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Sample records for solvent dependent binding

  1. Computational scheme for pH-dependent binding free energy calculation with explicit solvent.

    Science.gov (United States)

    Lee, Juyong; Miller, Benjamin T; Brooks, Bernard R

    2016-01-01

    We present a computational scheme to compute the pH-dependence of binding free energy with explicit solvent. Despite the importance of pH, the effect of pH has been generally neglected in binding free energy calculations because of a lack of accurate methods to model it. To address this limitation, we use a constant-pH methodology to obtain a true ensemble of multiple protonation states of a titratable system at a given pH and analyze the ensemble using the Bennett acceptance ratio (BAR) method. The constant pH method is based on the combination of enveloping distribution sampling (EDS) with the Hamiltonian replica exchange method (HREM), which yields an accurate semi-grand canonical ensemble of a titratable system. By considering the free energy change of constraining multiple protonation states to a single state or releasing a single protonation state to multiple states, the pH dependent binding free energy profile can be obtained. We perform benchmark simulations of a host-guest system: cucurbit[7]uril (CB[7]) and benzimidazole (BZ). BZ experiences a large pKa shift upon complex formation. The pH-dependent binding free energy profiles of the benchmark system are obtained with three different long-range interaction calculation schemes: a cutoff, the particle mesh Ewald (PME), and the isotropic periodic sum (IPS) method. Our scheme captures the pH-dependent behavior of binding free energy successfully. Absolute binding free energy values obtained with the PME and IPS methods are consistent, while cutoff method results are off by 2 kcal mol(-1) . We also discuss the characteristics of three long-range interaction calculation methods for constant-pH simulations. © 2015 The Protein Society.

  2. Dependence of protein binding capacity of dimethylamino-γ-butyric-acid (DMGABA)-immobilized porous membrane on composition of solvent used for DMGABA immobilization

    International Nuclear Information System (INIS)

    Iwanade, Akio; Umeno, Daisuke; Saito, Kyoichi; Sugo, Takanobu

    2013-01-01

    Dimethylamino-γ-butyric acid (DMGABA) as an ampholite was reacted with the epoxy group of the poly-glycidyl methacrylate chain grafted onto the pore surface of a porous hollow-fiber polyethylene membrane by radiation-induced graft polymerization. DMGABA was dissolved in a mixture of dioxane and water at various dioxane volume fractions, defined by dividing the dioxane volume by the total volume. The equilibrium binding capacity (EBC) of the DMGABA-immobilized porous hollow-fiber membrane for lysozyme was evaluated in the permeation mode. The EBC was varied from a 1/50-fold monolayer binding capacity to a 10-fold monolayer binding capacity by controlling the composition of the solvent used for DMGABA immobilization and the molar conversion of the epoxy group into the DMGABA group. - Highlights: ► A DMGABA membrane was immobilized by irradiation induced graft polymerization. ► The DMGABA was immobilized in a mixture of dioxane and water of various compositions. ► Lysozyme adsorptivity of DMGABA-immobilized membranes evaluated in the permeation mode. ► The composition of the DMGABA immobilized solvent can control adsorptivity

  3. Intra- versus Intermolecular Hydrogen Bonding: Solvent-Dependent Conformational Preferences of a Common Supramolecular Binding Motif from 1 H NMR and Vibrational Circular Dichroism Spectra.

    Science.gov (United States)

    Demarque, Daniel P; Merten, Christian

    2017-12-19

    When predicting binding properties of small molecules or larger supramolecular aggregates, intra- and intermolecular hydrogen bonds are often considered the most important factor. Spectroscopic techniques such as 1 H NMR spectroscopy are typically utilized to characterize such binding events, but interpretation is often qualitative and follows chemical intuition. In this study, we compare the effects of intramolecular hydrogen bonding and solvation on two chiral 2,6-pyridinediyl-dialkylamides. In comparison with 1 H NMR spectroscopy, vibrational circular dichroism (VCD) spectroscopy proved to be more sensitive to conformational changes. In fact, the change of the solvent from CDCl 3 to [D 6 ]DMSO generates mirror-image VCD spectra for the same enantiomer. Here, the common sense that the sterically less hindered group is more prone to solvation proved to be wrong according predicted VCD spectra, which clearly show that both asymmetric amide hydrogens are equally likely to be solvated, but never simultaneously. The competition between intra- and intermolecular hydrogen bonding and their importance for a correct prediction of spectral properties are discussed. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Properties of the manganese(II) binding site in ternary complexes of Mnter dot ADP and Mnter dot ATP with chloroplast coupling factor 1: Magnetic field dependence of solvent sup 1 H and sup 2 H NMR relaxation rates

    Energy Technology Data Exchange (ETDEWEB)

    Haddy, A.E.; Frasch, W.D.; Sharp, R.R. (Univ. of Michigan, Ann Arbor (USA))

    1989-05-02

    The influence of the binding of ADP and ATP on the high-affinity Mn(II) binding site of chloroplast coupling factor 1 (CF{sub 1}) was studied by analysis of field-dependent solvent proton and deuteron spin-lattice relaxation data. In order to characterize metal-nucleotide complexes of CF{sub 1} under conditions similar to those of the NMR experiments, the enzyme was analyzed for bound nucleotides and Mn(II) after incubation with AdN and MnCl{sub 2} and removal of labile ligands by extensive gel filtration chromatography. In the field-dependent NMR experiments, the Mn(II) binding site of CF{sub 1} was studied for three mole ratios of added Mn(II) to CF{sub 1}, 0.5, 1.0, and 1.5, in the presence of an excess of either ADP or ATP. The results were extrapolated to zero Mn(II) concentration to characterize the environment of the first Mn(II) binding site of Cf{sub 1}. In the presence of both adenine nucleotides, pronounced changes in the Mn(II) environment relative to that in Mn(II)-CF{sub 1} were evident; the local relaxation rate maxima were more pronounced and shifted to higher field strengths, and the relaxation rate per bound Mn(II) increased at all field strengths. Analysis of the data revealed that the number of exchangeable water molecules liganded to bound Mn(II) increased from one in the binary Mn(II)-CF{sub 1} complex to three and two in the ternary Mn(II)-ADP-CF{sub 1} and Mn(II)-ATP-CF{sub 1} complexes, respectively; these results suggest that a water ligand to bound Mn(II) in the Mn(II)-ADP-CF{sub 1} complex is replaced by the {gamma}-phosphate of ATP in the Mn(II)-ATP-CF{sub 1} complex. A binding model is presented to account for these observations.

  5. The spectral properties of (--epigallocatechin 3-O-gallate (EGCG fluorescence in different solvents: dependence on solvent polarity.

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    Vladislav Snitsarev

    Full Text Available (--Epigallocatechin 3-O-gallate (EGCG a molecule found in green tea and known for a plethora of bioactive properties is an inhibitor of heat shock protein 90 (HSP90, a protein of interest as a target for cancer and neuroprotection. Determination of the spectral properties of EGCG fluorescence in environments similar to those of binding sites found in proteins provides an important tool to directly study protein-EGCG interactions. The goal of this study is to examine the spectral properties of EGCG fluorescence in an aqueous buffer (AB at pH=7.0, acetonitrile (AN (a polar aprotic solvent, dimethylsulfoxide (DMSO (a polar aprotic solvent, and ethanol (EtOH (a polar protic solvent. We demonstrate that EGCG is a highly fluorescent molecule when excited at approximately 275 nm with emission maxima between 350 and 400 nm depending on solvent. Another smaller excitation peak was found when EGCG is excited at approximately 235 nm with maximum emission between 340 and 400 nm. We found that the fluorescence intensity (FI of EGCG in AB at pH=7.0 is significantly quenched, and that it is about 85 times higher in an aprotic solvent DMSO. The Stokes shifts of EGCG fluorescence were determined by solvent polarity. In addition, while the emission maxima of EGCG fluorescence in AB, DMSO, and EtOH follow the Lippert-Mataga equation, its fluorescence in AN points to non-specific solvent effects on EGCG fluorescence. We conclude that significant solvent-dependent changes in both fluorescence intensity and fluorescence emission shifts can be effectively used to distinguish EGCG in aqueous solutions from EGCG in environments of different polarity, and, thus, can be used to study specific EGCG binding to protein binding sites where the environment is often different from aqueous in terms of polarity.

  6. Sampling protein motion and solvent effect during ligand binding

    Science.gov (United States)

    Limongelli, Vittorio; Marinelli, Luciana; Cosconati, Sandro; La Motta, Concettina; Sartini, Stefania; Mugnaini, Laura; Da Settimo, Federico; Novellino, Ettore; Parrinello, Michele

    2012-01-01

    An exhaustive description of the molecular recognition mechanism between a ligand and its biological target is of great value because it provides the opportunity for an exogenous control of the related process. Very often this aim can be pursued using high resolution structures of the complex in combination with inexpensive computational protocols such as docking algorithms. Unfortunately, in many other cases a number of factors, like protein flexibility or solvent effects, increase the degree of complexity of ligand/protein interaction and these standard techniques are no longer sufficient to describe the binding event. We have experienced and tested these limits in the present study in which we have developed and revealed the mechanism of binding of a new series of potent inhibitors of Adenosine Deaminase. We have first performed a large number of docking calculations, which unfortunately failed to yield reliable results due to the dynamical character of the enzyme and the complex role of the solvent. Thus, we have stepped up the computational strategy using a protocol based on metadynamics. Our approach has allowed dealing with protein motion and solvation during ligand binding and finally identifying the lowest energy binding modes of the most potent compound of the series, 4-decyl-pyrazolo[1,5-a]pyrimidin-7-one. PMID:22238423

  7. Solvent annealing induced phase separation and dewetting in PMMA∕SAN blend film: film thickness and solvent dependence.

    Science.gov (United States)

    You, Jichun; Zhang, Shuangshuang; Huang, Gang; Shi, Tongfei; Li, Yongjin

    2013-06-28

    The competition between "dewetting" and "phase separation" behaviors in polymer blend films attracts significant attention in the last decade. The simultaneous phase separation and dewetting in PMMA∕SAN [poly(methyl methacrylate) and poly(styrene-ran-acrylonitrile)] blend ultrathin films upon solvent annealing have been observed for the first time in our previous work. In this work, film thickness and annealing solvent dependence of phase behaviors in this system has been investigated using atomic force microscopy and grazing incidence small-angle X-ray scattering (GISAXS). On one hand, both vertical phase separation and dewetting take place upon selective solvent vapor annealing, leading to the formation of droplet∕mimic-film structures with various sizes (depending on original film thickness). On the other hand, the whole blend film dewets the substrate and produces dispersed droplets on the silicon oxide upon common solvent annealing. GISAXS results demonstrate the phase separation in the big dewetted droplets resulted from the thicker film (39.8 nm). In contrast, no period structure is detected in small droplets from the thinner film (5.1 nm and 9.7 nm). This investigation indicates that dewetting and phase separation in PMMA∕SAN blend film upon solvent annealing depend crucially on the film thickness and the atmosphere during annealing.

  8. Solvent-dependent transformation of aflatoxin B1 in soil.

    Science.gov (United States)

    Starr, James M; Rushing, Blake R; Selim, Mustafa I

    2017-08-01

    To date, all studies of aflatoxin B 1 (AFB 1 ) transformation in soil or in purified mineral systems have identified aflatoxins B 2 (AFB 2 ) and G 2 (AFG 2 ) as the primary transformation products. However, identification in these studies was made using thin layer chromatography which has relatively low resolution, and these studies did not identify a viable mechanism by which such transformations would occur. Further, the use of methanol as the solvent delivery vehicle in these studies may have contributed to formation of artifactual transformation products. In this study, we investigated the role of the solvent vehicle in the transformation of AFB 1 in soil. To do this, we spiked soils with AFB 1 dissolved in water (93:7, water/methanol) or methanol and used HPLC-UV and HPLC-MS to identify the transformation products. Contrasting previous published reports, we did not detect AFB 2 or AFG 2 . In an aqueous-soil environment, we identified aflatoxin B 2a (AFB 2a ) as the single major transformation product. We propose that AFB 2a is formed from hydrolysis of AFB 1 with the soil acting as an acid catalyst. Alternatively, when methanol was used, we identified methoxy aflatoxin species likely formed via acid-catalyzed addition of methanol to AFB 1 . These results suggest that where soil moisture is adequate, AFB 1 is hydrolyzed to AFB 2a and that reactive organic solvents should be avoided when replicating natural conditions to study the fate of AFB 1 in soil.

  9. The effect of macromolecular crowding on the electrostatic component of barnase-barstar binding: a computational, implicit solvent-based study.

    Directory of Open Access Journals (Sweden)

    Helena W Qi

    Full Text Available Macromolecular crowding within the cell can impact both protein folding and binding. Earlier models of cellular crowding focused on the excluded volume, entropic effect of crowding agents, which generally favors compact protein states. Recently, other effects of crowding have been explored, including enthalpically-related crowder-protein interactions and changes in solvation properties. In this work, we explore the effects of macromolecular crowding on the electrostatic desolvation and solvent-screened interaction components of protein-protein binding. Our simple model enables us to focus exclusively on the electrostatic effects of water depletion on protein binding due to crowding, providing us with the ability to systematically analyze and quantify these potentially intuitive effects. We use the barnase-barstar complex as a model system and randomly placed, uncharged spheres within implicit solvent to model crowding in an aqueous environment. On average, we find that the desolvation free energy penalties incurred by partners upon binding are lowered in a crowded environment and solvent-screened interactions are amplified. At a constant crowder density (fraction of total available volume occupied by crowders, this effect generally increases as the radius of model crowders decreases, but the strength and nature of this trend can depend on the water probe radius used to generate the molecular surface in the continuum model. In general, there is huge variation in desolvation penalties as a function of the random crowder positions. Results with explicit model crowders can be qualitatively similar to those using a lowered "effective" solvent dielectric to account for crowding, although the "best" effective dielectric constant will likely depend on multiple system properties. Taken together, this work systematically demonstrates, quantifies, and analyzes qualitative intuition-based insights into the effects of water depletion due to crowding on the

  10. A Correlation between the Activity of Candida antarctica Lipase B and Differences in Binding Free Energies of Organic Solvent and Substrate

    DEFF Research Database (Denmark)

    Banik, Sindrila Dutta; Nordblad, Mathias; Woodley, John

    2016-01-01

    in an inhibitory effect which is also confirmed by the binding free energies for the solvent and substrate molecules estimated from the simulations. Consequently, the catalytic activity of CALB decreases in polar solvents. This effect is significant, and CALB is over 10 orders of magnitude more active in nonpolar...... of the enzyme may be ascribed to binding of solvent molecules to the enzyme active site region and the solvation energy of substrate molecules in the different solvents. Polar solvent molecules interact strongly with CALB and compete with the substrate to bind to the active site region, resulting...

  11. A novel technique to determine concentration-dependent solvent dispersion in Vapex

    Energy Technology Data Exchange (ETDEWEB)

    Abukhalifeh, H.; Lohi, A.; Upreti, S. R. [Department of Chemical Engineering, Ryerson University, 350 Victoria Street, Toronto, Ontario, M5B 2K3 (Canada)

    2009-07-01

    Vapex (vapor extraction of heavy oil and bitumen) is a promising recovery technology because it consumes low energy, and is very environmentally-friendly. The dispersion of solvents into heavy oil and bitumen is a crucial transport property governing Vapex. The accurate determination of solvent dispersion in Vapex is essential to effectively predict the amount and time scale of oil recovery as well to optimize the field operations. In this work, a novel technique is developed to experimentally determine the concentration-dependent dispersion coefficient of a solvent in Vapex process. The principles of variational calculus are utilized in conjunction with a mass transfer model of the experimental Vapex process. A computational algorithm is developed to optimally compute solvent dispersion as a function of its concentration in heavy oil. The developed technique is applied to Vapex utilizing propane as a solvent. The results show that dispersion of propane is a unimodal function of its concentration in bitumen. (author)

  12. A Novel Technique to Determine Concentration-Dependent Solvent Dispersion in Vapex

    Directory of Open Access Journals (Sweden)

    Hadil Abukhalifeh

    2009-10-01

    Full Text Available Vapex (vapor extraction of heavy oil and bitumen is a promising recovery technology because it consumes low energy, and is very environmentally-friendly. The dispersion of solvents into heavy oil and bitumen is a crucial transport property governing Vapex. The accurate determination of solvent dispersion in Vapex is essential to effectively predict the amount and time scale of oil recovery as well to optimize the field operations. In this work, a novel technique is developed to experimentally determine the concentration-dependent dispersion coefficient of a solvent in Vapex process. The principles of variational calculus are utilized in conjunction with a mass transfer model of the experimental Vapex process. A computational algorithm is developed to optimally compute solvent dispersion as a function of its concentration in heavy oil. The developed technique is applied to Vapex utilizing propane as a solvent. The results show that dispersion of propane is a unimodal function of its concentration in bitumen.

  13. Prediction of Water Binding to Protein Hydration Sites with a Discrete, Semiexplicit Solvent Model.

    Science.gov (United States)

    Setny, Piotr

    2015-12-08

    Buried water molecules are ubiquitous in protein structures and are found at the interface of most protein-ligand complexes. Determining their distribution and thermodynamic effect is a challenging yet important task, of great of practical value for the modeling of biomolecular structures and their interactions. In this study, we present a novel method aimed at the prediction of buried water molecules in protein structures and estimation of their binding free energies. It is based on a semiexplicit, discrete solvation model, which we previously introduced in the context of small molecule hydration. The method is applicable to all macromolecular structures described by a standard all-atom force field, and predicts complete solvent distribution within a single run with modest computational cost. We demonstrate that it indicates positions of buried hydration sites, including those filled by more than one water molecule, and accurately differentiates them from sterically accessible to water but void regions. The obtained estimates of water binding free energies are in fair agreement with reference results determined with the double decoupling method.

  14. Temperature-dependent binding of cyclosporine to an erythrocyte protein

    International Nuclear Information System (INIS)

    Agarwal, R.P.; Threatte, G.A.; McPherson, R.A.

    1987-01-01

    In this competitive binding assay to measure endogenous binding capacity for cyclosporine (CsA) in erythrocyte lysates, a fixed amount of [ 3 H]CsA plus various concentrations of unlabeled CsA is incubated with aliquots of a test hemolysate. Free CsA is then adsorbed onto charcoal and removed by centrifugation; CsA complexed with a cyclosporine-binding protein (CsBP) remains in the supernate. We confirmed the validity of this charcoal-separation mode of binding analysis by comparison with equilibrium dialysis. Scatchard plot analysis of the results at 4 degrees C yielded a straight line with slope corresponding to a binding constant of 1.9 X 10(7) L/mol and a saturation capacity of approximately 4 mumol per liter of packed erythrocytes. Similar analysis of binding data at 24 degrees C and 37 degrees C showed that the binding constant decreased with increasing temperature, but the saturation capacity did not change. CsBP was not membrane bound but appeared to be freely distributed within erythrocytes. 125 I-labeled CsA did not complex with the erythrocyte CsBP. Several antibiotics and other drugs did not inhibit binding between CsA and CsBP. These findings may explain the temperature-dependent uptake of CsA by erythrocytes in whole blood and suggest that measurement of CsBP in erythrocytes or lymphocytes may help predict therapeutic response or toxicity after administration of CsA

  15. Solvent-dependent fluorescence enhancement and piezochromism of a carbazole-substituted naphthopyran

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Lihui; Wang, Aixia [Faculty of Chemistry, Northeast Normal University, Changchun 130024 (China); Wang, Guang, E-mail: wangg923@nenu.edu.cn [Faculty of Chemistry, Northeast Normal University, Changchun 130024 (China); Munyentwari, Alexis [Faculty of Chemistry, Northeast Normal University, Changchun 130024 (China); Zhou, Yihan, E-mail: yhzhou@ciac.ac.cn [National Analytical Research Center of Electrochemistry and Spectroscopy, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022 (China)

    2015-09-15

    A novel carbazole-substituted naphthopyran, 3,3-bis-(4-carbazolylphenyl)-[3H]-naphtho[2,1-b]pyran (CzNP) was designed and synthesized. The new compound exhibited normal photochromism in dichloromethane solution and the UV irradiation did not influence its fluorescence. On the contrary, the fluorescence of CzNP in N,N-dimethylformamide (DMF) was intensively enhanced to 29 times after 60 min of the UV irradiation and this enhanced fluorescence can be quenched by addition of triethylamine (TEA). The study of enhanced extent of fluorescence of CzNP in solvents with different polarities and in mixed solvents demonstrated that the enhanced fluorescence is dependent on the polarity of solvents. The larger the polarity of solvent was, the stronger was the fluorescence of CzNP. CzNP also exhibited piezochromic performance and the pressure led to the cleavage of the C–O bond of pyran ring. - Highlights: • A carbazole-substituted photochromic naphthopyran was designed and synthesized. • The fluorescence was enhanced under the existence of DMF and UV irradiation. • The polarity of solvent was the dominating factor to affect the fluorescence. • The new compound also displayed piezochromic performance.

  16. Gaussian-Based Smooth Dielectric Function: A Surface-Free Approach for Modeling Macromolecular Binding in Solvents

    Directory of Open Access Journals (Sweden)

    Arghya Chakravorty

    2018-03-01

    Full Text Available Conventional modeling techniques to model macromolecular solvation and its effect on binding in the framework of Poisson-Boltzmann based implicit solvent models make use of a geometrically defined surface to depict the separation of macromolecular interior (low dielectric constant from the solvent phase (high dielectric constant. Though this simplification saves time and computational resources without significantly compromising the accuracy of free energy calculations, it bypasses some of the key physio-chemical properties of the solute-solvent interface, e.g., the altered flexibility of water molecules and that of side chains at the interface, which results in dielectric properties different from both bulk water and macromolecular interior, respectively. Here we present a Gaussian-based smooth dielectric model, an inhomogeneous dielectric distribution model that mimics the effect of macromolecular flexibility and captures the altered properties of surface bound water molecules. Thus, the model delivers a smooth transition of dielectric properties from the macromolecular interior to the solvent phase, eliminating any unphysical surface separating the two phases. Using various examples of macromolecular binding, we demonstrate its utility and illustrate the comparison with the conventional 2-dielectric model. We also showcase some additional abilities of this model, viz. to account for the effect of electrolytes in the solution and to render the distribution profile of water across a lipid membrane.

  17. Modification of crystal habit of ibuprofen using the phase partition technique: effect of aerosil and tween 80 in binding solvent.

    Science.gov (United States)

    Umprayn, K; Luengtummuen, A; Kitiyadisai, C; Pornpiputsakul, T

    2001-11-01

    A ternary diagram, representing the solubility of binding solvent (chloroform) in a mixture of ethanol and water, was constructed. For this study, the solvent mixture that gave the best ibuprofen pellets (IPs) was composed of chloroform.ethanol:water at a ratio of 1.5%:8%:90.5%. The suitable agitator speed, temperature, and mixing time were found to be 1,500 rpm, 25 degrees C +/- 2 degrees C, and 20 min, respectively. In addition, suitable stirring time when the phase partition process of IPs began was 15 min. IPs obtained from these conditions were small and round, approximately 1 mm; surface determination by scanning electron microscopy (SEM) indicated that the IPs were composed of drug microcrystals rearranged on the surface. For the dissolution, IPs showed lower drug release when compared with pure ibuprofen crystal (IC) (f2 analysis). An attempt to modify the dissolution property of IP by incorporating various concentrations of Aerosil and Tween 80 in the binding solvent was made. Microscopic appearance showed that both Aerosil and Tween 80 gave less spherical pellets when compared with the use of binding solvent alone. For both the Aerosil and Tween 80 employed, the results indicated a change in rearrangement of drug microcrystals and a change in crystal habit. However, Tween 80 gave more change of the crystallographic direction of drug microcrystals than Aerosil. In term of dissolution, the results showed that employing Tween 80 at 1.2% gave the highest drug release compared to the use of Aerosil and IC alone (f2 analysis). These pellets had a good flow property, as indicated by Carr's compressibility, flow rate, and angle of repose, and they can be compressed into a tablet, encapsulated by suitable polymer, or pulverized to obtain micronized crystals. In the case of compression into tablets, the dissolution profiles of these tablets compared with those of commercial product meet the USP 24 requirement (Q > or = 80% at 60 min).

  18. Changing the Mechanism for CO 2 Hydrogenation Using Solvent-Dependent Thermodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Burgess, Samantha A. [Catalysis Science Group, Pacific Northwest National Laboratory, P.O. Box 999 Richland WA 99352 USA; Appel, Aaron M. [Catalysis Science Group, Pacific Northwest National Laboratory, P.O. Box 999 Richland WA 99352 USA; Linehan, John C. [Catalysis Science Group, Pacific Northwest National Laboratory, P.O. Box 999 Richland WA 99352 USA; Wiedner, Eric S. [Catalysis Science Group, Pacific Northwest National Laboratory, P.O. Box 999 Richland WA 99352 USA

    2017-10-23

    A critical scientific challenge for utilization of CO2 is the development of catalyst systems that do not depend upon expensive or environmentally unfriendly reagents, such as precious metals, strong organic bases, and organic solvents. We have used thermodynamic insights to predict and demonstrate that the HCoI(dmpe)2 catalyst system, previously described for use in organic solvents, can hydrogenate CO2 to formate in water with bicarbonate as the only added reagent. Replacing tetrahydrofuran as the solvent with water changes the mechanism for catalysis by altering the thermodynamics for hydride transfer to CO2 from a key dihydride intermediate. The need for a strong organic base was eliminated by performing catalysis in water due to the change in mechanism. These studies demonstrate that the solvent plays a pivotal role in determining the reaction thermodynamics and thereby catalytic mechanism and activity. The research was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.

  19. Solvent-Dependent Dual Fluorescence of the Push-Pull System 2-Diethylamino-7-Nitrofluorene

    KAUST Repository

    Larsen, Martin A. B.; Stephansen, Anne B.; Alarousu, Erkki; Pittelkow, Michael; Mohammed, Omar F.; Sø lling, Theis I

    2018-01-01

    The solvent-dependent excited state behavior of the molecular push-pull system 2-diethylamino-7-nitrofluorene has been explored using femtosecond transient absorption spectroscopy in combination with density functional theory calculations. Several excited state minima have been identified computationally, all possessing significant intramolecular charge transfer character. The experimentally observed dual fluorescence is suggested to arise from a planar excited state minimum and another minimum reached by twisting of the aryl-nitrogen bond of the amino group. The majority of the excited state population, however, undergo non-radiative transitions and potential excited deactivation pathways are assessed in the computational investigation. A third excited state conformer, characterized by twisting around the aryl-nitrogen bond of the nitro group, is reasoned to be responsible for the majority of the non-radiative decays and a crossing between the excited state and ground state is localized. Additionally, ultrafast intersystem crossing is observed in the apolar solvent cyclohexane and rationalized to occur via an El-Sayed assisted transition from one of the identified excited state minima. The solvent thus determines more than just the fluorescence lifetime and shapes the potential energy landscape, thereby dictating the available excited state pathways.

  20. Solvent-Dependent Dual Fluorescence of the Push-Pull System 2-Diethylamino-7-Nitrofluorene

    KAUST Repository

    Larsen, Martin A. B.

    2018-01-31

    The solvent-dependent excited state behavior of the molecular push-pull system 2-diethylamino-7-nitrofluorene has been explored using femtosecond transient absorption spectroscopy in combination with density functional theory calculations. Several excited state minima have been identified computationally, all possessing significant intramolecular charge transfer character. The experimentally observed dual fluorescence is suggested to arise from a planar excited state minimum and another minimum reached by twisting of the aryl-nitrogen bond of the amino group. The majority of the excited state population, however, undergo non-radiative transitions and potential excited deactivation pathways are assessed in the computational investigation. A third excited state conformer, characterized by twisting around the aryl-nitrogen bond of the nitro group, is reasoned to be responsible for the majority of the non-radiative decays and a crossing between the excited state and ground state is localized. Additionally, ultrafast intersystem crossing is observed in the apolar solvent cyclohexane and rationalized to occur via an El-Sayed assisted transition from one of the identified excited state minima. The solvent thus determines more than just the fluorescence lifetime and shapes the potential energy landscape, thereby dictating the available excited state pathways.

  1. Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding.

    Science.gov (United States)

    Katkova, E V; Onufriev, A V; Aguilar, B; Sulimov, V B

    2017-03-01

    In this study several commonly used implicit solvent models are compared with respect to their accuracy of estimating solvation energies of small molecules and proteins, as well as desolvation penalty in protein-ligand binding. The test set consists of 19 small proteins, 104 small molecules, and 15 protein-ligand complexes. We compared predicted hydration energies of small molecules with their experimental values; the results of the solvation and desolvation energy calculations for small molecules, proteins and protein-ligand complexes in water were also compared with Thermodynamic Integration calculations based on TIP3P water model and Amber12 force field. The following implicit solvent (water) models considered here are: PCM (Polarized Continuum Model implemented in DISOLV and MCBHSOLV programs), GB (Generalized Born method implemented in DISOLV program, S-GB, and GBNSR6 stand-alone version), COSMO (COnductor-like Screening Model implemented in the DISOLV program and the MOPAC package) and the Poisson-Boltzmann model (implemented in the APBS program). Different parameterizations of the molecules were examined: we compared MMFF94 force field, Amber12 force field and the quantum-chemical semi-empirical PM7 method implemented in the MOPAC package. For small molecules, all of the implicit solvent models tested here yield high correlation coefficients (0.87-0.93) between the calculated solvation energies and the experimental values of hydration energies. For small molecules high correlation (0.82-0.97) with the explicit solvent energies is seen as well. On the other hand, estimated protein solvation energies and protein-ligand binding desolvation energies show substantial discrepancy (up to 10kcal/mol) with the explicit solvent reference. The correlation of polar protein solvation energies and protein-ligand desolvation energies with the corresponding explicit solvent results is 0.65-0.99 and 0.76-0.96 respectively, though this difference in correlations is caused

  2. Symmetry- and Solvent-Dependent Photophysics of Fluorenes Containing Donor and Acceptor Groups (Postprint)

    Science.gov (United States)

    2014-07-01

    for exciplex forma- tion.29,30 Solvent-dependent studies by Belfield et al. on similar dyes31 and BT2F32 revealed strong solvatochromism on the emission...Swiger, R. N.; Orseno, D. L.; Haley, J. E.; Cooper, T. M.; Tan, L.-S. Exciplex Formation in Solid State Blends of Charge-Transfer-Type Afx Dyes and...Tan, L.-S. Exciplex Formation in Blended Spin-Cast Films of Fluorene-Linked Dyes and Bisphthalimide Quenchers. J. Phys. Chem. A 2013, 117, 3909−3917

  3. Solvent Dependency of the UV-Vis Spectrum of Indenoisoquinolines: Role of Keto-Oxygens as Polarity Interaction Probes

    Science.gov (United States)

    Coletta, Andrea; Castelli, Silvia; Chillemi, Giovanni; Sanna, Nico; Cushman, Mark; Pommier, Yves; Desideri, Alessandro

    2013-01-01

    Indenoisoquinolines are the most promising non-campthotecins topoisomerase IB inhibitors. We present an integrated experimental/computational investigation of the UV-Vis spectra of the IQNs parental compound (NSC314622) and two of its derivatives (NSC724998 and NSC725776) currently undergoing Phase I clinical trials. In all the three compounds a similar dependence of the relative absorption intensities at 270 nm and 290 nm on solvent polarity is found. The keto-oxygens in positions 5 and 11 of the molecular scaffold of the molecule are the principal chromophores involved in this dependence. Protic interactions on these sites are also found to give rise to absorptions at wavelength <250 nm observed in water solution, due to the stabilization of highly polarized tautomers of the molecule. These results suggest that the keto-oxygens are important polarizable groups that can act as useful interactors with the molecular receptor, providing at the same time an useful fingerprint for the monitoring of the drug binding to topoisomerase IB. PMID:24086299

  4. General Solvent-dependent Strategy toward Enhanced Oxygen Reduction Reaction in Graphene/Metal Oxide Nanohybrids: Effects of Nitrogen-containing Solvent

    Science.gov (United States)

    Kao, Wei-Yao; Chen, Wei-Quan; Chiu, Yu-Hsiang; Ho, Yu-Hsuan; Chen, Chun-Hu

    2016-11-01

    A general solvent-dependent protocol directly influencing the oxygen reduction reaction (ORR) in metal oxide/graphene nanohybrids has been demonstrated. We conducted the two-step synthesis of cobalt oxide/N-doped graphene nanohybrids (CNG) with solvents of water, ethanol, and dimethylformamide (DMF), representing tree typical categories of aqueous, polar organic, and organic N-containing solvents commonly adopted for graphene nanocomposites preparation. The superior ORR performance of the DMF-hybrids can be attributed to the high nitrogen-doping, aggregation-free hybridization, and unique graphene porous structures. As DMF is the more effective N-source, the spectroscopic results support a catalytic nitrogenation potentially mediated by cobalt-DMF coordination complexes. The wide-distribution of porosity (covering micro-, meso-, to macro-pore) and micron-void assembly of graphene may further enhance the diffusion kinetics for ORR. As the results, CNG by DMF-synthesis exhibits the high ORR activities close to Pt/C (i.e. only 8 mV difference of half-wave potential with electron transfer number of 3.96) with the better durability in the alkaline condition. Additional graphene hybrids comprised of iron and manganese oxides also show the superior ORR activities by DMF-synthesis, confirming the general solvent-dependent protocol to achieve enhanced ORR activities.

  5. ATP binding cassette G1-dependent cholesterol efflux during inflammation.

    Science.gov (United States)

    de Beer, Maria C; Ji, Ailing; Jahangiri, Anisa; Vaughan, Ashley M; de Beer, Frederick C; van der Westhuyzen, Deneys R; Webb, Nancy R

    2011-02-01

    ATP binding cassette transporter G1 (ABCG1) mediates the transport of cellular cholesterol to HDL, and it plays a key role in maintaining macrophage cholesterol homeostasis. During inflammation, HDL undergoes substantial remodeling, acquiring lipid changes and serum amyloid A (SAA) as a major apolipoprotein. In the current study, we investigated whether remodeling of HDL that occurs during acute inflammation impacts ABCG1-dependent efflux. Our data indicate that lipid free SAA acts similarly to apolipoprotein A-I (apoA-I) in mediating sequential efflux from ABCA1 and ABCG1. Compared with normal mouse HDL, acute phase (AP) mouse HDL containing SAA exhibited a modest but significant 17% increase in ABCG1-dependent efflux. Interestingly, AP HDL isolated from mice lacking SAA (SAAKO mice) was even more effective in promoting ABCG1 efflux. Hydrolysis with Group IIA secretory phospholipase A(2) (sPLA(2)-IIA) significantly reduced the ability of AP HDL from SAAKO mice to serve as a substrate for ABCG1-mediated cholesterol transfer, indicating that phospholipid (PL) enrichment, and not the presence of SAA, is responsible for alterations in efflux. AP human HDL, which is not PL-enriched, was somewhat less effective in mediating ABCG1-dependent efflux compared with normal human HDL. Our data indicate that inflammatory remodeling of HDL impacts ABCG1-dependent efflux independent of SAA.

  6. NMR determination of solvent dependent behavior and XRD structural properties of 4-carboxy phenylboronic acid: A DFT supported study

    Science.gov (United States)

    Dikmen, Gökhan; Alver, Özgür; Parlak, Cemal

    2018-04-01

    Solvent dependent structural properties of 4-carboxy phenylboronic acid (4-cpba) were investigated by X-ray diffraction (XRD) and nuclear magnetic resonance (NMR) spectroscopic methods. The molecular structure and geometric parameters were determined by some computational methods such as B3LYP/6-31 + G(3df,p), HF/aug-cc-pvtz and MP2/6-31G(d). Detailed elucidation of the structural and spectroscopic properties of 4-cpba was carried out with 1H, HETCOR and DOSY NMR experiments. Solvent effects on the structural properties were monitored on the changes of 1H NMR spectra by using various solvents and it was observed that 4-cpba shows serious structural preferences depending on the solvent used.

  7. Influence of Solvent Polarity and DNA-Binding on Spectral Properties of Quaternary Benzo[c]phenanthridine Alkaloids.

    Directory of Open Access Journals (Sweden)

    Michal Rájecký

    Full Text Available Quaternary benzo[c]phenanthridine alkaloids are secondary metabolites of the plant families Papaveraceae, Rutaceae, and Ranunculaceae with anti-inflammatory, antifungal, antimicrobial and anticancer activities. Their spectral changes induced by the environment could be used to understand their interaction with biomolecules as well as for analytical purposes. Spectral shifts, quantum yield and changes in lifetime are presented for the free form of alkaloids in solvents of different polarity and for alkaloids bound to DNA. Quantum yields range from 0.098 to 0.345 for the alkanolamine form and are below 0.033 for the iminium form. Rise of fluorescence lifetimes (from 2-5 ns to 3-10 ns and fluorescence intensity are observed after binding of the iminium form to the DNA for most studied alkaloids. The alkanolamine form does not bind to DNA. Acid-base equilibrium constant of macarpine is determined to be 8.2-8.3. Macarpine is found to have the highest increase of fluorescence upon DNA binding, even under unfavourable pH conditions. This is probably a result of its unique methoxy substitution at C12 a characteristic not shared with other studied alkaloids. Association constant for macarpine-DNA interaction is 700000 M(-1.

  8. Deltamethrin Binding to Triatoma infestans (Hemiptera: Reduviidae) Lipoproteins. Analysis by Solvent Bar Microextraction Coupled to Gas Chromatography.

    Science.gov (United States)

    Dulbecco, A B; Mijailovsky, S J; Girotti, J R; Juárez, M P

    2015-11-01

    The binding of deltamethrin (DLM) to the hemipteran Triatoma infestans (Klug) hemolymph lipoproteins was evaluated in vitro. After DLM incubation with the insect hemolymph, lipoproteins were fractioned by ultracentrifugation. DLM binding was analyzed by a microextractive technique-solvent bar microextraction-a solventless methodology to extract DLM from each lipoprotein fraction. This is a novel use of the technique applied to extract an insecticide from an insect fluid. Capillary gas chromatography with microelectron capture detection was used to detect DLM bound by the T. infestans hemolymph lipoproteins and to identify the preferred DLM carrier. We show that Lp and VHDLp I lipoproteins are mainly responsible for DLM transport in T. infestans, both in DLM-resistant and DLM-susceptible bugs. Our results also indicate that DLM amounts transported are not related to DLM susceptibility. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  9. Solvent dependence of organic exciplex fluorescence studied by magnetic effect on reaction yield (M.A.R.Y) spectroscopy

    International Nuclear Information System (INIS)

    Pal, K.

    2011-01-01

    This work aims at understanding the various facets of one of the elementary reactions in nature, the electron transfer reaction using MARY (Magnetic effect on Reaction Yield) spectroscopy as a tool. The prime focus of study by the use this technique was the solvent dependence of organic exciplex fluorescence. Apart from that temperature dependent measurements using MARY spectroscopy have been performed to extract the activation energy parameters of electron transfer reaction. The discovery of magnetic field effect on new system was also a part of our study. The study of solvent dependence of organic exciplex fluorescence using MARY spectroscopy was carried out on the system of 9,10-dimethylanthracene (as the fluorophore) and N,N'-dimethylaniline and 4,4'-Bis(dimethylamino) diphenylmethane (as quenchers) in binary solvent mixtures of toluene/dimethylsulfoxide, benzylacetate/dimethylsulfoxide, toluene/propylenecarbonate and propylacetate/butyronitrile. The work focuses on the use of solvent mixtures rather than pure solvents. The solvent mixtures, tailored to simulate different microenvironemets, were employed to find out the effect of preferential solvation on electron transfer reaction. The contrast in the absolute field effect and linewidth values of the MARY spectra obtained in the four system as a function of dielectric constant scan suggest the imperative effect of concentration fluctuation on the electron transfer reaction. Temperature dependent measurements were performed on the system of N,N,N',N'- tetramethylparaphenylendiamin, photo-ionizing in a mixture of toluene/dimethylsulfoxide. However the sluggish response of the system to temperature changes does not really permit us to extract fruitful results. The magnetic field effect on the much studied system of Perylene/ N.N'-dimethylaniline was discovered for the first time. (author) [de

  10. Heavy atoms as molecular probes in studying the solvent dependence of the dynamics of triplet exciplexes

    International Nuclear Information System (INIS)

    Steiner, U.; Winter, G.

    1981-01-01

    Electron transfer reactions between thiopyronine triplet (acceptor 3 A + ) and the electron donors (D), aniline, p-Br-aniline and p-I-aniline, are investigated by flash spectroscopy in solvents of different viscosity and polarity. Due to the heavy-atom effect the radical yield becomes very sensitive to the solvent influence, which can be explained by the dynamic properties of a triplet exciplex ( 3 (AD + )) formed as a primary product in the reaction between acceptor triplet and donor. Whereas on variation of solvent viscosity the solvent cage effect on the dissociation of 3 (AD + ) is observed, a change in solvent polarity is suggested to affect the radiationless deactivation of 3 (AD + ) to the ground state of the components. (author)

  11. Temperature dependence measurements and structural characterization of trimethyl ammonium ionic liquids with a highly polar solvent.

    Science.gov (United States)

    Attri, Pankaj; Venkatesu, Pannuru; Hofman, T

    2011-08-25

    We report the synthesis and characterization of a series of an ammonium ionic liquids (ILs) containing acetate, dihydrogen phosphate, and hydrogen sulfate anions with a common cation. To characterize the thermophysical properties of these newly synthesized ILs with the highly polar solvent N,N-dimethylformamide (DMF), precise measurements such as densities (ρ) and ultrasonic sound velocities (u) over the whole composition range have been performed at atmospheric pressure and over wide temperature ranges (25-50 °C). The excess molar volume (V(E)) and the deviation in isentropic compressibilities (Δκ(s)) were predicted using these temperature dependence properties as a function of the concentration of ILs. The Redlich-Kister polynomial was used to correlate the results. The ILs investigated in the present study included trimethylammonium acetate [(CH(3))(3)NH][CH(3)COO] (TMAA), trimethylammonium dihydrogen phosphate [(CH(3))(3)NH][H(2)PO(4)] (TMAP), and trimethylammonium hydrogen sulfate [(CH(3))(3)NH][HSO(4)] (TMAS). The intermolecular interactions and structural effects were analyzed on the basis of the measured and the derived properties. In addition, the hydrogen bonding between ILs and DMF has been demonstrated using semiempirical calculations with help of Hyperchem 7. A qualitative analysis of the results is discussed in terms of the ion-dipole, ion-pair interactions, and hydrogen bonding between ILs and DMF molecules and their structural factors. The influence of the anion of the protic IL, namely, acetate (CH(3)COO), dihydrogen phosphate (H(2)PO(4)), and hydrogen sulfate (HSO(4)), on the thermophysical properties is also provided. © 2011 American Chemical Society

  12. Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process.

    Science.gov (United States)

    Reshetnikov, Roman V; Sponer, Jiri; Rassokhina, Olga I; Kopylov, Alexei M; Tsvetkov, Philipp O; Makarov, Alexander A; Golovin, Andrey V

    2011-12-01

    A combination of explicit solvent molecular dynamics simulation (30 simulations reaching 4 µs in total), hybrid quantum mechanics/molecular mechanics approach and isothermal titration calorimetry was used to investigate the atomistic picture of ion binding to 15-mer thrombin-binding quadruplex DNA (G-DNA) aptamer. Binding of ions to G-DNA is complex multiple pathway process, which is strongly affected by the type of the cation. The individual ion-binding events are substantially modulated by the connecting loops of the aptamer, which play several roles. They stabilize the molecule during time periods when the bound ions are not present, they modulate the route of the ion into the stem and they also stabilize the internal ions by closing the gates through which the ions enter the quadruplex. Using our extensive simulations, we for the first time observed full spontaneous exchange of internal cation between quadruplex molecule and bulk solvent at atomistic resolution. The simulation suggests that expulsion of the internally bound ion is correlated with initial binding of the incoming ion. The incoming ion then readily replaces the bound ion while minimizing any destabilization of the solute molecule during the exchange. © The Author(s) 2011. Published by Oxford University Press.

  13. Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process

    Science.gov (United States)

    Reshetnikov, Roman V.; Sponer, Jiri; Rassokhina, Olga I.; Kopylov, Alexei M.; Tsvetkov, Philipp O.; Makarov, Alexander A.; Golovin, Andrey V.

    2011-01-01

    A combination of explicit solvent molecular dynamics simulation (30 simulations reaching 4 µs in total), hybrid quantum mechanics/molecular mechanics approach and isothermal titration calorimetry was used to investigate the atomistic picture of ion binding to 15-mer thrombin-binding quadruplex DNA (G-DNA) aptamer. Binding of ions to G-DNA is complex multiple pathway process, which is strongly affected by the type of the cation. The individual ion-binding events are substantially modulated by the connecting loops of the aptamer, which play several roles. They stabilize the molecule during time periods when the bound ions are not present, they modulate the route of the ion into the stem and they also stabilize the internal ions by closing the gates through which the ions enter the quadruplex. Using our extensive simulations, we for the first time observed full spontaneous exchange of internal cation between quadruplex molecule and bulk solvent at atomistic resolution. The simulation suggests that expulsion of the internally bound ion is correlated with initial binding of the incoming ion. The incoming ion then readily replaces the bound ion while minimizing any destabilization of the solute molecule during the exchange. PMID:21893589

  14. Role of excited state solvent fluctuations on time-dependent fluorescence Stokes shift

    Energy Technology Data Exchange (ETDEWEB)

    Li, Tanping, E-mail: tanping@lsu.edu, E-mail: revatik@lsu.edu; Kumar, Revati, E-mail: tanping@lsu.edu, E-mail: revatik@lsu.edu [Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803 (United States)

    2015-11-07

    We explore the connection between the solvation dynamics of a chromophore upon photon excitation and equilibrium fluctuations of the solvent. Using molecular dynamics simulations, fluorescence Stokes shift for the tryptophan in Staphylococcus nuclease was examined using both nonequilibrium calculations and linear response theory. When the perturbed and unperturbed surfaces exhibit different solvent equilibrium fluctuations, the linear response approach on the former surface shows agreement with the nonequilibrium process. This agreement is excellent when the perturbed surface exhibits Gaussian statistics and qualitative in the case of an isomerization induced non-Gaussian statistics. However, the linear response theory on the unperturbed surface breaks down even in the presence of Gaussian fluctuations. Experiments also provide evidence of the connection between the excited state solvent fluctuations and the total fluorescence shift. These observations indicate that the equilibrium statistics on the excited state surface characterize the relaxation dynamics of the fluorescence Stokes shift. Our studies specifically analyze the Gaussian fluctuations of the solvent in the complex protein environment and further confirm the role of solvent fluctuations on the excited state surface. The results are consistent with previous investigations, found in the literature, of solutes dissolved in liquids.

  15. Solvent-dependent excited-state hydrogen transfer and intersystem crossing in 2-(2′-hydroxyphenyl)-benzothiazole

    KAUST Repository

    Aly, Shawkat Mohammede

    2015-02-12

    The excited-state intramolecular hydrogen transfer (ESIHT) of 2-(2′-hydroxyphenyl) benzothiazole (HBT) has been investigated in a series of nonpolar, polar aprotic, and polar protic solvents. A variety of state-of-the-art experimental methods were employed, including femto- and nanosecond transient absorption and fluorescence upconversion spectroscopy with broadband capabilities. We show that the dynamics and mechanism of ESIHT of the singlet excited HBT are strongly solvent-dependent. In nonpolar solvents, the data demonstrate that HBT molecules adopt a closed form stabilized by O-H⋯N chelated hydrogen bonds with no twisting angle, and the photoinduced H transfer occurs within 120 fs, leading to the formation of a keto tautomer. In polar solvents, owing to dipole-dipole cross talk and hydrogen bonding interactions, the H transfer process is followed by ultrafast nonradiative deactivation channels, including ultrafast internal conversion (IC) and intersystem crossing (ISC). This is likely to be driven by the twisting motion around the C-C bond between the hydroxyphenyl and thiazole moieties, facilitating the IC back to the enol ground state or to the keto triplet state. In addition, our femtosecond time-resolved fluorescence experiments indicate, for the first time, that the lifetime of the enol form in ACN is approximately 280 fs. This observation indicates that the solvent plays a crucial role in breaking the H bond and deactivating the excited state of the HBT. Interestingly, the broadband transient absorption and fluorescence up-conversion data clearly demonstrate that the intermolecular proton transfer from the excited HBT to the DMSO solvent is about 190 fs, forming the HBT anion excited state.

  16. Solvent-dependent excited-state hydrogen transfer and intersystem crossing in 2-(2′-hydroxyphenyl)-benzothiazole

    KAUST Repository

    Aly, Shawkat Mohammede; Usman, Anwar; Alzayer, Maytham; Hamdi, Ghada A.; Alarousu, Erkki; Mohammed, Omar F.

    2015-01-01

    The excited-state intramolecular hydrogen transfer (ESIHT) of 2-(2′-hydroxyphenyl) benzothiazole (HBT) has been investigated in a series of nonpolar, polar aprotic, and polar protic solvents. A variety of state-of-the-art experimental methods were employed, including femto- and nanosecond transient absorption and fluorescence upconversion spectroscopy with broadband capabilities. We show that the dynamics and mechanism of ESIHT of the singlet excited HBT are strongly solvent-dependent. In nonpolar solvents, the data demonstrate that HBT molecules adopt a closed form stabilized by O-H⋯N chelated hydrogen bonds with no twisting angle, and the photoinduced H transfer occurs within 120 fs, leading to the formation of a keto tautomer. In polar solvents, owing to dipole-dipole cross talk and hydrogen bonding interactions, the H transfer process is followed by ultrafast nonradiative deactivation channels, including ultrafast internal conversion (IC) and intersystem crossing (ISC). This is likely to be driven by the twisting motion around the C-C bond between the hydroxyphenyl and thiazole moieties, facilitating the IC back to the enol ground state or to the keto triplet state. In addition, our femtosecond time-resolved fluorescence experiments indicate, for the first time, that the lifetime of the enol form in ACN is approximately 280 fs. This observation indicates that the solvent plays a crucial role in breaking the H bond and deactivating the excited state of the HBT. Interestingly, the broadband transient absorption and fluorescence up-conversion data clearly demonstrate that the intermolecular proton transfer from the excited HBT to the DMSO solvent is about 190 fs, forming the HBT anion excited state.

  17. Determination of solvent concentration-dependent dispersion in the vapor extraction (VAPEX) process

    Energy Technology Data Exchange (ETDEWEB)

    Abukhalifeh, H.; Lohi, A.; Upreti, S. [Ryerson Polytechnic Univ., Toronto, ON (Canada)

    2008-07-01

    This paper presented the results of a computational algorithm that revealed the optimal conditions required for vapor extraction (VAPEX) for a solvent gas-heavy oil system. VAPEX is a promising recovery process because it requires low energy use and emits fewer greenhouse gases to the atmosphere compared to other enhanced oil recovery methods. The process is governed by the dispersion of solvent gases into heavy oil and bitumen. As such, it is essential to accurately determine solvent dispersion in VAPEX in order to effectively predict the amount and time scale of oil recovery, and to optimize field operations. VAPEX experiments were conducted in this study to determined the dispersion coefficient of a solvent as a function of its concentration in heavy oil and bitumen. The principles of variational calculus were used together with a mass transfer model of the experimental process. It was concluded that the oil production determined by the model should agree with its experimental counterpart, given the optimal gas dispersion versus concentration function.

  18. Single molecule studies of solvent-dependent diffusion and entrapment in poly(dimethylsiloxane) thin films.

    Science.gov (United States)

    Lange, Jeffrey J; Culbertson, Christopher T; Higgins, Daniel A

    2008-12-15

    Single molecule microscopic and spectroscopic methods are employed to probe the mobility and physical entrapment of dye molecules in dry and solvent-loaded poly(dimethylsiloxane) (PDMS) films. PDMS films of approximately 220 nm thickness are prepared by spin casting dilute solutions of Sylgard 184 onto glass coverslips, followed by low temperature curing. A perylene diimide dye (BPPDI) is used to probe diffusion and molecule-matrix interactions. Two classes of dye-loaded samples are investigated: (i) those incorporating dye dispersed throughout the films ("in film" samples) and (ii) those in which the dye is restricted primarily to the PDMS surface ("on film" samples). Experiments are performed under dry nitrogen and at various levels of isopropyl alcohol (IPA) loading from the vapor phase. A PDMS-coated quartz-crystal microbalance is employed to monitor solvent loading and drying of the PDMS and to ensure equilibrium conditions are achieved. Single molecules are shown to be predominantly immobile under dry conditions and mostly mobile under IPA-saturated conditions. Quantitative methods for counting the fluorescent spots produced by immobile single molecules in optical images of the samples demonstrate that the population of mobile molecules increases nonlinearly with IPA loading. Even under IPA saturated conditions, the population of fixed molecules is found to be greater than zero and is greatest for "in film" samples. Fluorescence correlation spectroscopy is used to measure the apparent diffusion coefficient for the mobile molecules, yielding a mean value of D = 1.4(+/-0.4) x 10(-8) cm(2)/s that is virtually independent of IPA loading and sample class. It is concluded that a nonzero population of dye molecules is physically entrapped within the PDMS matrix under all conditions. The increase in the population of mobile molecules under high IPA conditions is attributed to the filling of film micropores with solvent, rather than by incorporation of molecularly

  19. Dependence of the surface roughness of MAPLE-deposited films on the solvent parameters

    Science.gov (United States)

    Caricato, A. P.; Leggieri, G.; Martino, M.; Vantaggiato, A.; Valerini, D.; Cretì, A.; Lomascolo, M.; Manera, M. G.; Rella, R.; Anni, M.

    2010-12-01

    Matrix-assisted pulsed laser evaporation (MAPLE) was used to deposit layers of poly(9,9-dioctylfluorene) (PFO) to study the relation between the solvent properties (laser light absorption, boiling temperature and solubility parameters) and the morphology of the deposited films. To this end, the polymer was diluted (0.5 wt%) in tetrahydrofuran—THF, toluene and toluene/hexane mixtures. The thickness of the films was equal to 70±20 nm. The morphology and uniformity of the films was investigated by Atomic Force Microscopy and by the photoluminescence emission properties of the polymer films, respectively. It is shown that, although the solubility parameters of the solvents are important in controlling the film roughness and morphology, the optical absorption properties and boiling temperature play a very important role, too. In fact, for matrices characterized by the same total solubility parameter, lower roughness values are obtained for films prepared using solvents with lower penetration depth of the laser radiation and higher boiling temperatures.

  20. Canyon solvent cleaning

    International Nuclear Information System (INIS)

    Reif, D.J.

    1986-01-01

    The HM Process at the Savannah River Plant (SRP) uses 7.5% tributylphosphate in n-paraffin as an extraction solvent. During use, the solvent is altered due to hydrolysis and radiolysis, forming materials that influence product losses, produce decontamination, and separation efficiencies. Laboratory studies to improve online solvent cleaning have shown the carbonate washing, although removing residual solvent activity does not remove binding ligands that hold fission products in the solvent. Treatment of solvent by an alumina adsorption process removes binding ligands and significantly improves recycle solvent performance. Both laboratory work defining a full-scale alumina adsorption process and the use of the process to clean HM Process first cycle solvent are presented

  1. Electric Dipole Transition Moments and Solvent-Dependent Interactions of Fluorescent Boron-Nitrogen Substituted Indole Derivatives.

    Science.gov (United States)

    Saif, Mari; Widom, Julia R; Xu, Senmiao; Abbey, Eric R; Liu, Shih-Yuan; Marcus, Andrew H

    2015-06-25

    Fluorescent analogues of the indole side chain of tryptophan can be useful spectroscopic probes of protein-protein and protein-DNA interactions. Here we present linear dichroism and solvent-dependent spectroscopic studies of two fluorescent analogues of indole, in which the organic C═C unit is substituted with the isosteric inorganic B-N unit. We studied the so-called "external" BN indole, which has C2v symmetry, and the "fused" BN indole with Cs symmetry. We performed a combination of absorption and fluorescence spectroscopy, ultraviolet linear dichroism (UV-LD) in stretched poly(ethylene) (PE) films, and quantum chemical calculations on both BN indole compounds. Our measurements allowed us to characterize the degree of alignment for both molecules in stretched PE films. We thus determined the orientations and magnitudes of the two lowest energy electric dipole transition moments (EDTMs) for external BN indole, and the two lowest energy EDTMs for fused BN indole within the 30 000-45 000 cm(-1) spectral range. We compared our experimental results to those of quantum chemical calculations using standard density functional theory (DFT). Our theoretical predictions for the low-energy EDTMs are in good agreement with our experimental data. The absorption and fluorescence spectra of the external and the fused BN indoles are sensitive to solvent polarity. Our results indicate that the fused BN indole experiences much greater solvation interactions with polar solvents than does the external BN indole.

  2. LRRK2 kinase activity is dependent on LRRK2 GTP binding capacity but independent of LRRK2 GTP binding.

    Directory of Open Access Journals (Sweden)

    Jean-Marc Taymans

    Full Text Available Leucine rich repeat kinase 2 (LRRK2 is a Parkinson's disease (PD gene that encodes a large multidomain protein including both a GTPase and a kinase domain. GTPases often regulate kinases within signal transduction cascades, where GTPases act as molecular switches cycling between a GTP bound "on" state and a GDP bound "off" state. It has been proposed that LRRK2 kinase activity may be increased upon GTP binding at the LRRK2 Ras of complex proteins (ROC GTPase domain. Here we extensively test this hypothesis by measuring LRRK2 phosphorylation activity under influence of GDP, GTP or non-hydrolyzable GTP analogues GTPγS or GMPPCP. We show that autophosphorylation and lrrktide phosphorylation activity of recombinant LRRK2 protein is unaltered by guanine nucleotides, when co-incubated with LRRK2 during phosphorylation reactions. Also phosphorylation activity of LRRK2 is unchanged when the LRRK2 guanine nucleotide binding pocket is previously saturated with various nucleotides, in contrast to the greatly reduced activity measured for the guanine nucleotide binding site mutant T1348N. Interestingly, when nucleotides were incubated with cell lysates prior to purification of LRRK2, kinase activity was slightly enhanced by GTPγS or GMPPCP compared to GDP, pointing to an upstream guanine nucleotide binding protein that may activate LRRK2 in a GTP-dependent manner. Using metabolic labeling, we also found that cellular phosphorylation of LRRK2 was not significantly modulated by nucleotides, although labeling is significantly reduced by guanine nucleotide binding site mutants. We conclude that while kinase activity of LRRK2 requires an intact ROC-GTPase domain, it is independent of GDP or GTP binding to ROC.

  3. Rifampicin-dependent antibodies bind a similar or identical epitope to glycoprotein IX-specific quinine-dependent antibodies

    NARCIS (Netherlands)

    Burgess, Janette K.; Lopez, Jose A.; Gaudry, Leonie E.; Chong, Beng H.

    2000-01-01

    The drug-dependent antibody of a patient with rifampicin-induced thrombocytopenia was characterized using the antigen-capture enzyme-linked immunosorbent assay (MAIPA assay), flow cytometry, and immunoprecipitation. The antibody was found to bind glycoprotein (GP) Ib-IX but not GPIIb-IIIa because

  4. Solvent-dependent deuterium isotope effects in the 15N NMR spectra of an ammonium ion

    International Nuclear Information System (INIS)

    Wielogorska, E.; Jackowski, K.

    2000-01-01

    Deuterium isotope effects on 15 N NMR chemical shifts and spin-spin coupling constants have been investigated for the 15 N enriched ammonium chloride (conc. 15 NH 4 + ion has been observed in water, methanol, ethanol and dimethylsulfoxide, while the 15 ND 4 + has been monitored in the analogous deuterated liquids. It is shown that the isotope effect in nitrogen chemical shifts ( 1 Δ 15 N( 2/1 H)), significantly different in various solvents, changes from -1.392 ppm in dimethylsulfoxide to -0.071 ppm in ethanol. The 1 J(N,H) and 1 J(N,D) coupling constants have been measured for acidic solutions under conditions of slow proton (or deuterium) exchange. The reduced coupling constants have been estimated to present isotope effects in the spin-spin coupling constants. The latter isotope effects are fairly small. (author)

  5. Catalytic recruitment in the inactivation of acetylcholinesterase by soman: temperature dependence of the solvent isotope effect

    International Nuclear Information System (INIS)

    Kovach, I.M.; Huber, J.H.A.; Schowen, R.L.

    1988-01-01

    3,3-Dimethyl-2-butyl methylphosphonofluoridate (soman) recruits at least 60-70% of the catalytic power of acetylcholinesterase during phosphonylation of the active-site serine, as compared with the acetylation by acetylcholine. The solvent isotope effect is 1.34 +/- 0.11 and is temperature independent within experimental error between 5 and 45 0 C. This observation is quite similar to what has been found for the reactions of aryl acetates and anilides. Average activation parameters for the same temperature range are ΔH* = 7.3 +/- 0.6 kcal/mol and ΔS* = -4 +/- 2 eu (H 2 O) and ΔH* = 7.1 +/- 0.4 kcal/mol and ΔS* = -6 +/- 1 eu (D 2 O). A rate-limiting process with 50% contribution of an induced-fit conformational change is supported by the data

  6. Rationalization of Anomalous Pseudocontact Shifts and Their Solvent Dependence in a Series of C3-Symmetric Lanthanide Complexes.

    Science.gov (United States)

    Vonci, Michele; Mason, Kevin; Suturina, Elizaveta A; Frawley, Andrew T; Worswick, Steven G; Kuprov, Ilya; Parker, David; McInnes, Eric J L; Chilton, Nicholas F

    2017-10-11

    Bleaney's long-standing theory of magnetic anisotropy has been employed with some success for many decades to explain paramagnetic NMR pseudocontact shifts, and has been the subject of many subsequent approximations. Here, we present a detailed experimental and theoretical investigation accounting for the anomalous solvent dependence of NMR shifts for a series of lanthanide(III) complexes, namely [LnL 1 ] (Ln = Eu, Tb, Dy, Ho, Er, Tm, and Yb; L 1 : 1,4,7-tris[(6-carboxypyridin-2-yl)methyl]-1,4,7-triazacyclononane), taking into account the effect of subtle ligand flexibility on the electronic structure. We show that the anisotropy of the room temperature magnetic susceptibility tensor, which in turn affects the sign and magnitude of the pseudocontact chemical shift, is extremely sensitive to minimal structural changes in the first coordination sphere of L 1 . We show that DFT structural optimizations do not give accurate structural models, as assessed by the experimental chemical shifts, and thus we determine a magnetostructural correlation and employ this to evaluate the accurate solution structure for each [LnL 1 ]. This approach allows us to explain the counterintuitive pseudocontact shift behavior, as well as a striking solvent dependence. These results have important consequences for the analysis and design of novel magnetic resonance shift and optical emission probes that are sensitive to the local solution environment and polarity.

  7. Systematic studies of binding energy dependence of neutron-proton momentum correlation function

    International Nuclear Information System (INIS)

    Wei, Y B; Ma, Y G; Shen, W Q; Ma, G L; Wang, K; Cai, X Z; Zhong, C; Guo, W; Chen, J G; Fang, D Q; Tian, W D; Zhou, X F

    2004-01-01

    Hanbury Brown-Twiss (HBT) results of the neutron-proton correlation function have been systematically investigated for a series of nuclear reactions with light projectiles with the help of the isospin-dependent quantum molecular dynamics model. The relationship between the binding energy per nucleon of the projectiles and the strength of the neutron-proton HBT at small relative momentum has been obtained. Results show that neutron-proton HBT results are sensitive to the binding energy per nucleon

  8. Solvent Dependency in the Quantum Efficiency of 4-[(4-Aminophenyl)-(4-imino-1-cyclohexa-2, 5- dienylidene) methyl] Aniline Hydrochloride.

    Science.gov (United States)

    Pathrose, Bini; Nampoori, V P N; Radhakrishnan, P; Sahira, H; Mujeeb, A

    2015-05-01

    In the present work dual beam thermal lens technique is used for studying the solvent dependency on the quantum efficiency of a novel dye used for biomedical applications. The role of solvent in the absolute fluorescence quantum yield of 4-[(4-Aminophenyl)-(4-imino-1-cyclohexa-2, 5- dienylidene) methyl] aniline hydrochloride is studied using thermal lens technique. It is observed that the variation in solvents and its concentration results considerable variations in the fluorescence quantum yield. These variations are due to the non-radiative relaxation of the absorbed energy and because of the different solvent properties. The highest quantum yield of the dye is observed in the polar protic solvent-water.

  9. Frequency-dependent solvent friction and torsional damping in liquid 1,2-difluoroethane

    Science.gov (United States)

    MacPhail, Richard A.; Monroe, Frances C.

    1991-04-01

    We have used Raman spectroscopy to study the torsional dynamics, rotational dynamics, and conformational solvation energy of liquid 1,2-difluoroethane. From the Raman intensities, we obtain Δ H(g-t) = -2.4±0.1 kcal/mol, indicating strong dipolar solvation of the gauche conformer. We analyze the Raman linewidths of the CCF bending bands to obtain the zero-frequency torsional damping coefficient or well friction for the gauche conformer, and from the linewidth of the torsion band we obtain the friction evaluated at the torsional frequency. The zero-frequency well friction shows deviations from hydrodynamic behavior reminiscent of those observed for barrier friction, whereas the high-frequency friction is considerably smaller in magnitude and independent of temperature and viscosity. The zero-frequency torsional friction correlates linearly with the rotational friction. It is argued that the small amplitude of the torsional fluctuations emphasizes the short distance, or high wavevector components of the solvent friction. Dielectric friction apparently does not contribute to the torsional friction at the observed frequencies.

  10. Direct Probing of Solvent Accessibility and Mobility at the Binding Interface of Polymerase (Dpo4)-DNA Complex

    OpenAIRE

    Qin, Yangzhong; Yang, Yi; Zhang, Luyuan; Fowler, Jason D.; Qiu, Weihong; Wang, Lijuan; Suo, Zucai; Zhong, Dongping

    2013-01-01

    Water plays essential structural and dynamical roles in protein-DNA recognition through contributing to enthalpic or entropic stabilization of binding complex and by mediating intermolecular interactions and fluctuations for biological function. These interfacial water molecules are confined by the binding partners in nanospace but in many cases they are highly mobile and exchange with outside bulk solution. Here, we report our studies of the interfacial water dynamics in the binary and terna...

  11. Solvent effects in time-dependent self-consistent field methods. II. Variational formulations and analytical gradients

    International Nuclear Information System (INIS)

    Bjorgaard, J. A.; Velizhanin, K. A.; Tretiak, S.

    2015-01-01

    This study describes variational energy expressions and analytical excited state energy gradients for time-dependent self-consistent field methods with polarizable solvent effects. Linear response, vertical excitation, and state-specific solventmodels are examined. Enforcing a variational ground stateenergy expression in the state-specific model is found to reduce it to the vertical excitation model. Variational excited state energy expressions are then provided for the linear response and vertical excitation models and analytical gradients are formulated. Using semiempiricalmodel chemistry, the variational expressions are verified by numerical and analytical differentiation with respect to a static external electric field. Lastly, analytical gradients are further tested by performing microcanonical excited state molecular dynamics with p-nitroaniline

  12. Vibrationally resolved UV/Vis spectroscopy with time-dependent density functional based tight binding

    NARCIS (Netherlands)

    Ruger, R.; Niehaus, T.; van Lenthe, E.; Heine, T.; Visscher, L.

    2016-01-01

    We report a time-dependent density functional based tight-binding (TD-DFTB) scheme for the calculation of UV/Vis spectra, explicitly taking into account the excitation of nuclear vibrations via the adiabatic Hessian Franck-Condon method with a harmonic approximation for the nu- clear wavefunction.

  13. Photo-isomerization and oxidation of bilirubin in mammals is dependent on albumin binding.

    Science.gov (United States)

    Goncharova, Iryna; Jašprová, Jana; Vítek, Libor; Urbanová, Marie

    2015-12-01

    The bilirubin (BR) photo-conversion in the human body is a protein-dependent process; an effective photo-isomerization of the potentially neurotoxic Z,Z-BR as well as its oxidation to biliverdin in the antioxidant redox cycle is possible only when BR is bound on serum albumin. We present a novel analytical concept in the study of linear tetrapyrroles metabolic processes based on an in-depth mapping of binding sites in the structure of human serum albumin (HSA). A combination of fluorescence spectroscopy, circular dichroism (CD) spectroscopy, and molecular modeling methods was used for recognition of the binding site for BR, its derivatives (mesobilirubin and bilirubin ditaurate), and the products of the photo-isomerization and oxidation (lumirubin, biliverdin, and xanthobilirubic acid) on HSA. The CD spectra and fluorescent quenching of the Trp-HSA were used to calculate the binding constants. The results of the CD displacement experiments performed with hemin were interpreted together with the findings of molecular docking performed on the pigment-HSA complexes. We estimated that Z,Z-BR and its metabolic products bind on two independent binding sites. Our findings support the existence of a reversible antioxidant redox cycle for BR and explain an additional pathway of the photo-isomerization process (increase of HSA binding capacity; the excess free [unbound] BR can be converted and also bound to HSA). Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Oxygen dependency of epidermal growth factor receptor binding and DNA synthesis of rat hepatocytes

    International Nuclear Information System (INIS)

    Hirose, Tetsuro; Terajima, Hiroaki; Yamauchi, Akira

    1997-01-01

    Background/Aims: Changes in oxygen availability modulate replicative responses in several cell types, but the effects on hepatocyte replication remain unclear. We have studied the effects of transient nonlethal hypoxia on epidermal growth factor receptor binding and epidermal growth factor-induced DNA synthesis of rat hepatocytes. Methods: Lactate dehydrogenase activity in culture supernatant, intracellular adenosine triphosphate content, 125 I-epidermal growth factor specific binding, epidermal growth factor receptor protein expression, and 3 H-thymidine incorporation were compared between hepatocytes cultured in hypoxia and normoxia. Results: Hypoxia up to 3 h caused no significant increase in lactate dehydrogenase activity in the culture supernatant, while intracellular adenosine triphosphate content decreased time-dependently and was restored to normoxic levels by reoxygenation (nonlethal hypoxia). Concomitantly, 125 I-epidermal growth factor specific binding to hepatocytes decreased time-dependently (to 54.1% of normoxia) and was restored to control levels by reoxygenation, although 125 I-insulin specific binding was not affected. The decrease in 125 I-epidermal growth factor specific binding was explained by the decrease in the number or available epidermal growth factor receptors (21.37±3.08 to 12.16±1.42 fmol/10 5 cells), while the dissociation constant of the receptor was not affected. The change in the number of available receptors was not considered to be due to receptor degradation-resynthesis, since immuno-detection of the epidermal growth factor receptor revealed that the receptor protein expression did not change during hypoxia and reoxygenation, and since neither actinomycin D nor cycloheximide affected the recovery of 125 I-epidermal growth factor binding by reoxygenation. Inhibition of epidermal growth factor-induced DNA synthesis after hypoxia (to 75.4% of normoxia by 3 h hypoxia) paralleled the decrease in 125 I-epidermal growth factor binding

  15. Phosphopeptide binding by Sld3 links Dbf4-dependent kinase to MCM replicative helicase activation.

    Science.gov (United States)

    Deegan, Tom D; Yeeles, Joseph Tp; Diffley, John Fx

    2016-05-02

    The initiation of eukaryotic DNA replication requires the assembly of active CMG (Cdc45-MCM-GINS) helicases at replication origins by a set of conserved and essential firing factors. This process is controlled during the cell cycle by cyclin-dependent kinase (CDK) and Dbf4-dependent kinase (DDK), and in response to DNA damage by the checkpoint kinase Rad53/Chk1. Here we show that Sld3, previously shown to be an essential CDK and Rad53 substrate, is recruited to the inactive MCM double hexamer in a DDK-dependent manner. Sld3 binds specifically to DDK-phosphorylated peptides from two MCM subunits (Mcm4, 6) and then recruits Cdc45. MCM mutants that cannot bind Sld3 or Sld3 mutants that cannot bind phospho-MCM or Cdc45 do not support replication. Moreover, phosphomimicking mutants in Mcm4 and Mcm6 bind Sld3 without DDK and facilitate DDK-independent replication. Thus, Sld3 is an essential "reader" of DDK phosphorylation, integrating signals from three distinct protein kinase pathways to coordinate DNA replication during S phase. © 2016 The Authors. Published under the terms of the CC BY 4.0 license.

  16. Pressure-dependent shallow donor binding energy in InGaN/GaN square QWWs

    International Nuclear Information System (INIS)

    Ghazi, Haddou El; Jorio, Anouar; Zorkani, Izeddine

    2013-01-01

    Using a variational approach, we perform a theoretical study of hydrostatic pressure effect on the ground-state of axial hydrogenic shallow-donor impurity binding energy in InGaN/GaN square quantum well wire (SQWWs) as a function of the side length within the effective-mass scheme and finite potential barrier. The pressure dependence of wire length, effective mass, dielectric constant and potential barrier are taken into account. Numerical results show that: (i) the binding energy is strongly affected by the wire length and the external applied pressure and (ii) its maximum moves to the narrow wire in particular for height pressure.

  17. Calcium-dependent binding of Escherichia coli alpha-hemolysin to erythrocytes

    International Nuclear Information System (INIS)

    Boehm, D.F.

    1989-01-01

    Alpha hemolysin (AH), a protein secreted by certain strains of Escherichia coli, causes lysis of erythrocytes (RBCs) and is cytotoxic for other cells. The primary structure of AH contains an eight amino acid sequence tandemly repeated 13 times near the C-terminus. These repeated sequences are essential for hemolytic activity. AH also requires an unknown modification by an accessory protein, Hly C, for hemolytic activity. The role of calcium in the interaction of Ah with RBCs was investigated using recombinant strains which produced active and inactive forms of the toxin. Hemolytic activity was calcium-dependent. Osmotic protection experiments and immunoblots of SDS-PAGE separated proteins from washed, toxin-treated RBCs showed that the binding of active AH to RBCs was calcium-dependent. Binding of active AH to RBCs increased the calcium permeability of RBC membranes and resulted in changes in membrane protein profiles. The changes in membrane proteins did not cause the lysis of the cells. These results were consistent with a mechanism of lysis involving the formation of cation-selective pores in the membranes of target cells. 45 Ca-autoradiography of the recombinant hemolysins separated by SDS-PAGE and transferred to nitrocellulose showed that active AH bound calcium. The domain involved in binding calcium was identified as the tandemly repeated sequences since a deletion hemolysin missing 11 of the 13 repeated sequences did not bind calcium. This deletion hemolysin was non-hemolytic and did not bind to RBC membranes. Hemolysin lacking the Hly C modification was also non-hemolytic and did not bind to RBC membranes. This unmodified AH contained the repeated sequences and bound calcium as efficiently as active AH

  18. Species dependence of [64Cu]Cu-Bis(thiosemicarbazone) radiopharmaceutical binding to serum albumins

    International Nuclear Information System (INIS)

    Basken, Nathan E.; Mathias, Carla J.; Lipka, Alexander E.; Green, Mark A.

    2008-01-01

    Introduction: Interactions of three copper(II) bis(thiosemicarbazone) positron emission tomography radiopharmaceuticals with human serum albumin, and the serum albumins of four additional mammalian species, were evaluated. Methods: 64 Cu-labeled diacetyl bis(N 4 -methylthiosemicarbazonato)copper(II) (Cu-ATSM), pyruvaldehyde bis(N 4 -methylthiosemicarbazonato)copper(II) (Cu-PTSM) and ethylglyoxal bis(thiosemicarbazonato)copper(II) (Cu-ETS) were synthesized and their binding to human, canine, rat, baboon and porcine serum albumins quantified by ultrafiltration. Protein binding was also measured for each tracer in human, porcine, rat and mouse serum. Results: The interaction of these neutral, lipophilic copper chelates with serum albumin is highly compound- and species-dependent. Cu-PTSM and Cu-ATSM exhibit particularly high affinity for human serum albumin (HSA), while the albumin binding of Cu-ETS is relatively insensitive to species. At HSA concentrations of 40 mg/ml, '% free' (non-albumin-bound) levels of radiopharmaceutical were 4.0±0.1%, 5.3±0.2% and 38.6±0.8% for Cu-PTSM, Cu-ATSM and Cu-ETS, respectively. Conclusions: Species-dependent variations in radiopharmaceutical binding to serum albumin may need to be considered when using animal models to predict the distribution and kinetics of these compounds in humans

  19. Species dependence of [{sup 64}Cu]Cu-Bis(thiosemicarbazone) radiopharmaceutical binding to serum albumins

    Energy Technology Data Exchange (ETDEWEB)

    Basken, Nathan E. [Division of Nuclear Pharmacy, Department of Industrial and Physical Pharmacy, Purdue University, West Lafayette, IN 47907 (United States)], E-mail: nbasken@purdue.edu; Mathias, Carla J. [Division of Nuclear Pharmacy, Department of Industrial and Physical Pharmacy, Purdue University, West Lafayette, IN 47907 (United States); Lipka, Alexander E. [Department of Statistics, Purdue University, West Lafayette, IN 47907 (United States); Green, Mark A. [Division of Nuclear Pharmacy, Department of Industrial and Physical Pharmacy, Purdue University, West Lafayette, IN 47907 (United States)], E-mail: magreen@purdue.edu

    2008-04-15

    Introduction: Interactions of three copper(II) bis(thiosemicarbazone) positron emission tomography radiopharmaceuticals with human serum albumin, and the serum albumins of four additional mammalian species, were evaluated. Methods: {sup 64}Cu-labeled diacetyl bis(N{sup 4}-methylthiosemicarbazonato)copper(II) (Cu-ATSM), pyruvaldehyde bis(N{sup 4}-methylthiosemicarbazonato)copper(II) (Cu-PTSM) and ethylglyoxal bis(thiosemicarbazonato)copper(II) (Cu-ETS) were synthesized and their binding to human, canine, rat, baboon and porcine serum albumins quantified by ultrafiltration. Protein binding was also measured for each tracer in human, porcine, rat and mouse serum. Results: The interaction of these neutral, lipophilic copper chelates with serum albumin is highly compound- and species-dependent. Cu-PTSM and Cu-ATSM exhibit particularly high affinity for human serum albumin (HSA), while the albumin binding of Cu-ETS is relatively insensitive to species. At HSA concentrations of 40 mg/ml, '% free' (non-albumin-bound) levels of radiopharmaceutical were 4.0{+-}0.1%, 5.3{+-}0.2% and 38.6{+-}0.8% for Cu-PTSM, Cu-ATSM and Cu-ETS, respectively. Conclusions: Species-dependent variations in radiopharmaceutical binding to serum albumin may need to be considered when using animal models to predict the distribution and kinetics of these compounds in humans.

  20. Reversibly Switchable, pH-Dependent Peptide Ligand Binding via 3,5-Diiodotyrosine Substitutions.

    Science.gov (United States)

    Ngambenjawong, Chayanon; Sylvestre, Meilyn; Gustafson, Heather H; Pineda, Julio Marco B; Pun, Suzie H

    2018-04-20

    Cell type-specific targeting ligands utilized in drug delivery applications typically recognize receptors that are overexpressed on the cells of interest. Nonetheless, these receptors may also be expressed, to varying extents, on off-target cells, contributing to unintended side effects. For the selectivity profile of targeting ligands in cancer therapy to be improved, stimuli-responsive masking of these ligands with acid-, redox-, or enzyme-cleavable molecules has been reported, whereby the targeting ligands are exposed in specific environments, e.g., acidic tumor hypoxia. One possible drawback of these systems lies in their one-time, permanent trigger, which enables the "demasked" ligands to bind off-target cells if released back into the systemic circulation. A promising strategy to address the aforementioned problem is to design ligands that show selective binding based on ionization state, which may be microenvironment-dependent. In this study, we report a systematic strategy to engineer low pH-selective targeting peptides using an M2 macrophage-targeting peptide (M2pep) as an example. 3,5-Diiodotyrosine mutagenesis into native tyrosine residues of M2pep confers pH-dependent binding behavior specific to acidic environment (pH 6) when the amino acid is protonated into the native tyrosine-like state. At physiological pH of 7.4, the hydroxyl group of 3,5-diiodotyrosine on the peptide is deprotonated leading to interruption of the peptide native binding property. Our engineered pH-responsive M2pep (Ac-Y-Î-Î) binds target M2 macrophages more selectively at pH 6 than at pH 7.4. In addition, 3,5-diiodotyrosine substitutions also improve serum stability of the peptide. Finally, we demonstrate pH-dependent reversibility in target binding via a postbinding peptide elution study. The strategy presented here should be applicable for engineering pH-dependent functionality of other targeting peptides with potential applications in physiology-dependent in vivo targeting

  1. Temperature dependence of charge-transfer fluorescence from extended and U-shaped donor-bridge-acceptor systems in glass-forming solvents.

    NARCIS (Netherlands)

    Goes, M.; de Groot, M.; Koeberg, M.; Verhoeven, J.W.; Lokan, N.R.; Shephard, M.J.; Paddon-Row, M.N.

    2001-01-01

    Abstract: The behavior is reported of three fluorescent D-bridge-A systems that display a fascinating temperature dependence in glass forming solvents over the temperature range between 77 and 293 K. In two of these systems, a rigid, saturated alkane bridge maintains an extended conformation, and as

  2. Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects.

    Science.gov (United States)

    Rocklin, Gabriel J; Mobley, David L; Dill, Ken A; Hünenberger, Philippe H

    2013-11-14

    calculations for a given system, its dependence on the box size being analytical. The latter scheme also provides insight into the physical origin of the finite-size effects. These two schemes also encompass a correction for discrete solvent effects that persists even in the limit of infinite box sizes. Application of either scheme essentially eliminates the size dependence of the corrected charging free energies (maximal deviation of 1.5 kJ mol(-1)). Because it is simple to apply, the analytical correction scheme offers a general solution to the problem of finite-size effects in free-energy calculations involving charged solutes, as encountered in calculations concerning, e.g., protein-ligand binding, biomolecular association, residue mutation, pKa and redox potential estimation, substrate transformation, solvation, and solvent-solvent partitioning.

  3. Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

    Energy Technology Data Exchange (ETDEWEB)

    Rocklin, Gabriel J. [Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th St., San Francisco, California 94143-2550, USA and Biophysics Graduate Program, University of California San Francisco, 1700 4th St., San Francisco, California 94143-2550 (United States); Mobley, David L. [Departments of Pharmaceutical Sciences and Chemistry, University of California Irvine, 147 Bison Modular, Building 515, Irvine, California 92697-0001, USA and Department of Chemistry, University of New Orleans, 2000 Lakeshore Drive, New Orleans, Louisiana 70148 (United States); Dill, Ken A. [Laufer Center for Physical and Quantitative Biology, 5252 Stony Brook University, Stony Brook, New York 11794-0001 (United States); Hünenberger, Philippe H., E-mail: phil@igc.phys.chem.ethz.ch [Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich (Switzerland)

    2013-11-14

    -periodic PB calculations for a given system, its dependence on the box size being analytical. The latter scheme also provides insight into the physical origin of the finite-size effects. These two schemes also encompass a correction for discrete solvent effects that persists even in the limit of infinite box sizes. Application of either scheme essentially eliminates the size dependence of the corrected charging free energies (maximal deviation of 1.5 kJ mol{sup −1}). Because it is simple to apply, the analytical correction scheme offers a general solution to the problem of finite-size effects in free-energy calculations involving charged solutes, as encountered in calculations concerning, e.g., protein-ligand binding, biomolecular association, residue mutation, pK{sub a} and redox potential estimation, substrate transformation, solvation, and solvent-solvent partitioning.

  4. Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

    Science.gov (United States)

    Rocklin, Gabriel J.; Mobley, David L.; Dill, Ken A.; Hünenberger, Philippe H.

    2013-11-01

    calculations for a given system, its dependence on the box size being analytical. The latter scheme also provides insight into the physical origin of the finite-size effects. These two schemes also encompass a correction for discrete solvent effects that persists even in the limit of infinite box sizes. Application of either scheme essentially eliminates the size dependence of the corrected charging free energies (maximal deviation of 1.5 kJ mol-1). Because it is simple to apply, the analytical correction scheme offers a general solution to the problem of finite-size effects in free-energy calculations involving charged solutes, as encountered in calculations concerning, e.g., protein-ligand binding, biomolecular association, residue mutation, pKa and redox potential estimation, substrate transformation, solvation, and solvent-solvent partitioning.

  5. MIT domain of Vps4 is a Ca2+-dependent phosphoinositide-binding domain.

    Science.gov (United States)

    Iwaya, Naoko; Takasu, Hirotoshi; Goda, Natsuko; Shirakawa, Masahiro; Tanaka, Toshiki; Hamada, Daizo; Hiroaki, Hidekazu

    2013-05-01

    The microtubule interacting and trafficking (MIT) domain is a small protein module that is conserved in proteins of diverged function, such as Vps4, spastin and sorting nexin 15 (SNX15). The molecular function of the MIT domain is protein-protein interaction, in which the domain recognizes peptides containing MIT-interacting motifs. Recently, we identified an evolutionarily related domain, 'variant' MIT domain at the N-terminal region of the microtubule severing enzyme katanin p60. We found that the domain was responsible for binding to microtubules and Ca(2+). Here, we have examined whether the authentic MIT domains also bind Ca(2+). We found that the loop between the first and second α-helices of the MIT domain binds a Ca(2+) ion. Furthermore, the MIT domains derived from Vps4b and SNX15a showed phosphoinositide-binding activities in a Ca(2+)-dependent manner. We propose that the MIT domain is a novel membrane-associating domain involved in endosomal trafficking.

  6. A fluorescent glycolipid-binding peptide probe traces cholesterol dependent microdomain-derived trafficking pathways.

    Directory of Open Access Journals (Sweden)

    Steffen Steinert

    Full Text Available BACKGROUND: The uptake and intracellular trafficking of sphingolipids, which self-associate into plasma membrane microdomains, is associated with many pathological conditions, including viral and toxin infection, lipid storage disease, and neurodegenerative disease. However, the means available to label the trafficking pathways of sphingolipids in live cells are extremely limited. In order to address this problem, we have developed an exogenous, non-toxic probe consisting of a 25-amino acid sphingolipid binding domain, the SBD, derived from the amyloid peptide Abeta, and conjugated by a neutral linker with an organic fluorophore. The current work presents the characterization of the sphingolipid binding and live cell trafficking of this novel probe, the SBD peptide. SBD was the name given to a motif originally recognized by Fantini et al in a number of glycolipid-associated proteins, and was proposed to interact with sphingolipids in membrane microdomains. METHODOLOGY/PRINCIPAL FINDINGS: In accordance with Fantini's model, optimal SBD binding to membranes depends on the presence of sphingolipids and cholesterol. In synthetic membrane binding assays, SBD interacts preferentially with raft-like lipid mixtures containing sphingomyelin, cholesterol, and complex gangliosides in a pH-dependent manner, but is less glycolipid-specific than Cholera toxin B (CtxB. Using quantitative time-course colocalization in live cells, we show that the uptake and intracellular trafficking route of SBD is unlike that of either the non-raft marker Transferrin or the raft markers CtxB and Flotillin2-GFP. However, SBD traverses an endolysosomal route that partially intersects with raft-associated pathways, with a major portion being diverted at a late time point to rab11-positive recycling endosomes. Trafficking of SBD to acidified compartments is strongly disrupted by cholesterol perturbations, consistent with the regulation of sphingolipid trafficking by cholesterol

  7. Solubility-Parameter-Guided Solvent Selection to Initiate Ostwald Ripening for Interior Space-Tunable Structures with Architecture-Dependent Electrochemical Performance.

    Science.gov (United States)

    Mao, Baoguang; Guo, Donglei; Qin, Jinwen; Meng, Tao; Wang, Xin; Cao, Minhua

    2018-01-08

    Despite significant advancement in preparing various hollow structures by Ostwald ripening, one common problem is the intractable uncontrollability of initiating Ostwald ripening due to the complexity of the reaction processes. Here, a new strategy on Hansen solubility parameter (HSP)-guided solvent selection to initiate Ostwald ripening is proposed. Based on this comprehensive principle for solvent optimization, N,N-dimethylformamide (DMF) was screened out, achieving accurate synthesis of interior space-tunable MoSe 2 spherical structures (solid, core-shell, yolk-shell and hollow spheres). The resultant MoSe 2 structures exhibit architecture-dependent electrochemical performances towards hydrogen evolution reaction and sodium-ion batteries. This pre-solvent selection strategy can effectively provide researchers great possibility in efficiently synthesizing various hollow structures. This work paves a new pathway for deeply understanding Ostwald ripening. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Nonspecific DNA Binding and Bending by HUαβ: Interfaces of the Three Binding Modes Characterized by Salt Dependent Thermodynamics

    Science.gov (United States)

    Koh, Junseock; Shkel, Irina; Saecker, Ruth M.; Record, M. Thomas

    2011-01-01

    Previous ITC and FRET studies demonstrated that Escherichia coli HUαβ binds nonspecifically to duplex DNA in three different binding modes: a tighter-binding 34 bp mode which interacts with DNA in large (>34 bp) gaps between bound proteins, reversibly bending it 140° and thereby increasing its flexibility, and two weaker, modestly cooperative small-site-size modes (10 bp, 6 bp) useful for filling gaps between bound proteins shorter than 34 bp. Here we use ITC to determine the thermodynamics of these binding modes as a function of salt concentration, and deduce that DNA in the 34 bp mode is bent around but not wrapped on the body of HU, in contrast to specific binding of IHF. Analyses of binding isotherms (8, 15, 34 bp DNA) and initial binding heats (34, 38, 160 bp DNA) reveal that all three modes have similar log-log salt concentration derivatives of the binding constants (Ski) even though their binding site sizes differ greatly; most probable values of Ski on 34 bp or larger DNA are − 7.5 ± 0.5. From the similarity of Ski values, we conclude that binding interfaces of all three modes involve the same region of the arms and saddle of HU. All modes are entropy-driven, as expected for nonspecific binding driven by the polyelectrolyte effect. The bent-DNA 34 bp mode is most endothermic, presumably because of the cost of HU-induced DNA bending, while the 6 bp mode is modestly exothermic at all salt concentrations examined. Structural models consistent with the observed Ski values are proposed. PMID:21513716

  9. Dimensionality of hallucinogen and inhalant/solvent abuse and dependence criteria: implications for the Diagnostic and Statistical Manual of Mental Disorders-Fifth Edition.

    Science.gov (United States)

    Kerridge, Bradley T; Saha, Tulshi D; Smith, Sharon; Chou, Patricia S; Pickering, Roger P; Huang, Boji; Ruan, June W; Pulay, Attila J

    2011-09-01

    Prior research has demonstrated the dimensionality of Diagnostic and Statistical Manual of Mental Disorders-Fourth Edition (DSM-IV) alcohol, nicotine, cannabis, cocaine and amphetamine abuse and dependence criteria. The purpose of this study was to examine the dimensionality of hallucinogen and inhalant/solvent abuse and dependence criteria. In addition, we assessed the impact of elimination of the legal problems abuse criterion on the information value of the aggregate abuse and dependence criteria, another proposed change for DSM-IV currently lacking empirical justification. Factor analyses and item response theory (IRT) analyses were used to explore the unidimisionality and psychometric properties of hallucinogen and inhalant/solvent abuse and dependence criteria using a large representative sample of the United States (U.S.) general population. Hallucinogen and inhalant/solvent abuse and dependence criteria formed unidimensional latent traits. For both substances, IRT models without the legal problems abuse criterion demonstrated better fit than the corresponding model with the legal problem abuse criterion. Further, there were no differences in the information value of the IRT models with and without the legal problems abuse criterion, supporting the elimination of that criterion. No bias in the new diagnoses was observed by sex, age and race-ethnicity. Consistent with findings for alcohol, nicotine, cannabis, cocaine and amphetamine abuse and dependence criteria, hallucinogen and inhalant/solvent criteria reflect underlying dimensions of severity. The legal problems criterion associated with each of these substance use disorders can be eliminated with no loss in informational value and an advantage of parsimony. Taken together, these findings support the changes to substance use disorder diagnoses recommended by the DSM-V Substance and Related Disorders Workgroup, that is, combining DSM-IV abuse and dependence criteria and eliminating the legal problems abuse

  10. Gate dielectric strength dependent performance of CNT MOSFET and CNT TFET: A tight binding study

    Directory of Open Access Journals (Sweden)

    Md. Shamim Sarker

    Full Text Available This paper presents a comparative study between CNT MOSFET and CNT TFET taking into account of different dielectric strength of gate oxide materials. Here we have studied the transfer characteristics, on/off current (ION/IOFF ratio and subthreshold slope of the device using Non Equilibrium Greens Function (NEGF formalism in tight binding frameworks. The results are obtained by solving the NEGF and Poisson’s equation self-consistently in NanoTCADViDES environment and found that the ON state performance of CNT MOSFET and CNT TFET have significant dependency on the dielectric strength of the gate oxide materials. The figure of merits of the devices also demonstrates that the CNT TFET is promising for high-speed and low-power logic applications. Keywords: CNT TFET, Subthreshold slop, Barrier width, Conduction band (C.B and Valance band (V.B, Oxide dielectric strength, Tight binding approach

  11. Structure-dependent binding and activation of perfluorinated compounds on human peroxisome proliferator-activated receptor γ

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Lianying [State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, 18 Shuangqing Road, Beijing 100085 (China); College of Life Science, Dezhou University, Dezhou 253023 (China); Ren, Xiao-Min; Wan, Bin [State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, 18 Shuangqing Road, Beijing 100085 (China); Guo, Liang-Hong, E-mail: LHGuo@rcees.ac.cn [State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, 18 Shuangqing Road, Beijing 100085 (China)

    2014-09-15

    Perfluorinated compounds (PFCs) have been shown to disrupt lipid metabolism and even induce cancer in rodents through activation of peroxisome proliferator-activated receptors (PPARs). Lines of evidence showed that PPARα was activated by PFCs. However, the information on the binding interactions between PPARγ and PFCs and subsequent alteration of PPARγ activity is still limited and sometimes inconsistent. In the present study, in vitro binding of 16 PFCs to human PPARγ ligand binding domain (hPPARγ-LBD) and their activity on the receptor in cells were investigated. The results showed that the binding affinity was strongly dependent on their carbon number and functional group. For the eleven perfluorinated carboxylic acids (PFCAs), the binding affinity increased with their carbon number from 4 to 11, and then decreased slightly. The binding affinity of the three perfluorinated sulfonic acids (PFSAs) was stronger than their PFCA counterparts. No binding was detected for the two fluorotelomer alcohols (FTOHs). Circular dichroim spectroscopy showed that PFC binding induced distinctive structural change of the receptor. In dual luciferase reporter assays using transiently transfected Hep G2 cells, PFCs acted as hPPARγ agonists, and their potency correlated with their binding affinity with hPPARγ-LBD. Molecular docking showed that PFCs with different chain length bind with the receptor in different geometry, which may contribute to their differences in binding affinity and transcriptional activity. - Highlights: • Binding affinity between PFCs and PPARγ was evaluated for the first time. • The binding strength was dependent on fluorinated carbon chain and functional group. • PFC binding induced distinctive structural change of the receptor. • PFCs could act as hPPARγ agonists in Hep G2 cells.

  12. Heparin-independent, PF4-dependent binding of HIT antibodies to platelets: implications for HIT pathogenesis.

    Science.gov (United States)

    Padmanabhan, Anand; Jones, Curtis G; Bougie, Daniel W; Curtis, Brian R; McFarland, Janice G; Wang, Demin; Aster, Richard H

    2015-01-01

    Antibodies specific for platelet factor 4 (PF4)/heparin complexes are the hallmark of heparin-induced thrombocytopenia and thrombosis (HIT), but many antibody-positive patients have normal platelet counts. The basis for this is not fully understood, but it is believed that antibodies testing positive in the serotonin release assay (SRA) are the most likely to cause disease. We addressed this issue by characterizing PF4-dependent binding of HIT antibodies to intact platelets and found that most antibodies testing positive in the SRA, but none of those testing negative, bind to and activate platelets when PF4 is present without any requirement for heparin (P HIT antibodies recognize PF4 in a complex with heparin, only a subset of these antibodies recognize more subtle epitopes induced in PF4 when it binds to CS, the major platelet glycosaminoglycan. Antibodies having this property could explain "delayed HIT" seen in some individuals after discontinuation of heparin and the high risk for thrombosis that persists for weeks in patients recovered from HIT. © 2015 by The American Society of Hematology.

  13. Circadian clock protein KaiC forms ATP-dependent hexameric rings and binds DNA.

    Science.gov (United States)

    Mori, Tetsuya; Saveliev, Sergei V; Xu, Yao; Stafford, Walter F; Cox, Michael M; Inman, Ross B; Johnson, Carl H

    2002-12-24

    KaiC from Synechococcus elongatus PCC 7942 (KaiC) is an essential circadian clock protein in cyanobacteria. Previous sequence analyses suggested its inclusion in the RecADnaB superfamily. A characteristic of the proteins of this superfamily is that they form homohexameric complexes that bind DNA. We show here that KaiC also forms ring complexes with a central pore that can be visualized by electron microscopy. A combination of analytical ultracentrifugation and chromatographic analyses demonstrates that these complexes are hexameric. The association of KaiC molecules into hexamers depends on the presence of ATP. The KaiC sequence does not include the obvious DNA-binding motifs found in RecA or DnaB. Nevertheless, KaiC binds forked DNA substrates. These data support the inclusion of KaiC into the RecADnaB superfamily and have important implications for enzymatic activity of KaiC in the circadian clock mechanism that regulates global changes in gene expression patterns.

  14. Calcium binding properties of calcium dependent protein kinase 1 (CaCDPK1) from Cicer arietinum.

    Science.gov (United States)

    Dixit, Ajay Kumar; Jayabaskaran, Chelliah

    2015-05-01

    Calcium plays a crucial role as a secondary messenger in all aspects of plant growth, development and survival. Calcium dependent protein kinases (CDPKs) are the major calcium decoders, which couple the changes in calcium level to an appropriate physiological response. The mechanism by which calcium regulates CDPK protein is not well understood. In this study, we investigated the interactions of Ca(2+) ions with the CDPK1 isoform of Cicer arietinum (CaCDPK1) using a combination of biophysical tools. CaCDPK1 has four different EF hands as predicted by protein sequence analysis. The fluorescence emission spectrum of CaCDPK1 showed quenching with a 5 nm red shift upon addition of calcium, indicating conformational changes in the tertiary structure. The plot of changes in intensity against calcium concentrations showed a biphasic curve with binding constants of 1.29 μM and 120 μM indicating two kinds of binding sites. Isothermal calorimetric (ITC) titration with CaCl2 also showed a biphasic curve with two binding constants of 0.027 μM and 1.7 μM. Circular dichroism (CD) spectra showed two prominent peaks at 208 and 222 nm indicating that CaCDPK1 is a α-helical rich protein. Calcium binding further increased the α-helical content of CaCDPK1 from 75 to 81%. Addition of calcium to CaCDPK1 also increased fluorescence of 8-anilinonaphthalene-1-sulfonic acid (ANS) indicating exposure of hydrophobic surfaces. Thus, on the whole this study provides evidence for calcium induced conformational changes, exposure of hydrophobic surfaces and heterogeneity of EF hands in CaCDPK1. Copyright © 2015 Elsevier GmbH. All rights reserved.

  15. Mechanistic Insights into Solvent and Ligand Dependency in Cu(I)-Catalyzed Allylic Alkylation with gem-Diborylalkanes.

    Science.gov (United States)

    Zhang, Qi; Wang, Bing; Liu, Jia-Qin; Fu, Yao; Wu, Yu-Cheng

    2018-01-19

    The recent Cu-catalyzed allylic substitution reaction between gem-diboryalkane and allyl electrophiles shows intriguing solvent and ligand-controlled regioselectivity. The α-alkylation product was obtained in DMF solvent, while γ-alkylation product was obtained in dioxane solvent and the dioxane and NHC ligand situation. In the present study, density functional theory calculations have been used to investigate the reaction mechanism and origin of the regioselectivity. For both dioxane and DMF, γ-alkylation undergoes successive oxidative addition (CH 2 Bpin trans to leaving group) and direct Cγ-C reductive elimination. The α-alkylation is found to undergo oxidative addition (CH 2 Bpin trans to leaving group), isomerization, and Cα-C reductive elimination rather than the previously proposed oxidative addition (-CH 2 Bpin cis to the leaving group) and Cα-C reductive elimination. The γ-alkylation and α-alkylation is, respectively, favorable for dioxane and DMF solvent, which is consistent with the γ- and α-selectivity in experiment. The solvent interferes the isomerization step, thereby affects the relative facility of the α- and γ-alkylation. Further investigation shows that η 1 -intermediate formation promoted by solvent is the rate-determining step of the isomerization. The stronger electron-donating ability of DMF than dioxane facilitates the η 1 -intermediate formation and finally results in the easier isomerization in DMF. For dioxane and NHC situation, in the presence of neutral NHC ligand, the -PO 4 Et 2 group tightly coordinates with the Cu center after the oxidative addition, preventing the isomerization process. The regioselectivity is determined by the relative facility of the oxidative addition step. Therefore, the favorable oxidative addition (in which -CH 2 Bpin trans to the leaving group) results in the facility of γ-alkylation.

  16. Solvent-Dependent Self-Assembly of 4,7-Dibromo-5,6-bis(octyloxybenzo[c][1,2,5] Thiadiazole on Graphite Surface by Scanning Tunneling Microscopy

    Directory of Open Access Journals (Sweden)

    Bao Zha

    2013-01-01

    Full Text Available Solvent effect on self-assembly of 4,7-dibromo-5,6-bis(octyloxybenzo[c][1,2,5] thiadiazole (DBT on a highly oriented graphite (HOPG surface was investigated by scanning tunneling microscopy (STM by using 1-phenyloctane, 1-octanoic acid, and 1-octanol as the solvents. Two different patterns were obtained in 1-phenyloctane and 1-octanoic acid, suggesting that the self-assembly of DBT was solvent dependent. At the 1-phenyloctane/HOPG interface, a linear structure was revealed due to the intermolecular halogen bonding. When 1-octanoic acid and 1-octanol are used as the solvents, the coadsorption of solvent molecules resulting from the hydrogen bonding between DBT and solvent made an important contribution to the formation of a lamellar structure. The results demonstrate that solvents could affect the molecular self-assembly according to the variational intermolecular interactions.

  17. Solvent Composition-Dependent Signal-Reduction of Molecular Ions Generated from Aromatic Compounds in (+) Atmospheric Pressure Photo Ionization Mass Spectrometry.

    Science.gov (United States)

    Lee, Seulgidaun; Ahmed, Arif; Kim, Sunghwan

    2018-03-30

    The ionization process is essential for successful mass spectrometry (MS) analysis because of its influence on selectivity and sensitivity. In particular, certain solvents reduce the ionization of the analyte, thereby reducing the overall sensitivity in APPI. Since the sensitivity varies greatly depending on the solvents, a fundamental understanding of the mechanism is required. Standard solutions were analyzed by (+) Atmospheric pressure photo ionization (APPI) QExactive ion trap mass spectrometer (Thermo Scientific). Each solution was infused directly to the APPI source at a flow rate 100 μl/min and the APPI source temperature was 300 °C. Other operating mass spectrometric parameters were maintained under the same conditions. Quantum mechanical calculations were carried out using the Gaussian 09 suite program. Density functional theory was used to calculate the reaction enthalpies (∆H) of reaction between toluene and other solvents. The experimental and theoretical results showed good agreement. The abundances of analyte ions were well correlated with the calculated ∆H values. Therefore, the results strongly support the suggested signal reduction mechanism. In addition, linear correlations between the abundance of toluene and analyte molecular ions were observed, which also supports the suggested mechanism. A solvent composition-dependent signal reduction mechanism was suggested and evaluated for the (+) atmospheric pressure photo ionization (APPI) mass spectrometry analysis of poly-aromatic hydrocarbons (PAHs) generating mainly molecular ions. Overall, the evidence provided in this work suggests that reactions between solvent cluster(s) and toluene molecular ions are responsible for the observed signal reductions. This article is protected by copyright. All rights reserved.

  18. Calcium-dependent and -independent binding of the pentraxin serum amyloid P component to glycosaminoglycans and amyloid proteins

    DEFF Research Database (Denmark)

    Danielsen, B; Sørensen, I J; Nybo, Mads

    1997-01-01

    precursor protein beta2M was observed. This binding was also enhanced at slightly acid pH, most pronounced at pH 5.0. The results of this study indicate that SAP can exhibit both Ca2(+)-dependent and -independent binding to ligands involved in amyloid fibril formation and that the binding is enhanced under...... and beta2M) by ELISA. An increase in the dose-dependent binding of SAP to heparan sulfate, AA-protein and beta2M was observed as the pH decreased from 8.0 to 5.0. Furthermore, a lower, but significant Ca2(+)-independent binding of SAP to heparan sulfate, dermatan sulfate, AA protein and the amyloid...

  19. Hemin binding by Porphyromonas gingivalis strains is dependent on the presence of A-LPS.

    Science.gov (United States)

    Rangarajan, M; Aduse-Opoku, J; Paramonov, N A; Hashim, A; Curtis, M A

    2017-10-01

    Porphyromonas gingivalis is a Gram-negative black pigmenting anaerobe that is unable to synthesize heme [Fe(II)-protoporphyrin IX] or hemin [Fe(III)-protoporphyrin IX-Cl], which are important growth/virulence factors, and must therefore derive them from the host. Porphyromonas gingivalis expresses several proteinaceous hemin-binding sites, which are important in the binding/transport of heme/hemin from the host. It also synthesizes several virulence factors, namely cysteine-proteases Arg- and Lys-gingipains and two lipopolysaccharides (LPS), O-LPS and A-LPS. The gingipains are required for the production of the black pigment, μ-oxo-bisheme {[Fe(III)PPIX] 2 O}, which is derived from hemoglobin and deposited on the bacterial cell-surface leading to the characteristic black colonies when grown on blood agar. In this study we investigated the role of LPS in the deposition of μ-oxo-bisheme on the cell-surface. A P. gingivalis mutant defective in the biosynthesis of Arg-gingipains, namely rgpA/rgpB, produces brown colonies on blood agar and mutants defective in Lys-gingipain (kgp) and LPS biosynthesis namely porR, waaL, wzy, and pg0129 (α-1, 3-mannosyltransferase) produce non-pigmented colonies. However, only those mutants lacking A-LPS showed reduced hemin-binding when cells in suspension were incubated with hemin. Using native, de-O-phosphorylated and de-lipidated LPS from P. gingivalis W50 and porR strains, we demonstrated that hemin-binding to O-polysaccharide (PS) and to the lipid A moiety of LPS was reduced compared with hemin-binding to A-PS. We conclude that A-LPS in the outer-membrane of P. gingivalis serves as a scaffold/anchor for the retention of μ-oxo-bisheme on the cell surface and pigmentation is dependent on the presence of A-LPS. © 2017 The Authors. Molecular Oral Microbiology Published by John Wiley & Sons Ltd.

  20. DNA Binding in High Salt: Analysing the Salt Dependence of Replication Protein A3 from the Halophile Haloferax volcanii

    Directory of Open Access Journals (Sweden)

    Jody A. Winter

    2012-01-01

    Full Text Available Halophilic archaea maintain intracellular salt concentrations close to saturation to survive in high-salt environments and their cellular processes have adapted to function under these conditions. Little is known regarding halophilic adaptation of the DNA processing machinery, particularly intriguing since protein-DNA interactions are classically salt sensitive. To investigate such adaptation, we characterised the DNA-binding capabilities of recombinant RPA3 from Haloferax volcanii (HvRPA3. Under physiological salt conditions (3 M KCl, HvRPA3 is monomeric, binding 18 nucleotide ssDNA with nanomolar affinity, demonstrating that RPAs containing the single OB-fold/zinc finger architecture bind with broadly comparable affinity to two OB-fold/zinc finger RPAs. Reducing the salt concentration to 1 M KCl induces dimerisation of the protein, which retains its ability to bind DNA. On circular ssDNA, two concentration-dependent binding modes are observed. Conventionally, increased salt concentration adversely affects DNA binding but HvRPA3 does not bind DNA in 0.2 M KCl, although multimerisation may occlude the binding site. The single N-terminal OB-fold is competent to bind DNA in the absence of the C-terminal zinc finger, albeit with reduced affinity. This study represents the first quantitative characterisation of DNA binding in a halophilic protein in extreme salt concentrations.

  1. Nuclear size is sensitive to NTF2 protein levels in a manner dependent on Ran binding

    Science.gov (United States)

    Vuković, Lidija D.; Jevtić, Predrag; Zhang, Zhaojie; Stohr, Bradley A.; Levy, Daniel L.

    2016-01-01

    ABSTRACT Altered nuclear size is associated with many cancers, and determining whether cancer-associated changes in nuclear size contribute to carcinogenesis necessitates an understanding of mechanisms of nuclear size regulation. Although nuclear import rates generally positively correlate with nuclear size, NTF2 levels negatively affect nuclear size, despite the role of NTF2 (also known as NUTF2) in nuclear recycling of the import factor Ran. We show that binding of Ran to NTF2 is required for NTF2 to inhibit nuclear expansion and import of large cargo molecules in Xenopus laevis egg and embryo extracts, consistent with our observation that NTF2 reduces the diameter of the nuclear pore complex (NPC) in a Ran-binding-dependent manner. Furthermore, we demonstrate that ectopic NTF2 expression in Xenopus embryos and mammalian tissue culture cells alters nuclear size. Finally, we show that increases in nuclear size during melanoma progression correlate with reduced NTF2 expression, and increasing NTF2 levels in melanoma cells is sufficient to reduce nuclear size. These results show a conserved capacity for NTF2 to impact on nuclear size, and we propose that NTF2 might be a new cancer biomarker. PMID:26823604

  2. Binding-dependent disorder-order transition in PKI alpha: a fluorescence anisotropy study.

    Science.gov (United States)

    Hauer, J A; Taylor, S S; Johnson, D A

    1999-05-25

    The conformational flexibility of peptidyl ligands may be an essential element of many peptide-macromolecular interactions. Consequently, the alpha-carbonyl backbone flexibility of the 8 kDa protein kinase inhibitor (PKI alpha) peptide of cAMP-dependent protein kinase (cAPK) free in solution and bound to cAPK was assessed by time-resolved fluorescence anisotropy. Specifically, three full-length, single-site PKI alpha mutants (V3C, S28C, and S59C) were prepared, and fluorescein iodoacetamide (FI) was selectively conjugated to the side chains of each substituted cysteine. The time-resolved anisotropy decay profiles of the labeled mutants were well fit to a model-free nonassociative biexponential equation. Free in solution, the three labeled proteins had very similar anisotropy decays arising primarily from local alpha-carbonyl backbone movements. Only a small fraction of the anisotropy decay was associated with slower, whole-body tumbling, confirming that PKI alpha is highly disordered at all three locations. Complexation of the mutants with the catalytic (C) subunit of cAPK decreased the rate of whole-body tumbling for all three mutants. The effects on the rapid decay processes, however, were dependent upon the site of conjugation. The anisotropy decay profiles of both FI-V3C- and FI-S28C-PKI alpha were associated with significantly reduced contributions from the fast decay processes, while that of FI-S59C-PKI alpha was largely unaffected by binding to the C-subunit. The results suggest that the cAPK-binding domain of PKI alpha extends from the its N-terminus to residues beyond Ser28 but does not include the segment around Ser59, which is still part of a highly flexible domain when bound to the C-subunit.

  3. Temperature dependence and GABA modulation of [3H]triazolam binding in the rat brain

    International Nuclear Information System (INIS)

    Earle, M.E.; Concas, A.; Wamsley, J.K.; Yamamura, H.I.

    1987-01-01

    The hypnotic triazolam (TZ), a triazolobenzodiazepine displays a short physiological half life and has been used for the treatment of insomnia related to anxiety states. The authors major objectives were the direct measurement of the temperature dependence and the gamma-aminobutyric acid (GABA) effect of [ 3 H]TZ binding in the rat brain. Saturation studies showed a shift to lower affinity with increasing temperatures (K/sub d/ = 0.27 +/- 08 nM at 0 0 C; K/sub d/ = 1.96 +/- 0.85 nM at 37 0 C) while the B/sub max/ values remained unchanged (1220 +/- 176 fmoles/mg protein at 0 0 C and 1160 +/- 383 fmoles/mg protein at 37 0 C). Saturation studies of [ 3 H]TZ binding in the presence or absence of GABA (100μM) showed a GABA-shift. At 0 0 C the K/sub d/ values were (K/sub d/ = 0.24 +/- 0.03 nM/-GABA; K/sub d/ = 0.16 +/- 0.04/+GABA) and at 37 0 C the K/sub d/ values were (K/sub d/ = 1.84 +/- 0.44 nM/-GABA; K/sub d/ = 0.95 +/- 0.29 nM/+GABA). In contrast to reported literature, the authors findings show that TZ interacts with benzodiazepine receptors with a temperature dependence and GABA-shift consistent with predicted behavior for benzodiazepine agonists. 20 references, 3 tables

  4. Solvent-dependent self-assembly and ordering in slow-drying semi-crystalline conjugated polymer solutions

    KAUST Repository

    Zhao, Kui

    2015-09-07

    The mechanistic understanding of the intrinsic molecular self-assembly of conjugated polymers is of immense importance to controlling the microstructure development in organic semiconducting thin films, with meaningful impact on charge transport and optoelectronic properties. Yet, to date the vast majority of studies have focused on the fast solution process itself, with studies of slower intrinsic molecular self-assembly in formulations lagging behind. Here we have investigated molecular self-assembly during spontaneous organization and uncovered how changes in formulation influence the microstructure, morphology and transport properties of conjugated polymer thin films. Our results suggest that the polymer-solvent interaction is the key factor for the molecular self-assembly and changes in macroscopic charge transport, which is in contrast with most solution processes, such as spin-coating and blade coating, where solvent drying kinetics dominates the aggregation and crystallization processes. Energetically favourable interactions between the polymer and its solvent are shown to cause chain expansion, resulting in a large hydrodynamic volume and few chain entanglements in solution. This provides molecular freedom for self-assembly and is shown to greatly enhance the local and long range order of the polymer, intra-chain backbone planarity and crystallite size. These improvements, in turn, are shown to endow the conjugated polymer with high carrier transport, as demonstrated by organic thin film transistors.

  5. A fluorescence polarization binding assay to identify inhibitors of flavin-dependent monooxygenases.

    Science.gov (United States)

    Qi, Jun; Kizjakina, Karina; Robinson, Reeder; Tolani, Karishma; Sobrado, Pablo

    2012-06-01

    N-Hydroxylating monooxygenases (NMOs) are essential for pathogenesis in fungi and bacteria. NMOs catalyze the hydroxylation of sine and ornithine in the biosynthesis of hydroxamate-containing siderophores. Inhibition of kynurenine monooxygenase (KMO), which catalyzes the conversion of kynurenine to 3-hydroxykynurenine, alleviates neurodegenerative disorders such as Huntington's and Alzheimer's diseases and brain infections caused by the parasite Trypanosoma brucei. These enzymes are examples of flavin-dependent monooxygenases, which are validated drug targets. Here, we describe the development and optimization of a fluorescence polarization assay to identify potential inhibitors of flavin-dependent monooxygenases. Fluorescently labeled ADP molecules were synthesized and tested. An ADP-TAMRA chromophore bound to KMO with a K(d) value of 0.60 ± 0.05 μM and to the NMOs from Aspergillus fumigatus and Mycobacterium smegmatis with K(d) values of 2.1 ± 0.2 and 4.0 ± 0.2 μM, respectively. The assay was tested in competitive binding experiments with substrates and products of KMO and an NMO. Furthermore, we show that this assay can be used to identify inhibitors of NMOs. A Z' factor of 0.77 was calculated, and we show that the assay exhibits good tolerance to temperature, incubation time, and dimethyl sulfoxide concentration. Copyright © 2012 Elsevier Inc. All rights reserved.

  6. Mechanistic Inferences from the Binding of Ligands to LpxC, A Metal-Dependent Deacetylase

    International Nuclear Information System (INIS)

    Gennadios, H.; Whittington, D.; Li, X.; Fierke, C.; Christianson, D.

    2006-01-01

    The metal-dependent deacetylase LpxC catalyzes the first committed step of lipid A biosynthesis in Gram-negative bacteria. Accordingly, LpxC is an attractive target for the development of inhibitors that may serve as potential new antibiotics for the treatment of Gram-negative bacterial infections. Here, we report the 2.7 Angstroms resolution X-ray crystal structure of LpxC complexed with the substrate analogue inhibitor TU-514 and the 2.0 Angstroms resolution structure of LpxC complexed with imidazole. The X-ray crystal structure of LpxC complexed with TU-514 allows for a detailed examination of the coordination geometry of the catalytic zinc ion and other enzyme-inhibitor interactions in the active site. The hydroxamate group of TU-514 forms a bidentate chelate complex with the zinc ion and makes hydrogen bond interactions with conserved active site residues E78, H265, and T191. The inhibitor C-4 hydroxyl group makes direct hydrogen bond interactions with E197 and H58. Finally, the C-3 myristate moiety of the inhibitor binds in the hydrophobic tunnel of the active site. These intermolecular interactions provide a foundation for understanding structural aspects of enzyme-substrate and enzyme-inhibitor affinity. Comparison of the TU-514 complex with cacodylate and imidazole complexes suggests a possible substrate diphosphate binding site and highlights residues that may stabilize the tetrahedral intermediate and its flanking transition states in catalysis. Evidence of a catalytic zinc ion in the native zinc enzyme coordinated by H79, H238, D242, and two water molecules with square pyramidal geometry is also presented. These results suggest that the native state of this metallohydrolase may contain a pentacoordinate zinc ion, which contrasts with the native states of archetypical zinc hydrolases such as thermolysin and carboxypeptidase A

  7. Calcium ion binding properties of Medicago truncatula calcium/calmodulin-dependent protein kinase.

    Science.gov (United States)

    Swainsbury, David J K; Zhou, Liang; Oldroyd, Giles E D; Bornemann, Stephen

    2012-09-04

    A calcium/calmodulin-dependent protein kinase (CCaMK) is essential in the interpretation of calcium oscillations in plant root cells for the establishment of symbiotic relationships with rhizobia and mycorrhizal fungi. Some of its properties have been studied in detail, but its calcium ion binding properties and subsequent conformational change have not. A biophysical approach was taken with constructs comprising either the visinin-like domain of Medicago truncatula CCaMK, which contains EF-hand motifs, or this domain together with the autoinhibitory domain. The visinin-like domain binds three calcium ions, leading to a conformational change involving the exposure of hydrophobic surfaces and a change in tertiary but not net secondary or quaternary structure. The affinity for calcium ions of visinin-like domain EF-hands 1 and 2 (K(d) = 200 ± 50 nM) was appropriate for the interpretation of calcium oscillations (~125-850 nM), while that of EF-hand 3 (K(d) ≤ 20 nM) implied occupancy at basal calcium ion levels. Calcium dissociation rate constants were determined for the visinin-like domain of CCaMK, M. truncatula calmodulin 1, and the complex between these two proteins (the slowest of which was 0.123 ± 0.002 s(-1)), suggesting the corresponding calcium association rate constants were at or near the diffusion-limited rate. In addition, the dissociation of calmodulin from the protein complex was shown to be on the same time scale as the dissociation of calcium ions. These observations suggest that the formation and dissociation of the complex between calmodulin and CCaMK would substantially mirror calcium oscillations, which typically have a 90 s periodicity.

  8. Feline leukemia virus infection requires a post-receptor binding envelope-dependent cellular component.

    Science.gov (United States)

    Hussain, Naveen; Thickett, Kelly R; Na, Hong; Leung, Cherry; Tailor, Chetankumar S

    2011-12-01

    Gammaretrovirus receptors have been suggested to contain the necessary determinants to mediate virus binding and entry. Here, we show that murine NIH 3T3 and baby hamster kidney (BHK) cells overexpressing receptors for subgroup A, B, and C feline leukemia viruses (FeLVs) are weakly susceptible (10(1) to 10(2) CFU/ml) to FeLV pseudotype viruses containing murine leukemia virus (MLV) core (Gag-Pol) proteins, whereas FeLV receptor-expressing murine Mus dunni tail fibroblast (MDTF) cells are highly susceptible (10(4) to 10(6) CFU/ml). However, NIH 3T3 cells expressing the FeLV subgroup B receptor PiT1 are highly susceptible to gibbon ape leukemia virus pseudotype virus, which differs from the FeLV pseudotype viruses only in the envelope protein. FeLV resistance is not caused by a defect in envelope binding, low receptor expression levels, or N-linked glycosylation. Resistance is not alleviated by substitution of the MLV core in the FeLV pseudotype virus with FeLV core proteins. Interestingly, FeLV resistance is alleviated by fusion of receptor-expressing NIH 3T3 and BHK cells with MDTF or human TE671 cells, suggesting the absence of an additional cellular component in NIH 3T3 and BHK cells that is required for FeLV infection. The putative FeLV-specific cellular component is not a secreted factor, as MDTF conditioned medium does not alleviate the block to FeLV infection. Together, our findings suggest that FeLV infection requires an additional envelope-dependent cellular component that is absent in NIH 3T3 and BHK cells but that is present in MDTF and TE671 cells.

  9. Investigation on the pH-dependent binding of Eosin Y and bovine serum albumin by spectral methods

    International Nuclear Information System (INIS)

    Gao Dejiang; Tian Yuan; Liang Fanghui; Jin Danhong; Chen Yanhua; Zhang Hanqi; Yu Aimin

    2007-01-01

    In this paper, the pH-dependent binding of Eosin Y and bovine serum albumin (BSA) was investigated by spectral methods, including resonance light scattering (RLS), absorption and fluorescence spectrometry. Due to the pH-dependent structure of Eosin Y and BSA, the interaction of BSA and Eosin Y depended on the solution pH value. Especially at pH 2.6 and 9.2, the RLS intensity of BSA was obviously enhanced in the presence of Eosin Y. However, the fluorescence intensity of BSA was quenched in the presence of Eosin Y. To fully understand the pH-dependent binding of BSA and Eosin Y, fluorescence quenching technique was introduced. Based on the fluorescence data obtained, the style of binding, the binding constant, the binding site number and the thermodynamic parameters for the interaction of BSA and Eosin Y were studied. Based on Foerster non-radiation energy transfer theory, the distance between donor BSA and acceptor Eosin Y was obtained

  10. Investigation on the pH-dependent binding of Eosin Y and bovine serum albumin by spectral methods

    Energy Technology Data Exchange (ETDEWEB)

    Gao Dejiang; Tian Yuan [College of Chemistry, Jilin University, Changchun 130012 (China); Liang Fanghui; Jin Danhong [Changchun Medical College, Changchun 130031 (China); Chen Yanhua; Zhang Hanqi [College of Chemistry, Jilin University, Changchun 130012 (China); Yu Aimin [College of Chemistry, Jilin University, Changchun 130012 (China)], E-mail: analchem@mail.jlu.edu.cn

    2007-12-15

    In this paper, the pH-dependent binding of Eosin Y and bovine serum albumin (BSA) was investigated by spectral methods, including resonance light scattering (RLS), absorption and fluorescence spectrometry. Due to the pH-dependent structure of Eosin Y and BSA, the interaction of BSA and Eosin Y depended on the solution pH value. Especially at pH 2.6 and 9.2, the RLS intensity of BSA was obviously enhanced in the presence of Eosin Y. However, the fluorescence intensity of BSA was quenched in the presence of Eosin Y. To fully understand the pH-dependent binding of BSA and Eosin Y, fluorescence quenching technique was introduced. Based on the fluorescence data obtained, the style of binding, the binding constant, the binding site number and the thermodynamic parameters for the interaction of BSA and Eosin Y were studied. Based on Foerster non-radiation energy transfer theory, the distance between donor BSA and acceptor Eosin Y was obtained.

  11. GTP-dependent binding and nuclear transport of RNA polymerase II by Npa3 protein

    DEFF Research Database (Denmark)

    Staresincic, Lidija; Walker, Jane; Dirac-Svejstrup, A Barbara

    2011-01-01

    in yeast extracts. Indeed, Npa3 depletion in vivo affects nuclear localization of RNAPII; the polymerase accumulates in the cytoplasm. Npa3 is a member of the GPN-LOOP family of GTPases. Npa3 mutants that either cannot bind GTP or that bind but cannot hydrolyze it are inviable and unable to support nuclear...... transport of RNAPII. Surprisingly, we were unable to detect interactions between Npa3 and proteins in the classical importin a/ß pathway for nuclear import. Interestingly, Npa3-RNAPII binding is significantly increased by the addition of GTP or its slowly hydrolyzable analogue guanosine 5'-3-O......-(thio)triphosphate (GTP¿S). Moreover, the Npa3 mutant that binds GTP, but cannot hydrolyze it, binds RNAPII even in the absence of added GTP, whereas the mutant that cannot bind GTP is unable to bind the polymerase. Together, our data suggest that Npa3 defines an unconventional pathway for nuclear import of RNAPII, which...

  12. Cu(II) bis(thiosemicarbazone) radiopharmaceutical binding to serum albumin: further definition of species dependence and associated substituent effects

    International Nuclear Information System (INIS)

    Basken, Nathan E.; Green, Mark A.

    2009-01-01

    Introduction: The pyruvaldehyde bis(N 4 -methylthiosemicarbazonato)copper(II) (Cu-PTSM) and diacetyl bis(N 4 -methylthiosemicarbazonato)copper(II) (Cu-ATSM) radiopharmaceuticals exhibit strong, species-dependent binding to the IIA site of human serum albumin (HSA), while the related ethylglyoxal bis(thiosemicarbazonato)copper(II) (Cu-ETS) radiopharmaceutical appears to exhibit only nonspecific binding to HSA and animal serum albumins. Methods: To further probe the structural basis for the species dependence of this albumin binding interaction, we examined protein binding of these three radiopharmaceuticals in solutions of albumin and/or serum from a broader array of mammalian species (rat, sheep, donkey, rabbit, cow, pig, dog, baboon, mouse, cat and elephant). We also evaluated the albumin binding of several copper(II) bis(thiosemicarbazone) chelates offering more diverse substitution of the ligand backbone. Results: Cu-PTSM and Cu-ATSM exhibit a strong interaction with HSA that is not apparent with the albumins of other species, while the binding of Cu-ETS to albumin is much less species dependent. The strong interaction of Cu-PTSM with HSA does not appear to simply correlate with variation, relative to the animal albumins, of a single amino acid lining HSA's IIA site. Those agents that selectively interact with HSA share the common feature of only methyl or hydrogen substitution at the carbon atoms of the diimine fragment of the ligand backbone. Conclusions: The interspecies variations in albumin binding of Cu-PTSM and Cu-ATSM are not simply explained by unique amino acid substitutions in the IIA binding pocket of the serum albumins. However, the specific affinity for this region of HSA is disrupted when substituents bulkier than a methyl group appear on the imine carbons of the copper bis(thiosemicarbazone) chelate.

  13. Cu(II) bis(thiosemicarbazone) radiopharmaceutical binding to serum albumin: further definition of species dependence and associated substituent effects

    Energy Technology Data Exchange (ETDEWEB)

    Basken, Nathan E. [Division of Nuclear Pharmacy, Department of Industrial and Physical Pharmacy, Purdue University, West Lafayette, IN 47907 (United States); Green, Mark A. [Division of Nuclear Pharmacy, Department of Industrial and Physical Pharmacy, Purdue University, West Lafayette, IN 47907 (United States)], E-mail: magreen@purdue.edu

    2009-07-15

    Introduction: The pyruvaldehyde bis(N{sup 4}-methylthiosemicarbazonato)copper(II) (Cu-PTSM) and diacetyl bis(N{sup 4}-methylthiosemicarbazonato)copper(II) (Cu-ATSM) radiopharmaceuticals exhibit strong, species-dependent binding to the IIA site of human serum albumin (HSA), while the related ethylglyoxal bis(thiosemicarbazonato)copper(II) (Cu-ETS) radiopharmaceutical appears to exhibit only nonspecific binding to HSA and animal serum albumins. Methods: To further probe the structural basis for the species dependence of this albumin binding interaction, we examined protein binding of these three radiopharmaceuticals in solutions of albumin and/or serum from a broader array of mammalian species (rat, sheep, donkey, rabbit, cow, pig, dog, baboon, mouse, cat and elephant). We also evaluated the albumin binding of several copper(II) bis(thiosemicarbazone) chelates offering more diverse substitution of the ligand backbone. Results: Cu-PTSM and Cu-ATSM exhibit a strong interaction with HSA that is not apparent with the albumins of other species, while the binding of Cu-ETS to albumin is much less species dependent. The strong interaction of Cu-PTSM with HSA does not appear to simply correlate with variation, relative to the animal albumins, of a single amino acid lining HSA's IIA site. Those agents that selectively interact with HSA share the common feature of only methyl or hydrogen substitution at the carbon atoms of the diimine fragment of the ligand backbone. Conclusions: The interspecies variations in albumin binding of Cu-PTSM and Cu-ATSM are not simply explained by unique amino acid substitutions in the IIA binding pocket of the serum albumins. However, the specific affinity for this region of HSA is disrupted when substituents bulkier than a methyl group appear on the imine carbons of the copper bis(thiosemicarbazone) chelate.

  14. A solvent-dependent fluorescent detection method for Fe(3+) and Hg(2+) based on a rhodamine B derivative.

    Science.gov (United States)

    Li, Xutian; Yin, Yue; Deng, Junjie; Zhong, Huixian; Tang, Jian; Chen, Zhi; Yang, Liting; Ma, Li-Jun

    2016-07-01

    A new rhodamine B-benzofurazan based fluorescent probe (1) for Fe(3+) and Hg(2+) was synthesized. In aqueous solution containing 30% (v/v) ethanol, probe 1 shows a high selective fluorescent enhancement recognition to Fe(3+) with a binding ratio of 1:1 (probe 1: Fe(3+)), when the concentration of Fe(3+) is less than that of the probe. When the concentration of Fe(3+) is higher than that of the probe, it shows fluorescent "turn-on" response to Fe(3+) by opening the rhodamine spirolactam with a binding ratio of 1:2 (probe 1: Fe(3+)). Furthermore, probe 1 displays a high selectivity and a hypersensitivity (detection limit is 4.4nM) to Hg(2+) with a binding ratio of 1:1 in ethanol. NMR and UV-vis experiments indicate that the different fluorescent recognition signals to Fe(3+) and Hg(2+) are derived from different binding modes of 1-Fe(3+) and 1-Hg(2+). Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Alpha-amylase inhibitor, CS-1036 binds to serum amylase in a concentration-dependent and saturable manner.

    Science.gov (United States)

    Honda, Tomohiro; Kaneno-Urasaki, Yoko; Ito, Takashi; Kimura, Takako; Matsushima, Nobuko; Okabe, Hiromi; Yamasaki, Atsushi; Izumi, Takashi

    2014-03-01

    (2R,3R,4R)-4-hydroxy-2-(hydroxymethyl)pyrrolidin-3-yl 4-O-(6-deoxy-β-D-glucopyranosyl)-α-D-glucopyranoside (CS-1036), which is an α-amylase inhibitor, exhibited biphasic and sustained elimination with a long t1/2 (18.4-30.0 hours) in rats and monkeys, but exhibited a short t1/2 (3.7-7.9 hours) in humans. To clarify the species differences in the t1/2, the plasma protein binding of CS-1036 was evaluated by ultrafiltration. A concentration-dependent and saturable plasma protein binding of CS-1036 was observed in rats and monkeys with the dissociation rate constant (KD) of 8.95 and 27.2 nM, and maximal binding capacity (Bmax) of 52.8 and 22.1 nM, respectively. By the assessments of the recombinant amylase and immunoprecipitation, the major binding protein of CS-1036 in rats was identified as salivary amylase (KD 5.64 nM). CS-1036 also showed concentration-dependent and saturable binding to human salivary and pancreatic amylase, with similar binding affinity in rats. However, the protein binding of CS-1036 was constant in human plasma (≤10.2%) due to the lower serum amylase level compared with rats and monkeys. From the calculation of the unbound fraction (fu) in plasma based on in vitro KD and Bmax, the dose-dependent increase in fu after oral administration is speculated to lead to a dose-dependent increase in total body clearance and a high area under the curve/dose at lower doses, such as 0.3 mg/kg in rats.

  16. Solvent extraction

    Energy Technology Data Exchange (ETDEWEB)

    Coombs, D.M.; Latimer, E.G.

    1988-01-05

    It is an object of this invention to provide for the demetallization and general upgrading of heavy oil via a solvent extracton process, and to improve the efficiency of solvent extraction operations. The yield and demetallization of product oil form heavy high-metal content oil is maximized by solvent extractions which employ either or all of the following techniques: premixing of a minor amount of the solvent with feed and using countercurrent flow for the remaining solvent; use of certain solvent/free ratios; use of segmental baffle tray extraction column internals and the proper extraction column residence time. The solvent premix/countercurrent flow feature of the invention substantially improves extractions where temperatures and pressures above the critical point of the solvent are used. By using this technique, a greater yield of extract oil can be obtained at the same metals content or a lower metals-containing extract oil product can be obtained at the same yield. Furthermore, the premixing of part of the solvent with the feed before countercurrent extraction gives high extract oil yields and high quality demetallization. The solvent/feed ratio features of the invention substanially lower the captial and operating costs for such processes while not suffering a loss in selectivity for metals rejection. The column internals and rsidence time features of the invention further improve the extractor metals rejection at a constant yield or allow for an increase in extract oil yield at a constant extract oil metals content. 13 figs., 3 tabs.

  17. Characterization of little skate (Leucoraja erinacea) recombinant transthyretin: Zinc-dependent 3,3',5-triiodo-l-thyronine binding.

    Science.gov (United States)

    Suzuki, Shunsuke; Kasai, Kentaro; Yamauchi, Kiyoshi

    2015-01-01

    Transthyretin (TTR) diverged from an ancestral 5-hydroxyisourate hydrolase (HIUHase) by gene duplication at some early stage of chordate evolution. To clarify how TTR had participated in the thyroid system as an extracellular thyroid hormone (TH) binding protein, TH binding properties of recombinant little skate Leucoraja erinacea TTR was investigated. At the amino acid level, skate TTR showed 37-46% identities with the other vertebrate TTRs. Because the skate TTR had a unique histidine-rich segment in the N-terminal region, it could be purified by Ni-affinity chromatography. The skate TTR was a 46-kDa homotetramer of 14.5kDa subunits, and had one order of magnitude higher affinity for 3,3',5-triiodo-l-thyronine (T3) and some halogenated phenols than for l-thyroxine. However, the skate TTR had no HIUHase activity. Ethylenediaminetetraacetic acid (EDTA) treatment inhibited [(125)I]T3 binding activity whereas the addition of Zn(2+) to the EDTA-treated TTR recovered [(125)I]T3 binding activity in a Zn(2+) concentration-dependent manner. Scatchard analysis revealed the presence of two classes of binding site for T3, with dissociation constants of 0.24 and 17nM. However, the high-affinity sites were completely abolished with 1mM EDTA, whereas the remaining low-affinity sites decreased binding capacity. The number of zinc per TTR was quantified to be 4.5-6.3. Our results suggest that skate TTR has tight Zn(2+)-binding sites, which are essential for T3 binding to at least the high-affinity sites. Zn(2+) binding to the N-terminal histidine-rich segment may play an important role in acquisition or reinforcement of TH binding ability during early evolution of TTR. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Time-dependent recovery of in vivo binding sites after drug dosing: A method for radiotracer evaluation

    International Nuclear Information System (INIS)

    Kilbourn, Michael R.

    1997-01-01

    The recovery of in vivo binding sites for (±)-α-[ 11 C]methoxytetrabenazine, a radioligand for the monoamine vesicular transporter (VMAT2), was determined in mouse brain at various times following a pharmacological dose of tetrabenazine. Concentrations of in vivo radioligand binding sites progressively increased and had reached control values by 8.5 h, and this recovery was consistent with the pharmacokinetics of the competing drug tetrabenazine and its active metabolite, dihydrotetrabenazine. This study demonstrates a simple experimental protocol of using a single dose of a reversible competing drug and time-dependent measurements of in vivo binding of a radioligand. This protocol is suitable for testing the sensitivity of an in vivo radiotracer for measurement of varying concentrations of in vivo binding sites

  19. Role of codeposited impurities during growth. II. Dependence of morphology on binding and barrier energies

    Science.gov (United States)

    Sathiyanarayanan, Rajesh; Hamouda, Ajmi Bh.; Pimpinelli, A.; Einstein, T. L.

    2011-01-01

    In an accompanying article we showed that surface morphologies obtained through codeposition of a small quantity (2%) of impurities with Cu during growth (step-flow mode, θ = 40 ML) significantly depends on the lateral nearest-neighbor binding energy (ENN) to Cu adatom and the diffusion barrier (Ed) of the impurity atom on Cu(0 0 1). Based on these two energy parameters, ENN and Ed, we classify impurity atoms into four sets. We study island nucleation and growth in the presence of codeposited impurities from different sets in the submonolayer (θ⩽ 0.7 ML) regime. Similar to growth in the step-flow mode, we find different nucleation and growth behavior for impurities from different sets. We characterize these differences through variations of the number of islands (Ni) and the average island size with coverage (θ). Further, we compute the critical nucleus size (i) for all of these cases from the distribution of capture-zone areas using the generalized Wigner distribution.

  20. Insight into temperature dependence of GTPase activity in human guanylate binding protein-1.

    Directory of Open Access Journals (Sweden)

    Anjana Rani

    Full Text Available Interferon-γ induced human guanylate binding protein-1(hGBP1 belongs to a family of dynamin related large GTPases. Unlike all other GTPases, hGBP1 hydrolyzes GTP to a mixture of GDP and GMP with GMP being the major product at 37°C but GDP became significant when the hydrolysis reaction was carried out at 15°C. The hydrolysis reaction in hGBP1 is believed to involve with a number of catalytic steps. To investigate the effect of temperature in the product formation and on the different catalytic complexes of hGBP1, we carried out temperature dependent GTPase assays, mutational analysis, chemical and thermal denaturation studies. The Arrhenius plot for both GDP and GMP interestingly showed nonlinear behaviour, suggesting that the product formation from the GTP-bound enzyme complex is associated with at least more than one step. The negative activation energy for GDP formation and GTPase assay with external GDP together indicate that GDP formation occurs through the reversible dissociation of GDP-bound enzyme dimer to monomer, which further reversibly dissociates to give the product. Denaturation studies of different catalytic complexes show that unlike other complexes the free energy of GDP-bound hGBP1 decreases significantly at lower temperature. GDP formation is found to be dependent on the free energy of the GDP-bound enzyme complex. The decrease in the free energy of this complex at low temperature compared to at high is the reason for higher GDP formation at low temperature. Thermal denaturation studies also suggest that the difference in the free energy of the GTP-bound enzyme dimer compared to its monomer plays a crucial role in the product formation; higher stability favours GMP but lower favours GDP. Thus, this study provides the first thermodynamic insight into the effect of temperature in the product formation of hGBP1.

  1. Involvement of histidine residues in the pH-dependent β-galactoside binding activity of human galectin-1.

    Science.gov (United States)

    Hiramatsu, Hirotsugu; Takeuchi, Katsuyuki; Takeuchi, Hideo

    2013-04-02

    The pH dependence of the β-galactoside binding activity of human galectin-1 (hGal-1) was investigated by fluorescence spectroscopy using lactose as a ligand. The obtained binding constant Kb was 2.94 ± 0.10 mM(-1) at pH 7.5. The Kb value decreased at acidic pH with a midpoint of transition at pH 6.0 ± 0.1. To elucidate the molecular mechanism of the pH dependence, we investigated the structures of hGal-1 and its two His mutants (H44Q and H52Q) using fluorescence, circular dichroism, UV absorption, and UV resonance Raman spectroscopy. Analysis of the spectra has shown that the pKa values of His44 and His52 are 5.7 ± 0.2 and 6.3 ± 0.1, respectively. The protonation of His52 below pH 6.3 induces a small change in secondary structure and partly reduces the galactoside binding activity. On the other hand, the protonation of His44 below pH 5.7 exerts a cation-π interaction with Trp68 and largely diminishes the galactoside binding activity. With reference to the literature X-ray structures at pH 7.0 and 5.6, protonated His52 is proposed to move slightly away from the galactoside-binding region with a partial unfolding of the β-strand containing His52. On the other hand, protonated His44 becomes unable to form a hydrogen bond with galactoside and additionally induces a reorientation and/or displacement of Trp68 through cation-π interaction, leading to a loosening of the galactoside-binding pocket. These structural changes associated with His protonation are likely to be the origin of the pH dependence of the galactoside binding activity of hGal-1.

  2. Deasphalting solvents

    International Nuclear Information System (INIS)

    Carrillo, J. A; Caceres, J; Vela, G; Bueno, H

    1996-01-01

    This paper describes how the deasphalted oil (DMO) or demetalized oil (DMO) quality (CCR, Ni, V end asphaltenes contents) changes with: DAO or DMO yield, solvent/feed ratio, type of vacuum reside (from paraffinic to blends with vis breaking bottoms), extraction temperature and extraction solvent (propane, propylene, n-butane and I butane)

  3. A Central Nervous System-Dependent Intron-Embedded Gene Encodes a Novel Murine Fyn Binding Protein.

    Science.gov (United States)

    Ben Khalaf, Noureddine; Taha, Safa; Bakhiet, Moiz; Fathallah, M Dahmani

    2016-01-01

    The interplay between the nervous and immune systems is gradually being unraveled. We previously reported in the mouse the novel soluble immune system factor ISRAA, whose activation in the spleen is central nervous system-dependent. We also showed that ISRAA plays a role in modulating anti-infection immunity. Herein, we report the genomic description of the israa locus, along with some insights into the structure-function relationship of the protein. Our findings revealed that israa is nested within intron 6 of the mouse zmiz1 gene. Protein sequence analysis revealed a typical SH2 binding motif (Y102TEV), with Fyn being the most likely binding partner. Docking simulation showed a favorable conformation for the ISRAA-Fyn complex, with a specific binding mode for the binding of the YTEV motif to the SH2 domain. Experimental studies showed that in vitro, recombinant ISRAA is phosphorylated by Fyn at tyrosine 102. Cell transfection and pull-down experiments revealed Fyn as a binding partner of ISRAA in the EL4 mouse T-cell line. Indeed, we demonstrated that ISRAA downregulates T-cell activation and the phosphorylation of an activation tyrosine (Y416) of Src-family kinases in mouse splenocytes. Our observations highlight ISRAA as a novel Fyn binding protein that is likely to be involved in a signaling pathway driven by the nervous system.

  4. A Central Nervous System-Dependent Intron-Embedded Gene Encodes a Novel Murine Fyn Binding Protein.

    Directory of Open Access Journals (Sweden)

    Noureddine Ben Khalaf

    Full Text Available The interplay between the nervous and immune systems is gradually being unraveled. We previously reported in the mouse the novel soluble immune system factor ISRAA, whose activation in the spleen is central nervous system-dependent. We also showed that ISRAA plays a role in modulating anti-infection immunity. Herein, we report the genomic description of the israa locus, along with some insights into the structure-function relationship of the protein. Our findings revealed that israa is nested within intron 6 of the mouse zmiz1 gene. Protein sequence analysis revealed a typical SH2 binding motif (Y102TEV, with Fyn being the most likely binding partner. Docking simulation showed a favorable conformation for the ISRAA-Fyn complex, with a specific binding mode for the binding of the YTEV motif to the SH2 domain. Experimental studies showed that in vitro, recombinant ISRAA is phosphorylated by Fyn at tyrosine 102. Cell transfection and pull-down experiments revealed Fyn as a binding partner of ISRAA in the EL4 mouse T-cell line. Indeed, we demonstrated that ISRAA downregulates T-cell activation and the phosphorylation of an activation tyrosine (Y416 of Src-family kinases in mouse splenocytes. Our observations highlight ISRAA as a novel Fyn binding protein that is likely to be involved in a signaling pathway driven by the nervous system.

  5. Por secretion system-dependent secretion and glycosylation of Porphyromonas gingivalis hemin-binding protein 35.

    Directory of Open Access Journals (Sweden)

    Mikio Shoji

    Full Text Available The anaerobic Gram-negative bacterium Porphyromonas gingivalis is a major pathogen in severe forms of periodontal disease and refractory periapical perodontitis. We have recently found that P. gingivalis has a novel secretion system named the Por secretion system (PorSS, which is responsible for secretion of major extracellular proteinases, Arg-gingipains (Rgps and Lys-gingipain. These proteinases contain conserved C-terminal domains (CTDs in their C-termini. Hemin-binding protein 35 (HBP35, which is one of the outer membrane proteins of P. gingivalis and contributes to its haem utilization, also contains a CTD, suggesting that HBP35 is translocated to the cell surface via the PorSS. In this study, immunoblot analysis of P. gingivalis mutants deficient in the PorSS or in the biosynthesis of anionic polysaccharide-lipopolysaccharide (A-LPS revealed that HBP35 is translocated to the cell surface via the PorSS and is glycosylated with A-LPS. From deletion analysis with a GFP-CTD[HBP35] green fluorescent protein fusion, the C-terminal 22 amino acid residues of CTD[HBP35] were found to be required for cell surface translocation and glycosylation. The GFP-CTD fusion study also revealed that the CTDs of CPG70, peptidylarginine deiminase, P27 and RgpB play roles in PorSS-dependent translocation and glycosylation. However, CTD-region peptides were not found in samples of glycosylated HBP35 protein by peptide map fingerprinting analysis, and antibodies against CTD-regions peptides did not react with glycosylated HBP35 protein. These results suggest both that the CTD region functions as a recognition signal for the PorSS and that glycosylation of CTD proteins occurs after removal of the CTD region. Rabbits were used for making antisera against bacterial proteins in this study.

  6. Endogenously generated plasmin at the vascular wall injury site amplifies lysine binding site-dependent plasminogen accumulation in microthrombi.

    Directory of Open Access Journals (Sweden)

    Tomasz Brzoska

    Full Text Available The fibrinolytic system plays a pivotal role in the regulation of hemostasis; however, it remains unclear how and when the system is triggered to induce thrombolysis. Using intra-vital confocal fluorescence microscopy, we investigated the process of plasminogen binding to laser-induced platelet-rich microthrombi generated in the mesenteric vein of transgenic mice expressing green fluorescent protein (GFP. The accumulation of GFP-expressing platelets as well as exogenously infused Alexa Fluor 568-labeled Glu-plasminogen (Glu-plg on the injured vessel wall was assessed by measuring the increase in the corresponding fluorescence intensities. Glu-plg accumulated in a time-dependent manner in the center of the microthrombus, where phosphatidylserine is exposed on platelet surfaces and fibrin formation takes place. The rates of binding of Glu-plg in the presence of ε-aminocaproic acid and carboxypeptidase B, as well as the rates of binding of mini-plasminogen lacking kringle domains 1-4 and lysine binding sites, were significantly lower than that of Glu-plg alone, suggesting that the binding was dependent on lysine binding sites. Furthermore, aprotinin significantly suppressed the accumulation of Glu-plg, suggesting that endogenously generated plasmin activity is a prerequisite for the accumulation. In spite of the endogenous generation of plasmin and accumulation of Glu-plg in the center of microthrombi, the microthrombi did not change in size during the 2-hour observation period. When human tissue plasminogen activator was administered intravenously, Glu-plg further accumulated and the microthrombi were lysed. Glu-plg appeared to accumulate in the center of microthrombi in the early phase of microthrombus formation, and plasmin activity and lysine binding sites were required for this accumulation.

  7. Cyclophilin B binding to platelets supports calcium-dependent adhesion to collagen.

    Science.gov (United States)

    Allain, F; Durieux, S; Denys, A; Carpentier, M; Spik, G

    1999-08-01

    We have recently reported that cyclophilin B (CyPB), a secreted cyclosporine-binding protein, could bind to T lymphocytes through interactions with two types of binding sites. The first ones, referred to as type I, involve interactions with the conserved domain of CyPB and promote the endocytosis of surface-bound ligand, while the second type of binding sites, termed type II, are represented by glycosaminoglycans (GAG). Here, we further investigated the interactions of CyPB with blood cell populations. In addition to lymphocytes, CyPB was found to interact mainly with platelets. The binding is specific, with a dissociation constant (kd) of 9 +/- 3 nmol/L and the number of sites estimated at 960 +/- 60 per cell. Platelet glycosaminoglycans are not required for the interactions, but the binding is dramatically reduced by active cyclosporine derivatives. We then analyzed the biologic effects of CyPB and found a significant increase in platelet adhesion to collagen. Concurrently, CyPB initiates a transmembranous influx of Ca(2+) and induces the phosphorylation of the P-20 light chains of myosin. Taken together, the present results demonstrate for the first time that extracellular CyPB specifically interacts with platelets through a functional receptor related to the lymphocyte type I binding sites and might act by regulating the activity of a receptor-operated membrane Ca(2+) channel.

  8. Activity of cAMP-dependent protein kinases and cAMP-binding proteins of rat kidney cytosol during dehydration

    International Nuclear Information System (INIS)

    Zelenina, M.N.; Solenov, E.I.; Ivanova, L.N.

    1985-01-01

    The activity of cAMP-dependent protein kinases, the binding of cAMP, and the spectrum of cAMP-binding proteins in the cytosol of the renal papilla was studied in intact rats and in rats after 24 h on a water-deprived diet. It was found that the activation of protein kinases by 10 -6 M cAMP is significantly higher in the experimental animals than in the intact animals. In chromatography on DEAE-cellulose, the positions of the peaks of specific reception of cAMP corresponded to the peaks of the regulatory subunits of cAMP-dependent protein kinases of types I and II. In this case, in intact animals more than 80% of the binding activity was detected in peaks II, whereas in rats subjected to water deprivation, more than 60% of the binding was observed in peak I. The general regulatory activity of the cytosol was unchanged in the experimental animals in comparison with intact animals. It is suggested that during dehydration there is an induction of the synthesis of the regulatory subunit of type I cAMP-dependent protein kinase in the renal papilla

  9. Canyon solvent cleaning with solid adsorbents

    International Nuclear Information System (INIS)

    Reif, D.J.

    1987-01-01

    The HM Process at the Savannah River Plant (SRP) uses 7.5% tributyl phosphate in n-paraffin as an extraction solvent. During use, the solvent is altered due to hydrolysis and radiolysis, forming materials that influence product losses, product decontamination, and separation efficiencies. Laboratory studies to improve online solvent cleaning have shown that carbonate washing, although removing residual solvent activity, does not remove binding ligands that hold fission products in the solvent. Treatment of solvent with a solid adsorbent removes binding ligands and significantly improves recycle solvent performance. Both laboratory work defining a full-scale adsorption process and the use of the process to clean HM Process first cycle solvent are presented

  10. Mechanistic study on lowering the sensitivity of positive atmospheric pressure photoionization mass spectrometric analyses: size-dependent reactivity of solvent clusters.

    Science.gov (United States)

    Ahmed, Arif; Choi, Cheol Ho; Kim, Sunghwan

    2015-11-15

    Understanding the mechanism of atmospheric pressure photoionization (APPI) is important for studies employing APPI liquid chromatography/mass spectrometry (LC/MS). In this study, the APPI mechanism for polyaromatic hydrocarbon (PAH) compounds dissolved in toluene and methanol or water mixture was investigated by use of MS analysis and quantum mechanical simulation. In particular, four different mechanisms that could contribute to the signal reduction were considered based on a combination of MS data and quantum mechanical calculations. The APPI mechanism is clarified by combining MS data and density functional theory (DFT) calculations. To obtain MS data, a positive-mode (+) APPI Q Exactive Orbitrap mass spectrometer was used to analyze each solution. DFT calculations were performed using the general atomic and molecular electronic structure system (GAMESS). The experimental results indicated that methanol significantly reduced the signal in (+) APPI, but no significative signal reduction was observed when water was used as a co-solvent with toluene. The signal reduction is more significant especially for molecular ions than for protonated ions. Therefore, important information about the mechanism of methanol-induced signal reduction in (+) APPI-MS can be gained due its negative impact on APPI efficiency. The size-dependent reactivity of methanol clusters ((CH3 OH)n , n = 1-8) is an important factor in determining the sensitivity of (+) APPI-MS analyses. Clusters can compete with toluene radical ions for electrons. The reactivity increases as the sizes of the methanol clusters increase and this effect can be caused by the size-dependent ionization energy of the solvent clusters. The resulting increase in cluster reactivity explains the flow rate and temperature-dependent signal reduction observed in the analytes. Based on the results presented here, minimizing the sizes of methanol clusters can improve the sensitivity of LC/(+)-APPI-MS. Copyright © 2015 John

  11. Binding modes and pathway of RHPS4 to human telomeric G-quadruplex and duplex DNA probed by all-atom molecular dynamics simulations with explicit solvent.

    Science.gov (United States)

    Mulholland, Kelly; Siddiquei, Farzana; Wu, Chun

    2017-07-19

    RHPS4, a potent binder to human telomeric DNA G-quadruplex, shows high efficacy in tumor cell growth inhibition. However, it's preferential binding to DNA G-quadruplex over DNA duplex (about 10 fold) remains to be improved toward its clinical application. A high resolution structure of the single-stranded telomeric DNA G-quadruplexes, or B-DNA duplex, in complex with RHPS4 is not available yet, and the binding nature of this ligand to these DNA forms remains to be elusive. In this study, we carried out 40 μs molecular dynamics binding simulations with a free ligand to decipher the binding pathway of RHPS4 to a DNA duplex and three G-quadruplex folders (parallel, antiparallel and hybrid) of the human telomeric DNA sequence. The most stable binding mode identified for the duplex, parallel, antiparallel and hybrid G-quadruplexes is an intercalation, bottom stacking, top intercalation and bottom intercalation mode, respectively. The intercalation mode with similar binding strength to both the duplex and the G-quadruplexes, explains the lack of binding selectivity of RHPS4 to the G-quadruplex form. Therefore, a ligand modification that destabilizes the duplex intercalation mode but stabilizes the G-quadruplex intercalation mode will improve the binding selectivity toward G-quadruplex. The intercalation mode of RHPS4 to both the duplex and the antiparallel and the hybrid G-quadruplex follows a base flipping-insertion mechanism rather than an open-insertion mechanism. The groove binding, the side binding and the intercalation with flipping out of base were observed to be intermediate states before the full intercalation state with paired bases.

  12. Solvent substitution

    International Nuclear Information System (INIS)

    1990-01-01

    The DOE Environmental Restoration and Waste Management Office of Technology Development and the Air Force Engineering and Services Center convened the First Annual International Workshop on Solvent Substitution on December 4--7, 1990. The primary objectives of this joint effort were to share information and ideas among attendees in order to enhance the development and implementation of required new technologies for the elimination of pollutants associated with industrial use of hazardous and toxic solvents; and to aid in accelerating collaborative efforts and technology transfer between government and industry for solvent substitution. There were workshop sessions focusing on Alternative Technologies, Alternative Solvents, Recovery/Recycling, Low VOC Materials and Treatment for Environmentally Safe Disposal. The 35 invited papers presented covered a wide range of solvent substitution activities including: hardware and weapons production and maintenance, paint stripping, coating applications, printed circuit boards, metal cleaning, metal finishing, manufacturing, compliance monitoring and process control monitoring. This publication includes the majority of these presentations. In addition, in order to further facilitate information exchange and technology transfer, the US Air Force and DOE solicited additional papers under a general ''Call for Papers.'' These papers, which underwent review and final selection by a peer review committee, are also included in this combined Proceedings/Compendium. For those involved in handling, using or managing hazardous and toxic solvents, this document should prove to be a valuable resource, providing the most up-to-date information on current technologies and practices in solvent substitution. Individual papers are abstracted separated

  13. Solvent substitution

    Energy Technology Data Exchange (ETDEWEB)

    1990-01-01

    The DOE Environmental Restoration and Waste Management Office of Technology Development and the Air Force Engineering and Services Center convened the First Annual International Workshop on Solvent Substitution on December 4--7, 1990. The primary objectives of this joint effort were to share information and ideas among attendees in order to enhance the development and implementation of required new technologies for the elimination of pollutants associated with industrial use of hazardous and toxic solvents; and to aid in accelerating collaborative efforts and technology transfer between government and industry for solvent substitution. There were workshop sessions focusing on Alternative Technologies, Alternative Solvents, Recovery/Recycling, Low VOC Materials and Treatment for Environmentally Safe Disposal. The 35 invited papers presented covered a wide range of solvent substitution activities including: hardware and weapons production and maintenance, paint stripping, coating applications, printed circuit boards, metal cleaning, metal finishing, manufacturing, compliance monitoring and process control monitoring. This publication includes the majority of these presentations. In addition, in order to further facilitate information exchange and technology transfer, the US Air Force and DOE solicited additional papers under a general Call for Papers.'' These papers, which underwent review and final selection by a peer review committee, are also included in this combined Proceedings/Compendium. For those involved in handling, using or managing hazardous and toxic solvents, this document should prove to be a valuable resource, providing the most up-to-date information on current technologies and practices in solvent substitution. Individual papers are abstracted separated.

  14. Item-location binding in working memory: is it hippocampus-dependent?

    Science.gov (United States)

    Allen, Richard J; Vargha-Khadem, Faraneh; Baddeley, Alan D

    2014-07-01

    A general consensus is emerging that the hippocampus has an important and active role in the creation of new long-term memory representations of associations or bindings between elements. However, it is less clear whether this contribution can be extended to the creation of temporary bound representations in working memory, involving the retention of small numbers of items over short delays. We examined this by administering a series of recognition and recall tests of working memory for colour-location binding and object-location binding to a patient with highly selective hippocampal damage (Jon), and groups of control participants. Jon achieved high levels of accuracy in all working memory tests of recognition and recall binding across retention intervals of up to 10s. In contrast, Jon performed at chance on an unexpected delayed test of the same object-location binding information. These findings indicate a clear dissociation between working memory and long-term memory, with no evidence for a critical hippocampal contribution to item-location binding in working memory. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Environment-dependent crystal-field tight-binding based on density-functional theory

    International Nuclear Information System (INIS)

    Urban, Alexander

    2012-01-01

    systematic derivation of Slater-Koster parameters from the results of DFT calculations. In our approach, the DFT wave functions (Kohn-Sham orbitals) in a numerically converged basis of atom-centered functions and plane waves are mapped onto a minimal basis of atomic orbitals (AOs) using a projection formalism. This allows the computation of the minimal basis representation of the converged DFT Hamiltonian. The quality of TB parameters obtained using the projection methodology crucially depends on the choice of the minimal AO basis. We have therefore developed several schemes for the optimization of AO basis sets, which are discussed in detail in this thesis. The projection formalism described above is not limited to the calculation of conventional TB parameters, i.e., to bond and overlap integrals over two orbitals that are located at two different atomic sites. It also can be used to analyze crystal field interactions. We introduce an extended crystal-field tight-binding (CF-TB) method, which includes an environment-dependent on-site parametrization. It is demonstrated that the CF-TB method is substantially more accurate for low-symmetry structures. A common potential energy reference is a necessary condition to be able to compare Hamilton matrices and eigenvalues from different structures. We point out that the structure-dependent on-site parameters of a CF-TB model are suitable to gauge eigenvalues and bond integrals of different atomic and molecular structures. Most importantly, with an appropriate choice of potential energy reference, the structure sensitivity of bond integrals can be significantly reduced, thus leading to a substantial increase of the transferability of the TB models. In addition to the Slater-Koster parametrization of the electronic structure, for the calculation of cohesion energies and atomic forces in TB, a description of the ionic core repulsion and the double-counting corrections is required. We have explored various options for the partitioning

  16. Solvent extraction of some fission products using tetracycline as a complexing agent : dependence on the ph of the aqueous phase and on the nature of some inorganic anions

    International Nuclear Information System (INIS)

    Cunha, I.I.L.; Nastasi, M.J.C.

    1982-10-01

    The behavior of tetracycline as a complexing agent in solvent extraction studies is presented. The extraction curves for the fission products 90 Sr, 140 Ba, 99 Mo, sup(99m)Tc, 95 Zr, 95 Nb, 103 Ru and also for U have been determined for the extraction system tetracycline-benzyl alcohol. The extraction dependence on the pH of the aqueous phase as well as on the kind of electrolyte present was examined. As a practical application, the possiblity of using the tetracycline-benzyl alcohol system for separation of the fission products present in a mixture of them, as well as for the separation of uranium from those elements, was tested. (Author) [pt

  17. Visualizing double-stranded RNA distribution and dynamics in living cells by dsRNA binding-dependent fluorescence complementation

    International Nuclear Information System (INIS)

    Cheng, Xiaofei; Deng, Ping; Cui, Hongguang; Wang, Aiming

    2015-01-01

    Double-stranded RNA (dsRNA) is an important type of RNA that plays essential roles in diverse cellular processes in eukaryotic organisms and a hallmark in infections by positive-sense RNA viruses. Currently, no in vivo technology has been developed for visualizing dsRNA in living cells. Here, we report a dsRNA binding-dependent fluorescence complementation (dRBFC) assay that can be used to efficiently monitor dsRNA distribution and dynamics in vivo. The system consists of two dsRNA-binding proteins, which are fused to the N- and C-terminal halves of the yellow fluorescent protein (YFP). Binding of the two fusion proteins to a common dsRNA brings the split YFP halves in close proximity, leading to the reconstitution of the fluorescence-competent structure and restoration of fluorescence. Using this technique, we were able to visualize the distribution and trafficking of the replicative RNA intermediates of positive-sense RNA viruses in living cells. - Highlights: • A live-cell imaging system was developed for visualizing dsRNA in vivo. • It uses dsRNA binding proteins fused with two halves of a fluorescent protein. • Binding to a common dsRNA enables the reporter to become fluorescent. • The system can efficiently monitor viral RNA replication in living cells.

  18. Visualizing double-stranded RNA distribution and dynamics in living cells by dsRNA binding-dependent fluorescence complementation

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Xiaofei [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada); College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 310036 (China); Deng, Ping; Cui, Hongguang [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada); Wang, Aiming, E-mail: aiming.wang@agr.gc.ca [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada)

    2015-11-15

    Double-stranded RNA (dsRNA) is an important type of RNA that plays essential roles in diverse cellular processes in eukaryotic organisms and a hallmark in infections by positive-sense RNA viruses. Currently, no in vivo technology has been developed for visualizing dsRNA in living cells. Here, we report a dsRNA binding-dependent fluorescence complementation (dRBFC) assay that can be used to efficiently monitor dsRNA distribution and dynamics in vivo. The system consists of two dsRNA-binding proteins, which are fused to the N- and C-terminal halves of the yellow fluorescent protein (YFP). Binding of the two fusion proteins to a common dsRNA brings the split YFP halves in close proximity, leading to the reconstitution of the fluorescence-competent structure and restoration of fluorescence. Using this technique, we were able to visualize the distribution and trafficking of the replicative RNA intermediates of positive-sense RNA viruses in living cells. - Highlights: • A live-cell imaging system was developed for visualizing dsRNA in vivo. • It uses dsRNA binding proteins fused with two halves of a fluorescent protein. • Binding to a common dsRNA enables the reporter to become fluorescent. • The system can efficiently monitor viral RNA replication in living cells.

  19. CO2-Binding Organic Liquids Gas Capture with Polarity-Swing-Assisted Regeneration Full Technology Feasibility Study B1 - Solvent-based Systems

    Energy Technology Data Exchange (ETDEWEB)

    Heldebrant, David J

    2014-08-31

    PNNL, Fluor Corporation and Queens University (Kingston, ON) successfully completed a three year comprehensive study of the CO2BOL water-lean solvent platform with Polarity Swing Assisted Regeneration (PSAR). This study encompassed solvent synthesis, characterization, environmental toxicology, physical, thermodynamic and kinetic property measurements, Aspen Plus™ modeling and bench-scale testing of a candidate CO2BOL solvent molecule. Key Program Findings The key program findings are summarized as follows: • PSAR favorably reduced stripper duties and reboiler temperatures with little/no impact to absorption column • >90% CO2 capture was achievable at reasonable liquid-gas ratios in the absorber • High rich solvent viscosities (up to 600 cP) were successfully demonstrated in the bench-scale system. However, the projected impacts of high viscosity to capital cost and operational limits compromised the other levelized cost of electricity benefits. • Low thermal conductivity of organics significantly increased the required cross exchanger surface area, and potentially other heat exchange surfaces. • CO2BOL had low evaporative losses during bench-scale testing • There was no evidence of foaming during bench scale testing • Current CO2BOL formulation costs project to be $35/kg • Ecotoxicity (Water Daphnia) was comparable between CO2BOL and MEA (169.47 versus 103.63 mg/L) • Full dehydration of the flue gas was determined to not be economically feasible. However, modest refrigeration (13 MW for the 550 MW reference system) was determined to be potentially economically feasible, and still produce a water-lean condition for the CO2BOLs (5 wt% steady-state water loading). • CO2BOLs testing with 5 wt% water loading did not compromise anhydrous performance behavior, and showed actual enhancement of CO2 capture performance. • Mass transfer of CO2BOLs was not greatly impeded by viscosity • Facile separation of antisolvent from lean CO2BOL was

  20. RNA-binding protein PSPC1 promotes the differentiation-dependent nuclear export of adipocyte RNAs

    DEFF Research Database (Denmark)

    Wang, Jiexin; Rajbhandari, Prashant; Damianov, Andrey

    2017-01-01

    A highly orchestrated gene expression program establishes the properties that define mature adipocytes, but the contribution of posttranscriptional factors to the adipocyte phenotype is poorly understood. Here we have shown that the RNA-binding protein PSPC1, a component of the paraspeckle complex...

  1. Mycobacterial laminin-binding histone-like protein mediates collagen-dependent cytoadherence

    Directory of Open Access Journals (Sweden)

    André Alves Dias

    2012-12-01

    Full Text Available When grown in the presence of exogenous collagen I, Mycobacterium bovis BCG was shown to form clumps. Scanning electron microscopy examination of these clumps revealed the presence of collagen fibres cross-linking the bacilli. Since collagen is a major constituent of the eukaryotic extracellular matrices, we assayed BCG cytoadherence in the presence of exogenous collagen I. Collagen increased the interaction of the bacilli with A549 type II pneumocytes or U937 macrophages, suggesting that BCG is able to recruit collagen to facilitate its attachment to host cells. Using an affinity chromatography approach, we have isolated a BCG collagen-binding protein corresponding to the previously described mycobacterial laminin-binding histone-like protein (LBP/Hlp, a highly conserved protein associated with the mycobacterial cell wall. Moreover, Mycobacterium leprae LBP/Hlp, a well-characterized adhesin, was also able to bind collagen I. Finally, using recombinant fragments of M. leprae LBP/Hlp, we mapped the collagen-binding activity within the C-terminal domain of the adhesin. Since this protein was already shown to be involved in the recognition of laminin and heparan sulphate-containing proteoglycans, the present observations reinforce the adhesive activities of LBP/Hlp, which can be therefore considered as a multifaceted mycobacterial adhesin, playing an important role in both leprosy and tuberculosis pathogenesis.

  2. Deciphering the binding behavior of flavonoids to the cyclin dependent kinase 6/cyclin D complex.

    Directory of Open Access Journals (Sweden)

    Jingxiao Zhang

    Full Text Available Flavonoids, a class of natural compounds with variable phenolic structures, have been found to possess anti-cancer activities by modulating different enzymes and receptors like CDK6. To understand the binding behavior of flavonoids that inhibit the active CDK6, molecular dynamics (MD simulations were performed on six inhibitors, chrysin (M01, fisetin (M03, galangin (M04, genistein (M05, quercetin (M06 and kaempferol (M07, complexed with CDK6/cyclin D. For all six flavonoids, the 3'-OH and 4'-OH of B-ring were found to be favorable for hydrogen bond formation, but the 3-OH on the C-ring and 5-OH on the A-ring were unfavorable, which were confirmed by the MD simulation results of the test molecule, 3', 4', 7-trihydroxyflavone (M15. The binding efficiencies of flavonoids against the CDK6/cyclin D complex were mainly through the electrostatic (especially the H-bond force and vdW interactions with residues ILE19, VAL27, ALA41, GLU61, PHE98, GLN103, ASP163 and LEU152. The order of binding affinities of these flavonoids toward the CDK6/cyclin D was M03 > M01 > M07 > M15 > M06 > M05 > M04. It is anticipated that the binding features of flavonoid inhibitors studied in the present work may provide valuable insights for the development of CDK6 inhibitors.

  3. High-Throughput Testing of Antibody-Dependent Binding Inhibition of Placental Malaria Parasites

    DEFF Research Database (Denmark)

    Nielsen, Morten A; Salanti, Ali

    2015-01-01

    The particular virulence of Plasmodium falciparum manifests in diverse severe malaria syndromes as cerebral malaria, severe anemia and placental malaria. The cause of both the severity and the diversity of infection outcome, is the ability of the infected erythrocyte (IE) to bind a range......-throughput assay used in the preclinical and clinical development of a VAR2CSA based vaccine against placental malaria....

  4. Serum albumin promotes ATP-binding cassette transporter-dependent sterol uptake in yeast

    DEFF Research Database (Denmark)

    Marek, Magdalena; Silvestro, Daniele; Fredslund, Maria D.

    2014-01-01

    Sterol uptake in fungi is a multistep process that involves interaction between external sterols and the cell wall, incorporation of sterol molecules into the plasma membrane, and subsequent integration into intracellular membranes for turnover. ATP-binding cassette (ABC) transporters have been...

  5. Effect of hydrogen bonding of a solvent on the thermodynamic stability of cadmium complexes of ethylenediamine

    International Nuclear Information System (INIS)

    Ledenkov, S.F.; Sharnin, V.A.; Chistyakova, G.V.

    2004-01-01

    The composition and stability of cadmium(II) ethylenediamine complexes in water-dimethylsulfoxide (DMSO) mixed solvents, depending on the content of organic component, were studied by the methods of pH-metry and calorimetry. It is shown that increase in DMSO content in the solvent gives rise to higher stability of cadmium complexes. The greatest growth of stability constant was pointed out for coordination-saturated compounds. The complexing thermodynamics was discussed from the viewpoint of solvation approach. Protolytic solvents were shown to produce destabilizing effect on the polyligand complexes owing to participation of coordination sphere in H-binding [ru

  6. Clostridium Perfringens Epsilon Toxin Binds to Membrane Lipids and Its Cytotoxic Action Depends on Sulfatide.

    Directory of Open Access Journals (Sweden)

    Carles Gil

    Full Text Available Epsilon toxin (Etx is one of the major lethal toxins produced by Clostridium perfringens types B and D, being the causal agent of fatal enterotoxemia in animals, mainly sheep and goats. Etx is synthesized as a non-active prototoxin form (proEtx that becomes active upon proteolytic activation. Etx exhibits a cytotoxic effect through the formation of a pore in the plasma membrane of selected cell targets where Etx specifically binds due to the presence of specific receptors. However, the identity and nature of host receptors of Etx remain a matter of controversy. In the present study, the interactions between Etx and membrane lipids from the synaptosome-enriched fraction from rat brain (P2 fraction and MDCK cell plasma membrane preparations were analyzed. Our findings show that both Etx and proEtx bind to lipids extracted from lipid rafts from the two different models as assessed by protein-lipid overlay assay. Lipid rafts are membrane microdomains enriched in cholesterol and sphingolipids. Binding of proEtx to sulfatide, phosphatidylserine, phosphatidylinositol (3-phosphate and phosphatidylinositol (5-phosphate was detected. Removal of the sulphate groups via sulfatase treatment led to a dramatic decrease in Etx-induced cytotoxicity, but not in proEtx-GFP binding to MDCK cells or a significant shift in oligomer formation, pointing to a role of sulfatide in pore formation in rafts but not in toxin binding to the target cell membrane. These results show for the first time the interaction between Etx and membrane lipids from host tissue and point to a major role for sulfatides in C. perfringens epsilon toxin pathophysiology.

  7. Effect of trastuzumab interchain disulfide bond cleavage on Fcγ receptor binding and antibody-dependent tumour cell phagocytosis.

    Science.gov (United States)

    Suzuki, Mami; Yamanoi, Ayaka; Machino, Yusuke; Ootsubo, Michiko; Izawa, Ken-ichi; Kohroki, Junya; Masuho, Yasuhiko

    2016-01-01

    The Fc domain of human IgG1 binds to Fcγ receptors (FcγRs) to induce effector functions such as phagocytosis. There are four interchain disulfide bonds between the H and L chains. In this study, the disulfide bonds within the IgG1 trastuzumab (TRA), which is specific for HER2, were cleaved by mild S-sulfonation or by mild reduction followed by S-alkylation with three different reagents. The cleavage did not change the binding activities of TRA to HER2-bearing SK-BR-3 cells. The binding activities of TRA to FcγRIIA and FcγRIIB were greatly enhanced by modification with mild reduction and S-alkylation with ICH2CONH2 or N-(4-aminophenyl) maleimide, while the binding activities of TRA to FcγRI and FcγRIIIA were decreased by any of the four modifications. However, the interchain disulfide bond cleavage by the different modifications did not change the antibody-dependent cell-mediated phagocytosis (ADCP) of SK-BR-3 cells by activated THP-1 cells. The order of FcγR expression levels on the THP-1 cells was FcγRII > FcγRI > FcγRIII and ADCP was inhibited by blocking antibodies against FcγRI and FcγRII. These results imply that the effect of the interchain disulfide bond cleavage on FcγRs binding and ADCP is dependent on modifications of the cysteine residues and the FcγR isotypes. © The Authors 2015. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

  8. Photoaffinity labeling with cholesterol analogues precisely maps a cholesterol-binding site in voltage-dependent anion channel-1.

    Science.gov (United States)

    Budelier, Melissa M; Cheng, Wayland W L; Bergdoll, Lucie; Chen, Zi-Wei; Janetka, James W; Abramson, Jeff; Krishnan, Kathiresan; Mydock-McGrane, Laurel; Covey, Douglas F; Whitelegge, Julian P; Evers, Alex S

    2017-06-02

    Voltage-dependent anion channel-1 (VDAC1) is a highly regulated β-barrel membrane protein that mediates transport of ions and metabolites between the mitochondria and cytosol of the cell. VDAC1 co-purifies with cholesterol and is functionally regulated by cholesterol, among other endogenous lipids. Molecular modeling studies based on NMR observations have suggested five cholesterol-binding sites in VDAC1, but direct experimental evidence for these sites is lacking. Here, to determine the sites of cholesterol binding, we photolabeled purified mouse VDAC1 (mVDAC1) with photoactivatable cholesterol analogues and analyzed the photolabeled sites with both top-down mass spectrometry (MS), and bottom-up MS paired with a clickable, stable isotope-labeled tag, FLI -tag. Using cholesterol analogues with a diazirine in either the 7 position of the steroid ring (LKM38) or the aliphatic tail (KK174), we mapped a binding pocket in mVDAC1 localized to Thr 83 and Glu 73 , respectively. When Glu 73 was mutated to a glutamine, KK174 no longer photolabeled this residue, but instead labeled the nearby Tyr 62 within this same binding pocket. The combination of analytical strategies employed in this work permits detailed molecular mapping of a cholesterol-binding site in a protein, including an orientation of the sterol within the site. Our work raises the interesting possibility that cholesterol-mediated regulation of VDAC1 may be facilitated through a specific binding site at the functionally important Glu 73 residue. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  9. Human IGF-I propeptide A promotes articular chondrocyte biosynthesis and employs glycosylation-dependent heparin binding.

    Science.gov (United States)

    Shi, Shuiliang; Kelly, Brian J; Wang, Congrong; Klingler, Ken; Chan, Albert; Eckert, George J; Trippel, Stephen B

    2018-03-01

    Insulin-like growth factor I (IGF-I) is a key regulator of chondrogenesis, but its therapeutic application to articular cartilage damage is limited by rapid elimination from the repair site. The human IGF-I gene gives rise to three IGF-I propeptides (proIGF-IA, proIGF-IB and proIGF-IC) that are cleaved to create mature IGF-I. In this study, we elucidate the processing of IGF-I precursors by articular chondrocytes, and test the hypotheses that proIGF-I isoforms bind to heparin and regulate articular chondrocyte biosynthesis. Human IGF-I propeptides and mutants were overexpressed in bovine articular chondrocytes. IGF-I products were characterized by ELISA, western blot and FPLC using a heparin column. The biosynthetic activity of IGF-I products on articular chondrocytes was assayed for DNA and glycosaminoglycan that the cells produced. Secreted IGF-I propeptides stimulated articular chondrocyte biosynthetic activity to the same degree as mature IGF-I. Of the three IGF-I propeptides, only one, proIGF-IA, strongly bound to heparin. Interestingly, heparin binding of proIGF-IA depended on N-glycosylation at Asn92 in the EA peptide. To our knowledge, this is the first demonstration that N-glycosylation determines the binding of a heparin-binding protein to heparin. The biosynthetic and heparin binding abilities of proIGF-IA, coupled with its generation of IGF-I, suggest that proIGF-IA may have therapeutic value for articular cartilage repair. These data identify human pro-insulin-like growth factor IA as a bifunctional protein. Its combined ability to bind heparin and augment chondrocyte biosynthesis makes it a promising therapeutic agent for cartilage damage due to trauma and osteoarthritis. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. The HTLV-1 Tax protein binding domain of cyclin-dependent kinase 4 (CDK4 includes the regulatory PSTAIRE helix

    Directory of Open Access Journals (Sweden)

    Grassmann Ralph

    2005-09-01

    Full Text Available Abstract Background The Tax oncoprotein of human T-cell leukemia virus type 1 (HTLV-1 is leukemogenic in transgenic mice and induces permanent T-cell growth in vitro. It is found in active CDK holoenzyme complexes from adult T-cell leukemia-derived cultures and stimulates the G1- to-S phase transition by activating the cyclin-dependent kinase (CDK CDK4. The Tax protein directly and specifically interacts with CDK4 and cyclin D2 and binding is required for enhanced CDK4 kinase activity. The protein-protein contact between Tax and the components of the cyclin D/CDK complexes increases the association of CDK4 and its positive regulatory subunit cyclin D and renders the complex resistant to p21CIP inhibition. Tax mutants affecting the N-terminus cannot bind cyclin D and CDK4. Results To analyze, whether the N-terminus of Tax is capable of CDK4-binding, in vitro binding -, pull down -, and mammalian two-hybrid analyses were performed. These experiments revealed that a segment of 40 amino acids is sufficient to interact with CDK4 and cyclin D2. To define a Tax-binding domain and analyze how Tax influences the kinase activity, a series of CDK4 deletion mutants was tested. Different assays revealed two regions which upon deletion consistently result in reduced binding activity. These were isolated and subjected to mammalian two-hybrid analysis to test their potential to interact with the Tax N-terminus. These experiments concurrently revealed binding at the N- and C-terminus of CDK4. The N-terminal segment contains the PSTAIRE helix, which is known to control the access of substrate to the active cleft of CDK4 and thus the kinase activity. Conclusion Since the N- and C-terminus of CDK4 are neighboring in the predicted three-dimensional protein structure, it is conceivable that they comprise a single binding domain, which interacts with the Tax N-terminus.

  11. Behavior of solvent-exposed hydrophobic groove in the anti-apoptotic Bcl-XL protein: clues for its ability to bind diverse BH3 ligands from MD simulations.

    Directory of Open Access Journals (Sweden)

    Dilraj Lama

    Full Text Available Bcl-XL is a member of Bcl-2 family of proteins involved in the regulation of intrinsic pathway of apoptosis. Its overexpression in many human cancers makes it an important target for anti-cancer drugs. Bcl-XL interacts with the BH3 domain of several pro-apoptotic Bcl-2 partners. This helical bundle protein has a pronounced hydrophobic groove which acts as a binding region for the BH3 domains. Eight independent molecular dynamics simulations of the apo/holo forms of Bcl-XL were carried out to investigate the behavior of solvent-exposed hydrophobic groove. The simulations used either a twin-range cut-off or particle mesh Ewald (PME scheme to treat long-range interactions. Destabilization of the BH3 domain-containing helix H2 was observed in all four twin-range cut-off simulations. Most of the other major helices remained stable. The unwinding of H2 can be related to the ability of Bcl-XL to bind diverse BH3 ligands. The loss of helical character can also be linked to the formation of homo- or hetero-dimers in Bcl-2 proteins. Several experimental studies have suggested that exposure of BH3 domain is a crucial event before they form dimers. Thus unwinding of H2 seems to be functionally very important. The four PME simulations, however, revealed a stable helix H2. It is possible that the H2 unfolding might occur in PME simulations at longer time scales. Hydrophobic residues in the hydrophobic groove are involved in stable interactions among themselves. The solvent accessible surface areas of bulky hydrophobic residues in the groove are significantly buried by the loop LB connecting the helix H2 and subsequent helix. These observations help to understand how the hydrophobic patch in Bcl-XL remains stable in the solvent-exposed state. We suggest that both the destabilization of helix H2 and the conformational heterogeneity of loop LB are important factors for binding of diverse ligands in the hydrophobic groove of Bcl-XL.

  12. Solvent substitutes

    International Nuclear Information System (INIS)

    Evanoff, S.P.

    1995-01-01

    The environmental and industrial hygiene regulations promulgated since 1980, most notably the Superfund Amendments and Reauthorization Act (SARA), the Hazardous and Solid Waste Amendments to the Resources Conservation and Recovery Act (RCRA), and the Clean Air Act Amendments of 1990, have brought about an increased emphasis on user exposure, hazardous waste generation, and air emissions. As a result, industry is performing a fundamental reassessment of cleaning solvents, processes, and procedures. The more progressive organizations have made their goal the elimination of solvents that may pose significant potential human health and environmental hazards. This chapter discusses solvent cleaning in metal-finishing, metal-manufacturing, and industrial maintenance applications; precision cleaning; and electronics manufacturing. Nonmetallic cleaning, adhesives, coatings, inks, and aerosols also will be addressed, but in a more cursory manner

  13. Cleanup of 7.5% tributyl phosphate/n-paraffin solvent-extraction solvent

    International Nuclear Information System (INIS)

    Reif, D.J.

    1987-02-01

    The HM process at the Savannah River Plant uses 7.5% tributyl phosphate in n-paraffin as an extraction solvent. During use, the solvent is altered due to hydrolysis and radiolysis, forming materials which influence product losses, product decontamination, and separation efficiencies. Laboratory studies to improve online solvent cleaning have shown that carbonate washing, although removing residual solvent activity, does not remove binding ligands which hold fission products in the solvent. Treatment of solvent by an alumina adsorption process removes binding ligands and significantly improves recycle solvent performance. Both laboratory work defining a full-scale alumina adsorption process and the use of the process to clean HM process first cycle solvent is discussed

  14. Restoring solvent for nuclear separation processes

    International Nuclear Information System (INIS)

    Reif, D.J.

    1987-01-01

    Solvent extraction separation processes are used to recover usable nuclear materials from spent fuels. These processes involve the use of an extractant/diluent (solvent) for separation of the reusable actinides from unwanted fission products. The most widely used processes employ tributyl phosphate as an extractant diluted with a normal-paraffin hydrocarbon. During use, the solvent is altered due to hydrolysis and radiolysis, forming materials that influence product losses, product decontamination, and separation efficiencies. In most processes, the solvent is recycled after cleaning. Solvent cleaning generally involves scrubbing with a sodium carbonate solution. Studies at the Savannah River Laboratory have shown that carbonate washing, although removing residual solvent activity, does not remove more solvent-soluble binding ligands (formed by solvent degradation), which hold fission products in the solvent. Treatment of the solvent with a solid adsorbent after carbonate washing removes binding ligands and significantly improves recycled solvent performance. Laboratory work to establish the advantage of adsorbent cleaning and the development of a full-scale adsorption process is described. The application of this process for cleaning the first cycle solvent of a Savannah River Plant production process is discussed

  15. Magnetic field-dependent of binding energy in GaN/InGaN/GaN spherical QDQW nanoparticles

    International Nuclear Information System (INIS)

    El Ghazi, Haddou; Jorio, Anouar; Zorkani, Izeddine

    2013-01-01

    Simultaneous study of magnetic field and impurity's position effects on the ground-state shallow-donor binding energy in GaN|InGaN|GaN (core|well|shell) spherical quantum dot–quantum well (SQDQW) as a function of the ratio of the inner and the outer radius is reported. The calculations are investigated within the framework of the effective-mass approximation and an infinite deep potential describing the quantum confinement effect. A Ritz variational approach is used taking into account of the electron-impurity correlation and the magnetic field effect in the trial wave-function. It appears that the binding energy depends strongly on the external magnetic field, the impurity's position and the structure radius. It has been found that: (i) the magnetic field effect is more marked in large layer than in thin layer and (ii) it is more pronounced in the spherical layer center than in its extremities

  16. The molecular basis of FHA domain:phosphopeptide binding specificity and implications for phospho-dependent signaling mechanisms.

    Science.gov (United States)

    Durocher, D; Taylor, I A; Sarbassova, D; Haire, L F; Westcott, S L; Jackson, S P; Smerdon, S J; Yaffe, M B

    2000-11-01

    Forkhead-associated (FHA) domains are a class of ubiquitous signaling modules that appear to function through interactions with phosphorylated target molecules. We have used oriented peptide library screening to determine the optimal phosphopeptide binding motifs recognized by several FHA domains, including those within a number of DNA damage checkpoint kinases, and determined the X-ray structure of Rad53p-FHA1, in complex with a phospho-threonine peptide, at 1.6 A resolution. The structure reveals a striking similarity to the MH2 domains of Smad tumor suppressor proteins and reveals a mode of peptide binding that differs from SH2, 14-3-3, or PTB domain complexes. These results have important implications for DNA damage signaling and CHK2-dependent tumor suppression, and they indicate that FHA domains play important and unsuspected roles in S/T kinase signaling mechanisms in prokaryotes and eukaryotes.

  17. Dynamic regulation of GDP binding to G proteins revealed by magnetic field-dependent NMR relaxation analyses.

    Science.gov (United States)

    Toyama, Yuki; Kano, Hanaho; Mase, Yoko; Yokogawa, Mariko; Osawa, Masanori; Shimada, Ichio

    2017-02-22

    Heterotrimeric guanine-nucleotide-binding proteins (G proteins) serve as molecular switches in signalling pathways, by coupling the activation of cell surface receptors to intracellular responses. Mutations in the G protein α-subunit (Gα) that accelerate guanosine diphosphate (GDP) dissociation cause hyperactivation of the downstream effector proteins, leading to oncogenesis. However, the structural mechanism of the accelerated GDP dissociation has remained unclear. Here, we use magnetic field-dependent nuclear magnetic resonance relaxation analyses to investigate the structural and dynamic properties of GDP bound Gα on a microsecond timescale. We show that Gα rapidly exchanges between a ground-state conformation, which tightly binds to GDP and an excited conformation with reduced GDP affinity. The oncogenic D150N mutation accelerates GDP dissociation by shifting the equilibrium towards the excited conformation.

  18. Molecular Binding Contributes to Concentration Dependent Acrolein Deposition in Rat Upper Airways: CFD and Molecular Dynamics Analyses

    Directory of Open Access Journals (Sweden)

    Jinxiang Xi

    2018-03-01

    Full Text Available Existing in vivo experiments show significantly decreased acrolein uptake in rats with increasing inhaled acrolein concentrations. Considering that high-polarity chemicals are prone to bond with each other, it is hypothesized that molecular binding between acrolein and water will contribute to the experimentally observed deposition decrease by decreasing the effective diffusivity. The objective of this study is to quantify the probability of molecular binding for acrolein, as well as its effects on acrolein deposition, using multiscale simulations. An image-based rat airway geometry was used to predict the transport and deposition of acrolein using the chemical species model. The low Reynolds number turbulence model was used to simulate the airflows. Molecular dynamic (MD simulations were used to study the molecular binding of acrolein in different media and at different acrolein concentrations. MD results show that significant molecular binding can happen between acrolein and water molecules in human and rat airways. With 72 acrolein embedded in 800 water molecules, about 48% of acrolein compounds contain one hydrogen bond and 10% contain two hydrogen bonds, which agreed favorably with previous MD results. The percentage of hydrogen-bonded acrolein compounds is higher at higher acrolein concentrations or in a medium with higher polarity. Computational dosimetry results show that the size increase caused by the molecular binding reduces the effective diffusivity of acrolein and lowers the chemical deposition onto the airway surfaces. This result is consistent with the experimentally observed deposition decrease at higher concentrations. However, this size increase can only explain part of the concentration-dependent variation of the acrolein uptake and acts as a concurrent mechanism with the uptake-limiting tissue ration rate. Intermolecular interactions and associated variation in diffusivity should be considered in future dosimetry modeling of

  19. Molecular Binding Contributes to Concentration Dependent Acrolein Deposition in Rat Upper Airways: CFD and Molecular Dynamics Analyses.

    Science.gov (United States)

    Xi, Jinxiang; Hu, Qin; Zhao, Linlin; Si, Xiuhua April

    2018-03-27

    Existing in vivo experiments show significantly decreased acrolein uptake in rats with increasing inhaled acrolein concentrations. Considering that high-polarity chemicals are prone to bond with each other, it is hypothesized that molecular binding between acrolein and water will contribute to the experimentally observed deposition decrease by decreasing the effective diffusivity. The objective of this study is to quantify the probability of molecular binding for acrolein, as well as its effects on acrolein deposition, using multiscale simulations. An image-based rat airway geometry was used to predict the transport and deposition of acrolein using the chemical species model. The low Reynolds number turbulence model was used to simulate the airflows. Molecular dynamic (MD) simulations were used to study the molecular binding of acrolein in different media and at different acrolein concentrations. MD results show that significant molecular binding can happen between acrolein and water molecules in human and rat airways. With 72 acrolein embedded in 800 water molecules, about 48% of acrolein compounds contain one hydrogen bond and 10% contain two hydrogen bonds, which agreed favorably with previous MD results. The percentage of hydrogen-bonded acrolein compounds is higher at higher acrolein concentrations or in a medium with higher polarity. Computational dosimetry results show that the size increase caused by the molecular binding reduces the effective diffusivity of acrolein and lowers the chemical deposition onto the airway surfaces. This result is consistent with the experimentally observed deposition decrease at higher concentrations. However, this size increase can only explain part of the concentration-dependent variation of the acrolein uptake and acts as a concurrent mechanism with the uptake-limiting tissue ration rate. Intermolecular interactions and associated variation in diffusivity should be considered in future dosimetry modeling of high

  20. Revealing kinetics and state-dependent binding properties of IKur-targeting drugs that maximize atrial fibrillation selectivity

    Science.gov (United States)

    Ellinwood, Nicholas; Dobrev, Dobromir; Morotti, Stefano; Grandi, Eleonora

    2017-09-01

    The KV1.5 potassium channel, which underlies the ultra-rapid delayed-rectifier current (IKur) and is predominantly expressed in atria vs. ventricles, has emerged as a promising target to treat atrial fibrillation (AF). However, while numerous KV1.5-selective compounds have been screened, characterized, and tested in various animal models of AF, evidence of antiarrhythmic efficacy in humans is still lacking. Moreover, current guidelines for pre-clinical assessment of candidate drugs heavily rely on steady-state concentration-response curves or IC50 values, which can overlook adverse cardiotoxic effects. We sought to investigate the effects of kinetics and state-dependent binding of IKur-targeting drugs on atrial electrophysiology in silico and reveal the ideal properties of IKur blockers that maximize anti-AF efficacy and minimize pro-arrhythmic risk. To this aim, we developed a new Markov model of IKur that describes KV1.5 gating based on experimental voltage-clamp data in atrial myocytes from patient right-atrial samples in normal sinus rhythm. We extended the IKur formulation to account for state-specificity and kinetics of KV1.5-drug interactions and incorporated it into our human atrial cell model. We simulated 1- and 3-Hz pacing protocols in drug-free conditions and with a [drug] equal to the IC50 value. The effects of binding and unbinding kinetics were determined by examining permutations of the forward (kon) and reverse (koff) binding rates to the closed, open, and inactivated states of the KV1.5 channel. We identified a subset of ideal drugs exhibiting anti-AF electrophysiological parameter changes at fast pacing rates (effective refractory period prolongation), while having little effect on normal sinus rhythm (limited action potential prolongation). Our results highlight that accurately accounting for channel interactions with drugs, including kinetics and state-dependent binding, is critical for developing safer and more effective pharmacological anti

  1. Carbohydrate-dependent binding of langerin to SodC, a cell wall glycoprotein of Mycobacterium leprae.

    Science.gov (United States)

    Kim, Hee Jin; Brennan, Patrick J; Heaslip, Darragh; Udey, Mark C; Modlin, Robert L; Belisle, John T

    2015-02-01

    Langerhans cells participate in the immune response in leprosy by their ability to activate T cells that recognize the pathogen, Mycobacterium leprae, in a langerin-dependent manner. We hypothesized that langerin, the distinguishing C-type lectin of Langerhans cells, would recognize the highly mannosylated structures in pathogenic Mycobacterium spp. The coding region for the extracellular and neck domain of human langerin was cloned and expressed to produce a recombinant active trimeric form of human langerin (r-langerin). Binding assays performed in microtiter plates, by two-dimensional (2D) Western blotting, and by surface plasmon resonance demonstrated that r-langerin possessed carbohydrate-dependent affinity to glycoproteins in the cell wall of M. leprae. This lectin, however, yielded less binding to mannose-capped lipoarabinomannan (ManLAM) and even lower levels of binding to phosphatidylinositol mannosides. However, the superoxide dismutase C (SodC) protein of the M. leprae cell wall was identified as a langerin-reactive ligand. Tandem mass spectrometry verified the glycosylation of a recombinant form of M. leprae SodC (rSodC) produced in Mycobacterium smegmatis. Analysis of r-langerin affinity by surface plasmon resonance revealed a carbohydrate-dependent affinity of rSodC (equilibrium dissociation constant [KD] = 0.862 μM) that was 20-fold greater than for M. leprae ManLAM (KD = 18.69 μM). These data strongly suggest that a subset of the presumptively mannosylated M. leprae glycoproteins act as ligands for langerin and may facilitate the interaction of M. leprae with Langerhans cells. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  2. PICK1 regulates the trafficking of ASIC1a and acidotoxicity in a BAR domain lipid binding-dependent manner

    Directory of Open Access Journals (Sweden)

    Jin Wenying

    2010-12-01

    Full Text Available Abstract Background Acid-sensing ion channel 1a (ASIC1a is the major ASIC subunit determining acid-activated currents in brain neurons. Recent studies show that ASIC1a play critical roles in acid-induced cell toxicity. While these studies raise the importance of ASIC1a in diseases, mechanisms for ASIC1a trafficking are not well understood. Interestingly, ASIC1a interacts with PICK1 (protein interacting with C-kinase 1, an intracellular protein that regulates trafficking of several membrane proteins. However, whether PICK1 regulates ASIC1a surface expression remains unknown. Results Here, we show that PICK1 overexpression increases ASIC1a surface level. A BAR domain mutant of PICK1, which impairs its lipid binding capability, blocks this increase. Lipid binding of PICK1 is also required for PICK1-induced clustering of ASIC1a. Consistent with the effect on ASIC1a surface levels, PICK1 increases ASIC1a-mediated acidotoxicity and this effect requires both the PDZ and BAR domains of PICK1. Conclusions Taken together, our results indicate that PICK1 regulates trafficking and function of ASIC1a in a lipid binding-dependent manner.

  3. Binding and distribution studies in the SENCAR mouse of compounds demonstrating a route-dependent tumorigenic effect

    International Nuclear Information System (INIS)

    Carlson, G.P.; Fossa, A.A.; Morse, M.A.; Weaver, P.M.

    1986-01-01

    Previous investigators have determined that benzo(a)pyrene [B(a)P] was much more effective in causing skin papillomas if applied topically than when administered orally in the initiation-promotion assay in SENCAR mouse. Conversely, urethane and acrylamide caused a higher percentage of mice to develop papillomas and induced more tumors per mouse when given orally. In an attempt to understand the reason for this discrepancy in route dependency, 3 H-benzo(a)pyrene, 14 C-acrylamide were administered as single doses orally or topically to male SENCAR mice. Distribution in skin, stomach, liver, and lung was determined for time periods up to 48 hr. The binding of these compounds to DNA, RNA, and protein in these tissues was determined 6 and 48 hr after administration. For all three compounds, high concentrations were found in the skin following topical application, but very little material reached this target organ following oral administration. In contrast, the internal organs generally contained more material after oral administration. The binding of label compounds to DNA, RNA, and protein generally reflected the distribution data, thus more compound was bound in the stomach, liver, and lung after oral administration compared to topical application, whereas the opposite was true for the skin. This finding was particularly evident for B(a)P. The results suggest that differences in distribution to the skin and binding to macromolecules following oral or topical administration cannot explain the greater tumorigenicity of urethane and acrylamide after oral administration in the SENCAR mouse

  4. EXPRESSION OF CALCIUM-BINDING PROTEINS IN THE NEUROTROPHIN-3-DEPENDENT SUBPOPULATION OF RAT EMBRYONIC DORSAL-ROOT GANGLION-CELLS IN CULTURE

    NARCIS (Netherlands)

    COPRAY, JCVM; MANTINGHOTTER, IJ; BROUWER, N

    1994-01-01

    In this study we have examined the calcium-binding protein expression in rat embryonic (E16) dorsal root ganglia (DRG) neurons in vitro in the presence of neurotrophin-3 (NT-3). A comparison was made with the expression of calcium-binding proteins in DRG subpopulations that depended in vitro on

  5. Extrastriatal binding of [123I]FP-CIT in the thalamus and pons: gender and age dependencies assessed in a European multicentre database of healthy controls

    International Nuclear Information System (INIS)

    Koch, Walter; Unterrainer, Marcus; Xiong, Guoming; Bartenstein, Peter; Diemling, Markus; Varrone, Andrea; Dickson, John C.; Tossici-Bolt, Livia; Sera, Terez; Asenbaum, Susanne; Booij, Jan; Kapucu, Ozlem L.; Kluge, Andreas; Ziebell, Morten; Darcourt, Jacques; Nobili, Flavio; Pagani, Marco; Hesse, Swen; Borght, Thierry Vander; Laere, Koen van; Tatsch, Klaus; La Fougere, Christian

    2014-01-01

    Apart from binding to the dopamine transporter (DAT), [ 123 I]FP-CIT shows moderate affinity for the serotonin transporter (SERT), allowing imaging of both monoamine transporters in a single imaging session in different brain areas. The aim of this study was to systematically evaluate extrastriatal binding (predominantly due to SERT) and its age and gender dependencies in a large cohort of healthy controls. SPECT data from 103 healthy controls with well-defined criteria of normality acquired at 13 different imaging centres were analysed for extrastriatal binding using volumes of interest analysis for the thalamus and the pons. Data were examined for gender and age effects as well as for potential influence of striatal DAT radiotracer binding. Thalamic binding was significantly higher than pons binding. Partial correlations showed an influence of putaminal DAT binding on measured binding in the thalamus but not on the pons. Data showed high interindividual variation in extrastriatal binding. Significant gender effects with 31 % higher binding in women than in men were observed in the thalamus, but not in the pons. An age dependency with a decline per decade (±standard error) of 8.2 ± 1.3 % for the thalamus and 6.8 ± 2.9 % for the pons was shown. The potential to evaluate extrastriatal predominant SERT binding in addition to the striatal DAT in a single imaging session was shown using a large database of [ 123 I]FP-CIT scans in healthy controls. For both the thalamus and the pons, an age-related decline in radiotracer binding was observed. Gender effects were demonstrated for binding in the thalamus only. As a potential clinical application, the data could be used as a reference to estimate SERT occupancy in addition to nigrostriatal integrity when using [ 123 I]FP-CIT for DAT imaging in patients treated with selective serotonin reuptake inhibitors. (orig.)

  6. Extrastriatal binding of [{sup 123}I]FP-CIT in the thalamus and pons: gender and age dependencies assessed in a European multicentre database of healthy controls

    Energy Technology Data Exchange (ETDEWEB)

    Koch, Walter; Unterrainer, Marcus; Xiong, Guoming; Bartenstein, Peter [University of Munich, Department of Nuclear Medicine, Munich (Germany); Diemling, Markus [Hermes Medical Solutions, Stockholm (Sweden); Varrone, Andrea [Karolinska University Hospital, Karolinska Institutet, Department of Clinical Neuroscience, Centre for Psychiatry Research, Stockholm (Sweden); Dickson, John C. [UCLH NHS Foundation Trust and University College, Institute of Nuclear Medicine, London (United Kingdom); Tossici-Bolt, Livia [University Hospitals Southampton NHS Trust, Department of Medical Physics, Southampton (United Kingdom); Sera, Terez [University of Szeged, Department of Nuclear Medicine and Euromedic Szeged, Szeged (Hungary); Asenbaum, Susanne [Medical University of Vienna, Department of Neurology, Vienna (Austria); Booij, Jan [University of Amsterdam, Department of Nuclear Medicine, Academic Medical Centre, Amsterdam (Netherlands); Kapucu, Ozlem L. [Gazi University, Department of Nuclear Medicine, Faculty of Medicine, Ankara (Turkey); Kluge, Andreas [ABX-CRO, Dresden (Germany); Ziebell, Morten [Rigshospitalet and University of Copenhagen, Neurobiology Research Unit, Copenhagen (Denmark); Darcourt, Jacques [University of Nice-Sophia Antipolis, Nuclear Medicine Department, Centre Antoine Lacassagne, Nice (France); Nobili, Flavio [University of Genoa, Clinical Neurology Unit, Department of Neuroscience (DINOGMI), Genoa (Italy); Pagani, Marco [CNR, Institute of Cognitive Sciences and Technologies, Rome (Italy); Karolinska Hospital, Department of Nuclear Medicine, Stockholm (Sweden); Hesse, Swen [University of Leipzig, Department of Nuclear Medicine, Leipzig (Germany); Leipzig University Medical Centre, Molecular Neuroimaging IFB Adiposity Diseases, Leipzig (Germany); Borght, Thierry Vander [Universite Catholique de Louvain, Nuclear Medicine Division, CHU Dinant Godinne, Yvoir (Belgium); Laere, Koen van [University Hospital and K.U. Leuven, Nuclear Medicine, Leuven (Belgium); Tatsch, Klaus [Staedtisches Klinikum Karlsruhe, Department of Nuclear Medicine, Karlsruhe (Germany); La Fougere, Christian [University of Munich, Department of Nuclear Medicine, Munich (Germany); University of Tuebingen, Department of Nuclear Medicine, Tuebingen (Germany)

    2014-10-15

    Apart from binding to the dopamine transporter (DAT), [{sup 123}I]FP-CIT shows moderate affinity for the serotonin transporter (SERT), allowing imaging of both monoamine transporters in a single imaging session in different brain areas. The aim of this study was to systematically evaluate extrastriatal binding (predominantly due to SERT) and its age and gender dependencies in a large cohort of healthy controls. SPECT data from 103 healthy controls with well-defined criteria of normality acquired at 13 different imaging centres were analysed for extrastriatal binding using volumes of interest analysis for the thalamus and the pons. Data were examined for gender and age effects as well as for potential influence of striatal DAT radiotracer binding. Thalamic binding was significantly higher than pons binding. Partial correlations showed an influence of putaminal DAT binding on measured binding in the thalamus but not on the pons. Data showed high interindividual variation in extrastriatal binding. Significant gender effects with 31 % higher binding in women than in men were observed in the thalamus, but not in the pons. An age dependency with a decline per decade (±standard error) of 8.2 ± 1.3 % for the thalamus and 6.8 ± 2.9 % for the pons was shown. The potential to evaluate extrastriatal predominant SERT binding in addition to the striatal DAT in a single imaging session was shown using a large database of [{sup 123}I]FP-CIT scans in healthy controls. For both the thalamus and the pons, an age-related decline in radiotracer binding was observed. Gender effects were demonstrated for binding in the thalamus only. As a potential clinical application, the data could be used as a reference to estimate SERT occupancy in addition to nigrostriatal integrity when using [{sup 123}I]FP-CIT for DAT imaging in patients treated with selective serotonin reuptake inhibitors. (orig.)

  7. Dishevelled binds the Discs large 'Hook' domain to activate GukHolder-dependent spindle positioning in Drosophila.

    Directory of Open Access Journals (Sweden)

    Joshua D Garcia

    Full Text Available Communication between cortical cell polarity cues and the mitotic spindle ensures proper orientation of cell divisions within complex tissues. Defects in mitotic spindle positioning have been linked to various developmental disorders and have recently emerged as a potential contributor to tumorigenesis. Despite the importance of this process to human health, the molecular mechanisms that regulate spindle orientation are not fully understood. Moreover, it remains unclear how diverse cortical polarity complexes might cooperate to influence spindle positioning. We and others have demonstrated spindle orientation roles for Dishevelled (Dsh, a key regulator of planar cell polarity, and Discs large (Dlg, a conserved apico-basal cell polarity regulator, effects which were previously thought to operate within distinct molecular pathways. Here we identify a novel direct interaction between the Dsh-PDZ domain and the alternatively spliced "I3-insert" of the Dlg-Hook domain, thus establishing a potential convergent Dsh/Dlg pathway. Furthermore, we identify a Dlg sequence motif necessary for the Dsh interaction that shares homology to the site of Dsh binding in the Frizzled receptor. Expression of Dsh enhanced Dlg-mediated spindle positioning similar to deletion of the Hook domain. This Dsh-mediated activation was dependent on the Dlg-binding partner, GukHolder (GukH. These results suggest that Dsh binding may regulate core interdomain conformational dynamics previously described for Dlg. Together, our results identify Dlg as an effector of Dsh signaling and demonstrate a Dsh-mediated mechanism for the activation of Dlg/GukH-dependent spindle positioning. Cooperation between these two evolutionarily-conserved cell polarity pathways could have important implications to both the development and maintenance of tissue homeostasis in animals.

  8. Time-dependent density-functional tight-binding method with the third-order expansion of electron density.

    Science.gov (United States)

    Nishimoto, Yoshio

    2015-09-07

    We develop a formalism for the calculation of excitation energies and excited state gradients for the self-consistent-charge density-functional tight-binding method with the third-order contributions of a Taylor series of the density functional theory energy with respect to the fluctuation of electron density (time-dependent density-functional tight-binding (TD-DFTB3)). The formulation of the excitation energy is based on the existing time-dependent density functional theory and the older TD-DFTB2 formulae. The analytical gradient is computed by solving Z-vector equations, and it requires one to calculate the third-order derivative of the total energy with respect to density matrix elements due to the inclusion of the third-order contributions. The comparison of adiabatic excitation energies for selected small and medium-size molecules using the TD-DFTB2 and TD-DFTB3 methods shows that the inclusion of the third-order contributions does not affect excitation energies significantly. A different set of parameters, which are optimized for DFTB3, slightly improves the prediction of adiabatic excitation energies statistically. The application of TD-DFTB for the prediction of absorption and fluorescence energies of cresyl violet demonstrates that TD-DFTB3 reproduced the experimental fluorescence energy quite well.

  9. Developmental pathways from child maltreatment to adolescent marijuana dependence: Examining moderation by FK506 binding protein 5 gene (FKBP5).

    Science.gov (United States)

    Handley, Elizabeth D; Rogosch, Fred A; Cicchetti, Dante

    2015-11-01

    The current study examined the prospective association between child maltreatment and the development of substance use disorder in adolescence with the aim of investigating pathways underlying this relation, as well as genetic moderation of these developmental mechanisms. Specifically, we tested whether youth who experienced maltreatment prior to age 8 were at risk for the development of marijuana dependence in adolescence by way of a childhood externalizing pathway and a childhood internalizing pathway. Moreover, we tested whether variation in FK506 binding protein 5 gene (FKBP5) CATT haplotype moderated these pathways. The participants were 326 children (n =179 maltreated; n = 147 nonmaltreated) assessed across two waves of data collection (childhood: ages 7-9 and adolescence: ages 15-18). Results indicated that higher levels of child externalizing symptoms significantly mediated the effect of child maltreatment on adolescent marijuana dependence symptoms for individuals with one or two copies of the FKBP5 CATT haplotype only. We did not find support for an internalizing pathway from child maltreatment to adolescent marijuana dependence, nor did we find evidence of moderation of the internalizing pathway by FKBP5 haplotype variation. Findings extend previous research by demonstrating that whether a maltreated child will traverse an externalizing pathway toward substance use disorder in adolescence is dependent on FKBP5 genetic variation.

  10. Distinct roles of beta1 metal ion-dependent adhesion site (MIDAS), adjacent to MIDAS (ADMIDAS), and ligand-associated metal-binding site (LIMBS) cation-binding sites in ligand recognition by integrin alpha2beta1.

    Science.gov (United States)

    Valdramidou, Dimitra; Humphries, Martin J; Mould, A Paul

    2008-11-21

    Integrin-ligand interactions are regulated in a complex manner by divalent cations, and previous studies have identified ligand-competent, stimulatory, and inhibitory cation-binding sites. In collagen-binding integrins, such as alpha2beta1, ligand recognition takes place exclusively at the alpha subunit I domain. However, activation of the alphaI domain depends on its interaction with a structurally similar domain in the beta subunit known as the I-like or betaI domain. The top face of the betaI domain contains three cation-binding sites: the metal-ion dependent adhesion site (MIDAS), the ADMIDAS (adjacent to MIDAS), and LIMBS (ligand-associated metal-binding site). The role of these sites in controlling ligand binding to the alphaI domain has yet to be elucidated. Mutation of the MIDAS or LIMBS completely blocked collagen binding to alpha2beta1; in contrast mutation of the ADMIDAS reduced ligand recognition but this effect could be overcome by the activating monoclonal antibody TS2/16. Hence, the MIDAS and LIMBS appear to be essential for the interaction between alphaI and betaI, whereas occupancy of the ADMIDAS has an allosteric effect on the conformation of betaI. An activating mutation in the alpha2 I domain partially restored ligand binding to the MIDAS and LIMBS mutants. Analysis of the effects of Ca(2+), Mg(2+), and Mn(2+) on ligand binding to these mutants showed that the MIDAS is a ligand-competent site through which Mn(2+) stimulates ligand binding, whereas the LIMBS is a stimulatory Ca(2+)-binding site, occupancy of which increases the affinity of Mg(2+) for the MIDAS.

  11. Protection against Mitochondrial and Metal Toxicity Depends on Functional Lipid Binding Sites in ATP13A2

    Directory of Open Access Journals (Sweden)

    Shaun Martin

    2016-01-01

    Full Text Available The late endo-/lysosomal P-type ATPase ATP13A2 (PARK9 is implicated in Parkinson’s disease (PD and Kufor-Rakeb syndrome, early-onset atypical Parkinsonism. ATP13A2 interacts at the N-terminus with the signaling lipids phosphatidic acid (PA and phosphatidylinositol (3,5 bisphosphate (PI(3,5P2, which modulate ATP13A2 activity under cellular stress conditions. Here, we analyzed stable human SHSY5Y cell lines overexpressing wild-type (WT or ATP13A2 mutants in which three N-terminal lipid binding sites (LBS1–3 were mutated. We explored the regulatory role of LBS1–3 in the cellular protection by ATP13A2 against mitochondrial stress induced by rotenone and found that the LBS2-3 mutants displayed an abrogated protective effect. Moreover, in contrast to WT, the LBS2 and LBS3 mutants responded poorly to pharmacological inhibition of, respectively, PI(3,5P2 and PA formation. We further demonstrate that PA and PI(3,5P2 are also required for the ATP13A2-mediated protection against the toxic metals Mn2+, Zn2+, and Fe3+, suggesting a general lipid-dependent activation mechanism of ATP13A2 in various PD-related stress conditions. Our results indicate that the ATP13A2-mediated protection requires binding of PI(3,5P2 to LBS2 and PA to LBS3. Thus, targeting the N-terminal lipid binding sites of ATP13A2 might offer a therapeutic approach to reduce cellular toxicity of various PD insults including mitochondrial stress.

  12. Vitamin D-dependent rat renal calcium-binding protein: development of a radioimmunoassay, tissue distribution, and immunologic identification

    International Nuclear Information System (INIS)

    Sonnenberg, J.; Pansini, A.R.; Christakos, S.

    1984-01-01

    A sensitive double antibody RIA has been developed for the 28,000 mol wt rat renal vitamin D-dependent calcium-binding protein. Using this assay, concentrations of calcium-binding protein (CaBP) as low as 30 ng can be measured. The assay is precise (intraassay variability, 5.0%) and reproductible (interassay variability, 8.2%). Measurements of renal CaBP by RIA showed a good correlation with measurements of CaBP by the chelex resin assay and by polyacrylamide gel analysis by densitometric tracing using a purified CaBP marker. The concentration of CaBP in the vitamin D-replete rat kidney is 7.3 +/- 1.0 (mean +/- SEM) micrograms/mg protein. In vitamin D-deficient rats the level of renal CaBP is 2.6 +/- 0.3 micrograms/mg protein. Tissue distribution of immunoreactive rat renal CaBP showed the highest concentration of CaBP in the rat cerebellum (38.3 +/- 5.1 micrograms/mg protein). Lower concentrations of immunoreactive CaBP were detected in several other rat tissues. No immunoreactive CaBP was detected in rat or human serum. In necropsy human kidney and cerebellum, high levels of immunoreactive CaBP were also detected (1.5 +/- 0.1 and 27.3 +/- 2.1 micrograms/mg protein, respectively). When extracts of rat kidney and brain and human cerebellum and kidney were assayed at several dilutions, immunodisplacement curves parallel to that of pure renal CaBP were observed, indicating immunochemical similarity. Fractionation of extracts of rat cerebellum, human kidney, and human cerebellum on Sephadex G-100 revealed immunoreactivity and calcium-binding activity in the 28,000 mol wt region similar to rat kidney

  13. Maximizing in vivo target clearance by design of pH-dependent target binding antibodies with altered affinity to FcRn.

    Science.gov (United States)

    Yang, Danlin; Giragossian, Craig; Castellano, Steven; Lasaro, Marcio; Xiao, Haiguang; Saraf, Himanshu; Hess Kenny, Cynthia; Rybina, Irina; Huang, Zhong-Fu; Ahlberg, Jennifer; Bigwarfe, Tammy; Myzithras, Maria; Waltz, Erica; Roberts, Simon; Kroe-Barrett, Rachel; Singh, Sanjaya

    2017-10-01

    Antibodies with pH-dependent binding to both target antigens and neonatal Fc receptor (FcRn) provide an alternative tool to conventional neutralizing antibodies, particularly for therapies where reduction in antigen level is challenging due to high target burden. However, the requirements for optimal binding kinetic framework and extent of pH dependence for these antibodies to maximize target clearance from circulation are not well understood. We have identified a series of naturally-occurring high affinity antibodies with pH-dependent target binding properties. By in vivo studies in cynomolgus monkeys, we show that pH-dependent binding to the target alone is not sufficient for effective target removal from circulation, but requires Fc mutations that increase antibody binding to FcRn. Affinity-enhanced pH-dependent FcRn binding that is double-digit nM at pH 7.4 and single-digit nM at pH 6 achieved maximal target reduction when combined with similar target binding affinities in reverse pH directions. Sustained target clearance below the baseline level was achieved 3 weeks after single-dose administration at 1.5 mg/kg. Using the experimentally derived mechanistic model, we demonstrate the essential kinetic interplay between target turnover and antibody pH-dependent binding during the FcRn recycling, and identify the key components for achieving maximal target clearance. These results bridge the demand for improved patient dosing convenience with the "know-how" of therapeutic modality by design.

  14. pH-dependent kinetics of copper ions binding to amyloid-β peptide.

    Science.gov (United States)

    Bin, Yannan; Chen, Shu; Xiang, Juan

    2013-02-01

    Interactions of amyloid-β peptide (Aβ) with Cu(2+) are known to be pH-dependent and believed to play a crucial role in the neurotoxicity of Alzheimer's disease (AD). Some research has revealed that injured brains with lowered pH have higher risks of developing AD. However, reported experiments were performed under neutral or mildly acidic conditions, and no reports about the affinity of Aβ-Cu(2+) below pH6.0. In this study, surface plasmon resonance (SPR) sensor with immobilized Aβ was used to investigate the formation of Aβ-Cu(2+) complexes under acidic pH conditions. Dissociation constants were calculated and shown to be pH-dependent, ranging from 3.5×10(-8)M to 8.7×10(-3)M in the pH range from 7.0 to 4.0. The physiological significance of K(d) was preliminarily investigated by monitoring the generation of OH() in aerobic solutions containing Aβ-Cu(2+) and Cu(2+). The results imply that acidic conditions could aggravate the oxidative stress in the presence of Cu(2+), and the weak affinities of Aβ-Cu(2+) under mildly acidic pH of 5.0-6.0 could further enhance the oxidative damage. However, the oxidative stress effect of Aβ is negligible due to the suppressed formation of Aβ-Cu(2+) below pH5.0. This work is useful for the in-depth understanding of the role of Aβ-Cu(2+) in AD neuropathology. Crown Copyright © 2012. Published by Elsevier Inc. All rights reserved.

  15. The Potato Nucleotide-binding Leucine-rich Repeat (NLR) Immune Receptor Rx1 Is a Pathogen-dependent DNA-deforming Protein.

    Science.gov (United States)

    Fenyk, Stepan; Townsend, Philip D; Dixon, Christopher H; Spies, Gerhard B; de San Eustaquio Campillo, Alba; Slootweg, Erik J; Westerhof, Lotte B; Gawehns, Fleur K K; Knight, Marc R; Sharples, Gary J; Goverse, Aska; Pålsson, Lars-Olof; Takken, Frank L W; Cann, Martin J

    2015-10-09

    Plant nucleotide-binding leucine-rich repeat (NLR) proteins enable cells to respond to pathogen attack. Several NLRs act in the nucleus; however, conserved nuclear targets that support their role in immunity are unknown. Previously, we noted a structural homology between the nucleotide-binding domain of NLRs and DNA replication origin-binding Cdc6/Orc1 proteins. Here we show that the NB-ARC (nucleotide-binding, Apaf-1, R-proteins, and CED-4) domain of the Rx1 NLR of potato binds nucleic acids. Rx1 induces ATP-dependent bending and melting of DNA in vitro, dependent upon a functional P-loop. In situ full-length Rx1 binds nuclear DNA following activation by its cognate pathogen-derived effector protein, the coat protein of potato virus X. In line with its obligatory nucleocytoplasmic distribution, DNA binding was only observed when Rx1 was allowed to freely translocate between both compartments and was activated in the cytoplasm. Immune activation induced by an unrelated NLR-effector pair did not trigger an Rx1-DNA interaction. DNA binding is therefore not merely a consequence of immune activation. These data establish a role for DNA distortion in Rx1 immune signaling and define DNA as a molecular target of an activated NLR. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  16. The Potato Nucleotide-binding Leucine-rich Repeat (NLR) Immune Receptor Rx1 Is a Pathogen-dependent DNA-deforming Protein*

    Science.gov (United States)

    Fenyk, Stepan; Townsend, Philip D.; Dixon, Christopher H.; Spies, Gerhard B.; de San Eustaquio Campillo, Alba; Slootweg, Erik J.; Westerhof, Lotte B.; Gawehns, Fleur K. K.; Knight, Marc R.; Sharples, Gary J.; Goverse, Aska; Pålsson, Lars-Olof; Takken, Frank L. W.; Cann, Martin J.

    2015-01-01

    Plant nucleotide-binding leucine-rich repeat (NLR) proteins enable cells to respond to pathogen attack. Several NLRs act in the nucleus; however, conserved nuclear targets that support their role in immunity are unknown. Previously, we noted a structural homology between the nucleotide-binding domain of NLRs and DNA replication origin-binding Cdc6/Orc1 proteins. Here we show that the NB-ARC (nucleotide-binding, Apaf-1, R-proteins, and CED-4) domain of the Rx1 NLR of potato binds nucleic acids. Rx1 induces ATP-dependent bending and melting of DNA in vitro, dependent upon a functional P-loop. In situ full-length Rx1 binds nuclear DNA following activation by its cognate pathogen-derived effector protein, the coat protein of potato virus X. In line with its obligatory nucleocytoplasmic distribution, DNA binding was only observed when Rx1 was allowed to freely translocate between both compartments and was activated in the cytoplasm. Immune activation induced by an unrelated NLR-effector pair did not trigger an Rx1-DNA interaction. DNA binding is therefore not merely a consequence of immune activation. These data establish a role for DNA distortion in Rx1 immune signaling and define DNA as a molecular target of an activated NLR. PMID:26306038

  17. Magnetic field-dependent of binding energy in GaN/InGaN/GaN spherical QDQW nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    El Ghazi, Haddou, E-mail: hadghazi@gmail.com [Solid State Laboratory, Faculty of science, Dhar EL Mehrez, BP 1796 Fes-Atlas (Morocco); Special mathematics, CPGE Kénitra, Chakib Arsalane Street (Morocco); Jorio, Anouar; Zorkani, Izeddine [Solid State Laboratory, Faculty of science, Dhar EL Mehrez, BP 1796 Fes-Atlas (Morocco)

    2013-10-15

    Simultaneous study of magnetic field and impurity's position effects on the ground-state shallow-donor binding energy in GaN|InGaN|GaN (core|well|shell) spherical quantum dot–quantum well (SQDQW) as a function of the ratio of the inner and the outer radius is reported. The calculations are investigated within the framework of the effective-mass approximation and an infinite deep potential describing the quantum confinement effect. A Ritz variational approach is used taking into account of the electron-impurity correlation and the magnetic field effect in the trial wave-function. It appears that the binding energy depends strongly on the external magnetic field, the impurity's position and the structure radius. It has been found that: (i) the magnetic field effect is more marked in large layer than in thin layer and (ii) it is more pronounced in the spherical layer center than in its extremities.

  18. Cuz1/Ynl155w, a Zinc-dependent Ubiquitin-binding Protein, Protects Cells from Metalloid-induced Proteotoxicity*

    Science.gov (United States)

    Hanna, John; Waterman, David; Isasa, Marta; Elsasser, Suzanne; Shi, Yuan; Gygi, Steven; Finley, Daniel

    2014-01-01

    Protein misfolding is a universal threat to cells. The ubiquitin-proteasome system mediates a cellular stress response capable of eliminating misfolded proteins. Here we identify Cuz1/Ynl155w as a component of the ubiquitin system, capable of interacting with both the proteasome and Cdc48. Cuz1/Ynl155w is regulated by the transcription factor Rpn4, and is required for cells to survive exposure to the trivalent metalloids arsenic and antimony. A related protein, Yor052c, shows similar phenotypes, suggesting a multicomponent stress response pathway. Cuz1/Ynl155w functions as a zinc-dependent ubiquitin-binding protein. Thus, Cuz1/Ynl155w is proposed to protect cells from metalloid-induced proteotoxicity by delivering ubiquitinated substrates to Cdc48 and the proteasome for destruction. PMID:24297164

  19. Ebselen and congeners inhibit NADPH oxidase 2-dependent superoxide generation by interrupting the binding of regulatory subunits.

    Science.gov (United States)

    Smith, Susan M E; Min, Jaeki; Ganesh, Thota; Diebold, Becky; Kawahara, Tsukasa; Zhu, Yerun; McCoy, James; Sun, Aiming; Snyder, James P; Fu, Haian; Du, Yuhong; Lewis, Iestyn; Lambeth, J David

    2012-06-22

    NADPH oxidases (Nox) are a primary source of reactive oxygen species (ROS), which function in normal physiology and, when overproduced, in pathophysiology. Recent studies using mice deficient in Nox2 identify this isoform as a novel target against Nox2-implicated inflammatory diseases. Nox2 activation depends on the binding of the proline-rich domain of its heterodimeric partner p22phox to p47phox. A high-throughput screen that monitored this interaction via fluorescence polarization identified ebselen and several of its analogs as inhibitors. Medicinal chemistry was performed to explore structure-activity relationships and to optimize potency. Ebselen and analogs potently inhibited Nox1 and Nox2 activity but were less effective against other isoforms. Ebselen also blocked translocation of p47phox to neutrophil membranes. Thus, ebselen and its analogs represent a class of compounds that inhibit ROS generation by interrupting the assembly of Nox2-activating regulatory subunits. Copyright © 2012 Elsevier Ltd. All rights reserved.

  20. Organic solvent topical report

    Energy Technology Data Exchange (ETDEWEB)

    COWLEY, W.L.

    1999-05-13

    This report provides the basis for closing the organic solvent safety issue. Sufficient information is presented to conclude that risk posed by an organic solvent fire is within risk evaluation guidelines. This report updates information contained in Analysis of Consequences of Postulated Solvent Fires in Hanford Site Waste Tanks. WHC-SD-WM-CN-032. Rev. 0A (Cowley et al. 1996). However, this document will not replace Cowley et al (1996) as the primary reference for the Basis for Interim Operation (BIO) until the recently submitted BIO amendment (Hanson 1999) is approved by the US Department of Energy. This conclusion depends on the use of controls for preventing vehicle fuel fires and for limiting the use of flame cutting in areas where hot metal can fall on the waste surface.The required controls are given in the Tank Waste Remediation System Technical Safety Requirements (Noorani 1997b). This is a significant change from the conclusions presented in Revision 0 of this report. Revision 0 of this calcnote concluded that some organic solvent fire scenarios exceeded risk evaluation guidelines, even with controls imposed.

  1. Organic solvent topical report

    International Nuclear Information System (INIS)

    COWLEY, W.L.

    1999-01-01

    This report provides the basis for closing the organic solvent safety issue. Sufficient information is presented to conclude that risk posed by an organic solvent fire is within risk evaluation guidelines. This report updates information contained in Analysis of Consequences of Postulated Solvent Fires in Hanford Site Waste Tanks. WHC-SD-WM-CN-032. Rev. 0A (Cowley et al. 1996). However, this document will not replace Cowley et al (1996) as the primary reference for the Basis for Interim Operation (BIO) until the recently submitted BIO amendment (Hanson 1999) is approved by the US Department of Energy. This conclusion depends on the use of controls for preventing vehicle fuel fires and for limiting the use of flame cutting in areas where hot metal can fall on the waste surface.The required controls are given in the Tank Waste Remediation System Technical Safety Requirements (Noorani 1997b). This is a significant change from the conclusions presented in Revision 0 of this report. Revision 0 of this calcnote concluded that some organic solvent fire scenarios exceeded risk evaluation guidelines, even with controls imposed

  2. Thermodynamics of cooperative binding of FAD to human NQO1: Implications to understanding cofactor-dependent function and stability of the flavoproteome.

    Science.gov (United States)

    Clavería-Gimeno, Rafael; Velazquez-Campoy, Adrian; Pey, Angel Luis

    2017-12-15

    The stability of human flavoproteins strongly depends on flavin levels, although the structural and energetic basis of this relationship is poorly understood. Here, we report an in-depth analysis on the thermodynamics of FAD binding to one of the most representative examples of such relationship, NAD(P)H:quinone oxidoreductase 1 (NQO1). NQO1 is a dimeric enzyme that tightly binds FAD, which triggers large structural changes upon binding. A common cancer-associated polymorphism (P187S) severely compromises FAD binding. We show that FAD binding is described well by a thermodynamic model explicitly incorporating binding cooperativity when applied to different sets of calorimetric analyses and NQO1 variants, thus providing insight on the effects in vitro and in cells of cancer-associated P187S, its suppressor mutation H80R and the role of NQO1 C-terminal domain to modulate binding cooperativity and energetics. Furthermore, we show that FAD binding to NQO1 is very sensitive to physiologically relevant environmental conditions, such as the presence of phosphate buffer and salts. Overall, our results contribute to understanding at the molecular level the link between NQO1 stability and fluctuations of FAD levels intracellularly, and supports the notion that FAD binding energetics and cooperativity are fundamentally linked with the dynamic nature of apo-NQO1 conformational ensemble. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Hydrogenic-Donor Impurity Binding Energy Dependence of the Electric Field in GaAs/AlxGa1−xAs Quantum Rings

    Directory of Open Access Journals (Sweden)

    Guangxin Wang

    2013-01-01

    Full Text Available Using a variational method with two-parameter trial wave function and the effective mass approximation, the binding energy of a donor impurity in GaAs/AlxGa1−xAs cylindrical quantum ring (QR subjected to an external field is calculated. It is shown that the donor impurity binding energy is highly dependent on the QR structure parameters (radial thickness and height, impurity position, and external electric field. The binding energy increases inchmeal as the QR parameters (radial thickness and height decrease until a maximum value for a central impurity and then begins to drop quickly. The applied electric field can significantly modify the spread of electronic wave function in the QR and shift electronic wave function from the donor position and then leads to binding energy changes. In addition, results for the binding energies of a hydrogenic donor impurity as functions of the impurity position and applied electric field are also presented.

  4. Phospho-dependent binding of the clathrin AP2 adaptor complex to GABAA receptors regulates the efficacy of inhibitory synaptic transmission

    OpenAIRE

    Kittler, Josef T.; Chen, Guojun; Honing, Stephan; Bogdanov, Yury; McAinsh, Kristina; Arancibia-Carcamo, I. Lorena; Jovanovic, Jasmina N.; Pangalos, Menelas N.; Haucke, Volker; Yan, Zhen; Moss, Stephen J.

    2005-01-01

    The efficacy of synaptic inhibition depends on the number of γ-aminobutyric acid type A receptors (GABAARs) expressed on the cell surface of neurons. The clathrin adaptor protein 2 (AP2) complex is a critical regulator of GABAAR endocytosis and, hence, surface receptor number. Here, we identify a previously uncharacterized atypical AP2 binding motif conserved within the intracellular domains of all GABAAR β subunit isoforms. This AP2 binding motif (KTHLRRRSSQLK in the β3 subunit) incorporates...

  5. Response and binding elements for ligand-dependent positive transcription factors integrate positive and negative regulation of gene expression

    International Nuclear Information System (INIS)

    Rosenfeld, M.G.; Glass, C.K.; Adler, S.; Crenshaw, E.B. III; He, X.; Lira, S.A.; Elsholtz, H.P.; Mangalam, H.J.; Holloway, J.M.; Nelson, C.; Albert, V.R.; Ingraham, H.A.

    1988-01-01

    Accurate, regulated initiation of mRNA transcription by RNA polymerase II is dependent on the actions of a variety of positive and negative trans-acting factors that bind cis-acting promoter and enhancer elements. These transcription factors may exert their actions in a tissue-specific manner or function under control of plasma membrane or intracellular ligand-dependent receptors. A major goal in the authors' laboratory has been to identify the molecular mechanisms responsible for the serial activation of hormone-encoding genes in the pituitary during development and the positive and negative regulation of their transcription. The anterior pituitary gland contains phenotypically distinct cell types, each of which expresses unique trophic hormones: adrenocorticotropic hormone, thyroid-stimulating hormone, prolactin, growth hormone, and follicle-stimulating hormone/luteinizing hormone. The structurally related prolactin and growth hormone genes are expressed in lactotrophs and somatotrophs, respectively, with their expression virtually limited to the pituitary gland. The reported transient coexpression of these two structurally related neuroendocrine genes raises the possibility that the prolactin and growth hormone genes are developmentally controlled by a common factor(s)

  6. Phospho-dependent binding of the clathrin AP2 adaptor complex to GABAA receptors regulates the efficacy of inhibitory synaptic transmission.

    Science.gov (United States)

    Kittler, Josef T; Chen, Guojun; Honing, Stephan; Bogdanov, Yury; McAinsh, Kristina; Arancibia-Carcamo, I Lorena; Jovanovic, Jasmina N; Pangalos, Menelas N; Haucke, Volker; Yan, Zhen; Moss, Stephen J

    2005-10-11

    The efficacy of synaptic inhibition depends on the number of gamma-aminobutyric acid type A receptors (GABA(A)Rs) expressed on the cell surface of neurons. The clathrin adaptor protein 2 (AP2) complex is a critical regulator of GABA(A)R endocytosis and, hence, surface receptor number. Here, we identify a previously uncharacterized atypical AP2 binding motif conserved within the intracellular domains of all GABA(A)R beta subunit isoforms. This AP2 binding motif (KTHLRRRSSQLK in the beta3 subunit) incorporates the major sites of serine phosphorylation within receptor beta subunits, and phosphorylation within this site inhibits AP2 binding. Furthermore, by using surface plasmon resonance, we establish that a peptide (pepbeta3) corresponding to the AP2 binding motif in the GABA(A)R beta3 subunit binds to AP2 with high affinity only when dephosphorylated. Moreover, the pepbeta3 peptide, but not its phosphorylated equivalent (pepbeta3-phos), enhanced the amplitude of miniature inhibitory synaptic current and whole cell GABA(A)R current. These effects of pepbeta3 on GABA(A)R current were occluded by inhibitors of dynamin-dependent endocytosis supporting an action of pepbeta3 on GABA(A)R endocytosis. Therefore phospho-dependent regulation of AP2 binding to GABA(A)Rs provides a mechanism to specify receptor cell surface number and the efficacy of inhibitory synaptic transmission.

  7. Whole blood-oxygen binding properties of four cold-temperate marine fishes: blood affinity is independent of pH-dependent binding, routine swimming performance, and environmental hypoxia

    DEFF Research Database (Denmark)

    Herbert, Neill A; Skov, Peter V; Wells, Rufus M G

    2006-01-01

    performance and the predicted low O(2) response of each species. The ecotype of the four marine species was also unrelated to pH-dependent binding because no difference in the Bohr effect was apparent ( Phi varied insignificantly from -0.90 to -1.06), and differences in the magnitude of the cooperative...

  8. Acyl-CoA-binding protein (ACBP) localizes to the endoplasmic reticulum and Golgi in a ligand-dependent manner in mammalian cells

    DEFF Research Database (Denmark)

    Hansen, Jesper S; Færgeman, Nils J; Kragelund, Birthe B

    2008-01-01

    showed that ACBP targeted to the ER (endoplasmic reticulum) and Golgi in a ligand-binding-dependent manner. A variant Y28F/K32A-FACI-50, which is unable to bind acyl-CoA, did no longer show association with the ER and became segregated from the Golgi, as analysed by intensity correlation calculations....... Depletion of fatty acids from cells by addition of FAFBSA (fatty-acid-free BSA) significantly decreased FACI-50 association with the Golgi, whereas fatty acid overloading increased Golgi association, strongly supporting that ACBP associates with the Golgi in a ligand-dependent manner. FRAP (fluorescence...... recovery after photobleaching) showed that the fatty-acid-induced targeting of FACI-50 to the Golgi resulted in a 5-fold reduction in FACI-50 mobility. We suggest that ACBP is targeted to the ER and Golgi in a ligand-binding-dependent manner in living cells and propose that ACBP may be involved...

  9. COMPUTER-AIDED SOLVENT DESIGN FOR POLLUTION PREVENTION: PARIS II

    Science.gov (United States)

    Solvent substitution is an attractive way of elijminating the use of regulated solvents because it usually does not require major chanages in existing processes, equipment or operations. Successful solvent substitution is dependent on finding solvents that are as effective or be...

  10. Dependence of the enthalpies of formation of glycylglycinate complexes of nickel(II) on the composition of a mixed water-dimethylsulfoxide solvent

    Science.gov (United States)

    Naumov, V. V.; Kovaleva, Yu. A.; Isaeva, V. A.; Usacheva, T. R.; Sharnin, V. A.

    2014-06-01

    The heat effects of the complexation reactions of nickel(II) with a glycylglycinate ion in a water-dimethylsulfoxide solvent in a range of compositions of 0.00-0.60 molar parts of dimethylsulfoxide (DMSO) (an ionic strength of 0.1 was maintained using sodium perchlorate) were determined by means of calorimetry at 298.15 K. It is established that the exothermicity of complexation reactions rises by the first two steps and falls upon the addition of a third glycylglycinate anion with an increase in the concentration of DMSO. It is shown that the formation of mono- and bis-glycylglycinate complexes of nickel(II) in a water-DMSO solvent is determined mostly by the enthalpic contribution. It is concluded that the formation of tris-ligand complexes is more associated with the entropic contribution.

  11. Cesium Concentration in MCU Solvent

    International Nuclear Information System (INIS)

    Walker, D

    2006-01-01

    During Modular Caustic-Side Solvent Extraction (CSSX) Unit (MCU) operations, Cs-137 concentrations in product streams will vary depending on the location in the process and on the recent process conditions. Calculations of cesium concentrations under a variety of operating conditions reveal the following: (1) Under nominal operations with salt solution feed containing 1.1 Ci Cs-137 per gallon, the maximum Cs-137 concentration in the process will occur in the strip effluent (SE) and equal 15-16.5 Ci/gal. (2) Under these conditions, the majority of the solvent will contain 0.005 to 0.01 Ci/gal, with a limited portion of the solvent in the contactor stages containing ∼4 Ci/gal. (3) When operating conditions yield product near 0.1 Ci Cs-137/gal in the decontaminated salt solution (DSS), the SE cesium concentration will be the same or lower than in nominal operations, but majority of the stripped solvent will increase to ∼2-3 Ci/gal. (4) Deviations in strip and waste stream flow rates cause the largest variations in cesium content: (a) If strip flow rates deviate by -30% of nominal, the SE will contain ∼23 Ci/gal, although the cesium content of the solvent will increase to only 0.03 Ci/gal; (b) If strip flow rate deviates by -77% (i.e., 23% of nominal), the SE will contain 54 Ci/gal and solvent will contain 1.65 Ci/gal. At this point, the product DSS will just reach the limit of 0.1 Ci/gal, causing the DSS gamma monitors to alarm; and (c) Moderate (+10 to +30%) deviations in waste flow rate cause approximately proportional increases in the SE and solvent cesium concentrations. Recovery from a process failure due to poor cesium stripping can achieve any low cesium concentration required. Passing the solvent back through the contactors while recycling DSS product will produce a ∼70% reduction during one pass through the contactors (assuming the stripping D value is no worse than 0.36). If the solvent is returned to the solvent hold tank (containing additional

  12. Probing Temperature- and pH-Dependent Binding between Quantum Dots and Bovine Serum Albumin by Fluorescence Correlation Spectroscopy

    Directory of Open Access Journals (Sweden)

    Zonghua Wang

    2017-04-01

    Full Text Available Luminescent quantum dots (QDs with unique optical properties have potential applications in bio-imaging. The interaction between QDs and bio-molecules is important to the biological effect of QDs in vivo. In this paper, we have employed fluorescence correlation spectroscopy (FCS to probe the temperature- and pH-dependent interactions between CdSe QDs with carboxyl (QDs-COOH and bovine serum albumin (BSA in buffer solutions. The results have shown that microscopic dissociation constant K′D is in the range of (1.5 ± 0.2 × 10−5 to (8.6 ± 0.1 × 10−7 M, the Hill coefficient n is from 0.4 to 2.3, and the protein corona thickness is from 3.0 to 9.4 nm. Variable-temperature measurements have shown both negative values of ∆H and ∆S for BSA adsorption on QDs-COOH, while pH has a profound effect on the adsorption. Additional, FCS measurement QDs-COOH and proteins in whole mice serum and plasma samples has also been conducted. Finally, simulation results have shown four favored QD binding sites in BSA.

  13. Inhibition of herpes simplex virus infection by lactoferrin is dependent on interference with the virus binding to glycosaminoglycans

    International Nuclear Information System (INIS)

    Marchetti, Magda; Trybala, Edward; Superti, Fabiana; Johansson, Maria; Bergstroem, Tomas

    2004-01-01

    Previous reports have indicated that lactoferrin inhibits herpes simplex virus (HSV) infection during the very early phases of the viral replicative cycle. In the present work we investigated the mechanism of the antiviral activity of lactoferrin in mutant glycosaminoglycan (GAG)-deficient cells. Bovine lactoferrin (BLf) was a strong inhibitor of HSV-1 infection in cells expressing either heparan sulfate (HS) or chondroitin sulfate (CS) or both, but was ineffective or less efficient in GAG-deficient cells or in cells treated with GAG-degrading enzymes. In contrast to wild-type HSV-1, virus mutants devoid of glycoprotein C (gC) were significantly less inhibited by lactoferrin in GAG-expressing cells, indicating that lactoferrin interfered with the binding of viral gC to cell surface HS and/or CS. Finally, we demonstrated that lactoferrin bound directly to both HS and CS isolated from surfaces of the studied cells, as well as to commercial preparations of GAG chains. The results support the hypothesis that the inhibition of HSV-1 infectivity by lactoferrin is dependent on its interaction with cell surface GAG chains of HS and CS

  14. Reactivity of solvent alcohol on degradation of CFC113

    International Nuclear Information System (INIS)

    Nakagawa, Seiko

    2003-01-01

    1,1,2-Trichloro-trifluoroethane (CFC113) was dissolved in alkaline 1-butanol, 2-butanol, iso-butyl alcohol, and phenyl ethyl alcohol and irradiated with 60 Co gamma rays after purged with pure nitrogen gas. In all these solvents, the concentration of CFC113 and hydroxide ion decreased and that of chloride ion increased with a dose observed in 2-propanol solution. The reaction efficiency increases in order of 1-butanol< iso-butyl alcohol< phenyl ethyl alcohol<2-butanol<2-propanol. The solvent effect will depend on the binding energy of the αC-H of the alcohol molecule and electron affinity and dipole moment of the ketones or aldehydes produced from the alcohols

  15. pH-dependence of the specific binding of Cu(II) and Zn(II) ions to the amyloid-β peptide

    International Nuclear Information System (INIS)

    Ghalebani, Leila; Wahlström, Anna; Danielsson, Jens; Wärmländer, Sebastian K.T.S.; Gräslund, Astrid

    2012-01-01

    Highlights: ► Cu(II) and Zn(II) display pH-dependent binding to the Aβ(1–40) peptide. ► At pH 7.4 both metal ions display residue-specific binding to the Aβ peptide. ► At pH 5.5 the binding specificity is lost for Zn(II). ► Differential Cu(II) and Zn(II) binding may help explain metal-induced AD toxicity. -- Abstract: Metal ions like Cu(II) and Zn(II) are accumulated in Alzheimer’s disease amyloid plaques. The amyloid-β (Aβ) peptide involved in the disease interacts with these metal ions at neutral pH via ligands provided by the N-terminal histidines and the N-terminus. The present study uses high-resolution NMR spectroscopy to monitor the residue-specific interactions of Cu(II) and Zn(II) with 15 N- and 13 C, 15 N-labeled Aβ(1–40) peptides at varying pH levels. At pH 7.4 both ions bind to the specific ligands, competing with one another. At pH 5.5 Cu(II) retains its specific histidine ligands, while Zn(II) seems to lack residue-specific interactions. The low pH mimics acidosis which is linked to inflammatory processes in vivo. The results suggest that the cell toxic effects of redox active Cu(II) binding to Aβ may be reversed by the protective activity of non-redox active Zn(II) binding to the same major binding site under non-acidic conditions. Under acidic conditions, the protective effect of Zn(II) may be decreased or changed, since Zn(II) is less able to compete with Cu(II) for the specific binding site on the Aβ peptide under these conditions.

  16. Variation in one residue associated with the metal ion-dependent adhesion site regulates αIIbβ3 integrin ligand binding affinity.

    Directory of Open Access Journals (Sweden)

    Joel Raborn

    Full Text Available The Asp of the RGD motif of the ligand coordinates with the β I domain metal ion dependent adhesion site (MIDAS divalent cation, emphasizing the importance of the MIDAS in ligand binding. There appears to be two distinct groups of integrins that differ in their ligand binding affinity and adhesion ability. These differences may be due to a specific residue associated with the MIDAS, particularly the β3 residue Ala(252 and corresponding Ala in the β1 integrin compared to the analogous Asp residue in the β2 and β7 integrins. Interestingly, mutations in the adjacent to MIDAS (ADMIDAS of integrins α4β7 and αLβ2 increased the binding and adhesion abilities compared to the wild-type, while the same mutations in the α2β1, α5β1, αVβ3, and αIIbβ3 integrins demonstrated decreased ligand binding and adhesion. We introduced a mutation in the αIIbβ3 to convert this MIDAS associated Ala(252 to Asp. By combination of this mutant with mutations of one or two ADMIDAS residues, we studied the effects of this residue on ligand binding and adhesion. Then, we performed molecular dynamics simulations on the wild-type and mutant αIIbβ3 integrin β I domains, and investigated the dynamics of metal ion binding sites in different integrin-RGD complexes. We found that the tendency of calculated binding free energies was in excellent agreement with the experimental results, suggesting that the variation in this MIDAS associated residue accounts for the differences in ligand binding and adhesion among different integrins, and it accounts for the conflicting results of ADMIDAS mutations within different integrins. This study sheds more light on the role of the MIDAS associated residue pertaining to ligand binding and adhesion and suggests that this residue may play a pivotal role in integrin-mediated cell rolling and firm adhesion.

  17. Unexpected solvent effects on the UV/Vis absorption spectra of o-cresol in toluene and benzene: in contrast with non-aromatic solvents.

    Science.gov (United States)

    Zheng, Dong; Yuan, Xiang-Ai; Ma, Haibo; Li, Xiaoxiong; Wang, Xizhang; Liu, Ziteng; Ma, Jing

    2018-03-01

    Cresol is a prototype molecule in understanding intermolecular interactions in material and biological systems, because it offers different binding sites with various solvents and protonation states under different pH values. It is found that the UV/Vis absorption spectra of o -cresol in aromatic solvents (benzene, toluene) are characterized by a sharp peak, unlike the broad double-peaks in 11 non-aromatic solvents. Both molecular dynamics simulations and electronic structure calculations revealed the formation of intermolecular π-complexation between o -cresol and aromatic solvents. The thermal movements of solvent and solute molecules render the conformations of o -cresol changing between trans and cis isomers. The π-interaction makes the cis configuration a dominant isomer, hence leading to the single keen-edged UV/Vis absorption peak at approximately 283 nm. The free conformation changes between trans and cis in aqueous solution rationalize the broader absorption peaks in the range of 260-280 nm. The pH dependence of the UV/Vis absorption spectra in aqueous solutions is also rationalized by different protonation states of o -cresol. The explicit solvent model with long-ranged interactions is vital to describe the effects of π-complexation and electrostatic interaction on the UV/Vis absorption spectra of o -cresol in toluene and alkaline aqueous (pH > 10.3) solutions, respectively.

  18. Host factor I, Hfq, binds to Escherichia coli ompA mRNA in a growth rate-dependent fashion and regulates its stability

    DEFF Research Database (Denmark)

    Vytvytska, O; Jakobsen, J S; Balcunaite, G

    1998-01-01

    RNA. In hfq mutant cells with a deficient Hfq gene product, the RNA-binding activity is missing, and analysis of the ompA mRNA showed that the growth-rate dependence of degradation is lost. Furthermore, the half-life of the ompA mRNA is prolonged in the mutant cells, irrespective of growth rate. Hfq has...

  19. Predicting the activity coefficients of free-solvent for concentrated globular protein solutions using independently determined physical parameters.

    Directory of Open Access Journals (Sweden)

    Devin W McBride

    Full Text Available The activity coefficient is largely considered an empirical parameter that was traditionally introduced to correct the non-ideality observed in thermodynamic systems such as osmotic pressure. Here, the activity coefficient of free-solvent is related to physically realistic parameters and a mathematical expression is developed to directly predict the activity coefficients of free-solvent, for aqueous protein solutions up to near-saturation concentrations. The model is based on the free-solvent model, which has previously been shown to provide excellent prediction of the osmotic pressure of concentrated and crowded globular proteins in aqueous solutions up to near-saturation concentrations. Thus, this model uses only the independently determined, physically realizable quantities: mole fraction, solvent accessible surface area, and ion binding, in its prediction. Predictions are presented for the activity coefficients of free-solvent for near-saturated protein solutions containing either bovine serum albumin or hemoglobin. As a verification step, the predictability of the model for the activity coefficient of sucrose solutions was evaluated. The predicted activity coefficients of free-solvent are compared to the calculated activity coefficients of free-solvent based on osmotic pressure data. It is observed that the predicted activity coefficients are increasingly dependent on the solute-solvent parameters as the protein concentration increases to near-saturation concentrations.

  20. A tandem sequence motif acts as a distance-dependent enhancer in a set of genes involved in translation by binding the proteins NonO and SFPQ

    Directory of Open Access Journals (Sweden)

    Roepcke Stefan

    2011-12-01

    Full Text Available Abstract Background Bioinformatic analyses of expression control sequences in promoters of co-expressed or functionally related genes enable the discovery of common regulatory sequence motifs that might be involved in co-ordinated gene expression. By studying promoter sequences of the human ribosomal protein genes we recently identified a novel highly specific Localized Tandem Sequence Motif (LTSM. In this work we sought to identify additional genes and LTSM-binding proteins to elucidate potential regulatory mechanisms. Results Genome-wide analyses allowed finding a considerable number of additional LTSM-positive genes, the products of which are involved in translation, among them, translation initiation and elongation factors, and 5S rRNA. Electromobility shift assays then showed specific signals demonstrating the binding of protein complexes to LTSM in ribosomal protein gene promoters. Pull-down assays with LTSM-containing oligonucleotides and subsequent mass spectrometric analysis identified the related multifunctional nucleotide binding proteins NonO and SFPQ in the binding complex. Functional characterization then revealed that LTSM enhances the transcriptional activity of the promoters in dependency of the distance from the transcription start site. Conclusions Our data demonstrate the power of bioinformatic analyses for the identification of biologically relevant sequence motifs. LTSM and the here found LTSM-binding proteins NonO and SFPQ were discovered through a synergistic combination of bioinformatic and biochemical methods and are regulators of the expression of a set of genes of the translational apparatus in a distance-dependent manner.

  1. HTLV-1 Tax Oncoprotein Subverts the Cellular DNA Damage Response via Binding to DNA-dependent Protein Kinase*S⃞

    Science.gov (United States)

    Durkin, Sarah S.; Guo, Xin; Fryrear, Kimberly A.; Mihaylova, Valia T.; Gupta, Saurabh K.; Belgnaoui, S. Mehdi; Haoudi, Abdelali; Kupfer, Gary M.; Semmes, O. John

    2008-01-01

    Human T-cell leukemia virus type-1 is the causative agent for adult T-cell leukemia. Previous research has established that the viral oncoprotein Tax mediates the transformation process by impairing cell cycle control and cellular response to DNA damage. We showed previously that Tax sequesters huChk2 within chromatin and impairs the response to ionizing radiation. Here we demonstrate that DNA-dependent protein kinase (DNA-PK) is a member of the Tax·Chk2 nuclear complex. The catalytic subunit, DNA-PKcs, and the regulatory subunit, Ku70, were present. Tax-containing nuclear extracts showed increased DNA-PK activity, and specific inhibition of DNA-PK prevented Tax-induced activation of Chk2 kinase activity. Expression of Tax induced foci formation and phosphorylation of H2AX. However, Tax-induced constitutive signaling of the DNA-PK pathway impaired cellular response to new damage, as reflected in suppression of ionizing radiation-induced DNA-PK phosphorylation and γH2AX stabilization. Tax co-localized with phospho-DNA-PK into nuclear speckles and a nuclear excluded Tax mutant sequestered endogenous phospho-DNA-PK into the cytoplasm, suggesting that Tax interaction with DNA-PK is an initiating event. We also describe a novel interaction between DNA-PK and Chk2 that requires Tax. We propose that Tax binds to and stabilizes a protein complex with DNA-PK and Chk2, resulting in a saturation of DNA-PK-mediated damage repair response. PMID:18957425

  2. Two solvent and temperature dependent copper(II) compounds formed by a flexible ligand: syntheses, structures and SC-SC transformation.

    Science.gov (United States)

    Sun, Haixia; Xie, Wenli; Lv, Shenghong; Xu, Yan; Wu, Yong; Zhou, Yaoming; Ma, Zhenmao; Fang, Min; Liu, Hong-Ke

    2012-07-07

    A nonporous neutral framework [CuCl(2)(m-bttmb)(2)](n) (1) was changed into a porous ionic {[Cu(m-bttmb)(2)(H(2)O)Cl]Cl(CH(3)CN)(0.5)(H(2)O)(2.75)}(n) (2) by simply increasing the amount of CH(3)CN in the mixed solvent (CH(3)CN and H(2)O) or temperature in the reactions of CuCl(2)·2H(2)O with 1,3-bis(triazol-1-ylmethyl)-2,4,6-trimethylbenzene (m-bttmb). 1 undergoes transformation into 2 when treated with CH(3)CN. Both 1 and 2 have 2D 4-connected (4,4) network architectures but in different packing arrangements. These compounds have been characterized by single-crystal X-ray diffraction analysis, elemental analysis, IR spectra and thermogravimetric analysis. This work may provide a way to control the formation of neutral or ionic frameworks, as well as porosities by adjusting the polarity and components of the solvents.

  3. Solvent sorting in (mixed solvent electrolyte) systems: Time-resolved ...

    Indian Academy of Sciences (India)

    lar solvents as an effective single component dipo- lar liquid that is characterized ... and time (t) dependent solvation energy of mobile dipo- lar solute with density ..... Even though this way for modification of C is purely ad- hoc, the observation ...

  4. Linker length dependent binding of a focal adhesion kinase derived peptide to the Src SH3-SH2 domains.

    Science.gov (United States)

    Lindfors, Hanna E; Venkata, Bharat Somireddy; Drijfhout, Jan W; Ubbink, Marcellus

    2011-02-18

    The interaction between a peptide encompassing the SH3 and SH2 binding motifs of focal adhesion kinase (FAK) and the Src SH3-SH2 domains has been investigated with NMR spectroscopy and calorimetry. The binding to both motifs is anti-cooperative. Reduction of the long linker connecting the motifs does not lead to cooperativity. Short linkers that do not allow simultaneous intramolecular binding of the peptide to both motifs cause peptide-mediated dimerisation, even with a linker of only three amino acids. The role of the SH3 binding motif is discussed in view of the independent nature of the SH interactions. Copyright © 2011 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  5. Conserved epitope on several human vitamin K-dependent proteins: location of the antigenic site and influence of metal ions on antibody binding

    International Nuclear Information System (INIS)

    Church, W.R.; Messier, T.; Howard, P.R.; Amiral, J.; Meyer, D.; Mann, K.G.

    1988-01-01

    A murine monoclonal antibody (designated H-11) produced by injecting mice with purified human protein C was found to bind several human vitamin K-dependent proteins. Using a solid-phase competitive radioimmunoassay with antibody immobilized onto microtiter plates, binding of 125 I-labeled protein C to the antibody was inhibited by increasing amounts of protein C, prothrombin, and Factors X and VII over a concentration range of 1 x 10 -8 to 1 x 10 -6 M. Chemical treatment of prothrombin with a variety of agents did not destroy the antigenic site recognized by the antibody as measured by immunoblotting of prothrombin or prothrombin derivative immobilized onto nitrocellulose. Immunoblotting of purified vitamin K-dependent polypeptides with the monoclonal antibody following sodium dodecyl sulfate-polyacrylamide gel electrophoresis and electrophoretic transfer to nitrocellulose indicated that the antigenic site was found on the light chains of protein C and Factor X. The exact location of the antigenic determinant for antibody H-11 was established using synthetic peptides. Comparison of protein sequences of bovine and human vitamin K-dependent proteins suggests that the sequence Phe-Leu-Glu-Glu-Xaa-Arg/Lys is required for antibody binding. Increasing concentrations of Ca 2+ , Mg 2+ , or Mn 2+ partially inhibited binding of 125 I-protein C to the antibody in a solid-phase assay system with half-maximal binding observed at divalent metal ion concentrations of 2, 4, and 0.6 mM, respectively. The antigenic site thus recognized by monoclonal antibody H-11 is located at the amino-terminal region in the highly conserved γ-carboxyglutamic acid-containing domains of several, but not all, vitamin K-dependent proteins

  6. FcγRII-binding Centyrins mediate agonism and antibody-dependent cellular phagocytosis when fused to an anti-OX40 antibody.

    Science.gov (United States)

    Zhang, Di; Whitaker, Brian; Derebe, Mehabaw G; Chiu, Mark L

    2018-04-01

    Immunostimulatory antibodies against the tumor necrosis factor receptors (TNFR) are emerging as promising cancer immunotherapies. The agonism activity of such antibodies depends on crosslinking to Fc gamma RIIB receptor (FcγRIIB) to enable the antibody multimerization that drives TNFR activation. Previously, Fc engineering was used to enhance the binding of such antibodies to Fcγ receptors. Here, we report the identification of Centyrins as alternative scaffold proteins with binding affinities to homologous FcγRIIB and FcγRIIA, but not to other types of Fcγ receptors. One Centyrin, S29, was engineered at distinct positions of an anti-OX40 SF2 antibody to generate bispecific and tetravalent molecules named as mAbtyrins. Regardless of the position of S29 on the SF2 antibody, SF2-S29 mAbtyrins could bind FcγRIIB and FcγRIIA specifically while maintaining binding to OX40 receptors. In a NFκB reporter assay, attachment of S29 Centyrin molecules at the C-termini, but not the N-termini, resulted in SF2 antibodies with increased agonism owing to FcγRIIB crosslinking. The mAbtyrins also showed agonism in T-cell activation assays with immobilized FcγRIIB and FcγRIIA, but this activity was confined to mAbtyrins with S29 specifically at the C-termini of antibody heavy chains. Furthermore, regardless of the position of the molecule, S29 Centyrin could equip an otherwise Fc-silent antibody with antibody-dependent cellular phagocytosis activity without affecting the antibody's intrinsic antibody-dependent cell-meditated cytotoxicity and complement-dependent cytotoxicity. In summary, the appropriate adoption FcγRII-binding Centyrins as functional modules represents a novel strategy to engineer therapeutic antibodies with improved functionalities.

  7. Identification of a phosphorylation-dependent nuclear localization motif in interferon regulatory factor 2 binding protein 2.

    Directory of Open Access Journals (Sweden)

    Allen C T Teng

    Full Text Available Interferon regulatory factor 2 binding protein 2 (IRF2BP2 is a muscle-enriched transcription factor required to activate vascular endothelial growth factor-A (VEGFA expression in muscle. IRF2BP2 is found in the nucleus of cardiac and skeletal muscle cells. During the process of skeletal muscle differentiation, some IRF2BP2 becomes relocated to the cytoplasm, although the functional significance of this relocation and the mechanisms that control nucleocytoplasmic localization of IRF2BP2 are not yet known.Here, by fusing IRF2BP2 to green fluorescent protein and testing a series of deletion and site-directed mutagenesis constructs, we mapped the nuclear localization signal (NLS to an evolutionarily conserved sequence (354ARKRKPSP(361 in IRF2BP2. This sequence corresponds to a classical nuclear localization motif bearing positively charged arginine and lysine residues. Substitution of arginine and lysine with negatively charged aspartic acid residues blocked nuclear localization. However, these residues were not sufficient because nuclear targeting of IRF2BP2 also required phosphorylation of serine 360 (S360. Many large-scale phosphopeptide proteomic studies had reported previously that serine 360 of IRF2BP2 is phosphorylated in numerous human cell types. Alanine substitution at this site abolished IRF2BP2 nuclear localization in C(2C(12 myoblasts and CV1 cells. In contrast, substituting serine 360 with aspartic acid forced nuclear retention and prevented cytoplasmic redistribution in differentiated C(2C(12 muscle cells. As for the effects of these mutations on VEGFA promoter activity, the S360A mutation interfered with VEGFA activation, as expected. Surprisingly, the S360D mutation also interfered with VEGFA activation, suggesting that this mutation, while enforcing nuclear entry, may disrupt an essential activation function of IRF2BP2.Nuclear localization of IRF2BP2 depends on phosphorylation near a conserved NLS. Changes in phosphorylation status

  8. The C-terminus of H-Ras as a target for the covalent binding of reactive compounds modulating Ras-dependent pathways.

    Directory of Open Access Journals (Sweden)

    Clara L Oeste

    2011-01-01

    Full Text Available Ras proteins are crucial players in differentiation and oncogenesis and constitute important drug targets. The localization and activity of Ras proteins are highly dependent on posttranslational modifications at their C-termini. In addition to an isoprenylated cysteine, H-Ras, but not other Ras proteins, possesses two cysteine residues (C181 and C184 in the C-terminal hypervariable domain that act as palmitoylation sites in cells. Cyclopentenone prostaglandins (cyPG are reactive lipidic mediators that covalently bind to H-Ras and activate H-Ras dependent pathways. Dienone cyPG, such as 15-deoxy-Δ(12,14-PGJ(2 (15d-PGJ(2 and Δ(12-PGJ(2 selectively bind to the H-Ras hypervariable domain. Here we show that these cyPG bind simultaneously C181 and C184 of H-Ras, thus potentially altering the conformational tendencies of the hypervariable domain. Based on these results, we have explored the capacity of several bifunctional cysteine reactive small molecules to bind to the hypervariable domain of H-Ras proteins. Interestingly, phenylarsine oxide (PAO, a widely used tyrosine phosphatase inhibitor, and dibromobimane, a cross-linking agent used for cysteine mapping, effectively bind H-Ras hypervariable domain. The interaction of PAO with H-Ras takes place in vitro and in cells and blocks modification of H-Ras by 15d-PGJ(2. Moreover, PAO treatment selectively alters H-Ras membrane partition and the pattern of H-Ras activation in cells, from the plasma membrane to endomembranes. These results identify H-Ras as a novel target for PAO. More importantly, these observations reveal that small molecules or reactive intermediates interacting with spatially vicinal cysteines induce intramolecular cross-linking of H-Ras C-terminus potentially contributing to the modulation of Ras-dependent pathways.

  9. Solvents and solvent effects in organic chemistry

    National Research Council Canada - National Science Library

    Reichardt, C; Welton, T

    2011-01-01

    .../guest complexation equilibria and reactions in biphasic solvent systems and neoteric solvents, respectively. More than 900 new references have been added, giving preference to review articles, and many older ones have been deleted. New references either replace older ones or are added to the end of the respective reference list of each chapter. Th...

  10. Dynamics of α-Hb chain binding to its chaperone AHSP depends on heme coordination and redox state.

    Science.gov (United States)

    Kiger, Laurent; Vasseur, Corinne; Domingues-Hamdi, Elisa; Truan, Gilles; Marden, Michael C; Baudin-Creuza, Véronique

    2014-01-01

    AHSP is an erythroid molecular chaperone of the α-hemoglobin chains (α-Hb). Upon AHSP binding, native ferric α-Hb undergoes an unprecedented structural rearrangement at the heme site giving rise to a 6th coordination bond with His(E7). Recombinant AHSP, WT α-Hb:AHSP and α-Hb(HE7Q):AHSP complexes were expressed in Escherichia coli. Thermal denaturation curves were measured by circular dichroism for the isolated α-Hb and bound to AHSP. Kinetics of ligand binding and redox reactions of α-Hb bound to AHSP as well as α-Hb release from the α-Hb:AHSP complex were measured by time-resolved absorption spectroscopy. AHSP binding to α-Hb is kinetically controlled to prevail over direct binding with β-chains and is also thermodynamically controlled by the α-Hb redox state and not the liganded state of the ferrous α-Hb. The dramatic instability of isolated ferric α-Hb is greatly decreased upon AHSP binding. Removing the bis-histidyl hexacoordination in α-HbH58(E7)Q:AHSP complex reduces the stabilizing effect of AHSP binding. Once the ferric α-Hb is bound to AHSP, the globin can be more easily reduced by several chemical and enzymatic systems compared to α-Hb within the Hb-tetramer. α-Hb reduction could trigger its release from AHSP toward its final Hb β-chain partner producing functional ferrous Hb-tetramers. This work indicates a preferred kinetic pathway for Hb-synthesis. The cellular redox balance in Hb-synthesis should be considered as important as the relative proportional synthesis of both Hb-subunits and their heme cofactor. The in vivo role of AHSP is discussed in the context of the molecular disorders observed in thalassemia. © 2013 Elsevier B.V. All rights reserved.

  11. Identification of an hexapeptide that binds to a surface pocket in cyclin A and inhibits the catalytic activity of the complex cyclin-dependent kinase 2-cyclin A.

    Science.gov (United States)

    Canela, Núria; Orzáez, Mar; Fucho, Raquel; Mateo, Francesca; Gutierrez, Ricardo; Pineda-Lucena, Antonio; Bachs, Oriol; Pérez-Payá, Enrique

    2006-11-24

    The protein-protein complexes formed between different cyclins and cyclin-dependent kinases (CDKs) are central to cell cycle regulation. These complexes represent interesting points of chemical intervention for the development of antineoplastic molecules. Here we describe the identification of an all d-amino acid hexapeptide, termed NBI1, that inhibits the kinase activity of the cyclin-dependent kinase 2 (cdk2)-cyclin A complex through selective binding to cyclin A. The mechanism of inhibition is non-competitive for ATP and non-competitive for protein substrates. In contrast to the existing CDKs peptide inhibitors, the hexapeptide NBI1 interferes with the formation of the cdk2-cyclin A complex. Furthermore, a cell-permeable derivative of NBI1 induces apoptosis and inhibits proliferation of tumor cell lines. Thus, the NBI1-binding site on cyclin A may represent a new target site for the selective inhibition of activity cdk2-cyclin A complex.

  12. Processivity and Subcellular Localization of Glycogen Synthase Depend on a Non-catalytic High Affinity Glycogen-binding Site*

    OpenAIRE

    Díaz, Adelaida; Martínez-Pons, Carlos; Fita, Ignacio; Ferrer, Juan C.; Guinovart, Joan J.

    2011-01-01

    Glycogen synthase, a central enzyme in glucose metabolism, catalyzes the successive addition of α-1,4-linked glucose residues to the non-reducing end of a growing glycogen molecule. A non-catalytic glycogen-binding site, identified by x-ray crystallography on the surface of the glycogen synthase from the archaeon Pyrococcus abyssi, has been found to be functionally conserved in the eukaryotic enzymes. The disruption of this binding site in both the archaeal and the human muscle glycogen synth...

  13. Phospholipid-binding protein EhC2A mediates calcium-dependent translocation of transcription factor URE3-BP to the plasma membrane of Entamoeba histolytica.

    Science.gov (United States)

    Moreno, Heriberto; Linford, Alicia S; Gilchrist, Carol A; Petri, William A

    2010-05-01

    The Entamoeba histolytica upstream regulatory element 3-binding protein (URE3-BP) is a transcription factor that binds DNA in a Ca(2+)-inhibitable manner. The protein is located in both the nucleus and the cytoplasm but has also been found to be enriched in the plasma membrane of amebic trophozoites. We investigated the reason for the unusual localization of URE3-BP at the amebic plasma membrane. Here we identify and characterize a 22-kDa Ca(2+)-dependent binding partner of URE3-BP, EhC2A, a novel member of the C2-domain superfamily. Immunoprecipitations of URE3-BP and EhC2A showed that the proteins interact and that such interaction was enhanced in the presence of Ca(2+). Recombinant and native EhC2A bound phospholipid liposomes in a Ca(2+)-dependent manner, with half-maximal binding occurring at 3.4 muM free Ca(2+). A direct interaction between EhC2A and URE3-BP was demonstrated by the ability of recombinant EhC2A to recruit recombinant URE3-BP to phospholipid liposomes in a Ca(2+)-dependent manner. URE3-BP and EhC2A were observed to translocate to the amebic plasma membrane upon an increase in the intracellular Ca(2+) concentration of trophozoites, as revealed by subcellular fractionation and immunofluorescent staining. Short hairpin RNA-mediated knockdown of EhC2A protein expression significantly modulated the mRNA levels of URE3-BP-regulated transcripts. Based on these results, we propose a model for EhC2A-mediated regulation of the transcriptional activities of URE3-BP via Ca(2+)-dependent anchoring of the transcription factor to the amebic plasma membrane.

  14. Organic Solvent Tropical Report

    International Nuclear Information System (INIS)

    COWLEY, W.L.

    2000-01-01

    This report provides the basis for closing the organic solvent safety issue. Sufficient information is presented to conclude that risk posed by an unmitigated organic solvent fire is within risk evaluation guidelines

  15. Solvent wash solution

    International Nuclear Information System (INIS)

    Neace, J.C.

    1986-01-01

    This patent describes a process for removing diluent degradation products from a solvent extraction solution comprising an admixture of an organic extractant for uranium and plutonium and a non-polar organic liquid diluent, which has been used to recover uranium and plutonium from spent nuclear fuel. Comprising combining a wash solution consisting of: (a) water; and (b) a positive amount up to about, an including, 50 volume percent of at least one highly-polar water-miscible organic solvent, based on the total volume of the water and the highly-polar organic solvent, with the solvent extraction solution after uranium and plutonium values have been stripped from the solvent extraction solution, the diluent degradation products dissolving in the highly-polar organic solvent and the extractant and diluent of the extraction solution not dissolving in the highly-polar organic solvent, and separating the highly-polar organic solvent and the extraction solution to obtain a purified extraction solution

  16. Indium recovery by solvent extraction

    International Nuclear Information System (INIS)

    Fortes, Marilia Camargos Botelho

    1999-04-01

    Indium has been recovered as a byproduct from residues generated from the sulfuric acid leaching circuits in mineral plants for zinc recovery. Once its recovery comes from the slags of other metals recovery, it is necessary to separate it from the other elements which usually are present in high concentrations. Many works have been approaching this separation and indicate the solvent extraction process as the main technique used. In Brazilian case, indium recovery depends on the knowledge of this technique and its development. This paper describes the solvent extraction knowledge for the indium recovery from aqueous solutions generated in mineral plants. The results for determination of the best experimental conditions to obtain a high indium concentration solution and minimum iron poisoning by solvent extraction with di (2-ethylhexyl)-phosphoric acid (D2EHPA) solubilized in isoparafin and exxsol has been presented. (author)

  17. Anti-Inflammatory Oxicams as Multi-donor Ligand Systems: pH- and Solvent-Dependent Coordination Modes of Meloxicam and Piroxicam to Ru and Os.

    Science.gov (United States)

    Aman, Farhana; Hanif, Muhammad; Kubanik, Mario; Ashraf, Adnan; Söhnel, Tilo; Jamieson, Stephen M F; Siddiqui, Waseeq Ahmad; Hartinger, Christian G

    2017-04-06

    The nitrogen- and sulfur-containing 1,2-benzothiazines meloxicam and piroxicam are widely used as nonsteroidal anti-inflammatory drugs. Intrigued by the presence of multiple donor atoms and therefore potentially rich coordination chemistry, we prepared a series of organometallic Ru and Os compounds with meloxicam and piroxicam featuring either as mono- or bidentate ligand systems. The choice of the solvent and the pH value was identified as the critical parameter to achieve selectively mono- or bidentate coordination. The coordination modes were confirmed experimentally by NMR spectroscopy and single crystal X-ray diffraction analysis. Using DFT calculations, it was established that complexes in which meloxicam acts as a bidentate N,O donor are energetically more favorable than coordination as O,O and S,O donor systems. Since meloxicam and piroxicam derivatives have shown anticancer activity in the past, we aimed to compare the complexes with mono- and bidentate ligands on their in vitro anticancer activity. However, stability studies revealed that only the latter complexes were stable in [D 6 ]DMSO/D 2 O (5:95) and therefore no direct comparisons could be made. The meloxicam complexes 1 and 2 showed moderate cytotoxicity, whereas the piroxicam derivatives 5 and 6 were hardly active against the utilized cell lines. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Distinct solvent- and temperature-dependent packing arrangements of anti-parallel β-sheet polyalanines studied with solid-state 13C NMR and MD simulation.

    Science.gov (United States)

    Kametani, Shunsuke; Tasei, Yugo; Nishimura, Akio; Asakura, Tetsuo

    2017-08-09

    Polyalanine (polyA) sequences are well known as the simplest sequence that naturally forms anti-parallel β-sheets and constitute a key element in the structure of spider and wild silkworm silk fibers. We have carried out a systematic analysis of the packing of anti-parallel β-sheets for (Ala) n , n = 5, 6, 7 and 12, using primarily 13 C solid-state NMR and MD simulation. HFIP and TFA are frequently used as the dope solvents for recombinant silks, and polyA was solidified from both HFIP and TFA solutions by drying. An analysis of Ala Cβ peaks in the 13 C CP/MAS NMR spectra indicated that polyA from HFIP was mainly rectangular but polyA from TFA was mainly staggered. The transition from the rectangular to the staggered arrangement in (Ala) 6 was observed for the first time from the change in the Ala Cβ peak through heat treatment at 200 °C for 4 h. The removal of the bound water was confirmed by thermal analysis. This transition could be reproduced by MD simulation of (Ala) 6 molecules at 200 °C after removal of the bound water molecules. In this way, the origin of the stability of the different packing arrangements of polyA was clarified.

  19. The solvent at antigen-binding site regulated C3d-CR2 interactions through the C-terminal tail of C3d at different ion strengths: insights from molecular dynamics simulation.

    Science.gov (United States)

    Zhang, Yan; Guo, Jingjing; Li, Lanlan; Liu, Xuewei; Yao, Xiaojun; Liu, Huanxiang

    2016-10-01

    The interactions of complement receptor 2 (CR2) and the degradation fragment C3d of complement component C3 play important links between the innate and adaptive immune systems. Due to the importance of C3d-CR2 interaction in the design of vaccines and inhibitors, a number of studies have been performed to investigate C3d-CR2 interaction. Many studies have indicated C3d-CR2 interactions are ionic strength-dependent. To investigate the molecular mechanism of C3d-CR2 interaction and the origin of effects of ionic strength, molecular dynamics simulations for C3d-CR2 complex together with the energetic and structural analysis were performed. Our results revealed the increased interactions between charged protein and ions weaken C3d-CR2 association, as ionic strengths increase. Moreover, ion strengths have similar effects on antigen-binding site and CR2 binding site. Meanwhile, Ala17 and Gln20 will transform between the activated and non-activated states mediated by His133 and Glu135 at different ion strengths. Our results reveal the origins of the effects of ionic strengths on C3d-CR2 interactions are due to the changes of water, ion occupancies and distributions. This study uncovers the origin of the effect of ionic strength on C3d-CR2 interaction and deepens the understanding of the molecular mechanism of their interaction, which is valuable for the design of vaccines and small molecule inhibitors. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. Hexanucleotide Repeats in ALS/FTD Form Length-Dependent RNA Foci, Sequester RNA Binding Proteins, and Are Neurotoxic

    Directory of Open Access Journals (Sweden)

    Youn-Bok Lee

    2013-12-01

    Full Text Available The GGGGCC (G4C2 intronic repeat expansion within C9ORF72 is the most common genetic cause of amyotrophic lateral sclerosis (ALS and frontotemporal dementia (FTD. Intranuclear neuronal RNA foci have been observed in ALS and FTD tissues, suggesting that G4C2 RNA may be toxic. Here, we demonstrate that the expression of 38× and 72× G4C2 repeats form intranuclear RNA foci that initiate apoptotic cell death in neuronal cell lines and zebrafish embryos. The foci colocalize with a subset of RNA binding proteins, including SF2, SC35, and hnRNP-H in transfected cells. Only hnRNP-H binds directly to G4C2 repeats following RNA immunoprecipitation, and only hnRNP-H colocalizes with 70% of G4C2 RNA foci detected in C9ORF72 mutant ALS and FTD brain tissues. We show that expanded G4C2 repeats are potently neurotoxic and bind hnRNP-H and other RNA binding proteins. We propose that RNA toxicity and protein sequestration may disrupt RNA processing and contribute to neurodegeneration.

  1. Unsaturated free fatty acids increase benzodiazepine receptor agonist binding depending on the subunit composition of the GABAA receptor complex.

    Science.gov (United States)

    Witt, M R; Westh-Hansen, S E; Rasmussen, P B; Hastrup, S; Nielsen, M

    1996-11-01

    It has been shown previously that unsaturated free fatty acids (FFAs) strongly enhance the binding of agonist benzodiazepine receptor ligands and GABAA receptor ligands in the CNS in vitro. To investigate the selectivity of this effect, recombinant human GABAA/benzodiazepine receptor complexes formed by different subunit compositions (alpha x beta y gamma 2, x = 1, 2, 3, and 5; y = 1, 2, and 3) were expressed using the baculovirus-transfected Sf9 insect cell system. At 10(-4) M, unsaturated FFAs, particularly arachidonic (20:4) and docosahexaenoic (22:6) acids, strongly stimulated (> 200% of control values) the binding of [3H]flunitrazepam ([3H]FNM) to the alpha 3 beta 2 gamma 2 receptor combination in whole cell preparations. No effect or small increases in levels of unsaturated FFAs on [3H]FNM binding to alpha 1 beta x gamma 2 and alpha 2 beta x gamma 2 receptor combinations were observed, and weak effects (130% of control values) were detected using the alpha 5 beta 2 gamma 2 receptor combination. The saturated FFAs, stearic and palmitic acids, were without effect on [3H]FNM binding to any combination of receptor complexes. The hydroxylated unsaturated FFAs, ricinoleic and ricinelaidic acids, were shown to decrease the binding of [3H]FNM only if an alpha 1 beta 2 gamma 2 receptor combination was used. Given the heterogeneity of the GABAA/ benzodiazepine receptor subunit distribution in the CNS, the effects of FFAs on the benzodiazepine receptor can be assumed to vary at both cellular and regional levels.

  2. Structure of an N276-Dependent HIV-1 Neutralizing Antibody Targeting a Rare V5 Glycan Hole Adjacent to the CD4 Binding Site

    Energy Technology Data Exchange (ETDEWEB)

    Wibmer, Constantinos Kurt; Gorman, Jason; Anthony, Colin S.; Mkhize, Nonhlanhla N.; Druz, Aliaksandr; York, Talita; Schmidt, Stephen D.; Labuschagne, Phillip; Louder, Mark K.; Bailer, Robert T.; Karim, Salim S. Abdool; Mascola, John R.; Williamson, Carolyn; Moore, Penny L.; Kwong, Peter D.; Morris, Lynn (NHLS-South Africa); (NIH); (Witwatersrand); (KwaZulu-Natal)

    2016-08-31

    ABSTRACT

    All HIV-1-infected individuals develop strain-specific neutralizing antibodies to their infecting virus, which in some cases mature into broadly neutralizing antibodies. Defining the epitopes of strain-specific antibodies that overlap conserved sites of vulnerability might provide mechanistic insights into how broadly neutralizing antibodies arise. We previously described an HIV-1 clade C-infected donor, CAP257, who developed broadly neutralizing plasma antibodies targeting an N276 glycan-dependent epitope in the CD4 binding site. The initial CD4 binding site response potently neutralized the heterologous tier 2 clade B viral strain RHPA, which was used to design resurfaced gp120 antigens for single-B-cell sorting. Here we report the isolation and structural characterization of CAP257-RH1, an N276 glycan-dependent CD4 binding site antibody representative of the early CD4 binding site plasma response in donor CAP257. The cocrystal structure of CAP257-RH1 bound to RHPA gp120 revealed critical interactions with the N276 glycan, loop D, and V5, but not with aspartic acid 368, similarly to HJ16 and 179NC75. The CAP257-RH1 monoclonal antibody was derived from the immunoglobulin-variable IGHV3-33 and IGLV3-10 genes and neutralized RHPA but not the transmitted/founder virus from donor CAP257. Its narrow neutralization breadth was attributed to a binding angle that was incompatible with glycosylated V5 loops present in almost all HIV-1 strains, including the CAP257 transmitted/founder virus. Deep sequencing of autologous CAP257 viruses, however, revealed minority variants early in infection that lacked V5 glycans. These glycan-free V5 loops are unusual holes in the glycan shield that may have been necessary for initiating this N276 glycan-dependent CD4 binding site B-cell lineage.

    IMPORTANCEThe conserved CD4 binding site on gp120 is a major target for HIV-1 vaccine design, but key events in the elicitation and maturation of

  3. One amino acid in mouse activated factor VII defines its endothelial protein C receptor (EPCR) binding and modulates its EPCR-dependent hemostatic activity in vivo.

    Science.gov (United States)

    Pavani, G; Zintner, S M; Ivanciu, L; Small, J C; Stafford, K A; Szeto, J H; Margaritis, P

    2017-03-01

    Essentials The lack of factor (F) VIIa-endothelial protein C receptor (EPCR) binding in mice is unresolved. A single substitution of Leu4 to Phe in mouse FVIIa (mFVIIa) enables its interaction with EPCR. mFVIIa with a Phe4 shows EPCR binding-dependent enhanced hemostatic function in vivo vs. mFVIIa. Defining the FVIIa-EPCR interaction in mice allows for further investigating its biology in vivo. Background Human activated factor VII (hFVIIa), which is used in hemophilia treatment, binds to the endothelial protein C (PC) receptor (EPCR) with unclear hemostatic consequences. Interestingly, mice lack the activated FVII (FVIIa)-EPCR interaction. Therefore, to investigate the hemostatic consequences of this interaction in hemophilia, we previously engineered a mouse FVIIa (mFVIIa) molecule that bound mouse EPCR (mEPCR) by using three substitutions from mouse PC (mPC), i.e. Leu4→Phe, Leu8→Met, and Trp9→Arg. The resulting molecule, mFVIIa-FMR, modeled the EPCR-binding properties of hFVIIa and showed enhanced hemostatic capacity in hemophilic mice versus mFVIIa. These data implied a role of EPCR in the action of hFVIIa in hemophilia treatment. However, the substitutions in mFVIIa-FMR only broadly defined the sequence determinants for its mEPCR interaction and enhanced function in vivo. Objectives To determine the individual contributions of mPC Phe4, Met8 and Arg9 to the in vitro/in vivo properties of mFVIIa-FMR. Methods The mEPCR-binding properties of single amino acid variants of mFVIIa or mPC at position 4, 8 or 9 were investigated. Results and conclusions Phe4 in mFVIIa or mPC was solely critical for interaction with mEPCR. In hemophilic mice, administration of mFVIIa harboring a Phe4 resulted in a 1.9-2.5-fold increased hemostatic capacity versus mFVIIa that was EPCR binding-dependent. This recapitulated previous observations made with triple-mutant mFVIIa-FMR. As Leu8 is crucial for hFVIIa-EPCR binding, we describe the sequence divergence of this interaction in

  4. MeCP2 regulates Tet1-catalyzed demethylation, CTCF binding, and learning-dependent alternative splicing of the BDNF gene in Turtle

    Science.gov (United States)

    Zheng, Zhaoqing; Ambigapathy, Ganesh; Keifer, Joyce

    2017-01-01

    MECP2 mutations underlying Rett syndrome cause widespread misregulation of gene expression. Functions for MeCP2 other than transcriptional are not well understood. In an ex vivo brain preparation from the pond turtle Trachemys scripta elegans, an intraexonic splicing event in the brain-derived neurotrophic factor (BDNF) gene generates a truncated mRNA transcript in naïve brain that is suppressed upon classical conditioning. MeCP2 and its partners, splicing factor Y-box binding protein 1 (YB-1) and methylcytosine dioxygenase 1 (Tet1), bind to BDNF chromatin in naïve but dissociate during conditioning; the dissociation correlating with decreased DNA methylation. Surprisingly, conditioning results in new occupancy of BDNF chromatin by DNA insulator protein CCCTC-binding factor (CTCF), which is associated with suppression of splicing in conditioning. Knockdown of MeCP2 shows it is instrumental for splicing and inhibits Tet1 and CTCF binding thereby negatively impacting DNA methylation and conditioning-dependent splicing regulation. Thus, mutations in MECP2 can have secondary effects on DNA methylation and alternative splicing. DOI: http://dx.doi.org/10.7554/eLife.25384.001 PMID:28594324

  5. RNA-dependent RNA polymerase of hepatitis C virus binds to its coding region RNA stem-loop structure, 5BSL3.2, and its negative strand.

    Science.gov (United States)

    Kanamori, Hiroshi; Yuhashi, Kazuhito; Ohnishi, Shin; Koike, Kazuhiko; Kodama, Tatsuhiko

    2010-05-01

    The hepatitis C virus NS5B RNA-dependent RNA polymerase (RdRp) is a key enzyme involved in viral replication. Interaction between NS5B RdRp and the viral RNA sequence is likely to be an important step in viral RNA replication. The C-terminal half of the NS5B-coding sequence, which contains the important cis-acting replication element, has been identified as an NS5B-binding sequence. In the present study, we confirm the specific binding of NS5B to one of the RNA stem-loop structures in the region, 5BSL3.2. In addition, we show that NS5B binds to the complementary strand of 5BSL3.2 (5BSL3.2N). The bulge structure of 5BSL3.2N was shown to be indispensable for tight binding to NS5B. In vitro RdRp activity was inhibited by 5BSL3.2N, indicating the importance of the RNA element in the polymerization by RdRp. These results suggest the involvement of the RNA stem-loop structure of the negative strand in the replication process.

  6. Chorion gene activation and repression is dependent on BmC/EBP expression and binding to cognate cis-elements.

    Science.gov (United States)

    Papantonis, Argyris; Sourmeli, Sissy; Lecanidou, Rena

    2008-05-09

    From the different cis-elements clustered on silkmoth chorion gene promoters, C/EBP binding sites predominate. Their sequence composition and dispersal vary amongst promoters of diverse developmental specificity. Occupancy of these sites by BmC/EBP was examined through Southwestern and ChIP assays modified to suit ovarian follicular cells. For the genes studied, binding of BmC/EBP coincided with the respective stages of transcriptional activation. However, the factor was reloaded on promoter sequences long after individual gene repression. Furthermore, suppression of BmC/EBP transcription in developing follicles resulted in de-regulation of chorion gene expression. A biphasic function of BmC/EBP, according to which it may act as both an activator and a repressor during silkmoth choriogenesis, is considered under the light of the presented data.

  7. Supervised machine learning techniques to predict binding affinity. A study for cyclin-dependent kinase 2.

    Science.gov (United States)

    de Ávila, Maurício Boff; Xavier, Mariana Morrone; Pintro, Val Oliveira; de Azevedo, Walter Filgueira

    2017-12-09

    Here we report the development of a machine-learning model to predict binding affinity based on the crystallographic structures of protein-ligand complexes. We used an ensemble of crystallographic structures (resolution better than 1.5 Å resolution) for which half-maximal inhibitory concentration (IC 50 ) data is available. Polynomial scoring functions were built using as explanatory variables the energy terms present in the MolDock and PLANTS scoring functions. Prediction performance was tested and the supervised machine learning models showed improvement in the prediction power, when compared with PLANTS and MolDock scoring functions. In addition, the machine-learning model was applied to predict binding affinity of CDK2, which showed a better performance when compared with AutoDock4, AutoDock Vina, MolDock, and PLANTS scores. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Millisecond dynamics in glutaredoxin during catalytic turnover is dependent on substrate binding and absent in the resting states

    DEFF Research Database (Denmark)

    Jensen, Kristine Steen; Winther, Jakob R; Teilum, Kaare

    2011-01-01

    to the glutathione exchange rate was observed for 23 residues. Binding of reduced glutathione resulted in competitive inhibition of the reduced enzyme having kinetics similar to that of the reaction. This observation couples the motions observed during catalysis directly to substrate binding. Backbone motions......Conformational dynamics is important for enzyme function. Which motions of enzymes determine catalytic efficiency and whether the same motions are important for all enzymes, however, are not well understood. Here we address conformational dynamics in glutaredoxin during catalytic turnover...... with a combination of NMR magnetization transfer, R(2) relaxation dispersion, and ligand titration experiments. Glutaredoxins catalyze a glutathione exchange reaction, forming a stable glutathinoylated enzyme intermediate. The equilibrium between the reduced state and the glutathionylated state was biochemically...

  9. Paxillin and embryonic PolyAdenylation Binding Protein (ePABP) engage to regulate androgen-dependent Xenopus laevis oocyte maturation - A model of kinase-dependent regulation of protein expression.

    Science.gov (United States)

    Miedlich, Susanne U; Taya, Manisha; Young, Melissa Rasar; Hammes, Stephen R

    2017-06-15

    Steroid-triggered Xenopus laevis oocyte maturation is an elegant physiologic model of nongenomic steroid signaling, as it proceeds completely independent of transcription. We previously demonstrated that androgens are the main physiologic stimulator of oocyte maturation in Xenopus oocytes, and that the adaptor protein paxillin plays a crucial role in mediating this process through a positive feedback loop in which paxillin first enhances Mos protein translation, ensued by Erk2 activation and Erk-dependent phosphorylation of paxillin on serine residues. Phosphoserine-paxillin then further augments Mos protein translation and downstream Erk2 activation, resulting in meiotic progression. We hypothesized that paxillin enhances Mos translation by interacting with embryonic PolyAdenylation Binding Protein (ePABP) on polyadenylated Mos mRNA. Knockdown of ePABP phenocopied paxillin knockdown, with reduced Mos protein expression, Erk2 and Cdk1 activation, as well as oocyte maturation. In both Xenopus oocytes and mammalian cells (HEK-293), paxillin and ePABP constitutively interacted. Testosterone (Xenopus) or EGF (HEK-293) augmented ePABP-paxillin binding, as well as ePABP binding to Mos mRNA (Xenopus), in an Erk-dependent fashion. Thus, ePABP and paxillin work together in an Erk-dependent fashion to enhance Mos protein translation and promote oocyte maturation. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. High-affinity DNA-binding Domains of Replication Protein A (RPA) Direct SMARCAL1-dependent Replication Fork Remodeling*

    Science.gov (United States)

    Bhat, Kamakoti P.; Bétous, Rémy; Cortez, David

    2015-01-01

    SMARCAL1 catalyzes replication fork remodeling to maintain genome stability. It is recruited to replication forks via an interaction with replication protein A (RPA), the major ssDNA-binding protein in eukaryotic cells. In addition to directing its localization, RPA also activates SMARCAL1 on some fork substrates but inhibits it on others, thereby conferring substrate specificity to SMARCAL1 fork-remodeling reactions. We investigated the mechanism by which RPA regulates SMARCAL1. Our results indicate that although an interaction between SMARCAL1 and RPA is essential for SMARCAL1 activation, the location of the interacting surface on RPA is not. Counterintuitively, high-affinity DNA binding of RPA DNA-binding domain (DBD) A and DBD-B near the fork junction makes it easier for SMARCAL1 to remodel the fork, which requires removing RPA. We also found that RPA DBD-C and DBD-D are not required for SMARCAL1 regulation. Thus, the orientation of the high-affinity RPA DBDs at forks dictates SMARCAL1 substrate specificity. PMID:25552480

  11. High-affinity DNA-binding domains of replication protein A (RPA) direct SMARCAL1-dependent replication fork remodeling.

    Science.gov (United States)

    Bhat, Kamakoti P; Bétous, Rémy; Cortez, David

    2015-02-13

    SMARCAL1 catalyzes replication fork remodeling to maintain genome stability. It is recruited to replication forks via an interaction with replication protein A (RPA), the major ssDNA-binding protein in eukaryotic cells. In addition to directing its localization, RPA also activates SMARCAL1 on some fork substrates but inhibits it on others, thereby conferring substrate specificity to SMARCAL1 fork-remodeling reactions. We investigated the mechanism by which RPA regulates SMARCAL1. Our results indicate that although an interaction between SMARCAL1 and RPA is essential for SMARCAL1 activation, the location of the interacting surface on RPA is not. Counterintuitively, high-affinity DNA binding of RPA DNA-binding domain (DBD) A and DBD-B near the fork junction makes it easier for SMARCAL1 to remodel the fork, which requires removing RPA. We also found that RPA DBD-C and DBD-D are not required for SMARCAL1 regulation. Thus, the orientation of the high-affinity RPA DBDs at forks dictates SMARCAL1 substrate specificity. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  12. Stark effect-dependent of ground-state donor binding energy in InGaN/GaN parabolic QWW

    International Nuclear Information System (INIS)

    El Ghazi, Haddou; Zorkani, Izeddine; Jorio, Anouar

    2013-01-01

    Using the finite-difference method within the quasi-one-dimensional effective potential model and effective mass approximation, the ground-state binding energy of hydrogenic shallow-donor impurity in wurtzite (WZ) (In,Ga)N/GaN parabolic transversal-section quantum-well wires (PQWWs) subjected to external electric field is investigated. An effective radius of a cylindrical QWW describing the strength of the lateral confinement is introduced. The results show that (i) the position of the largest electron probability density in x–y plane is located at a point and it is pushed along the negative sense by the electric field directed along the positive sense, (ii) the ground-state binding energy is largest for the impurity located at this point and starts to decrease when the impurity is away from this point, (iii) the ground-state binding energy decreases with increase in the external electric field and effective radius, and (iv) the Stark-shift increases with the increase of the external electric field and the effective radius

  13. A chimeric protein composed of NuMA fused to the DNA binding domain of LANA is sufficient for the ori-P-dependent DNA replication

    International Nuclear Information System (INIS)

    Ohsaki, Eriko; Ueda, Keiji

    2017-01-01

    The Kaposi's sarcoma-associated herpesvirus (KSHV) genome is stably maintained in KSHV-infected PEL cell lines during cell division. We previously showed that accumulation of LANA in the nuclear matrix fraction could be important for the latent DNA replication, and that the functional significance of LANA should be its recruitment of ori-P to the nuclear matrix. Here, we investigated whether the forced localization of the LANA-DNA binding domain (DBD) to the nuclear matrix facilitated ori-P-containing plasmid replication. We demonstrated that chimeric proteins constructed by fusion of LANA DBD with the nuclear mitotic apparatus protein (NuMA), which is one of the components of the nuclear matrix, could bind with ori-P and enhance replication of an ori-P-containing plasmid, compared with that in the presence of DBD alone. These results further suggested that the ori-P recruitment to the nuclear matrix through the binding with DBD is important for latent viral DNA replication. - Highlights: •KSHV replication in latency depends on LANA localization to the nuclear matrix. •LANA DBD was fused with NuMA, a nuclear matrix protein, at the N- and C-terminus. •NuMA-DBD was in the nuclear matrix and supported the ori-P dependent replication. •LANA in the nuclear matrix should be important for the KSHV replication in latency.

  14. A chimeric protein composed of NuMA fused to the DNA binding domain of LANA is sufficient for the ori-P-dependent DNA replication

    Energy Technology Data Exchange (ETDEWEB)

    Ohsaki, Eriko; Ueda, Keiji, E-mail: kueda@virus.med.osaka-u.ac.jp

    2017-01-15

    The Kaposi's sarcoma-associated herpesvirus (KSHV) genome is stably maintained in KSHV-infected PEL cell lines during cell division. We previously showed that accumulation of LANA in the nuclear matrix fraction could be important for the latent DNA replication, and that the functional significance of LANA should be its recruitment of ori-P to the nuclear matrix. Here, we investigated whether the forced localization of the LANA-DNA binding domain (DBD) to the nuclear matrix facilitated ori-P-containing plasmid replication. We demonstrated that chimeric proteins constructed by fusion of LANA DBD with the nuclear mitotic apparatus protein (NuMA), which is one of the components of the nuclear matrix, could bind with ori-P and enhance replication of an ori-P-containing plasmid, compared with that in the presence of DBD alone. These results further suggested that the ori-P recruitment to the nuclear matrix through the binding with DBD is important for latent viral DNA replication. - Highlights: •KSHV replication in latency depends on LANA localization to the nuclear matrix. •LANA DBD was fused with NuMA, a nuclear matrix protein, at the N- and C-terminus. •NuMA-DBD was in the nuclear matrix and supported the ori-P dependent replication. •LANA in the nuclear matrix should be important for the KSHV replication in latency.

  15. Solvent-dependent reactions for the synthesis of β-keto-benzo-δ-sultone scaffolds via DBU-catalyzed O-sulfonylation/intramolecular Baylis-Hillman/1,3-H shift or dehydration tandem sequences.

    Science.gov (United States)

    Ghandi, Mehdi; Bozcheloei, Abolfazl Hasani; Nazari, Seyed Hadi; Sadeghzadeh, Masoud

    2011-12-16

    We have developed a solvent-dependent method for the synthesis of novel benzo-δ-sultone scaffolds. A variety of benzylbenzo[e][1,2]oxathiin-4(3H)-one-2,2-dioxides were obtained in high yields in DMF using a one-pot, DBU-catalyzed condensation of 2-hydroxybenzaldehydes with a number of (E)-2-phenylethenesulfonyl chlorides. On the other hand, the initially prepared 2-formylphenyl-(E)-2-phenylethenesulfonate derivatives underwent DBU-catalyzed reactions to a series of 3-[methoxy(phenyl)methyl]benzo[e][1,2]oxathiine-2,2-dioxides in moderate to good yields in MeOH. These reactions presumably proceed via DBU-catalyzed O-sulfonylation/intramolecular Baylis-Hillman/1,3-H shift or dehydration tandem sequences, respectively.

  16. UV-induced modifications in the peptidyl transferase loop of 23S rRNA dependent on binding of the streptogramin B antibiotic, pristinamycin IA

    DEFF Research Database (Denmark)

    Porse, B T; Kirillov, S V; Awayez, M J

    1999-01-01

    The naturally occurring streptogramin B antibiotic, pristinamycin IA, which inhibits peptide elongation, can produce two modifications in 23S rRNA when bound to the Escherichia coli 70S ribosome and irradiated at 365 nm. Both drug-induced effects map to highly conserved nucleotides within...... in the latter modification to A2062/C2063. Pristinamycin IA can also produce a modification on binding to deproteinized, mature 23S rRNA, at position U2500/C2501. The same modification occurs on an approximately 37-nt fragment, encompassing positions approximately 2496-2532 of the peptidyl transferase loop...... the sequence Cm-C-U-C-G-m2A-psi-G2505 are important for pristinamycin IA binding and/or the antibiotic-dependent modification of 23S rRNA....

  17. Presenilins Regulate Neurotrypsin Gene Expression and Neurotrypsin-dependent Agrin Cleavage via Cyclic AMP Response Element-binding Protein (CREB) Modulation*

    Science.gov (United States)

    Almenar-Queralt, Angels; Kim, Sonia N.; Benner, Christopher; Herrera, Cheryl M.; Kang, David E.; Garcia-Bassets, Ivan; Goldstein, Lawrence S. B.

    2013-01-01

    Presenilins, the catalytic components of the γ-secretase complex, are upstream regulators of multiple cellular pathways via regulation of gene transcription. However, the underlying mechanisms and the genes regulated by these pathways are poorly characterized. In this study, we identify Tequila and its mammalian ortholog Prss12 as genes negatively regulated by presenilins in Drosophila larval brains and mouse embryonic fibroblasts, respectively. Prss12 encodes the serine protease neurotrypsin, which cleaves the heparan sulfate proteoglycan agrin. Altered neurotrypsin activity causes serious synaptic and cognitive defects; despite this, the molecular processes regulating neurotrypsin expression and activity are poorly understood. Using γ-secretase drug inhibitors and presenilin mutants in mouse embryonic fibroblasts, we found that a mature γ-secretase complex was required to repress neurotrypsin expression and agrin cleavage. We also determined that PSEN1 endoproteolysis or processing of well known γ-secretase substrates was not essential for this process. At the transcriptional level, PSEN1/2 removal induced cyclic AMP response element-binding protein (CREB)/CREB-binding protein binding, accumulation of activating histone marks at the neurotrypsin promoter, and neurotrypsin transcriptional and functional up-regulation that was dependent on GSK3 activity. Upon PSEN1/2 reintroduction, this active epigenetic state was replaced by a methyl CpG-binding protein 2 (MeCP2)-containing repressive state and reduced neurotrypsin expression. Genome-wide analysis revealed hundreds of other mouse promoters in which CREB binding is similarly modulated by the presence/absence of presenilins. Our study thus identifies Tequila and neurotrypsin as new genes repressed by presenilins and reveals a novel mechanism used by presenilins to modulate CREB signaling based on controlling CREB recruitment. PMID:24145027

  18. Presenilins regulate neurotrypsin gene expression and neurotrypsin-dependent agrin cleavage via cyclic AMP response element-binding protein (CREB) modulation.

    Science.gov (United States)

    Almenar-Queralt, Angels; Kim, Sonia N; Benner, Christopher; Herrera, Cheryl M; Kang, David E; Garcia-Bassets, Ivan; Goldstein, Lawrence S B

    2013-12-06

    Presenilins, the catalytic components of the γ-secretase complex, are upstream regulators of multiple cellular pathways via regulation of gene transcription. However, the underlying mechanisms and the genes regulated by these pathways are poorly characterized. In this study, we identify Tequila and its mammalian ortholog Prss12 as genes negatively regulated by presenilins in Drosophila larval brains and mouse embryonic fibroblasts, respectively. Prss12 encodes the serine protease neurotrypsin, which cleaves the heparan sulfate proteoglycan agrin. Altered neurotrypsin activity causes serious synaptic and cognitive defects; despite this, the molecular processes regulating neurotrypsin expression and activity are poorly understood. Using γ-secretase drug inhibitors and presenilin mutants in mouse embryonic fibroblasts, we found that a mature γ-secretase complex was required to repress neurotrypsin expression and agrin cleavage. We also determined that PSEN1 endoproteolysis or processing of well known γ-secretase substrates was not essential for this process. At the transcriptional level, PSEN1/2 removal induced cyclic AMP response element-binding protein (CREB)/CREB-binding protein binding, accumulation of activating histone marks at the neurotrypsin promoter, and neurotrypsin transcriptional and functional up-regulation that was dependent on GSK3 activity. Upon PSEN1/2 reintroduction, this active epigenetic state was replaced by a methyl CpG-binding protein 2 (MeCP2)-containing repressive state and reduced neurotrypsin expression. Genome-wide analysis revealed hundreds of other mouse promoters in which CREB binding is similarly modulated by the presence/absence of presenilins. Our study thus identifies Tequila and neurotrypsin as new genes repressed by presenilins and reveals a novel mechanism used by presenilins to modulate CREB signaling based on controlling CREB recruitment.

  19. Fluorescence-Based Comparative Binding Studies of the Supramolecular Host Properties of PAMAM Dendrimers Using Anilinonaphthalene Sulfonates: Unusual Host-Dependent Fluorescence Titration Behavior

    Directory of Open Access Journals (Sweden)

    Natasa Stojanovic

    2010-04-01

    Full Text Available This work describes the fluorescence enhancement of the anilinonaphthalene sulfonate probes 1,8-ANS, 2,6-ANS, and 2,6-TNS via complexation with PAMAM dendrimer hosts of Generation 4, 5 and 6. The use of this set of three very closely related probes allows for comparative binding studies, with specific pairs of probes differing only in shape (1,8-ANS and 2,6-ANS, or in the presence of a methyl substituent (2,6-TNS vs. 2,6-ANS. The fluorescence of all three probes was significantly enhanced upon binding with PAMAM dendrimers, however in all cases except one, a very unusual spike was consistently observed in the host fluorescence titration plots (fluorescence enhancement vs. host concentration at low dendrimer concentration. This unprecedented fluorescence titration curve shape makes fitting the data to a simple model such as 1:1 or 2:1 host: guest complexation very difficult; thus only qualitative comparisons of the relative binding of the three guests could be made based on host titrations. In the case of G4 and G5 dendrimers, the order of binding strength was qualitatively determined to be 1,8-ANS < 2,6-ANS indicating that the more streamlined 2,6-substituted probes are a better match for the dendrimer cavity shape than the bulkier 1,8-substituted probe. This order of binding strength was also indicated by double fluorometric titration experiments, involving both host and guest titrations. Further double fluorometric titration experiments on 2,6-ANS in G4 dendrimer revealed a host concentration-dependent change in the nature of the host: guest complexation, with multiple guests complexed per host molecule at very low host concentrations, but less than one guest per host at higher concentrations.

  20. Simultaneous fluorescence light-up and selective multicolor nucleobase recognition based on sequence-dependent strong binding of berberine to DNA abasic site.

    Science.gov (United States)

    Wu, Fei; Shao, Yong; Ma, Kun; Cui, Qinghua; Liu, Guiying; Xu, Shujuan

    2012-04-28

    Label-free DNA nucleobase recognition by fluorescent small molecules has received much attention due to its simplicity in mutation identification and drug screening. However, sequence-dependent fluorescence light-up nucleobase recognition and multicolor emission with individual emission energy for individual nucleobases have been seldom realized. Herein, an abasic site (AP site) in a DNA duplex was employed as a binding field for berberine, one of isoquinoline alkaloids. Unlike weak binding of berberine to the fully matched DNAs without the AP site, strong binding of berberine to the AP site occurs and the berberine's fluorescence light-up behaviors are highly dependent on the target nucleobases opposite the AP site in which the targets thymine and cytosine produce dual emission bands, while the targets guanine and adenine only give a single emission band. Furthermore, more intense emissions are observed for the target pyrimidines than purines. The flanking bases of the AP site also produce some modifications of the berberine's emission behavior. The binding selectivity of berberine at the AP site is also confirmed by measurements of fluorescence resonance energy transfer, excited-state lifetime, DNA melting and fluorescence quenching by ferrocyanide and sodium chloride. It is expected that the target pyrimidines cause berberine to be stacked well within DNA base pairs near the AP site, which results in a strong resonance coupling of the electronic transitions to the particular vibration mode to produce the dual emissions. The fluorescent signal-on and emission energy-modulated sensing for nucleobases based on this fluorophore is substantially advantageous over the previously used fluorophores. We expect that this approach will be developed as a practical device for differentiating pyrimidines from purines by positioning an AP site toward a target that is available for readout by this alkaloid probe. This journal is © The Royal Society of Chemistry 2012

  1. Activity of the rat osteocalcin basal promoter in osteoblastic cells is dependent upon homeodomain and CP1 binding motifs.

    Science.gov (United States)

    Towler, D A; Bennett, C D; Rodan, G A

    1994-05-01

    A detailed analysis of the transcriptional machinery responsible for osteoblast-specific gene expression should provide tools useful for understanding osteoblast commitment and differentiation. We have defined three cis-elements important for basal activity of the rat osteocalcin (OC) promoter, located at about -200 to -180, -170 to -138, and -121 to -64 relative to the transcription initiation site. A motif (TCTGATTGTGT) present in the region between -200 and -170 that binds a multisubunit CP1/NFY/CBF-like CAAT factor complex contributes significantly to high level basal activity and presumably functions as the CAAT box for the rat OC promoter. We show that the region -121 to 32 is sufficient to confer osteoblastic cell type specificity in transient transfection assays of cultured cell lines using luciferase as a reporter. The basal promoter is active in rodent osteoblastic cell lines, but not in rodent fibroblastic or muscle cell lines. Although the rat OC box (-100 to -74) contains a CAAT motif, we could not detect CP1-like CAAT factor binding to this region. In fact, we demonstrate that a Msx-1 (Hox 7.1) homeodomain binding motif (ACTAATTG; bottom strand) in the 3'-end of the rat OC box is necessary for high level activity of the rat OC basal promoter in osteoblastic cells. A nuclear factor that recognizes this motif appears to be present in osteoblastic ROS 17/2.8 cells, which produce OC, but not in fibroblastic ROS 25/1 cells, which fail to express OC. This ROS 17/2.8 nuclear factor also recognizes the A/T-rich DNA cognates of the homeodomain-containing POU family of transcription factors. Taken together, these data suggest that a ubiquitous CP1-like CAAT factor and a cell type-restricted homeodomain containing (Msx or POU family) transcription factor interact with the proximal rat OC promoter to direct appropriate basal OC transcription in osteoblastic cells.

  2. Molecule-binding dependent assembly of split aptamer and γ-cyclodextrin: A sensitive excimer signaling approach for aptamer biosensors

    International Nuclear Information System (INIS)

    Jin, Fen; Lian, Yan; Li, Jishan; Zheng, Jing; Hu, Yaping; Liu, Jinhua; Huang, Jin; Yang, Ronghua

    2013-01-01

    Graphical abstract: Adenosine-binding aptamer was splitted into two fragments P2 and P3 which labeled pyrene molecules, mainly produce monomer signal. γ-CD cavity brings P2 and P3 in close proximity, allowing for weak excimer emission. In the presence of target, P2 and P3 are expected to bind ATP and form an aptamer/target complex, leads to large increase of the pyrene excimer fluorescence. -- Highlights: •We assembled split aptamer and γ-cyclodextrin fluorescence biosensors for ATP detection. •The biosensor increased quantum yield and emission lifetime of the excimer. •Time-resolved fluorescence is effective for ATP assay in complicated environment. -- Abstract: A highly sensitive and selective fluorescence aptamer biosensors for the determination of adenosine triphosphate (ATP) was developed. Binding of a target with splitting aptamers labeled with pyrene molecules form stable pyrene dimer in the γ-cyclodextrin (γ-CD) cavity, yielding a strong excimer emission. We have found that inclusion of pyrene dimer in γ-cyclodextrin cavity not only exhibits additive increases in quantum yield and emission lifetime of the excimer, but also facilitates target-induced fusion of the splitting aptamers to form the aptamer/target complex. As proof-of-principle, the approach was applied to fluorescence detection of adenosine triphosphate. With an anti-ATP aptamer, the approach exhibits excimer fluorescence response toward ATP with a maximum signal-to-background ratio of 32.1 and remarkably low detection limit of 80 nM ATP in buffer solution. Moreover, due to the additive fluorescence lifetime of excimer induced by γ-cyclodextrin, time-resolved measurements could be conveniently used to detect as low as 0.5 μM ATP in blood serum quantitatively

  3. NAD-Dependent DNA-Binding Activity of the Bifunctional NadR Regulator of Salmonella typhimurium

    OpenAIRE

    Penfound, Thomas; Foster, John W.

    1999-01-01

    NadR is a 45-kDa bifunctional regulator protein. In vivo genetic studies indicate that NadR represses three genes involved in the biosynthesis of NAD. It also participates with an integral membrane protein (PnuC) in the import of nicotinamide mononucleotide, an NAD precursor. NadR was overexpressed and purified as a His-tagged fusion in order to study its DNA-binding properties. The protein bound to DNA fragments containing NAD box consensus sequences. NAD proved to be the relevant in vivo co...

  4. Structural requirements of the human sodium-dependent bile acid transporter (hASBT): Role of 3- and 7-OH moieties on binding and translocation of bile acids

    Science.gov (United States)

    González, Pablo M.; Lagos, Carlos F.; Ward, Weslyn C.; Polli, James E.

    2014-01-01

    Bile acids (BAs) are the end products of cholesterol metabolism. One of the critical steps in their biosynthesis involves the isomerization of the 3β-hydroxyl (-OH) group on the cholestane ring to the common 3α-configuration on BAs. BAs are actively recaptured from the small intestine by the human Apical Sodium-dependent Bile Acid Transporter (hASBT) with high affinity and capacity. Previous studies have suggested that no particular hydroxyl group on BAs is critical for binding or transport by hASBT, even though 3β-hydroxylated BAs were not examined. The aim of this study was to elucidate the role of the 3α-OH group on BAs binding and translocation by hASBT. Ten 3β-hydroxylated BAs (Iso-bile acids, iBAs) were synthesized, characterized, and subjected to hASBT inhibition and uptake studies. hASBT inhibition and uptake kinetics of iBAs were compared to that of native 3α-OH BAs. Glycine conjugates of native and isomeric BAs were subjected to molecular dynamics simulations in order to identify topological descriptors related to binding and translocation by hASBT. Iso-BAs bound to hASBT with lower affinity and exhibited reduced translocation than their respective 3α-epimers. Kinetic data suggests that, in contrast to native BAs where hASBT binding is the rate-limiting step, iBAs transport was rate-limited by translocation and not binding. Remarkably, 7-dehydroxylated iBAs were not hASBT substrates, highlighting the critical role of 7-OH group on BA translocation by hASBT, especially for iBAs. Conformational analysis of gly-iBAs and native BAs identified topological features for optimal binding as: concave steroidal nucleus, 3-OH “on-” or below-steroidal plane, 7-OH below-plane, and 12-OH moiety towards-plane. Our results emphasize the relevance of the 3α-OH group on BAs for proper hASBT binding and transport and revealed the critical role of 7-OH group on BA translocation, particularly in the absence of a 3α-OH group. Results have implications for BA

  5. Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism.

    Science.gov (United States)

    Goh, Garrett B; Hulbert, Benjamin S; Zhou, Huiqing; Brooks, Charles L

    2014-07-01

    pH is a ubiquitous regulator of biological activity, including protein-folding, protein-protein interactions, and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH-dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolvation energy of buried charged residues, increasing the error associated with predictions that involve internal ionizable residue that are important in processes like hydrogen transport and electron transfer. Furthermore, discrete water and ions cannot be modeled in implicit solvent, which are important in systems like membrane proteins and ion channels. We report on an explicit solvent constant pH molecular dynamics framework based on multi-site λ-dynamics (CPHMD(MSλD)). In the CPHMD(MSλD) framework, we performed seamless alchemical transitions between protonation and tautomeric states using multi-site λ-dynamics, and designed novel biasing potentials to ensure that the physical end-states are predominantly sampled. We show that explicit solvent CPHMD(MSλD) simulations model realistic pH-dependent properties of proteins such as the Hen-Egg White Lysozyme (HEWL), binding domain of 2-oxoglutarate dehydrogenase (BBL) and N-terminal domain of ribosomal protein L9 (NTL9), and the pKa predictions are in excellent agreement with experimental values, with a RMSE ranging from 0.72 to 0.84 pKa units. With the recent development of the explicit solvent CPHMD(MSλD) framework for nucleic acids, accurate modeling of pH-dependent properties of both major class of biomolecules-proteins and nucleic acids is now possible. © 2013 Wiley Periodicals, Inc.

  6. State-dependent electron delocalization dynamics at the solute-solvent interface: soft-x-ray absorption spectroscopy and ab initio calculations.

    Science.gov (United States)

    Bokarev, Sergey I; Dantz, Marcus; Suljoti, Edlira; Kühn, Oliver; Aziz, Emad F

    2013-08-23

    Nonradiative decay channels in the L-edge fluorescence yield spectra from transition-metal-aqueous solutions give rise to spectral distortions with respect to x-ray transmission spectra. Their origin is unraveled here using partial and inverse partial fluorescence yields on the microjet combined with multireference ab initio electronic structure calculations. Comparing Fe2+, Fe3+, and Co2+ systems we demonstrate and quantify unequivocally the state-dependent electron delocalization within the manifold of d orbitals as one origin of this observation.

  7. Structure of the Mr 140,000 growth hormone-dependent insulin-like growth factor binding protein complex: Determination by reconstitution and affinity-labeling

    International Nuclear Information System (INIS)

    Baxter, R.C.; Martin, J.L.

    1989-01-01

    To determine the structure of the high molecular weight, growth hormone-dependent complex between the insulin-like growth factors (IGF-I and IGF-II) and their binding proteins in human serum, we have reconstituted the complex from its purified component proteins and analyzed it by gel electrophoresis and autoradiography after covalent cross-linking. The proteins tested in reconstitution mixtures were an acid-labile Mr 84,000-86,000 glycoprotein doublet (alpha subunit), an acid-stable Mr 47,000-53,000 glycoprotein doublet with IGF-binding activity (BP-53 or beta subunit), and IGF-I or IGF-II (gamma subunit). In incubations containing any one of the three subunits 125I-labeled and the other two unlabeled, identical 125I-labeled alpha-beta-gamma complexes of Mr 140,000 were formed. Minor bands of Mr 120,000 and 90,000 were also seen, thought to represent a partially deglycosylated form of the alpha-beta-gamma complex, and an alpha-gamma complex arising as a cross-linking artifact. When serum samples from subjects of various growth hormone status were affinity-labeled with IGF-II tracer, a growth hormone-dependent Mr 140,000 band was seen, corresponding to the reconstituted alpha-beta-gamma complex. Other growth hormone-dependent labeled bands, of Mr 90,000 (corresponding to alpha-gamma), Mr 55,000-60,000 (corresponding to labeled beta-subunit doublet), and smaller bands of Mr 38,000, 28,000, and 23,000-25,000 (corresponding to labeled beta-subunit degradation products), were also seen in the affinity-labeled serum samples and in the complex reconstituted from pure proteins. All were immunoprecipitable with an anti-BP-53 antiserum. We conclude that the growth hormone-dependent Mr 140,000 IGF-binding protein complex in human serum has three components: the alpha (acid-labile) subunit, the beta (binding) subunit, and the gamma (growth factor) subunit

  8. Influence of Solvent-Solvent and Solute-Solvent Interaction Properties on Solvent-Mediated Potential

    International Nuclear Information System (INIS)

    Zhou Shiqi

    2005-01-01

    A recently proposed universal calculational recipe for solvent-mediated potential is applied to calculate excess potential of mean force between two large Lennard-Jones (LJ) or hard core attractive Yukawa particles immersed in small LJ solvent bath at supercritical state. Comparison between the present prediction with a hypernetted chain approximation adopted for solute-solute correlation at infinitely dilute limit and existing simulation data shows high accuracy for the region with large separation, and qualitative reliability for the solute particle contact region. The calculational simplicity of the present recipe allows for a detailed investigation on the effect of the solute-solvent and solvent-solvent interaction details on the excess potential of mean force. The resultant conclusion is that gathering of solvent particles near a solute particle leads to repulsive excess PMF, while depletion of solvent particles away from the solute particle leads to attractive excess PMF, and minor change of the solvent-solvent interaction range has large influence on the excess PMF.

  9. Binding of Human Fibrinogen to MRP Enhances Streptococcus suis Survival in Host Blood in a αXβ2 Integrin-dependent Manner.

    Science.gov (United States)

    Pian, Yaya; Li, Xueqin; Zheng, Yuling; Wu, Xiaohong; Yuan, Yuan; Jiang, Yongqiang

    2016-05-27

    The Gram-positive bacterium Streptococcus suis serotype 2 (S. suis 2), an important zoonotic pathogen, induces strong systemic infections in humans; sepsis and meningitis are the most common clinical manifestations and are often accompanied by bacteremia. However, the mechanisms of S. suis 2 survival in human blood are not well understood. In our previous study, we identified muramidase-released protein (MRP), a novel human fibrinogen (hFg)-binding protein (FBP) in S. suis 2 that is an important epidemic infection marker with an unknown mechanism in pathogenesis. The present study demonstrates that the N-terminus of MRP (a.a. 283-721) binds to both the Aα and Bβ chains of the D fragment of hFg. Strikingly, the hFg-MRP interaction improved the survival of S. suis 2 in human blood and led to the aggregation and exhaustion of polymorphonuclear neutrophils (PMNs) via an αXβ2 integrin-dependent mechanism. Other Fg-binding proteins, such as M1 (GAS) and FOG (GGS), also induced PMNs aggregation; however, the mechanisms of these FBP-hFg complexes in the evasion of PMN-mediated innate immunity remain unclear. MRP is conserved across highly virulent strains in Europe and Asia, and these data shed new light on the function of MRP in S. suis pathogenesis.

  10. Structure of thrombospondin type 3 repeats in bacterial outer membrane protein A reveals its intra-repeat disulfide bond-dependent calcium-binding capability

    Energy Technology Data Exchange (ETDEWEB)

    Dai, Shuyan; Sun, Cancan; Tan, Kemin; Ye, Sheng; Zhang, Rongguang

    2017-09-01

    Eukaryotic thrombospondin type 3 repeat (TT3R) is an efficient calcium ion (Ca2+) binding motif only found in mammalian thrombospondin family. TT3R has also been found in prokaryotic cellulase Cel5G, which was thought to forfeit the Ca2+-binding capability due to the formation of intra-repeat disulfide bonds, instead of the inter-repeat ones possessed by eukaryotic TT3Rs. In this study, we have identified an enormous number of prokaryotic TT3R-containing proteins belonging to several different protein families, including outer membrane protein A (OmpA), an important structural protein connecting the outer membrane and the periplasmic peptidoglycan layer in gram-negative bacteria. Here, we report the crystal structure of the periplasmic region of OmpA from Capnocytophaga gingivalis, which contains a linker region comprising five consecutive TT3Rs. The structure of OmpA-TT3R exhibits a well-ordered architecture organized around two tightly-coordinated Ca2+ and confirms the presence of abnormal intra-repeat disulfide bonds. Further mutagenesis studies showed that the Ca2+-binding capability of OmpA-TT3R is indeed dependent on the proper formation of intra-repeat disulfide bonds, which help to fix a conserved glycine residue at its proper position for Ca2+ coordination. Additionally, despite lacking inter repeat disulfide bonds, the interfaces between adjacent OmpA-TT3Rs are enhanced by both hydrophobic and conserved aromatic-proline interactions.

  11. A SAM-dependent methyltransferase cotranscribed with arsenate reductase alters resistance to peptidyl transferase center-binding antibiotics in Azospirillum brasilense Sp7.

    Science.gov (United States)

    Singh, Sudhir; Singh, Chhaya; Tripathi, Anil Kumar

    2014-05-01

    The genome of Azospirillum brasilense harbors a gene encoding S-adenosylmethionine-dependent methyltransferase, which is located downstream of an arsenate reductase gene. Both genes are cotranscribed and translationally coupled. When they were cloned and expressed individually in an arsenate-sensitive strain of Escherichia coli, arsenate reductase conferred tolerance to arsenate; however, methyltransferase failed to do so. Sequence analysis revealed that methyltransferase was more closely related to a PrmB-type N5-glutamine methyltransferase than to the arsenate detoxifying methyltransferase ArsM. Insertional inactivation of prmB gene in A. brasilense resulted in an increased sensitivity to chloramphenicol and resistance to tiamulin and clindamycin, which are known to bind at the peptidyl transferase center (PTC) in the ribosome. These observations suggested that the inability of prmB:km mutant to methylate L3 protein might alter hydrophobicity in the antibiotic-binding pocket of the PTC, which might affect the binding of chloramphenicol, clindamycin, and tiamulin differentially. This is the first report showing the role of PrmB-type N5-glutamine methyltransferases in conferring resistance to tiamulin and clindamycin in any bacterium.

  12. Elimination of Endogenous Toxin, Creatinine from Blood Plasma Depends on Albumin Conformation: Site Specific Uremic Toxicity & Impaired Drug Binding

    Science.gov (United States)

    Varshney, Ankita; Rehan, Mohd; Subbarao, Naidu; Rabbani, Gulam; Khan, Rizwan Hasan

    2011-01-01

    Uremic syndrome results from malfunctioning of various organ systems due to the retention of uremic toxins which, under normal conditions, would be excreted into the urine and/or metabolized by the kidneys. The aim of this study was to elucidate the mechanisms underlying the renal elimination of uremic toxin creatinine that accumulate in chronic renal failure. Quantitative investigation of the plausible correlations was performed by spectroscopy, calorimetry, molecular docking and accessibility of surface area. Alkalinization of normal plasma from pH 7.0 to 9.0 modifies the distribution of toxin in the body and therefore may affect both the accumulation and the rate of toxin elimination. The ligand loading of HSA with uremic toxin predicts several key side chain interactions of site I that presumably have the potential to impact the specificity and impaired drug binding. These findings provide useful information for elucidating the complicated mechanism of toxin disposition in renal disease state. PMID:21386972

  13. Chirality dependence of dipole matrix element of carbon nanotubes in axial magnetic field: A third neighbor tight binding approach

    Science.gov (United States)

    Chegel, Raad; Behzad, Somayeh

    2014-02-01

    We have studied the electronic structure and dipole matrix element, D, of carbon nanotubes (CNTs) under magnetic field, using the third nearest neighbor tight binding model. It is shown that the 1NN and 3NN-TB band structures show differences such as the spacing and mixing of neighbor subbands. Applying the magnetic field leads to breaking the degeneracy behavior in the D transitions and creates new allowed transitions corresponding to the band modifications. It is found that |D| is proportional to the inverse tube radius and chiral angle. Our numerical results show that amount of filed induced splitting for the first optical peak is proportional to the magnetic field by the splitting rate ν11. It is shown that ν11 changes linearly and parabolicly with the chiral angle and radius, respectively.

  14. HIF-1-dependent regulation of lifespan in Caenorhabditis elegans by the acyl-CoA-binding protein MAA-1

    DEFF Research Database (Denmark)

    Shamalnasab, Mehrnaz; Dhaoui, Manel; Thondamal, Manjunatha

    2017-01-01

    In yeast, the broadly conserved acyl-CoA-binding protein (ACBP) is a negative regulator of stress resistance and longevity. Here, we have turned to the nematode C. elegans as a model organism in which to determine whether ACBPs play similar roles in multicellular organisms. We systematically...... inactivated each of the seven C. elegans ACBP paralogs and found that one of them, maa-1 (which encodes membrane-associated ACBP 1), is indeed involved in the regulation of longevity. In fact, loss of maa-1 promotes lifespan extension and resistance to different types of stress. Through genetic and gene...... of the proteome. Our work extends to C. elegans the role of ACBP in aging, implicates HIF-1 in the increase of lifespan of maa-1-deficient worms, and sheds light on the anti-aging function of HIF-1. Given that both ACBP and HIF-1 are highly conserved, our results suggest the possible involvement of these proteins...

  15. Modulation of microtubule assembly by the HIV-1 Tat protein is strongly dependent on zinc binding to Tat

    Directory of Open Access Journals (Sweden)

    Muller Sylviane

    2008-07-01

    Full Text Available Abstract Background During HIV-1 infection, the Tat protein plays a key role by transactivating the transcription of the HIV-1 proviral DNA. In addition, Tat induces apoptosis of non-infected T lymphocytes, leading to a massive loss of immune competence. This apoptosis is notably mediated by the interaction of Tat with microtubules, which are dynamic components essential for cell structure and division. Tat binds two Zn2+ ions through its conserved cysteine-rich region in vitro, but the role of zinc in the structure and properties of Tat is still controversial. Results To investigate the role of zinc, we first characterized Tat apo- and holo-forms by fluorescence correlation spectroscopy and time-resolved fluorescence spectroscopy. Both of the Tat forms are monomeric and poorly folded but differ by local conformational changes in the vicinity of the cysteine-rich region. The interaction of the two Tat forms with tubulin dimers and microtubules was monitored by analytical ultracentrifugation, turbidity measurements and electron microscopy. At 20°C, both of the Tat forms bind tubulin dimers, but only the holo-Tat was found to form discrete complexes. At 37°C, both forms promoted the nucleation and increased the elongation rates of tubulin assembly. However, only the holo-Tat increased the amount of microtubules, decreased the tubulin critical concentration, and stabilized the microtubules. In contrast, apo-Tat induced a large amount of tubulin aggregates. Conclusion Our data suggest that holo-Tat corresponds to the active form, responsible for the Tat-mediated apoptosis.

  16. Promiscuous ligand-dependent activation of the Ah receptor: chemicals in crude extracts from commercial and consumer products bind to and activate the Ah receptor and Ah receptor-dependent gene expression

    Energy Technology Data Exchange (ETDEWEB)

    Denison, M.; Rogers, W.; Bohonowych, J.; Zhao, B. [Dept. of Environmental Toxicology, Univ. of California, Davis (United States)

    2004-09-15

    2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD, dioxin) and related halogenated and polycyclic aromatic hydrocarbons (HAHs and PAHs) produce a variety of toxic and biological effects, the majority of which are mediated by their ability to bind to and activate the Ah receptor (AhR) and AhR-dependent gene expression. While previous studies suggested that the physiochemical characteristics of AhR ligands (i.e. HAH and PAH agonists) must meet a defined set of criteria, it has recently become abundantly clear that the AhR can be bound and activated by structurally diverse range of synthetic and naturally occurring chemicals. Based on the spectrum of AhR ligands identified to date, the structural promiscuity of AhR ligands is significantly more diverse than that observed for other liganddependent nuclear receptors. However, a detailed understanding of the structural diversity of AhR ligands and their respective biological and toxicological activities remains to be established and could provide insights into the identity of endogenous ligands. Over the past several years we have developed and utilized several AhR-based in vitro and cell-based bioassay systems to screen pure chemicals and chemical libraries as well as mixtures of chemicals with the goal of defining the spectrum of chemicals that can bind to and activate/inhibit the AhR and AhR-dependent gene expression. In addition, demonstration of the presence of AhR agonists/antagonists in extracts containing complex mixtures of chemicals from a variety of biological and environmental samples, coupled with AhR bioassay-based fractionation procedures, provides an avenue in which to identify novel AhR ligands. In previous preliminary screening studies we demonstrated the presence of AhR agonists in extracts of commercial and consumer products using an in vitro guinea pig hepatic AhR DNA binding and mouse gene induction assays. Here we have extended these studies and have examined the ability of crude DMSO and ethanol extracts

  17. Modeling of Salt Solubilities in Mixed Solvents

    DEFF Research Database (Denmark)

    Chiavone-Filho, O.; Rasmussen, Peter

    2000-01-01

    A method to correlate and predict salt solubilities in mixed solvents using a UNIQUAC+Debye-Huckel model is developed. The UNIQUAC equation is applied in a form with temperature-dependent parameters. The Debye-Huckel model is extended to mixed solvents by properly evaluating the dielectric...... constants and the liquid densities of the solvent media. To normalize the activity coefficients, the symmetric convention is adopted. Thermochemical properties of the salt are used to estimate the solubility product. It is shown that the proposed procedure can describe with good accuracy a series of salt...

  18. Tight-binding approximations to time-dependent density functional theory — A fast approach for the calculation of electronically excited states

    Energy Technology Data Exchange (ETDEWEB)

    Rüger, Robert, E-mail: rueger@scm.com [Scientific Computing & Modelling NV, De Boelelaan 1083, 1081 HV Amsterdam (Netherlands); Department of Theoretical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam (Netherlands); Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Linnéstr. 2, 04103 Leipzig (Germany); Lenthe, Erik van [Scientific Computing & Modelling NV, De Boelelaan 1083, 1081 HV Amsterdam (Netherlands); Heine, Thomas [Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Linnéstr. 2, 04103 Leipzig (Germany); Visscher, Lucas [Department of Theoretical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam (Netherlands)

    2016-05-14

    We propose a new method of calculating electronically excited states that combines a density functional theory based ground state calculation with a linear response treatment that employs approximations used in the time-dependent density functional based tight binding (TD-DFTB) approach. The new method termed time-dependent density functional theory TD-DFT+TB does not rely on the DFTB parametrization and is therefore applicable to systems involving all combinations of elements. We show that the new method yields UV/Vis absorption spectra that are in excellent agreement with computationally much more expensive TD-DFT calculations. Errors in vertical excitation energies are reduced by a factor of two compared to TD-DFTB.

  19. Heparin/heparan sulfates bind to and modulate neuronal L-type (Cav1.2) voltage-dependent Ca2+ channels

    DEFF Research Database (Denmark)

    Garau, Gianpiero; Magotti, Paola; Heine, Martin

    2015-01-01

    Our previous studies revealed that L-type voltage-dependent Ca2+ channels (Cav1.2 L-VDCCs) are modulated by the neural extracellular matrix backbone, polyanionic glycan hyaluronic acid. Here we used isothermal titration calorimetry and screened a set of peptides derived from the extracellular......M), integrating their enthalpic and entropic binding contributions. Interaction between heparin and recombinant as well as native full-length neuronal Cav1.2α1 channels was confirmed using the heparin–agarose pull down assay. Whole cell patch clamp recordings in HEK293 cells transfected with neuronal Cav1.......2 channels revealed that enzymatic digestion of highly sulfated heparan sulfates with heparinase 1 affects neither voltage-dependence of channel activation nor the level of steady state inactivation, but did speed up channel inactivation. Treatment of hippocampal cultures with heparinase 1 reduced the firing...

  20. The 3D protein of duck hepatitis A virus type 1 binds to a viral genomic 3' UTR and shows RNA-dependent RNA polymerase activity.

    Science.gov (United States)

    Zhang, Yu; Cao, Qianda; Wang, Mingshu; Jia, Renyong; Chen, Shun; Zhu, Dekang; Liu, Mafeng; Sun, Kunfeng; Yang, Qiao; Wu, Ying; Zhao, Xinxin; Chen, Xiaoyue; Cheng, Anchun

    2017-12-01

    To explore the RNA-dependent RNA polymerase (RdRP) function of the 3D protein of duck hepatitis A virus type 1 (DHAV-1), the gene was cloned into the pET-32a(+) vector for prokaryotic expression. The 3' untranslated region (3' UTR) of DHAV-1 together with a T7 promoter was cloned into the pMD19-T vector for in vitro transcription of 3' UTR RNA, which was further used as a template in RNA-dependent RNA polymerization. In this study, three methods were applied to analyze the RdRP function of the 3D protein: (1) ammonium molybdate spectrophotometry to detect pyrophosphate produced during polymerization; (2) quantitative reverse transcription PCR (RT-qPCR) to investigate the changes in RNA quantity during polymerization; and (3) electrophoresis mobility shift assay to examine the interaction between the 3D protein and 3' UTR. The results showed the 3D protein was successfully expressed in bacteria culture supernatant in a soluble form, which could be purified by affinity chromatography. In 3D enzymatic activity assays, pyrophosphate and RNA were produced, the amounts of which increased based on approximative kinetics, and binding of the 3D protein to the 3' UTR was observed. These results indicate that prokaryotically expressed soluble DHAV-13D protein can bind to a viral genomic 3' UTR and exhibit RdRP activity.

  1. Maize DRE-binding proteins DBF1 and DBF2 are involved in rab17 regulation through the drought-responsive element in an ABA-dependent pathway.

    Science.gov (United States)

    Kizis, Dimosthenis; Pagès, Montserrat

    2002-06-01

    The abscisic acid-responsive gene rab17 of maize is expressed during late embryogenesis, and is induced by ABA and desiccation in embryo and vegetative tissues. ABRE and DRE cis-elements are involved in regulation of the gene by ABA and drought. Using yeast one-hybrid screening, we isolated two cDNAs encoding two new DRE-binding proteins, designated DBF1 and DBF2, that are members of the AP2/EREBP transcription factor family. Analysis of mRNA accumulation profiles showed that DBF1 is induced during maize embryogenesis and after desiccation, NaCl and ABA treatments in plant seedlings, whereas the DBF2 mRNA is not induced. DNA-binding preferences of DBFs were analysed by electrophoretic mobility shift assays, and showed that both DBF1 and DBF2 bound to the wild-type DRE2 element, but not to the DRE2 mutant or to the DRE1 element which differs only in a single nucleotide. Transactivation activity using particle bombardment showed that DBF1 functioned as activator of DRE2-dependent transcription of rab17 promoter by ABA, whereas DBF2 overexpression had a repression action downregulating not only the basal promoter activity, but also the ABA effect. These results show that ABA plays a role in the regulation of DBF activity, and suggests the existence of an ABA-dependent pathway for the regulation of genes through the C-repeat/DRE element.

  2. Evaluations of in vitro metabolism, drug-drug interactions mediated by reversible and time-dependent inhibition of CYPs, and plasma protein binding of MMB4 DMS.

    Science.gov (United States)

    Hong, S Peter; Lusiak, Bozena D; Burback, Brian L; Johnson, Jerry D

    2013-01-01

    1,1'-Methylenebis[4-[(hydroxyimino)methyl]-pyridinium] (MMB4) dimethanesulfonate (DMS) is a bisquaternary pyridinium aldoxime that reactivates acetylcholinesterase inhibited by organophosphorus nerve agent. Drug metabolism and plasma protein binding for MMB4 DMS were examined using various techniques and a wide range of species. When (14)C-MMB4 DMS was incubated in liver microsomes, 4-pyridine aldoxime (4-PA) and an additional metabolite were detected in all species tested. Identity of the additional metabolite was postulated to be isonicotinic acid (INA) based on liquid chromatography with a tandem mass spectrometry analysis, which was confirmed by comparison with authentic INA. Formation of INA was dependent on species, with the highest level found in monkey liver microsomes. The MMB4 DMS exhibited reversible inhibition in a concentration-dependent manner toward cytochrome P450 1A2 (CYP1A2), CYP2C9, CYP2C19, CYP2D6, and CYP3A4 in human liver microsomes showing the highest inhibition for CYP2D6. Human recombinant CYPs were used to evaluate inhibitory curves more adequately and determine detailed kinetic constants for reversible inhibition and potential time-dependent inhibition (TDI). The MMB4 DMS exhibited reversible inhibition toward human-recombinant CYP2D6 with an inhibition constant (K i) value of 66.6 µmol/L. Based on the k inact/K I values, MMB4 DMS was found to exhibit the most potent TDI toward CYP2D6. The MMB4 DMS at 5 different concentrations was incubated in plasma for 5 hours using an equilibrium dialysis device. For all species tested, there were no concentration-dependent changes in plasma protein binding, ranging from 10% to 17%. These results suggest that MMB4 was not extensively bound to plasma protein, and there were no overt species-related differences in the extent of MMB4 bound to plasma protein.

  3. ATP-dependent chromatin remodeling and histone binding by the Cockayne syndrome B DNA repair-transcription coupling factor.

    NARCIS (Netherlands)

    E. Citterio (Elisabetta); V. van den Boom (Vincent); G. Schnitzler; R. Kanaar (Roland); E. Bonte (Edgar); R.E. Kingston; J.H.J. Hoeijmakers (Jan); W. Vermeulen (Wim)

    2000-01-01

    textabstractThe Cockayne syndrome B protein (CSB) is required for coupling DNA excision repair to transcription in a process known as transcription-coupled repair (TCR). Cockayne syndrome patients show UV sensitivity and severe neurodevelopmental abnormalities. CSB is a DNA-dependent ATPase of the

  4. Hazardous solvent substitution

    International Nuclear Information System (INIS)

    Twitchell, K.E.

    1995-01-01

    This article is an overview of efforts at INEL to reduce the generation of hazardous wastes through the elimination of hazardous solvents. To aid in their efforts, a number of databases have been developed and will become a part of an Integrated Solvent Substitution Data System. This latter data system will be accessible through Internet

  5. Characterization of a Highly Conserved Binding Site of Mlh1 Required for Exonuclease I-Dependent Mismatch Repair

    DEFF Research Database (Denmark)

    Dherin, Claudine; Gueneau, Emeric; Francin, Mathilde

    2009-01-01

    Mlh1 is an essential factor of mismatch repair (MMR) and meiotic recombination. It interacts through its C-terminal region with MutL homologs and proteins involved in DNA repair and replication. In this study, we identified the site of yeast Mlh1 critical for the interaction with Exo1, Ntg2......, and Sgs1 proteins, designated as site S2 by reference to the Mlh1/Pms1 heterodimerization site S1. We show that site S2 is also involved in the interaction between human MLH1 and EXO1 or BLM. Binding at this site involves a common motif on Mlh1 partners that we called the MIP-box for the Mlh1 interacting...... protein box. Direct and specific interactions between yeast Mlh1 and peptides derived from Exo1, Ntg2, and Sgs1 and between human MLH1 and peptide derived from EXO1 and BLM were measured with K(d) values ranging from 8.1 to 17.4 microM. In Saccharomyces cerevisiae, a mutant of Mlh1 targeted at site S2...

  6. Binding mode dependent signaling for the detection of Cu2 +: An experimental and theoretical approach with practical applications

    Science.gov (United States)

    Ghosh, Soumen; Khan, Mehebub Ali; Ganguly, Aniruddha; Masum, Abdulla Al; Alam, Md. Akhtarul; Guchhait, Nikhil

    2018-02-01

    Two amido-schiff bases (3-Hydroxy-naphthalene-2-carboxylic acid pyren-1-ylmethylene-hydrazide and Naphthalene-2-carboxylic acid pyren-1-ylmethylene-hydrazide) have been synthesized having a common structural unit and only differs by a -OH group in the naphthalene ring. Both of them can detect Cu2 + ion selectively in semi-aqueous medium in distinctly different output modes (one detects Cu2 + by naked-eye color change where as the other detects Cu2 + by fluorescence enhancement). The difference in the binding of Cu 2 + with the compounds is the reason for this observation. The detection limit is found to be micromolar region for compound which contains -OH group whereas the compound without -OH group detects copper in nano-molar region. DFT calculations have been performed in order to demonstrate the structure of the compounds and their copper complexes. Practical utility has been explored by successful paper strip response of both the compounds. The biological applications have been evaluated in RAW 264.7.

  7. Binding of TFIIIC to sine elements controls the relocation of activity-dependent neuronal genes to transcription factories.

    Directory of Open Access Journals (Sweden)

    Luca Crepaldi

    Full Text Available In neurons, the timely and accurate expression of genes in response to synaptic activity relies on the interplay between epigenetic modifications of histones, recruitment of regulatory proteins to chromatin and changes to nuclear structure. To identify genes and regulatory elements responsive to synaptic activation in vivo, we performed a genome-wide ChIPseq analysis of acetylated histone H3 using somatosensory cortex of mice exposed to novel enriched environmental (NEE conditions. We discovered that Short Interspersed Elements (SINEs located distal to promoters of activity-dependent genes became acetylated following exposure to NEE and were bound by the general transcription factor TFIIIC. Importantly, under depolarizing conditions, inducible genes relocated to transcription factories (TFs, and this event was controlled by TFIIIC. Silencing of the TFIIIC subunit Gtf3c5 in non-stimulated neurons induced uncontrolled relocation to TFs and transcription of activity-dependent genes. Remarkably, in cortical neurons, silencing of Gtf3c5 mimicked the effects of chronic depolarization, inducing a dramatic increase of both dendritic length and branching. These findings reveal a novel and essential regulatory function of both SINEs and TFIIIC in mediating gene relocation and transcription. They also suggest that TFIIIC may regulate the rearrangement of nuclear architecture, allowing the coordinated expression of activity-dependent neuronal genes.

  8. Binding of TFIIIC to sine elements controls the relocation of activity-dependent neuronal genes to transcription factories.

    Science.gov (United States)

    Crepaldi, Luca; Policarpi, Cristina; Coatti, Alessandro; Sherlock, William T; Jongbloets, Bart C; Down, Thomas A; Riccio, Antonella

    2013-01-01

    In neurons, the timely and accurate expression of genes in response to synaptic activity relies on the interplay between epigenetic modifications of histones, recruitment of regulatory proteins to chromatin and changes to nuclear structure. To identify genes and regulatory elements responsive to synaptic activation in vivo, we performed a genome-wide ChIPseq analysis of acetylated histone H3 using somatosensory cortex of mice exposed to novel enriched environmental (NEE) conditions. We discovered that Short Interspersed Elements (SINEs) located distal to promoters of activity-dependent genes became acetylated following exposure to NEE and were bound by the general transcription factor TFIIIC. Importantly, under depolarizing conditions, inducible genes relocated to transcription factories (TFs), and this event was controlled by TFIIIC. Silencing of the TFIIIC subunit Gtf3c5 in non-stimulated neurons induced uncontrolled relocation to TFs and transcription of activity-dependent genes. Remarkably, in cortical neurons, silencing of Gtf3c5 mimicked the effects of chronic depolarization, inducing a dramatic increase of both dendritic length and branching. These findings reveal a novel and essential regulatory function of both SINEs and TFIIIC in mediating gene relocation and transcription. They also suggest that TFIIIC may regulate the rearrangement of nuclear architecture, allowing the coordinated expression of activity-dependent neuronal genes.

  9. pH dependence of cyanide binding to the ferric heme domain of the direct oxygen sensor from Escherichia coli and the effect of alkaline denaturation.

    Science.gov (United States)

    Bidwai, Anil K; Ok, Esther Y; Erman, James E

    2008-09-30

    The spectrum of the ferric heme domain of the direct oxygen sensor protein from Escherichia coli ( EcDosH) has been measured between pH 3.0 and 12.6. EcDosH undergoes acid denaturation with an apparent p K a of 4.24 +/- 0.05 and a Hill coefficient of 3.1 +/- 0.6 and reversible alkaline denaturation with a p K a of 9.86 +/- 0.04 and a Hill coefficient of 1.1 +/- 0.1. Cyanide binding to EcDosH has been investigated between pH 4 and 11. The EcDosH-cyanide complex is most stable at pH 9 with a K D of 0.29 +/- 0.06 microM. The kinetics of cyanide binding are monophasic between pH 4 and 8. At pH >or=8.5, the reaction is biphasic with the fast phase dependent upon the cyanide concentration and the slow phase independent of cyanide. The slow phase is attributed to conversion of denatured EcDosH to the native state, with a pH-independent rate of 0.052 +/- 0.006 s (-1). The apparent association rate constant for cyanide binding to EcDosH increases from 3.6 +/- 0.1 M (-1) s (-1) at pH 4 to 520 +/- 20 M (-1) s (-1) at pH 11. The dissociation rate constant averages (8.6 +/- 1.3) x 10 (-5) s (-1) between pH 5 and 9, increasing to (1.4 +/- 0.1) x 10 (-3) s (-1) at pH 4 and (2.5 +/- 0.1) x 10 (-3) s (-1) at pH 12.2. The mechanism of cyanide binding is consistent with preferential binding of the cyanide anion to native EcDosH. The reactions of imidazole and H 2O 2 with ferric EcDosH were also investigated and show little reactivity.

  10. Membrane-Dependent Effects of a Cytoplasmic Helix on the Structure and Drug Binding of the Influenza Virus M2 Protein

    Science.gov (United States)

    Cady, Sarah; Wang, Tuo; Hong, Mei

    2011-01-01

    The influenza A M2 protein forms a proton channel for virus infection and also mediates virus assembly and budding. The minimum protein length that encodes both functions contains the transmembrane (TM) domain (roughly residues 22 to 46) for the amantadine-sensitive proton-channel activity and an amphipathic cytoplasmic helix (roughly residues 45 to 62) for curvature induction and virus budding. However, structural studies involving the TM domain with or without the amphipathic helix differed on the drug-binding site. Here we use solid-state NMR spectroscopy to determine the amantadine binding site in the cytoplasmic-helix-containing M2(21–61). 13C-2H distance measurements of 13C-labeled protein and 2H-labeled amantadine showed that in DMPC bilayers, the first equivalent of drug bound S31 inside the M2(21–61) pore, similar to the behavior of M2TM in DMPC bilayers. The non-specific surface site of D44 observed in M2TM is disfavored in the longer peptide. Thus, the pharmacologically relevant drug-binding site in the fully functional M2(21–61) is S31 in the TM pore. Interestingly, when M2(21–61) was reconstituted into a virus-mimetic membrane containing 30% cholesterol, no chemical shift perturbation was observed for pore-lining residues, while M2TM in the same membrane exhibited drug-induced chemical shift changes. Reduction of the cholesterol level and the use of unsaturated phospholipids shifted the conformational equilibrium of M2TM fully to the bound state, but did not rescue drug binding to M2(21–61). These results suggest that the amphipathic helix, together with cholesterol, modulates the ability of the TM helices to bind amantadine. Thus, the M2 protein interacts with the lipid membrane and small-molecule inhibitors in a complex fashion, and a careful examination of the environmental dependence of the protein conformation is required to fully understand the structure-function relation of this protein. PMID:21661724

  11. Caustic-Side Solvent Extraction: Chemical and Physical Properties of the Optimized Solvent

    Energy Technology Data Exchange (ETDEWEB)

    Delmau, L.H.

    2002-10-08

    This work was undertaken to optimize the solvent used in the Caustic Side Solvent Extraction (CSSX) process and to measure key chemical and physical properties related to its performance in the removal of cesium from the alkaline high-level salt waste stored in tanks at the Savannah River Site. The need to adjust the solvent composition arose from the prior discovery that the previous baseline solvent was supersaturated with respect to the calixarene extractant. The following solvent-component concentrations in Isopar{reg_sign} L diluent are recommended: 0.007 M calix[4]arene-bis(tert-octylbenzo-crown-6) (BOBCalixC6) extractant, 0.75 M 1-(2,2,3,3-tetrafluoropropoxy)-3-(4-sec-butylphenoxy)-2-propanol (Cs-7SB) phase modifier, and 0.003 M tri-n-octylamine (TOA) stripping aid. Criteria for this selection included BOBCalixC6 solubility, batch cesium distribution ratios (D{sub Cs}), calculated flowsheet robustness, third-phase formation, coalescence rate (dispersion numbers), and solvent density. Although minor compromises within acceptable limits were made in flowsheet robustness and solvent density, significant benefits were gained in lower risk of third-phase formation and lower solvent cost. Data are also reported for the optimized solvent regarding the temperature dependence of D{sub Cs} in extraction, scrubbing, and stripping (ESS); ESS performance on recycle; partitioning of BOBCalixC6, Cs-7SB, and TOA to aqueous process solutions; partitioning of organic anions; distribution of metals; solvent phase separation at low temperatures; solvent stability to elevated temperatures; and solvent density and viscosity. Overall, the technical risk of the CSSX process has been reduced by resolving previously identified issues and raising no new issues.

  12. Being First Matters: Topographical Representational Similarity Analysis of ERP Signals Reveals Separate Networks for Audiovisual Temporal Binding Depending on the Leading Sense.

    Science.gov (United States)

    Cecere, Roberto; Gross, Joachim; Willis, Ashleigh; Thut, Gregor

    2017-05-24

    In multisensory integration, processing in one sensory modality is enhanced by complementary information from other modalities. Intersensory timing is crucial in this process because only inputs reaching the brain within a restricted temporal window are perceptually bound. Previous research in the audiovisual field has investigated various features of the temporal binding window, revealing asymmetries in its size and plasticity depending on the leading input: auditory-visual (AV) or visual-auditory (VA). Here, we tested whether separate neuronal mechanisms underlie this AV-VA dichotomy in humans. We recorded high-density EEG while participants performed an audiovisual simultaneity judgment task including various AV-VA asynchronies and unisensory control conditions (visual-only, auditory-only) and tested whether AV and VA processing generate different patterns of brain activity. After isolating the multisensory components of AV-VA event-related potentials (ERPs) from the sum of their unisensory constituents, we ran a time-resolved topographical representational similarity analysis (tRSA) comparing the AV and VA ERP maps. Spatial cross-correlation matrices were built from real data to index the similarity between the AV and VA maps at each time point (500 ms window after stimulus) and then correlated with two alternative similarity model matrices: AV maps = VA maps versus AV maps ≠ VA maps The tRSA results favored the AV maps ≠ VA maps model across all time points, suggesting that audiovisual temporal binding (indexed by synchrony perception) engages different neural pathways depending on the leading sense. The existence of such dual route supports recent theoretical accounts proposing that multiple binding mechanisms are implemented in the brain to accommodate different information parsing strategies in auditory and visual sensory systems. SIGNIFICANCE STATEMENT Intersensory timing is a crucial aspect of multisensory integration, determining whether and how

  13. LSD1 demethylase and the methyl-binding protein PHF20L1 prevent SET7 methyltransferase-dependent proteolysis of the stem-cell protein SOX2.

    Science.gov (United States)

    Zhang, Chunxiao; Hoang, Nam; Leng, Feng; Saxena, Lovely; Lee, Logan; Alejo, Salvador; Qi, Dandan; Khal, Anthony; Sun, Hong; Lu, Fei; Zhang, Hui

    2018-03-09

    The pluripotency-controlling stem-cell protein SRY-box 2 (SOX2) plays a pivotal role in maintaining the self-renewal and pluripotency of embryonic stem cells and also of teratocarcinoma or embryonic carcinoma cells. SOX2 is monomethylated at lysine 119 (Lys-119) in mouse embryonic stem cells by the SET7 methyltransferase, and this methylation triggers ubiquitin-dependent SOX2 proteolysis. However, the molecular regulators and mechanisms controlling SET7-induced SOX2 proteolysis are unknown. Here, we report that in human ovarian teratocarcinoma PA-1 cells, methylation-dependent SOX2 proteolysis is dynamically regulated by the LSD1 lysine demethylase and a methyl-binding protein, PHD finger protein 20-like 1 (PHF20L1). We found that LSD1 not only removes the methyl group from monomethylated Lys-117 (equivalent to Lys-119 in mouse SOX2), but it also demethylates monomethylated Lys-42 in SOX2, a reaction that SET7 also regulated and that also triggered SOX2 proteolysis. Our studies further revealed that PHF20L1 binds both monomethylated Lys-42 and Lys-117 in SOX2 and thereby prevents SOX2 proteolysis. Down-regulation of either LSD1 or PHF20L1 promoted SOX2 proteolysis, which was prevented by SET7 inactivation in both PA-1 and mouse embryonic stem cells. Our studies also disclosed that LSD1 and PHF20L1 normally regulate the growth of pluripotent mouse embryonic stem cells and PA-1 cells by preventing methylation-dependent SOX2 proteolysis. In conclusion, our findings reveal an important mechanism by which the stability of the pluripotency-controlling stem-cell protein SOX2 is dynamically regulated by the activities of SET7, LSD1, and PHF20L1 in pluripotent stem cells. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. Manipulation of the membrane binding site of vitamin K-dependent proteins: Enhanced biological function of human factor VII

    OpenAIRE

    Shah, Amit M.; Kisiel, Walter; Foster, Donald C.; Nelsestuen, Gary L.

    1998-01-01

    Recent studies suggested that modification of the membrane contact site of vitamin K-dependent proteins may enhance the membrane affinity and function of members of this protein family. The properties of a factor VII mutant, factor VII-Q10E32, relative to wild-type factor VII (VII, containing P10K32), have been compared. Membrane affinity of VII-Q10E32 was about 20-fold higher than that of wild-type factor VII. The rate of autoactivation VII-Q10E32 with soluble tissue factor was 100-fold fast...

  15. Preferential binding effects on protein structure and dynamics revealed by coarse-grained Monte Carlo simulation

    Science.gov (United States)

    Pandey, R. B.; Jacobs, D. J.; Farmer, B. L.

    2017-05-01

    The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered. While the radius of gyration (Rg) of the protein exhibits a non-monotonic dependence on solvent interaction over a wide range of f within an effective medium, an abrupt collapse in Rg occurs in a narrow range of f when solute molecules rapidly bind to a preferential set of sites on the protein. The structure factor S(q) of the protein with wave vector (q) becomes oscillatory in the collapsed state, which reflects segmental correlations caused by spatial fluctuations in solute-protein binding. Spatial fluctuations in solute binding also modify the effective dimension (D) of the protein in fibrous (D ˜ 1.3), random-coil (D ˜ 1.75), and globular (D ˜ 3) conformational ensembles as the interaction strength increases, which differ from an effective medium with respect to the magnitude of D and the length scale.

  16. Second site escape of a T20-dependent HIV-1 variant by a single amino acid change in the CD4 binding region of the envelope glycoprotein

    Directory of Open Access Journals (Sweden)

    Berkhout Ben

    2006-11-01

    Full Text Available Abstract Background We previously described the selection of a T20-dependent human immunodeficiency virus type-1 (HIV-1 variant in a patient on T20 therapy. The fusion inhibitor T20 targets the viral envelope (Env protein by blocking a conformational switch that is critical for viral entry into the host cell. T20-dependent viral entry is the result of 2 mutations in Env (GIA-SKY, creating a protein that undergoes a premature conformational switch, and the presence of T20 prevents this premature switch and rescues viral entry. In the present study, we performed 6 independent evolution experiments with the T20-dependent HIV-1 variant in the absence of T20, with the aim to identify second site compensatory changes, which may provide new mechanistic insights into Env function and the T20-dependence mechanism. Results Escape variants with improved replication capacity appeared within 42 days in 5 evolution cultures. Strikingly, 3 cultures revealed the same single amino acid change in the CD4 binding region of Env (glycine at position 431 substituted for arginine: G431R. This mutation was sufficient to abolish the T20-dependence phenotype and restore viral replication in the absence of T20. The GIA-SKY-G431R escape variant produces an Env protein that exhibits reduced syncytia formation and reduced cell-cell fusion activity. The escape variant was more sensitive to an antibody acting on an early gp41 intermediate, suggesting that the G431R mutation helps preserve a pre-fusion Env conformation, similar to T20 action. The escape variant was also less sensitive to soluble CD4, suggesting a reduced CD4 receptor affinity. Conclusion The forced evolution experiments indicate that the premature conformational switch of the T20-dependent HIV-1 Env variant (GIA-SKY can be corrected by a second site mutation in Env (GIA-SKY-G431R that affects the interaction with the CD4 receptor.

  17. Crystal complexes of a predicted S-adenosylmethionine-dependent methyltransferase reveal a typical AdoMet binding domain and a substrate recognition domain

    Energy Technology Data Exchange (ETDEWEB)

    Miller, D.J.; Ouellette, N.; Evodokimova, E.; Savchenko, A.; Edwards, A.; Anderson, W.F. (Toronto); (NWU)

    2010-03-08

    S-adenosyl-L-methionine-dependent methyltransferases (MTs) are abundant, and highly conserved across phylogeny. These enzymes use the cofactor AdoMet to methylate a wide variety of molecular targets, thereby modulating important cellular and metabolic activities. Thermotoga maritima protein 0872 (TM0872) belongs to a large sequence family of predicted MTs, ranging phylogenetically from relatively simple bacteria to humans. The genes for many of the bacterial homologs are located within operons involved in cell wall synthesis and cell division. Despite preliminary biochemical studies in E. coli and B. subtilis, the substrate specificity of this group of more than 150 proteins is unknown. As part of the Midwest Center for Structural Genomics initiative (www.mcsg.anl.gov), we have determined the structure of TM0872 in complexes with AdoMet and with S-adenosyl-L-homocysteine (AdoHcy). As predicted, TM0872 has a typical MT domain, and binds endogenous AdoMet, or co-crystallized AdoHcy, in a manner consistent with other known MT structures. In addition, TM0872 has a second domain that is novel among MTs in both its location in the sequence and its structure. The second domain likely acts in substrate recognition and binding, and there is a potential substrate-binding cleft spanning the two domains. This long and narrow cleft is lined with positively charged residues which are located opposite the S{sup +}-CH{sub 3} bond, suggesting that a negatively charged molecule might be targeted for catalysis. However, AdoMet and AdoHcy are both buried, and access to the methyl group would presumably require structural rearrangement. These TM0872 crystal structures offer the first structural glimpses at this phylogenetically conserved sequence family.

  18. Hepatic 123I-insulin binding kinetics in non-insulin-dependent (Type 2) diabetic patients after i.v. bolus administration

    International Nuclear Information System (INIS)

    Oolbekkink, M.; Veen, E.A. van der; Heine, R.J.; Hollander, W. den; Nauta, J.J.P.

    1989-01-01

    Insulin binding kinetics in the liver were studied in non insulin dependent (Type 2) diabetic patients, by i.v. bolus administration of 123 I-insulin. Eight Type 2 diabetic patients were compared with six male volunteers. Uptake of 123 I-insulin by liver and kidneys was measured by dynamic scintigraphy with a gamma camera during 30 min. Images of liver and kidneys appeared within 2-3 min after administration of 123 I-insulin at a dose of 1 mCi (37 MBq). Peak radioactivity for the liver was found 7.5±0.2 and 6.9±0.3 min after injection for the healthy and the diabetic subjects, respectively (N.S.). The percentage 123 I-insulin hepatic uptake was not significantly different for the diabetic and the healthy subjects. Although a large variation exists for maximal uptake of radioactivity within both groups, the data suggest that binding differences in the liver in Type 2 diabetic patients, as compared to healthy subjects, may not account for hepatic insulin resistance. (orig.)

  19. Solvent - solute interaction

    International Nuclear Information System (INIS)

    Urbanczyk, A.; Kalinowski, M.K.

    1983-01-01

    The electronic absorption spectrum of vanadyl acetylacetonate has been studied in 15 organic solvents. It has been found that wavenumbers and molar absorptivities of the long-wavelength bands (d-d transitions) can be well described by a complementary Lewis acid-base model including Gutmann's donor number [Gutmann V., Wychera E., Inorg. Nucl. Chem. Letters 2, 257 (1966)] and acceptor number [Mayer U., Gutmann V., Gerger W., Monatsh. Chem. 106, 1235 (1975)] of a solvent. This model describes also the solvent effect of the hyperfine splitting constant, Asub(iso)( 51 V), from e.s.r. spectra of VOacac 2 . These observations are discussed in terms of the donor-acceptor concept for solvent-solute interactions. (Author)

  20. Solvent induced supramolecular anisotropy in molecular gels

    Energy Technology Data Exchange (ETDEWEB)

    Rogers, Michael A., E-mail: mroger09@uoguelph.ca [Department of Food Science, University of Guelph, Guelph, Ontario, N3C3X9 (Canada); Corradini, Maria G. [Department of Food Science, University of Massachusetts Amherst, Amherst, MA, 01003 (United States); Emge, Thomas [Department of Chemistry and Biochemistry, Rutgers University, New Brunswick, NJ, 08901 (United States)

    2017-06-15

    Herein is the first report of solvent induced anisotropy in 12-hydroxystearic acid self-assembled fibrillar networks. Increasing the chain length of polar solvent, such as nitriles and ketones, tailored the anisotropy of the fibrillar aggregates. 12HSA molecular gels, comprised of alkanes, exhibited an isotropic fibrillar network irrespective of the alkane chain length. In polar solvents, anisotropy, observed using 2D powder x-ray diffraction profiles, is correlated to a fibrillar supramolecular morphologies in long chain nitriles and ketones while sphereulitic crystals are correlated to x-ray diffraction patterns with an isotropic scatter intensity in short chain ketones and nitriles. These changes directly modify the final physical properties of the gels. - Highlights: • 12-HSA self-assembles into crystalline supramolecular morphologies depending on the solvent. • Alkanes, short chain nitriles and ketones led to 12-HSA displaying supramolecular isotropy. • In long chain nitriles and ketones, 12-HSA displays supramolecular anisotropy.

  1. Solvent induced supramolecular anisotropy in molecular gels

    International Nuclear Information System (INIS)

    Rogers, Michael A.; Corradini, Maria G.; Emge, Thomas

    2017-01-01

    Herein is the first report of solvent induced anisotropy in 12-hydroxystearic acid self-assembled fibrillar networks. Increasing the chain length of polar solvent, such as nitriles and ketones, tailored the anisotropy of the fibrillar aggregates. 12HSA molecular gels, comprised of alkanes, exhibited an isotropic fibrillar network irrespective of the alkane chain length. In polar solvents, anisotropy, observed using 2D powder x-ray diffraction profiles, is correlated to a fibrillar supramolecular morphologies in long chain nitriles and ketones while sphereulitic crystals are correlated to x-ray diffraction patterns with an isotropic scatter intensity in short chain ketones and nitriles. These changes directly modify the final physical properties of the gels. - Highlights: • 12-HSA self-assembles into crystalline supramolecular morphologies depending on the solvent. • Alkanes, short chain nitriles and ketones led to 12-HSA displaying supramolecular isotropy. • In long chain nitriles and ketones, 12-HSA displays supramolecular anisotropy.

  2. Full scale solvent extraction remedial results

    International Nuclear Information System (INIS)

    Cash, A.B.

    1992-01-01

    Sevenson Extraction Technology, Inc. has completed the development of the Soil Restoration Unit (initially developed by Terra-Kleen Corporation), a mobile, totally enclosed solvent extraction treatment facility for the removal of organic contaminated media is greater by a closed loop, counter current process that recycles all solvents. The solvents used are selected for the individual site dependant upon the contaminants, such as PCB's, oil, etc. and the soil conditions. A mixture of up to fourteen non-toxic solvents can be used for complicated sites. The full scale unit has been used to treat one superfund site, the Traband Site in Tulsa, Oklahoma, and is currently treating another superfund site, the Pinette's Salvage Yard Site in Washburn, Maine. The full scale Soil Restoration Unit has also been used at a non-superfund site, as part of a TSCA Research and Development permit. The results from these sites will be discussed in brief herein, and in more detail in the full paper

  3. Green and Bio-Based Solvents.

    Science.gov (United States)

    Calvo-Flores, Francisco G; Monteagudo-Arrebola, María José; Dobado, José A; Isac-García, Joaquín

    2018-04-24

    Chemical reactions and many of the procedures of separation and purification employed in industry, research or chemistry teaching utilize solvents massively. In the last decades, with the birth of Green Chemistry, concerns about the employment of solvents and the effects on human health, as well as its environmental impacts and its dependence on non-renewable raw materials for manufacturing most of them, has drawn the attention of the scientific community. In this work, we review the concept of green solvent and the properties and characteristics to be considered green. Additionally, we discuss the different possible routes to prepare many solvents from biomass, as an alternative way to those methods currently applied in the petrochemical industry.

  4. Thymosin-β4 (Tβ4) Blunts PDGF-Dependent Phosphorylation and Binding of AKT to Actin in Hepatic Stellate Cells

    Science.gov (United States)

    Reyes-Gordillo, Karina; Shah, Ruchi; Popratiloff, Anastas; Fu, Sidney; Hindle, Anna; Brody, Frederick; Rojkind, Marcos

    2011-01-01

    Hepatic stellate cell transdifferentiation is a key event in the fibrogenic cascade. Therefore, attempts to prevent and/or revert the myofibroblastic phenotype could result in novel therapeutic approaches to treat liver cirrhosis. The expression of platelet-derived growth factor (PDGF)-β receptor and the proliferative response to platelet-derived growth factor-ββ (PDGF-ββ) are hallmarks of the transdifferentiation of hepatic stellate cells (HSC). In this communication, we investigated whether thymosin-β4 (Tβ4), a chemokine expressed by HSC could prevent PDGF-BB-mediated proliferation and migration of cultured HSC. Using early passages of human HSC, we showed that Tβ4 inhibited cell proliferation and migration and prevented the expression of PDGF-β receptor (PDGF-βr), α-smooth muscle actin and α1(I) collagen mRNAs. Tβ4 also inhibited the reappearance of PDGF-βr after its PDGF-BB-dependent degradation. These PDGF-dependent events were associated with the inhibition of AKT phosphorylation at both T308 and S473 amino acid residues. The lack of AKT phosphorylation was not due to the inhibition of PDGF-βr phosphorylation, the activation of phosphoinositide 3-kinase (PI3K), pyruvate dehydrogenase kinase isozyme 1 (PDK1), and mammalian target of rapamycin (mTOR). We found that PDGF-BB induced AKT binding to actin, and that Tβ4 prevented this effect. Tβ4 also prevented the activation of freshly isolated HSC cultured in the presence of Dulbecco's modified Eagle's medium or Dulbecco's minimal essential medium containing 10% fetal bovine serum. In conclusion, overall, our findings suggest that Tβ4 by sequestering actin prevents binding of AKT, thus inhibiting its phosphorylation. Therefore, Tβ4 has the potential to be an antifibrogenic agent. PMID:21514425

  5. Guanosine 5'-triphosphate binding protein (G/sub i/) and two additional pertussis toxin substrates associated with muscarinic receptors in rat heart myocytes: characterization and age dependency

    International Nuclear Information System (INIS)

    Moscona-Amir, E.; Henis, Y.I.; Sokolovsky, M.

    1988-01-01

    The coupling of muscarinic receptors with G-proteins was investigated in cultured myocytes prepared from the hearts of newborn rats. The coupling was investigated in both young (5 days after plating) and aged (14 days after plating) cultures, in view of the completely different effects of 5'-guanylyl imidodiphosphate [Gpp(NH)p] on muscarinic agonist binding to homogenates from young vs aged cultures. Pretreatment of cultures from both ages by Bordetella pertussis toxin (IAP) was found to eliminate any Gpp(NH)p effect on carbamylcholine binding. IAP by itself induced a rightward shift in the carbamylcholine competition curve in homogenates from aged cultures, but no such effect was observed in homogenates from young cultures. IAP-catalyzed [ 32 P]ADP-ribosylation of membrane preparations from young and aged cultures revealed major differences between them. Young cultures exhibited a major IAP substrate at 40 kDa, which was also recognized by anti-α/sub i/ antibodies, and two novel IAP substrates at 28 and 42 kDa, which were weakly ADP-ribosylated by the toxin and were not recognized with either anti-α/sub i/ or anti-α 0 antibodies. In aged cultures, only the 40-kDa band (ribosylated to a lower degree) was detected. The parallel age-dependent changes in the three IAP substrates (28, 40, and 42 kDa) and in the interactions of the G-protein(s) with the muscarinic receptors strongly suggest close association between the two phenomena. All of these age-dependent changes in the G-protein related parameters were prevented by phosphatidylcholine-liposome treatment of the aged cultures. The role of the membrane lipid composition in these phenomena is discussed

  6. A simple model for solvation in mixed solvents. Applications to the stabilization and destabilization of macromolecular structures.

    Science.gov (United States)

    Schellman, J A

    1990-08-31

    The properties of a simple model for solvation in mixed solvents are explored in this paper. The model is based on the supposition that solvent replacement is a simple one-for-one substitution reaction at macromolecular sites which are independent of one another. This leads to a new form for the binding polynomial in which all terms are associated with ligand interchange rather than ligand addition. The principal solvent acts as one of the ligands. Thermodynamic analysis then shows that thermodynamic binding (i.e., selective interaction) depends on the properties of K'-1, whereas stoichiometric binding (site occupation) depends on K'. K' is a 'practical' interchange equilibrium constant given by (f3/f1)K, where K is the true equilibrium constant for the interchange of components 3 and 1 on the site and f3 and f4 denote their respective activity coefficients on the mole fraction scale. Values of K' less than unity lead to negative selective interaction. It is selective interaction and not occupation number which determines the thermodynamic effects of solvation. When K' greater than 100 on the mole fraction scale or K' greater than 2 on the molality scale (in water), the differences between stoichiometric binding and selective interaction become less than 1%. The theory of this paper is therefore necessary only for very weak binding constants. When K'-1 is small, large concentrations of the added solvent component are required to produce a thermodynamic effect. Under these circumstances the isotherms for the selective interaction and for the excess (or transfer) free energy are strongly dependent on the behavior of the activity coefficients of both solvent components. Two classes of behavior are described depending on whether the components display positive or negative deviations from Raoult's law. Examples which are discussed are aqueous solutions of urea and guanidinium chloride for positive deviations and of sucrose and glucose for negative deviations

  7. Effect of solvent alcohol on degradation of chlorinated hydrocarbons by γ-irradiation

    International Nuclear Information System (INIS)

    Nakagawa, Seiko

    2002-01-01

    1,1,2-Trichloro-trifluoroethane (CFC113) was dissolved in alkaline 1-butanol, 2-butanol, iso-butyl alcohol, and phenyl ethyl alcohol and irradiated with 60 Co gamma rays after being purged with pure nitrogen gas. In all these solvents, the concentration of CFC113 and hydroxide ion decreased and that of chloride ion increased with a dose observed in 2-propanol solution. The reaction efficiency increases in the following order: 1-butanol < iso-butyl alcohol < phenyl ethyl alcohol < 2-butanol < 2-propanol. The solvent effect will depend on the binding energy of the αC-H of the alcohol molecule and electron affinity and dipole moment of the ketones or aldehydes produced from the alcohols. (author)

  8. Anti-HIV-1 B cell responses are dependent on B cell precursor frequency and antigen-binding affinity.

    Science.gov (United States)

    Dosenovic, Pia; Kara, Ervin E; Pettersson, Anna-Klara; McGuire, Andrew T; Gray, Matthew; Hartweger, Harald; Thientosapol, Eddy S; Stamatatos, Leonidas; Nussenzweig, Michel C

    2018-04-16

    The discovery that humans can produce potent broadly neutralizing antibodies (bNAbs) to several different epitopes on the HIV-1 spike has reinvigorated efforts to develop an antibody-based HIV-1 vaccine. Antibody cloning from single cells revealed that nearly all bNAbs show unusual features that could help explain why it has not been possible to elicit them by traditional vaccination and instead would require a sequence of different immunogens. This idea is supported by experiments with genetically modified immunoglobulin (Ig) knock-in mice. Sequential immunization with a series of specifically designed immunogens was required to shepherd the development of bNAbs. However, knock-in mice contain superphysiologic numbers of bNAb precursor-expressing B cells, and therefore how these results can be translated to a more physiologic setting remains to be determined. Here we make use of adoptive transfer experiments using knock-in B cells that carry a synthetic intermediate in the pathway to anti-HIV-1 bNAb development to examine how the relationship between B cell receptor affinity and precursor frequency affects germinal center (GC) B cell recruitment and clonal expansion. Immunization with soluble HIV-1 antigens can recruit bNAb precursor B cells to the GC when there are as few as 10 such cells per mouse. However, at low precursor frequencies, the extent of clonal expansion is directly proportional to the affinity of the antigen for the B cell receptor, and recruitment to GCs is variable and dependent on recirculation.

  9. Lipopolysaccharide (LPS)-binding protein stimulates CD14-dependent Toll-like receptor 4 internalization and LPS-induced TBK1-IKKϵ-IRF3 axis activation.

    Science.gov (United States)

    Tsukamoto, Hiroki; Takeuchi, Shino; Kubota, Kanae; Kobayashi, Yohei; Kozakai, Sao; Ukai, Ippo; Shichiku, Ayumi; Okubo, Misaki; Numasaki, Muneo; Kanemitsu, Yoshitomi; Matsumoto, Yotaro; Nochi, Tomonori; Watanabe, Kouichi; Aso, Hisashi; Tomioka, Yoshihisa

    2018-05-14

    Toll-like receptor 4 (TLR4) is an indispensable immune receptor for lipopolysaccharide (LPS), a major component of the Gram-negative bacterial cell wall. Following LPS stimulation, TLR4 transmits the signal from the cell surface and becomes internalized in an endosome. However, the spatial regulation of TLR4 signaling is not fully understood. Here, we investigated the mechanisms of LPS-induced TLR4 internalization and clarified the roles of the extracellular LPS-binding molecules, LPS-binding protein (LBP), and glycerophosphatidylinositol-anchored protein (CD14). LPS stimulation of CD14-expressing cells induced TLR4 internalization in the presence of serum, and an inhibitory anti-LBP mAb blocked its internalization. Addition of LBP to serum-free cultures restored LPS-induced TLR4 internalization to comparable levels of serum. The secretory form of the CD14 (sCD14) induced internalization but required a much higher concentration than LBP. An inhibitory anti-sCD14 mAb was ineffective for serum-mediated internalization. LBP lacking the domain for LPS transfer to CD14 and a CD14 mutant with reduced LPS binding both attenuated TLR4 internalization. Accordingly, LBP is an essential serum molecule for TLR4 internalization, and its LPS transfer to membrane-anchored CD14 (mCD14) is a prerequisite. LBP induced the LPS-stimulated phosphorylation of TBK1, IKKϵ, and IRF3, leading to IFN-β expression. However, LPS-stimulated late activation of NFκB or necroptosis were not affected. Collectively, our results indicate that LBP controls LPS-induced TLR4 internalization, which induces TLR adaptor molecule 1 (TRIF)-dependent activation of the TBK1-IKKϵ-IRF3-IFN-β pathway. In summary, we showed that LBP-mediated LPS transfer to mCD14 is required for serum-dependent TLR4 internalization and activation of the TRIF pathway. Copyright © 2018, The American Society for Biochemistry and Molecular Biology.

  10. Permeability of commercial solvents through living human skin

    DEFF Research Database (Denmark)

    Ursin, C; Hansen, C M; Van Dyk, J W

    1995-01-01

    A procedure has been developed for measuring the steady state rate of permeation of commercial solvents through living human skin. To get the most consistent results, it was necessary with some solvents to normalize the solvent permeation rate of a given skin sample with its [3H]water permeation...... rate. For other solvents this was not necessary, so the un-normalized data were used. High [3H]water permeation rate also was used as a criterion for "defective" skin samples that gave erroneous permeability rates, especially for solvents having slow permeability. The linearity of the steady state data...... of DMSO and octyl acetate were measured. No octyl acetate was detected and the permeability of DMSO was proportional to its mole fraction in the mixture. The effect of two hours of solvent exposure on the viability of skin (based on DNA synthesis) was measured and found to be very dependent on the solvent....

  11. MOLECULAR DYNAMICS SIMULATION OF KINETIC RESOLUTION OF RACEMIC ALCOHOL USING BURKHOLDERIA CEPACIA LIPASE IN ORGANIC SOLVENTS

    Directory of Open Access Journals (Sweden)

    A. C. Mathpati

    2018-03-01

    Full Text Available Lipases, a subclass of hydrolases, have gained a lot of importance as they can catalyze esterification, transesterification and hydrolysis reaction in non-aqueous media. Lipases are also widely used for kinetic resolution of racemic alcohols into enantiopure compounds. The lipase activity is affected by organic solvents due to changes in the conformational rigidity of enzymes, the active site, or altering the solvation of the transition state. The activity of lipases strongly depends on the logP value of solvents. Molecular dynamics (MD can help to understand the effect of solvents on lipase conformation as well as protein-ligand complex. In this work, MD simulations of Burkholderia cepacia lipase (BCL and complex between R and S conformation of acetylated form of 1-phenylethanol with BCL using gromacs have been carried in various organic solvents. The RMSD values were within the range of 0.15 to 0.20 nm and radius of gyration was found to be with 1.65 to 1.9 nm. Major changes in the B factor compared to reference structure were observed between residues 60 to 80, 120 to 150 and 240 to 260. Higher unfolding was observed in toluene and diethyl ether compared to hexane and acetonitrile. R acetylated complex was found to favorably bind BCL compared to S form. The predicted enantioselectivity were in good agreement with the experimental data.

  12. ATP-Binding Cassette Transporter VcaM from Vibrio cholerae is Dependent on the Outer Membrane Factor Family for Its Function

    Directory of Open Access Journals (Sweden)

    Wen-Jung Lu

    2018-03-01

    Full Text Available Vibrio cholerae ATP-binding cassette transporter VcaM (V. cholerae ABC multidrug resistance pump has previously been shown to confer resistance to a variety of medically important drugs. In this study, we set to analyse its properties both in vitro in detergent-solubilised state and in vivo to differentiate its dependency on auxiliary proteins for its function. We report the first detailed kinetic parameters of purified VcaM and the rate of phosphate (Pi production. To determine the possible functional dependencies of VcaM on the tripartite efflux pumps we then utilized different E. coli strains lacking the principal secondary transporter AcrB (Acriflavine resistance protein, as well as cells lacking the outer membrane factor (OMF TolC (Tolerance to colicins. Consistent with the ATPase function of VcaM we found it to be susceptible to sodium orthovanadate (NaOV, however, we also found a clear dependency of VcaM function on TolC. Inhibitors targeting secondary active transporters had no effects on either VcaM-conferred resistance or Hoechst 33342 accumulation, suggesting that VcaM might be capable of engaging with the TolC-channel without periplasmic mediation by additional transporters. Our findings are indicative of VcaM being capable of a one-step substrate translocation from cytosol to extracellular space utilising the TolC-channel, making it the only multidrug ABC-transporter outside of the MacB-family with demonstrable TolC-dependency.

  13. Purex process solvent: literature review

    Energy Technology Data Exchange (ETDEWEB)

    Geier, R.G.

    1979-10-01

    This document summarizes the data on Purex process solvent presently published in a variety of sources. Extracts from these various sources are presented herein and contain the work done, the salient results obtained, and the original, unaltered conclusions of the author of each paper. Three major areas are addressed: solvent stability, solvent quality testing, and solvent treatment processes. 34 references, 44 tables.

  14. Purex process solvent: literature review

    International Nuclear Information System (INIS)

    Geier, R.G.

    1979-10-01

    This document summarizes the data on Purex process solvent presently published in a variety of sources. Extracts from these various sources are presented herein and contain the work done, the salient results obtained, and the original, unaltered conclusions of the author of each paper. Three major areas are addressed: solvent stability, solvent quality testing, and solvent treatment processes. 34 references, 44 tables

  15. Activity-dependent shedding of the NMDA receptor glycine binding site by matrix metalloproteinase 3: a PUTATIVE mechanism of postsynaptic plasticity.

    Directory of Open Access Journals (Sweden)

    Thorsten Pauly

    Full Text Available Functional and structural alterations of clustered postsynaptic ligand gated ion channels in neuronal cells are thought to contribute to synaptic plasticity and memory formation in the human brain. Here, we describe a novel molecular mechanism for structural alterations of NR1 subunits of the NMDA receptor. In cultured rat spinal cord neurons, chronic NMDA receptor stimulation induces disappearance of extracellular epitopes of NMDA receptor NR1 subunits, which was prevented by inhibiting matrix metalloproteinases (MMPs. Immunoblotting revealed the digestion of solubilized NR1 subunits by MMP-3 and identified a fragment of about 60 kDa as MMPs-activity-dependent cleavage product of the NR1 subunit in cultured neurons. The expression of MMP-3 in the spinal cord culture was shown by immunoblotting and immunofluorescence microscopy. Recombinant NR1 glycine binding protein was used to identify MMP-3 cleavage sites within the extracellular S1 and S2-domains. N-terminal sequencing and site-directed mutagenesis revealed S542 and L790 as two putative major MMP-3 cleavage sites of the NR1 subunit. In conclusion, our data indicate that MMPs, and in particular MMP-3, are involved in the activity dependent alteration of NMDA receptor structure at postsynaptic membrane specializations in the CNS.

  16. Activity-dependent shedding of the NMDA receptor glycine binding site by matrix metalloproteinase 3: a PUTATIVE mechanism of postsynaptic plasticity.

    Science.gov (United States)

    Pauly, Thorsten; Ratliff, Miriam; Pietrowski, Eweline; Neugebauer, Rainer; Schlicksupp, Andrea; Kirsch, Joachim; Kuhse, Jochen

    2008-07-16

    Functional and structural alterations of clustered postsynaptic ligand gated ion channels in neuronal cells are thought to contribute to synaptic plasticity and memory formation in the human brain. Here, we describe a novel molecular mechanism for structural alterations of NR1 subunits of the NMDA receptor. In cultured rat spinal cord neurons, chronic NMDA receptor stimulation induces disappearance of extracellular epitopes of NMDA receptor NR1 subunits, which was prevented by inhibiting matrix metalloproteinases (MMPs). Immunoblotting revealed the digestion of solubilized NR1 subunits by MMP-3 and identified a fragment of about 60 kDa as MMPs-activity-dependent cleavage product of the NR1 subunit in cultured neurons. The expression of MMP-3 in the spinal cord culture was shown by immunoblotting and immunofluorescence microscopy. Recombinant NR1 glycine binding protein was used to identify MMP-3 cleavage sites within the extracellular S1 and S2-domains. N-terminal sequencing and site-directed mutagenesis revealed S542 and L790 as two putative major MMP-3 cleavage sites of the NR1 subunit. In conclusion, our data indicate that MMPs, and in particular MMP-3, are involved in the activity dependent alteration of NMDA receptor structure at postsynaptic membrane specializations in the CNS.

  17. Specificity of the Cyclic GMP-Binding Activity and of a Cyclic GMP-Dependent Cyclic GMP Phosphodiesterase in Dictyostelium discoideum

    NARCIS (Netherlands)

    Haastert, Peter J.M. van; Walsum, Hans van; Meer, Rob C. van der; Bulgakov, Roman; Konijn, Theo M.

    1982-01-01

    The nucleotide specificity of the cyclic GMP-binding activity in a homogenate of Dictyostelium discoideum was determined by competition of cyclic GMP derivatives with [8-3H] cyclic GMP for the binding sites. The results indicate that cyclic GMP is bound to the binding proteins by hydrogen bonds at

  18. Lipid-binding proteins modulate ligand-dependent trans-activation by peroxisome proliferator-activated receptors and localize to the nucleus as well as the cytoplasm

    DEFF Research Database (Denmark)

    Helledie, T; Antonius, M; Sorensen, R V

    2000-01-01

    Peroxisome proliferator-activated receptors (PPARs) are activated by a variety of fatty acids, eicosanoids, and hypolipidemic and insulin-sensitizing drugs. Many of these compounds bind avidly to members of a family of small lipid-binding proteins, the fatty acid-binding proteins (FABPs). Fatty...

  19. Mechanistic deductions from multiple kinetic and solvent deuterium isotope effects and pH studies of pyridoxal phosphate dependent carbon-carbon lyases: escherichia coli tryptophan indole-lyase

    International Nuclear Information System (INIS)

    Kiick, D.M.; Phillips, R.S.

    1988-01-01

    Analysis of the pH dependence of the kinetic parameters and competitive inhibitor Ki values for tryptophan indole-lyase suggests two enzymic groups must be unprotonated in order to facilitate binding and catalysis of tryptophan. The V/K for tryptophan and the pKi for oxindolyl-L-alanine, a putative transition state analogue and competitive inhibitor, decrease below two pK values of 7.6 and 6.0, while the Ki for L-alanine, also a competitive inhibitor, is 3300-fold larger (20 mM) than that for oxindolyl-L-alanine and increases below a single pK of 7.6. A single pK of 7.6 is also observed in the V/K profile for the alternate substrate, S-methyl-L-cysteine. Therefore, the enzymic group with a pK of 7.6 is responsible for proton abstraction at the 2-position of tryptophan, while the enzymic group with a pK of 6.0 interacts with the indole portion of tryptophan and probably catalyzes formation of the indolenine tautomer of tryptophan (in concert with proton transfer to C-3 of indole from the group with pK 7.6) to facilitate carbon-carbon bond cleavage and elimination of indole. The pH variation of the primary deuterium isotope effects for proton abstraction at the 2-position of tryptophan (DV = 2.5 and D(V/Ktrp) = 2.8) are pH independent, while the Vmax for tryptophan or S-methyl-L-cysteine is the same and also pH independent. Thus, substrates bind only to the correctly protonated form of the enzyme. Further, tryptophan is not sticky, and the pK values observed in both V/K profiles are the correct ones

  20. Separation by solvent extraction

    International Nuclear Information System (INIS)

    Holt, C.H. Jr.

    1976-01-01

    In a process for separating fission product values from U and Pu values contained in an aqueous solution, an oxidizing agent is added to the solution to secure U and Pu in their hexavalent state. The aqueous solution is contacted with a substantially water-immiscible organic solvent with agitation while the temperature is maintained at from -1 to -2 0 C until the major part of the water present is frozen. The solid ice phase is continuously separated as it is formed and a remaining aqueous liquid phase containing fission product values and a solvent phase containing Pu and U values are separated from each other. The last obtained part of the ice phase is melted and added to the separated liquid phase. The resulting liquid is treated with a new supply of solvent whereby it is practically depleted of U and Pu

  1. Solvent-mediated pathways to gelation and phase separation in suspensions of grafted nanoparticles

    KAUST Repository

    Anyfantakis, Manos; Bourlinos, Athanasios; Vlassopoulos, Dimitris; Fytas, George; Giannelis, Emmanuel; Kumar, Sanat K.

    2009-01-01

    , rheology and visual observations, and different routes to gelation, depending on the solvent used. In agreement with earlier works, the solvent quality for the grafted chains at a given temperature controls the balance between attractions and repulsions

  2. Organic solvent topical report

    Energy Technology Data Exchange (ETDEWEB)

    Cowley, W.L.

    1998-04-30

    This report is the technical basis for the accident and consequence analyses used in the Hanford Tank Farms Basis for Interim Operation. The report also contains the scientific and engineering information and reference material needed to understand the organic solvent safety issue. This report includes comments received from the Chemical Reactions Subcommittee of the Tank Advisory Panel.

  3. Organic solvent topical report

    International Nuclear Information System (INIS)

    Cowley, W.L.

    1998-01-01

    This report is the technical basis for the accident and consequence analyses used in the Hanford Tank Farms Basis for Interim Operation. The report also contains the scientific and engineering information and reference material needed to understand the organic solvent safety issue. This report includes comments received from the Chemical Reactions Subcommittee of the Tank Advisory Panel

  4. DESIGNING GREENER SOLVENTS

    Science.gov (United States)

    Computer-aided design of chemicals and chemical mixtures provides a powerful tool to help engineers identify cleaner process designs and more-benign alternatives to toxic industrial solvents. Three software programs are discussed: (1) PARIS II (Program for Assisting the Replaceme...

  5. Evidence of two different Na/sup +/-dependent (/sup 3/H)-ouabain binding sites of a Na/sup +/-K/sup +/-ATPase of guinea-pig hearts

    Energy Technology Data Exchange (ETDEWEB)

    Fricke, U; Klaus, W [Koeln Univ. (Germany, F.R.)

    1977-11-01

    The influence of various Na/sup +/ concentrations on (/sup 3/H)-ouabain binding was studied in experiments on a microsomal Na/sup +/-K/sup +/-adenosine triphosphatase (ATPase) from guinea-pig hearts. The ATP-independent cardiac glycoside binding was not influenced by increasing Na/sup +/ concentrations. However, a good correlation was found between the ATP-dependent (/sup 3/H)-ouabain binding and Na/sup +/ concentration. A more detailed analysis of these results revealed two distinct processes involved in this interaction: one ouabain binding process was activated at rather low Na/sup +/ concentrations, (Ksub(0.5) = 4.5 mM); this type of (/sup 3/H)-ouabain binding was strongly correlated to the Na/sup +/ concentration necessary for half maximum phosphorylation (Ksub(0.5) = 1 mM). The other ouabain binding process was predominant at high Na/sup +/ concentrations (Ksub(0.5 = 69 mM). On the basis of the commonly accepted ATPase reaction cycle a model for the interaction of cardiac glycosides with the Na/sup +/-K/sup +/-ATPase is proposed, assuming two different binding sites for cardiac glycosides (E/sub 2/ -P and Esub(l) -P) and involving a translocation of these drugs from an outer to an inner compartment of the cell membrane.

  6. Detection of Specific Solvent Rearrangement Regions of an Enzyme: NMR and ITC Studies with Aminoglycoside Phosphotransferase(3 )-IIIa

    International Nuclear Information System (INIS)

    Ozen, C.; Norris, Adrianne; Land, Miriam Louise; Tjioe, Elina; Serpersu, Engin H

    2008-01-01

    This work describes differential effects of solvent in complexes of the aminoglycoside phosphotransferase(3 and cent;)-IIIa (APH) with different aminoglycosides and the detection of change in solvent structure at specific sites away from substrates. Binding of kanamycins to APH occurs with a larger negative and cent;H in H2O relative to D2O ( and cent; and cent;H(H2O-D2O) < 0), while the reverse is true for neomycins. Unusually large negative and cent;Cp values were observed for binding of aminoglycosides to APH. and cent;Cp for the APHneomycin complex was -1.6 kcal and acirc;mol-1 and acirc;deg-1. A break at 30 C was observed in the APH-kanamycin complex yielding and cent;Cp values of -0.7 kcal and acirc;mol-1 and acirc;deg-1 and -3.8 kcal and acirc;mol-1 and acirc;deg-1 below and above 30 C, respectively. Neither the change in accessible surface area ( and cent;ASA) nor contributions from heats of ionization were sufficient to explain the large negative and cent;Cp values. Most significantly, 15N-1H HSQC experiments showed that temperature-dependent shifts of the backbone amide protons of Leu 88, Ser 91, Cys 98, and Leu143 revealed a break at 30 C only in the APH-kanamycin complex in spectra collected between 21 C and 38 C. These amino acids represent solVent reorganization sites that experience a change in solvent structure in their immediate environment as structurally different ligands bind to the enzyme. These residues were away from the substrate binding site and distributed in three hydrophobic patches in APH. Overall, our results show that a large number of factors affect and cent;Cp and binding of structurally different ligand groups cause different solvent structure in the active site as well as differentially affecting specific sites away from the ligand binding site

  7. DJ-1-dependent protective activity of DJ-1-binding compound no. 23 against neuronal cell death in MPTP-treated mouse model of Parkinson's disease

    Directory of Open Access Journals (Sweden)

    Kazuko Takahashi-Niki

    2015-03-01

    Full Text Available Parkinson's disease (PD is caused by dopaminergic cell death in the substantia nigra, leading to a reduced level of dopamine in the striatum. Oxidative stress is one of the causes of PD. Since symptomatic PD therapies are used, identification of compounds or proteins that inhibit oxidative stress-induced neuronal cell death is necessary. DJ-1 is a causative gene product of familial PD and plays a role in anti-oxidative stress reaction. We have identified various DJ-1-binding compounds, including compound-23, that restored neuronal cell death and locomotion defects observed in neurotoxin-induced PD models. In this study, wild-type and DJ-1-knockout mice were injected intraperitoneally with 1 mg/kg of compound-23 and then with 30 mg/kg of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP at 1 h after injection. Five days after administration, the effects of compound-23 on MPTP-induced locomotion deficits, on dopaminergic cell death and on brain dopamine levels were analyzed by rotor rod tests, by staining cells with an anti-TH antibody and by an HPLC, respectively. The results showed that compound-23 inhibited MPTP-induced reduction of retention time on the rotor rod bar, neuronal cell death in the substantia nigra and striatum and dopamine content in wild-type mice but not in DJ-1-knockout mice, indicating a DJ-1-dependent effect of compound-23.

  8. Probes of eukaryotic DNA-dependent RNA polymerase II-I. Binding of 9-beta-D-arabinofuranosyl-6-mercaptopurine to the elongation subsite.

    Science.gov (United States)

    Cho, J M; Kimball, A P

    1982-08-15

    9-beta-D-Arabinofuranosyl-6-mercaptopurine (ara-6-MP) was used to affinity-label wheat germ DNA-dependent RNA polymerase II (or B) (nucleosidetriphosphate:RNA nucleotidyltransferase, EC 2.7.7.6). This nucleoside analogue was found to be a competitive inhibitor with respect to [3H]UMP incorporation. Natural substrates protected the enzyme from inactivation by ara-6-MP when the enzyme was preincubated with excess concentrations of substrates, suggesting that the inhibitor binds at the elongation subsite. The inhibitor bound the catalytic center of the enzyme with a stoichiometry of 0.6:1. The sulfhydryl reagent, dithiothreitol, reversed the inhibition by ara-6-MP, suggesting that the 6-thiol group of the inhibitor was interacting closely with an essential cysteine residue in the catalytic center of the enzyme. Chromatographic analysis of the pronase-digestion products of the RNA polymerase II-ara-6-MP complex also showed that ara-6-MP had bound a cysteine residue. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the denatured [6-35S]ara-6-MP-labeled RNA polymerase II revealed that over 80% of the radioactivity was associated with the IIb subunit of the enzyme.

  9. An environment-dependent semi-empirical tight binding model suitable for electron transport in bulk metals, metal alloys, metallic interfaces, and metallic nanostructures. I. Model and validation

    Energy Technology Data Exchange (ETDEWEB)

    Hegde, Ganesh, E-mail: ghegde@purdue.edu; Povolotskyi, Michael; Kubis, Tillmann; Klimeck, Gerhard, E-mail: gekco@purdue.edu [Network for Computational Nanotechnology (NCN), Department of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana 47907 (United States); Boykin, Timothy [Department of Electrical and Computer Engineering, University of Alabama, Huntsville, Alabama (United States)

    2014-03-28

    Semi-empirical Tight Binding (TB) is known to be a scalable and accurate atomistic representation for electron transport for realistically extended nano-scaled semiconductor devices that might contain millions of atoms. In this paper, an environment-aware and transferable TB model suitable for electronic structure and transport simulations in technologically relevant metals, metallic alloys, metal nanostructures, and metallic interface systems are described. Part I of this paper describes the development and validation of the new TB model. The new model incorporates intra-atomic diagonal and off-diagonal elements for implicit self-consistency and greater transferability across bonding environments. The dependence of the on-site energies on strain has been obtained by appealing to the Moments Theorem that links closed electron paths in the system to energy moments of angular momentum resolved local density of states obtained ab initio. The model matches self-consistent density functional theory electronic structure results for bulk face centered cubic metals with and without strain, metallic alloys, metallic interfaces, and metallic nanostructures with high accuracy and can be used in predictive electronic structure and transport problems in metallic systems at realistically extended length scales.

  10. An environment-dependent semi-empirical tight binding model suitable for electron transport in bulk metals, metal alloys, metallic interfaces, and metallic nanostructures. I. Model and validation

    International Nuclear Information System (INIS)

    Hegde, Ganesh; Povolotskyi, Michael; Kubis, Tillmann; Klimeck, Gerhard; Boykin, Timothy

    2014-01-01

    Semi-empirical Tight Binding (TB) is known to be a scalable and accurate atomistic representation for electron transport for realistically extended nano-scaled semiconductor devices that might contain millions of atoms. In this paper, an environment-aware and transferable TB model suitable for electronic structure and transport simulations in technologically relevant metals, metallic alloys, metal nanostructures, and metallic interface systems are described. Part I of this paper describes the development and validation of the new TB model. The new model incorporates intra-atomic diagonal and off-diagonal elements for implicit self-consistency and greater transferability across bonding environments. The dependence of the on-site energies on strain has been obtained by appealing to the Moments Theorem that links closed electron paths in the system to energy moments of angular momentum resolved local density of states obtained ab initio. The model matches self-consistent density functional theory electronic structure results for bulk face centered cubic metals with and without strain, metallic alloys, metallic interfaces, and metallic nanostructures with high accuracy and can be used in predictive electronic structure and transport problems in metallic systems at realistically extended length scales

  11. An environment-dependent semi-empirical tight binding model suitable for electron transport in bulk metals, metal alloys, metallic interfaces, and metallic nanostructures. I. Model and validation

    Science.gov (United States)

    Hegde, Ganesh; Povolotskyi, Michael; Kubis, Tillmann; Boykin, Timothy; Klimeck, Gerhard

    2014-03-01

    Semi-empirical Tight Binding (TB) is known to be a scalable and accurate atomistic representation for electron transport for realistically extended nano-scaled semiconductor devices that might contain millions of atoms. In this paper, an environment-aware and transferable TB model suitable for electronic structure and transport simulations in technologically relevant metals, metallic alloys, metal nanostructures, and metallic interface systems are described. Part I of this paper describes the development and validation of the new TB model. The new model incorporates intra-atomic diagonal and off-diagonal elements for implicit self-consistency and greater transferability across bonding environments. The dependence of the on-site energies on strain has been obtained by appealing to the Moments Theorem that links closed electron paths in the system to energy moments of angular momentum resolved local density of states obtained ab initio. The model matches self-consistent density functional theory electronic structure results for bulk face centered cubic metals with and without strain, metallic alloys, metallic interfaces, and metallic nanostructures with high accuracy and can be used in predictive electronic structure and transport problems in metallic systems at realistically extended length scales.

  12. ω-3 and ω-6 Fatty Acids Modulate Conventional and Atypical Protein Kinase C Activities in a Brain Fatty Acid Binding Protein Dependent Manner in Glioblastoma Multiforme

    Directory of Open Access Journals (Sweden)

    Marwa E. Elsherbiny

    2018-04-01

    Full Text Available Glioblastoma multiforme (GBM is a highly infiltrative brain cancer with a dismal prognosis. High levels of brain fatty acid binding protein (B-FABP are associated with increased migration/infiltration in GBM cells, with a high ratio of arachidonic acid (AA to docosahexaenoic acid (DHA driving B-FABP-mediated migration. Since several protein kinase Cs (PKCs are overexpressed in GBM and linked to migration, we explored a possible relationship between B-FABP and levels/activity of different PKCs, as a function of AA and DHA supplementation. We report that ectopic expression of B-FABP in U87 cells alters the levels of several PKCs, particularly PKCζ. Upon analysis of PKCζ RNA levels in a panel of GBM cell lines and patient-derived GBM neurospheres, we observed a trend towards moderate positive correlation (r = 0.624, p = 0.054 between B-FABP and PKCζ RNA levels. Analysis of PKC activity in U87 GBM cells revealed decreased typical PKC activity (23.4% in B-FABP-expressing cells compared with nonexpressing cells, with no difference in novel and atypical PKC activities. AA and DHA modulated both conventional and atypical PKC activities in a B-FABP-dependent manner, but had no effect on novel PKC activity. These results suggest that conventional and atypical PKCs are potential downstream effectors of B-FABP/fatty acid-mediated alterations in GBM growth properties.

  13. Universal dependence of hydrogen oxidation and evolution reaction activity of platinum-group metals on pH and hydrogen binding energy.

    Science.gov (United States)

    Zheng, Jie; Sheng, Wenchao; Zhuang, Zhongbin; Xu, Bingjun; Yan, Yushan

    2016-03-01

    Understanding how pH affects the activity of hydrogen oxidation reaction (HOR) and hydrogen evolution reaction (HER) is key to developing active, stable, and affordable HOR/HER catalysts for hydroxide exchange membrane fuel cells and electrolyzers. A common linear correlation between hydrogen binding energy (HBE) and pH is observed for four supported platinum-group metal catalysts (Pt/C, Ir/C, Pd/C, and Rh/C) over a broad pH range (0 to 13), suggesting that the pH dependence of HBE is metal-independent. A universal correlation between exchange current density and HBE is also observed on the four metals, indicating that they may share the same elementary steps and rate-determining steps and that the HBE is the dominant descriptor for HOR/HER activities. The onset potential of CO stripping on the four metals decreases with pH, indicating a stronger OH adsorption, which provides evidence against the promoting effect of adsorbed OH on HOR/HER.

  14. pH-Dependent Binding of Chloride to a Marine Alkaline Phosphatase Affects the Catalysis, Active Site Stability, and Dimer Equilibrium.

    Science.gov (United States)

    Hjörleifsson, Jens G; Ásgeirsson, Bjarni

    2017-09-26

    The effect of ionic strength on enzyme activity and stability varies considerably between enzymes. Ionic strength is known to affect the catalytic activity of some alkaline phosphatases (APs), such as Escherichia coli AP, but how ions affect APs is debated. Here, we studied the effect of various ions on a cold-adapted AP from Vibrio splendidus (VAP). Previously, we have found that the active form of VAP is extremely unstable at low ionic strengths. Here we show that NaCl increased the activity and stability of VAP and that the effect was pH-dependent in the range of pH 7-10. The activity profile as a function of pH formed two maxima, indicating a possible conformational change. Bringing the pH from the neutral to the alkaline range was accompanied by a large increase in both the K i for inorganic phosphate (product inhibition) and the K M for p-nitrophenyl phosphate. The activity transitions observed as the pH was varied correlated with structural changes as monitored by tryptophan fluorescence. Thermal and urea-induced inactivation was shown to be accompanied by neither dissociation of the active site metal ions nor dimer dissociation. This would suggest that the inactivation involved subtle changes in active site conformation. Furthermore, the VAP dimer equilibrium was studied for the first time and shown to highly favor dimerization, which was dependent on pH and NaCl concentration. Taken together, the data support a model in which anions bind to some specific acceptor in the active site of VAP, resulting in great stabilization and catalytic rate enhancement, presumably through a different mechanism.

  15. Identification of constrained peptides that bind to and preferentially inhibit the activity of the hepatitis C viral RNA-dependent RNA polymerase

    International Nuclear Information System (INIS)

    Amin, Anthony; Zaccardi, Joe; Mullen, Stanley; Olland, Stephane; Orlowski, Mark; Feld, Boris; Labonte, Patrick; Mak, Paul

    2003-01-01

    A class of disulfide constrained peptides containing a core motif FPWG was identified from a screen of phage displayed library using the HCV RNA-dependent RNA polymerase (NS5B) as a bait. Surface plasmon resonance studies showed that three highly purified synthetic constrained peptides bound to immobilized NS5B with estimated K d values ranging from 30 to 60 μM. In addition, these peptides inhibited the NS5B activity in vitro with IC 50 ranging from 6 to 48 μM, whereas in contrast they had no inhibitory effect on the enzymatic activities of calf thymus polymerase α, human polymerase β, RSV polymerase, and HIV reverse transcriptase in vitro. Two peptides demonstrated conformation-dependent inhibition since their synthetic linear versions were not inhibitory in the NS5B assay. A constrained peptide with the minimum core motif FPWG retained selective inhibition of NS5B activity with an IC 50 of 50 μM. Alanine scan analyses of a representative constrained peptide, FPWGNTW, indicated that residues F1 and W7 were critical for the inhibitory effect of this peptide, although residues P2 and N5 had some measurable inhibitory effect as well. Further analyses of the mechanism of inhibition indicated that these peptides inhibited the formation of preelongation complexes required for the elongation reaction. However, once the preelongation complex was formed, its activity was refractory to peptide inhibition. Furthermore, the constrained peptide FPWGNTW inhibited de novo initiated RNA synthesis by NS5B from a poly(rC) template. These data indicate that the peptides confer selective inhibition of NS5B activity by binding to the enzyme and perturbing an early step preceding the processive elongation step of RNA synthesis

  16. Enhancement of antibody-dependent cell-mediated cytotoxicity by endowing IgG with FcαRI (CD89) binding.

    Science.gov (United States)

    Borrok, M Jack; Luheshi, Nadia M; Beyaz, Nurten; Davies, Gareth C; Legg, James W; Wu, Herren; Dall'Acqua, William F; Tsui, Ping

    2015-01-01

    Fc effector functions such as antibody-dependent cell-mediated cytotoxicity (ADCC) and antibody-dependent cell-mediated phagocytosis (ADCP) are crucial to the efficacy of many antibody therapeutics. In addition to IgG, antibodies of the IgA isotype can also promote cell killing through engagement of myeloid lineage cells via interactions between the IgA-Fc and FcαRI (CD89). Herein, we describe a unique, tandem IgG1/IgA2 antibody format in the context of a trastuzumab variable domain that exhibits enhanced ADCC and ADCP capabilities. The IgG1/IgA2 tandem Fc format retains IgG1 FcγR binding as well as FcRn-mediated serum persistence, yet is augmented with myeloid cell-mediated effector functions via FcαRI/IgA Fc interactions. In this work, we demonstrate anti-human epidermal growth factor receptor-2 antibodies with the unique tandem IgG1/IgA2 Fc can better recruit and engage cytotoxic polymorphonuclear (PMN) cells than either the parental IgG1 or IgA2. Pharmacokinetics of IgG1/IgA2 in BALB/c mice are similar to the parental IgG, and far surpass the poor serum persistence of IgA2. The IgG1/IgA2 format is expressed at similar levels and with similar thermal stability to IgG1, and can be purified via standard protein A chromatography. The tandem IgG1/IgA2 format could potentially augment IgG-based immunotherapeutics with enhanced PMN-mediated cytotoxicity while avoiding many of the problems associated with developing IgAs.

  17. SN2 fluorination reactions in ionic liquids: a mechanistic study towards solvent engineering.

    Science.gov (United States)

    Oh, Young-Ho; Jang, Hyeong Bin; Im, Suk; Song, Myoung Jong; Kim, So-Yeon; Park, Sung-Woo; Chi, Dae Yoon; Song, Choong Eui; Lee, Sungyul

    2011-01-21

    In the catalysis of S(N)2 fluorination reactions, the ionic liquid anion plays a key role as a Lewis base by binding to the counterion Cs(+) and thereby reducing the retarding Coulombic influence of Cs(+) on the nucleophile F(-). The reaction rates also depend critically on the structures of ionic liquid cation, for example, n-butyl imidazolium gives no S(N)2 products, whereas n-butylmethyl imidazolium works well. The origin of the observed phenomenal synergetic effects by the ionic liquid [mim-(t)OH][OMs], in which t-butanol is bonded covalently to the cation [mim], is that the t-butanol moiety binds to the leaving group of the substrate, moderating the retarding interactions between the acidic hydrogen and F(-). This work is a significant step toward designing and engineering solvents for promoting specific chemical reactions.

  18. Theory of polyelectrolytes in solvents.

    Science.gov (United States)

    Chitanvis, Shirish M

    2003-12-01

    Using a continuum description, we account for fluctuations in the ionic solvent surrounding a Gaussian, charged chain and derive an effective short-ranged potential between the charges on the chain. This potential is repulsive at short separations and attractive at longer distances. The chemical potential can be derived from this potential. When the chemical potential is positive, it leads to a meltlike state. For a vanishingly low concentration of segments, this state exhibits scaling behavior for long chains. The Flory exponent characterizing the radius of gyration for long chains is calculated to be approximately 0.63, close to the classical value obtained for second order phase transitions. For short chains, the radius of gyration varies linearly with N, the chain length, and is sensitive to the parameters in the interaction potential. The linear dependence on the chain length N indicates a stiff behavior. The chemical potential associated with this interaction changes sign, when the screening length in the ionic solvent exceeds a critical value. This leads to condensation when the chemical potential is negative. In this state, it is shown using the mean-field approximation that spherical and toroidal condensed shapes can be obtained. The thickness of the toroidal polyelectrolyte is studied as a function of the parameters of the model, such as the ionic screening length. The predictions of this theory should be amenable to experimental verification.

  19. Solvent selection methodology for pharmaceutical processes: Solvent swap

    DEFF Research Database (Denmark)

    Papadakis, Emmanouil; Kumar Tula, Anjan; Gani, Rafiqul

    2016-01-01

    A method for the selection of appropriate solvents for the solvent swap task in pharmaceutical processes has been developed. This solvent swap method is based on the solvent selection method of Gani et al. (2006) and considers additional selection criteria such as boiling point difference...... in pharmaceutical processes as well as new solvent swap alternatives. The method takes into account process considerations such as batch distillation and crystallization to achieve the swap task. Rigorous model based simulations of the swap operation are performed to evaluate and compare the performance...

  20. Improvements in solvent extraction columns

    International Nuclear Information System (INIS)

    Aughwane, K.R.

    1987-01-01

    Solvent extraction columns are used in the reprocessing of irradiated nuclear fuel. For an effective reprocessing operation a solvent extraction column is required which is capable of distributing the feed over most of the column. The patent describes improvements in solvent extractions columns which allows the feed to be distributed over an increased length of column than was previously possible. (U.K.)

  1. Solvent extraction columns

    International Nuclear Information System (INIS)

    Middleton, P.; Smith, J.R.

    1979-01-01

    In pulsed columns for use in solvent extraction processes, e.g. the reprocessing of nuclear fuel, the horizontal perforated plates inside the column are separated by interplate spacers manufactured from metallic neutron absorbing material. The spacer may be in the form of a spiral or concentric circles separated by radial limbs, or may be of egg-box construction. Suitable neutron absorbing materials include stainless steel containing boron or gadolinium, hafnium metal or alloys of hafnium. (UK)

  2. Hazardous solvent substitution

    International Nuclear Information System (INIS)

    Twitchell, K.E.

    1995-01-01

    Eliminating hazardous solvents is good for the environment, worker safety, and the bottom line. However, even though we are motivated to find replacements, the big question is 'What can we use as replacements for hazardous solvents?'You, too, can find replacements for your hazardous solvents. All you have to do is search for them. Search through the vendor literature of hundreds of companies with thousands of products. Ponder the associated material safety data sheets, assuming of course that you can obtain them and, having obtained them, that you can read them. You will want to search the trade magazines and other sources for product reviews. You will want to talk to users about how well the product actually works. You may also want to check US Environmental Protection Agency (EPA) and other government reports for toxicity and other safety information. And, of course, you will want to compare the product's constituent chemicals with the many hazardous constituency lists to ensure the safe and legal use of the product in your workplace

  3. Insulin-like growth factor binding protein-3 induces angiogenesis through IGF-I- and SphK1-dependent mechanisms.

    Science.gov (United States)

    Granata, R; Trovato, L; Lupia, E; Sala, G; Settanni, F; Camussi, G; Ghidoni, R; Ghigo, E

    2007-04-01

    Angiogenesis is critical for development and repair, and is a prominent feature of many pathological conditions. Based on evidence that insulin-like growth factor binding protein (IGFBP)-3 enhances cell motility and activates sphingosine kinase (SphK) in human endothelial cells, we have investigated whether IGFBP-3 plays a role in promoting angiogenesis. IGFBP-3 potently induced network formation by human endothelial cells on Matrigel. Moreover, it up-regulated proangiogenic genes, such as vascular endothelial growth factor (VEGF) and matrix metalloproteinases (MMP)-2 and -9. IGFBP-3 even induced membrane-type 1 MMP (MT1-MMP), which regulates MMP-2 activation. Decreasing SphK1 expression by small interfering RNA (siRNA), blocked IGFBP-3-induced network formation and inhibited VEGF, MT1-MMP but not IGF-I up-regulation. IGF-I activated SphK, leading to sphingosine-1-phosphate (S1P) formation. The IGF-I effect on SphK activity was blocked by specific inhibitors of IGF-IR, PI3K/Akt and ERK1/2 phosphorylation. The disruption of IGF-I signaling prevented the IGFBP-3 effect on tube formation, SphK activity and VEGF release. Blocking ERK1/2 signaling caused the loss of SphK activation and VEGF and IGF-I up-regulation. Finally, IGFBP-3 dose-dependently stimulated neovessel formation into subcutaneous implants of Matrigel in vivo. Thus, IGFBP-3 positively regulates angiogenesis through involvement of IGF-IR signaling and subsequent SphK/S1P activation.

  4. SOLVENT FIRE BY-PRODUCTS

    Energy Technology Data Exchange (ETDEWEB)

    Walker, D; Samuel Fink, S

    2006-05-22

    Southwest Research Institute (SwRI) conducted a burn test of the Caustic-Side Solvent Extraction (CSSX) solvent to determine the combustion products. The testing showed hydrogen fluoride gas is not a combustion product from a solvent fire when up to 70% of the solvent is consumed. The absence of HF in the combustion gases may reflect concentration of the modifier containing the fluoride groups in the unburned portion. SwRI reported results for other gases (CO, HCN, NOx, formaldehyde, and hydrocarbons). The results, with other supporting information, can be used for evaluating the consequences of a facility fire involving the CSSX solvent inventory.

  5. Solvents effect on n→π*and π→π* transition of 9- fluorenone

    African Journals Online (AJOL)

    STORAGESEVER

    2008-08-04

    Aug 4, 2008 ... tation to bind with the excited state charge distribution. Blue shift will therefore ... of fluorenone by oxime formation test on the spectra. The disappearance of ... ties and the oscillator strength of 9-fluorenone in various solvents.

  6. The solvent effects on dimethyl phthalate investigated by FTIR characterization, solvent parameter correlation and DFT computation

    Science.gov (United States)

    Chen, Yi; Zhang, Hui; Zhou, Wenzhao; Deng, Chao; Liao, Jian

    2018-06-01

    This study set out with the aim of investigating the solvent effects on dimethyl phthalate (DMP) using FTIR characterization, solvent parameter correlation and DFT calculation. DMP exposed to 17 organic solvents manifested varying shift in the carbonyl stretching vibration frequency (νCdbnd O). Non-alkanols induced Band I and alkanols produced Band I and Band II. Through correlating the νCdbnd O with the empirical solvent scales including acceptor parameter (AN), Schleyer's linear free energy parameter (G), and linear free salvation energy relationships (LSER), Band I was mainly ascribed to non-specific effects from either non-alkanols or alkanol polymers ((alkanol)n). νCdbnd O of the latter indicated minor red shift and less variability compared to the former. An assumption was made and validated about the sequestering of hydroxyl group by the bulky hydrophobic chain in (alkanol)n, creating what we refer to as "screening effects". Ab initio calculation, on the other hand, provided insights for possible hydrogen binding between DMP and (ethanol)n or between ethanol monomers. The two components of Band I observed in inert solvents were assigned to the two Cdbnd O groups adopting differentiated conformations. This in turn prompted our consideration that hydrogen binding was highly selective in favor of lowly associated (alkanol)n and the particular Cdbnd O group having relatively less steric hindrance and stronger electron-donating capacity. Band II was therefore believed to derive from hydrogen-bond interactions mainly in manner of 1:1 and 1:2 DMP-(alkanol)n complexes.

  7. Dendritic brushes under theta and poor solvent conditions

    Science.gov (United States)

    Gergidis, Leonidas N.; Kalogirou, Andreas; Charalambopoulos, Antonios; Vlahos, Costas

    2013-07-01

    The effects of solvent quality on the internal stratification of polymer brushes formed by dendron polymers up to third generation were studied by means of molecular dynamics simulations with Langevin thermostat. The distributions of polymer units, of the free ends, the radii of gyration, and the back folding probabilities of the dendritic spacers were studied at the macroscopic states of theta and poor solvent. For high grafting densities we observed a small decrease in the height of the brush as the solvent quality decreases. The internal stratification in theta solvent was similar to the one we found in good solvent, with two and in some cases three kinds of populations containing short dendrons with weakly extended spacers, intermediate-height dendrons, and tall dendrons with highly stretched spacers. The differences increase as the grafting density decreases and single dendron populations were evident in theta and poor solvent. In poor solvent at low grafting densities, solvent micelles, polymeric pinned lamellae, spherical and single chain collapsed micelles were observed. The scaling dependence of the height of the dendritic brush at high density brushes for both solvents was found to be in agreement with existing analytical results.

  8. Binding of ouabain and marinobufagenin leads to different structural changes in Na,K-ATPase and depends on the enzyme conformation.

    Science.gov (United States)

    Klimanova, Elizaveta A; Petrushanko, Irina Yu; Mitkevich, Vladimir A; Anashkina, Anastasia A; Orlov, Sergey N; Makarov, Alexander A; Lopina, Olga D

    2015-09-14

    Ion pump, Na,K-ATPase specifically binds cardiotonic steroids (CTS), which leads to inhibition of the enzyme activity and activation of signaling network in the cell. We have studied interaction of Na,K-ATPase with CTS of two different types - marinobufagenin and ouabain. We have shown that both CTS inhibit activity of Na,K-ATPase with the same Ki values, but binding of ouabain is sensitive to the conformation of Na,K-ATPase while binding of marinobufagenin is not. Furthermore, binding of ouabain and marinobufagenin results in different structural changes in Na,K-ATPase. Our data allow to explain the diversity of effects on the receptor function of Na,K-ATPase caused by different types of CTS. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  9. The Role of Interfacial Potential in Adsorbate Bonding: Electrode Potential-Dependent Infrared Spectra for Saturated CO Adlayers on Pt(110) and Related Electrochemical Surfaces in Varying Solvent Environments

    Science.gov (United States)

    1992-05-01

    as supporting electrolytes were recrystallized from methanol, water and ethanol , and water, respectively, and dried under vacuum at 110°C. Electrode...under these conditions 8,17 (vide infra). All measurements were performed at room temperature , 23±1*C. RESULTS AND DISCUSSION The experimental strategy...of interferometer scans during a suitably slow (2 mV s- ) positive-going potential sweep. For solvents containing traces of water, electrooxidative

  10. Binding proteins for the regulatory subunit (RII-B) of brain cAMP-dependent protein kinase II: isolation and initial characterization of cDNA clones

    International Nuclear Information System (INIS)

    Bregman, D.B.; Hu, E.; Rubin, C.S.

    1987-01-01

    In mammalian brain several proteins bind RII-B with high affinity. An example is P75, which co-purifies with RII-B and also complexes Ca 2+ -calmodulin. Thus, RII-B binding proteins (RBPs) might play a role in integrating the Ca 2+ and cAMP signalling pathways in the CNS. In order to study the structure and function of these polypeptides they have isolated cloned cDNAs for RBPs by screening brain λgt11 expression libraries using a functional assay: the binding of 32 P-labeled RII to fusion proteins produced by recombinants expressing RII binding domains. Inserts from rat brain recombinant clones λ7B and λ10B both hybridize to a brain mRNA of 7000 nucleotides. Northern gel analyses indicate that the putative RBP mRNA is also expressed in lung, but not in several other tissues. The λ7B insert was subcloned into the expression plasmid pINIA. A 50 kDa high affinity RII-B binding polypeptide accumulated in E. coli transformed with pINIA-7B. Two RBP cDNAs (λ77, λ100A) have been retrieved from a bovine λgt 11 library using a monoclonal antibody directed against P75 and the binding assay respectively. On Southern blots the insert from λ100A hybridizes to the cDNA insert from clones λ77, suggesting that λ 77 cDNA might contain sequences coding for both an RII binding domain and a P75 epitope. The bovine λ100A insert also hybridizes with the rat λ7B clone indicating that an RII binding domain is conserved in the two species

  11. A hierarchy of functionally important relaxations within myoglobin based on solvent effects, mutations and kinetic model.

    Science.gov (United States)

    Dantsker, David; Samuni, Uri; Friedman, Joel M; Agmon, Noam

    2005-06-01

    Geminate CO rebinding in myoglobin is studied for two viscous solvents, trehalose and sol-gel (bathed in 100% glycerol) at several temperatures. Mutations in key distal hemepocket residues are used to eliminate or enhance specific relaxation modes. The time-resolved data are analyzed with a modified Agmon-Hopfield model which is capable of providing excellent fits in cases where a single relaxation mode is dominant. Using this approach, we determine the relaxation rate constants of specific functionally important modes, obtaining also their Arrhenius activation energies. We find a hierarchy of distal pocket modes controlling the rebinding kinetics. The "heme access mode" (HAM) is responsible for the major slow-down in rebinding. It is a solvent-coupled cooperative mode which restricts ligand return from the xenon cavities. Bulky side-chains, like those His64 and Trp29 (in the L29W mutant), operate like overdamped pendulums which move over and block the binding site. They may be either unslaved (His64) or moderately slaved (Trp29) to the solvent. Small side-chain relaxations, most notably of leucines, are revealed in some mutants (V68L, V68A). They are conjectured to facilitate inter-cavity ligand motion. When all relaxations are arrested (H64L in trehalose), we observe pure inhomogeneous kinetics with no temperature dependence, suggesting that proximal relaxation is not a factor on the investigated timescale.

  12. Solvent effects in chemistry

    CERN Document Server

    Buncel, Erwin

    2015-01-01

    This book introduces the concepts, theory and experimental knowledge concerning solvent effects on the rate and equilibrium of chemical reactions of all kinds.  It begins with basic thermodynamics and kinetics, building on this foundation to demonstrate how a more detailed understanding of these effects may be used to aid in determination of reaction mechanisms, and to aid in planning syntheses. Consideration is given to theoretical calculations (quantum chemistry, molecular dynamics, etc.), to statistical methods (chemometrics), and to modern day concerns such as ""green"" chemistry, where ut

  13. On the Evaporation Kinetics of [60] Fullerene in Aromatic Organic Solvents

    KAUST Repository

    Amer, Maher S.; Wang, Wenhu; Kollins, Kaitlin N; Altalebi, Hasanain; Schwingenschlö gl, Udo

    2018-01-01

    We investigate the effect of C60 fullerene nanospheres on the evaporation kinetics of a number of aromatic solvents with different levels of molecular association, namely, benzene, toluene, and chlorobenzene. The dependence of the evaporation rate on the fullerene concentration is not monotonic but rather exhibits maxima and minima. The results strongly support the notion of molecular structuring within the liquid solvent controlled by the nature of fullerene/solvent interaction and the level of molecular association within the solvent itself.

  14. On the Evaporation Kinetics of [60] Fullerene in Aromatic Organic Solvents

    KAUST Repository

    Amer, Maher S.

    2018-04-03

    We investigate the effect of C60 fullerene nanospheres on the evaporation kinetics of a number of aromatic solvents with different levels of molecular association, namely, benzene, toluene, and chlorobenzene. The dependence of the evaporation rate on the fullerene concentration is not monotonic but rather exhibits maxima and minima. The results strongly support the notion of molecular structuring within the liquid solvent controlled by the nature of fullerene/solvent interaction and the level of molecular association within the solvent itself.

  15. Solvent effects in the synergistic solvent extraction of Co2+

    International Nuclear Information System (INIS)

    Kandil, A.T.; Ramadan, A.

    1979-01-01

    The extraction of Co 2+ from a 0.1M ionic strength aqueous phase (Na + , CH 3 COOH) of pH = 5.1 was studied using thenoyltrifluoroacetone, HTTA, in eight different solvents and HTTA + trioctylphosphine oxide, TOPO, in the same solvents. A comparison of the effect of solvent dielectric constant on the equilibrium constant shows a synergism as a result of the increased hydrophobic character imparted to the metal complex due to the formation of the TOPO adduct. (author)

  16. Passivating ligand and solvent contribution to the electronics properties of semiconductor nanocrystals

    Energy Technology Data Exchange (ETDEWEB)

    Tretiak, Sergei [Los Alamos National Laboratory; Crotty, Angela [Los Alamos National Laboratory; Fischer, Sean [Los Alamos National Laboratory; Kilina, Svetlana [NON LANL

    2010-10-04

    Expanding on previous work, we examine in detail the impact passivating ligands have on the electronic properties of CdSe quantum dots (QDs). We also explore the importance of the inclusion of solvent in simulating passivated QDs. Most ligand states are found well removed from the band edges, with pyridine being the exception and contributing states that sit right on the conduction band edge. Localized trap states are found for trimethylphosphine and pyridine capped QDs, with solvent helping to eliminate these. The effect of losing a ligand on the electronic properties of the system is observed to vary in proportion with the binding energy and steric bulk of the ligand. More disruption of the electronic properties is seen for tight-binding, sterically large ligands. We also look at the validity of using the single-particle Kohn-Sham (KS) representation to approximate optical absorption spectra. Besides a systematic blue-shift relative to the time-dependent density functional theory spectra, the KS spectra are in very good agreement with the more accurate method for these systems. Such agreement here justifies the use of the KS approach for calculating absorption spectra of QD systems.

  17. Rheb Protein Binds CAD (Carbamoyl-phosphate Synthetase 2, Aspartate Transcarbamoylase, and Dihydroorotase) Protein in a GTP- and Effector Domain-dependent Manner and Influences Its Cellular Localization and Carbamoyl-phosphate Synthetase (CPSase) Activity*

    Science.gov (United States)

    Sato, Tatsuhiro; Akasu, Hitomi; Shimono, Wataru; Matsu, Chisa; Fujiwara, Yuki; Shibagaki, Yoshio; Heard, Jeffrey J.; Tamanoi, Fuyuhiko; Hattori, Seisuke

    2015-01-01

    Rheb small GTPases, which consist of Rheb1 and Rheb2 (also known as RhebL1) in mammalian cells, are unique members of the Ras superfamily and play central roles in regulating protein synthesis and cell growth by activating mTOR. To gain further insight into the function of Rheb, we carried out a search for Rheb-binding proteins and found that Rheb binds to CAD protein (carbamoyl-phosphate synthetase 2, aspartate transcarbamoylase, and dihydroorotase), a multifunctional enzyme required for the de novo synthesis of pyrimidine nucleotides. CAD binding is more pronounced with Rheb2 than with Rheb1. Rheb binds CAD in a GTP- and effector domain-dependent manner. The region of CAD where Rheb binds is located at the C-terminal region of the carbamoyl-phosphate synthetase domain and not in the dihydroorotase and aspartate transcarbamoylase domains. Rheb stimulated carbamoyl-phosphate synthetase activity of CAD in vitro. In addition, an elevated level of intracellular UTP pyrimidine nucleotide was observed in Tsc2-deficient cells, which was attenuated by knocking down of Rheb. Immunostaining analysis showed that expression of Rheb leads to increased accumulation of CAD on lysosomes. Both a farnesyltransferase inhibitor that blocks membrane association of Rheb and knockdown of Rheb mislocalized CAD. These results establish CAD as a downstream effector of Rheb and suggest a possible role of Rheb in regulating de novo pyrimidine nucleotide synthesis. PMID:25422319

  18. Rheb protein binds CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamoylase, and dihydroorotase) protein in a GTP- and effector domain-dependent manner and influences its cellular localization and carbamoyl-phosphate synthetase (CPSase) activity.

    Science.gov (United States)

    Sato, Tatsuhiro; Akasu, Hitomi; Shimono, Wataru; Matsu, Chisa; Fujiwara, Yuki; Shibagaki, Yoshio; Heard, Jeffrey J; Tamanoi, Fuyuhiko; Hattori, Seisuke

    2015-01-09

    Rheb small GTPases, which consist of Rheb1 and Rheb2 (also known as RhebL1) in mammalian cells, are unique members of the Ras superfamily and play central roles in regulating protein synthesis and cell growth by activating mTOR. To gain further insight into the function of Rheb, we carried out a search for Rheb-binding proteins and found that Rheb binds to CAD protein (carbamoyl-phosphate synthetase 2, aspartate transcarbamoylase, and dihydroorotase), a multifunctional enzyme required for the de novo synthesis of pyrimidine nucleotides. CAD binding is more pronounced with Rheb2 than with Rheb1. Rheb binds CAD in a GTP- and effector domain-dependent manner. The region of CAD where Rheb binds is located at the C-terminal region of the carbamoyl-phosphate synthetase domain and not in the dihydroorotase and aspartate transcarbamoylase domains. Rheb stimulated carbamoyl-phosphate synthetase activity of CAD in vitro. In addition, an elevated level of intracellular UTP pyrimidine nucleotide was observed in Tsc2-deficient cells, which was attenuated by knocking down of Rheb. Immunostaining analysis showed that expression of Rheb leads to increased accumulation of CAD on lysosomes. Both a farnesyltransferase inhibitor that blocks membrane association of Rheb and knockdown of Rheb mislocalized CAD. These results establish CAD as a downstream effector of Rheb and suggest a possible role of Rheb in regulating de novo pyrimidine nucleotide synthesis. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  19. Solvent extraction of zirconium

    International Nuclear Information System (INIS)

    Kim, S.S.; Yoon, J.H.

    1981-01-01

    The extraction of zirconium(VI) from an aqueous solution of constant ionic strength with versatic acid-10 dissolved in benzen was studied as a function of pH and the concentration of zirconium(VI) and organic acid. The effects of sulphate and chlorine ions on the extraction of the zirconium(VI) were briefly examined. It was revealed that (ZrOR 2 .2RH) is the predominant species of extracted zirconium(VI) in the versatic acid-10. The chemical equation and the apparent equilibrium constants thereof have been determined as follows. (ZrOsup(2+))aq+ 2(R 2 H 2 )sub(org) = (ZrOR 2 .2RH)sub(org)+2(H + )aq Ksub(Zr) = (ZrOR 2 .2RH)sub(org)(H + ) 2 /(ZrOsup(2+))sub(aq)(R 2 H 2 )sup(2)sub(org) = 3.3 x 10 -7 . The synergistic effects of TBP and D2EHPA were also studied. In the mixed solvent with 0.1M TBP, the synergistic effect was observed, while the mixed solvent with D2EHPA showed the antisynergistic effect. (Author)

  20. Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: Comparison between hard-sphere solvent and water

    International Nuclear Information System (INIS)

    Oshima, Hiraku; Kinoshita, Masahiro

    2015-01-01

    In earlier works, we showed that the entropic effect originating from the translational displacement of water molecules plays the pivotal role in protein folding and denaturation. The two different solvent models, hard-sphere solvent and model water, were employed in theoretical methods wherein the entropic effect was treated as an essential factor. However, there were similarities and differences in the results obtained from the two solvent models. In the present work, to unveil the physical origins of the similarities and differences, we simultaneously consider structural transition, cold denaturation, and pressure denaturation for the same protein by employing the two solvent models and considering three different thermodynamic states for each solvent model. The solvent-entropy change upon protein folding/unfolding is decomposed into the protein-solvent pair (PA) and many-body (MB) correlation components using the integral equation theories. Each component is further decomposed into the excluded-volume (EV) and solvent-accessible surface (SAS) terms by applying the morphometric approach. The four physically insightful constituents, (PA, EV), (PA, SAS), (MB, EV), and (MB, SAS), are thus obtained. Moreover, (MB, SAS) is discussed by dividing it into two factors. This all-inclusive investigation leads to the following results: (1) the protein-water many-body correlation always plays critical roles in a variety of folding/unfolding processes; (2) the hard-sphere solvent model fails when it does not correctly reproduce the protein-water many-body correlation; (3) the hard-sphere solvent model becomes problematic when the dependence of the many-body correlation on the solvent number density and temperature is essential: it is not quite suited to studies on cold and pressure denaturating of a protein; (4) when the temperature and solvent number density are limited to the ambient values, the hard-sphere solvent model is usually successful; and (5) even at the ambient

  1. Cellular expression or binding of desLys58-beta2 microglobulin is not dependent on the presence of the tri-molecular MHC class I complex

    DEFF Research Database (Denmark)

    Wang, M; Corlin, D B; Heegaard, N H H

    2008-01-01

    -exposure to dbeta2m. Binding of 332-01 antibody could not be displaced by addition of high concentrations of native beta2m. In conclusion, our data indicate that dbeta2m - in contrast to native beta2m - binds to a hitherto unknown cell surface receptor independent of classical MHC class I molecules. As beta2m has...... previously been shown to display biological activities such as the induction of both growth promotion and apoptosis, C1 complement activity, shown to mediate cleavage of beta2m, could be involved in these processes....

  2. Cell adhesion to fibrillin-1: identification of an Arg-Gly-Asp-dependent synergy region and a heparin-binding site that regulates focal adhesion formation

    DEFF Research Database (Denmark)

    Bax, Daniel V; Mahalingam, Yashithra; Cain, Stuart

    2007-01-01

    We have defined the molecular basis of cell adhesion to fibrillin-1, the major structural component of extracellular microfibrils that are associated with elastic fibres. Using human dermal fibroblasts, and recombinant domain swap fragments containing the Arg-Gly-Asp motif, we have demonstrated...... a requirement for upstream domains for integrin-alpha(5)beta(1)-mediated cell adhesion and migration. An adjacent heparin-binding site, which supports focal adhesion formation, was mapped to the fibrillin-1 TB5 motif. Site-directed mutagenesis revealed two arginine residues that are crucial for heparin binding...

  3. Solvent Extraction and Characterization of Neutral Lipids in Oocystis sp

    Energy Technology Data Exchange (ETDEWEB)

    Anthony, Renil [Department of Mechanical Engineering, Ohio University, Athens, OH (United States); Stuart, Ben, E-mail: stuart@ohio.edu [Department of Civil Engineering, Ohio University, Athens, OH (United States)

    2015-01-20

    Microalgae are a favorable feedstock for bioproducts and biofuels due to their high oil content, fast growth rates, and low resource demands. Solvent lipid extraction efficiency from microalgae is dependent on algal strain and the extraction solvent. Four non-polar extraction solvents were evaluated for the recovery of neutral cellular lipids from microalgae Oocystis sp. (University of Texas at Austin LB2396). Methylene chloride, hexane, diethyl ether, and cyclohexane were selected as the extraction solvents. The lipid extracts were derivatized and analyzed using gas chromatography–mass spectroscopy. All solvent extracts contained hexadecanoic acid, linoleic acid, and linolenic acid; accounting for 70% of total lipid content with a proportional wt% composition of the three fatty acids, except for the hexane extracts that showed only hexadecanoic acid and linoleic acid. While not statistically differentiated, methylene chloride proved to be the most effective solvent for Oocystis sp. among the four solvents tested with a total average neutral lipid recovery of 0.25% of dry weight followed by diethyl ether (0.18%), cyclohexane (0.14%), and hexane (0.11%). This research presents a simple methodology to optimize the selection of lipid specific extraction solvents for the microalgal strain selected.

  4. Solvent Extraction and Characterization of Neutral Lipids in Oocystis sp.

    Directory of Open Access Journals (Sweden)

    Renil eAnthony

    2015-01-01

    Full Text Available Microalgae are a favorable feedstock for bioproducts and biofuels due to their high oil content, fast growth rates and low resource demands. Solvent lipid extraction efficiency from microalgae is dependent on algal strain and the extraction solvent. Four non-polar extraction solvents were evaluated for the recovery of neutral cellular lipids from microalgae Oocystis sp. (UTEX LB2396. Methylene chloride, hexane, diethyl ether, and cyclohexane were selected as the extraction solvents. All solvent extracts contained hexadecanoic acid, linoleic acid and linolenic acid; accounting for 70% of total lipid content with a proportional wt% composition of the three fatty acids, except for the hexane extracts that showed only hexadecanoic acid and linoleic acid. While not statistically differentiated, methylene chloride proved to be the most effective solvent for Oocystis sp. among the four solvents tested with a total average neutral lipid recovery of 0.25% of dry weight followed by diethyl ether (0.18%, cyclohexane (0.14% and hexane (0.11%. This research presents a simple methodology to optimize the selection of lipid specific extraction solvents for the microalgal strain selected.

  5. Solvent Extraction and Characterization of Neutral Lipids in Oocystis sp

    International Nuclear Information System (INIS)

    Anthony, Renil; Stuart, Ben

    2015-01-01

    Microalgae are a favorable feedstock for bioproducts and biofuels due to their high oil content, fast growth rates, and low resource demands. Solvent lipid extraction efficiency from microalgae is dependent on algal strain and the extraction solvent. Four non-polar extraction solvents were evaluated for the recovery of neutral cellular lipids from microalgae Oocystis sp. (University of Texas at Austin LB2396). Methylene chloride, hexane, diethyl ether, and cyclohexane were selected as the extraction solvents. The lipid extracts were derivatized and analyzed using gas chromatography–mass spectroscopy. All solvent extracts contained hexadecanoic acid, linoleic acid, and linolenic acid; accounting for 70% of total lipid content with a proportional wt% composition of the three fatty acids, except for the hexane extracts that showed only hexadecanoic acid and linoleic acid. While not statistically differentiated, methylene chloride proved to be the most effective solvent for Oocystis sp. among the four solvents tested with a total average neutral lipid recovery of 0.25% of dry weight followed by diethyl ether (0.18%), cyclohexane (0.14%), and hexane (0.11%). This research presents a simple methodology to optimize the selection of lipid specific extraction solvents for the microalgal strain selected.

  6. Protein-solvent preferential interactions, protein hydration, and the modulation of biochemical reactions by solvent components.

    Science.gov (United States)

    Timasheff, Serge N

    2002-07-23

    Solvent additives (cosolvents, osmolytes) modulate biochemical reactions if, during the course of the reaction, there is a change in preferential interactions of solvent components with the reacting system. Preferential interactions can be expressed in terms of preferential binding of the cosolvent or its preferential exclusion (preferential hydration). The driving force is the perturbation by the protein of the chemical potential of the cosolvent. It is shown that the measured change of the amount of water in contact with protein during the course of the reaction modulated by an osmolyte is a change in preferential hydration that is strictly a measure of the cosolvent chemical potential perturbation by the protein in the ternary water-protein-cosolvent system. It is not equal to the change in water of hydration, because water of hydration is a reflection strictly of protein-water forces in a binary system. There is no direct relation between water of preferential hydration and water of hydration.

  7. Stimulation of a Cd-binding protein, and inhibition of the vitamin D-dependent calcium-binding protein, by zinc or cadmium in organ-cultured embryonic chick duodenum

    International Nuclear Information System (INIS)

    Corradino, R.A.; Fullmer, C.S.

    1980-01-01

    Embryonic chick duodenum maintained in organ culture responds to 1 α,25-dihydroxy vitamin D 3 in the culture medium by de novo synthesis of a specific calcium-binding protein (CaBP). The addition of Cd 2+ (3-5 x 10 -5 M) or Zn 2+ (10 -5 -10 -4 M) to the medium inhibited CaBP, but stimulated biosynthesis of a Cd-binding protein (CdBP). CdBP in duodenal homogenate supernatants was assessed in two ways: first, by its 109 Cd-binding activity ( 109 CdBA) using a competitive ion exchange procedure; and, second, by the extent of [ 35 S]-cystine incorporation into a specific peak or band after gel filtration or analytical polyacrylamide disc gel electrophoresis, respectively. Regardless of whether cadmium- or zinc-stimulated, the 35 S-labeled CdBP - the only protein significantly labeled under the conditions employed - migrated identically upon gel filtration and electrophoresis, and comigrated with purified chick liver Cd-metallothionein. Neither actinomycin D nor α-amanitin, in concentrations sufficient to severely inhibit CaBP, significantly reduced CdBP production. However, cycloheximide did inhibit either Cd 2+ - or Zn 2+ -stimulated CdBP by about 50% at an inhibitor concentration which abolished CaBP. The inhibitor studies, coupled with the observations of extensive incorporation of [ 35 S]cystine into CdBP, suggest that the metals stimulated biosynthesis by a mechanism operating at the translational level. The organ-cultured duodenum seems well suited for studies of the regulation of CdBP biosynthesis especially since it responds predictably to the steroid hormone, 1α,25-dihydroxy vitamin D 3 , in the induction of another specific protein, CaBP, at the transcriptional level. The biosynthesis of CaBP thus may serve as a convenient control in studies of CdBP production under various experimental conditions

  8. How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations.

    Science.gov (United States)

    Kaus, Joseph W; Harder, Edward; Lin, Teng; Abel, Robert; McCammon, J Andrew; Wang, Lingle

    2015-06-09

    Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conformations that are important for ligand binding, the calculated free energy may depend on the initial conformation used in the simulation due to the lack of complete sampling of all the important regions in phase space. This is particularly true for ligands with multiple possible binding modes separated by high energy barriers, making it difficult to sample all relevant binding modes even with modern enhanced sampling methods. In this paper, we apply a previously developed method that provides a corrected binding free energy for ligands with multiple binding modes by combining the free energy results from multiple alchemical FEP calculations starting from all enumerated poses, and the results are compared with Glide docking and MM-GBSA calculations. From these calculations, the dominant ligand binding mode can also be predicted. We apply this method to a series of ligands that bind to c-Jun N-terminal kinase-1 (JNK1) and obtain improved free energy results. The dominant ligand binding modes predicted by this method agree with the available crystallography, while both Glide docking and MM-GBSA calculations incorrectly predict the binding modes for some ligands. The method also helps separate the force field error from the ligand sampling error, such that deviations in the predicted binding free energy from the experimental values likely indicate possible inaccuracies in the force field. An error in the force field for a subset of the ligands studied was identified using this method, and improved free energy results were obtained by correcting the partial charges assigned to the

  9. How To Deal with Multiple Binding Poses in Alchemical Relative Protein–Ligand Binding Free Energy Calculations

    Science.gov (United States)

    2016-01-01

    Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conformations that are important for ligand binding, the calculated free energy may depend on the initial conformation used in the simulation due to the lack of complete sampling of all the important regions in phase space. This is particularly true for ligands with multiple possible binding modes separated by high energy barriers, making it difficult to sample all relevant binding modes even with modern enhanced sampling methods. In this paper, we apply a previously developed method that provides a corrected binding free energy for ligands with multiple binding modes by combining the free energy results from multiple alchemical FEP calculations starting from all enumerated poses, and the results are compared with Glide docking and MM-GBSA calculations. From these calculations, the dominant ligand binding mode can also be predicted. We apply this method to a series of ligands that bind to c-Jun N-terminal kinase-1 (JNK1) and obtain improved free energy results. The dominant ligand binding modes predicted by this method agree with the available crystallography, while both Glide docking and MM-GBSA calculations incorrectly predict the binding modes for some ligands. The method also helps separate the force field error from the ligand sampling error, such that deviations in the predicted binding free energy from the experimental values likely indicate possible inaccuracies in the force field. An error in the force field for a subset of the ligands studied was identified using this method, and improved free energy results were obtained by correcting the partial charges assigned to the

  10. Recent Advances in Anhydrous Solvents for CO{sub 2} Capture: Ionic Liquids, Switchable Solvents, and Nanoparticle Organic Hybrid Materials

    Energy Technology Data Exchange (ETDEWEB)

    Park, Youngjune [School of Environmental Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju (Korea, Republic of); Lin, Kun-Yi Andrew [Department of Environmental Engineering, National Chung Hsing University, Taichung City (China); Park, Ah-Hyung Alissa, E-mail: ap2622@columbia.edu [Department of Earth and Environmental Engineering, Lenfest Center for Sustainable Energy, Columbia University, New York, NY (United States); Department of Chemical Engineering, Lenfest Center for Sustainable Energy, Columbia University, New York, NY (United States); Petit, Camille, E-mail: ap2622@columbia.edu [Department of Chemical Engineering, Imperial College London, London (United Kingdom)

    2015-10-01

    CO{sub 2} capture by amine scrubbing, which has a high CO{sub 2} capture capacity and a rapid reaction rate, is the most employed and investigated approach to date. There are a number of recent large-scale demonstrations including the Boundary Dam Carbon Capture Project by SaskPower in Canada that have reported successful implementations of aqueous amine solvent in CO{sub 2} capture from flue gases. The findings from these demonstrations will significantly advance the field of CO{sub 2} capture in the coming years. While the latest efforts in aqueous amine solvents are exciting and promising, there are still several drawbacks to amine-based CO{sub 2} capture solvents including high volatility and corrosiveness of the amine solutions as well as the high parasitic energy penalty during the solvent regeneration step. Thus, in a parallel effort, alternative CO{sub 2} capture solvents, which are often anhydrous, have been developed as the third-generation CO{sub 2} capture solvents. These novel classes of liquid materials include ionic liquids, CO{sub 2}-triggered switchable solvents (i.e., CO{sub 2}-binding organic liquids, reversible ionic liquids), and nanoparticle organic hybrid materials. This paper provides a review of these various anhydrous solvents and their potential for CO{sub 2} capture. Particular attention is given to the mechanisms of CO{sub 2} absorption in these solvents, their regeneration and their processability – especially taking into account their viscosity. While not intended to provide a complete coverage of the existing literature, this review aims at pointing the major findings reported for these new classes of CO{sub 2} capture media.

  11. Recent Advances in Anhydrous Solvents for CO2 Capture: Ionic Liquids, Switchable Solvents, and Nanoparticle Organic Hybrid Materials

    Directory of Open Access Journals (Sweden)

    YOUNGJUNE ePARK

    2015-10-01

    Full Text Available CO2 capture by amine scrubbing, which has a high CO2 capture capacity and a rapid reaction rate, is the most employed and investigated approach to date. There are a number of recent large-scale demonstrations including the Boundary Dam Carbon Capture Project by SaskPower in Canada that have reported successful implementations of aqueous amine solvent in CO2 capture from flue gases. The findings from these demonstrations will significantly advance the field of CO2 capture in the coming years. While the latest efforts in aqueous amine solvents are exciting and promising, there are still several drawbacks to amine-based CO2 capture solvents including high volatility and corrosiveness of the amine solutions, as well as the high parasitic energy penalty during the solvent regeneration step. Thus, in a parallel effort, alternative CO2 capture solvents, which are often anhydrous, have been developed as the third-generation CO2 capture solvents. These novel classes of liquid materials include: Ionic Liquids (ILs, CO2-triggered switchable solvents (i.e., CO2 Binding Organic Liquids (CO2BOLs, Reversible Ionic Liquids (RevILs, and Nanoparticle Organic Hybrid Materials (NOHMs. This paper provides a review of these various anhydrous solvents and their potential for CO2 capture. Particular attention is given to the mechanisms of CO2 absorption in these solvents, their regeneration and their processability – especially taking into account their viscosity. While not intended to provide a complete coverage of the existing literature, this review aims at pointing the major findings reported for these new classes of CO2 capture media.

  12. Recent Advances in Anhydrous Solvents for CO2 Capture: Ionic Liquids, Switchable Solvents, and Nanoparticle Organic Hybrid Materials

    International Nuclear Information System (INIS)

    Park, Youngjune; Lin, Kun-Yi Andrew; Park, Ah-Hyung Alissa; Petit, Camille

    2015-01-01

    CO 2 capture by amine scrubbing, which has a high CO 2 capture capacity and a rapid reaction rate, is the most employed and investigated approach to date. There are a number of recent large-scale demonstrations including the Boundary Dam Carbon Capture Project by SaskPower in Canada that have reported successful implementations of aqueous amine solvent in CO 2 capture from flue gases. The findings from these demonstrations will significantly advance the field of CO 2 capture in the coming years. While the latest efforts in aqueous amine solvents are exciting and promising, there are still several drawbacks to amine-based CO 2 capture solvents including high volatility and corrosiveness of the amine solutions as well as the high parasitic energy penalty during the solvent regeneration step. Thus, in a parallel effort, alternative CO 2 capture solvents, which are often anhydrous, have been developed as the third-generation CO 2 capture solvents. These novel classes of liquid materials include ionic liquids, CO 2 -triggered switchable solvents (i.e., CO 2 -binding organic liquids, reversible ionic liquids), and nanoparticle organic hybrid materials. This paper provides a review of these various anhydrous solvents and their potential for CO 2 capture. Particular attention is given to the mechanisms of CO 2 absorption in these solvents, their regeneration and their processability – especially taking into account their viscosity. While not intended to provide a complete coverage of the existing literature, this review aims at pointing the major findings reported for these new classes of CO 2 capture media.

  13. The Potato Nucleotide-Binding Leucine-Rich Repeat (NLR) Immune Receptor Rx1 is a Pathogen Dependent DNA-Deforming Protein

    NARCIS (Netherlands)

    Fenyk, S.; Townsend, P.D.; Dixon, C.H.; Spies, G.B.; Campillo, A.S.E.; Slootweg, E.J.; Westerhof, L.B.; Gawehns, F.K.K.; Knight, M.R.; Sharples, G.J.; Goverse, A.; Palsson, L.O.; Takken, F.L.W.; Cann, M.J.

    2015-01-01

    Plant NLR proteins enable cells to respond to pathogen attack. Several NLRs act in the nucleus, however, conserved nuclear targets that support their role in immunity are unknown. Previously we noted a structural homology between the NB domain of NLRs and DNA replication origin-binding Cdc6/Orc1

  14. Inhibition of nuclear T3 binding by fatty acids: dependence on chain length, unsaturated bonds, cis-trans configuration and esterification

    NARCIS (Netherlands)

    Wiersinga, W. M.; Platvoet-ter Schiphorst, M.

    1990-01-01

    1. Fatty acids have the capacity for inhibition of nuclear T3 binding (INB). The present studies were undertaken to describe the INB-activity of fatty acids as a function of chain length, unsaturated bonds, cis-trans configuration, and esterification. 2. Isolated rat liver nuclei were incubated with

  15. Direct binding of the N-terminus of HTLV-1 tax oncoprotein to cyclin-dependent kinase 4 is a dominant path to stimulate the kinase activity.

    Science.gov (United States)

    Li, Junan; Li, Hongyuan; Tsai, Ming-Daw

    2003-06-10

    The involvement of Tax oncoprotein in the INK4-CDK4/6-Rb pathway has been regarded as a key factor for immortalization and transformation of human T-cell leukemia virus 1 (HTLV-1) infected cells. In both p16 -/- and +/+ cells, expression of Tax has been correlated with an increase in CDK4 activity, which subsequently increases the phosphorylation of Rb and drives the infected cells into cell cycle progression. In relation to these effects, Tax has been shown to interact with two components of the INK4-CDK4/6-Rb pathway, p16 and cyclin D(s). While Tax competes with CDK4 for p16 binding, thus suppressing p16 inhibition of CDK4, Tax also binds to cyclin D(s) with concomitant increases in both CDK4 activity and the phosphorylation of cyclin D(s). Here we show that both Tax and residues 1-40 of the N-terminus of Tax, Tax40N, bind to and activate CDK4 in vitro. In the presence of INK4 proteins, binding of Tax and Tax40N to CDK4 counteracts against the inhibition of p16 and p18 and acts as the major path to regulate Tax-mediated activation of CDK4. We also report that Tax40N retains the transactivation ability. These results of in vitro studies demonstrate a potentially novel, p16-independent route to regulate CDK4 activity by the Tax oncoprotein in HTLV-1 infected cells.

  16. Porous fiber formation in polymer-solvent system undergoing solvent evaporation

    Science.gov (United States)

    Dayal, Pratyush; Kyu, Thein

    2006-08-01

    Temporal evolution of the fiber morphology during dry spinning has been investigated in the framework of Cahn-Hilliard equation [J. Chem. Phys. 28, 258 (1958)] pertaining to the concentration order parameter or volume fraction given by the Flory-Huggins free energy of mixing [P. J. Flory, Principles of Polymer Chemistry (Cornell University Press, Ithaca, NY, 1953), p. 672] in conjunction with the solvent evaporation rate. To guide the solvent evaporation induced phase separation, equilibrium phase diagram of the starting polymer solution was established on the basis of the Flory-Huggins free energy of mixing. The quasi-steady-state approximation has been adopted to account for the nonconserved nature of the concentration field caused by the solvent loss. The process of solvent evaporation across the fiber skin-air interface was treated in accordance with the classical Fick's law [R. B. Bird et al., Transport Phenomena (J. Wiley, New York, 1960), p. 780]. The simulated morphologies include gradient type, hollow fiber type, bicontinuous type, and host-guest type. The development of these diverse fiber morphologies is explicable in terms of the phase diagram of the polymer solution in a manner dependent on the competition between the phase separation dynamics and rate of solvent evaporation.

  17. Use of eluted peptide sequence data to identify the binding characteristics of peptides to the insulin-dependent diabetes susceptibility allele HLA-DQ8 (DQ 3.2).

    Science.gov (United States)

    Godkin, A; Friede, T; Davenport, M; Stevanovic, S; Willis, A; Jewell, D; Hill, A; Rammensee, H G

    1997-06-01

    HLA-DQ8 (A1*0301, B1*0302) and -DQ2 (A1*0501, B1*0201) are both associated with diseases such as insulin-dependent diabetes mellitus and coeliac disease. We used the technique of pool sequencing to look at the requirements of peptides binding to HLA-DQ8, and combined these data with naturally sequenced ligands and in vitro binding assays to describe a novel motif for HLA-DQ8. The motif, which has the same basic format as many HLA-DR molecules, consists of four or five anchor regions, in the positions from the N-terminus of the binding core of n, n + 3, n + 5/6 and n + 8, i.e. P1, P4, P6/7 and P9. P1 and P9 require negative or polar residues, with mainly aliphatic residues at P4 and P6/7. The features of the HLA-DQ8 motif were then compared to a pool sequence of peptides eluted from HLA-DQ2. A consensus motif for the binding of a common peptide which may be involved in disease pathogenesis is described. Neither of the disease-associated alleles HLA-DQ2 and -DQ8 have Asp at position 57 of the beta-chain. This Asp, if present, may form a salt bridge with an Arg at position 79 of the alpha-chain and so alter the binding specificity of P9. HLA-DQ2 and -DQ8 both appear to prefer negatively charged amino acids at P9. In contrast, HLA-DQ7 (A1*0301, B1*0301), which is not associated with diabetes, has Asp at beta 57, allowing positively charged amino acids at P9. This analysis of the sequence features of DQ-binding peptides suggests molecular characteristics which may be useful to predict epitopes involved in disease pathogenesis.

  18. Comparative responses of river biofilms at the community level to common organic solvent and herbicide exposure.

    Science.gov (United States)

    Paule, A; Roubeix, V; Swerhone, G D W; Roy, J; Lauga, B; Duran, R; Delmas, F; Paul, E; Rols, J L; Lawrence, J R

    2016-03-01

    Residual pesticides applied to crops migrate from agricultural lands to surface and ground waters. River biofilms are the first aquatic non-target organisms which interact with pesticides. Therefore, ecotoxicological experiments were performed at laboratory scale under controlled conditions to investigate the community-level responses of river biofilms to a chloroacetanilide herbicide (alachlor) and organic solvent (methanol) exposure through the development referenced to control. Triplicate rotating annular bioreactors, inoculated with river water, were used to cultivate river biofilms under the influence of 1 and 10 μg L(-1) of alachlor and 25 mg L(-1) of methanol. For this purpose, functional (thymidine incorporation and carbon utilization spectra) and structural responses of microbial communities were assessed after 5 weeks of development. Structural aspects included biomass (chlorophyll a, confocal laser scanning microscopy) and composition (fluor-conjugated lectin binding, molecular fingerprinting, and diatom species composition). The addition of alachlor resulted in a significant reduction of bacterial biomass at 1 μg L(-1), whereas at 10 μg L(-1), it induced a significant reduction of exopolymer lectin binding, algal, bacterial, and cyanobacterial biomass. However, there were no changes in biofilm thickness or thymidine incorporation. No significant difference between the bacterial community structures of control and alachlor-treated biofilms was revealed by terminal restriction fragment length polymorphism (T-RFLP) analyses. However, the methanol-treated bacterial communities appeared different from control and alachlor-treated communities. Moreover, methanol treatment resulted in an increase of bacterial biomass and thymidine incorporation as well. Changes in dominant lectin binding suggested changes in the exopolymeric substances and community composition. Chlorophyll a and cyanobacterial biomass were also altered by methanol. This study suggested

  19. Comparative studies on the human serum albumin binding of the clinically approved EGFR inhibitors gefitinib, erlotinib, afatinib, osimertinib and the investigational inhibitor KP2187.

    Science.gov (United States)

    Dömötör, Orsolya; Pelivan, Karla; Borics, Attila; Keppler, Bernhard K; Kowol, Christian R; Enyedy, Éva A

    2018-05-30

    Binding interactions between human serum albumin (HSA) and four approved epidermal growth factor receptor (EGFR) inhibitors gefitinib (GEF), erlotinib (ERL), afatinib (AFA), osimertinib (OSI), as well as the experimental drug KP2187, were investigated by means of spectrofluorometric and molecular modelling methods. Steady-state and time resolved spectrofluorometric techniques were carried out, including direct quenching of protein fluorescence and site marker displacement measurements. Proton dissociation processes and solvent dependent fluorescence properties were investigated as well. The EGFR inhibitors were predominantly presented in their single protonated form (HL + ) at physiological pH except ERL, which is charge-neutral. Significant solvent dependent fluorescence properties were found for GEF, ERL and KP2187, namely their emission spectra show strong dependence on the polarity and the hydrogen bonding ability of the solvents. The inhibitors proved to be bound at site I of HSA (in subdomain IIA) in a weak-to-moderate fashion (logK' 3.9-4.9) using spectrofluorometry. OSI (logK' 4.3) and KP2187 can additionally bind in site II (in subdomain IIIA), while GEF, ERL and AFA clearly show no interaction here. Docking methods qualitatively confirmed binding site preferences of compounds GEF and KP2187, and indicated that they probably bind to HSA in their neutral forms. Binding constants calculated on the basis of the various experimental data indicate a weak-to-moderate binding on HSA, only OSI exhibits somewhat higher affinity towards this protein. However, model calculations performed at physiological blood concentrations of HSA resulted in high (ca. 90%) bound fractions for the inhibitors, highlighting the importance of plasma protein binding. Copyright © 2018 Elsevier B.V. All rights reserved.

  20. Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Shenggao, E-mail: sgzhou@suda.edu.cn, E-mail: bli@math.ucsd.edu [Department of Mathematics and Mathematical Center for Interdiscipline Research, Soochow University, 1 Shizi Street, Jiangsu, Suzhou 215006 (China); Sun, Hui; Cheng, Li-Tien [Department of Mathematics, University of California, San Diego, La Jolla, California 92093-0112 (United States); Dzubiella, Joachim [Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, 14109 Berlin, Germany and Institut für Physik, Humboldt-Universität zu Berlin, 12489 Berlin (Germany); Li, Bo, E-mail: sgzhou@suda.edu.cn, E-mail: bli@math.ucsd.edu [Department of Mathematics and Quantitative Biology Graduate Program, University of California, San Diego, La Jolla, California 92093-0112 (United States); McCammon, J. Andrew [Department of Chemistry and Biochemistry, Department of Pharmacology, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093-0365 (United States)

    2016-08-07

    Recent years have seen the initial success of a variational implicit-solvent model (VISM), implemented with a robust level-set method, in capturing efficiently different hydration states and providing quantitatively good estimation of solvation free energies of biomolecules. The level-set minimization of the VISM solvation free-energy functional of all possible solute-solvent interfaces or dielectric boundaries predicts an equilibrium biomolecular conformation that is often close to an initial guess. In this work, we develop a theory in the form of Langevin geometrical flow to incorporate solute-solvent interfacial fluctuations into the VISM. Such fluctuations are crucial to biomolecular conformational changes and binding process. We also develop a stochastic level-set method to numerically implement such a theory. We describe the interfacial fluctuation through the “normal velocity” that is the solute-solvent interfacial force, derive the corresponding stochastic level-set equation in the sense of Stratonovich so that the surface representation is independent of the choice of implicit function, and develop numerical techniques for solving such an equation and processing the numerical data. We apply our computational method to study the dewetting transition in the system of two hydrophobic plates and a hydrophobic cavity of a synthetic host molecule cucurbit[7]uril. Numerical simulations demonstrate that our approach can describe an underlying system jumping out of a local minimum of the free-energy functional and can capture dewetting transitions of hydrophobic systems. In the case of two hydrophobic plates, we find that the wavelength of interfacial fluctuations has a strong influence to the dewetting transition. In addition, we find that the estimated energy barrier of the dewetting transition scales quadratically with the inter-plate distance, agreeing well with existing studies of molecular dynamics simulations. Our work is a first step toward the

  1. Selective solvent extraction of oils

    Energy Technology Data Exchange (ETDEWEB)

    1938-04-09

    In the selective solvent extraction of naphthenic base oils, the solvent used consists of the extract obtained by treating a paraffinic base oil with a selective solvent. The extract, or partially spent solvent is less selective than the solvent itself. Selective solvents specified for the extraction of the paraffinic base oil are phenol, sulphur dioxide, cresylic acid, nitrobenzene, B:B/sup 1/-dichlorethyl ether, furfural, nitroaniline and benzaldehyde. Oils treated are Coastal lubricating oils, or naphthenic oils from the cracking, or destructive hydrogenation of coal, tar, lignite, peat, shale, bitumen, or petroleum. The extraction may be effected by a batch or counter-current method, and in the presence of (1) liquefied propane, or butane, or naphtha, or (2) agents which modify the solvent power such as, water, ammonia, acetonitrile, glycerine, glycol, caustic soda or potash. Treatment (2) may form a post-treatment effected on the extract phase. In counter-current treatment in a tower some pure selective solvent may be introduced near the raffinate outlet to wash out any extract therefrom.

  2. Mutating the Conserved Q-loop Glutamine 1291 Selectively Disrupts Adenylate Kinase-dependent Channel Gating of the ATP-binding Cassette (ABC) Adenylate Kinase Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) and Reduces Channel Function in Primary Human Airway Epithelia.

    Science.gov (United States)

    Dong, Qian; Ernst, Sarah E; Ostedgaard, Lynda S; Shah, Viral S; Ver Heul, Amanda R; Welsh, Michael J; Randak, Christoph O

    2015-05-29

    The ATP-binding cassette (ABC) transporter cystic fibrosis transmembrane conductance regulator (CFTR) and two other non-membrane-bound ABC proteins, Rad50 and a structural maintenance of chromosome (SMC) protein, exhibit adenylate kinase activity in the presence of physiologic concentrations of ATP and AMP or ADP (ATP + AMP ⇆ 2 ADP). The crystal structure of the nucleotide-binding domain of an SMC protein in complex with the adenylate kinase bisubstrate inhibitor P(1),P(5)-di(adenosine-5') pentaphosphate (Ap5A) suggests that AMP binds to the conserved Q-loop glutamine during the adenylate kinase reaction. Therefore, we hypothesized that mutating the corresponding residue in CFTR, Gln-1291, selectively disrupts adenylate kinase-dependent channel gating at physiologic nucleotide concentrations. We found that substituting Gln-1291 with bulky side-chain amino acids abolished the effects of Ap5A, AMP, and adenosine 5'-monophosphoramidate on CFTR channel function. 8-Azidoadenosine 5'-monophosphate photolabeling of the AMP-binding site and adenylate kinase activity were disrupted in Q1291F CFTR. The Gln-1291 mutations did not alter the potency of ATP at stimulating current or ATP-dependent gating when ATP was the only nucleotide present. However, when physiologic concentrations of ADP and AMP were added, adenylate kinase-deficient Q1291F channels opened significantly less than wild type. Consistent with this result, we found that Q1291F CFTR displayed significantly reduced Cl(-) channel function in well differentiated primary human airway epithelia. These results indicate that a highly conserved residue of an ABC transporter plays an important role in adenylate kinase-dependent CFTR gating. Furthermore, the results suggest that adenylate kinase activity is important for normal CFTR channel function in airway epithelia. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  3. Structural insights into the T6SS effector protein Tse3 and the Tse3-Tsi3 complex from Pseudomonas aeruginosa reveal a calcium-dependent membrane-binding mechanism.

    Science.gov (United States)

    Lu, Defen; Shang, Guijun; Zhang, Heqiao; Yu, Qian; Cong, Xiaoyan; Yuan, Jupeng; He, Fengjuan; Zhu, Chunyuan; Zhao, Yanyu; Yin, Kun; Chen, Yuanyuan; Hu, Junqiang; Zhang, Xiaodan; Yuan, Zenglin; Xu, Sujuan; Hu, Wei; Cang, Huaixing; Gu, Lichuan

    2014-06-01

    The opportunistic pathogen Pseudomonas aeruginosa uses the type VI secretion system (T6SS) to deliver the muramidase Tse3 into the periplasm of rival bacteria to degrade their peptidoglycan (PG). Concomitantly, P. aeruginosa uses the periplasm-localized immunity protein Tsi3 to prevent potential self-intoxication caused by Tse3, and thus gains an edge over rival bacteria in fierce niche competition. Here, we report the crystal structures of Tse3 and the Tse3-Tsi3 complex. Tse3 contains an annexin repeat-like fold at the N-terminus and a G-type lysozyme fold at the C-terminus. One loop in the N-terminal domain (Loop 12) and one helix (α9) from the C-terminal domain together anchor Tse3 and the Tse3-Tsi3 complex to membrane in a calcium-dependent manner in vitro, and this membrane-binding ability is essential for Tse3's activity. In the C-terminal domain, a Y-shaped groove present on the surface likely serves as the PG binding site. Two calcium-binding motifs are also observed in the groove and these are necessary for Tse3 activity. In the Tse3-Tsi3 structure, three loops of Tsi3 insert into the substrate-binding groove of Tse3, and three calcium ions present at the interface of the complex are indispensable for the formation of the Tse3-Tsi3 complex. © 2014 John Wiley & Sons Ltd.

  4. The protein inhibitor of nNOS (PIN/DLC1/LC8) binding does not inhibit the NADPH-dependent heme reduction in nNOS, a key step in NO synthesis.

    Science.gov (United States)

    Parhad, Swapnil S; Jaiswal, Deepa; Ray, Krishanu; Mazumdar, Shyamalava

    2016-03-25

    The neuronal nitric oxide synthase (nNOS) is an essential enzyme involved in the synthesis of nitric oxide (NO), a potent neurotransmitter. Although previous studies have indicated that the dynein light chain 1 (DLC1) binding to nNOS could inhibit the NO synthesis, the claim is challenged by contradicting reports. Thus, the mechanism of nNOS regulation remained unclear. nNOS has a heme-bearing, Cytochrome P450 core, and the functional enzyme is a dimer. The electron flow from NADPH to Flavin, and finally to the heme of the paired nNOS subunit within a dimer, is facilitated upon calmodulin (CaM) binding. Here, we show that DLC1 binding to nNOS-CaM complex does not affect the electron transport from the reductase to the oxygenase domain. Therefore, it cannot inhibit the rate of NADPH-dependent heme reduction in nNOS, which results in l-Arginine oxidation. Also, the NO release activity does not decrease with increasing DLC1 concentration in the reaction mix, which further confirmed that DLC1 does not inhibit nNOS activity. These findings suggest that the DLC1 binding may have other implications for the nNOS function in the cell. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Selection and design of solvents

    DEFF Research Database (Denmark)

    Gani, Rafiqul

    and design of solvents will be presented together with application examples. The selection problem is defined as finding known chemicals that match the desired functions of a solvent for a specified set of applications. The design problem is defined as finding the molecular structure (or mixture of molecules....... With increasing interest on issues such as waste, sustainability, environmental impact and green chemistry, the selection and design of solvents have become important problems that need to be addressed during chemical product-process design and development. Systematic methods and tools suitable for selection......) that match the desired functions of a solvent for a specified set of applications. Use of organic chemicals and ionic liquids as solvents will be covered....

  6. Synthetic, XRD, non-covalent interactions and solvent dependent nonlinear optical studies of Sulfadiazine-Ortho-Vanillin Schiff base: (E)-4-((2-hydroxy-3-methoxy- benzylidene) amino)-N-(pyrimidin-2-yl)benzene-sulfonamide

    Science.gov (United States)

    Shahid, Muhammad; Salim, Muhammad; Khalid, Muhammad; Tahir, Muhammad Nawaz; Khan, Muhammad Usman; Braga, Ataualpa Albert Carmo

    2018-06-01

    In this study, Sulfadiazine-Ortho-Vanillin Schiff base namely (E)-4-((2-hydroxy-3-methoxybenzylidene)amino)sbnd N-(pyrimidin-2-yl)benzene-sulfonamide (BS) was synthesized. Chemical characterization and computational studies using different techniques like XRD, FT-IR, UV-Vis, NBO, FMO, and MEP have been employed. Density functional theory (DFT) calculations have been performed at M06-2X/6-311 + G(d,p) level of theory to obtain optimized geometry and vibrational wave numbers for (E)-4-((2-hydroxy-3-methoxybenzylidene)amino)sbnd N-(pyrimidin-2-yl)benzene-sulfonamide (BS). The DFT optimized geometry supports the experimental XRD parameters. Frontier molecular orbital (FMO) energies and molecular electrostatic potential (MEP) surfaces have been executed at M06-2X/6-311 + G(d,p) level of theory. NBO analysis has been carried out at M06-2X/6-311 + G(d,p) level which not only discovered the hyper conjugative interactions and stability in title molecule but also reconfirmed the existence of Nsbnd H⋯N hydrogen bonds between the dimer. The findings of small EHOMO-ELUMO gap shows less hardness and larger softness values which suggested the bioactiveness of the title molecule. Finally, the effect of solvent on nonlinear optical (NLO) properties has been executed using M06-2X level of theory and 6-311 + G (d,p) basis set. The solvent polarity enhanced the NLO response from 3.62 × 10-30 esu to 4.66 × 10-30 esu indicating the considerable NLO character hence in general may have potential applications in the development of non-linear optical materials.

  7. The TAL effector PthA4 interacts with nuclear factors involved in RNA-dependent processes including a HMG protein that selectively binds poly(U RNA.

    Directory of Open Access Journals (Sweden)

    Tiago Antonio de Souza

    Full Text Available Plant pathogenic bacteria utilize an array of effector proteins to cause disease. Among them, transcriptional activator-like (TAL effectors are unusual in the sense that they modulate transcription in the host. Although target genes and DNA specificity of TAL effectors have been elucidated, how TAL proteins control host transcription is poorly understood. Previously, we showed that the Xanthomonas citri TAL effectors, PthAs 2 and 3, preferentially targeted a citrus protein complex associated with transcription control and DNA repair. To extend our knowledge on the mode of action of PthAs, we have identified new protein targets of the PthA4 variant, required to elicit canker on citrus. Here we show that all the PthA4-interacting proteins are DNA and/or RNA-binding factors implicated in chromatin remodeling and repair, gene regulation and mRNA stabilization/modification. The majority of these proteins, including a structural maintenance of chromosomes protein (CsSMC, a translin-associated factor X (CsTRAX, a VirE2-interacting protein (CsVIP2, a high mobility group (CsHMG and two poly(A-binding proteins (CsPABP1 and 2, interacted with each other, suggesting that they assemble into a multiprotein complex. CsHMG was shown to bind DNA and to interact with the invariable leucine-rich repeat region of PthAs. Surprisingly, both CsHMG and PthA4 interacted with PABP1 and 2 and showed selective binding to poly(U RNA, a property that is novel among HMGs and TAL effectors. Given that homologs of CsHMG, CsPABP1, CsPABP2, CsSMC and CsTRAX in other organisms assemble into protein complexes to regulate mRNA stability and translation, we suggest a novel role of TAL effectors in mRNA processing and translational control.

  8. In vivo estradiol-dependent dephosphorylation of the repressor MDBP-2-H1 correlates with the loss of in vitro preferential binding to methylated DNA.

    Science.gov (United States)

    Bruhat, A; Jost, J P

    1995-01-01

    We have previously shown that estradiol treatment of roosters resulted in a rapid loss of binding activity of the repressor MDBP-2-H1 (a member of the histone H1 family) to methylated DNA that was not due to a decrease in MDBP-2-H1 concentration. Here we demonstrate that MDBP-2-H1 from rooster liver nuclear extracts is a phosphoprotein. Phosphoamino acid analysis reveals that the phosphorylation occurs exclusively on serine residues. Two-dimensional gel electrophoresis and tryptic phosphopeptide analysis show that MDBP-2-H1 is phosphorylated at several sites. Treatment of roosters with estradiol triggers a dephosphorylation of at least two sites in the protein. Phosphatase treatment of purified rooster MDBP-2-H1 combined with gel mobility shift assay indicates that phosphorylation of MDBP-2-H1 is essential for the binding to methylated DNA and that the dephosphorylation can occur on the protein bound to methylated DNA causing its release from DNA. Thus, these results suggest that in vivo modification of the phosphorylation status of MDBP-2-H1 caused by estradiol treatment may be a key step for the down regulation of its binding to methylated DNA. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 Fig. 6 PMID:7731964

  9. Solvent extraction of Zn and metals in Zn ores by nonphosphorous solvents

    International Nuclear Information System (INIS)

    Auchapt, J.M.; Tostain, Jacqueline.

    1975-07-01

    This bibliography follows a first work on Zn solvent extraction by organo-phosphorous compounds. The other solvents used in Zn extraction, are studied: oxygenated nonphosphorous solvents (ketones, alcohols, carboxylic acids, sulfonates), nitrogenous solvents and hydrocarbons [fr

  10. The protein inhibitor of nNOS (PIN/DLC1/LC8) binding does not inhibit the NADPH-dependent heme reduction in nNOS, a key step in NO synthesis

    International Nuclear Information System (INIS)

    Parhad, Swapnil S.; Jaiswal, Deepa; Ray, Krishanu; Mazumdar, Shyamalava

    2016-01-01

    The neuronal nitric oxide synthase (nNOS) is an essential enzyme involved in the synthesis of nitric oxide (NO), a potent neurotransmitter. Although previous studies have indicated that the dynein light chain 1 (DLC1) binding to nNOS could inhibit the NO synthesis, the claim is challenged by contradicting reports. Thus, the mechanism of nNOS regulation remained unclear. nNOS has a heme-bearing, Cytochrome P450 core, and the functional enzyme is a dimer. The electron flow from NADPH to Flavin, and finally to the heme of the paired nNOS subunit within a dimer, is facilitated upon calmodulin (CaM) binding. Here, we show that DLC1 binding to nNOS-CaM complex does not affect the electron transport from the reductase to the oxygenase domain. Therefore, it cannot inhibit the rate of NADPH-dependent heme reduction in nNOS, which results in L-Arginine oxidation. Also, the NO release activity does not decrease with increasing DLC1 concentration in the reaction mix, which further confirmed that DLC1 does not inhibit nNOS activity. These findings suggest that the DLC1 binding may have other implications for the nNOS function in the cell. - Highlights: • The effect of interaction of nNOS with DLC1 has been debatable with contradicting reports in literature. • Purified DLC1 has no effect on electron transport between reductase and oxygenase domain of purified nNOS-CaM. • The NO release activity of nNOS was not altered by DLC1, supporting that DLC1 does not inhibit the enzyme. • These findings suggest that the DLC1 binding may have other implications for the nNOS function in the cell.

  11. The protein inhibitor of nNOS (PIN/DLC1/LC8) binding does not inhibit the NADPH-dependent heme reduction in nNOS, a key step in NO synthesis

    Energy Technology Data Exchange (ETDEWEB)

    Parhad, Swapnil S. [Tata Institute of Fundamental Research (TIFR), Homi Bhabha Road, Mumbai 400 005 (India); Jaiswal, Deepa [Tata Institute of Fundamental Research (TIFR), Homi Bhabha Road, Mumbai 400 005 (India); TIFR Centre for Interdisciplinary Sciences, 21 Brundavan Colony, Narsingi, Hyderabad 500075 (India); Ray, Krishanu, E-mail: krishanu@tifr.res.in [Tata Institute of Fundamental Research (TIFR), Homi Bhabha Road, Mumbai 400 005 (India); Mazumdar, Shyamalava, E-mail: shyamal@tifr.res.in [Tata Institute of Fundamental Research (TIFR), Homi Bhabha Road, Mumbai 400 005 (India)

    2016-03-25

    The neuronal nitric oxide synthase (nNOS) is an essential enzyme involved in the synthesis of nitric oxide (NO), a potent neurotransmitter. Although previous studies have indicated that the dynein light chain 1 (DLC1) binding to nNOS could inhibit the NO synthesis, the claim is challenged by contradicting reports. Thus, the mechanism of nNOS regulation remained unclear. nNOS has a heme-bearing, Cytochrome P450 core, and the functional enzyme is a dimer. The electron flow from NADPH to Flavin, and finally to the heme of the paired nNOS subunit within a dimer, is facilitated upon calmodulin (CaM) binding. Here, we show that DLC1 binding to nNOS-CaM complex does not affect the electron transport from the reductase to the oxygenase domain. Therefore, it cannot inhibit the rate of NADPH-dependent heme reduction in nNOS, which results in L-Arginine oxidation. Also, the NO release activity does not decrease with increasing DLC1 concentration in the reaction mix, which further confirmed that DLC1 does not inhibit nNOS activity. These findings suggest that the DLC1 binding may have other implications for the nNOS function in the cell. - Highlights: • The effect of interaction of nNOS with DLC1 has been debatable with contradicting reports in literature. • Purified DLC1 has no effect on electron transport between reductase and oxygenase domain of purified nNOS-CaM. • The NO release activity of nNOS was not altered by DLC1, supporting that DLC1 does not inhibit the enzyme. • These findings suggest that the DLC1 binding may have other implications for the nNOS function in the cell.

  12. Processing of polymers using reactive solvents

    NARCIS (Netherlands)

    Lemstra, P.J.; Kurja, J.; Meijer, H.E.H.; Meijer, H.E.H.

    1997-01-01

    A review with many refs. on processing of polymers using reactive solvents including classification of synthetic polymers, guidelines for the selection of reactive solvents, basic aspects of processing, examples of intractable and tractable polymer/reactive solvent system

  13. The pH dependence of the spectral and anion binding properties of iron containing superoxide dismutase from E. coli B

    International Nuclear Information System (INIS)

    Fee, J.A.; McClune, G.J.; Lees, A.C.; Zidovetzki, R.; Pecht, I.

    1981-01-01

    Examination of the optical and EPR properties of the ferric form of the iron containing superoxide dismutase from E.coli B, at pH values ranging from 4.5 to 10.9, has revealed two reversible structural transitions affecting the Fe 3+ ion. The apparent pKsub(a) values of these transitions are 5.1+-0.3 and 9.O+-0.3. The binding of azide has been studied over the pH range 4.5 to 10.7; the affinity of the Fe 3+ for N 3 - is independent of pH from 4.5 to approximately 7.5, after which the dissociation constant decreased by a factor of 10 per unit increase in pH. The apparent pKsub(a) which affects N 3 - binding to the iron is 8.6+-0.2. The association of N 3 - with the iron has been examined using the temperature-jump method at pH 7.4 and 9.3. The kinetics of ligand association were shown to conform to the minimal mechanism: P-Fe 3+ + N 3 - reversible K 1 N 3 - - P-Fe 3+ reversible K 2 P-Fe 3+ - N 3 - . K 1 was found to be essentially unaffected by pH whereas K 2 was much lower at pH 9.3 than at 7.4. The value of K 1 at pH 7.4 (100 M -1 ) corresponds very closely to that obtained for the inhibition constant of azide, 10mM. A scheme is presented in which N 3 - inhibits the iron containing dismutase by competing with O 2 - for an anion binding site near, but not on the Fe 3+ . (author)

  14. Handbook of organic solvent properties

    CERN Document Server

    Smallwood, Ian

    2012-01-01

    The properties of 72 of the most commonly used solvents are given, tabulated in the most convenient way, making this book a joy for industrial chemists to use as a desk reference. The properties covered are those which answer the basic questions of: Will it do the job? Will it harm the user? Will it pollute the air? Is it easy to handle? Will it pollute the water? Can it be recovered or incinerated? These are all factors that need to be considered at the early stages of choosing a solvent for a new product or process.A collection of the physical properties of most commonly used solvents, their

  15. Acetone-based cellulose solvent.

    Science.gov (United States)

    Kostag, Marc; Liebert, Tim; Heinze, Thomas

    2014-08-01

    Acetone containing tetraalkylammonium chloride is found to be an efficient solvent for cellulose. The addition of an amount of 10 mol% (based on acetone) of well-soluble salt triethyloctylammonium chloride (Et3 OctN Cl) adjusts the solvent's properties (increases the polarity) to promote cellulose dissolution. Cellulose solutions in acetone/Et3 OctN Cl have the lowest viscosity reported for comparable aprotic solutions making it a promising system for shaping processes and homogeneous chemical modification of the biopolymer. Recovery of the polymer and recycling of the solvent components can be easily achieved. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Photophysical properties of coumarin-120: Unusual behavior in nonpolar solvents

    International Nuclear Information System (INIS)

    Pal, Haridas; Nad, Sanjukta; Kumbhakar, Manoj

    2003-01-01

    Photophysical properties of coumarin-120 (C120; 7-amino-4-methyl-1,2-benzopyrone) dye have been investigated in different solvents using steady-state and time-resolved fluorescence and picosecond laser flash photolysis (LFP) and nanosecond pulse radiolysis (PR) techniques. C120 shows unusual photophysical properties in nonpolar solvents compared to those in other solvents of moderate to higher polarities. Where the Stokes shifts (Δν-bar=ν-bar abs -ν-bar fl ), fluorescence quantum yields (Φ f ), and fluorescence lifetimes (τ f ) show more or less linear correlation with the solvent polarity function Δf={(ε-1)/(2ε+1)-(n 2 -1)/(2n 2 +1)}, all these parameters are unusually lower in nonpolar solvents. Unlike in other solvents, both Φ f and τ f in nonpolar solvents are also strongly temperature dependent. It is indicated that the excited singlet (S 1 ) state of C120 undergoes a fast activation-controlled nonradiative deexcitation in nonpolar solvents, which is absent in all other solvents. LFP and PR studies indicate that the intersystem crossing process is negligible for the present dye in all the solvents studied. Photophysical behavior of C120 in nonpolar solvent has been rationalized assuming that in these solvents the dye exists in a nonpolar structure, with its 7-NH 2 group in a pyramidal configuration. In this structure, since the 7-NH 2 group is bonded to the 1,2-benzopyrone moiety by a single bond, the former group can undergo a fast flip-flop motion, which in effect causes the fast nonradiative deexcitation of the dye excited state. In moderate to higher polarity solvents, it is indicated that the dye exists in an intramolecular charge-transfer structure, where the bond between 7-NH 2 group and the 1,2-benzopyrone moiety attains substantial double bond character. In this structure, the flip-flop motion of the 7-NH 2 group is highly restricted and thus there is no fast nonradiative deexcitation process for the excited dye

  17. Crystal structure of clustered regularly interspaced short palindromic repeats (CRISPR)-associated Csn2 protein revealed Ca2+-dependent double-stranded DNA binding activity.

    Science.gov (United States)

    Nam, Ki Hyun; Kurinov, Igor; Ke, Ailong

    2011-09-02

    Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated protein genes (cas genes) are widespread in bacteria and archaea. They form a line of RNA-based immunity to eradicate invading bacteriophages and malicious plasmids. A key molecular event during this process is the acquisition of new spacers into the CRISPR loci to guide the selective degradation of the matching foreign genetic elements. Csn2 is a Nmeni subtype-specific cas gene required for new spacer acquisition. Here we characterize the Enterococcus faecalis Csn2 protein as a double-stranded (ds-) DNA-binding protein and report its 2.7 Å tetrameric ring structure. The inner circle of the Csn2 tetrameric ring is ∼26 Å wide and populated with conserved lysine residues poised for nonspecific interactions with ds-DNA. Each Csn2 protomer contains an α/β domain and an α-helical domain; significant hinge motion was observed between these two domains. Ca(2+) was located at strategic positions in the oligomerization interface. We further showed that removal of Ca(2+) ions altered the oligomerization state of Csn2, which in turn severely decreased its affinity for ds-DNA. In summary, our results provided the first insight into the function of the Csn2 protein in CRISPR adaptation by revealing that it is a ds-DNA-binding protein functioning at the quaternary structure level and regulated by Ca(2+) ions.

  18. CK2 phospho-dependent binding of R2TP complex to TEL2 is essential for mTOR and SMG1 stability.

    Science.gov (United States)

    Horejsí, Zuzana; Takai, Hiroyuki; Adelman, Carrie A; Collis, Spencer J; Flynn, Helen; Maslen, Sarah; Skehel, J Mark; de Lange, Titia; Boulton, Simon J

    2010-09-24

    TEL2 interacts with and is essential for the stability of all phosphatidylinositol 3-kinase-related kinases (PIKKs), but its mechanism of action remains unclear. Here, we show that TEL2 is constitutively phosphorylated on conserved serines 487 and 491 by casein kinase 2 (CK2). Proteomic analyses establish that the CK2 phosphosite of TEL2 confers binding to the R2TP/prefoldin-like complex, which possesses chaperon/prefoldin activities required during protein complex assembly. The PIH1D1 subunit of the R2TP complex binds directly to the CK2 phosphosite of TEL2 in vitro and is required for the TEL2-R2TP/prefoldin-like complex interaction in vivo. Although the CK2 phosphosite mutant of TEL2 retains association with the PIKKs and HSP90 in cells, failure to interact with the R2TP/prefoldin-like complex results in instability of the PIKKs, principally mTOR and SMG1. We propose that TEL2 acts as a scaffold to coordinate the activities of R2TP/prefoldin-like and HSP90 chaperone complexes during the assembly of the PIKKs. Copyright © 2010 Elsevier Inc. All rights reserved.

  19. Regulation of synaptic inhibition by phospho-dependent binding of the AP2 complex to a YECL motif in the GABAA receptor γ2 subunit

    Science.gov (United States)

    Kittler, Josef T.; Chen, Guojun; Kukhtina, Viktoria; Vahedi-Faridi, Ardeschir; Gu, Zhenglin; Tretter, Verena; Smith, Katharine R.; McAinsh, Kristina; Arancibia-Carcamo, I. Lorena; Saenger, Wolfram; Haucke, Volker; Yan, Zhen; Moss, Stephen J.

    2008-01-01

    The regulation of the number of γ2-subunit-containing GABAA receptors (GABAARs) present at synapses is critical for correct synaptic inhibition and animal behavior. This regulation occurs, in part, by the controlled removal of receptors from the membrane in clathrin-coated vesicles, but it remains unclear how clathrin recruitment to surface γ2-subunit-containing GABAARs is regulated. Here, we identify a γ2-subunit-specific Yxxφ-type-binding motif for the clathrin adaptor protein, AP2, which is located within a site for γ2-subunit tyrosine phosphorylation. Blocking GABAAR-AP2 interactions via this motif increases synaptic responses within minutes. Crystallographic and biochemical studies reveal that phosphorylation of the Yxxφ motif inhibits AP2 binding, leading to increased surface receptor number. In addition, the crystal structure provides an explanation for the high affinity of this motif for AP2 and suggests that γ2-subunit-containing heteromeric GABAARs may be internalized as dimers or multimers. These data define a mechanism for tyrosine kinase regulation of GABAAR surface levels and synaptic inhibition. PMID:18305175

  20. Regulation of synaptic inhibition by phospho-dependent binding of the AP2 complex to a YECL motif in the GABAA receptor gamma2 subunit.

    Science.gov (United States)

    Kittler, Josef T; Chen, Guojun; Kukhtina, Viktoria; Vahedi-Faridi, Ardeschir; Gu, Zhenglin; Tretter, Verena; Smith, Katharine R; McAinsh, Kristina; Arancibia-Carcamo, I Lorena; Saenger, Wolfram; Haucke, Volker; Yan, Zhen; Moss, Stephen J

    2008-03-04

    The regulation of the number of gamma2-subunit-containing GABA(A) receptors (GABA(A)Rs) present at synapses is critical for correct synaptic inhibition and animal behavior. This regulation occurs, in part, by the controlled removal of receptors from the membrane in clathrin-coated vesicles, but it remains unclear how clathrin recruitment to surface gamma2-subunit-containing GABA(A)Rs is regulated. Here, we identify a gamma2-subunit-specific Yxxvarphi-type-binding motif for the clathrin adaptor protein, AP2, which is located within a site for gamma2-subunit tyrosine phosphorylation. Blocking GABA(A)R-AP2 interactions via this motif increases synaptic responses within minutes. Crystallographic and biochemical studies reveal that phosphorylation of the Yxxvarphi motif inhibits AP2 binding, leading to increased surface receptor number. In addition, the crystal structure provides an explanation for the high affinity of this motif for AP2 and suggests that gamma2-subunit-containing heteromeric GABA(A)Rs may be internalized as dimers or multimers. These data define a mechanism for tyrosine kinase regulation of GABA(A)R surface levels and synaptic inhibition.

  1. Crystal Structure of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated Csn2 Protein Revealed Ca[superscript 2+]-dependent Double-stranded DNA Binding Activity

    Energy Technology Data Exchange (ETDEWEB)

    Nam, Ki Hyun; Kurinov, Igor; Ke, Ailong (Cornell); (NWU)

    2012-05-22

    Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated protein genes (cas genes) are widespread in bacteria and archaea. They form a line of RNA-based immunity to eradicate invading bacteriophages and malicious plasmids. A key molecular event during this process is the acquisition of new spacers into the CRISPR loci to guide the selective degradation of the matching foreign genetic elements. Csn2 is a Nmeni subtype-specific cas gene required for new spacer acquisition. Here we characterize the Enterococcus faecalis Csn2 protein as a double-stranded (ds-) DNA-binding protein and report its 2.7 {angstrom} tetrameric ring structure. The inner circle of the Csn2 tetrameric ring is {approx}26 {angstrom} wide and populated with conserved lysine residues poised for nonspecific interactions with ds-DNA. Each Csn2 protomer contains an {alpha}/{beta} domain and an {alpha}-helical domain; significant hinge motion was observed between these two domains. Ca{sup 2+} was located at strategic positions in the oligomerization interface. We further showed that removal of Ca{sup 2+} ions altered the oligomerization state of Csn2, which in turn severely decreased its affinity for ds-DNA. In summary, our results provided the first insight into the function of the Csn2 protein in CRISPR adaptation by revealing that it is a ds-DNA-binding protein functioning at the quaternary structure level and regulated by Ca{sup 2+} ions.

  2. Extraction of Aromatics from Heavy Naphtha Using Different Solvents

    International Nuclear Information System (INIS)

    EI-Bassuoni, A.A.; Esmael, K.K.

    2004-01-01

    Aromatic hydrocarbons are very important to the petrochemical industry. Among these are benzene, toluene and xylene (BTX), which are basic raw materials for the production of a number of important petrochemicals. There are many processes used to separate aromatic from non aromatic such as fractionation, azeotropic distillation and liquid I liquid extraction, etc. Liquid - liquid extraction is unique, efficiently used for heat sensitive, close boiling components and for separation of components not possible by other unit operations and it could be done at ambient temperature makes it more energy efficient. The choice of solvent depends on the properties and boiling range of the feedstock. Through the years, a lot of selective solvents has been proposed and selected for the physical separation of aromatics in liquid liquid extraction. Among the selection criteria are the stability,. chemical compatibility, availability, environmental hazards and price of the solvent. But the basic solvent properties that make it efficient are selectivity and capacity

  3. Effect of Ca2+ on the promiscuous target-protein binding of calmodulin.

    Directory of Open Access Journals (Sweden)

    Annie M Westerlund

    2018-04-01

    Full Text Available Calmodulin (CaM is a calcium sensing protein that regulates the function of a large number of proteins, thus playing a crucial part in many cell signaling pathways. CaM has the ability to bind more than 300 different target peptides in a Ca2+-dependent manner, mainly through the exposure of hydrophobic residues. How CaM can bind a large number of targets while retaining some selectivity is a fascinating open question. Here, we explore the mechanism of CaM selective promiscuity for selected target proteins. Analyzing enhanced sampling molecular dynamics simulations of Ca2+-bound and Ca2+-free CaM via spectral clustering has allowed us to identify distinct conformational states, characterized by interhelical angles, secondary structure determinants and the solvent exposure of specific residues. We searched for indicators of conformational selection by mapping solvent exposure of residues in these conformational states to contacts in structures of CaM/target peptide complexes. We thereby identified CaM states involved in various binding classes arranged along a depth binding gradient. Binding Ca2+ modifies the accessible hydrophobic surface of the two lobes and allows for deeper binding. Apo CaM indeed shows shallow binding involving predominantly polar and charged residues. Furthermore, binding to the C-terminal lobe of CaM appears selective and involves specific conformational states that can facilitate deep binding to target proteins, while binding to the N-terminal lobe appears to happen through a more flexible mechanism. Thus the long-ranged electrostatic interactions of the charged residues of the N-terminal lobe of CaM may initiate binding, while the short-ranged interactions of hydrophobic residues in the C-terminal lobe of CaM may account for selectivity. This work furthers our understanding of the mechanism of CaM binding and selectivity to different target proteins and paves the way towards a comprehensive model of CaM selectivity.

  4. Uranium refining by solvent extraction

    International Nuclear Information System (INIS)

    Kraikaew, J.

    1996-01-01

    The yellow cake refining was studied in both laboratory and semi-pilot scales. The process units mainly consist of dissolution and filtration, solvent extraction, and precipitation and filtration. Effect of flow ratio (organic flow rate/ aqueous flow rate) on working efficiencies of solvent extraction process was studied. Detailed studies were carried out on extraction, scrubbing and stripping processes. Purity of yellow cake product obtained is high as 90.32% U 3 O 8

  5. PH dependence of the spectral and anion binding properties of iron containing superoxide dismutase from E. coli B. An explanation for the azide inhibition of dismutase activity

    Energy Technology Data Exchange (ETDEWEB)

    Fee, J A; McClune, G J; Lees, A C [Michigan Univ., Ann Arbor (USA). Dept. of Biological Chemistry; Zidovetzki, R; Pecht, I [Weizmann Inst. of Science, Rehovoth (Israel). Dept. of Chemical Immunology

    1981-01-01

    Examination of the optical and EPR properties of the ferric form of the iron containing superoxide dismutase from E.coli B, at pH values ranging from 4.5 to 10.9, has revealed two reversible structural transitions affecting the Fe/sup 3 +/ ion. The apparent pKsub(a) values of these transitions are 5.1+-0.3 and 9.O+-0.3. The binding of azide has been studied over the pH range 4.5 to 10.7; the affinity of the Fe/sup 3 +/ for N/sub 3//sup -/ is independent of pH from 4.5 to approximately 7.5, after which the dissociation constant decreased by a factor of 10 per unit increase in pH. The apparent pKsub(a) which affects N/sub 3//sup -/ binding to the iron is 8.6+-0.2. The association of N/sub 3//sup -/ with the iron has been examined using the temperature-jump method at pH 7.4 and 9.3. The kinetics of ligand association were shown to conform to the minimal mechanism: P-Fe/sup 3 +/ + N/sub 3//sup -/reversible K/sub 1/N/sub 3//sup -/ - P-Fe/sup 3 +/reversible K/sub 2/P-Fe/sup 3 +/ - N/sub 3//sup -/. K/sub 1/ was found to be essentially unaffected by pH whereas K/sub 2/ was much lower at pH 9.3 than at 7.4. The value of K/sub 1/ at pH 7.4 (100 M/sup -1/) corresponds very closely to that obtained for the inhibition constant of azide, 10mM. A scheme is presented in which N/sub 3//sup -/ inhibits the iron containing dismutase by competing with O/sub 2//sup -/ for an anion binding site near, but not on the Fe/sup 3 +/.

  6. Molecular and ionic hydrogen bond formation in fluorous solvents.

    Science.gov (United States)

    O'Neal, Kristi L; Weber, Stephen G

    2009-01-08

    There are only a few studies of noncovalent association in fluorous solvents and even fewer that are quantitative. A full understanding, particularly of stoichiometry and binding strength of noncovalent interactions in fluorous solvents could be very useful in improved molecular-receptor-based extractions, advancements in sensor technologies, crystal engineering, and supramolecular chemistry. This work investigates hydrogen bonding between heterocyclic bases and a perfluoropolyether with a terminal carboxylic acid group (Krytox 157FSH (1)), chiefly in FC-72 (a mixture of perfluorohexanes). In particular, we were interested in whether or not proton transfer occurs, and if so, under what conditions in H-bonded complexes. Continuous variations experiments show that in FC-72 weaker bases (pyrazine, pyrimidine, and quinazoline) form 1:1 complexes with 1, whereas stronger bases (quinoline, pyridine, and isoquinoline) form 1:3 complexes. Ultraviolet and infrared spectral signatures reveal that the 1:1 complexes are molecular (B.HA) whereas the 1:3 complexes are ionic (BH+.A-HAHA). Infrared spectra of 1:3 ionic complexes are discussed in detail. Literature and experimental data on complexes between N-heterocyclic bases and carboxylic acids in a range of solvents are compiled to compare solvent effects on proton transfer. Polar solvents support ionic hydrogen bonds at a 1:1 mol ratio. In nonpolar organic solvents, ionic hydrogen bonds are only observed in complexes with 1:2 (base/acid) stoichiometries. In fluorous solvents, a larger excess of acid, 1:3, is necessary to facilitate proton transfer in hydrogen bonds between carboxylic acids and the bases studied.

  7. The interaction between the iron-responsive element binding protein and its cognate RNA is highly dependent upon both RNA sequence and structure.

    Science.gov (United States)

    Jaffrey, S R; Haile, D J; Klausner, R D; Harford, J B

    1993-09-25

    To assess the influence of RNA sequence/structure on the interaction RNAs with the iron-responsive element binding protein (IRE-BP), twenty eight altered RNAs were tested as competitors for an RNA corresponding to the ferritin H chain IRE. All changes in the loop of the predicted IRE hairpin and in the unpaired cytosine residue characteristically found in IRE stems significantly decreased the apparent affinity of the RNA for the IRE-BP. Similarly, alteration in the spacing and/or orientation of the loop and the unpaired cytosine of the stem by either increasing or decreasing the number of base pairs separating them significantly reduced efficacy as a competitor. It is inferred that the IRE-BP forms multiple contacts with its cognate RNA, and that these contacts, acting in concert, provide the basis for the high affinity of this interaction.

  8. The phosphomimetic mutation of syndecan-4 binds and inhibits Tiam1 modulating Rac1 activity in PDZ interaction-dependent manner.

    Directory of Open Access Journals (Sweden)

    Aniko Keller-Pinter

    Full Text Available The small GTPases of the Rho family comprising RhoA, Rac1 and Cdc42 function as molecular switches controlling several essential biochemical pathways in eukaryotic cells. Their activity is cycling between an active GTP-bound and an inactive GDP-bound conformation. The exchange of GDP to GTP is catalyzed by guanine nucleotide exchange factors (GEFs. Here we report a novel regulatory mechanism of Rac1 activity, which is controlled by a phosphomimetic (Ser179Glu mutant of syndecan-4 (SDC4. SDC4 is a ubiquitously expressed transmembrane, heparan sulfate proteoglycan. In this study we show that the Ser179Glu mutant binds strongly Tiam1, a Rac1-GEF reducing Rac1-GTP by 3-fold in MCF-7 breast adenocarcinoma cells. Mutational analysis unravels the PDZ interaction between SDC4 and Tiam1 is indispensable for the suppression of the Rac1 activity. Neither of the SDC4 interactions is effective alone to block the Rac1 activity, on the contrary, lack of either of interactions can increase the activity of Rac1, therefore the Rac1 activity is the resultant of the inhibitory and stimulatory effects. In addition, SDC4 can bind and tether RhoGDI1 (GDP-dissociation inhibitor 1 to the membrane. Expression of the phosphomimetic SDC4 results in the accumulation of the Rac1-RhoGDI1 complex. Co-immunoprecipitation assays (co-IP-s reveal that SDC4 can form complexes with RhoGDI1. Together, the regulation of the basal activity of Rac1 is fine tuned and SDC4 is implicated in multiple ways.

  9. The phosphomimetic mutation of syndecan-4 binds and inhibits Tiam1 modulating Rac1 activity in PDZ interaction–dependent manner

    Science.gov (United States)

    Keller-Pinter, Aniko; Ughy, Bettina; Domoki, Monika; Pettko-Szandtner, Aladar; Letoha, Tamas; Tovari, Jozsef; Timar, Jozsef

    2017-01-01

    The small GTPases of the Rho family comprising RhoA, Rac1 and Cdc42 function as molecular switches controlling several essential biochemical pathways in eukaryotic cells. Their activity is cycling between an active GTP-bound and an inactive GDP-bound conformation. The exchange of GDP to GTP is catalyzed by guanine nucleotide exchange factors (GEFs). Here we report a novel regulatory mechanism of Rac1 activity, which is controlled by a phosphomimetic (Ser179Glu) mutant of syndecan-4 (SDC4). SDC4 is a ubiquitously expressed transmembrane, heparan sulfate proteoglycan. In this study we show that the Ser179Glu mutant binds strongly Tiam1, a Rac1-GEF reducing Rac1-GTP by 3-fold in MCF-7 breast adenocarcinoma cells. Mutational analysis unravels the PDZ interaction between SDC4 and Tiam1 is indispensable for the suppression of the Rac1 activity. Neither of the SDC4 interactions is effective alone to block the Rac1 activity, on the contrary, lack of either of interactions can increase the activity of Rac1, therefore the Rac1 activity is the resultant of the inhibitory and stimulatory effects. In addition, SDC4 can bind and tether RhoGDI1 (GDP-dissociation inhibitor 1) to the membrane. Expression of the phosphomimetic SDC4 results in the accumulation of the Rac1–RhoGDI1 complex. Co-immunoprecipitation assays (co-IP-s) reveal that SDC4 can form complexes with RhoGDI1. Together, the regulation of the basal activity of Rac1 is fine tuned and SDC4 is implicated in multiple ways. PMID:29121646

  10. The phosphomimetic mutation of syndecan-4 binds and inhibits Tiam1 modulating Rac1 activity in PDZ interaction-dependent manner.

    Science.gov (United States)

    Keller-Pinter, Aniko; Ughy, Bettina; Domoki, Monika; Pettko-Szandtner, Aladar; Letoha, Tamas; Tovari, Jozsef; Timar, Jozsef; Szilak, Laszlo

    2017-01-01

    The small GTPases of the Rho family comprising RhoA, Rac1 and Cdc42 function as molecular switches controlling several essential biochemical pathways in eukaryotic cells. Their activity is cycling between an active GTP-bound and an inactive GDP-bound conformation. The exchange of GDP to GTP is catalyzed by guanine nucleotide exchange factors (GEFs). Here we report a novel regulatory mechanism of Rac1 activity, which is controlled by a phosphomimetic (Ser179Glu) mutant of syndecan-4 (SDC4). SDC4 is a ubiquitously expressed transmembrane, heparan sulfate proteoglycan. In this study we show that the Ser179Glu mutant binds strongly Tiam1, a Rac1-GEF reducing Rac1-GTP by 3-fold in MCF-7 breast adenocarcinoma cells. Mutational analysis unravels the PDZ interaction between SDC4 and Tiam1 is indispensable for the suppression of the Rac1 activity. Neither of the SDC4 interactions is effective alone to block the Rac1 activity, on the contrary, lack of either of interactions can increase the activity of Rac1, therefore the Rac1 activity is the resultant of the inhibitory and stimulatory effects. In addition, SDC4 can bind and tether RhoGDI1 (GDP-dissociation inhibitor 1) to the membrane. Expression of the phosphomimetic SDC4 results in the accumulation of the Rac1-RhoGDI1 complex. Co-immunoprecipitation assays (co-IP-s) reveal that SDC4 can form complexes with RhoGDI1. Together, the regulation of the basal activity of Rac1 is fine tuned and SDC4 is implicated in multiple ways.

  11. Methylene blue binding to DNA with alternating AT base sequence: minor groove binding is favored over intercalation.

    Science.gov (United States)

    Rohs, Remo; Sklenar, Heinz

    2004-04-01

    The results presented in this paper on methylene blue (MB) binding to DNA with AT alternating base sequence complement the data obtained in two former modeling studies of MB binding to GC alternating DNA. In the light of the large amount of experimental data for both systems, this theoretical study is focused on a detailed energetic analysis and comparison in order to understand their different behavior. Since experimental high-resolution structures of the complexes are not available, the analysis is based on energy minimized structural models of the complexes in different binding modes. For both sequences, four different intercalation structures and two models for MB binding in the minor and major groove have been proposed. Solvent electrostatic effects were included in the energetic analysis by using electrostatic continuum theory, and the dependence of MB binding on salt concentration was investigated by solving the non-linear Poisson-Boltzmann equation. We find that the relative stability of the different complexes is similar for the two sequences, in agreement with the interpretation of spectroscopic data. Subtle differences, however, are seen in energy decompositions and can be attributed to the change from symmetric 5'-YpR-3' intercalation to minor groove binding with increasing salt concentration, which is experimentally observed for the AT sequence at lower salt concentration than for the GC sequence. According to our results, this difference is due to the significantly lower non-electrostatic energy for the minor groove complex with AT alternating DNA, whereas the slightly lower binding energy to this sequence is caused by a higher deformation energy of DNA. The energetic data are in agreement with the conclusions derived from different spectroscopic studies and can also be structurally interpreted on the basis of the modeled complexes. The simple static modeling technique and the neglect of entropy terms and of non-electrostatic solute-solvent

  12. Effect of solvent polarity and temperature on the spectral and thermodynamic properties of exciplexes of 1-cyanonaphthalene with hexamethylbenzene in organic solvents

    International Nuclear Information System (INIS)

    Asim, Sadia; Mansha, Asim; Grampp, Günter; Landgraf, Stephan; Zahid, Muhammad; Bhatti, Ijaz Ahmad

    2014-01-01

    Study of the effect of solvent polarity and temperature is done on the exciplex emission spectra of 1-cyanonaphthalene with hexamethylbenzene. Exciplex system is studied in the range of partially polar solvents and in solvent mixture of propyl acetate and butyronitrile. The unique feature of this solvent mixture is that only the solvent polarity changes (6.0≤ε s ≤24.7) with the change in the mole fraction of solvents whereas the solvent viscosity and refractive index remains unaffected. Thermodynamic properties are calculated according to the models developed by Weller and Kuzmin. Fluorescence lifetimes for both the fluorophore as well as the exciplex are evaluated in all used solvents. Exciplex energetics as a function of solvent polarity and temperature are also discussed. Kuzmin model of self-consistent polarization is used for the explanation of the exciplex emission spectra. The effects of solvent polarity and temperature on energy of zero–zero transitions (hv 0 / ), Huang–Rhys factor (S), Gauss broadening of vibronic level (σ) and the dominant high-frequency vibration (hν ν ) are investigated. The strong dependence of exciplex stability and energetics upon the solvent polarity and temperature are observed. Full charge transfer exciplexes were observed in solvents of all polarities and stronger exciplex with large emission intensities were found in solvents of low polarities but with the increase in solvent polarity the exciplex becomes weak and they dissociate fastly into radical ion pairs. The kinetic model of Kuzmin was observed to reduce into the Weller kinetic model for this exciplex system with ∆G ET = −0.22 eV and the spectral shift, h∆ν>0.2 eV. - Highlights: • Exciplex formed as a result of mixing of charge transfer and locally excited states. • Effect of solvents polarity and temperature on the exciplex stability and thermodynamics. • Solvent polarity will decide the formation of contact radical ion pair or solvent separated

  13. Effect of solvent polarity and temperature on the spectral and thermodynamic properties of exciplexes of 1-cyanonaphthalene with hexamethylbenzene in organic solvents

    Energy Technology Data Exchange (ETDEWEB)

    Asim, Sadia [Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremaryrgasse 9, A-8010 Graz (Austria); Department of Chemistry and Biochemistry, University of Agriculture, Faisalabad (Pakistan); Mansha, Asim [Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremaryrgasse 9, A-8010 Graz (Austria); Department of Chemistry, Government College University, Faisalabad (Pakistan); Grampp, Günter, E-mail: grampp@tugraz.at [Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremaryrgasse 9, A-8010 Graz (Austria); Landgraf, Stephan [Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremaryrgasse 9, A-8010 Graz (Austria); Zahid, Muhammad [Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremaryrgasse 9, A-8010 Graz (Austria); Department of Chemistry and Biochemistry, University of Agriculture, Faisalabad (Pakistan); Bhatti, Ijaz Ahmad [Department of Chemistry and Biochemistry, University of Agriculture, Faisalabad (Pakistan)

    2014-09-15

    Study of the effect of solvent polarity and temperature is done on the exciplex emission spectra of 1-cyanonaphthalene with hexamethylbenzene. Exciplex system is studied in the range of partially polar solvents and in solvent mixture of propyl acetate and butyronitrile. The unique feature of this solvent mixture is that only the solvent polarity changes (6.0≤ε{sub s}≤24.7) with the change in the mole fraction of solvents whereas the solvent viscosity and refractive index remains unaffected. Thermodynamic properties are calculated according to the models developed by Weller and Kuzmin. Fluorescence lifetimes for both the fluorophore as well as the exciplex are evaluated in all used solvents. Exciplex energetics as a function of solvent polarity and temperature are also discussed. Kuzmin model of self-consistent polarization is used for the explanation of the exciplex emission spectra. The effects of solvent polarity and temperature on energy of zero–zero transitions (hv{sub 0}{sup /}), Huang–Rhys factor (S), Gauss broadening of vibronic level (σ) and the dominant high-frequency vibration (hν{sub ν}) are investigated. The strong dependence of exciplex stability and energetics upon the solvent polarity and temperature are observed. Full charge transfer exciplexes were observed in solvents of all polarities and stronger exciplex with large emission intensities were found in solvents of low polarities but with the increase in solvent polarity the exciplex becomes weak and they dissociate fastly into radical ion pairs. The kinetic model of Kuzmin was observed to reduce into the Weller kinetic model for this exciplex system with ∆G{sub ET} = −0.22 eV and the spectral shift, h∆ν>0.2 eV. - Highlights: • Exciplex formed as a result of mixing of charge transfer and locally excited states. • Effect of solvents polarity and temperature on the exciplex stability and thermodynamics. • Solvent polarity will decide the formation of contact radical ion pair

  14. Fasting and feeding variations of insulin requirements and insulin binding to erythrocytes at different times of the day in insulin dependent diabetics--assessed under the condition of glucose-controlled insulin infusion.

    Science.gov (United States)

    Hung, C T; Beyer, J; Schulz, G

    1986-07-01

    Nine insulin-dependent diabetic patients were examined for insulin requirement, counterregulatory hormones, and receptor binding during their connection to glucose-controlled insulin infusion system. They were of 103% ideal body weight. A diet of 45% carbohydrate, 20% protein and 35% fat was divided into three meals and three snacks averaging the daily calorie intake of 1859 kcal. Following an equilibrating phase of 14 hours after the connection to the glucose-controlled insulin infusion system the blood samples were taken at 0800, 1200 and 1800. The insulin infusion rate increased at 0300 in the early morning from 0.128 mU/kg/min to 0.221 mU/kg/min (P less than 0.02). The postprandial insulin infusion rate jumped from 0.7 U/h (0700-0800) to 7.5 U/h (0800-0900). The calorie related and carbohydrate related insulin demands after breakfast were also highest and declined after lunch respectively (1.16 uU/kg/min kj vs. 0.61 uU/kg/min kj, P less than 0.05 and 236 mU/g CHO vs. 129 mU/g CHO and 143 mU/g CHO). Of the counterregulatory hormones the cortisol showed a significant diurnal rhythm to insulin demands. The insulin tracer binding was higher at 0800 before breakfast than that at 1200 before lunch (P less than 0.05). The increased binding could be better attributed to receptor concentration change than to affinity change. The cause of insulin relative insensitivity in the morning could be due to altered liver response to the cortisol peak in type 1 diabetics. The preserved variation of insulin binding in our patients might be referred to feeding.

  15. Solvent/Non-Solvent Sintering To Make Microsphere Scaffolds

    Science.gov (United States)

    Laurencin, Cato T.; Brown, Justin L.; Nair, Lakshmi

    2011-01-01

    A solvent/non-solvent sintering technique has been devised for joining polymeric microspheres to make porous matrices for use as drug-delivery devices or scaffolds that could be seeded with cells for growing tissues. Unlike traditional sintering at elevated temperature and pressure, this technique is practiced at room temperature and pressure and, therefore, does not cause thermal degradation of any drug, protein, or other biochemical with which the microspheres might be loaded to impart properties desired in a specific application. Also, properties of scaffolds made by this technique are more reproducible than are properties of comparable scaffolds made by traditional sintering. The technique involves the use of two miscible organic liquids: one that is and one that is not a solvent for the affected polymer. The polymeric microspheres are placed in a mold having the size and shape of the desired scaffold, then the solvent/non-solvent mixture is poured into the mold to fill the void volume between the microspheres, then the liquid mixture is allowed to evaporate. Some of the properties of the resulting scaffold can be tailored through choice of the proportions of the liquids and the diameter of the microspheres.

  16. Solvent effects in ionic liquids: empirical linear energy-density relationships.

    Science.gov (United States)

    Cerda-Monje, A; Aizman, A; Tapia, R A; Chiappe, C; Contreras, R

    2012-07-28

    Multiparameter linear energy-density relationships to model solvent effects in room temperature ionic liquids (RTILs) are introduced and tested. The model incorporates two solvent dependent and two specific solute-solvent parameters represented by a set of electronic indexes derived from the conceptual density functional theory. The specific solute-solvent interactions are described in terms of the electronic chemical potential for proton migration between the anion or cation and the transition state structure of a specific reaction. These indexes provide a quantitative estimation of the hydrogen bond (HB) acceptor basicity and the hydrogen bond donor acidity of the ionic solvent, respectively. A sound quantitative scale of HB strength is thereby obtained. The solvent dependent contributions are described by the global electrophilicity of the cation and nucleophilicity of the anion forming the ionic liquid. The model is illustrated for the kinetics of cycloaddition of cyclopentadiene towards acrolein. In general, cation HB acidity outweighs the remaining parameters for this reaction.

  17. Substituent Effects on the Coordination Chemistry of Metal-Binding Pharmacophores

    Energy Technology Data Exchange (ETDEWEB)

    Craig, Whitney R. [Department; Baker, Tessa W. [Department; Marts, Amy R. [Department; DeGenova, Daniel T. [Department; Martin, David P. [Department; Reed, Garrett C. [Department; McCarrick, Robert M. [Department; Crowder, Michael W. [Department; Cohen, Seth M. [Department; Tierney, David L. [Department

    2017-09-12

    A combination of XAS, UV–vis, NMR, and EPR was used to examine the binding of a series of α-hydroxythiones to CoCA. All three appear to bind preferentially in their neutral, protonated forms. Two of the three clearly bind in a monodentate fashion, through the thione sulfur alone. Thiomaltol (TM) appears to show some orientational preference, on the basis of the NMR, while it appears that thiopyromeconic acid (TPMA) retains rotational freedom. In contrast, allothiomaltol (ATM), after initially binding in its neutral form, presumably through the thione sulfur, forms a final complex that is five-coordinate via bidentate coordination of ATM. On the basis of optical titrations, we speculate that this may be due to the lower initial pKa of ATM (8.3) relative to those of TM (9.0) and TPMA (9.5). Binding through the thione is shown to reduce the hydroxyl pKa by ~0.7 pH unit on metal binding, bringing only ATM’s pKa close to the pH of the experiment, facilitating deprotonation and subsequent coordination of the hydroxyl. The data predict the presence of a solvent-exchangeable proton on TM and TPMA, and Q-band 2-pulse ESEEM experiments on CoCA + TM suggest that the proton is present. ESE-detected EPR also showed a surprising frequency dependence, giving only a subset of the expected resonances at X-band.

  18. Transpeptidase activity of penicillin-binding protein SpoVD in peptidoglycan synthesis conditionally depends on the disulfide reductase StoA.

    Science.gov (United States)

    Bukowska-Faniband, Ewa; Hederstedt, Lars

    2017-07-01

    Endospore cortex peptidoglycan synthesis is not required for bacterial growth but essential for endospore heat resistance. It therefore constitutes an amenable system for research on peptidoglycan biogenesis. The Bacillus subtilis sporulation-specific class B penicillin-binding protein (PBP) SpoVD and many homologous PBPs contain two conserved cysteine residues of unknown function in the transpeptidase domain - one as residue x in the SxN catalytic site motif and the other in a flexible loop near the catalytic site. A disulfide bond between these residues blocks the function of SpoVD in cortex synthesis. With a combination of experiments with purified proteins and B. subtilis mutant cells, it was shown that in active SpoVD the two cysteine residues most probably interact by hydrogen bonding and that this is important for peptidoglycan synthesis in vivo. It was furthermore demonstrated that the sporulation-specific thiol-disulfide oxidoreductase StoA reduces SpoVD and that requirement of StoA for cortex synthesis can be suppressed by two completely different types of structural alterations in SpoVD. It is concluded that StoA plays a critical role mainly during maturation of SpoVD in the forespore outer membrane. The findings advance our understanding of essential PBPs and redox control of extra-cytoplasmic protein disulfides in bacterial cells. © 2017 The Authors. Molecular Microbiology Published by John Wiley & Sons Ltd.

  19. Crystal structure and size-dependent neutralization properties of HK20, a human monoclonal antibody binding to the highly conserved heptad repeat 1 of gp41.

    Science.gov (United States)

    Sabin, Charles; Corti, Davide; Buzon, Victor; Seaman, Mike S; Lutje Hulsik, David; Hinz, Andreas; Vanzetta, Fabrizia; Agatic, Gloria; Silacci, Chiara; Mainetti, Lara; Scarlatti, Gabriella; Sallusto, Federica; Weiss, Robin; Lanzavecchia, Antonio; Weissenhorn, Winfried

    2010-11-18

    The human monoclonal antibody (mAb) HK20 neutralizes a broad spectrum of primary HIV-1 isolates by targeting the highly conserved heptad repeat 1 (HR1) of gp41, which is transiently exposed during HIV-1 entry. Here we present the crystal structure of the HK20 Fab in complex with a gp41 mimetic 5-Helix at 2.3 Å resolution. HK20 employs its heavy chain CDR H2 and H3 loops to bind into a conserved hydrophobic HR1 pocket that is occupied by HR2 residues in the gp41 post fusion conformation. Compared to the previously described HR1-specific mAb D5, HK20 approaches its epitope with a different angle which might favor epitope access and thus contribute to its higher neutralization breadth and potency. Comparison of the neutralization activities of HK20 IgG, Fab and scFv employing both single cycle and multiple cycle neutralization assays revealed much higher potencies for the smaller Fab and scFv over IgG, implying that the target site is difficult to access for complete antibodies. Nevertheless, two thirds of sera from HIV-1 infected individuals contain significant titers of HK20-inhibiting antibodies. The breadth of neutralization of primary isolates across all clades, the higher potencies for C-clade viruses and the targeting of a distinct site as compared to the fusion inhibitor T-20 demonstrate the potential of HK20 scFv as a therapeutic tool.

  20. Vacuolar ATPases, like F1,F0-ATPases, show a strong dependence of the reaction velocity on the binding of more than one ATP per enzyme

    International Nuclear Information System (INIS)

    Kasho, V.N.; Boyer, P.D.

    1989-01-01

    Recent studies with vacuolar ATPases have shown that multiple copies catalytic subunits are present and that these have definite sequence homology with catalytic subunits of the F 1 , F 0 -ATPases. Experiments are reported that assess whether the vacuolar ATPases may have the unusual catalytic cooperativity with sequential catalytic site participation as in the binding change mechanism for the F 1 ,F 0 -ATPases. The extent of reversal of bound ATP hydrolysis to bound ADP and P i as medium ATP concentration was lowered was determined by 18 O-exchange measurements for yeast and neurospora vacuolar ATPases. The results show a pronounced increase in the extent of water oxygen incorporation into the P i formed as ATP concentration is decreased to the micromolar range. The F 1 ,F 0 -ATPase from neurospora mitochondria showed an event more pronounced modulation, similar to that of other F 1 -type ATPases. The vacuolar ATPases thus appear to have a catalytic mechanism quite analogous to that of the F 1 ,F 0 -ATPases

  1. Importin alpha binding and nuclear localization of PARP-2 is dependent on lysine 36, which is located within a predicted classical NLS

    Directory of Open Access Journals (Sweden)

    Valovka Taras

    2008-07-01

    Full Text Available Abstract Background The enzymes responsible for the synthesis of poly-ADP-ribose are named poly-ADP-ribose polymerases (PARP. PARP-2 is a nuclear protein, which regulates a variety of cellular functions that are mainly controlled by protein-protein interactions. A previously described non-conventional bipartite nuclear localization sequence (NLS lies in the amino-terminal DNA binding domain of PARP-2 between amino acids 1–69; however, this targeting sequence has not been experimentally examined or validated. Results Using a site-directed mutagenesis approach, we found that lysines 19 and 20, located within a previously described bipartite NLS, are not required for nuclear localization of PARP-2. In contrast, lysine 36, which is located within a predicted classical monopartite NLS, was required for PARP-2 nuclear localization. While wild type PARP-2 interacted with importin α3 and to a very weak extent with importin α1 and importin α5, the mutant PARP-2 (K36R did not interact with importin α3, providing a molecular explanation why PARP-2 (K36R is not targeted to the nucleus. Conclusion Our results provide strong evidence that lysine 36 of PARP-2 is a critical residue for proper nuclear targeting of PARP-2 and consequently for the execution of its biological functions.

  2. Quantum mechanics/molecular mechanics modeling of photoelectron spectra: the carbon 1s core-electron binding energies of ethanol-water solutions.

    Science.gov (United States)

    Löytynoja, T; Niskanen, J; Jänkälä, K; Vahtras, O; Rinkevicius, Z; Ågren, H

    2014-11-20

    Using ethanol-water solutions as illustration, we demonstrate the capability of the hybrid quantum mechanics/molecular mechanics (QM/MM) paradigm to simulate core photoelectron spectroscopy: the binding energies and the chemical shifts. An integrated approach with QM/MM binding energy calculations coupled to preceding molecular dynamics sampling is adopted to generate binding energies averaged over the solute-solvent configurations available at a particular temperature and pressure and thus allowing for a statistical assessment with confidence levels for the final binding energies. The results are analyzed in terms of the contributions in the molecular mechanics model-electrostatic, polarization, and van der Waals-with atom or bond granulation of the corresponding MM charge and polarizability force-fields. The role of extramolecular charge transfer screening of the core-hole and explicit hydrogen bonding is studied by extending the QM core to cover the first solvation shell. The results are compared to those obtained from pure electrostatic and polarizable continuum models. Particularly, the dependence of the carbon 1s binding energies with respect to the ethanol concentration is studied. Our results indicate that QM/MM can be used as an all-encompassing model to study photoelectron binding energies and chemical shifts in solvent environments.

  3. Influences of surface and solvent on retention of HEMA/mixture components after evaporation.

    Science.gov (United States)

    Garcia, Fernanda C P; Wang, Linda; Pereira, Lúcia C G; de Andrade e Silva, Safira M; Júnior, Luiz M; Carrilho, Marcela Rocha de Oliveira

    2010-01-01

    This study examined the retention of solvents within experimental HEMA/solvent primers after two conditions for solvent evaporation: from a free surface or from dentine surface. Experimental primers were prepared by mixing 35% HEMA with 65% water, methanol, ethanol or acetone (v/v). Aliquots of each primer (50 microl) were placed on glass wells or they were applied to the surface of acid-etched dentine cubes (2mm x 2mm x 2mm) (n=5). For both conditions (i.e. from free surface or dentine cubes), change in primers mass due to solvent evaporation was gravimetrically measured for 10min at 51% RH and 21 degrees C. The rate of solvent evaporation was calculated as a function of loss of primers mass (%) over time. Data were analysed by two-way ANOVA and Student-Newman-Keuls (pevaporation rate (%/min) depending on the solvent present in the primer and the condition for evaporation (from free surface or dentine cubes) (pevaporation for HEMA/acetone primer was almost 2- to 10-times higher than for HEMA/water primer depending whether evaporation occurred, respectively, from a free surface or dentine cubes. The rate of solvent evaporation varied with time, being in general highest at the earliest periods. The rate of solvent evaporation and its retention into HEMA/solvent primers was influenced by the type of the solvent and condition allowed for their evaporation.

  4. Solvents interactions with thermochromic print

    Directory of Open Access Journals (Sweden)

    Mirela Rožić

    2017-12-01

    Full Text Available In this study, the interactions between different solvents (benzene, acetone, cyclohexanone, various alcohols and water and thermochromic printing ink were investigated. Thermochromic printing ink was printed on metal surface. Components of thermochromic printing inks are polymeric microcapsules and classic yellow offset printing ink. Below its activation temperature, dye and developer within the microcapsules form a blue coloured complex. Therefore, thermochromic print is green. By heating above the activation temperature, blue colour of the complex turns into the leuco dye colourless state and the green colour of the prints turns into the yellow colour of the classic offset pigment. The results of the interaction with various solvents show that the thermochromic print is stable in all tested solvents except in ethanol, acetone and cyclohexanone. In ethanol, the green colour of the print becomes yellow. SEM analysis shows that microcapsules are dissolved. In acetone and cyclohexanone, the green colour of the print turns into blue, and the microcapsules become significantly more visible. Thus, the yellow pigment interacts with examined ketones. Based on the obtained interactions it can be concluded that the microcapsules have more polar nature than the classical pigment particles. Solvent-thermocromic print interactions were analysed using Hansen solubility parameters that rank the solvents based on their estimated interaction capabilities.

  5. Drug and Solvent Abuse Among Ahwaz\\'s Elderlies

    Directory of Open Access Journals (Sweden)

    Abdolrahim Asadollahi

    2007-10-01

    Full Text Available Objectives: There are researches to point epidemiology of addiction to drugs, chemical and solvent abuse in elderlies. Drug and Solvent abuse is considered as one of these addictions. This study was point to chemical abuse among elderly population of Ahwaz an Iranian city during year of 2007. Methods & Materials: Research method is description-exploration with use to questionnaire, clinical interview and survey of medical and clinical reports among volunteer clients. Statistical community is all elderly population at one of citizen region in Ahwaz city (Iran. Seventy four dossiers were considered via random sampling; with 30 Elder volunteer clients been interviewed and replied to Elderly Drug Abuse Questionnaire (EDAQ. Results: Signification of hypothesis with X2 test was considered significant relation between age and addiction record variables to solvent abuse; this relation is very significant to second value of drug's derivations such as Morphine, Codeine, Tebaine and Heroine. Interview showed psychological dependent due to appeal them to solvent abuse. Kind of abuse among elderly was snuffing and abuse of medicine drugs which were been recommended to them by their physician. Conclusion: Although study of solvent and chemical abuse's epidemiology pointed less average of this addiction in samples, should be considered important and notice in studies. Finally, researchers were suggested to avoid of this new drug abuse and so to control behavior and interaction of these addicted and their behavior development; it's better to control on distribution of solvent and glue materials and recommending of medicine drug via physicians visiting exderlies.

  6. Size-dependent binding energies and fine-structure splitting of excitonic complexes in single InAs/GaAs quantum dots

    International Nuclear Information System (INIS)

    Rodt, S.; Seguin, R.; Schliwa, A.; Guffarth, F.; Poetschke, K.; Pohl, U.W.; Bimberg, D.

    2007-01-01

    A systematic study of excitonic complexes confined in single InAs/GaAs quantum dots is presented. Emphasis is placed on the recombination energies of the excitonic complexes and on the fine-structure splitting of the bright exciton ground state. The values depend in a characteristic way on the size of the respective quantum dot which controls the number of bound hole states and the piezoelectric potential

  7. Probing protein surface with a solvent mimetic carbene coupled to detection by mass spectrometry.

    Science.gov (United States)

    Gómez, Gabriela E; Mundo, Mariana R; Craig, Patricio O; Delfino, José M

    2012-01-01

    Much knowledge into protein folding, ligand binding, and complex formation can be derived from the examination of the nature and size of the accessible surface area (SASA) of the polypeptide chain, a key parameter in protein science not directly measurable in an experimental fashion. To this end, an ideal chemical approach should aim at exerting solvent mimicry and achieving minimal selectivity to probe the protein surface regardless of its chemical nature. The choice of the photoreagent diazirine to fulfill these goals arises from its size comparable to water and from being a convenient source of the extremely reactive methylene carbene (:CH(2)). The ensuing methylation depends primarily on the solvent accessibility of the polypeptide chain, turning it into a valuable signal to address experimentally the measurement of SASA in proteins. The superb sensitivity and high resolution of modern mass spectrometry techniques allows us to derive a quantitative signal proportional to the extent of modification (EM) of the sample. Thus, diazirine labeling coupled to electrospray mass spectrometry (ESI-MS) detection can shed light on conformational features of the native as well as non-native states, not easily addressable by other methods. Enzymatic fragmentation of the polypeptide chain at the level of small peptides allows us to locate the covalent tag along the amino acid sequence, therefore enabling the construction of a map of solvent accessibility. Moreover, by subsequent MS/MS analysis of peptides, we demonstrate here the feasibility of attaining amino acid resolution in defining the target sites. © American Society for Mass Spectrometry, 2011

  8. Glutathione reductase: solvent equilibrium and kinetic isotope effects

    International Nuclear Information System (INIS)

    Wong, K.K.; Vanoni, M.A.; Blanchard, J.S.

    1988-01-01

    Glutathione reductase catalyzes the NADPH-dependent reduction of oxidized glutathione (GSSG). The kinetic mechanism is ping-pong, and we have investigated the rate-limiting nature of proton-transfer steps in the reactions catalyzed by the spinach, yeast, and human erythrocyte glutathione reductases using a combination of alternate substrate and solvent kinetic isotope effects. With NADPH or GSSG as the variable substrate, at a fixed, saturating concentration of the other substrate, solvent kinetic isotope effects were observed on V but not V/K. Plots of Vm vs mole fraction of D 2 O (proton inventories) were linear in both cases for the yeast, spinach, and human erythrocyte enzymes. When solvent kinetic isotope effect studies were performed with DTNB instead of GSSG as an alternate substrate, a solvent kinetic isotope effect of 1.0 was observed. Solvent kinetic isotope effect measurements were also performed on the asymmetric disulfides GSSNB and GSSNP by using human erythrocyte glutathione reductase. The Km values for GSSNB and GSSNP were 70 microM and 13 microM, respectively, and V values were 62 and 57% of the one calculated for GSSG, respectively. Both of these substrates yield solvent kinetic isotope effects greater than 1.0 on both V and V/K and linear proton inventories, indicating that a single proton-transfer step is still rate limiting. These data are discussed in relationship to the chemical mechanism of GSSG reduction and the identity of the proton-transfer step whose rate is sensitive to solvent isotopic composition. Finally, the solvent equilibrium isotope effect measured with yeast glutathione reductase is 4.98, which allows us to calculate a fractionation factor for the thiol moiety of GSH of 0.456

  9. Mapping the surface of Escherichia coli peptide deformylase by NMR with organic solvents.

    Science.gov (United States)

    Byerly, Douglas W; McElroy, Craig A; Foster, Mark P

    2002-07-01

    Identifying potential ligand binding sites on a protein surface is an important first step for targeted structure-based drug discovery. While performing control experiments with Escherichia coli peptide deformylase (PDF), we noted that the organic solvents used to solubilize some ligands perturbed many of the same resonances in PDF as the small molecule inhibitors. To further explore this observation, we recorded (15)N HSQC spectra of E. coli peptide deformylase (PDF) in the presence of trace quantities of several simple organic solvents (acetone, DMSO, ethanol, isopropanol) and identified their sites of interaction from local perturbation of amide chemical shifts. Analysis of the protein surface structure revealed that the ligand-induced shift perturbations map to the active site and one additional surface pocket. The correlation between sites of solvent and inhibitor binding highlights the utility of organic solvents to rapidly and effectively validate and characterize binding sites on proteins prior to designing a drug discovery screen. Further, the solvent-induced perturbations have implications for the use of organic solvents to dissolve candidate ligands in NMR-based screens.

  10. Crystal structure and size-dependent neutralization properties of HK20, a human monoclonal antibody binding to the highly conserved heptad repeat 1 of gp41.

    Directory of Open Access Journals (Sweden)

    Charles Sabin

    Full Text Available The human monoclonal antibody (mAb HK20 neutralizes a broad spectrum of primary HIV-1 isolates by targeting the highly conserved heptad repeat 1 (HR1 of gp41, which is transiently exposed during HIV-1 entry. Here we present the crystal structure of the HK20 Fab in complex with a gp41 mimetic 5-Helix at 2.3 Å resolution. HK20 employs its heavy chain CDR H2 and H3 loops to bind into a conserved hydrophobic HR1 pocket that is occupied by HR2 residues in the gp41 post fusion conformation. Compared to the previously described HR1-specific mAb D5, HK20 approaches its epitope with a different angle which might favor epitope access and thus contribute to its higher neutralization breadth and potency. Comparison of the neutralization activities of HK20 IgG, Fab and scFv employing both single cycle and multiple cycle neutralization assays revealed much higher potencies for the smaller Fab and scFv over IgG, implying that the target site is difficult to access for complete antibodies. Nevertheless, two thirds of sera from HIV-1 infected individuals contain significant titers of HK20-inhibiting antibodies. The breadth of neutralization of primary isolates across all clades, the higher potencies for C-clade viruses and the targeting of a distinct site as compared to the fusion inhibitor T-20 demonstrate the potential of HK20 scFv as a therapeutic tool.

  11. Aryl hydrocarbon receptor-dependent retention of nuclear HuR suppresses cigarette smoke-induced cyclooxygenase-2 expression independent of DNA-binding.

    Science.gov (United States)

    Zago, Michela; Sheridan, Jared A; Nair, Parameswaran; Rico de Souza, Angela; Gallouzi, Imed-Eddine; Rousseau, Simon; Di Marco, Sergio; Hamid, Qutayba; Eidelman, David H; Baglole, Carolyn J

    2013-01-01

    The aryl hydrocarbon receptor (AhR), a ligand-activated transcription factor that responds to man-made environmental toxicants, has emerged as an endogenous regulator of cyclooxygenase-2 (Cox-2) by a mechanism that is poorly understood. In this study, we first used AhR-deficient (AhR(-/-) ) primary pulmonary cells, together with pharmacological tools to inhibit new RNA synthesis, to show that the AhR is a prominent factor in the destabilization of Cox-2 mRNA. The destabilization of Cox-2 mRNA and subsequent suppression of cigarette smoke-induced COX-2 protein expression by the AhR was independent of its ability to bind the dioxin response element (DRE), thereby differentiating the DRE-driven toxicological AhR pathway from its anti-inflammatory abilities. We further describe that the AhR destabilizes Cox-2 mRNA by sequestering HuR within the nucleus. The role of HuR in AhR stabilization of Cox-2 mRNA was confirmed by knockdown of HuR, which resulted in rapid Cox-2 mRNA degradation. Finally, in the lungs of AhR(-/-) mice exposed to cigarette smoke, there was little Cox-2 mRNA despite robust COX-2 protein expression, a finding that correlates with almost exclusive cytoplasmic HuR within the lungs of AhR(-/-) mice. Therefore, we propose that the AhR plays an important role in suppressing the expression of inflammatory proteins, a function that extends beyond the ability of the AhR to respond to man-made toxicants. These findings open the possibility that a DRE-independent AhR pathway may be exploited therapeutically as an anti-inflammatory target.

  12. Loss of the zona pellucida-binding protein 2 (Zpbp2) gene in mice impacts airway hypersensitivity and lung lipid metabolism in a sex-dependent fashion.

    Science.gov (United States)

    Kanagaratham, Cynthia; Chiwara, Victoria; Ho, Bianca; Moussette, Sanny; Youssef, Mina; Venuto, David; Jeannotte, Lucie; Bourque, Guillaume; de Sanctis, Juan Bautista; Radzioch, Danuta; Naumova, Anna K

    2018-04-01

    The human chromosomal region 17q12-q21 is one of the best replicated genome-wide association study loci for childhood asthma. The associated SNPs span a large genomic interval that includes several protein-coding genes. Here, we tested the hypothesis that the zona pellucida-binding protein 2 (ZPBP2) gene residing in this region contributes to asthma pathogenesis using a mouse model. We tested the lung phenotypes of knock-out (KO) mice that carry a deletion of the Zpbp2 gene. The deletion attenuated airway hypersensitivity (AHR) in female, but not male, mice in the absence of allergic sensitization. Analysis of the lipid profiles of their lungs showed that female, but not male, KO mice had significantly lower levels of sphingosine-1-phosphate (S1P), very long-chain ceramides (VLCCs), and higher levels of long-chain ceramides compared to wild-type controls. Furthermore, in females, lung resistance following methacholine challenge correlated with lung S1P levels (Pearson correlation coefficient 0.57) suggesting a link between reduced AHR in KO females, Zpbp2 deletion, and S1P level regulation. In livers, spleens and blood plasma, however, VLCC, S1P, and sphingosine levels were reduced in both KO females and males. We also find that the Zpbp2 deletion was associated with gain of methylation in the adjacent DNA regions. Thus, we demonstrate that the mouse ortholog of ZPBP2 has a role in controlling AHR in female mice. Our data also suggest that Zpbp2 may act through regulation of ceramide metabolism. These findings highlight the importance of phospholipid metabolism for sexual dimorphism in AHR.

  13. Multiple sclerosis and organic solvents

    DEFF Research Database (Denmark)

    Mortensen, J T; Brønnum-Hansen, Henrik; Rasmussen, K

    1998-01-01

    We investigated a possible causal relation between exposure to organic solvents in Danish workers (housepainters, typographers/printers, carpenters/cabinetmakers) and onset of multiple sclerosis. Data on men included in the Danish Multiple Sclerosis Register (3,241 men) were linked with data from......, and butchers. Over a follow-up period of 20 years, we observed no increase in the incidence of multiple sclerosis among men presumed to be exposed to organic solvents. It was not possible to obtain data on potential confounders, and the study design has some potential for selection bias. Nevertheless......, the study does not support existing hypotheses regarding an association between occupational exposure to organic solvents and multiple sclerosis....

  14. Computational Calorimetry: High-Precision Calculation of Host–Guest Binding Thermodynamics

    Science.gov (United States)

    2015-01-01

    We present a strategy for carrying out high-precision calculations of binding free energy and binding enthalpy values from molecular dynamics simulations with explicit solvent. The approach is used to calculate the thermodynamic profiles for binding of nine small molecule guests to either the cucurbit[7]uril (CB7) or β-cyclodextrin (βCD) host. For these systems, calculations using commodity hardware can yield binding free energy and binding enthalpy values with a precision of ∼0.5 kcal/mol (95% CI) in a matter of days. Crucially, the self-consistency of the approach is established by calculating the binding enthalpy directly, via end point potential energy calculations, and indirectly, via the temperature dependence of the binding free energy, i.e., by the van’t Hoff equation. Excellent agreement between the direct and van’t Hoff methods is demonstrated for both host–guest systems and an ion-pair model system for which particularly well-converged results are attainable. Additionally, we find that hydrogen mass repartitioning allows marked acceleration of the calculations with no discernible cost in precision or accuracy. Finally, we provide guidance for accurately assessing numerical uncertainty of the results in settings where complex correlations in the time series can pose challenges to statistical analysis. The routine nature and high precision of these binding calculations opens the possibility of including measured binding thermodynamics as target data in force field optimization so that simulations may be used to reliably interpret experimental data and guide molecular design. PMID:26523125

  15. Defect of Fe-S cluster binding by DNA polymerase δ in yeast suppresses UV-induced mutagenesis, but enhances DNA polymerase ζ - dependent spontaneous mutagenesis.

    Science.gov (United States)

    Stepchenkova, E I; Tarakhovskaya, E R; Siebler, H M; Pavlov, Y I

    2017-01-01

    Eukaryotic genomes are duplicated by a complex machinery, utilizing high fidelity replicative B-family DNA polymerases (pols) α, δ and ε. Specialized error-prone pol ζ, the fourth B-family member, is recruited when DNA synthesis by the accurate trio is impeded by replication stress or DNA damage. The damage tolerance mechanism dependent on pol ζ prevents DNA/genome instability and cell death at the expense of increased mutation rates. The pol switches occurring during this specialized replication are not fully understood. The loss of pol ζ results in the absence of induced mutagenesis and suppression of spontaneous mutagenesis. Disruption of the Fe-S cluster motif that abolish the interaction of the C-terminal domain (CTD) of the catalytic subunit of pol ζ with its accessory subunits, which are shared with pol δ, leads to a similar defect in induced mutagenesis. Intriguingly, the pol3-13 mutation that affects the Fe-S cluster in the CTD of the catalytic subunit of pol δ also leads to defective induced mutagenesis, suggesting the possibility that Fe-S clusters are essential for the pol switches during replication of damaged DNA. We confirmed that yeast strains with the pol3-13 mutation are UV-sensitive and defective in UV-induced mutagenesis. However, they have increased spontaneous mutation rates. We found that this increase is dependent on functional pol ζ. In the pol3-13 mutant strain with defective pol δ, there is a sharp increase in transversions and complex mutations, which require functional pol ζ, and an increase in the occurrence of large deletions, whose size is controlled by pol ζ. Therefore, the pol3-13 mutation abrogates pol ζ-dependent induced mutagenesis, but allows for pol ζ recruitment for the generation of spontaneous mutations and prevention of larger deletions. These results reveal differential control of the two major types of pol ζ-dependent mutagenesis by the Fe-S cluster present in replicative pol δ. Copyright © 2016

  16. Theoretical investigation of the weak interaction between graphene and alcohol solvents

    Science.gov (United States)

    Wang, Haining; Chen, Sian; Lu, Shanfu; Xiang, Yan

    2017-05-01

    The dispersion of graphene in five different alcohol solvents was investigated by evaluating the binding energy between graphene and alcohol molecules using DFT-D method. The calculation showed the most stable binding energy appeared at the distance of ∼3.5 Å between graphene and alcohol molecules and increased linearly as changing the alcohol from methanol to 1-pentanol. The weak interaction was further graphically illustrated using the reduced density gradient method. The theoretical study revealed alcohols with more carbon atoms could be a good starting point for screening suitable solvents for graphene dispersion.

  17. Solvent isotope effect on the fluorescence of azoalkanes

    International Nuclear Information System (INIS)

    Mirbach, M.J.; Mirbach, M.F.; Cherry, W.R.; Turro, N.J.; Engel, P.

    1977-01-01

    A study of fluorescence quantum yields and fluorescence lifetimes of two cyclic azoalkanes reveal a striking dependence of phisub(F) and tausub(F) on solvent and on isotopic substitution (OH → OD). A mechanism involving specific deactivation of the fluorescent state from a hydrogen bonded complex is proposed to rationalize the data. (orig./HK) [de

  18. Improved Purex solvent scrubbing methods

    International Nuclear Information System (INIS)

    Mailen, J.C.; Tallent, O.K.

    1984-01-01

    Studies of hydrazine and hydroxylamine salts as solvent scrubbing agents that can be decomposed into gases are summarized. Results from testing of countercurrent scrubbers and solid sorber columns that produce lesser amounts of permanent salts are reported. The status of studies of the acid-degradation of paraffin diluent and the options for removal of long-chain organic acids is given

  19. Risk assessment for halogenated solvents

    International Nuclear Information System (INIS)

    Travis, C.C.

    1988-01-01

    A recent development in the cancer risk area is the advent of biologically based pharmacokinetic and pharmacodynamic models. These models allow for the incorporation of biological and mechanistic data into the risk assessment process. These advances will not only improve the risk assessment process for halogenated solvents but will stimulate and guide basic research in the biological area

  20. Immune hierarchy among HIV-1 CD8+ T cell epitopes delivered by dendritic cells depends on MHC-I binding irrespective of mode of loading and immunization in HLA-A*0201 mice

    DEFF Research Database (Denmark)

    Kloverpris, Henrik N; Karlsson, Ingrid; Thorn, Mette

    2009-01-01

    Recent human immunodeficiency virus type 1 (HIV-1) vaccination strategies aim at targeting a broad range of cytotoxic T lymphocyte (CTL) epitopes from different HIV-1 proteins by immunization with multiple CTL epitopes simultaneously. However, this may establish an immune hierarchical response......, where the immune system responds to only a small number of the epitopes administered. To evaluate the feasibility of such vaccine strategies, we used the human leukocyte antigen (HLA)-A*0201 transgenic (tg) HHD murine in vivo model and immunized with dendritic cells pulsed with seven HIV-1-derived HLA......-gamma)-producing CD8(+) T cells, mainly focused on two of seven administered epitopes. The magnitude of individual T-cell responses induced by immunization with multiple peptides correlated with their individual immunogenicity that depended on major histocompatibility class I binding and was not influenced by mode...

  1. A radioligand immunoassay for 1,25-dihydroxyvitamin D3 receptors using monoclonal antibody: detection of a phenotypic receptor variant in vitamin D-dependency rickets (type II) which does not bind hormone

    International Nuclear Information System (INIS)

    Pike, J.W.; Dokoh, Shigeharu; Liberman, U.A.; Eil, C.; Haussler, M.R.; Marx, S.J.

    1984-01-01

    Vitamin D-dependency rickets, type II (VDDRII), is a well recognized heritable disorder characterized by peripheral target organ resistance to 1,25-dihydroxyvitamin D 3 (1,25(OH) 2 D 3 ), the hormonally active form of the vitamin. Recently, cultured skin fibroblasts obtained from a number of patients with VDDRII have been utilized to characterize the underlying molecular defects associated with this malady. Recently monoclonal antibodies to the vitamin D receptor have been generated, and a radioligand immunoassay (RLIA) for the detection of this molecule has been developed which is independent of its hormone-binding capacity. This report describes the application of the immunoassay in the detection of receptor-like molecules in fibroblasts derived from patients with VDDRII. The results indicate that the molecule is generally present in all patients, and provides a mechanism for individual responsiveness to pharmacologic treatment with vitamin D 3 metabolites. 8 refs.; 3 figs.; 1 table

  2. Green biochemistry approach for synthesis of silver and gold nanoparticles using Ficus racemosa latex and their pH-dependent binding study with different amino acids using UV/Vis absorption spectroscopy.

    Science.gov (United States)

    Tetgure, Sandesh R; Borse, Amulrao U; Sankapal, Babasaheb R; Garole, Vaman J; Garole, Dipak J

    2015-04-01

    Simple and eco-friendly biosynthesis approach was developed to synthesize silver nanoparticles (SNPs) and gold nanoparticles (GNPs) using Ficus racemosa latex as reducing agent. The presence of sunlight is utilized with latex and achieved the nanoparticles whose average size was in the range of 50-120 nm for SNPs and 20-50 nm for GNPs. The synthesized nanoparticles were characterized by UV/Visible absorption spectroscopy, X-ray diffraction, and field emission-scanning electron microscopy techniques toget understand the obtained nanoparticles. The pH-dependent binding studies of SNPs and GNPs with four amino acids, namely L-lysine, L-arginine, L-glutamine and glycin have been reported.

  3. Characterization and antioxidant activity of bovine serum albumin and sulforaphane complex in different solvent systems

    Energy Technology Data Exchange (ETDEWEB)

    Dong, Xueyan; Zhou, Rui; Jing, Hao, E-mail: h200521@cau.edu.cn

    2014-02-15

    Modes and influencing factors of bovine serum albumin (BSA) and sulforaphane (SFN) interaction will help us understand the interaction mechanisms and functional changes of bioactive small molecule and biomacromolecule. This study investigated interaction mechanisms of BSA and SFN and associated antioxidant activity in three solvent systems of deionized water (dH{sub 2}O), dimethyl sulfoxide (DMSO) and ethanol (EtOH), using Fourier transform infrared spectroscopy (FT-IR), fluorescence spectroscopy, synchronous fluorescence spectroscopy, DPPH and ABTS radical scavenging assays. The results revealed that SFN had ability to quench BSA's fluorescence in static modes, and to interact with BSA at both tyrosine (Tyr) and tryptophan (Trp) residues, while the Trp residues were highly sensitive, which was demonstrated by fluorescence at 340 nm. Hydrophobic forces, hydrogen bonds and van der Waals interactions were all involved in BSA and SFN interaction, which were not significantly changed by three solvents. The binding constant values and binding site numbers were in a descending order of dH{sub 2}O>DMSO>EtOH. The values of free energy change were in a descending order of dH{sub 2}O>DMSO>EtOH, which indicated that the binding forces were in a descending order of dH{sub 2}O>DMSO>EtOH. There was no significant difference in antioxidant activity between SFN and BSA–SFN. Moreover, three solvents had not significant influence on antioxidant activity of SFN and BSA–SFN. -- Highlights: • We report interaction mechanisms of BSA and sulforaphane in three solvent systems. • We report antioxidant activity of BSA–sulforaphane complex in three solvent systems. • Decreasing the solvent polarity will decrease the binding of BSA and sulforaphane. • Three solvents had not influence on antioxidant activity of BSA–sulforaphane.

  4. Two CGTCA motifs and a GHF1/Pit1 binding site mediate cAMP-dependent protein kinase A regulation of human growth hormone gene expression in rat anterior pituitary GC cells.

    Science.gov (United States)

    Shepard, A R; Zhang, W; Eberhardt, N L

    1994-01-21

    We established the cis-acting elements which mediate cAMP responsiveness of the human growth hormone (hGH) gene in transiently transfected rat anterior pituitary tumor GC cells. Analysis of the intact hGH gene or hGH 5'-flanking DNA (5'-FR) coupled to the hGh cDNA or chloramphenicol acetyltransferase or luciferase genes, indicated that cAMP primarily stimulated hGH promoter activity. Cotransfection of a protein kinase A inhibitory protein cDNA demonstrated that the cAMP response was mediated by protein kinase A. Mutational analysis of the hGH promoter identified two core cAMP response element motifs (CGTCA) located at nucleotides -187/-183 (distal cAMP response element; dCRE) and -99/-95 (proximal cAMP response element; pCRE) and a pituitary-specific transcription factor (GHF1/Pit1) binding site at nucleotides -123/-112 (dGHF1) which were required for cAMP responsiveness. GHF1 was not a limiting factor, since overexpression of GHF1 in cotransfections increased basal but not forskolin induction levels. Gel shift analyses indicated that similar, ubiquitous, thermostable protein(s) specifically bound the pCRE and dCRE motifs. The CGTCA motif-binding factors were cAMP response element binding protein (CREB)/activating transcription factor-1 (ATF-1)-related, since the DNA-protein complex was competed by unlabeled CREB consensus oligonucleotide, specifically supershifted by antisera to CREB and ATF-1 but not ATF-2, and was bound by purified CREB with the same relative binding affinity (pCRE < dCRE < CREB) and mobility as the GC nuclear extract. UV cross-linking and Southwestern blot analyses revealed multiple DNA-protein interactions of which approximately 100- and approximately 45-kDa proteins were predominant; the approximately 45-kDa protein may represent CREB. These results indicate that CREB/ATF-1-related factors act coordinately with the cell-specific factor GHF1 to mediate cAMP-dependent regulation of hGH-1 gene transcription in anterior pituitary somatotrophs.

  5. Solvent Flux Method (SFM): A Case Study of Water Access to Candida antarctica Lipase B.

    Science.gov (United States)

    Benson, Sven P; Pleiss, Jürgen

    2014-11-11

    The solvent flux method (SFM) was developed to comprehensively characterize the influx of solvent molecules from the solvent environment into the active site of a protein in the framework of molecular dynamics simulations. This was achieved by introducing a solvent concentration gradient as well as partially reorienting and rescaling the velocity vector of all solvent molecules contained within a spherical volume enclosing the protein, thus inducing an accelerated solvent influx toward the active site. In addition to the detection of solvent access pathway within the protein structure, it is hereby possible to identify potential amino acid positions relevant to solvent-related enzyme engineering with high statistical significance. The method is particularly aimed at improving the reverse hydrolysis reaction rates in nonaqueous media. Candida antarctica lipase B (CALB) binds to a triglyceride-water interface with its substrate entrance channel oriented toward the hydrophobic substrate interface. The lipase-triglyceride-water system served as a model system for SFM to evaluate the influx of water molecules to the active site. As a proof of principle for SFM, a previously known water access pathway in CALB was identified as the primary water channel. In addition, a secondary water channel and two pathways for water access which contribute to water leakage between the protein and the triglyceride-water interface were identified.

  6. Uranium reextraction from D2EHPA-TOPO solvent

    International Nuclear Information System (INIS)

    Duarte Neto, J.

    1985-01-01

    A comparative study for recovering uranium from the solvent D 2 EHPA-TOPO (di-2-ethyl hexyl phosphoric acid - tri-n-octyl phosphine oxide) with ammonium carbonate and sodium carbonate solutions has been made. The paper discusses the precipitation of iron during stripping and the extracctant solubilization in the aqueous phases. Continuous tests showed that uranium is efficiently stripped from the solvent by using both solutions and that the choice of a specific system is dependent on the uranium precipitation mechanism to be employed. (Author) [pt

  7. Effect of solvent composition on dispersing ability of reaction sialon suspensions.

    Science.gov (United States)

    Xu, Xin; Oliveira, Marta; Ferreira, José M F

    2003-03-15

    This work focuses on the optimization of the rheological behavior of suspensions considering different solvent compositions. The effects of methyl ethyl ketone (MEK)/ethanol (E) solvent mixtures on reaction sialon suspensions were investigated by measuring sedimentation behavior, adsorption of dispersant, and flow behavior. It was shown that both the flow behavior and the sedimentation behavior strongly depended on selection of solvent composition. Using 3 wt% KD1 as dispersant, well-dispersed colloidal suspensions could be obtained in MEK-rich solvents. The suspensions with 60 vol% MEK/40 vol% E as solvent could be fitted to the Bingham model with very low yield stress, while suspensions with pure MEK or ethanol-rich mixtures as solvent showed pseudo plastic behavior with relatively high yield stress values. A model was proposed to explain the different flow behaviors of suspensions considering the different configurations of dispersant at particles' surfaces.

  8. Combined effect of solvents and gamma irradiation on the infrared absorption spectra of polyethylene terephthalate

    International Nuclear Information System (INIS)

    Rabie, S.M.; ElBially, A.; Elshourbaguie, S.

    1991-01-01

    The combined effect of solvents and gamma irradiation on the intensities of infrared absorption bands of polyethylene terephthalate, particularly the bands sensitive to conformational changes, were studied. The results revealed that solvent treatment of PET results in significant changes in the intensities of its infrared absorption bands and the exposure of PET to gamma radiation in the presence of solvents helps in the appearance of the two bands at 1550 and 1630 cm . Also, the combined effect of solvents and gamma irradiation on the intensities of the absorption bands is greater than the effect of each agent alone. The extent of the induced changes depends on the nature of solvent and the applied dosage. Further more, for any given solvent or dosage, the rate of change of the intensities of the trans band is not equal to that of the gauche bands.3 fig

  9. Channel formation by the binding component of Clostridium botulinum C2 toxin: glutamate 307 of C2II affects channel properties in vitro and pH-dependent C2I translocation in vivo.

    Science.gov (United States)

    Blöcker, Dagmar; Bachmeyer, Christoph; Benz, Roland; Aktories, Klaus; Barth, Holger

    2003-05-13

    The binding component (C2II) of the binary Clostridium botulinum C2 toxin mediates transport of the actin ADP-ribosylating enzyme component (C2I) into the cytosol of target cells. C2II (80 kDa) is activated by trypsin cleavage, and proteolytically activated C2II (60 kDa) oligomerizes to heptamers in solution. Activated C2II forms channels in lipid bilayer membranes which are highly cation selective and voltage-gated. A role for this channel in C2I translocation across the cell membrane into the cytosol is discussed. Amino acid residues 303-331 of C2II contain a conserved pattern of alternating hydrophobic and hydrophilic residues, which likely facilitates membrane insertion and channel formation by creating two antiparallel beta-strands. Some of the residues are in strategic positions within the putative C2II channel, in particular, glutamate 307 (E307) localized in its center and glycine 316 (G316) localized on the trans side of the membrane. Here, single-lysine substitutions of these amino acids and the double mutant E307K/G316K of C2II were analyzed in vivo and in artificial lipid bilayer experiments. The pH dependence of C2I transport across cellular membranes was altered, and a pH of properties of C2II were substantially changed by the mutations, as evidenced by reduced cation selectivity. Interestingly, the voltage dependence of wild-type C2II was completely lost for the E307K mutant, which means that E307 is responsible for voltage gating. Chloroquine blocked the E307K mutant channel and intoxication of Vero cells by mutant C2II and C2I, indicating that chloroquine binding does not involve E307. Overall, the voltage gating and cation selectivity of the C2II channel do not play an important role in translocation of C2I into the cytosol.

  10. Chiral halogenated Schiff base compounds: green synthesis, anticancer activity and DNA-binding study

    Science.gov (United States)

    Ariyaeifar, Mahnaz; Amiri Rudbari, Hadi; Sahihi, Mehdi; Kazemi, Zahra; Kajani, Abolghasem Abbasi; Zali-Boeini, Hassan; Kordestani, Nazanin; Bruno, Giuseppe; Gharaghani, Sajjad

    2018-06-01

    Eight enantiomerically pure halogenated Schiff base compounds were synthesized by reaction of halogenated salicylaldehydes with 3-Amino-1,2-propanediol (R or S) in water as green solvent at ambient temperature. All compounds were characterized by elemental analyses, NMR (1H and 13C), circular dichroism (CD) and FT-IR spectroscopy. FS-DNA binding studies of these compounds carried out by fluorescence quenching and UV-vis spectroscopy. The obtained results revealed that the ligands bind to DNA as: (Rsbnd ClBr) > (Rsbnd Cl2) > (Rsbnd Br2) > (Rsbnd I2) and (Ssbnd ClBr) > (Ssbnd Cl2) > (Ssbnd Br2) > (Ssbnd I2), indicating the effect of halogen on binding constant. In addition, DNA-binding constant of the Ssbnd and R-enantiomers are different from each other. The ligands can form halogen bonds with DNA that were confirmed by molecular docking. This method was also measured the bond distances and bond angles. The study of obtained data can have concluded that binding affinity of the ligands to DNA depends on strength of halogen bonds. The potential anticancer activity of ligands were also evaluated on MCF-7 and HeLa cancer cell lines by using MTT assay. The results showed that the anticancer activity and FS-DNA interaction is significantly dependent on the stereoisomers of Schiff base compounds as R-enantiomers displayed significantly higher activity than S-enantiomers. The molecular docking was also used to illustrate the specific DNA-binding of synthesized compounds and groove binding mode of DNA interaction was proposed for them. In addition, molecular docking results indicated that there are three types of bonds (Hsbnd and X-bond and hX-bond) between synthesized compounds and base pairs of DNA.

  11. A smallest 6 kda metalloprotease, mini-matrilysin, in living world: a revolutionary conserved zinc-dependent proteolytic domain- helix-loop-helix catalytic zinc binding domain (ZBD

    Directory of Open Access Journals (Sweden)

    Yu Wei-Hsuan

    2012-05-01

    Full Text Available Abstract Background The Aim of this study is to study the minimum zinc dependent metalloprotease catalytic folding motif, helix B Met loop-helix C, with proteolytic catalytic activities in metzincin super family. The metzincin super family share a catalytic domain consisting of a twisted five-stranded β sheet and three long α helices (A, B and C. The catalytic zinc is at the bottom of the cleft and is ligated by three His residues in the consensus sequence motif, HEXXHXXGXXH, which is located in helix B and part of the adjacent Met turn region. An interesting question is - what is the minimum portion of the enzyme that still possesses catalytic and inhibitor recognition?” Methods We have expressed a 60-residue truncated form of matrilysin which retains only the helix B-Met turn-helix C region and deletes helix A and the five-stranded β sheet which form the upper portion of the active cleft. This is only 1/4 of the full catalytic domain. The E. coli derived 6 kDa MMP-7 ZBD fragments were purified and refolded. The proteolytic activities were analyzed by Mca-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH2 peptide assay and CM-transferrin zymography analysis. SC44463, BB94 and Phosphoramidon were computationally docked into the 3day structure of the human MMP7 ZBD and TAD and thermolysin using the docking program GOLD. Results This minimal 6 kDa matrilysin has been refolded and shown to have proteolytic activity in the Mca-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH2 peptide assay. Triton X-100 and heparin are important factors in the refolding environment for this mini-enzyme matrilysin. This minienzyme has the proteolytic activity towards peptide substrate, but the hexamer and octamer of the mini MMP-7 complex demonstrates the CM-transferrin proteolytic activities in zymographic analysis. Peptide digestion is inhibited by SC44463, specific MMP7 inhibitors, but not phosphorimadon. Interestingly, the mini MMP-7 can be processed by autolysis and producing ~ 6

  12. Iodine removing method in organic solvent

    International Nuclear Information System (INIS)

    Suzuki, Takeo; Sakurai, Manabu

    1988-01-01

    Purpose: To effectively remove iodine in an organic solvent to thereby remove iodine in the solvent that can be re-used or put to purning treatment. Method: Organic solvent formed from wastes of nuclear facilities is mixed with basic lead acetate, or silica gel or activated carbon incorporated with such a compound to adsorb iodine in the organic solvent to the basic lead acetate. Then, iodine in the organic solvent is removed by separating to eliminate the basic lead acetate adsorbing iodine from the organic solvent or by passing the organic solvent through a tower or column charged or pre-coated with silica gel or activated carbon incorporated with lead acetate. By using basic lead acetate as the adsorbents, iodine can effective by adsorbed and eliminated. Thus, the possibility of circumstantial release of iodine can be reduced upon reusing or burning treatment of the organic solvent. (Kamimura, M.)

  13. Computer Aided Solvent Selection and Design Framework

    DEFF Research Database (Denmark)

    Mitrofanov, Igor; Conte, Elisa; Abildskov, Jens

    and computer-aided tools and methods for property prediction and computer-aided molecular design (CAMD) principles. This framework is applicable for solvent selection and design in product design as well as process design. The first module of the framework is dedicated to the solvent selection and design...... in terms of: physical and chemical properties (solvent-pure properties); Environment, Health and Safety (EHS) characteristic (solvent-EHS properties); operational properties (solvent–solute properties). 3. Performing the search. The search step consists of two stages. The first is a generation and property...... identification of solvent candidates using special software ProCAMD and ProPred, which are the implementations of computer-aided molecular techniques. The second consists of assigning the RS-indices following the reaction–solvent and then consulting the known solvent database and identifying the set of solvents...

  14. Recent solvent extraction experience at Savannah River

    International Nuclear Information System (INIS)

    Gray, L.W.; Burney, G.A.; Gray, J.H.; Hodges, M.E.; Holt, D.L.; Macafee, I.M.; Reif, D.J.; Shook, H.E.

    1986-01-01

    Tributyl phosphate-based solvent extraction processes have been used at Savannah River for more than 30 years to separate and purify thorium, uranium, neptunium, plutonium, americium, and curium isotopes. This report summarizes the advancement of solvent extraction technology at Savannah River during the 1980's. Topics that are discussed include equipment improvements, solvent treatment, waste reduction, and an improved understanding of the various chemistries in the process streams entering, within, and leaving the solvent extraction processes

  15. Solvent extraction studies of RERTR silicide fuels

    International Nuclear Information System (INIS)

    Gouge, Anthony P.

    1983-01-01

    Uranium silicide fuels, which are candidate RERTR fuel compositions, may require special considerations in solvent extraction reprocessing. Since Savannah River Plant may be reprocessing RERTR fuels as early as 1985, studies have been conducted at Savannah River Laboratory to demonstrate the solvent extraction behavior of this fuel. Results of solvent extraction studies with both unirradiated and irradiated fuel are presented along with the preliminary RERTR solvent extraction reprocessing flow sheet for Savannah River Plant. (author)

  16. Translation initiation on mRNAs bound by nuclear cap-binding protein complex CBP80/20 requires interaction between CBP80/20-dependent translation initiation factor and eukaryotic translation initiation factor 3g.

    Science.gov (United States)

    Choe, Junho; Oh, Nara; Park, Sungjin; Lee, Ye Kyung; Song, Ok-Kyu; Locker, Nicolas; Chi, Sung-Gil; Kim, Yoon Ki

    2012-05-25

    In the cytoplasm of mammalian cells, either cap-binding proteins 80 and 20 (CBP80/20) or eukaryotic translation initiation factor (eIF) 4E can direct the initiation of translation. Although the recruitment of ribosomes to mRNAs during eIF4E-dependent translation (ET) is well characterized, the molecular mechanism for CBP80/20-dependent translation (CT) remains obscure. Here, we show that CBP80/20-dependent translation initiation factor (CTIF), which has been shown to be preferentially involved in CT but not ET, specifically interacts with eIF3g, a component of the eIF3 complex involved in ribosome recruitment. By interacting with eIF3g, CTIF serves as an adaptor protein to bridge the CBP80/20 and the eIF3 complex, leading to efficient ribosome recruitment during CT. Accordingly, down-regulation of CTIF using a small interfering RNA causes a redistribution of CBP80 from polysome fractions to subpolysome fractions, without significant consequence to eIF4E distribution. In addition, down-regulation of eIF3g inhibits the efficiency of nonsense-mediated mRNA decay, which is tightly coupled to CT but not to ET. Moreover, the artificial tethering of CTIF to an intercistronic region of dicistronic mRNA results in translation of the downstream cistron in an eIF3-dependent manner. These findings support the idea that CT mechanistically differs from ET.

  17. Effect of solvent blending on cycling characteristics of lithium

    Energy Technology Data Exchange (ETDEWEB)

    Morita, Masayuki; Matsuda, Yoshiharu

    1987-07-01

    The suitability of electrolytes using mixed solvents has been examined for ambient temperature, rechargeable lithium batteries. Sulfolane (S) and dimethylsulfoxide (DMSO) have been used as base solvents because of their high permittivity, and ethers such as 1,2-dimethoxyethane (DME) have been blended as a low viscosity co-solvent. This blending has been found to yield electrolytes with a high conductivity, and maximum values are observed in solutions with 40-90 mol% ether. The cycling characteristics of lithium are also improved by blending the ethers. The coulombic efficiencies on a nickel substrate are greater than or equal to 80% in S-DME/LiPF/sub 6/ and DMSO-DME/LiPF/sub 6/ solutions. The lithium electrode characteristics are markedly dependent on the type of co-solvent ether, as well as on the electrolytic salt. The results of the conductance behaviour and the electrode characteristics are discussed in terms of ionic structure in the mixed solvent and the state of the electrode/electrolyte interphase.

  18. Aerosols released from solvent fire accidents in reprocessing plants

    International Nuclear Information System (INIS)

    Jordan, S.; Lindner, W.

    1985-01-01

    Thermodynamic, aerosol characterizing and radiological data of solvent fires in reprocessing plants have been established in experiments. These are the main results: Depending on the ventilation in the containment, kerosene-TBP mixtures burn at a rate up to 120 kg/m 2 h. The aqueous phase of inorganic-organic mixtures might be released during the fire. The gaseous reaction products contain unburnable acidic compounds. Solvents with TBP-nitrate complex shows higher (up to 25%) burning rates than pure solvents (kerosene-TBP). The nitrate complex decomposes violently at about 130 0 C with a release of acid and unburnable gases. Up to 20% of the burned kerosene-TBP solvents are released during the fire in the form of soot particles, phosphoric acid and TBP decomposition products. The particles have an aerodynamic mass median diameter of about 0.5 μm and up to 1.5% of the uranium fixed in the TBP-nitrate complex is released during solvent fires. (orig.)

  19. Directed Assembly of Janus Cylinders by Controlling the Solvent Polarity.

    Science.gov (United States)

    Kim, Jongmin; Choi, Chang-Hyung; Yeom, Su-Jin; Eom, Naye; Kang, Kyoung-Ku; Lee, Chang-Soo

    2017-08-01

    This study demonstrates the possibility of controlling the directed self-assembly of microsized Janus cylinders by changing the solvent polarity of the assembly media. Experimental results are analyzed and theoretical calculations of the free energy of adhesion (ΔG ad ) are performed to elucidate the underlying basic principles and investigate the effects of the solvent on the self-assembled structures. This approach will pave a predictive route for controlling the structures of assembly depending on the solvent polarity. In particular, we find that a binary solvent system with precisely controlled polarity induces directional assembly of the microsized Janus cylinders. Thus, the formation of two-dimensional (2D) and three-dimensional (3D) assembled clusters can be reliably tuned by controlling the numbers of constituent Janus cylinders in a binary solvent system. Finally, this approach is expanded to stepwise assembly, which forms unique microstructures via secondary growth of primary seed clusters formed by the Janus cylinders. We envision that this investigation is highly promising for the construction of desired superstructures using a wide variety of polymeric Janus microparticles with chemical and physical multicompartments.

  20. Solvent Extraction of Furfural From Biomass

    Science.gov (United States)

    Humphrey, M. F.

    1984-01-01

    Solvent-extraction method reduces energy required to remove furfural produced during acid hydrolysis of biomass. Acid hydrolysis performed in vessel containing both solvents and reacting ingredients. With intimate contact between solvents and aqueous hydrolyis liqour, furfural removed form liquor almost as fast as it forms.

  1. Adaptive Resolution Simulation of MARTINI Solvents

    NARCIS (Netherlands)

    Zavadlav, Julija; Melo, Manuel N.; Cunha, Ana V.; de Vries, Alex H.; Marrink, Siewert J.; Praprotnik, Matej

    We present adaptive resolution dynamics simulations of aqueous and apolar solvents coarse-grained molecular models that are compatible with the MARTINI force field. As representatives of both classes solvents we have chosen liquid water and butane, respectively, at ambient temperature. The solvent

  2. The Solvent Selection framework: solvents for organic synthesis, separation processes and ionic-organic synthesis

    DEFF Research Database (Denmark)

    Mitrofanov, Igor; Sansonetti, Sascha; Abildskov, Jens

    2012-01-01

    This paper presents a systematic integrated framework for solvent selection and solvent design. The framework is divided into several modules, which can tackle specific problems in various solvent-based applications. In particular, three modules corresponding to the following solvent selection pr...

  3. Solvent cleaning system and method for removing contaminants from solvent used in resin recycling

    Science.gov (United States)

    Bohnert, George W [Harrisonville, MO; Hand, Thomas E [Lee's Summit, MO; DeLaurentiis, Gary M [Jamestown, CA

    2009-01-06

    A two step solvent and carbon dioxide based system that produces essentially contaminant-free synthetic resin material and which further includes a solvent cleaning system for periodically removing the contaminants from the solvent so that the solvent can be reused and the contaminants can be collected and safely discarded in an environmentally safe manner.

  4. Ion association thermodynamics of alkali metal tetraphenylborates in the mixed solvent propylenecarbonate-1,2-dimethoxyethane

    International Nuclear Information System (INIS)

    Fialkov, Yu.Ya.; Gorbachev, V.Yu.

    1997-01-01

    Polythermal dependences of constants of ion association of (Li + -Cs + )BPh 4 salts in mixed solvent differ significantly in permittivity. Thermodynamic characteristics of this process are calculated and their relation with solvation processes is analyzed. (author)

  5. Cloning and expression of the translocator protein (18 kDa), voltage-dependent anion channel, and diazepam binding inhibitor in the gonad of largemouth bass (Micropterus salmoides) across the reproductive cycle.

    Science.gov (United States)

    Doperalski, Nicholas J; Martyniuk, Christopher J; Prucha, Melinda S; Kroll, Kevin J; Denslow, Nancy D; Barber, David S

    2011-08-01

    Cholesterol transport across the mitochondrial membrane is rate-limiting for steroidogenesis in vertebrates. Previous studies in fish have characterized expression of the steroidogenic acute regulatory protein, however the function and regulation of other genes and proteins involved in piscine cholesterol transport have not been evaluated. In the current study, mRNA sequences of the 18 kDa translocator protein (tspo; formerly peripheral benzodiazepine receptor), voltage-dependent anion channel (vdac), and diazepam binding inhibitor (dbi; also acyl-CoA binding protein) were cloned from largemouth bass. Gonadal expression was examined across reproductive stages to determine if expression is correlated with changes in steroid levels and with indicators of reproductive maturation. In testis, transcript abundance of tspo and dbi increased with reproductive maturation (6- and 23-fold maximal increase, respectively) and expression of tspo and dbi was positively correlated with reproductive stage, gonadosomatic index (GSI), and circulating levels of testosterone. Testis vdac expression was positively correlated with reproductive stage and GSI. In females, gonadal tspo and vdac expression was negatively correlated with GSI and levels of plasma testosterone and 17β-estradiol. Ovarian dbi expression was not correlated with indicators of reproductive maturation. These studies represent the first investigation of the steroidogenic role of tspo, vdac, and dbi in fish. Findings suggest that cholesterol transport in largemouth bass testis, but not in ovary, may be transcriptionally-regulated, however further investigation will be necessary to fully elucidate the role of these genes in largemouth bass steroidogenesis. Copyright © 2011 Elsevier Inc. All rights reserved.

  6. Understanding cAMP-dependent allostery by NMR spectroscopy: comparative analysis of the EPAC1 cAMP-binding domain in its apo and cAMP-bound states.

    Science.gov (United States)

    Mazhab-Jafari, Mohammad T; Das, Rahul; Fotheringham, Steven A; SilDas, Soumita; Chowdhury, Somenath; Melacini, Giuseppe

    2007-11-21

    cAMP (adenosine 3',5'-cyclic monophosphate) is a ubiquitous second messenger that activates a multitude of essential cellular responses. Two key receptors for cAMP in eukaryotes are protein kinase A (PKA) and the exchange protein directly activated by cAMP (EPAC), which is a recently discovered guanine nucleotide exchange factor (GEF) for the small GTPases Rap1 and Rap2. Previous attempts to investigate the mechanism of allosteric activation of eukaryotic cAMP-binding domains (CBDs) at atomic or residue resolution have been hampered by the instability of the apo form, which requires the use of mixed apo/holo systems, that have provided only a partial picture of the CBD apo state and of the allosteric networks controlled by cAMP. Here, we show that, unlike other eukaryotic CBDs, both apo and cAMP-bound states of the EPAC1 CBD are stable under our experimental conditions, providing a unique opportunity to define at an unprecedented level of detail the allosteric interactions linking two critical functional sites of this CBD. These are the phosphate binding cassette (PBC), where cAMP binds, and the N-terminal helical bundle (NTHB), which is the site of the inhibitory interactions between the regulatory and catalytic regions of EPAC. Specifically, the combined analysis of the cAMP-dependent changes in chemical shifts, 2 degrees structure probabilities, hydrogen/hydrogen exchange (H/H) and hydrogen/deuterium exchange (H/D) protection factors reveals that the long-range communication between the PBC and the NTHB is implemented by two distinct intramolecular cAMP-signaling pathways, respectively, mediated by the beta2-beta3 loop and the alpha6 helix. Docking of cAMP into the PBC perturbs the NTHB inner core packing and the helical probabilities of selected NTHB residues. The proposed model is consistent with the allosteric role previously hypothesized for L273 and F300 based on site-directed mutagenesis; however, our data show that such a contact is part of a

  7. Insecticide solvents: interference with insecticidal action.

    Science.gov (United States)

    Brattsten, L B; Wilkinson, C F

    1977-06-10

    Several commercial solvent mixtures commonly used as insecticide carriers in spray formulations increase by more than threefold the microsomal N-demethylation of p-chloro N-methylaniline in midgut preparations of southern army-worm (Spodoptera eridania) larvae exposed orally to the test solvents. Under laboratory conditions, the same solvent mixtures exhibit a protective action against the in vivo toxicity of the insecticide carbaryl to the larvae. The data are discussed with respect to possible solvent-insecticide interactions occurring under field conditions and, more broadly, to potential toxicological hazards of these solvents to humans.

  8. Organic solvents in electromembrane extraction: recent insights

    DEFF Research Database (Denmark)

    Huang, Chuixiu; Gjelstad, Astrid; Pedersen-Bjergaard, Stig

    2016-01-01

    the introduction. Under the influence of an electrical field, EME is based on electrokinetic migration of the analytes through a supported liquid membrane (SLM), which is an organic solvent immobilized in the pores of the polymeric membrane, and into the acceptor solution. Up to date, close to 150 research...... articles with focus on EME have been published. The current review summarizes the performance of EME with different organic solvents and discusses several criteria for efficient solvents in EME. In addition, the authors highlight their personal perspective about the most promising organic solvents for EME...... and have indicated that more fundamental work is required to investigate and discover new organic solvents for EME....

  9. A new combined computational and NMR-spectroscopical strategy for the identification of additional conformational constraints of the bound ligand in an aprotic solvent

    NARCIS (Netherlands)

    Vliegenthart, J.F.G.; Siebert, H.-C; André, S.; Asensio, J.l.; Cañada, F.J.; Dong, X.; Espinosa, M.; Frank, M.

    2000-01-01

    This study documents the feasibility of switching to an aprotic medium in sugar receptor research. The solvent change offers additional insights into mechanistic details of receptor-carbohydrate ligand interactions. If a receptor retained binding capacity in an aprotic medium, solvent-exchangeable

  10. Mechanism of Protein Denaturation: Partial Unfolding of the P22 Coat Protein I-Domain by Urea Binding

    Science.gov (United States)

    Newcomer, Rebecca L.; Fraser, LaTasha C.R.; Teschke, Carolyn M.; Alexandrescu, Andrei T.

    2015-01-01

    The I-domain is an insertion domain of the bacteriophage P22 coat protein that drives rapid folding and accounts for over half of the stability of the full-length protein. We sought to determine the role of hydrogen bonds (H-bonds) in the unfolding of the I-domain by examining 3JNC’ couplings transmitted through H-bonds, the temperature and urea-concentration dependence of 1HN and 15N chemical shifts, and native-state hydrogen exchange at urea concentrations where the domain is predominantly folded. The native-state hydrogen-exchange data suggest that the six-stranded β-barrel core of the I-domain is more stable against unfolding than a smaller subdomain comprised of a short α-helix and three-stranded β-sheet. H-bonds, separately determined from solvent protection and 3JNC’ H-bond couplings, are identified with an accuracy of 90% by 1HN temperature coefficients. The accuracy is improved to 95% when 15N temperature coefficients are also included. In contrast, the urea dependence of 1HN and 15N chemical shifts is unrelated to H-bonding. The protein segments with the largest chemical-shift changes in the presence of urea show curved or sigmoidal titration curves suggestive of direct urea binding. Nuclear Overhauser effects to urea for these segments are also consistent with specific urea-binding sites in the I-domain. Taken together, the results support a mechanism of urea unfolding in which denaturant binds to distinct sites in the I-domain. Disordered segments bind urea more readily than regions in stable secondary structure. The locations of the putative urea-binding sites correlate with the lower stability of the structure against solvent exchange, suggesting that partial unfolding of the structure is related to urea accessibility. PMID:26682823

  11. Binding and thermodynamics of REV peptide-ctDNA interaction.

    Science.gov (United States)

    Upadhyay, Santosh Kumar

    2017-03-01

    driven. ITC based analysis of salt dependence of binding constant gave a charge value (Z) = +4.01, as determined for the δlnK/δln[Na + ] parameter, suggesting the participation of only 3-4 Arg out of 11 Arg charge from REV peptide. The stoichiometry observed for the complex was three molar charge of REV peptide binding per molar charge of ctDNA. ITC based analysis further confirmed that the binding between ctDNA and REV peptide is governed by electrostatic interaction. Molecular interactions including H-bonding, van der Waals forces, and solvent molecules rearrangement, underlie the binding of REV peptide to ctDNA. © 2016 Wiley Periodicals, Inc.

  12. Reformulation of Maxwell's equations to incorporate near-solute solvent structure.

    Science.gov (United States)

    Yang, Pei-Kun; Lim, Carmay

    2008-09-04

    Maxwell's equations, which treat electromagnetic interactions between macroscopic charged objects in materials, have explained many phenomena and contributed to many applications in our lives. Derived in 1861 when no methods were available to determine the atomic structure of macromolecules, Maxwell's equations assume the solvent to be a structureless continuum. However, near-solute solvent molecules are highly structured, unlike far-solute bulk solvent molecules. Current methods cannot treat both the near-solute solvent structure and time-dependent electromagnetic interactions in a macroscopic system. Here, we derive "microscopic" electrodynamics equations that can treat macroscopic time-dependent electromagnetic field problems like Maxwell's equations and reproduce the solvent molecular and dipole density distributions observed in molecular dynamics simulations. These equations greatly reduce computational expense by not having to include explicit solvent molecules, yet they treat the solvent electrostatic and van der Waals effects more accurately than continuum models. They provide a foundation to study electromagnetic interactions between molecules in a macroscopic system that are ubiquitous in biology, bioelectromagnetism, and nanotechnology. The general strategy presented herein to incorporate the near-solute solvent structure would enable studies on how complex cellular protein-ligand interactions are affected by electromagnetic radiation, which could help to prevent harmful electromagnetic spectra or find potential therapeutic applications.

  13. Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies.

    Science.gov (United States)

    Deng, Nanjie; Zhang, Bin W; Levy, Ronald M

    2015-06-09

    The ability to accurately model solvent effects on free energy surfaces is important for understanding many biophysical processes including protein folding and misfolding, allosteric transitions, and protein–ligand binding. Although all-atom simulations in explicit solvent can provide an accurate model for biomolecules in solution, explicit solvent simulations are hampered by the slow equilibration on rugged landscapes containing multiple basins separated by barriers. In many cases, implicit solvent models can be used to significantly speed up the conformational sampling; however, implicit solvent simulations do not fully capture the effects of a molecular solvent, and this can lead to loss of accuracy in the estimated free energies. Here we introduce a new approach to compute free energy changes in which the molecular details of explicit solvent simulations are retained while also taking advantage of the speed of the implicit solvent simulations. In this approach, the slow equilibration in explicit solvent, due to the long waiting times before barrier crossing, is avoided by using a thermodynamic cycle which connects the free energy basins in implicit solvent and explicit solvent using a localized decoupling scheme. We test this method by computing conformational free energy differences and solvation free energies of the model system alanine dipeptide in water. The free energy changes between basins in explicit solvent calculated using fully explicit solvent paths agree with the corresponding free energy differences obtained using the implicit/explicit thermodynamic cycle to within 0.3 kcal/mol out of ∼3 kcal/mol at only ∼8% of the computational cost. We note that WHAM methods can be used to further improve the efficiency and accuracy of the implicit/explicit thermodynamic cycle.

  14. Potential of mean force for ion pairs in non-aqueous solvents. Comparison of polarizable and non-polarizable MD simulations

    Science.gov (United States)

    Odinokov, A. V.; Leontyev, I. V.; Basilevsky, M. V.; Petrov, N. Ch.

    2011-01-01

    Potentials of mean force (PMF) are calculated for two model ion pairs in two non-aqueous solvents. Standard non-polarizable molecular dynamics simulation (NPMD) and approximate polarizable simulation (PMD) are implemented and compared as tools for monitoring PMF profiles. For the polar solvent (dimethylsulfoxide, DMSO) the PMF generated in terms of the NPMD reproduces fairly well the refined PMD-PMF profile. For the non-polar solvent (benzene) the conventional NPMD computation proves to be deficient. The validity of the correction found in terms of the approximate PMD approach is verified by its comparison with the result of the explicit PMD computation in benzene. The shapes of the PMF profiles in DMSO and in benzene are quite different. In DMSO, owing to dielectric screening, the PMF presents a flat plot with a shallow minimum positioned in the vicinity of the van der Waals contact of the ion pair. For the benzene case, the observed minimum proves to be unexpectedly deep, which manifests the formation of a tightly-binded contact ion pair. This remarkable effect arises owing to the strong electrostatic interaction that is incompletely screened by a non-polar medium. The PMFs for the binary benzene/DMSO mixtures display intermediate behaviour depending on the DMSO content.

  15. Advanced integrated solvent extraction systems

    Energy Technology Data Exchange (ETDEWEB)

    Horwitz, E.P.; Dietz, M.L.; Leonard, R.A. [Argonne National Lab., IL (United States)

    1997-10-01

    Advanced integrated solvent extraction systems are a series of novel solvent extraction (SX) processes that will remove and recover all of the major radioisotopes from acidic-dissolved sludge or other acidic high-level wastes. The major focus of this effort during the last 2 years has been the development of a combined cesium-strontium extraction/recovery process, the Combined CSEX-SREX Process. The Combined CSEX-SREX Process relies on a mixture of a strontium-selective macrocyclic polyether and a novel cesium-selective extractant based on dibenzo 18-crown-6. The process offers several potential advantages over possible alternatives in a chemical processing scheme for high-level waste treatment. First, if the process is applied as the first step in chemical pretreatment, the radiation level for all subsequent processing steps (e.g., transuranic extraction/recovery, or TRUEX) will be significantly reduced. Thus, less costly shielding would be required. The second advantage of the Combined CSEX-SREX Process is that the recovered Cs-Sr fraction is non-transuranic, and therefore will decay to low-level waste after only a few hundred years. Finally, combining individual processes into a single process will reduce the amount of equipment required to pretreat the waste and therefore reduce the size and cost of the waste processing facility. In an ongoing collaboration with Lockheed Martin Idaho Technology Company (LMITCO), the authors have successfully tested various segments of the Advanced Integrated Solvent Extraction Systems. Eichrom Industries, Inc. (Darien, IL) synthesizes and markets the Sr extractant and can supply the Cs extractant on a limited basis. Plans are under way to perform a test of the Combined CSEX-SREX Process with real waste at LMITCO in the near future.

  16. Reverse Non-Equilibrium Molecular Dynamics Demonstrate That Surface Passivation Controls Thermal Transport at Semiconductor-Solvent Interfaces.

    Science.gov (United States)

    Hannah, Daniel C; Gezelter, J Daniel; Schaller, Richard D; Schatz, George C

    2015-06-23

    We examine the role played by surface structure and passivation in thermal transport at semiconductor/organic interfaces. Such interfaces dominate thermal transport in semiconductor nanomaterials owing to material dimensions much smaller than the bulk phonon mean free path. Utilizing reverse nonequilibrium molecular dynamics simulations, we calculate the interfacial thermal conductance (G) between a hexane solvent and chemically passivated wurtzite CdSe surfaces. In particular, we examine the dependence of G on the CdSe slab thickness, the particular exposed crystal facet, and the extent of surface passivation. Our results indicate a nonmonotonic dependence of G on ligand-grafting density, with interfaces generally exhibiting higher thermal conductance for increasing surface coverage up to ∼0.08 ligands/Å(2) (75-100% of a monolayer, depending on the particular exposed facet) and decreasing for still higher coverages. By analyzing orientational ordering and solvent penetration into the ligand layer, we show that a balance of competing effects is responsible for this nonmonotonic dependence. Although the various unpassivated CdSe surfaces exhibit similar G values, the crystal structure of an exposed facet nevertheless plays an important role in determining the interfacial thermal conductance of passivated surfaces, as the density of binding sites on a surface determines the ligand-grafting densities that may ultimately be achieved. We demonstrate that surface passivation can increase G relative to a bare surface by roughly 1 order of magnitude and that, for a given extent of passivation, thermal conductance can vary by up to a factor of ∼2 between different surfaces, suggesting that appropriately tailored nanostructures may direct heat flow in an anisotropic fashion for interface-limited thermal transport.

  17. Solvent friction effects propagate over the entire protein molecule through low-frequency collective modes.

    Science.gov (United States)

    Moritsugu, Kei; Kidera, Akinori; Smith, Jeremy C

    2014-07-24

    Protein solvation dynamics has been investigated using atom-dependent Langevin friction coefficients derived directly from molecular dynamics (MD) simulations. To determine the effect of solvation on the atomic friction coefficients, solution and vacuum MD simulations were performed for lysozyme and staphylococcal nuclease and analyzed by Langevin mode analysis. The coefficients thus derived are roughly correlated with the atomic solvent-accessible surface area (ASA), as expected from the fact that friction occurs as the result of collisions with solvent molecules. However, a considerable number of atoms with higher friction coefficients are found inside the core region. Hence, the influence of solvent friction propagates into the protein core. The internal coefficients have large contributions from the low-frequency modes, yielding a simple picture of the surface-to-core long-range damping via solvation governed by collective low-frequency modes. To make use of these findings in implicit-solvent modeling, we compare the all-atom friction results with those obtained using Langevin dynamics (LD) with two empirical representations: the constant-friction and the ASA-dependent (Pastor-Karplus) friction models. The constant-friction model overestimates the core and underestimates the surface damping whereas the ASA-dependent friction model, which damps protein atoms only on the solvent-accessible surface, reproduces well the friction coefficients for both the surface and core regions observed in the explicit-solvent MD simulations. Therefore, in LD simulation, the solvent friction coefficients should be imposed only on the protein surface.

  18. Thin porphyrin composite membranes with enhanced organic solvent transport

    KAUST Repository

    Phuoc, Duong

    2018-05-01

    Extending the stability of polymeric membranes in organic solvents is important for applications in chemical and pharmaceutical industry. Thin-film composite membranes with enhanced solvent permeance are proposed, using porphyrin as a building block. Hybrid polyamide films are formed by interfacial polymerization of 5,10,15,20-(tetra-4-aminophenyl)porphyrin/m-phenylene diamine (MPD) mixtures with trimesoyl chloride. Porphyrin is a non-planar molecule, containing a heterocyclic tetrapyrrole unit. Its incorporation into a polyamide film leads to higher free volume than that of a standard polyamide film. Polyamide films derived from porphyrin and MPD amines with a fixed total amine concentration of 1wt% and various porphyrin/MPD ratios were fabricated and characterized. The porphyrin/MPD polyamide film was complexed with Cu(II), due to the binding capacity of porphyrin to metal ions. By coupling scanning transmission electron microscopy (STEM) with electron energy-loss spectroscopy (EELS), Cu mapping was obtained, revealing the distribution of porphyrin in the interfacial polymerized layer. By using porphyrin as amine-functionalized monomer a membrane with thin selective skin and enhanced solvent transport is obtained, with good dye selectivity in the nanofiltration range. For instance, an ultra-fast hexane permeance, 40-fold increased, was confirmed when using 0.5/0.5 porphyrin/MPD mixtures, instead of only MPD as amine monomer. A rejection of 94.2% Brilliant Blue R (826g/mol) in methanol was measured.

  19. Thermodynamics of ligand binding to acyl-coenzyme A binding protein studied by titration calorimetry

    DEFF Research Database (Denmark)

    Færgeman, Nils J.; Sigurskjold, B W; Kragelund, B B

    1996-01-01

    Ligand binding to recombinant bovine acyl-CoA binding protein (ACBP) was examined using isothermal microcalorimetry. Microcalorimetric measurements confirm that the binding affinity of acyl-CoA esters for ACBP is strongly dependent on the length of the acyl chain with a clear preference for acyl-...

  20. Vasohibin 2 promotes epithelial-mesenchymal transition in human breast cancer via activation of transforming growth factor β 1 and hypoxia dependent repression of GATA-binding factor 3.

    Science.gov (United States)

    Tu, Min; Li, Zhanjun; Liu, Xian; Lv, Nan; Xi, Chunhua; Lu, Zipeng; Wei, Jishu; Song, Guoxin; Chen, Jianmin; Guo, Feng; Jiang, Kuirong; Wang, Shui; Gao, Wentao; Miao, Yi

    2017-03-01

    Vasohibin 2 (VASH2) is identified as an angiogenic factor, and has been implicated in tumor angiogenesis, proliferation and epithelial-mesenchymal transition (EMT). To investigate the EMT role of VASH2 in breast cancer, we overexpressed or knocked down expression of VASH2 in human breast cancer cell lines. We observed that VASH2 induced EMT in vitro and in vivo. The transforming growth factor β1 (TGFβ1) pathway was activated by VASH2, and expression of a dominant negative TGFβ type II receptor could block VASH2-mediated EMT. In clinical breast cancer tissues VASH2 positively correlated with TGFβ1 expression, but negatively correlated with E-cadherin (a marker of EMT) expression. Under hypoxic conditions in vitro or in vivo, we found that down-regulation of estrogen receptor 1 (ESR1) in VASH2 overexpressing ESR1 positive cells suppressed E-cadherin. Correlation coefficient analysis indicated that VASH2 and ESR1 expression were negatively correlated in clinical human breast cancer tissues. Further study revealed that a transcription factor of ESR1, GATA-binding factor 3 (GATA3), was down-regulated by VASH2 under hypoxia or in vivo. These findings suggest that VASH2 drives breast cancer cells to undergo EMT by activation of the TGFβ1 pathway and hypoxia dependent repression GATA3-ESR1 pathway, leading to cancer metastasis. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  1. PspF-binding domain PspA1-144 and the PspA·F complex: New insights into the coiled-coil-dependent regulation of AAA+ proteins.

    Science.gov (United States)

    Osadnik, Hendrik; Schöpfel, Michael; Heidrich, Eyleen; Mehner, Denise; Lilie, Hauke; Parthier, Christoph; Risselada, H Jelger; Grubmüller, Helmut; Stubbs, Milton T; Brüser, Thomas

    2015-11-01

    Phage shock protein A (PspA) belongs to the highy conserved PspA/IM30 family and is a key component of the stress inducible Psp system in Escherichia coli. One of its central roles is the regulatory interaction with the transcriptional activator of this system, the σ(54) enhancer-binding protein PspF, a member of the AAA+ protein family. The PspA/F regulatory system has been intensively studied and serves as a paradigm for AAA+ enzyme regulation by trans-acting factors. However, the molecular mechanism of how exactly PspA controls the activity of PspF and hence σ(54) -dependent expression of the psp genes is still unclear. To approach this question, we identified the minimal PspF-interacting domain of PspA, solved its structure, determined its affinity to PspF and the dissociation kinetics, identified residues that are potentially important for PspF regulation and analyzed effects of their mutation on PspF in vivo and in vitro. Our data indicate that several characteristics of AAA+ regulation in the PspA·F complex resemble those of the AAA+ unfoldase ClpB, with both proteins being regulated by a structurally highly conserved coiled-coil domain. The convergent evolution of both regulatory domains points to a general mechanism to control AAA+ activity for divergent physiologic tasks via coiled-coil domains. © 2015 John Wiley & Sons Ltd.

  2. Extracellular Membrane-proximal Domain of HAb18G/CD147 Binds to Metal Ion-dependent Adhesion Site (MIDAS) Motif of Integrin β1 to Modulate Malignant Properties of Hepatoma Cells*

    Science.gov (United States)

    Li, Yong; Wu, Jiao; Song, Fei; Tang, Juan; Wang, Shi-Jie; Yu, Xiao-Ling; Chen, Zhi-Nan; Jiang, Jian-Li

    2012-01-01

    Several lines of evidence suggest that HAb18G/CD147 interacts with the integrin variants α3β1 and α6β1. However, the mechanism of the interaction remains largely unknown. In this study, mammalian protein-protein interaction trap (MAPPIT), a mammalian two-hybrid method, was used to study the CD147-integrin β1 subunit interaction. CD147 in human hepatocellular carcinoma (HCC) cells was interfered with by small hairpin RNA. Nude mouse xenograft model and metastatic model of HCC were used to detect the role of CD147 in carcinogenesis and metastasis. We found that the extracellular membrane-proximal domain of HAb18G/CD147 (I-type domain) binds at the metal ion-dependent adhesion site in the βA domain of the integrin β1 subunit, and Asp179 in the I-type domain of HAb18G/CD147 plays an important role in the interaction. The levels of the proteins that act downstream of integrin, including focal adhesion kinase (FAK) and phospho-FAK, were decreased, and the cytoskeletal structures of HCC cells were rearranged bearing the HAb18G/CD147 deletion. Simultaneously, the migration and invasion capacities, secretion of matrix metalloproteinases, colony formation rate in vitro, and tumor growth and metastatic potential in vivo were decreased. These results indicate that the interaction of HAb18G/CD147 extracellular I-type domain with the integrin β1 metal ion-dependent adhesion site motif activates the downstream FAK signaling pathway, subsequently enhancing the malignant properties of HCC cells. PMID:22130661

  3. Phospholipid electrospun nanofibers: effect of solvents and co-axial processing on morphology and fiber diameter

    DEFF Research Database (Denmark)

    Jørgensen, Lars; Qvortrup, Klaus; Chronakis, Ioannis S.

    2015-01-01

    Asolectin phospholipid nano-microfibers were prepared using electrospinning processing. The asolectin fibers were studied by scanning electron microscopy, and the fiber morphology was found to be strongly dependent on the phospholipid concentration and the solvents used. The solvents studied were...... chloroform : dimethylformamide (CHCl3 : DMF, 3 : 2 v/v), isooctane, cyclohexane and limonene, producing phospholipid fibers with average diameters in the range of 2.57 +/- 0.59 mu m, similar to 3-8 mu m, similar to 4-5 mu m and 14.3 +/- 2.7 mu m, respectively. The diameter of asolectin electrospun fibers...... solvent and the inner needle contains the asolectin solution in CHCl3: DMF, a substantial reduction in the average fiber diameter was observed. In particular, the average diameter of the fibers when DMF (a solvent with a high dielectric constant) was used as a sheath solvent was reduced by a factor...

  4. Influence of Solvent Composition on the Performance of Spray-Dried Co-Amorphous Formulations

    DEFF Research Database (Denmark)

    Mishra, Jaya; Rades, Thomas; Löbmann, Korbinian

    2018-01-01

    Ball-milling is usually used to prepare co-amorphous drug–amino acid (AA) mixtures. In this study, co-amorphous drug–AA mixtures were produced using spray-drying, a scalable industrially preferred preparation method. The influence of the solvent type and solvent composition was investigated....... Mixtures of indomethacin (IND) and each of the three AAs arginine, histidine, and lysine were ball-milled and spray-dried at a 1:1 molar ratio, respectively. Spray-drying was performed at different solvent ratios in (a) ethanol and water mixtures and (b) acetone and water mixtures. Different ratios...... that using spray-drying as a preparation method, all IND–AA mixtures could be successfully converted into the respective co-amorphous forms, irrespective of the type of solvent used, but depending on the solvent mixture ratios. Both ball-milled and spray-dried co-amorphous samples showed an enhanced...

  5. Sustainable development of gree solvent separation process

    OpenAIRE

    Lisickov, Kiril; Fidancevska, Emilija; Grujic, Radoslav; Srebrenkoska, Vineta; Kuvendziev, Stefan

    2011-01-01

    Solvents defi ne a major part of the environmental performance of processes in the chemical industry and impact on cost, safety and health issues. The idea of green solvents expresses the goal to minimize the environmental impact resulting from the use of solvents in chemical production. In spite of conventional separation methods, precise process green technologies are based on the application of modern processes and process equipment as well as control and management...

  6. Supercritical solvent extraction of oil sand bitumen

    Science.gov (United States)

    Imanbayev, Ye. I.; Ongarbayev, Ye. K.; Tileuberdi, Ye.; Mansurov, Z. A.; Golovko, A. K.; Rudyk, S.

    2017-08-01

    The supercritical solvent extraction of bitumen from oil sand studied with organic solvents. The experiments were performed in autoclave reactor at temperature above 255 °C and pressure 29 atm with stirring for 6 h. The reaction resulted in the formation of coke products with mineral part of oil sands. The remaining products separated into SARA fractions. The properties of the obtained products were studied. The supercritical solvent extraction significantly upgraded extracted natural bitumen.

  7. Canyon solvent cleaning with activated alumina

    International Nuclear Information System (INIS)

    Reif, D.J.

    1987-01-01

    This paper presents recent work at SRL concerning the cleaning of solvent extraction solvent used at SRP. The paper explains why we undertook the work, and some laboratory studies on two approaches to solvent cleaning, namely extended carbonate washing and use of solid adsorbents. The paper then discusses scale-up of the preferred method and the results of the full-scale cleaning. 19 figs

  8. Solvent cleanup using base-treated silica gel solid adsorbent

    International Nuclear Information System (INIS)

    Tallent, O.K.; Mailen, J.C.; Pannell, K.D.

    1984-06-01

    A solvent cleanup method using silica gel columns treated with either sodium hydroxide (NaOH) or lithium hydroxide (LiOH) has been investigated. Its effectiveness compares favorably with that of traditional wash methods. After treatment with NaOH solution, the gels adsorb HNO 3 , dibutyl phosphate (DBP), UO 2 2+ , Pu 4+ , various metal-ion fission products, and other species from the solvent. Adsorption mechanisms include neutralization, hydrolysis, polymerization, and precipitation, depending on the species adsorbed. Sodium dibutyl phosphate, which partially distributes to the solvent from the gels, can be stripped with water; the stripping coefficient ranges from 280 to 540. Adsorption rates are diffusion controlled such that temperature effects are relatively small. Recycle of the gels is achieved either by an aqueous elution and recycle sequence or by a thermal treatment method, which may be preferable. Potential advantages of this solvent cleanup method are that (1) some operational problems are avoided and (2) the amount of NaNO 3 waste generated per metric ton of nuclear fuel reprocessed would be reduced significantly. 19 references, 6 figures, 12 tables

  9. Effect of solvents on the enzyme mediated degradation of copolymers

    International Nuclear Information System (INIS)

    Banerjee, Aditi; Chatterjee, Kaushik; Madras, Giridhar

    2015-01-01

    The biodegradation of polycaprolactone (PCL), polylactic acid (PLA), polyglycolide (PGA) and their copolymers, poly (lactide-co-glycolide) and poly (D, L-lactide-co-caprolactone) (PLCL) was investigated. The influence of different solvents on the degradation of these polymers at 37 °C in the presence of two different lipases namely Novozym 435 and the free lipase of porcine pancreas was investigated. The rate coefficients for the polymer degradation and enzyme deactivation were determined using continuous distribution kinetics. Among the homopolymers, the degradation of PGA was nearly an order of magnitude lower than that for PCL and PLA. The overall rate coefficients of the copolymers were higher than their respective homopolymers. Thus, PLCL degraded faster than either PCL or PLA. The degradation was highly dependent on the viscosity of the solvent used with the highest degradation observed in acetone. The degradation of the polymers in acetone was nearly twice that observed in dimethyl sulfoxide indicating that the degradation decreases with increase in the solvent viscosity. The degradation of the polymers in water-solvent mixtures indicated an optimal water content of 2.5 wt% of water. (paper)

  10. Process for hydrogenating coal and coal solvents

    Energy Technology Data Exchange (ETDEWEB)

    Shridharani, K.G.; Tarrer, A.R.

    1983-02-15

    A novel process is described for the hydrogenation of coal by the hydrogenation of a solvent for the coal in which the hydrogenation of the coal solvent is conducted in the presence of a solvent hydrogenation catalyst of increased activity, wherein the hydrogenation catalyst is produced by reacting ferric oxide with hydrogen sulfide at a temperature range of 260/sup 0/ C to 315/sup 0/ C in an inert atmosphere to produce an iron sulfide hydrogenation catalyst for the solvent. Optimally, the reaction temperature is 275/sup 0/ C. Alternately, the reaction can be conducted in a hydrogen atmosphere at 350/sup 0/ C.

  11. Process for hydrogenating coal and coal solvents

    Science.gov (United States)

    Tarrer, Arthur R.; Shridharani, Ketan G.

    1983-01-01

    A novel process is described for the hydrogenation of coal by the hydrogenation of a solvent for the coal in which the hydrogenation of the coal solvent is conducted in the presence of a solvent hydrogenation catalyst of increased activity, wherein the hydrogenation catalyst is produced by reacting ferric oxide with hydrogen sulfide at a temperature range of 260.degree. C. to 315.degree. C. in an inert atmosphere to produce an iron sulfide hydrogenation catalyst for the solvent. Optimally, the reaction temperature is 275.degree. C. Alternately, the reaction can be conducted in a hydrogen atmosphere at 350.degree. C.

  12. Aminosilicone solvent recovery methods and systems

    Science.gov (United States)

    Spiry, Irina Pavlovna; Perry, Robert James; Wood, Benjamin Rue; Singh, Surinder Prabhjot; Farnum, Rachel Lizabeth; Genovese, Sarah Elizabeth

    2018-02-13

    The present invention is directed to aminosilicone solvent recovery methods and systems. The methods and systems disclosed herein may be used to recover aminosilicone solvent from a carbon dioxide containing vapor stream, for example, a vapor stream that leaves an aminosilicone solvent desorber apparatus. The methods and systems of the invention utilize a first condensation process at a temperature from about 80.degree. C. to about 150.degree. C. and a second condensation process at a temperature from about 5.degree. C. to about 75.degree. C. The first condensation process yields recovered aminosilicone solvent. The second condensation process yields water.

  13. Molecular Thermodynamic Modeling of Mixed Solvent Solubility

    DEFF Research Database (Denmark)

    Ellegaard, Martin Dela; Abildskov, Jens; O’Connell, John P.

    2010-01-01

    A method based on statistical mechanical fluctuation solution theory for composition derivatives of activity coefficients is employed for estimating dilute solubilities of 11 solid pharmaceutical solutes in nearly 70 mixed aqueous and nonaqueous solvent systems. The solvent mixtures range from...... nearly ideal to strongly nonideal. The database covers a temperature range from 293 to 323 K. Comparisons with available data and other existing solubility methods show that the method successfully describes a variety of observed mixed solvent solubility behaviors using solute−solvent parameters from...

  14. Characterization of molecularly imprinted polymers using a new polar solvent titration method.

    Science.gov (United States)

    Song, Di; Zhang, Yagang; Geer, Michael F; Shimizu, Ken D

    2014-07-01

    A new method of characterizing molecularly imprinted polymers (MIPs) was developed and tested, which provides a more accurate means of identifying and measuring the molecular imprinting effect. In the new polar solvent titration method, a series of imprinted and non-imprinted polymers were prepared in solutions containing increasing concentrations of a polar solvent. The polar solvent additives systematically disrupted the templation and monomer aggregation processes in the prepolymerization solutions, and the extent of disruption was captured by the polymerization process. The changes in binding capacity within each series of polymers were measured, providing a quantitative assessment of the templation and monomer aggregation processes in the imprinted and non-imprinted polymers. The new method was tested using three different diphenyl phosphate imprinted polymers made using three different urea functional monomers. Each monomer had varying efficiencies of templation and monomer aggregation. The new MIP characterization method was found to have several advantages. To independently verify the new characterization method, the MIPs were also characterized using traditional binding isotherm analyses. The two methods appeared to give consistent conclusions. First, the polar solvent titration method is less susceptible to false positives in identifying the imprinting effect. Second, the method is able to differentiate and quantify changes in binding capacity, as measured at a fixed guest and polymer concentration, arising from templation or monomer aggregation processes in the prepolymerization solution. Third, the method was also easy to carry out, taking advantage of the ease of preparing MIPs. Copyright © 2014 John Wiley & Sons, Ltd.

  15. Kinetics and thermodynamics of small molecule binding to pincer-PCP rhodium(I) complexes

    KAUST Repository

    Doherty, Mark D.

    2013-04-15

    The kinetics and thermodynamics of the binding of several small molecules, L (L = N2, H2, D2, and C2H 4), to the coordinatively unsaturated pincer-PCP rhodium(I) complexes Rh[tBu2PCH2(C6H3)CH 2PtBu2] (1) and Rh[tBu 2P(CH2)2(CH)(CH2)2P tBu2] (2) in organic solvents (n-heptane, toluene, THF, and cyclohexane-d12) have been investigated by a combination of kinetic flash photolysis methods, NMR equilibrium studies, and density functional theory (DFT) calculations. Using various gas mixtures and monitoring by NMR until equilibrium was established, the relative free energies of binding of N2, H2, and C2H4 in cyclohexane-d12 were found to increase in the order C 2H4 < N2 < H2. Time-resolved infrared (TRIR) and UV-vis transient absorption spectroscopy revealed that 355 nm excitation of 1-L and 2-L results in the photoejection of ligand L. The subsequent mechanism of binding of L to 1 and 2 to regenerate 1-L and 2-L is determined by the structure of the PCP ligand framework and the nature of the solvent. In both cases, the primary transient is a long-lived, unsolvated species (τ = 50-800 ns, depending on L and its concentration in solution). For 2, this so-called less-reactive form (LRF) is in equilibrium with a more-reactive form (MRF), which reacts with L at diffusion-controlled rates to regenerate 2-L. These two intermediates are proposed to be different conformers of the three-coordinate (PCP)Rh fragment. For 1, a similar mechanism is proposed to occur, but the LRF to MRF step is irreversible. In addition, a parallel reaction pathway was observed that involves the direct reaction of the LRF of 1 with L, with second-order rate constants that vary by almost 3 orders of magnitude, depending on the nature of L (in n-heptane, k = 6.7 × 10 5 M-1 s-1 for L = C2H4; 4.0 × 106 M-1 s-1 for L = N2; 5.5 × 108 M-1 s-1 for L = H2). Experiments in the more coordinating solvent, THF, revealed the binding of THF to 1 to generate 1-THF, and its subsequent reaction with L, as a

  16. Kinetics and thermodynamics of small molecule binding to pincer-PCP rhodium(I) complexes

    KAUST Repository

    Doherty, Mark D.; Grills, David C.; Huang, Kuo-Wei; Muckerman, James T.; Polyansky, Dmitry E.; Van Eldik, Rudi V.; Fujita, Etsuko

    2013-01-01

    The kinetics and thermodynamics of the binding of several small molecules, L (L = N2, H2, D2, and C2H 4), to the coordinatively unsaturated pincer-PCP rhodium(I) complexes Rh[tBu2PCH2(C6H3)CH 2PtBu2] (1) and Rh[tBu 2P(CH2)2(CH)(CH2)2P tBu2] (2) in organic solvents (n-heptane, toluene, THF, and cyclohexane-d12) have been investigated by a combination of kinetic flash photolysis methods, NMR equilibrium studies, and density functional theory (DFT) calculations. Using various gas mixtures and monitoring by NMR until equilibrium was established, the relative free energies of binding of N2, H2, and C2H4 in cyclohexane-d12 were found to increase in the order C 2H4 < N2 < H2. Time-resolved infrared (TRIR) and UV-vis transient absorption spectroscopy revealed that 355 nm excitation of 1-L and 2-L results in the photoejection of ligand L. The subsequent mechanism of binding of L to 1 and 2 to regenerate 1-L and 2-L is determined by the structure of the PCP ligand framework and the nature of the solvent. In both cases, the primary transient is a long-lived, unsolvated species (τ = 50-800 ns, depending on L and its concentration in solution). For 2, this so-called less-reactive form (LRF) is in equilibrium with a more-reactive form (MRF), which reacts with L at diffusion-controlled rates to regenerate 2-L. These two intermediates are proposed to be different conformers of the three-coordinate (PCP)Rh fragment. For 1, a similar mechanism is proposed to occur, but the LRF to MRF step is irreversible. In addition, a parallel reaction pathway was observed that involves the direct reaction of the LRF of 1 with L, with second-order rate constants that vary by almost 3 orders of magnitude, depending on the nature of L (in n-heptane, k = 6.7 × 10 5 M-1 s-1 for L = C2H4; 4.0 × 106 M-1 s-1 for L = N2; 5.5 × 108 M-1 s-1 for L = H2). Experiments in the more coordinating solvent, THF, revealed the binding of THF to 1 to generate 1-THF, and its subsequent reaction with L, as a

  17. Solvent anode for plutonium purification

    International Nuclear Information System (INIS)

    Bowersox, D.F.; Fife, K.W.; Christensen, D.C.

    1986-01-01

    The purpose of this study is to develop a technique to allow complete oxidation of plutonium from the anode during plutonium electrorefining. This will eliminate the generation of a ''spent'' anode heel which requires further treatment for recovery. Our approach is to employ a solvent metal in the anode to provide a liquid anode pool throughout electrorefining. We use molten salts and metals in ceramic crucibles at 700 0 C. Our goal is to produce plutonium metal at 99.9% purity with oxidation and transfer of more than 98% of the impure plutonium feed metal from the anode into the salt and product phases. We have met these criteria in experiments on the 100 to 1000 g scale. We plan to scale our operations to 4 kg of feed plutonium and to optimize the process parameters

  18. Quantitation of buried contamination by use of solvents. [degradation of silicone polymers by amine solvents

    Science.gov (United States)

    Pappas, S. P.; Hsiao, Y. C.; Hill, L. W.

    1973-01-01

    Spore recovery form cured silicone potting compounds using amine solvents to degrade the cured polymers was investigated. A complete list of solvents and a description of the effect of each on two different silicone polymers is provided.

  19. Implicit solvent simulations of DNA and DNA-protein complexes: Agreement with explicit solvent vs experiment

    Czech Academy of Sciences Publication Activity Database

    Chocholoušová, Jana; Feig, M.

    2006-01-01

    Roč. 110, č. 34 (2006), s. 17240-17251 ISSN 1520-6106 Keywords : implicit solvent * explicit solvent * protein DNA complex Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.115, year: 2006

  20. Activity and conformation of lysozyme in molecular solvents, protic ionic liquids (PILs) and salt-water systems.

    Science.gov (United States)

    Wijaya, Emmy C; Separovic, Frances; Drummond, Calum J; Greaves, Tamar L

    2016-09-21

    Improving protein stabilisation is important for the further development of many applications in the pharmaceutical, specialty chemical, consumer product and agricultural sectors. However, protein stabilization is highly dependent on the solvent environment and, hence, it is very complex to tailor protein-solvent combinations for stable protein maintenance. Understanding solvent features that govern protein stabilization will enable selection or design of suitable media with favourable solution environments to retain protein native conformation. In this work the structural conformation and activity of lysozyme in 29 solvent systems were investigated to determine the role of various solvent features on the stability of the enzyme. The solvent systems consisted of 19 low molecular weight polar solvents and 4 protic ionic liquids (PILs), both at different water content levels, and 6 aqueous salt solutions. Small angle X-ray scattering, Fourier transform infrared spectroscopy and UV-vis spectroscopy were used to investigate the tertiary and secondary structure of lysozyme along with the corresponding activity in various solvation systems. At low non-aqueous solvent concentrations (high water content), the presence of solvents and salts generally maintained lysozyme in its native structure and enhanced its activity. Due to the presence of a net surface charge on lysozyme, electrostatic interactions in PIL-water systems and salt solutions enhanced lysozyme activity more than the specific hydrogen-bond interactions present in non-ionic molecular solvents. At higher solvent concentrations (lower water content), solvents with a propensity to exhibit the solvophobic effect, analogous to the hydrophobic effect in water, retained lysozyme native conformation and activity. This solvophobic effect was observed particularly for solvents which contained hydroxyl moieties. Preferential solvophobic effects along with bulky chemical structures were postulated to result in less

  1. Crystal Nucleation of Tolbutamide in Solution: Relationship to Solvent, Solute Conformation, and Solution Structure.

    Science.gov (United States)

    Zeglinski, Jacek; Kuhs, Manuel; Khamar, Dikshitkumar; Hegarty, Avril C; Devi, Renuka K; Rasmuson, Åke C

    2018-04-03

    The influence of the solvent in nucleation of tolbutamide, a medium-sized, flexible and polymorphic organic molecule, has been explored by measuring nucleation induction times, estimating solvent-solute interaction enthalpies using molecular modelling and calorimetric data, probing interactions and clustering with spectroscopy, and modelling solvent-dependence of molecular conformation in solution. The nucleation driving force required to reach the same induction time is strongly solvent-dependent, increasing in the order: acetonitrilenucleation difficulty is a function of the strength of solvent-solute interaction, with emphasis on the interaction with specific H-bonding polar sites of importance in the crystal structure. A clear exception from this rule is the most difficult nucleation in toluene despite the weakest solvent-solute interactions. However molecular dynamics modelling predicts that tolbutamide assumes an intramolecularly H-bonded conformation in toluene, substantially different from and more stable than the conformation in the crystal structure, and thus presenting an additional barrier to nucleation. This explains why nucleation in toluene is the most difficult and why the relatively higher propensity for aggregation of tolbutamide molecules in toluene solution, as observed with FTIR spectroscopy, does not translate into easier nucleation. Thus, our combined experimental and molecular modelling study suggests that the solvent can influence on the nucleation not only via differences in the desolvation but also through the influence on molecular conformation. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. A sequential binding mechanism in a PDZ domain

    DEFF Research Database (Denmark)

    Chi, Celestine N; Bach, Anders; Engström, Åke

    2009-01-01

    that ligand binding involves at least a two-step process. By using an ultrarapid continuous-flow mixer, we then detected a hyperbolic dependence of binding rate constants on peptide concentration, corroborating the two-step binding mechanism. Furthermore, we found a similar dependence of the rate constants...

  3. Selective nonspecific solvation under dielectric saturation and fluorescence spectra of dye solutions in binary solvents.

    Science.gov (United States)

    Bakhshiev, N G; Kiselev, M B

    1991-09-01

    The influence of selective nonspecific solvation on the fluorescence spectra of three substitutedN-methylphthalimides in a binary solvent system consisting of a nonpolar (n-heptane) and a polar (pyridine) component has been studied under conditions close to dielectric saturation. The substantially nonlinearity of the effect is confirmation that the spectral shifts of fluorescence bands depend on the number of polar solvent molecules involved in solvating the dye molecule. The measured fluorescence spectral shifts determined by substituting one nonpolar solvent molecula with a polar one in the proximity of the dye molecule agree quantitatively with the forecasts of the previously proposed semiempirical theory which describes this nonlinear solvation phenomenon.

  4. XBP1 (X-Box-Binding Protein-1)-Dependent O-GlcNAcylation Is Neuroprotective in Ischemic Stroke in Young Mice and Its Impairment in Aged Mice Is Rescued by Thiamet-G.

    Science.gov (United States)

    Jiang, Meng; Yu, Shu; Yu, Zhui; Sheng, Huaxin; Li, Ying; Liu, Shuai; Warner, David S; Paschen, Wulf; Yang, Wei

    2017-06-01

    Impaired protein homeostasis induced by endoplasmic reticulum dysfunction is a key feature of a variety of age-related brain diseases including stroke. To restore endoplasmic reticulum function impaired by stress, the unfolded protein response is activated. A key unfolded protein response prosurvival pathway is controlled by the endoplasmic reticulum stress sensor (inositol-requiring enzyme-1), XBP1 (downstream X-box-binding protein-1), and O-GlcNAc (O-linked β-N-acetylglucosamine) modification of proteins (O-GlcNAcylation). Stroke impairs endoplasmic reticulum function, which activates unfolded protein response. The rationale of this study was to explore the potentials of the IRE1/XBP1/O-GlcNAc axis as a target for neuroprotection in ischemic stroke. Mice with Xbp1 loss and gain of function in neurons were generated. Stroke was induced by transient or permanent occlusion of the middle cerebral artery in young and aged mice. Thiamet-G was used to increase O-GlcNAcylation. Deletion of Xbp1 worsened outcome after transient and permanent middle cerebral artery occlusion. After stroke, O-GlcNAcylation was activated in neurons of the stroke penumbra in young mice, which was largely Xbp1 dependent. This activation of O-GlcNAcylation was impaired in aged mice. Pharmacological increase of O-GlcNAcylation before or after stroke improved outcome in both young and aged mice. Our study indicates a critical role for the IRE1/XBP1 unfolded protein response branch in stroke outcome. O-GlcNAcylation is a prosurvival pathway that is activated in the stroke penumbra in young mice but impaired in aged mice. Boosting prosurvival pathways to counterbalance the age-related decline in the brain's self-healing capacity could be a promising strategy to improve ischemic stroke outcome in aged brains. © 2017 American Heart Association, Inc.

  5. Combining Solvent Isotope Effects with Substrate Isotope Effects in Mechanistic Studies of Alcohol and Amine Oxidation by Enzymes*

    Science.gov (United States)

    Fitzpatrick, Paul F.

    2014-01-01

    Oxidation of alcohols and amines is catalyzed by multiple families of flavin-and pyridine nucleotide-dependent enzymes. Measurement of solvent isotope effects provides a unique mechanistic probe of the timing of the cleavage of the OH and NH bonds, necessary information for a complete description of the catalytic mechanism. The inherent ambiguities in interpretation of solvent isotope effects can be significantly decreased if isotope effects arising from isotopically labeled substrates are measured in combination with solvent isotope effects. The application of combined solvent and substrate (mainly deuterium) isotope effects to multiple enzymes is described here to illustrate the range of mechanistic insights that such an approach can provide. PMID:25448013

  6. Solvent-vapor-assisted imprint lithography

    NARCIS (Netherlands)

    Voicu, Nicoleta E.; Ludwigs, Sabine; Crossland, Edward J. W.; Andrew, Piers; Steiner, Ullrich

    2007-01-01

    Sub-micrometer features are replicated into high-molecular-weight polymer resists by using solvent-assisted nanoimprint lithography (see figure). By swelling the polymer in a controlled solvent-vapor atmosphere, millibar pressures and ambient temperatures are sufficient to achieve high-fidelity

  7. Into the depths of deep eutectic solvents

    NARCIS (Netherlands)

    Rodriguez, N.; Alves da Rocha, M.A.; Kroon, M.C.

    2015-01-01

    Ionic liquids (ILs) have been successfully tested in a wide range of applications; however, their high price and complicated synthesis make them infeasible for large scale implementation. A decade ago, a new generation of solvents so called deep eutectic solvents (DESs) was reported for the first

  8. Remediation of Contaminated Soils by Solvent Flushing

    NARCIS (Netherlands)

    Augustijn, Dionysius C.M.; Jessup, Ron E.; Rao, P. Suresh C.; Wood, A. Lynn

    1994-01-01

    Solvent flushing is a potential technique for remediating a waste disposal/spill site contaminated with organic chemicals. This technique involves the injection of a solvent mixture (e.g., water plus alcohols) that enhances contaminant solubility, reduces the retardation factor, and increases the

  9. Structuring of polymer solutions upon solvent evaporation

    NARCIS (Netherlands)

    Schaefer, C.; van der Schoot, P.|info:eu-repo/dai/nl/102140618; Michels, J. J.

    2015-01-01

    The morphology of solution-cast, phase-separated polymers becomes finer with increasing solvent evaporation rate. We address this observation theoretically for a model polymer where demixing is induced by steady solvent evaporation. In contrast to what is the case for a classical, thermal quench

  10. Asymmetric cation-binding catalysis

    DEFF Research Database (Denmark)

    Oliveira, Maria Teresa; Lee, Jiwoong

    2017-01-01

    The employment of metal salts is quite limited in asymmetric catalysis, although it would provide an additional arsenal of safe and inexpensive reagents to create molecular functions with high optical purity. Cation chelation by polyethers increases the salts' solubility in conventional organic...... solvents, thus increasing their applicability in synthesis. The expansion of this concept to chiral polyethers led to the emergence of asymmetric cation-binding catalysis, where chiral counter anions are generated from metal salts, particularly using BINOL-based polyethers. Alkali metal salts, namely KF...... highly enantioselective silylation reactions in polyether-generated chiral environments, and leading to a record-high turnover in asymmetric organocatalysis. This can lead to further applications by the asymmetric use of other inorganic salts in various organic transformations....

  11. Solvent distillations studies for a reprocessing plant

    International Nuclear Information System (INIS)

    Ginisty, C.; Guillaume, B.

    1989-01-01

    The substantial amounts of solvent used in large reprocessing plants are such that considerable care must be paid to solvent management to limit the production of organic wastes. The installation of intensive treatment by chemical regeneration serves to increase the service life of the solvent. General solvent management, combined with a distillation unit under reduced pressure also helps to recycle the two components of the solvent at a low activity level. Distillation also serves to remove the heavy degradation products that are generally responsible for poor hydraulic behavior and for the holdup of radioactive products such as plutonium, zirconium and ruthenium. From the safety standpoint, the flashpoint of the distilled diluent tends to rise. It can therefore be recycled without risk

  12. Method of decomposing radioactive organic solvent wastes

    International Nuclear Information System (INIS)

    Uki, Kazuo; Ichihashi, Toshio; Hasegawa, Akira; Sato, Tatsuaki

    1986-01-01

    Purpose: To decompose radioactive organic solvent wastes or radioactive hydrocarbon solvents separated therefrom into organic materials under moderate conditions, as well as greatly decrease the amount of secondary wastes generated. Method: Radioactive organic solvent wastes comprising an organic phosphoric acid ester ingredient and a hydrocarbon ingredient as a diluent therefor, or radioactive hydrocarbon solvents separated therefrom are oxidatively decomposed by hydrogen peroxide in an aqueous phosphoric acid solution of phosphoric acid metal salts finally into organic materials to perform decomposing treatment for the radioactive organic solvent wastes. The decomposing reaction is carried out under relatively moderate conditions and cause less burden to facilities or the likes. Further, since the decomposed liquid after the treatment can be reused for the decomposing reaction as a catalyst solution secondary wastes can significantly be decreased. (Yoshihara, H.)

  13. Effect of solvent extraction on Tunisian esparto wax composition

    Directory of Open Access Journals (Sweden)

    Saâd Inès

    2016-08-01

    Full Text Available The increase of needs for renewable and vegetable based materials will help to drive the market growth of vegetable waxes. Because of their highly variable composition and physicochemical properties, plant waxes have found numerous applications in the: food, cosmetic, candle, coating, polish etc... The aim of this project is to determine the effect of solvent extraction (petroleum ether and ethanol on Tunisian esparto wax composition. The GC-MS was applied in order to determine the waxes compositions. Then, physicochemical parameters of these two samples of waxes: acid value, saponification value, iodine value and melting point were measured in order to deduct their properties and possible fields of uses. Results showed that esparto wax composition depended on the solvent extraction and that major components of the two samples of waxes were: alkanes, esters of fatty acids and phenols. Furthermore, esparto waxes were characterized by an antioxidant and antibacterial activities but the potential of these activities depended on the solvent of wax extraction.

  14. Influence of molecular geometry, exchange-correlation functional, and solvent effects in the modeling of vertical excitation energies in phthalocyanines using time-dependent density functional theory (TDDFT) and polarized continuum model TDDFT methods: can modern computational chemistry methods explain experimental controversies?

    Science.gov (United States)

    Nemykin, Victor N; Hadt, Ryan G; Belosludov, Rodion V; Mizuseki, Hiroshi; Kawazoe, Yoshiyuki

    2007-12-20

    A time-dependent density functional theory (TDDFT) approach coupled with 14 different exchange-correlation functionals was used for the prediction of vertical excitation energies in zinc phthalocyanine (PcZn). In general, the TDDFT approach provides a more accurate description of both visible and ultraviolet regions of the UV-vis and magnetic circular dichroism (MCD) spectra of PcZn in comparison to the more popular semiempirical ZINDO/S and PM3 methods. It was found that the calculated vertical excitation energies of PcZn correlate with the amount of Hartree-Fock exchange involved in the exchange-correlation functional. The correlation was explained on the basis of the calculated difference in energy between occupied and unoccupied molecular orbitals. The influence of PcZn geometry, optimized using different exchange-correlation functionals, on the calculated vertical excitation energies in PcZn was found to be relatively small. The influence of solvents on the calculated vertical excitation energies in PcZn was considered for the first time using a polarized continuum model TDDFT (PCM-TDDFT) method and was found to be relatively small in excellent agreement with the experimental data. For all tested TDDFT and PCM-TDDFT cases, an assignment of the Q-band as an almost pure a1u (HOMO)-->eg (LUMO) transition, initially suggested by Gouterman, was confirmed. Pure exchange-correlation functionals indicate the presence of six 1Eu states in the B-band region of the UV-vis spectrum of PcZn, while hybrid exchange-correlation functionals predict only five 1Eu states for the same energy envelope. The first two symmetry-forbidden n-->pi* transitions were predicted in the Q0-2 region and in the low-energy tail of the B-band, while the first two symmetry-allowed n-->pi* transitions were found within the B-band energy envelope when pure exchange-correlation functionals were used for TDDFT calculations. The presence of a symmetry-forbidden but vibronically allowed n

  15. The chemistry of nonaqueous solvents v.4 solution phenomena and aprotic solvents

    CERN Document Server

    Lagowski, J J

    1976-01-01

    The Chemistry of Nonaqueous Solvents, Volume IV: Solution Phenomena and Aprotic Solvents focuses on the chemistry of nonaqueous solvents, with emphasis on solution phenomena and aprotic solvents such as tetramethylurea, inorganic acid chlorides, cyclic carbonates, and sulfolane. This book is organized into seven chapters and begins with an overview of the theory of electrical conductivity and elementary experimental considerations, along with some of the interesting research on nonaqueous solvents. It then turns to a discussion on hydrogen bonding phenomena in nonaqueous systems as probed

  16. PARIS II: Computer Aided Solvent Design for Pollution Prevention

    Science.gov (United States)

    This product is a summary of U.S. EPA researchers' work developing the solvent substitution software tool PARIS II (Program for Assisting the Replacement of Industrial Solvents, version 2.0). PARIS II finds less toxic solvents or solvent mixtures to replace more toxic solvents co...