytes was saturable, whereas nonspecific binding was linear with ligand concentration. Arterioles had more specific grain counts than muscle cells (P less than 0.0001), and Scatchard analysis showed that the arterioles had a much higher affinity for (3H)DHA than myocytes. In a second study with lower concentrations of (3H)DHA (0.19-1.98 nM), binding to the arterioles saturated, whereas binding to the cardiac myocytes did not. Specific binding to arterioles was significantly higher (P less than 0.0001) than binding to myocytes at all concentrations of (3H)DHA. The dissociation constants for the subendocardial and subepicardial myocytes were 1.57 and 1.71 nM, respectively, while the dissociation constant for the arterioles was 0.26 nM. The maximum number of binding sites was 911 grains/0.9 X 10(-2) mm2 for subepicardial myocytes, 936 for subendocardial myocytes, and 986 for arterioles. The large nerves accompanying an epicardial artery also demonstrated specific (3H)DHA binding. Thus this study has demonstrated major differences in the distribution and affinity of beta-adrenergic receptors, which may help to explain various physiological responses to beta-adrenergic stimulation.

  15. Trematode hemoglobins show exceptionally high oxygen affinity.

    PubMed

    Kiger, L; Rashid, A K; Griffon, N; Haque, M; Moens, L; Gibson, Q H; Poyart, C; Marden, M C

    1998-08-01

    Ligand binding studies were made with hemoglobin (Hb) isolated from trematode species Gastrothylax crumenifer (Gc), Paramphistomum epiclitum (Pe), Explanatum explanatum (Ee), parasitic worms of water buffalo Bubalus bubalis, and Isoparorchis hypselobagri (Ih) parasitic in the catfish Wallago attu. The kinetics of oxygen and carbon monoxide binding show very fast association rates. Whereas oxygen can be displaced on a millisecond time scale from human Hb at 25 degrees C, the dissociation of oxygen from trematode Hb may require a few seconds to over 20 s (for Hb Pe). Carbon monoxide dissociation is faster, however, than for other monomeric hemoglobins or myoglobins. Trematode hemoglobins also show a reduced rate of autoxidation; the oxy form is not readily oxidized by potassium ferricyanide, indicating that only the deoxy form reacts rapidly with this oxidizing agent. Unlike most vertebrate Hbs, the trematodes have a tyrosine residue at position E7 instead of the usual distal histidine. As for Hb Ascaris, which also displays a high oxygen affinity, the trematodes have a tyrosine in position B10; two H-bonds to the oxygen molecule are thought to be responsible for the very high oxygen affinity. The trematode hemoglobins display a combination of high association rates and very low dissociation rates, resulting in some of the highest oxygen affinities ever observed.

  16. Binding affinities of CRBPI and CRBPII for 9-cis-retinoids

    PubMed Central

    Kane, Maureen A.; Bright, Frank V.; Napoli, Joseph L.

    2014-01-01

    Background Cellular retinol binding-protein I (CRBPI) and cellular retinol binding-protein II (CRBPII) serve as intracellular retinoid chaperones that bind retinol and retinal with high affinity and facilitate substrate delivery to select enzymes that catalyze retinoic acid (RA) and retinyl ester biosynthesis. Recently, 9-cis-RA has been identified in vivo in the pancreas, where it contributes to regulating glucose-stimulated insulin secretion. In vitro, 9-cis-RA activates RXR (retinoid×receptors), which serve as therapeutic targets for treating cancer and metabolic diseases. Binding affinities and structure–function relationships have been well characterized for CRBPI and CRBPII with all-trans-retinoids, but not for 9-cis-retinoids. This study extended current knowledge by establishing binding affinities for CRBPI and CRBPII with 9-cis-retinoids. Methods We have determined apparent dissociation constants, Kd′, through monitoring binding of 9-cis-retinol, 9-cis-retinal, and 9-cis-RA with CRBPI and CRBPII by fluorescence spectroscopy, and analyzing the data with non-linear regression. We compared these data to the data we obtained for all-trans- and 13-cis-retinoids under identical conditions. Results CRBPI and CRBPII, respectively, bind 9-cis-retinol ( Kd′, 11 nM and 68 nM) and 9-cis-retinal ( Kd′, 8 nM and 5 nM) with high affinity. No significant 9-cis-RA binding was observed with CRBPI or CRBPII. Conclusions CRBPI and CRBPII bind 9-cis-retinol and 9-cis-retinal with high affinities, albeit with affinities somewhat lower than for all-trans-retinol and all-trans-retinal. General significance These data provide further insight into structure–binding relationships of cellular retinol binding-proteins and are consistent with a model of 9-cis-RA biosynthesis that involves chaperoned delivery of 9-cis-retinoids to enzymes that recognize retinoid binding-proteins. PMID:21382444

  17. Omega-conotoxin GVIA binding to a high-affinity receptor in brain: characterization, calcium sensitivity, and solubilization

    SciTech Connect

    Wagner, J.A.; Snowman, A.M.; Biswas, A.; Olivera, B.M.; Snyder, S.H.

    1988-09-01

    We describe unique, high-affinity binding sites for omega(/sup 125/I)conotoxin GVIA in membranes from rat brain and rabbit sympathetic ganglia which appear to be primarily associated with N-type voltage-dependent calcium channels. The dissociation constant (KD) for the toxin in rat brain membranes is 60 pM. Physiologic extracellular concentrations of calcium inhibit toxin binding noncompetitively (IC50 = 0.2 mM). The regional distribution of the binding sites in rat brain differs markedly from that of dihydropyridine calcium antagonist receptors associated with L-type calcium channels. In detergent-solubilized brain membranes, toxin binding retains the same affinity, specificity, and ionic sensitivity as in particulate preparations.

  18. Structure-Affinity Properties of a High-Affinity Ligand of FKBP12 Studied by Molecular Simulations of a Binding Intermediate

    PubMed Central

    Olivieri, Lilian; Gardebien, Fabrice

    2014-01-01

    With a view to explaining the structure-affinity properties of the ligands of the protein FKBP12, we characterized a binding intermediate state between this protein and a high-affinity ligand. Indeed, the nature and extent of the intermolecular contacts developed in such a species may play a role on its stability and, hence, on the overall association rate. To find the binding intermediate, a molecular simulation protocol was used to unbind the ligand by gradually decreasing the biasing forces introduced. The intermediate was subsequently refined with 17 independent stochastic boundary molecular dynamics simulations that provide a consistent picture of the intermediate state. In this state, the core region of the ligand remains stable, notably because of the two anchoring oxygen atoms that correspond to recurrent motifs found in all FKBP12 ligand core structures. Besides, the non-core regions participate in numerous transient intermolecular and intramolecular contacts. The dynamic aspect of most of the contacts seems important both for the ligand to retain at least a part of its configurational entropy and for avoiding a trapped state along the binding pathway. Since the transient and anchoring contacts contribute to increasing the stability of the intermediate, as a corollary, the dissociation rate constant of this intermediate should be decreased, resulting in an increase of the affinity constant . The present results support our previous conclusions and provide a coherent rationale for explaining the prevalence in high-affinity ligands of (i) the two oxygen atoms found in carbonyl or sulfonyl groups of dissimilar core structures and of (ii) symmetric or pseudo-symmetric mobile groups of atoms found as non-core moieties. Another interesting aspect of the intermediate is the distortion of the flexible 80 s loop of the protein, mainly in its tip region, that promotes the accessibility to the bound state. PMID:25502559

  19. Are Fundamental Constants Really Constant?

    ERIC Educational Resources Information Center

    Swetman, T. P.

    1972-01-01

    Dirac's classical conclusions, that the values of e2, M and m are constants and the quantity of G decreases with time. Evoked considerable interest among researchers and traces historical development by which further experimental evidence points out that both e and G are constant values. (PS)

  20. BIOINTERACTION ANALYSIS BY HIGH-PERFORMANCE AFFINITY CHROMATOGRAPHY: KINETIC STUDIES OF IMMOBILIZED ANTIBODIES

    PubMed Central

    Nelson, Mary Anne; Moser, Annette; Hage, David S.

    2009-01-01

    A system based on high-performance affinity chromatography was developed for characterizing the binding, elution and regeneration kinetics of immobilized antibodies and immunoaffinity supports. This information was provided by using a combination of frontal analysis, split-peak analysis and peak decay analysis to determine the rate constants for antibody-antigen interactions under typical sample application and elution conditions. This technique was tested using immunoaffinity supports that contained monoclonal antibodies for 2,4-dichlorophenoxyacetic acid (2,4-D). Association equilibrium constants measured by frontal analysis for 2,4-D and related compounds with the immobilized antibodies were 1.7–12 × 106 M−1 at pH 7.0 and 25°C. Split-peak analysis gave association rate constants of 1.4–12 × 105 M−1s−1 and calculated dissociation rate constants of 0.01–0.4 s−1 under the application conditions. Elution at pH 2.5 for the analytes from the antibodies was examined by peak decay analysis and gave dissociation rate constants of 0.056–0.17 s−1. A comparison of frontal analysis results after various periods of column regeneration allowed the rate of antibody regeneration to be examined, with the results giving a first-order regeneration rate constant of 2.4 × 10−4 s−1. This combined approach and the information it provides should be useful in the design and optimization of immunoaffinity chromatography and other analytical methods that employ immobilized antibodies. The methods described are not limited to the particular analytes and antibodies employed in this study but should be useful in characterizing other targets, ligands and supports. PMID:19394281

  1. Tuning the Binding Affinities and Reversion Kinetics of a Light Inducible Dimer Allows Control of Transmembrane Protein Localization.

    PubMed

    Zimmerman, Seth P; Hallett, Ryan A; Bourke, Ashley M; Bear, James E; Kennedy, Matthew J; Kuhlman, Brian

    2016-09-20

    Inducible dimers are powerful tools for controlling biological processes through colocalizing signaling molecules. To be effective, an inducible system should have a dissociation constant in the "off" state that is greater (i.e., weaker affinity) than the concentrations of the molecules that are being controlled, and in the "on" state a dissociation constant that is less (i.e., stronger affinity) than the relevant protein concentrations. Here, we reengineer the interaction between the light inducible dimer, iLID, and its binding partner SspB, to better control proteins present at high effective concentrations (5-100 μM). iLID contains a light-oxygen-voltage (LOV) domain that undergoes a conformational change upon activation with blue light and exposes a peptide motif, ssrA, that binds to SspB. The new variant of the dimer system contains a single SspB point mutation (A58V), and displays a 42-fold change in binding affinity when activated with blue light (from 3 ± 2 μM to 125 ± 40 μM) and allows for light-activated colocalization of transmembrane proteins in neurons, where a higher affinity switch (0.8-47 μM) was less effective because more colocalization was seen in the dark. Additionally, with a point mutation in the LOV domain (N414L), we lengthened the reversion half-life of iLID. This expanded suite of light induced dimers increases the variety of cellular pathways that can be targeted with light.

  2. Tuning the Binding Affinities and Reversion Kinetics of a Light Inducible Dimer Allows Control of Transmembrane Protein Localization.

    PubMed

    Zimmerman, Seth P; Hallett, Ryan A; Bourke, Ashley M; Bear, James E; Kennedy, Matthew J; Kuhlman, Brian

    2016-09-20

    Inducible dimers are powerful tools for controlling biological processes through colocalizing signaling molecules. To be effective, an inducible system should have a dissociation constant in the "off" state that is greater (i.e., weaker affinity) than the concentrations of the molecules that are being controlled, and in the "on" state a dissociation constant that is less (i.e., stronger affinity) than the relevant protein concentrations. Here, we reengineer the interaction between the light inducible dimer, iLID, and its binding partner SspB, to better control proteins present at high effective concentrations (5-100 μM). iLID contains a light-oxygen-voltage (LOV) domain that undergoes a conformational change upon activation with blue light and exposes a peptide motif, ssrA, that binds to SspB. The new variant of the dimer system contains a single SspB point mutation (A58V), and displays a 42-fold change in binding affinity when activated with blue light (from 3 ± 2 μM to 125 ± 40 μM) and allows for light-activated colocalization of transmembrane proteins in neurons, where a higher affinity switch (0.8-47 μM) was less effective because more colocalization was seen in the dark. Additionally, with a point mutation in the LOV domain (N414L), we lengthened the reversion half-life of iLID. This expanded suite of light induced dimers increases the variety of cellular pathways that can be targeted with light. PMID:27529180

  3. Estimation of the rate constants associated with the inhibitory effect of okadaic acid on type 2A protein phosphatase by time-course analysis.

    PubMed Central

    Takai, A; Ohno, Y; Yasumoto, T; Mieskes, G

    1992-01-01

    As is often the case with tightly binding inhibitors, okadaic acid produces its inhibitory effect on type 2A protein phosphatase (PP2A) in a time-dependent manner. We measured the rate constants associated with the binding of okadaic acid to PP2A by analysing the time-course of the reduction of the p-nitrophenyl phosphate (pNPP) phosphatase activity of the enzyme after application of okadaic acid. The rate constants for dissociation of okadaic acid from PP2A were also estimated from the time-course of the recovery of the activity from inhibition by okadaic acid after addition of a mouse IgG1 monoclonal antibody raised against the inhibitor. Our results show that the rate constants for the binding of okadaic acid and PP2A are of the order of 10(7) M-1.s-1, a typical value for reactions involving relatively large molecules, whereas those for their dissociation are in the range 10(-4)-10(-3) s-1. The very low values of the latter seems to be the determining factor for the exceedingly high affinity of okadaic acid for PP2A. The dissociation constants for the interaction of okadaic acid with the free enzyme and the enzyme-substrate complex, estimated as the ratio of the rate constants, are both in the range 30-40 pM, in agreement with the results of previous dose-inhibition analyses. PMID:1329723

  4. The neonatal Fc receptor (FcRn) binds independently to both sites of the IgG homodimer with identical affinity

    PubMed Central

    Abdiche, Yasmina Noubia; Yeung, Yik Andy; Chaparro-Riggers, Javier; Barman, Ishita; Strop, Pavel; Chin, Sherman Michael; Pham, Amber; Bolton, Gary; McDonough, Dan; Lindquist, Kevin; Pons, Jaume; Rajpal, Arvind

    2015-01-01

    The neonatal Fc receptor (FcRn) is expressed by cells of epithelial, endothelial and myeloid lineages and performs multiple roles in adaptive immunity. Characterizing the FcRn/IgG interaction is fundamental to designing therapeutic antibodies because IgGs with moderately increased binding affinities for FcRn exhibit superior serum half-lives and efficacy. It has been hypothesized that 2 FcRn molecules bind an IgG homodimer with disparate affinities, yet their affinity constants are inconsistent across the literature. Using surface plasmon resonance biosensor assays that eliminated confounding experimental artifacts, we present data supporting an alternate hypothesis: 2 FcRn molecules saturate an IgG homodimer with identical affinities at independent sites, consistent with the symmetrical arrangement of the FcRn/Fc complex observed in the crystal structure published by Burmeister et al. in 1994. We find that human FcRn binds human IgG1 with an equilibrium dissociation constant (KD) of 760 ± 60 nM (N = 14) at 25°C and pH 5.8, and shows less than 25% variation across the other human subtypes. Human IgG1 binds cynomolgus monkey FcRn with a 2-fold higher affinity than human FcRn, and binds both mouse and rat FcRn with a 10-fold higher affinity than human FcRn. FcRn/IgG interactions from multiple species show less than a 2-fold weaker affinity at 37°C than at 25°C and appear independent of an IgG's variable region. Our in vivo data in mouse and rat models demonstrate that both affinity and avidity influence an IgG's serum half-life, which should be considered when choosing animals, especially transgenic systems, as surrogates. PMID:25658443

  5. Computational and ESR studies of electron attachment to decafluorocyclopentane, octafluorocyclobutane, and hexafluorocyclopropane: electron affinities of the molecules and the structures of their stable negative ions as determined from 13C and 19F hyperfine coupling constants.

    PubMed

    ElSohly, Adel M; Tschumper, Gregory S; Crocombe, Richard A; Wang, Jih Tzong; Williams, Ffrancon

    2005-08-01

    High-resolution ESR spectra of the ground-state negative ions of hexafluorocyclopropane (c-C3F6*-), octafluorocyclobutane (c-C4F8*-), and decafluorocyclopentane (c-C5F10*-) are reported and their isotropic 19F hyperfine coupling constants (hfcc) of 198.6 +/- 0.4 G, 147.6 +/- 0.4 G, and 117.9 +/- 0.4 G, respectively, are in inverse ratio to the total number of fluorine atoms per anion. Together with the small value of 5.2 +/- 0.4 G determined for the isotropic 13C hfcc of c-C4F8*-, these results indicate that in each case the singly occupied molecular orbital (SOMO) is delocalized over the equivalent fluorines and possesses a nodal plane through the carbon atoms of a time-averaged D(nh) structure. A series of quantum chemical computations were carried out to further characterize these anions and their neutral counterparts. Both the B3LYP density functional and second-order Møller-Plesset perturbation theory (MP2) indicate that c-C3F6*- adopts a D(3h) geometry and a (2)A2'' ground electronic state, that c-C4F8*- adopts a D(4h) geometry and a (2)A2u ground electronic state, and that c-C5F10*- adopts a C(s) structure and a (2)A' electronic state. Moreover, the 19F hyperfine coupling constants computed with the MP2 method and a high quality triple-zeta basis set are within 1% of the experimental values. Also, the values computed for the 13C hfcc of c-C4F8*- are consistent with the experimental value of 5.2 G. Therefore, in keeping with the ESR results, these negative ions derived from first-row elements can be characterized as pi* species. In addition, the hypervalency of these perfluorocycloalkane radical anions has been clarified.

  6. Identification and characterization of high affinity antisense PNAs for the human unr (upstream of N-ras) mRNA which is uniquely overexpressed in MCF-7 breast cancer cells

    PubMed Central

    Fang, Huafeng; Yue, Xuan; Li, Xiaoxu; Taylor, John-Stephen

    2005-01-01

    We have recently shown that an MCF-7 tumor can be imaged in a mouse by PET with 64Cu-labeled Peptide nucleic acids (PNAs) tethered to the permeation peptide Lys4 that recognize the uniquely overexpressed and very abundant upstream of N-ras or N-ras related gene (unr mRNA) expressed in these cells. Herein we describe how the high affinity antisense PNAs to the unr mRNA were identified and characterized. First, antisense binding sites on the unr mRNA were mapped by an reverse transcriptase random oligonucleotide library (RT-ROL) method that we have improved, and by a serial analysis of antisense binding sites (SAABS) method that we have developed which is similar to another recently described method. The relative binding affinities of oligodeoxynucleotides (ODNs) complementary to the antisense binding sites were then qualitatively ranked by a new Dynabead-based dot blot assay. Dissociation constants for a subset of the ODNs were determined by a new Dynabead-based solution assay and were found to be 300 pM for the best binders in 1 M salt. PNAs corresponding to the ODNs with the highest affinities were synthesized with an N-terminal CysTyr and C-terminal Lys4 sequence. Dissociation constants of these hybrid PNAs were determined by the Dynabead-based solution assay to be about 10 pM for the highest affinity binders. PMID:16314303

  7. Effect of receptor-ligand affinity on the strength of endothelial cell adhesion.

    PubMed Central

    Xiao, Y; Truskey, G A

    1996-01-01

    The objective of this study was to determine the effect of receptor-ligand affinity on the strength of endothelial cell adhesion. Linear and cyclic forms of the fibronectin (Fn) cell-binding domain peptide Arg-Gly-Asp (RGD) were covalently immobilized to glass, and Fn was adsorbed onto glass slides. Bovine aortic endothelial cells attached to the surfaces for 15 min. The critical wall shear stress at which 50% of the cells detached increased nonlinearly with ligand density and was greater with immobilized cyclic RGD than with immobilized linear RGD or adsorbed Fn. To directly compare results for the different ligand densities, the receptor-ligand dissociation constant and force per bond were estimated from data for the critical shear stress and contact area. Total internal reflection fluorescence microscopy was used to measure the contact area as a function of separation distance. Contact area increased with increasing ligand density. Contact areas were similar for the immobilized peptides but were greater on surfaces with adsorbed Fn. The dissociation constant was determined by nonlinear regression of the net force on the cells to models that assumed that bonds were either uniformly stressed or that only bonds on the periphery of the contact region were stressed (peeling model). Both models provided equally good fits for cells attached to immobilized peptides whereas the peeling model produced a better fit of data for cells attached to adsorbed Fn. Cyclic RGD and linear RGD both bind to the integrin alpha v beta 3, but immobilized cyclic RGD exhibited a greater affinity than did linear RGD. Receptor affinities of Fn adsorbed to glycophase glass and Fn adsorbed to glass were similar. The number of bonds was calculated assuming binding equilibrium. The peeling model produced good linear fits between bond force and number of bonds. Results of this study indicate that 1) bovine aortic endothelial cells are more adherent on immobilized cyclic RGD peptide than linear

  8. A novel technique for measurement of thermal rate constants and temperature dependences of dissociative recombination: CO2(+), CF3(+), N2O(+), C7H8(+), C7H7(+), C6H6(+), C6H5(+), C5H6(+), C4H4(+), and C3H3(+).

    PubMed

    Fournier, Joseph A; Shuman, Nicholas S; Melko, Joshua J; Ard, Shaun G; Viggiano, Albert A

    2013-04-21

    A novel technique using a flowing afterglow-Langmuir probe apparatus for measurement of temperature dependences of rate constants for dissociative recombination (DR) is presented. Low (~10(11) cm(-3)) concentrations of a neutral precursor are added to a noble gas∕electron afterglow plasma thermalized at 300-500 K. Charge exchange yields one or many cation species, each of which may undergo DR. Relative ion concentrations are monitored at a fixed reaction time while the initial plasma density is varied between 10(9) and 10(10) cm(-3). Modeling of the decrease in concentration of each cation relative to the non-recombining noble gas cation yields the rate constant for DR. The technique is applied to several species (O2(+), CO2(+), CF3(+), N2O(+)) with previously determined 300 K values, showing excellent agreement. The measurements of those species are extended to 500 K, with good agreement to literature values where they exist. Measurements are also made for a range of CnHm(+) (C7H7(+), C7H8(+), C5H6(+), C4H4(+), C6H5(+), C3H3(+), and C6H6(+)) derived from benzene and toluene neutral precursors. CnHm(+) DR rate constants vary from 8-12 × 10(-7) cm(3) s(-1) at 300 K with temperature dependences of approximately T(-0.7). Where prior measurements exist these results are in agreement, with the exception of C3H3(+) where the present results disagree with a previously reported flat temperature dependence. PMID:23614415

  9. Affinity of molecular interactions in the bacteriophage φ29 DNA packaging motor

    PubMed Central

    Robinson, Mark A.; Wood, Jonathan P.A.; Capaldi, Stephanie A.; Baron, Andrew J.; Gell, Christopher; Smith, D. Alastair; Stonehouse, Nicola J.

    2006-01-01

    DNA packaging in the bacteriophage φ29 involves a molecular motor with protein and RNA components, including interactions between the viral connector protein and molecules of pRNA, both of which form multimeric complexes. Data are presented to demonstrate the higher order assembly of pRNA together with the affinity of pRNA:pRNA and pRNA:connector interactions, which are used to propose a model for motor function. In solution, pRNA can form dimeric and trimeric multimers in a magnesium-dependent manner, with dissociation constants for multimerization in the micromolar range. pRNA:connector binding is also facilitated by the presence of magnesium ions, with a nanomolar apparent dissociation constant for the interaction. From studies with a mutant pRNA, it appears that multimerization of pRNA is not essential for connector binding and it is likely that connector protein is involved in the stabilization of higher order RNA multimers. It is proposed that magnesium ions may promote conformational change that facilitate pRNA:connector interactions, essential for motor function. PMID:16714447

  10. Affinity of molecular interactions in the bacteriophage phi29 DNA packaging motor.

    PubMed

    Robinson, Mark A; Wood, Jonathan P A; Capaldi, Stephanie A; Baron, Andrew J; Gell, Christopher; Smith, D Alastair; Stonehouse, Nicola J

    2006-01-01

    DNA packaging in the bacteriophage phi29 involves a molecular motor with protein and RNA components, including interactions between the viral connector protein and molecules of pRNA, both of which form multimeric complexes. Data are presented to demonstrate the higher order assembly of pRNA together with the affinity of pRNA:pRNA and pRNA:connector interactions, which are used to propose a model for motor function. In solution, pRNA can form dimeric and trimeric multimers in a magnesium-dependent manner, with dissociation constants for multimerization in the micromolar range. pRNA:connector binding is also facilitated by the presence of magnesium ions, with a nanomolar apparent dissociation constant for the interaction. From studies with a mutant pRNA, it appears that multimerization of pRNA is not essential for connector binding and it is likely that connector protein is involved in the stabilization of higher order RNA multimers. It is proposed that magnesium ions may promote conformational change that facilitate pRNA:connector interactions, essential for motor function.

  11. Swirling flow of a dissociated gas

    NASA Technical Reports Server (NTRS)

    Wolfram, W. R., Jr.; Walker, W. F.

    1975-01-01

    Most physical applications of the swirling flow, defined as a vortex superimposed on an axial flow in the nozzle, involve high temperatures and the possibility of real gas effects. The generalized one-dimensional swirling flow in a converging-diverging nozzle is analyzed for equilibrium and frozen dissociation using the ideal dissociating gas model. Numerical results are provided to illustrate the major effects and to compare with results obtained for a perfect gas with constant ratio of specific heats. It is found that, even in the case of real gases, perfect gas calculations can give a good estimate of the reduction in mass flow due to swirl.

  12. Choline uptake in Agrobacterium tumefaciens by the high-affinity ChoXWV transporter.

    PubMed

    Aktas, Meriyem; Jost, Kathinka A; Fritz, Christiane; Narberhaus, Franz

    2011-10-01

    Agrobacterium tumefaciens is a facultative phytopathogen that causes crown gall disease. For successful plant transformation A. tumefaciens requires the membrane lipid phosphatidylcholine (PC), which is produced via the methylation and the PC synthase (Pcs) pathways. The latter route is dependent on choline. Although choline uptake has been demonstrated in A. tumefaciens, the responsible transporter(s) remained elusive. In this study, we identified the first choline transport system in A. tumefaciens. The ABC-type choline transporter is encoded by the chromosomally located choXWV operon (ChoX, binding protein; ChoW, permease; and ChoV, ATPase). The Cho system is not critical for growth and PC synthesis. However, [14C]choline uptake is severely reduced in A. tumefaciens choX mutants. Recombinant ChoX is able to bind choline with high affinity (equilibrium dissociation constant [KD] of ≈2 μM). Since other quaternary amines are bound by ChoX with much lower affinities (acetylcholine, KD of ≈80 μM; betaine, KD of ≈470 μM), the ChoXWV system functions as a high-affinity transporter with a preference for choline. Two tryptophan residues (W40 and W87) located in the predicted ligand-binding pocket are essential for choline binding. The structural model of ChoX built on Sinorhizobium meliloti ChoX resembles the typical structure of substrate binding proteins with a so-called "Venus flytrap mechanism" of substrate binding. PMID:21803998

  13. Probing high-affinity 11-mer DNA aptamer against Lup an 1 (β-conglutin).

    PubMed

    Nadal, P; Svobodova, M; Mairal, T; O'Sullivan, C K

    2013-11-01

    Aptamers are synthetic nucleic acids with great potential as analytical tools. However, the length of selected aptamers (typically 60-100 bases) can affect affinity, due to the presence of bases not required for interaction with the target, and therefore, the truncation of these selected sequences and identification of binding domains is a critical step to produce potent aptamers with higher affinities and specificities and lowered production costs. In this paper we report the truncation of an aptamer that specifically binds to β-conglutin (Lup an 1), an anaphylactic allergen. Through comparing the predicted secondary structures of the aptamers, a hairpin structure with a G-rich loop was determined to be the binding motif. The highest affinity was observed with a truncation resulting in an 11-mer sequence that had an apparent equilibrium dissociation constant (K D) of 1.7 × 10(-9) M. This 11-mer sequence was demonstrated to have high specificity for β-conglutin and showed no cross-reactivity to other lupin conglutins (α-, δ-, γ-conglutins) and closely related proteins such as gliadin. Finally, the structure of the truncated 11-mer aptamer was preliminarily elucidated, and the GQRS Mapper strongly predicted the presence of a G-quadruplex, which was subsequently corroborated using one-dimensional NMR, thus highlighting the stability of the truncated structure. PMID:24126837

  14. Complementary metal oxide semiconductor-compatible silicon nanowire biofield-effect transistors as affinity biosensors.

    PubMed

    Duan, Xuexin; Rajan, Nitin K; Izadi, Mohammad Hadi; Reed, Mark A

    2013-11-01

    Affinity biosensors use biorecognition elements and transducers to convert a biochemical event into a recordable signal. They provides the molecule binding information, which includes the dynamics of biomolecular association and dissociation, and the equilibrium association constant. Complementary metal oxide semiconductor-compatible silicon (Si) nanowires configured as a field-effect transistor (NW FET) have shown significant advantages for real-time, label-free and highly sensitive detection of a wide range of biomolecules. Most research has focused on reducing the detection limit of Si-NW FETs but has provided less information about the real binding parameters of the biomolecular interactions. Recently, Si-NW FETs have been demonstrated as affinity biosensors to quantify biomolecular binding affinities and kinetics. They open new applications for NW FETs in the nanomedicine field and will bring such sensor technology a step closer to commercial point-of-care applications. This article summarizes the recent advances in bioaffinity measurement using Si-NW FETs, with an emphasis on the different approaches used to address the issues of sensor calibration, regeneration, binding kinetic measurements, limit of detection, sensor surface modification, biomolecule charge screening, reference electrode integration and nonspecific molecular binding.

  15. Monoclonal IgM antibody exhibiting high-affinity binding and cryoglobulin properties.

    PubMed Central

    Ballard, D W; Kranz, D M; Voss, E W

    1983-01-01

    A monoclonal IgM antibody (18-2-3) derived from cell fusion of (NZB X NZW) F1 splenocytes following secondary immunization with fluorescein-conjugated keyhole limpet hemocyanin was shown to exhibit high intrinsic binding affinity and cryoinsolubility. Affinity-purified preparations were determined to be IgM by immunochemical, electrophoretic, and chromatographic analyses. An intrinsic association constant (Ka) of 2.9 X 10(10) M-1 (at 2 degrees C) was measured by first-order dissociation-rate analysis. Antibody solubility at low concentration (approximately equal to 50 micrograms/ml) was shown, by absorption spectroscopy, to be temperature dependent between 4 degrees C and 32 degrees C. Insolubility at low temperature (4 degrees C) was reversible in the presence of homologous fluorescyl hapten, indicative of active site involvement in the mechanism of cryoglobulin-18-2-3 complex formation. Characteristics of clone 18-2-3 are discussed in terms of (i) its potential use as a model for examining the mechanism of cryoprecipitation and (ii) the proposed relationship between affinity maturation and the IgM to IgG class switch. Images PMID:6348779

  16. A structure-based benchmark for protein-protein binding affinity.

    PubMed

    Kastritis, Panagiotis L; Moal, Iain H; Hwang, Howook; Weng, Zhiping; Bates, Paul A; Bonvin, Alexandre M J J; Janin, Joël

    2011-03-01

    We have assembled a nonredundant set of 144 protein-protein complexes that have high-resolution structures available for both the complexes and their unbound components, and for which dissociation constants have been measured by biophysical methods. The set is diverse in terms of the biological functions it represents, with complexes that involve G-proteins and receptor extracellular domains, as well as antigen/antibody, enzyme/inhibitor, and enzyme/substrate complexes. It is also diverse in terms of the partners' affinity for each other, with K(d) ranging between 10(-5) and 10(-14) M. Nine pairs of entries represent closely related complexes that have a similar structure, but a very different affinity, each pair comprising a cognate and a noncognate assembly. The unbound structures of the component proteins being available, conformation changes can be assessed. They are significant in most of the complexes, and large movements or disorder-to-order transitions are frequently observed. The set may be used to benchmark biophysical models aiming to relate affinity to structure in protein-protein interactions, taking into account the reactants and the conformation changes that accompany the association reaction, instead of just the final product.

  17. Enzyme activity assay of glycoprotein enzymes based on a boronate affinity molecularly imprinted 96-well microplate.

    PubMed

    Bi, Xiaodong; Liu, Zhen

    2014-12-16

    Enzyme activity assay is an important method in clinical diagnostics. However, conventional enzyme activity assay suffers from apparent interference from the sample matrix. Herein, we present a new format of enzyme activity assay that can effectively eliminate the effects of the sample matrix. The key is a 96-well microplate modified with molecularly imprinted polymer (MIP) prepared according to a newly proposed method called boronate affinity-based oriented surface imprinting. Alkaline phosphatase (ALP), a glycoprotein enzyme that has been routinely used as an indicator for several diseases in clinical tests, was taken as a representative target enzyme. The prepared MIP exhibited strong affinity toward the template enzyme (with a dissociation constant of 10(-10) M) as well as superb tolerance for interference. Thus, the enzyme molecules in a complicated sample matrix could be specifically captured and cleaned up for enzyme activity assay, which eliminated the interference from the sample matrix. On the other hand, because the boronate affinity MIP could well retain the enzymatic activity of glycoprotein enzymes, the enzyme captured by the MIP was directly used for activity assay. Thus, additional assay time and possible enzyme or activity loss due to an enzyme release step required by other methods were avoided. Assay of ALP in human serum was successfully demonstrated, suggesting a promising prospect of the proposed method in real-world applications.

  18. Weak affinity chromatography as a new approach for fragment screening in drug discovery.

    PubMed

    Duong-Thi, Minh-Dao; Meiby, Elinor; Bergström, Maria; Fex, Tomas; Isaksson, Roland; Ohlson, Sten

    2011-07-01

    Fragment-based drug design (FBDD) is currently being implemented in drug discovery, creating a demand for developing efficient techniques for fragment screening. Due to the intrinsic weak or transient binding of fragments (mM-μM in dissociation constant (K(D))) to targets, methods must be sensitive enough to accurately detect and quantify an interaction. This study presents weak affinity chromatography (WAC) as an alternative tool for screening of small fragments. The technology was demonstrated by screening of a selected 23-compound fragment collection of documented binders, mostly amidines, using trypsin and thrombin as model target protease proteins. WAC was proven to be a sensitive, robust, and reproducible technique that also provides information about affinity of a fragment in the range of 1 mM-10 μM. Furthermore, it has potential for high throughput as was evidenced by analyzing mixtures in the range of 10 substances by WAC-MS. The accessibility and flexibility of the technology were shown as fragment screening can be performed on standard HPLC equipment. The technology can further be miniaturized and adapted to the requirements of affinity ranges of the fragment library. All these features of WAC make it a potential method in drug discovery for fragment screening. PMID:21352794

  19. Characteristics of the interaction of calcium with casein submicelles as determined by analytical affinity chromatography

    SciTech Connect

    Jang, H.D.; Swaisgood, H.E. )

    1990-12-01

    Interaction of calcium with casein submicelles was investigated in CaCl2 and calcium phosphate buffers and with synthetic milk salt solutions using the technique of analytical affinity chromatography. Micelles that had been prepared by size exclusion chromatography with glycerolpropyl controlled-pore glass from fresh raw skim milk that had never been cooled, were dialyzed at room temperature against calcium-free imidazole buffer, pH 6.7. Resulting submicelles were covalently immobilized on succinamidopropyl controlled-pore glass (300-nm pore size). Using 45Ca to monitor the elution retardation, the affinity of free Ca2+ and calcium salt species was determined at temperatures of 20 to 40 degrees C and pH 6.0 to 7.5. Increasing the pH in this range or increasing the temperature strengthened the binding of calcium to submicelles, similar to previous observations with individual caseins. However, the enthalpy change obtained from the temperature dependence was considerably greater than that reported for alpha s1- and beta-caseins. Furthermore, the elution profiles for 45Ca in milk salt solutions were decidedly different from those in CaCl2 or calcium phosphate buffers and the affinities were also greater. For example, at pH 6.7 and 30 degrees C the average dissociation constant for the submicelle-calcium complex is 0.074 mM for CaCl2 and calcium phosphate buffers, vs 0.016 mM for the milk salt solution. The asymmetric frontal boundaries and higher average affinities observed with milk salts may be due to binding of calcium salts with greater affinity in addition to the binding of free Ca2+ in these solutions.

  20. Theoretical and experimental studies on zone-interference chromatography as a new method for determining macromolecular kinetic constants.

    PubMed

    Endo, S; Wada, A

    1983-11-01

    Zone-interference chromatography is a new method for studying macromolecular interactions (S. Endo and A. Wada, Anal. Biochem. 124 (1982) 372). This method is a new style of affinity chromatography which requires no preparation of affinity-column materials but utilizes the velocity difference in a column between interacting molecular species. Using the stochastic theory on the behavior of solute molecules, both the association and the dissociation rate constants can be analytically obtained from the degree of deformation of elution patterns, i.e., the change of the first and second moments. In order to verify the present theory, computer simulation of elution profiles by the extended plate theory and a binding experiment between glutamate dehydrogenase and ADP have been carried out. PMID:6661497

  1. The dissociative bond.

    PubMed

    Gordon, Nirit

    2013-01-01

    Dissociation leaves a psychic void and a lingering sense of psychic absence. How do 2 people bond while they are both suffering from dissociation? The author explores the notion of a dissociative bond that occurs in the aftermath of trauma--a bond that holds at its core an understanding and shared detachment from the self. Such a bond is confined to unspoken terms that are established in the relational unconscious. The author proposes understanding the dissociative bond as a transitional space that may not lead to full integration of dissociated knowledge yet offers some healing. This is exemplified by R. Prince's (2009) clinical case study. A relational perspective is adopted, focusing on the intersubjective aspects of a dyadic relationship. In the dissociative bond, recognition of the need to experience mutual dissociation can accommodate a psychic state that yearns for relationship when the psyche cannot fully confront past wounds. Such a bond speaks to the need to reestablish a sense of human relatedness and connection when both parties in the relationship suffer from disconnection. This bond is bound to a silence that becomes both a means of protection against the horror of traumatic memory and a way to convey unspoken gestures toward the other.

  2. The dissociative bond.

    PubMed

    Gordon, Nirit

    2013-01-01

    Dissociation leaves a psychic void and a lingering sense of psychic absence. How do 2 people bond while they are both suffering from dissociation? The author explores the notion of a dissociative bond that occurs in the aftermath of trauma--a bond that holds at its core an understanding and shared detachment from the self. Such a bond is confined to unspoken terms that are established in the relational unconscious. The author proposes understanding the dissociative bond as a transitional space that may not lead to full integration of dissociated knowledge yet offers some healing. This is exemplified by R. Prince's (2009) clinical case study. A relational perspective is adopted, focusing on the intersubjective aspects of a dyadic relationship. In the dissociative bond, recognition of the need to experience mutual dissociation can accommodate a psychic state that yearns for relationship when the psyche cannot fully confront past wounds. Such a bond speaks to the need to reestablish a sense of human relatedness and connection when both parties in the relationship suffer from disconnection. This bond is bound to a silence that becomes both a means of protection against the horror of traumatic memory and a way to convey unspoken gestures toward the other. PMID:23282044

  3. The region of antithrombin interacting with full-length heparin chains outside the high-affinity pentasaccharide sequence extends to Lys136 but not to Lys139.

    PubMed

    Arocas, V; Turk, B; Bock, S C; Olson, S T; Björk, I

    2000-07-25

    The interaction of a well-defined pentasaccharide sequence of heparin with a specific binding site on antithrombin activates the inhibitor through a conformational change. This change increases the rate of antithrombin inhibition of factor Xa, whereas acceleration of thrombin inhibition requires binding of both inhibitor and proteinase to the same heparin chain. An extended heparin binding site of antithrombin outside the specific pentasaccharide site has been proposed to account for the higher affinity of the inhibitor for full-length heparin chains by interacting with saccharides adjacent to the pentasaccharide sequence. To resolve conflicting evidence regarding the roles of Lys136 and Lys139 in this extended site, we have mutated the two residues to Ala or Gln. Mutation of Lys136 decreased the antithrombin affinity for full-length heparin by at least 5-fold but minimally altered the affinity for the pentasaccharide. As a result, the full-length heparin and pentasaccharide affinities were comparable. The reduced affinity for full-length heparin was associated with the loss of one ionic interaction and was caused by both a lower overall association rate constant and a higher overall dissociation rate constant. In contrast, mutation of Lys139 affected neither full-length heparin nor pentasaccharide affinity. The rate constants for inhibition of thrombin and factor Xa by the complexes between antithrombin and full-length heparin or pentasaccharide were unaffected by both mutations, indicating that neither Lys136 nor Lys139 is involved in heparin activation of the inhibitor. Together, these results show that Lys136 forms part of the extended heparin binding site of antithrombin that participates in the binding of full-length heparin chains, whereas Lys139 is located outside this site. PMID:10913257

  4. Mu/sub 1/: A very high affinity subtype of enkephalin binding sites in rat brain

    SciTech Connect

    Lutz, R.A.; Cruciani, R.A.; Munson, P.J.; Rodbard, D.

    1985-06-10

    Displacement studies of (/sup 3/H)-(D-Ala/sup 2/-MePhe/sup 4/-Gly-ol/sup 5/)-enkephalin ((/sup 3/H)-DAGO) and (/sup 3/H)-(D-Ala/sup 2/-D-Leu/sup 5/)-enkephalin ((/sup 3/H)-DADL) by the corresponding unlabeled ligands show that there are at least three classes of sites which bind these enkephalin analogs with high affinity. Using computer modeling, the introduction of the third site significantly improved the goodness of fit in ten consecutive experiments. These sites appear to correspond to the ..mu.., delta, and ..mu../sub 1/ sites, with mean dissociation constants of 11, 1.3 and 0.9 nM for DADL and 2.5, 300 and 0.3 nM for DAGO, respectively. 15 reference, 3 figures, 1 table.

  5. Afi-Chip: An Equipment-Free, Low-Cost, and Universal Binding Ligand Affinity Evaluation Platform.

    PubMed

    Song, Yanling; Shi, Yuanzhi; Li, Xingrui; Ma, Yanli; Gao, Mingxuan; Liu, Dan; Mao, Yu; Zhu, Zhi; Lin, Hui; Yang, Chaoyong

    2016-08-16

    Binding affinity characterization is of great importance for aptamer screening because the dissociation constant (Kd) value is a key parameter for evaluating molecular interaction. However, conventional methods often require sophisticated equipment and time-consuming processing. Here, we present a portable device, Afi-Chip, as an equipment-free, rapid, low-cost, and universal platform for evaluation of the aptamer affinity. The Afi-Chip displays a distance readout based on the reaction of an enzyme catalyzing the decomposition of H2O2 for gas generation to push the movement of ink bar. Taking advantage of translating the recognition signal to distance signal and realizing the regents mixing and quantitative readout on the chip, we successfully monitored the aptamer evolution process and characterized binding affinity of aptamers against multiple types of targets, including small molecule glucose, cancer biomarker protein EpCAM, and tumor cell SW620. We also applied the Afi-Chip for rapid characterization of the affinity between anti-HCG and HCG to demonstrate the generality for the molecular interaction study. All of the Kd values obtained are comparable to those reported in the literature or obtained by sophisticated instruments such as a flow cytometer. The Afi-Chip offers a new approach for equipment-free investigation of molecular interactions, such as aptamer identification, ligand selection monitoring, and drug screening. PMID:27454185

  6. Afi-Chip: An Equipment-Free, Low-Cost, and Universal Binding Ligand Affinity Evaluation Platform.

    PubMed

    Song, Yanling; Shi, Yuanzhi; Li, Xingrui; Ma, Yanli; Gao, Mingxuan; Liu, Dan; Mao, Yu; Zhu, Zhi; Lin, Hui; Yang, Chaoyong

    2016-08-16

    Binding affinity characterization is of great importance for aptamer screening because the dissociation constant (Kd) value is a key parameter for evaluating molecular interaction. However, conventional methods often require sophisticated equipment and time-consuming processing. Here, we present a portable device, Afi-Chip, as an equipment-free, rapid, low-cost, and universal platform for evaluation of the aptamer affinity. The Afi-Chip displays a distance readout based on the reaction of an enzyme catalyzing the decomposition of H2O2 for gas generation to push the movement of ink bar. Taking advantage of translating the recognition signal to distance signal and realizing the regents mixing and quantitative readout on the chip, we successfully monitored the aptamer evolution process and characterized binding affinity of aptamers against multiple types of targets, including small molecule glucose, cancer biomarker protein EpCAM, and tumor cell SW620. We also applied the Afi-Chip for rapid characterization of the affinity between anti-HCG and HCG to demonstrate the generality for the molecular interaction study. All of the Kd values obtained are comparable to those reported in the literature or obtained by sophisticated instruments such as a flow cytometer. The Afi-Chip offers a new approach for equipment-free investigation of molecular interactions, such as aptamer identification, ligand selection monitoring, and drug screening.

  7. The sodium ion affinities of asparagine, glutamine, histidine and arginine

    NASA Astrophysics Data System (ADS)

    Wang, Ping; Ohanessian, Gilles; Wesdemiotis, Chrys

    2008-01-01

    The sodium ion affinities of the amino acids Asn, Gln, His and Arg have been determined by experimental and computational approaches (for Asn, His and Arg). Na+-bound heterodimers with amino acid and peptide ligands (Pep1, Pep2) were produced by electrospray ionization. From the dissociation kinetics of these Pep1-Na+-Pep2 ions to Pep1-Na+ and Pep2-Na+, determined by collisionally activated dissociation, a ladder of relative affinities was constructed and subsequently converted to absolute affinities by anchoring the relative values to known Na+ affinities. The Na+ affinities of Asn, His and Arg, were calculated at the MP2(full)/6-311+G(2d,2p)//MP2/6-31G(d) level of ab initio theory. The resulting experimental and computed Na+ affinities are in excellent agreement with one another. These results, combined with those of our previous studies, yield the sodium ion affinities of 18 out of the 20 [alpha]-amino acids naturally occurring in peptides and proteins of living systems.

  8. A new method of quantitative affinity chromatography and its application to the study of myosin.

    PubMed Central

    Bottomley, R C; Storer, A C; Trayer, I P

    1976-01-01

    A new method of quantifying the interactions between two or three components of an interacting system, one of which is insoluble, is described. The method differs from those previously applied to affinity chromatography systems in that it does not require that elution volumes be measured, but is instead dependent on measurements of the quantity of affinity-bound material. Theoretical expressions are derived for systems in which the acceptor is immobilized. Examples presented to illustrate the validity of the theory are of the latter type and are from studies on the myosin-adenosine nucleotide-PPi system. With Sepharose-myosin columns (myosin covalently coupled to CNBr-activated Sepharose) a dissociation constant of 1.8 muM for ATP4- was found. Data were also obtained under conditions that closely approximate to those found in vivo, i.e. on columns packed with a slurry of Sephadex G-50 and precipitated myosin filaments formed at low ionic strength. The binding of MgATP2-, MgADP-, ATP4- and MgPPi2- to "filamentous" myosin in both two- (myosin and nucleotide) and three- (myosin, nucleotide and PPi) component systems at different temperatures was studied and the dissociation constants obtained agreed well with previously published values. Except for the binding of ATP4- to filamentous myosin at 4 degrees when 85% of the protein was interacting with the nucleotide, much lower values for the number of available sites occupied by the nucleotides were as a routine found in this system. Although this apparent discrepancy is difficult to explain, it is not an anomaly of the theoretical approach and may reflect the present state of understanding of the myosin system. PMID:1008824

  9. Kinetic analysis of a high-affinity antibody/antigen interaction performed by multiple Biacore users.

    PubMed

    Katsamba, Phinikoula S; Navratilova, Iva; Calderon-Cacia, Maria; Fan, Linsey; Thornton, Kevin; Zhu, Mingde; Bos, Tim Vanden; Forte, Carla; Friend, Della; Laird-Offringa, Ite; Tavares, Gisele; Whatley, John; Shi, Ergang; Widom, Angela; Lindquist, Kevin C; Klakamp, Scott; Drake, Andrew; Bohmann, David; Roell, Marina; Rose, Larry; Dorocke, Jill; Roth, Bruce; Luginbühl, Béatrice; Myszka, David G

    2006-05-15

    To explore the reliability of Biacore-based assays, 22 study participants measured the binding of prostate-specific antigen (PSA) to a monoclonal antibody (mAb). Each participant was provided with the same reagents and a detailed experimental protocol. The mAb was immobilized on the sensor chip at three different densities and a two-step assay was used to determine the kinetic and affinity parameters of the PSA/mAb complex. First, PSA was tested over a concentration range of 2.5-600 nM to obtain k(a) information. Second, to define the k(d) of this stable antigen/antibody complex accurately, the highest PSA concentration was retested with the dissociation phase of each binding cycle monitored for 1h. All participants collected data that could be analyzed to obtain kinetic parameters for the interaction. The association and the extended-dissociation data derived from the three antibody surfaces were globally fit using a simple 1:1 interaction model. The average k(a) and k(d) for the PSA/mAb interaction as calculated from the 22 analyses were (4.1+/-0.6) x 10(4) M(-1) s(-1) and (4.5+/-0.6) x 10(-5) s(-1), respectively. Overall, the experimental standard errors in the rate constants were only approximately 14%. Based on the kinetic rate constants, the affinity (K(D)) of the PSA/mAb interaction was 1.1+/-0.2 nM.

  10. Generalised dissociative amnesia.

    PubMed

    Sengupta, S N; Jena, S; Saxena, S

    1993-12-01

    A case of generalised dissociative amnesia is presented, which illustrates several characteristic features of this uncommon condition. The case showed poor response to thiopentone interviews and in vivo cueing. Amnesia had persisted at six months follow up.

  11. BC(50): a generalized, unifying affinity descriptor.

    PubMed

    Vacca, Alberto; Francesconi, Oscar; Roelens, Stefano

    2012-12-01

    Assessing binding affinities is an unavoidable step that we come across any time interactions between binding species are investigated. A quantitative evaluation of binding affinities relies on the determination of binding constants but, whilst the binding constant fully defines the affinity of a reagent for a ligand when only one complex species is formed, the same is not true when the interacting partners form more than one complex of different stoichiometry, because all complexes contribute to the overall binding affinity. Unfortunately, this situation is the rule rather than the exception in chemical systems, but a generally accepted solution for this issue has not yet been settled. In this Personal Account, we describe the evolution, from the initial idea to a fully developed stage, of a binding descriptor that has been developed with the aim of filling this gap, thereby providing scientists in all fields of chemistry with a unifying tool for the assessment of binding affinities based on the knowledge of the binding constants in systems that involve any number of complex species.

  12. Limited proteolysis for assaying ligand binding affinities of nuclear receptors.

    PubMed

    Benkoussa, M; Nominé, B; Mouchon, A; Lefebvre, B; Bernardon, J M; Formstecher, P; Lefebvre, P

    1997-01-01

    The binding of natural or synthetic ligands to nuclear receptors is the triggering event leading to gene transcription activation or repression. Ligand binding to the ligand binding domain of these receptors induces conformational changes that are evidenced by an increased resistance of this domain to proteases. In vitro labeled receptors were incubated with various synthetic or natural agonists or antagonists and submitted to trypsin digestion. Proteolysis products were separated by SDS-PAGE and quantified. The amount of trypsin-resistant fragments was proportional to receptor occupancy by the ligand, and allowed the determination of dissociation constants (kDa). Using the wild-type or mutated human retinoic acid receptor alpha as a model, kDa values determined by classical competition binding assays using tritiated ligands are in agreement with those measured by the proteolytic assay. This method was successfully extended to human retinoic X receptor alpha, glucocorticoid receptor, and progesterone receptor, thus providing a basis for a new, faster assay to determine simultaneously the affinity and conformation of receptors when bound to a given ligand.

  13. Directed evolution to low nanomolar affinity of a tumor-targeting epidermal growth factor receptor-binding affibody molecule.

    PubMed

    Friedman, Mikaela; Orlova, Anna; Johansson, Eva; Eriksson, Tove L J; Höidén-Guthenberg, Ingmarie; Tolmachev, Vladimir; Nilsson, Fredrik Y; Ståhl, Stefan

    2008-03-01

    The epidermal growth factor receptor 1 (EGFR) is overexpressed in various malignancies and is associated with a poor patient prognosis. A small, receptor-specific, high-affinity imaging agent would be a useful tool in diagnosing malignant tumors and in deciding upon treatment and assessing the response to treatment. We describe here the affinity maturation procedure for the generation of Affibody molecules binding with high affinity and specificity to EGFR. A library for affinity maturation was constructed by rerandomization of selected positions after the alignment of first-generation binding variants. New binders were selected with phage display technology, using a single oligonucleotide in a single-library effort, and the best second-generation binders had an approximately 30-fold improvement in affinity (K(d)=5-10 nM) for the soluble extracellular domain of EGFR in biospecific interaction analysis using Biacore. The dissociation equilibrium constant, K(d), was also determined for the Affibody with highest affinity using EGFR-expressing A431 cells in flow cytometric analysis (K(d)=2.8 nM). A retained high specificity for EGFR was verified by a dot blot assay showing staining only of EGFR proteins among a panel of serum proteins and other EGFR family member proteins (HER2, HER3, and HER4). The EGFR-binding Affibody molecules were radiolabeled with indium-111, showing specific binding to EGFR-expressing A431 cells and successful targeting of the A431 tumor xenografts with 4-6% injected activity per gram accumulated in the tumor 4 h postinjection. PMID:18207161

  14. Two high-affinity ligand binding states of uterine estrogen receptor distinguished by modulation of hydrophobic environment

    SciTech Connect

    Hutchens, T.W.; Li, C.M.; Zamah, N.M.; Besch, P.K.

    1987-02-10

    The steroid binding function of soluble (cytosolic) estrogen receptors from calf uteri was evaluated under conditions known to modify the extent of hydrophobic interaction with receptor-associated proteins. Receptor preparations were equilibrated into 6 M urea buffers and control buffers by chromatography through small columns of Sephadex G-25 or by dialysis at 0.6 /sup 0/C. Equilibrium dissociation constants (K/sub d/) and binding capacities (n) of experimental and control receptor preparations were determined by 13-point Scatchard analyses using concentrations of 17..beta..-(/sup 3/H)estradiol from 0.05 to 10 nM. Nonspecific binding was determined at each concentration by parallel incubations with a 200-fold molar excess of the receptor-specific competitor diethylstilbestrol. The control receptor population was consistently found to be a single class of binding sites with a high affinity for estradiol which was unaffected by G-25 chromatography, by dialysis, by dilution, or by the presence of 0.4 M KCl. However, equilibration into 6 M urea induced a discrete (10-fold) reduction in receptor affinity to reveal a second, thermodynamically stable, high-affinity binding state. The presence of 0.4 M KCl did not significantly influence the discrete change in receptor affinity induced by urea. The effects of urea on both receptor affinity and binding capacity were reversible, suggesting a lack of covalent modification. These results demonstrate nonenzymatic means by which not only the binding capacity but also the affinity of receptor for estradiol can be reversibly controlled, suggesting that high concentrations of urea might be more effectively utilized during the physicochemical characterization and purification of steroid receptor proteins.

  15. Observed drug-receptor association rates are governed by membrane affinity: the importance of establishing "micro-pharmacokinetic/pharmacodynamic relationships" at the β2-adrenoceptor.

    PubMed

    Sykes, David A; Parry, Cheryl; Reilly, John; Wright, Penny; Fairhurst, Robin A; Charlton, Steven J

    2014-04-01

    Current pharmacological models for determining affinity and kinetics of drugs for membrane receptors assume the interacting molecules are homogeneously distributed in the bulk aqueous phase. The phospholipid membrane can, however, provide a second compartment into which drugs can partition, particularly lipophilic/basic compounds. In this study we measured the phospholipid affinity and receptor binding kinetics of several clinically relevant β2-adrenoceptor agonists and antagonists and demonstrated that the degree of phospholipid interaction directly affects the observed kinetic association rate (k on) and dissociation constant (Kd), but not the dissociation rate (k off) from the target, by concentrating drug in the local environment around the receptor. When the local drug concentration was accounted for, the k on was comparable across the cohort and the corrected Kd was directly related to the k off. In conclusion, we propose a new approach to determining the pharmacology of drugs for membrane targets that accounts for differences in local drug concentration brought about by direct affinity for phospholipids, establishing "micro-pharmacokinetic/pharmacodynamic relationships" for drugs.

  16. Affine projective Osserman structures

    NASA Astrophysics Data System (ADS)

    Gilkey, P.; Nikčević, S.

    2013-08-01

    By considering the projectivized spectrum of the Jacobi operator, we introduce the concept of projective Osserman manifold in both the affine and in the pseudo-Riemannian settings. If M is an affine projective Osserman manifold, then the deformed Riemannian extension metric on the cotangent bundle is both spacelike and timelike projective Osserman. Since any rank-1-symmetric space is affine projective Osserman, this provides additional information concerning the cotangent bundle of a rank-1 Riemannian symmetric space with the deformed Riemannian extension metric. We construct other examples of affine projective Osserman manifolds where the Ricci tensor is not symmetric and thus the connection in question is not the Levi-Civita connection of any metric. If the dimension is odd, we use methods of algebraic topology to show the Jacobi operator of an affine projective Osserman manifold has only one non-zero eigenvalue and that eigenvalue is real.

  17. II. Dissociation free energies in drug-receptor systems via nonequilibrium alchemical simulations: application to the FK506-related immunophilin ligands.

    PubMed

    Nerattini, Francesca; Chelli, Riccardo; Procacci, Piero

    2016-06-01

    The recently proposed fast switching double annihilation (FS-DAM) [Cardelli et al., J. Chem. Theory Comput., 2015, 11, 423] is aimed at computing the absolute standard dissociation free energies for the chemical equilibrium RL ⇌ R + L occurring in solution through molecular dynamics (MD) simulations at the atomistic level. The technique is based on the production of fast nonequilibrium annihilation trajectories of one of the species (the ligand) in the solvated RL complex and in the bulk solvent. As detailed in the companion theoretical paper, the free energies of these two nonequilibrium annihilation processes are recovered by using an unbiased unidirectional estimate derived from the Crooks theorem exploiting the inherent Gaussian nature of the annihilation work. The FS-DAM technique was successfully applied to the evaluation of the dissociation free energy of the complexes of Zn(ii) cations with an inhibitor of the Tumor Necrosis Factor α converting enzyme. Here we apply the technique to a real drug-receptor system, by satisfactorily reproducing the experimental dissociation free energies of FK506-related bulky ligands towards the native FKBP12 enzyme and by predicting the dissociation constants for the same ligands towards the mutant I56D. The effect of such mutations on the binding affinity of FK506-related ligands is relevant for assessing the thermodynamic forces regulating molecular recognition in FKBP12 inhibition. PMID:27193181

  18. Molecular Basis of Ligand Dissociation from the Adenosine A2A Receptor.

    PubMed

    Guo, Dong; Pan, Albert C; Dror, Ron O; Mocking, Tamara; Liu, Rongfang; Heitman, Laura H; Shaw, David E; IJzerman, Adriaan P

    2016-05-01

    How drugs dissociate from their targets is largely unknown. We investigated the molecular basis of this process in the adenosine A2Areceptor (A2AR), a prototypical G protein-coupled receptor (GPCR). Through kinetic radioligand binding experiments, we characterized mutant receptors selected based on molecular dynamic simulations of the antagonist ZM241385 dissociating from the A2AR. We discovered mutations that dramatically altered the ligand's dissociation rate despite only marginally influencing its binding affinity, demonstrating that even receptor features with little contribution to affinity may prove critical to the dissociation process. Our results also suggest that ZM241385 follows a multistep dissociation pathway, consecutively interacting with distinct receptor regions, a mechanism that may also be common to many other GPCRs.

  19. Binding of L-(/sup 3/H)nicotine to a single class of high affinity sites in rat brain membranes

    SciTech Connect

    Lippiello, P.M.; Fernandes, K.G.

    1986-05-01

    The binding of optically pure L-(/sup 3/H)nicotine to rat brain membrane preparations was studied using a rapid filtration method. The binding properties observed depended on the method used for tissue isolation. The most consistent results were obtained with membranes prepared in the presence of protease inhibitors, without divalent cations. Binding was saturable, reversible, and stereospecific. Scatchard analysis revealed a single class of high affinity sites with an average KD of 2 nM and a Bmax of approximately 200 fmol/mg of protein. The Hill coefficient was near unity. The KD calculated from the kinetic rate constants for association (k1 = 0.012 min-1 nM-1) and dissociation (k-1 = 0.04 min-1) was around 3 nM, in good agreement with the dissociation constant determined from equilibrium binding. In competition studies, cholinergic agonists were generally the most effective in inhibiting L-(/sup 3/H)nicotine binding, whereas antagonists were relatively ineffective. The D-isomer of nicotine was about 60-fold less potent than the L-isomer in inhibiting binding. The results were unaffected by temperature, with the exception that Bmax was somewhat lower at 37 degrees. The equilibrium binding properties of these sites were essentially identical in adult male and female brain. However, Bmax was lower in fetal brain tissue. The present findings are consistent with the idea that there is a single class of high affinity nicotinic binding sites in rat brain with cholinoceptive properties.

  20. Mathematical model accurately predicts protein release from an affinity-based delivery system.

    PubMed

    Vulic, Katarina; Pakulska, Malgosia M; Sonthalia, Rohit; Ramachandran, Arun; Shoichet, Molly S

    2015-01-10

    Affinity-based controlled release modulates the delivery of protein or small molecule therapeutics through transient dissociation/association. To understand which parameters can be used to tune release, we used a mathematical model based on simple binding kinetics. A comprehensive asymptotic analysis revealed three characteristic regimes for therapeutic release from affinity-based systems. These regimes can be controlled by diffusion or unbinding kinetics, and can exhibit release over either a single stage or two stages. This analysis fundamentally changes the way we think of controlling release from affinity-based systems and thereby explains some of the discrepancies in the literature on which parameters influence affinity-based release. The rate of protein release from affinity-based systems is determined by the balance of diffusion of the therapeutic agent through the hydrogel and the dissociation kinetics of the affinity pair. Equations for tuning protein release rate by altering the strength (KD) of the affinity interaction, the concentration of binding ligand in the system, the rate of dissociation (koff) of the complex, and the hydrogel size and geometry, are provided. We validated our model by collapsing the model simulations and the experimental data from a recently described affinity release system, to a single master curve. Importantly, this mathematical analysis can be applied to any single species affinity-based system to determine the parameters required for a desired release profile. PMID:25449806

  1. Dissociation as complex adaptation.

    PubMed

    Sel, R

    1997-03-01

    In this article the general theory of complex adaptive systems, substantiated by non-linear dynamics, will be used to put the dissociative disorders into a theoretical framework and clarify their genesis and presentation. When a system is far out of equilibrium, dissipative structures may be formed ('order out of chaos', as Prigogine (1) has put it). These structures provide the starting point for further evolution and co-evolution of competing groups of functional schemata divided on a bifurcation surface. Complex adaptation is almost inevitable in a complicated system (such as the brain) driven by non-linear dynamics. Dissociation is thus regarded as a consequence of adaptation to a chaotic environment rich in contrasts. In a sufficiently complex environment a person with dissociative identity disorder is more adapted and thus more likely to occur than a 'normal' monopersonality individual.

  2. The serotonin transporter: Examination of the changes in transporter affinity induced by ligand binding

    SciTech Connect

    Humphreys, C.J.

    1989-01-01

    The plasmalemmal serotonin transporter uses transmembrane gradients of Na{sup +}, Cl{sup {minus}} and K{sup +} to accumulate serotonin within blood platelets. Transport is competitively inhibited by the antidepressant imipramine. Like serotonin transport, imipramine binding requires Na{sup +}. Unlike serotonin, however, imipramine does not appear to be transported. To gain insight into the mechanism of serotonin transport the author have analyzed the influences of Na{sup +} and Cl{sup {minus}}, the two ions cotransported with serotonin, on both serotonin transport and the interaction of imipramine and other antidepressant drugs with the plasmalemmal serotonin transporter of human platelets. Additionally, the author have synthesized, purified and characterized the binding of 2-iodoimipramine to the serotonin transporter. Finally, the author have conducted a preliminary study of the inhibition of serotonin transport and imipramine binding produced by dicyclohexylcarbodiimide. My results reveal many instances of positive heterotropic cooperativity in ligand binding to the serotonin transporter. Na{sup +} binding enhances the transporters affinity for imipramine and several other antidepressant drugs, and also increases the affinity for Cl{sup {minus}}. Cl{sup {minus}} enhances the transporters affinity for imipramine, as well as for Na{sup +}. At concentrations in the range of its K{sub M} for transport serotonin is a competitive inhibitor of imipramine binding. At much higher concentrations, however, serotonin also inhibits imipramines dissociation rate constant. This latter effect which is Na{sup +}-independent and species specific, is apparently produced by serotonin binding at a second, low affinity site on, or near, the transporter complex. Iodoimipramine competitively inhibit both ({sup 3}H)imipramine binding and ({sup 3}H)serotonin transport.

  3. Achieving high affinity towards a bacterial lectin through multivalent topological isomers of calix[4]arene glycoconjugates.

    PubMed

    Cecioni, Samy; Lalor, Ruth; Blanchard, Bertrand; Praly, Jean-Pierre; Imberty, Anne; Matthews, Susan E; Vidal, Sébastien

    2009-12-01

    A family of seven topologically isomeric calix[4]arene glycoconjugates was prepared through the synthesis of a series of alkyne-derivatised calix[4]arene precursors that are suitable for the attachment of sugar moieties by microwave-assisted copper(I)-catalysed azide-alkyne cycloaddition (CuAAC). The glycoconjugates thus synthesised comprised one mono-functionalised derivative, two 1,2- or 1,3-divalent regioisomers, one trivalent and three tetravalent topoisomers in the cone, partial cone or 1,3-alternate conformations. The designed glycoconjugates were evaluated as ligands for the galactose-binding lectin PA-IL from the opportunistic bacterium Pseudomonas aeruginosa, a major causative agent of lung infections in cystic fibrosis patients. Binding affinities were determined by isothermal titration calorimetry (ITC), and the interaction with the lectin was shown to be strongly dependant on both the valence and the topology. Whereas the trivalent conjugate displayed enhanced affinity when compared to a monosaccharide model, the tetravalent conjugates are to-date the highest-affinity ligands measured by ITC. The topologies presenting carbohydrates on both faces of calixarene are the most potent ones with dissociation constants of approximately 200 nM. Molecular modelling suggests that such a multivalent molecule can efficiently chelate two of the binding sites of the tetrameric lectin; this explains the 800-fold increase of affinity achieved by the tetravalent molecule. Surface plasmon resonance (SPR) experiments confirmed that this glycoconjugate is the strongest inhibitor for binding of PA-IL to galactosylated surfaces for potential applications as an anti-adhesive agent.

  4. Performance of dye-affinity beads for aluminium removal in magnetically stabilized fluidized bed

    PubMed Central

    Yavuz, Handan; Say, Ridvan; Andaç, Müge; Bayraktar, Necmi; Denizli, Adil

    2004-01-01

    Background Aluminum has recently been recognized as a causative agent in dialysis encephalopathy, osteodystrophy, and microcytic anemia occurring in patients with chronic renal failure who undergo long-term hemodialysis. Only a small amount of Al(III) in dialysis solutions may give rise to these disorders. Methods Magnetic poly(2-hydroxyethyl methacrylate) (mPHEMA) beads in the size range of 80–120 μm were produced by free radical co-polymerization of HEMA and ethylene dimethacrylate (EDMA) in the presence of magnetite particles (Fe3O4). Then, metal complexing ligand alizarin yellow was covalently attached onto mPHEMA beads. Alizarin yellow loading was 208 μmol/g. These beads were used for the removal of Al(III) ions from tap and dialysis water in a magnetically stabilized fluidized bed. Results Al(III) adsorption capacity of the beads decreased with an increase in the flow-rate. The maximum Al(III) adsorption was observed at pH 5.0. Comparison of batch and magnetically stabilized fluidized bed (MSFB) maximum capacities determined using Langmuir isotherms showed that dynamic capacity (17.5 mg/g) was somewhat higher than the batch capacity (11.8 mg/g). The dissociation constants for Al(III) were determined using the Langmuir isotherm equation to be 27.3 mM (MSFB) and 6.7 mM (batch system), indicating medium affinity, which was typical for pseudospecific affinity ligands. Al(III) ions could be repeatedly adsorbed and desorbed with these beads without noticeable loss in their Al(III) adsorption capacity. Conclusions Adsorption of Al(III) demonstrate the affinity of magnetic dye-affinity beads. The MSFB experiments allowed us to conclude that this inexpensive sorbent system may be an important alternative to the existing adsorbents in the removal of aluminium. PMID:15329149

  5. LOVTRAP: an optogenetic system for photoinduced protein dissociation.

    PubMed

    Wang, Hui; Vilela, Marco; Winkler, Andreas; Tarnawski, Miroslaw; Schlichting, Ilme; Yumerefendi, Hayretin; Kuhlman, Brian; Liu, Rihe; Danuser, Gaudenz; Hahn, Klaus M

    2016-09-01

    LOVTRAP is an optogenetic approach for reversible light-induced protein dissociation using protein A fragments that bind to the LOV domain only in the dark, with tunable kinetics and a >150-fold change in the dissociation constant (Kd). By reversibly sequestering proteins at mitochondria, we precisely modulated the proteins' access to the cell edge, demonstrating a naturally occurring 3-mHz cell-edge oscillation driven by interactions of Vav2, Rac1, and PI3K proteins. PMID:27427858

  6. Special Report: Affinity Chromatography.

    ERIC Educational Resources Information Center

    Parikh, Indu; Cuatrecasas, Pedro

    1985-01-01

    Describes the nature of affinity chromatography and its use in purifying enzymes, studying cell interactions, exploring hormone receptors, and other areas. The potential the technique may have in treating disease is also considered. (JN)

  7. Blackbody Infrared Radiative Dissociation of Protonated Oligosaccharides

    NASA Astrophysics Data System (ADS)

    Fentabil, Messele A.; Daneshfar, Rambod; Kitova, Elena N.; Klassen, John S.

    2011-12-01

    The dissociation pathways, kinetics, and energetics of protonated oligosaccharides in the gas phase were investigated using blackbody infrared radiative dissociation (BIRD). Time-resolved BIRD measurements were performed on singly protonated ions of cellohexaose (Cel6), which is composed of β-(1 → 4)-linked glucopyranose rings, and five malto-oligosaccharides (Malx, where x = 4-8), which are composed of α-(1 → 4)-linked glucopyranose units. At the temperatures investigated (85-160 °C), the oligosaccharides dissociate at the glycosidic linkages or by the loss of a water molecule to produce B- or Y-type ions. The Y ions dissociate to smaller Y or B ions, while the B ions yield exclusively smaller B ions. The sequential loss of water molecules from the smallest B ions (B1 and B2) also occurs. Rate constants for dissociation of the protonated oligosaccharides and the corresponding Arrhenius activation parameters (Ea and A) were determined. The Ea and A-factors measured for protonated Malx (x > 4) are indistinguishable within error (~19 kcal mol-1, 1010 s-1), which is consistent with the ions being in the rapid energy exchange limit. In contrast, the Arrhenius parameters for protonated Cel6 (24 kcal mol-1, 1012 s-1) are significantly larger. These results indicate that both the energy and entropy changes associated with the glycosidic bond cleavage are sensitive to the anomeric configuration. Based on the results of this study, it is proposed that formation of B and Y ions occurs through a common dissociation mechanism, with the position of the proton establishing whether a B or Y ion is formed upon glycosidic bond cleavage.

  8. [Determination of the interaction kinetics between meloxicam and β-cyclodextrin using the quantitative high-performance affinity chromatography coupled with mass spectrometry].

    PubMed

    Wang, Cai-fen; Li, Zhuo; Wang, Xiao-bo; Li, Hai-yan; Zhang, Ji-wen; Sun, Li-xin

    2015-09-01

    The association rate constant and dissociation rate constant are important parameters of the drug-cyclodextrin supermolecule systems, which determine the dissociation of drugs from the complex and the further in vivo absorption of drugs. However, the current studies of drug-cyclodextrin interactions mostly focus on the thermodynamic parameter of equilibrium constants (K). In this paper, a method based on quantitative high performance affinity chromatography coupled with mass spectrometry was developed to determine the apparent dissociation rate constant (k(off,app)) of drug-cyclodextrin supermolecule systems. This method was employed to measure the k(off,app) of meloxicam and acetaminophen. Firstly, chromatographic peaks of drugs and non-retained solute (uracil) on β-cyclodextrin column at different flow rates were acquired, and the retention time and variance values were obtained via the fitting the peaks. Then, the plate heights of drugs (H(R)) and uracil (H(M,C)) were calculated. The plate height of theoretical non-retained solute (H(M,T)) was calculated based on the differences of diffusion coefficient and the stagnant mobile phase mass transfer between drugs and uracil. Finally, the k(off,app) was calculated from the slope of the regression equation between (H(R)-H(M,T)) and uk/(1+k)2, (0.13 ± 0.00) s(-1) and (4.83 ± 0.10) s(-1) for meloxicam and acetaminophen (control drug), respectively. In addition, the apparent association rate constant (k(on,app)) was also calculated through the product of K (12.53 L x mol(-1)) and k(off,app). In summary, it has been proved that the method established in our study was simple, efficiently fast and reproducible for investigation on the kinetics of drug-cyclodextrin interactions. PMID:26757555

  9. Dissociative Identity Disorder

    ERIC Educational Resources Information Center

    Schmidt, Tom

    2007-01-01

    Few psychological disorders in the Diagnostic Statistical Manual have generated as much controversy as Dissociative Identity Disorder (DID). For the past 35 years diagnoses of DID, previously referred to as Multiple Personality Disorder (MPD), have increased exponentially, causing various psychological researchers and clinicians to question the…

  10. Dissociation: the clinical realities.

    PubMed

    Frankel, F H

    1996-07-01

    An attempt was made by the authors of DSM-III to restrict its focus to the experimental, the observable, and the measurable. The intention was to free the nosology from the influence of unproven theories, and the philosophy was driven largely by the importance of research being able to identify diagnostic categories to facilitate the study of homogeneous groups. So it is of interest that the authors accepted dissociation-an ambiguous event linked to an explicit theoretical concept that had been introduced by Janet-as the basis for classification of clinical presentations that were formerly included under the rubric of hysteria, a similarly unclear category. Since DSM-III, there have been an increasing number of reports of dissociative experiences and dissociative identity disorder (formerly known as multiple personality disorder), but neither of these clinical presentations seems able to withstand the concern that it is dramatically influenced by environmental cues, e.g., the expectations of the therapist. Thus, a restricted phenomenological perspective does not fully appreciate the distorting potential of suggestibility and imagination on the nature of the emerging clinical picture. These factors might well have contributed to and laid the conceptual groundwork for the growth in the number of reports of dissociation.

  11. Dissociation and psychosis in dissociative identity disorder and schizophrenia.

    PubMed

    Laddis, Andreas; Dell, Paul F

    2012-01-01

    Dissociative symptoms, first-rank symptoms of schizophrenia, and delusions were assessed in 40 schizophrenia patients and 40 dissociative identity disorder (DID) patients with the Multidimensional Inventory of Dissociation (MID). Schizophrenia patients were diagnosed with the Structured Clinical Interview for the DSM-IV Axis I Disorders; DID patients were diagnosed with the Structured Clinical Interview for DSM-IV Dissociative Disorders-Revised. DID patients obtained significantly (a) higher dissociation scores; (b) higher passive-influence scores (first-rank symptoms); and (c) higher scores on scales that measure child voices, angry voices, persecutory voices, voices arguing, and voices commenting. Schizophrenia patients obtained significantly higher delusion scores than did DID patients. What is odd is that the dissociation scores of schizophrenia patients were unrelated to their reports of childhood maltreatment. Multiple regression analyses indicated that 81% of the variance in DID patients' dissociation scores was predicted by the MID's Ego-Alien Experiences Scale, whereas 92% of the variance in schizophrenia patients' dissociation scores was predicted by the MID's Voices Scale. We propose that schizophrenia patients' responses to the MID do not index the same pathology as do the responses of DID patients. We argue that neither phenomenological definitions of dissociation nor the current generation of dissociation instruments (which are uniformly phenomenological in nature) can distinguish between the dissociative phenomena of DID and what we suspect are just the dissociation-like phenomena of schizophrenia.

  12. Pathological Dissociation as Measured by the Child Dissociative Checklist

    ERIC Educational Resources Information Center

    Wherry, Jeffrey N.; Neil, Debra A.; Taylor, Tamara N.

    2009-01-01

    The component structure of the Child Dissociative Checklist was examined among abused children. A factor described as pathological dissociation emerged that was predicted by participants being male. There also were differences in pathological dissociation between groups of sexually abused and physically abused children. Replication of this factor…

  13. Evaluation of kinetic constants of biomolecular interaction on optical surface plasmon resonance sensor with Newton Iteration Method

    NASA Astrophysics Data System (ADS)

    Zhao, Yuanyuan; Jiang, Guoliang; Hu, Jiandong; Hu, Fengjiang; Wei, Jianguang; Shi, Liang

    2010-10-01

    In the immunology, there are two important types of biomolecular interaction: antigens-antibodies and receptors-ligands. Monitoring the response rate and affinity of biomolecular interaction can help analyze the protein function, drug discover, genomics and proteomics research. Moreover the association rate constant and dissociation rate constant of receptors-ligands are the important parameters for the study of signal transmission between cells. Recent advances in bioanalyzer instruments have greatly simplified the measurement of the kinetics of molecular interactions. Non-destructive and real-time monitoring the response to evaluate the parameters between antigens and antibodies can be performed by using optical surface plasmon resonance (SPR) biosensor technology. This technology provides a quantitative analysis that is carried out rapidly with label-free high-throughput detection using the binding curves of antigens-antibodies. Consequently, the kinetic parameters of interaction between antigens and antibodies can be obtained. This article presents a low cost integrated SPR-based bioanalyzer (HPSPR-6000) designed by ourselves. This bioanalyzer is mainly composed of a biosensor TSPR1K23, a touch-screen monitor, a microprocessor PIC24F128, a microflow cell with three channels, a clamp and a photoelectric conversion device. To obtain the kinetic parameters, sensorgrams may be modeled using one of several binding models provided with BIAevaluation software 3.0, SensiQ or Autolab. This allows calculation of the association rate constant (ka) and the dissociation rate constant (kd). The ratio of ka to kd can be used to estimate the equilibrium constant. Another kind is the analysis software OriginPro, which can process the obtained data by nonlinear fitting and then get some correlative parameters, but it can't be embedded into the bioanalyzer, so the bioanalyzer don't support the use of OriginPro. This paper proposes a novel method to evaluate the kinetic parameters

  14. Affine group formulation of the Standard Model coupled to gravity

    SciTech Connect

    Chou, Ching-Yi; Ita, Eyo; Soo, Chopin

    2014-04-15

    In this work we apply the affine group formalism for four dimensional gravity of Lorentzian signature, which is based on Klauder’s affine algebraic program, to the formulation of the Hamiltonian constraint of the interaction of matter and all forces, including gravity with non-vanishing cosmological constant Λ, as an affine Lie algebra. We use the hermitian action of fermions coupled to gravitation and Yang–Mills theory to find the density weight one fermionic super-Hamiltonian constraint. This term, combined with the Yang–Mills and Higgs energy densities, are composed with York’s integrated time functional. The result, when combined with the imaginary part of the Chern–Simons functional Q, forms the affine commutation relation with the volume element V(x). Affine algebraic quantization of gravitation and matter on equal footing implies a fundamental uncertainty relation which is predicated upon a non-vanishing cosmological constant. -- Highlights: •Wheeler–DeWitt equation (WDW) quantized as affine algebra, realizing Klauder’s program. •WDW formulated for interaction of matter and all forces, including gravity, as affine algebra. •WDW features Hermitian generators in spite of fermionic content: Standard Model addressed. •Constructed a family of physical states for the full, coupled theory via affine coherent states. •Fundamental uncertainty relation, predicated on non-vanishing cosmological constant.

  15. Affinity ligands for glycoprotein purification based on the multi-component Ugi reaction.

    PubMed

    Chen, Chen; Khoury, Graziella El; Lowe, Christopher R

    2014-10-15

    One challenge facing the purification of therapeutic glycoproteins by affinity chromatography is creating ligands specific for the glycan moiety. Affinity chromatography of glycoproteins is currently conducted with immobilized lectins or boronates, although biomimetic ligands could present a more desirable option. This work describes the rational design and combinatorial synthesis of carbohydrate-binding ligands based on the solid phase multi-component Ugi reaction. An aldehyde-functionalized Sepharose™ solid support constitutes one component (aldehyde) in the four-component reaction, while the other three components (a primary/secondary amine, a carboxylic acid and an isocyanide) are varied in a combinatorial fashion to generate a tri-substituted Ugi scaffold which provides a degree of rigidity and is functionally suitable for interacting with the glycan moiety of glycoproteins. An Ugi library containing 48 ligands was initially screened against glucose oxidase (GOx) as the model glycoprotein to identify a candidate ligand, A13C24I8, which showed affinity to GOx through its carbohydrate moiety. Immobilized ligand A13C24I8 demonstrated a static binding capacity of 16.7mg GOx/ml resin and an apparent dissociation constant (Kd) of 1.45×10(-6)M at pH 7.4. The adsorbent can also bind 8.1mg AGP/ml resin and displays an apparent affinity constant Kd=1.44×10(-5)M. The ligand has a sugar specificity in the following sequence: sorbitol>fructose>mannitol>ribose>arabinose>xylose>galactose>mannose>glucose>fructose; however, it did not display any specificity for sialic acid or methyl α-D-glycosides. A control ligand, generated by substitution of C24 (3-carboxyphenylboronic acid) with C7 (4-hydroxyphenyl acetic acid), failed to show affinity to the carbohydrate moiety, supporting the importance of the role that boronic acid group plays in sugar binding. GOx spiked E. coli samples were loaded onto immobilized ligand A13C24I8, 3-aminophenylboronic acid (APBA) and

  16. Affinity ligands for glycoprotein purification based on the multi-component Ugi reaction.

    PubMed

    Chen, Chen; Khoury, Graziella El; Lowe, Christopher R

    2014-10-15

    One challenge facing the purification of therapeutic glycoproteins by affinity chromatography is creating ligands specific for the glycan moiety. Affinity chromatography of glycoproteins is currently conducted with immobilized lectins or boronates, although biomimetic ligands could present a more desirable option. This work describes the rational design and combinatorial synthesis of carbohydrate-binding ligands based on the solid phase multi-component Ugi reaction. An aldehyde-functionalized Sepharose™ solid support constitutes one component (aldehyde) in the four-component reaction, while the other three components (a primary/secondary amine, a carboxylic acid and an isocyanide) are varied in a combinatorial fashion to generate a tri-substituted Ugi scaffold which provides a degree of rigidity and is functionally suitable for interacting with the glycan moiety of glycoproteins. An Ugi library containing 48 ligands was initially screened against glucose oxidase (GOx) as the model glycoprotein to identify a candidate ligand, A13C24I8, which showed affinity to GOx through its carbohydrate moiety. Immobilized ligand A13C24I8 demonstrated a static binding capacity of 16.7mg GOx/ml resin and an apparent dissociation constant (Kd) of 1.45×10(-6)M at pH 7.4. The adsorbent can also bind 8.1mg AGP/ml resin and displays an apparent affinity constant Kd=1.44×10(-5)M. The ligand has a sugar specificity in the following sequence: sorbitol>fructose>mannitol>ribose>arabinose>xylose>galactose>mannose>glucose>fructose; however, it did not display any specificity for sialic acid or methyl α-D-glycosides. A control ligand, generated by substitution of C24 (3-carboxyphenylboronic acid) with C7 (4-hydroxyphenyl acetic acid), failed to show affinity to the carbohydrate moiety, supporting the importance of the role that boronic acid group plays in sugar binding. GOx spiked E. coli samples were loaded onto immobilized ligand A13C24I8, 3-aminophenylboronic acid (APBA) and

  17. Affinity purification of human granulocyte macrophage colony-stimulating factor receptor alpha-chain. Demonstration of binding by photoaffinity labeling

    SciTech Connect

    Chiba, S.; Shibuya, K.; Miyazono, K.; Tojo, A.; Oka, Y.; Miyagawa, K.; Takaku, F. )

    1990-11-15

    The human granulocyte macrophage colony-stimulating factor (GM-CSF) receptor alpha-chain, a low affinity component of the receptor, was solubilized and affinity-purified from human placenta using biotinylated GM-CSF. Scatchard analysis of {sup 125}I-GM-CSF binding to the placental membrane extract disclosed that the GM-CSF receptor had a dissociation constant (Kd) of 0.5-0.8 nM, corresponding to the Kd value of the GM-CSF receptor alpha-chain on the intact placental membrane. Affinity labeling of the solubilized protein using a photoreactive cross-linking agent, N-hydroxysuccinimidyl-4-azidobenzoate (HSAB), demonstrated a single specific band of 70-95 kDa representing a ligand-receptor complex. Approximately 2 g of the placental membrane extract was subjected to a biotinylated GM-CSF-fixed streptavidin-agarose column, resulting in a single major band at 70 kDa on a silver-stained sodium dodecyl sulfate gel. The radioiodination for the purified material disclosed that the purified protein had an approximate molecular mass of 70 kDa and a pI of 6.6. Binding activity of the purified material was demonstrated by photoaffinity labeling using HSAB-{sup 125}I-GM-CSF, producing a similar specific band at 70-95 kDa as was demonstrated for the crude protein.

  18. Crystal structure and ligand affinity of avidin in the complex with 4‧-hydroxyazobenzene-2-carboxylic acid

    NASA Astrophysics Data System (ADS)

    Strzelczyk, Paweł; Bujacz, Grzegorz

    2016-04-01

    Avidin is a protein found in egg white that binds numerous organic compounds with high affinity, especially biotin and its derivatives. Due to its extraordinary affinity for its ligands, avidin is extensively used in biotechnology. X-ray crystallography and fluorescence-based biophysical techniques were used to show that avidin binds the dye 4‧-hydroxyazobenzene-2-carboxylic acid (HABA) with a lower affinity than biotin. The apparent dissociation constant determined for the avidin complex with HABA by microscale thermophoresis (MST) is 4.12 μM. The crystal structure of avidin-HABA complex was determined at a resolution of 2.2 Å (PDB entry 5chk). The crystals belong to a hexagonal system, in the space group P6422. In that structure, the hydrazone tautomer of HABA is bound at the bottom part of the central calyx near the polar residues. We show interactions of the dye with avidin and compare them with the previously reported avidin-biotin complex.

  19. Selection of ceramic fluorapatite-binding peptides from a phage display combinatorial peptide library: optimum affinity tags for fluorapatite chromatography.

    PubMed

    Islam, Tuhidul; Bibi, Noor Shad; Vennapusa, Rami Reddy; Fernandez-Lahore, Marcelo

    2013-08-01

    Peptide affinity tags have become efficient tools for the purification of recombinant proteins from biological mixtures. The most commonly used ligands in this type of affinity chromatography are immobilized metal ions, proteins, antibodies, and complementary peptides. However, the major bottlenecks of this technique are still related to the ligands, including their low stability, difficulties in immobilization, and leakage into the final products. A model approach is presented here to overcome these bottlenecks by utilizing macroporous ceramic fluorapatite (CFA) as the stationary phase in chromatography and the CFA-specific short peptides as tags. The CFA chromatographic materials act as both the support matrix and the ligand. Peptides that bind with affinity to CFA were identified from a randomized phage display heptapeptide library. A total of five rounds of phage selection were performed. A common N-terminal sequence was found in two selected peptides: F4-2 (KPRSMLH) and F5-4 (KPRSVSG). The peptide F5-4, displayed by more than 40% of the phages analyzed in the fifth round of selection, was subjected to further studies. Selectivity of the peptide for the chemical composition and morphology of CFA was assured by the adsorption studies. The dissociation constant, obtained from the F5-4/CFA adsorption isotherm, was in the micromolar range, and the maximum capacity was 39.4 nmol/mg. The chromatographic behavior of the peptides was characterized on a CFA stationary phase with different buffers. Preferential affinity and specific retention properties suggest the possible application of the phage-derived peptides as a tag in CFA affinity chromatography for enhancing the selective recovery of proteins.

  20. Isomer-Specific Binding Affinity of Perfluorooctanesulfonate (PFOS) and Perfluorooctanoate (PFOA) to Serum Proteins.

    PubMed

    Beesoon, Sanjay; Martin, Jonathan W

    2015-05-01

    Perfluorooctanesulfonate (PFOS) and perfluorooctanoate (PFOA) are among the most prominent contaminants in human serum, and these were historically manufactured as technical mixtures of linear and branched isomers. The isomers display unique pharmacokinetics in humans and in animal models, but molecular mechanisms underlying isomer-specific PFOS and PFOA disposition have not previously been studied. Here, ultrafiltration devices were used to examine (i) the dissociation constants (Kd) of individual PFOS and PFOA isomers with human serum albumin (HSA) and (ii) relative binding affinity of isomers in technical mixtures spiked to whole calf serum and human serum. Measurement of HSA Kd's demonstrated that linear PFOS (Kd=8(±4)×10(-8) M) was much more tightly bound than branched PFOS isomers (Kd range from 8(±1)×10(-5) M to 4(±2)×10(-4) M). Similarly, linear PFOA (Kd=1(±0.9)×10(-4) M) was more strongly bound to HSA compared to branched PFOA isomers (Kd range from 4(±2)×10(-4) M to 3(±2)×10(-4) M). The higher binding affinities of linear PFOS and PFOA to total serum protein were confirmed when both calf serum and human serum were spiked with technical mixtures. Overall, these data provide a mechanistic explanation for the longer biological half-life of PFOS in humans, compared to PFOA, and for the higher transplacental transfer efficiencies and renal clearance of branched PFOS and PFOA isomers, compared to the respective linear isomer.

  1. Affinity of neuroleptics for D1 receptor of human brain striatum.

    PubMed Central

    Kanba, S; Suzuki, E; Nomura, S; Nakaki, T; Yagi, G; Asai, M; Richelson, E

    1994-01-01

    We determined the inhibition-dissociation constant (Ki) of a number of neuroleptics for D1 receptors of normal human brain tissue using [3H]SCH23390 [R-(+)-8-chloro-2,3,4,5-tetrahydro-3-methyl-5-phenyl-1H-3[benzazepine-7- ol]. SCH23390 had the highest affinity with a Ki of 0.76 nM. Among clinically used drugs, propericiazine showed the highest affinity with a Ki of 10 nM. When neuroleptics were classified according to chemical structures, the Ki values were as follows. Phenothiazines ranged from 10 nM to 250 nM. Butyrophenones ranged from 45 nM to 250 nM. Thioxanthenes ranged from 12 nM to 340 nM. Orthopramines were more than 10,000 nM. The Ki values for the binding site of this study were significantly correlated with those reported in studies using animal brain. The possible relationship between D1 receptors and negative symptoms is discussed. PMID:7918347

  2. Hsp70 chaperones are non-equilibrium machines that achieve ultra-affinity by energy consumption.

    PubMed

    De Los Rios, Paolo; Barducci, Alessandro

    2014-05-27

    70-kDa Heat shock proteins are ATP-driven molecular chaperones that perform a myriad of essential cellular tasks. Although structural and biochemical studies have shed some light on their functional mechanism, the fundamental issue of the role of energy consumption, due to ATP-hydrolysis, has remained unaddressed. Here we establish a clear connection between the non-equilibrium nature of Hsp70, due to ATP hydrolysis, and the determining feature of its function, namely its high affinity for its substrates. Energy consumption can indeed decrease the dissociation constant of the chaperone-substrate complex by several orders of magnitude with respect to an equilibrium scenario. We find that the biochemical requirements for observing such ultra-affinity coincide with the physiological conditions in the cell. Our results rationalize several experimental observations and pave the way for further analysis of non-equilibrium effects underlying chaperone functions.DOI: http://dx.doi.org/10.7554/eLife.02218.001.

  3. High-affinity receptors for bombesin-like peptides in normal guinea pig lung membranes

    SciTech Connect

    Lach, E.; Trifilieff, A.; Landry, Y.; Gies, J.P. )

    1991-01-01

    The binding of the radiolabeled bombesin analogue ({sup 125}I-Tyr{sup 4})bombesin to guinea-pig lung membranes was investigated. Binding of ({sup 125}I-Tyr{sup 4})bombesin was specific, saturable, reversible and linearly related to the protein concentration. Scatchard analysis of equilibrium binding data at 25C indicated the presence of a single class of non-interacting binding sites for bombesin (B{sub max} = 7.7 fmol/mg protein). The value of the equilibrium dissociation constant (K{sub D} = 90 pM) agrees with a high-affinity binding site. Bombesin and structurally related peptides such as ({sup 125}I-Tyr{sup 4})bombesin, neuromedin B and neuromedin C inhibited the binding of ({sup 125}I-Tyr{sup 4})bombesin in an order of potencies as follows: ({sup 125}I-Tyr{sup 4})bombesin {gt} bombesin {ge} neuromedin C {much gt} neuromedin B. These results indicate that guinea-pig lung membranes possess a single class of bombesin receptors with a high affinity for bombesin and a lower one for neuromedin B.

  4. Three dimensions of dissociative amnesia.

    PubMed

    Dell, Paul F

    2013-01-01

    Principal axis factor analysis with promax rotation extracted 3 factors from the 42 memory and amnesia items of the Multidimensional Inventory of Dissociation (MID) database (N = 2,569): Discovering Dissociated Actions, Lapses of Recent Memory and Skills, and Gaps in Remote Memory. The 3 factors' shared variance ranged from 36% to 64%. Construed as scales, the 3 factor scales had Cronbach's alpha coefficients of .96, .94, and .93, respectively. The scales correlated strongly with mean Dissociative Experiences Scale scores, mean MID scores, and total scores on the Structured Clinical Interview for DSM-IV Dissociative Disorders-Revised (SCID-D-R). What is interesting is that the 3 amnesia factors exhibited a range of correlations with SCID-D-R Amnesia scores (.52, .63, and .70, respectively), suggesting that the SCID-D-R Amnesia score emphasizes gaps in remote memory over amnesias related to dissociative identity disorder. The 3 amnesia factor scales exhibited a clinically meaningful pattern of significant differences among dissociative identity disorder, dissociative disorder not otherwise specified-1, dissociative amnesia, depersonalization disorder, and nonclinical participants. The 3 amnesia factors may have greater clinical utility for frontline clinicians than (a) amnesia as discussed in the context of the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, nosology of the dissociative disorders or (b) P. Janet's (1893/1977 ) 4-fold classification of dissociative amnesia. The author recommends systematic study of the phenomenological differences within specific dissociative symptoms and their differential relationship to specific dissociative disorders. PMID:23282045

  5. Three dimensions of dissociative amnesia.

    PubMed

    Dell, Paul F

    2013-01-01

    Principal axis factor analysis with promax rotation extracted 3 factors from the 42 memory and amnesia items of the Multidimensional Inventory of Dissociation (MID) database (N = 2,569): Discovering Dissociated Actions, Lapses of Recent Memory and Skills, and Gaps in Remote Memory. The 3 factors' shared variance ranged from 36% to 64%. Construed as scales, the 3 factor scales had Cronbach's alpha coefficients of .96, .94, and .93, respectively. The scales correlated strongly with mean Dissociative Experiences Scale scores, mean MID scores, and total scores on the Structured Clinical Interview for DSM-IV Dissociative Disorders-Revised (SCID-D-R). What is interesting is that the 3 amnesia factors exhibited a range of correlations with SCID-D-R Amnesia scores (.52, .63, and .70, respectively), suggesting that the SCID-D-R Amnesia score emphasizes gaps in remote memory over amnesias related to dissociative identity disorder. The 3 amnesia factor scales exhibited a clinically meaningful pattern of significant differences among dissociative identity disorder, dissociative disorder not otherwise specified-1, dissociative amnesia, depersonalization disorder, and nonclinical participants. The 3 amnesia factors may have greater clinical utility for frontline clinicians than (a) amnesia as discussed in the context of the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, nosology of the dissociative disorders or (b) P. Janet's (1893/1977 ) 4-fold classification of dissociative amnesia. The author recommends systematic study of the phenomenological differences within specific dissociative symptoms and their differential relationship to specific dissociative disorders.

  6. Subunit affinities and stoichiometries of the human papillomavirus type 11 E1:E2:DNA complex.

    PubMed

    Chao, S F; Rocque, W J; Daniel, S; Czyzyk, L E; Phelps, W C; Alexander, K A

    1999-04-01

    The association between the papillomavirus E1 and E2 proteins is an important regulatory interaction, imparting coordinated control of viral transcription and replication. Using fluorescence polarization, we have characterized the interactions between HPV-11 E1, HPV-11 E2, and DNA in solution at equilibrium. For these studies, two double-stranded fluorescein-labeled oligonucleotides were prepared. The first fluorescent oligonucleotide, designated Fl-E2BS and containing a single E2 binding-site palindrome (ACCGN6CGGT), was used to determine the affinity of E2 for its DNA binding site. HPV-11 E2 bound Fl-E2BS with an apparent Kd of 0.84 nM. Binding was saturable and consistent with a single class of noninteracting sites. The second oligonucleotide, designated Fl-E1E2BS, contained both E1 and E2 sites in sequence derived directly from the HPV-11 origin of replication. Under titration conditions identical to those used for Fl-E2BS, the E2 protein exhibited reduced affinity for Fl-E1E2BS (Kd > 100 nM). E1 binding to Fl-E1E2BS was of very low affinity. Addition of excess HPV-11 E1 to Fl-E1E2BS lowered the dissociation constant for the E2:Fl-E1E2BS interaction to 2 nM. This effect was not dependent upon ATP or magnesium ion. Fluorescence polarization and other data suggest formation of a complex containing six E1 molecules and a single dimer of E2 bound to a single Fl-E1E2BS oligonucleotide; E2 dissociation from the final complex did not occur. In summary, physical interaction between E1 and E2 increases the DNA binding affinity of each. The role of this energy coupling may be to promote origin-specific binding of both E1 and E2 to DNA.

  7. Determination of individual proton affinities of ofloxacin from its UV-Vis absorption, fluorescence and charge-transfer spectra: effect of inclusion in beta-cyclodextrin on the proton affinities.

    PubMed

    Ghosh, Bankim Chandra; Deb, Nipamanjari; Mukherjee, Asok K

    2010-08-01

    Individual proton affinities of the four dissociable functional groups of (+/-)-9-fluoro-2,3-dihydro-3-methyl-10-(4-methyl-1-piperazinyl)-7-oxo-7H-pyrido[1,2,3-de]-1,4-benzoxazine-6-carboxylic acid (commonly called "ofloxacin" and to be denoted henceforth as OflH), have been determined from the pH-dependent variation of the UV-vis absorption and fluorescence spectra of the compound itself and of its charge transfer complexes (CT) with p-bromanil and p-chloranil (in aqueous medium containing 0.1% ethanol, v/v). To utilize the CT spectra for determination of the proton affinity of the anilinic N, the CT absorption band of the ofloxacin-p-bromanil complex has been studied by changing the pH of the medium. Further, the effect of inclusion on the proton affinities of the four dissociable groups of OflH has been studied in presence of beta-cyclodextrin (beta-CD). Two pK(a) values corresponding to anilinic and tertiary N atoms change, whereas those corresponding to phenolic -OH and aromatic -COOH groups remain unchanged by the addition of beta-CD, a fact that indicates partial inclusion of the ofloxacin molecule in beta-CD. Formation constant and related thermodynamic parameters for the OflH(2)(+).beta-CD inclusion complex in aqueous solution have been determined from absorption intensities. A general relation between pK(a) values of guests having proton-releasing functional groups and formation constants of the inclusion complexes of the protonated and deprotonated forms with a host molecule has been utilized for determination of the formation constant of the OflH(3)(+2).beta-CD complex from the pK(a) values of OflH(3)(+2) in the presence and absence of beta-CD, along with the formation constant of the OflH(2)(+).beta-CD complex. Results of the present study reveal that the N-methylpiperazinyl moiety of ofloxacin is included in beta-CD, and the remaining part of the guest molecule remains outside. Also, in molecular interaction with quinone-type electron acceptors

  8. Dissociative ionization of biomolecules

    NASA Astrophysics Data System (ADS)

    Huo, Winifred

    2004-09-01

    Dissociative ionization (DI) by electron impact plays a role in many different applications, including low-temperature plasma processing, the study of space and astrophysical plasmas, and the study of biological damages by high-energy radiation. In the present study, our goal is to understand the health hazard to humans from exposure to radiation during an extended space flight. DI by secondary electrons can damage the DNA, either directly by causing a DNA lesion, or indirectly by producing radicals and cations that attack the DNA. The theoretical model employed makes use of the fact that electronic motion is much faster than nuclear motion, allowing DI to be treated as a two-step process. The first step is electron-impact ionization resulting in a dissociative state of the molecular ion with the same geometry as the neutral molecule. In the second step the ion relaxes from the initial geometry and undergoes unimolecular dissociation. Thus the DI cross section is given by the product of the ionization cross section and the dissociation probability. For the ionization process we use the improved binary-encounter dipole (iBED) model. For unimolecular dissociation, we use the multiconfigurational self-consistent field (MCSCF) method to determine the minimum energy pathways to possible product channels. This model has been applied to study the DI of H_2O, NH_3, and CH_4, and the results are in good agreement with experiment. The DI from the low-lying channels of benzene has also been studied and the dissociation products are compared with photoionization measurements. The DI of the DNA bases guanine and cytosine are then discussed. Of the four DNA bases, guanine has the largest ionization cross section and cytosine has the smallest. The guanine radical cation is considered to be one of the precursors to the primary, direct-type lesions formed in DNA when it is irradiated. Comparison of DI products of guanine and cytosine will be made to understand the differences in

  9. A theoretical study on ascorbic acid dissociation in water clusters.

    PubMed

    Demianenko, Eugeniy; Ilchenko, Mykola; Grebenyuk, Anatoliy; Lobanov, Victor; Tsendra, Oksana

    2014-03-01

    Dissociation of ascorbic acid in water has been studied by using a cluster model. It was examined by density functional theory (DFT) with the В3LYP, M06, and wB97XD functionals and a 6-311++G(d,p) basis set. The thermodynamic and kinetic characteristics of proton transfer from ascorbic acid molecule to water clusters were calculated as well as the equilibrium constants (pK a ) for the related processes. The used functionals in the DFT method together with continuum solvent models provided results close to the experimental data for the dissociation constant of ascorbic acid in aqueous solution.

  10. [A dissociative patient].

    PubMed

    de Jongh, A; Abkhezr, S; Broers, D L M

    2009-08-01

    A 45-year-old woman attended a centre for special dental care. Initially, it seemed that the patient suffered from an extreme form of dental anxiety. However, the fact that she displayed 'dissociations' suggested that she had a severe psychiatric disorder, in this case Dissociative Identity Disorder. The key feature of this condition is a dysfunction of the normal integrative functions of identity, memory and consciousness. In such instances it is recommended to contact a psychologist or psychiatrist and the referring care provider to consider the consequences of the psychiatric condition regarding informed consent, treatment plan and actual treatment. Because it was not likely that the patient would respond to an intervention specifically aimed to reduce anxiety in the dental setting, dental treatment under general anesthesia was the best suited option.

  11. Dissociation and psychotic symptoms.

    PubMed

    Steingard, S; Frankel, F H

    1985-08-01

    The literature on hysterical or brief reactive psychosis reflects great diversity both in clinical description and theoretical formulation. The authors describe the case of a 17-year-old girl who presented with a diagnosis of bipolar affective disorder, rapid cycling type, but who, in fact, was experiencing dissociative episodes manifested as psychotic states. The patient's successful treatment with hypnosis is described, along with the clinical and theoretical implications of the case.

  12. Calculation of antibody affinity in homogeneous and heterogeneous systems.

    PubMed

    Chalquest, R R

    1988-12-01

    Antibody affinity is an important determinant of all antibody-antigen reactions. A new computer program, AFCRV, was developed to calculate binding constants with data from a radioimmunoassay on most microcomputers in the laboratory by using constant-ratio dilution curves. Evaluation of a homogeneous or heterogeneous antibody in the presence of a single antigen can be accomplished.

  13. Copper dissociation from estuarine humic materials

    NASA Astrophysics Data System (ADS)

    Olson, Dean L.; Shuman, Mark S.

    1985-06-01

    Dissolved humic material from three locations on the Ogeechee River Estuary near Savannah, GA, was ultrafiltered into three size fractions and used for kinetic experiments with Cu(II). A Cu(II)-humic mixture was reacted with a colorimetric reagent for Cu(II) and absorbance observed from 50 msec to at least 1835 sec corresponding to rate constants from 0.001-40 sec -1. The apparent dissociation rate constants were distributed over a wide range, with most bound Cu(II) having k > 1 sec-1 ( t 1/2 < 0.7 sec ). Nearly all the variation seen in the kinetic distribution was among size fractions; as size fraction decreased, the distribution of bound Cu(II) shifted to larger rate constants. Location of sampling stations on the estuary had little effect on results.

  14. Experimental Dissociation of Methane Hydrates Through Depressurization

    NASA Astrophysics Data System (ADS)

    Borgfeldt, T.; Flemings, P. B.; Meyer, D.; You, K.

    2015-12-01

    We dissociated methane hydrates by stepwise depressurization. The initial hydrates were formed by injecting gas into a cylindrical sample of brine-saturated, coarse-grained sand at hydrate-stable conditions with the intention of reaching three-phase equilibrium. The sample was initially at 1°C with a pore pressure of 1775 psi and a salinity of 7 wt. % NaBr. The depressurization setup consisted of one pump filled with tap water attached to the confining fluid port and a second pump attached to the inlet port where the methane was injected. Depressurization was conducted over sixteen hours at a constant temperature of 1°C. The pore pressure was stepwise reduced from 1775 psi to atmospheric pressure by pulling known volumes of gas from the sample. After each extraction, we recorded the instantaneous and equilibrium pore pressure. 0.503 moles of methane were removed from the sample. The pore pressure decreased smoothly and nonlinearly with the cumulative gas withdrawn from the sample. We interpret that hydrate began to dissociate immediately with depressurization, and it continued to dissociate when the pressure decreased below the three-phase pressure for 1°C and 0 wt. % salinity. Two breaks in slope in the pressure vs. mass extracted data are bounded by smooth, nonlinear curves with differing slopes on either side. We attribute the breaks to dissociation of three zones of hydrate concentration. We created a box model to simulate the experimental behavior. For a 10% initial gas saturation (estimated from the hydrate formation experiment and based on mass conservation), an initial hydrate saturation of 55% is required to match the total methane extracted from the sample. Future experiments will be conducted over a longer timespan while monitoring hydrate dissociation with CT imaging throughout the process.

  15. CHARACTERIZATION OF INTERACTION KINETICS BETWEEN CHIRAL SOLUTES AND HUMAN SERUM ALBUMIN BY USING HIGH-PERFORMANCE AFFINITY CHROMATOGRAPHY AND PEAK PROFILING

    PubMed Central

    Tong, Zenghan; Hage, David S.

    2011-01-01

    Peak profiling and high-performance columns containing immobilized human serum albumin (HSA) were used to study the interaction kinetics of chiral solutes with this protein. This approach was tested using the phenytoin metabolites 5-(3-hydroxyphenyl)-5-phenylhydantoin (m-HPPH) and 5-(4-hydroxyphenyl)-5-phenylhydantoin (p-HPPH) as model analytes. HSA columns provided some resolution of the enantiomers for each phenytoin metabolite, which made it possible to simultaneously conduct kinetic studies on each chiral form. The dissociation rate constants for these interactions were determined by using both the single flow rate and multiple flow rate peak profiling methods. Corrections for non-specific interactions with the support were also considered. The final estimates obtained at pH 7.4 and 37°C for the dissociation rate constants of these interactions were 8.2–9.6 s−1 for the two enantiomers of m-HPPH and 3.2–4.1 s−1 for the enantiomers of p-HPPH. These rate constants agreed with previous values that have been reported for other drugs and solutes that have similar affinities and binding regions on HSA. The approach used in this report was not limited to phenytoin metabolites or HSA but could be applied to a variety of other chiral solutes and proteins. This method could also be adopted for use in the rapid screening of drug-protein interactions. PMID:21872871

  16. Dynamics of light-induced FeB pair dissociation in crystalline silicon

    SciTech Connect

    Geerligs, L.J.; Macdonald, Daniel

    2004-11-29

    The dynamics of light-induced dissociation of iron-boron (FeB) pairs in p-type crystalline silicon is investigated. The dissociation is observed to be a single-exponential process which is balanced with thermal repairing. The dissociation rate is proportional to the square of the carrier generation rate and the inverse square of the FeB concentration. This suggests that the dissociation process involves two recombination or electron capture events. A proportionality constant of 5x10{sup -15} s describes the dissociation rate well in the absence of other significant recombination channels. The dissociation rate decreases in the presence of other recombination channels. These results can be used for reliable detection of iron in silicon devices and materials, and for further elucidation of the electronically driven FeB dissociation reaction.

  17. The Linkage Between Oxygenation and Subunit Dissociation in Human Hemoglobin

    PubMed Central

    Ackers, Gary K.; Halvorson, Herbert R.

    1974-01-01

    The use of subunit dissociation as a means of probing intersubunit contact energy changes which accompany cooperative ligand binding has been studied for the case of human hemoglobin. An analysis is presented delineating the information that can be obtained from the linkage relationships between ligand binding and subunit dissociation of hemoglobin tetramers into dimers. The analysis defines (a) the variation of the saturation function, Ȳ, with total protein concentration, (b) the variation of the subunit dissociation constant xK2 with ligand concentration (X) and (c) the correlations between changes in dimer-dimer contact energy and the sequential ligand binding steps. Sensitivity of the linkage function has been explored by numerical simulation. It is shown that subunit dissociation may appreciably affect oxygenation curves under usual conditions of measurement and that relying solely on either xK2 or Ȳ may lead to incorrect picutres of the energetics, whereas the combination defines the system much more exactly. PMID:4530985

  18. A set of robust fluorescent peptide probes for quantification of Cu(ii) binding affinities in the micromolar to femtomolar range.

    PubMed

    Young, Tessa R; Wijekoon, Chathuri J K; Spyrou, Benjamin; Donnelly, Paul S; Wedd, Anthony G; Xiao, Zhiguang

    2015-03-01

    Reliable quantification of copper binding affinities and identification of the binding sites provide a molecular basis for an understanding of the nutritional roles and toxic effects of copper ions. Sets of chromophoric probes are now available that can quantify Cu(i) binding affinities from nanomolar to attomolar concentrations on a unified scale under in vitro conditions. Equivalent probes for Cu(ii) are lacking. This work reports development of a set of four fluorescent dansyl peptide probes (DP1-4) that can quantify Cu(ii) binding affinities from micromolar to femtomolar concentrations, also on a unified scale. The probes were constructed by conjugation of a dansyl group to four short peptides of specific design. Each was characterised by its dissociation constant KD, its pH dependence and the nature of its binding site. One equivalent of Cu(ii) is bound by the individual probes that display different and well-separated affinities at pH 7.4 (log KD = -8.1, -10.1, -12.3 and -14.1, respectively). Intense fluorescence is emitted at λmax ∼ 550 nm upon excitation at ∼330 nm. Binding of Cu(ii) quenches the fluorescence intensity linearly until one equivalent of Cu(ii) is bound. Multiple approaches and multiple affinity standards were employed to ensure reliability. Selected examples of application to well-characterised Cu(ii) binding peptides and proteins are presented. These include Aβ16 peptides, two naturally occurring Cu(ii)-chelating motifs in human serum and cerebrospinal fluid with sequences GHK and DAHK and two copper binding proteins, CopC from Pseudomonas syringae and PcoC from Escherichia coli. Previously reported affinities are reproduced, demonstrating that peptides DP1-4 form a set of robust and reliable probes for Cu(ii) binding to peptides and protein targets. PMID:25715324

  19. A set of robust fluorescent peptide probes for quantification of Cu(ii) binding affinities in the micromolar to femtomolar range.

    PubMed

    Young, Tessa R; Wijekoon, Chathuri J K; Spyrou, Benjamin; Donnelly, Paul S; Wedd, Anthony G; Xiao, Zhiguang

    2015-03-01

    Reliable quantification of copper binding affinities and identification of the binding sites provide a molecular basis for an understanding of the nutritional roles and toxic effects of copper ions. Sets of chromophoric probes are now available that can quantify Cu(i) binding affinities from nanomolar to attomolar concentrations on a unified scale under in vitro conditions. Equivalent probes for Cu(ii) are lacking. This work reports development of a set of four fluorescent dansyl peptide probes (DP1-4) that can quantify Cu(ii) binding affinities from micromolar to femtomolar concentrations, also on a unified scale. The probes were constructed by conjugation of a dansyl group to four short peptides of specific design. Each was characterised by its dissociation constant KD, its pH dependence and the nature of its binding site. One equivalent of Cu(ii) is bound by the individual probes that display different and well-separated affinities at pH 7.4 (log KD = -8.1, -10.1, -12.3 and -14.1, respectively). Intense fluorescence is emitted at λmax ∼ 550 nm upon excitation at ∼330 nm. Binding of Cu(ii) quenches the fluorescence intensity linearly until one equivalent of Cu(ii) is bound. Multiple approaches and multiple affinity standards were employed to ensure reliability. Selected examples of application to well-characterised Cu(ii) binding peptides and proteins are presented. These include Aβ16 peptides, two naturally occurring Cu(ii)-chelating motifs in human serum and cerebrospinal fluid with sequences GHK and DAHK and two copper binding proteins, CopC from Pseudomonas syringae and PcoC from Escherichia coli. Previously reported affinities are reproduced, demonstrating that peptides DP1-4 form a set of robust and reliable probes for Cu(ii) binding to peptides and protein targets.

  20. ( sup 3 H)-DOB(4-bromo-2,5-dimethoxyphenylisopropylamine) and ( sup 3 H) ketanserin label two affinity states of the cloned human 5-hydroxytryptamine2 receptor

    SciTech Connect

    Branchek, T.; Adham, N.; Macchi, M.; Kao, H.T.; Hartig, P.R. )

    1990-11-01

    The binding properties of the 5-hydroxytryptamine2 (5-HT2) receptor have been the subject of much interest and debate in recent years. The hallucinogenic amphetamine derivative 4-bromo-2,5-dimethoxyphenylisopropylamine (DOB) has been shown to bind to a small number of binding sites with properties very similar to (3H)ketanserin-labeled 5-HT2 receptors, but with much higher agonist affinities. Some researchers have interpreted this as evidence for the existence of a new subtype of 5-HT2 receptor (termed 5-HT2A), whereas others have interpreted these data as indicative of agonist high affinity and agonist low affinity states for the 5-HT2 receptor. In this investigation, a cDNA clone encoding the serotonin 5-HT2 receptor was transiently transfected into monkey kidney Cos-7 cells and stably transfected into mouse fibroblast L-M(TK-) cells. In both systems, expression of this single serotonin receptor cDNA led to the appearance of both (3H)DOB and (3H)ketanserin binding sites with properties that matched their binding characteristics in mammalian brain homogenates. Addition of guanosine 5'-(beta, gamma-imido) triphosphate (Gpp(NH)p) to this system caused a rightward shift and steepening of agonist competition curves for (3H) ketanserin binding, converting a two-site binding curve to a single low affinity binding state. Gpp(NH)p addition also caused a 50% decrease in the number of high affinity (3H)DOB binding sites, with no change in the dissociation constant of the remaining high affinity states. These data on a single human 5-HT2 receptor cDNA expressed in two different transfection host cells indicate that (3H)DOB and (3H)ketanserin binding reside on the same gene product, apparently interacting with agonist and antagonist conformations of a single human 5-HT2 receptor protein.

  1. DNA-binding affinity and sequence permutation preference of the telomere protein from Euplotes crassus

    PubMed Central

    Suzuki, Takahito; McKenzie, Margaret; Ott, Elizabeth; Ilkun, Olesya; Horvath, Martin P.

    2008-01-01

    Telomere end binding proteins from diverse organisms use various forms of an ancient protein structure to recognize and bind with single strand DNA found at the ends of telomeres. To further understand the biochemistry and evolution of these proteins we have characterized the DNA-binding properties of the telomere end binding protein from Euplotes crassus (EcTEBP). EcTEBP and its predicted amino-terminal DNA-binding domain, EcTEBP-N, were expressed in E. coli and purified. Each protein formed stoichiometric (1:1) complexes with single strand DNA oligos derived from the precisely defined d(TTTTGGGGTTTTGG) sequence found at DNA termini in Euplotes. Dissociation constants for DNA•EcTEBP and DNA•EcTEBP-N were comparable, with KD-DNA = 38 ± 2 nM for the full-length protein and KD-DNA = 60 ± 4 nM for the N-terminal domain, indicating that the N-terminal domain retains high affinity for DNA even in the absence of potentially stabilizing moieties located in the C-terminal domain. Rate constants for DNA association and DNA dissociation corroborated a slightly improved DNA binding performance for the full-length protein (ka = 45 ± 4 μM-1 s-1, kd = 0.10 ± 0.02 s-1) relative to the N-terminal domain (ka = 18 ± 1 μM-1 s-1, kd = 0.15 ± 0.01 s-1). Equilibrium dissociation constants measured for sequence permutations of the telomere repeat spanned a 55 – 1400 nM range, with EcTEBP and EcTEBP-N binding most tightly to d(TTGGGGTTTTGG) — the sequence corresponding with that of mature DNA termini. Additionally, competition experiments showed that EcTEBP recognizes and binds the telomere-derived 14-nucleotide DNA in preference to shorter 5′ -truncation variants. Compared with multi-subunit complexes assembled with telomere single strand DNA from Oxytricha nova, our results highlight the relative simplicity of the Euplotes crassus system where a telomere end binding protein has biochemical properties indicating one protein subunit caps the single strand DNA. PMID

  2. High-affinity antibodies to the 1,4-dihydropyridine Ca2+-channel blockers

    SciTech Connect

    Campbell, K.P.; Sharp, A.; Strom, M.; Kahl, S.D.

    1986-05-01

    Antibodies with high affinity and specificity for the 1,4-dihydropyridine Ca2+-channel blockers have been produced in rabbits by immunization with dihydropyridine-protein conjugates. Anti-dihydropyridine antibodies were found to specifically bind (/sup 3/H)nitrendipine, (/sup 3/H)-nimodipine, (/sup 3/H)nisoldipine, and (/sup 3/H)PN 200-110 (all 1,4-dihydropyridine Ca2+-channel blockers) with high affinity, while (/sup 3/H)verapamil, (/sup 3/H)diltiazem, and (/sup 3/H)trifluoperazine were not recognized. The average dissociation constant of the (/sup 3/H)nitrendipine-antibody complex was 0.06 (+/- 0.02) X 10(-9) M for an antiserum studied in detail and ranged from 0.01 to 0.24 X 10(-9) M for all antisera. Inhibition of (/sup 3/H)nitrendipine binding was specific for the 1,4-dihydropyridine Ca2+-channel modifiers and the concentrations required for half-maximal inhibition ranged between 0.25 and 0.90 nM. Structurally unrelated Ca2+-channel blockers, calmodulin antagonists, inactive metabolites of nitrendipine, and UV-inactivated nisoldipine did not modify (/sup 3/H)nitrendipine binding to the anti-dihydropyridine antibodies. Dihydropyridines without a bulky substituent in the 4-position of the heterocycle were able to displace (/sup 3/H)nitrendipine binding, but the concentrations required for half-maximal inhibition were greater than 800 nM. In summary, anti-dihydropyridine antibodies have been shown to have high affinity and specificity for the 1,4-dihydropyridine Ca2+-channel blockers and to exhibit dihydropyridine binding properties similar to the membrane receptor for the 1,4-dihydropyridine Ca2+-channel blockers.

  3. Determination of protein binding affinities within hydrogel-based molecularly imprinted polymers (HydroMIPs).

    PubMed

    EL-Sharif, Hazim F; Hawkins, Daniel M; Stevenson, Derek; Reddy, Subrayal M

    2014-08-01

    Hydrogel-based molecularly imprinted polymers (HydroMIPs) were prepared for several proteins (haemoglobin, myoglobin and catalase) using a family of acrylamide-based monomers. Protein affinity towards the HydroMIPs was investigated under equilibrium conditions and over a range of concentrations using specific binding with Hill slope saturation profiles. We report HydroMIP binding affinities, in terms of equilibrium dissociation constants (Kd) within the micro-molar range (25 ± 4 μM, 44 ± 3 μM, 17 ± 2 μM for haemoglobin, myoglobin and catalase respectively within a polyacrylamide-based MIP). The extent of non-specific binding or cross-selectivity for non-target proteins has also been assessed. It is concluded that both selectivity and affinity for both cognate and non-cognate proteins towards the MIPs were dependent on the concentration and the complementarity of their structures and size. This is tentatively attributed to the formation of protein complexes during both the polymerisation and rebinding stages at high protein concentrations. We have used atomic force spectroscopy to characterize molecular interactions in the MIP cavities using protein-modified AFM tips. Attractive and repulsive force curves were obtained for the MIP and NIP (non-imprinted polymer) surfaces (under protein loaded or unloaded states). Our force data suggest that we have produced selective cavities for the template protein in the MIPs and we have been able to quantify the extent of non-specific protein binding on, for example, a non-imprinted polymer (NIP) control surface.

  4. KW-3902, a selective high affinity antagonist for adenosine A1 receptors.

    PubMed Central

    Nonaka, H.; Ichimura, M.; Takeda, M.; Kanda, T.; Shimada, J.; Suzuki, F.; Kase, H.

    1996-01-01

    1. We demonstrate that 8-(noradamantan-3-yl)-1,3-dipropylxanthine (KW-3902) is a very potent and selective adenosine A1 receptor antagonist, assessed by radioligand binding and cyclic AMP response in cells. 2. In rat forebrain adenosine A1 receptors labelled with [3H]-cyclohexyladenosine (CHA), KW-3902 had a Ki value of 0.19 nM, whereas it showed a Ki value of 170 nM in rat striatal A2A receptors labelled with [3H]-2-[p-(2-carboxyethyl)-phenethylamino]-5'-N-ethylcarboxamidoad enosine (CGS21680), indicating 890 fold A1 receptor selectivity versus the A2A receptor. KW-3902 at 10 microM showed no effect on recombinant rat A3 receptors expressed on CHO cells. 3. Saturation studies with [3H]-KW-3902 revealed that it bound with high affinity (Kd = 77 pM) and limited capacity (Bmax = 470 fmol mg-1 of protein) to a single class of recognition sites. A high positive correlation was observed between the pharmacological profile of adenosine ligands inhibiting the binding of [3H]-KW-3902 and that of [3H]-CHA. 4. KW-3902 showed potent A1 antagonism against the inhibition of forskolin-induced cyclic AMP accumulation in DDT1 MF-2 cells by the A1-selective agonist, cyclopentyladenosine with a dissociation constant (KB value) of 0.34 nM. KW-3902 antagonized 5'-N-ethylcarboxamidoadenosine-elicited cyclic AMP accumulation via A2B receptors with a KB value of 52 nM. 5. KW-3902 exhibited marked species-dependent differences in the binding affinities. The highest affinity was for the rat A1 receptor (ki = 0.19 nM) and these values for guinea-pig and dog A1 receptors were 1.3 and 10 nM, respectively. PMID:8732272

  5. Pyrrolic tripodal receptors effectively recognizing monosaccharides. Affinity assessment through a generalized binding descriptor.

    PubMed

    Nativi, Cristina; Cacciarini, Martina; Francesconi, Oscar; Vacca, Alberto; Moneti, Gloriano; Ienco, Andrea; Roelens, Stefano

    2007-04-11

    Pyrrolic and imino (3) or amino (4) H-bonding ligands were incorporated into a benzene-based tripodal scaffold to develop a new generation of receptors for molecular recognition of carbohydrates. Receptors 3 and 4 effectively bound a set of octylglycosides of biologically relevant monosaccharides, including glucose (Glc), galactose (Gal), mannose (Man), and N-acetyl-glucosamine (GlcNAc), showing micromolar affinities in CDCl3 and millimolar affinities in CD3CN by NMR titrations. Both receptors selectively recognized Glc among the investigated monosaccharides, with 3 generally less effective than 4 but showing selectivities for the all-equatorial beta-glycosides of Glc and GlcNAc among the largest reported for H-bonding synthetic receptors. Selectivities in CDCl3 spanned a range of nearly 250-fold for 3 and over 30-fold for 4. Affinities and selectivities were univocally assessed through the BC50 descriptor, for which a generalized treatment is described that extends the scope of the descriptor to include any two-reagent host-guest system featuring any number of binding constants. ITC titrations of betaGlc in acetonitrile evidenced, for both receptors, a strong enthalpic contribution to the binding interaction, suggesting multiple H bonding. Selectivity trends toward alphaGlc and betaGlc analogous to those obtained in solution were also observed in the gas phase for 3 and 4 by collision-induced dissociation experiments. From comparison with appropriate reference compounds, a substantial contribution to carbohydrate binding emerged for both the imino/amino and the pyrrolic H-bonding groups but not for the amidic group. This previously undocumented behavior, supported by crystallographic evidence, has been discussed in terms of geometric, functional, and coordinative complementarity between H-bonding groups and glycosidic hydroxyls and opens the way to a new designer strategy of H-bonding receptors for carbohydrates.

  6. Characterization of the ER-Targeted Low Affinity Ca2+ Probe D4ER

    PubMed Central

    Greotti, Elisa; Wong, Andrea; Pozzan, Tullio; Pendin, Diana; Pizzo, Paola

    2016-01-01

    Calcium ion (Ca2+) is a ubiquitous intracellular messenger and changes in its concentration impact on nearly every aspect of cell life. Endoplasmic reticulum (ER) represents the major intracellular Ca2+ store and the free Ca2+ concentration ([Ca2+]) within its lumen ([Ca2+]ER) can reach levels higher than 1 mM. Several genetically-encoded ER-targeted Ca2+ sensors have been developed over the last years. However, most of them are non-ratiometric and, thus, their signal is difficult to calibrate in live cells and is affected by shifts in the focal plane and artifactual movements of the sample. On the other hand, existing ratiometric Ca2+ probes are plagued by different drawbacks, such as a double dissociation constant (Kd) for Ca2+, low dynamic range, and an affinity for the cation that is too high for the levels of [Ca2+] in the ER lumen. Here, we report the characterization of a recently generated ER-targeted, Förster resonance energy transfer (FRET)-based, Cameleon probe, named D4ER, characterized by suitable Ca2+ affinity and dynamic range for monitoring [Ca2+] variations within the ER. As an example, resting [Ca2+]ER have been evaluated in a known paradigm of altered ER Ca2+ homeostasis, i.e., in cells expressing a mutated form of the familial Alzheimer’s Disease-linked protein Presenilin 2 (PS2). The lower Ca2+ affinity of the D4ER probe, compared to that of the previously generated D1ER, allowed the detection of a conspicuous, more clear-cut, reduction in ER Ca2+ content in cells expressing mutated PS2, compared to controls. PMID:27598166

  7. Characterization of the ER-Targeted Low Affinity Ca(2+) Probe D4ER.

    PubMed

    Greotti, Elisa; Wong, Andrea; Pozzan, Tullio; Pendin, Diana; Pizzo, Paola

    2016-01-01

    Calcium ion (Ca(2+)) is a ubiquitous intracellular messenger and changes in its concentration impact on nearly every aspect of cell life. Endoplasmic reticulum (ER) represents the major intracellular Ca(2+) store and the free Ca(2+) concentration ([Ca(2+)]) within its lumen ([Ca(2+)]ER) can reach levels higher than 1 mM. Several genetically-encoded ER-targeted Ca(2+) sensors have been developed over the last years. However, most of them are non-ratiometric and, thus, their signal is difficult to calibrate in live cells and is affected by shifts in the focal plane and artifactual movements of the sample. On the other hand, existing ratiometric Ca(2+) probes are plagued by different drawbacks, such as a double dissociation constant (Kd) for Ca(2+), low dynamic range, and an affinity for the cation that is too high for the levels of [Ca(2+)] in the ER lumen. Here, we report the characterization of a recently generated ER-targeted, Förster resonance energy transfer (FRET)-based, Cameleon probe, named D4ER, characterized by suitable Ca(2+) affinity and dynamic range for monitoring [Ca(2+)] variations within the ER. As an example, resting [Ca(2+)]ER have been evaluated in a known paradigm of altered ER Ca(2+) homeostasis, i.e., in cells expressing a mutated form of the familial Alzheimer's Disease-linked protein Presenilin 2 (PS2). The lower Ca(2+) affinity of the D4ER probe, compared to that of the previously generated D1ER, allowed the detection of a conspicuous, more clear-cut, reduction in ER Ca(2+) content in cells expressing mutated PS2, compared to controls. PMID:27598166

  8. Determination of protein binding affinities within hydrogel-based molecularly imprinted polymers (HydroMIPs).

    PubMed

    EL-Sharif, Hazim F; Hawkins, Daniel M; Stevenson, Derek; Reddy, Subrayal M

    2014-08-01

    Hydrogel-based molecularly imprinted polymers (HydroMIPs) were prepared for several proteins (haemoglobin, myoglobin and catalase) using a family of acrylamide-based monomers. Protein affinity towards the HydroMIPs was investigated under equilibrium conditions and over a range of concentrations using specific binding with Hill slope saturation profiles. We report HydroMIP binding affinities, in terms of equilibrium dissociation constants (Kd) within the micro-molar range (25 ± 4 μM, 44 ± 3 μM, 17 ± 2 μM for haemoglobin, myoglobin and catalase respectively within a polyacrylamide-based MIP). The extent of non-specific binding or cross-selectivity for non-target proteins has also been assessed. It is concluded that both selectivity and affinity for both cognate and non-cognate proteins towards the MIPs were dependent on the concentration and the complementarity of their structures and size. This is tentatively attributed to the formation of protein complexes during both the polymerisation and rebinding stages at high protein concentrations. We have used atomic force spectroscopy to characterize molecular interactions in the MIP cavities using protein-modified AFM tips. Attractive and repulsive force curves were obtained for the MIP and NIP (non-imprinted polymer) surfaces (under protein loaded or unloaded states). Our force data suggest that we have produced selective cavities for the template protein in the MIPs and we have been able to quantify the extent of non-specific protein binding on, for example, a non-imprinted polymer (NIP) control surface. PMID:24950144

  9. Fragment screening of cyclin G-associated kinase by weak affinity chromatography.

    PubMed

    Meiby, Elinor; Knapp, Stefan; Elkins, Jonathan M; Ohlson, Sten

    2012-11-01

    Fragment-based drug discovery (FBDD) has become a new strategy for drug discovery where lead compounds are evolved from small molecules. These fragments form low affinity interactions (dissociation constant (K(D)) = mM - μM) with protein targets, which require fragment screening methods of sufficient sensitivity. Weak affinity chromatography (WAC) is a promising new technology for fragment screening based on selective retention of fragments by a drug target. Kinases are a major pharmaceutical target, and FBDD has been successfully applied to several of these targets. In this work, we have demonstrated the potential to use WAC in combination with mass spectrometry (MS) detection for fragment screening of a kinase target-cyclin G-associated kinase (GAK). One hundred seventy fragments were selected for WAC screening by virtual screening of a commercial fragment library against the ATP-binding site of five different proteins. GAK protein was immobilized on a capillary HPLC column, and compound binding was characterized by frontal affinity chromatography. Compounds were screened in sets of 13 or 14, in combination with MS detection for enhanced throughput. Seventy-eight fragments (46 %) with K(D) < 200 μM were detected, including a few highly efficient GAK binders (K(D) of 2 μM; ligand efficiency = 0.51). Of special interest is that chiral screening by WAC may be possible, as two stereoisomeric fragments, which both contained one chiral center, demonstrated twin peaks. This ability, in combination with the robustness, sensitivity, and simplicity of WAC makes it a new method for fragment screening of considerable potential. PMID:22918538

  10. Energetics from Slow Infrared Multiphoton Dissociation of Biomolecules

    PubMed Central

    Jockusch, Rebecca A.; Paech, Kolja

    2005-01-01

    Photodissociation kinetics of the protonated pentapeptide leucine enkephalin measured using a cw CO2 laser and a Fourier-transform mass spectrometer are reported. A short induction period, corresponding to the time required to raise the internal energy of the ion population to a (dissociating) steady state, is observed. After this induction period, the dissociation data are accurately fit by first-order kinetics. A plot of the log of the unimolecular dissociation rate constant, kuni, as a function of the log of laser power is linear at low laser powers (<9 W, kuni <0.05 s−1), but tapers off at high laser power (9–33 W, kuni = 0.05–7 s−1). The entire measured dissociation curve can be accurately fit by an exponential function plus a constant. The experiment is simulated using a master equation formalism. In the model, the laser radiation is described as an energetically flat-topped distribution which is spatially uniform. This description is consistent with experimental results which indicate that ion motion within the cell averages out spatial inhomogeneities in the laser light. The model has several adjustable parameters. The effect of varying these parameters on the calculated kinetics and power dependence curves is discussed. A procedure for determining a limited range of threshold dissociation energy, Eo, which fits both the measured induction period and power dependence curves, is presented. Using this procedure, Eo of leucine enkephalin is determined to be 1.12–1.46 eV. This result is consistent with, although less precise than, values measured previously using blackbody infrared radiative dissociation. Although the blackbody dissociation results were used as a starting point to search for fits of the master equation model to experiment, these results demonstrate that it is, in principle, possible to determine a limited range of Eo from slow infrared multiphoton dissociation data alone. PMID:16467893

  11. Selective induction of high-ouabain-affinity isoform of Na sup + -K sup + -ATPase by thyroid hormone

    SciTech Connect

    Haber, R.S.; Loeb, J.N. )

    1988-12-01

    The administration of thyroid hormone is known to result in an induction of the Na{sup +}-K{sup +}-adenosinetriphosphatase (Na{sup +}-K{sup +}-ATPase) in rat skeletal muscle and other thyroid hormone-responsive tissues. Since the Na{sup +}-K{sup +}-ATPase in a variety of mammalian tissues has recently been reported to exist in at least two forms distinguishable by differing affinities for the inhibitory cardiac glycoside ouabain. The authors have studied the effects of 3,3{prime},5-triiodo-L-thyronine (T{sub 3}) treatment on these two forms of the enzyme in rat diaphragm. The inhibition of Na{sup +}-K{sup +}-ATPase activity in a crude membrane fraction by varying concentrations of ouabain conformed to a biphasic pattern consistent with the presence of two distinct isoforms with inhibition constants (K{sub I}s) for ouabain of {approximately}10{sup {minus}7} and 10{sup {minus}4} M, respectively. Measurement of the specific binding of ({sup 3}H)ouabain to these membranes confirmed the presence of a class of high-affinity ouabain binding sites with a dissociation constant (K{sub d}) of slightly less than 10{sup {minus}7}M, whose maximal binding capacity was increased by T{sub 3} treatment by 185%. Binding studies in unfractionated homogenates of diaphragm similarly demonstrated the presence of high-affinity sites whose maximal binding capacity was increased by T{sub 3} treatment. Quantitation of both the high- and low-ouabain-affinity forms of the Na{sup +}-K{sup +}-ATPase by ouabain-dependent phosphorylation from ({sup 32}P)orthophosphate confirmed that T{sub 3} treatment markedly increased the number of high-affinity sites while having little effect on the number of low-affinity sites. These observations provide, to our knowledge, the first demonstration that these two forms of the Na{sup +}-K{sup +}-ATPase are subject to selective hormonal induction.

  12. Affinity purification of metalloprotease from marine bacterium using immobilized metal affinity chromatography.

    PubMed

    Li, Shangyong; Wang, Linna; Yang, Juan; Bao, Jing; Liu, Junzhong; Lin, Shengxiang; Hao, Jianhua; Sun, Mi

    2016-06-01

    In this study, an efficient affinity purification protocol for an alkaline metalloprotease from marine bacterium was developed using immobilized metal affinity chromatography. After screening and optimization of the affinity ligands and spacer arm lengths, Cu-iminmodiacetic acid was chosen as the optimal affinity ligand, which was coupled to Sepharose 6B via a 14-atom spacer arm. The absorption analysis of this medium revealed a desorption constant Kd of 21.5 μg/mL and a theoretical maximum absorption Qmax of 24.9 mg/g. Thanks to this affinity medium, the enzyme could be purified by only one affinity purification step with a purity of approximately 95% pure when analyzed by high-performance liquid chromatography and reducing sodium dodecyl sulfate polyacrylamide gel electrophoresis. The recovery of the protease activity reached 74.6%, which is much higher than the value obtained by traditional protocols (8.9%). These results contribute to the industrial purifications and contribute a significant reference for the purification of other metalloproteases. PMID:27058973

  13. Dissociative recombination of CH4(+).

    PubMed

    Thomas, Richard D; Kashperka, Iryna; Vigren, E; Geppert, Wolf D; Hamberg, Mathias; Larsson, Mats; af Ugglas, Magnus; Zhaunerchyk, Vitali

    2013-10-01

    CH4(+) is an important molecular ion in the astrochemistry of diffuse clouds, dense clouds, cometary comae, and planetary ionospheres. However, the rate of one of the common destruction mechanisms for molecular ions in these regions, dissociative recombination (DR), is somewhat uncertain. Here, we present absolute measurements for the DR of CH4(+) made using the heavy ion storage ring CRYRING in Stockholm, Sweden. From our collision-energy dependent cross-sections, we infer a thermal rate constant of k(Te) = 1.71(±0.02) × 10(–6)(Te/300)(−0.66(±0.02)) cm3 s(–1) over the region of electron temperatures 10 ≤ Te ≤ 1000 K. At low collision energies, we have measured the branching fractions of the DR products to be CH4 (0.00 ± 0.00); CH3 + H (0.18 ± 0.03); CH2 + 2H (0.51 ± 0.03); CH2 + H2 (0.06 ± 0.01); CH + H2 + H (0.23 ± 0.01); and CH + 2H2 (0.02 ± 0.01), indicating that two or more C–H bonds are broken in 80% of all collisions.

  14. Recurrent dissociative fugue.

    PubMed

    Mamarde, Abhishek; Navkhare, Praveen; Singam, Amrita; Kanoje, Akash

    2013-10-01

    Dissociative fugue is a rarely reported diagnostic entity. It is one of the least understood and yet clinically one of the most fascinating disorders in mental health. Here, we describe a case of fugue in a 32-year-old man who was brought to mental hospital with complete loss of memory for events pertaining to identity of self. This case illustrates the nature of presentation in hospital setting like mental hospital and effort taken to reintegrate his identity and reunite with his family. PMID:24379504

  15. Recurrent dissociative fugue.

    PubMed

    Mamarde, Abhishek; Navkhare, Praveen; Singam, Amrita; Kanoje, Akash

    2013-10-01

    Dissociative fugue is a rarely reported diagnostic entity. It is one of the least understood and yet clinically one of the most fascinating disorders in mental health. Here, we describe a case of fugue in a 32-year-old man who was brought to mental hospital with complete loss of memory for events pertaining to identity of self. This case illustrates the nature of presentation in hospital setting like mental hospital and effort taken to reintegrate his identity and reunite with his family.

  16. Recurrent Dissociative Fugue

    PubMed Central

    Mamarde, Abhishek; Navkhare, Praveen; Singam, Amrita; Kanoje, Akash

    2013-01-01

    Dissociative fugue is a rarely reported diagnostic entity. It is one of the least understood and yet clinically one of the most fascinating disorders in mental health. Here, we describe a case of fugue in a 32-year-old man who was brought to mental hospital with complete loss of memory for events pertaining to identity of self. This case illustrates the nature of presentation in hospital setting like mental hospital and effort taken to reintegrate his identity and reunite with his family. PMID:24379504

  17. Comparison of biosensor platforms in the evaluation of high affinity antibody-antigen binding kinetics.

    PubMed

    Yang, Danlin; Singh, Ajit; Wu, Helen; Kroe-Barrett, Rachel

    2016-09-01

    The acquisition of reliable kinetic parameters for the characterization of biomolecular interactions is an important component of the drug discovery and development process. While several benchmark studies have explored the variability of kinetic rate constants obtained from multiple laboratories and biosensors, a direct comparison of these instruments' performance has not been undertaken, and systematic factors contributing to data variability from these systems have not been discussed. To address these questions, a panel of ten high-affinity monoclonal antibodies was simultaneously evaluated for their binding kinetics against the same antigen on four biosensor platforms: GE Healthcare's Biacore T100, Bio-Rad's ProteOn XPR36, ForteBio's Octet RED384, and Wasatch Microfluidics's IBIS MX96. We compared the strengths and weaknesses of these systems and found that despite certain inherent systematic limitations in instrumentation, the rank orders of both the association and dissociation rate constants were highly correlated between these instruments. Our results also revealed a trade-off between data reliability and sample throughput. Biacore T100, followed by ProteOn XPR36, exhibited excellent data quality and consistency, whereas Octet RED384 and IBIS MX96 demonstrated high flexibility and throughput with compromises in data accuracy and reproducibility. Our results support the need for a "fit-for-purpose" approach in instrument selection for biosensor studies. PMID:27365220

  18. High affinity dopamine D2 receptor radioligands. 1. Regional rat brain distribution of iodinated benzamides

    SciTech Connect

    Kessler, R.M.; Ansari, M.S.; de Paulis, T.; Schmidt, D.E.; Clanton, J.A.; Smith, H.E.; Manning, R.G.; Gillespie, D.; Ebert, M.H. )

    1991-08-01

    Five 125I-labeled substituted benzamides, which are close structural analogues of (S)-sulpiride, eticlopride, and isoremoxipride, were evaluated for their selective in vivo uptake into dopamine D2 receptor rich tissue of the rat brain. Iodopride (KD 0.88 nM), an iodine substituted benzamide structurally related to sulpiride, displayed a maximal striatum: cerebellar uptake ratio of 7.6. Demonstration of saturation of the receptor with (125I)iodopride in striatum required uptake in frontal cortex to be used, rather than cerebellar uptake, to define nonspecific binding. Two other ligands structurally related to eticlopride, iclopride (KD 0.23 nM) and itopride (KD 0.16 nM), displayed maximal striatal: cerebellar uptake ratios of 9.8 and 3.3, respectively. The most potent ligands, epidepride (KD 0.057 nM) and ioxipride (KD 0.070 nM) showed striatal:cerebellar uptake ratios of 234 and 65, respectively. The observed uptake ratios correlated poorly with the affinity constants for the dopamine D2 receptor alone, but were highly correlated (r = 0.92) with the product of the receptor dissociation constant (KD) and the apparent lipophilicity (kw), as determined by reverse-phase HPLC at pH 7.5. Total striatal uptake also appeared dependent on lipophilicity, with maximal uptake occurring for ligands having log kw 2.4-2.8.

  19. THE DISSOCIATIVE TURN IN PSYCHOANALYSIS.

    PubMed

    Itzkowitz, Sheldon

    2015-06-01

    In his response to the Roundtable Discussions on what is effective in psychoanalytic psychotherapy, the author focuses on the renewed interest in the concept of dissociation that began to emerge toward the end of the 20th century. A contemporary psychoanalytic position informed by the impact of developmental trauma has led to an understanding of and interest in the dissociative mind. The actuality of trauma during infancy and early childhood is recognized as a key factor leading to the emergence of dissociative processes, the potential dissociative structuring of the mind, and mind being characterized by multiple, discontinuous, centers of consciousness. The therapeutic goal in the psychoanalytic work with fragmented patients is to establish communication and understanding between the dissociated self-states. The author offers two brief clinical examples of working with dissociated self-states.

  20. Kinetic rate constant prediction supports the conformational selection mechanism of protein binding.

    PubMed

    Moal, Iain H; Bates, Paul A

    2012-01-01

    The prediction of protein-protein kinetic rate constants provides a fundamental test of our understanding of molecular recognition, and will play an important role in the modeling of complex biological systems. In this paper, a feature selection and regression algorithm is applied to mine a large set of molecular descriptors and construct simple models for association and dissociation rate constants using empirical data. Using separate test data for validation, the predicted rate constants can be combined to calculate binding affinity with accuracy matching that of state of the art empirical free energy functions. The models show that the rate of association is linearly related to the proportion of unbound proteins in the bound conformational ensemble relative to the unbound conformational ensemble, indicating that the binding partners must adopt a geometry near to that of the bound prior to binding. Mirroring the conformational selection and population shift mechanism of protein binding, the models provide a strong separate line of evidence for the preponderance of this mechanism in protein-protein binding, complementing structural and theoretical studies.

  1. Affinity driven social networks

    NASA Astrophysics Data System (ADS)

    Ruyú, B.; Kuperman, M. N.

    2007-04-01

    In this work we present a model for evolving networks, where the driven force is related to the social affinity between individuals of a population. In the model, a set of individuals initially arranged on a regular ordered network and thus linked with their closest neighbors are allowed to rearrange their connections according to a dynamics closely related to that of the stable marriage problem. We show that the behavior of some topological properties of the resulting networks follows a non trivial pattern.

  2. Dissociative state and competence.

    PubMed

    Lin, Yu-Ju; Hsieh, Ming-Hsien; Liu, Shi-Kai

    2007-10-01

    This report presents the results of forensic evaluation of the civil competence of a case of alleged dissociative identity disorder (DID) and discusses whether such dissociative states substantially jeopardize civil competence. A 40-year-old woman claimed that she had had many personalities since her college days. From the age of 37 to 40, she shopped excessively, which left her with millions of dollars of debt. She ascribed her shopping to a certain identity state, over which she had no control. (In this article, we use the term identity state to replace personality as an objective description of a mental state.) She thus raised the petition of civil incompetence. During the forensic evaluation, it was found that the identity states were relatively stable and mutually aware of each other. The switch into another identity state was sometimes under voluntary control. The subject showed consistency and continuity in behavioral patterns across the different identity states, and no matter which identity state she was in, there was no evidence of impairment in her factual knowledge of social situations and her capacity for managing personal affairs. We hence concluded that she was civilly competent despite the claimed DID. Considering that the existence and diagnosis of DID are still under dispute and a diagnosis of DID alone is not sufficient to interdict a persons civil right, important clinical and forensic issues remain to be answered.

  3. Dissociative Electron Attachment

    NASA Astrophysics Data System (ADS)

    Arreola, Esmeralda; Esmeralda Arreola Collaboration; Leigh Hargreaves Collaboration

    Since the pioneering work of Boudiaffa et al., it has been understood that electrons, even with energies near or below the ionization threshold, are capable of initiating strand-breaks in human DNA. This discovery raised important questions for cancer treatments, since sub-ionizing electrons are known to be the most copiously produced secondary product of radiation therapy. But even to date these factors are largely excluded from dosimetry calculations. This lack of inclusion is, at least in part, certainly due to the dearth of fundamental data describing low-energy electron interactions with nucleotide molecules that form the basis of DNA. Understanding of how such slow electrons are able to damage DNA remains incomplete, but the strongly peaked nature of Boudiaffa et al.'s data gives strong hints at resonantly driven collision processes. DNA damage is therefore most likely driven by ``dissociative electron attachment'' (DEA). DEA is a rather complicated process to model due to the coupling of electronic and nuclear degrees of freedom in the molecule. At the California State University Fullerton, we are currently commissioning a new spectrometer to study dissociation channels, reaction rates and orientation effects in DEA collisions between slow electrons and nucleotide molecules. At the meeting we will present design parameters and commissioning data for this new apparatus.

  4. DIFFRACTION DISSOCIATION - 50 YEARS LATER.

    SciTech Connect

    WHITE, S.N.

    2005-04-27

    The field of Diffraction Dissociation, which is the subject of this workshop, began 50 years ago with the analysis of deuteron stripping in low energy collisions with nuclei. We return to the subject in a modern context- deuteron dissociation in {radical}s{sub NN} = 200 GeV d-Au collisions recorded during the 2003 RHIC run in the PHENIX experiment. At RHIC energy, d {yields} n+p proceeds predominantly (90%) through Electromagnetic Dissociation and the remaining fraction via the hadronic shadowing described by Glauber. Since the dissociation cross section has a small theoretical error we adopt this process to normalize other cross sections measured in RHIC.

  5. High Affinity Binding of Indium and Ruthenium Ions by Gastrins.

    PubMed

    Baldwin, Graham S; George, Graham N; Pushie, M Jake

    2015-01-01

    The peptide hormone gastrin binds two ferric ions with high affinity, and iron binding is essential for the biological activity of non-amidated forms of the hormone. Since gastrins act as growth factors in gastrointestinal cancers, and as peptides labelled with Ga and In isotopes are increasingly used for cancer diagnosis, the ability of gastrins to bind other metal ions was investigated systematically by absorption spectroscopy. The coordination structures of the complexes were characterized by extended X-ray absorption fine structure (EXAFS) spectroscopy. Changes in the absorption of gastrin in the presence of increasing concentrations of Ga3+ were fitted by a 2 site model with dissociation constants (Kd) of 3.3 x 10-7 and 1.1 x 10-6 M. Although the absorption of gastrin did not change upon the addition of In3+ ions, the changes in absorbance on Fe3+ ion binding in the presence of indium ions were fitted by a 2 site model with Kd values for In3+ of 6.5 x 10-15 and 1.7 x 10-7 M. Similar results were obtained with Ru3+ ions, although the Kd values for Ru3+ of 2.6 x 10-13 and 1.2 x 10-5 M were slightly larger than observed for In3+. The structures determined by EXAFS all had metal:gastrin stoichiometries of 2:1 but, while the metal ions in the Fe, Ga and In complexes were bridged by a carboxylate and an oxygen with a metal-metal separation of 3.0-3.3 Å, the Ru complex clearly demonstrated a short range Ru-Ru separation, which was significantly shorter, at 2.4 Å, indicative of a metal-metal bond. We conclude that gastrin selectively binds two In3+ or Ru3+ ions, and that the affinity of the first site for In3+ or Ru3+ ions is higher than for ferric ions. Some of the metal ion-gastrin complexes may be useful for cancer diagnosis and therapy.

  6. High Affinity Binding of Indium and Ruthenium Ions by Gastrins

    PubMed Central

    Baldwin, Graham S.; George, Graham N.; Pushie, M. Jake

    2015-01-01

    The peptide hormone gastrin binds two ferric ions with high affinity, and iron binding is essential for the biological activity of non-amidated forms of the hormone. Since gastrins act as growth factors in gastrointestinal cancers, and as peptides labelled with Ga and In isotopes are increasingly used for cancer diagnosis, the ability of gastrins to bind other metal ions was investigated systematically by absorption spectroscopy. The coordination structures of the complexes were characterized by extended X-ray absorption fine structure (EXAFS) spectroscopy. Changes in the absorption of gastrin in the presence of increasing concentrations of Ga3+ were fitted by a 2 site model with dissociation constants (Kd) of 3.3 x 10−7 and 1.1 x 10−6 M. Although the absorption of gastrin did not change upon the addition of In3+ ions, the changes in absorbance on Fe3+ ion binding in the presence of indium ions were fitted by a 2 site model with Kd values for In3+ of 6.5 x 10−15 and 1.7 x 10−7 M. Similar results were obtained with Ru3+ ions, although the Kd values for Ru3+ of 2.6 x 10−13 and 1.2 x 10−5 M were slightly larger than observed for In3+. The structures determined by EXAFS all had metal:gastrin stoichiometries of 2:1 but, while the metal ions in the Fe, Ga and In complexes were bridged by a carboxylate and an oxygen with a metal-metal separation of 3.0–3.3 Å, the Ru complex clearly demonstrated a short range Ru—Ru separation, which was significantly shorter, at 2.4 Å, indicative of a metal-metal bond. We conclude that gastrin selectively binds two In3+ or Ru3+ ions, and that the affinity of the first site for In3+ or Ru3+ ions is higher than for ferric ions. Some of the metal ion-gastrin complexes may be useful for cancer diagnosis and therapy. PMID:26457677

  7. Evaluation of adhesion force and binding affinity of phytohemagglutinin erythroagglutinating to EGF receptor on human lung cancer cells.

    PubMed

    Kuo, W-T; Dong, G-C; Yao, C-H; Huang, J-Y; Lin, F-H

    2013-01-01

    PHA-E is a natural product extracted from red kidney beans, and it has been reported to induce cell apoptosis by blocking EGFR in lung cancer cells. Because EGF is the major in vivo competitor to PHA-E in clinical application, PHA-E must be proved that has better affinity to EGFR than EGF. This study would focus on how PHA-E tightly bind to EGFR and the results would compare with EGF. The adhesion force, measured by AFM, between EGFR and PHA-E was 207.14±74.42 pN that was higher than EGF (183.65±86.93 pN). The equilibrium dissociation constant of PHA-E and EGF to EGFR was 2.4 10(-9)±1.4 10(-9) and 7.3 10(-8)±2.7 10(-8), respectively, that could evaluate binding affinity. The result showed that binding affinity of PHA-E to EGFR was one order higher than EGF to EGFR. In the results of flow cytometer and confocal microscope, we found binding efficiency of EGF to EGFR was decrease as the concentration of PHA-E increased. In the analysis of Western blot, treatment of A-549 cells with PHA-E resulted in a dose-dependent decrease in EGFR phosphorylation. In conclusion, we found that PHA-E had better adhesion force and binding affinity to EGFR than that of the EGF. The interaction between PHA-E and EGFR could block EGF binding and then inhibit EGFR phosphorylation. PHA-E could be developed into a new target molecule for lung cancer treatment that could be immobilized on the drug carrier to guide therapeutic particles to the tumor site. PMID:23394551

  8. Evidence for monomeric and oligomeric hormone-binding domains in affinity-purified gonadotropin receptor from rat ovary

    SciTech Connect

    Zhang, Q.Y.; Menon, K.M.J. )

    1989-11-01

    Rat ovarian lutropin/choriogonadotropin receptor was purified from a Triton X-100-solubilized membrane preparation by affinity chromatography with Affi-Gel 10 coupled to purified human choriogonadotropin. The affinity-purified receptor preparations contained a single class of high-affinity binding sites for {sup 125}I-labeled human choriogonadotropin, with an equilibrium dissociation constant (K{sub d}) of 2.5 {times} 10{sup {minus}9} M, which is comparable to the K{sub d} values for membrane-bound and solubilized receptors. The purified receptor appeared as two dominant bands with molecular weights of 135,000 and 92,000 after sodium dodecyl sulfate/polyacrylamide gel electrophoresis (SDS/PAGE) under nonreducing conditions. When the individual affinity-purified receptor bands were electroeluted from the gel and analyzed again by SDS/PAGE under nonreducing conditions, both the M{sub r} 92,000 and the 135,000 proteins retained their original molecular form even when 8 M urea was included in the gel. However, when the electrophoretically purified M{sub r} 92,000 and 135,000 bands were subjected to SDS/PAGE under reducing conditions, the M{sub r} 135,000 species was almost completely converted to a M{sub r} 92,000 band, but the M{sub r} 92,000 species did not undergo any alteration in molecular weight. The results suggest that the lutropin/choriogonadotropin receptor from rat ovary exists in two molecular forms, and the higher molecular weight form appears to be composed of disulfide-linked M{sup r} 92,000 subunit, which comprises the hormone-binding domain.

  9. Sulfated Metabolites of Polychlorinated Biphenyls Are High-Affinity Ligands for the Thyroid Hormone Transport Protein Transthyretin

    PubMed Central

    Grimm, Fabian A.; Lehmler, Hans-Joachim; He, Xianran; Robertson, Larry W.

    2013-01-01

    Background: The displacement of l-thyroxine (T4) from binding sites on transthyretin (TTR) is considered a significant contributing mechanism in polychlorinated biphenyl (PCB)-induced thyroid disruption. Previous research has discovered hydroxylated PCB metabolites (OH-PCBs) as high-affinity ligands for TTR, but the binding potential of conjugated PCB metabolites such as PCB sulfates has not been explored. Objectives: We evaluated the binding of five lower-chlorinated PCB sulfates to human TTR and compared their binding characteristics to those determined for their OH-PCB precursors and for T4. Methods: We used fluorescence probe displacement studies and molecular docking simulations to characterize the binding of PCB sulfates to TTR. The stability of PCB sulfates and the reversibility of these interactions were characterized by HPLC analysis of PCB sulfates after their binding to TTR. The ability of OH-PCBs to serve as substrates for human cytosolic sulfotransferase 1A1 (hSULT1A1) was assessed by OH-PCB–dependent formation of adenosine-3´,5´-diphosphate, an end product of the sulfation reaction. Results: All five PCB sulfates were able to bind to the high-affinity binding site of TTR with equilibrium dissociation constants (Kd values) in the low nanomolar range (4.8–16.8 nM), similar to that observed for T4 (4.7 nM). Docking simulations provided corroborating evidence for these binding interactions and indicated multiple high-affinity modes of binding. All OH-PCB precursors for these sulfates were found to be substrates for hSULT1A1. Conclusions: Our findings show that PCB sulfates are high-affinity ligands for human TTR and therefore indicate, for the first time, a potential relevance for these metabolites in PCB-induced thyroid disruption. PMID:23584369

  10. Hyperglycemia associated dissociative fugue (organic dissociative disorder) in an elderly

    PubMed Central

    Ram, Dushad; Ashoka, H. G; Gowdappa, Basavnna

    2015-01-01

    Inadequate glycemic control in patients with diabetes is known to be associated with psychiatric disorders such as depression, anxiety disorder, and cognitive impairment. However, dissociative syndrome has not been reported so far. Here we are reporting a case of repeated dissociative fugue associated with hyperglycemia, in an elderly with type II diabetes. Possible neurobiological mechanism has been discussed. PMID:26286620

  11. Ionic molal conductivities, activity coefficients, and dissociation constants of HAsO42 − and H2AsO4− from 5 to 90 °C and ionic strengths from 0.001 up to 3 mol kg− 1 and applications in natural systems

    USGS Publications Warehouse

    Zhu, Xiangyu; Nordstrom, D Kirk; McCleskey, R. Blaine; Wang, Rucheng

    2016-01-01

    Arsenic is known to be one of the most toxic inorganic elements, causing worldwide environmental contamination. However, many fundamental properties related to aqueous arsenic species are not well known which will inhibit our ability to understand the geochemical behavior of arsenic (e.g. speciation, transport, and solubility). Here, the electrical conductivity of Na2HAsO4 solutions has been measured over the concentration range of 0.001–1 mol kg− 1 and the temperature range of 5–90 °C. Ionic strength and temperature-dependent equations were derived for the molal conductivity of HAsO42 −and H2AsO4− aqueous ions. Combined with speciation calculations and the approach used by McCleskey et al. (2012b), these equations can be used to calculate the electrical conductivities of arsenic-rich waters having a large range of effective ionic strengths (0.001–3 mol kg− 1) and temperatures (5–90 °C). Individual ion activity coefficients for HAsO42 − and H2AsO4− in the form of the Hückel equation were also derived using the mean salt method and the mean activity coefficients of K2HAsO4 (0.001–1 mol kg− 1) and KH2AsO4 (0.001–1.3 mol kg− 1). A check on these activity coefficients was made by calculating mean activity coefficients for Na2HAsO4 and NaH2AsO4 solutions and comparing them to measured values. At the same time Na-arsenate complexes were evaluated. The NaH2AsO40 ion pair is negligible in NaH2AsO4 solutions up to 1.3 mol kg− 1. The NaHAsO4− ion pair is important in NaHAsO4 solutions > 0.1 mol kg− 1 and the formation constant of 100.69 was confirmed. The enthalpy, entropy, free energy and heat capacity for the second and third arsenic acid dissociation reactions were calculated from pH measurements. These properties have been incorporated into a widely used geochemical calculation code WATEQ4F and applied to natural arsenic waters. For arsenic spiked water samples from Yellowstone National Park, the mean difference

  12. Effect of heme modification on oxygen affinity of myoglobin and equilibrium of the acid-alkaline transition in metmyoglobin.

    PubMed

    Shibata, Tomokazu; Nagao, Satoshi; Fukaya, Masashi; Tai, Hulin; Nagatomo, Shigenori; Morihashi, Kenji; Matsuo, Takashi; Hirota, Shun; Suzuki, Akihiro; Imai, Kiyohiro; Yamamoto, Yasuhiko

    2010-05-01

    Functional regulation of myoglobin (Mb) is thought to be achieved through the heme environment furnished by nearby amino acid residues, and subtle tuning of the intrinsic heme Fe reactivity. We have performed substitution of strongly electron-withdrawing perfluoromethyl (CF(3)) group(s) as heme side chain(s) of Mb to obtain large alterations of the heme electronic structure in order to elucidate the relationship between the O(2) affinity of Mb and the electronic properties of heme peripheral side chains. We have utilized the equilibrium constant (pK(a)) of the "acid-alkaline transition" in metmyoglobin in order to quantitatively assess the effects of the CF(3) substitutions for the electron density of heme Fe atom (rho(Fe)) of the protein. The pK(a) value of the protein was found to decrease by approximately 1 pH unit upon the introduction of one CF(3) group, and the decrease in the pK(a) value with decreasing the rho(Fe) value was confirmed by density functional theory calculations on some model compounds. The O(2) affinity of Mb was found to correlate well with the pK(a) value in such a manner that the P(50) value, which is the partial pressure of O(2) required to achieve 50% oxygenation, increases by a factor of 2.7 with a decrease of 1 pK(a) unit. Kinetic studies on the proteins revealed that the decrease in O(2) affinity upon the introduction of an electron-withdrawing CF(3) group is due to an increase in the O(2) dissociation rate. Since the introduction of a CF(3) group substitution is thought to prevent further Fe(2+)-O(2) bond polarization and hence formation of a putative Fe(3+)-O(2)(-)-like species of the oxy form of the protein [Maxwell, J. C.; Volpe, J. A.; Barlow, C. H.; Caughey, W. S. Biochem. Biophys. Res. Commun. 1974, 58, 166-171], the O(2) dissociation is expected to be enhanced by the substitution of electron-withdrawing groups as heme side chains. We also found that, in sharp contrast to the case of the O(2) binding to the protein, the CO

  13. Surfactant protein A binds TGF-β1 with high affinity and stimulates the TGF-β pathway.

    PubMed

    Willems, Coen H M P; Zimmermann, Luc J I; Kloosterboer, Nico; Kramer, Boris W; van Iwaarden, J Freek

    2014-02-01

    We were able to demonstrate reversible, specific and high-affinity binding of radioactively-labelled TGF-β1 ((125)I-TGF-β1) to immobilized surfactant protein A (SP-A), with an apparent dissociation constant of 53 picomolar at ∼21. Addition of a 200-fold molar excess of the latency associated peptide (LAP) prevented and dissociated the binding of (125)I-TGF-β1 to SP-A, whereas latent TGF-β1 had no effect. Using a bioassay for TGF-β1 activity--a luciferase reporter assay--we were able to show that SP-A in the presence of TGF-β1 stimulated the TGF-β1 pathway, whereas SP-A alone had no effect. Studies with structural analogues of the distinct SP-A tail domain and head domain indicated that stimulatory activity of SP-A resided in the head domain. No activation of latent TGF-β1 by SP-A was observed. In addition, we observed that SP-A inhibited TGF-β1 inactivation by LAP. These results indicate that SP-A may have a regulatory role in the TGF-β1-mediated processes in the lung. PMID:23685990

  14. Dissociative States and Neural Complexity

    ERIC Educational Resources Information Center

    Bob, Petr; Svetlak, Miroslav

    2011-01-01

    Recent findings indicate that neural mechanisms of consciousness are related to integration of distributed neural assemblies. This neural integration is particularly vulnerable to past stressful experiences that can lead to disintegration and dissociation of consciousness. These findings suggest that dissociation could be described as a level of…

  15. Dissociation Patterns in Evolving Populations

    NASA Astrophysics Data System (ADS)

    Moreno, F. J.; Hernández, J. A.; Sánchez, F.

    2011-09-01

    The recent explosion and availability of mobility based technologies such as geographic information systems, cell phones equipped with built-in GPS, among others, are a valuable source of spatio-temporal data. However, only recently there have been works focused on identifying movement patterns in groups of moving entities. We focus on a particular movement pattern: dissociation. A dissociation pattern occurs when an entity that was once associated to a population, eventually separated from it and subsequently reintegrated it again. The backwarding and forwarding patterns are a type of dissociation where an entity stays behind or ahead of another entity, respectively. Dissociation really is a diversity generator, so instead avoiding it, taking advantage could be better to prevent premature convergence in evolutionary algorithms. In this work, we present formal mathematical definitions for these patterns. A discussion of how to use dissociation patterns as a mean to preserve diversity in evolutionary algorithms is also shown.

  16. Presynaptic alpha-2 adrenoceptor activation and coupling of the receptor-presynaptic effector system in the perfused rat heart: affinity and efficacy of phenethylamines and imidazoline derivatives.

    PubMed

    Fuder, H; Braun, H J; Schimkus, R

    1986-04-01

    The right sympathetic nerves of perfused rat hearts were stimulated in the presence of inhibitors of neuronal and extraneuronal uptake and propranolol. The inhibition by alpha adrenoceptor agonists of stimulation-evoked (10 pulses, 0.1 Hz) [3H]norepinephrine (NE) overflow into the perfusate was taken as a parameter of presynaptic adrenoceptor activation. Under the present conditions, autoinhibition of NE release is not activated by endogenous NE as evident from ineffectiveness of adrenoceptor antagonists in facilitating evoked [3H]NE overflow. The potency (EC50, -log10), affinity (agonist-presynaptic receptor dissociation constant KA, -log10) and relative efficacies (RE) were determined for phenethylamines (NE or alpha-methylepinephrine) and for imidazoline derivatives. NE (-log EC50, 7.76) was 0.88 log units more potent than alpha-methylepinephrine (-log EC50, 6.88) and about the same difference was observed for the -log KA values (5.92 vs. 4.75). RE were similar (NE, 100%; alpha methylepinephrine, 98%) and 22- to 50-fold higher than efficacies of imidazoline derivatives. Hydroxylations in positions 3 and 4 of the phenyl moiety of phenylaminoimidazoline (-log EC50, less than 5; -log KA, less than 5; RE, less than 1%) resulted in a marked increase in potency (-log EC50, 8.32) of the resulting dihydroxyphenylaminoimidazoline due to a high affinity (-log KA, 8.22) at a low efficacy (2% of NE). In contrast, hydroxylation in positions 3 and 4 of the phenyl ring of tolazoline (no agonist activity under the present conditions; antagonist affinity constant from the literature, 6.4-6.6) produced dihydroxytolazoline, a moderately potent agonist (-log EC50, 7.25) with an efficacy of 3.5% at an affinity (-log KA, 6.92) not much different from that of tolazine.(ABSTRACT TRUNCATED AT 250 WORDS)

  17. Magneto-nanosensor platform for probing low-affinity protein-protein interactions and identification of a low-affinity PD-L1/PD-L2 interaction.

    PubMed

    Lee, Jung-Rok; Bechstein, Daniel J B; Ooi, Chin Chun; Patel, Ashka; Gaster, Richard S; Ng, Elaine; Gonzalez, Lino C; Wang, Shan X

    2016-01-01

    Substantial efforts have been made to understand the interactions between immune checkpoint receptors and their ligands targeted in immunotherapies against cancer. To carefully characterize the complete network of interactions involved and the binding affinities between their extracellular domains, an improved kinetic assay is needed to overcome limitations with surface plasmon resonance (SPR). Here, we present a magneto-nanosensor platform integrated with a microfluidic chip that allows measurement of dissociation constants in the micromolar-range. High-density conjugation of magnetic nanoparticles with prey proteins allows multivalent receptor interactions with sensor-immobilized bait proteins, more closely mimicking natural-receptor clustering on cells. The platform has advantages over traditional SPR in terms of insensitivity of signal responses to pH and salinity, less consumption of proteins and better sensitivities. Using this platform, we characterized the binding affinities of the PD-1-PD-L1/PD-L2 co-inhibitory receptor system, and discovered an unexpected interaction between the two known PD-1 ligands, PD-L1 and PD-L2. PMID:27447090

  18. Magneto-nanosensor platform for probing low-affinity protein–protein interactions and identification of a low-affinity PD-L1/PD-L2 interaction

    PubMed Central

    Lee, Jung-Rok; Bechstein, Daniel J. B.; Ooi, Chin Chun; Patel, Ashka; Gaster, Richard S.; Ng, Elaine; Gonzalez, Lino C.; Wang, Shan X.

    2016-01-01

    Substantial efforts have been made to understand the interactions between immune checkpoint receptors and their ligands targeted in immunotherapies against cancer. To carefully characterize the complete network of interactions involved and the binding affinities between their extracellular domains, an improved kinetic assay is needed to overcome limitations with surface plasmon resonance (SPR). Here, we present a magneto-nanosensor platform integrated with a microfluidic chip that allows measurement of dissociation constants in the micromolar-range. High-density conjugation of magnetic nanoparticles with prey proteins allows multivalent receptor interactions with sensor-immobilized bait proteins, more closely mimicking natural-receptor clustering on cells. The platform has advantages over traditional SPR in terms of insensitivity of signal responses to pH and salinity, less consumption of proteins and better sensitivities. Using this platform, we characterized the binding affinities of the PD-1—PD-L1/PD-L2 co-inhibitory receptor system, and discovered an unexpected interaction between the two known PD-1 ligands, PD-L1 and PD-L2. PMID:27447090

  19. A mutant trypsin-like enzyme from Streptomyces fradiae, created by site-directed mutagenesis, improves affinity chromatography for protein trypsin inhibitors.

    PubMed

    Katoh, T; Kikuchi, N; Nagata, K; Yoshida, N

    1996-08-01

    The Ser-170 residue of a trypsin-like enzyme from Streptomyces fradiae (SFT), which is considered to be the active-site serine, was replaced with alanine by site-directed mutagenesis to improve the affinity chromatography step for a Kazal-type trypsin inhibitor pancreatic secretory trypsin inhibitor (PSTI). The resulting mutant SFT, designated as [S170A]SFT, was expressed in Streptomyces lividans and purified to homogeneity. [S170A]SFT was catalytically inactive, but still had the ability to bind tightly to PSTI and to soybean trypsin inhibitor with dissociation constants of 3.1 x 10(-7) M and 1.9 x 10(-8) M respectively. We further demonstrated that recombinant human PSTI secreted into Saccharomyces cerevisiae culture broth could be purified to homogeneity with a one-step [S170A]SFT-affinity column. The purified PSTI contained no molecules intramolecularly cleaved by active trypsin, which are found when trypsin-affinity chromatography is used for the purification. This eliminated the need for further separation of intact PSTI from intramolecularly cleaved PSTI by high-performance liquid chromatography, thus simplifying and improving its purification process.

  20. FYWHCLDE-based affinity chromatography of IgG: effect of ligand density and purifications of human IgG and monoclonal antibody.

    PubMed

    Zhao, Wei-Wei; Shi, Qing-Hong; Sun, Yan

    2014-08-15

    This work reports the development of an octapeptide-based affinity adsorbent for the purification of human IgG (hIgG) and monoclonal antibody (mAb). The octapeptide was FYWHCLDE selected earlier by the biomimetic design of affinity peptide ligands for hIgG. The ligand was coupled to Sepharose gel at four densities from 10.4 to 31.0μmol/mL, and the effect of peptide density on the adsorption of hIgG and bovine serum albumin (BSA) was first investigated. The binding capacity of hIgG increased from 104.2 to 176.4mg/mL within the ligand density range, and the binding affinity (dissociation constant) kept at 2.4-3.7μM. Batch adsorption revealed that the selectivity of FYWHCLDE-Sepharose for IgG was 30-40 times over BSA. The effective pore diffusivity of IgG decreased somewhat with increasing ligand density, but the dynamic binding capacity at 10% breakthrough, measured by using 10-fold diluted human serum as feedstock, doubled with increasing ligand density from 10.4 to 31.0μmol/mL due to the remarkable increase of static binding capacity. By using the affinity column with a ligand density of 23.9μmol/mL, hIgG and humanized mAb purifications from human serum and cell culture supernatant, respectively, were achieved at high purities and recovery yields. Finally, the robustness of the peptide gel was demonstrated by recycled use of the affinity column in 20 breakthrough cycles. PMID:24947889

  1. Solubilization of high affinity corticotropin-releasing factor receptors from rat brain: Characterization of an active digitonin-solubilized receptor complex

    SciTech Connect

    Grigoriadis, D.E.; Zaczek, R.; Pearsall, D.M.; De Souza, E.B. )

    1989-12-01

    The binding characteristics of CRF receptors in rat frontal cerebral cortex membranes solubilized in 1% digitonin were determined. The binding of (125I)Tyro-ovine CRF ((125I)oCRF) to solubilized membrane proteins was dependent on incubation time, temperature, and protein concentration, was saturable and of high affinity, and was absent in boiled tissue. The solubilized receptors retained their high affinity for (125I) oCRF in the solubilized state, exhibiting a dissociation constant (KD) of approximately 200 pM, as determined by direct binding saturation isotherms. Solubilized CRF receptors maintained the rank order of potencies for various related and unrelated CRF peptides characteristic of the membrane CRF receptor: rat/human CRF congruent to ovine CRF congruent to Nle21,38-rat CRF greater than alpha-helical oCRF-(9-41) greater than oCRF-(7-41) much greater than vasoactive intestinal peptide, arginine vasopressin, or the substance-P antagonist. Furthermore, the absolute potencies (Ki values) for the various CRF-related peptides in solubilized receptors were almost identical to those observed in the membrane preparations, indicating that the CRF receptor retained its high affinity binding capacity in the digitonin-solubilized state. Chemical affinity cross-linking of digitonin-solubilized rat cortical membrane proteins revealed a specifically labeled protein with an apparent mol wt of 58,000 which was similar to the labeled protein in native membrane homogenates. Although solubilized CRF receptors retained their high affinity for agonists, their sensitivity for guanine nucleotide was lost. Size exclusion chromatography substantiated these results, demonstrating that in the presence or absence of guanine nucleotides, (125I)oCRF labeled the same size receptor complex.

  2. PHARMACEUTICAL AND BIOMEDICAL APPLICATIONS OF AFFINITY CHROMATOGRAPHY: RECENT TRENDS AND DEVELOPMENTS

    PubMed Central

    Hage, David S.; Anguizola, Jeanethe A.; Bi, Cong; Li, Rong; Matsuda, Ryan; Papastavros, Efthimia; Pfaunmiller, Erika; Vargas, John; Zheng, Xiwei

    2012-01-01

    Affinity chromatography is a separation technique that has become increasingly important in work with biological samples and pharmaceutical agents. This method is based on the use of a biologically-related agent as a stationary phase to selectively retain analytes or to study biological interactions. This review discusses the basic principles behind affinity chromatography and examines recent developments that have occurred in the use of this method for biomedical and pharmaceutical analysis. Techniques based on traditional affinity supports are discussed, but an emphasis is placed on methods in which affinity columns are used as part of HPLC systems or in combination with other analytical methods. General formats for affinity chromatography that are considered include step elution schemes, weak affinity chromatography, affinity extraction and affinity depletion. Specific separation techniques that are examined include lectin affinity chromatography, boronate affinity chromatography, immunoaffinity chromatography, and immobilized metal ion affinity chromatography. Approaches for the study of biological interactions by affinity chromatography are also presented, such as the measurement of equilibrium constants, rate constants, or competition and displacement effects. In addition, related developments in the use of immobilized enzyme reactors, molecularly imprinted polymers, dye ligands and aptamers are briefly considered. PMID:22305083

  3. The dissociative disorders. Rarely considered and underdiagnosed.

    PubMed

    Coons, P M

    1998-09-01

    A wide variety of dissociative disorders, including dissociative amnesia, dissociative fugue, depersonalization disorder, dissociative identity disorder, and various forms of dissociative disorder not otherwise specified. In many instances, these disorders are either underdiagnosed or misdiagnosed secondary to the clinician's mistaken belief that dissociative disorders are rare. Recent research shows that dissociative disorders may comprise 5% to 10% of psychiatric populations. This article reviews the epidemiology and clinical symptomatology of these disorders. In addition, various screening and diagnostic instruments, such as the DES, Structured Clinical Interview for Dissociative Disorders, and MMPI, are discussed.

  4. Affine differential geometry analysis of human arm movements.

    PubMed

    Flash, Tamar; Handzel, Amir A

    2007-06-01

    Humans interact with their environment through sensory information and motor actions. These interactions may be understood via the underlying geometry of both perception and action. While the motor space is typically considered by default to be Euclidean, persistent behavioral observations point to a different underlying geometric structure. These observed regularities include the "two-thirds power law", which connects path curvature with velocity, and "local isochrony", which prescribes the relation between movement time and its extent. Starting with these empirical observations, we have developed a mathematical framework based on differential geometry, Lie group theory and Cartan's moving frame method for the analysis of human hand trajectories. We also use this method to identify possible motion primitives, i.e., elementary building blocks from which more complicated movements are constructed. We show that a natural geometric description of continuous repetitive hand trajectories is not Euclidean but equi-affine. Specifically, equi-affine velocity is piecewise constant along movement segments, and movement execution time for a given segment is proportional to its equi-affine arc-length. Using this mathematical framework, we then analyze experimentally recorded drawing movements. To examine movement segmentation and classification, the two fundamental equi-affine differential invariants-equi-affine arc-length and curvature are calculated for the recorded movements. We also discuss the possible role of conic sections, i.e., curves with constant equi-affine curvature, as motor primitives and focus in more detail on parabolas, the equi-affine geodesics. Finally, we explore possible schemes for the internal neural coding of motor commands by showing that the equi-affine framework is compatible with the common model of population coding of the hand velocity vector when combined with a simple assumption on its dynamics. We then discuss several alternative explanations

  5. Effects of Peptide Backbone Amide-to-Ester Bond Substitution on the Cleavage Frequency in Electron Capture Dissociation and Collision-Activated Dissociation

    NASA Astrophysics Data System (ADS)

    Kjeldsen, Frank; Zubarev, Roman A.

    2011-08-01

    Probing the mechanism of electron capture dissociation on variously modified model peptide polycations has resulted in discovering many ways to prevent or reduce {{N}} - {{{C}}_α } bond fragmentation. Here we report on a rare finding of how to increase the backbone bond dissociation rate. In a number of model peptides, amide-to-ester backbone bond substitution increased the frequency of {{O}} - {{{C}}_α } bond cleavage (an analogue of {{N}} - {{{C}}_α } bonds in normal peptides) by several times, at the expense of reduced frequency of cleavages of the neighboring {{N}} - {{{C}}_α } bonds. In contrast, the ester linkage was only marginally broken in collisional dissociation. These results further highlight the complementarity of the reaction mechanisms in electron capture dissociation (ECD) and collision-activated dissociation (CAD). It is proposed that the effects of amide-to-ester bond substitution on fragmentation are mainly due to the differences in product ion stability (ECD, CAD) as well as proton affinity (CAD). This proposal is substantiated by calculations using density functional theory. The implications of these results in relation to the current understanding of the mechanisms of electron capture dissociation and electron transfer dissociation are discussed.

  6. Effectors of hemoglobin. Separation of allosteric and affinity factors.

    PubMed Central

    Marden, M C; Bohn, B; Kister, J; Poyart, C

    1990-01-01

    The relative contributions of the allosteric and affinity factors toward the change in p50 have been calculated for a series of effectors of hemoglobin (Hb). Shifts in the ligand affinity of deoxy Hb and the values for 50% ligand saturation (p50) were obtained from oxygen equilibrium data. Because the high-affinity parameters (liganded conformation) are poorly determined from the equilibrium curves, they were determined from kinetic measurements of the association and dissociation rates with CO as ligand. The CO on-rates were obtained by flash photolysis measurements. The off-rates were determined from the rate of oxidation of HbCO by ferricyanide, or by replacement of CO with NO. The partition function of fully liganded hemoglobin for oxygen and CO is only slightly changed by the effectors. Measurements were made in the presence of the effectors 2,3-diphosphoglycerate (DPG), inositol hexakisphosphate (IHP), bezafibrate (Bzf), and two recently synthesized derivatives of Bzf (LR16 and L35). Values of p50 change by over a factor of 60; the on-rates decrease by nearly a factor of 8, with little change in the off-rates for the liganded conformation. The data indicate that both allosteric and affinity parameters are changed by the effectors; the changes in ligand affinity represent the larger contribution toward shifts in p50. PMID:2306490

  7. Critical factors governing the difference in antizyme-binding affinities between human ornithine decarboxylase and antizyme inhibitor.

    PubMed

    Liu, Yen-Chin; Liu, Yi-Liang; Su, Jia-Yang; Liu, Guang-Yaw; Hung, Hui-Chih

    2011-01-01

    Both ornithine decarboxylase (ODC) and its regulatory protein, antizyme inhibitor (AZI), can bind with antizyme (AZ), but the latter has a higher AZ-binding affinity. The results of this study clearly identify the critical amino acid residues governing the difference in AZ-binding affinities between human ODC and AZI. Inhibition experiments using a series of ODC mutants suggested that residues 125 and 140 may be the key residues responsible for the differential AZ-binding affinities. The ODC_N125K/M140K double mutant demonstrated a significant inhibition by AZ, and the IC(50) value of this mutant was 0.08 µM, three-fold smaller than that of ODC_WT. Furthermore, the activity of the AZ-inhibited ODC_N125K/M140K enzyme was hardly rescued by AZI. The dissociation constant (K(d)) of the [ODC_N125K/M140K]-AZ heterodimer was approximately 0.02 µM, which is smaller than that of WT_ODC by approximately 10-fold and is very close to the K(d) value of AZI_WT, suggesting that ODC_N125K/M140K has an AZ-binding affinity higher than that of ODC_WT and similar to that of AZI. The efficiency of the AZI_K125N/K140M double mutant in the rescue of AZ-inhibited ODC enzyme activity was less than that of AZI_WT. The K(d) value of [AZI_K125N/K140M]-AZ was 0.18 µM, nine-fold larger than that of AZI_WT and close to the K(d) value of ODC_WT, suggesting that AZI_K125N/K140M has an AZ-binding affinity lower than that of AZI_WT and similar to that of ODC. These data support the hypothesis that the differences in residues 125 and 140 in ODC and AZI are responsible for the differential AZ-binding affinities. PMID:21552531

  8. Adjoint affine fusion and tadpoles

    NASA Astrophysics Data System (ADS)

    Urichuk, Andrew; Walton, Mark A.

    2016-06-01

    We study affine fusion with the adjoint representation. For simple Lie algebras, elementary and universal formulas determine the decomposition of a tensor product of an integrable highest-weight representation with the adjoint representation. Using the (refined) affine depth rule, we prove that equally striking results apply to adjoint affine fusion. For diagonal fusion, a coefficient equals the number of nonzero Dynkin labels of the relevant affine highest weight, minus 1. A nice lattice-polytope interpretation follows and allows the straightforward calculation of the genus-1 1-point adjoint Verlinde dimension, the adjoint affine fusion tadpole. Explicit formulas, (piecewise) polynomial in the level, are written for the adjoint tadpoles of all classical Lie algebras. We show that off-diagonal adjoint affine fusion is obtained from the corresponding tensor product by simply dropping non-dominant representations.

  9. Are major dissociative disorders characterized by a qualitatively different kind of dissociation?

    PubMed

    Rodewald, Frauke; Dell, Paul F; Wilhelm-Gossling, Claudia; Gast, Ursula

    2011-01-01

    A total of 66 patients with a major dissociative disorder, 54 patients with nondissociative disorders, and 30 nonclinical controls were administered the Structured Clinical Interview for DSM-IV Dissociative Disorders-Revised, the Dissociative Experiences Scale, the Multidimensional Inventory of Dissociation, and the Symptom Checklist 90-Revised. Dissociative patients reported significantly more dissociative and nondissociative symptoms than did nondissociative patients and nonclinical controls. When general psychopathology was controlled, the dissociation scores of dissociative patients were still significantly higher than those of both other groups, whereas the dissociation scores of nondissociative patients and nonclinical controls no longer differed. These findings appear to be congruent with a typological model of dissociation that distinguishes between 2 qualitatively different kinds of dissociation. Specifically, the results of this study suggest that the dissociation that occurs in major dissociative disorders (i.e., dissociative identity disorder [DID] and dissociative disorder not otherwise specified, Type 1 [DDNOS-1]) is qualitatively different from the dissociation that occurs in persons who do not have a dissociative disorder. In contrast to previous research, the dissociation of persons who do not have a dissociative disorder is not limited to absorption; it covers a much wider range of phenomena. The authors hypothesize that different mechanisms produce the dissociation of persons with DID and DDNOS-1 as opposed to the dissociation of persons who do not have a dissociative disorder.

  10. Structural Basis of Low-Affinity Nickel Binding to the Nickel-Responsive Transcription Factor NikR from Escherichia coli

    SciTech Connect

    Phillips, C.; Schreiter, E; Stultz, C; Drennan, C

    2010-01-01

    Escherichia coli NikR regulates cellular nickel uptake by binding to the nik operon in the presence of nickel and blocking transcription of genes encoding the nickel uptake transporter. NikR has two binding affinities for the nik operon: a nanomolar dissociation constant with stoichiometric nickel and a picomolar dissociation constant with excess nickel [Bloom, S. L., and Zamble, D. B. (2004) Biochemistry 43, 10029-10038; Chivers, P. T., and Sauer, R. T. (2002) Chem. Biol. 9, 1141-1148]. While it is known that the stoichiometric nickel ions bind at the NikR tetrameric interface [Schreiter, E. R., et al. (2003) Nat. Struct. Biol. 10, 794-799; Schreiter, E. R., et al. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 13676-13681], the binding sites for excess nickel ions have not been fully described. Here we have determined the crystal structure of NikR in the presence of excess nickel to 2.6 {angstrom} resolution and have obtained nickel anomalous data (1.4845 {angstrom}) in the presence of excess nickel for both NikR alone and NikR cocrystallized with a 30-nucleotide piece of double-stranded DNA containing the nik operon. These anomalous data show that excess nickel ions do not bind to a single location on NikR but instead reveal a total of 22 possible low-affinity nickel sites on the NikR tetramer. These sites, for which there are six different types, are all on the surface of NikR, and most are found in both the NikR alone and NikR-DNA structures. Using a combination of crystallographic data and molecular dynamics simulations, the nickel sites can be described as preferring octahedral geometry, utilizing one to three protein ligands (typically histidine) and at least two water molecules.

  11. Allowance for antibody bivalence in the determination of association rate constants by kinetic exclusion assay.

    PubMed

    Winzor, Donald J

    2013-10-15

    This investigation completes the amendment of theoretical expressions for the characterization of antigen-antibody interactions by kinetic exclusion assay-an endeavor that has been marred by inadequate allowance for the consequences of antibody bivalence in its uptake by the affinity matrix (immobilized antigen) that is used to ascertain the fraction of free antibody sites in a solution with defined total concentrations of antigen and antibody. A simple illustration of reacted site probability considerations in action confirms that the square root of the fluorescence response ratio, R(Ag)/R₀, needs to be taken in order to determine the fraction of unoccupied antibody sites, which is the parameter employed to describe the kinetics of antigen uptake in the mixture of antigen and antibody with defined initial composition. The approximately 2-fold underestimation of the association rate constant (k(a)) that emanates from the usual practice of omitting the square root factor gives rise to a corresponding overestimate of the equilibrium dissociation constant (K(d))--a situation that is also encountered in the thermodynamic characterization of antigen-antibody interactions by kinetic exclusion assay. PMID:23851342

  12. Somatostatin binding to dissociated cells from rat cerebral cortex

    SciTech Connect

    Colas, B.; Prieto, J.C.; Arilla, E. )

    1990-11-01

    A method has been developed for the study of somatostatin (SS) binding to dissociated cells from rat cerebral cortex. Binding of {sup 125}I (Tyr11)SS to cells obtained by mechanical dissociation of rat cerebral cortex was dependent on time and temperature, saturable, reversible and highly specific. Under conditions of equilibrium, i.e., 60 min at 25 degrees C, native SS inhibited tracer binding in a dose-dependent manner. The Scatchard analysis of binding data was linear and yielded a dissociation constant of 0.60 +/- 0.08 nM with a maximal binding capacity of 160 +/- 16 fmol/mg protein. The binding of {sup 125}I (Tyr11)SS was specific as shown in experiments on tracer displacement by the native peptides, SS analogues, and unrelated peptides.

  13. KINETIC STUDIES OF DRUG-PROTEIN INTERACTIONS BY USING PEAK PROFILING AND HIGH-PERFORMANCE AFFINITY CHROMATOGRAPHY: EXAMINATION OF MULTI-SITE INTERACTIONS OF DRUGS WITH HUMAN SERUM ALBUMIN COLUMNS

    PubMed Central

    Tong, Zenghan; Schiel, John E.; Papastavros, Efthimia; Ohnmacht, Corey M.; Smith, Quentin R.; Hage, David S.

    2010-01-01

    Carbamazepine and imipramine are drugs that have significant binding to human serum albumin (HSA), the most abundant serum protein in blood and a common transport protein for many drugs in the body. Information on the kinetics of these drug interactions with HSA would be valuable in understanding the pharmacokinetic behavior of these drugs and could provide data that might lead to the creation of improved assays for these analytes in biological samples. In this report, an approach based on peak profiling was used with high-performance affinity chromatography to measure the dissociation rate constants for carbamazepine and imipramine with HSA. This approach compared the elution profiles for each drug and a non-retained species on an HSA column and control column over a board range of flow rates. Various approaches for the corrections of non-specific binding between these drugs and the support were considered and compared in this process. Dissociation rate constants of 1.7 (± 0.2) s-1 and 0.67 (± 0.04) s-1 at pH 7.4 and 37 °C were estimated by this approach for HSA in its interactions with carbamazepine and imipramine, respectively. These results gave good agreement with rate constants that have determined by other methods or for similar solute interactions with HSA. The approach described in this report for kinetic studies is not limited to these particular drugs or HSA but can also be extended to other drugs and proteins. PMID:21067755

  14. Molar absorption coefficients and stability constants of metal complexes of 4-(2-pyridylazo)resorcinol (PAR): Revisiting common chelating probe for the study of metalloproteins.

    PubMed

    Kocyła, Anna; Pomorski, Adam; Krężel, Artur

    2015-11-01

    4-(2-Pyridylazo)resorcinol (PAR) is one of the most popular chromogenic chelator used in the determination of the concentrations of various metal ions from the d, p and f blocks and their affinities for metal ion-binding biomolecules. The most important characteristics of such a sensor are the molar absorption coefficient and the metal-ligand complex dissociation constant. However, it must be remembered that these values are dependent on the specific experimental conditions (e.g. pH, solvent components, and reactant ratios). If one uses these values to process data obtained in different conditions, the final result can be under- or overestimated. We aimed to establish the spectral properties and the stability of PAR and its complexes accurately with Zn(2+), Cd(2+), Hg(2+), Co(2+), Ni(2+), Cu(2+), Mn(2+) and Pb(2+) at a multiple pH values. The obtained results account for the presence of different species of metal-PAR complexes in the physiological pH range of 5 to 8 and have been frequently neglected in previous studies. The effective molar absorption coefficient at 492 nm for the ZnHx(PAR)2 complex at pH7.4 in buffered water solution is 71,500 M(-1) cm(-1), and the dissociation constant of the complex in these conditions is 7.08×10(-13) M(2). To confirm these values and estimate the range of the dissociation constants of zinc-binding biomolecules that can be measured using PAR, we performed several titrations of zinc finger peptides and zinc chelators. Taken together, our results provide the updated parameters that are applicable to any experiment conducted using inexpensive and commercially available PAR.

  15. Dissociative disorders in DSM-5.

    PubMed

    Spiegel, David; Lewis-Fernández, Roberto; Lanius, Ruth; Vermetten, Eric; Simeon, Daphne; Friedman, Matthew

    2013-01-01

    The rationale, research literature, and proposed changes to the dissociative disorders and conversion disorder in the fifth edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) are presented. Dissociative identity disorder will include reference to possession as well as identity fragmentation, to make the disorder more applicable to culturally diverse situations. Dissociative amnesia will include dissociative fugue as a subtype, since fugue is a rare disorder that always involves amnesia but does not always include confused wandering or loss of personality identity. Depersonalization disorder will include derealization as well, since the two often co-occur. A dissociative subtype of posttraumatic stress disorder (PTSD), defined by the presence of depersonalization or derealization in addition to other PTSD symptoms, is being recommended, based upon new epidemiological and neuroimaging evidence linking it to an early life history of adversity and a combination of frontal activation and limbic inhibition. Conversion disorder (functional neurological symptom disorder) will likely remain with the somatic symptom disorders, despite considerable dissociative comorbidity. PMID:23394228

  16. Dissociative disorders in DSM-5.

    PubMed

    Spiegel, David; Lewis-Fernández, Roberto; Lanius, Ruth; Vermetten, Eric; Simeon, Daphne; Friedman, Matthew

    2013-01-01

    The rationale, research literature, and proposed changes to the dissociative disorders and conversion disorder in the fifth edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) are presented. Dissociative identity disorder will include reference to possession as well as identity fragmentation, to make the disorder more applicable to culturally diverse situations. Dissociative amnesia will include dissociative fugue as a subtype, since fugue is a rare disorder that always involves amnesia but does not always include confused wandering or loss of personality identity. Depersonalization disorder will include derealization as well, since the two often co-occur. A dissociative subtype of posttraumatic stress disorder (PTSD), defined by the presence of depersonalization or derealization in addition to other PTSD symptoms, is being recommended, based upon new epidemiological and neuroimaging evidence linking it to an early life history of adversity and a combination of frontal activation and limbic inhibition. Conversion disorder (functional neurological symptom disorder) will likely remain with the somatic symptom disorders, despite considerable dissociative comorbidity.

  17. Electrochemical and theoretical analysis of the reactivity of shikonin derivatives: dissociative electron transfer in esterified compounds.

    PubMed

    Armendáriz-Vidales, Georgina; Frontana, Carlos

    2014-09-01

    An electrochemical and theoretical analysis of a series of shikonin derivatives in aprotic media is presented. Results showed that the first electrochemical reduction signal is a reversible monoelectronic transfer, generating a stable semiquinone intermediate; the corresponding E(I)⁰ values were correlated with calculated values of electroaccepting power (ω(+)) and adiabatic electron affinities (A(Ad)), obtained with BH and HLYP/6-311++G(2d,2p) and considering the solvent effect, revealing the influence of intramolecular hydrogen bonding and the substituting group at position C-2 in the experimental reduction potential. For the second reduction step, esterified compounds isobutyryl and isovalerylshikonin presented a coupled chemical reaction following dianion formation. Analysis of the variation of the dimensionless cathodic peak potential values (ξ(p)) as a function of the scan rate (v) functions and complementary experiments in benzonitrile suggested that this process follows a dissociative electron transfer, in which the rate of heterogeneous electron transfer is slow (~0.2 cm s(-1)), and the rate constant of the chemical process is at least 10(5) larger. PMID:25007856

  18. Affinity and efficacy of racemic, (+)-, and (-)-methacholine in muscarinic inhibition of [3H]-noradrenaline release.

    PubMed

    Fuder, H; Jung, B

    1985-02-01

    The right postganglionic sympathetic nerves of rat isolated perfused hearts (previously loaded with [3H]-noradrenaline) were stimulated electrically with 10 trains of 10 pulses at 10 Hz. The inhibition by methacholine of stimulation-evoked [3H]-noradrenaline overflow into the perfusate (determined in the presence of corticosterone, desipramine, phentolamine, and propranolol) was taken as a measure for activation of presynaptic muscarinic receptors. The evoked [3H]-noradrenaline overflow was inhibited by (+)-, racemic, and (-)-methacholine in a reversible and concentration-dependent manner. The concentration causing 50% inhibition (IC50) was 0.1, 0.26, and 65 microM, respectively, resulting in an isomeric potency ratio IC50 (+)/IC50(-) of 650. The dissociation constant KA of the (+/-)- or (+)-methacholine-presynaptic receptor complex was determined after fractional receptor inactivation according to Furchgott & Bursztyn (1967) with phenoxybenzamine or propylbenzilylcholine mustard as irreversible antagonists of muscarinic receptors. KA for (-)-methacholine was estimated according to Mackay (1966). KA of (+)-, (+/-)-, and (-)-methacholine were 2.5, 4 and 440 microM, resulting in an isomeric affinity ratio KA (+)/KA(-) of 180. The discrepancy between the isomeric IC50 ratio and the isomeric KA ratio is explained by a higher intrinsic efficacy of the (+)-enantiomer compared to the (-)-enantiomer. Thus, (+)-methacholine has to occupy fewer receptors to induce a given inhibition of release than its antipode as revealed by a plot of fractional receptor occupancy vs response. The results show that, in the effector system of presynaptic muscarinic inhibition, methacholine enantiomers differ greatly not only in affinity for the receptor, but also to some extent in the efficiency of signal transmission, and both parameters contribute to the high isomeric potency ratio. The activity of the racemate is fully accounted for by the activity of the (+)-enantiomer.

  19. A MEMS Dielectric Affinity Glucose Biosensor

    PubMed Central

    Huang, Xian; Li, Siqi; Davis, Erin; Li, Dachao; Wang, Qian; Lin, Qiao

    2013-01-01

    Continuous glucose monitoring (CGM) sensors based on affinity detection are desirable for long-term and stable glucose management. However, most affinity sensors contain mechanical moving structures and complex design in sensor actuation and signal readout, limiting their reliability in subcutaneously implantable glucose detection. We have previously demonstrated a proof-of-concept dielectric glucose sensor that measured pre-mixed glucose-sensitive polymer solutions at various glucose concentrations. This sensor features simplicity in sensor design, and possesses high specificity and accuracy in glucose detection. However, lack of glucose diffusion passage, this device is unable to fulfill real-time in-vivo monitoring. As a major improvement to this device, we present in this paper a fully implantable MEMS dielectric affinity glucose biosensor that contains a perforated electrode embedded in a suspended diaphragm. This capacitive-based sensor contains no moving parts, and enables glucose diffusion and real-time monitoring. The experimental results indicate that this sensor can detect glucose solutions at physiological concentrations and possesses good reversibility and reliability. This sensor has a time constant to glucose concentration change at approximately 3 min, which is comparable to commercial systems. The sensor has potential applications in fully implantable CGM that require excellent long-term stability and reliability. PMID:24511215

  20. Global functioning and disability in dissociative disorders.

    PubMed

    Mueller-Pfeiffer, Christoph; Rufibach, Kaspar; Perron, Noelle; Wyss, Daniela; Kuenzler, Cornelia; Prezewowsky, Cornelia; Pitman, Roger K; Rufer, Michael

    2012-12-30

    Dissociative disorders are frequent comorbid conditions of other mental disorders. Yet, there is controversy about their clinical relevance, and little systematic research has been done on how they influence global functioning. Outpatients and day care patients (N=160) of several psychiatric units in Switzerland were assessed with the Structured Clinical Interview for Diagnostic and Statistical Manual of Mental Disorders (DSM)-IV Axis I Disorders, Structured Clinical Interview for DSM-IV Dissociative Disorders, Global Assessment of Functioning Scale, and World Health Organization Disability Assessment Schedule-II. The association between subjects with a dissociative disorder (N=30) and functional impairment after accounting for non-dissociative axis I disorders was evaluated by linear regression models. We found a proportion of 18.8% dissociative disorders (dissociative amnesia=0%, dissociative fugue=0.6%, depersonalization disorder=4.4%, dissociative identity disorder=7.5%, dissociative disorder-not-otherwise-specified=6.3%) across treatment settings. Adjusted for other axis I disorders, subjects with a comorbid dissociative identity disorder or dissociative disorder-not-otherwise-specified had a median global assessment of functioning score that was 0.86 and 0.88 times, respectively, the score of subjects without a comorbid dissociative disorder. These findings support the hypothesis that complex dissociative disorders, i.e., dissociative identity disorder and dissociative disorder-not-otherwise-specified, contribute to functional impairment above and beyond the impact of co-existing non-dissociative axis I disorders, and that they qualify as "serious mental illness".

  1. Quantification of transcription factor-DNA binding affinity in a living cell.

    PubMed

    Belikov, Sergey; Berg, Otto G; Wrange, Örjan

    2016-04-20

    The apparent dissociation constant (Kd) for specific binding of glucocorticoid receptor (GR) and androgen receptor (AR) to DNA was determined in vivo in Xenopus oocytes. The total nuclear receptor concentration was quantified as specifically retained [(3)H]-hormone in manually isolated oocyte nuclei. DNA was introduced by nuclear microinjection of single stranded phagemid DNA, chromatin is then formed during second strand synthesis. The fraction of DNA sites occupied by the expressed receptor was determined by dimethylsulphate in vivo footprinting and used for calculation of the receptor-DNA binding affinity. The forkhead transcription factor FoxA1 enhanced the DNA binding by GR with an apparent Kd of ∼1 μM and dramatically stimulated DNA binding by AR with an apparent Kd of ∼0.13 μM at a composite androgen responsive DNA element containing one FoxA1 binding site and one palindromic hormone receptor binding site known to bind one receptor homodimer. FoxA1 exerted a weak constitutive- and strongly cooperative DNA binding together with AR but had a less prominent effect with GR, the difference reflecting the licensing function of FoxA1 at this androgen responsive DNA element.

  2. Rapid screening of textile dyes employed as affinity ligands to purify enzymes from yeast.

    PubMed

    Raya-Tonetti, G; Perotti, N

    1999-04-01

    A rapid method for screening potential dye ligands for use in affinity chromatography is described. Textile dyes were non-covalently coupled to a cross-linked polysaccharide Sepharose(R) matrix. Yeast alcohol dehydrogenase (ADH) was used as the model protein for evaluating the screening system. A homogenate from baker's yeast was used as the crude source of enzyme. Batchwise adsorption and elution were used to evaluate the individual dyes. The influence of pH and ionic strength in the binding and elution steps was evaluated. Batch isotherms were used to evaluate parameter characteristics. Experimental data obtained were fitted to Langmuir isotherms to determine the maximum binding capacity and the dissociation constant for each dye evaluated in this study. A dynamic binding capacity of 107.6 units of ADH/g of resin was determined for Procion Turquoise MXG dye by frontal analysis. Specific elution with NAD+ and non-specific elution with 50 mM Tris/HCl buffer, pH 8.5, were tested when Procion Turquoise MXG was used, giving purification factors of 53.5 and 4.4 respectively. This screening technique is inexpensive and can be performed in a few hours. It was possible to predict the performance of different reactive dyes in this way, and the influence of pH and salt on the binding behaviour was demonstrated. PMID:10075911

  3. Rapid screening of textile dyes employed as affinity ligands to purify enzymes from yeast.

    PubMed

    Raya-Tonetti, G; Perotti, N

    1999-04-01

    A rapid method for screening potential dye ligands for use in affinity chromatography is described. Textile dyes were non-covalently coupled to a cross-linked polysaccharide Sepharose(R) matrix. Yeast alcohol dehydrogenase (ADH) was used as the model protein for evaluating the screening system. A homogenate from baker's yeast was used as the crude source of enzyme. Batchwise adsorption and elution were used to evaluate the individual dyes. The influence of pH and ionic strength in the binding and elution steps was evaluated. Batch isotherms were used to evaluate parameter characteristics. Experimental data obtained were fitted to Langmuir isotherms to determine the maximum binding capacity and the dissociation constant for each dye evaluated in this study. A dynamic binding capacity of 107.6 units of ADH/g of resin was determined for Procion Turquoise MXG dye by frontal analysis. Specific elution with NAD+ and non-specific elution with 50 mM Tris/HCl buffer, pH 8.5, were tested when Procion Turquoise MXG was used, giving purification factors of 53.5 and 4.4 respectively. This screening technique is inexpensive and can be performed in a few hours. It was possible to predict the performance of different reactive dyes in this way, and the influence of pH and salt on the binding behaviour was demonstrated.

  4. Determining force dependence of two-dimensional receptor-ligand binding affinity by centrifugation.

    PubMed Central

    Piper, J W; Swerlick, R A; Zhu, C

    1998-01-01

    Analyses of receptor-ligand interactions are important to the understanding of cellular adhesion. Traditional methods of measuring the three-dimensional (3D) dissociation constant (Kd) require at least one of the molecular species in solution and hence cannot be directly applied to the case of cell adhesion. We describe a novel method of measuring 2D binding characteristics of receptors and ligands that are attached to surfaces and whose bonds are subjected to forces. The method utilizes a common centrifugation assay to quantify adhesion. A model for the experiment has been formulated, solved exactly, and tested carefully. The model is stochastically based and couples the bond force to the binding affinity. The method was applied to examine tumor cell adherence to recombinant E-selectin. Satisfactory agreement was found between predictions and data. The estimated zero-force 2D Kd for E-selectin/carbohydrate ligand binding was approximately 5 x 10(3) microm(-2), and the bond interaction range was subangstrom. Our results also suggest that the number of bonds mediating adhesion was small (<5). PMID:9449350

  5. Quantification of helix–helix binding affinities in micelles and lipid bilayers

    PubMed Central

    Lomize, Andrei L.; Pogozheva, I.D.; Mosberg, H.I.

    2004-01-01

    A theoretical approach for estimating association free energies of α-helices in nonpolar media has been developed. The parameters of energy functions have been derived from ΔΔG values of mutants in water-soluble proteins and partitioning of organic solutes between water and nonpolar solvents. The proposed approach was verified successfully against three sets of published data: (1) dissociation constants of α-helical oligomers formed by 27 hydrophobic peptides; (2) stabilities of 22 bacteriorhodopsin mutants, and (3) protein-ligand binding affinities in aqueous solution. It has been found that coalescence of helices is driven exclusively by van der Waals interactions and H-bonds, whereas the principal destabilizing contributions are represented by side-chain conformational entropy and transfer energy of atoms from a detergent or lipid to the protein interior. Electrostatic interactions of α-helices were relatively weak but important for reproducing the experimental data. Immobilization free energy, which originates from restricting rotational and translational rigid-body movements of molecules during their association, was found to be less than 1 kcal/mole. The energetics of amino acid substitutions in bacteriorhodopsin was complicated by specific binding of lipid and water molecules to cavities created in certain mutants. PMID:15340167

  6. Identification and characterization of a novel high affinity metal-binding site in the hammerhead ribozyme.

    PubMed Central

    Hansen, M R; Simorre, J P; Hanson, P; Mokler, V; Bellon, L; Beigelman, L; Pardi, A

    1999-01-01

    A novel metal-binding site has been identified in the hammerhead ribozyme by 31P NMR. The metal-binding site is associated with the A13 phosphate in the catalytic core of the hammerhead ribozyme and is distinct from any previously identified metal-binding sites. 31P NMR spectroscopy was used to measure the metal-binding affinity for this site and leads to an apparent dissociation constant of 250-570 microM at 25 degrees C for binding of a single Mg2+ ion. The NMR data also show evidence of a structural change at this site upon metal binding and these results are compared with previous data on metal-induced structural changes in the core of the hammerhead ribozyme. These NMR data were combined with the X-ray structure of the hammerhead ribozyme (Pley HW, Flaherty KM, McKay DB. 1994. Nature 372:68-74) to model RNA ligands involved in binding the metal at this A13 site. In this model, the A13 metal-binding site is structurally similar to the previously identified A(g) metal-binding site and illustrates the symmetrical nature of the tandem G x A base pairs in domain 2 of the hammerhead ribozyme. These results demonstrate that 31P NMR represents an important method for both identification and characterization of metal-binding sites in nucleic acids. PMID:10445883

  7. CHARACTERIZATION OF DRUG INTERACTIONS WITH SERUM PROTEINS BY USING HIGH-PERFORMANCE AFFINITY CHROMATOGRAPHY

    PubMed Central

    Hage, David S.; Anguizola, Jeanethe; Barnaby, Omar; Jackson, Abby; Yoo, Michelle J.; Papastavros, Efthimia; Pfaunmiller, Erika; Sobansky, Matt; Tong, Zenghan

    2011-01-01

    The binding of drugs with serum proteins can affect the activity, distribution, rate of excretion, and toxicity of pharmaceutical agents in the body. One tool that can be used to quickly analyze and characterize these interactions is high-performance affinity chromatography (HPAC). This review shows how HPAC can be used to study drug-protein binding and describes the various applications of this approach when examining drug interactions with serum proteins. Methods for determining binding constants, characterizing binding sites, examining drug-drug interactions, and studying drug-protein dissociation rates will be discussed. Applications that illustrate the use of HPAC with serum binding agents such as human serum albumin, α1-acid glycoprotein, and lipoproteins will be presented. Recent developments will also be examined, such as new methods for immobilizing serum proteins in HPAC columns, the utilization of HPAC as a tool in personalized medicine, and HPAC methods for the high-throughput screening and characterization of drug-protein binding. PMID:21395530

  8. The Lectin Frontier Database (LfDB), and data generation based on frontal affinity chromatography.

    PubMed

    Hirabayashi, Jun; Tateno, Hiroaki; Shikanai, Toshihide; Aoki-Kinoshita, Kiyoko F; Narimatsu, Hisashi

    2015-01-01

    Lectins are a large group of carbohydrate-binding proteins, having been shown to comprise at least 48 protein scaffolds or protein family entries. They occur ubiquitously in living organisms-from humans to microorganisms, including viruses-and while their functions are yet to be fully elucidated, their main underlying actions are thought to mediate cell-cell and cell-glycoconjugate interactions, which play important roles in an extensive range of biological processes. The basic feature of each lectin's function resides in its specific sugar-binding properties. In this regard, it is beneficial for researchers to have access to fundamental information about the detailed oligosaccharide specificities of diverse lectins. In this review, the authors describe a publicly available lectin database named "Lectin frontier DataBase (LfDB)", which undertakes the continuous publication and updating of comprehensive data for lectin-standard oligosaccharide interactions in terms of dissociation constants (Kd's). For Kd determination, an advanced system of frontal affinity chromatography (FAC) is used, with which quantitative datasets of interactions between immobilized lectins and >100 fluorescently labeled standard glycans have been generated. The FAC system is unique in its clear principle, simple procedure and high sensitivity, with an increasing number (>67) of associated publications that attest to its reliability. Thus, LfDB, is expected to play an essential role in lectin research, not only in basic but also in applied fields of glycoscience. PMID:25580689

  9. The affinity and activity of compounds related to nicotine on the rectus abdominis muscle of the frog (Rana pipiens)

    PubMed Central

    Barlow, R. B.; Thompson, G. M.

    1969-01-01

    1. Series of pyridylalkyl- and substituted phenylalkyl-trimethylammonium salts, triethylammonium salts, diethylamines and di-n-propylamines have been made. The substituents in the benzene ring were nitro, chloro, bromo, methoxy, hydroxy and amino groups and the alkyl residues had one, two, or three methylene groups separating the aromatic nucleus from the cationic head. 2. Most of the trimethylammonium compounds caused a contracture of the frog rectus muscle, but some were partial agonists and a few were antagonists. The di-n-propylamines were all antagonists, as were most of the diethylamines and triethylammonium compounds, though some of these were partial agonists and a few triethylammonium compounds were agonists. The affinities of the antagonists and partial agonists for the receptors stimulated by β-pyridylmethyltrimethylammonium (and by nicotine) were measured. The equipotent molar ratios of all the agonists were measured relative to β-pyridylmethyltrimethylammonium. 3. The dissociation constants of the pyridylmethyldiethylamines and substituted benzyldiethylamines were measured. The effects of substituents on the pKa of benzyldiethylamine were similar to their effects on the pKa of aniline, though there were differences with some of the o-substituted compounds, which could be attributed to internal hydrogen-bond formation. 4. There is no obvious correlation between the effects of a substituent on the pKa of benzyldiethylamine and its effects on affinity. Although increasing the size of the cationic group usually increased affinity, it did not always do so. The compounds with the highest affinity, p-hydroxybenzyldiethylamine (log K, 5·90) had about half the affinity of (+)-tubocurarine (log K, 6·11), but the triethylammonium analogue (log K, 4·17) had only about one-fiftieth of the affinity of the tertiary base. The binding of the drug to the receptor appears to involve many factors which include the size of the groups as well as their electron

  10. Affinity maturation of T-cell receptor-like antibodies for Wilms tumor 1 peptide greatly enhances therapeutic potential

    PubMed Central

    Zhao, Qi; Ahmed, Mahiuddin; Tassev, Dimiter V.; Hasan, Aisha; Kuo, Tzu-Yun; Guo, Hong-fen; O’Reilly, Richard J.; Cheung, Nai-Kong V.

    2016-01-01

    WT1126 (RMFPNAPYL) is a human leukocyte antigen-A2 (HLA-A2) restricted peptide derived from Wilms tumor protein (WT1), which is widely expressed in a broad spectrum of leukemias, lymphomas and solid tumors. A novel T-cell-receptor (TCR)-like single chain variable fragment (scFv) antibody specific for the T cell epitope consisting of the WT1/HLA-A2 complex was isolated from a human scFv phage library. This scFv was affinity-matured by mutagenesis combined with yeast display, and structurally analyzed using a homology model. This monovalent scFv showed a 100-fold affinity improvement (dissociation constant [KD]= 3nM) and exquisite specificity towards its targeted epitope or HLA-A2+/WT1+ tumor cells. Bivalent scFv-huIgG1-Fc fusion protein demonstrated an even higher avidity (KD = 2pM) binding to the T cell epitope and to tumor targets, and was capable of mediating antibody-dependent cell-mediated cytotoxicity or tumor lysis by chimeric antigen receptor (CAR)-expressing human T or NK-92-MI transfected cells. This antibody demonstrated specific and potent cytotoxicity in vivo towards WT1-positive leukemia xenograft that was HLA-A2 restricted. In summary, T cell epitopes can provide novel targets for antibody-based therapeutics. By combining phage and yeast displays and scFv-Fc fusion platforms, a strategy for developing high affinity TCR-like antibodies could be rapidly explored for potential clinical development. PMID:25987253

  11. Local release from affinity-based polymers increases urethral concentration of the stem cell chemokine CCL7 in rats.

    PubMed

    Rivera-Delgado, Edgardo; Sadeghi, Zhina; Wang, Nick X; Kenyon, Jonathan; Satyanarayan, Sapna; Kavran, Michael; Flask, Chris; Hijaz, Adonis Z; von Recum, Horst A

    2016-04-01

    The protein chemokine (C-C motif) ligand 7 (CCL7) is significantly over-expressed in urethral and vaginal tissues immediately following vaginal distention in a rat model of stress urinary incontinence. Further evidence, in this scenario and other clinical scenarios, indicates CCL7 stimulates stem cell homing for regenerative repair. This CCL7 gradient is likely absent or compromised in the natural repair process of women who continue to suffer from SUI into advanced age. We evaluated the feasibility of locally providing this missing CCL7 gradient by means of an affinity-based implantable polymer. To engineer these polymers we screened the affinity of different proteoglycans, to use them as CCL7-binding hosts. We found heparin to be the strongest binding host for CCL7 with a 0.323 nM dissociation constant. Our experimental approach indicates conjugation of heparin to a polymer backbone (using either bovine serum albumin or poly (ethylene glycol) as the base polymer) can be used as a delivery system capable of providing sustained concentrations of CCL7 in a therapeutically useful range up to a month in vitro. With this approach we are able to detect, after polymer implantation, significant increase in CCL7 in the urethral tissue directly surrounding the polymer implants with only trace amounts of human CCL7 present in the blood of the animals. Whole animal serial sectioning shows evidence of retention of locally injected human mesenchymal stem cells (hMSCs) only in animals with sustained CCL7 delivery, 2 weeks after affinity-polymers were implanted. PMID:27097800

  12. Biochemical characterization of ThiT from Lactococcus lactis: a thiamin transporter with picomolar substrate binding affinity.

    PubMed

    Erkens, Guus B; Slotboom, Dirk Jan

    2010-04-13

    The putative thiamin transporter ThiT from Lactococcus lactis was overproduced in the membrane of lactococcal cells. In vivo transport assays using radiolabeled thiamin demonstrated that ThiT indeed was involved in thiamin transport. The protein was solubilized from the membranes and purified in detergent solution. Size exclusion chromatography coupled to static light scattering, refractive index, and UV absorbance measurements (SEC-MALLS) showed that ThiT is a monomer of 22.7 kDa in detergent solution. When the cells overexpressing ThiT had been cultivated in complex growth medium, all binding sites of the purified protein were occupied with substrate, which had copurified with the protein. MALDI-TOF mass spectrometry analysis confirmed that the copurified substance was thiamin. Substrate-depleted ThiT was obtained by expressing the protein in cells that were cultivated in chemically defined growth medium without thiamin. The intrinsic tryptophan fluorescence of substrate-depleted ThiT was strongly quenched upon thiamin binding. The quenching of the fluorescence was used to determine dissociation constants for thiamin and related compounds. ThiT had an unusually high affinity for thiamin (K(D) = 122 +/- 13 pM) and bound the substrate with a 1:1 (protein:ligand) stoichiometry. TPP, TMP, and pyrithiamin bound to ThiT with nanomolar affinity. A multiple sequence alignment of ThiT homologues revealed that well-conserved residues were clustered in a tryptophan-rich stretch comprising the loop between the predicted membrane spanning segments 5 and 6. Mutational analysis of the conserved residues in this region combined with binding assays of thiamin and related compounds was used to build a model of the high-affinity binding site. The model was compared with thiamin binding sites of other proteins and interpreted in terms of the transport mechanism.

  13. Kinetic analysis of drug-protein interactions by affinity chromatography.

    PubMed

    Bi, Cong; Beeram, Sandya; Li, Zhao; Zheng, Xiwei; Hage, David S

    2015-10-01

    Information on the kinetics of drug-protein interactions is of crucial importance in drug discovery and development. Several methods based on affinity chromatography have been developed in recent years to examine the association and dissociation rates of these processes. These techniques include band-broadening measurements, the peak decay method, peak fitting methods, the split-peak method, and free fraction analysis. This review will examine the general principles and applications of these approaches and discuss their use in the characterization, screening and analysis of drug-protein interactions in the body. PMID:26724332

  14. Affinity chromatography: a historical perspective.

    PubMed

    Hage, David S; Matsuda, Ryan

    2015-01-01

    Affinity chromatography is one of the most selective and versatile forms of liquid chromatography for the separation or analysis of chemicals in complex mixtures. This method makes use of a biologically related agent as the stationary phase, which provides an affinity column with the ability to bind selectively and reversibly to a given target in a sample. This review examines the early work in this method and various developments that have lead to the current status of this technique. The general principles of affinity chromatography are briefly described as part of this discussion. Past and recent efforts in the generation of new binding agents, supports, and immobilization methods for this method are considered. Various applications of affinity chromatography are also summarized, as well as the influence this field has played in the creation of other affinity-based separation or analysis methods. PMID:25749941

  15. Dissociative experiences and dissociative minds: Exploring a nomological network of dissociative functioning.

    PubMed

    Schimmenti, Adriano

    2016-01-01

    In this study, the psychometric properties of the Dissociative Experiences Scale-II (DES-II) were tested in a sample of Italian adults, and a nomological network of dissociative functioning based on current psychodynamic research was examined. A total of 794 participants (55% females) ranging in age from 18 to 64 completed the DES-II and other measures of theory of mind, alexithymia, attachment style, and empathy. The Italian translation of the DES-II showed high internal consistency, adequate item-to-scale homogeneity, and good split-half reliability. A single-factor solution including the 8 items of pathological dissociation (DES-T) adequately fit the data. Participants who reported higher levels of dissociative experiences showed significantly lower scores on theory of mind and empathy than other participants. They also showed significantly higher scores on alexithymia, preoccupied attachment, and fearful attachment. Results of the study support the view that people who suffer from severe dissociative experiences may also have difficulties mentalizing and regulating affects and that they may feel uncomfortable in close relationships because they have a negative view of the self. This can inform clinical work with dissociative individuals, who could benefit from therapies that consider their potential problems with mentalization, empathy, affect regulation, and attachment.

  16. Vibrational nonequilibrium effects on diatomic dissociation rates

    NASA Technical Reports Server (NTRS)

    Hansen, C. F.

    1993-01-01

    The collision-induced dissociation rate of diatomic molecules from a ladder of rotational and anharmonic vibrational states is developed, and the correction for vibrational nonequilibrium is considered. The result is similar to an analytic correction derived by Hammerling et al. (1959) for harmonic oscillators. An empirical correction algorithm suggested by Park (1987, 1990) gives similar results when vibrational temperature is comparable to kinetic temperature but underestimates the dissociation rate when vibrational temperature is small compared with the kinetic temperature. This algorithm uses an effective temperature in the experimentally determined Arrhenius expression for the rate coefficient, which is a weighted average of the vibrational and kinetic temperature, whereas theory indicates that kinetic temperature should appear only in the exponential term of the Arrhenius expression. Nevertheless, an effective temperature can always be found that will numerically duplicate the proper rate coefficient at any given condition, but a constant weighting factor cannot be expected to provide this. However, the algorithm can he adjusted to give reasonable results over a range of conditions if the geometric weighting factor is taken to be a simple linear function of the ratio of vibrational to kinetic temperature in the gas.

  17. Affine conformal vectors in space-time

    NASA Astrophysics Data System (ADS)

    Coley, A. A.; Tupper, B. O. J.

    1992-05-01

    All space-times admitting a proper affine conformal vector (ACV) are found. By using a theorem of Hall and da Costa, it is shown that such space-times either (i) admit a covariantly constant vector (timelike, spacelike, or null) and the ACV is the sum of a proper affine vector and a conformal Killing vector or (ii) the space-time is 2+2 decomposable, in which case it is shown that no ACV can exist (unless the space-time decomposes further). Furthermore, it is proved that all space-times admitting an ACV and a null covariantly constant vector (which are necessarily generalized pp-wave space-times) must have Ricci tensor of Segré type {2,(1,1)}. It follows that, among space-times admitting proper ACV, the Einstein static universe is the only perfect fluid space-time, there are no non-null Einstein-Maxwell space-times, and only the pp-wave space-times are representative of null Einstein-Maxwell solutions. Otherwise, the space-times can represent anisotropic fluids and viscous heat-conducting fluids, but only with restricted equations of state in each case.

  18. Visuomotor Dissociation in Cerebral Scaling of Size.

    PubMed

    Potgieser, Adriaan R E; de Jong, Bauke M

    2016-01-01

    Estimating size and distance is crucial in effective visuomotor control. The concept of an internal coordinate system implies that visual and motor size parameters are scaled onto a common template. To dissociate perceptual and motor components in such scaling, we performed an fMRI experiment in which 16 right-handed subjects copied geometric figures while the result of drawing remained out of sight. Either the size of the example figure varied while maintaining a constant size of drawing (visual incongruity) or the size of the examples remained constant while subjects were instructed to make changes in size (motor incongruity). These incongruent were compared to congruent conditions. Statistical Parametric Mapping (SPM8) revealed brain activations related to size incongruity in the dorsolateral prefrontal and inferior parietal cortex, pre-SMA / anterior cingulate and anterior insula, dominant in the right hemisphere. This pattern represented simultaneous use of a 'resized' virtual template and actual picture information requiring spatial working memory, early-stage attention shifting and inhibitory control. Activations were strongest in motor incongruity while right pre-dorsal premotor activation specifically occurred in this condition. Visual incongruity additionally relied on a ventral visual pathway. Left ventral premotor activation occurred in all variably sized drawing while constant visuomotor size, compared to congruent size variation, uniquely activated the lateral occipital cortex additional to superior parietal regions. These results highlight size as a fundamental parameter in both general hand movement and movement guided by objects perceived in the context of surrounding 3D space. PMID:26963705

  19. Visuomotor Dissociation in Cerebral Scaling of Size.

    PubMed

    Potgieser, Adriaan R E; de Jong, Bauke M

    2016-01-01

    Estimating size and distance is crucial in effective visuomotor control. The concept of an internal coordinate system implies that visual and motor size parameters are scaled onto a common template. To dissociate perceptual and motor components in such scaling, we performed an fMRI experiment in which 16 right-handed subjects copied geometric figures while the result of drawing remained out of sight. Either the size of the example figure varied while maintaining a constant size of drawing (visual incongruity) or the size of the examples remained constant while subjects were instructed to make changes in size (motor incongruity). These incongruent were compared to congruent conditions. Statistical Parametric Mapping (SPM8) revealed brain activations related to size incongruity in the dorsolateral prefrontal and inferior parietal cortex, pre-SMA / anterior cingulate and anterior insula, dominant in the right hemisphere. This pattern represented simultaneous use of a 'resized' virtual template and actual picture information requiring spatial working memory, early-stage attention shifting and inhibitory control. Activations were strongest in motor incongruity while right pre-dorsal premotor activation specifically occurred in this condition. Visual incongruity additionally relied on a ventral visual pathway. Left ventral premotor activation occurred in all variably sized drawing while constant visuomotor size, compared to congruent size variation, uniquely activated the lateral occipital cortex additional to superior parietal regions. These results highlight size as a fundamental parameter in both general hand movement and movement guided by objects perceived in the context of surrounding 3D space.

  20. Visuomotor Dissociation in Cerebral Scaling of Size

    PubMed Central

    Potgieser, Adriaan R. E.; de Jong, Bauke M.

    2016-01-01

    Estimating size and distance is crucial in effective visuomotor control. The concept of an internal coordinate system implies that visual and motor size parameters are scaled onto a common template. To dissociate perceptual and motor components in such scaling, we performed an fMRI experiment in which 16 right-handed subjects copied geometric figures while the result of drawing remained out of sight. Either the size of the example figure varied while maintaining a constant size of drawing (visual incongruity) or the size of the examples remained constant while subjects were instructed to make changes in size (motor incongruity). These incongruent were compared to congruent conditions. Statistical Parametric Mapping (SPM8) revealed brain activations related to size incongruity in the dorsolateral prefrontal and inferior parietal cortex, pre-SMA / anterior cingulate and anterior insula, dominant in the right hemisphere. This pattern represented simultaneous use of a ‘resized’ virtual template and actual picture information requiring spatial working memory, early-stage attention shifting and inhibitory control. Activations were strongest in motor incongruity while right pre-dorsal premotor activation specifically occurred in this condition. Visual incongruity additionally relied on a ventral visual pathway. Left ventral premotor activation occurred in all variably sized drawing while constant visuomotor size, compared to congruent size variation, uniquely activated the lateral occipital cortex additional to superior parietal regions. These results highlight size as a fundamental parameter in both general hand movement and movement guided by objects perceived in the context of surrounding 3D space. PMID:26963705

  1. Mechanisms of peptide fragmentation from time- and energy-resolved surface-induced dissociation studies: Dissociation of angiotensin analogs

    NASA Astrophysics Data System (ADS)

    Laskin, Julia; Bailey, Thomas H.; Futrell, Jean H.

    2006-03-01

    Energetics and mechanism of dissociation of singly protonated angiotensin III (RVYIHPF) and its analogs RVYIFPF, RVYIYPF, RVYIHAF and RVYIHDF was studied using surface-induced dissociation (SID) in a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially configured for studying ion activation by collisions with surfaces. The energetics and dynamics of peptide fragmentation were deduced by modeling the time- and energy-resolved survival curves for each precursor ion using an RRKM-based approach developed in our laboratory. Fragmentation mechanisms were inferred from comparison of time- and energy-resolved fragmentation efficiency curves (TFECs) of different fragment ions followed by RRKM modeling of dissociation of angiotensin III into six major families of fragment ions. Detailed modeling demonstrated that dissociation of these peptides is dominated by loss of ammonia from the precursor ion and characterized by a high-energy barrier of 1.6 eV. Loss of NH3 and subsequent rearrangement of the MH+-NH3 ion results in proton mobilization and release of ca. 30 kcal/mol into internal excitation of the MH+-NH3 ion. The resulting highly excited ion accesses a variety of non-specific dissociation pathways with very high rate constants. Fast fragmentation of excited MH+-NH3 ion forms a variety of abundant bn-NH3 and an-NH3 fragment ions. Abundant XH and HX internal fragments are also formed, reflecting the stability of histidine-containing diketopiperazine structures.

  2. Competitive Inhibition of High-Affinity Oryzalin Binding to Plant Tubulin by the Phosphoric Amide Herbicide Amiprophos-Methyl.

    PubMed Central

    Murthy, J. V.; Kim, H. H.; Hanesworth, V. R.; Hugdahl, J. D.; Morejohn, L. C.

    1994-01-01

    Amiprophos-methyl (APM), a phosphoric amide herbicide, was previously reported to inhibit the in vitro polymerization of isolated plant tubulin (L.C. Morejohn, D.E. Fosket [1984] Science 224: 874-876), yet little other biochemical information exists concerning this compound. To characterize further the mechanism of action of APM, its interactions with tubulin and microtubules purified from cultured cells of tobacco (Nicotiana tabacum cv Bright Yellow-2) were investigated. Low micromolar concentrations of APM depolymerized preformed, taxol-stabilized tobacco microtubules. Remarkably, at the lowest APM concentration examined, many short microtubules were redistributed into fewer but 2.7-fold longer microtubules without a substantial decrease in total polymer mass, a result consistent with an end-to-end annealing of microtubules with enhanced kinetic properties. Quasi-equilibrium binding measurements showed that tobacco tubulin binds [14C]oryzalin with high affinity to produce a tubulin-oryzalin complex having a dissociation constant (Kd) = 117 nM (pH 6.9; 23[deg]C). Also, an estimated maximum molar binding stoichiometry of 0.32 indicates pharamacological heterogeneity of tobacco dimers and may be related to structural heterogeneity of tobacco tubulin subunits. APM inhibits competitively the binding of [14C]oryzalin to tubulin with an inhibition constant (Ki) = 5 [mu]M, indicating the formation of a moderate affinity tubulin-APM complex that may interact with the ends of microtubules. APM concentrations inhibiting tobacco cell growth were within the threshold range of APM concentrations that depolymerized cellular microtubules, indicating that growth inhibition is caused by microtubules depolymerization. APM had no apparent effect on microtubules in mouse 3T3 fibroblasts. Because cellular microtubules were depolymerized at APM and oryzalin concentrations below their respective Ki and Kd values, both herbicides are proposed to depolymerize microtubules by a

  3. Dataset of the binding kinetic rate constants of anti-PCSK9 antibodies obtained using the Biacore T100, ProteOn XPR36, Octet RED384, and IBIS MX96 biosensor platforms.

    PubMed

    Yang, Danlin; Singh, Ajit; Wu, Helen; Kroe-Barrett, Rachel

    2016-09-01

    Here we provide data from a head-to-head comparison study using four biosensor platforms: GE Healthcare׳s Biacore T100, Bio-Rad׳s ProteOn XPR36, ForteBio׳s Octet RED384, and Wasatch Microfluidics׳s IBIS MX96. We used these instruments to analyze the binding interactions of a panel of ten high-affinity monoclonal antibodies with their antigen, human proprotein convertase subtilisin kexin type 9 (PCSK9). For each instrument, binding curves obtained at multiple densities of surface antibodies were fit to the 1:1 Langmuir kinetic model, and the association and dissociation rate constants and corresponding affinity constants were calculated. The data supplied in this article accompany the research article entitled, "Comparison of biosensor platforms in the evaluation of high affinity antibody-antigen binding kinetics" (Yang et al., 2016) [1], which further discusses the strengths and weaknesses of each biosensor platform with an emphasis on data consistency, comparability, and operational efficiency. PMID:27547794

  4. Kinetic Studies of Biological Interactions By Affinity Chromatography

    PubMed Central

    Schiel, John E.; Hage, David S.

    2009-01-01

    The rates at which biological interactions occur can provide important information on the mechanism and behavior of such processes in living systems. This review will discuss how affinity chromatography can be used as a tool to examine the kinetics of biological interactions. This approach, referred to here as biointeraction chromatography, uses a column with an immobilized binding agent to examine the association or dissociation of this agent with other compounds. The use of HPLC-based affinity columns in kinetic studies has received particular attention in recent years. Advantages of using HPLC with affinity chromatography for this purpose include the ability to reuse the same ligand within a column for a large number of experiments, and the good precision and accuracy of this approach. A number of techniques are available for kinetic studies through the use of affinity columns and biointeraction chromatography. These approaches include plate height measurements, peak profiling, peak fitting, split-peak measurements, and peak decay analysis. The general principles for each of these methods are discussed in this review and some recent applications of these techniques are presented. The advantages and potential limitations of each approach are also considered. PMID:19391173

  5. Molecular dynamics simulation of ligand dissociation from liver fatty acid binding protein.

    PubMed

    Long, Dong; Mu, Yuguang; Yang, Daiwen

    2009-06-30

    The mechanisms of how ligands enter and leave the binding cavity of fatty acid binding proteins (FABPs) have been a puzzling question over decades. Liver fatty acid binding protein (LFABP) is a unique family member which accommodates two molecules of fatty acids in its cavity and exhibits the capability of interacting with a variety of ligands with different chemical structures and properties. Investigating the ligand dissociation processes of LFABP is thus a quite interesting topic, which however is rather difficult for both experimental approaches and ordinary simulation strategies. In the current study, random expulsion molecular dynamics simulation, which accelerates ligand motions for rapid dissociation, was used to explore the potential egress routes of ligands from LFABP. The results showed that the previously hypothesized "portal region" could be readily used for the dissociation of ligands at both the low affinity site and the high affinity site. Besides, one alternative portal was shown to be highly favorable for ligand egress from the high affinity site and be related to the unique structural feature of LFABP. This result lends strong support to the hypothesis from the previous NMR exchange studies, which in turn indicates an important role for this alternative portal. Another less favored potential portal located near the N-terminal end was also identified. Identification of the dissociation pathways will allow further mechanistic understanding of fatty acid uptake and release by computational and/or experimental techniques.

  6. Multiphoton dissociative ionization of CS+

    NASA Astrophysics Data System (ADS)

    Rajput, Jyoti; Jochim, Bethany; Zohrabi, M.; Betsch, K. J.; Ablikim, U.; Berry, Ben; Severt, T.; Summers, A. M.; Armstrong, G. S. J.; Esry, B. D.; Carnes, K. D.; Ben-Itzhak, I.

    2015-05-01

    We have studied the dissociative photoionization of a CS+ molecular ion beam in the strong-field regime using <50 fs IR laser pulses (λ ~ 790 nm) from a 10 kHz, ~2 mJ (per pulse) Ti:Sapphire laser system. A coincidence three-dimensional momentum imaging method was used to measure all ions and neutrals formed during this multiphoton process. Two prominent channels were observed: charge-symmetric dissociation, yielding C+ + S+, and charge-asymmetric dissociation, yielding C + S2+. The differences between these two channels with reference to their relative production probability, energetics, and angular distributions is the focus of this work. This work was supported by the Chemical Sciences, Geosciences, and Biosciences Division, Office of Basic Energy Sciences, Office of Science, U.S. Department of Energy. BJ is also supported by DOE-SCGF (DE-AC05-06OR23100).

  7. 3- and 4-O-sulfoconjugated and methylated dopamine: highly reduced binding affinity to dopamine D2 receptors in rat striatal membranes.

    PubMed

    Werle, E; Lenz, T; Strobel, G; Weicker, H

    1988-07-01

    The binding properties of 3- and 4-O-sulfo-conjugated dopamine (DA-3-O-S, DA-4-O-S) as well as 3-O-methylated dopamine (MT) to rat striatal dopamine D2 receptors were investigated. 3H-spiperone was used as a radioligand in the binding studies. In saturation binding experiments (+)butaclamol, which has been reported to bind to dopaminergic D2 and serotoninergic 5HT2 receptors, was used in conjunction with ketanserin and sulpiride, which preferentially label 5HT2 and D2 receptors, respectively, in order to discriminate between 3H-spiperone binding to D2 and to 5HT2 receptors. Under our particular membrane preparation and assay conditions, 3H-spiperone binds to D2 and 5HT2 receptors with a maximal binding capacity (Bmax) of 340 fmol/mg protein in proportions of about 75%:25% with similar dissociation constants KD (35 pmol/l; 43 pmol/l). This result was verified by the biphasic competition curve of ketanserin, which revealed about 20% high (KD = 24 nmol/l) and 80% low (KD = 420 nmol/l) affinity binding sites corresponding to 5HT2 and D2 receptors, respectively. Therefore, all further competition experiments at a tracer concentration of 50 pmol/l were performed in the presence of 0.1 mumol/l ketanserin to mask the 5HT2 receptors. DA competition curves were best fitted assuming two binding sites, with high (KH = 0.12 mumol/l) and low (KL = 18 mumol/l) affinity, present in a ratio of 3:1. The high affinity binding sites were interconvertible by 100 mumol/l guanyl-5-yl imidodiphosphate [Gpp(NH)p], resulting in a homogenous affinity state of DA receptors (KD = 2.8 mumol/l).2+ off PMID:2853303

  8. 3- and 4-O-sulfoconjugated and methylated dopamine: highly reduced binding affinity to dopamine D2 receptors in rat striatal membranes.

    PubMed

    Werle, E; Lenz, T; Strobel, G; Weicker, H

    1988-07-01

    The binding properties of 3- and 4-O-sulfo-conjugated dopamine (DA-3-O-S, DA-4-O-S) as well as 3-O-methylated dopamine (MT) to rat striatal dopamine D2 receptors were investigated. 3H-spiperone was used as a radioligand in the binding studies. In saturation binding experiments (+)butaclamol, which has been reported to bind to dopaminergic D2 and serotoninergic 5HT2 receptors, was used in conjunction with ketanserin and sulpiride, which preferentially label 5HT2 and D2 receptors, respectively, in order to discriminate between 3H-spiperone binding to D2 and to 5HT2 receptors. Under our particular membrane preparation and assay conditions, 3H-spiperone binds to D2 and 5HT2 receptors with a maximal binding capacity (Bmax) of 340 fmol/mg protein in proportions of about 75%:25% with similar dissociation constants KD (35 pmol/l; 43 pmol/l). This result was verified by the biphasic competition curve of ketanserin, which revealed about 20% high (KD = 24 nmol/l) and 80% low (KD = 420 nmol/l) affinity binding sites corresponding to 5HT2 and D2 receptors, respectively. Therefore, all further competition experiments at a tracer concentration of 50 pmol/l were performed in the presence of 0.1 mumol/l ketanserin to mask the 5HT2 receptors. DA competition curves were best fitted assuming two binding sites, with high (KH = 0.12 mumol/l) and low (KL = 18 mumol/l) affinity, present in a ratio of 3:1. The high affinity binding sites were interconvertible by 100 mumol/l guanyl-5-yl imidodiphosphate [Gpp(NH)p], resulting in a homogenous affinity state of DA receptors (KD = 2.8 mumol/l).2+ off

  9. [Dissociative identity disorder or schizophrenia?].

    PubMed

    Tschöke, S; Steinert, T

    2010-01-01

    We present a case of dissociative identity disorder in which Schneiderian first rank symptoms were present besides of various states of consciousness. Thus the diagnosis of schizophrenia had to be considered. Formally, the symptoms met ICD-10 criteria for schizophrenia. However, taking into account the lack of formal thought disorder and of negative symptoms as well as a typical history of severe and prolonged traumatisation, we did not diagnose a co-morbid schizophrenic disorder. There is good evidence for the existence of psychotic symptoms among patients with dissociative disorders. However, in clinical practice this differential diagnosis is rarely considered.

  10. Formation and dissociation of semiperketals under conditions of liquid-phase oxidation of hydrocarbons

    SciTech Connect

    Lipes, V.V.; Levina, O.V.; Kazantseva, L.K.; Morozova, V.I.

    1988-06-01

    It was found that during the thermolysis of cyclooctyl hydroperoxide (solvent - cyclooctane, 110-120/sup 0/C), cyclohexanone accelerates the dissociation of the hydroperoxide, while addition of cyclododecanone does not influence the rate of the dissociation. The decomposition of a mixed semiperketal, 1-hydroxycyclohexyl-cyclooctyl peroxide was studied. Analysis of the reaciton products showed that for ..cap alpha..-hydroxyalkoxy radicals, the isomerization rate constant is one order of magnitude higher than that for alkoxy radicals.

  11. On the Khinchin Constant

    NASA Technical Reports Server (NTRS)

    Bailey, David H.; Borwein, Jonathan M.; Crandall, Richard E.; Craw, James M. (Technical Monitor)

    1995-01-01

    We prove known identities for the Khinchin constant and develop new identities for the more general Hoelder mean limits of continued fractions. Any of these constants can be developed as a rapidly converging series involving values of the Riemann zeta function and rational coefficients. Such identities allow for efficient numerical evaluation of the relevant constants. We present free-parameter, optimizable versions of the identities, and report numerical results.

  12. Affine generalization of the Komar complex of general relativity

    NASA Astrophysics Data System (ADS)

    Mielke, Eckehard W.

    2001-02-01

    On the basis of the ``on shell'' Noether identities of the metric-affine gauge approach of gravity, an affine superpotential is derived which comprises the energy- and angular-momentum content of exact solutions. In the special case of general relativity (GR) or its teleparallel equivalent, the Komar or Freud complex, respectively, are recovered. Applying this to the spontaneously broken anti-de Sitter gauge model of McDowell and Mansouri with an induced Euler term automatically yields the correct mass and spin of the Kerr-AdS solution of GR with a (induced) cosmological constant without the factor two discrepancy of the Komar formula.

  13. The hubble constant.

    PubMed

    Huchra, J P

    1992-04-17

    The Hubble constant is the constant of proportionality between recession velocity and distance in the expanding universe. It is a fundamental property of cosmology that sets both the scale and the expansion age of the universe. It is determined by measurement of galaxy The Hubble constant is the constant of proportionality between recession velocity and development of new techniques for the measurements of galaxy distances, both calibration uncertainties and debates over systematic errors remain. Current determinations still range over nearly a factor of 2; the higher values favored by most local measurements are not consistent with many theories of the origin of large-scale structure and stellar evolution. PMID:17743107

  14. The cosmological constant

    NASA Technical Reports Server (NTRS)

    Carroll, Sean M.; Press, William H.; Turner, Edwin L.

    1992-01-01

    The cosmological constant problem is examined in the context of both astronomy and physics. Effects of a nonzero cosmological constant are discussed with reference to expansion dynamics, the age of the universe, distance measures, comoving density of objects, growth of linear perturbations, and gravitational lens probabilities. The observational status of the cosmological constant is reviewed, with attention given to the existence of high-redshift objects, age derivation from globular clusters and cosmic nuclear data, dynamical tests of Omega sub Lambda, quasar absorption line statistics, gravitational lensing, and astrophysics of distant objects. Finally, possible solutions to the physicist's cosmological constant problem are examined.

  15. Theoretical dissociation energies for the alkali and alkaline-earth monofluorides and monochlorides

    NASA Technical Reports Server (NTRS)

    Langhoff, S. R.; Bauschlicher, C. W., Jr.; Partridge, H.

    1986-01-01

    Spectroscopic parameters are accurately determined for the alkali and alkaline-earth monofluorides and monochlorides by means of ab initio self-consistent field and correlated wave function calculations. Numerical Hartree-Fock calculations are performed on selected systems to ensure that the extended Slater basis sets employed are near the Hartree-Fock limit. Since the bonding is predominantly electrostatic in origin, a strong correlation exists between the dissociation energy (to ions) and the spectroscopic parameter r(e). By dissociating to the ionic limits, most of the differential correlation effects can be embedded in the accurate experimental electron affinities and ionization potentials.

  16. [Traditional and modern views of dissociation].

    PubMed

    Merza, Katalin; Kuritárné Szabó, Ildikó

    2012-01-01

    Dissociation is a failure to integrate aspects of identity, memory, perception, and consciousness. Dissociation is conceptualized as a dimensional process existing along a continuum from normal and relatively common dissociative experiences to severe and clinically relevant forms. There is a growing body of clinical and empirical evidence that dissociation may occur especially as a defense during trauma. In case of traumatic events dissociation considered as an attempt to maintain mental control just as physical control is lost. Dissociation can be either a symptom of some complex mental disorder or a distinct clinical entity categorized among dissociative and somatoform disorders in DSM-IV. The article describes the conceptual issues of dissociation and presents a new classification by Nijenhuis where the so-called somatoform dissociative symptoms are included as well in the list of dissociative symptoms. Finally, this paper summarizes the measures of dissociative phenomena and the cognitive-behavioral approaches of dissociation, and highlights the main features of the new structural dissociation model.

  17. Fundamental Physical Constants

    National Institute of Standards and Technology Data Gateway

    SRD 121 CODATA Fundamental Physical Constants (Web, free access)   This site, developed in the Physics Laboratory at NIST, addresses three topics: fundamental physical constants, the International System of Units (SI), which is the modern metric system, and expressing the uncertainty of measurement results.

  18. Calculation of magnetostriction constants

    NASA Astrophysics Data System (ADS)

    Tatebayashi, T.; Ohtsuka, S.; Ukai, T.; Mori, N.

    1986-02-01

    The magnetostriction constants h1 and h2 for Ni and Fe metals and the anisotropy constants K1 and K2 for Fe metal are calculated on the basis of the approximate d bands obtained by Deegan's prescription, by using Gilat-Raubenheimer's method. The obtained results are compared with the experimental ones.

  19. Transmission of electronic effects through the {closo-1-CB9} and {closo-1-CB11} cages: apparent dissociation constants for series of [closo-1-CB9H8-1-COOH-10-X] and [closo-1-CB11H10-1-COOH-12-X] acids.

    PubMed

    Pecyna, Jacek G; Ringstrand, Bryan; Kaszyński, Piotr

    2012-05-01

    The apparent ionization constants pK(a)' for series of carboxylic acids [closo-1-CB(9)H(8)-1-COOH-10-X](-) (1) and [closo-1-CB(11)H(10)-1-COOH-12-X](-) (2), where X = H, I, n-C(6)H(13), (+)NMe(3), (+)N(2), (+)SMe(2), OC(5)H(11), were measured in EtOH/H(2)O (1/1, v/v) at 24 °C. Correlation analysis of the pK(a)' values using Hammett substituent constants σ(p)(X) gave the reaction constant ρ = 0.87 ± 0.04 for series 1 and ρ = 1.00 ± 0.09 for series 2. These values are higher than for derivatives of PhCH═CHCOOH (ρ = 0.70 ± 0.09 in 55% EtOH) and correspond to 56% and 65% efficiencies in transmission of electronic effects by [closo-1-CB(9)H(10)](-) (E) and [closo-1-CB(11)H(12)](-) (F), respectively, as compared to benzene (A). Experimental results were supported with DFT calculations of relative acidity for series of acids derived from A, E, and F in aqueous medium.

  20. Separate Einstein-Eddington Spaces and the Cosmological Constant

    NASA Astrophysics Data System (ADS)

    Azri, Hemza

    2016-07-01

    In affine variational principle, a symmetric linear connection is taken as a fundamental field. The metric tensor is generated dynamically, and it appears as a canonically conjugate to the connection. From this picture, Einstein's gravity with a cosmological constant can be obtained by a covariant Legendre transformation of the affine Lagrangian. In this talk, we apply this formalism (first proposed by Kijowski) to product spaces and the cosmological constant problem. From pure affine variational principle, we derive the separate Einstein space described by its Ricci tensor. The derived equations spite into two field equations of motion that describe two maximally symmetric spaces with two non independent cosmological constants. We propose that the invariance of the bi-field equations under projections on the separate spaces, may render one of the cosmological constants to zero. We also formulate the model in the presence of matter fields. The resulted separate Einstein-Eddington spaces maybe considered as two states that describe the universe before and after inflation. A possibly interesting affine action for a general perfect fluid is also proposed. It turns out that the condition which leads to zero cosmological constant in the vacuum case, eliminates here the effects of the gravitational mass density of the perfect fluid, and the dynamic of the universe in its final state is governed by only the inertial mass density of the fluid. We present no new solutions to the problems associated with inflation.

  1. Affinity Interaction between Hexamer Peptide Ligand HWRGWV and Immunoglobulin G Studied by Quartz Crystal Microbalance and Surface Plasmon Resonance

    NASA Astrophysics Data System (ADS)

    Shen, Fei

    sensors for the immobilization of peptide ligands with low nonspecific binding. The silica surface was first modified by the formation of self-assembling monolayer (SAM) of 3-amino-propyl triethoxy silane as an anchor layer. Short chains of poly(ethylene glycol) (PEG) with Fmoc-protected amino groups at one end and carboxyl groups at the other end were then coupled through the carboxyl terminal to the amino groups on the silane. The short PEG chains served as spacer arms to reduce nonspecific binding to the substrate. The gold surface was modified by a two-component SAM using mixtures of HS(CH 2)11(CH2CH2O)6NH2 and HS(CH2)11(CH2CH2O)3OH. The advantage of using a modified silica surface is its relatively higher stability than the SAM on gold during the peptide functionalization step, however the SPR sensors do not work on silica surfaces. In addition, the modification process of the gold surface is relatively simple compared with that of the silica surface. The peptide immobilization process was optimized with silica surfaces and the best conditions were applied for the immobilization on gold surfaces. The results of surface modifications and peptide immobilizations were characterized by various surface analysis techniques including, ellipsometry, contact angle goniometer, chemical force microscopy (CFM), x-ray photoelectron spectroscopy (XPS) and time of flight secondary ion mass spectroscopy (ToF-SIMS). QCM and SPR results indicated that this peptide ligand HWRGWV immobilized on modified silica or gold surfaces has high affinity and specificity to hIgG binding even in a complex medium such as cMEM. Both thermodynamic and kinetic parameters of affinity interaction were obtained by the analysis of QCM and SPR data. Compared with QCM, SPR is more suitable for quantitative analysis of the protein binding, which is essential for the investigation of thermodynamics and kinetics parameters. The maximum binding capacity (4.15 mg m-2 ) and the dissociation constant (1.83 mu

  2. Binding affinity of full-length and extracellular domains of recombinant human (pro)renin receptor to human renin when expressed in the fat body and hemolymph of silkworm larvae.

    PubMed

    Du, Dongning; Kato, Tatsuya; Suzuki, Fumiaki; Park, Enoch Y

    2009-10-01

    Transmembrane domains of some receptors have been found to be very important in the process of constitutive oligomerization, and in the stability and functioning of the receptor. In this study, full-length of human (pro)renin receptor (hPRR) and hPRR lacking cytoplasmic domain (hPRR-DeltaCD) were expressed in fat body of silkworm larvae, and the extracellular domain of hPRR (hPRR-DeltaTMDeltaCD) in hemolymph. Three forms of hPRR were used for investigation of the interaction between receptor and ligand using surface plasmon resonance (SPR). As a result, the cytoplasmic domain was not an essential requirement for binding affinity, but the transmembrane domain of hPRR was indispensable in the formation of functional hPRR. The dissociation equilibrium constants (K(D)) of purified hPRR and hPRR-DeltaCD were estimated to be 46 nM and 330 nM, respectively. No evidence of binding by the extracellular domain of hPRR located in hemolymph was found. However, the solubilized microsomal fraction of the extracellular domain of hPRR expressed in the fat body showed specific affinity, but lost its binding affinity after purification. Its binding affinity was recovered by mixing microsomal fraction of mock-injected fat body to the purified extracellular domain. It is probable that an artificial transmembrane domain stabilizes the extracellular domain of hPRR and native conformation may be structurally recovered. To our knowledge, these are the first findings describing the interaction of transmembrane and extracellular domains of hPRR with ligand and this may help towards the understanding of binding affinity of hPRR to ligand.

  3. The high affinity ligand binding conformation of the nuclear 1,25-dihydroxyvitamin D3 receptor is functionally linked to the transactivation domain 2 (AF-2).

    PubMed Central

    Nayeri, S; Kahlen, J P; Carlberg, C

    1996-01-01

    The nuclear receptor for 1,25-dihydroxyvitamin D3 (VD), VDR, is a transcription factor that mediates all genomic actions of the hormone. The activation of VDR by ligand induces a conformational change within its ligand binding domain (LBD). Due to the lack of a crystal structure analysis, biochemical methods have to be applied in order to investigate the details of this receptor-ligand interaction. The limited protease digestion assay can be used as a tool for the determination of a functional dissociation constant (K(df)) of VDR with any potential ligand. This method provided with the natural hormone VD two protease-resistant fragments of the VDR LBD and with the 20-epi conformation of VD, known as MC1288, even an additional fragment of intermediate size. These fragments were interpreted as different receptor conformations and their decreasing size was found to be associated with decreasing ligand binding affinity. A critical amino acid for VDR's high ligand binding conformation has been identified by C-terminal receptor truncations and point mutations as phenylalanine 422. This amino acid appears to directly contact the ligand and belongs to the ligand-inducible activation function-2 (AF-2) domain. Moreover, functional assays supported the observation that high affinity ligand binding is directly linked to transactivation function. PMID:8948643

  4. Development of a specific affinity-matured exosite inhibitor to MT1-MMP that efficiently inhibits tumor cell invasion in vitro and metastasis in vivo

    PubMed Central

    Botkjaer, Kenneth A.; Kwok, Hang Fai; Terp, Mikkel G.; Karatt-Vellatt, Aneesh; Santamaria, Salvatore; McCafferty, John; Andreasen, Peter A.; Itoh, Yoshifumi; Ditzel, Henrik J.; Murphy, Gillian

    2016-01-01

    The membrane-associated matrix metalloproteinase-14, MT1-MMP, has been implicated in pericellular proteolysis with an important role in cellular invasion of collagenous tissues. It is substantially upregulated in various cancers and rheumatoid arthritis, and has been considered as a potential therapeutic target. Here, we report the identification of antibody fragments to MT1-MMP that potently and specifically inhibit its cell surface functions. Lead antibody clones displayed inhibitory activity towards pro-MMP-2 activation, collagen-film degradation and gelatin-film degradation, and were shown to bind to the MT1-MMP catalytic domain outside the active site cleft, inhibiting binding to triple helical collagen. Affinity maturation using CDR3 randomization created a second generation of antibody fragments with dissociation constants down to 0.11 nM, corresponding to an improved affinity of 332-fold with the ability to interfere with cell-surface MT1-MMP functions, displaying IC50 values down to 5 nM. Importantly, the new inhibitors were able to inhibit collagen invasion by tumor-cells in vitro and in vivo primary tumor growth and metastasis of MDA-MB-231 cells in a mouse orthotopic xenograft model. Herein is the first demonstration that an inhibitory antibody targeting sites outside the catalytic cleft of MT1-MMP can effectively abrogate its in vivo activity during tumorigenesis and metastasis. PMID:26934448

  5. The single Cys2-His2 zinc finger domain of the GAGA protein flanked by basic residues is sufficient for high-affinity specific DNA binding.

    PubMed

    Pedone, P V; Ghirlando, R; Clore, G M; Gronenborn, A M; Felsenfeld, G; Omichinski, J G

    1996-04-01

    Specific DNA binding to the core consensus site GAGAGAG has been shown with an 82-residue peptide (residues 310-391) taken from the Drosophila transcription factor GAGA. Using a series of deletion mutants, it was demonstrated that the minimal domain required for specific binding (residues 310-372) includes a single zinc finger of the Cys2-His2 family and a stretch of basic amino acids located on the N-terminal end of the zinc finger. In gel retardation assays, the specific binding seen with either the peptide or the whole protein is zinc dependent and corresponds to a dissociation constant of approximately 5 x 10(-9) M for the purified peptide. It has previously been thought that a single zinc finger of the Cys2-His2 family is incapable of specific, high-affinity binding to DNA. The combination of an N-terminal basic region with a single Cys2-His2 zinc finger in the GAGA protein can thus be viewed as a novel DNA binding domain. This raises the possibility that other proteins carrying only one Cys2-His2 finger are also capable of high-affinity specific binding to DNA. PMID:8610125

  6. Study of the dissociation of molecular hydrogen

    NASA Technical Reports Server (NTRS)

    Vessot, R. F. C.

    1981-01-01

    Dissociators used to obtain an RF plasma discharge for hydrogen masers and the test system used for operation and evaluation of the dissociators are described. A compact sorption cartridge using a graphite matrix is tested as part of a hydrogen scavenging system. Testing of a vacuum enclosed hydrogen dissociator suitable for long term operation in space is described.

  7. Two-temperature models for nitrogen dissociation

    NASA Astrophysics Data System (ADS)

    da Silva, M. Lino; Guerra, V.; Loureiro, J.

    2007-12-01

    Accurate sets of nitrogen state-resolved dissociation rates have been reduced to two-temperature (translational T and vibrational Tv) dissociation rates. The analysis of such two-temperature dissociation rates shows evidence of two different dissociation behaviors. For Tv < 0.3 T dissociation proceeds predominantly from the lower-lying vibrational levels, whereas for Tv > 0.3 T dissociation proceeds predominantly form the near-dissociative vibrational levels, with an abrupt change of behavior at Tv = 0.3 T. These two-temperature sets have then been utilized as a benchmark for the comparison against popular multitemperature dissociation models (Park, Hansen, Marrone-Treanor, Hammerling, Losev-Shatalov, Gordiets, Kuznetsov, and Macheret-Fridman). This has allowed verifying the accuracy of each theoretical model, and additionally proposing adequate values for any semi-empirical parameters present in the different theories. The Macheret-Fridman model, who acknowledges the existence of the two aforementioned dissociation regimes, has been found to provide significantly more accurate results than the other models. Although these different theoretical approaches have been tested and validated solely for nitrogen dissociation processes, it is reasonable to expect that the general conclusions of this work, regarding the adequacy of the different dissociation models, could be extended to the description of arbitrary diatomic dissociation processes.

  8. Dissociative Functions in the Normal Mourning Process.

    ERIC Educational Resources Information Center

    Kauffman, Jeffrey

    1994-01-01

    Sees dissociative functions in mourning process as occurring in conjunction with integrative trends. Considers initial shock reaction in mourning as model of normal dissociation in mourning process. Dissociation is understood to be related to traumatic significance of death in human consciousness. Discerns four psychological categories of…

  9. Mutations in TFIIIA that increase stability of the TFIIIA-5 S rRNA gene complex: unusual effects on the kinetics of complex assembly and dissociation.

    PubMed

    Brady, Kristina L; Ponnampalam, Stephen N; Bumbulis, Michael J; Setzer, David R

    2005-07-22

    We have identified four mutations in Xenopus TFIIIA that increase the stability of TFIIIA-5 S rRNA gene complexes. In each case, the mutation has a relatively modest effect on equilibrium binding affinity. In three cases, these equilibrium binding effects can be ascribed primarily to decreases in the rate constant for protein-DNA complex dissociation. In the fourth case, however, a substitution of phenylalanine for the wild-type leucine at position 148 in TFIIIA results in much larger compensating changes in the kinetics of complex assembly and dissociation. The data support a model in which a relatively unstable population of complexes with multi-component dissociation kinetics forms rapidly; complexes then undergo a slow conformational change that results in very stable, kinetically homogeneous TFIIIA-DNA complexes. The L148F mutant protein acts as a particularly potent transcriptional activator when it is fused to the VP16 activation domain and expressed in yeast cells. Substitution of L148 to tyrosine or tryptophan produces an equally strong transcriptional activator. Substitution to histidine results in genetic and biochemical effects that are more modest than, but similar to, those observed with the L148F mutation. We propose that an amino acid with a planar side chain at position 148 can intercalate between adjacent base pairs in the intermediate element of the 5 S rRNA gene. Intercalation occurs slowly but results in a very stable DNA-protein complex. These results suggest that transcriptional activation by a cis-acting sequence element is largely dependent on the kinetic, rather than the thermodynamic, stability of the complex formed with an activator protein. Thus, transcriptional activation is dependent in large part on the lifetime of the activator-DNA complex rather than on binding site occupancy at steady state. Introduction of intercalating amino acids into zinc finger proteins may be a useful tool for producing artificial transcription factors with

  10. Interplay between binding affinity and kinetics in protein-protein interactions.

    PubMed

    Cao, Huaiqing; Huang, Yongqi; Liu, Zhirong

    2016-07-01

    To clarify the interplay between the binding affinity and kinetics of protein-protein interactions, and the possible role of intrinsically disordered proteins in such interactions, molecular simulations were carried out on 20 protein complexes. With bias potential and reweighting techniques, the free energy profiles were obtained under physiological affinities, which showed that the bound-state valley is deep with a barrier height of 12 - 33 RT. From the dependence of the affinity on interface interactions, the entropic contribution to the binding affinity is approximated to be proportional to the interface area. The extracted dissociation rates based on the Arrhenius law correlate reasonably well with the experimental values (Pearson correlation coefficient R = 0.79). For each protein complex, a linear free energy relationship between binding affinity and the dissociation rate was confirmed, but the distribution of the slopes for intrinsically disordered proteins showed no essential difference with that observed for ordered proteins. A comparison with protein folding was also performed. Proteins 2016; 84:920-933. © 2016 Wiley Periodicals, Inc. PMID:27018856

  11. Interplay between binding affinity and kinetics in protein-protein interactions.

    PubMed

    Cao, Huaiqing; Huang, Yongqi; Liu, Zhirong

    2016-07-01

    To clarify the interplay between the binding affinity and kinetics of protein-protein interactions, and the possible role of intrinsically disordered proteins in such interactions, molecular simulations were carried out on 20 protein complexes. With bias potential and reweighting techniques, the free energy profiles were obtained under physiological affinities, which showed that the bound-state valley is deep with a barrier height of 12 - 33 RT. From the dependence of the affinity on interface interactions, the entropic contribution to the binding affinity is approximated to be proportional to the interface area. The extracted dissociation rates based on the Arrhenius law correlate reasonably well with the experimental values (Pearson correlation coefficient R = 0.79). For each protein complex, a linear free energy relationship between binding affinity and the dissociation rate was confirmed, but the distribution of the slopes for intrinsically disordered proteins showed no essential difference with that observed for ordered proteins. A comparison with protein folding was also performed. Proteins 2016; 84:920-933. © 2016 Wiley Periodicals, Inc.

  12. Cesium cation affinities and basicities

    NASA Astrophysics Data System (ADS)

    Gal, Jean-François; Maria, Pierre-Charles; Massi, Lionel; Mayeux, Charly; Burk, Peeter; Tammiku-Taul, Jaana

    2007-11-01

    This review focuses on the quantitative data related to cesium cation interaction with neutral or negatively charged ligands. The techniques used for measuring the cesium cation affinity (enthalpies, CCA), and cesium cation basicities (Gibbs free energies, CCB) are briefly described. The quantum chemical calculations methods that were specifically designed for the determination of cesium cation adduct structures and the energetic aspects of the interaction are discussed. The experimental results, obtained essentially from mass spectrometry techniques, and complemented by thermochemical data, are tabulated and commented. In particular, the correlations between cesium cation affinities and lithium cation affinities for the various kinds of ligands (rare gases, polyatomic neutral molecules, among them aromatic compounds and negative ions) serve as a basis for the interpretation of the diverse electrostatic modes of interaction. A brief account of some recent analytical applications of ion/molecule reactions with Cs+, as well as other cationization approaches by Cs+, is given.

  13. Kinetics of CH4 and CO2 hydrate dissociation and gas bubble evolution via MD simulation.

    PubMed

    Uddin, M; Coombe, D

    2014-03-20

    Molecular dynamics simulations of gas hydrate dissociation comparing the behavior of CH4 and CO2 hydrates are presented. These simulations were based on a structurally correct theoretical gas hydrate crystal, coexisting with water. The MD system was first initialized and stabilized via a thorough energy minimization, constant volume-temperature ensemble and constant volume-energy ensemble simulations before proceeding to constant pressure-temperature simulations for targeted dissociation pressure and temperature responses. Gas bubble evolution mechanisms are demonstrated as well as key investigative properties such as system volume, density, energy, mean square displacements of the guest molecules, radial distribution functions, H2O order parameter, and statistics of hydrogen bonds. These simulations have established the essential similarities between CH4 and CO2 hydrate dissociation. The limiting behaviors at lower temperature (no dissociation) and higher temperature (complete melting and formation of a gas bubble) have been illustrated for both hydrates. Due to the shift in the known hydrate stability curves between guest molecules caused by the choice of water model as noted by other authors, the intermediate behavior (e.g., 260 K) showed distinct differences however. Also, because of the more hydrogen-bonding capability of CO2 in water, as reflected in its molecular parameters, higher solubility of dissociated CO2 in water was observed with a consequence of a smaller size of gas bubble formation. Additionally, a novel method for analyzing hydrate dissociation based on H-bond breakage has been proposed and used to quantify the dissociation behaviors of both CH4 and CO2 hydrates. Activation energies Ea values from our MD studies were obtained and evaluated against several other published laboratory and MD values. Intrinsic rate constants were estimated and upscaled. A kinetic reaction model consistent with macroscale fitted kinetic models has been proposed to

  14. Space Shuttle astrodynamical constants

    NASA Technical Reports Server (NTRS)

    Cockrell, B. F.; Williamson, B.

    1978-01-01

    Basic space shuttle astrodynamic constants are reported for use in mission planning and construction of ground and onboard software input loads. The data included here are provided to facilitate the use of consistent numerical values throughout the project.

  15. The cosmological constant problem

    SciTech Connect

    Dolgov, A.D.

    1989-05-01

    A review of the cosmological term problem is presented. Baby universe model and the compensating field model are discussed. The importance of more accurate data on the Hubble constant and the Universe age is stressed. 18 refs.

  16. [Dis-social personality disorder].

    PubMed

    Habermeyer, E; Herpertz, S C

    2006-05-01

    Deviant behavior is gaining in clinical importance if it is founded on stable, characteristic, and enduring patterns of psychopathologically relevant personality traits which have their onset in childhood or adolescence. The classification of these traits shows variations, so that a distinction between the ICD-10 diagnosis of dis-social personality disorder, DSM-IV diagnosis of antisocial personality disorder, and the concept "psychopathy" is necessary. Our knowledge about the biological basis of antisocial behavior includes neurophysiologic, psychophysiologic, and genetic findings. Also relevant are results of neurotransmitter studies and structural resp. functional neuroimaging findings. Psychosocial risk factors include parental deficits, rejection, disregard, unstable relations, and abuse. Efficient psychotherapeutic treatment is cognitive-behavioral. Pharmacologic treatment is largely "off-label". The diagnosis of antisocial and dis-social personality disorders allows no conclusions on criminal responsibility. In addition to psychiatric diagnostics, considerations on the severity of the disorder and its effects on the ability to inhibit actions are necessary.

  17. "Clickable" agarose for affinity chromatography.

    PubMed

    Punna, Sreenivas; Kaltgrad, Eiton; Finn, M G

    2005-01-01

    Successful purification of biological molecules by affinity chromatography requires the attachment of desired ligands to biocompatible chromatographic supports. The Cu(I)-catalyzed cycloaddition of azides and alkynes-the premier example of "click chemistry"-is an efficient way to make covalent connections among diverse molecules and materials. Both azide and alkyne units are highly selective in their reactivity, being inert to most chemical functionalities and stable to wide ranges of solvent, temperature, and pH. We show that agarose beads bearing alkyne and azide groups can be easily made and are practical precursors to functionalized agarose materials for affinity chromatography.

  18. Constant potential pulse polarography

    USGS Publications Warehouse

    Christie, J.H.; Jackson, L.L.; Osteryoung, R.A.

    1976-01-01

    The new technique of constant potential pulse polarography, In which all pulses are to be the same potential, is presented theoretically and evaluated experimentally. The response obtained is in the form of a faradaic current wave superimposed on a constant capacitative component. Results obtained with a computer-controlled system exhibit a capillary response current similar to that observed In normal pulse polarography. Calibration curves for Pb obtained using a modified commercial pulse polarographic instrument are in good accord with theoretical predictions.

  19. Paraphilia from a dissociative perspective.

    PubMed

    Ross, Colin A

    2008-12-01

    A dissociative structural model of the psyche can account for a wide range of symptoms across many DSM-IV categories, including sexual compulsions and addictions. The model leads to a distinct overall plan of treatment and a set of operationalized interventions aimed at integration of the self, rather than suppression of impulses. The model could be tested first in epidemiological studies and later in treatment outcome studies.

  20. Dissociative Photoionization of Diethyl Ether.

    PubMed

    Voronova, Krisztina; Mozaffari Easter, Chrissa M; Covert, Kyle J; Bodi, Andras; Hemberger, Patrick; Sztáray, Bálint

    2015-10-29

    The dissociative photoionization of internal energy selected diethyl ether ions was investigated by imaging photoelectron photoion coincidence spectroscopy. In a large, 5 eV energy range Et2O(+) cations decay by two parallel and three sequential dissociative photoionization channels, which can be modeled well using statistical theory. The 0 K appearance energies of the CH3CHOCH2CH3(+) (H-loss, m/z = 73) and CH3CH2O═CH2(+) (methyl-loss, m/z = 59) fragment ions were determined to be 10.419 ± 0.015 and 10.484 ± 0.008 eV, respectively. The reemergence of the hydrogen-loss ion above 11 eV is attributed to transition-state (TS) switching, in which the second, outer TS is rate-determining at high internal energies. At 11.81 ± 0.05 eV, a secondary fragment of the CH3CHOCH2CH3(+) (m/z = 73) ion, protonated acetaldehyde, CH3CH═OH(+) (m/z = 45) appears. On the basis of the known thermochemical onset of this fragment, a reverse barrier of 325 meV was found. Two more sequential dissociation reactions were examined, namely, ethylene and formaldehyde losses from the methyl-loss daughter ion. The 0 K appearance energies of 11.85 ± 0.07 and 12.20 ± 0.08 eV, respectively, indicate no reverse barrier in these processes. The statistical model of the dissociative photoionization can also be used to predict the fractional ion abundances in threshold photoionization at large temperatures, which could be of use in, for example, combustion diagnostics. PMID:26444101

  1. Dissociative symptoms and REM sleep.

    PubMed

    van Heugten-van der Kloet, Dalena; Merckelbach, Harald; Lynn, Steven Jay

    2013-12-01

    Llewellyn has written a fascinating article about rapid eye movement (REM) dreams and how they promote the elaborative encoding of recent memories. The main message of her article is that hyperassociative and fluid cognitive processes during REM dreaming facilitate consolidation. We consider one potential implication of this analysis: the possibility that excessive or out-of-phase REM sleep fuels dissociative symptomatology. Further research is warranted to explore the psychopathological ramifications of Llewellyn's theory. PMID:24304772

  2. Single-cell measurement of red blood cell oxygen affinity

    PubMed Central

    Di Caprio, Giuseppe; Stokes, Chris; Higgins, John M.; Schonbrun, Ethan

    2015-01-01

    Oxygen is transported throughout the body by hemoglobin (Hb) in red blood cells (RBCs). Although the oxygen affinity of blood is well-understood and routinely assessed in patients by pulse oximetry, variability at the single-cell level has not been previously measured. In contrast, single-cell measurements of RBC volume and Hb concentration are taken millions of times per day by clinical hematology analyzers, and they are important factors in determining the health of the hematologic system. To better understand the variability and determinants of oxygen affinity on a cellular level, we have developed a system that quantifies the oxygen saturation, cell volume, and Hb concentration for individual RBCs in high throughput. We find that the variability in single-cell saturation peaks at an oxygen partial pressure of 2.9%, which corresponds to the maximum slope of the oxygen–Hb dissociation curve. In addition, single-cell oxygen affinity is positively correlated with Hb concentration but independent of osmolarity, which suggests variation in the Hb to 2,3-diphosphoglycerate (2–3 DPG) ratio on a cellular level. By quantifying the functional behavior of a cellular population, our system adds a dimension to blood cell analysis and other measurements of single-cell variability. PMID:26216973

  3. The dissociation of shock-heated carbon monoxide

    NASA Technical Reports Server (NTRS)

    Hanson, R. K.

    1973-01-01

    Investigation of the dissociation kinetics of undiluted carbon monoxide over the 5,600 to 12,000 K temperature range. Data are presented that have been obtained as time-resolved pressure measurements on the end wall of a shock tube and radiation emission of a C2 Swan system (0-0 band) behind incident shock waves. The decomposition of CO is complex and includes a chain with C2 as an intermediate species. The dissociation rate for the overall process has been found to be independent of the proportions of the collision partners M = CO, C, and O. The rate constant found is on the average about 10 times that previously measured with argon as the collision partner.

  4. Dissociative excitation and fragmentation of S8 by electron impact.

    PubMed

    Brotton, S J; McConkey, J W

    2011-05-28

    The vacuum-ultraviolet emission spectrum from 136 nm to 168 nm following the dissociative excitation of a predominantly S(8) target by electron impact at 100 eV incident energy was measured. The relative cross sections for the dominant multiplets at 138.9, 142.9, 147.9, and 166.7 nm are presented. Excitation functions are shown for electron-impact energies from below threshold to 360 eV for the two most prominent emissions at 142.5 nm and 147.4 nm. Five thresholds are clearly apparent in both excitation functions. For the four highest energy channels, the energy separation between the adjacent thresholds is approximately constant and the cross sections reduce regularly as the threshold energies increase. We suggest possible fragmentation pathways of the dissociating S(8) molecule that reproduce the energies of our observed thresholds.

  5. [Differential diagnosis between dissociative disorders and schizophrenia].

    PubMed

    Shibayama, Masatoshi

    2011-01-01

    The differential diagnosis of dissociative disorders includes many psychiatric disorders, such as schizophrenia, bipolar disorders (especially bipolar II disorder), depressive disorder (especially atypical depression), epilepsy, Asperger syndrome, and borderline personality disorder. The theme of this paper is the differential diagnosis between dissociative disorders and schizophrenia. Schneiderian first-rank symptoms in schizophrenia are common in dissociative disorders, especially in dissociative identity disorder (DID). Many DID patients have been misdiagnosed as schizophrenics and treated with neuroleptics. We compared and examined Schneiderian symptoms of schizophrenia and those of dissociative disorders from a structural viewpoint. In dissociative disorders, delusional perception and somatic passivity are not seen. "Lateness" and "Precedence of the Other" originated from the concept of "Pattern Reversal" (H. Yasunaga)" is characteristic of schizophrenia. It is important to check these basic structure of schizophrenia in subjective experiences in differential diagnosis between dissociative disorders and schizophrenia.

  6. Overview of affinity tags for protein purification.

    PubMed

    Kimple, Michelle E; Brill, Allison L; Pasker, Renee L

    2013-01-01

    Addition of an affinity tag is a useful method for differentiating recombinant proteins expressed in bacterial and eukaryotic expression systems from the background of total cellular proteins, as well as for detecting protein-protein interactions. This overview describes the historical basis for the development of affinity tags, affinity tags that are commonly used today, how to choose an appropriate affinity tag for a particular purpose, and several recently developed affinity tag technologies that may prove useful in the near future. PMID:24510596

  7. Coenzyme-like ligands for affinity isolation of cholesterol oxidase.

    PubMed

    Xin, Yu; Lu, Liushen; Wang, Qing; Zhang, Ling; Tong, Yanjun; Wang, Wu

    2016-05-15

    Two coenzyme-like chemical ligands were designed and synthesized for affinity isolation of cholesterol oxidase (COD). To simulate the structure of natural coenzyme of COD (flavin adenine dinucleotide (FAD)), on Sepharose beads, 5-aminouracil, cyanuric chloride and 1, 4-butanediamine were composed and then modified. The COD gene from Brevibacterium sp. (DQ345780) was expressed in Escherichia coli BL21 (DE3), and then the sorbents were applied to adsorption analysis with the pure enzyme. Subsequently, the captured enzyme was applied to SDS-PAGE and activity analysis. As calculated, the theoretical maximum adsorption (Qmax) of the two affinity sorbents (RL-1 and RL-2) were ∼83.5 and 46.3mg/g wet gel; and the desorption constant Kd of the two sorbents were ∼6.02×10(-4) and 1.19×10(-4)μM. The proteins after cell lysis were applied to affinity isolation, and then after one step of affinity binding on the two sorbents, the protein recoveries of RL-1 and RL-2 were 9.2% and 9.7%; the bioactivity recoveries were 92.7% and 91.3%, respectively. SDS-PAGE analysis revealed that the purities of COD isolated with the two affinity sorbents were approximately 95%. PMID:26856529

  8. Fluorogen-Activating-Proteins as Universal Affinity Biosensors for Immunodetection

    PubMed Central

    Gallo, Eugenio; Vasilev, Kalin V.; Jarvik, Jonathan

    2014-01-01

    Fluorogen-activating-proteins (FAPs) are a novel platform of fluorescence biosensors utilized for protein discovery. The technology currently demands molecular manipulation methods that limit its application and adaptability. Here, we highlight an alternative approach based on universal affinity reagents for protein detection. The affinity reagents were engineered as bi-partite fusion proteins, where the specificity moiety is derived from IgG-binding proteins –Protein-A or Protein-G – and the signaling element is a FAP. In this manner, primary antibodies provide the antigenic selectivity against a desired protein in biological samples, while FAP affinity reagents target the constant region (Fc) of antibodies and provide the biosensor component of detection. Fluorescence results using various techniques indicate minimal background and high target specificity for exogenous and endogenous proteins in mammalian cells. Additionally, FAP-based affinity reagents provide enhanced properties of detection previously absent using conventional affinity systems. Distinct features explored in this report include: (1) unfixed signal wavelengths (excitation and emission) determined by the particular fluorogen chosen, (2) real-time user controlled fluorescence on-set and off-set, (3) signal wavelength substitution while performing live analysis, and (4) enhanced resistance to photobleaching. PMID:24122476

  9. Yeast Display-Based Antibody Affinity Maturation Using Detergent-Solubilized Cell Lysates.

    PubMed

    Tillotson, Benjamin J; Lajoie, Jason M; Shusta, Eric V

    2015-01-01

    It is often desired to identify or engineer antibodies that target membrane proteins (MPs). However, due to their inherent insolubility in aqueous solutions, MPs are often incompatible with in vitro antibody discovery and optimization platforms. Recently, we adapted yeast display technology to accommodate detergent-solubilized cell lysates as sources of MP antigens. The following protocol details the incorporation of cell lysates into a kinetic screen designed to obtain antibodies with improved affinity via slowed dissociation from an MP antigen. PMID:26060070

  10. Yeast display-based antibody affinity maturation using detergent-solubilized cell lysates

    PubMed Central

    Tillotson, Benjamin J.; Lajoie, Jason M.; Shusta, Eric V.

    2016-01-01

    Summary It is often desired to identify or engineer antibodies that target membrane proteins (MPs). However, due to their inherent insolubility in aqueous solutions, MPs are often incompatible with in vitro antibody discovery and optimization platforms. Recently, we adapted yeast display technology to accommodate detergent-solubilized cell lysates as sources of MP antigens. The following protocol details the incorporation of cell lysates into a kinetic screen designed to obtain antibodies with improved affinity via slowed dissociation from an MP antigen. PMID:26060070

  11. [Clinical Handling of Patients with Dissociative Disorders].

    PubMed

    Okano, Kenichiro

    2015-01-01

    This paper discusses the way informed psychiatrists are expected to handle dissociative patients in clinical situations, with a specific focus on dissociative identity disorders and dissociative fugue. On the initial interview with dissociative patients, information on their history of trauma and any nascent dissociative symptoms in their childhood should be carefully obtained. Their level of stress in their current life should also be assessed in order to understand their symptomatology, as well as to predict their future clinical course. A psychoeducational approach is crucial; it might be helpful to give information on dissociative disorder to these patients as well as their family members in order to promote their adherence to treatment. Regarding the symptomatology of dissociative disorders, detailed symptoms and the general clinical course are presented. It was stressed that dissociative identity disorder and dissociative fugue, the most high-profile dissociative disorders, are essentially different in their etiology and clinical presentation. Dissociative disorders are often confused with and misdiagnosed as psychotic disorders, such as schizophrenia. Other conditions considered in terms of the differential diagnosis include borderline personality disorder as well as temporal lobe epilepsy. Lastly, the therapeutic approach to dissociative identity disorder is discussed. Each dissociative identity should be understood as potentially representing some traumatically stressful event in the past. The therapist should be careful not to excessively promote the creation or elaboration of any dissociative identities. Three stages are proposed in the individual psychotherapeutic process. In the initial stage, a secure environment and stabilization of symptoms should be sought. The second stage consists of aiding the "host" personality to make use of other more adaptive coping skills in their life. The third stage involves coaching as well as continuous awareness of

  12. [Clinical Handling of Patients with Dissociative Disorders].

    PubMed

    Okano, Kenichiro

    2015-01-01

    This paper discusses the way informed psychiatrists are expected to handle dissociative patients in clinical situations, with a specific focus on dissociative identity disorders and dissociative fugue. On the initial interview with dissociative patients, information on their history of trauma and any nascent dissociative symptoms in their childhood should be carefully obtained. Their level of stress in their current life should also be assessed in order to understand their symptomatology, as well as to predict their future clinical course. A psychoeducational approach is crucial; it might be helpful to give information on dissociative disorder to these patients as well as their family members in order to promote their adherence to treatment. Regarding the symptomatology of dissociative disorders, detailed symptoms and the general clinical course are presented. It was stressed that dissociative identity disorder and dissociative fugue, the most high-profile dissociative disorders, are essentially different in their etiology and clinical presentation. Dissociative disorders are often confused with and misdiagnosed as psychotic disorders, such as schizophrenia. Other conditions considered in terms of the differential diagnosis include borderline personality disorder as well as temporal lobe epilepsy. Lastly, the therapeutic approach to dissociative identity disorder is discussed. Each dissociative identity should be understood as potentially representing some traumatically stressful event in the past. The therapist should be careful not to excessively promote the creation or elaboration of any dissociative identities. Three stages are proposed in the individual psychotherapeutic process. In the initial stage, a secure environment and stabilization of symptoms should be sought. The second stage consists of aiding the "host" personality to make use of other more adaptive coping skills in their life. The third stage involves coaching as well as continuous awareness of

  13. [Dynamic model of protein behavior in water. Possible mechanism of association and dissociation of specific complexes].

    PubMed

    Kiaiviariainen, A I

    1979-01-01

    The proposed mechanism of association and dissociation of specific protein complex with ligands is based on the assumption that thermal fluctuations in the non-polar cavities of protein are interrelated due to the co-operative properties of macromolecules. The non-polar cavities, representing the active centres and clefts in the globule jump from the "open" state to the "closed" one with a certain amount of water being removed to the external medium. It is assumed that the association of ligand with the active centre is accompanied by stabilization of the chest state and destibilization of the open one, dissociation being a reverse process. A rapid change in the state of the active centre under the influence of ligand induces a slow relaxation process resulting in similar alterations in the state of the auxiliary non-polar cavities of protein. As a result, the binding constant of ligand increases, while the free energy of protein decreases. Expressions have been obtained which relate the rate constants of association, dissociation and the binding constant to the rate-constant of the nonpolar cavities transitions from the closed state to the open one, and vice versa. They gave a possibility for a qualitative interpretation of the effect of some specific and non-specific agents upon the stability of immunoglobulins, on the influence of salts upon the association and dissociation of antibody-antigene complexes and on the increase in the constant of binding between antibodies and haptens in the course of prolonged immunisation.

  14. STABILITY OF A SPHERICAL ACCRETION SHOCK WITH NUCLEAR DISSOCIATION

    SciTech Connect

    Fernandez, Rodrigo; Thompson, Christopher

    2009-06-01

    We examine the stability of a standing shock wave within a spherical accretion flow onto a gravitating star, in the context of core-collapse supernova explosions. Our focus is on the effect of nuclear dissociation below the shock on the linear growth, and nonlinear saturation, of nonradial oscillations of the shocked fluid. We combine two-dimensional, time-dependent hydrodynamic simulations using FLASH2.5 with a solution to the linear eigenvalue problem, and demonstrate the consistency of the two approaches. Previous studies of this 'standing accretion shock instability' (SASI) have focused either on zero-energy accretion flows without nuclear dissociation, or made use of a detailed finite-temperature nuclear equation of state and included strong neutrino heating. Our main goal in this and subsequent papers is to introduce equations of state of increasing complexity, in order to isolate the various competing effects. In this work, we employ an ideal gas equation of state with a constant rate of nuclear dissociation below the shock, and do not include neutrino heating. We find that a negative Bernoulli parameter below the shock significantly lowers the real frequency, growth rate, and saturation amplitude of the SASI. A decrease in the adiabatic index has similar effects. The nonlinear development of the instability is characterized by an expansion of the shock driven by turbulent kinetic energy at nearly constant internal energy. Our results also provide further insight into the instability mechanism: the rate of growth of a particular mode is fastest when the radial advection time from the shock to the accretor overlaps with the period of a standing lateral sound wave. The fastest-growing mode can therefore be modified by nuclear dissociation.

  15. Stability of a Spherical Accretion Shock with Nuclear Dissociation

    NASA Astrophysics Data System (ADS)

    Fernández, Rodrigo; Thompson, Christopher

    2009-06-01

    We examine the stability of a standing shock wave within a spherical accretion flow onto a gravitating star, in the context of core-collapse supernova explosions. Our focus is on the effect of nuclear dissociation below the shock on the linear growth, and nonlinear saturation, of nonradial oscillations of the shocked fluid. We combine two-dimensional, time-dependent hydrodynamic simulations using FLASH2.5 with a solution to the linear eigenvalue problem, and demonstrate the consistency of the two approaches. Previous studies of this "standing accretion shock instability" (SASI) have focused either on zero-energy accretion flows without nuclear dissociation, or made use of a detailed finite-temperature nuclear equation of state and included strong neutrino heating. Our main goal in this and subsequent papers is to introduce equations of state of increasing complexity, in order to isolate the various competing effects. In this work, we employ an ideal gas equation of state with a constant rate of nuclear dissociation below the shock, and do not include neutrino heating. We find that a negative Bernoulli parameter below the shock significantly lowers the real frequency, growth rate, and saturation amplitude of the SASI. A decrease in the adiabatic index has similar effects. The nonlinear development of the instability is characterized by an expansion of the shock driven by turbulent kinetic energy at nearly constant internal energy. Our results also provide further insight into the instability mechanism: the rate of growth of a particular mode is fastest when the radial advection time from the shock to the accretor overlaps with the period of a standing lateral sound wave. The fastest-growing mode can therefore be modified by nuclear dissociation.

  16. Affinity hydrogels for controlled protein release using nucleic acid aptamers and complementary oligonucleotides.

    PubMed

    Soontornworajit, Boonchoy; Zhou, Jing; Snipes, Matthew P; Battig, Mark R; Wang, Yong

    2011-10-01

    Biomaterials for the precise control of protein release are important to the development of new strategies for treating human diseases. This study aimed to fundamentally understand aptamer--protein dissociation triggered by complementary oligonucleotides, and to apply this understanding to develop affinity hydrogels for controlled protein release. The results showed that the oligonucleotide tails of the aptamers played a critical role in inducing intermolecular hybridization and triggering aptamer--protein dissociation. In addition, the attachment of the oligonucleotide tails to the aptamers and the increase of hybridizing length could produce a synergistic effect on the dissociation of bound proteins from their aptamers. More importantly, pegylated complementary oligonucleotides could successfully trigger protein release from the aptamer-functionalized hydrogels at multiple time points. Based on these results, it is believed that aptamer-functionalized hydrogels and complementary oligonucleotides hold great potential of controlling the release of protein drugs to treat human diseases.

  17. Quantifying Affinity among Chinese Dialects.

    ERIC Educational Resources Information Center

    Cheng, Chin-Chuan

    A study of the relationships between Chinese dialects based on a quantitative measure of dialect affinity is summarized. First, tone values in all the dialect localities available in the early 1970s were used to calculate the dialectal differences in terms of tone height with respect to the "yin and yang" split. In the late 1970s, calculations of…

  18. Affine Contractions on the Plane

    ERIC Educational Resources Information Center

    Celik, D.; Ozdemir, Y.; Ureyen, M.

    2007-01-01

    Contractions play a considerable role in the theory of fractals. However, it is not easy to find contractions which are not similitudes. In this study, it is shown by counter examples that an affine transformation of the plane carrying a given triangle onto another triangle may not be a contraction even if it contracts edges, heights or medians.…

  19. Measurement of free glucocorticoids: quantifying corticosteroid-binding globulin binding affinity and its variation within and among mammalian species

    PubMed Central

    Delehanty, Brendan; Hossain, Sabrina; Jen, Chao Ching; Crawshaw, Graham J.; Boonstra, Rudy

    2015-01-01

    Plasma glucocorticoids (GCs) are commonly used as measures of stress in wildlife. A great deal of evidence indicates that only free GC (GC not bound by the specific binding protein, corticosteroid-binding globulin, CBG) leaves the circulation and exerts biological effects on GC-sensitive tissues. Free hormone concentrations are difficult to measure directly, so researchers estimate free GC using two measures: the binding affinity and the binding capacity in plasma. We provide an inexpensive saturation binding method for calculating the binding affinity (equilibrium dissociation constant, Kd) of CBG that can be run without specialized laboratory equipment. Given that other plasma proteins, such as albumin, also bind GCs, the method compensates for this non-specific binding. Separation of bound GC from free GC was achieved with dextran-coated charcoal. The method provides repeatable estimates (12% coefficient of variation in the red squirrel, Tamiasciurus hudsonicus), and there is little evidence of inter-individual variation in Kd (range 2.0–7.3 nM for 16 Richardson's ground squirrels, Urocitellus richardsonii). The Kd values of 28 mammalian species we assessed were mostly clustered around a median of 4 nM, but five species had values between 13 and 61 nM. This pattern may be distinct from birds, for which published values are more tightly distributed (1.5–5.1 nM). The charcoal separation method provides a reliable and robust method for measuring the Kd in a wide range of species. It uses basic laboratory equipment to provide rapid results at very low cost. Given the importance of CBG in regulating the biological activity of GCs, this method is a useful tool for physiological ecologists. PMID:27293705

  20. Measurement of free glucocorticoids: quantifying corticosteroid-binding globulin binding affinity and its variation within and among mammalian species.

    PubMed

    Delehanty, Brendan; Hossain, Sabrina; Jen, Chao Ching; Crawshaw, Graham J; Boonstra, Rudy

    2015-01-01

    Plasma glucocorticoids (GCs) are commonly used as measures of stress in wildlife. A great deal of evidence indicates that only free GC (GC not bound by the specific binding protein, corticosteroid-binding globulin, CBG) leaves the circulation and exerts biological effects on GC-sensitive tissues. Free hormone concentrations are difficult to measure directly, so researchers estimate free GC using two measures: the binding affinity and the binding capacity in plasma. We provide an inexpensive saturation binding method for calculating the binding affinity (equilibrium dissociation constant, K d) of CBG that can be run without specialized laboratory equipment. Given that other plasma proteins, such as albumin, also bind GCs, the method compensates for this non-specific binding. Separation of bound GC from free GC was achieved with dextran-coated charcoal. The method provides repeatable estimates (12% coefficient of variation in the red squirrel, Tamiasciurus hudsonicus), and there is little evidence of inter-individual variation in K d (range 2.0-7.3 nM for 16 Richardson's ground squirrels, Urocitellus richardsonii). The K d values of 28 mammalian species we assessed were mostly clustered around a median of 4 nM, but five species had values between 13 and 61 nM. This pattern may be distinct from birds, for which published values are more tightly distributed (1.5-5.1 nM). The charcoal separation method provides a reliable and robust method for measuring the K d in a wide range of species. It uses basic laboratory equipment to provide rapid results at very low cost. Given the importance of CBG in regulating the biological activity of GCs, this method is a useful tool for physiological ecologists.

  1. Variation of Fundamental Constants

    NASA Astrophysics Data System (ADS)

    Flambaum, V. V.

    2006-11-01

    Theories unifying gravity with other interactions suggest temporal and spatial variation of the fundamental ``constants'' in expanding Universe. The spatial variation can explain a fine tuning of the fundamental constants which allows humans (and any life) to appear. We appeared in the area of the Universe where the values of the fundamental constants are consistent with our existence. We present a review of recent works devoted to the variation of the fine structure constant α, strong interaction and fundamental masses. There are some hints for the variation in quasar absorption spectra. Big Bang nucleosynthesis, and Oklo natural nuclear reactor data. A very promising method to search for the variation of the fundamental constants consists in comparison of different atomic clocks. Huge enhancement of the variation effects happens in transition between accidentally degenerate atomic and molecular energy levels. A new idea is to build a ``nuclear'' clock based on the ultraviolet transition between very low excited state and ground state in Thorium nucleus. This may allow to improve sensitivity to the variation up to 10 orders of magnitude! Huge enhancement of the variation effects is also possible in cold atomic and molecular collisions near Feshbach resonance.

  2. Uptake of oleate from albumin solutions by rat liver. Failure to detect catalysis of the dissociation of oleate from albumin by an albumin receptor.

    PubMed Central

    Weisiger, R A; Ma, W L

    1987-01-01

    The hepatic removal of albumin-bound substances from plasma requires that they dissociate from albumin. Using indirect methods, we and others have proposed that dissociation may be catalyzed by interaction of albumin with the liver cell surface. This study looked for direct evidence of catalysis by comparing the rate of dissociation of oleate from albumin in vitro with the rate observed within the sinusoids of perfused rat liver. No evidence for catalysis was found. The rate of hepatic oleate removal from dilute albumin solutions did not exceed but instead closely paralleled the rate predicted from the in vitro dissociation rate constant (0.14s-1). These results suggest that under some conditions the liver can remove unbound material from the sinusoids faster than it can be replenished by dissociation from albumin, resulting in dissociation-limited removal. However, dissociation of oleate does not appear to be catalyzed by the liver. PMID:3031131

  3. The influence of porosity and structural parameters on different kinds of gas hydrate dissociation

    PubMed Central

    Misyura, S. Y.

    2016-01-01

    Methane hydrate dissociation at negative temperatures was studied experimentally for different artificial and natural samples, differing by macro- and micro-structural parameters. Four characteristic dissociation types are discussed in the paper. The internal kinetics of artificial granule gas hydrates and clathrate hydrates in coal is dependent on the porosity, defectiveness and gas filtration rate. The density of pores distribution in the crust of formed ice decreases by the several orders of magnitude and this change significantly the rate of decay. Existing models for describing dissociation at negative temperatures do not take into account the structural parameters of samples. The dissociation is regulated by internal physical processes that must be considered in the simulation. Non-isothermal dissociation with constant external heat flux was simulated numerically. The dissociation is simulated with consideration of heat and mass transfer, kinetics of phase transformation and gas filtering through a porous medium of granules for the negative temperatures. It is shown that the gas hydrate dissociation in the presence of mainly microporous structures is fundamentally different from the disintegration of gas hydrates containing meso and macropores. PMID:27445113

  4. The influence of porosity and structural parameters on different kinds of gas hydrate dissociation.

    PubMed

    Misyura, S Y

    2016-01-01

    Methane hydrate dissociation at negative temperatures was studied experimentally for different artificial and natural samples, differing by macro- and micro-structural parameters. Four characteristic dissociation types are discussed in the paper. The internal kinetics of artificial granule gas hydrates and clathrate hydrates in coal is dependent on the porosity, defectiveness and gas filtration rate. The density of pores distribution in the crust of formed ice decreases by the several orders of magnitude and this change significantly the rate of decay. Existing models for describing dissociation at negative temperatures do not take into account the structural parameters of samples. The dissociation is regulated by internal physical processes that must be considered in the simulation. Non-isothermal dissociation with constant external heat flux was simulated numerically. The dissociation is simulated with consideration of heat and mass transfer, kinetics of phase transformation and gas filtering through a porous medium of granules for the negative temperatures. It is shown that the gas hydrate dissociation in the presence of mainly microporous structures is fundamentally different from the disintegration of gas hydrates containing meso and macropores. PMID:27445113

  5. The influence of porosity and structural parameters on different kinds of gas hydrate dissociation

    NASA Astrophysics Data System (ADS)

    Misyura, S. Y.

    2016-07-01

    Methane hydrate dissociation at negative temperatures was studied experimentally for different artificial and natural samples, differing by macro- and micro-structural parameters. Four characteristic dissociation types are discussed in the paper. The internal kinetics of artificial granule gas hydrates and clathrate hydrates in coal is dependent on the porosity, defectiveness and gas filtration rate. The density of pores distribution in the crust of formed ice decreases by the several orders of magnitude and this change significantly the rate of decay. Existing models for describing dissociation at negative temperatures do not take into account the structural parameters of samples. The dissociation is regulated by internal physical processes that must be considered in the simulation. Non-isothermal dissociation with constant external heat flux was simulated numerically. The dissociation is simulated with consideration of heat and mass transfer, kinetics of phase transformation and gas filtering through a porous medium of granules for the negative temperatures. It is shown that the gas hydrate dissociation in the presence of mainly microporous structures is fundamentally different from the disintegration of gas hydrates containing meso and macropores.

  6. The influence of porosity and structural parameters on different kinds of gas hydrate dissociation.

    PubMed

    Misyura, S Y

    2016-07-22

    Methane hydrate dissociation at negative temperatures was studied experimentally for different artificial and natural samples, differing by macro- and micro-structural parameters. Four characteristic dissociation types are discussed in the paper. The internal kinetics of artificial granule gas hydrates and clathrate hydrates in coal is dependent on the porosity, defectiveness and gas filtration rate. The density of pores distribution in the crust of formed ice decreases by the several orders of magnitude and this change significantly the rate of decay. Existing models for describing dissociation at negative temperatures do not take into account the structural parameters of samples. The dissociation is regulated by internal physical processes that must be considered in the simulation. Non-isothermal dissociation with constant external heat flux was simulated numerically. The dissociation is simulated with consideration of heat and mass transfer, kinetics of phase transformation and gas filtering through a porous medium of granules for the negative temperatures. It is shown that the gas hydrate dissociation in the presence of mainly microporous structures is fundamentally different from the disintegration of gas hydrates containing meso and macropores.

  7. Dynamics of nitrogen dissociation from direct molecular simulation

    NASA Astrophysics Data System (ADS)

    Valentini, Paolo; Schwartzentruber, Thomas E.; Bender, Jason D.; Candler, Graham V.

    2016-08-01

    We present a molecular-level investigation of nitrogen dissociation at high temperature. The computational technique, called direct molecular simulation (DMS), solely relies on an ab initio potential energy surface and both N2+N2 and N +N2 processes are simulated as they concurrently take place in an evolving nonequilibrium gas system. Quasiclassical trajectory calculations (QCT) reveal that dissociation rate coefficients calculated at thermal equilibrium, i.e., assuming Boltzmann energy distributions, are approximately equal (within less than 15%) for both N2+N2 and N +N2 collisions for the range of temperatures considered. The DMS (nonequilibrium) results indicate, however, that the presence of atomic nitrogen significantly affects the dissociation rate of molecular nitrogen, but indirectly. In fact, the presence of atomic nitrogen causes an important reduction of the vibrational relaxation time of N2, by almost one order of magnitude. This, in turn, speeds up the replenishment of high-v states that are otherwise significantly depleted if only N2+N2 collisions are considered. Because of the strong favoring of dissociation from high-v states, this results in dissociation rates that are 2-3 times higher when significant atomic nitrogen is present compared to systems composed of mainly diatomic nitrogen, such as during the initial onset of dissociation. Specifically, we find that exchange events occur frequently during N +N2 collisions and that such exchange collisions constitute an effective mechanism of scrambling the internal energy states, resulting in multiquantum jumps in vibrational energy levels that effectively promote energy transfers. The resulting vibrational relaxation time constant we calculate for N +N2 collisions is significantly lower than the widely used Millikan-White model. Significant discrepancies are found between predictions of the Park two-temperature model (using the Millikan-White vibrational relaxation model) and the DMS results for

  8. Dissociation Energetics and Mechanisms of Leucine Enkephalin (M + H)+ and (2M + X)+ Ions (X = H, Li, Na, K, and Rb) Measured by Blackbody Infrared Radiative Dissociation

    PubMed Central

    Schnier, Paul D.; Price, William D.; Strittmatter, Eric F.; Williams, Evan R.

    2005-01-01

    The dissociation kinetics of protonated leucine enkephalin and its proton and alkali metal bound dimers were investigated by blackbody infrared radiative dissociation in a Fourier-transform mass spectrometer. From the temperature dependence of the unimolecular dissociation rate constants, Arrhenius activation parameters in the zero-pressure limit are obtained. Protonated leucine enkephalin dissociates to form b4 and (M−H2O)+ ions with an average activation energy (Ea) of 1.1 eV and an A factor of 1010.5 s−1. The value of the A factor indicates that these dissociation processes are rearrangements. The b4 ions subsequently dissociate to form a4 ions via a process with a relatively high activation energy (1.3 eV), but one that is entropically favored. For the cationized dimers, the thermal stability decreases with increasing cation size, consistent with a simple electrostatic interaction in these noncovalent ion–molecule complexes. The Ea and A factors are indistinguishable within experimental error with values of ~1.5 eV and 1017 s−1, respectively. Although not conclusive, results from master equation modeling indicate that all these BIRD processes, except for b4 → a4, are in the rapid energy exchange limit. In this limit, the internal energy of the precursor ion population is given by a Boltzmann distribution and information about the energetics and dynamics of the reaction are obtained directly from the measured Arrhenius parameters. PMID:16554908

  9. The Interaction Affinity between Vascular Cell Adhesion Molecule-1 (VCAM-1) and Very Late Antigen-4 (VLA-4) Analyzed by Quantitative FRET

    PubMed Central

    Wu, Shu-Han; Karmenyan, Artashes; Chiou, Arthur

    2015-01-01

    Very late antigen-4 (VLA-4), a member of integrin superfamily, interacts with its major counter ligand vascular cell adhesion molecule-1 (VCAM-1) and plays an important role in leukocyte adhesion to vascular endothelium and immunological synapse formation. However, irregular expressions of these proteins may also lead to several autoimmune diseases and metastasis cancer. Thus, quantifying the interaction affinity of the VCAM-1/VLA-4 interaction is of fundamental importance in further understanding the nature of this interaction and drug discovery. In this study, we report an ‘in solution’ steady state organic fluorophore based quantitative fluorescence resonance energy transfer (FRET) assay to quantify this interaction in terms of the dissociation constant (Kd). We have used, in our FRET assay, the Alexa Fluor 488-VLA-4 conjugate as the donor, and Alexa Fluor 546-VCAM-1 as the acceptor. From the FRET signal analysis, Kd of this interaction was determined to be 41.82 ± 2.36 nM. To further confirm our estimation, we have employed surface plasmon resonance (SPR) technique to obtain Kd = 39.60 ± 1.78 nM, which is in good agreement with the result obtained by FRET. This is the first reported work which applies organic fluorophore based ‘in solution’ simple quantitative FRET assay to obtain the dissociation constant of the VCAM-1/VLA-4 interaction, and is also the first quantification of this interaction. Moreover, the value of Kd can serve as an indicator of abnormal protein-protein interactions; hence, this assay can potentially be further developed into a drug screening platform of VLA-4/VCAM-1 as well as other protein-ligand interactions. PMID:25793408

  10. Distinct dissociation kinetics between ion pairs: Solvent-coordinate free-energy landscape analysis.

    PubMed

    Yonetani, Yoshiteru

    2015-07-28

    Different ion pairs exhibit different dissociation kinetics; however, while the nature of this process is vital for understanding various molecular systems, the underlying mechanism remains unclear. In this study, to examine the origin of different kinetic rate constants for this process, molecular dynamics simulations were conducted for LiCl, NaCl, KCl, and CsCl in water. The results showed substantial differences in dissociation rate constant, following the trend kLiCl < kNaCl < kKCl < kCsCl. Analysis of the free-energy landscape with a solvent reaction coordinate and subsequent rate component analysis showed that the differences in these rate constants arose predominantly from the variation in solvent-state distribution between the ion pairs. The formation of a water-bridging configuration, in which the water molecule binds to an anion and a cation simultaneously, was identified as a key step in this process: water-bridge formation lowers the related dissociation free-energy barrier, thereby increasing the probability of ion-pair dissociation. Consequently, a higher probability of water-bridge formation leads to a higher ion-pair dissociation rate.

  11. Distinct dissociation kinetics between ion pairs: Solvent-coordinate free-energy landscape analysis

    NASA Astrophysics Data System (ADS)

    Yonetani, Yoshiteru

    2015-07-01

    Different ion pairs exhibit different dissociation kinetics; however, while the nature of this process is vital for understanding various molecular systems, the underlying mechanism remains unclear. In this study, to examine the origin of different kinetic rate constants for this process, molecular dynamics simulations were conducted for LiCl, NaCl, KCl, and CsCl in water. The results showed substantial differences in dissociation rate constant, following the trend kLiCl < kNaCl < kKCl < kCsCl. Analysis of the free-energy landscape with a solvent reaction coordinate and subsequent rate component analysis showed that the differences in these rate constants arose predominantly from the variation in solvent-state distribution between the ion pairs. The formation of a water-bridging configuration, in which the water molecule binds to an anion and a cation simultaneously, was identified as a key step in this process: water-bridge formation lowers the related dissociation free-energy barrier, thereby increasing the probability of ion-pair dissociation. Consequently, a higher probability of water-bridge formation leads to a higher ion-pair dissociation rate.

  12. Elastic constants of calcite

    USGS Publications Warehouse

    Peselnick, L.; Robie, R.A.

    1962-01-01

    The recent measurements of the elastic constants of calcite by Reddy and Subrahmanyam (1960) disagree with the values obtained independently by Voigt (1910) and Bhimasenachar (1945). The present authors, using an ultrasonic pulse technique at 3 Mc and 25??C, determined the elastic constants of calcite using the exact equations governing the wave velocities in the single crystal. The results are C11=13.7, C33=8.11, C44=3.50, C12=4.82, C13=5.68, and C14=-2.00, in units of 1011 dyncm2. Independent checks of several of the elastic constants were made employing other directions and polarizations of the wave velocities. With the exception of C13, these values substantially agree with the data of Voigt and Bhimasenachar. ?? 1962 The American Institute of Physics.

  13. The Hubble constant

    NASA Technical Reports Server (NTRS)

    Huchra, John P.

    1992-01-01

    The Hubble constant is the constant of proportionality between recession velocity and distance in the expanding universe. It is a fundamental property of cosmology that sets both the scale and the expansion age of the universe. It is determined by measurement of galaxy radial velocities and distances. Although there has been considerable progress in the development of new techniques for the measurements of galaxy distances, both calibration uncertainties and debates over systematic errors remain. Current determinations still range over nearly a factor of 2; the higher values favored by most local measurements are not consistent with many theories of the origin of large-scale structure and stellar evolution.

  14. Truncated Amyloid-β(11-40/42) from Alzheimer Disease Binds Cu2+ with a Femtomolar Affinity and Influences Fiber Assembly.

    PubMed

    Barritt, Joseph D; Viles, John H

    2015-11-13

    Alzheimer disease coincides with the formation of extracellular amyloid plaques composed of the amyloid-β (Aβ) peptide. Aβ is typically 40 residues long (Aβ(1-40)) but can have variable C and N termini. Naturally occurring N-terminally truncated Aβ(11-40/42) is found in the cerebrospinal fluid and has a similar abundance to Aβ(1-42), constituting one-fifth of the plaque load. Based on its specific N-terminal sequence we hypothesized that truncated Aβ(11-40/42) would have an elevated affinity for Cu(2+). Various spectroscopic techniques, complemented with transmission electron microscopy, were used to determine the properties of the Cu(2+)-Aβ(11-40/42) interaction and how Cu(2+) influences amyloid fiber formation. We show that Cu(2+)-Aβ(11-40) forms a tetragonal complex with a 34 ± 5 fm dissociation constant at pH 7.4. This affinity is 3 orders of magnitude tighter than Cu(2+) binding to Aβ(1-40/42) and more than an order of magnitude tighter than that of serum albumin, the extracellular Cu(2+) transport protein. Furthermore, Aβ(11-40/42) forms fibers twice as fast as Aβ(1-40) with a very different morphology, forming bundles of very short amyloid rods. Substoichiometric Cu(2+) drastically perturbs Aβ(11-40/42) assembly, stabilizing much longer fibers. The very tight fm affinity of Cu(2+) for Aβ(11-40/42) explains the high levels of Cu(2+) observed in Alzheimer disease plaques.

  15. The Interaction of Arp2/3 Complex with Actin: Nucleation, High Affinity Pointed End Capping, and Formation of Branching Networks of Filaments

    NASA Astrophysics Data System (ADS)

    Dyche Mullins, R.; Heuser, John A.; Pollard, Thomas D.

    1998-05-01

    The Arp2/3 complex is a stable assembly of seven protein subunits including two actin-related proteins (Arp2 and Arp3) and five novel proteins. Previous work showed that this complex binds to the sides of actin filaments and is concentrated at the leading edges of motile cells. Here, we show that Arp2/3 complex purified from Acanthamoeba caps the pointed ends of actin filaments with high affinity. Arp2/3 complex inhibits both monomer addition and dissociation at the pointed ends of actin filaments with apparent nanomolar affinity and increases the critical concentration for polymerization at the pointed end from 0.6 to 1.0 μ M. The high affinity of Arp2/3 complex for pointed ends and its abundance in amoebae suggest that in vivo all actin filament pointed ends are capped by Arp2/3 complex. Arp2/3 complex also nucleates formation of actin filaments that elongate only from their barbed ends. From kinetic analysis, the nucleation mechanism appears to involve stabilization of polymerization intermediates (probably actin dimers). In electron micrographs of quick-frozen, deep-etched samples, we see Arp2/3 bound to sides and pointed ends of actin filaments and examples of Arp2/3 complex attaching pointed ends of filaments to sides of other filaments. In these cases, the angle of attachment is a remarkably constant 70 ± 7 degrees. From these in vitro biochemical properties, we propose a model for how Arp2/3 complex controls the assembly of a branching network of actin filaments at the leading edge of motile cells.

  16. Reduced affinity of the androgen receptor for 5 alpha-dihydrotestosterone but not methyltrienolone in a form of partial androgen resistance. Studies on cultured genital skin fibroblasts.

    PubMed Central

    Pinsky, L; Kaufman, M; Chudley, A E

    1985-01-01

    We have studied a child with posterior labial fusion, clitoral phallus, female urethra, and a short, blind vagina born to a mother with decreased axillary and pubic hair. Her karyotype is 46,XY. At 2 yr of age, the child's basal level of plasma testosterone was less than 0.35 nM and after human chorionic gonadotropin stimulation, it rose to 2.6. Testis and epididymis histology were normal. Her cultured genital (labial) skin fibroblasts have normal testosterone 5 alpha-reductase activity, and metabolize 5 alpha-dihydrotestosterone (DHT) normally, but they do not augment (up-regulate) their basal androgen-receptor binding activity during prolonged incubation with DHT. With DHT, the androgen receptor in her genital skin fibroblasts has a normal binding capacity (maximum binding capacity = 25 fmol/mg protein), but an increased rate constant of dissociation (k = 11.6 X 10(-3) min-1; normal, 6 +/- 1.2 (+/- SD)), and a decreased apparent equilibrium binding affinity (Kd = 0.6 nM; normal, 0.22 +/- 0.09) that is evident in the results of 2-h assays but not of those lasting 0.5 h. With the synthetic androgen, methyltrienolone, all three binding properties of the receptor are normal, and her receptor activity up-regulates normally. We interpret these results to mean that the subject has a ligand-selective defect in the time-dependent transformation of initial, low-affinity androgen-receptor complexes to serial states of higher affinity, presumably as the result of a structural mutation at the X-linked locus that encodes the androgen receptor protein. PMID:3872888

  17. The dissociation kinetics of Cu-dissolved organic matter complexes from soil and soil amendments.

    PubMed

    Amery, F; Degryse, F; Van Moorleghem, C; Duyck, M; Smolders, E

    2010-06-18

    Complexes between dissolved organic matter (DOM) and copper (Cu) that dissociate very slowly can theoretically facilitate Cu leaching to the groundwater. Data on dissociation kinetics of Cu-DOM complexes present in soil and in soil amendments are limited. The dissociation kinetics of different Cu-DOM complexes from soil, wastewater, pig manure and sewage sludge was measured with the Competitive Ligand Exchange Method (CLEM) and Diffusive Gradient in Thin films (DGT) technique. The solutions were set at constant pH, Ca concentration and free Cu(2+) activity to allow comparison between the different samples. The average dissociation rate constant k(d) of the complexes, as measured by CLEM, was about 10(-3) s(-1) and the fractions of dissolved Cu that were undissociated after 8 h ranged from <1% to 25%. These fractions determined by CLEM were significantly correlated with the non-labile fractions (0-82%) determined in the DGT tests and data analysis show that DGT data can be predicted from CLEM data. The dissociation rates decreased when Cu-DOM complexes had been equilibrated at lower Cu(2+) activities. Increasing the Cu-DOM contact time (7-297 days) decreased the dissociation rate. The non-labile fractions were positively correlated with the specific UV absorbance suggesting that aromatic moieties in DOM hold non-labile Cu. All natural Cu-DOM complexes contained a detectable fraction with a dissociation rate constant k(d) lower than 10(-5)s(-1) which can theoretically lead to non-equilibrium conditions and leaching risks in soil.

  18. Calcium ion gradients modulate the zinc affinity and antibacterial activity of human calprotectin.

    PubMed

    Brophy, Megan Brunjes; Hayden, Joshua A; Nolan, Elizabeth M

    2012-10-31

    Calprotectin (CP) is an antimicrobial protein produced and released by neutrophils that inhibits the growth of pathogenic microorganisms by sequestering essential metal nutrients in the extracellular space. In this work, spectroscopic and thermodynamic metal-binding studies are presented to delineate the zinc-binding properties of CP. Unique optical absorption and EPR spectroscopic signatures for the interfacial His(3)Asp and His(4) sites of human calprotectin are identified by using Co(II) as a spectroscopic probe. Zinc competition titrations employing chromophoric Zn(II) indicators provide a 2:1 Zn(II):CP stoichiometry, confirm that the His(3)Asp and His(4) sites of CP coordinate Zn(II), and reveal that the Zn(II) affinity of both sites is calcium-dependent. The calcium-insensitive Zn(II) competitor ZP4 affords dissociation constants of K(d1) = 133 ± 58 pM and K(d2) = 185 ± 219 nM for CP in the absence of Ca(II). These values decrease to K(d1) ≤ 10 pM and K(d2) ≤ 240 pM in the presence of excess Ca(II). The K(d1) and K(d2) values are assigned to the His(3)Asp and His(4) sites, respectively. In vitro antibacterial activity assays indicate that the metal-binding sites and Ca(II)-replete conditions are required for CP to inhibit the growth of both Gram-negative and -positive bacteria. Taken together, these data provide a working model whereby calprotectin responds to physiological Ca(II) gradients to become a potent Zn(II) chelator in the extracellular space. PMID:23082970

  19. Coronary response to large decreases of hemoglobin-O2 affinity in isolated rat heart.

    PubMed

    Stücker, O; Vicaut, E; Villereal, M C; Ropars, C; Teisseire, B P; Duvelleroy, M A

    1985-12-01

    In this study, the consequences of large increases of P50 (O2 partial pressure at 50% oxyhemoglobin saturation) on coronary blood flow (CBF) were investigated in isolated Wistar rat heart. Rightward shifts of the O2 dissociation curve (ODC), obtained by lysing and resealing erythrocytes to encapsulate inositol hexaphosphate (IHP), led to a very large increase in P50 without side effects. Each heart was perfused alternatively with control stored human blood [P50 = 18.8 +/- 0.3 (SE) mmHg] and IHP-treated human blood (P50 = 47.1 +/- 1.7 mmHg), according to the technique of Langendorff (mean perfusion pressure 80 mmHg; hematocrit 25%). Arterial PO2 of 180 mmHg was maintained to keep arterial O2 content identical for both types of blood. When hemoglobin affinity was lowered, CBF decreased from 5.32 +/- 0.20 to 3.40 +/- 0.14 ml X min-1 X g-1, coronary sinus PO2 (PcsO2) rose from 39.9 +/- 0.9 to 69.9 +/- 4.2 mmHg, and myocardial O2 consumption (MVO2) rose slightly from 0.125 +/- 0.005 to 0.149 +/- 0.010 ml O2 X min-1 X g-1 (P less than 0.05). A significant negative correlation was found between CBF and P50 (r = -0.90; n = 32) and a significant positive correlation between PcsO2 and P50 (r = +0.84; n = 28). The coronary blood flow response to high P50 values was not abolished when maximal dilation was induced by adenosine, so this response seems independent of metabolic needs. These experiments have demonstrated that if O2 uptake by erythrocytes remains constant, in the presence of a high P50, sufficient O2 supply may be achieved with substantially less blood flow.(ABSTRACT TRUNCATED AT 250 WORDS)

  20. Compassion is a constant.

    PubMed

    Scott, Tricia

    2015-11-01

    Compassion is a powerful word that describes an intense feeling of commiseration and a desire to help those struck by misfortune. Most people know intuitively how and when to offer compassion to relieve another person's suffering. In health care, compassion is a constant; it cannot be rationed because emergency nurses have limited time or resources to manage increasing demands.

  1. XrayOpticsConstants

    2005-06-20

    This application (XrayOpticsConstants) is a tool for displaying X-ray and Optical properties for a given material, x-ray photon energy, and in the case of a gas, pressure. The display includes fields such as the photo-electric absorption attenuation length, density, material composition, index of refraction, and emission properties (for scintillator materials).

  2. Compassion is a constant.

    PubMed

    Scott, Tricia

    2015-11-01

    Compassion is a powerful word that describes an intense feeling of commiseration and a desire to help those struck by misfortune. Most people know intuitively how and when to offer compassion to relieve another person's suffering. In health care, compassion is a constant; it cannot be rationed because emergency nurses have limited time or resources to manage increasing demands. PMID:26542898

  3. Dissociative Tendencies and Facilitated Emotional Processing

    PubMed Central

    Oathes, Desmond J.; Ray, William J.

    2009-01-01

    Dissociation is a process linked to lapses of attention, history of abuse or trauma, compromised emotional memory, and a disintegrated sense of self. It is theorized that dissociation stems from avoiding emotional information, especially negative emotion, to protect a fragile psyche. The present study tested whether or not dissociaters do actually avoid processing emotion by asking groups scoring high or low on the Dissociative Experiences Scale to judge the affective valence of several types of emotional stimuli. Manipulations of valence, modality (pictures or words), task complexity, and personal relevance lead to results suggesting that dissociation is linked to facilitated rather than deficient emotional processing. Our results are consistent with a theory that sensitivity to emotional material may be a contributing factor in subsequent dissociation to avoid further elaboration of upsetting emotion in these individuals. The findings for dissociation further exemplify the influence of individual differences in the link between cognition and emotion. PMID:18837615

  4. Shock-tube study of carbon monoxide dissociation kinetics

    NASA Technical Reports Server (NTRS)

    Hanson, R. K.

    1974-01-01

    Carbon monoxide dissociation-rate data were obtained over the temperature range 5600-12,000 K. The experiments were conducted with undiluted CO to emphasize rate constants applicable to molecular gas systems. Data were obtained as time-resolved pressure measurements on the end wall of a shock tube and, in some cases, as emission histories of the C2 Swan system (0-0 band) behind incident shock waves. Results confirm the presence of C2 as an intermediate species in CO decomposition.

  5. Dissociation rate of bromine diatomics in an argon heat bath

    NASA Technical Reports Server (NTRS)

    Razner, R.; Hopkins, D.

    1973-01-01

    The evolution of a collection of 300 K bromine diatomics embedded in a heat bath of argon atoms at 1800 K was studied by computer, and a dissociation-rate constant for the reaction Br2 + BR + Ar yields Br + Ar was determined. Previously published probability distributions for energy and angular momentum transfers in classical three-dimensional Br2-Ar collisions were used in conjunction with a newly developed Monte Carlo scheme for this purpose. Results are compared with experimental shock-tube data and the predictions of several other theoretical models. A departure from equilibrium is obtained which is significantly greater than that predicted by any of these other theories.

  6. Fluorotrimethylsilane affinities of anionic nucleophiles: a study of fluoride-induced desilylation.

    PubMed

    Krouse, Ian H; Wenthold, Paul G

    2005-05-01

    In this study, preparation and decomposition of five novel pentavalent fluorosiliconates, RSi(CH3)3F- (R = CH3CH2O, CF3CH2O, (CH3)2CHO, (CH3)3SiO, and (CH3)3SiNH) is used to investigate the process of fluoride-induced desilylation. The siliconates were characterized by collision-induced dissociation and energy-resolved mass spectrometry. Decomposition of RSi(CH3)3F- leads to loss of the nucleophile R- and FSi(CH3)3, except in the case of (CH3)3SiNHSi(CH3)3F-, where HF loss is also observed. Ion affinities for FSi(CH3)3 have been measured for all five nucleophiles, and compare well with computational predictions. The observed trend of the bond dissociation energies resembles the trend of deltaH(acid) values for the corresponding conjugate acids, RH. Additionally, this data has been incorporated with existing thermochemistry to derive fluoride affinities for four of the silanes (R = CH3CH2O, (CH3)2CHO, (CH3)3SiO, and (CH3)3SiNH). We use the fluoride affinity of the silanes and the FSi(CH3)3 affinity of the departing nucleophilic anion to assess the feasibility of fluoride-induced desilylation of the silanes examined in this work. PMID:15862771

  7. Lectin affinity chromatography of glycolipids

    SciTech Connect

    Torres, B.V.; Smith, D.F.

    1987-05-01

    Since glycolipids (GLs) are either insoluble or form mixed micelles in water, lectin affinity chromatography in aqueous systems has not been applied to their separation. They have overcome this problem by using tetrahydrofuran (THF) in the mobile phase during chromatography. Affinity columns prepared with the GalNAc-specific Helix pomatia agglutinin (HPA) and equilibrated in THF specifically bind the (/sup 3/H)oligosaccharide derived from Forssman GL indicating that the immobilized HPA retained its carbohydrate-binding specificity in this solvent. Intact Forssman GL was bound by the HPA-column equilibrated in THF and was specifically eluted with 0.1 mg/ml GalNAc in THF. Purification of the Forssman GL was achieved when a crude lipid extract of sheep erythrocyte membranes was applied to the HPA-column in THF. Non-specifically bound GLs were eluted from the column using a step gradient of aqueous buffer in THF, while the addition of GalNAc was required to elute the specifically bound GLs. Using this procedure the A-active GLs were purified from a crude lipid extract of type A human erythrocytes in a single chromatographic step. The use of solvents that maintain carbohydrate-binding specificity and lipid solubility will permit the application of affinity chromatography on immobilized carbohydrate-binding proteins to intact GLs.

  8. Vibrational photodetachment spectroscopy near the electron affinity of S2

    NASA Astrophysics Data System (ADS)

    Barrick, J. B.; Yukich, J. N.

    2016-02-01

    We have conducted laser photodetachment spectroscopy near the detachment threshold of the electron affinity of S2 in a 1.8-T field. The ions are prepared by dissociative electron attachment to carbonyl sulfide. The experiment is conducted in a Penning ion trap and with a narrow-band, tunable, Ti:sapphire laser. A hybrid model for photodetachment in an ion trap is fit to the data using the appropriate Franck-Condon factors. The observations reveal detachment from and to the first few vibrational levels of the anion and the neutral molecule, respectively. Evaporative cooling of the anion ensemble condenses the thermal distribution to the lowest initial vibrational states. The subsequent detachment spectroscopy yields results consistent with a vibrationally cooled anion population.

  9. Dissociative identity disorder: Medicolegal challenges.

    PubMed

    Farrell, Helen M

    2011-01-01

    Persons with dissociative identity disorder (DID) often present in the criminal justice system rather than the mental health system and perplex experts in both professions. DID is a controversial diagnosis with important medicolegal implications. Defendants have claimed that they committed serious crimes, including rape or murder, while they were in a dissociated state. Asserting that their alter personality committed the bad act, defendants have pleaded not guilty by reason of insanity (NGRI). In such instances, forensic experts are asked to assess the defendant for DID and provide testimony in court. Debate continues over whether DID truly exists, whether expert testimony should be allowed into evidence, and whether it should exculpate defendants for their criminal acts. This article reviews historical and theoretical perspectives on DID, presents cases that illustrate the legal implications and controversies of raising an insanity defense based on multiple personalities, and examines the role of forensic experts asked to comment on DID with the goal of assisting clinicians in the medicolegal assessment of DID in relation to crimes.

  10. Dissociative recombination in planetary ionospheres

    NASA Technical Reports Server (NTRS)

    Fox, J. L.

    1993-01-01

    Ionization in planetary atmospheres can be produced by solar photoionization, photoelectron impact ionization, and, in auroral regions, by impact of precipitating particles. This ionization is lost mainly in dissociative recombination (DR) of molecular ions. Although atomic ions cannot undergo DR, they can be transformed locally through ion-molecule reactions into molecular ions, or they may be transported vertically or horizontally to regions of the atmosphere where such transformations are possible. Because DR reactions tend to be very exothermic, they can be an important source of kinetically or internally excited fragments. In interplanetary thermospheres, the neutral densities decrease exponentially with altitude. Below the homopause (or turbopause), the atmosphere is assumed to be throughly mixed by convection and/or turbulence. Above the homopause, diffusion is the major transport mechanism, and each species is distributed according to its mass, with the logarithmic derivative of the density with repect to altitude given approximately by -1/H, where H = kT/mg is the scale height. In this expression, T is the neutral temperature, g is the local acceleratiion of gravity, and m is the mass of the species. Thus lighter species become relatively more abundant, and heavier species less abundant, as the altitude increases. This variation of the neutral composition can lead to changes in the ion composition; furthermore, as the neutral densities decrease, dissociative recombination becomes more important relative to ion-neutral reactions as a loss mechanism for molecular ions.

  11. Mirror writing and a dissociative identity disorder.

    PubMed

    Le, Catherine; Smith, Joyce; Cohen, Lewis

    2009-01-01

    Individuals with dissociative identity disorder (DID) have been known to show varied skills and talents as they change from one dissociative state to another. For example, case reports have described people who have changed their handedness or have spoken foreign languages during their dissociative states. During an interview with a patient with DID, a surprising talent emerged when she wrote a sentence for the Folstein Mini-Mental State Exam-mirror writing. It is not known whether her mirror writing had a deeper level of meaning; however, it does emphasize the idiosyncratic nature of dissociative identity disorder.

  12. Dissociative Recombination without a Curve Crossing

    NASA Technical Reports Server (NTRS)

    Guberman, Steven L.

    1994-01-01

    Ab initio calculations show that a curve crossing is not always needed for a high dissociative- recombination cross section. For HeH(+), in which no neutral states cross the ion potential curve, dissociative recombination is driven by the nuclear kinetic-energy operator on adiabatic potential curves. The kinetic-energy derivative operator allows for capture into repulsive curves that are outside of the classical turning points for the nuclear motion. The dominant dissociative route is the C (2)Sigma(+) state leading to H(n = 2) atoms. An analogous mechanism is proposed for the dissociative recombination of H3(+).

  13. Expression of high-affinity IL-4 receptors on human melanoma, ovarian and breast carcinoma cells.

    PubMed Central

    Obiri, N I; Siegel, J P; Varricchio, F; Puri, R K

    1994-01-01

    It has previously been shown that murine sarcoma cells express high-affinity IL-4 receptors (IL-4R) which are internalized after binding to the ligand (Puri et al., Cancer Res 1991; 51:3011-7). We have also reported that human renal cell carcinoma cells express high-affinity IL-4R, and IL-4 inhibits tumour growth in vitro (Obiri et al., J Clin Invest 1993; 91:88). In this study we investigated the expression and function of IL-4R on other human solid tumours. Human melanoma, ovarian carcinoma and breast carcinoma cell lines were assessed for the cell surface expression of IL-4R by radio-ligand receptor binding and for IL-4R gene expression by Northern blot analysis. Primary cultures of mesothelioma and neurofibrosarcoma cells were similarly investigated. Human melanoma, ovarian carcinoma and breast carcinoma cell lines expressed IL-4R on their cell surface with a dissociation constant (Kd) of 140-549 pM. These tumour lines expressed a single 4 kb species of mRNA for IL-4R. Similarly, primary cultures of mesothelioma and neurofibrosarcoma cells were positive for the IL-4R mRNA by Northern blot analysis. Fresh, non-cultured mesothelioma and neurofibrosarcoma tumour sections were also positive for the presence of IL-4R as determined by immunohistochemistry of frozen sections using anti-IL-4R antibody. In order to study possible functions of IL-4R, we evaluated the effects of IL-4 on cell growth and its effect on MHC antigen expression in the presence or absence of interferon-gamma (IFN-gamma). In tissue culture, IL-4 reduced the growth of tumour cell lines and primary cell cultures studied. IL-4 had very little effect on MHC class I antigen expression on ovarian, breast and melanoma cell lines; however, MHC class II (HLA-DR) expression was enhanced on melanoma and breast carcinoma cells. IL-4 also enhanced the IFN-gamma-induced class II expression on melanoma and breast carcinoma cells. Taken together, our observations indicate that IL-4R are expressed on a variety of

  14. Work function and electron affinity of the fluorine-terminated (100) diamond surface

    NASA Astrophysics Data System (ADS)

    Rietwyk, K. J.; Wong, S. L.; Cao, L.; O'Donnell, K. M.; Ley, L.; Wee, A. T. S.; Pakes, C. I.

    2013-03-01

    The work function and electron affinity of fluorine-terminated (100) diamond surfaces prepared by exposure to dissociated XeF2 have been determined using synchrotron-based photoemission. After vacuum annealing to 350 °C a clean, monofluoride terminated C(100):F surface was obtained for which an electron affinity of 2.56 eV was measured. This is the highest electron affinity reported for any diamond surface termination so far, and it exceeds the value predicted by recent density functional theory calculations by 0.43 eV. The work function of 7.24 eV measured for the same surface places the Fermi energy of 0.79 eV above the valence band maximum.

  15. Affinity maturation of an anti-V antigen IgG expressed in situ through adenovirus gene delivery confers enhanced protection against Yersinia pestis challenge.

    PubMed

    Van Blarcom, T J; Sofer-Podesta, C; Ang, J; Boyer, J L; Crystal, R G; Georgiou, G

    2010-07-01

    Genetic transfer of neutralizing antibodies (Abs) has been shown to confer strong and persistent protection against bacterial and viral infectious agents. Although it is well established that for many exogenous neutralizing Abs increased antigen affinity correlates with protection, the effect of antigen affinity on Abs produced in situ after adenoviral gene transfer has not been examined. The mouse IgG2b monoclonal Ab, 2C12.4, recognizes the Yersinia pestis type III secretion apparatus protein, LcrV (V antigen), and confers protection in mice when administered as an IgG intraperitoneally or after genetic immunization with engineered, replication-defective serotype 5 human adenovirus (Ad). The 2C12.4 Ab was expressed as a single-chain variable fragment (scFv) in Escherichia coli and was shown to display an equilibrium dissociation constant (K(D))=3.5 nM by surface plasmon resonance analysis. The 2C12.4 scFv was subjected to random mutagenesis, and variants with increased affinity were isolated by flow cytometry using the anchored periplasmic expression bacterial display system. After a single round of mutagenesis, variants displaying up to 35-fold lower K(D) values (H8, K(D)=100 pM) were isolated. The variable domains of the H8 scFv were used to replace those of the parental 2C12.4 IgG encoded in the Ad vector, AdalphaV, giving rise to AdalphaV.H8. The two adenoviral vectors resulted in similar titers of anti-V antigen Abs 3 days after immunization, with 10(9), 10(10) or 10(11) particle units (pu). After intranasal challenge with 363 LD(50) (lethal dose, 50%) of Y. pestis CO92, 54% of the mice immunized with 10(10) pu of AdalphaV.H8 survived through the 14 day end point compared with only 15% survivors for the group immunized with AdalphaV expressing the lower-affinity 2C12.4 (P<0.04; AdalphaV versus AdalphaV.H8). These results indicate that affinity maturation of a neutralizing Ab delivered by genetic transfer may confer increased protection not only for Y. pestis

  16. Wall of fundamental constants

    SciTech Connect

    Olive, Keith A.; Peloso, Marco; Uzan, Jean-Philippe

    2011-02-15

    We consider the signatures of a domain wall produced in the spontaneous symmetry breaking involving a dilatonlike scalar field coupled to electromagnetism. Domains on either side of the wall exhibit slight differences in their respective values of the fine-structure constant, {alpha}. If such a wall is present within our Hubble volume, absorption spectra at large redshifts may or may not provide a variation in {alpha} relative to the terrestrial value, depending on our relative position with respect to the wall. This wall could resolve the contradiction between claims of a variation of {alpha} based on Keck/Hires data and of the constancy of {alpha} based on Very Large Telescope data. We derive the properties of the wall and the parameters of the underlying microscopic model required to reproduce the possible spatial variation of {alpha}. We discuss the constraints on the existence of the low-energy domain wall and describe its observational implications concerning the variation of the fundamental constants.

  17. Dissociative symptoms and dissociative disorder comorbidity in patients with obsessive-compulsive disorder.

    PubMed

    Belli, Hasan; Ural, Cenk; Vardar, Melek Kanarya; Yesılyurt, Sema; Oncu, Fatıh

    2012-10-01

    The present study attempted to assess the dissociative symptoms and overall dissociative disorder comorbidity in patients with obsessive-compulsive disorder (OCD). In addition, we examined the relationship between the severity of obsessive-compulsive symptoms and dissociative symptoms. All patients admitted for the first time to the psychiatric outpatient unit were included in the study. Seventy-eight patients had been diagnosed as having OCD during the 2-year study period. Patients had to meet the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition criteria for OCD. Most (76.9%; n = 60) of the patients were female, and 23.1% (n = 18) of the patients were male. Dissociation Questionnaire was used to measure dissociative symptoms. The Structured Clinical Interview for Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition Dissociative Disorders interviews and Yale-Brown Obsessive Compulsive Checklist and Severity Scale were used. Eleven (14%) of the patients with OCD had comorbid dissociative disorder. The most prevalent disorder in our study was dissociative depersonalization disorder. Dissociative amnesia and dissociative identity disorder were common as well. The mean Yale-Brown score was 23.37 ± 7.27 points. Dissociation Questionnaire scores were between 0.40 and 3.87 points, and the mean was 2.23 ± 0.76 points. There was a statistically significant positive correlation between Yale-Brown points and Dissociation Questionnaire points. We conclude that dissociative symptoms among patients with OCD should alert clinicians for the presence of a chronic and complex dissociative disorder. Clinicians may overlook an underlying dissociative process in patients who have severe symptoms of OCD. However, a lack of adequate response to cognitive-behavioral and drug therapy may be a consequence of dissociative process.

  18. Quantum dot-induced viral capsid assembling in dissociation buffer.

    PubMed

    Gao, Ding; Zhang, Zhi-Ping; Li, Feng; Men, Dong; Deng, Jiao-Yu; Wei, Hong-Ping; Zhang, Xian-En; Cui, Zong-Qiang

    2013-01-01

    Viruses encapsulating inorganic nanoparticles are a novel type of nanostructure with applications in biomedicine and biosensors. However, the encapsulation and assembly mechanisms of these hybridized virus-based nanoparticles (VNPs) are still unknown. In this article, it was found that quantum dots (QDs) can induce simian virus 40 (SV40) capsid assembly in dissociation buffer, where viral capsids should be disassembled. The analysis of the transmission electron microscope, dynamic light scattering, sucrose density gradient centrifugation, and cryo-electron microscopy single particle reconstruction experimental results showed that the SV40 major capsid protein 1 (VP1) can be assembled into ≈25 nm capsids in the dissociation buffer when QDs are present and that the QDs are encapsulated in the SV40 capsids. Moreover, it was determined that there is a strong affinity between QDs and the SV40 VP1 proteins (KD=2.19E-10 M), which should play an important role in QD encapsulation in the SV40 viral capsids. This study provides a new understanding of the assembly mechanism of SV40 virus-based nanoparticles with QDs, which may help in the design and construction of other similar virus-based nanoparticles.

  19. Quantum dot-induced viral capsid assembling in dissociation buffer

    PubMed Central

    Gao, Ding; Zhang, Zhi-Ping; Li, Feng; Men, Dong; Deng, Jiao-Yu; Wei, Hong-Ping; Zhang, Xian-En; Cui, Zong-Qiang

    2013-01-01

    Viruses encapsulating inorganic nanoparticles are a novel type of nanostructure with applications in biomedicine and biosensors. However, the encapsulation and assembly mechanisms of these hybridized virus-based nanoparticles (VNPs) are still unknown. In this article, it was found that quantum dots (QDs) can induce simian virus 40 (SV40) capsid assembly in dissociation buffer, where viral capsids should be disassembled. The analysis of the transmission electron microscope, dynamic light scattering, sucrose density gradient centrifugation, and cryo-electron microscopy single particle reconstruction experimental results showed that the SV40 major capsid protein 1 (VP1) can be assembled into ≈25 nm capsids in the dissociation buffer when QDs are present and that the QDs are encapsulated in the SV40 capsids. Moreover, it was determined that there is a strong affinity between QDs and the SV40 VP1 proteins (KD = 2.19E-10 M), which should play an important role in QD encapsulation in the SV40 viral capsids. This study provides a new understanding of the assembly mechanism of SV40 virus-based nanoparticles with QDs, which may help in the design and construction of other similar virus-based nanoparticles. PMID:23776332

  20. Varying constants quantum cosmology

    SciTech Connect

    Leszczyńska, Katarzyna; Balcerzak, Adam; Dabrowski, Mariusz P. E-mail: abalcerz@wmf.univ.szczecin.pl

    2015-02-01

    We discuss minisuperspace models within the framework of varying physical constants theories including Λ-term. In particular, we consider the varying speed of light (VSL) theory and varying gravitational constant theory (VG) using the specific ansätze for the variability of constants: c(a) = c{sub 0} a{sup n} and G(a)=G{sub 0} a{sup q}. We find that most of the varying c and G minisuperspace potentials are of the tunneling type which allows to use WKB approximation of quantum mechanics. Using this method we show that the probability of tunneling of the universe ''from nothing'' (a=0) to a Friedmann geometry with the scale factor a{sub t} is large for growing c models and is strongly suppressed for diminishing c models. As for G varying, the probability of tunneling is large for G diminishing, while it is small for G increasing. In general, both varying c and G change the probability of tunneling in comparison to the standard matter content (cosmological term, dust, radiation) universe models.

  1. A Redetermination of the Dissociation Energy of MgO(+)

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Partridge, Harry

    1994-01-01

    In 1986, we reported a dissociation energy (D(sub 0) of 2.31 eV for the X(sup 2)Pi ground state of MgO(+). This value was determined by computing the dissociation energy to the Mg(2+) + O(-) limit and adjusting the value to the Mg(+) + O limit using the experimental Ionization Potential (IP) of Mg(+) and the Electron Affinity (EA) of O. The success of this method relies on the assumption that there is little covalent contribution to the bonding. The very small (0.04 eV) correlation contribution to the binding energy was taken as corroboration for the validity of this approach. Our earlier theoretical value was estimated to be accurate to at least 0.2 eV. It is in excellent agreement with the subsequent value of 2.30 +/- 0.13 eV determined by Freiser and co-workers from photodissociation experiments. It is also consistent with the upper (less than 3.1 eV) and lower (greater than 1.1 eV) bounds determined by Rowe obtained by studying the reactions of Mg(+) with 03 and NO2. However, it is inconsistent with an upper bound of 1.7 eV reported by Kappes and Staley based on their failure to observe MgO(+) in the reaction of Mg(+) with N2O. The picture became somewhat clouded, however, by the recent guided-ion beam mass spectrometric studies of Dalleska and Armentrout. Their initial analysis of the reaction data for Mg(+) + O2 lead to a bond dissociation energy of 2.92 +/- 0.25 eV, which is considerably larger than the value of 2.47 +/- 0.06 eV deduced from their studies of the Mg(+)+NO2 reaction.

  2. Dissociative attachment reactions of electrons with strong acid molecules

    SciTech Connect

    Adams, N.G.; Smith, D.; Viggiano, A.A.; Paulson, J.F.; Henchman, M.J.

    1986-06-15

    Using the flowing afterglow/Langmuir probe (FALP) technique, we have determined (at variously 300 and 570 K) the dissociative attachment coefficients ..beta.. for the reactions of electrons with the common acids HNO/sub 3/ (producing NO/sup -//sub 2/) and H/sub 2/SO/sub 4/ (HSO/sup -//sub 4/), the superacids FSO/sub 3/H (FSO/sup -//sub 3/), CF/sub 3/SO/sub 3/H (CF/sub 3/SO/sup -//sub 3/), ClSO/sub 3/H (ClSO/sup -//sub 3/,Cl/sup -/), the acid anhydride (CF/sub 3/SO/sub 2/)/sub 2/O (CF/sub 3/SO/sup -//sub 3/), and the halogen halides HBr (Br/sup -/) and HI (I/sup -/). The anions formed in the reactions are those given in the parentheses. The reactions with HF and HCl were investigated, but did not occur at a measurable rate since they are very endothermic. Dissociative attachment is rapid for the common acids, the superacids, and the anhydride, the measured ..beta.. being appreciable fractions of the theoretical maximum ..beta.. for such reactions, ..beta../sub max/. The HI reaction is very fast ( ..beta..approx...beta../sub max/) but the HBr reaction occurs much more slowly because it is significantly endothermic. The data indicate that the extreme acidity of the (Bronsted-type) superacids has its equivalence in the very efficient gas-phase dissociative attachment which these species undergo when reacting with free electrons. The anions of the superacids generated in these reactions, notably FSO/sup -//sub 3/ and CF/sub 3/SO/sup -//sub 3/, are very stable (unreactive) implying exceptionally large electron affinities for the FSO/sub 3/ and CF/sub 3/SO/sub 3/ radicals.

  3. Multiple GPCR conformations and signalling pathways: implications for antagonist affinity estimates

    PubMed Central

    Baker, Jillian G.; Hill, Stephen J.

    2007-01-01

    Antagonist affinity measurements have traditionally been considered important in characterizing the cell-surface receptors present in a particular cell or tissue. A central assumption has been that antagonist affinity is constant for a given receptor–antagonist interaction, regardless of the agonist used to stimulate that receptor or the downstream response that is measured. As a consequence, changes in antagonist affinity values have been taken as initial evidence for the presence of novel receptor subtypes. Emerging evidence suggests, however, that receptors can possess multiple binding sites and the same receptor can show different antagonist affinity measurements under distinct experimental conditions. Here, we discuss several mechanisms by which antagonists have different affinities for the same receptor as a consequence of allosterism, coupling to different G proteins, multiple (but non-interacting) receptor sites, and signal-pathway-dependent pharmacology (where the pharmacology observed varies depending on the signalling pathway measured). PMID:17629959

  4. General approach for characterizing in vitro selected peptides with protein binding affinity.

    PubMed

    Larsen, Andrew C; Gillig, Annabelle; Shah, Pankti; Sau, Sujay P; Fenton, Kathryn E; Chaput, John C

    2014-08-01

    In vitro selection technologies are important tools for identifying high affinity peptides to proteins of broad medical and biological interest. However, the technological advances that have made it possible to generate long lists of candidate peptides have far outpaced our ability to characterize the binding properties of individual peptides. Here, we describe a low cost strategy to rapidly synthesize, purify, screen, and characterize peptides for high binding affinity. Peptides are assayed in a 96-well dot blot apparatus using membranes that enable partitioning of bound and unbound peptide-protein complexes. We have validated the binding affinity constants produced by this method using known peptide ligands and applied this process to discover five new peptides with nanomolar affinity to human α-thrombin. Given the need for new analytical tools that can accelerate peptide discovery and characterization, we feel that this approach would be useful to a wide range of technologies that utilize high affinity peptides.

  5. The multidimensional inventory of dissociation (MID): A comprehensive measure of pathological dissociation.

    PubMed

    Dell, Paul F

    2006-01-01

    This article describes the development and validation of the Multidimensional Inventory of Dissociation (MID). The MID is a 218-item, self-administered, multiscale instrument that comprehensively assesses the phenomenological domain of pathological dissociation and diagnoses the dissociative disorders. The MID measures 14 major facets of pathological dissociation; it has 23 dissociation diagnostic scales that simultaneously operationalize (1) the subjective/ phenomenological domain of pathological dissociation and (2) the hypothesized dissociative symptoms of dissociative identity disorder (Dell, 2001a). The MID was designed for clinical research and for diagnostic assessment of patients who present with a mixture of dissociative, posttraumatic, and borderline symptoms. The MID demonstrated internal reliability, temporal stability, convergent validity, discriminant validity, and construct validity. The MID also exhibited incremental validity over the Dissociative Experiences Scale (DES) by predicting an additional 18% of the variance in weighted abuse scores on the Traumatic Experiences Questionnaire (TEQ). Confirmatory factor analysis (CFA) did not support a one-factor model of the MID's clinical scales (i.e., the 14 facets and the 23 diagnostic symptoms). In contrast, however, CFA of the MID's factor scales (Dell & Lawson, 2005) has strongly supported a one-factor model. It was concluded that both the MID's 168 dissociation items and the construct of pathological dissociation have a second-order, unifactorial structure.

  6. The differential diagnosis of epilepsy, pseudoseizures, dissociative identity disorder, and dissociative disorder not otherwise specified.

    PubMed

    Bowman, E S; Coons, P M

    2000-01-01

    The authors review the co-occurrences of dissociative symptoms and disorders with epilepsy and pseudo-seizures and examine newer diagnostic instruments that assist in accurate diagnosis of persons with concomitant seizure behaviors and dissociative symptoms. They also review seizure behaviors and electroencephalographic findings in persons with dissociative identity disorder (DID) and dissociative disorder not otherwise specified (DDNOS) and dissociative symptoms in persons with epilepsy and with pseudoseizures. Dissociative symptoms in 15 patients with epilepsy and 15 with pseudo-seizures were examined using the Dissociative Experiences Scale (DES) and the Structured Clinical Interview for DSM-IV Dissociative Disorders (SCID-D). On the SCID-D, pseudo-seizure patients had significantly higher dissociative symptom scores than epileptic patients, but DES scores did not reliably distinguish epileptic and pseudo-seizure patients. Misdiagnosis of persons with seizures and dissociative symptoms can be avoided by careful adherence to DSM dissociative disorder criteria, the use of video-EEG monitoring, and systematic assessment of dissociative symptoms with the SCID-D.

  7. Two-parameter twisted quantum affine algebras

    NASA Astrophysics Data System (ADS)

    Jing, Naihuan; Zhang, Honglian

    2016-09-01

    We establish Drinfeld realization for the two-parameter twisted quantum affine algebras using a new method. The Hopf algebra structure for Drinfeld generators is given for both untwisted and twisted two-parameter quantum affine algebras, which include the quantum affine algebras as special cases.

  8. Native Elution of Yeast Protein Complexes Obtained by Affinity Capture.

    PubMed

    LaCava, John; Fernandez-Martinez, Javier; Rout, Michael P

    2016-01-01

    This protocol describes two options for the native (nondenaturing) elution of protein complexes obtained by affinity capture. The first approach involves the elution of complexes purified through a tag that includes a human rhinovirus 3C protease (PreScission protease) cleavage site sequence between the protein of interest and the tag. Incubation with the protease cleaves immobilized complexes from the affinity medium. The second approach involves the release of protein A-tagged protein complexes using a competitive elution reagent called PEGylOx. The degree of purity of the native assemblies eluted is sample dependent and strongly influenced by the affinity capture. It should be noted that the efficiency of native elution is commonly lower than that of elution by a denaturing agent (e.g., SDS) and the release of the complex will be limited by the activity of the protease or the inhibition constant (Ki) of the competitive release agent. However, an advantage of native release is that some nonspecifically bound materials tend to stay adsorbed to the affinity medium, providing an eluted fraction of higher purity. Finally, keep in mind that the presence of the protease or elution peptide could potentially affect downstream applications; thus, their removal should be considered. PMID:27371597

  9. Binding affinities of anti-acetylcholine receptor autoantibodies in myasthenia gravis

    SciTech Connect

    Bray, J.J.; Drachman, D.B.

    1982-01-01

    Antibodies directed against acetylcholine (ACh) receptors are present in the sera of nearly 90% of patients with myasthenia gravis (MG), and are involved in the pathogenesis of this autoimmune disease. However, the antibody titers measured by the standard radioimmunoassay correspond poorly with the clinical severity of the disease. To determine whether this disparity could be accounted for by differences in the binding affinities of anti-ACh receptor antibodies in different patients, we have measured the binding affinities of these autoantibodies in 15 sera from MG patients. The affinity constants (K/sub o/), as determined by Scatchard analysis, were all in the range of 10/sup 10/ M/sup -1/, comparable to the highest values reported in immunized animals. The affinity constants were truly representative of the population of autoantibodies detected by the radioimmunoassay, as shown by the remarkable linearity of the Scatchard plots (r/sup 2/>0.90) and the close correlation between the antibody titers determined by extrapolation of the Scatchard plots and by saturation analysis (r = 0.99; p < 0.001). There was only a 6-fold variation in affinity constants measured in this series of patients despite widely differing antibody titers and severity of the disease. Factors other than the titer and affinity of anti-ACh receptor antibodies may correlate better with the clinical manifestations of MG.

  10. Dissociative recombination of cold H3+ and its interstellar implications.

    PubMed

    McCall, Benjamin J

    2006-11-15

    H3+ plays a key role in interstellar chemistry as the initiator of ion-molecule chemistry. The amount of H3+ observed in dense interstellar clouds is consistent with expectations, but the large abundance of H3+ seen in diffuse clouds is not easily explained by simple chemical models. A crucial parameter in predicting the abundance of H3+ in diffuse clouds is the rate constant for dissociative recombination (DR) with electrons. The value of this constant has been very controversial, because different experimental techniques have yielded very different results, perhaps owing to varying degrees of rotational and vibrational excitation of the H3+ ions. If the value of this rate constant under interstellar conditions were much lower than usually assumed, the large H3+ abundance could be easily explained. In an attempt to pin down this crucial rate constant, we have performed DR measurements at the CRYRING ion storage ring in Stockholm, using a supersonic expansion ion source to produce rotationally cold H3+ ions. These measurements suggest that the DR rate constant in diffuse clouds is not much lower than usually assumed and that the abundant H3+ must be due to either a low electron fraction or a high ionization rate.

  11. Molecular dissociation in dilute gas

    SciTech Connect

    Renfrow, S.N.; Duggan, J.L.; McDaniel, F.D. |

    1999-06-01

    The charge state distributions (CSD) produced during molecular dissociation are important to both Trace Element Accelerator Mass Spectrometry (TEAMS) and the ion implantation industry. The CSD of 1.3{endash}1.7 MeV SiN{sup +}, SiMg{sup +}, SiMn{sup +}, and SiZn{sup +} molecules have been measured for elements that do not form atomic negative ions (N, Mg, Mn, and Zn) using a NEC Tandem Pelletron accelerator. The molecules were produced in a Cs sputter negative ion source, accelerated, magnetically analyzed, and then passed through an N{sub 2} gas cell. The neutral and charged breakups where analyzed using an electrostatic deflector and measured with particle detectors. Equilibrium CSD were determined and comparisons made between molecular and atomic ion data. {copyright} {ital 1999 American Institute of Physics.}

  12. The Dissociative Recombination of OH(+)

    NASA Technical Reports Server (NTRS)

    Guberman, Steven L.

    1995-01-01

    Theoretical quantum chemical calculations of the cross sections and rates for the dissociative recombination of the upsilon = 0 level of the ground state of OH(+) show that recombination occurs primarily along the 2 (2)Pi diabatic route. The products are 0((1)D) and a hot H atom with 6.1 eV kinetic energy. The coupling to the resonances is very small and the indirect recombination mechanism plays only a minor role. The recommended value for the rate coefficient is (6.3 +/- 0.7) x 10(exp -9)x (T(e)/1300)(exp -0.48) cu.cm/s for 10 less than T(e) less than 1000 K.

  13. Dissociative depression among women in the community.

    PubMed

    Sar, Vedat; Akyüz, Gamze; Oztürk, Erdinç; Alioğlu, Firdevs

    2013-01-01

    This study screened the prevalence and correlates of dissociative disorders among depressive women in the general population. The Dissociative Disorders Interview Schedule and the posttraumatic stress disorder (PTSD) and borderline personality disorder sections of the Structured Clinical Interview for DSM-IV were administered to 628 women in 500 homes. The prevalence of current major depressive episode was 10.0%. Of the women, 26 (40.6%) had the lifetime diagnosis of a DSM-IV, dissociative disorder, yielding a prevalence of 4.1% for dissociative depression. This group was younger (mean age = 30.7 years) than the nondissociative depression women (mean age = 39.6 years). There was no difference between the 2 groups on comorbid somatization disorder, PTSD, or borderline personality disorder. Besides suicide attempts, the dissociative group was characterized by secondary features of dissociative identity disorder; Schneiderian symptoms; borderline personality disorder criteria; and extrasensory perceptions, including possession experiences. They reported suicidality, thoughts of guilt and worthlessness, diminished concentration and indecisiveness, and appetite and weight changes more frequently than the nondissociative group. Early cessation of school education and childhood sexual abuse were frequently reported by the dissociative depression group. With its distinct features, the concept of dissociative depression may facilitate understanding of treatment resistance in, development of better psychotherapy strategies for, and new thinking on the neurobiology and pharmacotherapy of depressive disorders. PMID:23796173

  14. Dissociation and the Development of Psychopathology.

    ERIC Educational Resources Information Center

    Putnam, Frank W.; Trickett, Penelope K.

    This paper reviews the research on dissociation and the development of psychopathology in children and adolescents. Definitions and dimensions of dissociation are addressed, noting its range from normative daydreaming to the extremes found in individuals with multiple personality disorder. Memory dysfunctions, disturbances of identity, passive…

  15. Dissociative depression among women in the community.

    PubMed

    Sar, Vedat; Akyüz, Gamze; Oztürk, Erdinç; Alioğlu, Firdevs

    2013-01-01

    This study screened the prevalence and correlates of dissociative disorders among depressive women in the general population. The Dissociative Disorders Interview Schedule and the posttraumatic stress disorder (PTSD) and borderline personality disorder sections of the Structured Clinical Interview for DSM-IV were administered to 628 women in 500 homes. The prevalence of current major depressive episode was 10.0%. Of the women, 26 (40.6%) had the lifetime diagnosis of a DSM-IV, dissociative disorder, yielding a prevalence of 4.1% for dissociative depression. This group was younger (mean age = 30.7 years) than the nondissociative depression women (mean age = 39.6 years). There was no difference between the 2 groups on comorbid somatization disorder, PTSD, or borderline personality disorder. Besides suicide attempts, the dissociative group was characterized by secondary features of dissociative identity disorder; Schneiderian symptoms; borderline personality disorder criteria; and extrasensory perceptions, including possession experiences. They reported suicidality, thoughts of guilt and worthlessness, diminished concentration and indecisiveness, and appetite and weight changes more frequently than the nondissociative group. Early cessation of school education and childhood sexual abuse were frequently reported by the dissociative depression group. With its distinct features, the concept of dissociative depression may facilitate understanding of treatment resistance in, development of better psychotherapy strategies for, and new thinking on the neurobiology and pharmacotherapy of depressive disorders.

  16. Childhood Stuttering and Dissociations across Linguistic Domains

    ERIC Educational Resources Information Center

    Anderson, Julie D.; Pellowski, Mark W.; Conture, Edward G.

    2005-01-01

    The purpose of this investigation was to evaluate the possible presence of dissociations in the speech and language skills of young children who do (CWS) and do not stutter (CWNS) using a correlation-based statistical procedure [Bates, E., Appelbaum, M., Salcedo, J., Saygin, A. P., & Pizzamiglio, L. (2003). Quantifying dissociations in…

  17. [Dissociative disorder and self-injury].

    PubMed

    Noma, Shun'ichi

    2011-01-01

    Both the number of patients with dissociative disorder and that of those with self-injury have been increasing since the end of the twentieth century, suggesting that dissociation and self-injury might be closely related. When dissociative disorder coexists with self-injury, it implies self-punishment and a wish to be understood by others. Although many cases of self-injury observed since 2000 lacked traumatic experiences and were not accompanied by pathological dissociative symptoms, the patients did have dissociative tendencies. According to the results of our study examining self-injury in patients with eating disorders, we observed that self-injury, dissociative tendency and insulation from others are related to each other. This suggests that affects, sensations and representations are dissociated, losing their normal response order, and that the pervasive idea that "pain=secure" is formed in a patient from childhood based on influence from their parents. Self-injury appears to be an activation of this pervasive idea that is triggered by a stressful situation, when the dissociative psychological segmentation of effects and their representations are present in the background.

  18. Cognitive and dissociative manifestations in fibromyalgia.

    PubMed

    Leavitt, Frank; Katz, Robert S; Mills, Megan; Heard, Amy R

    2002-04-01

    Memory decline and mental confusion frequently complicate the clinical presentation of fibromyalgia; however, formal cognitive examination often does not support deterioration. This paradox was examined in the context of dissociation, a condition with many cognitive similarities. Dissociation refers to the separation of parts of experience from the mainstream of consciousness. A common example is highway hypnosis. Eighty-nine fibromyalgia (FM) patients and 64 other rheumatic disease patients were screened for memory decline and mental confusion using a questionnaire format. Pain, dissociation, affective distress, fatigue, sleep difficulty, and mental confusion were also assessed. Cognitive complaints (76.4%-43.8%) and dissociative symptoms (37.1%-1.9%) were overrepresented in patients with FM. Among FM patients with high dissociation, cognitive difficulties were reported by 95%; 100% of these cases reported that both memory and mental clarity were affected, a condition referred to as fibrofog. Dissociation in combination with fibrofog was associated with higher levels of FM symptom intensity and decreased mental well being. These findings suggest that dissociation may play a role in FM symptom amplification and may aid in comprehending the regularity of cognitive symptoms. Separating cases of fibrofog from cognitive conditions with actual brain damage is important. It may be prudent to add a test of dissociation as an adjunct to the evaluation of FM patients in cases of suspected fibrofog. Otherwise, test results may prove normal even in patients with disabling cognitive symptoms.

  19. A Hierarchical Process-Dissociation Model

    ERIC Educational Resources Information Center

    Rouder, Jeffrey N.; Lu, Jun; Morey, Richard D.; Sun, Dongchu; Speckman, Paul L.

    2008-01-01

    In fitting the process-dissociation model (L. L. Jacoby, 1991) to observed data, researchers aggregate outcomes across participant, items, or both. T. Curran and D. L. Hintzman (1995) demonstrated how biases from aggregation may lead to artifactual support for the model. The authors develop a hierarchical process-dissociation model that does not…

  20. Change is a Constant.

    PubMed

    Lubowitz, James H; Provencher, Matthew T; Brand, Jefferson C; Rossi, Michael J; Poehling, Gary G

    2015-06-01

    In 2015, Henry P. Hackett, Managing Editor, Arthroscopy, retires, and Edward A. Goss, Executive Director, Arthroscopy Association of North America (AANA), retires. Association is a positive constant, in a time of change. With change comes a need for continuing education, research, and sharing of ideas. While the quality of education at AANA and ISAKOS is superior and most relevant, the unique reason to travel and meet is the opportunity to interact with innovative colleagues. Personal interaction best stimulates new ideas to improve patient care, research, and teaching. Through our network, we best create innovation.

  1. Cosmology with varying constants.

    PubMed

    Martins, Carlos J A P

    2002-12-15

    The idea of possible time or space variations of the 'fundamental' constants of nature, although not new, is only now beginning to be actively considered by large numbers of researchers in the particle physics, cosmology and astrophysics communities. This revival is mostly due to the claims of possible detection of such variations, in various different contexts and by several groups. I present the current theoretical motivations and expectations for such variations, review the current observational status and discuss the impact of a possible confirmation of these results in our views of cosmology and physics as a whole.

  2. The expectancy of threat and peritraumatic dissociation

    PubMed Central

    McDonald, Pamela; Bryant, Richard A.; Silove, Derrick; Creamer, Mark; O'Donnell, Meaghan; McFarlane, Alexander C.

    2013-01-01

    Background Peritraumatic dissociation is one of the most critical acute responses to a traumatic experience, partly because it predicts subsequent posttraumatic stress disorder. Despite this, there is little understanding about the factors that influence peritraumatic dissociation. This study investigated the extent to which peritraumatic dissociation is predicted by the amount of perceived warning that participants had of the impact of the trauma. Method Randomized eligible admissions to four major trauma hospitals (N=243) were assessed during hospital admission with the Peritraumatic Dissociation Experiences Questionnaire (PDEQ) and the perceived warning that participants had before the trauma impact occurred. Results Whereas female gender predicted both Awareness and Derealization subscale scores on the PDEQ, perceived warning also predicted scores on the Derealization subscale. Conclusions This finding suggests that the degree of anticipated threat may contribute to peritraumatic dissociation. PMID:24363835

  3. Comparative kinetics of cofactor association and dissociation for the human and trypanosomal S-adenosylhomocysteine hydrolases. 3. Role of lysyl and tyrosyl residues of the C-terminal extension.

    PubMed

    Cai, Sumin; Fang, Jianwen; Li, Qing-Shan; Borchardt, Ronald T; Kuczera, Krzysztof; Middaugh, C Russell; Schowen, Richard L

    2010-09-28

    On the basis of the available X-ray structures of S-adenosylhomocysteine hydrolases (SAHHs), free energy simulations employing the MM-GBSA approach were applied to predict residues important to the differential cofactor binding properties of human and trypanosomal SAHHs (Hs-SAHH and Tc-SAHH), within 5 Å of the cofactor NAD(+)/NADH binding site. Among the 38 residues in this region, only four are different between the two enzymes. Surprisingly, the four nonidentical residues make no major contribution to differential cofactor binding between Hs-SAHH and Tc-SAHH. On the other hand, four pairs of identical residues are shown by free energy simulations to differentiate cofactor binding between Hs-SAHH and Tc-SAHH. Experimental mutagenesis was performed to test these predictions for a lysine residue and a tyrosine residue of the C-terminal extension that penetrates a partner subunit to form part of the cofactor binding site. The K431A mutant of Tc-SAHH (TcK431A) loses its cofactor binding affinity but retains the wild type's tetrameric structure, while the corresponding mutant of Hs-SAHH (HsK426A) loses both cofactor affinity and tetrameric structure [Ault-Riche, D. B., et al. (1994) J. Biol. Chem. 269, 31472-31478]. The tyrosine mutants HsY430A and TcY435A alter the NAD(+) association and dissociation kinetics, with HsY430A increasing the cofactor equilibrium dissociation constant from approximately 10 nM (Hs-SAHH) to ∼800 nM and TcY435A increasing the cofactor equilibrium dissociation constant from approximately 100 nM (Tc-SAHH) to ∼1 mM. Both changes result from larger increases in the off rate combined with smaller decreases in the on rate. These investigations demonstrate that computational free energy decomposition may be used to guide experimental studies by suggesting sensitive sites for mutagenesis. Our finding that identical residues in two orthologous proteins may give significantly different binding free energy contributions strongly suggests that

  4. High fidelity modeling of thermal relaxation and dissociation of oxygen

    SciTech Connect

    Andrienko, Daniil A. Boyd, Iain D.

    2015-11-15

    A master equation study of vibrational relaxation and dissociation of oxygen is conducted using state-specific O{sub 2}–O transition rates, generated by extensive trajectory simulations. Both O{sub 2}–O and O{sub 2}–O{sub 2} collisions are concurrently simulated in the evolving nonequilibrium gas system under constant heat bath conditions. The forced harmonic oscillator model is incorporated to simulate the state-to-state relaxation of oxygen in O{sub 2}–O{sub 2} collisions. The system of master equations is solved to simulate heating and cooling flows. The present study demonstrates the importance of atom-diatom collisions due to the extremely efficient energy randomization in the intermediate O{sub 3} complex. It is shown that the presence of atomic oxygen has a significant impact on vibrational relaxation time at temperatures observed in hypersonic flow. The population of highly-excited O{sub 2} vibrational states is affected by the amount of atomic oxygen when modeling the relaxation under constant heat bath conditions. A model of coupled state-to-state vibrational relaxation and dissociation of oxygen is also discussed.

  5. High fidelity modeling of thermal relaxation and dissociation of oxygen

    NASA Astrophysics Data System (ADS)

    Andrienko, Daniil A.; Boyd, Iain D.

    2015-11-01

    A master equation study of vibrational relaxation and dissociation of oxygen is conducted using state-specific O2-O transition rates, generated by extensive trajectory simulations. Both O2-O and O2-O2 collisions are concurrently simulated in the evolving nonequilibrium gas system under constant heat bath conditions. The forced harmonic oscillator model is incorporated to simulate the state-to-state relaxation of oxygen in O2-O2 collisions. The system of master equations is solved to simulate heating and cooling flows. The present study demonstrates the importance of atom-diatom collisions due to the extremely efficient energy randomization in the intermediate O3 complex. It is shown that the presence of atomic oxygen has a significant impact on vibrational relaxation time at temperatures observed in hypersonic flow. The population of highly-excited O2 vibrational states is affected by the amount of atomic oxygen when modeling the relaxation under constant heat bath conditions. A model of coupled state-to-state vibrational relaxation and dissociation of oxygen is also discussed.

  6. Expression and affinity purification of recombinant proteins from plants

    NASA Technical Reports Server (NTRS)

    Desai, Urvee A.; Sur, Gargi; Daunert, Sylvia; Babbitt, Ruth; Li, Qingshun

    2002-01-01

    With recent advances in plant biotechnology, transgenic plants have been targeted as an inexpensive means for the mass production of proteins for biopharmaceutical and industrial uses. However, the current plant purification techniques lack a generally applicable, economic, large-scale strategy. In this study, we demonstrate the purification of a model protein, beta-glucuronidase (GUS), by employing the protein calmodulin (CaM) as an affinity tag. In the proposed system, CaM is fused to GUS. In the presence of calcium, the calmodulin fusion protein binds specifically to a phenothiazine-modified surface of an affinity column. When calcium is removed with a complexing agent, e.g., EDTA, calmodulin undergoes a conformational change allowing the dissociation of the calmodulin-phenothiazine complex and, therefore, permitting the elution of the GUS-CaM fusion protein. The advantages of this approach are the fast, efficient, and economical isolation of the target protein under mild elution conditions, thus preserving the activity of the target protein. Two types of transformation methods were used in this study, namely, the Agrobacterium-mediated system and the viral-vector-mediated transformation system. Copyright 2002 Elsevier Science (USA).

  7. The Shutdown Dissociation Scale (Shut-D)

    PubMed Central

    Schalinski, Inga; Schauer, Maggie; Elbert, Thomas

    2015-01-01

    The evolutionary model of the defense cascade by Schauer and Elbert (2010) provides a theoretical frame for a short interview to assess problems underlying and leading to the dissociative subtype of posttraumatic stress disorder. Based on known characteristics of the defense stages “fright,” “flag,” and “faint,” we designed a structured interview to assess the vulnerability for the respective types of dissociation. Most of the scales that assess dissociative phenomena are designed as self-report questionnaires. Their items are usually selected based on more heuristic considerations rather than a theoretical model and thus include anything from minor dissociative experiences to major pathological dissociation. The shutdown dissociation scale (Shut-D) was applied in several studies in patients with a history of multiple traumatic events and different disorders that have been shown previously to be prone to symptoms of dissociation. The goal of the present investigation was to obtain psychometric characteristics of the Shut-D (including factor structure, internal consistency, retest reliability, predictive, convergent and criterion-related concurrent validity). A total population of 225 patients and 68 healthy controls were accessed. Shut-D appears to have sufficient internal reliability, excellent retest reliability, high convergent validity, and satisfactory predictive validity, while the summed score of the scale reliably separates patients with exposure to trauma (in different diagnostic groups) from healthy controls. The Shut-D is a brief structured interview for assessing the vulnerability to dissociate as a consequence of exposure to traumatic stressors. The scale demonstrates high-quality psychometric properties and may be useful for researchers and clinicians in assessing shutdown dissociation as well as in predicting the risk of dissociative responding. PMID:25976478

  8. A strategy of designing the ligand of antibody affinity chromatography based on molecular dynamics simulation.

    PubMed

    Dai, Lu; Li, Weikang; Sun, Fei; Li, Baizhi; Li, Hongrui; Zhang, Hongxing; Zheng, Qingchuan; Liang, Chongyang

    2016-09-01

    Designing affinity ligands has always been the development focus of affinity chromatography. Previous antibody affinity ligand designs were mostly based on the crystal structure of protein A (UniProt code number: P38507), and the antibody-binding domains were modified according to the properties of amino acid residues. Currently, more effective bioinformatic prediction and experimental validation has been used to improve the design of antibody affinity ligands. In the present study, the complex crystal structure (the domain D of protein A and the Fab segment of IgM, PDB code: 1DEE) was used as the model. The vital site that inhibits the binding between domain D and IgM was estimated by means of molecular dynamics (MD) simulation, then MM-GBSA calculations were used to design a mutant of domain D (K46E) for improving affinity on the above vital site. The binding analysis using Biacore showed the association and dissociation parameters of K46E mutant that were optimized with IgM. The affinity increase of K46E mutant preferred for IgM, the affinity order is K46E tetramer (KD=6.02×10(-9)M)>K46E mutant (KD=6.66×10(-8)M)>domain D (KD=2.17×10(-7)M). Similar results were obtained when the optimized ligands were immobilized to the chromatography medium. A complete designing strategy was validated in this study, which will provide a novel insight into designing new ligands of antibody affinity chromatography media.

  9. A strategy of designing the ligand of antibody affinity chromatography based on molecular dynamics simulation.

    PubMed

    Dai, Lu; Li, Weikang; Sun, Fei; Li, Baizhi; Li, Hongrui; Zhang, Hongxing; Zheng, Qingchuan; Liang, Chongyang

    2016-09-01

    Designing affinity ligands has always been the development focus of affinity chromatography. Previous antibody affinity ligand designs were mostly based on the crystal structure of protein A (UniProt code number: P38507), and the antibody-binding domains were modified according to the properties of amino acid residues. Currently, more effective bioinformatic prediction and experimental validation has been used to improve the design of antibody affinity ligands. In the present study, the complex crystal structure (the domain D of protein A and the Fab segment of IgM, PDB code: 1DEE) was used as the model. The vital site that inhibits the binding between domain D and IgM was estimated by means of molecular dynamics (MD) simulation, then MM-GBSA calculations were used to design a mutant of domain D (K46E) for improving affinity on the above vital site. The binding analysis using Biacore showed the association and dissociation parameters of K46E mutant that were optimized with IgM. The affinity increase of K46E mutant preferred for IgM, the affinity order is K46E tetramer (KD=6.02×10(-9)M)>K46E mutant (KD=6.66×10(-8)M)>domain D (KD=2.17×10(-7)M). Similar results were obtained when the optimized ligands were immobilized to the chromatography medium. A complete designing strategy was validated in this study, which will provide a novel insight into designing new ligands of antibody affinity chromatography media. PMID:27524303

  10. Complex high affinity interactions occur between MHCI and superantigens

    NASA Technical Reports Server (NTRS)

    Chapes, S. K.; Herpich, A. R.; Spooner, B. S. (Principal Investigator)

    1998-01-01

    Staphylococcal enterotoxins A and C1 (SEA or SEC1) bound to major histocompatibility-I (MHCI) molecules with high affinity (binding constants ranging from 1.1 microM to 79 nM). SEA and SEC1 directly bound MHCI molecules that had been captured by monoclonal antibodies specific for H-2Kk, H-2Dk, or both. In addition, MHCI-specific antibodies inhibited the binding of SEC1 to LM929 cells and SEA competitively inhibited SEC1 binding; indicating that the superantigens bound to MHCI on the cell surface. The affinity and number of superantigen binding sites differed depending on whether MHCI was expressed in the membrane of LM929 cells or whether it was captured. These data support the hypothesis that MHCI molecules can serve as superantigen receptors.

  11. Banach frames in the affine synthesis problem

    NASA Astrophysics Data System (ADS)

    Terekhin, Pavel A.

    2009-10-01

    We consider the problem of representing functions f\\in L^p(\\mathbb R^d) by a series in elements of the affine system \\displaystyle \\psi_{j,k}(x)=\\lvert\\det a_j\\rvert^{1/2}\\psi(a_jx-bk), \\qquad j\\in\\mathbb N, \\quad k\\in\\mathbb Z^d. The corresponding representation theorems are established on the basis of the frame inequalities \\displaystyle A\\Vert g\\Vert _q\\le\\Vert\\{(g,\\psi_{j,k})\\}\\Vert _Y\\le B\\Vert g\\Vert _q for the Fourier coefficients \\displaystyle(g,\\psi_{j,k})=\\int_{\\mathbb R^d}g(x)\\psi_{j,k}(x)\\,dx of functions g\\in L^q(\\mathbb R^d), 1/p+1/q=1, where {\\Vert\\cdot\\Vert}_Y is the norm in some Banach space of number families \\{y_{j,k}\\} and 0 are constants. In particular, it is proved that if the integral of a function \\psi\\in L^1\\cap L^p(\\mathbb R^d), 1, is nonzero, so \\displaystyle\\int_{\\mathbb R^d}\\psi(x)\\,dx\

  12. Dissociation and Memory Fragmentation in Posttraumatic Stress Disorder: An Evaluation of the Dissociative Encoding Hypothesis

    PubMed Central

    Bedard-Gilligan, Michele; Zoellner, Lori A.

    2012-01-01

    Several prominent theories of posttraumatic stress disorder (PTSD) posit that peritraumatic dissociation results in insufficient encoding of the trauma memory and that persistent dissociation prevents memory elaboration, resulting in memory fragmentation and PTSD. In this review, we summarize the empirical literature on peritraumatic and trait dissociation and trauma narrative fragmentation as measured by meta-memory and rater/objective coding. Across 16 studies to date, the association between dissociation and fragmentation was most prominent when examining peritraumatic dissociation and patient's own ratings of memory fragmentation. This relationship did not hold when examining trait dissociation or rater-coded or computer-generated measures of fragmentation. Thus, initial evidence points more toward a strong self-reported association between constructs that is not supported on more objective fragmentation coding. Measurement overlap, construct ambiguity, and exclusion of potential confounds may underlie lack of a strong association between dissociation and objective-rated fragmentation. PMID:22348400

  13. Exciton dissociation at organic small molecule donor-acceptor interfaces (Presentation Recording)

    NASA Astrophysics Data System (ADS)

    Robey, Steven W.

    2015-08-01

    Exciton dissociation at organic semiconductor donor-acceptor (D-A) heterojunctions is critical for the performance of organic photovoltaic (OPV) structures. Interfacial charge separation and recombination processes control device efficiency. We have investigated these fundamental interfacial issues using time-resolved two-photon photoemission (TR-2PPE), coupled with the formation of well-controlled D-A structures by organic molecular beam epitaxy. The interfacial electronic and molecular structure of these model interfaces was well-characterized using scanning tunneling microscopy and ultraviolet photoemission. Exciton dissociation dynamics were investigated by using a sub-picosecond pump pulse to create Pc π-->π* transitions, producing a population of singlet (S1) Pc excitons. The subsequent decay dynamics of this population was monitored via photoemission with a time-delayed UV pulse. For CuPcC60 interfaces, S1 exciton population decay in the interfacial CuPc layer was much faster than decay in the bulk due to interfacial charge separation. The rate constant for exciton dissociation was found to be ≍ 7 x 10 12 sec-1 (≍ 140 fs). Excitons that lose energy via intersystem crossing (ISC) to triplet levels dissociate approximately 500 to 1000 times slower. The dependence of exciton dissociation on separation was also studied. Exciton dissociation falls of rapidly with distance from the interface. Dissociation from the 2nd, and subsequent, layers of H2Pc is reduced by at least a factor of 10 from that in the interfacial layer. Finally, investigations of the relative efficiency for interfacial exciton dissociation by alternative acceptors based on perylene cores, (perylene tetracarboxylic dianhydride, or PTCDA) compared to fullerene-based acceptors such as C60 will also be discussed.

  14. High affinity DNA-microtubule associated protein interaction.

    PubMed

    Marx, K A

    1992-07-01

    We have isolated the MAP/tau proteins from twice-cycled chick brain microtubule preparations and demonstrated that they are responsible for the nitrocellulose DNA binding activity we and others have measured. Using the isolated MAP/tau proteins we then measured the apparent affinity constant K(app) for the homologous chick DNA interaction and found evidence for two equilibrium affinity classes-a K(app) = 6 x 10(7) M-1, responsible for the bulk of the DNA binding activity and a small (less than 10%) higher affinity K(app) = 10(8) - 10(9) M-1, likely due to sequence specific binding protein species. Using the same chick brain MAP-tau protein, a heterologous interaction with D. melanogaster DNA, was found to possess just the lower affinity class-K(app) = 2 x 10(7) M-1. Under stringent binding conditions we carried out equilibrium nitrocellulose filter binding experiments in a ternary reaction mixture at constant MAP/tau protein and 35S radiolabelled chick DNA concentration using increasing and excess concentrations of competitor DNAs of different sources. The order of competitor strengths found was-chick DNA greater than mouse DNA greater than D. melanogaster = E. coli. DNA. These data and specifically the homologous DNA: protein case being the strongest competitor corroborate our previous studies using total microtubule protein and provide new evidence for a conserved interaction of a small DNA sequence class with MAP/tau protein species. Moreover, these data allow us to conclude that the conserved DNA sequence: MAP/tau protein interactions do not critically depend upon any energetic feature co-involving tubulin for their properties since tubulin is absent from these preparations.

  15. Computational study of coagulation factor VIIa's affinity for phospholipid membranes.

    PubMed

    Taboureau, Olivier; Olsen, Ole Hvilsted

    2007-02-01

    The interaction between the gamma-carboxyglutamic acid-rich domain of coagulation factor VIIa (FVIIa), a vitamin-K-dependent enzyme, and phospholipid membranes plays a major role in initiation of blood coagulation. However, despite a high sequence and structural similarity to the Gla domain of other vitamin-K-dependent enzymes with a high membrane affinity, its affinity for negatively charged phospholipids is poor. A few amino acid differences are responsible for this observation. Based on the X-ray structure of lysophosphatidylserine (lysoPS) bound to the Gla domain of bovine prothrombin (Prth), models of the Gla domain of wildtype FVIIa and mutated FVIIa Gla domains in complex with lysoPS were built. Molecular dynamics (MD) and steered molecular dynamics (SMD) simulations on the complexes were applied to investigate the significant difference in the binding affinity. The MD simulation approach provides a structural and dynamic support to the role of P10Q and K32E mutations in the improvement of the membrane contact. Hence, rotation of the Gly11 main chain generated during the MD simulation results in a hydrogen bond with Q10 side chain as well as the appearance of a hydrogen bond between E32 and Q10 forcing the loop harbouring Arg9 and Arg15 to shrink and thereby enhances the accessibility of the phospholipids to the calcium ions. Furthermore, the application of the SMD simulation method to dissociate C6-lysoPS from a series of Gla domain models exhibits a ranking of the rupture force that can be useful in the interpretation of the PS interaction with Gla domains. Finally, adiabatic mapping of Gla6 residue in FVIIa with or without insertion of Tyr4 confirms the critical role of the insertion on the conformation of the side chain Gla6 in FVIIa and the corresponding Gla7 in Prth. PMID:17131117

  16. Dissociative recombination study of N{sub 3}{sup +}: Cross section and branching fraction measurements

    SciTech Connect

    Zhaunerchyk, V.; Geppert, W. D.; Vigren, E.; Hamberg, M.; Danielsson, M.; Larsson, M.; Thomas, R. D.; Kaminska, M.; Oesterdahl, F.

    2007-07-07

    We report an investigation into the dissociative recombination of the azide radical cation, N{sub 3}{sup +}. The reaction rate constant has been measured to be 6.47x10{sup -7} cm{sup 3} s{sup -1} at room temperature. This value is smaller than those reported earlier for the ion-electron neutralization of N{sub 3}{sup +} at nitrogen atmospheric pressure. A strong propensity to dissociate through the N{sub 2}+N channel has been observed.

  17. Models for direct Monte Carlo simulation of coupled vibration-dissociation

    NASA Technical Reports Server (NTRS)

    Haas, Brian L.; Boyd, Iain D.

    1993-01-01

    A new model for reactive collisions is developed within the framework of a particle method, which simulates coupled vibration-dissociation (CVD) behavior in high-temperature gases. The fundamental principles of particle simulation methods are introduced with particular attention given to the probability functions employed to select thermal and reactive collisions. Reaction probability functions are derived which favor vibrationally excited molecules as reaction candidates. The new models derived here are used to simulate CVD behavior during thermochemical relaxation of constant-volume O2 reservoirs, as well as the dissociation incubation behavior of postshock N2 flows for comparisons with previous models and experimental data.

  18. Trajectory study of energy partition in CF 3CN → CF 3 + CN dissociation dynamics

    NASA Astrophysics Data System (ADS)

    Nyman, Gunnar; Rynefors, Kjell; Hase, William L.

    1986-12-01

    The classical trajectory method has been used to study the internal dynamics and unimolecular dissociation of CF 3CN at energies consistent with infrared multiphoton excitation conditions. A model potential energy function consisting of Morse stretches and attenuated bending terms is used in the trajectory study. At an excitation energy of 150 kcal/mol the CN K. The vibrational and rotational distributions are approximately Boltzmann. This energy partitioning is in good agreement with recent experimental results. The trajectory unimolecular rate constants and lifetime distributions for CF 3CN dissociation are consistent with intrinsic RRKM behaviour.

  19. Dissociation dynamics in the dissociative electron attachment to carbon dioxide

    NASA Astrophysics Data System (ADS)

    Nag, Pamir; Nandi, Dhananjay

    2015-05-01

    Dissociative electron attachment (DEA) to gas phase CO2 has been probed using a velocity slice imaging technique. DEA to CO2 produces only an O- ionic fragment and shows two major resonances located at 4.4 and 8.2 eV, respectively. The kinetic energy and angular distribution of the O- ions are measured around the second resonance with higher efficiency and sensitivity that provide details of the DEA dynamics. The kinetic energy distributions are in good agreement with the previous reports. However, the distinct angular distributions show substantial difference from the two recent studies within the limited electron energies. Our angular distribution results show two negative ion resonant states are involved in the underlying DEA process at the entire electron energies over the second resonance. We discussed the recent conflicting findings in the angular distribution results. The forward-backward asymmetry observed in the angular distributions is explained due to the interference effect of different partial waves associated with the attaching electron.

  20. Probing the electrostatics and pharmacologic modulation of sequence-specific binding by the DNA-binding domain of the ETS-family transcription factor PU.1: a binding affinity and kinetics investigation

    PubMed Central

    Munde, Manoj; Poon, Gregory M. K.; Wilson, W. David

    2013-01-01

    Members of the ETS family of transcription factors regulate a functionally diverse array of genes. All ETS proteins share a structurally-conserved but sequence-divergent DNA-binding domain, known as the ETS domain. Although the structure and thermodynamics of the ETS-DNA complexes are well known, little is known about the kinetics of sequence recognition, a facet that offers potential insight into its molecular mechanism. We have characterized DNA binding by the ETS domain of PU.1 by biosensor-surface plasmon resonance (SPR). SPR analysis revealed a striking kinetic profile for DNA binding by the PU.1 ETS domain. At low salt concentrations, it binds high-affinity cognate DNA with a very slow association rate constant (≤105 M−1 s−1), compensated by a correspondingly small dissociation rate constant. The kinetics are strongly salt-dependent but mutually balance to produce a relatively weak dependence in the equilibrium constant. This profile contrasts sharply with reported data for other ETS domains (e.g., Ets-1, TEL) for which high-affinity binding is driven by rapid association (>107 M−1 s−1). We interpret this difference in terms of the hydration properties of ETS-DNA binding and propose that at least two mechanisms of sequence recognition are employed by this family of DNA-binding domain. Additionally, we use SPR to demonstrate the potential for pharmacological inhibition of sequence-specific ETS-DNA binding, using the minor groove-binding distamycin as a model compound. Our work establishes SPR as a valuable technique for extending our understanding of the molecular mechanisms of ETS-DNA interactions as well as developing potential small-molecule agents for biotechnological and therapeutic purposes. PMID:23416556